10,000 Matching Annotations
  1. Jan 2026
    1. Author response:

      The following is the authors’ response to the original reviews.

      Public Reviews:

      Reviewer #1 (Public review):

      The key discovery of the manuscript is that the authors found that genetically wild type females descended from Khdc3 mutants shows abnormal gene expression relating to hepatic metabolism, which persist over multiple generations and pass through both female and male lineages. They also find dysregulation of hepatically-metabolized molecules in the blood of these wild type mice with Khdc3 mutant ancestry. These data provide solid evidence further support that phenotype can be transmitted to multiple generations without altering DNA sequence, supporting the involvement of epigenetic mechanisms. The authors further performed exploratory studies on the small RNA profiles in the oocytes of Khdc3-null females, and their wild type descendants, suggesting that altered small RNA expression could be a contributor of the observed phenotype transmission, although this has not been functionally validated.

      Reviewer #2 (Public review):

      Summary:

      This manuscript aimed to investigate the non-genetic impact of KHDC3 mutation on the liver metabolism. To do that they analyzed the female liver transcriptome of genetically wild type mice descended from female ancestors with a mutation in the Khdc3 gene. They found that genetically wild type females descended from Khdc3 mutants have hepatic transcriptional dysregulation which persist over multiple generations in the progenies descended from female ancestors with a mutation in the Khdc3 gene. This transcriptomic deregulation was associated with dysregulation of hepatically-metabolized molecules in the blood of these wild type mice with female mutational ancestry. Furthermore, to determine whether small non-coding RNA could be involved in the maternal non-genetic transmission of the hepatic transcriptomic deregulation, they performed small RNA-seq of oocytes from Khdc3-/- mice and genetically wild type female mice descended from female ancestors with a Khdc3 mutation and claimed that oocytes of wild type female offspring from Khdc3-null females has dysregulation of multiple small RNAs.

      Finally, they claimed that their data demonstrates that ancestral mutation in Khdc3 can produce transgenerational inherited phenotypes.

      However, at this stage and considering the information provided in the paper, I think that these conclusions are too preliminary. Indeed, several controls/experiments need to be added to reach those conclusions.

      Additional context you think would help readers interpret or understand the significance of the work

      Line 25: this first sentence is very strong and needs to be documented in the introduction.

      Line 48: Reference 5 is not appropriate since the paper shows the remodeling of small RNA during post-testicular maturation of mammalian sperm and their sensibility to environment. Please, change it

      Line 51: "implies" is too strong and should be replaced by « suggests »

      Line 67: reference is missing

      Database, the accession numbers are lacking.

      References showing the maternal transmission of non-genetically inherited phenotypes in mice via small RNA need to be added

      Line 378: All RNA-Seq and small RNA-Seq data are available in the NCBI GEO

      We have changed references as requested, and updated portions of the introduction in order to mention specifically genes that seem to regulate an RNA-based genetic nurture effect.  We are not aware of any published work that has demonstrated maternal transmission of non-genetic phenotypes via small RNAs; if the reviewer has a specific reference in mind, we would be happy to read it and add it to our manuscript.  We did add a few sentences describing why this work has primarily been performed in males/fathers.

      Reviewer #1 (Recommendations for the authors):

      (1) In addition to the altered hepatic gene expression and metabolites, did the authors notice any overall phenotypes? including body weight, overall growth, eating behavior, etc?

      We have added information on more general phenotypes of the mice, including litter size, birth weights, and weights at 3 and 8 weeks of age.  We have also performed a metabolic analysis of WT****** mice at 8 months of age.  Overall, there are no striking differences in the WT* mice in these broad phenotypic measures, and also no indication that a smaller litter size or larger birthweight are the drivers of our observed hepatic abnormalities.

      (2) When analyzing the small RNAs, the authors mentioned that they have mapped the reads aging rRNAs. This should have resulted in the identifications of many rRNA-derived small RNAs (rsRNAs). The authors should also perform analyses on the differential expression of rsRNAs in this context. Both tsRNAs and rsRNAs has been shown to be involved in epigenetic inheritance (at least in sperm) (Nat Cell Biol 2018, PMID: 29695786).

      In the oocyte small RNA data, we did not notice many differences in either piRNAs or rRNAs between either the WT and KO oocytes, or the WT and WT** oocytes.  The most significant differences by far were in miRNA and tsRNA.  We have added that we do not see any differences in rRNAs.

      Reviewer #2 (Recommendations for the authors):

      To support your conclusion, you should include the following Data/experiments:

      (1) In the abstract, you wrote "Our results demonstrate that ancestral mutation in Khdc3 can produce transgenerational inherited phenotypes". The full phenotypic description of the phenotype (weight at birth, 3-weeks, 8weights old, phenotype of the liver...) of each progeny should carefully described/analyzed.

      Female KHDC3-deficient mice showed reduced fertility with smaller litter. Given the fact that litter size influences early growth and adult physiology (DOI: 10.1016/j.cmet.2020.07.014), all the metabolic effects observed in the paper could be the result of the litter size. Information about the litter size should be provided. Without this information, it is difficult to evaluate the non-genetic impact of KHDC3 mutation on the metabolism of the progenies.

      We have added information on more general phenotypes of the mice, including litter size, birth weights, and weights at 3 and 8 weeks of age (Figure 3). We have also performed a metabolic analysis of WT****** mice at 8 months of age.  Overall, there were no striking differences in the WT* mice in these broad phenotypic measures, and also no indication that a smaller litter size or larger birthweight are the drivers of our observed hepatic abnormalities.

      We have also added a new figure in order to examine the mechanism of transmission of our observed transcriptional abnormalities (Figure 5).  By transferring serum from WT* mice into wild type recipients, we observe alterations to hepatic gene expression, suggesting that serum-based molecules are driving the altered non-genetic factors in the oocyte.  This lends further support to the conclusion that the observed changes in WT* mice are from inherited germ cell abnormalities (informed by somatic metabolic abnormalities and communicated via blood), and not a consequence of litter sizes or growth rates.

      (2) In addition to the lack of phenotypic information of the progenies, the DEG for the small RNA-seq should be filtered on padj(FDR)<0.05 and not on pvalue<0.05. In Figure 4a, the legend is missing.

      We did not alter the filtering on the small RNA-Seq data.  We are not focusing on any specific small RNA, rather we are stating that these groups (miRNA, tsRNA) of small RNAs are dysregulated; accordingly we believe that using pval is not inappropriate in this circumstance.  The analysis was performed similarly to 4 cell embryo RNA-Seq performed by Harris et al, Cell Reports (PMID 38573852).

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      dweb.link: setup-indy0wiki.pad.html

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      Using the latest indy0pad that produces HTML documents that on Peergos at the point of creation of an index,htmlk file in the right path do - embed hypothesis social annotation tool - set encoding to UTF8 - set title based on the as the last three elements of the path - has a folly operational counterpart in the Inter Planetary Constellation wich is now ready for prime time as IPFS Desktop is now able to share because it is using the new sweep algorithm

      The current verison as of 2025-12-09

      take this published version as the basis and will be edited with the InterPlanetary Indy0Pad

      will use the annotation margin to save updated dweb.links and add them to the document using the Indy0Pad editor @ IPFS which actually save changes into local Storage

      and will be able to save to IPFS in the next round of development

    1. Reviewer #3 (Public review):

      In this manuscript, the authors present data on the supposed composition of pulmonary surfactant obtained from bronchoalveolar lavages (BALs) of a small cohort of dolphins, a group of them suffering from pneumonia. The lipid compositional differences of the sample group are consistent with the different pathological situations of the specimens, suggesting that differences in surfactant composition are somehow associated (as a cause or as a consequence) with the particular pathophysiological contexts. It is particularly remarkable that an increase in cardiolipins and plasmalogens appears as an abnormal composition in pathological surfactants. The study is completed by analyzing the differences in membrane properties (order, packing, phase) of abnormal versus "control" membranes, concluding that pneumonia in dolphins is associated with a significant alteration of surfactant membranes that become more rigid, packed and thicker than those in surfactant from animals with no lung disease.

      In general terms, the data provided are of interest as they somehow offer a framework of effects that may extend what is known about alterations of composition, biophysical properties and functional performance of pulmonary surfactant as a consequence of respiratory pathologies. A collection of pertinent biophysical methodologies (fluorescence, X-ray scattering, AFM) have been applied to complete a full characterization of membrane properties in the different samples.

      However, they way the samples have been processed, i.e. by making organic extracts of hydrophobic (lipid and protein) components before surfactant membranes have been purified or at least, separated from bulk lavage, open the question of how much of the altered composition is actually occurring in surfactant or comes from other membranes (from cells, bacteria) that have been completely intermixed as a consequence of the organic extraction. Without an appropriate surfactant membrane obtention, the results of the study should be taken with caution and await confirmation. Specific questions that need to be considered include:

      (1) As said, the direct organic extract of BAL samples ends in a full mix of lipid and protein components that in origin could be part of different membranes, either from different surfactant assemblies, or even from pulmonary cells or membrane debris, or microorganisms, collected within the lavage. Obtaining conclusions about the structure and properties of membranes artefactually reconstituted from such lipid and protein mixtures is far from correct.

      It is mentioned that "subsequentially" to the organic extraction, the samples were subjected to ultracentrifugation to separate debris and membrane cells. I do not see what the ultracentrifugation is going to change if it is done after the organic extraction. It should have been done before the extraction, for the organic solvents to solubilize exclusively the large, and relatively light, surfactant membrane complexes.

      On the other hand, the ulterior reconstitution of the obtained full lipid mixture surely ends in membrane assemblies whose compositional distribution and organization may differ significantly from those in the original membranes.

      Taking all this into account, statements such as "These aggregate forms reproduce the expected membrane microstructures observed in native alveolar hypophase" or "pulmonary membranes can be successfully extracted and reconstituted from BALs of Navy dolphins" are simply not true and should be rephrased.

      One can understand that the limitation of material may make it difficult to obtain first the purified surfactant membranes and then their organic extract. However, the limitation should be acknowledged to make the readers clear that the actual compositional effects caused in surfactant by pneumonia need confirmation.

      (2) In some of the experiments, i.e. in the AFM characterization, supported membranes were prepared by the spray-dry method applied to organic solutions. Again, the spray-dry of organic lipid solutions ends in a lipid dispersion that may be very far from the real organization of the lipids in actual surfactant membranes.

      (3) When stated that phospholipid concentrations are greater in BAL from pinnipeds than in humans, how has the actual concentration been determined? BAL volumes are typically subjected to large variations depending on the conditions used to obtain the lavage (including volume of saline instilled, level of atelectasia in the lung tissue, presence of inflammation and edema, etc). If total amounts of phospholipids in BAL are to be compared, certain normalization procedures should be applied, such as for instance, with respect to the urea concentration in serum.

      (4) All the differences regarding membrane phase and lipid order/packing have been interpreted in terms of the potential coexistence of Lbeta (gel)/Lalpha (liquid crystalline) phases. However, it has been well established that in lipid systems containing cholesterol, such as pulmonary surfactant, phase coexistence can actually be of the type liquid-ordered (Lo)/liquid-disordered (Ld), very different in terms of mobility and true molecular order. Why do the authors consider that Lbeta is the phase observed in the surfactant membranes they have reconstituted? The presence of round-shaped domains seems to indicate that a liquid/liquid phase segregation is actually occurring.

      (5) In the same line as the previous comment, the authors state that SAXS shows that bovine-extracted pulmonary membranes exhibit a coexistence of two lamellar phases, one rich in unsaturated lipids and one in saturated lipids. SAXS and WAXS cannot provide compositional information, but structural parameters such as membrane thickness, or molecular order. This should be clarified.

      (6) It is mentioned that the surfactant monolayer at the air-liquid interface is interconnected to tubular membranous structures (tubular myelin, TM). It is true that TM, when present, appears interconnected with the interface. However, it is widely recognized that there are many other structures connected with the interfacial film, including multilamellar membrane arrays or reservoirs that have not been mentioned here. Furthermore, TM is not required for surfactant function, because it is absent, for instance, in mice lacking expression of surfactant protein SP-A, which can breathe perfectly.

      (7) In the Discussion, the authors mention that "...after squeeze-out, the excluded multilayers remain closely associated with the interfacial monolayer rather than escaping into the subphase". The authors may like to complete this discussion by specifying that the stable association of excluded assemblies with the interfacial film is actually possible thanks to the surfactant proteins.

    1. Reviewer #2 (Public review):

      Summary:

      This work extends a previous recurrent neural network model of activity-silent working memory to account for well-established findings from psychology and neuroscience suggesting that working memory capacity constraints can be partially overcome when stimuli can be organized into chunks. This is accomplished via the introduction of specialized chunking clusters of neurons to the original model. When these chunking clusters are activated by a cue (such as a longer delay between stimuli), they rapidly suppress recently active stimulus clusters. This makes these stimulus clusters available for later retrieval via a synaptic augmentation mechanism, thereby expanding the network's overall effective capacity. Furthermore, these chunking clusters can be arranged in a hierarchical fashion, where chunking clusters are themselves chunked by higher-level chunking clusters, further expanding the network's overall effective capacity to a new "magic number", 2^{C-1} (where C is the basic capacity without chunking). In addition to illustrating the basic dynamics of the model with detailed simulations (Figures 1 and 2), the paper also utilizes qualitative predictions from the model to (re-)analyze data collected in previous experiments, including single-unit recordings from human medial temporal lobe as well as behavioral findings from a classic study of human memory.

      Strengths:

      The writing and figures are very clear, and the general topic is relevant to a broad interdisciplinary audience. The work is strongly theory-driven, but also makes some effort to engage with existing data from two empirical studies. The basic results showcasing how chunking can be achieved in an activity-silent working memory model via suppression and synaptic augmentation dynamics are interesting. Furthermore, we agree with the authors that the derivation of their new "magic number" is relatively general and could apply to other models, so those findings in particular may be of interest even to researchers using different modeling frameworks.

      Weaknesses:

      (1) Very important aspects of the model are assumed / hard-coded, raising the concern that it relies too much on an external controller, and that it would therefore be difficult to implement the same principles in a fully behaving model responsible for producing its own outputs from a sequence of stimuli (i.e., without a priori knowledge of the structure of incoming sequences).

      (i) One such aspect is the use of external chunking cues provided to the model at critical times to activate the chunking clusters. The simulations reported in the paper were conducted in a setting where signals to chunk are conveniently indicated by longer delays between stimuli. In this case, it is not difficult to imagine how an external component could detect the presence of such a delay and activate a chunking cluster in response. However, in order for the model to be more broadly applicable to different memory tasks that elicit chunking-related phenomena, a more general-purpose detector would be required (see further comments below and alternative models).

      (ii) Relatedly, and as the authors acknowledge in the discussion, the network relies on a pretty sophisticated external controller that decides when the individual chunking clusters are activated or deactivated during readout/retrieval. This seems especially complex in the hierarchical case. How might a network decide which chunking/meta-chunking clusters are activated/deactivated in which order? This was hard-coded in their simulations, but we imagine that it would be difficult to implement a general solution to this problem, especially in cases where there is ambiguity about which stimuli should be chunked, or where the structure of the incoming sequence is not known in advance.

      (iii) One of the central mechanisms of the model is the rapid synaptic plasticity in the inhibitory connections responsible for binding chunking clusters to their corresponding stimulus clusters. This mechanism again appears to have been hard-coded in the main simulations. Although we appreciate that the authors worked on one possible way that this could be implemented (Methods section D, Supplementary Figure S2), in the end, their solution seems to rely on precisely fine-tuning the timing with which stimuli are presented - a factor that seems unlikely to matter very much in humans/animals. This stands in contrast with models of working memory that rely on persistent activity, which are more robust to changes in timing. Note that we do not discount the possibility of activity-silent WM, and indeed it should be studied in its own right, but it is then even more important to highlight which of its features are dependent on the time constants, etc.

      (2) Another key shortcoming of this work is its limited direct engagement with empirical evidence and alternative computational accounts of chunking in WM. Although the efforts to re-analyze existing empirical results in light of the new predictions made by the model are commendable, in the end, we think they fall short of being convincing. As noted above, the model doesn't actually perform the same two tasks used in the human experiments, so direct quantitative comparisons between the model and human behavior or neural data are not possible. Instead, the authors rely on isolating two qualitative predictions of the model - the "dip" and "ramp" phenomena observed after a chunking cluster is activated (Figure 3), and the new magic number for effective capacity derived from the model in the case where stimuli are chunkable, which approximately converges with human recall performance in a memory study (Figure 4). Below, we highlight some specific issues related to these two sets of analyses, but the larger point is that if the model is making a commitment about how these neural mechanisms relate to behavioral phenomena, it would be important to test if the model can produce the behavioral patterns of data in experimental paradigms that have been extensively used to characterize those phenomena. For example, modern paradigms characterizing capacity limits have been more careful to isolate the contributions of WM per se (whereas the original magic number 7 is now thought to reflect a combination of episodic and working memory; see Cowan 2010). There are several existing models that more directly engage with this literature (e.g., Edin et al., 2009; Matthey et al., 2015; Nassar et al., 2018; Soni & Frank, 2025; Swan & Wyble, 2014; van den Berg et al., 2014; Wei et al., 2012), some of which also account for chunking-related phenomena (e.g., Wei et al, 2012; Nassar et al., 2018; Panichello et al., 2019; Soni & Frank, 2025). A number of related proposals suggest that WM capacity limits emerge from fundamentally different mechanisms than the one considered here - for example, content-related interference (Bays, 2014; Ma et al., 2014; Schurgin et al., 2020), or limitations in the number of content-independent pointers that can be deployed at a given time (Awh & Vogel, 2025), and/or the inherent difficulty of learning this binding problem (Soni & Frank, 2025). We think it would be worth discussing how these ideas could be considered complementary or alternatives to the ones presented here.

      (i) Single unit recordings. We found it odd that the authors chose to focus on evidence from single-unit recordings in the medial temporal lobe from a study focused on episodic memory. It was unclear how exactly these data are supposed to relate to their proposal. Is the suggestion that a mechanism similar to the boundary neurons might be operative in the case of working memory over shorter timescales in WM-related areas such as the prefrontal cortex, or that their chunking mechanism may relate not only to working memory but also to episodic memory in the medial temporal lobe?

      (ii) N-gram memory experiment. Our main complaint about the analysis of the behavioral data from the human memory study (Figure 4) is that the model clearly does not account for the main effect observed in that study - namely, the better recall observed for higher-order n-gram approximations to English. We acknowledge that this was perhaps not the main point of the analysis (which related more to the prediction about the absolute capacity limit M*), but it relates to a more general criticism that the model cannot account for chunking behavior associated with statistical learning or semantic similarity. Most of the examples used in the introduction and discussion are of this kind (e.g., expressions such as "Oh my God" or "Easier said than done", etc.). However, the chunking mechanism of the model should not have any preference for segmenting based on statistical regularities or semantic similarity - it should work just as well if statistical anomalies or semantic dissimilarity were used as external chunking cues. In our view, these kinds of effects are likely to relate to the brain's use of distributed representations that can capture semantic similarity and learn statistical regularities in the environment. Although these kinds of effects may be beyond the scope of this model, some effort could be made to highlight this in the discussion. But again, more generally, the paper would be more compelling if the model were challenged to simulate more modern experimental paradigms aimed at testing the nature of capacity limits in WM, or chunking, etc.

      (iii) There are a number of other empirical phenomena that we're not sure the model can explain. In particular, one of the hallmarks of WM capacity limits is that it suffers from a recency bias, where people are more likely to remember the most recent items at the expense of items presented prior to that (Oberauer et al 2012). [There are also studies showing primacy effects in addition to recency effects, but the primacy effects are generally attributed to episodic rather than working memory - for example, introducing a distractor task abolishes the recency but not primacy effect]. But the current model seems to make the opposite prediction: when the stimuli exceed its base capacity, it appears to forget the most recent stimuli rather than the earliest ones (Figure 1d). This seems to result from the number of representations that can be reactivated within a cycle and thus seems inherent to the dynamics of the model, but the authors can clarify if, instead, it depends on the particular values of certain parameters. (In contrast, this recency effect is captured in other models with chunking capabilities based on attractive dynamics and/or gating mechanisms - eg Boboeva et al 2023; Soni & Frank (2025)). Relatedly, we're not sure if the model could account for the more recent finding that recall is specifically enhanced when chunks occur in early serial positions compared to later ones (Thalmann, Souza, Oberauer, 2019).

    2. Reviewer #3 (Public review):

      The paper presents a synaptic mechanism for chunking in working memory, extending previous work of the last author by introducing specialized "chunking clusters", neural populations that can dynamically segment incoming items into chunks. The idea is that this enables hierarchical representations that increase the effective capacity of working memory. They also derive a theoretical bound for working memory capacity based on this idea, suggesting that hierarchical chunking expands the number of retrievable items beyond the basic WM capacity. Finally, they present neural and behavioral data related to their hypothesis.

      Strengths

      A major strength of the paper is its clear theoretical ambition of developing a mechanistic model of working memory chunking.

      Weaknesses

      Despite the inspiration in biophysical mechanisms (short-term synaptic plasticity with different time constants), the model is "cartoonish". It is unclear whether the proposed mechanism would work reliably in the presence of noise and non-zero background activity or in a more realistic implementation (e.g., a spiking network).

      As far as I know, there is no evidence for cyclic neural activation patterns, which are supposed to limit WM capacity (such as in Figure 1d). In fact, I believe there is no evidence for population bursts in WM, which are a crucial ingredient of the model. For example, Panicello et al. 2024 have found evidence for periods during which working memory decoding accuracy decreases, but no population bursts were observed in their data. In brief, my critique is that including some biophysical mechanism in an abstract model does not make the model plausible per se.

      It is claimed that "our proposed chunking mechanism applies to both the persistent-activity and periodic-activity regimes, with chunking clusters serving the same function in each", but this is not shown. If the results and model predictions are the same, irrespective of whether WM is activity-silent or persistent, I suggest highlighting this more and including the corresponding simulations.

      The empirical validations of the model are weak. The single-unit analysis is purely descriptive, without any statistical quantification of the apparent dip-ramp pattern. I agree that the dip-ramp pattern may be consistent with the proposed model, but I don't believe that this pattern is a specific prediction of the proposed model. It seems just to be an interesting observation that may be compatible with several network mechanisms involving some inhibition and a rebound.

      Moreover, the reanalyses of n-gram behavioral data do not constitute a mechanistic test of the model. The "new magic number" depends strongly on structural assumptions about how chunking operates, and it is unclear whether human working memory uses the specific hierarchical scheme required to achieve the predicted limit.

      The presentation of the modeling results is highly compressed in two figures and is rather hard to follow. Plotting the activity of different neural clusters in separate subplots or as heatmaps (x-axis time, y-axis neural population, color = firing rate) would help to clarify (Figure 1d). Also, control signals that activate the chunking clusters should be shown.

      Overall, the theoretical proposal is interesting, but its empirical grounding and biological plausibility need to be substantially reinforced.

    1. Robert Sapolsky, “Life Without Free Will: Does it Preclude Possibilities Download Life Without Free Will: Does it Preclude Possibilities ?” Possibility Studies & Society 2024, Vol 2(3) 272-81.

      Author arguing that there is no free will because of biology (which we did not control, and its interactions with the environment which we also did not control)

    1. The primary spermatocyte undergoes meiosis I to form two haploid secondary spermatocytes. These two cells undergo Meiosis II to form four spermatids, which then develop into mature sperm.

      Maybe a reference here that further discussion of Meiosis is coming in the next section.

    1. Aldosterone, a hormone produced by the adrenal cortex, increases the reabsorption of Na+, which then increases the reabsorption of water. Antidiuretic hormone (ADH), a hormone released by the posterior pituitary gland, also increases the reabsorption of water. ADH exerts its effect farther along in the nephron at the distal collecting tubule and collecting duct. It influences how dilute or concentrated the final urine will be

      Do we want to have a quick conversation about obligatory vs selective reabsorption here? I worry that this section implies that these hormones impact all reabsorption instead of only selective.

    2. The distal convoluted tubule will recover another 10–15 percent before the filtrate enters the collecting ducts

      I agree with calling out the specific percentage here, but I feel that if we are going to do so we should also do it in the PCT and loop discussion.

    3. About 99 percent of the water and most of the solutes filtered by the nephron are reabsorbed

      I feel like this sentence should be earlier, because it's inclusion here implies that 99% of reabsorption is happening in the PCT.

    4. See Figure 15.3[2] for an illustration of the location of the kidneys.

      Neither diagram nor text reflect that right kidney is slightly inferior to the left due to the presence of the liver.

    1. Metaphor is further used in act II, scene 3: "I have been feasting with mine enemy" – Metaphor. The Capulet feast was a "feast." Juliet, a Capulet, is the "enemy." He was wounded by love there.

    2. Characterization in act II, scene 3: Friar: "Holy Saint Francis, what a change is here!" – He's shocked by the speed of the change from Rosaline to Juliet. He doubts Romeo's emotional depth. "Young men's love then lies / Not truly in their hearts, but in their eyes" – He criticizes Romeo for loving based on physical appearance (eyes), not deep feeling. "Jesu Maria, what a deal of brine / Hath wash'd thy sallow cheeks for Rosaline!" – "Brine" = salt tears. He mocks Romeo's exaggerated, performative past grief.

    3. Romeo's character traits are described in act II, scene 3: Romeo: "Good morrow, father." – His cheerful greeting contrasts with the Friar's philosophical mood. Shows Romeo's youthful energy and distraction by love. Friar: "Young son, it argues a distemper'd head" – "Distemper'd" = disordered, sick. He assumes Romeo is unwell to be up so early. He's right—love-sick. "Our Romeo hath not been in bed to-night" – The Friar deduces the truth. Romeo's behavior is so unusual it reveals his all-night adventure.

    4. Paradox and key themes in act II, scene 3: "The earth that's nature's mother is her tomb" – Paradox. The earth gives life (womb) and receives death (tomb). Central theme: life and death are intertwined. "For nought so vile that on the earth doth live / But to the earth some special good doth give" – Nothing is so evil it doesn't have some potential good use. "Virtue itself turns vice, being misapplied" – Key theme. Good things (like herbs, or love) can become harmful if used incorrectly. Foreshadows the plan's failure.

    5. Simile and personification are used in act II, scene 3: "The grey-eyed morn smiles on the frowning night" – Personification. Dawn ("grey-eyed morn") smiles; night frowns. A peaceful, hopeful image of a new day. "Flecked darkness like a drunkard reels" – Simile. The remaining darkness staggers away like a drunkard. Vivid image of night being pushed out by day

    1. The digestion of proteins and carbohydrates begins in the mouth with salivary amylase

      This sentence seems to imply that salivary amylase chemically digests proteins, which would not be accurate.

    2. Although one might think that the size of a person’s stomach is related to how much food that individual consumes, body weight does not correlate with stomach size. Rather, when greater quantities of food are eaten—such as at holiday dinner—the stomach stretches more than when less is eaten.

      Should we discuss emesis as a protective mechanism either here or in the disorders section?

    3. Salivary amylase, an enzyme in saliva, begins the chemical digestion of starches in the mouth.

      I think this would flow better if we discuss salivary amylase before we state that chemical digestion is continued in the stomach.

    4. The stomach is equipped for its churning function by the addition of a third layer,

      Should we point out that the muscularis of the stomach is composed of smooth muscle before we discuss the third layer?

    1. Stap 3: Gevangenhouding door de Raadkamer rechtbank

      Wie beslist? De Raadkamer van de rechtbank (dit volgt na de rechter-commissaris).

      De beslissing: De Raadkamer besluit of de minderjarige langer vast moet blijven zitten (gevangenhouding) of naar huis mag (schorsing met voorwaarden).

      De termijnen:

      De zitting moet binnen 30 dagen plaatsvinden.

      Dit mag twee keer verlengd worden.

      De totale duur van dit voorarrest is maximaal 90 dagen.

      Wat gebeurt er ondertussen? Hoewel de echte rechtszaak nog moet komen, wordt er direct een plan van aanpak gemaakt (hulpverlening, toezicht, school/werk, etc.). De hulpverlening start dus al vóór de veroordeling.

    2. Stap 1: Politiebureau en cellencomplex

      1. Het Proces op het Politiebureau

      **Identificatie: ** Gebeurt volledig geautomatiseerd (biometrie/paspoort).

      Opsluiting: Mag maximaal 6 dagen (inverzekeringstelling is max 2x 3 dagen).

      Kritiek: Cellen zijn traumatisch voor kinderen. De RSJ adviseert daarom: max 24 uur opsluiten en sneller verhoren.

      2. Rollen & Rechten

      Advocaat: Is verplicht. Heeft eigen bevoegdheden en mag beslissingen nemen, zelfs als ouders het er niet mee eens zijn.

      Ouders: Hebben het recht om bij het verhoor te zijn.

      Bewijs: Rapporten van hulpverleners (Jeugdzorg/artsen) gelden niet als wettig bewijs.

      3. Theorie (Beccaria)

      **Doelen: ** Speciale preventie (dader leert ervan) vs. Algemene preventie (signaal naar samenleving).

      Beginselen:

      **Proportionaliteit: ** Zo min mogelijk leed toevoegen (straf moet in verhouding staan). ** Subsidiariteit: ** De lichtste straf kiezen die nog effect heeft.

      4. Het Grote Dilemma (Juridisch vs. Pedagogisch) Er is een spanning tussen het opvoeden en het strafproces:

      Pedagogisch: Je wilt dat een kind leert van zijn fouten (speciale preventie).

      Juridisch: Als je vrijspraak wilt, is het strategisch vaak slim om niet mee te werken of te zwijgen.

      Gevolg: Dit zorgt voor wrijving. De advocaat zit er tussenin: moet hij gaan voor het beste juridische resultaat (vrijspraak/zwijgen) of voor het pedagogische effect (meewerken/verantwoordelijkheid nemen)?

      **5. Theorie van Galanter ** Naast Beccaria wordt ook Galanter genoemd. Hij maakt onderscheid tussen twee soorten verdachten:

      **One-shotters: ** Mensen die eenmalig of zelden met justitie in aanraking komen.

      **Repeat players: ** Mensen die vaak met de politie te maken hebben (draaideurcriminelen).

      De advocaat en rechter moeten rekening houden met dit verschil in hun aanpak en beslismodel. ** 6. De Wetboeken Het jeugdstrafrecht** staat niet in één boekje, maar is verspreid over twee belangrijke wetboeken:

      Wetboek van Strafvordering: De regels over het proces (arrestatie, verhoor, etc.).

      Wetboek van Strafrecht: De regels over de straffen en feiten.

      Belangrijk: Deze regels gelden voor minderjarigen (<18), maar soms ook voor jongvolwassenen (>18).

    1. Reviewer #1 (Public review):

      Summary:

      This study addresses the encoding of forelimb movement parameters using a reach-to-grasp task in mice. The authors use a modified version of the water-reaching paradigm developed by Galinanes and Huber. Two-photon calcium imaging was then performed with GCaMP6f to measure activity across both the contralateral caudal forelimb area (CFA) and the forelimb portion of primary somatosensory cortex (fS1) as mice perform the reaching behavior. Established methods were used to extract the activity of imaged neurons in layer 2/3, including methods for deconvolving the calcium indicator's response function from fluorescence time series. Video-based limb tracking was performed to track the positions of several sites on the forelimb during reaching and extract numerous low-level (joint angle) and high-level (reach direction) parameters. The authors find substantial encoding of parameters for both the proximal and distal parts of the limb across both CFA and fS1, with individual neurons showing heterogeneous parameter encoding. Limb movement can be decoded similarly well from both CFA and fS1, though CFA activity enables decoding of reach direction earlier and for a more extended duration than fS1 activity. Collectively, these results indicate involvement of a broadly distributed sensorimotor region in mouse cortex in determining low-level features of limb movement during reach-to-grasp.

      Strengths:

      The technical approach is of very high quality. In particular, the decoding methods are well designed and rigorous. The use of partial correlations to distinguish correlation between cortical activity and either proximal or distal limb parameters or either low- or high-level movement parameters was very nice. The limb tracking was also of extremely high quality, and critical here to revealing the richness of distal limb movement during task performance.

      The task itself also reflects an important extension of the original work by Galinanes and Huber. The demonstration of a clear, trackable grasp component in a paradigm where mice will perform hundreds of trials per day expands the experimental opportunities for the field. This is an exciting development.

      The findings here are important and the support for them is solid. The work represents an important step forward toward understanding the cortical origins of limb control signals. One can imagine numerous extensions of this work to address basic questions that have not been reachable in other model systems.

      Collectively, these strengths made this manuscript a pleasure to read and review.

    2. Author response:

      The following is the authors’ response to the original reviews.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      This study addresses the encoding of forelimb movement parameters using a reach-to-grasp task in mice. The authors use a modified version of the water-reaching paradigm developed by Galinanes and Huber. Two-photon calcium imaging was then performed with GCaMP6f to measure activity across both the contralateral caudal forelimb area (CFA) and the forelimb portion of primary somatosensory cortex (fS1) as mice perform the reaching behavior. Established methods were used to extract the activity of imaged neurons in layer 2/3, including methods for deconvolving the calcium indicator's response function from fluorescence time series. Video-based limb tracking was performed to track the positions of several sites on the forelimb during reaching and extract numerous low-level (joint angle) and high-level (reach direction) parameters. The authors find substantial encoding of parameters for both the proximal and distal parts of the limb across both CFA and fS1, with individual neurons showing heterogeneous parameter encoding. Limb movement can be decoded similarly well from both CFA and fS1, though CFA activity enables decoding of reach direction earlier and for a more extended duration than fS1 activity. Collectively, these results indicate involvement of a broadly distributed sensorimotor region in mouse cortex in determining low-level features of limb movement during reach-to-grasp.

      Strengths:

      The technical approach is of very high quality. In particular, the decoding methods are well designed and rigorous. The use of partial correlations to distinguish correlation between cortical activity and either proximal or distal limb parameters or either low- or high-level movement parameters was very nice. The limb tracking was also of extremely high quality, and critical here to revealing the richness of distal limb movement during task performance.

      The task itself also reflects an important extension of the original work by Galinanes and Huber. The demonstration of a clear, trackable grasp component in a paradigm where mice will perform hundreds of trials per day expands the experimental opportunities for the field. This is an exciting development.

      The findings here are important and the support for them is solid. The work represents an important step forward toward understanding the cortical origins of limb control signals. One can imagine numerous extensions of this work to address basic questions that have not been reachable in other model systems.

      Collectively, these strengths made this manuscript a pleasure to read and review.

      Thank you!

      Weaknesses:

      In the last section of the results, the authors purport to examine the representation of "higher-level target-related signals," using the decoding of reach direction. While I think the authors are careful in their phrasing here, I think they should be more explicit about what these signals could be reflecting. The "signals" here that are used to decode direction could relate to anything - low-level signals related to limb or postural muscles, or true high-level commands that dictate only what movement downstream motor centers should execute, rather than the muscle commands that dictate how. One could imagine using a partial correlation-type approach again here to extract a signal uncorrelated with all the measured low-level parameters, but there would still be all the unmeasured ones. Again, I think it is still ok to call these "high-level signals," but I think some explicit discussion of what these signals could reflect is necessary.

      Thank you for this excellent suggestion. We have followed both pieces of the reviewer’s advice. First, we performed the suggested analysis, partialing off the kinematics then performing target classification on the residuals. This is now Figure 6S1. The analysis revealed the presence of target-related information in the neural activity after subtracting off all linear correlations with kinematics, supporting our claims that higher-level information is present in both populations. The exact timing of classifier performances varied substantially across mice, potentially due to differences in reach-to-grasp strategy, kinematic tracking fidelity, and exact spatial locations of each recorded FOV. Following the second suggestion, we have made the relevant text more careful. We now conclude simply that higher-level signals, meaning those signals that are largely unrelated to forelimb joint angle kinematics, are present but with variable timing and strengths in each area. That text now reads:

      “Target decoding performance could result from truly higher-level signals that code abstractly for target location, or alternatively could be supported by strong encoding of kinematic variables that differed between targets. To disambiguate these possibilities, we refit the linear classifier to neural data after regressing off variance related to the joint angle kinematics. The strength and exact time course of the resulting target decoding varied somewhat across animals, but the earliest portion of target decoding performance persisted in all animals after the removal of kinematics and performance remained stronger for M1-fl than S1-fl (Fig. 6S1B). We thus conclude that higher-level signals are present in both areas, but differ in their exact timing and strength. However, we note that other possible signals, such as postural changes, could not be controlled for here.”

      Related to this, I think the manuscript in general does not do an adequate job of explicitly raising the important caveats in interpreting parametric correlations in motor system signals, like those raised by Todorov, 2000. The authors do an expert job of handling the correlations, using PCA to extract uncorrelated components and using the partial correlation approach. However, more clarity about the range of possible signal types the recorded activity could reflect seems necessary.

      This is an important point, and our text could have unintentionally misled readers. We have now attempted to make this point explicit in the Discussion and in the Results for Figure 6. This Discussion text now reads:

      “Moreover, as is widely known (Todorov 2000), the exact role of these kinematically-related signals is challenging to determine from correlative measures alone; thus, determining whether these signals are used for direct movement control or instead indirectly reflect control performed elsewhere is left as a topic for future work.”

      The manuscript could also do a better job of clarifying relevant similarities and differences between the rodent and primate systems, especially given the claims about the rodent being a "first-class" system for examining the cellular and circuit basis of motor control, which I certainly agree with. Interspecies similarities and differences could be better addressed both in the Introduction, where results from both rodents and primates are intermixed (second paragraph), and in the Discussion, where more clarity on how results here agree and disagree with those from primates would be helpful. For example, the ratio of corticospinal projections targeting sensory and motor divisions of the spinal cord differs substantially between rodents and primates. As another example, the relatively high physical proximity between the typical neurons in mouse M1 and S1 compared to primates seems likely to yoke their activity together to a greater extent. There is also the relatively large extent of fS1 from which forelimb movements can be elicited through intracortical microstimulation at current levels similar to those for evoking movement from M1. All of these seem relevant in the context of findings that activity in mouse M1 and S1 are similar.

      We understand two points to address here. The first point is that we needed to be more careful to attribute previous results as being from the rodent vs. monkey. We agree. We have now revised several parts of the paper to make these distinctions clearer. The second point is about the potential benefit of a thorough review of the many ways in which primate and rodent sensorimotor systems differ. We entirely agree that this could be useful for the field. However, this is a sizable endeavor and doing it full justice is beyond what we know how to fit in the space allotted for framing our results here. We therefore sought a compromise, acknowledging how our results correspond to existing results in the primate without exhaustively accounting for how they differ. Future work will be necessary to more carefully disambiguate whether species-specific differences are due to biomechanical, neurological, ethological, or as-of-yet undetermined sources. We have incorporated your final specific points about what could produce similar information in M1 and S1 into the Discussion.

      “This may simply be a consequence of widely distributed representations of movement across mouse cortex (Musall et al. 2019; Steinmetz et al. 2019; Stringer et al. 2019), including forelimb somatosensory areas, or may be a consequence of the close physical proximity of M1-fl and S1-fl hindering development of functionally distinct representations (Tennant et al. 2011).”

      In addition, there are a number of other issues related to the interpretation of findings here that are not adequately addressed. These are described in the Recommendations for improvement.

      Reviewer #2 (Public review):

      Summary:

      In this manuscript, Grier, Salimian, and Kaufman characterize the relationship between the activity of neurons in sensorimotor cortex and forelimb kinematics in mice performing a reach-to-grasp task. First, they train animals to reach to two cued targets to retrieve water reward, measure limb motion with high resolution, and characterize the stereotyped kinematics of the shoulder, elbow, wrist, and digits. Next, they find that inactivation of the caudal forelimb motor area severely impairs coordination of the limb and prevents successful performance of the task. They then use calcium imaging to measure the activity of neurons in motor and somatosensory cortex, and demonstrate that fine details of limb kinematics can be decoded with high fidelity from this activity. Finally, they show reach direction (left vs right target) can be decoded earlier in the trial from motor than from somatosensory cortex.

      Strengths:

      In my opinion, this manuscript is technically outstanding and really sets a new bar for motor systems neurophysiology in the mouse. The writing and figures are clear, and the claims are supported by the data. This study is timely, as there has been a recent trend towards recording large numbers of neurons across the brain in relatively uncontrolled tasks and inferring a widespread but coarse encoding of high-level task variables. The central finding here, that sensorimotor cortical activity reflects fine details of forelimb movement, argues against the resurgent idea of cortical equipotentiality, and in favor of a high degree of specificity in the responses of individual neurons and of the specialization of cortical areas.

      Thank you!

      Weaknesses:

      It would be helpful for the authors to be more explicit about which models of mouse cortical function their results support or rule out, and how their findings break new conceptual ground.

      We appreciate this feedback and have attempted to make these details clearer through changes to the Introduction and Discussion. One key change is noted below:

      “The presence of detailed kinematic signals in the sensorimotor cortex supports a model of mouse sensorimotor cortex in which M1-fl and S1-fl play a strong role in shaping the fine details of reaching and grasping movements.”

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      In addition to the weaknesses noted above, I suggest the authors also address the following:

      The last results section is generally lacking in statistical support for claims. Statistical support should be added.

      Thank you for pointing this out, we have added more statistical support to this section.

      The consideration in the Discussion of relevant previous findings and potential explanations for the distal limb signals in mouse sensorimotor cortex is somewhat lacking. There are several specific issues:

      (1) In contrast to the present study, the studies cited in regards to a lack of motor cortical involvement did not involve dexterous movements - in fact, Kawai et al. explicitly engineered a task that did not involve dexterity to distinguish the role of motor cortex in learning from its known role in dextrous movement execution. In Kawai et al., the authors note one rat who adopted a more dexterous approach to the lever pressing task; in this rat, a motor cortical lesion did cause a longer-lasting reduction in task performance. In additional experiments reported in Kawai's PhD thesis, performance of a dextrous task does erode with motor cortex lesion, as seen in other studies, like the early rodent reaching work of Whishaw and colleagues.

      (2) Other possible explanations for the persistence of non-dexterous tasks following motor cortical removal are compensation by, or redundant functionality in, other motor system regions.

      (3) It is also worth noting that stimulation in different regions of mouse M1 and S1 evokes alternately, digit, wrist, and elbow movements in fairly similar proportions (Tennant, 2011), suggesting that descending pathways substantially target spinal circuits that control all forelimb joints.

      (4) It also seems relevant that although the recovery time course is longer, nonhuman primates also retain substantial hand control after motor cortical removal (e.g. Lashley, 1925; Glees and Cole, 1950; Passingham et al., 1983). Humans of course, appear to be a different story.

      These are good points. We have tried to make the Discussion better reflect the tension in the literature, including with this new text:

      “However, several other previous results have indirectly suggested that M1 and S1 may be involved in the details of forelimb movement. Performance suffers with inactivation or lesioning of M1 and S1 in skilled, complex manual behaviors (Guo et al 2015, Mizes et al 2024, Whishaw et al 1990) or idiosyncratic use of digits to accomplish non-dexterous tasks (Kawai 2014). The sparing of non-dexterous tasks with these lesions may also reflect redundancy in control as opposed to irrelevance of M1 and S1. Nevertheless, our finding of low-level kinematic information in sensorimotor cortex supports a role for cortex beyond simply providing redundant high-level commands to these subcortical areas.”

      We have avoided mentioning points 3 and 4 in the paper; the stimulation results might follow from activating projections not normally involved in this behavior, and discussing primates in this context would require a long list of caveats. We agree that these points are worth thinking about, but are concerned that they are too circumstantial to include in interpreting the results formally.

      Although similar decoding performance is achieved using neurons from both CFA and fS1, I am left wondering whether you would do substantially better with CFA using activity at additional preceding time points, or when using exclusively time points from the past. The primary model used here appears to use neural signals from corresponding time points to decode limb parameters, but results seemingly could be different when using preceding time points as regressors.

      We appreciate this suggestion and have added the analysis to an additional supplementary panel for Figure 5 (Figure 5S3). Incorporating lags into the decoder via a Wiener filter does indeed improve the decoding performance, but this could simply be due to the increase in the number of predictor variables. This analysis did not, however, further disambiguate M1-fl and S1-fl: the performance improvement was similar across areas for both causal and acausal lag configurations. This could be a consequence of the time resolution of calcium imaging, so further experiments with electrophysiology would be required to rule this possibility out. We now note this new result:

      “Including additional causal (-100 ms preceding) and/or acausal (-100 ms preceding to 100 following) lags improved decoding performance modestly and similarly for both areas (Fig. 5S3E-F).”

      Related to this, I am also worried about the bleeding of signals across time here. If you deconvolve and interpolate between time points, the interpolation seemingly will pull information into the past, up to half the sampling period, which here is on the order of how long it takes signals to travel to and from the limb. The authors do not make any inappropriate claims about the neural signals here reflecting causes or consequences of what is happening at the limb, but readers (like me) will still try to draw these sorts of conclusions. Is it possible that, although decoding from instantaneous signals is similar for the two regions, the M1 signals are actually motor signals related to future limb state while the S1 signals are sensory consequences? Even if many of the relevant details related to conduction times are not known, perhaps the authors could clarify what can and can't be said related to causal interpretation here.

      Thank you for suggesting further explanation here. We agree that our interpretation could be made more specific. We have added text in the Discussion section to speak more directly to what can and cannot be concluded from our analyses. In short, it is hard to be certain of lags in calcium imaging data for many reasons, and using recording methods with finer temporal resolution (like electrophysiology) will be necessary for determining the precise temporal relationships between kinematics and neural activity. In the absence of these recordings, we limit our claim to kinematic information being present in M1-fl and S1-fl neural activity and leave determining the causal role of this information to future work.

      New clarifying text in the Discussion:

      “The use of calcium imaging further prevents strong conclusions about whether activity reflects future limb states or sensory consequences. Confirming this limitation, inclusion of lagged data in the decoding models, whether causal or acausal, resulted in similar performance changes in both areas.”

      An alternative reason why lift onset is less decodable in CFA is that CFA activates substantially before lift onset, as has been observed in previous rodent studies (Kargo and Nitz, 2004; Miri et al., 2017; Veuthey et al., 2020), perhaps as some sort of movement preparation. S1, on the other hand, may not have this early activity, and so may show a clearer transient at onset when the hand and limb start to move. This seems more likely than the explanations provided by the authors.

      This is a valid possible alternative explanation and we have updated the Discussion to reflect this. This difference in the structure of M1-fl activity versus S1-fl is apparent in the projections of Figure 6A, which show M1-fl projections more clearly aligned to cue-onset than S1-fl projections.

      “Our lift time decoding results are consistent with this view and align with recent observations characterizing mouse proprioceptive forelimb cortex, (Alonso et al 2023), although an alternative explanation may be simply that M1-fl activates earlier than S1-fl during reaching (Kargo and Nitz 2004; Miri et al 2017; Veuthey et al 2020).”

      To better clarify relevant similarities and differences between the rodent and primate systems, the Introduction could include some of these similarities and differences exposed by the literature currently cited, and the Discussion could include an additional paragraph specifically relating findings here to previous observations in the primate.

      We appreciate the reviewer’s thoughtfulness on possible framings of our results. When writing this paper, framing was a major challenge for us and we drafted quite a few versions of the Introduction including some that focused more on mouse-primate comparison. In the end, we decided the most critical function of the Intro was to set up our central question, of “levels-of-sensorimotor-control”. The rich primate literature was valuable here, but getting into a protracted compare-and-contrast exercise quickly became a distraction from the point. Further, we sought to highlight the relevance and importance of the question answered in our work as the mouse has gained prominence for filling gaps that are challenging to address with primates. This paper serves as one of many early steps towards the ultimate goal of revealing general properties of sensorimotor cortical function with the mouse model. We have made some subtle changes to the Introduction that we hope will more clearly communicate this narrative. 

      We agree that a Discussion paragraph directly relating our results to those in primates would benefit our conclusions and have added one:

      “These results expand our understanding of the rodent sensorimotor system and highlight similarities to nonhuman primates. We show here evidence in mice of detailed joint angle kinematic signals from the full forelimb in M1 and S1, as has been shown in macaque cortex during tasks involving reaching and grasping objects (Vargas-Irwin et al. 2010; Saleh et al. 2010, 2012; Goodman et al. 2019; Okorokova et al. 2020). Additionally, the earlier onset of movement-related activity in M1-fl compared to S1-fl is similar to macaque M1 and S1 (Tanji and Evarts 1976). Taken together these results suggest that the mouse can be employed to address questions traditionally explored in primates about how cortical activity encodes detailed movement commands.”

      Although this is outside the scope of the present study, it would be interesting to image descending projection neurons to see what signals are conveyed downstream, and to what targets. Some signals observed in layer 2/3 may not be strongly reflected in descending projections.

      We agree that recording from descending projection neurons in this task would be of deep interest – and also agree that these experiments are beyond the scope of the present study. We look forward to performing these additional experiments in future work.

      Minor:

      (1) The use of "CFA" and “fS1” is a bit confusing. S1, like M1, is defined primarily based on histological criteria, while CFA is defined by intracortical microstimulation. CFA contains a substantial fraction of fS1, seemingly most of it based on the maps shown in Tennant et al., 2011. This is not really a criticism, as the field has not reached any sort of consensus on this nomenclature yet.

      We are similarly unhappy with the inconsistency of the terminology in the field, and struggled with how not to make it worse.  After much debate and consultation with colleagues, we decided to use “M1” and “S1” to evoke the century of literature on these areas; and “-fl” to indicate forelimb because it is more intuitive than “-ul” and avoids using the illegible “-ll” for hindlimb (relevant to our subsequent paper). For what we called M1-fl, we recorded where we did because anecdotally we saw similar responses across that swath; but note that this definition is also consistent with the definition of “MOp-ul” found with multimodal mapping by

      Munoz-Castaneda (2021), which extends a little anteriorly of MOp as defined by the Allen CCF. As the field continues to mature, we hope future work can converge on a set of shared terms.

      (2) Page 4: "Inactivations and lesions of M1 and S1 have shown that M1 is required for the execution of dexterous reach-to-grasp movements" - to me, earlier work from Whishaw and colleagues deserves to be cited here.

      We appreciate the suggestion and have updated the references in this section to better reflect the prior work from Whishaw and other researchers.

      (3) Page 5: "evoking sufficient trial-to-trial variability to avoid model overfitting." - what I think the authors are referring to here is a particular kind of "overfitting," the consequence of not exploring the full movement space, as opposed to model overfitting from issues with the model-fitting method itself. Rather than just saying overfitting, the authors could be clearer about what they are referring to.

      The reviewer is right; the phenomenon we intended to refer to is not properly termed overfitting. Specifically, we meant that data with restricted range does not necessarily express global structure, and models can therefore incorrectly fit them. For example, fitting a linear model to data including many periods of a sine wave will correctly show a zero-slope linear component, but fitting to only a portion of a single cycle will typically yield a nonzero slope. This is not overfitting, is not exactly underfitting (because the relevant structure is barely present in the data, as opposed to missed by an insufficiently powerful model), is not bias (the data are fit well), and is not even necessarily a problem (the local relationship may be what you are interested in). Yet, it does not reflect the larger structure of the data.

      We do not know of a standard term for this phenomenon, so instead of dragging the reader through this tangential argument, we have tried to offer a simpler motivation for using multiple targets:

      “Assessing the relationship between neural activity and the details of movement requires striking a balance between achieving repeatable behavior and evoking sufficient trial-to-trial variability to broadly sample movement space”.

      (4) Page 5: Caudal Forelimb Area should not be capitalized.

      Obviated with the change in area nomenclature.

      (5) Page 7: "of linearly independent degrees of freedom" - for a neuroscience audience, I think it is better to explicitly mention that the resulting PCs are uncorrelated.

      We agree that this section could benefit from clarification. We have attempted to provide additional nuance to indicate what the analysis was intended to test.

      “Despite the strong coupling between the proximal and distal joint angles, rich variation remained in the action of different joints over time. The presence of strong correlations across joints suggested that the kinematics may be well described by a smaller number of independent degrees of freedom than the total number of recorded angles. To assess the number of linearly independent (uncorrelated) degrees of freedom amongst the 24 joint angles and velocities, we used double-cross-validated PCA (Yu et al. 2009); Methods; Fig. 3D), finding intermediate dimensionalities of 7 (median for joint angles) and 10 (velocities; Fig. 3E). This is consistent with the idea that joint angles across the limb are coordinated instead of controlled independently, and that this coordination is flexible enough over time to enable accurately performing reaching and grasping to different targets.”

      (6) Page 7: In the Results, the authors should mention what indicator is being used, the imaging frame rate, and summarize briefly how cells were defined.

      Thank you for the suggestion, these details have been added to the relevant results section for clarity.

      “To do so, we recorded neural activity from neurons in layer 2/3 M1-fl extending into the immediately adjacent secondary motor cortex (M2), and the forelimb region of S1 (S1-fl) using two-photon calcium imaging of GCaMP6f-expressing neurons in layer 2/3 (185-230 μm deep, imaged at 31 Hz, cells extracted with Suite2p (Pachitariu et al 2017)).”

      (7) Page 7: "corrected at n=2" - n doesn't typically refer to the number of tests, so for clarity I would say "corrected for dual tests."

      Thank you for pointing this out, we have corrected the text and added additional explanation in the methods for our approach to determining statistical significance across the targets and locking events.

      “P-values obtained through the ZETA were then Bonferroni corrected for dual tests when measuring the number of cells modulated to a given event and corrected for six tests (2 targets and 3 events) when measuring the overall number of modulated cells.”

      (8) Page 7: In the Results, when the decoding is introduced, it would be helpful to have a few details without having to hunt through the Methods. For example, were things regularized, how was cross-validation handled, etc?

      Thank you for the suggestion, these details have been added to the relevant results section for clarity.

      A simple linear regression model related the single-trial joint angles at all time points to single-trial neural activity at the corresponding moments. The model was fit with ridge regression, the ridge penalty was determined via a heuristic (Karabatsos 2018), and performance was measured on held-out trials (80/20 train/test split, 50 folds).

      (9) Page 8: I think it is worth noting how much mouse reaching involves shoulder rotation as opposed to movement in other joints, as this seems very different from primates.

      Thank you for pointing this out. We think this is mostly a task difference: our mice were in a quadrupedal stance, whereas monkeys are typically asked to reach from a sitting position. We now mention this in the Results. 

      “Reaching evoked particularly large rotation of the shoulder, likely because the mice reached from a quadrupedal position to targets on either side of the snout.”

      (10) Page 8: Should provide quantification to clarify what is meant by "closely tracked."

      We have updated the text to indicate that this claim was meant to be qualitative, and to more clearly highlight that the interest here is the first demonstration of the ability to reconstruct valid forelimb postures from decoded joint angles in the mouse. Quantifying the reconstruction properly would require substantially more manual data labeling, and the successful decoding itself demonstrates indirectly that the reconstructions are good enough to obtain the results of interest.

      Additionally, we reconstructed the skeletal representation of the forelimb from the decoded joint angles and found that, as intended, the reconstructed postures had strong qualitative resemblance to the true postures, even of “minor” angles like cylindrical paw deformation or digit splay (Fig. 5C,G).

      (11) Page 8: "Overall, these results suggest that instantaneous movement-related signals are similarly distributed across CFA and fS1." - I know we are being succinct here, but this sentence sounds like a non sequitur in the context of this paragraph - perhaps include a conclusion from the results in this paragraph first, then summarize the whole section.

      Thank you for the suggestion, we have updated this text to more clearly conclude the results of this section.

      Overall, these results reveal that neural activity in M1-fl and S1-fl is closely related to the kinematic details of reach-to-grasp movements. The ability to decode substantial variance in proximal and distal joints suggests that this relationship extends to the entire forelimb and the similar performance obtained from each area suggests that this information is similarly distributed across M1-fl and S1-fl. 

      (12) Page 10: Mention of projections from fS1 does not explicitly specify their preferential targeting of the dorsal horn, which seems relevant.

      We appreciate the suggestion and have added this detail to the text.

      Rodent S1-fl is known to influence interneuron populations in the spinal cord through direct and indirect projections that predominantly target the dorsal horn (Ueno et al. 2018), thus these signals may also reflect S1-fl’s important role in modulating reflex circuits to coordinate sensory feedback with movement generation (Moreno-López et al. 2016; Moreno-Lopez et al. 2021; Seki et al. 2003).

      (13) Page 31: Labels on the figure indicating what blue and red stand for would be helpful.

      Thank you for the suggestion, labels have been added to indicate left and right trials for Figure 5 C/F and Figure 6A.

      (14) Page 32: Legend does not include panel D.

      Thank you for catching this, the corresponding caption has been added.

      Reviewer #2 (Recommendations for the authors):

      (1) The Introduction could perhaps set the central question in starker relief. What specifically do the authors mean by high- vs low-level control? As suggested by the cited studies, this has been a fraught issue in primate work for decades, and I think a finer-grained framing of alternative hypotheses would help set up the results. For example, would better performance at decoding joint angles than paw position be evidence for lower-level control? The clarity of the Introduction might also be improved if the facts and unknowns were broken down by species throughout.

      We have tried to further improve the focus of the Introduction on the central question, clarify what we mean, and make clearer in the review of the literature which species a finding comes from.

      The clarifying text from the introduction is quoted below:

      Extensive motor mapping experiments in rodents have revealed that activating different parts of the sensorimotor cortex evokes movements of different body parts or different kinds of movements of the same body part, as it does in primates (for review, see (Harrison and Murphy 2014)). Yet it is unclear how the topography of stimulation-evoked movements relates to the roles of these areas during volitional actions. Perturbations during behavioral tasks in mice involving forelimb lever or reaching movements have provided a coarse-level understanding of how these areas contribute during behavior. Inactivations and lesions of M1 and S1 have shown that M1 is required for the execution of dexterous reach-to-grasp movements (Guo et al. 2015; Sauerbrei et al. 2020; Galiñanes et al. 2018; Wang et al. 2017; Whishaw et al. 1991; Whishaw 2000) and that S1 is essential for adapting learned movements to external perturbations of a joystick (Mathis et al. 2017). However, spinal cord projections from mouse M1 and S1 primarily target spinal interneurons rather than directly synapsing onto motor neurons (Gu et al. 2017; Ueno et al. 2018; Wang et al. 2017), suggesting cortical activity might play a more modulatory role. Further, stimulation of brainstem nuclei alone can evoke naturalistic forelimb actions, including realistic reaching movements involving coordinated flexion and extension of the proximal and distal limb (Esposito et al. 2014; Ruder et al. 2021; Yang et al. 2023). Taken together, these results have raised the question of what role mouse M1 and S1 play in the control of goal-directed forelimb movements. 

      One route to answering this question involves characterizing the signals present in mouse M1 and S1 during movement. If mouse M1 and S1 were to control only high-level aspects of forelimb movements, activity should be dominated by ‘abstract’ signals like target location and reflect little trial-to-trial variability in reach kinematics. If instead M1 and S1 control low-level movement features then activity should correlate strongly with forelimb joint angle kinematics and their trial-to-trial variation when reaching to different targets. While the presence of high- or low-level signals in a cortical area does not necessarily imply that they are causally responsible for these aspects of movement, characterizing what signals are present serves as a first step toward determining how these areas relate to movement.

      (2) The kinematics and calcium traces appear to be highly stereotyped across trials. If the population encodes joint angles, would one expect to find correlations between the neural and kinematic residuals after subtraction of the time-varying means? Some additional analysis and/or discussion on this point would be helpful, especially as there are only two targets.

      This is a great idea. As suggested, we implemented regression models on the residuals for each target in the new Figure 5S3. Figure 5S3 A and B show the performance when decoding the residuals for right trials and C and D show performance for left trials. Decoding remained well above chance, despite shrinking down due to predicting this relatively small within-target variation. This analysis supports our claims from the main regression models in Figure 5 and 5S1-2, and also suggests that movements ipsilateral to the reaching limb (contralateral to the recording hemisphere) may be better encoded than movements contralateral to the reaching limb. We have added a reference to this additional residual analysis in the final paragraph of the decoding section of the Results section:

      “Finally, we tested whether the ability to decode these many joint angles was a direct consequence of inter-joint correlations, and might not be indicative of the presence of “real” information about some of these joints. To do so, we fit partial correlation models that removed correlations between proximal and distal joints, or removed correlations of the joint angles with a high-level parameter – the overall distance of the paw centroid to the spout. Despite substantially lowering the behavioral variance, in each case the residuals could still be decoded from neural activity (Fig 5S2A-D). Similar decoding performance for M1-fl and S1-fl was obtained from models fit to decode single-trial residuals separately for left and right trials (Fig 5S3A-D), indicating that trial-to-trial variations on each basic movement were decodable from these populations.”

      Along similar lines, binary classification is used to characterize cue-, lift-, and contact-responsive neurons. Is it possible to exploit trial-to-trial variation in the cue-lift and lift-contact latencies to extract the time-varying marginal effects of each event (e.g., using a GLM)?

      For the detection of single-cell modulations by different events, we have elected to retain our simple statistical test to determine modulation; in our experience, encoding models typically involve a surprising number of steps to get them to do what you actually intend. We leave more extensive encoding model-style analysis to future work, currently in progress.

      (3) The authors mention prior studies suggesting that the control of some forelimb tasks can be gradually transferred from the cortex to the subcortical centers. Have they performed the inactivation at different time points across learning, and if so, do they have evidence for a diminishing effect over time (e.g., blocking of both initiation and coordination early in training)? In addition, the effects of motor cortex inactivation are similar to, but slightly different from, effects shown in reaching tasks in prior studies. Some additional discussion on this point would be useful.

      Our inactivation experiments in this study were intended to coarsely demonstrate the involvement of mouse forelimb sensorimotor cortex in our task. We have not performed the inactivations over learning and leave such experiments to future work. 

      We agree that a little more clarity relating our results to previous ones was warranted. Previous studies (Guo et al. 2015 and Galinanes et al. 2018) have demonstrated inactivation impacts on similar tasks, but for thoroughness we sought to show the same for our task as it varied from the pellet and motorized water spout tasks in both training time and target configurations. Our results are strongly in line with those of Galinanes et al. 2018 which used a fairly similar water spout target configuration. In the inactivation experiments of that paper, 3 out of 13 animals with initiation-triggered inactivations were able to initiate reaching within a time window similar to control trials. Additionally, a proportion of trials across multiple mice proceeded with little perturbation from the inactivations. This is consistent with our observation that M1-fl inactivations may either abolish movement initiation or allow movement initiation but impair task completion on a trial-by-trial and animal-to-animal basis. Further work is required to determine what factors influence these differential responses to inactivation and to determine how these effects differ across task variations (i.e., pellet vs water spout). We have added a brief description of these nuances to the text for clarity. 

      “These inactivations blocked the execution of the reach to grasp sequence, preventing the animal from making contact with the spout during the 3-second laser stimulation period (Fig. 1F; 86.5% control trials with contact within 3 seconds of cue, 5.1% inactivation trials with contact, P < 10<sup>-191</sup>, Mann-Whitney U test, 2 mice, 495 stimulation trials). Interestingly, inactivation at the time of cue often did not prevent reach initiation (mouse 1: 54.7%, mouse 2: 34.2% of inactivation trials with lift within 3 seconds; 93.5%, 86.2% control trials). Yet the movement stalled once the paw and digits extended towards the spout, producing uncoordinated and unsuccessful reaching trajectories (Fig. 1I, two representative datasets). Taken together, these results support the involvement of M1-fl in the water-reaching task and suggest that the strength of inactivation effects may depend on specific task details like training time or target configuration (c.f. Galinanes et al. 2018).”

      Minor points

      (1) The rationale for the multiple comparisons procedure in identifying event-locked responses should be explained in more detail. If I understand correctly, the authors are not correcting for comparisons across ROIs, but instead control the family-wise error rate across brain regions and event types (dividing alpha by two or six). Why not instead control the false discovery rate across ROIs? 

      Thank you for pointing this out, it was confusing as written and we received a similar comment from Reviewer 1. We have fixed the wording now to make it clearer why we did this. We simply aimed to describe how many of the recorded neurons in each area were modulated by the task as a proxy for the engagement of these areas during the behavior, and to use this measure of modulation as a criterion for including the neuron in subsequent analysis. In other words, if the question had been “are any neurons in this area modulated by the task?” then correcting for the number of ROIs would be the correct method; but if the question is, “is this neuron probably modulated and therefore worth including in my decoder?” correcting for the number of ROIs will typically be much too conservative. Thus, we only sought to correct for the false discovery rate across events and targets for each ROI. We have added additional text in the methods to clarify these choices, below. Please also see response to (7) from Reviewer 1 above.

      “Note that we did not correct for the number of ROIs tested for two reasons. First, the goal of this testing was to serve as a criterion for inclusion in subsequent decoding analyses, not to determine whether any neurons in the area at all were modulated; and second, correcting for the number of ROIs would bias comparison between areas if different numbers of ROIs were recorded in one area vs. the other.”

      (2) It appears joint angles are treated as linear variables in the decoding analysis; is this correct? This seems reasonable as long as the range of motion is not too large, but the authors might briefly comment on the issue in the Methods. 

      Yes, all joint angles are treated as linear variables in the linear regression model. We observed empirically (as can be seen in Figure 3B and Figure 5B/F) that the joint angle variables were relatively constrained to specific ranges during the task, with no angles displaying substantial wrap-around during the reaching and grasping movements. It is true that use of nonlinear decoding would almost surely improve performance further. Future work could also compare decoding of joint angles with muscle forces, which correlate and which we made no effort to distinguish here. In this work, though, the demonstration of a substantial relationship between neural activity and kinematics already tells us that fine details of movement are present in the M1 and S1-fl populations, which is a critical fact to understand these areas and was not previously known. We now comment explicitly on this, as suggested.

      “Joint angle or velocity kinematics were linearly interpolated from their original 6.66 ms to 10 ms and smoothed with a Gaussian (15 ms s.d.). These angular variables were then treated linearly in decoding analyses as their ranges were relatively constrained during the reaching and grasping movements; although the true relationships are likely nonlinear, this serves as a sufficient approximation to demonstrate the presence of a relationship between neural activity and kinematics.”

      (3) Are the limb pose estimates mirrored along the mediolateral axis? Figures 1C and 2D appear to show reaches to the left spout on the animal's right.

      Thank you for pointing out the ambiguity in the display of these data. The reach trajectories were not mirrored along the mediolateral axis, but they are displayed from the perspective of the behavioral imaging cameras as shown in Figure 1A. Thus the right target reaches (ipsilateral to the animal’s reaching arm) are on the left side of the camera image and the left target reaches (contralateral to the animal’s reaching arm) are on the right side of the image. We have clarified this in the figure captions.

    1. Reviewer #3 (Public review):

      This study makes excellent use of a uniquely large dataset of reaching movements collected over several decades to evaluate the origins of systematic motor biases. The analyses convincingly demonstrate that these biases are not explained by errors in sensed hand position or by biomechanical constraints, but instead arise from a misalignment between eye-centric and body-centric representations of position. By testing multiple computational models across diverse contexts-including different effectors, visible versus occluded start positions-the authors provide strong evidence for their transformation model. My earlier concerns have been addressed, and I find the work to be a significant and timely contribution that will be of broad interest to researchers studying visuomotor control, perception, and sensorimotor integration.

      Comments on revisions:

      None

    2. Author response:

      The following is the authors’ response to the previous reviews

      General recommendations (from the Reviewing Editor):

      The reviewers agreed that addressing some specific concerns would improve the clarity of the paper and the strength of the conclusions. These points are listed below, and described in more detail in the reviewer-specific 'Recommendations for Authors':

      We thanks the editor and reviewers for the encouraging feedback and constructive comments. We provide our point-by-point response below.

      (1) The details of the new experiment including number of subjects and a description of the analysis should be provided in the main text.

      We now provide a detailed description of the methods (including the number of subjects; N = 30) and analyses for the new experiment. See our response to Reviewer 2 for more details.

      (2) It would be informative to see how the amplitude biases observed, agree with those found by Gordon et al. 1994.

      Addressed. Please see our response to Reviewer 1, comment 1.

      (3) Each of the models lead to different bias patterns. It would be very helpful to hear the author's interpretation, ideally with a mathematical explanation, of what leads to these distinct patterns.

      Addressed. Please see our response to Reviewer 1, comment 2.

      Reviewer #1 (Recommendations for the authors):

      (1) Most of my points have been addressed convincingly in this revision. The new experiment in which also biases in movement amplitude were determined is a welcome addition to the paper. However, I could not see the results of this study, as the authors did not include Fig. 4 in the manuscript, but repeated Fig. 3. That's unfortunate as I would have like to see the similarity between the biases in direction and amplitude. Moreover, I would have liked to see how the amplitude biases agree with those found by Gordon et al. EBR (1994) 99:112-130, and to which extent Gordon et al.'s explanation can explain the pattern.

      We apologize for including the incorrect figure in the previous version of our manuscript. We did make a correction and submitted a corrected version, but it appears that it didn’t make its way to you. The correct Figure 4 is now in the manuscript.

      The motor biases in amplitude (extent) observed in Experiment 4 (Author response image 1) are qualitatively similar to the pattern reported by Gordon et al. 1994. While the exact peaks do not match perfectly, both datasets show a two-peaked pattern.

      Gordon et al. (1994) attributed the bias in amplitude to direction-dependent variation in movement speed which, in their view, arise from anisotropies in limb inertia. Specifically, moving the upper arm along its quasiorthogonal direction (i.e., rotation about the elbow) requires lower effective inertia than moving parallel to the upper-arm axis. Given the arm posture in both datasets, the upper limb points toward ~135°/315°, with the orthogonal direction corresponding to ~45°/225°. The two-peaked speed profiles in both our data Author response image 1 and Gordon et al. are consistent with this prediction.

      Author response image 1.

      Gordon et al (1994) noted that, while the extent bias function should mirror the speed bias function, the motor planning system might proactively compensate for the speed bias. Indeed, while the extent and speed bias functions are roughly aligned in their study, the two are misaligned in our Experiment 4. For example, the speed function peaks around 45° which corresponds to a valley in the extent bias function. The difference between their data and ours could be due to a difference in the starting point configuration. However, their model predicts alignment of the speed and extent functions independent of starting point configuration. In contrast, the TR+TG model does predict our observed extent bias function and yields predictions about how this should change with different start point configurations. As such, while heterogeneity in movement speed may contribute to extent bias to some degree, we think the transformation bias and visual-target bias likely play a larger role in determining the amplitude bias observed extent bias at movement endpoint.

      We have added a discussion section about the bias function reported by Gordon et al. (1994) and their account in the manuscript (lines 482-493). We do not repeat it here, as the content largely overlaps with the response above.

      (2) One of the most important new insights from this study is that the three single-source models lead to different bias patterns, with 1, 2 or 4 peaks. However, what I miss in the paper is an intuitive explanation why they do so. Now, the models are described and their predictions are shown, but it remains unclear where these distinct patterns come from. As scientists, we want to understand things, so I would very much appreciate if the authors can provide such an intuitive explanation, for instance using a mathematical proof. That could also identify how general these patterns are, or if there are certain requirements for them to occur (such as a certain shape of the transformation bias).

      Note that the closed-form mathematical expression for the motor bias function is not straight forward. As such, the intuition comes primarily from inspection, that is, the model simulations themselves, what we show Figure 1 of the paper. Importantly, the model predictions are insensitive to the parameter values over a reasonable range. Thus, the number of peaks predicted by each model is a core distinguishing feature. We present in the Supplementary Results a formalized mathematical analysis to illustrate how different models produce different numbers of peaks in the movement-bias function.

      (3) I think it's a good idea to change the previous "Visual Bias" into a "Target Bias". This raises the question whether the "Prioprioceptive Bias" should not be changed into a "Hand Bias" or "Start Bias"?

      While we appreciate the reviewer’s point here, we prefer the term “Proprioceptive Bias” given that this term has been used in the literature and provides a contrast with sources of bias arising from vision. “Hand Bias” and "Start Bias” seem more ambiguous.

      L51: I think "would fall short" should be replaced by "would overshoot".

      L127: I think "biased toward the vertical axis" should be replaced by "biased away from the vertical axis". Figure 3 still contains the old terminology like T+V. Please replace by the new terminology. L255: Replace "Exp 1a" by "Exp 1b".

      L376: Replace 60 by 6.

      L831-2: I hope the summed LL was maximized, not minimized.

      Thanks for catching the typos. We have corrected all of them.

      Reviewer #2 (Recommendations for the authors):

      I think that Experiment 4 does not mention how many participants performed the study. (Only in the response to the reviewers I found this)

      We have added information regarding the number of participants in the Fig 4 (N=30).

      I am very happy that the authors added the biomechanical simulation into the paper. I am not convinced that this addressed my concerns exactly but it is an excellent addition and the authors have now adjusted the text appropriately.

      We appreciate the positive response to our additional assessment of biomechanical factors. We welcome any additional information on how we might fully address this issue.

      line 826: extend -> extent

      Corrected.

      Figure 4. I think that the authors have put the wrong figure here. I cannot see any data for extent. I would need to see this figure (or please correct me - but the caption doesn't match the figure and I don't see the results clearly. (I think the review might have the correct figure).

      We apologize for this mistake. We now provided the correct Figure 4 in the paper (also included in the first page of the response letter).

      I am missing the detailed description on when the direction error and distance error were calculated for exp 4 - and what exactly was used? How did the authors examine the values without correction? What time point was used? Did I miss the analysis section for this?

      Participants were instructed to make fast, straight movement without any corrections and were given up to 1 s to complete the movement. Hand position was recorded once the movement speed dropped below 1 cm/s. On 99.8% of trials, movement speed did not increase once this threshold was passed, indicating that the participants adhered to the instructions. On the remaining trials, we detected a secondary corrective movement (increase in speed >5 cm/s). On these trials, we used the position recorded when the movement speed initially dropped below 1 cm/s as the endpoint position. The pattern of results would be the same were we to exclude these trials.

      This information has been added to the Methods section (line 661-666).

    1. Author response:

      The following is the authors’ response to the original reviews.

      Reviewer #1:

      SOM+ interneurons such as Martinotti cells target the apical tufts of pyramidals in the cortex. Since interneurons in general are strongly implicated in mediating rhythmic population activity over a range of timescales, it is quite appropriate to study the consequence of rhythmic inhibition provided by SOM+ interneurons for synaptic integration, including the phenomenon of dendritic spikes. However, using conclusions from a singular study (ref 22) to identify the beta band as the rhythm mediated by SOM+ is not very accurate. SOM+ interneurons have been implicated in regulating rhythms centered just below 30 Hz (refs 22, 21). It is a range that lies in the grey zone of the traditional definition of beta and gamma. However, it is significantly higher than the 16 Hz rhythms explored in this study. It thus remains unknown how a 25-30 Hz rhythmic inhibition (that has an experimentally suggested role for dendrite targeting SOM+ INs) in apical tufts regulates dendritic spikes.

      We agree with the reviewer that the rhythms arising from SOM+ interneurons can extend their frequencies higher than the 16 Hz analyzed in this study. To address this, we have conducted a new set of simulations where we delivered distal dendritic inhibition across a range of frequencies, from 0.5 to 80 Hz (see new Results section “Frequency specific effects of rhythmic inhibition on neuronal integration”). These results revealed, surprisingly, that at 30 Hz their ability to entrain Ca<sup>2+</sup> and NMDA spikes degrades (but not Na<sup>+</sup> spikes). This suggests that beta rhythms in the 20-30 Hz range are operating at the highest frequency for which dendritically targeting inhibition will be effective. The implications are covered in the Discussion section “Interaction with microcircuitry”. They are:

      “Particularly in the visual cortex, SOM interneurons can generate a rhythm in the 25-30 Hz range [22]. We found this to be at the upper end of the frequency range for dendritic inhibitory rhythms to be effective in modulating NMDA and Ca<sup>2+</sup> spikes. If this rhythm solely recruited SOM interneurons, its effectiveness would be marginal. Potentially compensating for this, recent work has found that PV interneurons also participate in beta/low-gamma [23, 24] (but see [21, 22]). In our model, on its own when beta rhythmic inhibition was delivered perisomatically we found that it was less able to entrain spiking and had an overall hyperpolarizing effect. However, if delivered in conjunction with the distal dendritic inhibition arising from SOM interneurons, this may strengthen entrainment.”

      Distal dendritic inhibition has been previously shown to be more effective in controlling dendritic spikes. However, given the slow timescale of dendritic spikes, it can be hypothesized that high-frequency rhythmic inhibition would be ineffective in entraining the dendritic spikes either in distal or proximal location, as demonstrated by 4H and 5F, and vice versa. A computational study can take this further by exploring the robustness of this hypothesis. By sticking to a single-frequency definition of what constitutes Gamma (64 Hz) and Beta (16 Hz) inhibition, the current exploration does support the core hypothesis. However, given the temporal dynamics of dendritic spikes, it is valuable to learn, for example, the upper bound of "Beta" range (13-30Hz) inhibition that fails to phasically modulate them. In addition to the reason stated in the earlier paragraph, Alpha band activity (8-12 Hz), has been implicated (e.g. van Kerkoerle, 2014) in signaling of inter-areal feedback to the superficial layer in the cortex, potentially targeting apical tufts of pyramidals from multiple layers and resulting in alpha-range rhythmic inhibition. To make the findings significant, it might therefore be more pertinent to understand the consequences of ~10Hz rhythmic inhibition (in addition to the ~25-30 Hz Beta/Gamma) in the apical tufts for phasic modulation of dendritic spikes.

      We added an additional set of simulations that address this in the Results section ‘Frequency specific effects of rhythmic inhibition on neuronal integration’. In general, we found that dendritic and perisomatic inhibitory rhythms at lower frequencies could entrain AP generation, but with less functional specialization. This is explored in our Discussion section ‘Interneuron specializations and rhythm timescales’.

      The differential effect of Gamma and Beta range inhibition on basal and apical excitatory clusters is not convincing from the information provided. The basal cluster appears to overlap with perisomatic inhibitory synapses. The description in the methods does not have enough information to negate the visual perception (ln 979-81). With this understanding, it is not surprising that the correlation between excitation and APs is high (during the trough of gamma) for basal and not apical excitation. A more comparable scenario would be a more distal location of the basal excitatory cluster.

      While we stated in the original manuscript that we were contrasting ‘basal’ vs. ‘apical’ clustered inputs, this terminology did not reflect our intent with these analyses. We meant to contrast proximal vs. distal dendritic clustered synaptic inputs, which the reviewer correctly noted is confounded in the apical vs. basal comparison. We have rewritten these results, their discussion, and corresponding figure, to clearly state that we are contrasting proximal vs. distal synaptic input.

      Reviewer #2:

      The weaknesses are probably in some of the parameterizations of inhibitory synaptic dynamics. A unitary peak conductance of 1nS is very high for inhibitory synapses. This high value could invariably skew some of the network-level predictions. The authors could obtain specific parameters from the Neocortical Collaboration Portal (https://bbp.epfl.ch/nmcportal/microcircuit.html), which is an incredible resource for cortical neurons and synapses.

      We appreciate the valuable resource mentioned by the reviewer and will consult it when constructing future models. Regarding the present one, our choice of peak conductance was based on previous studies, namely:

      Egger R, Narayanan RT, Guest JM, Bast A, Udvary D, Messore LF, Das S, de Kock CPJ, Oberlaender M (2020) Cortical output is gated by horizontally projecting neurons in the deep layers. Neuron 105, 122-137.e128.

      and

      Xiang Z, Huguenard JR, Prince DA (2002) Synaptic inhibition of pyramidal cells evoked by different interneuronal subtypes in layer v of rat visual cortex. J Neurophysiol 88, 740-750.

      The study by Egger et al. used an inhibitory peak conductance of 1 nS and was simulating circuitry very similar to ours. We validated these synapses in pilot simulations that sought to characterize the resulting IPSPs and IPSCs, and whose results can be seen in Table 1 of our methods. These synapses exhibited IPSCs whose peak amplitudes ranged over values (~24162 pA) that agreed with the experimental literature, such as Xiang et al.

      Given this, we feel our parameterization of inhibitory synapses does not warrant any changes.

      Reviewer #3:

      What disappointed me a bit was the lack of a concise summary of what we learned beyond the fact that beta and gamma act differently on dendritic integration. The individual paragraphs of the discussion often are 80% summary of existing theories and only a single vague statement about how the results in this study relate. I think a summarizing schematic or similar would help immensely.

      We agree with the reviewer that a summary schematic would help the reader. This has been added to the manuscript as Figure 11. It demonstrates the principal findings of the paper and is referenced in the opening paragraph of the discussion section.

      Orthogonal to that, there were some points where the authors could have offered more depth on specific features. For example, the authors summarized that their "results suggest that the timescales of these rhythms align with the specialized impacts of SOM and PV interneurons on neuronal integration". Here they could go deeper and try to explain why SOM impact is specialized at slower time scales. (I think their results provide enough for a speculative outlook.)

      This discussion has been expanded under the section “Interneuron specializations and rhythm timescales”. The added text is:

      “So, while our results suggest that spatial targeting of SOM and PV interneurons aligns with the timescales of their network-level rhythms, it could also be that their timing and subcellular localization interact to produce specialized neuron-level functions [85]. For instance, NMDA and Ca<sup>2+</sup> spikes in the distal dendrites last for ~50 ms, making the slower beta rhythm more appropriate for bidirectionally controlling them. Both can be described as dynamical systems with distinct phases with differing sensitivity to inhibition. Ca<sup>2+</sup> spikes are dynamical events comprised of an initiation, plateau, and termination phase. Inhibition delivered during the plateau phase shortens their duration [86]. If the beta rhythm is comprised of cycling between periods of elevated excitation (increased NMDA spike generation) followed by elevated inhibition, then Ca<sup>2+</sup> spike initiation will tend to occur during the excitatory phase, and its plateau during the subsequent inhibitory phase. A plateau during the inhibitory phase will more quickly enter termination. This is bidirectional control. On the other hand, slower rhythms (e.g. 1 Hz) initiate Ca<sup>2+</sup> spikes during the excitatory phase that plateau and enter termination autonomously, before the inhibitory phase is reached. The same principle holds for NMDA spikes [87]. As a result, rhythms in the range from 15-30 Hz are optimal for synchronizing the onsets and offsets of dendritic spikes across a population of neurons.

      The integrative effects of gamma (>40 Hz) are also specialized. Low frequency inhibitory rhythms delivered to the soma tended to shift the membrane potential higher or lower with the rhythm’s phase, effectively bringing it closer or farther from AP generation but not changing the neuron’s sensitivity to fast synaptic inputs. In the gamma frequency range, this is reversed, with the mean membrane potential not varying with rhythm phase but with a shifting bias to positive or negative membrane potential fluctuations. In addition, the trough phase of gamma lowers the threshold for AP generation, while slower rhythms like beta only raise the threshold. Consequently, the timing of gamma is ideal for increasing the sensitivity of the neuron to rapid excitation. This agrees with the observation that gamma oscillations accompany rapid excitation-inhibition balancing [88].”

      We also extended our discussion section ‘Relevance to coding’ to explore how beta and gamma rhythms can support sparse vs. dense population coding, respectively. It reads:

      “One interpretation of rhythms arising from local inhibitory feedback is that they maintain the balance between excitation and inhibition. This can be thought of as a normalization operation that maintains activity within a set range. Normalization can be achieved either through a subtractive effect that raises the threshold for initiating an action potential, or a multiplicative effect that lowers the slope of the relationship between excitation and action potential firing rate. When considered at the population level, these normalization effects impact coding in different ways. Subtractive normalization increases sparsity by dropping out neurons whose excitation is below the raised threshold. Multiplicative normalization, however, encourages dense codes by scaling down firing rates and compressing the range of firing rates. This study found that while both perisomatic and distal dendritic inhibition produced subtractive effects, only perisomatic had a multiplicative effect. Tying this to beta and gamma, beta rhythms may encourage sparse population codes while gamma allows for dense.”

      Beyond that, the authors invite the community to reappraise the role of gamma and beta in coding. This idea seems to be hindered by the fact that I cannot find a mention of a release of the model used in this work. The base pyramidal cell model is of course available from the original study, but it would be helpful for follow-up work to release the complete setup including excitatory and inhibitory synapses and their activation in the different simulation paradigms used. As well as code related to that.

      We have added a Code and Data Availability section that addresses this. It reads: “Simulation code is deposited at ModelDB athttps://modeldb.science/2019883 . The raw simulation data are available from DBH upon request. Analysis code is posted as a github repo at https://github.com/dbheadley/InhibOnDendComp.”

    1. Reviewer #1 (Public review):

      Summary:

      The authors investigate the determinants of population-level cell size variability, quantified via the coefficient of variation, in budding yeast populations. Using a combination of computational modeling and experimental readouts, they conclude that mother-daughter division asymmetry is the dominant factor shaping the coefficient of variation of cell size. In particular, through parameter sensitivity analysis of the Chandler-Brown model and empirical perturbations, the authors show that size-control mutations have limited effects on CV, whereas modulating mother-daughter asymmetry, by changing the growth environment, produces substantially larger shifts.

      Strengths:

      (1) The study addresses a fundamental question in biophysics, i.e., what are the mechanisms that produce and maintain population size heterogeneity?

      (2) It provides a conceptual reconciliation for previous observations that size-control mutants often alter mean size but not CV.

      (3) The modeling framework is clearly explained and compared to the data.

      (4) The parameter sensitivity analysis is thoughtfully performed and provides transparent intuition about which parameters influence variability.

      (5) The writing is clear, and the figures are well-organized.

      Weaknesses:

      (1) The work focuses on the Chandler-Brown model, so it is not clear to what extent the conclusions depend on it. A sensitivity or robustness check using an alternative model would strengthen generality.

      (2) CV is the sole descriptor used to quantify heterogeneity; while this is an efficient descriptor, it must be handled with care when used on experimental data, as it may vary due to differences in the chosen observables (e.g., if size is identified via cell volume, length, area, number of proteins, etc.) instead of real differences in the distribution.

      (3) The experimental validation using varied nutrient conditions is interesting; however, the statistical significance of the found correlations should be provided/discussed.

    2. Reviewer #2 (Public review):

      Summary:

      This paper provides a new framework for understanding how cell size variability arises in budding yeast populations. Whereas previous studies emphasized G1/S size control in daughter cells as the main regulator of size homeostasis, the authors show that perturbations to this control checkpoint have only modest effects on population-wide size variability.

      By extending a stochastic model of the yeast cell cycle to include both mother and daughter lineages, the authors demonstrate that division asymmetry-stemming from slower growth and longer post-Start phases in mother cells-is the key factor determining the population coefficient of variation (CV). As mothers grow larger and daughters smaller, the overall size distribution broadens. Experimental measurements across multiple mutants and conditions support the predicted correlation between asymmetry and CV.

      Strengths:

      The main conceptual advance of this study is to consider the full proliferating population, and in particular the dominant mother lineages, rather than single-cycle daughters, thereby offering a population-level explanation for size variability that is consistent with several previous but seemingly conflicting results.

      Weaknesses:

      Nevertheless, the modelling is described superficially and has notable limitations.

      (1) The extended Chandler-Brown model was originally parameterized only for daughter cells, and its generalization to mothers introduces several new assumptions that are not directly tested.

      (2) The model treats asymmetry phenomenologically, without a mechanistic basis, so while it correctly identifies correlations, causality remains uncertain.

      (3) Moreover, since population CVs emerge from steady-state lineage dynamics, they could be sensitive to parameter choices or growth-related details not fully explored in the current analysis.

      In summary, this study provides a useful conceptual synthesis and a useful quantitative framework, but it should be clear that readers should interpret the modeling as heuristic. The central message-that division asymmetry dominates population size variability-remains interesting and well supported at the phenomenological level.

    3. Reviewer #3 (Public review):

      Summary:

      The article studies the origins of cell size random variability in budding yeast. Different strains with different average cell sizes have very similar noise measured using the coefficient of variability defined as the standard deviation over the mean. Manipulating the noise in key variables such as the duration of cell stages, the growth rate or the division strategy (adder, timer, sizer) was not enough to explain the observed noise in mutants. The proposed solution for the origin of most of the cell size noise is related to the asymmetry in the average cell size for cells with two different phenotypes: daughter cells (New cells that have not passed the first division) AND 'Mother cells' (the rest). The origin of the cell size noise is mainly related to the fact that the distributions of these phenotypes have different cell size distributions. The article includes simple statistical methods for hypothesis analysis and explanatory figures.

      Strengths:

      The article provides different approaches: experimental (mutants and different growth conditions) and computational (simulations) to explain and test the hypothesis. The methods are based on previous articles with simple conclusions and explanations easy to follow.

      The rigor level in both mathematical and biological approaches looks fair to me. The terms are well defined and consistent throughout the article. Authors use well-established analysis techniques.

      The proposed theoretical analysis is coarse-grained and therefore can explain different strains and mutations using mathematical tools (noise analysis), aiming to reach general (mathematically) claims. This approach strengthens the conclusions and provides a good language to set a bridge between the biological community and mathematicians (quantitative biologists).

      The concept that the population heterogeneity (mothers vs daughters) is a fundamental reason behind the cell size variability is not new, but this article presents a clear experimental justification for the development of complete models of cell size regulation. I consider this contribution very relevant to the community modelling cell size.

      Weaknesses:

      The concept that population heterogeneity (mother and daughters) with different cell size distributions explains the observed size variability in a heterogeneous population. It is not clear how the population composition can affect this heterogeneity. Intuitively, I would expect that the fraction (number of daughters)/(number of mothers) changes in different stages of the population expansion due to the mean duration of both stages can change in different growth conditions. I would suggest studying how different (or not) these fractions are in different conditions. The authors should acknowledge this effect and discuss briefly using, for instance, simple models of random variables addition (adding different fractions of individuals with different cell size distributions) in which cases (different fractions or different means and noises in their respective distribution) their contribution is relevant. Finally. Do different simulations (gradient or sizer, timer) predict different moments (mean and CV) in distributions of both mother size and daughter size?

      Related to the previous comment, I would also include the fraction (number of daughters)/(number of mothers) or the percentage in different growth conditions with their respective size moments (mean and CV) to test whether the resultant cell size moments are related to the addition of two variables with different fractions with their respective moments.

      It is interesting how the G1 timer and G1 Sizer are located in different quadrants of Figure 4D, while the studied mutants belong to the other quadrant. I expected them to be closer to the G1 timer, similar to that observed in Figure 4G. I think the authors should discuss this dissimilarity.

      Although the authors are working using a definite model, other models would predict different results, especially in synthetic data. For instance, the same models for obtaining sizers can predict different noise levels.

      Nieto, C. et al., 2024. npj Systems Biology and Applications, 10(1), p.61.

      Barber, Felix, et al., Frontiers in cell and developmental biology 5 (2017): 92.

      Teimouri, H. et al,.2020. The Journal of Physical Chemistry Letters, 11(20), pp.8777-8782.

      I would mention that the noise level also depends on whether the population has reached steady-state conditions. This would require multiple generations, and measure over at least a couple of thousand cells. Therefore, experiments with single-cell-derived colonies would present different levels of noise than the noise in steady conditions, especially if few cells were sampled. However, I acknowledge that the purpose of the article is not a detailed description of the system but rather the presentation of the concept and for that matter, this level of detail is not mandatory.

    1. Reviewer #3 (Public review):

      In this manuscript, authors use the Drosophila wing as model system and combine state-of-the-arte genetic engineering to identify and validate the molecular players mediating the activity of one of the cis-regulatory enhancers of the apterous gene involved in the regulation of its expression domain in the dorsal compartment of the wing primordium during larval development. The paper is subdivided into the following chapters/figures:

      (1) In the first couple of figures, authors describe the methodology to genetically manipulate the apE enhancer (a cartoon summarizing all the previous work with this enhancer might help) and identify two well-conserved domains in the OR463 enhancer required for wing development (the m3 region whose deletion phenocopies OR463 deletion: loss of wing, and the m1 region, whose deletion gives rise to AP identify changes in the P compartment).

      (2) In the following three figures, authors characterize the m1 regulatory region, identify HOX and ETS binding sites, functionally validate their role in wing development and the activity of the genes/proteins regulating their activity (eg-. Hth and Pointed) by their ability to phenocopy (when depleted) the m1 loss of function wing phenotype. Authors conclude that Hth and Pointed regulate apterous expression through the m1 region.

      (3) In the last few figures, authors perform similar experiments with the m3 regulatory region to conclude that the Grn and Antennapedia regulate apterous expression through the m3 enhancer.

      My comments:

      Technically sound: As stated in my previous review, the work is technically excellent (authors use state-of-the-art genetic engineering to manipulate the enhancer and combine it with genetic analysis through RNAi and CRISPR/Cas9 and phenotypic characterization to functionally validate their findings), figures are nicely done and cartoons are self-explanatory.

      Poor paper writing: The paper is too long and difficult to read/understand, many grammatical mistakes are found, and formatting is in some cases heterodox.

      Science:

      (1) The question of "who is locating the relative position of the AP and DV boundaries in the developing wing?" is not resolved. I would then change the intro or reduce the tone of this question. Having said that, I agree that these results shed light on the wing phenotypes of some apterous alleles related to AP identify and growth and, as such, I congratulate the authors.

      (2) Identification of two TFs (Grain and Antp) mediating the regulation of apterous expression is interesting but some contextualization might be required. Data on Antp is not as convincing as data on Grn. I wonder whether Antp data can be removed at all.

      (3) I am not sure whether the term hemizygous is used properly

    2. Author response:

      The following is the authors’ response to the original reviews.

      Public Reviews:

      Reviewer #1 (Public Review):

      Summary:

      The Drosophila wing disc is an epithelial tissue, the study of which has provided many insights into the genetic regulation of organ patterning and growth. One fundamental aspect of wing development is the positioning of the wing primordia, which occurs at the confluence of two developmental boundaries, the anterior-posterior and the dorsal-ventral. The dorsal-ventral boundary is determined by the domain of expression of the gene apterous, which is set early in the development of the wing disc. For this reason, the regulation of apterous expression is a fundamental aspect of wing formation.

      In this manuscript, the authors used state-of-the-art genomic engineering and a bottom-up approach to analyze the contribution of a 463 base pair fragment of apterous regulatory DNA. They find compelling evidence about the inner structure of this regulatory DNA and the upstream transcription factors that likely bind to this DNA to regulate apterous early expression in the Drosophila wing disc.

      Strengths:

      This manuscript has several strengths concerning both the experimental techniques used to address the problem of gene regulation and the relevance of the subject. To identify the mode of operation of the 463 bp enhancer, the authors use a balanced combination of different experimental approaches. First, they use bioinformatic analysis (sequence conservation and identification of transcription factors binding sites) to identify individual modules within the 463 bp enhancer. Second, they identify the functional modules through genetic analysis by generating Drosophila strains with individual deletions. Each deletion is characterized by looking at the resulting adult phenotype and also by monitoring apterous expression in the mutant wing discs. They then use a clever method to interfere in a more dynamic manner with the function of the enhancer, by directing the expression of catalytically inactive Cas9 to specific regions of this DNA. Finally, they recur to a more classical genetic approach to uncover the relevance of candidate transcription factors, some of them previously known and others suggested by the bioinformatic analysis of the 463 bp sequence. This workflow is clearly reflected in the manuscript, and constitutes a great example of how to proceed experimentally in the analysis of regulatory DNA.

      We thank the reviewer for these positive comments on the manuscript.

      Weaknesses:

      There are several caveats with the data that might be constructed as weaknesses, some of them are intrinsic to this detailed analysis or to the experimental difficulties of dealing with the wing disc in its earliest stages, and others are more conceptual and are offered here in case the authors may wish to consider them.

      (1) The primordium of the wing region of the wing imaginal disc is defined by the expression of the gen vestigial, which is regulated by inputs coming from the dorsal-ventral boundary (Notch and wg) and from the anterior-posterior boundary (Dpp). Having such a principal role in wing primordium specification and expansion, I am surprised that this manuscript does not mention this gene in the main text and only contains indirect references to it. I consider that the manuscript would have benefited a lot by including vestigial in the analysis, at least as a marker of early wing primordium. This might allow us to visualize directly the positioning of the primordium in the apterous mutants generated in this study, adding more verisimilitude to the interpretations that place this domain based on indirect evidence.

      Vg does indeed play a critical role on the formation of the wing disc, and it is an ideal marker for the identification of the wing pouch. In the updated version of the article, we have now followed the expression of vg in some of the OR463 mutants via immunostaining of the Vg protein (Supplementary Figure 6). Cells within posterior wing outgrowths in Δm1flies were invariably positive for Vg. This result further supports our previous identification of these cells as pouch cells. In those mutants in which no cross-over between DV and AP was observed, vg expression was severely reduced or absent, indicating that the wing pouch had not been specified. We thank the reviewer for this experimental idea, which we believe strengthens the final manuscript.

      We have added to the text:

      “To identify the nature of the posterior outgrowths, we performed anti-Vestigal (Vg) antibody staining of Δm1 mutants (Supplementary Figure 6). Vg is a key regulator of wing specifications and also participates in wing growth and patterning (Baena-Lopez & García-Bellido, 2006; Kim et al., 1996; Zecca & Struhl, 2007a). In those discs, in which the stripe was extended and the P compartment was enlarged, Vg was detected throughout the outgrowth, supporting the wing pouch identity of this region (Supplementary Figure 6B). Hemizygous Δm3 mutants presented a highly reduced anti-Vg signal, which suggests that no wing pouch is specified in these mutants (Supplementary Figure 6C).”

      (2) The authors place some emphasis on the idea that their work addresses possible coordination between setting the D/V boundary and the A/P boundary:

      Abstract: "Thus, the correct establishment of ap expression pattern with respect to en must be tightly controlled", "...challenging the mechanism by which apE miss-regulation leads to AP defects." "Detailed mutational analyses using CRISPR/Cas revealed a role of apE in positioning the DV boundary with respect to the AP boundary"

      Introduction: "However, little is known about how the expression pattern of ap is set up with respect that of en. In other words, how is the DV boundary positioned with respect to the AP boundary?"

      "How such interaction between ap and the AP specification program arises is unknown."

      Results: "Some of these phenotypes are reminiscent of those reported for apBlot (Whittle, 1979) and point towards a yet undescribed crosstalk between ap early expression and the AP specification program."

      At the same time, they express the notion, with which this reviewer agrees, that all defects observed in A/P patterning arising as a result of apterous miss-regulation are due to the fact that in their mutants, apterous expression is lost mainly in the posterior dorsal compartment, bringing novel confrontations between the A/P and the D/V boundaries.

      To me, the key point is why the expression of apterous in different mutants of the OR463 enhancer affects only the posterior compartment. This should be discussed because it is far from obvious that apterous expression has different regulatory requirements in the anterior and posterior compartments.

      We agree with the reviewer that the differential effect of the mutations on the expression of ap in the A and P compartment is a key factor underlying our explanation of how the phenotypes arise. To clarify this point, we have now extended our first discussion point. Moreover, we have included some other references of differential enhancer regulation in different wing disc compartments. In addition, we have discussed whether this effect has to do with the different regulation of the enhancer in the A and P compartment or due to regulation of downstream effectors.

      Added paragraph:

      “Although apE is active throughout the dorsal compartment, its disruption leads to a preferential loss of ap expression in posterior cells. The asymmetric effect of apE perturbation on the anterior and posterior compartments suggests that apE transcriptional control is not equivalent across the A/P axis. Compartment-dependent differences in enhancer regulation have also been documented in other developmental contexts; for example, the Distal-less DMX-R element is interpreted through distinct cofactor combinations (Sloppy paired anteriorly and Engrailed posteriorly) (Gebelein et al., 2004), and specific mutations within DMX-R preferentially disrupt enhancer function in anterior versus posterior cells. It is possible that apE is more sensitive to misregulation due to differential transcriptional regulation across compartments. Nevertheless, we cannot exclude the possibility that the posterior bias we observe arises not from enhancer logic per se, but from intrinsic differences in tissue architecture or the dynamics of boundary positioning during wing disc development.”

      (3) The description of gene expression in the wing disc of novel apterous mutants is only carried out in late third instar discs (Figs. 2, 3, 5, and 7). This is understandable given the technical difficulties of dealing with early discs, as those shown in the analysis of candidate apterous regulatory transcription factors (Fig. 4F, Fig. 6 C-D). However, because the effects of the mutants on apterous expression are expected to occur much earlier than the time of expression analysis, this fact should be discussed.

      We agree with the reviewer regarding the limitations of our analysis whenever we analyzed third instar larvae to assess the expression of the OE463 enhancer. We have included a statement in which this is mentioned in the discussion:

      “It is important to acknowledge that all expression analyses were conducted in third-instar discs, a stage that follows the initial establishment of ap expression. Earlier effects are therefore inferred rather than directly observed, as imaging and staging of early discs present significant technical challenges due to their small size and fragility. A direct observation of the early wing disc across mutant conditions would likely help to clarify the role of the discovered factors during early ap expression.”

      Reviewer #2 (Public Review):

      In their manuscript, "Transcriptional control of compartmental boundary positioning during Drosophila wing development," Aguilar and colleagues do an exceptional job of exploring how tissue axes are established across Drosophila development. The authors perform a series of functional perturbations using mutational analyses at the native locus of apterous (ap), and perform tissue-specific enhancer disruption via dCas9 expression. This innovative approach allowed them to explore the spatio-temporal requirements of an apterous enhancer. Combining these techniques allowed the authors to explore the molecular basis of apterous expression, connecting the genotypes to the phenotypical effects of enhancer perturbations. To me, this paper was a beautiful example of what can be done using modern drosophila genetics to understand classic questions in developmental biology and transcriptional regulation.

      In sum, this was a rigorous paper bridging scales from the molecular to phenotypes, with new insight into how enhancers control compartmental boundary positioning during Drosophila wing development.

      We would like to thank the reviewer for its positive and encouraging comments, as well as for the careful review of the manuscript and figures. We have adapted most of the suggestions in the new manuscript.

      Reviewer #3 (Public Review):

      In this manuscript, authors use the Drosophila wing as a model system and combine state-ofthe-art genetic engineering to identify and validate the molecular players mediating the activity of one of the cis-regulatory enhancers of the apterous gene involved in the regulation of its expression domain in the dorsal compartment of the wing primordium during larval development.

      (1) The authors raise two very important questions in the Introduction: (1) who is locating the relative position of the AP and DV boundaries in the developing wing, and (2) who is responsible for the maintenance of the apterous expression domain late in larval development. None of these two questions have been responded to and, indeed, the summary of the work (as stated in the conclusions of the last paragraph of the Introduction) does not resolve any of these questions.

      We believe the results presented, together with those added during the revision, shed some on the positioning of the boundary. We proposed that the combined integration of four TFs by the OR463 enhancer is fundamental for the correct positioning. Additionally, we proposed a model on how these positioning problems result in the phenotypes observed (Supplementary figure 7, now also shown in Figure 2D). Our results indicate that ap expression in the PD quadrant is particularly sensitive to mutations in the enhancer, which we have now further elaborated on in the first part of the discussion. Together, we believe that our results do tackle the first problem posed in the introduction, while not completely solving them. As for the second question, we have tried to remove any suggestions that this article tries to explain later regulation of apterous. Probably this misunderstanding arises from a sentence in the introduction which has now been deleted. The means of the maintenance of ap expression in later stages has been partially explored previously (See Bieli et al 2015) and it is subject of our current studies.

      (2) The authors have identified two different regions whose deletions give very interesting phenotypes in the adult wing (AP identify change & outgrowths, and loss of wing), and have bioinformatically identified and functionally verified 4 TFs that mediate the activity of these regions by their capacity to phenocopy the wing phenotype. While identification of the 2 TFs acting on the m1 is incremental with respect to previous work on the identification of the enhancer responsible for the early expression of Ap, identification of Antp and Grn does not explain the loss of function phenotype of the m3 enhancer. Does any of these results shed any light on the first two Qs? Do these results explain the compartment boundary position in the wing as stated in the title? Expression of lacZ reporter assays is fundamental to demonstrate their model of Figure 8. The reduction of the PD compartment is difficult to understand by the sole reduction in ap expression in this region (which has not been demonstrated).

      We agree that the identification of Antp and Grn does not by itself explain the loss-of-function phenotype of the m3 enhancer. However, these transcription factors represent the best current candidates for direct regulators for this enhancer. We have clarified in the text that Antp and Grn may not act as instructive inputs but rather play a permissive role in enabling ap expression through m3. Importantly, the dCas9-mediated perturbation experiments directly demonstrate that targeted manipulation of apE in this region is sufficient to produce the characteristic duplications, providing functional evidence that apE activity underlies the observed phenotypes. In addition, lacZ reporter assays confirm that apE expression is indeed affected in all cases where the experimental setup permitted detection. Together, these results validate that the observed morphological phenotypes stem from perturbation of apE activity and support the proposed model for enhancer regulation and its role in compartment boundary maintenance.

      (3) The authors state in one of the sections "Spatio-temporal analysis of apE via dCas9 ". No temporal manipulation of gene activity is shown. The authors should combine GAL4/UAs with the Gal80ts to demonstrate the temporal requirements of Antp/Grn and Pnt/Hth as depicted in their model of Figure 8.

      We agree with the reviewer that the temporal dimension was not explored in the first version of the manuscript (aside of the temporal constrains of en-Gal4 driver). As suggested by the reviewer, we have now used a tub-Gal80ts allele to temporally control the enhancer perturbation and delimit its window of activity. The results are included in two new panels in the figure 3 (H and H’). The new data agrees with the notion that apE enhancer is important up to L2 stages but dispensable later in development. We have added the following paragraph to the text:

      “To define the developmental time window during which the apE enhancer remains sensitive to repression, we combined the temperature-sensitive tub-Gal80<sup>ts</sup> system with temporally controlled expression of dCas9. Animals carrying the en-Gal4, tub-Gal80<sup>ts</sup>, UAS-dCas9 and U6-OR463gRNA(4x) transgenes were maintained at 18 °C to suppress dCas9 expression. Independent sets of embryos were then shifted to 29 °C at successive developmental intervals ranging from 0 to 168 h after egg laying (AEL), so that dCas9 induction occurred at distinct time points in development (Figure 3H). Under these conditions, dCas9 transcription was induced only after the temperature shift, while the gRNAs were expressed constitutively. Wing phenotypes were quantified in adult progeny as a readout of apE enhancer perturbation. When dCas9 was expressed from embryonic or early larval stages (0–48 h AEL), nearly all wings (70–90%) displayed severe ap-like phenotypes, including posterior compartment duplication and loss of anterior–posterior boundary integrity. Shifting animals later (48–72 h AEL) still produced a majority (~66%) of abnormal wings, whereas induction after 72 h AEL resulted in progressively weaker effects and complete loss of phenotypes by 96 h AEL (Figure 3H’).

      These results delineate the developmental period during which apE activity is required for proper wing patterning. Perturbation during the first half of the second larval instar (≤ 96 h at 18 °C) was sufficient to elicit strong ap-like transformations, consistent with the enhancer being functionally required during early larval stages and becoming dispensable thereafter. The temporal decline in phenotype penetrance thus reflects the progressive loss of apE sensitivity to dCas9-mediated repression, providing a precise estimate of when its activity is no longer required for wing morphogenesis.”

      (4) The authors have not managed to explain the AP phenotype. Thus, this work opens many unresolved questions and does not resolve the title, which is a big overstatement. Thus, strengths (technically excellent), weakness (there is not much to learn about wing development and apterous regulation from these results besides the incremental identification of 4 additional TFs mediating the regulation of ap expression by their ability to phenocopy regulatory mutations of the apterous gene).

      As mentioned in response to reviewer 1, we have indeed no concrete explanation  for why the P compartment seems more sensitive to mutations. We have now further discussed this point (see below paragraph, now included in  the discussion). As for how the adult phenotypes arise from the mutant wing discs, we have a good idea (see Supplementary figure 7 and Figure 2). 

      We are pleased to hear that the reviewer considers our article technically valuable. Therefore, we have reformulated the title such as the technical merits play a bigger role in it:

      ”in situ mutational screening and CRISPR interference demonstrate that the apterous Early enhancer is required for developmental boundary positioning”

      Paragraph added to the discussion:

      " Although apE is active throughout the dorsal compartment, its disruption leads to a preferential loss of ap expression in posterior cells. The asymmetric effect of apE perturbation on the anterior and posterior compartments suggests that apE transcriptional control is not equivalent across the A/P axis. Compartment-dependent differences in enhancer regulation have also been documented in other developmental contexts; for example, the Distal-less DMX-R element is interpreted through distinct cofactor combinations (Sloppy paired anteriorly and Engrailed posteriorly) (Gebelein et al., 2004), and specific mutations within DMX-R preferentially disrupt enhancer function in anterior versus posterior cells. It is possible that apE is more sensitive to misregulation due to differential transcriptional regulation across compartments. Nevertheless, we cannot exclude the possibility that the posterior bias we observe arises not from enhancer logic per se, but from intrinsic differences in tissue architecture or the dynamics of boundary positioning during wing disc development.”

      Recommendations for the authors:

      Reviewer #1 (Recommendations For The Authors):

      Formatting of references should be checked throughout the manuscript

      Reviewer #2 (Recommendations For The Authors):

      Here, I note a few points that would help clarify the manuscript and connect it with a broader community.

      Figure 1: it could help the reader to add the landing site genetic scheme to the main figure.

      In a first draft that was exactly the original configuration, but after comparing both versions we determined that the presence of the landing site removes a bit of the focus of the phenotypes.

      Figure 1: what species were used for the conservation alignment? Further details would be nice to add here.

      We have now added a section of bioinformatical analysis, which was missing in the original manuscript:

      Sequence conservation of the OR463 fragment within the ap upstream intergenic region was analysed across different dipteran species using the “Cons 124 Insects” multiple-alignment track of the D. melanogaster dm6 genome on the UCSC Genome Browser (Kent et al., 2002, https://genome.ucsc.edu). Conservation scores were obtained from the phastCons (Siepel et al., 2005) and used to delineate conserved and less conserved blocks within OR463. Conserved transcription factor binding sites were predicted with MotEvo (Arnold et al., 2011), which defined four conserved modules (m1–m4) and six inter-modules (N1–N6). Additional motif analysis was performed using the JASPAR CORE Insecta database and the Target Explorer tool to cross-validate conserved binding-site predictions and refine motif assignments within the enhancer.

      From Figure 2: I would consider moving the model or portions of it to a main figure. These models, while descriptive, really help make the manuscript more approachable. Note that eLife does not have forced figure requirements.

      We have adapted the reviewer’s suggestion and we are very grateful for it. We think the figure has greatly improved. The final figure now highlights a small part of the model, which is still included in the Supplementary Figure.

      Figure 5: This figure is fantastic, and the results are particularly important. I would recommend increasing the weight of the arrows from D to E, making it more obvious. Did the authors consider any temperature or other perturbations to look at robustness? They mention "robustness" a few times, and this could be an excellent system to explore a bit further. For panels F and G, it would be nice to have a bit of biochemistry here to test the spacing requirements' effects on the distances (but it's great phenotypical data, regardless).

      We have chosen a darker grey to highlight the lines. 

      We appreciate the reviewer’s suggestions. With respect to robustness assays, such as temperature perturbations, we agree that the apE enhancer would be a suitable system for such experiments. However, these analyses would move the study beyond its current scope, which is focused on defining the regulatory logic of boundary positioning through mutational dissection and CRISPRi. We therefore prefer not to expand the work in this direction here, but we note that this would be an interesting avenue for future investigation.

      Similarly, biochemical assays probing spacing requirements would provide additional mechanistic insight but would represent a separate line of work. In this manuscript, we aimed to establish the functional consequences of motif spacing using in vivo genetic and phenotypic analyses, which we believe sufficiently support our conclusions.

      Thank you for the insight.

      Discussion: To the point "most point mutations or short deletions in enhancer regions have little effect on gene expression" I would push the authors to discuss their work in relation to Fuqua et al., (Nature 2020) and Kvon et al., (Cell 2020). Their work is consistent with enhancers being sensitive to mutations, and this warrants further discussion because it could be important for the transcription field.

      Hox genes as pioneer factors, I would recommend citing Loker et al., (Curr Biol 2021), as an example of Hox genes functioning as a pioneer factor.

      We thank the reviewer for this suggestion. We have now added a short paragraph in the Discussion noting how our observations may relate to the mutational patterns described in Fuqua et al. (2020) and Kvon et al. (2020), while keeping the interpretation tentative. The text now says:

      “Recent large-scale enhancer mutagenesis studies have shown that the mutational consequences within enhancers can vary widely. In some cases, many nucleotide positions appear tolerant to single-base changes and only a small subset of mutations produce clear functional effects (Kvon et al., 2020). In other enhancers, regulatory information is distributed more densely, and mutations at multiple positions can alter output (Fuqua et al., 2020). Together, these studies illustrate that enhancer sensitivity is not uniform but depends on enhancer-specific features such as motif organization, cooperativity, and redundancy. Within this broader landscape, the apE enhancer appears to represent a particularly sensitive case.”

      We also included a citation to Loker et al. (2021) in connection with the possible pioneer-like contribution of HOX input to apE.

      We would like to thank all reviewers for their effort.

    1. Reviewer #3 (Public review):

      Parrotta et al provide a convincing and thorough revision of their manuscript "Exposure to false cardiac feedback alters pain perception and anticipatory cardiac frequency". The authors addressed my previous concerns regarding theoretical framing and methodological clarity. For example:

      They provided additional detail on the experimental design, procedure and statistical analyses.

      The predictive coding rationale for the hypotheses has been clarified.

      The limitations of the study are discussed comprehensively

      Additional analyses were performed to investigate the role of learning effects and across-experiment effects

      New supplementary figures allow a closer look at the feedback-related response patterns

      In sum, the revisions improve the manuscript. However, some issues remain present.

      (1) Potential learning/ habituation effects. In my first review of the manuscript, I raised the concern that learning effects may have contributed to the observed differences between interoceptive & exteroceptive cues.<br /> The authors argue that the small number of six trials per condition could limit aversive effects of differential learning between experiments. However, electric nociceptive stimuli are exceptionally potent in classical conditioning experiments and humans can develop conditioned responses to these types of stimuli after a single trial [1-2]. Therefore, six trials are sufficient to allow for associative or expectancy-based learning processes.

      However, the authors are also presenting additional analyses, i.e. LME models which included trial rank as a predictor. While these models do not show a statistically significant learning effect, they do indicate a noteworthy larger effect in earlier trials compared to later ones. However, in my reading, this speaks towards the presence of unspecific effects of attention or arousal. This pattern is compatible with early learning or, alternatively, with non-specific attentional or arousal responses that diminish across repetitions. This is potentially a limitation of the design: repetition-related effects (attention reduction, arousal habituation, early learning) may contribute to the results, and distinguishing between interoceptive inference and non-specific effects remains challenging within this paradigm.

      (1) Haesen K, Beckers T, Baeyens F, Vervliet B. One-trial overshadowing: Evidence for fast specific fear learning in humans. Behav Res Ther. 2017 Mar;90:16-24. doi: 10.1016/j.brat.2016.12.001. Epub 2016 Dec 8. PMID: 27960093.

      (2) Glenn CR, Lieberman L, Hajcak G. Comparing electric shock and a fearful screaming face as unconditioned stimuli for fear learning. Int J Psychophysiol. 2012 Dec;86(3):214-9. doi: 10.1016/j.ijpsycho.2012.09.006. Epub 2012 Sep 21. PMID: 23007035; PMCID: PMC3627354.

      (2) SESOI and power rationale. The authors elaborated on the sensitivity analyses and the rationale of reporting SESOI rather than traditional a-priori power analyses and included this information in the manuscript, which improves transparency.

      (3) Unspecific arousal/ attention mechanisms. The authors argue against unspecific arousal mechanisms based on the absence of main effects in pain ratings and heart rate. This reduces the likelihood of a purely unspecific arousal account, however, these unspecific effects may not need to manifest as main effects. Unspecific mechanisms are likely adding (at least residual) effects onto the results.

      Regarding attention-based mechanisms, the authors have clarified that in Experiment 2 (exteroceptive cue), the participants are instructed that the sound does not have any relation with their heart rate. If participants did not receive any instructions on the meaning of the knocking sounds, they may have simply ignored it - not unlikely, also because the exteroceptive feedback did not elicit any systematic effect on the outcome variables (minus the slowing of HR with slower exteroceptive feedback, which may reflect noise, altering, multiple comparisons?). Ultimately, how the participants did or did not process the exteroceptive cue is unclear.

      (4) The authors provided more context to their hypothesis and strengthened its theoretical motivation (increased pain intensity with incongruent-high cardiac feedback), rooting it in predictive coding accounts of interoception. For instance, their prior study shows that participants report an increased cardiac frequency while anticipating pain. The reasoning behind this study is hence that if pain shapes cardiac perception, cardiac perception should in turn shape pain perception. The introduction has been revised accordingly, adding more references on the interplay between cardiac feedback and pain and emotional responses. While this rooting within the predictive processing framework is now clearly developed, it also underscores a gap between the proposed theoretical mechanism and the current analytical approach. The hypothesis is formulated in a mechanistic, computational-level language, yet the statistical analysis remains primarily descriptive, at a group level, and does not directly test the predictive-coding account.

      New concerns introduced by the revision:

      (1) Some of the newly added paragraphs interrupt the narrative flow. For example, the justification of the supradiaphragmatic focus based on the BPQ questionnaire feels too long for this section and might fit more naturally in the theoretical background or introduction. Similarly, the predictive-coding paragraph appearing after the hypotheses seems better suited to the earlier conceptual framing rather than following the hypothesis statements. It would be better for the argumentative flow if hypotheses followed from theoretical considerations.

      (2) The authors now note that the administration of the BPQ questionnaire was exploratory, explaining the null-results in the methods section as resulting from an underpowered design. But if the design is not appropriate for discovering a connection between self-reported body awareness and pain ratings, why was it administered in the first place? The rationale here is unclear.

      (3) The discussion is longer than before and would benefit greatly from streamlining the arguments.

    2. Author response:

      The following is the authors’ response to the original reviews.

      Public Reviews:

      Reviewer #1 (Public Review):

      Summary:

      I read the paper by Parrotta et al with great interest. The authors are asking an interesting and important question regarding pain perception, which is derived from predictive processing accounts of brain function. They ask: If the brain indeed integrates information coming from within the body (interoceptive information) to comprise predictions about the expected incoming input and how to respond to it, could we provide false interoceptive information to modulate its predictions, and subsequently alter the perception of such input? To test this question, they use pain as the input and the sounds of heartbeats (falsified or accurate) as the interoceptive signal.

      Strengths:

      I found the question well-established, interesting, and important, with important implications and contributions for several fields, including neuroscience of prediction-perception, pain research, placebo research, and health psychology. The paper is well-written, the methods are adequate, and the findings largely support the hypothesis of the authors. The authors carried out a control experiment to rule out an alternative explanation of their finding, which was important.

      Weaknesses:

      I will list here one theoretical weakness or concern I had, and several methodological weaknesses.

      The theoretical concern regards what I see as a misalignment between a hypothesis and a result, which could influence our understanding of the manipulation of heartbeats, and its meaning: The authors indicate from prior literature and find in their own findings, that when preparing for an aversive incoming stimulus, heartbeats *decrease*. However, in their findings, manipulating the heartbeats that participants hear to be slower than their own prior to receiving a painful stimulus had *no effect* on participants' actual heartbeats, nor on their pain perceptions. What authors did find is that when listening to heartbeats that are *increased* in frequency - that was when their own heartbeats decreased (meaning they expected an aversive stimulus) and their pain perceptions increased.

      This is quite complex - but here is my concern: If the assumption is that the brain is collecting evidence from both outside and inside the body to prepare for an upcoming stimulus, and we know that *slowing down* of heartbeats predicts an aversive stimulus, why is it that participants responded in a change in pain perception and physiological response when listened to *increased heartbeats* and not decreased? My interpretation is that the manipulation did not fool the interoceptive signals that the brain collects, but rather the more conscious experience of participants, which may then have been translated to fear/preparation for the incoming stimulus. As the authors indicate in the discussion (lines 704-705), participants do not *know* that decreased heartbeats indicate upcoming aversive stimulus, and I would even argue the opposite - the common knowledge or intuitive response is to increase alertness when we hear increased heartbeats, like in horror films or similar scenarios. Therefore, the unfortunate conclusion is that what the authors assume is a manipulation of interoception - to me seems like a manipulation of participants' alertness or conscious experience of possible danger. I hope the (important) distinction between the two is clear enough because I find this issue of utmost importance for the point the paper is trying to make. If to summarize in one sentence - if it is decreased heartbeats that lead the brain to predict an approaching aversive input, and we assume the manipulation is altering the brain's interoceptive data collection, why isn't it responding to the decreased signal? --> My conclusion is, that this is not in fact a manipulation of interoception, unfortunately

      We thank the reviewer for their comment, which gives us the opportunity to clarify what we believe is a theoretical misunderstanding that we have not sufficiently made clear in the previous version of the manuscript. The reviewer suggests that a decreased heart rate itself might act as an internal cue for a forthcoming aversive stimulus, and questions why our manipulation of slower heartbeats then did not produce measurable effects.

      The central point is this: decreased heart rate is not a signal the brain uses to predict a threat, but is a consequence of the brain having already predicted the threat. This distinction is crucial. The well-known anticipatory decrease of heartrate serves an allostatic function: preparing the body in advance so that physiological responses to the actual stressor (such as an increase in sympathetic activation) do not overshoot. In other words, the deceleration is an output of the predictive model, not an input from which predictions are inferred. It would be maladaptive for the brain to predict threat through a decrease in heartrate, as this would then call for a further decrease, creating a potential runaway cycle.

      Instead, increased heart rate is a salient and evolutionarily conserved cue for arousal, threat, and pain. This association is reinforced both culturally - for example, through the use of accelerating heartbeats in films and media to signal urgency, as R1 mentions - and physiologically, as elevated heart rates reliably occur in response to actual (not anticipated) stressors. Decreased heartrates, in contrast, are reliably associated with the absence of stressors, for example during relaxation and before (and during) sleep. Thus, across various everyday experiences, increased (instead of decreased) heartrates are robustly associated with actual stressors, and there is no a priori reason to assume that the brain would treat decelerating heartrates as cue for threat. As we argued in previous work, “the relationship between the increase in cardiac activity and the anticipation of a threat may have emerged from participants’ first-hand experience of increased heart rates to actual, not anticipated, pain” (Parrotta et al., 2024). The changes in heart rate and pain perception that we hypothesize (and observe) are therefore fully in line with the prior literature on the anticipatory compensatory heartrate response (Bradley et al., 2008, 2005; Colloca et al., 2006; Lykken et al., 1972; Taggart et al., 1976; Tracy et al., 2017; Skora et al., 2022), as well as with Embodied Predictive Coding models (Barrett & Simmons, 2015; Pezzulo, 2014; Seth, 2013; Seth et al., 2012), which assume that our body is regulated through embodied simulations that anticipate likely bodily responses to upcoming events, thereby enabling anticipatory or allostatic regulation of physiological states (Barrett, 2017).

      We now add further explanation to this point to the Discussion (lines 740-758) and Introduction (lines 145-148; 154-156) of our manuscript to make this important point clearer.

      Barrett, L. F., & Simmons, W. K. (2015). Interoceptive predictions in the brain. Nature reviews neuroscience, 16(7), 419-429.

      Barrett, L. F. (2017). The theory of constructed emotion: An active inference account of interoception and categorization. Social cognitive and affective neuroscience, 12(1), 1-23.

      Bradley, M. M., Moulder, B., & Lang, P. J. (2005). When good things go bad: The reflex physiology of defense. Psychological science, 16(6), 468-473.

      Bradley, M. M., Silakowski, T., & Lang, P. J. (2008). Fear of pain and defensive activation. PAIN®, 137(1), 156-163.

      Colloca, L., Petrovic, P., Wager, T. D., Ingvar, M., & Benedetti, F. (2010). How the number of learning trials affects placebo and nocebo responses. Pain®, 151(2), 430-439.

      Lykken, D., Macindoe, I., & Tellegen, A. (1972). Preception: Autonomic response to shock as a function of predictability in time and locus. Psychophysiology, 9(3), 318-333.

      Taggart, P., Hedworth-Whitty, R., Carruthers, M., & Gordon, P. D. (1976). Observations on electrocardiogram and plasma catecholamines during dental procedures: The forgotten vagus. British Medical Journal, 2(6039), 787-789.

      Tracy, L. M., Gibson, S. J., Georgiou-Karistianis, N., & Giummarra, M. J. (2017). Effects of explicit cueing and ambiguity on the anticipation and experience of a painful thermal stimulus. PloS One, 12(8), e0183650.

      Parrotta, E., Bach, P., Perrucci, M. G., Costantini, M., & Ferri, F. (2024). Heart is deceitful above all things: Threat expectancy induces the illusory perception of increased heartrate. Cognition, 245, 105719.

      Pezzulo, G. (2014). Why do you fear the bogeyman? An embodied predictive coding model of perceptual inference. Cognitive, Affective & Behavioral Neuroscience, 14(3), 902-911.

      Seth, A., Suzuki, K., & Critchley, H. (2012). An Interoceptive Predictive Coding Model of Conscious Presence. Frontiers in Psychology, 2. https://www.frontiersin.org/articles/10.3389/fpsyg.2011.00395

      Seth, A. K. (2013). Interoceptive inference, emotion, and the embodied self. Trends in Cognitive Sciences, 17(11), 565-573.

      Skora, L. I., Livermore, J. J. A., & Roelofs, K. (2022). The functional role of cardiac activity in perception and action. Neuroscience & Biobehavioral Reviews, 104655.

      I will add that the control experiment - with an exteroceptive signal (knocking of wood) manipulated in a similar manner - could be seen as evidence of the fact that heartbeats are regarded as an interoceptive signal, and it is an important control experiment, however, to me it seems that what it is showing is the importance of human-relevant signals to pain prediction/perception, and not directly proves that it is considered interoceptive. For example, it could be experienced as a social cue of human anxiety/fear etc, and induce alertness.

      The reviewer asks us to consider whether our measured changes in pain response happen not because the brain treats the heartrate feedback in Experiment 1 as interoceptive stimulus, but because heartbeat sounds could have signalled threat on a more abstract, perhaps metacognitive or affective, level, in contrast to the less visceral control sounds in Experiment 2. We deem this highly unlikely for several reasons.

      First, as we point out in our response to Reviewer 3 (Point 3), if this were the case, the different sounds in both experiments should have induced overall (between-experiment) differences in pain perception and heart rate, induced by the (supposedly) generally more threatening heart beat sounds. However, when we added such comparisons, no such between-experiment differences were obtained (See Results Experiment 2, and Supplementary Materials, Cross-experiment analysis between-subjects model). Instead, we only find a significant interaction between experiment and feedback (faster, slower). Thus, it is not the heartbeat sounds per se that induce the measured changes to pain perception, but the modulation of their rate, and that identical changes to the rate of non-heartrate sounds produce no such effects. In other words, pain perception is sensitive to a change in heart rate feedback, as we predicted, instead of the overall presence of heartbeat sounds (as one would need to predict if heart beat sounds had more generally induced threat or stress).

      Second, one may suspect that it is precisely the acceleration of heartrate feedback that could act as cue to arousal, while accelerated exteroceptive feedback would not. However, if this were the case, one would need to predict a general heart rate increase with accelerated feedback, as this is the general physiological marker of increasing alertness and arousal (e.g. Tousignant-Laflamme et al., 2005; Terkelsen et al., 2005; for a review, see Forte et al., 2022). However, the data shows the opposite, with real heartrates decreasing when the heartrate feedback increases. This result is again fully in line with the predicted interoceptive consequences of accelerated heartrate feedback, which mandates an immediate autonomic regulation, especially when preparing for an anticipated stressor.

      Third, our view is further supported by neurophysiological evidence showing that heartbeat sounds, particularly under the belief they reflect one’s own body, are not processed merely as generic aversive or “human-relevant” signals. For instance, Vicentin et al. (2024) showed that simulated faster heartbeat sounds elicited stronger EEG alpha-band suppression, indicative of increased cortical activation  over frontocentral and right frontal areas, compatible with the localization of brain regions contributing to interoceptive processes (Kleint et al., 2015). Importantly, Kleint et al. also demonstrated via fMRI that heartbeat sounds, compared to acoustically matched tones, selectively activate bilateral anterior insula and frontal operculum, key hubs of the interoceptive network. This suggests that the semantic identity of the sound as a heartbeat is sufficient to elicit internal body representations, despite its exteroceptive nature. Further evidence comes from van Elk et al. (2014), who found that heartbeat sounds suppress the auditory N1 component, a neural marker of sensory attenuation typically associated with self-generated or predicted stimuli. The authors interpret this as evidence that the brain treats heartbeat sounds as internally predicted bodily signals, supporting interoceptive predictive coding accounts in which exteroceptive cues (i.e., auditory cardiac feedback) are integrated with visceral information to generate coherent internal body representations.

      Finally, it is worth noting that the manipulation of heartrate feedback in our study elicited measurable compensatory changes in participants’ actual heart rate. This is striking compared to our previous work (Parrotta et al., 2024), wherein we used a highly similar design as here, combined with a very strong threat manipulation. Specifically, we presented participants with highly salient threat cues (knives directed at an anatomical depiction of a heart), which predicted forthcoming pain with 100% validity (compared to flowers that did predict the absence of pain with 100%). In other words, these cues perfectly predicted actual pain, through highly visceral stimuli. Nevertheless, we found no measurable decrease in actual heartrate. From an abstract threat perspective, it is therefore striking that the much weaker manipulation of slightly increased or decreased heartrates we used here would induce such a change. The difference therefore suggests that what caused the response here is not due to an abstract feeling of threat, but because the brain indeed treated the increased heartrate feedback as an interoceptive signal for (stressor-induced) sympathetic activation, which would then be immediately down-regulated.

      Together, we hope you agree that these considerations make a strong case against a non-specific, arousal or alertness-related explanation of our data. We now make this point clearer in the new paragraph of the Discussion (Accounting for general unspecific contributionslines 796-830), and have added the relevant between experiment comparisons to the Results of Experiment 2.

      Forte, G., Troisi, G., Pazzaglia, M., Pascalis, V. D., & Casagrande, M. (2022). Heart rate variability and pain: a systematic review. Brain sciences, 12(2), 153.

      Vicentin, S., Guglielmi, S., Stramucci, G., Bisiacchi, P., & Cainelli, E. (2024). Listen to the beat: behavioral and neurophysiological correlates of slow and fast heartbeat sounds. International Journal of Psychophysiology, 206, 112447.

      Kleint, N. I., Wittchen, H. U., & Lueken, U. (2015). Probing the interoceptive network by listening to heartbeats: an fMRI study. PloS one, 10(7), e0133164.

      Parrotta, E., Bach, P., Perrucci, M. G., Costantini, M., & Ferri, F. (2024). Heart is deceitful above all things: Threat expectancy induces the illusory perception of increased heartrate. Cognition, 245, 105719.

      Terkelsen, A. J., Mølgaard, H., Hansen, J., Andersen, O. K., & Jensen, T. S. (2005). Acute pain increases heart rate: differential mechanisms during rest and mental stress. Autonomic Neuroscience, 121(1-2), 101-109.

      Tousignant-Laflamme, Y., Rainville, P., & Marchand, S. (2005). Establishing a link between heart rate and pain in healthy subjects: a gender effect. The journal of pain, 6(6), 341-347.

      van Elk, M., Lenggenhager, B., Heydrich, L., & Blanke, O. (2014). Suppression of the auditory N1-component for heartbeat-related sounds reflects interoceptive predictive coding. Biological psychology, 99, 172-182.

      Several additional, more methodological weaknesses include the very small number of trials per condition - the methods mention 18 test trials per participant for the 3 conditions, with varying pain intensities, which are later averaged (and whether this is appropriate is a different issue). This means 6 trials per condition, and only 2 trials per condition and pain intensity. I thought that this number could be increased, though it is not a huge concern of the paper. It is, however, needed to show some statistics about the distribution of responses, given the very small trial number (see recommendations for authors). The sample size is also rather small, on the verge of "just right" to meet the required sample size according to the authors' calculations.

      We provide detailed responses to these points in the “Recommendations for The Authors” section, where each of these issues is addressed point by point in response to the specific questions raised.

      Finally, and just as important, the data exists to analyze participants' physiological responses (ECG) after receiving the painful stimulus - this could support the authors' claims about the change in both subjective and objective responses to pain. It could also strengthen the physiological evidence, which is rather weak in terms of its effect. Nevertheless, this is missing from the paper.

      This is indeed an interesting point, and we agree that analyzing physiological responses such as ECG following the painful stimulus could offer additional insights into the objective correlates of pain. However, it is important to clarify that the experiment was not designed to investigate post-stimulus physiological responses. Our primary focus was on the anticipatory processes leading up to the pain event. Notably, in the time window immediately following the stimulus - when one might typically expect to observe physiological changes such as an increase in heart rate - participants were asked to provide subjective ratings of their nociceptive experience. It is therefore not a “clean” interval that would lend itself for measurement, especially as a substantial body of evidence indicates that one’s heart rate is strongly modulated by higher-order cognitive processes, including attentional control, executive functioning, decision-making and action itself (e.g., Forte et al., 2021a; Forte et al., 2021b; Luque-Casado et al., 2016).

      This limitation is particularly important as the induced change in pain ratings by our heart rate manipulation is substantially smaller than the changes in heart rate induced by actual pain (e.g., Loggia et al., 2011). To confirm this for our study, we simply estimated how much change in heart rate is produced by a change in actual stimulus intensity in the initial no feedback phase of our experiment. There, we find that a change between stimulus intensities 2 and 4 induces a NPS change of 32.95 and a heart rate acceleration response of 1.19 (difference in heart rate response relative to baseline, Colloca et al., 2006), d = .52, p < .001. The change of NPS induced by our implicit heart rate manipulation, however, is only a seventh of this (4.81 on the NPS). This means that the expected effect size of heart rate acceleration produced by our manipulation would only be d = .17. A power analysis, using GPower, reveals that a sample size of n = 266 would be required to detect such an effect, if it exists. Thus, while we agree that this is an exciting hypothesis to be tested, it requires a specifically designed study, and a much larger sample than was possible here.

      Colloca, L., Benedetti, F., & Pollo, A. (2006). Repeatability of autonomic responses to pain anticipation and pain stimulation. European Journal of Pain, 10(7), 659-665.

      Forte, G., Morelli, M., & Casagrande, M. (2021a). Heart rate variability and decision-making: Autonomic responses in making decisions. Brain sciences, 11(2), 243.

      Forte, G., Favieri, F., Oliha, E. O., Marotta, A., & Casagrande, M. (2021b). Anxiety and attentional processes: the role of resting heart rate variability. Brain sciences, 11(4), 480.

      Loggia, M. L., Juneau, M., & Bushnell, M. C. (2011). Autonomic responses to heat pain: Heart rate, skin conductance, and their relation to verbal ratings and stimulus intensity. PAIN®, 152(3), 592-598.

      Luque-Casado, A., Perales, J. C., Cárdenas, D., & Sanabria, D. (2016). Heart rate variability and cognitive processing: The autonomic response to task demands. Biological psychology, 113, 83-90

      I have several additional recommendations regarding data analysis (using an ANOVA rather than multiple t-tests, using raw normalized data rather than change scores, questioning the averaging across 3 pain intensities) - which I will detail in the "recommendations for authors" section.

      We provide detailed responses to these points in the “Recommendations for The Authors” section, where each of these issues is addressed point by point in response to the specific questions raised.

      Conclusion:

      To conclude, the authors have shown in their findings that predictions about an upcoming aversive (pain) stimulus - and its subsequent subjective perception - can be altered not only by external expectations, or manipulating the pain cue, as was done in studies so far, but also by manipulating a cue that has fundamental importance to human physiological status, namely heartbeats. Whether this is a manipulation of actual interoception as sensed by the brain is - in my view - left to be proven.

      Still, the paper has important implications in several fields of science ranging from neuroscience prediction-perception research, to pain and placebo research, and may have implications for clinical disorders, as the authors propose. Furthermore, it may lead - either the authors or someone else - to further test this interesting question of manipulation of interoception in a different or more controlled manner.

      I salute the authors for coming up with this interesting question and encourage them to continue and explore ways to study it and related follow-up questions.

      We sincerely thank the reviewer for the thoughtful and encouraging feedback. We hope our responses to your points below convince you a bit more that what we are measuring does indeed capture interoceptive processes, but we of course fully acknowledge that additional measures - for example from brain imaging (or computational modelling, see Reviewer 3) - could further support our interpretation, and highlights in the Limitations and Future directions section.

      Reviewer #2 (Public Review):

      In this manuscript, Parrotta et al. tested whether it is possible to modulate pain perception and heart rate by providing false HR acoustic feedback before administering electrical cutaneous shocks. To this end, they performed two experiments. The first experiment tested whether false HR acoustic feedback alters pain perception and the cardiac anticipatory response. The second experiment tested whether the same perceptual and physiological changes are observed when participants are exposed to a non-interoceptive feedback. The main results of the first experiment showed a modulatory effect for faster HR acoustic feedback on pain intensity, unpleasantness, and cardiac anticipatory response compared to a control (acoustic feedback congruent to the participant's actual HR). However, the results of the second experiment also showed an increase in pain ratings for the faster non-interoceptive acoustic feedback compared to the control condition, with no differences in pain unpleasantness or cardiac response.

      The main strengths of the manuscript are the clarity with which it was written, and its solid theoretical and conceptual framework. The researchers make an in-depth review of predictive processing models to account for the complex experience of pain, and how these models are updated by perceptual and active inference. They follow with an account of how pain expectations modulate physiological responses and draw attention to the fact that most previous studies focus on exteroceptive cues. At this point, they make the link between pain experience and heart rate changes, and introduce their own previous work showing that people may illusorily perceive a higher cardiac frequency when expecting painful stimulation, even though anticipating pain typically goes along with a decrease in HR. From here, they hypothesize that false HR acoustic feedback evokes more intense and unpleasant pain perception, although the actual HR actually decreases due to the orienting cardiac response. Furthermore, they also test the hypothesis that an exteroceptive cue will lead to no (or less) changes in those variables. The discussion of their results is also well-rooted in the existing bibliography, and for the most part, provides a credible account of the findings.

      Thank you for the clear and thoughtful review. We appreciate your positive comments on the manuscript’s clarity, theoretical framework, and interpretation of results.

      The main weaknesses of the manuscript lies in a few choices in methodology and data analysis that hinder the interpretation of the results and the conclusions as they stand.

      The first peculiar choice is the convoluted definition of the outcomes. Specifically, pain intensity and unpleasantness are first normalized and then transformed into variation rates (sic) or deltas, which makes the interpretation of the results unnecessarily complicated. This is also linked to the definitions of the smallest effect of interest (SESOI) in terms of these outcomes, which is crucial to determining the sample size and gauging the differences between conditions. However, the choice of SESOI is not properly justified, and strangely, it changes from the first experiment to the second.

      We thank the reviewer for this important observation. In the revised manuscript, we have made substantial changes and clarifications to address both aspects of this concern: (1) the definition of outcome variables and their normalization, and (2) the definition of the SESOI.

      First, As explained in our response to Reviewer #1, we have revised the analyses and removed the difference-based change scores from the main results, addressing concerns about interpretability. However, we retained the normalization procedure: all variables (heart rate, pain intensity, unpleasantness) are normalized relative to the no-feedback baseline using a standard proportional change formula (X−bX)/bX(X - bX)/bX(X−bX)/bX, where X is the feedback-phase mean and bX is the no-feedback baseline. This is a widely used normalization procedure (e.g., Bartolo et al., 2013; Cecchini et al., 2020). This method controls for interindividual variability by expressing responses relative to each participant’s own baseline. The resulting normalized values are then used directly in all analyses, and not further transformed into deltas.

      To address potential concerns about this baseline correction approach and its interpretability, we also conducted a new set of supplementary analyses (now reported in the supplementary materials) that include the no-feedback condition explicitly in the models, rather than treating it as a baseline for normalization. These models confirm that our main effects are not driven by the choice of normalization and hold even when no-feedback is analyzed as an independent condition. The new analyses and results are now reported in the Supplementary Materials.

      Second, concerning the SESOI values and their justification: The difference in SESOI values between Experiment 1 and Experiment 2 reflects the outcome of sensitivity analyses conducted for each dataset separately, rather than a post-hoc reinterpretation of our results. Specifically, we followed current methodological recommendations (Anderson, Kelley & Maxwell, 2017; Albers & Lakens, 2017; Lakens, 2022), which advise against estimating statistical power based on previously published effect sizes, especially when working with novel paradigms or when effect sizes in the literature may be inflated or imprecise. Instead, we used the sensitivity analysis function in G*Power (Version 3.1) to determine the smallest effect size our design was capable of detecting with high statistical power (90%), given the actual sample size, test type, and alpha level used in each experiment. This is a prospective, design-based estimation rather than a post-hoc analysis of observed effects. The slight differences in SESOI are due to more participants falling below our exclusions criteria in Experiment 2, leading to slightly larger effect sizes that can be detected (d = 0.62 vs d = 0.57). Importantly, both experiments remain adequately powered to detect effects of a size commonly reported in the literature on top-down pain modulation. For instance, Iodice et al. (2019) reported effects of approximately d = 0.7, which is well above the minimum detectable thresholds of our designs.

      We have now clarified the logic in the Participant section of Experiment 1 (193-218).

      Anderson, S. F., Kelley, K., & Maxwell, S. E. (2017). Sample-Size Planning for More Accurate Statistical Power: A Method Adjusting Sample Effect Sizes for Publication Bias and Uncertainty. Psychological Science, 28(11), 1547-1562.

      Bartolo, M., Serrao, M., Gamgebeli, Z., Alpaidze, M., Perrotta, A., Padua, L., Pierelli, F., Nappi, G., & Sandrini, G. (2013). Modulation of the human nociceptive flexion reflex by pleasant and unpleasant odors. PAIN®, 154(10), 2054-2059.

      Cecchini, M. P., Riello, M., Sandri, A., Zanini, A., Fiorio, M., & Tinazzi, M. (2020). Smell and taste dissociations in the modulation of tonic pain perception induced by a capsaicin cream application. European Journal of Pain, 24(10), 1946-1955.

      Lakens, D. (2022). Sample size justification. Collabra: psychology, 8(1), 33267.

      Albers, C., & Lakens, D. (2018). When power analyses based on pilot data are biased: Inaccurate effect size estimators and follow-up bias. Journal of experimental social psychology, 74, 187-195.

      Furthermore, the researchers propose the comparison of faster vs. slower delta HR acoustic feedback throughout the manuscript when the natural comparison is the incongruent vs. the congruent feedback.

      We very much disagree that the natural comparison is congruent vs incongruent feedback. First, please note that congruency simply refers to whether the heartrate feedback was congruent with (i.e., matched) the participant’s heartrate measurements in the no feedback trials, or whether it was incongruent, and was therefore either faster or slower than this baseline frequency. As such, simply comparing congruent with incongruent feedback could only indicate that pain ratings change when the feedback does not match the real heart rate, irrespective of whether it is faster or slower. Such a test can therefore only reveal potential general effects of surprise or salience, when the feedback heartrate does not match the real one.

      We therefore assume that the reviewer specifically refers to the comparison of congruent vs incongruent faster feedback. However, this is not a good test either, as this comparison is, by necessity, confounded with the factor of surprise described above. In other words, if a difference would be found, it would not be clear if it emerges because, as we assume, that faster feedback is represented as an interoceptive signal for threat, or simply because participants are surprised about heartrate feedback that diverges from their real heartrate. Note that even a non-significant result in the analogous comparison of congruent vs incongruent slower feedback would not be able to resolve this confound, as in null hypothesis testing the absence of a significant effect does, per definition, not indicate that there is no effect - only that it could not be detected here.

      Instead, the only possible test of our hypothesis is the one we have designed our experiment around and focussed on with our central t-test: the comparison of incongruent faster with incongruent slower feedback. This keeps any possible effects of surprise/salience from generally altered feedback constant and allows us to test our specific hypothesis: that real heart rates will decrease and pain ratings will increase when receiving false interoceptive feedback about increased compared to decreasing heartrates. Note that this test of faster vs slower feedback is also statistically the most appropriate, as it collapses our prediction onto a single and highest-powered hypothesis test: As faster and slower heartrate feedback are assumed to induce effects in the opposite direction, the effect size of their difference is, per definition, double than the averaged effect size for the two separate tests of faster vs congruent feedback and slower vs congruent feedback.

      That being said, we also included comparisons with the congruent condition in our revised analysis, in line with the reviewer’s suggestion and previous studies. These analyses help explore potential asymmetries in the effect of false feedback. While faster feedback (both interoceptive and exteroceptive) significantly modulated pain relative to congruent feedback, the slower feedback did not, consistent with previous literature showing stronger effects for arousal-increasing cues (e.g., Valins, 1966; Iodice et al., 2019). To address this point, in the revised manuscript we have added a paragraph to the Data Analysis section of Experiment 1 (lines 405-437) to make this logic clearer.

      Valins, S. (1966). Cognitive effects of false heart-rate feedback. Journal of personality and social psychology, 4(4), 400.

      Iodice, P., Porciello, G., Bufalari, I., Barca, L., & Pezzulo, G. (2019). An interoceptive illusion of effort induced by false heart-rate feedback. Proceedings of the National Academy of Sciences, 116(28), 13897-13902.

      This could be influenced by the fact that the faster HR exteroceptive cue in experiment 2 also shows a significant modulatory effect on pain intensity compared to congruent HR feedback, which puts into question the hypothesized differences between interoceptive vs. exteroceptive cues. These results could also be influenced by the specific choice of exteroceptive cue: the researchers imply that the main driver of the effect is the nature of the cue (interoceptive vs. exteroceptive) and not its frequency. However, they attempt to generalize their findings using knocking wood sounds to all possible sounds, but it is possible that some features of these sounds (e.g., auditory roughness or loomingness) could be the drivers behind the observed effects.

      We appreciate this thoughtful comment. We agree that low-level auditory features can potentially introduce confounds in the experimental design, and we acknowledge the importance of distinguishing these factors from the higher-order distinction that is central to our study: whether the sound is perceived as interoceptive (originating from within the body) or exteroceptive (perceived as external). To this end, the knocking sound was chosen not for its specific acoustic profile, but because it lacked bodily relevance, thus allowing us to test whether the same temporal manipulations (faster, congruent, slower) would have different effects depending on whether the cue was interpreted as reflecting an internal bodily state or not. In this context, the exteroceptive cue served as a conceptual contrast rather than an exhaustive control for all auditory dimensions.

      Several aspects of our data make it unlikely that the observed effects are driven by unspecific acoustic characteristics of the sounds used in the exteroceptive and interoceptive experiments (see also our responses to Reviewer 1 and Reviewer 3 who raised similar points).

      First, if the knocking sound had inherent acoustic features that strongly influenced perception or physiological responses, we would expect it to have produced consistent effects across all feedback conditions (Faster, Slower, Congruent), regardless of the interpretive context. This would have manifested as an overall difference between experiments in the between-subjects analyses and in the supplementary mixed-effects models that included Experiment as a fixed factor. Yet, we observed no such main effects in any of our variables. Instead, significant differences emerged only in specific theoretically predicted comparisons (e.g., Faster vs. Slower), and critically, these effects depended on the cue type (interoceptive vs. exteroceptive), suggesting that perceived bodily relevance, rather than a specific acoustic property, was the critical modulator. In other words, any alternative explanation based on acoustic features would need to be able to explain why these acoustic properties would induce not an overall change in heart rate and pain perception (i.e., similarly across slower, faster, and congruent feedback), but the brain’s response to changes in the rate of this feedback – increasing pain ratings and decreasing heartrates for faster relative to slower feedback. We hope you agree that a simple effect of acoustic features would not predict such a sensitivity to the rate with which the sound was played.

      Please refer to our responses to Reviewers 1 and 2 for further aspects of the data, arguing strongly against other features associated with the sounds (e.g., alertness, arousal) could be responsible for the results, as the data pattern again goes in the opposite direction than that predicted by such accounts (e.g., faster heartrate feedback decreased real heartrate, instead of increasing them, as would be expected if accelerated heartrate feedback increased arousal).

      Finally, to further support this interpretation, we refer to neurophysiological evidence showing that heartbeat sounds are not processed as generic auditory signals, but as internal, bodily relevant cues especially when believed to reflect one’s own physiological state. For instance, fMRI research (Kleint et al., 2015) shows that heartbeat sounds engage key interoceptive regions such as the anterior insula and frontal operculum more than acoustically matched control tones. EEG data (Vicentin et al., 2024) showed that faster heartbeat sounds produce stronger alpha suppression over frontocentral areas, suggesting enhanced processing in networks associated with interoceptive attention. Moreover, van Elk et al. (2014) found that heartbeat sounds attenuate the auditory N1 response, a neural signature typically linked to self-generated or predicted bodily signals. These findings consistently demonstrate that heartbeats sounds are processed as interoceptive and self-generated signals, which is in line with our rationale that the critical factor at play concern whether it is semantically perceived as reflecting one’s own bodily state, rather than the physical properties of the sound.

      We now explicitly discuss these issues in the revised Discussion section (lines 740-758).

      Kleint, N. I., Wittchen, H. U., & Lueken, U. (2015). Probing the interoceptive network by listening to heartbeats: an fMRI study. PloS one, 10(7), e0133164.

      van Elk, M., Lenggenhager, B., Heydrich, L., & Blanke, O. (2014). Suppression of the auditory N1-component for heartbeat-related sounds reflects interoceptive predictive coding. Biological psychology, 99, 172-182.

      Vicentin, S., Guglielmi, S., Stramucci, G., Bisiacchi, P., & Cainelli, E. (2024). Listen to the beat: behavioral and neurophysiological correlates of slow and fast heartbeat sounds. International Journal of Psychophysiology, 206, 112447.

      Finally, it is noteworthy that the researchers divided the study into two experiments when it would have been optimal to test all the conditions with the same subjects in a randomized order in a single cross-over experiment to reduce between-subject variability. Taking this into consideration, I believe that the conclusions are only partially supported by the evidence. Despite of the outcome transformations, a clear effect of faster HR acoustic feedback can be observed in the first experiment, which is larger than the proposed exteroceptive counterpart. This work could be of broad interest to pain researchers, particularly those working on predictive coding of pain.

      We appreciate the reviewer’s suggestion regarding a within-subject crossover design. While such a design indeed offers increased statistical power by reducing interindividual variability (Charness, Gneezy, & Kuhn, 2012), we intentionally opted for a between-subjects design due to theoretical and methodological considerations specific to studies involving deceptive feedback. Most importantly, carryover effects are a major concern in deception paradigms. Participants exposed to one type of feedback initially (e.g., interoceptive), and then the other (exteroceptive) would be more likely to develop suspicion or adaptive strategies that would alter their responses. Such expectancy effects could contaminate results in a crossover design, particularly when participants realize that feedback is manipulated. In line with this idea, past studies on false cardiac feedback (e.g., Valins, 1966; Pennebaker & Lightner, 1980) often employed between-subjects or blocked designs to mitigate this risk.

      Pennebaker, J. W., & Lightner, J. M. (1980). Competition of internal and external information in an exercise setting. Journal of personality and social psychology, 39(1), 165.

      Valins, S. (1966). Cognitive effects of false heart-rate feedback. Journal of personality and social psychology, 4(4), 400.

      Reviewer #3 (Public Review):

      In their manuscript titled "Exposure to false cardiac feedback alters pain perception and anticipatory cardiac frequency", Parrotta and colleagues describe an experimental study on the interplay between false heart rate feedback and pain experience in healthy, adult humans. The experimental design is derived from Bayesian perspectives on interoceptive inference. In Experiment 1 (N=34), participants rated the intensity and unpleasantness of an electrical pulse presented to their middle fingers. Participants received auditory cardiac feedback prior to the electrical pulse. This feedback was congruent with the participant's heart rate or manipulated to have a higher or lower frequency than the participant's true heart rate (incongruent high/ low feedback). The authors find heightened ratings of pain intensity and unpleasantness as well as a decreased heart rate in participants who were exposed to the incongruent-high cardiac feedback. Experiment 2 (N=29) is equivalent to Experiment 1 with the exception that non-interoceptive auditory feedback was presented. Here, mean pain intensity and unpleasantness ratings were unaffected by feedback frequency.

      Strengths:

      The authors present interesting experimental data that was derived from modern theoretical accounts of interoceptive inference and pain processing.

      (1) The motivation for the study is well-explained and rooted within the current literature, whereas pain is the result of a multimodal, inferential process. The separation of nociceptive stimulation and pain experience is explained clearly and stringently throughout the text.

      (2) The idea of manipulating pain-related expectations via an internal, instead of an external cue, is very innovative.

      (3) An appropriate control experiment was implemented, where an external (non-physiological) auditory cue with parallel frequency to the cardiac cue was presented.

      (4) The chosen statistical methods are appropriate, albeit averaging may limit the opportunity for mechanistic insight, see weaknesses section.

      (5) The behavioral data, showing increased unpleasantness and intensity ratings after exposure to incongruent-high cardiac feedback, but not exteroceptive high-frequency auditory feedback, is backed up by ECG data. Here, the decrease in heart rate during the incongruent-high condition speaks towards a specific, expectation-induced physiological effect that can be seen as resulting from interoceptive inference.

      We thank the reviewer for their positive feedback. We are glad that the study’s theoretical foundation, innovative design, appropriate control conditions, and convergence of behavioral and physiological data were well received.

      Weaknesses:

      Additional analyses and/ or more extensive discussion are needed to address these limitations:

      (1) I would like to know more about potential learning effects during the study. Is there a significant change in ∆ intensity and ∆ unpleasantness over time; e.g. in early trials compared to later trials? It would be helpful to exclude the alternative explanation that over time, participants learned to interpret the exteroceptive cue more in line with the cardiac cue, and the effect is driven by a lack of learning about the slightly less familiar cue (the exteroceptive cue) in early trials. In other words, the heartbeat-like auditory feedback might be "overlearned", compared to the less naturalistic tone, and more exposure to the less naturalistic cue might rule out any differences between them w.r.t. pain unpleasantness ratings.

      We thank the reviewer for raising this important point. Please note that the repetitions in our task were relatively limited (6 trials per condition), which limits the potential influence of such differential learning effects between experiments. To address this concern, we performed an additional analysis, reported in the Supplementary Materials, using a Linear Mixed-Effects Model approach. This method allowed us to include "Trial" (the rank order of each trial) as a variable to account for potential time-on-task effects such as learning, adaptation, or fatigue (e.g., Möckel et al., 2015). All feedback conditions (no-feedback, congruent, faster, slower) and all stimulus intensity levels were included.

      Specifically, we tested the following models:

      Likert Pain Unpleasantness Ratings ~ Experiment × Feedback × StimInt × Trial + (StimInt + Trial | Subject)

      Numeric Pain Scale of Intensity Ratings ~ Experiment × Feedback × StimInt × Trial + (StimInt + Trial | Subject)

      In both models, no significant interactions involving Trial × Experiment or Trial × Feedback × Experiment were found. Instead, we just find generally larger effects in early trials compared to later ones (Main effect of Trial within each Experiment), similar to other cognitive illusions where repeated exposure diminishes effects. Thus, although some unspecific changes over time may have occurred (e.g., due to general task exposure), these changes did not differ systematically across experimental conditions (interoceptive vs. exteroceptive) or feedback types. However, we are fully aware that the absence of significant higher-order interactions does not conclusively rule out the possibility of learning-related effects. It is possible that our models lacked the statistical power to detect more subtle or complex time-dependent modulations, particularly if such effects differ in magnitude or direction across feedback conditions.

      We report the full description of these analyses and results in the Supplementary materials 1. Cross-experiment analysis (between-subjects model).

      (2) The origin of the difference in Cohen's d (Exp. 1: .57, Exp. 2: .62) and subsequently sample size in the sensitivity analyses remains unclear, it would be helpful to clarify where these values are coming from (are they related to the effects reported in the results? If so, they should be marked as post-hoc analyses).

      Following recommendations (Anderson, Kelley & Maxwell, 2017; Albers &  Lakens, 2017), we do not report theoretical power based on previously reported effect sizes as this neglects uncertainty around effect size measurements, especially for new effects for which no reliable expected effect size estimates can be derived across the literature. Instead, the power analysis is based on a sensitivity analysis, conducted in G*Power (Version 3.1). Importantly, these are not post-hoc analyses, as they are not based on observed effect sizes in our study, but derived a priori. Sensitivity analyses estimate effect sizes that our design is well-powered (90%) to detect (i.e. given target power, sample size, type of test), for the crucial comparison between faster and slower feedback in both experiments (Lakens, 2022). Following recommendations, we also report the smallest effect size this test can in principle detect in our study (SESOI, Lakens, 2022). This yields effect sizes of d = .57 in Experiment 1 and d = .62 in Experiment 2 at 90% power and SESOIs of d = .34 and .37, respectively. Note that values are slightly higher in Experiment 2, as more participants were excluded based on our exclusion criteria. Importantly, detectable effect sizes in both experiments are smaller than reported effect sizes for comparable top-down effects on pain measurements of d = .7 (Iodice et al., 2019).  We have now added more information to the power analysis sections to make this clearer (lines 208-217).

      Albers, C., & Lakens, D. (2018). When power analyses based on pilot data are biased: Inaccurate effect size estimators and follow-up bias. Journal of experimental social psychology, 74, 187-195.

      Anderson, S. F., Kelley, K., & Maxwell, S. E. (2017). Sample-Size Planning for More Accurate Statistical Power: A Method Adjusting Sample Effect Sizes for Publication Bias and Uncertainty. Psychological Science, 28(11), 1547-1562.

      Lakens, D. (2022). Sample size justification. Collabra: psychology, 8(1), 33267.

      (3) As an alternative explanation, it is conceivable that the cardiac cue may have just increased unspecific arousal or attention to a larger extent than the exteroceptive cue. It would be helpful to discuss the role of these rather unspecific mechanisms, and how it may have differed between experiments.

      We thank the reviewer for raising this important point. We agree that, in principle, unspecific mechanisms such as increased arousal or attention driven by cardiac feedback could be an alternative explanation for the observed effects. However, several aspects of our data indicate that this is unlikely:

      (1) No main effect of Experiment on pain ratings:

      If the cardiac feedback had simply increased arousal or attention in a general (non-specific) way, we would expect a main effect of Experiment (i.e., interoceptive vs exteroceptive condition) on pain intensity or unpleasantness ratings, regardless of feedback frequency. However, such a main effect was never observed when we compared between experiments (see between-experiment t-tests in results, and in supplementary analyses). Instead, effects were specific to the manipulation of feedback frequency.

      (2) Heart rate as an arousal measure:

      Heart rate (HR) is a classical physiological index of arousal. If there had been an unspecific increase in arousal in the interoceptive condition, we would expect a main effect of Experiment on HR. However, no such main effect was found. Instead, our HR analyses revealed a significant interaction between feedback and experiment, suggesting that HR changes depended specifically on the feedback manipulation rather than reflecting a general arousal increase.

      (3) Arousal predicts faster, not slower, heart rates

      In Experiment 1, faster interoceptive cardiac feedback led to a slowdown in heartrates both when compared to slower feedback and to congruent cardiac feedback. This is in line with the predicted compensatory response to faster heart rates. In contrast, if faster feedback would have only generally increased arousal, heart rates should have increased instead of decreased, as indicated by several prior studies (Tousignant-Laflamme et al., 2005; Terkelsen et al., 2005; for a review, see Forte et al., 2022), predicting the opposite pattern of responses than was found in Experiment 1.

      Taken together, these findings indicate that the effects observed are unlikely to be driven by unspecific arousal or attention mechanisms, but rather are consistent with feedback-specific modulations, in line with our interoceptive inference framework.

      We have now integrated these considerations in the revised discussion (lines 796-830), and added the relevant between-experiment comparisons to the Results of Experiment 2 and the supplementary analysis.

      Terkelsen, A. J., Mølgaard, H., Hansen, J., Andersen, O. K., & Jensen, T. S. (2005). Acute pain increases heart rate: differential mechanisms during rest and mental stress. Autonomic Neuroscience, 121(1-2), 101-109.

      Tousignant-Laflamme, Y., Rainville, P., & Marchand, S. (2005). Establishing a link between heart rate and pain in healthy subjects: a gender effect. The journal of pain, 6(6), 341-347.

      Forte, G., Troisi, G., Pazzaglia, M., Pascalis, V. D., & Casagrande, M. (2022). Heart rate variability and pain: a systematic review. Brain sciences, 12(2), 153.

      (4) The hypothesis (increased pain intensity with incongruent-high cardiac feedback) should be motivated by some additional literature.

      We thank the reviewer for this helpful suggestion. Please note that the current phenomenon was tested in this experiment for the first time. Therefore, there is no specific prior study that motivated our hypotheses; they were driven theoretically, and derived from our model of interoceptive integration of pain and cardiac perception. The idea that accelerated cardiac feedback (relative to decelerated feedback) will increase pain perception and reduce heart rates is grounded on Embodied Predictive coding frameworks. Accordingly, expectations and signals from different sensory modalities (sensory, proprioceptive, interoceptive) are integrated both to efficiently infer crucial homeostatic and physiological variables, such as hunger, thirst, and, in this case, pain, and regulate the body’s own autonomic responses based on these inferences.

      Within this framework, the concept of an interoceptive schema (Tschantz et al., 2022; Iodice et al., 2019; Parrotta et al., 2024; Schoeller et al., 2022) offers the basis for understanding interoceptive illusions, wherein inferred levels of interoceptive states (i.e., pain) deviate from the actual physiological state. Cardiac signals conveyed by the feedback manipulation act as a misleading prior, shaping the internal generative model of pain. Specifically, an increased heart rate may signal a state of threat, establishing a prior expectation of heightened pain. Building on predictive models of interoception, we predict that this cardiac prior is integrated with interoceptive (i.e., actual nociceptive signal) and exteroceptive inputs (i.e., auditory feedback input), leading to a subjective experience of increased pain even when there is no corresponding increase in the nociceptive input.

      This idea is not completely new, but it is based on our previous findings of an interoceptive cardiac illusion driven by misleading priors about anticipated threat (i.e., pain). Specifically, in Parrotta et al. (2024), we tested whether a common false belief that heart rate increases in response to threat lead to an illusory perception of accelerated cardiac activity when anticipating pain. In two experiments, we asked participants to monitor and report their heartbeat while their ECG was recorded. Participants performed these tasks while visual cues reliably predicted a forthcoming harmless (low-intensity) vs. threatening (high-intensity) cutaneous electrical stimulus. We showed that anticipating a painful vs. harmless stimulus causes participants to report an increased cardiac frequency, which does not reflect their real cardiac response, but the common (false) belief that heart rates would accelerate under threat, reflecting the hypothesised integration of prior expectations and interoceptive inputs when estimating cardiac activity.

      Here we tested the counterpart of such a cardiac illusion. We reasoned that if cardiac interoception is shaped by expectations about pain, then the inverse should also be true: manipulating beliefs about cardiac activity (via cardiac feedback) in the context of pain anticipation should influence the perception of pain. Specifically, we hypothesized that presenting accelerated cardiac feedback would act as a misleading prior, leading to an illusory increase in pain experience, even in the absence of an actual change in nociceptive input.

      Moreover, next to the references already provided in the last version of the manuscript, there is ample prior research that provides more general support for such relationships. Specifically, studies have shown that providing mismatched cardiac feedback in contexts where cardiovascular changes are typically expected (i.e. sexual arousal, Rupp & Wallen, 2008; Valins, 1996; physical exercise, Iodice et al., 2019) can enhance the perception of interoceptive states associated with those experiences. Furthermore, findings that false cardiac feedback can influence emotional experience suggest that it is the conscious perception of physiological arousal, combined with the cognitive interpretation of the stimulus, that plays a key role in shaping emotional responses (Crucian et al., 2000).

      This point is now addressed in the revised Introduction, wherein additional references have been integrated (lines 157-170).

      Crucian, G. P., Hughes, J. D., Barrett, A. M., Williamson, D. J. G., Bauer, R. M., Bowers, D., & Heilman, K. M. (2000). Emotional and physiological responses to false feedback. Cortex, 36(5), 623-647.

      Iodice, P., Porciello, G., Bufalari, I., Barca, L., & Pezzulo, G. (2019). An interoceptive illusion of effort induced by false heart-rate feedback. Proceedings of the National Academy of Sciences, 116(28), 13897-13902.

      Parrotta, E., Bach, P., Perrucci, M. G., Costantini, M., & Ferri, F. (2024). Heart is deceitful above all things: Threat expectancy induces the illusory perception of increased heartrate. Cognition, 245, 105719.

      Rupp, H. A., & Wallen, K. (2008). Sex differences in response to visual sexual stimuli: A review. Archives of sexual behavior, 37(2), 206-218.

      Schoeller, F., Horowitz, A., Maes, P., Jain, A., Reggente, N., Moore, L. C., Trousselard, M., Klein, A., Barca, L., & Pezzulo, G. (2022). Interoceptive technologies for clinical neuroscience.

      Tschantz, A., Barca, L., Maisto, D., Buckley, C. L., Seth, A. K., & Pezzulo, G. (2022). Simulating homeostatic, allostatic and goal-directed forms of interoceptive control using active inference. Biological Psychology, 169, 108266.

      Valins, S. (1966). Cognitive effects of false heart-rate feedback. Journal of personality and social psychology, 4(4), 400.

      (5) The discussion section does not address the study's limitations in a sufficient manner. For example, I would expect a more thorough discussion on the lack of correlation between participant ratings and self-reported bodily awareness and reactivity, as assessed with the BPQ.

      We thank the reviewer for this valuable observation. In response, we have revised the Discussion section to explicitly acknowledge and elaborate on the lack of significant correlations between participants’ pain ratings and their self-reported bodily awareness and reactivity as assessed with the BPQ.

      We now clarify that the inclusion of this questionnaire was exploratory. While it would be theoretically interesting to observe a relationship between subjective pain modulation and individual differences in interoceptive awareness, detecting robust correlations between within-subject experimental effects and between-subjects trait measures such as the BPQ typically requires much larger sample sizes (often exceeding N = 200) due to the inherently low reliability of such cross-level associations (see Hedge, Powell & Sumner, 2018; the “reliability paradox”). As such, the absence of a significant correlation in our study does not undermine the conclusions we draw from our main findings. Future studies with larger samples will be needed to systematically address this question. We now acknowledge this point explicitly in the revised manuscript (lines 501-504; 832-851).

      Hedge, C., Powell, G., & Sumner, P. (2018). The reliability paradox: Why robust cognitive tasks do not produce reliable individual differences. Behavior Research Methods, 50(3), 1166-1186. https://doi.org/10.3758/s13428-017-0935-1

      (a) Some short, additional information on why the authors chose to focus on body awareness and supradiaphragmatic reactivity subscales would be helpful.

      We chose to focus on the body awareness and supradiaphragmatic reactivity subscales because these aspects are closely tied to emotional and physiological processing, particularly in the context of interoception. Body awareness plays a critical role in how individuals perceive and interpret bodily signals, which in turn affects emotional regulation and self-awareness. Supradiaphragmatic reactivity refers specifically to organs located or occurring above the diaphragm (i.e., the muscle that separates the chest cavity from the abdomen), which includes the heart, compared to subdiaphragmatic reactivity subscales further down. Our decision to include these subscales is further motivated by recent research, including the work by Petzschner et al. (2021), which demonstrates that the focus of attention can modulate the heartbeat-evoked potential (HEP), and that this modulation is predicted by participants’ responses on the supradiaphragmatic reactivity subscales. Thus, this subscale, and the more general body awareness scale, allows us to explore the interplay between bodily awareness, physiological reactivity, and emotional processing in our study. We now clarify this point in the revised version of the Methods - Body Perception Questionnaire (lines 384-393).

      (6) The analyses presented in this version of the manuscript allow only limited mechanistic conclusions - a computational model of participants' behavior would be a very strong addition to the paper. While this may be out of the scope of the article, it would be helpful for the reader to discuss the limitations of the presented analyses and outline avenues towards a more mechanistic understanding and analysis of the data. The computational model in [7] might contain some starting ideas.

      Thank you for your valuable feedback. We agree that a computational model would enhance the mechanistic understanding of our findings. While this is beyond the current scope, we now discuss the limitations of our analysis in the Limitations and Future directions section (lines 852-863). Specifically, we acknowledge that future studies could use computational models to better understand the interactions between physiological, cognitive, and perceptual factors.

      Some additional topics were not considered in the first version of the manuscript:

      (1) The possible advantages of a computational model of task behavior should be discussed.

      We agree that a computational model of task behavior could provide several advantages. By formalizing principles of predictive processing and active inference, such a model could generate quantitative predictions about how heart rate (HR) and feedback interact, providing a more precise understanding of their respective contributions to pain modulation. However, this is a first demonstration of a theoretically predicted phenomenon, and computationally modelling it is currently outside the scope of the article. We would be excited to explore this in the future. We have added a brief discussion of these potential advantages in the revised manuscript and suggest that future work could integrate computational modelling to further deepen our understanding of these processes (lines 852-890).

      (2) Across both experiments, there was a slightly larger number of female participants. Research suggests significant sex-related differences in pain processing [1,2]. It would be interesting to see what role this may have played in this data.

      Thank you for your insightful comment. While we acknowledge that sex-related differences in pain processing are well-documented in the literature, we do not have enough participants in our sample to test this in a well-powered way. As such, exploring the role of sex differences in pain perception will need to be addressed in future studies with more balanced samples. It would be interesting if more sensitive individuals, with a more precise representation of pain, also show smaller effects on pain perception. We have noted this point in the revised manuscript (lines 845-851) and suggest that future research could specifically investigate how sex differences might influence the modulation of pain and physiological responses in similar experimental contexts.

      (3) There are a few very relevant papers that come to mind which may be of interest. These sources might be particularly useful when discussing the roadmap towards a mechanistic understanding of the inferential processes underlying the task responses [3,4] and their clinical implications.

      Thank you for highlighting these relevant papers. We appreciate your suggestion and have now cited them in the Limitations and Future directions paragraph (lines 852-863).

      (4) In this version of the paper, we only see plots that illustrate ∆ scores, averaged across pain intensities - to better understand participant responses and the relationship with stimulus intensity, it would be helpful to see a more descriptive plot of task behavior (e.g. stimulus intensity and raw pain ratings)

      To directly address the reviewer’s request, we now provide additional descriptive plots in the supplementary material of the revised manuscript, showing raw pain ratings across different stimulus intensities and feedback conditions. These plots offer a clearer view of participant behavior without averaging across pain levels, helping to better illustrate the relationship between stimulus intensity and reported pain.

      Mogil, J. S. (2020). Qualitative sex differences in pain processing: emerging evidence of a biased literature. Nature Reviews Neuroscience, 21(7), 353-365. https://www.nature.com/articles/s41583-020-0310-6

      Sorge, R. E., & Strath, L. J. (2018). Sex differences in pain responses. Current Opinion in Physiology, 6, 75-81. https://www.sciencedirect.com/science/article/abs/pii/S2468867318300786?via%3Dihub

      Unal, O., Eren, O. C., Alkan, G., Petzschner, F. H., Yao, Y., & Stephan, K. E. (2021). Inference on homeostatic belief precision. Biological Psychology, 165, 108190.

      Allen, M., Levy, A., Parr, T., & Friston, K. J. (2022). In the body's eye: the computational anatomy of interoceptive inference. PLoS Computational Biology, 18(9), e1010490.

      Stephan, K. E., Manjaly, Z. M., Mathys, C. D., Weber, L. A., Paliwal, S., Gard, T., ... & Petzschner, F. H. (2016). Allostatic self-efficacy: A metacognitive theory of dyshomeostasis-induced fatigue and depression. Frontiers in human neuroscience, 10, 550.

      Friston, K. J., Stephan, K. E., Montague, R., & Dolan, R. J. (2014). Computational psychiatry: the brain as a phantastic organ. The Lancet Psychiatry, 1(2), 148-158.

      Eckert, A. L., Pabst, K., & Endres, D. M. (2022). A Bayesian model for chronic pain. Frontiers in Pain Research, 3, 966034.

      We thank the reviewer for highlighting these relevant references which have now been integrated in the revised version of the manuscript.

      Recommendations For The Authors: 

      Reviewer #1 (Recommendations For The Authors):

      At the time I was reviewing this paper, I could not think of a detailed experiment that would answer my biggest concern: Is this a manipulation of the brain's interoceptive data integration, or rather a manipulation of participants' alertness which indirectly influences their pain prediction?

      One incomplete idea that came to mind was delivering this signal in a more "covert" manner (though I am not sure it will suffice), or perhaps correlating the effect size of a participant with their interoceptive abilities, as measured in a different task or through a questionnaire.... Another potential idea is to tell participants that  this is someone else's HR that they hear and see if that changes the results (though requires further thought). I leave it to the authors to think further, and perhaps this is to be answered in a different paper - but if so, I am sorry to say that I do not think the claims can remain as they are now, and the paper will need a revision of its arguments, unfortunately. I urge the authors to ask further questions if my point about the concern was not made clear enough for them to address or contemplate it.

      We thank the reviewer for raising this important point. As detailed in our previous response, this point invites an important clarification regarding the role of cardiac deceleration in threat processing. Rather than serving as an interoceptive input from which the brain infers the likelihood of a forthcoming aversive event, heart rate deceleration is better described as an output of an already ongoing predictive process, as it reflects an allostatic adjustment of the bodily state aimed at minimizing the impact of the predicted perturbation (e.g., pain) and preventing sympathetic overshoot. It would be maladaptive for the brain to use a decelerating heart rate as evidence of impending threat, since this would paradoxically trigger further parasympathetic activation, initiating a potentially destabilizing feedback loop. Conversely, increased heart rate represents an evolutionarily conserved cue for arousal, threat, and pain. Our results therefore align with the idea that the brain treats externally manipulated increases in cardiac signals as congruent with anticipated sympathetic activation, prompting a compensatory autonomic and perceptual response consistent with embodied predictive processing frameworks (e.g., Barrett & Simmons, 2015; Seth, 2013).

      We would also like to re-iterate that our results cannot be explained by general differences induced by the different heart rate sounds relative to the exteroceptive (see also our detailed comments to your point above, and our response to a similar point from Reviewer 3), for three main reasons.

      (1) No main effect of Experiment on pain ratings:

      If the cardiac feedback had simply increased arousal or attention in a general (non-specific) way, we would expect a main effect of Experiment (i.e., interoceptive vs exteroceptive condition) on pain intensity or unpleasantness ratings, regardless of feedback frequency. However, such a main effect was never observed. Instead, effects were specific to the manipulation of feedback frequency.

      (2) Heart rate as an arousal measure:

      Heart rate (HR) is a classical physiological index of arousal. If there had been an unspecific increase in arousal in the interoceptive condition, we would expect a main effect of Experiment on HR. However, no such main effect was found. Instead, our HR analyses revealed a significant interaction between feedback and experiment, suggesting that HR changes depended specifically on the feedback manipulation rather than reflecting a general arousal increase.

      (3) Arousal predicts faster, not slower, heart rates

      In Experiment 1, faster interoceptive cardiac feedback led to a slowdown in heartrates both when compared to slower feedback and to congruent cardiac feedback. This is in line with the predicted compensatory response to faster heart rates. In contrast, if faster feedback would have only generally increased arousal, heart rates should have increased instead of decreased, as indicated by several prior studies (for a review, see Forte et al., 2022), predicting the opposite pattern of responses than was found in Experiment 1.

      Taken together, these findings indicate that the effects observed are unlikely to be driven by unspecific arousal or attention mechanisms, but rather are consistent with feedback-specific modulations, in line with our interoceptive inference framework. We now integrate these considerations in the general discussion (lines 796-830).

      Barrett, L. F., & Simmons, W. K. (2015). Interoceptive predictions in the brain. Nature reviews neuroscience, 16(7), 419-429.

      Forte, G., Troisi, G., Pazzaglia, M., Pascalis, V. D., & Casagrande, M. (2022). Heart rate variability and pain: a systematic review. Brain sciences, 12(2), 153.

      Seth, A. K. (2013). Interoceptive inference, emotion, and the embodied self. Trends in Cognitive Sciences, 17(11), 565-573.

      Additional recommendations:

      Major (in order of importance):

      (1) Number of trials per participant, per condition: as I mentioned, having only 6 trials for each condition is very little. The minimum requirement to accept so few trials would be to show data about the distribution of participants' responses to these trials, both per pain intensity (which was later averaged across - another issue discussed later), and across pain intensities, and see that it allows averaging across and that it is not incredibly variable such that the mean is unreliable.

      We appreciate the reviewer’s concern regarding the limited number of trials per condition. This choice was driven by both theoretical and methodological considerations.

      First, as is common in body illusion paradigms (e.g., the Rubber Hand Illusion, Botvinick & Cohen, 1998; the Full Body Illusion, Ehrsson, 2007; the Cardio-visual full body illusion, Pratviel et al., 2022) only a few trials are typically employed due to the immediate effects these manipulations elicit. Repetition can reduce the strength of the illusion through habituation, increased awareness, or loss of believability.

      Second, the experiment was already quite long (1.5h to 2h per participant) and cognitively demanding. It would not have been feasible to expand it further without compromising data quality due to fatigue, attentional decline, or participant disengagement.

      Third, the need for a large number of trials is more relevant when using implicit measures such as response times or physiological indices, which are typically indirectly related to the psychological constructs of interest. In contrast, explicit ratings are often more sensitive and less noisy, and thus require fewer repetitions to yield reliable effects (e.g., Corneille et al., 2024).

      Importantly, we also addressed your concern analytically. We ran therefore linear mixed-effects model analyses across all dependent variables (See Supplementary materials), with Trial (i.e., the rank order of each trial) included as a predictor to account for potential time-on-task effects such as learning, adaptation, or fatigue (e.g., Möckel et al., 2015). These models captured trial-by-trial variability and allowed us to test for systematic changes in heart rate (HR) and pain ratings including interactions with feedback conditions (e.g., Klieg et al., 2011; Baayen et al., 2010; Ambrosini et al., 2019). The consistent effects of Trial suggest that repetition dampens the illusion, reinforcing our decision to limit the number of exposures.

      In the interoceptive experiment, these analyses revealed a significant Feedback × Trial interaction (F(3, 711.19) = 6.16, p < .001), indicating that the effect of feedback on HR was not constant over time. As we suspected, and in line with other illusion-like effects, the difference between Faster and Slower feedback, which was significant early on (estimate = 1.68 bpm, p = .0007), decreased by mid-session (estimate = 0.69 bpm, p = .0048), and was no longer significant in later trials (estimate = 0.30 bpm, p = .4775). At the end of the session, HR values in the Faster and Slower conditions even numerically converged (Faster: M = 74.4, Slower: M = 74.1), and the non-significant contrast confirms that the difference had effectively vanished (for further details about slope estimation, see Supplementary material).

      The same pattern emerged for pain-unpleasantness ratings. A significant Feedback × Trial interaction (F (3, 675.33) = 3.44, p = .0165) revealed that the difference between Faster and Slower feedback was strongest at the beginning of the session and progressively weakened. Specifically, Faster feedback produced higher unpleasantness than Slower in early trials (estimate= -0.28, p = .0058) and mid-session (estimate = - 0.19, p = .0001), but this contrast was no longer significant in the final trials, wherein all the differences between active feedback conditions vanished (all ps > .55).

      Finally, similar results were yielded for pain intensity ratings. A significant Feedback × Trial interaction (F (3, 669.15) = 9.86, p < .001) showed that the Faster vs Slower difference was greatest at the start of the session and progressively vanished over trials. In early trials Faster feedback exceeded Slower (estimate=-8.33, p = .0001); by mid-session this gap had shrunk to 4.48 points (p < .0001); and in the final trials it was no longer significant (all ps > .94).

      Taken together, our results show that the illusion induced by Faster relative to slower feedback fades with repetition; adding further trials would likely have masked this key effect, confirming the methodological choice to restrict each condition to fewer exposures. To conclude, given that this is the first study to investigate an illusion of pain using heartbeat-based manipulation, we intentionally limited repeated exposures to preserve the integrity of the illusion. The use of mixed models as complementary analyses strengthens the reliability of our conclusions within these necessary design constraints. We now clarify this point in the Procedure paragraph (lines 328-335)

      Ambrosini, E., Peressotti, F., Gennari, M., Benavides-Varela, S., & Montefinese, M. (2023). Aging-related effects on the controlled retrieval of semantic information. Psychology and Aging, 38(3), 219.

      Baayen, R. H., & Milin, P. (2010). Analyzing reaction times. International Journal of Psychological Research, 3(2), 12-28.

      Botvinick, M., & Cohen, J. (1998). Rubber hands ‘feel’touch that eyes see. Nature, 391(6669), 756-756.

      Corneille, O., & Gawronski, B. (2024). Self-reports are better measurement instruments than implicit measures. Nature Reviews Psychology, 3(12), 835–846.

      Ehrsson, H. H. (2007). The experimental induction of out-of-body experiences. Science, 317(5841), 1048-1048.

      Kliegl, R., Wei, P., Dambacher, M., Yan, M., & Zhou, X. (2011). Experimental effects and individual differences in linear mixed models: Estimating the relation of spatial, object, and attraction effects in visual attention. Frontiers in Psychology, 1, 238. https://doi.org/10.3389/fpsyg.2010.00238

      Möckel, T., Beste, C., & Wascher, E. (2015). The effects of time on task in response selection-an ERP study of mental fatigue. Scientific reports, 5(1), 10113.

      Pratviel, Y., Bouni, A., Deschodt-Arsac, V., Larrue, F., & Arsac, L. M. (2022). Avatar embodiment in VR: Are there individual susceptibilities to visuo-tactile or cardio-visual stimulations?. Frontiers in Virtual Reality, 3, 954808.

      (2) Using different pain intensities: what was the purpose of training participants on correctly identifying pain intensities? You state that the aim of having 5 intensities is to cause ambiguity. What is the purpose of making sure participants accurately identify the intensities? Also, why then only 3 intensities were used in the test phase? The rationale for these is lacking.

      We thank the reviewer for raising these important points regarding the use of different pain intensities. The purpose of using five levels during the calibration and training phases was to introduce variability and increase ambiguity in the participants’ sensory experience. This variability aimed to reduce predictability and prevent participants from forming fixed expectations about stimulus intensity, thereby enhancing the plausibility of the illusion. It also helped prevent habituation to a single intensity and made the manipulation subtler and more credible. We had no specific theoretical hypotheses about this manipulation. Regarding the accuracy training, although the paradigm introduced ambiguity, it was important to ensure that participants developed a stable and consistent internal representation of the pain scale. This step was essential to control for individual differences in sensory discrimination and to ensure that illusion effects were not confounded by participants’ inability to reliably distinguish between intensities.

      As for the use of only three pain intensities in the test phase, the rationale was to focus on a manageable subset that still covered a meaningful range of the stimulus spectrum. This approach followed the same logic as Iodice et al. (2019, PNAS), who used five (rather than all seven) intensity levels during their experimental session. Specifically, they excluded the extreme levels (45 W and 125 W) used during baseline, to avoid floor and ceiling effects and to ensure that each test intensity could be paired with both a “slower” and a “faster” feedback from an adjacent level. This would not have been possible at the extremes of the intensity range, where no adjacent level exists in one direction. We adopted the same strategy to preserve the internal consistency and plausibility of our feedback manipulation.

      We further clarified these points in the revised manuscript (lines 336-342).

      Iodice, P., Porciello, G., Bufalari, I., Barca, L., & Pezzulo, G. (2019). An interoceptive illusion of effort induced by false heart-rate feedback. Proceedings of the National Academy of Sciences, 116(28), 13897-13902.

      (3) Averaging across pain intensities: this is, in my opinion, not the best approach as by matching a participant's specific responses to a pain stimulus before and after the manipulation, you can more closely identify changes resulting from the manipulation. Nevertheless, the minimal requirement to do so is to show data of distributions of pain intensities so we know they did not differ between conditions per participant, and in general - as you indicate they were randomly distributed.

      We thank the reviewer for this thoughtful comment. The decision to average across pain intensities in our main analyses was driven by the specific aim of the study: we did not intend to determine at which exact intensity level the illusion was most effective, and the limited number of trials makes such an analysis difficult. Rather, we introduced variability in nociceptive input to increase ambiguity and reduce predictability in the participants’ sensory experience. This variability was critical for enhancing the plausibility of the illusion by preventing participants from forming fixed expectations about stimulus strength. Additionally, using a range of intensities helped to minimize habituation effects and made the feedback manipulation subtler and more credible.

      That said, we appreciate the reviewer’s point that matching specific responses before and after the manipulation at each intensity level could provide further insights into how the illusion operates across varying levels of nociceptive input. We therefore conducted supplementary analyses using linear mixed-effects models in which all three stimulus intensities were included as a continuous fixed factor. This allowed us to examine whether the effects of feedback were intensity-specific or generalized across different levels of stimulation

      These analyses revealed that, in both the interoceptive and exteroceptive experiments, the effect of feedback on pain ratings was significantly modulated by stimulus intensity, as indicated by a Feedback × Stimulus Intensity interaction (Interoceptive: unpleasantness F(3, 672.32)=3.90, p=.0088; intensity ratings F(3, 667.07)=3.46, p=.016. Exteroceptive: unpleasantness F(3, 569.16)=8.21, p<.0001; intensity ratings F(3, 570.65)=3.00, p=.0301). The interaction term confirmed that the impact of feedback varied with stimulus strength, yet the pattern that emerged in each study diverged markedly.

      In the interoceptive experiment, the accelerated-heartbeat feedback (Faster) systematically heightened pain relative to the decelerated version (Slower) at every level of noxious input: for low-intensity trials Faster exceeded Slower by 0.22 ± 0.08 points on the unpleasantness scale (t = 2.84, p = .0094) and by 3.87 ± 1.69 units on the numeric intensity scale (t = 2.29, p = .0448); at the medium intensity the corresponding differences were 0.19 ± 0.05 (t = -4.02, p = .0001) and 4.52 ± 1.06 (t = 4.28, p < .0001); and even at the highest intensity, Faster still surpassed Slower by 0.17 ± 0.08 on unpleasantness (t = 2.21, p = .0326) and by 5.16 ± 1.67 on intensity (t = 3.09, p = .0032). This uniform Faster > Slower pattern indicates that the interoceptive manipulation amplifies perceived pain in a stimulus-independent fashion.

      The exteroceptive control experiment told a different story: the Faster-Slower contrast reached significance only at the most noxious setting (unpleasantness: estimate = 0.24 ± 0.07, t = -3.24, p = .0019; intensity: estimate = - 5.14 ± 1.82, t = 2.83, p = .0072) and was absent at the medium level (intensity , p=0.29; unpleasantness,  p=0.45), while at the lowest level Slower actually produced numerically higher unpleasantness (2.56 versus 2.40) and intensity ratings (44.7 versus 42.2).

      Thus, although both studies show that feedback effects depend on the actual nociceptive level of the stimulus, the results suggest that the faster vs. slower interoceptive feedback manipulation delivers a robust and intensity-invariant enhancement of pain, whereas the exteroceptive cue exerts a sporadic influence that surfaces solely under maximal stimulation.

      These new results are now included in the Supplementary Materials, where we report the detailed analyses for both the Interoceptive and Exteroceptive experiments on the Likert unpleasantness ratings and the numeric pain intensity ratings.

      (4) Sample size: It seems that the sample size was determined after the experiment was conducted, as the required N is identical to the actual N. I would be transparent about that, and say that retrospective sample size analyses support the ability of your sample size to support your claims. In general, a larger sample size than is required is always recommended, and if you were to run another study, I suggest you increase the sample size.

      As also addressed in our responses to your later comments (see our detailed reply regarding the justification of SESOI and power analyses), the power analyses reported here were not post-hoc power analyses based on obtained results. In line with current recommendations (Anderson, Kelley & Maxwell, 2017; Albers & Lakens, 2018), we did not base our analyses on previously reported effect sizes, as these can carry considerable uncertainty, particularly for novel effects where robust estimates are lacking. Instead, we used sensitivity analyses, conducted using the sensitivity analysis function in G*Power (Version 3.1). Sensitivity analyses allow us to report effect sizes that our design was adequately powered (90%) to detect, given the actual sample size, desired power level, and the statistical test used in each experiment (Lakens, 2022). Following further guidance (Lakens, 2022), we also report the smallest effect size of interest (SESOI) that these tests could reliably detect.

      This approach indicated that our design was powered to detect effect sizes of d = 0.57 in Experiment 1 and d = 0.62 in Experiment 2, with corresponding SESOIs of d = 0.34 and d = 0.37, respectively. The slightly higher value in Experiment 2 reflects the greater number of participants excluded (from an equal number originally tested) based on pre-specified criteria. Importantly, both experiments were well-powered to detect effects smaller than those typically reported in similar top-down pain modulation studies, where effect sizes around d = 0.7 have been observed (Iodice et al., 2019).

      We have now clarified this rationale in the revised manuscript, Experiment 1- Methods - Participants (lines 208-217).

      Albers, C., & Lakens, D. (2018). When power analyses based on pilot data are biased: Inaccurate effect size estimators and follow-up bias. Journal of experimental social psychology, 74, 187-195.

      Anderson, S. F., Kelley, K., & Maxwell, S. E. (2017). Sample-Size Planning for More Accurate Statistical Power: A Method Adjusting Sample Effect Sizes for Publication Bias and Uncertainty. Psychological Science, 28(11), 1547-1562. https://doi.org/10.1177/0956797617723724

      Lakens, D. (2022). Sample size justification. Collabra: psychology, 8(1), 33267.

      (5) Analysis: the use of change scores instead of the actual scores is not recommended, as it is a loss of data, but could have been ignored if it didn't have a significant effect on the analyses conducted. Instead of conducting an RM-ANOVA of conditions (faster, slower, normal heartbeats) across participants, finding significant interaction, and then moving on to specific post-hoc paired comparisons between conditions, the authors begin with the change score but then move on to conduct the said paired comparisons without ever anchoring these analyses in an appropriate larger ANOVA. I strongly recommend the use of an ANOVA but if not, the authors would have to correct for multiple comparisons at the minimum.

      We thank the reviewer for their comment regarding the use of change scores. These were originally derived from the difference between the slower and faster feedback conditions relative to the congruent condition. In line with the reviewer’s recommendation, we have now removed these difference-based change scores from the main analysis. The results remain identical. Please note that we have retained the normalization procedure, relative to each participant’s initial baseline in the no feedback trials, as it is widely used in the interoceptive and pain literature (e.g., Bartolo et al., 2013; Cecchini et al., 2020; Riello et al., 2019). This approach helps to control for interindividual variability and baseline differences by expressing each participant’s response relative to their no-feedback baseline. As before, normalization was applied across all dependent variables (heart rate, pain intensity, and pain unpleasantness).

      To address the reviewer’s concern about statistical validity, we now first report a 1-factor repeated-measures ANOVA (Greenhouse-Geisser corrected) for each dependent variable, with feedback condition (slower, congruent, faster) as the within-subject factor.

      These show in each case a significant main effect, which we then follow with planned paired-sample t-tests comparing:

      Faster vs. slower feedback (our main hypothesis, as these manipulations are expected to produce largest, most powerful, test of our hypothesis, see response to Reviewer 3),

      Faster vs. congruent and slower vs. congruent (to test for potential asymmetries, as suggested  by previous false heart rate feedback studies).

      The rationale of these analyses is further discussed in the Data Analysis of Experiment 1 (lines 405-437).

      Although we report the omnibus one-factor RM-ANOVAs to satisfy conventional expectations, we note that such tests are not statistically necessary, nor even optimal, when the research question is fully captured by a priori, theory-driven contrasts. Extensive methodological work shows that, in this situation, going straight to planned contrasts maximises power without inflating Type I error and avoids the logical circularity of first testing an effect one does not predict (e.g., Rosenthal & Rosnow, 1985). In other words, an omnibus F is warranted only when one wishes to protect against unspecified patterns of differences. Here our hypotheses were precise (Faster ≠ Slower; potential asymmetry relative to Congruent), so the planned paired comparisons would have sufficed statistically. We therefore include the RM-ANOVAs solely for readers who expect to see them, but our inferential conclusions rest on the theoretically motivated contrasts.

      Rosenthal, R., & Rosnow, R. L. (1985). Contrast analysis. New York: Cambridge.

      (6) Correlations: were there correlations between subjects' own heartbeats (which are considered a predictive cue) and pain perceptions? This is critical to show that the two are in fact related.

      We thank the reviewer for this thoughtful suggestion. While we agree that testing for a correlation between anticipatory heart rate responses and subjective pain ratings is theoretically relevant. However, we have not conducted this analysis in the current manuscript, as our study was not designed or powered to reliably detect such individual differences. As noted by Hedge, Powell, and Sumner (2018), robust within-subject experimental designs tend to minimize between-subject variability in order to detect clear experimental effects. This reduction in variance at the between-subject level limits the reliability of correlational analyses involving trait-like or individual response patterns. This issue, known as the reliability paradox, highlights that measures showing robust within-subject effects may not show stable individual differences, and therefore correlations with other individual-level variables (like subjective ratings used here) require much larger samples to produce interpretable results than available here (and commonly used in the literature), typically more than 200 participants. For these reasons, we believe that running such an analysis in our current dataset would not yield informative results and could be misleading.

      We now explicitly acknowledge this point in the revised version of the manuscript (Limitations and future directions, lines 832-851) and suggest that future studies specifically designed to examine individual variability in anticipatory physiological responses and pain perception would be better suited to address this question.

      Hedge, C., Powell, G., & Sumner, P. (2018). The reliability paradox: Why robust cognitive tasks do not produce reliable individual differences. Behavior Research Methods, 50(3), 1166-1186. https://doi.org/10.3758/s13428-017-0935-1

      (7) The direct comparison between studies is great! and finally the use of ANOVA - but why without the appropriate post-hoc tests to support the bold claims in lines 542-544? This is needed. Same for 556-558.

      We apologize if our writing was not clear here, but the result of the ANOVAs fully warrants the claims in 542-544 (now lines 616-618) and 556-558 (now lines 601-603).

      In a 2x2 design, the interaction term is mathematically identical to comparing the difference induced by Factor 1 at one level of Factor 2 with the same difference induced at the other level of Factor 2. In our 2x2 analysis with the factors Experiment (Cardiac feedback, Exteroceptive feedback - between participants) and Feedback Frequency (faster, slower - within participants), the interaction therefore directly tests whether the effect of Feedback frequency differs statistically (i.e., is larger or smaller) in the participants in the interoceptive and exteroceptive experiments. Thus, the conclusion that “faster feedback affected the perceptual bias more strongly in the Experiment 1 than in Experiment 2” captures the outcome of the significant interaction exactly. Indeed, this test would be statistically equivalent (and would produce identical p values) to a simple between-group t-test between each participant’s difference between the faster and slower feedback in the interoceptive group and the analogous differences between the faster and slower feedback in the exteroceptive group, as illustrated in standard examples of factorial analysis (see, e.g., Maxwell, Delaney and Kelley, 2018).

      Please note that, for the above reason, mathematically the conclusion of larger effects in one experiment than the other is licensed by the significant interaction even without follow-up t-tests. However, if the reader would like to see these tests, they are simply the main analysis results reported in each of the two experiment sections, where significant (t-test) differences between faster and slower feedback were induced with interoceptive cues (Experiment 1) but not exteroceptive cues (Experiment 2). Reporting them in the between-experiment comparison section again would therefore be redundant.

      To avoid this lack of clarity, we have now re-written the results section of each experiment. First, as noted above, we now precede our main hypothesis test - the crucial t-test comparing heartrate and pain ratings after faster vs slower feedback - with an ANOVA including all three levels (faster, congruent, slower feedback). Moreover, we removed the separate between-experiment comparison section. Instead, in the Result section of the exteroceptive Experiment 2, we now directly compare the (absent or reversed) effects of faster vs slower feedback directly, with a between-groups t-test, with the present effects in the interoceptive Experiment 1. This shows conclusively, and hopefully more clearly, that the effects in both experiments differ. We hope that this makes the logic of our analyses clearer.

      Maxwell, S. E., Delaney, H. D., & Kelley, K. (2017). Designing experiments and analyzing data: A model comparison perspective. Routledge.

      (8) The discussion is missing a limitation paragraph.

      Thank you for the suggestion. We have now added a dedicated limitations paragraph in the Discussion section (lines 832-890).

      Additional recommendations:

      Minor (chronological order):

      (1) Sample size calculations for both experiments: what was the effect size based on? A citation or further information is needed. Also, clarify why the effect size differed between the two experiments.

      Please see above

      (2) "Participants were asked to either not drink coffee or smoke cigarettes" - either is implying that one of the two was asked. I suspect it is redundant as both were not permitted.

      The intention was to restrict both behaviors, so we have corrected the sentence to clarify that participants were asked not to drink coffee or smoke cigarettes before the session.

      (3) Normalization of ECG - what exactly was normalized, namely what measure of the ECG?

      The normalized measure was the heart rate, expressed in beats per minute (bpm). We now clarify this in the Data Analysis section of Experiment 1 (Measures of the heart rate recorded with the ECG (beats per minute) in the feedback phase were normalized)

      (4) Line 360: "Mean Δ pain unpleasantness ratings were analysed analogously" - this is unclear, if already described in methods then should be removed here, if not - should be further explained here.

      Thank you for your observation. We are no longer using change scores.

      (5) Lines 418-420: "Consequently, perceptual and cardiac modulations associated with the feedback manipulation should be reduced over the exposure to the faster exteroceptive sound." - why reduced and not unchanged? I didn't follow the logic.

      We chose the term “reduced” rather than “unchanged” to remain cautious in our interpretation. Statistically, the absence of a significant effect in one experiment does not necessarily mean that no effect is present; it simply means we did not detect one. For this reason, we avoided using language that would suggest complete absence of modulation. It also more closely matches the results of the between experiment comparisons that we report in the Result section of Experiment 2, which can in principle only show that the effect in Experiment 2 was smaller than that of Experiment 1, not that it was absent. Even the TOST analysis that we utilize to show the absence of an effect can only show that any effect that is present is smaller than we could reasonably expect to detect with our experimental design, not its complete absence.

      Also, on a theoretical level, pain is a complex, multidimensional experience influenced not only by sensory input but also by cognitive, emotional, social and expectancy factors. For this reason, we considered it important to remain open to the possibility that other mechanisms beyond the misleading cardiac prior induced by the feedback might have contributed to the observed effects. If such other influences had contributed to the induced differences between faster and slower feedback in Experiment 1, some remainder of this difference could have been observed in Experiment 2 as well.

      Thus, for both statistical and theoretical reasons, we were careful to predict a reduction of the crucial difference, not its complete elimination. However, to warrant the possibility that effects could be completely eliminated we now write that “perceptual and cardiac modulations associated with the feedback manipulation should be reduced or eliminated with exteroceptive feedback”

      (6) Study 2 generation of feedback - was this again tailored per participants (25% above and beyond their own HR at baseline + gradually increasing or decreasing), or identical for everyone?

      Yes, in Study 2, the generation of feedback was tailored to each participant, mirroring the procedure or Experiment 1. Specifically, the feedback was set to be 25% above or below their baseline heart rate, with the feedback gradually increasing or decreasing. This individualized approach ensured that each participant experienced feedback relative to their own baseline heart rate. We now clarify this in the Methods section (lines 306-318).

      (7) I did not follow why we need the TOST and how to interpret its results.

      We thank the reviewer for raising this important point. In classical null hypothesis significance testing (NHST), a non-significant p-value (e.g., p > .05) only indicates that we failed to find a statistically significant difference, not that there is no difference. It therefore does not allow us to conclude that two conditions are equivalent – only that we cannot confidently say they are different. In our case, to support the claim that exteroceptive feedback does not induce perceptual or physiological changes (unlike interoceptive feedback), we needed a method to test for the absence of a meaningful effect, not just the absence of a statistically detectable one.

      The TOST (Two One-Sided Tests) procedure reverses the logic of NHST by testing whether the observed effect falls within a predefined equivalence interval, called the smallest effect size of interest (SESOI) that is in principle measurable with our design parameters (e.g., type of test, number of participants). This approach is necessary when the goal is not to detect a difference, but rather to demonstrate that an observed effect is so small that it can be considered negligible – or at the least smaller than we could in principle expect to observe in the given experiment. We used the TOST procedure in Experiment 2 to test for statistical equivalence between the effects of faster and slower exteroceptive feedback on pain ratings and heart rate.

      We hope that the clearer explanation now provided in data analysis of Experiment 2 section (lines 5589-563) fully addresses the reviewer’s concern.

      (8) Lines 492-3: authors say TOST significant, while p value = 0.065

      We thank the reviewer for spotting this inconsistency. The discrepancy was due to a typographical error in the initial manuscript. During the revision of the paper, we rechecked and fully recomputed all TOST analyses, and the results have now been corrected throughout the manuscript to accurately reflect the statistical outcomes. In particular, for the comparison of heart rate between faster and slower exteroceptive feedback in Experiment 2, the corrected TOST analysis now shows a significant equivalence, with the observed effect size being d = -0.19 (90% CI [-0.36, -0.03]) and both one-sided tests yielding p = .025 and p < .001. These updated results are reported in the revised Results section.

      Reviewer #2 (Recommendations For The Authors):

      I would suggest the authors revise their definition of pain in the introduction, since it is not always a protective experience. The new IASP definition specifically takes this into consideration.

      We thank the reviewer for this suggestion. We have updated the definition of pain in the Introduction (lines 2-4) to align with the most recent IASP definition (2020), which characterizes pain as “an unpleasant sensory and emotional experience associated with, or resembling that associated with, actual or potential tissue damage” (lines 51-53).

      The work on exteroceptive cues does not necessarily neglect the role of interoceptive sources of information, although it is true that it has been comparatively less studied. I suggest rephrasing this sentence to reflect this.

      We thank the reviewer for pointing out this important nuance. We agree that studies employing exteroceptive cues to modulate pain perception do not necessarily neglect the role of interoceptive sources, even though these are not always the primary focus of investigation. Our intention was not to imply a strict dichotomy, but rather to highlight that interoceptive mechanisms have been comparatively under-investigated. We have revised the sentence in the Introduction accordingly to better reflect this perspective (Introduction, lines 110-112, “Although interoceptive processes may have contributed to the observed effects, these studies did not specifically target interoceptive sources of information within the inferential process.”).

      The last paragraph of the introduction (lines 158-164) contains generalizations beyond what can be supported by the data and the results, about the generation of predictive processes and the origins of these predictions. The statements regarding the understanding of pain-related pathologies in terms of chronic aberrant predictions in the context of this study are also unwarranted.

      We have deleted this paragraph now.

      I could not find the study registration (at least in clinicaltrials.gov). This is curious considering that the hypothesis and the experimental design seem in principle well thought out, and a study pre-registration improves the credibility of the research (Nosek et al., 2018). I also find the choice for the smallest effect of interest (SESOI) odd. Besides the unnecessary variable transformations (more on that later), there is no justification for why that particular SESOI was chosen, or why it changes between experiments (Dienes, 2021; King, 2011), which makes the choice look arbitrary. The SESOI is a fundamental component of a priori power analysis (Lakens, 2022), and without rationale and preregistration, it is impossible to tell whether this is a case of SPARKing or not (Sasaki & Yamada, 2023).

      We acknowledge that the study was not preregistered. Although our hypotheses and design were developed a priori and informed by established theoretical frameworks, the lack of formal preregistration is a limitation.

      The SESOI values for Experiments 1 and 2 were derived from sensitivity analyses based on the fixed design parameters (type of test, number of participants, alpha level) of our study, not from any post-hoc interpretation based on observed results - they can therefore not be a case of SPARKing. Following current recommendations (Anderson, Kelley & Maxwell, 2017; Albers & Lakens, 2017; Lakens, 2022), we avoided basing power estimates on published effect sizes, as no such values exist for in novel paradigms, and are typically inflated due to publication and other biases. Instead, sensitivity analyses (using G*Power, v 3.1) allows us to calculate, prospectively, the smallest effect each design could detect with 90 % power, given the actual sample size, test type, and α level. Because more participants were excluded in Experiment 2, this design can detect slightly larger effects (d = 0.62) than Experiment 1 (d = 0.57). Please note that both studies therefore remain well-powered to capture effects of the magnitude typically reported in previous research using feedback manipulations to explore interoceptive illusions (e.g., Iodice et al., 2019, d ≈ 0.7).

      We have added this clarification to the Participants section of Experiment 1 (Lines 208-217).

      Anderson, S. F., Kelley, K., & Maxwell, S. E. (2017). Sample-Size Planning for More Accurate Statistical Power: A Method Adjusting Sample Effect Sizes for Publication Bias and Uncertainty. Psychological Science, 28(11), 1547-1562.

      Lakens, D. (2022). Sample size justification. Collabra: psychology, 8(1), 33267.

      Albers, C., & Lakens, D. (2018). When power analyses based on pilot data are biased: Inaccurate effect size estimators and follow-up bias. Journal of experimental social psychology, 74, 187-195.

      In the Apparatus subsection, it is stated that the intensity of the electrical stimuli was fixed at 2 ms. I believe the authors refer to the duration of the stimulus, not its intensity.

      You are right, thank you for pointing that out. The text should refer to the duration of the electrical stimulus, not its intensity. We have corrected this wording in the revised manuscript to avoid confusion.

      It would be interesting to report (in graphical form) the stimulation intensities corresponding to the calibration procedure for the five different pain levels identified for all subjects.

      That's a good suggestion. We have included a supplementary figure showing the stimulation intensities corresponding to the five individually calibrated pain levels across all participants (Supplementary Figure 11.)

      It is questionable that researchers state that "pain and unpleasantness should be rated independently" but then the first level of the Likert scale for unpleasantness is "1=no pain". This is particularly relevant since simulation (and specifically electrical stimulation) can be unpleasant but non-painful at the same time. Since the experiments were already performed, the researchers should at least explain this choice.

      Thank you for raising this point. You are right in that the label of “no pain” in the pain unpleasantness scale was not ideal, and we now acknowledge this in the text (lines 886-890). Please note that this was always the second rating that participants gave (after pain intensity), and the strongest results come from this first rating.

      Discussion.

      I did not find in the manuscript the rationale for varying the frequency of the heart rate by 25% (instead of any other arbitrary quantity).

      We thank the Reviewer for this observation, which prompted us to clarify the rationale behind our choice of a ±25% manipulation of heart rate feedback. False feedback paradigms have historically relied on a variety of approaches to modulate perceived cardiac signals. Some studies have adopted non-individualised values, using fixed frequencies (e.g., 60 or 110 bpm) to evoke states of calm or arousal, independently of participants’ actual physiology (Valins, 1966; Shahidi & Baluch, 1991; Crucian et al., 2000; Tajadura-Jiménez et al., 2008). Others have used the participant’s real-time heart rate as a basis, introducing accelerations or decelerations without applying a specific percentage transformation (e.g., Iodice et al., 2019). More recently, a growing body of work has employed percentage-based alterations of the instantaneous heart rate, offering a controlled and participant-specific manipulation. These include studies using −20% (Azevedo et al., 2017), ±30% (Dey et al., 2018), and even ±50% (Gray et al., 2007).

      These different methodologies - non-individualised, absolute, or proportionally scaled - have all been shown to effectively modulate subjective and physiological responses. They suggest that the impact of false feedback does not depend on a single fixed method, but rather on the plausibility and salience of the manipulation within the context of the task. We chose to apply a ±25% variation because it falls well within the most commonly used range and strikes a balance between producing a detectable effect and maintaining the illusion of physiological realism. The magnitude is conceptually justified as being large enough to shape interoceptive and emotional experience (as shown by Azevedo and Dey), yet small enough to avoid implausible or disruptive alterations, such as those approaching ±50%. We have now clarified this rationale in the revised Procedure paragraph of Experiment 1 (lines 306-318).

      T. Azevedo, R., Bennett, N., Bilicki, A., Hooper, J., Markopoulou, F., & Tsakiris, M. (2017). The calming effect of a new wearable device during the anticipation of public speech. Scientific reports, 7(1), 2285.

      Crucian, G. P., Hughes, J. D., Barrett, A. M., Williamson, D. J. G., Bauer, R. M., Bowers, D., & Heilman, K. M. (2000). Emotional and physiological responses to false feedback. Cortex, 36(5), 623-647.

      Dey, A., Chen, H., Billinghurst, M., & Lindeman, R. W. (2018, October). Effects of manipulating physiological feedback in immersive virtual environments. In Proceedings of the 2018 Annual Symposium on Computer-Human Interaction in Play (pp. 101-111).

      Gray, M. A., Harrison, N. A., Wiens, S., & Critchley, H. D. (2007). Modulation of emotional appraisal by false physiological feedback during fMRI. PLoS one, 2(6), e546.

      Shahidi, S., & Baluch, B. (1991). False heart-rate feedback, social anxiety and self-attribution of embarrassment. Psychological reports, 69(3), 1024-1026.

      Tajadura-Jiménez, A., Väljamäe, A., & Västfjäll, D. (2008). Self-representation in mediated environments: the experience of emotions modulated by auditory-vibrotactile heartbeat. CyberPsychology & Behavior, 11(1), 33-38.

      Valins, S. (1966). Cognitive effects of false heart-rate feedback. Journal of personality and social psychology, 4(4), 400.

      The researchers state that pain ratings collected in the feedback phase were normalized to the no-feedback phase to control for inter-individual variability in pain perception, as established by previous research. They cite three studies involving smell and taste, of which the last two contain the same normalization presented in this study. However, unlike these studies, the outcomes here require no normalization whatsoever, because there should be no (or very little) inter-individual variability in pain intensity ratings. Indeed, pain intensity ratings in this study are anchored to 30, 50, and 70 / 100 as a condition of the experimental design. The researchers go to extreme lengths to ensure this is the case, by adjusting stimulation intensities until at least 75% of stimulation intensities are correctly matched to their pain ratings counterpart in the pre-experiment procedure. In other words, inter-individual variability in this study is in stimulation intensities, and not pain intensity ratings. Even if it could be argued that pain unpleasantness and heart rate still need to account for inter-individual variability, the best way to do this is by using the baseline (no-feedback) measures as covariates in a mixed linear model. Another advantage of this approach is that all the effects can be described in terms of the original scales and are readily understandable, and post hoc tests between levels can be corrected for multiple comparisons. On the contrary, the familywise error rate for the comparisons between conditions in the current analysis is larger than 5% (since there is a "main" paired t-test and additional "simple" tests).

      We disagree that there is little to no variability in the no feedback phase. Participants were tested in their ability to distinguish intensities in an initial pre-experiment calibration phase. In the no feedback phase, participants rated the pain stimuli in the full experimental context.

      In the pre-experiment calibration phase, participants were tested only once in their ability to match five electrical‐stimulation levels to the 0-100 NPS scale, before any feedback manipulation started. During this pre-experiment calibration we required that each level was classified correctly on ≥ 75 % of the four repetitions; “correct” meant falling within ± 5 NPS units of the target anchor (e.g., a response of 25–35 was accepted for the 30/100 anchor). This procedure served one purpose only: to make sure that every participant entered the main experiment with three unambiguously distinguishable stimulation levels (30 / 50 / 70). We integrated this point in the revised manuscript lines 263-270.

      Once the real task began, the context changed: shocks are unpredictable, attention is drawn to the heartbeat, and participants must judge both intensity and unpleasantness. In this full experimental setting the no-feedback block indeed shows considerable variability, even for the pain intensity ratings. Participants mean rating on the NPS scale was 46.4, with a standard deviation of 11.9 - thus participants vary quite strongly in their mean ratings (range 14.5 to 70). Moreover, while all participants show a positive correlation between actual intensities and their ratings (i.e., they rate the higher intensities as more intense than the lower ones), they vary in how much of the scale they use, with differences between reported highest and lowest intensities ranging between 8 and 91, for the participants showing the smallest and largest differences, respectively.

      Thus, while we simplified the analysis to remove the difference scoring relative to the congruent trials and now use these congruent trials as an additional condition in the analysis, we retained the normalisation procedure to account for the in-fact-existing between-participant variability, and ensure consistency with prior research (Bartolo et al., 2013; Cecchini et al., 2020; Riello et al., 2019) and our a priori analysis plan.

      However, to ensure we fully address your point here (and the other reviewers’ points about potential additional factors affecting the effects, like trial number and stimulus intensity), we also report an additional linear mixed-effects model analysis without normalization. It includes every feedback level as condition (No-Feedback, Congruent, Slower, Faster), plus additional predictors for actual stimulus intensity and trial rank within the experiment (as suggested by the other reviewers). This confirms that all relevant results remain intact once baseline and congruent trials are explicitly included in the model.

      In brief, cross‐experiment analyses demonstrated that the Faster vs Slower contrast was markedly larger when the feedback was interoceptive than when it was exteroceptive. This held for heart-rate deceleration (b = 0.94 bpm, p = .005), for increases in unpleasantness (b = -0.16 Likert units, p = .015), and in pain-intensity ratings (b = -3.27 NPS points, p = .037).

      These findings were then further confirmed by within-experiment analyses. Within the interoceptive experiment, the mixed-model on raw scores replicated every original effect: heart rate was lower after Faster than Slower feedback (estimate = –0.69 bpm, p = .005); unpleasantness was higher after Faster than Slower feedback (estimate = 0.19, p < .001); pain-intensity rose after Faster versus Slower (estimate=-4.285, p < .001). In the exteroceptive experiment, however, none of these Faster–Slower contrasts reached significance for heart rate (all ps > .33), unpleasantness (all ps > .43) or intensity (all ps > .10).  Because these effects remain significant even with No-Feedback and Congruent trials explicitly included in the model and vanish under exteroceptive control, the supplementary, non-normalised analyses confirm that the faster vs. slower interoceptive feedback uniquely lowers anticipatory heart rate while amplifying both intensity and unpleasantness of pain, independent of data transformation or reference conditions.  Please see Supplementary analyses for further details.

      Bartolo, M., Serrao, M., Gamgebeli, Z., Alpaidze, M., Perrotta, A., Padua, L., Pierelli, F., Nappi, G., & Sandrini, G. (2013). Modulation of the human nociceptive flexion reflex by pleasant and unpleasant odors. PAIN®, 154(10), 2054-2059.

      Cecchini, M. P., Riello, M., Sandri, A., Zanini, A., Fiorio, M., & Tinazzi, M. (2020). Smell and taste dissociations in the modulation of tonic pain perception induced by a capsaicin cream application. European Journal of Pain, 24(10), 1946-1955.

      Riello, M., Cecchini, M. P., Zanini, A., Di Chiappari, M., Tinazzi, M., & Fiorio, M. (2019). Perception of phasic pain is modulated by smell and taste. European Journal of Pain, 23(10), 1790-1800.

      I could initially not find a rationale for bringing upfront the comparison between faster vs. slower HR acoustic feedback when in principle the intuitive comparisons would be faster vs. congruent and slower vs. congruent feedback. This is even more relevant considering that in the proposed main comparison, the congruent feedback does not play a role: since Δ outcomes are calculated as (faster - congruent) and (slower - congruent), a paired t-test between Δ faster and Δ slower outcomes equals (faster - congruent) - (slower - congruent) = (faster - slower). I later realized that the statistical comparison (paired t-test) of pain intensity ratings of faster vs. slower acoustic feedback is significant in experiment 1 but not in experiment 2, which in principle would support the argument that interoceptive, but not exteroceptive, feedback modulates pain perception. However, the "simple" t-tests show that faster feedback modulates pain perception in both experiments, although the effect is larger in experiment 1 (interoceptive feedback) compared to experiment 2 (exteroceptive feedback).

      The comparison between faster and slower feedback is indeed crucial, and we regret not having made this clearer in the first version of the manuscript. As noted in our response to your point in the public review, this comparison is both statistically most powerful, and theoretically the most appropriate, as it controls for any influence of salience or surprise when heart rates deviate (in either direction) from what is expected. It therefore provides a clean measure of how much accelerated heartrate affects pain perception and physiological response, relative to an equal change in the opposite direction. However, as noted above, in the new version of the manuscript we have now removed the analysis via difference scores, and directly compared all three relevant conditions (faster, congruent, slower), first via an ANOVA and then with follow-up planned t-tests.

      Please refer to our previous response for further details (i.e., Furthermore, the researchers propose the comparison of faster vs. slower delta HR acoustic feedback throughout the manuscript when the natural comparison is the incongruent vs. the congruent feedback [..]).

      The design of experiment two involves the selection of knocking wood sounds to act as exteroceptive acoustic feedback. Since the purpose is to test whether sound affects pain intensity ratings, unpleasantness, and heart rate, it would have made sense to choose sounds that would be more likely to elicit such changes, e.g. Taffou et al. (2021), Chen & Wang (2022), Zhou et al. (2022), Tajadura-Jiménez et al. (2010). Whereas I acknowledge that there is a difference in effect sizes between experiment 1 and experiment 2 for the faster acoustic feedback, I am not fully convinced that this difference is due to the nature of the feedback (interoceptive vs. exteroceptive), since a similar difference could arguably be obtained by exteroceptive sound with looming or rough qualities. Since the experiment was already carried out and this hypothesis cannot be tested, I suggest that the researchers moderate the inferences made in the Discussion regarding these results.

      Please refer to our previous response for a previous detailed answer to this point in the Public Review (i.e., This could be influenced by the fact that the faster HR exteroceptive cue in experiment 2 also shows a significant modulatory effect [..]). As we describe there, we see little grounds to suspect such a non-specific influence of acoustic parameters, as it is specifically the sensitivity to the change in heart rate (faster vs slower) that is affected by our between-experiment manipulation, not the overall response to the different exteroceptive or interoceptive sounds. Moreover, the specific change induced by the faster interoceptive feedback - a heartrate deceleration - is not consistent with a change in arousal or alertness (which would have predicted an increase in heartrate with increasing arousal). See also Discussion-Accounting for general unspecific contributions.

      Additionally, the fact that no significant effects were found for unpleasantness ratings or heart rate (absence of evidence) should not be taken as proof that faster exteroceptive feedback does not induce an effect on these outcomes (evidence of absence). In this case, it could be that there is actually no effect on these variables, or that the experiment was not sufficiently powered to detect those effects. This would depend on the SESOIs for these variables, which as stated before, was not properly justified.

      We very much agree that the absence of significant effects should not be interpreted as definitive evidence of absence. Indeed, we were careful not to overinterpret the null findings for heart rate and unpleasantness ratings, and we conducted additional analyses to clarify their interpretation. First, the TOST analysis shows that any effects in Experiment 2 are (significantly) smaller than the smallest effect size that can possibly be detected in our experiment, given the experimental parameters (number of participants, type of test, alpha level). Second, and more importantly, we run between-experiments comparisons (see Results Experiment 2, and Supplementary materials, Cross-experiment analysis between-subjects model) of the crucial difference in the changes induced by faster and slower feedback. This showed that the differences were larger with interoceptive (Experiment 1) than exteroceptive cues (Experiment 2). Thus, even if a smaller than is in principle detectable effect is induced by the exteroceptive cues in Experiment 2, it is smaller than with interoceptive cues in Experiment 1.

      To ensure we fully address this point, we have now simplified our main analysis (main manuscript), replicated it with a different analysis (Supplementary material), we motivate more clearly (Methods Experiment 1), why the comparison between faster and slower feedback is crucial, and we make clearer that the difference between these conditions is larger in Experiment 1 than Experiment 2 (Results Experiment 2). Moreover, we went through the manuscript and ensured that our wording does not over-interpret the absence of effects in Experiment 2, as an absence of a difference.

      The section "Additional comparison analysis between experiments" encompasses in a way all possible comparisons between levels of the different factors in both experiments. My original suggestion regarding the use of a mixed linear model with covariates is still valid for this case. This analysis also brings into question another aspect of the experimental design: what is the rationale for dividing the study into two experiments, considering that variability and confounding factors would have been much better controlled in a single experimental session that includes all conditions?

      We thank the reviewer for their comment. We would like to note, first, that the between-experiment analyses did not encompass all possible comparisons between levels, as it just included faster and slower feedback for the within-experiment comparison Instead, they focus on the specific interaction between faster and slower feedback on the one hand, and interoceptive vs exteroceptive cues on the other. This interaction essentially compares, for each dependent measure (HR, pain unpleasantness, pain intensity), the difference between faster and slower feedback in Experiment 1 with that the same difference in Experiment 2 (and would produce identical p values to a between-experiment t-test). The significant interactions therefore indicate larger effects of interoceptive cues than exteroceptive ones for each of the measures. To make this clearer, we have now exchanged the analysis with between-experiment t-tests of the difference between faster and slower feedback for each measure (Results Experiment 2), producing identical results. Moreover, as suggested, we also now report linear mixed model analyses (see Supplementary Materials), which provide a comprehensive comparison across experiments.

      Regarding the experimental design, we appreciate the reviewer’s suggestion regarding a within-subject crossover design. While such an approach indeed offers greater statistical power by reducing interindividual variability (Charness, Gneezy, & Kuhn, 2012), we intentionally chose a between-subjects design due to theoretical and methodological considerations specific to deceptive feedback paradigms. First, carryover effects are a major concern in deception studies. Participants exposed to one type of feedback could develop suspicion or adaptive strategies that would alter their responses in subsequent conditions (Martin & Sayette, 1993). Expectancy effects could thus contaminate results in a crossover design, particularly when feedback manipulation becomes apparent. In line with this idea, past studies on false cardiac feedback (e.g., Valins, 1966; Pennebaker & Lightner, 1980) often employed between-subjects or blocked designs to maintain the ecological validity of the illusion.

      Charness, G., Gneezy, U., & Kuhn, M. A. (2012). Experimental methods: Between-subject and within-subject design. Journal of economic behavior & organization, 81(1), 1-8.

      Martin, C. S., & Sayette, M. A. (1993). Experimental design in alcohol administration research: limitations and alternatives in the manipulation of dosage-set. Journal of studies on alcohol, 54(6), 750-761.

      Pennebaker, J. W., & Lightner, J. M. (1980). Competition of internal and external information in an exercise setting. Journal of personality and social psychology, 39(1), 165.

      Valins, S. (1966). Cognitive effects of false heart-rate feedback. Journal of personality and social psychology, 4(4), 400.

      References

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      Dienes Z. Obtaining Evidence for No Effect. Collabra: Psychology 2021 Jan 4; 7 (1): 28202. doi: 10.1525/collabra.28202

      King MT. A point of minimal important difference (MID): a critique of terminology and methods. Expert Rev Pharmacoecon Outcomes Res. 2011 Apr;11(2):171-84. doi: 10.1586/erp.11.9.

      Lakens D. Sample Size Justification. Collabra: Psychology 2022 Jan 5; 8 (1): 33267. doi: 10.1525/collabra.33267

      Nosek BA, Ebersole CR, DeHaven AC, Mellor DT. The preregistration revolution. Proc Natl Acad Sci U S A. 2018 Mar 13;115(11):2600-2606. doi: 10.1073/pnas.1708274114.

      Sasaki K, Yamada Y. SPARKing: Sample-size planning after the results are known. Front Hum Neurosci. 2023 Feb 22;17:912338. doi: 10.3389/fnhum.2023.912338.

      Taffou M, Suied C, Viaud-Delmon I. Auditory roughness elicits defense reactions. Sci Rep. 2021 Jan 13;11(1):956. doi: 10.1038/s41598-020-79767-0.

      Tajadura-Jiménez A, Väljamäe A, Asutay E, Västfjäll D. Embodied auditory perception: The emotional impact of approaching and receding sound sources. Emotion. 2010, 10(2), 216-229.https://doi.org/10.1037/a0018422

      Zhou W, Ye C, Wang H, Mao Y, Zhang W, Liu A, Yang CL, Li T, Hayashi L, Zhao W, Chen L, Liu Y, Tao W, Zhang Z. Sound induces analgesia through corticothalamic circuits. Science. 2022 Jul 8;377(6602):198-204. doi: 10.1126/science.abn4663.

      Reviewer #3 (Recommendations For The Authors):

      The manuscript would benefit from some spelling- and grammar checking.

      Done

      Discussion:

      The discussion section is rather lengthy and would benefit from some re-structuring, editing, and sub-section headers.

      In response, we have restructured and edited the Discussion section to improve clarity and flow.

      I personally had a difficult time understanding how the data relates to the rubber hand illusion (l.623-630). I would recommend revising or deleting this section.

      We thank the reviewer for this valuable feedback. We have revised the paragraph and made the parallel clearer (lines 731-739).

      Other areas are a bit short and might benefit from some elaboration, such as clinical implications. Since they were mentioned in the abstract, I had expected a bit more thorough discussion here (l. 718).

      Thank you for this suggestion. We have expanded the discussion to more thoroughly address the clinical implications of our interoceptive pain illusion (See Limitations and Future Directions paragraph).

      Further, clarification is needed for the following:

      I would like some more details on participant instructions; in particular, the potential difference in instruction between Exp. 1 and 2, if any. In Exp. 1, it says: (l. 280) "Crucially, they were also informed that over the 60 seconds preceding the administration of the shock, they were exposed to acoustic feedback, which was equivalent to their ongoing heart rate". Was there a similar instruction for Exp. 2? If yes, it would suggest a more specific effect of cardiac auditory feedback; if no, the ramifications of this difference in instructions should be more thoroughly discussed.

      Thank you for this suggestion. We have clarified this point in the Procedure of Experiment 2 (548-550).

    1. Reviewer #2 (Public review):

      Summary:

      The manuscript by Sy SKH. et al. on pallium encoded chemosensory impact of eye-body coordination describes how the valence of chemosensory stimuli can affect the coordination of eye saccades with tail flips. They show that aversive valence stimuli can increase both the strength and frequency of tail flips through a pallium-mediated circuit.

      Overall, the manuscript is well-written and easy to follow, although the figures are quite dense, the methodology is mostly sound, and the improvement to the fish on chips system is very interesting. The methods description is thorough and welcome, making the experiments clear. The limited number of animals, and the spread between 5 and 6dpf is a concern as most of the statistics seem to have been done on the individual events, and not the number of biological samples.

      The initial behavioural experiments are very promising. However, the conclusions surrounding the role of the pallium are a lot more speculative and not supported by the results.

      Comments:

      (1) The fish on chips 2.0 methods show a lot of promise for future studies of chemosensory stimuli, combined with whole-brain imaging. This will provide new avenues of research for zebrafish neuroscientists.

      (2) Chemosensory cues would have a very different timing than visual cues; timing is very important for multisensory integration. How do the authors suggest those are integrated? How would they differentiate between an integration of various cues or a different arousal state, as they describe in the introduction?

      (3) Studies have looked at chemosensation in Drosophila, including multisensory integration, which should be discussed by the authors (see the work of Mark Frye, amongst others).

      (4) In the brain imaging methods, there is a mention of robustly behaving larvae. Does that mean that an exclusion criterion was used to select only 5 larvae? If so, this should be stated clearly. The authors also do not mention how they avoid the switch to a passive state that one of the coauthors has observed in closed closed-loop setup. The authors should comment on this point.

      (5) Were the statistics in Figure 2 done with an n of 5, or do they assume that each tail flip and saccade is an independent event? I would imagine the latter would have inflated p-values and should be avoided.

      (7) Page 7: Why do the authors think that the cumulative effect of these minor differences could lead to very different behavioural goals? Especially when comparing to actual startle responses, which are extremely strong and stereotypical. How do their observations compare to the thermosensory navigation of larval zebrafish observed by Martin Haesemeyer, for example, or the work of the RoLi lab?

      (8) Page 8: Figure 5, I am confused by the y-axis of g, in e and f, the values are capped at 2, whereas in g they go up to 6, with apparently a number of cells whose preference is out of the y-axis limit (especially in Q2). Having the number of cells in each quadrant would also help to assess if indeed there is some preference in the pallium towards Q1.

      (9) Figure 6: How is the onset of neuronal activity determined compared to the motor stimulus? Looking at Supplementary Figure 8, it is quite unclear how the pallium is different from the OB or subpallium. The label of onset delay is also confusing in this figure.

      (10) Page 9: I do not think that the small differences observed in the pallium are as clear-cut as the authors make them out to be, or that they provide such strong evidence of their importance. As there are no interventions showing any causality in the presence of these pallium responses and the sensorimotor responses, these could represent different arousal states rather than any integration of sensory information.

    2. Reviewer #3 (Public review):

      The manuscript investigates the coupling of saccadic eye movements (S) with directed tail flips (T). The remarkable discovery is that tail flips that are preceded by a conjugate sacced (S-T) can be credibly classified as specific "volitional" turns that are distinguished from the standard tail movements that seem to be more of a spontaneous and "impulsive" nature.

      They show that 'turning intent', as indicated by a small increase in S, is elevated by aversive odors, while 'gliding intent', as indicated by a decrease in S and an increase in undulation cycles, is elevated by appetitive odors.

      This is a very important finding, which is backed up by a thorough behavioral analysis, and the identification of neural populations in the pallium and sub-pallium that clearly distinguish between these kinds of turns is very promising. Here they identify neuronal populations that are preferentially active during - and predictive of - coupled (S-T) versus isolated (T) tail flips.

      Especially the fact that S-T turns (but not T turns) can be predicted already by pre-event, ramping, pallial activity is intriguing.

      The authors then go on and demonstrate that the frequency of (S-T) turns is modulated in fish exposed to appetitive or aversive odors.<br /> Specifically, they quantify the aversiveness and appetitive-ness of several odors in a free swimming assay. They select a couple of these odors based on their valence, and they demonstrate that these odors induce moderate modulation in the frequency of eye saccades (S) and tail flips (T) and (S-T) turns.

      The study is rigorous and thorough, and the findings are informative and novel.

      In important controls, they confirm that brain-wide imaging can distinguish between appetitive and aversive contexts, and they show that pallial activation by aversive odors is consistent with neural activity in the rhombencephalon that correlates with turning activity, whereas sub-pallial activation by appetitive odors correlates with rhombencephalic activity related to gliding.

      Overall, this manuscript is very good.

    1. Reviewer #1 (Public review):

      Summary:

      Witte et al. examined whether canonical behavioral functions attributed to the cerebellum decline with age. To test this, they recruited younger, old, and older-old adults in a comprehensive battery of tasks previously identified as cerebellar-dependent in the literature. Remarkably, they found that cerebellar function is largely preserved across the lifespan-and in some cases even enhanced. Structural imaging confirmed that their older adult cohort was representative in terms of both cerebellar gray- and white-matter volume. Overall, this is an important study with strong theoretical implications and convincing evidence supporting the motor reserve hypothesis, demonstrating that cerebellar-dependent measures remain largely intact with aging.

      Strengths:

      (1) Relatively large sample size.

      (2) Most comprehensive behavioral battery to date assessing cerebellar-dependent behavior.

      (3) Structural MRI confirmation of age-related decline in cerebellar gray and white matter, ensuring representativeness of the sample.

      Weaknesses:

      (1) Although the authors note this was outside the study's scope, the absence of a voxel-based morphometry (VBM) analysis limits anatomical and functional specificity. Such an analysis would clarify which functions are cerebellar-dependent rather than solely inferring this from prior neuropsychological literature.

      (2) As acknowledged in the Discussion, task classification (cerebellar-dependent vs. general measures) remains somewhat ambiguous. Some "general" measures may still rely on cerebellar processes based on the paper's own criteria - for example, tasks in which individuals with cerebellar degeneration show impairments.

      (3) Cerebellar-dependent and general measures may inherently differ in measurement noise, potentially biasing results toward detecting effects in general measures but not in cerebellar-dependent ones.

    1. Reviewer #1 (Public review):

      Summary

      Wang et al. address the challenge of tracking goal-relevant visual signals amidst distractions, a fundamental aspect of adaptive visual information processing. By employing functional magnetic resonance spectroscopy (fMRS) during a visual tracking task, they quantify changes in both inhibitory (GABA) and excitatory (glutamate) neurotransmitter concentrations in the parietal and visual cortices. The results reveal that increases in GABA and glutamate in the parietal cortex are closely tied to the number of targets, and individual differences in GABAergic and glutamatergic responses within the parietal cortex predict tracking performance and distractor suppression. These findings underscore a neural mechanism in which GABAergic inhibition in the parietal cortex actively suppresses goal-irrelevant distractors, thereby facilitating goal-directed visual tracking and highlighting the dynamic role of these key metabolites in cognitive control during visual processing. I found the study to be well-written and thoughtful from an experimental standpoint, although it would benefit from some targeted revisions.

      Strengths

      (1) The study employs robust and validated fMRS methodology, allowing for real-time monitoring of metabolite changes during goal-directed tasks.

      (2) Simultaneous measurement of both GABA and Glx in parietal and visual cortices yields nuanced insights into the neurochemical correlates of visual attention.

      (3) The link between neurochemical changes and behavioral performance is clearly established, providing strong evidence for GABAergic involvement in distractor suppression.

      (4) Experimental protocols align with current standards for MEGA-PRESS, bolstering the technical reliability of the findings.

      Weaknesses

      (1) Certain aspects of terminology, methodological reporting, and confound management are inconsistently described throughout the manuscript.

      (2) Important confounding factors are not systematically reported or controlled.

      (3) Opportunities for additional analysis (e.g., behavioral dynamics, use of alternate fitting methods, more comprehensive quality metrics) have not been fully explored.

      (4) Open access data and/or codes for the analysis are not shared in the main manuscript

    2. Reviewer #2 (Public review):

      Summary:

      This study investigates how the visual system is able to track target objects when these are presented in the visual field together with other irrelevant and distracting visual objects. The authors use functional Magnetic Resonance Spectroscopy to measure the two most important excitatory and inhibitory neurotransmitters, glutamate and GABA, in both the visual and parietal cortex.

      Strengths:

      (1) Well-designed functional challenge.

      (2) Number of subjects.

      (3) Good quality spectra and appropriate reporting of MRS methods and quality assurance.

      (4) Introduction and discussion are clear for non-experts in visual processing.

      Weaknesses:

      (1) Rejection of spectra based on high % CRLB may artificially remove data with the lowest metabolite concentration.

      (2) SN description as percentage does not make sense.

    3. Reviewer #3 (Public review):

      Wang et al. report multiple experiments using functional magnetic resonance spectroscopy (fMRS) in a multiple object tracking (MOT) task to investigate the effect of experimentally manipulating a) the number of targets, b) object size, and c) total number of objects in the display on GABA and glutamate (Glx) concentrations in parietal and visual cortex. Data is analyzed in two orthogonal ways throughout: via condition differences in behavorial performance (inverse efficiency), GABA, and Glx concentrations and through correlations between changes in inverse efficiency and GABA or Glx. All three experimental manipulations affected inverse efficiency, with worse performance with more targets, smaller objects, and a larger total number of objects. However, only the manipulation of the target number produced a condition difference in GABA and Glx, with higher concentrations of both in the parietal VOI and only of Glx in the visual VOI with more targets ('high load'). Correlational analyses revealed that participants with a larger change in GABA in the parietal VOI with a higher number of targets showed a smaller drop in behavioral performance with more targets. The opposite direction of correlation was observed for Glx in both the visual and parietal VOI.

      In the two control experiments, correlations were only investigated in the parietal VOI. There was a negative correlation between change in Glx and change in inverse efficiency with manipulation of object size, i.e. participants exhibiting a positive change in Glx showed no or little difference in performance, but those with an increase in Glx with smaller targets showed a more pronounced drop in performance. There was no correlation with GABA for the manipulation of object size. For the manipulation of total object number, participants exhibiting an increasing GABA concentration with more objects showed a smaller drop in performance.

      The authors' main claim is that GABAergic suppression of goal-irrelevant distractors in parietal cortex is key to goal-directed visual information processing.

      The study is, to my knowledge, the first to employ fMRS in an MOT paradigm, and I read it with great interest. I am admittedly not an expert on the fMRS technique and have therefore refrained from commenting on the technical aspects of its use. Although the application of fMRS to MOT is novel and adds new knowledge to the field, I have some critiques and believe that a much more nuanced interpretation of the findings is warranted.

      Major

      (1) Especially the control experiments lean heavily on Bettencourt and Somers (2009) and adopt and to some extent exaggerate claims from that paper uncritically. This is obvious in referring to the manipulations of object size and object number as high/low enhancement and high/low suppression, as if the association of these physical manipulations of the stimulus display with attentional mechanisms were so obvious and beyond doubt that drawing any distinction between these manipulations and their supposed effects is entirely superfluous. This seems far beyond what is warranted to me. It may seem plausible that adding distractors engages distractor suppression more, but whether this is truly the case is an empirical question, and Bettencourt and Somers (2009) have no direct measure of distractor suppression to substantiate this claim. Their study is purely behavioral, and there is no attempt to assess distractor processing separately. The case for the 'target enhancement' manipulation is even weaker: objects are of a sufficient size and at maximum contrast (white on black screen, but exact details are omitted) to be clearly visible in either condition, so why would smaller objects require more enhancement? Although the present data shows a clear effect of manipulating object size, the corresponding size of the effect in Bettencourt and Somers (2009) is rather underwhelming and does not warrant such a strong conclusion. In summary, the link between the object number and object size manipulations with suppression and enhancement is very far from the 1:1 that the authors seem to assume. Accordingly, I believe that the manipulations should be labelled as object number and object size rather than their hypothesized effects, throughout and that there should be a much more critical discussion as to whether these manipulations are indeed related to these effects as expected.

      (2) The author's interpretation of the results seems rather uncritical. What is observed (at least in the first experiment) is a change in GABA and Glx concentrations with changes in the number of tracked targets. Is the only conceivable way in which this could happen through target enhancement and distractor suppression? The processing of targets and distractors is not measured directly, so any claims are indirect, at best. The authors cite the recent 'Ten simple rules to study distractor suppression' paper (Wöstmann et al., 2022), which presents a consensus between leading researchers in the field. Neither Bettencourt & Somers (2009) nor the design of the current study live up to the rules established in that paper, so a much more nuanced interpretation and discussion of the current findings seems warranted. It is anything but obvious to me that the only activity in the parietal cortex that could possibly be suppressed by GABA is the representation of distractors. Indeed, cueing more targets (high load) decreases the number of distractors in the first experiment, so the need for distractor suppression in the high load condition is less than in the low load condition. So, shouldn't we observe lower GABA concentrations in the 'high load' condition?

      (3) It seems that the authors included data from both correctly tracked and incorrectly tracked trials in their fMRS analysis. In MOT, attending target objects is the task per se, so task errors indicate that participants did not actually track the targets. So when comparing conditions with different error levels, it is ambiguous whether changes in brain activity reflect the experimental manipulation as such, or rather the different mix of correctly tracked and incorrectly tracked trials that result from this physical manipulation. Are the correlations perhaps driven by the inclusion of different proportions of correctly tracked trials across participants? It seems that the authors may have to separate correct and error trials in the analysis to check for the possibility that effects are due to the inclusion of data from trials in which participants may have stopped tracking at least some of the target objects. Of course, such an analysis is somewhat limited by the fact that only one target was probed, yielding a 50% guessing chance (i.e. even if the response is correct, we do not know whether the other, unprobed, objects were tracked correctly on that trial).

      (4) The key findings from the control experiments are purely correlational. The supposed cause may be what the authors claim, but there is an infinity of alternative explanations. Correlational findings cannot simply be interpreted as if they resulted from an experimental manipulation (...although this is, unfortunately, by no means rare in the cognitive neuroscience literature). The authors should make a rigorous effort to consider the most plausible alternative explanations for these correlations and argue why or why not they believe that they can be discounted.

      (5) Related to the previous point: the experimental manipulations did not produce mean differences in GABA/Glx in the control experiments. Doesn't this speak against the authors' interpretation? They briefly acknowledge this in the discussion, but I think there is a deeper problem. The absence of these effects casts doubt on what these manipulations actually do, and therefore also on the interpretation of the correlations in these experiments. For example, the authors might also have concluded from the same data that the absence of increased GABA in the 'high suppression' condition refutes the very idea that GABA concentrations are related to distractor suppression.

      (6) 'Inverse Efficiency' is a highly unusual measure of MOT performance in the literature, and its use reduces the comparability of the findings with previous work. The standard is to assess the correctness ('accuracy') of responses with no focus on speed. This makes sense as responses are given after the object motion has stopped. At the same time, reaction time can be informative too (e.g., Störmer et al., 2013). I think the authors should justify their use of inverse efficiency as the dependent variable.

      (7) The choice of variable names is problematic: it is sometimes misleading and makes understanding the findings harder (see also points 1 and 6): obvious, unambiguous, and importantly, interpretation free names for conditions such as target number (2/4), object size (small/large), and total object number (8/12) become load (high/low), target enhancement (high/low) and distractor suppression (low/high). This reduces clarity and, especially in the case of enhancement and suppression, conflates the actual manipulation with its interpretation.

    1. After careful editorial assessment, I regret to inform you that we are unable to proceed with this manuscript for publication. The decision is rejection, based on fundamental concerns related to scientific novelty, conceptual framing, methodological validity, and public health relevance, which collectively preclude suitability for this journal.

      1. Limited novelty and incremental contribution The central research question whether caregiver “hot-to-touch” assessment accurately detects fever compared with thermometer measurement is well established in the literature. Multiple systematic reviews and primary studies over the past two decades have already demonstrated that tactile assessment has moderate sensitivity and poor specificity, often overestimating fever. The present manuscript largely reconfirms known findings without offering a novel conceptual framework, methodological advance, or actionable insight that substantially extends current knowledge. While the multi-country dataset is large, scale alone does not compensate for the lack of conceptual or analytical innovation expected for a general global public health journal.

      2. Conceptual and clinical misalignment The study population is restricted to children with medically attended diarrhea enrolled in a Shigella surveillance platform, yet the research question is framed broadly around caregiver fever detection. This creates a conceptual mismatch: fever in diarrheal illness is neither the dominant nor the most clinically decisive symptom driving triage, referral, or mortality risk in such settings. As a result, the findings have limited relevance for broader fever detection strategies, integrated community case management (iCCM), or child survival policies. The manuscript does not convincingly justify why this specific clinical subgroup provides a valid or generalizable test case for caregiver fever assessment.

      3. Methodological concerns affecting validity Several methodological choices substantially weaken interpretability: The dichotomization of caregiver accuracy using a ≥50% threshold is arbitrary, not clinically meaningful, and insufficiently justified. This approach risks misclassification and dilutes interpretive clarity. Clinical covariates (e.g., respiratory rate, heart rate, chest indrawing) are measured only at enrollment, yet are used to explain caregiver accuracy across a 14-day follow-up period, violating temporal plausibility. The analysis does not adequately address within-child correlation arising from repeated daily measurements, raising concerns about model specification and variance estimation. Extremely small sample size in Peru, combined with its inclusion in pooled analyses, further complicates cross-site inference. These issues are not minor and would require substantial redesign of the analytical framework, rather than revision.

      4. Overinterpretation and limited policy relevance The conclusions and discussion extend beyond what the data can reasonably support. While the manuscript reiterates the importance of thermometers and caregiver education, these recommendations are already well accepted and are not meaningfully advanced by the study’s findings. The manuscript stops short of providing concrete, evidence-based guidance on how caregiver assessment might be integrated, improved, or safely relied upon in real-world decision-making. Consequently, the policy and practice implications are weak and largely generic, limiting the manuscript’s impact for a global public health audience.

    1. condensed

      Here’s a thorough explanation of “condensed” in both English and 中文, now with appropriate illustrative images from the internet** to help you visualize the meanings. 👇


      🌧️ 1. “Condensed” — Gas → Liquid (Science/Physics)

      Meaning: When a gas cools down and turns into a liquid, that liquid is described as condensed. This is a common phase change in the water cycle (vapour → water droplets). (Wikipedia)

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      👉 English explanation:

      • Condensation is when gas molecules slow down, come together, and form liquid. (acs.org)
      • The liquid formed by this process is condensed water.

      👉 中文解释:

      • 凝结(condensation)是当气体(如水蒸气)冷却、运动变慢,并聚集成液体时发生的过程。 (Wikipedia)
      • 这种形成的液体称为凝结的(水)

      Examples:

      • Water vapour condenses on the glass. 水蒸气在玻璃上凝结成水滴
      • Rain forms when condensed water in clouds becomes heavy. 当云中的凝结水变得很重时就会下雨。

      🥛 2. “Condensed” — Concentrated Liquid (Food)

      Meaning: When much of the water is removed from a liquid (like milk), what’s left is thicker and more concentrated — we call it condensed. (Wikipedia)

      👉 English explanation:

      • Condensed milk is milk with most water removed — it’s thick and sweet (especially with added sugar). (Wikipedia)

      👉 中文解释:

      • 炼乳 / 奶浓缩液 是把牛奶的大部分水分蒸发掉后得到的厚而甜的牛奶。 (Wikipedia)

      Examples:

      • She stirred condensed milk into her coffee. 她往咖啡里加了炼乳

      📝 3. “Condensed” — Shortened Text / Summary

      Meaning: When extra details are removed and information is presented in a shorter, tighter form, that version is called condensed.

      👉 English:

      • A condensed summary keeps the main ideas but is much shorter.

      👉 中文:

      • 精简版 / 简写版 是指去掉细节,只保留重点内容的版本。

      Examples:

      • This is a condensed version of the report. 这是报告的精简版

      (Note: Internet images for “condensed text summary diagram” commonly show further visualizations but may be behind paid stock image sites. (Shutterstock))


      📌 Quick Bilingual Recap

      | Usage (English) | 中文解释 | Key Idea | | ---------------------------- | --------------- | --------------------------- | | condensed water | 凝结水 / 凝结的液体 | gas → liquid | | condensed milk | 炼乳 / 浓缩牛奶 | water removed, concentrated | | condensed summary / text | 精简版 / 简写版 | shorter, fewer details |


      If you’d like, I can also generate a printable infographic combining these meanings visually with labels in both English and Chinese. Would you like that? 😊

    2. complementary bases.

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      English — complementary bases (thorough explanation)

      1) What complementary bases means (core idea)

      Complementary bases are pairs of nitrogenous bases that fit together in a specific way in DNA (and RNA).

      Complementary bases = bases that pair in a fixed, matching pattern

      They are called complementary because:

      • One base always matches with only one other base
      • The pairing is predictable and consistent

      2) The complementary base-pairing rules (must know)

      In DNA:

      • Adenine (A) pairs with Thymine (T)
      • Cytosine (C) pairs with Guanine (G)

      In RNA:

      • Adenine (A) pairs with Uracil (U)
      • Cytosine (C) pairs with Guanine (G)

      📌 These rules never change.


      3) Why these bases pair together

      Complementary pairing happens because of:

      • Shape → bases fit together like puzzle pieces
      • Hydrogen bonding → specific bases can form hydrogen bonds with each other

      Details:

      • A–T form 2 hydrogen bonds
      • C–G form 3 hydrogen bonds (stronger)

      This keeps DNA:

      • Stable
      • Uniform in width

      4) Complementary bases in DNA structure

      DNA looks like a twisted ladder:

      • The sides → sugar–phosphate backbones
      • The rungs → complementary base pairs

      Each rung is:

      • One base from one strand
      • Its complementary base from the other strand

      5) Why complementary bases are essential (Science 10 focus)

      A) DNA replication

      • DNA strands separate
      • Each strand uses complementary bases to build a new strand
      • Result: two identical DNA molecules

      B) Transcription (DNA → RNA)

      • RNA is built using complementary base pairing
      • Ensures accurate genetic instructions

      C) Genetic accuracy

      • Complementary pairing prevents many errors
      • Maintains stable inheritance of traits

      6) Example (exam-style)

      If one DNA strand is:

      A T G C C A

      The complementary strand is:

      T A C G G T


      One-sentence exam summary

      Complementary bases are specific base pairs (A–T and C–G) that hold DNA strands together and allow accurate replication.


      中文 — complementary bases(互补碱基) 详细解释

      1) 什么是互补碱基(核心概念)

      互补碱基是指在 DNA(或 RNA)中,只能按照固定规则配对的碱基

      互补碱基 = 能一一对应配对的碱基


      2) 互补配对规则(必背)

      DNA 中:

      • A(腺嘌呤) ↔ T(胸腺嘧啶)
      • C(胞嘧啶) ↔ G(鸟嘌呤)

      RNA 中:

      • A ↔ U(尿嘧啶)
      • C ↔ G

      3) 为什么叫“互补”

      互补的原因是:

      • 形状匹配
      • 氢键数量固定

      具体来说:

      • A–T:2 条氢键
      • C–G:3 条氢键(更牢固)

      这保证了 DNA 结构:

      • 稳定
      • 宽度一致

      4) 互补碱基在 DNA 中的位置

      DNA 像一把梯子:

      • 两侧:糖—磷酸骨架
      • 横档:互补碱基对

      每一个“横档”就是一对互补碱基。


      5) 互补碱基为什么重要(考试重点)

      ① DNA 复制

      • 旧链作模板
      • 通过互补配对生成新链
      • 遗传信息准确复制

      ② 转录(DNA → RNA)

      • RNA 按互补规则合成
      • 遗传信息得以表达

      ③ 遗传稳定性

      • 减少错误
      • 保证性状正确遗传

      6) 考试例题示范

      如果 DNA 一条链是:

      A T G C

      互补链是:

      T A C G


      一句话考试版总结

      互补碱基是 DNA 中按照 A–T、C–G 规则配对的碱基,保证遗传信息准确复制。

      如果你愿意,我可以把 complementary bases → DNA replication → transcription 做成 Science 10 中英对照流程图 / 互动闪卡,直接用于课堂或复习。

    3. rung

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      English — rung (thorough explanation)

      1) What “rung” means (core idea)

      A rung is a horizontal step or bar that connects the two sides of a ladder.

      Rung = one step of a ladder

      You climb a ladder by stepping on its rungs.


      2) “Rung” as a metaphor in biology (Science 10 focus)

      In biology, rung is often used as a comparison (metaphor) when explaining DNA structure.

      • DNA is often described as a twisted ladder
      • The sides of the ladder → sugar–phosphate backbones
      • The rungs of the ladder → paired nitrogenous bases

      📌 Each DNA rung is made of a base pair:

      • A–T (adenine–thymine)
      • C–G (cytosine–guanine)

      These base pairs are held together by hydrogen bonds.


      3) What makes up a DNA “rung”

      Each rung consists of:

      • Two nitrogenous bases
      • Joined by hydrogen bonds
      • One base from each DNA strand

      Example:

      One rung = A on one strand + T on the other strand


      4) Why the “rung” idea helps understanding

      The ladder model helps students visualize that:

      • DNA has two strands
      • The strands are connected at regular intervals
      • The order of rungs carries genetic information

      📌 The sequence of rungs = genetic code.


      5) Everyday uses of “rung”

      • Ladder rung
      • A rung on a career ladder (metaphor)
      • A rung in a rope ladder

      One-sentence exam summary

      A rung is a horizontal step of a ladder; in DNA, rungs represent paired nitrogenous bases connecting the two strands.


      中文 — rung(梯级 / 横档) 详细解释

      1) “rung”的基本含义

      Rung 指的是梯子上的横档或踏板,用来踩踏和攀爬。

      Rung = 梯子的一格横档


      2) 生物学中的 rung(DNA 比喻,重点)

      在生物学中,DNA 常被比作一把梯子

      • 梯子的两侧 → 糖—磷酸骨架
      • 梯子的横档(rungs)→ 碱基对

      📌 每一个 DNA 的“rung”由一对碱基组成:

      • A–T
      • C–G

      3) DNA 横档的作用

      • 把两条 DNA 链连接在一起
      • 保持双螺旋结构稳定
      • 横档的排列顺序储存遗传信息

      一句话考试版总结

      Rung 指梯子的横档,在 DNA 中用来比喻连接两条链的碱基对。

      如果你需要,我可以把 ladder model → rung → base pair → hydrogen bond 做成 Science 10 中英对照图解或互动闪卡,非常适合课堂讲解与复习。

    4. strands

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      English — strands (thorough explanation)

      1) What “strands” means (core idea)

      Strands are long, thin lines or threads of material. In science, the word is often used to describe structures that are stretched out rather than clumped or round.

      Strand = a long, thin piece of something


      2) “Strands” in biology (Science 10 focus)

      A) DNA strands

      DNA is made of two strands that twist together to form a double helix.

      • Each strand is a long chain of nucleotides
      • The two strands are held together by base pairing
      • The strands run in opposite directions (antiparallel)

      📌 One strand is not enough for stable DNA → two strands are needed.


      B) RNA strand

      RNA usually has only one strand.

      • Single-stranded structure
      • Made of nucleotides like DNA
      • Used to carry and translate genetic information

      📌 This is why RNA is more flexible but less stable than DNA.


      C) Protein strands (fibers)

      Some proteins form strand-like fibers, such as:

      • Muscle proteins
      • Collagen fibers
      • Keratin in hair and nails

      3) “Strands” outside biology (quick examples)

      • Hair strands → individual hairs
      • Fiber strands → threads in fabric or rope
      • Data strands → sequences of information (metaphorical use)

      4) Strand vs chain vs helix (common confusion)

      | Term | Meaning | | ------------ | ---------------------------- | | Strand | One long, thin line | | Chain | Many units linked together | | Double helix | Two strands twisted together |

      📌 In DNA:

      • Each strand is a chain
      • Two strands form a double helix

      5) Why strands matter in genetics

      • The order of bases along a strand carries information
      • Complementary strands allow accurate copying
      • Strand separation is essential for replication and transcription

      One-sentence exam summary

      Strands are long, thin chains; DNA has two strands, while RNA usually has one.


      中文 — strands(链 / 丝状结构) 详细解释

      1) “strands”的基本含义

      Strands 指的是 细长、线状的结构

      Strand = 一条细长的链或丝


      2) 生物学中的 strands(重点)

      A) DNA 链

      DNA 由 两条链(两条 strand)组成:

      • 每条链由核苷酸连接而成
      • 两条链通过碱基配对结合
      • 共同形成 双螺旋结构

      B) RNA 链

      RNA 通常是 单链结构

      • 只有一条 strand
      • 用于传递和执行遗传信息

      C) 蛋白质纤维

      某些蛋白质呈丝状结构

      • 肌肉纤维
      • 胶原蛋白
      • 角蛋白(头发)

      3) strand 与相关词的区别

      | 英文 | 中文 | 说明 | | ------------ | --- | ------- | | strand | 链 | 一条细长结构 | | chain | 链条 | 多个单位连接 | | double helix | 双螺旋 | 两条链扭在一起 |


      一句话考试版总结

      DNA 是双链结构,RNA 通常是单链结构。

      如果你愿意,我可以把 strand → nucleotide → base pairing → double helix 做成 Science 10 中英对照概念图或互动闪卡,直接用于复习或教学。

    5. ribonucleic

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      English — ribonucleic (thorough explanation)

      1) What ribonucleic means (core idea)

      Ribonucleic means related to RNA (ribonucleic acid). The word is most commonly seen in ribonucleic acid, abbreviated as RNA.

      Ribonucleic = having to do with RNA


      2) Why it’s called “ribonucleic”

      The name comes from its components:

      • Ribo-ribose sugar
      • -nucleic → found in the nucleus (or related to genetic material)

      So:

      Ribonucleic acid = nucleic acid containing ribose sugar


      3) What ribonucleic acid (RNA) is

      RNA is a molecule that:

      • Carries genetic instructions
      • Helps make proteins
      • Works closely with DNA

      Unlike DNA, RNA is usually:

      • Single-stranded
      • Shorter
      • Less stable

      4) Structure of ribonucleic acid (exam focus)

      Each RNA nucleotide has:

      1. Phosphate group
      2. Ribose sugar
      3. Nitrogenous base

      RNA bases are:

      • Adenine (A)
      • Uracil (U) ← replaces thymine
      • Cytosine (C)
      • Guanine (G)

      📌 The presence of ribose sugar is what makes RNA “ribo”-nucleic.


      5) Main types of ribonucleic acid

      mRNA (messenger RNA)

      • Carries instructions from DNA to ribosomes

      tRNA (transfer RNA)

      • Brings amino acids to build proteins

      rRNA (ribosomal RNA)

      • Forms part of the ribosome

      All of these are ribonucleic acids.


      6) Ribonucleic vs deoxyribonucleic (RNA vs DNA)

      | Feature | Ribonucleic (RNA) | Deoxyribonucleic (DNA) | | --------- | ----------------- | ---------------------- | | Sugar | Ribose | Deoxyribose | | Strands | Single | Double | | Bases | A, U, C, G | A, T, C, G | | Function | Protein synthesis | Store genetic info | | Stability | Lower | Higher |


      7) Why ribonucleic acid is important

      Without ribonucleic acid:

      • Genetic information could not be used
      • Proteins could not be made
      • Cells could not function properly

      DNA stores information; ribonucleic acid uses it


      One-sentence exam summary

      Ribonucleic refers to RNA, a nucleic acid containing ribose sugar that helps convert genetic information into proteins.


      中文 — ribonucleic(核糖核酸的) 详细解释

      1) “ribonucleic”的基本含义

      Ribonucleic 指的是与 RNA(核糖核酸)有关的

      Ribonucleic = 核糖核酸的


      2) 为什么叫“核糖核酸”

      • ribo-:核糖
      • nucleic:核酸 / 遗传物质

      RNA 是含有核糖的核酸


      3) RNA 是什么

      RNA(核糖核酸)是:

      • 遗传信息的“执行者”
      • 参与蛋白质合成
      • 帮助细胞工作的重要分子

      4) RNA 的结构(考试重点)

      RNA 的每个核苷酸包括:

      1. 磷酸基团
      2. 核糖
      3. 含氮碱基

      RNA 的碱基是:

      • A、U、C、G

      5) RNA 的主要类型

      • 信使 RNA(mRNA):传递指令
      • 转运 RNA(tRNA):搬运氨基酸
      • 核糖体 RNA(rRNA):构成核糖体

      6) RNA 与 DNA 的区别(常考)

      | 项目 | RNA | DNA | | -- | ----- | ------ | | 糖 | 核糖 | 脱氧核糖 | | 结构 | 单链 | 双链 | | 功能 | 蛋白质合成 | 储存遗传信息 |


      一句话考试版总结

      Ribonucleic 指的是核糖核酸(RNA),一种含核糖、参与蛋白质合成的核酸。

      如果你愿意,我可以把 ribonucleic / deoxyribonucleic / nucleotide / base 做成 Science 10 中英对照概念链或互动闪卡,方便你系统复习。

    6. Thymine

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      English — Thymine (T) (thorough explanation)

      1) What thymine is (core idea)

      Thymine is a nitrogenous base found only in DNA. It is one of the four bases that make up the DNA genetic code.

      Thymine = a DNA base that pairs with adenine


      2) Where thymine is found

      • DNA
      • RNA ❌ (RNA uses uracil instead)

      Each thymine base is part of a nucleotide, attached to:

      • Deoxyribose sugar
      • Phosphate group

      3) Thymine’s base-pairing rule (exam essential)

      In DNA:

      • Thymine (T) pairs with Adenine (A)
      • Held together by 2 hydrogen bonds

      This specific pairing:

      • Keeps DNA strands aligned
      • Allows accurate DNA replication

      4) Chemical group of thymine

      Thymine belongs to the pyrimidines, which:

      • Have a single-ring structure
      • Are smaller than purines

      Pyrimidines: Cytosine (C), Thymine (T), Uracil (U) Purines: Adenine (A), Guanine (G)

      Purine–pyrimidine pairing keeps the DNA double helix a constant width.


      5) Role of thymine in DNA

      • Thymine helps store genetic information
      • The order of T bases (with A, C, G) determines genes
      • Correct T–A pairing ensures genetic stability

      A mistake involving thymine (a mutation) can:

      • Change a gene
      • Alter protein structure
      • Affect traits

      6) Thymine vs uracil (common exam comparison)

      | Feature | Thymine (T) | Uracil (U) | | ---------- | ----------- | ----------- | | Found in | DNA | RNA | | Pairs with | Adenine | Adenine | | Stability | More stable | Less stable |

      📌 Thymine makes DNA more stable for long-term information storage.


      One-sentence exam summary

      Thymine is a pyrimidine nitrogenous base found only in DNA that pairs with adenine using two hydrogen bonds.


      中文 — Thymine(胸腺嘧啶,T) 详细解释

      1) 什么是胸腺嘧啶(核心概念)

      胸腺嘧啶(Thymine,T)是一种只存在于 DNA 中的含氮碱基,是 DNA 遗传信息的重要组成部分。

      胸腺嘧啶 = DNA 中与腺嘌呤配对的碱基


      2) 胸腺嘧啶出现在哪里

      • DNA 中有
      • RNA 中没有(RNA 用的是尿嘧啶 U

      3) 胸腺嘧啶的配对规则(必考)

      DNA 中:

      • T ↔ A
      • 通过 2 条氢键连接

      这种精确配对保证 DNA 复制准确


      4) 胸腺嘧啶的类别

      胸腺嘧啶属于 嘧啶(pyrimidine)

      • 单环结构
      • 分子较小

      5) 胸腺嘧啶的作用

      • 参与遗传信息储存
      • 确保 DNA 双螺旋结构稳定
      • 维持遗传信息长期保存

      6) 胸腺嘧啶 vs 尿嘧啶(常考对比)

      | 项目 | 胸腺嘧啶 | 尿嘧啶 | | ---- | ---- | --- | | 所在分子 | DNA | RNA | | 配对对象 | 腺嘌呤 | 腺嘌呤 | | 稳定性 | 更高 | 较低 |


      一句话考试版总结

      胸腺嘧啶是 DNA 中与腺嘌呤配对、具有两条氢键的嘧啶碱基。

      如果你需要,我可以把 A–T vs C–G稳定性比较或把 四种 DNA 碱基整理成 Science 10 中英对照闪卡 / 互动图表,方便系统复习与教学。

    7. Guanine

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      English — Guanine (G) (thorough explanation)

      1) What guanine is (core idea)

      Guanine is a nitrogenous base found in DNA and RNA. It is one of the four bases that make up the genetic code.

      Guanine = a nitrogen-containing base that stores genetic information


      2) Where guanine is found

      Guanine appears in:

      • DNA
      • RNA

      It is always part of a nucleotide, attached to:

      • A sugar (deoxyribose in DNA, ribose in RNA)
      • A phosphate group

      3) Guanine’s base-pairing rule (exam essential)

      In DNA:

      • Guanine (G) pairs with Cytosine (C)
      • They are held together by 3 hydrogen bonds

      In RNA:

      • Guanine (G) pairs with Cytosine (C)

      📌 Because there are three hydrogen bonds, G–C pairs are stronger and more stable than A–T pairs.


      4) Guanine’s chemical group

      Guanine belongs to the purines, which:

      • Have a double-ring structure
      • Are larger than pyrimidines

      Purines: Adenine (A), Guanine (G) Pyrimidines: Cytosine (C), Thymine (T), Uracil (U)

      This size matching (purine–pyrimidine) keeps the DNA double helix uniform in width.


      5) Role of guanine in DNA

      In DNA:

      • Guanine attaches to the sugar to form a nucleotide
      • The sequence of G (with A, T, C) determines genetic instructions
      • Accurate G–C pairing ensures correct DNA replication

      Changes involving guanine can cause mutations, potentially affecting proteins and traits.


      6) Guanine and DNA stability

      • Regions with many G–C pairs are more thermally stable
      • Such regions often occur in important regulatory areas of DNA

      One-sentence exam summary

      Guanine is a purine nitrogenous base that pairs with cytosine using three hydrogen bonds in DNA and RNA.


      中文 — Guanine(鸟嘌呤,G) 详细解释

      1) 什么是鸟嘌呤(核心概念)

      鸟嘌呤(Guanine,G)是一种存在于 DNA 和 RNA 中的含氮碱基,是遗传信息的重要组成部分。

      鸟嘌呤 = DNA / RNA 中的遗传“字母”之一


      2) 鸟嘌呤出现在哪里

      鸟嘌呤存在于:

      • DNA
      • RNA

      它与:

      • 磷酸基团 一起组成 核苷酸

      3) 鸟嘌呤的配对规则(必考)

      DNA 中:

      • G ↔ C
      • 通过 3 条氢键连接

      RNA 中:

      • G ↔ C

      📌 三条氢键使 G–C 配对更加牢固。


      4) 鸟嘌呤的类别

      鸟嘌呤属于 嘌呤(purine)

      • 双环结构
      • 分子较大

      对比:

      • 嘌呤:A、G
      • 嘧啶:C、T、U

      5) 鸟嘌呤在 DNA 中的作用

      • 与脱氧核糖结合形成核苷酸
      • 与胞嘧啶精确配对
      • 确保 DNA 复制的准确性

      碱基变化可能导致突变


      一句话考试版总结

      鸟嘌呤是 DNA 和 RNA 中与胞嘧啶配对、具有三条氢键的嘌呤碱基。

      如果你需要,我可以把 A–T vs C–G稳定性对比、或把四种碱基做成 Science 10 中英对照闪卡 / 互动图解,直接用于复习或教学。

    8. Cytosine

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      English — Cytosine (C) (thorough explanation)

      1) What cytosine is (core idea)

      Cytosine is a nitrogenous base found in DNA and RNA. It is one of the four main bases that make up the genetic code.

      Cytosine = a nitrogen-containing base that helps store genetic information


      2) Where cytosine is found

      Cytosine occurs in:

      • DNA
      • RNA

      It is always part of a nucleotide, attached to:

      • A sugar (deoxyribose in DNA, ribose in RNA)
      • A phosphate group

      3) Cytosine’s base-pairing rule (exam essential)

      In DNA:

      • Cytosine (C) pairs with Guanine (G)
      • They are held together by 3 hydrogen bonds

      In RNA:

      • Cytosine (C) pairs with Guanine (G)

      📌 The three hydrogen bonds make the C–G pair stronger than the A–T pair.


      4) Cytosine’s chemical group

      Cytosine belongs to the pyrimidines, which:

      • Have a single-ring structure
      • Are smaller than purines

      Purines (double ring):

      • Adenine (A)
      • Guanine (G)

      Pyrimidines (single ring):

      • Cytosine (C)
      • Thymine (T)
      • Uracil (U)

      This size matching keeps the DNA double helix uniform in width.


      5) Role of cytosine in DNA

      In DNA:

      • Cytosine attaches to the sugar to form a nucleotide
      • The order of cytosine (with A, T, G) determines genetic instructions
      • Accurate C–G pairing ensures correct DNA replication

      A change in cytosine (mutation) can:

      • Alter genes
      • Affect proteins
      • Change traits

      6) Cytosine and genetic stability

      Because C–G pairs have three hydrogen bonds:

      • Regions rich in C and G are more stable
      • They often occur in important regulatory regions of DNA

      One-sentence exam summary

      Cytosine is a pyrimidine nitrogenous base that pairs with guanine using three hydrogen bonds in DNA and RNA.


      中文 — Cytosine(胞嘧啶,C) 详细解释

      1) 什么是胞嘧啶(核心概念)

      胞嘧啶(Cytosine,C)是一种存在于 DNA 和 RNA 中的含氮碱基,是遗传信息的基本组成单位之一。

      胞嘧啶 = DNA / RNA 中的重要碱基


      2) 胞嘧啶出现在哪里

      胞嘧啶存在于:

      • DNA
      • RNA

      它与:

      • 糖(DNA 中是脱氧核糖)
      • 磷酸基团 一起构成核苷酸

      3) 胞嘧啶的配对规则(必考)

      DNA 中:

      • C ↔ G
      • 通过 3 条氢键连接

      RNA 中:

      • C ↔ G

      📌 三条氢键使 C–G 配对更牢固。


      4) 胞嘧啶的类别

      胞嘧啶属于 嘧啶(pyrimidine)

      • 单环结构
      • 分子较小

      嘌呤(双环):A、G 嘧啶(单环):C、T、U


      5) 胞嘧啶在 DNA 中的作用

      • 与脱氧核糖结合形成核苷酸
      • 与鸟嘌呤精确配对
      • 保证 DNA 复制的准确性

      碱基变化可能导致突变


      6) 一句话考试版总结

      胞嘧啶是 DNA 和 RNA 中与鸟嘌呤配对的嘧啶碱基,具有三条氢键。

      如果你愿意,我可以把 Adenine / Thymine / Cytosine / Guanine 做成 Science 10 中英对照碱基配对表或互动闪卡,非常适合系统复习与教学。

    9. Adenine

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      English — Adenine (A) (thorough explanation)

      1) What adenine is (core idea)

      Adenine is a nitrogenous base found in DNA and RNA. It is one of the letters of the genetic code.

      Adenine = a nitrogen-containing base that carries genetic information


      2) Where adenine is found

      Adenine appears in several key biological molecules:

      • DNA → pairs with thymine (T)
      • RNA → pairs with uracil (U)
      • ATP → part of the energy molecule used by cells

      3) Adenine’s base-pairing rules (exam essential)

      In DNA:

      • A pairs with T
      • Held together by 2 hydrogen bonds

      In RNA:

      • A pairs with U

      These pairing rules ensure accurate DNA replication and correct protein synthesis.


      4) Adenine’s chemical group

      Adenine belongs to the purines, which:

      • Have a double-ring structure
      • Are larger than pyrimidines

      Purines: Adenine (A), Guanine (G) Pyrimidines: Cytosine (C), Thymine (T), Uracil (U)

      This size difference explains why:

      • Purine always pairs with pyrimidine
      • DNA maintains a uniform width

      5) Role of adenine in DNA

      In DNA:

      • Adenine attaches to deoxyribose sugar
      • Becomes part of a nucleotide
      • The sequence of adenine (with other bases) determines genetic instructions

      Changing adenine’s position can:

      • Alter genes
      • Cause mutations
      • Affect traits

      6) Adenine in energy (ATP connection)

      Adenine is part of ATP (adenosine triphosphate):

      • Adenine + ribose = adenosine
      • Adenosine + 3 phosphates = ATP

      ATP provides energy for:

      • Muscle contraction
      • Active transport
      • Chemical reactions

      One-sentence exam summary

      Adenine is a purine nitrogenous base that pairs with thymine in DNA and with uracil in RNA.


      中文 — Adenine(腺嘌呤,A) 详细解释

      1) 什么是腺嘌呤(核心概念)

      腺嘌呤(Adenine,A)是一种含氮碱基,存在于 DNA 和 RNA 中,是遗传信息的“字母”之一。

      腺嘌呤 = DNA / RNA 中的重要遗传碱基


      2) 腺嘌呤出现在哪里

      • DNA:与 胸腺嘧啶(T)配对
      • RNA:与 尿嘧啶(U)配对
      • ATP:能量分子的重要组成部分

      3) 腺嘌呤的配对规则(必考)

      DNA 中:

      • A ↔ T(2 条氢键)

      RNA 中:

      • A ↔ U

      这些规则保证了遗传信息的准确复制和表达


      4) 腺嘌呤的类别

      腺嘌呤属于 嘌呤(purine)

      • 结构为双环
      • 体积较大

      嘌呤:A、G 嘧啶:C、T、U


      5) 腺嘌呤在 DNA 中的作用

      • 与脱氧核糖结合
      • 构成核苷酸
      • 其排列顺序决定遗传信息

      碱基变化可能导致突变


      6) 腺嘌呤与能量(ATP)

      腺嘌呤是 ATP(三磷酸腺苷)的一部分:

      • 为细胞活动提供能量

      一句话考试版总结

      腺嘌呤是 DNA 中与 T 配对、RNA 中与 U 配对的嘌呤碱基。

      如果你需要,我可以把 Adenine / Thymine / Cytosine / Guanine 做成 Science 10 中英对照碱基配对表或互动闪卡,方便系统复习。

    10. nitrogenousbase

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      English — nitrogenous base (thorough explanation)

      1) What a nitrogenous base is (core idea)

      A nitrogenous base is a nitrogen-containing molecule that is part of a nucleotide, the building block of DNA and RNA.

      Nitrogenous base = the “letter” of the genetic code

      Each nucleotide has:

      1. A phosphate group
      2. A sugar
      3. A nitrogenous base

      The sequence of bases stores genetic information.


      2) The five nitrogenous bases (must know)

      In DNA:

      • Adenine (A)
      • Thymine (T)
      • Cytosine (C)
      • Guanine (G)

      In RNA:

      • Adenine (A)
      • Uracil (U) (replaces thymine)
      • Cytosine (C)
      • Guanine (G)

      📌 Only the bases change; the sugar–phosphate backbone stays the same.


      3) Two base groups: purines vs pyrimidines

      Purines (two rings):

      • Adenine (A)
      • Guanine (G)

      Pyrimidines (one ring):

      • Cytosine (C)
      • Thymine (T)
      • Uracil (U)

      This size difference explains base pairing rules.


      4) Base pairing rules (DNA vs RNA)

      DNA base pairing:

      • A pairs with T (2 hydrogen bonds)
      • C pairs with G (3 hydrogen bonds)

      RNA base pairing:

      • A pairs with U
      • C pairs with G

      Hydrogen bonds hold paired bases together, forming the double helix in DNA.


      5) Why nitrogenous bases matter

      Nitrogenous bases:

      • Store genetic information
      • Determine proteins made by a cell
      • Allow DNA to replicate accurately
      • Enable RNA to carry instructions for protein synthesis

      Changing a base (a mutation) can change traits.


      6) Base vs nucleotide (common confusion)

      • Nitrogenous base → one component (A, T/U, C, G)
      • Nucleotide → base + sugar + phosphate

      Bases encode information; nucleotides build the molecule.


      One-sentence exam summary

      Nitrogenous bases are nitrogen-containing molecules in DNA and RNA whose sequence stores genetic information.


      中文 — nitrogenous base(含氮碱基) 详细解释

      1) 什么是含氮碱基(核心概念)

      含氮碱基含有氮原子的分子,是 DNA 和 RNA 的核苷酸组成部分之一

      含氮碱基 = 遗传信息的“字母”

      每个核苷酸由:

      1. 磷酸
      2. 含氮碱基 组成。

      2) 五种含氮碱基(必背)

      DNA 中:

      • 腺嘌呤(A)
      • 胸腺嘧啶(T)
      • 胞嘧啶(C)
      • 鸟嘌呤(G)

      RNA 中:

      • 腺嘌呤(A)
      • 尿嘧啶(U)
      • 胞嘧啶(C)
      • 鸟嘌呤(G)

      3) 含氮碱基的两大类

      嘌呤(双环):

      • A、G

      嘧啶(单环):

      • C、T、U

      4) 碱基配对规则(考试重点)

      DNA:

      • A ↔ T
      • C ↔ G

      RNA:

      • A ↔ U
      • C ↔ G

      这些配对通过氢键连接,使 DNA 形成双螺旋结构


      5) 含氮碱基的重要性

      • 决定遗传信息
      • 指导蛋白质合成
      • 保证 DNA 复制准确
      • 碱基改变会导致突变

      一句话考试版总结

      含氮碱基是 DNA 和 RNA 中储存遗传信息的关键成分。

      如果你需要,我可以把 nitrogenous base → nucleotide → DNA → gene 做成 Science 10 中英对照速记卡或互动图解,非常适合系统复习。

    11. sugar

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      English — Sugar in DNA (thorough explanation)

      1) What the sugar in DNA is

      The sugar found in DNA is called deoxyribose. It is a five-carbon sugar (a pentose) and is one of the three essential parts of a DNA nucleotide.

      DNA sugar = deoxyribose

      Each DNA nucleotide contains:

      1. A phosphate group
      2. Deoxyribose sugar
      3. A nitrogenous base (A, T, C, or G)

      2) Why it’s called deoxyribose

      • Deoxy-” means missing an oxygen
      • Deoxyribose has one less oxygen atom than ribose (the sugar in RNA)

      📌 This small difference makes DNA:

      • More stable
      • Better for long-term information storage

      3) What the sugar does in DNA (key functions)

      A) Forms the backbone

      • Deoxyribose links to phosphate groups
      • Together they form the sugar–phosphate backbone
      • This backbone gives DNA its shape and strength

      B) Connects to bases

      • Each sugar attaches to one nitrogenous base
      • The sequence of bases carries genetic information
      • The sugar itself does not code information, but holds it in place

      4) How sugars link DNA together

      • The sugar of one nucleotide bonds to the phosphate of the next
      • This creates a long chain called a polynucleotide
      • The bonds are called phosphodiester bonds

      Two sugar–phosphate backbones twist together to form the double helix.


      5) DNA sugar vs RNA sugar (common exam comparison)

      | Feature | DNA | RNA | | ------------------- | ------------------ | ------------------ | | Sugar | Deoxyribose | Ribose | | Oxygen at 2′ carbon | ❌ Missing | ✅ Present | | Stability | More stable | Less stable | | Function | Store genetic info | Help make proteins |


      6) Why sugar matters (big picture)

      Without the sugar:

      • DNA nucleotides could not link
      • DNA would fall apart
      • Genetic information could not be stored or copied

      Sugar = the structural “frame” that holds DNA together


      One-sentence exam summary

      The sugar in DNA is deoxyribose, which forms the sugar–phosphate backbone and supports the structure of the DNA molecule.


      中文 — DNA 中的糖(详细解释)

      1) DNA 中的糖是什么

      DNA 中的糖叫 脱氧核糖(deoxyribose),是一种五碳糖

      DNA 的糖 = 脱氧核糖

      每个 DNA 核苷酸由三部分组成:

      1. 磷酸基团
      2. 脱氧核糖
      3. 含氮碱基(A、T、C、G)

      2) 为什么叫“脱氧”核糖

      • “脱氧”表示 少一个氧原子
      • 脱氧核糖比 RNA 中的核糖 少一个氧

      📌 这使 DNA:

      • 稳定
      • 适合长期储存遗传信息

      3) 糖在 DNA 中的作用(重点)

      ① 构成骨架

      • 脱氧核糖与磷酸交替连接
      • 形成 糖—磷酸骨架
      • 为 DNA 提供支撑和形状

      ② 连接碱基

      • 每个糖连接一个碱基
      • 碱基顺序决定遗传信息
      • 糖本身不存信息,但固定信息

      4) DNA 是如何连成链的

      • 一个核苷酸的糖
      • 与下一个核苷酸的磷酸相连
      • 形成 磷酸二酯键

      两条这样的链相互缠绕,形成 DNA 双螺旋结构


      5) DNA 糖 vs RNA 糖(常考对比)

      | 项目 | DNA | RNA | | --- | ------ | ----- | | 糖 | 脱氧核糖 | 核糖 | | 氧原子 | 少一个 | 多一个 | | 稳定性 | 高 | 低 | | 功能 | 储存遗传信息 | 蛋白质合成 |


      一句话考试版总结

      DNA 中的糖是脱氧核糖,它与磷酸一起形成 DNA 的骨架结构。

      如果你需要,我可以把 nucleotide → sugar → phosphate → DNA backbone 做成 中英对照闪卡或可交互 HTML 图解,直接用于 Science 10 复习或教学。

    12. phosphategroup

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      English — phosphate group (thorough explanation)

      1) What a phosphate group is (core idea)

      A phosphate group is a chemical group made of one phosphorus atom bonded to four oxygen atoms (PO₄³⁻).

      In biology, phosphate groups are extremely important because they:

      • Form part of DNA and RNA
      • Store and transfer energy
      • Help link molecules together

      Phosphate group = a key chemical unit for structure and energy


      2) Phosphate group in nucleotides (Science 10 focus)

      In DNA and RNA, every nucleotide contains:

      1. A phosphate group
      2. A sugar
      3. A nitrogenous base

      The phosphate group:

      • Connects to the sugar of one nucleotide
      • Links to the sugar of the next nucleotide

      This creates the sugar–phosphate backbone of DNA and RNA.

      📌 Without phosphate groups, nucleotides could not form long chains.


      3) Phosphodiester bonds (important term)

      Phosphate groups form phosphodiester bonds, which:

      • Join one sugar to the next sugar
      • Hold DNA and RNA strands together
      • Are very strong and stable

      This is why DNA can safely store genetic information.


      4) Phosphate groups and energy (ATP connection)

      Phosphate groups are also central to energy transfer.

      In ATP (adenosine triphosphate):

      • Energy is stored in the bonds between phosphate groups
      • When a phosphate group is removed, energy is released

      📌 This energy powers cell activities like:

      • Movement
      • Active transport
      • Protein synthesis

      5) Other roles of phosphate groups

      Phosphate groups also:

      • Help regulate enzymes (phosphorylation)
      • Are part of cell membranes (phospholipids)
      • Carry negative charge, helping DNA dissolve in water

      One-sentence exam summary

      A phosphate group links nucleotides together to form the sugar–phosphate backbone of DNA and stores energy in molecules like ATP.


      中文 — phosphate group(磷酸基团) 详细解释

      1) 什么是磷酸基团(核心概念)

      磷酸基团是一种由 1 个磷原子和 4 个氧原子组成的化学基团(PO₄³⁻)。

      在生物体内,磷酸基团非常重要,因为它:

      • 构成 DNA 和 RNA
      • 参与 能量储存和释放
      • 帮助分子彼此连接

      磷酸基团 = 结构与能量的关键单位


      2) 磷酸基团在核苷酸中的作用(必考)

      DNA 和 RNA 中的每个核苷酸都包含:

      1. 磷酸基团
      2. 含氮碱基

      磷酸基团的作用:

      • 把一个核苷酸的糖
      • 与下一个核苷酸的糖连接起来

      从而形成 糖—磷酸骨架


      3) 磷酸二酯键(重要名词)

      磷酸基团形成的磷酸二酯键

      • 把相邻核苷酸连接起来
      • 使 DNA / RNA 链稳定
      • 是遗传信息的“支架”

      4) 磷酸基团与能量(ATP)

      ATP(三磷酸腺苷)中:

      • 能量储存在磷酸基团之间的键中
      • 当磷酸基团被移除时,释放能量

      这些能量用于:

      • 肌肉收缩
      • 主动运输
      • 生物合成

      5) 磷酸基团的其他作用

      • 调控蛋白质活性(磷酸化)
      • 构成细胞膜(磷脂)
      • 使 DNA 带负电、易溶于水

      一句话考试版总结

      磷酸基团把核苷酸连接成 DNA 的骨架,并在 ATP 中储存和释放能量。

      如果你愿意,我可以把 phosphate group → nucleotide → DNA backbone → ATP 做成 Science 10 中英对照概念图或互动闪卡,非常适合你现在的生物复习进度。

    13. blooms

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      English — algal blooms (thorough explanation)

      1) What algal blooms are (core idea)

      Algal blooms occur when algae grow very quickly and in large numbers in a body of water, often turning the water green, blue-green, or brown.

      Algal bloom = rapid overgrowth of algae in water

      Blooms commonly happen in ponds, lakes, rivers, and coastal waters.


      2) Why algal blooms happen

      Algal blooms are caused by a combination of favorable conditions:

      • Excess nutrients (especially nitrogen and phosphorus)

      • From fertilizers, sewage, farm runoff

      • Warm temperatures
      • Strong sunlight
      • Still or slow-moving water

      This nutrient enrichment is called eutrophication.


      3) Types of algal blooms

      A) Non-toxic blooms

      • Algae grow rapidly
      • Water looks green or cloudy
      • Still harmful if oxygen drops

      B) Harmful algal blooms (HABs)

      • Often caused by cyanobacteria (blue-green algae)
      • Can release toxins
      • Dangerous to fish, pets, wildlife, and humans

      4) Why algal blooms are harmful (Science 10 focus)

      Even though algae are producers, blooms can damage ecosystems:

      • Block sunlight → underwater plants die
      • Reduce oxygen when algae die and decompose
      • Cause fish kills
      • Disrupt food webs
      • Some toxins cause illness if water is swallowed or touched

      📌 This oxygen loss is called hypoxia.


      5) Effects on humans

      Algal blooms can:

      • Contaminate drinking water
      • Close beaches and lakes
      • Kill fish and livestock
      • Cause skin irritation, stomach illness, or neurological symptoms

      6) Algal blooms in ponds (exam-friendly example)

      In a pond:

      1. Fertilizer runoff enters the water
      2. Algae multiply rapidly
      3. Oxygen levels drop
      4. Fish and insects may die
      5. Pond biodiversity decreases

      7) How algal blooms can be reduced

      • Reduce fertilizer use
      • Improve wastewater treatment
      • Protect shoreline vegetation
      • Control nutrient runoff

      One-sentence exam summary

      Algal blooms are rapid increases in algae caused by excess nutrients, often leading to low oxygen and ecosystem damage.


      中文 — algal blooms(藻华 / 藻类暴发) 详细解释

      1) 什么是藻华(核心概念)

      藻华(algal blooms)是指藻类在水体中迅速、大量繁殖的现象,常使水体呈现绿色、蓝绿色或褐色

      藻华 = 藻类数量突然暴增


      2) 藻华产生的原因

      藻华通常由以下因素共同引起:

      • 养分过多(氮、磷)
      • 水温升高
      • 阳光充足
      • 水流缓慢或静止

      这种水体富营养化过程叫 水体富营养化


      3) 藻华的类型

      ① 无毒藻华

      • 藻类大量繁殖
      • 会导致水体缺氧

      ② 有害藻华

      • 常由蓝藻(蓝绿藻)引起
      • 释放毒素
      • 对鱼类、人类和动物有危险

      4) 藻华为什么有害(考试重点)

      • 遮挡阳光,水草死亡
      • 藻类分解消耗氧气
      • 造成鱼类死亡
      • 破坏生态系统平衡

      5) 对人类的影响

      • 饮用水污染
      • 湖泊和海滩关闭
      • 人和动物中毒

      6) 池塘中的藻华示例(常考)

      1. 肥料进入池塘
      2. 藻类迅速繁殖
      3. 水中氧气下降
      4. 鱼类死亡
      5. 生物多样性下降

      一句话考试版总结

      藻华是由养分过多引起的藻类快速繁殖,会导致水体缺氧和生态破坏。

      如果你需要,我可以把 algae / algal / algal bloom / eutrophication 做成 Science 10 中英对照概念图或互动闪卡,直接用于考试复习。

    14. algal

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      English — algal (thorough explanation)

      1) What algal means (core idea)

      Algal is an adjective that means related to or caused by algae.

      Algal = having to do with algae

      It is used to describe things like algal cells, algal growth, or algal blooms.


      2) What algae are (quick reminder)

      Algae are mostly aquatic, photosynthetic organisms. They can be:

      • Microscopic (single-celled)
      • Macroscopic (large seaweeds)

      Algae are not true plants, but many behave like plants because they:

      • Contain chlorophyll
      • Perform photosynthesis

      3) Common uses of “algal” in science (Science 10 focus)

      Algal growth

      • Increase in algae due to sunlight and nutrients

      Algal bloom

      • A rapid increase in algae population
      • Often turns water green
      • Can reduce oxygen in water and harm animals

      Algal cells

      • Individual algae cells seen under a microscope

      Algal mats

      • Thick layers of algae covering water surfaces or rocks

      4) Algal blooms — important ecological example

      Algal blooms often occur when:

      • Nutrients (nitrogen, phosphorus) are high
      • Water is warm
      • Sunlight is abundant

      Effects:

      • Block sunlight for other plants
      • Reduce dissolved oxygen
      • May produce toxins (in some species)

      📌 This process is linked to eutrophication.


      5) Why algal organisms are important

      Algal organisms:

      • Are primary producers
      • Form the base of many aquatic food chains
      • Produce a large amount of Earth’s oxygen
      • Support ecosystems like ponds, lakes, and oceans

      6) Grammar note

      • Algae → noun (plural)
      • Alga → noun (singular)
      • Algal → adjective

      📌 Example:

      Algal growth increases in warm, nutrient-rich water.


      中文 — algal(藻类的 / 与藻类有关的) 详细解释

      1) “algal”的基本含义

      Algal 是一个形容词,意思是 “与藻类有关的”

      Algal = 藻类的


      2) 藻类是什么(简单回顾)

      藻类是大多生活在水中的能进行光合作用的生物,可以是:

      • 单细胞(显微藻类)
      • 多细胞(大型海藻)

      3) “algal”的常见科学用法(考试常见)

      • 藻类生长(algal growth)
      • 藻华 / 藻类暴发(algal bloom)
      • 藻类细胞(algal cells)
      • 藻毯(algal mats)

      4) 藻华(重点)

      藻华通常发生在:

      • 养分多
      • 温度高
      • 光照强

      影响:

      • 水体缺氧
      • 鱼类死亡
      • 水质恶化

      5) 藻类的重要性

      • 是水生生态系统的生产者
      • 是食物链的基础
      • 产生大量氧气

      6) 词性总结(考试加分点)

      • alga:单数,藻
      • algae:复数,藻类
      • algal:形容词,藻类的

      一句话考试版总结

      Algal means related to algae, especially in aquatic ecosystems. Algal 指与藻类有关的事物。

      如果你需要,我可以把 alga / algae / algal 做成 Science 10 中英对照速记卡或易错点练习题,非常适合考试复习。

    15. amoebas

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      English — amoebas (thorough explanation)

      1) What amoebas are (core idea)

      Amoebas are microscopic, single-celled protists that usually live in water or moist environments. They are famous for their constantly changing shape.

      Amoeba = one cell that changes shape to move and eat


      2) Where amoebas live

      Amoebas are commonly found in:

      • Ponds and lakes
      • Wet soil
      • Slow-moving freshwater
      • Inside other organisms (some species)

      Most amoebas are free-living and harmless, but a few can cause disease.


      3) How amoebas move — pseudopodia

      Amoebas move using pseudopodia (“false feet”).

      • The cell membrane pushes outward
      • Cytoplasm flows into the extension
      • The cell slowly pulls itself forward

      This movement is called amoeboid movement.


      4) How amoebas eat (ingestion by phagocytosis)

      Amoebas are heterotrophic (they must eat food).

      Steps:

      1. Amoeba surrounds food with pseudopodia
      2. Food is engulfed
      3. A food vacuole forms
      4. Enzymes digest the food
      5. Nutrients enter the cytoplasm
      6. Waste is released

      This feeding method is called phagocytosis.


      5) Important cell structures (Science 10 focus)

      | Structure | Function | | ------------------- | -------------------------- | | Pseudopodia | Movement and feeding | | Cell membrane | Controls entry and exit | | Cytoplasm | Site of chemical reactions | | Nucleus | Controls cell activities | | Food vacuole | Digestion | | Contractile vacuole | Pumps out excess water |


      6) Water balance (very important)

      Because amoebas live in freshwater:

      • Water constantly enters the cell by osmosis
      • The contractile vacuole removes extra water
      • This prevents the cell from bursting

      7) How amoebas reproduce

      • Reproduce by binary fission
      • One cell divides into two identical cells
      • This is asexual reproduction

      8) Why amoebas are important

      • Feed on bacteria → help control populations
      • Part of aquatic food webs
      • Used in biology to study cell movement and feeding
      • Show how one cell can perform all life functions

      One-sentence exam summary

      Amoebas are single-celled protists that move and eat using pseudopodia.


      中文 — amoebas(变形虫) 详细解释

      1) 变形虫是什么(核心概念)

      变形虫(amoebas)是生活在水或潮湿环境中的单细胞原生生物。 它们最显著的特点是形状不断变化

      变形虫 = 靠改变形状来运动和进食的单细胞生物


      2) 变形虫的生活环境

      • 池塘
      • 湖泊
      • 潮湿土壤
      • 其他生物体内

      大多数变形虫对人类无害。


      3) 变形虫如何运动 —— 伪足

      变形虫通过伪足运动:

      • 细胞向前伸出伪足
      • 细胞质流入
      • 整个细胞向前移动

      这种方式叫 变形运动


      4) 变形虫如何进食(吞噬作用)

      变形虫是异养生物,进食过程如下:

      1. 伪足包围食物
      2. 食物被吞入
      3. 形成食物泡
      4. 消化酶分解食物
      5. 营养进入细胞质
      6. 废物排出

      这种方式称为 吞噬作用(phagocytosis)


      5) 重要结构(考试重点)

      | 结构 | 功能 | | --- | ------- | | 伪足 | 运动、捕食 | | 细胞膜 | 控制物质进出 | | 细胞质 | 生命活动场所 | | 细胞核 | 控制细胞 | | 食物泡 | 消化 | | 伸缩泡 | 排水、防止胀破 |


      6) 一句话考试版总结

      变形虫是通过伪足运动和进食的单细胞原生生物。

      如果你需要,我可以把 Amoeba / Paramecium / Euglena 做成 Science 10 中英对照比较表或互动闪卡,非常适合系统复习与课堂讲解。

    16. Euglena

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      English — Euglena (thorough explanation)

      1) What Euglena is (core idea)

      Euglena is a microscopic, single-celled protist that lives mainly in freshwater. It is special because it can act like both a plant and an animal.

      Euglena = a mix of plant-like and animal-like traits


      2) Why Euglena is unique (exam favorite)

      Euglena is often used to show that living things do not always fit neatly into one group.

      • Plant-like:

      • Has chloroplasts

      • Can do photosynthesis
      • Animal-like:

      • Can move

      • Can feed on organic matter when light is unavailable

      This flexible nutrition is called mixotrophic.


      3) How Euglena moves

      Euglena moves using a flagellum (a long, whip-like structure).

      • The flagellum spins or whips
      • Pulls the cell through water
      • Allows Euglena to move toward light

      4) How Euglena gets energy (two ways)

      A) Photosynthesis (like plants)

      • Uses chloroplasts
      • Needs light, carbon dioxide, and water
      • Produces glucose and oxygen

      B) Heterotrophic feeding (like animals)

      • When light is limited
      • Absorbs nutrients from the environment

      5) Important cell structures (Science 10 focus)

      | Structure | Function | | ------------------- | -------------------------------------- | | Flagellum | Movement | | Eyespot (stigma) | Detects light | | Chloroplasts | Photosynthesis | | Nucleus | Controls cell activities | | Pellicle | Flexible outer layer (not a cell wall) | | Contractile vacuole | Removes excess water |


      6) Eyespot and light detection (very important)

      Euglena has a red eyespot that:

      • Detects the direction of light
      • Helps Euglena swim toward light
      • Increases photosynthesis efficiency

      This behavior is called phototaxis.


      7) Where Euglena lives

      • Ponds
      • Lakes
      • Slow-moving freshwater
      • Nutrient-rich water

      Euglena often thrives in water with plenty of light.


      8) How Euglena reproduces

      • Reproduces by binary fission
      • One cell divides into two identical cells

      One-sentence exam summary

      Euglena is a single-celled protist that can photosynthesize like a plant and move like an animal using a flagellum.


      中文 — Euglena(眼虫) 详细解释

      1) 眼虫是什么(核心概念)

      眼虫(Euglena)是一种生活在淡水中的单细胞原生生物。 它的最大特点是:既像植物,又像动物

      眼虫 = 兼具植物和动物特征的原生生物


      2) 眼虫为什么特殊(考试重点)

      • 像植物

      • 有叶绿体

      • 能进行光合作用
      • 像动物

      • 能主动运动

      • 缺光时可吸收有机物获取能量

      这种双重营养方式称为 混合营养(mixotrophic)


      3) 眼虫如何运动

      • 通过一根鞭毛运动
      • 鞭毛摆动,推动细胞前进

      4) 眼虫如何获取能量

      ① 光合作用(有光时)

      • 利用叶绿体
      • 制造葡萄糖

      ② 异养方式(无光时)

      • 从环境中吸收营养

      5) 重要结构(必考)

      | 结构 | 功能 | | --- | ------- | | 鞭毛 | 运动 | | 眼点 | 感光 | | 叶绿体 | 光合作用 | | 细胞核 | 控制生命活动 | | 表膜 | 保护并保持形状 | | 伸缩泡 | 排出多余水分 |


      6) 眼点的作用(高频考点)

      • 感知光线方向
      • 帮助眼虫向光移动
      • 提高光合作用效率

      这种向光移动的行为叫 趋光性


      一句话考试版总结

      眼虫是一种能进行光合作用、又能主动运动的单细胞原生生物。

      如果你愿意,我可以把 Euglena / Paramecium / Amoeba 做成 Science 10 中英对照对比表或互动闪卡,非常适合系统复习。

    17. Paramecium

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      English — Paramecium (thorough explanation)

      1) What Paramecium is (core idea)

      Paramecium is a microscopic, single-celled protist that lives mainly in freshwater, such as ponds.

      Even though it is only one cell, it can:

      • Move
      • Eat
      • Digest food
      • Remove waste
      • Respond to its environment

      Paramecium = a single cell that does everything a living organism needs to do


      2) Where Paramecium lives

      Paramecium is commonly found in:

      • Ponds
      • Lakes
      • Slow-moving freshwater
      • Water with decaying organic matter

      These environments contain many bacteria, which Paramecium feeds on.


      3) How Paramecium moves — cilia

      Paramecium is covered with tiny hair-like structures called cilia.

      Cilia:

      • Beat in coordinated waves
      • Pull Paramecium through water
      • Help sweep food into the cell mouth

      📌 This makes Paramecium very active compared to many other protists.


      4) How Paramecium eats (ingestion & digestion)

      Paramecium is heterotrophic (cannot make its own food).

      Steps:

      1. Cilia sweep food (bacteria, algae) into the oral groove
      2. Food enters the cell mouth
      3. A food vacuole forms
      4. Enzymes digest the food
      5. Nutrients move into the cytoplasm
      6. Waste exits the cell

      5) Important cell structures (exam focus)

      | Structure | Function | | ----------------------- | -------------------------------------- | | Cilia | Movement and feeding | | Oral groove | Directs food inward | | Food vacuole | Digests food | | Contractile vacuole | Pumps out excess water | | Nucleus (macro & micro) | Controls cell functions & reproduction | | Cell membrane | Protects cell and controls entry/exit |


      6) How Paramecium controls water (very important)

      Because it lives in freshwater:

      • Water constantly enters the cell by osmosis
      • The contractile vacuole collects excess water
      • It periodically squeezes the water out

      👉 This prevents the cell from bursting.


      7) How Paramecium reproduces

      Paramecium reproduces mainly by binary fission:

      • One cell divides into two identical cells

      Sometimes, Paramecium can exchange genetic material through conjugation, which increases genetic diversity.


      8) Why Paramecium is important

      • Eats bacteria → helps control bacterial populations
      • Is food for larger microscopic organisms
      • A classic model organism in biology classes
      • Helps scientists study cell functions

      One-sentence exam summary

      Paramecium is a microscopic, single-celled protist that moves using cilia and feeds on bacteria in freshwater environments.


      中文 — Paramecium(草履虫) 详细解释

      1) 草履虫是什么(核心概念)

      草履虫(Paramecium)是一种生活在淡水中的单细胞原生生物

      虽然只有一个细胞,但它可以:

      • 运动
      • 进食
      • 消化
      • 排出废物
      • 对环境作出反应

      2) 草履虫的生活环境

      • 池塘
      • 湖泊
      • 缓慢流动的淡水
      • 含有腐烂有机物的水体

      3) 草履虫如何运动 —— 纤毛

      草履虫表面布满纤毛

      • 纤毛协调摆动
      • 推动草履虫前进
      • 同时把食物扫入口沟

      4) 草履虫如何进食

      草履虫是异养生物,进食过程如下:

      1. 纤毛将细菌扫入口沟
      2. 食物进入细胞口
      3. 形成食物泡
      4. 消化酶分解食物
      5. 营养被吸收
      6. 废物排出体外

      5) 重要结构(考试重点)

      | 结构 | 功能 | | --- | ------ | | 纤毛 | 运动和进食 | | 口沟 | 引导食物 | | 食物泡 | 消化 | | 伸缩泡 | 排出多余水分 | | 细胞核 | 控制生命活动 | | 细胞膜 | 保护细胞 |


      6) 伸缩泡的作用(必考)

      由于生活在淡水中:

      • 水不断进入细胞
      • 伸缩泡负责把多余的水排出
      • 防止细胞涨破

      7) 繁殖方式

      • 二分裂:一个变成两个
      • 接合生殖:交换遗传物质(不增加数量,但增加多样性)

      一句话考试版总结

      草履虫是利用纤毛运动、以细菌为食的单细胞原生生物。

      如果你愿意,我可以把 Paramecium / Amoeba / Euglena 做成 Science 10 中英对照比较表或互动闪卡,非常适合你现在的生物复习节奏。

    18. Protists

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      English — Protists (thorough explanation)

      1) What protists are (core idea)

      Protists are a diverse group of mostly microscopic, eukaryotic organisms that do not fit into the plant, animal, or fungi kingdoms.

      Protists = mostly single-celled eukaryotes that are not plants, animals, or fungi

      Key point for Science 10:

      • They have a nucleus and membrane-bound organelles
      • Most live in water or moist environments

      2) Why protists are grouped together

      Protists are grouped not because they are similar, but because they are eukaryotes that don’t belong elsewhere.

      They are extremely diverse in:

      • Shape
      • Size
      • Movement
      • Nutrition

      3) Main types of protists (exam-friendly categories)

      A) Animal-like protists (Protozoa)

      • Heterotrophic (must ingest food)
      • Often move to find food

      Examples:

      • Amoeba → moves using pseudopods (“false feet”)
      • Paramecium → moves using cilia

      📌 These protists ingest other organisms.


      B) Plant-like protists (Algae)

      • Autotrophic (do photosynthesis)
      • Contain chlorophyll
      • Important producers in aquatic ecosystems

      Examples:

      • Green algae
      • Diatoms
      • Kelp (large multicellular algae)

      📌 Algae produce oxygen and form the base of many food chains.


      C) Fungus-like protists

      • Heterotrophic
      • Often decomposers
      • Absorb nutrients from dead or decaying matter

      Examples:

      • Slime molds
      • Water molds

      4) Where protists are found

      Protists usually live in:

      • Ponds and lakes
      • Oceans
      • Wet soil
      • Inside other organisms

      Anywhere there is water, protists can usually thrive.


      5) Why protists are important

      Protists play major roles in ecosystems:

      • Producers (algae) → photosynthesis
      • Consumers → feed on bacteria and other protists
      • Decomposers → recycle nutrients
      • Part of aquatic food webs
      • Some cause diseases (e.g., malaria)

      Even though they are microscopic, they have huge ecological impact.


      6) Protists vs bacteria (common confusion)

      | Feature | Protists | Bacteria | | ---------- | ---------- | ----------- | | Cell type | Eukaryotic | Prokaryotic | | Nucleus | ✅ Yes | ❌ No | | Size | Larger | Smaller | | Organelles | Present | Absent |


      One-sentence exam summary

      Protists are mostly microscopic eukaryotic organisms that live in water and do not belong to the plant, animal, or fungi kingdoms.


      中文 — Protists(原生生物) 详细解释

      1) 什么是原生生物(核心概念)

      原生生物(Protists)是一类大多为单细胞的真核生物,它们既不是植物、也不是动物或真菌

      原生生物 = 不属于植物、动物、真菌的真核生物

      关键点:

      • 细胞核
      • 多生活在水或潮湿环境

      2) 为什么要把它们归为一类

      原生生物被归在一起,并不是因为它们相似,而是因为:

      • 它们是真核生物
      • 又不适合归入其他界

      3) 原生生物的三大类型(考试常考)

      A) 类动物原生生物(原生动物)

      • 异养(需要摄食)
      • 通常可以运动

      例子:

      • 变形虫:用伪足移动和捕食
      • 草履虫:用纤毛运动

      B) 类植物原生生物(藻类)

      • 自养
      • 进行光合作用
      • 是水生生态系统的重要生产者

      C) 类真菌原生生物

      • 异养
      • 多为分解者
      • 从腐烂有机物中吸收养分

      4) 原生生物生活在哪里

      • 池塘
      • 湖泊
      • 海洋
      • 潮湿土壤
      • 其他生物体内

      只要有水,就可能发现原生生物。


      5) 原生生物的重要性

      • 藻类提供氧气
      • 是食物链的基础
      • 帮助分解和循环养分
      • 有些会引起疾病

      一句话考试版总结

      原生生物是主要生活在水中的单细胞真核生物。

      如果你需要,我可以把 Protists / Bacteria / Fungi 做成 Science 10 中英对照对比表或互动闪卡,直接用于考试复习或课堂教学。

    19. multitude

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      English — multitude (thorough explanation)

      1) What “multitude” means (core idea)

      Multitude means a very large number of people or thingsmany more than just “several” or “some.”

      Multitude = a great many / a large quantity

      It emphasizes quantity and abundance.


      2) How “multitude” is used

      • It is often used with “of”

      • a multitude of stars

      • a multitude of species
      • It can describe people, objects, or living organisms.

      3) “Multitude” in science (Science 10 context)

      In biology and ecology, multitude is commonly used to describe:

      • A multitude of species in a biodiverse ecosystem
      • A multitude of organisms in a pond or soil
      • A multitude of cells in living tissue

      📌 Example:

      A healthy pond contains a multitude of microscopic organisms.


      4) Multitude vs similar words

      | Word | Meaning | Strength | | ------------- | ----------------- | ---------- | | few | very small number | low | | several | more than a few | low–medium | | many | large number | medium | | multitude | very large number | high | | countless | too many to count | very high |


      5) Grammar note

      • Multitude is a noun
      • It can be treated as singular or plural, depending on meaning:

      • A multitude of species is found here. (focus on the group)

      • A multitude of people were waiting. (focus on individuals)

      中文 — multitude(大量;众多) 详细解释

      1) “multitude”的基本含义

      Multitude 表示 数量非常多的事物或人,强调“多”和“丰富”。

      Multitude = 大量的 / 众多的


      2) 常见用法

      • 常与 of 连用:

      • a multitude of 动植物

      • a multitude of 问题

      3) 科学语境中的用法(考试常见)

      在生物和生态学中,multitude常用来描述:

      • 一个生态系统中众多的物种
      • 池塘中大量的微生物
      • 生物体内数量巨大的细胞

      📌 例句:

      一个健康的生态系统中存在着众多不同的物种。


      4) 近义词对比

      | 英文 | 中文 | 数量感觉 | | ------------- | -- | ------- | | few | 很少 | 少 | | several | 几个 | 较少 | | many | 许多 | 多 | | multitude | 众多 | 非常多 |


      一句话考试版总结

      Multitude means a very large number of people or things. Multitude 表示数量极多的事物或人。

      如果你愿意,我可以把 multitude / many / several / few 做成 Science 10 中英对照速记卡或练习题,帮助学生准确选词。

    20. thrive

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      English — thrive (thorough explanation)

      1) What “thrive” means (core idea)

      Thrive means to grow well, stay healthy, and do better than just surviving. When something thrives, it is strong, active, and successful in its environment.

      Thrive = grow and do very well


      2) Thrive vs survive (important contrast)

      These two words are often compared:

      • Survive → stay alive, but possibly weak or stressed
      • Thrive → grow, reproduce, and function at a high level

      📌 Example:

      • A plant that barely stays alive in poor soil survives
      • A plant that grows tall, produces flowers, and spreads thrives

      3) How “thrive” is used in biology (Science 10 focus)

      In biology and ecology, thrive means an organism has:

      • Enough food
      • Suitable temperature
      • Enough water
      • Proper space
      • Few limiting factors

      📌 Example sentence:

      Fish thrive in clean, oxygen-rich water.


      4) Thrive in ecosystems

      An organism thrives when:

      • It is well adapted to its habitat
      • Abiotic factors (light, water, temperature) are ideal
      • Biotic factors (food availability, low competition) are favorable

      When many organisms thrive, the ecosystem is healthy.


      5) Everyday uses of “thrive”

      “Thrive” is not only for biology:

      • People can thrive in supportive environments
      • Businesses can thrive when conditions are good
      • Ideas can thrive with encouragement

      中文 — thrive(茁壮成长 / 蓬勃发展) 详细解释

      1) “thrive”的基本含义

      Thrive 指的是 生长良好、状态健康、不只是勉强活着

      Thrive = 茁壮成长、发展得很好


      2) thrive 与 survive 的区别(重点)

      • Survive(生存):只是活着,可能状态不好
      • Thrive(茁壮成长):生长旺盛、繁殖良好、状态优秀

      📌 例子:

      • 条件差的植物只是“活着” → survive
      • 条件好的植物长得高、开花结果 → thrive

      3) 生物学中的 thrive(考试常见)

      在生态学中,生物要“茁壮成长”,需要:

      • 足够的食物
      • 合适的温度
      • 充足的水分
      • 合适的空间
      • 较少限制因素

      📌 例句:

      青蛙在湿润的池塘环境中茁壮成长。


      4) 生态系统中的 thrive

      当生物适应环境、资源充足时:

      • 个体会茁壮成长
      • 种群数量稳定或增加
      • 生态系统保持健康和平衡

      一句话考试版总结

      To thrive means to grow well and be healthy, not just survive. Thrive 指的是在良好条件下茁壮成长,而不仅仅是生存。

      如果你需要,我可以把 thrive / survive / adapt 做成 Science 10 中英对照速记卡或互动闪卡,非常适合考试复习。

    21. microscopic

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      English — microscopic (thorough explanation)

      1) What “microscopic” means (core idea)

      Microscopic describes something that is so small it cannot be seen with the naked eye and must be viewed using a microscope.

      Microscopic = too small to see without a microscope


      2) Microscopic vs macroscopic (important contrast)

      • Microscopic → visible only with a microscope
      • Macroscopic → visible with the naked eye

      📌 Examples:

      • A cell → microscopic
      • A leaf → macroscopic
      • Bacteria → microscopic
      • Ant → macroscopic

      3) Common microscopic things (Science 10 focus)

      Many important living things are microscopic:

      Living microscopic organisms

      • Bacteria
      • Protozoa (e.g., amoeba, paramecium)
      • Some algae
      • Yeast

      Microscopic structures

      • Cells
      • Nuclei
      • Chloroplasts
      • Red blood cells

      4) Why microscopic life is important

      Even though microscopic organisms are tiny, they are extremely important:

      • Help decompose dead material
      • Recycle nutrients in ecosystems
      • Some cause disease
      • Some are useful (e.g., gut bacteria, yeast in bread)
      • Form the base of some food chains (e.g., plankton)

      5) Microscopic life in ecosystems (example: ponds)

      In pond ecosystems:

      • Microscopic algae are producers
      • Microscopic animals are primary consumers
      • They support larger organisms like insects and fish

      Without microscopic life, ecosystems would collapse.


      6) How we study microscopic things

      Scientists use:

      • Light microscopes (for cells and small organisms)
      • Electron microscopes (for viruses and cell details)

      Microscopes magnify objects many times to make them visible.


      中文 — microscopic(微观的 / 显微的) 详细解释

      1) “microscopic”的基本含义

      Microscopic(微观的、显微的)指的是小到肉眼无法看见,必须借助显微镜才能观察的事物。

      Microscopic = 需要显微镜才能看到的


      2) microscopic 与 macroscopic 的区别(重点)

      • Microscopic:只能用显微镜看到
      • Macroscopic:用肉眼就能看到

      📌 例子:

      • 细胞 → 微观
      • 树叶 → 宏观
      • 细菌 → 微观
      • 昆虫 → 宏观

      3) 常见的微观事物

      微生物

      • 细菌
      • 原生动物(如变形虫)
      • 一些藻类
      • 酵母

      微观结构

      • 细胞
      • 细胞核
      • 叶绿体
      • 红细胞

      4) 微观生物的重要性

      虽然它们很小,但作用巨大:

      • 分解死亡生物
      • 循环养分
      • 有些会引起疾病
      • 有些对人类有益
      • 支撑生态系统的食物链

      5) 生态系统中的微观世界(池塘例子)

      • 微观藻类是生产者
      • 微观动物是初级消费者
      • 为更大的生物提供能量来源

      一句话考试版总结

      Microscopic objects are too small to be seen without a microscope. 微观事物需要借助显微镜才能观察。

      如果你愿意,我可以把 microscopic / macroscopic / microscope 做成 Science 10 中英对照速记卡或互动闪卡,方便你系统复习。

    22. coniferous

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      English — coniferous (thorough explanation)

      1) What “coniferous” means (core idea)

      Coniferous describes trees and plants that produce cones and usually have needle-like or scale-like leaves. Most coniferous trees are evergreen, meaning they stay green all year.

      Coniferous = cone-bearing, usually evergreen trees


      2) Key characteristics of coniferous trees

      • Leaves: narrow needles or scales
      • Seeds: produced in cones (not flowers)
      • Color: usually green year-round
      • Shape: often tall with a cone-like shape (helps shed snow)

      3) Why needle leaves are an advantage

      Needle-shaped leaves help coniferous trees survive harsh environments:

      • Less surface area → reduces water loss
      • Waxy coating → protects from cold and drying winds
      • Flexible needles → snow slides off easily

      These features make coniferous trees well adapted to cold or dry climates.


      4) Where coniferous forests are found

      • Cold and cool regions
      • Mountainous areas
      • Northern regions (taiga / boreal forest)

      Large coniferous forests exist in Canada, Alaska, Scandinavia, and Russia.


      5) Examples of coniferous trees

      • Pine
      • Spruce
      • Fir
      • Cedar
      • Hemlock

      6) Coniferous vs deciduous (quick comparison)

      | Feature | Coniferous | Deciduous | | --------- | ------------------- | ------------------ | | Leaves | Needles or scales | Broad, flat | | Leaf loss | Usually keep leaves | Lose leaves yearly | | Seeds | Cones | Flowers / fruits | | Climate | Cold / dry | Temperate |


      7) Importance of coniferous forests

      Coniferous forests:

      • Provide habitat for wildlife
      • Store carbon and help regulate climate
      • Supply wood, paper, and lumber
      • Protect soil from erosion

      中文 — coniferous(针叶林的 / 针叶植物) 详细解释

      1) “coniferous”的基本含义

      Coniferous(针叶植物的)指的是结球果的植物,通常具有针状或鳞片状叶子,而且大多是常绿植物

      Coniferous = 结松果的常绿植物


      2) 针叶树的主要特征

      • 叶子:针状或鳞片状
      • 种子:生长在球果
      • 颜色:全年保持绿色
      • 树形:常呈锥形,利于积雪滑落

      3) 针状叶子的生存优势

      针叶结构有助于在恶劣环境中生存:

      • 表面积小,减少水分流失
      • 表面有蜡质层,防寒防风
      • 针叶柔韧,不易压断积雪

      4) 针叶林分布地区

      • 寒冷或凉爽地区
      • 高山地区
      • 北方地区(泰加林 / 北方针叶林)

      加拿大大部分森林都是针叶林。


      5) 常见针叶树

      • 松树
      • 云杉
      • 冷杉
      • 雪松
      • 铁杉

      6) 针叶林 vs 落叶林(对比)

      | 特点 | 针叶林 | 落叶林 | | ---- | ------- | ---- | | 叶子 | 针状 | 宽叶 | | 是否落叶 | 常绿 | 每年落叶 | | 繁殖 | 球果 | 花和果实 | | 气候 | 寒冷 / 干燥 | 温带 |


      一句话考试版总结

      Coniferous plants produce cones and usually keep their needle-like leaves year-round. 针叶植物通过结球果并保持针状叶来适应寒冷环境。

      如果你需要,我可以把 coniferous vs deciduous 做成 Science 10 中英对照速记卡 / 对比图表 / HTML 互动闪卡,非常适合考试复习。

    23. ponds

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      English — ponds (thorough explanation)

      1) What “ponds” are (core idea)

      Ponds are small, shallow bodies of freshwater. They are usually shallower than lakes, so sunlight can reach the bottom, allowing plants to grow throughout much of the pond.

      Pond = small, shallow freshwater ecosystem


      2) Key characteristics of ponds

      • Freshwater (not salty)
      • Shallow depth → light reaches the bottom
      • Often warmer than lakes
      • Can be natural or human-made
      • Support rich biodiversity

      Because light reaches the bottom, ponds often have many plants.


      3) Living things found in ponds

      Ponds support many forms of life:

      Plants

      • Algae
      • Duckweed
      • Water lilies
      • Reeds and cattails

      Animals

      • Frogs and tadpoles
      • Fish (small species)
      • Insects (dragonflies, water beetles)
      • Snails
      • Birds (ducks, herons)

      4) Pond food chain (Science 10 focus)

      A simple pond food chain:

      • Producers → algae, aquatic plants
      • Primary consumers → insects, snails, tadpoles
      • Secondary consumers → small fish, frogs
      • Top predators → larger fish, birds

      Energy flows from the Sun → plants → animals.


      5) Abiotic (non-living) factors in ponds

      Important non-living factors include:

      • Sunlight
      • Water temperature
      • Dissolved oxygen
      • Nutrients
      • Mud or sediment at the bottom

      Changes in these factors affect pond life.


      6) Seasonal changes in ponds

      Ponds change with the seasons:

      • Spring: increased plant growth, breeding season
      • Summer: warm water, high biological activity
      • Autumn: dying plants add nutrients to the bottom
      • Winter: surface may freeze, but life continues below

      Shallow ponds may freeze more easily than lakes.


      7) Why ponds are important

      Ponds:

      • Provide habitat for many species
      • Support breeding of amphibians
      • Help filter water naturally
      • Increase local biodiversity

      Even small ponds play a big role in ecosystems.


      中文 — ponds(池塘) 详细解释

      1) “ponds”的基本含义

      池塘(ponds)较小、较浅的淡水水体。 由于水浅,阳光可以照到水底,因此植物可以在池塘各处生长。

      池塘 = 小型、浅水的淡水生态系统


      2) 池塘的主要特征

      • 淡水
      • 水浅
      • 水温通常比湖泊高
      • 可以是天然人工
      • 生物种类丰富

      3) 池塘中的生物

      植物

      • 藻类
      • 浮萍
      • 睡莲
      • 芦苇

      动物

      • 青蛙和蝌蚪
      • 小型鱼类
      • 昆虫(蜻蜓幼虫)
      • 蜗牛
      • 鸟类(鸭子、苍鹭)

      4) 池塘中的食物链(考试重点)

      简单的池塘食物链:

      • 生产者:藻类、水生植物
      • 初级消费者:昆虫、蜗牛、蝌蚪
      • 次级消费者:小鱼、青蛙
      • 顶级捕食者:大鱼、鸟类

      能量来源于太阳。


      5) 池塘中的非生物因素

      • 阳光
      • 水温
      • 水中溶氧
      • 养分
      • 底部泥沙

      这些因素会影响池塘生态平衡。


      6) 池塘的季节变化

      • 春季:生物繁殖,植物生长旺盛
      • 夏季:水温高,生命活动活跃
      • 秋季:植物死亡,营养回到水中
      • 冬季:表面结冰,水下生物仍可存活

      一句话考试版总结

      Ponds are small, shallow freshwater ecosystems that support a wide variety of plants and animals. 池塘是浅水淡水生态系统,支持多样的动植物生存。

      如果你需要,我可以把 ponds / lakes / wetlands 做成 Science 10 对比表或互动闪卡,方便系统复习。

    24. deciduous

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      English — deciduous (thorough explanation)

      1) What “deciduous” means (core idea)

      Deciduous describes plants (especially trees) that lose their leaves once every year, usually in autumn (fall).

      Deciduous = sheds leaves seasonally

      After losing their leaves, deciduous plants:

      • Remain bare during winter
      • Grow new leaves in spring

      2) Why deciduous trees lose their leaves

      Leaf loss is a survival strategy, not a weakness.

      Main reasons:

      • Cold protection: leaves are easily damaged by freezing
      • Water conservation: frozen ground makes water hard to absorb
      • Energy saving: maintaining leaves in winter costs energy

      By dropping leaves, the tree reduces water loss and damage.


      3) What happens to the leaves (color change)

      Before leaves fall:

      • Chlorophyll (green pigment) breaks down
      • Other pigments become visible:

      • Yellow / orange (carotenoids)

      • Red / purple (anthocyanins)

      This causes the autumn colors seen in deciduous forests.


      4) Examples of deciduous trees

      Common deciduous trees include:

      • Maple
      • Oak
      • Birch
      • Elm
      • Beech

      Many trees in temperate climates are deciduous.


      5) Deciduous vs evergreen (key comparison)

      | Feature | Deciduous | Evergreen | | ----------------- | ------------- | ------------------------- | | Leaves | Broad, thin | Needle-like or thick | | Leaf loss | Once a year | Gradual / not all at once | | Winter appearance | Bare branches | Green year-round | | Climate | Temperate | Cold or dry regions |


      6) Where deciduous plants are commonly found

      • Temperate regions with four seasons
      • Areas with cold winters and warm summers
      • Common in eastern North America, Europe, East Asia

      7) “Deciduous” is also used beyond trees

      The word deciduous means “falling off” in biology:

      • Deciduous teeth = baby teeth that fall out
      • Deciduous antlers = antlers shed yearly (e.g., deer)

      中文 — deciduous(落叶的 / 落叶性) 详细解释

      1) “deciduous”的基本含义

      Deciduous(落叶性的)指的是每年在特定季节(通常是秋天)会落叶的植物,尤其是树木。

      Deciduous = 每年定期落叶

      冬天:

      • 树枝光秃 春天:
      • 重新长出新叶

      2) 为什么落叶树要落叶

      落叶是一种适应环境的生存策略

      主要原因包括:

      • 防寒:叶子容易被霜冻破坏
      • 节水:冬季土壤结冰,难以吸水
      • 节省能量:维持叶片需要消耗能量

      3) 秋天树叶为什么会变色

      在秋天:

      • 叶绿素分解
      • 其他色素显现:

      • 黄色、橙色(类胡萝卜素)

      • 红色、紫色(花青素)

      这就形成了秋季彩叶景观


      4) 常见的落叶树

      • 枫树
      • 橡树
      • 桦树
      • 榆树
      • 山毛榉

      这些树在温带地区非常常见。


      5) 落叶树 vs 常绿树(重点对比)

      | 特点 | 落叶树 | 常绿树 | | ---- | ---- | ------- | | 叶子 | 宽而薄 | 针状或厚 | | 是否落叶 | 每年一次 | 不同时全部脱落 | | 冬天外观 | 光秃 | 四季常绿 | | 适应环境 | 四季分明 | 寒冷或干燥 |


      6) 地理分布

      • 四季分明的温带地区
      • 冬冷夏暖
      • 北美东部、欧洲、东亚常见

      7) 拓展用法

      Deciduous 在生物学中也可表示“会脱落的”:

      • 乳牙(deciduous teeth)
      • 鹿角(每年脱落)

      一句话考试版总结

      Deciduous plants lose their leaves once each year to survive cold or dry seasons. 落叶植物通过季节性落叶来适应寒冷或干燥环境。

      如果你愿意,我可以把 deciduous vs evergreen 做成 Science 10 中英对照速记卡 / 对比表 / HTML 互动闪卡,方便你系统复习。

    25. limbs

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      English — limbs (thorough explanation)

      1) What “limbs” means (core idea)

      Limbs are movable body parts that extend from the main body of an animal. They are mainly used for movement, support, and interaction with the environment.

      In humans, the limbs are:

      • Arms (upper limbs)
      • Legs (lower limbs)

      Limbs = body extensions used for movement and function


      2) Main functions of limbs

      Limbs can have different roles depending on the organism:

      • Movement: walking, running, swimming, flying
      • Support: holding up body weight
      • Manipulation: grasping, holding, using tools (hands)
      • Feeding: catching or handling food
      • Defense: claws, kicks, strikes

      3) Types of limbs (with examples)

      1) Upper limbs (forelimbs)

      • Humans: arms (hands, fingers)
      • Animals: front legs, wings (birds), flippers (whales)

      2) Lower limbs (hindlimbs)

      • Humans: legs (feet, toes)
      • Animals: back legs (frogs, horses)

      3) Modified limbs Limbs can evolve to serve special purposes:

      • Wings → flying (birds, bats)
      • Flippers → swimming (seals, dolphins)
      • Claws → catching prey
      • Hooves → fast running

      4) Limbs in vertebrates (Science 10 focus)

      Most vertebrates share a similar limb bone structure, even if the limbs look different.

      Common bones include:

      • One upper bone (e.g., humerus)
      • Two lower bones (e.g., radius & ulna)
      • Wrist/ankle bones
      • Fingers or toes

      This similarity shows common ancestry and is evidence of evolution.


      5) Limbs vs appendages (quick clarification)

      • Limbs: arms, legs, wings, flippers (main movement parts)
      • Appendages: a broader term that can include antennae, tails, etc.

      All limbs are appendages, but not all appendages are limbs.


      中文 — limbs(四肢 / 肢体) 详细解释

      1) “limbs”的基本含义

      Limbs(肢体、四肢)是指从动物身体主干伸出的、可以活动的部分

      在人类中:

      • 上肢:手臂
      • 下肢:腿

      Limbs = 用来运动和操作的身体部分


      2) 肢体的主要功能

      不同动物的肢体功能不同,包括:

      • 运动:行走、奔跑、游泳、飞行
      • 支撑:支撑身体重量
      • 操作:抓握、使用工具
      • 进食:抓取食物
      • 防御:攻击或保护自己

      3) 肢体的类型

      1) 前肢(上肢)

      • 人类:手臂
      • 动物:前腿、翅膀、鳍状肢

      2) 后肢(下肢)

      • 人类:腿
      • 动物:后腿

      3) 变态肢体(特殊功能)

      • 翅膀:飞行
      • 鳍肢:游泳
      • :捕食
      • :快速奔跑

      4) 生物学重点(考试常考)

      许多脊椎动物的肢体内部结构相似,即使外形不同。 这说明它们有共同祖先,是进化的证据


      一句话记忆

      Limbs are movable body parts used for movement and interaction. 肢体是用于运动和与环境互动的可活动身体部位。

      如果你需要,我可以把 limbs / joints / muscles / bones 做成 Science 10 中英对照速记卡或互动闪卡,非常适合考试复习。

    26. ingest

      Image

      Image

      Image

      Image

      English — ingest (thorough explanation)

      1) What “ingest” means (core idea)

      Ingest means to take food or another substance into the body, usually through the mouth.

      In biology, it is the first step of nutrition.

      Ingest = take in (eat or swallow)


      2) Ingest vs digest vs absorb (very important distinction)

      These words are often confused, but they mean different steps:

      1. Ingest → taking food into the body
      2. Digest → breaking food down into smaller molecules
      3. Absorb → moving nutrients into the bloodstream or cells

      📌 Example:

      • You ingest an apple
      • Your stomach and intestines digest it
      • Your intestines absorb the nutrients

      3) How ingestion happens in animals

      • Humans & animals: ingest food through the mouth
      • Teeth, tongue, and saliva help prepare food for digestion
      • Food then moves to the stomach and intestines

      4) Ingest in simple organisms

      Some organisms do not have a mouth like humans:

      • Amoeba ingests food by engulfing it

      • This process is called phagocytosis

      • The food is trapped inside a food vacuole

      5) Ingest in food chains (Science 10 focus)

      • Herbivores ingest plants
      • Carnivores ingest animals
      • Omnivores ingest both plants and animals

      Energy flows through ecosystems because organisms ingest other organisms.


      6) “Ingest” in non-biological use

      • Humans can ingest medicine, water, or chemicals
      • In computing, “ingest data” means taking data into a system

      中文 — ingest(摄入 / 吃进) 详细解释

      1) “ingest”的基本意思

      Ingest 指的是 把食物或物质摄入体内,通常是通过口腔

      在生物学中,它是营养过程的第一步

      Ingest = 吃进 / 摄入


      2) ingest、digest、absorb 的区别(重点)

      这三个词代表不同阶段:

      1. Ingest(摄入):把食物吃进体内
      2. Digest(消化):把食物分解成小分子
      3. Absorb(吸收):把营养吸收到血液或细胞中

      📌 例子:

      • 吃苹果 → ingest
      • 胃和肠分解苹果 → digest
      • 营养进入血液 → absorb

      3) 动物如何摄入食物

      • 人类和大多数动物通过嘴巴摄入食物
      • 牙齿和舌头帮助咀嚼
      • 食物进入消化系统继续处理

      4) 单细胞生物中的 ingest

      一些简单生物(如变形虫):

      • 没有真正的嘴
      • 通过包围食物的方式摄入
      • 形成食物泡

      5) 食物链中的 ingest(考试常考)

      • 草食动物摄入植物
      • 肉食动物摄入其他动物
      • 杂食动物两者都摄入

      能量通过“摄入”在生态系统中传递。


      一句话记忆

      Ingest = take food into the body Ingest = 把食物吃进体内

      如果你愿意,我可以把 ingest / digest / absorb 做成 中英对照表或 Science 10 闪卡,非常适合考试快速区分。

    27. photosynthesis

      Image

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      English — Photosynthesis (thorough explanation)

      1) What photosynthesis is (core idea)

      Photosynthesis is the process by which green plants, algae, and some bacteria use light energy to make food (glucose) from carbon dioxide and water.

      In simple terms:

      Photosynthesis = using sunlight to make sugar

      This process is the foundation of almost all life on Earth, because it produces:

      • Food (chemical energy)
      • Oxygen for respiration

      2) The word itself (helpful for exams)

      • Photo = light
      • Synthesis = putting together

      So photosynthesis literally means:

      “Putting things together using light.”


      3) The photosynthesis equation (must-know)

      [ 6CO_2 + 6H_2O + \text{light energy} \rightarrow C_6H_{12}O_6 + 6O_2 ]

      Left side (inputs):

      • Carbon dioxide (from air)
      • Water (from roots)
      • Light energy (from the Sun)

      Right side (outputs):

      • Glucose (food for the plant)
      • Oxygen (released into the air)

      4) Where photosynthesis happens

      Photosynthesis occurs in chloroplasts, which are found mainly in leaf cells.

      Inside a chloroplast:

      • Thylakoids → where light reactions happen
      • Stroma → where sugar is made

      Chlorophyll, the green pigment in chloroplasts, absorbs sunlight.


      5) Two main stages of photosynthesis

      Stage 1: Light-dependent reactions

      Location: Thylakoid membranes Needs light: ✅ Yes

      What happens:

      • Light energy is absorbed by chlorophyll
      • Water is split into:

      • Oxygen (released)

      • Hydrogen (used later)
      • Energy carriers (ATP and NADPH) are produced

      Key idea: 👉 This stage captures energy from sunlight


      Stage 2: Calvin Cycle (light-independent reactions)

      Location: Stroma Needs light directly: ❌ No (but depends on Stage 1)

      What happens:

      • Carbon dioxide is taken from the air
      • Energy from Stage 1 is used
      • Glucose (sugar) is produced

      Key idea: 👉 This stage builds sugar


      6) Why photosynthesis is so important

      Photosynthesis:

      • Provides food for plants (and all food chains)
      • Produces oxygen for animals and humans
      • Removes carbon dioxide from the atmosphere
      • Stores sunlight as chemical energy

      Without photosynthesis:

      ❌ No plants → ❌ no animals → ❌ no humans


      7) Factors that affect photosynthesis (exam favorite)

      • Light intensity (more light → faster rate, up to a limit)
      • Carbon dioxide concentration
      • Temperature (enzymes work best in a certain range)
      • Water availability

      中文 — 光合作用(Photosynthesis) 详细解释

      1) 什么是光合作用(核心概念)

      光合作用是指绿色植物、藻类和某些细菌利用光能,把二氧化碳合成葡萄糖的过程。

      一句话记忆:

      光合作用 = 用阳光制造食物

      光合作用不仅制造食物,还产生氧气,是地球生命的基础。


      2) 光合作用这个词怎么理解

      • Photo(光)
      • Synthesis(合成)

      意思是:

      利用光把物质合成在一起


      3) 光合作用总反应式(必考)

      [ 6CO_2 + 6H_2O + 光能 \rightarrow C_6H_{12}O_6 + 6O_2 ]

      原料(左边):

      • 二氧化碳(来自空气)
      • 水(来自根)
      • 光能(来自太阳)

      产物(右边):

      • 葡萄糖(植物的食物)
      • 氧气(释放到空气中)

      4) 光合作用发生在哪里

      光合作用发生在叶绿体中,主要位于叶片细胞

      叶绿体内部:

      • 类囊体:进行光反应
      • 基质:制造葡萄糖

      叶绿素负责吸收光能,因此植物呈绿色。


      5) 光合作用的两个阶段

      第一阶段:光反应

      位置: 类囊体膜 是否需要光: ✅ 需要

      过程:

      • 叶绿素吸收光能
      • 水被分解
      • 释放氧气
      • 产生能量物质(ATP、NADPH)

      👉 作用:收集并储存光能


      第二阶段:暗反应(卡尔文循环)

      位置: 叶绿体基质 是否直接需要光: ❌ 不需要

      过程:

      • 利用二氧化碳
      • 使用第一阶段提供的能量
      • 合成葡萄糖

      👉 作用:制造糖类


      6) 为什么光合作用如此重要

      光合作用:

      • 为植物制造食物
      • 是所有食物链的起点
      • 产生氧气供人类和动物呼吸
      • 减少空气中的二氧化碳

      没有光合作用:

      ❌ 没有植物 → ❌ 没有动物 → ❌ 没有人类


      7) 影响光合作用速率的因素(常考)

      • 光照强度
      • 二氧化碳浓度
      • 温度
      • 水分供应

      一句话考试版总结

      Photosynthesis uses light energy to convert CO₂ and water into glucose and oxygen. 光合作用利用光能把二氧化碳和水转化为葡萄糖和氧气。

      如果你需要,我可以把这部分整理成 Science 10 考试速记卡 / 中英对照表 / HTML 互动闪卡,直接接进你现在的学习系统。

    28. Image

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      English — “stem” (thorough explanation)

      1) What “stem” means (core idea)

      A stem is the main supporting structure of a plant, usually growing above the ground. It connects the roots to the leaves, flowers, and fruits.

      In simple terms, the stem is the plant’s support pole + transport highway.


      2) Main functions of a stem

      A) Support

      • Holds leaves up toward sunlight
      • Supports flowers and fruits
      • Keeps the plant upright

      B) Transport (vascular function) Inside most stems are transport tissues:

      • Xylem → carries water and minerals from roots to leaves
      • Phloem → carries sugars (food) made in leaves to the rest of the plant

      This allows all parts of the plant to survive and grow.

      C) Storage Some stems store food or water:

      • Potato (a stem tuber) stores starch
      • Cactus stems store water in dry environments

      D) Growth

      • Stems grow longer from the tip (apical meristem)
      • Buds on the stem can develop into branches, leaves, or flowers

      3) Types of stems

      1) Herbaceous stems

      • Soft, green, flexible
      • Example: grasses, sunflowers

      2) Woody stems

      • Hard, thick, brown
      • Example: trees and shrubs
      • Provide long-term strength and height

      3) Modified stems Stems that are adapted for special jobs:

      • Rhizome (horizontal underground stem): ginger
      • Tuber (swollen storage stem): potato
      • Runner / stolon (horizontal above ground): strawberry
      • Bulb (short stem with thick leaves): onion
      • Cladode (photosynthetic stem): cactus

      4) How to tell a stem from a root

      A stem has:

      • Nodes (where leaves or buds grow)
      • Internodes (space between nodes)
      • Buds (“eyes” on a potato)

      A root:

      • Has root hairs
      • Has no nodes or buds

      中文 — “stem(茎)” 详细解释

      1) “茎”的基本含义

      茎(stem)是植物的主要支撑结构,通常位于地上。它把叶、花和果实连接起来。

      可以把茎理解为植物的 “骨架 + 运输通道”


      2) 茎的主要功能

      A) 支撑作用

      • 支撑叶子,使其更好接受阳光
      • 支撑花和果实
      • 使植物保持直立

      B) 运输作用(维管组织) 茎内部有两种重要的运输组织:

      • 木质部(xylem):将水和无机盐从根向上运输
      • 韧皮部(phloem):将叶子制造的糖类运输到植物各部分

      C) 储存作用 有些茎用于储存营养或水分:

      • 土豆(块茎)储存淀粉
      • 仙人掌的茎储存水分

      D) 生长作用

      • 茎的顶端有分生组织,使植物不断长高
      • 可以发育成新的枝、叶或花

      3) 茎的类型

      1) 草本茎

      • 柔软、绿色
      • 例:草类、向日葵

      2) 木本茎

      • 坚硬、粗壮
      • 例:树木、灌木

      3) 变态茎(特殊功能的茎)

      • 根状茎:姜
      • 块茎:土豆
      • 匍匐茎:草莓
      • 鳞茎:洋葱
      • 叶状茎:仙人掌

      4) 重点一句话记忆

      茎的作用 = 支撑 + 运输 + 生长 +(有时)储存

      如果你愿意,我可以把 stem 做成 Science 10 考试版速记卡 / 中英对照表 / HTML 互动闪卡,非常适合你现在的生物学习体系。

    1. (1)OLS全模型: 先对所有8个特征做普通最小二乘回归,结果显示:某些变量(如肿瘤体积、前列腺重量)系数显著,另一些(如年龄、某指标LCP等)变得不显著,甚至出现了符号反转现象。例如年龄与PSA在单变量散点图中呈微弱正相关,但在多元回归中年龄系数却为负。这并不意味着“年龄大PSA反而低”,而是由于年龄与其他变量相关,在控制了更主要的因素后,年龄的边际效应估计变为负值,用来“补偿”共线性带来的影响。类似地,一些本来正相关的特征在多元回归中可能出现负系数。这说明在强共线、小样本情形下,OLS系数的符号和大小不可靠,不能直接逐个解释因果作用。相应地,OLS的预测性能也可能受到共线性的损害。 (2)子集选择: 我们可以在训练集上尝试用前向/后向逐步法或最佳子集选择来挑选变量。对于8个特征,最佳子集需要评估28=256种模型。实际上可以发现,优化某些信息准则(如AIC、BIC)或直接看测试集误差,最终往往只需要其中很少的特征就能达到接近最佳的预测效果。在该例中,最佳子集方法选出的最优模型仅包含两个变量,其他全被剔除。如此激进的简化虽提升了解释性,但也有欠拟合风险。 (3)岭回归: 岭回归不会删除任何变量,而是将所有系数向零收缩。选取适当的λ后,岭回归在测试集上的预测性能明显优于OLS。由于惩罚项抑制了共线性导致的系数不稳定,岭回归的预测更稳健。比如在模拟中,真实β1,β2均为正,而OLS估计出现一个为负;岭回归估计则将两个系数都缩小且为正,更接近真实值。然而岭回归保留了所有8个特征,模型解释性没有提升。而且对于高度相关的一组变量,岭回归往往会给予它们相似的中等大小系数,让它们共同发挥作用,但因为不稀疏,我们难以明确哪几个是主要驱动因素。 (4)Lasso: Lasso通过调节λ可以产生从全入模到全零不同复杂度的模型。当λ=0时即为OLS全模型;随着λ增加,系数逐渐被压缩,不重要的变量系数会变为0。当λ大到某程度时,模型可能只剩下极少数非零系数甚至退化为零模型。在前列腺癌例子中,lasso在某个最佳λ下自动选出了与最佳子集法相似的一组变量。具体来说,lasso删去了大部分无关变量,仅保留了与PSA关系最强的三四个特征,且这些特征正是我们肉眼和专业知识预期的重要变量(如肿瘤体积、重量等)。在测试集上,lasso的预测误差与岭回归相当,同样远低于OLS。然而,相比岭回归保留所有变量,lasso提供了一个更简洁的模型,更便于解释——我们可以告诉医生或决策者,这几个变量对PSA有主要影响,其余变量作用很小可以忽略。 (5)主成分回归和偏最小二乘: 这两种方法通过提取综合变量来回归,也在该例中进行了比较。主成分回归(PCR)提取数据协方差矩阵的若干主成分,偏最小二乘(PLS)则综合考虑响应来提取分量。它们一定程度上也能缓解共线性、降低模型维度。在前列腺癌数据上,PCR和PLS的测试误差与岭回归、lasso处于同一量级。 (6)模型性能对比: 用独立测试集评估,各种正则化或降维方法(岭、lasso、PCR、PLS、best subset等)都显著优于OLS。其中某个方法略胜一筹,但差异很小,且测试误差的标准误显示这些差异在统计上可能并不显著。这说明只要进行了合理的变量选择或正则化,高维共线数据的泛化性能就会有大幅提升,而具体选择哪一种方法反而不是最关键的。 (7)解释性 vs 预测性: 不同方法在模型简洁度和预测准确度上有所不同,需要权衡。如果侧重预测,我们应选择测试误差最小的方法(例如某个λ下的岭回归或lasso);如果侧重解释,则更倾向于简单模型(例如只含两三个变量的最佳子集模型),即使它的预测误差稍高。前列腺癌例子中,最佳子集模型仅两个变量,极具解释性,但其测试误差略高且可能不稳定;岭回归和lasso包含更多变量但预测更准;决策者应根据需求在二者间权衡。在实际应用中,这是常见的取舍:简单可解释和复杂高精度不可兼得,需要结合具体场景决定。

      这部分文字太密集,应考虑加入一些公式

    1. Note: This preprint has been reviewed by subject experts for Review Commons. Content has not been altered except for formatting.

      Learn more at Review Commons


      Referee #3

      Evidence, reproducibility and clarity

      Summary

      In this study, Weethington et al investigate how the abundance/activity of signaling proteins change over time following stimulation of NK cells and if the dynamics of these changes are coupled to cell cycle progression. Using CyTOF to measure these proteins in single cells and using several NK cell models, the investigators categorize proteins by the dynamics of these changes as cells progress through G1, S, and G2/M. The investigators indicate that the majority of proteins increase monotonically or semi-monotonically during cell cycle progression, while others exhibit non-monotonic changes - increasing from G1 -> S and then decreasing form S -> G2/M or vice-versa. The authors then use these data to inform mathematical models to identify the cellular processes that may give rise to these non-monotonic changes, identifying protein synthesis, degradation, or signaling kinetics as potential mechanisms.

      Major comments

      I do not understand the rationale for comparing time points (post-stimulation) between progressive cell cycle phases. Although there is a fixed temporal ordering to cell cycle phases (G1 -> S -> G2/M), there is no temporal relationship between protein abundance measurements at a post-stimulation time point in different cell cycle phases. For example, take CD69 in Fig 2E,G: the authors cite non-monotonous changes occurring at the 32, 64, and 256 min timepoints and semi-monotonic changes at all other time points. The abundance of CD69 at 32 min post-stimulation in G1 has no temporal relationship to the 32 min time point in S or G2 phase, so it is not clear how a statement about monotonicity can be made in this context? I believe the appropriate analysis strategy to interrogate the question posed by the authors in this paper is to compare the entire time-course of protein abundance between phases (i.e. the shape/magnitude of change in protein abundance in G1 vs S vs G2). Through this lens, the CD69 data in Fig 2G would suggest that the decrease in protein abundance at later time points (relative to untreated within the same phase) is larger in S phase than in G1 or G2. It should also be noted that the CD69 dynamics following stimulation is completely different in primary cells (Fig 2) vs the NK cell line (Fig S3), making interpretation and generalization very difficult. It is also difficult to assess the magnitude of differences in protein abundance given that there are often no measures of variance indicated in the bar plots visualizing these changes (e.g. Fig 2G, Fig S2B). I am aware that the authors use a pair of one-sided t tests to make statements of statistic significance for these comparisons. However, in single-cell assays of this scale with hundred to thousands of data points per condition, t tests are prone to Type I error and often overpowered to identify truly meaningful differences. Is a >5% decrease in mean abundance from G1 to S phase in a single experiment (independent replicates do not appear to have been performed) and no follow-up validation experiments sufficient to make the statement that this decrease is biologically meaningful? And then stratify proteins into classes based on these relatively small changes?

      Significance

      Our current knowledge of the mammalian cell cycle comes mostly studies in epithelial and fibroblast cells. A better understanding of the cell cycles of other cell types, how it is regulated, and how it influences other cell biological events would be a significant benefit to the field

      General assessment: I believe that this study has fundamental concerns (described above) that must be addressed before this manuscript should advance to publication

      Audience: Basic research, cell cycle and immunology audiences.

      My background is in experimental and computational cell cycle biology

    2. Note: This preprint has been reviewed by subject experts for Review Commons. Content has not been altered except for formatting.

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      Referee #2

      Evidence, reproducibility and clarity

      Summary:

      Wethington, Nayak, Jensen et al. investigated changes within protein abundances in distinct NK cell cycle stages after NKG2D stimulation of primary human NK cells and the NK cell line NKL. In addition the authors use mathematical models to define distinct patterns of signaling protein abundances across different cell cycle stages.

      Overall, the manuscript is well written and of interest for the scientific community. However, the manuscript could benefit from additional improvements.

      Major comments

      1. It remains unclear how many replicates were used within the manuscript throughout. Please state the number of replicates clearly. Since there is considerable variation between different human donors an n=3-5 would be preferable for the NKG2D stimulation of primary human data to draw valuable conclusions.
      2. Did the authors compare non-reactive vs reactive NK cells after NKG2D stimulation and if yes, how does the pattern look for the signaling molecules between distinct cell cycle phases when comparing those? It would be interesting to see the distribuition of CD107a negative and positive NK cells within the different cell cycle stages upon stimulation. This would potentially also provide an internal negative control as the signaling proteins within the CD107a negative population are expected to go through less changes.
      3. The link between the first part (NKG2D stimulation) and second part (mathematical modeling) remains a bit unclear. Was any of the NKG2D stimulation data used to train the mathematical modeling? If not a potential way to improve the link would be to describe the mathematical modeling first and subsequently validate certain patterns in the NKG2D modeling or to compare cytokine only induced changes (only IL-2) to receptor signaling changes (NKG2D stimulation).

      Minor comments:

      1. The level of NKG2D is not shown within manuscript and could be added as an additional supplementary figure.
      2. The authors mention CDKs influencing cell signaling. Did the authors track the abundance of CDK molecules upon NK cell stimulation?
      3. Figure 2E shows a lot of information and is a bit crowded. Potentially it would be easier to split the information up? Show a heatmap of the expression of the significant proteins at all different timepoints and then show the abundance changes in detail for a few proteins for specific timepoints.

      Significance

      General assessment:

      The manuscript provides an interesting mathematical modeling as well as CyTOF data from NK cell stimulations about differences in protein abundances throughout different cell cycle stages of NK cells. The data of the NK cell stimulation could be better linked to the mathematical modeling to make a stronger case for the robustness of the model and for more mechanistic conclusions. The manuscript contains a lot of data which is sometimes presented to condensed (Figure 2), the manuscript could benefit from a clearer red line throughout/focus on key molecules.

      Audience:

      The data presented is of interest for the specialized NK cell community but the discussion section could be improved by making a stronger case of how the herein presented data/model will benefit further studies within the NK cell or general immunology field.

      My field of expertise: NK cell biology, tissue-resident NK cells.

    1. To the IDW, trans people and their advocates are destroying the pillars of our society with such free-speech–suppressing, postmodern concepts as: “trans women are women,” “gender-neutral pronouns,” or “there are more than two genders.” Asserting “basic biology” will not be ignored, the IDW proclaims. “Facts don’t care about your feelings.”
      1. The motivation behind the author's writing is their beliefs towards how the media talks about transphobia and allows it due to science. As someone who studies the brain, the author automatically incorporates tones inside of their writing, directly showing their motivation.
    2. Contrary to popular belief, scientific research helps us better understand the unique and real transgender experience. Specifically, through three subjects: (1) genetics, (2) neurobiology and (3) endocrinology.
      1. This quote also highlights the fact that this reading is sicientifically based that is heavily opinionated. The form that the text takes is that science is very accessible for people to learn.
    3. Antiscientific sentiment bombards our politics, or so says the Intellectual Dark Web (IDW)
      1. This is motivating the author to write this text because people are spreading false information to argue against transgender people.
    4. Contrary to popular belief, scientific research helps us better understand the unique and real transgender experience. Specifically, through three subjects: (1) genetics, (2) neurobiology and (3) endocrinology.

      This quote directly answers the first question of what is the main message. I think that it directly explains the question because it says science to explain sex and gender about transgender people.

    5. Specifically, through three subjects: (1) genetics, (2) neurobiology and (3) endocrinology.

      shows that the author is knowledgable within science by organizing the argument into different scientific fields. This knowledge from the author builds credibility with the reader.

    1. This lubrication reduces friction between the two layers. See Figure 13.10[11] for an illustration of the pleurae and pleural cavity.

      A discussion of the role of the pleura in keeping the lungs inflated seems important, particularly in relation to conditions such as pneumothorax.

    2. The glottis is the opening inside the larynx, which also contains the vocal folds or cords. Air passes through this opening when breathing and making speech.

      Maybe a quick functional discussion stating that the glottis is widened when breathing, but narrowed during phonation to allow the passing air to vibrate the vocal chords?

    3. males due to the effects of testosterone

      Maybe remove the gender reference and simply state that it is enlarged with increasing levels of testosterone?

    4. The sinuses produce mucus and lighten the weight of the skull.

      Do we want to discuss their impact on vocal resonance and why the voice sounds different when we have a cold?

    1. ment

      Add these bullet points from the cart page: Ask your questions and get support in the LIVE Challenge Community Join the LIVE Website Coworking Session to create your website design and copy together. Wednesday, January 14 from 3-4 PM CET. Join the LIVE Website Critiques and get feedback on your website from professional graphic designer Clàudia Orengo. Wednesday, January 28th from 5-6 PM CET

      1. agricultural revolution

      2. more food= more people

      3. improvment in medicine

      4. better health= less in fant death- more people

      5. growth in work force

      6. more people= more factories

      7. urbanization

      8. more factories= people move into the city from agragrian settings

    1. Issues, Campus Resources, and Potential Outcomes

      This whole layout is helpful in what steps needed to take if you are experiencing issues with academic, health, social and more. I think it's really great there are so many resources including physical and mental health which are really important part from reading this chapter. I will use most of what's in this chapter because it closely relates to how I am currently feeling. I resonated with the "Imposter syndrome" part in particular and it's helpful to know I am not alone.

    2. The relationships you build with your professors will be some of the most important ones you create during your college career. You will rely on them to help you find internships, write letters of recommendation, nominate you for honors or awards, and serve as references for jobs. You

      This stood out to me because I did not know professors can play such a big part in internships, letters of recommendation or nomination of awards. This is actually really awesome and makes it more human especially for online classes. This is so important because professors see what you put in and can advocate for ones needs.

    1. The septum prevents the impulse from spreading directly to the ventricles without passing through the AV node first.

      Do we want to mention why this is important in order to help lead us into the Cardiac Cycle conversation?

    1. Note: This response was posted by the corresponding author to Review Commons. The content has not been altered except for formatting.

      Learn more at Review Commons


      Reply to the reviewers

      We thank the Reviewers for their positive assessment of the quality and significance of our work, as well as for their insightful comments, which have helped us to further improve the manuscript. We have addressed the majority of the comments in the revised version and, for those that require additional time, we outline below a detailed plan of the experiments we intend to perform.

      We agree with Reviewer #2 that a more detailed mechanistic understanding of the drug effects would further strengthen the study, and we are grateful to both reviewers for the constructive experimental suggestions provided to address this point. In particular, we are highly motivated to better define the causal role of C18 sphingolipid alterations in mediating the effects of the drugs, as suggested by Reviewer #2, as well as to investigate the involvement of the retromer complex in the lysosome-to-Golgi connection, as suggested by Reviewer #1.

      Below, we provide a point-by-point description of the revisions already incorporated into the manuscript, along with the planned experiments that will address the remaining comments

      REVIEWER #1:

      VPS13B is a bridge-like lipid transfer protein, the loss or mutation of which is associated with Cohen syndrome (CS) involving Golgi fragmentation. In this study, the authors performed image-based chemical screens to identify compounds capable of rescuing the Golgi morphology in VPS13B-KO HeLa cells. They identified 50 compounds, the majority of which are lysosomotropic compounds or cationic amphiphilic drugs (CADs). Treatment of cells with several of these compounds causes lysosomal lipid storage, as assessed by BMP/LBPA staining, filipin staining, or LipidTOX staining. Interestingly, most LipidTOX puncta colocalized with transferrin receptor-positive compartments but not lysosomes. Similar to lysosomotropic compounds, knocking down NPC1 or SMPD1, mimicking lysosomal storage disease, also substantially rescued Golgi morphology. The authors show that VPS13B-KO cells have reduced C18 sphingolipids, which is reversed by treatment with CADs. Finally, the authors show that two CADs partially rescue neurite outgrowth in neuronal cultures. However, these drugs do not rescue the size of VPS13B KO organoids.

      Overall, this is an impressive study identifying CADs as potential therapeutics for CS and suggesting sphingolipid upregulation as a general strategy for CS treatment. The morphological and lipidomics analyses unravel important molecular basis of CS pathology. This study will be of high interest to the field of lipid biology and organelle homeostasis. I have a few comments to help improve the quality of this study.

      1. The reverse of lipid changes in VPS13B-KO cells by CADs is intriguing. Are CAD-mediated benefits such as Golgi morphology recovery permanent or only transient within 24 hours of treatment? How do the CADs affect the Golgi morphology in WT HeLa cells?

      RESPONSE:

      We thank the reviewer for this insightful question Indeed, the effects of CADs on Golgi organization are most evident in VPS13B KO cells, where the Golgi apparatus is severely fragmented and becomes more compact upon drug treatment, whereas the effect is much less apparent in wild-type cells. Nevertheless, a careful quantitative analysis of the images (now presented in the new Fig. S7) demonstrates that the impact of these compounds on Golgi morphology is not restricted to KO cells but is likely more general, supporting a link between lysosomal storage and Golgi organization. Although this observation indicates an indirect effect (consistent with the proposed mechanism of action), rather than a direct correction of VPS13B loss, it does not compromise in our opinion their potential beneficial effect for KO cells as shown also from the results obtained in organoid-derived neurons.

      Under continuous treatment, azelastine keeps the Golgi in a compact state for 72 hours without any noticeable deleterious effect on the cells (see new Fig. S10) Raloxifene, on the contrary proved to be toxic over the same time period. We believe this difference reflects the mechanism of action of CADs, which progressively accumulate within acidic organelles and may eventually reach a toxic threshold upon prolonged exposure. For this reason, lower drug concentrations administered over longer treatment periods may represent a viable alternative strategy. In this regard, we also refer the reviewer to our response to the comment on brain organoids below.

      1. Is it surprising that Azelastine-induced lipid storage in transferrin receptor compartments (early and recycling endosomes)? I suggest more controls to examine LipidTOX overlap with Golgi markers or other late endosome/lysosome markers such as LBPA and CD63.

      RESPONSE:

      We agree with the reviewer that this observation is somewhat unexpected. However, we would like to clarify that we do not intend to suggest that lipid storage occurs primarily in early or recycling endosomes, which would indeed contradict a substantial body of existing evidence. Rather, our data indicate that this particular dye (LipidTOX) labels recycling endosomes, at least in HeLa cells. This finding is consistent with the widely accepted view that lysosomal lipid storage exerts broader effects on intracellular trafficking, not limited to late endosomes/lysosomes. We corrected the text in order to clarify this concept.

      LipidTOX was specifically developed to detect drug-induced phospholipidosis, and based on our data, it appears suitable for this purpose. To our knowledge, there is no published information detailing its intracellular localization, which motivated us to perform these control experiments. Unfortunately, the proprietary formulation of this product does not allow informed speculations to explain the observed localization or whether this could refer to the intact molecule or to a catabolite.

      As suggested by the reviewer, we plan to perform co-staining with additional markers to further clarify this this point.

      1. Does the LipidTOX/TFRC overlap suggest potential roles of retrograde transport in supplying sphingolipids to the Golgi? The authors can quickly test if the knockdown of a retromer subunit (VPS35) blocks Azelastine-induced recovery of Golgi morphology.

      RESPONSE:

      We thank the reviewer for this insightful suggestion. Indeed, the retromer complex represents one of the best-characterized trafficking pathways from the endosomal system to the Golgi, and this relatively straightforward experiment could help to mechanistically clarify our observations. We plan to test whether VPS35 knockdown interferes with the effects of the drugs.

      What is the rationale to use 500 nM to 1 uM azelastine and raloxifene for neuronal cultures and organoids? At such concentrations, no obvious changes in Golgi morphology or lipid storage were observed (Fig 4). Also, the lipidomics analysis was performed after 10 uM compound treatment. It might be worth trying dose-response experiments in organoid tests.

      RESPONSE:

      We thank the reviewer for this question. The rationale about this choice was indeed missing from our previous version of the manuscript. The reason of lowering the concentrations comes indeed from toxicity tests, preliminarily performed over long-term treatment of both WT and VPS13B KO organoids. This information has now been explicitly included in the Results section of the revised manuscript, and the broader implications are also discussed in the Discussion section.

      MINOR COMMENTS:

      It is important to know whether the authors used TGN or cis-Golgi markers for Golgi morphology analysis. Please label the two channels in Fig. 2C and throughout all figures. In many cases, it is not clear what is stained in the green channel to show the Golgi morphology. It was not even stated in the legend.

      RESPONSE:

      We now included the antibody staining in all figure legends where it was previously missing.

      The authors stated that Recovery of Golgi morphology is dependent on lysosomal lipid storage. However, while the data show positive correlation between the two, no causal relationship is established by the data. It seems true that in all conditions (CADs or genetic knockdown) where lysosomal lipid storage was observed, the authors detect the Recovery of Golgi morphology. However, budesonide did not depend on lysosomal lipid storage to recover the Golgi morphology. Thus, the recovery of Golgi morphology is NOT dependent on lysosomal lipid storage, but inducing lysosomal lipid storage appears sufficient to recover Golgi morphology in VPS13B-KO HeLa cells.

      RESPONSE:

      We thank the reviewer for this comment and we agree that the previous title of the paragraph could have been misleading. This has been now changed in: “Lysosomal lipid storage mediates the recovery of Golgi morphology” which is probably less prone to ambiguous interpretations.

      Obviously, in the previous version of the title we wanted to mean that Golgi recovery is dependent on lipid storage “in the context of CAD treatment” and not as a general statement.

      With respect to the cause–effect relationship, we believe that the strongest evidence supporting this link is the observation that genetically induced lipid storage phenocopies the effects of drug treatment. We hope that this conclusion is now sufficiently clear from the revised text.

      Each figure needs a title before the detailed legends for specific panels.

      RESPONSE:

      Titles have now been included to all figure legends.

      Fig 8. Y axis labeling is missing.

      RESPONSE:

      Axes labels have now been included

      Does U18666A rescues Golgi morphology in VPS13B-KO cells?

      RESPONSE:

      We thank the reviewer for this comment. U18666A indeed also corrects Golgi morphology. The result is now included in the new figure S5.

      Please do not repeat the result section in discussion. Focus on the most important points.

      RESPONSE:

      We thank the reviewer for this comment. We shortened the descriptive part of the discussion trying as much as possible to avoid repetitions with the result session and keeping only the more essential information for the flow of the discussion.

      Reviewer #1 (Significance (Required)):

      This is an impressive study that identifies Cationic Amphiphilic Drugs (CADs) as potential therapeutics for Cohen syndrome (CS) and suggests sphingolipid upregulation as a general strategy for diseases driven by VPS13B loss-of-function. The unbiased approaches, notably the chemical screen and lipidomics, provide novel mechanistic insights into the underlying pathology of CS. This study will be of high interest to researchers in the fields of lipid biology and organelle homeostasis. It will also be highly valuable for clinical pediatricians managing CS patients.

      REVIEWER #2:

      This manuscript describes a compound screening aimed at identifying molecules that can restore Golgi organization in VPS13B knockout (KO) cells. The authors identify several compounds, most of which are lysosomotropic, and analyze their effects on Golgi morphology and lipid composition using multiple approaches. They report that VPS13B KO cells exhibit a reduction in C18-N-acyl sphingolipids, which can be restored by several of the identified compounds. Furthermore, two of these compounds, azelastine and raloxifene, promote neurite outgrowth in VPS13B KO cortical organoids. These findings are interesting and could potentially contribute to a better understanding of the pathophysiology of Cohen syndrome and the development of therapeutic strategies. However, despite the large number of analyses presented, the study remains largely descriptive, and there is no coherent mechanistic explanation for how these compounds restore Golgi structure in VPS13B KO cells. In addition to the reduction in C18-N-acyl sphingolipids, the KO cells display alterations in several other lipid species (LPC, LPE, PC40:1, PE42:1, TG, etc.), and treatment with the selected compounds induces further lipid accumulations, including cholesterol and BMP/LBPA. The relationship between these diverse lipid changes and the observed Golgi recovery lacks clarity and mechanistic consistency.

      MAJOR COMMENTS:

      The finding that compounds cannot prevent Golgi fragmentation caused by brefeldin A or nocodazole but can suppress statin-induced fragmentation is intriguing, but the underlying mechanism is not addressed. It is not evident whether this difference results from changes in membrane lipid composition or restoration of Rab/SNARE trafficking. The authors should examine Rab prenylation and SNARE localization by immunofluorescence or Western blotting to support their interpretation.

      RESPONSE:

      We thank the reviewer for this suggestion and agree that the ability of these compounds to counteract statin-induced Golgi fragmentation is indeed intriguing. The primary reason we did not further explore this aspect is that we evaluated the effects of statins not to be a central focus of the present study. Nevertheless, we fully agree that this observation represents a valuable opportunity to gain additional insight into the mechanism underlying drug-induced Golgi recovery.

      To address this point, we plan to analyze Rab prenylation by Western blot and Rab localization by microscopy, focusing on a Golgi-associated Rab protein such as Rab6. In addition, we will employ downstream inhibitors of Rab prenylation, such as 3-PEHPC (an inhibitor of type II protein geranylgeranyltransferase (GGTase-II)), which should allow us to formally distinguish effects related to impaired Rab prenylation from those arising from inhibition of cholesterol biosynthesis.

      Although restoration of C18 sphingolipids (SM 36:1, CER 36:1) is observed upon compound treatment, its causal role in Golgi recovery or neurite outgrowth is not established. The authors should test whether blocking the increase of C18 SM/CER prevents the rescue of Golgi or neuronal phenotypes.

      RESPONSE:

      We sincerely thank the reviewer for this comment. We agree that, based on the current data, a definitive cause–effect relationship between Golgi recovery and the increase in C18 sphingolipids cannot be firmly established, and we acknowledge that a deeper understanding of this issue will require further investigation. Furthermore, we believe that addressing this would not only provide a better mechanistic understanding of the biological processes behind the effect of the drugs but provide a potential avenue for therapeutic intervention. For these reasons, we are strongly motivated to pursue this aspect further.

      With respect to the reviewer’s specific suggestion, we agree that preventing the increase in C18 sphingolipids would be an ideal experimental approach. However, the limited understanding of the regulatory mechanisms controlling C18 sphingolipid homeostasis currently precludes a fully informed strategy. In principle, if the observed increase were due to enhanced synthesis, one could envisage blocking it by silencing ceramide synthases with C18 selectivity, such as CERS1. The experiment shown in Fig. 7E (azelastine treatment in the presence of sphingolipid synthesis inhibitors) was designed with this rationale in mind. However, these results suggest that azelastine-induced C18 sphingolipid accumulation is unlikely to result from increased synthesis, and is instead more consistent with reduced degradation, in line with the proposed mechanism of action of CADs.

      Based on these considerations, we propose to invert the experimental approach and test whether cellular re-complementation with C18 sphingolipids is sufficient to recapitulate the drug-induced Golgi recovery. We are aware of the technical challenges associated with the targeted delivery of exogenously supplied lipids, particularly given the likelihood that effective rescue would require lipid access to the Golgi apparatus. Based on current knowledge, we anticipate that externally supplied lipids would primarily traffic either to the ER via non-vesicular routes or to endosomes/lysosomes through endocytic uptake. From both locations they could eventually reach to some extent the Golgi. The route from endosomes to Golgi in particular as been intensively studied in the past with the use of fluorescent sphingolipid analogs1,2 and may well work also with native lipids.

      Since we are not able to predict in advance which lipid species would be more effective or the optimal delivery strategy, we plan to test re-complementation using C18 sphingomyelin and some of its potential precursors, including C18 ceramide as well as using alternative delivery strategies such as incorporation in liposomes of different formulations and delivery at the plasma membrane with bovine serum albumin or cyclodextrins as carriers.

      1. Puri et al., (2001). J Cell Biol.154:535-47 (doi: 10.1083/jcb.200102084)
      2. Koivusalo et al.,(2007). Mol Biol Cell. 18:5113-23 (doi: 10.1091/mbc.e07-04-0330)

        In Figure 7D, comparisons should include the LM and HM fractions isolated from WT cells.

      RESPONSE:

      Wild-type control were included in the figure as requested.

      The subcellular fractionation experiment should be repeated using AZL and RAL, the compounds used in organoid experiments, rather than TFPZ, to assess whether similar results are obtained. The compounds used differ across experiments, making it difficult to draw consistent conclusions.

      RESPONSE:

      We thank the reviewer for this comment and apology for some inconsistencies in the selection of the compounds to highlight in the figures which are mostly remnants of the drug prioritization history over the progression of the project. We tried to make it more consistent in the current version.

      In the new version of figure 7D, AZL is substituting TFPZ, while TFPZ data were moved to supplementary figure S19.

      Golgi morphology in VPS13B KO cells is reported to recover in NPC1 KD and SMPD1 KD cells, but it is not shown whether SM 36:1, CER 36:1, or other lipid levels also increase or change in these conditions. If Golgi morphology recovery occurs via the same mechanism as with compound treatment, a similar lipid pattern should be observed.

      RESPONSE:

      We thank the reviewer for this question that allowed us to expand our study including new interesting findings. We agree that this is an important point to strengthen the link between CAD and genetic perturbation effects. Given the availability of several published lipidomic datasets modelling LDS in HeLa and in other cell lines, we decided to perform a re-analysis of those to specifically focus on C18 sphingolipids. We found a relative increase of 36:1 upon depletion of LSD genes in all analyzed datasets for NPC1 and SMPD1, but also for more than 15 other LSD genes including NPC2, recapitulating what we find with all the CAD molecules tested in our study. These changes, were not noticed or at least not discussed by most of the authors. This is not surprising since those studies are focused on different biological questions. We believe that these findings, besides reinforcing our hypothesis of a common mechanism between CAD and NPC1/SMPD1 KO, have of general interest for the regulation of C18 sphingolipids, which are among the relative few lipid species with a bona fide specific protein binding partner and proposed to play a crucial role in Golgi traffic.

      MINOR POINTS:

      The manuscript lacks sufficient information about the compound library used for screening (number and source of compounds, compound type).

      RESPONSE:

      We apologize if this information was not sufficiently visible in the original version of the manuscript. The data about source, catalog number, formulation and several additional identifiers is included in the File S1. This is now clearly indicated in the methods so that I can be more easily visible to the readers

      Fig. 3A: a WT control image is required.

      RESPONSE:

      A WT control image is now included in the new version of Figure 3.

      Fig. 4: include representative images at concentrations higher than 1.25 µM.

      RESPONSE:

      Representative images are now included for all concentrations higher than 1.25 µM, as requested.

      Abbreviations such as BMP/LBPA should be defined when first mentioned.

      RESPONSE:

      The abbreviation of BMP/LBPA was already defined when first mentioned in the original version of the manuscript

      The abbreviation for raloxifene is inconsistent (RLX vs RAL) and should be unified.

      RESPONSE:

      Raloxifene is now abbreviated as RLX all over the manuscript.

      Fig. 5C: the meaning of the green and magenta bars is not explained.

      RESPONSE:

      Color code for figure 5C has been included.

      The definitions and centrifugation parameters for light and heavy membrane fractions should be clearly stated in the Methods.

      RESPONSE:

      The centrifugation parameters were already defined in the original manuscript. It is not clear to us, which parameter the Referee is referring to. Below is the sentence in the methods section:

      “Gradients were centrifuged at 165,000 g for 1.5 h at 4°C with a SW40Ti Swinging-Bucket rotor (Beckman-Coulter). The LM and HM fractions were collected at the 35%-HB and 35%-40.6% interfaces, respectively”

      The concentration and incubation times for BFA and nocodazole should be included in the main text or figure legends.

      RESPONSE:

      Concentrations and incubation times of BFA and nocodazole were already present in the legend of figure 5.

      Fig. 8C, D, G, H: y-axes lack labels and must be defined.

      RESPONSE:

      Axes labels have now been included

      There are multiple typographical errors, including "VPS12" instead of "VPS13B", that should be corrected.

      RESPONSE:

      We corrected this specific mistake as well as others that we could identify after careful reading of the manuscript.

      Reviewer #2 (Significance (Required)):

      While the dataset is extensive and technically detailed, the manuscript lacks a clear mechanistic explanation connecting lipid changes to Golgi restoration. The choice and comparison of compounds are inconsistent across experiments, and the interpretation remains speculative. Substantial revision and additional experiments are required before the study can be considered for publication.

    2. Note: This preprint has been reviewed by subject experts for Review Commons. Content has not been altered except for formatting.

      Learn more at Review Commons


      Referee #1

      Evidence, reproducibility and clarity

      VPS13B is a bridge-like lipid transfer protein, the loss or mutation of which is associated with Cohen syndrome (CS) involving Golgi fragmentation. In this study, the authors performed image-based chemical screens to identify compounds capable of rescuing the Golgi morphology in VPS13B-KO HeLa cells. They identified 50 compounds, the majority of which are lysosomotropic compounds or cationic amphiphilic drugs (CADs). Treatment of cells with several of these compounds causes lysosomal lipid storage, as assessed by BMP/LBPA staining, filipin staining, or LipidTOX staining. Interestingly, most LipidTOX puncta colocalized with transferrin receptor-positive compartments but not lysosomes. Similar to lysosomotropic compounds, knocking down NPC1 or SMPD1, mimicking lysosomal storage disease, also substantially rescued Golgi morphology. The authors show that VPS13B-KO cells have reduced C18 sphingolipids, which is reversed by treatment with CADs. Finally, the authors show that two CADs partially rescue neurite outgrowth in neuronal cultures. However, these drugs do not rescue the size of VPS13B KO organoids.

      Overall, this is an impressive study identifying CADs as potential therapeutics for CS and suggesting sphingolipid upregulation as a general strategy for CS treatment. The morphological and lipidomics analyses unravel important molecular basis of CS pathology. This study will be of high interest to the field of lipid biology and organelle homeostasis. I have a few comments to help improve the quality of this study.

      1. The reverse of lipid changes in VPS13B-KO cells by CADs is intriguing. Are CAD-mediated benefits such as Golgi morphology recovery permanent or only transient within 24 hours of treatment? How do the CADs affect the Golgi morphology in WT HeLa cells?
      2. Is it surprising that Azelastine-induced lipid storage in transferrin receptor compartments (early and recycling endosomes)? I suggest more controls to examine LipidTOX overlap with Golgi markers or other late endosome/lysosome markers such as LBPA and CD63.
      3. Does the LipidTOX/TFRC overlap suggest potential roles of retrograde transport in supplying sphingolipids to the Golgi? The authors can quickly test if the knockdown of a retromer subunit (VPS35) blocks Azelastine-induced recovery of Golgi morphology.
      4. What is the rationale to use 500 nM to 1 uM azelastine and raloxifene for neuronal cultures and organoids? At such concentrations, no obvious changes in Golgi morphology or lipid storage were observed (Fig 4). Also, the lipidomics analysis was performed after 10 uM compound treatment. It might be worth trying dose-response experiments in organoid tests.

      Minor:

      1. It is important to know whether the authors used TGN or cis-Golgi markers for Golgi morphology analysis. Please label the two channels in Fig. 2C and throughout all figures. In many cases, it is not clear what is stained in the green channel to show the Golgi morphology. It was not even stated in the legend.
      2. The authors stated that Recovery of Golgi morphology is dependent on lysosomal lipid storage. However, while the data show positive correlation between the two, no causal relationship is established by the data. It seems true that in all conditions (CADs or genetic knockdown) where lysosomal lipid storage was observed, the authors detect the Recovery of Golgi morphology. However, budesonide did not depend on lysosomal lipid storage to recover the Golgi morphology. Thus, the recovery of Golgi morphology is NOT dependent on lysosomal lipid storage, but inducing lysosomal lipid storage appears sufficient to recover Golgi morphology in VPS13B-KO HeLa cells.
      3. Each figure needs a title before the detailed legends for specific panels.
      4. Fig 8. Y axis labeling is missing.
      5. Does U18666A rescues Golgi morphology in VPS13B-KO cells?
      6. Please do not repeat the result section in discussion. Focus on the most important points.

      Significance

      This is an impressive study that identifies Cationic Amphiphilic Drugs (CADs) as potential therapeutics for Cohen syndrome (CS) and suggests sphingolipid upregulation as a general strategy for diseases driven by VPS13B loss-of-function. The unbiased approaches, notably the chemical screen and lipidomics, provide novel mechanistic insights into the underlying pathology of CS. This study will be of high interest to researchers in the fields of lipid biology and organelle homeostasis. It will also be highly valuable for clinical pediatricians managing CS patients.

    1. Adult females have an average of 4 to 5 liters of blood, and adult males have an average of 5 to 6 liters of blood.

      I like to clarify here that blood volume is dependent on size, not gender.

    1. Author response:

      The following is the authors’ response to the original reviews.

      Public Reviews: 

      Reviewer #1 (Public Review): 

      Summary:

      The manuscript submitted by Langenbacher et al., entitled " Rtf1-dependent transcriptional pausing regulates cardiogenesis", describes very interesting and highly impactful observations about the function of Rtf-1 in cardiac development. Over the last few years, the Chen lab has published novel insights into the genes involved in cardiac morphogenesis. Here, they used the mouse model, the zebrafish model, cellular assays, single cell transcription, chemical inhibition, and pathway analysis to provide a comprehensive view of Rtf1 in RNAPII (Pol2) transcription pausing during cardiac development. They also conducted knockdown-rescue experiments to dissect the functions of Rtf1 domains. 

      Strengths:

      The most interesting discovery is the connection between Rtf1 and CDK9 in regulating Pol2 pausing as an essential step in normal heart development. The design and execution of these experiments also demonstrate a thorough approach to revealing a previously underappreciated role of Pol2 transcription pausing in cardiac development. This study also highlights the potential amelioration of related cardiac deficiencies using small molecule inhibitors against cyclin dependent kinases, many of which are already clinically approved, while many other specific inhibitors are at various preclinical stages of development for the treatment of other human diseases. Thus, this work is impactful and highly significant. 

      We thank the reviewer for appreciating our work.

      Reviewer #2 (Public Review): 

      Summary: 

      Langenbacher at el. examine the requirement of Rtf1, a component of the PAF1C, which regulates transcriptional pausing in cardiac development. The authors first confirm their previous morphant study with newly generated rtf1 mutant alleles, which recapitulate the defects in cardiac progenitor and diUerentiation gene expression observed previously in morphants. They then examine the conservation of Rtf1 in mouse embryos and embryonic stem cell-derived cardiomyocytes. Conditional loss of Rtf1 in mesodermal lineages and depletion in murine ESCs demonstrates a failure to turn on cardiac progenitor and diUerentiation marker genes, supporting conservation of Rtf1 in promoting cardiac development. The authors subsequently employ bulk RNA-seq on flow-sorted hand2:GFP+ cells and multiomic single-cell RNA-seq on whole Rtf1-depleted embryos at the 10-12 stage. These experiments corroborate that genes associated with cardiac and muscle development are lost. Furthermore, the diUerentiation trajectories suggest that the expression of genes associated with cardiac maturation is not initiated.  Structure-function analysis supports that the Plus3 domain is necessary for its function in promoting cardiac progenitor formation. ChIP-seq for RNA Pol II on 1012 somite stage embryos suggests that Rtf1 is required for proper promoter pausing. This defect can partially be rescued through use of a pharmacological inhibitor for Cdk9, which inhibits elongation, can partially restore elongation in rtf1 mutants.  

      Strengths: 

      Many aspects of the data are strong, which support the basic conclusions of the authors that Rtf1 is required for transcriptional pausing and has a conserved requirement in vertebrate cardiac development. Areas of strength include the genetic data supporting the conserved requirement for Rtf1 in promoting cardiac development, the complementary bulk and single-cell RNA-sequencing approaches providing some insight into the gene expression changes of the cardiac progenitors, the structure-function analysis supporting the requirement of the Plus3 domain, and the pharmacological epistasis combined with the RNA Pol II ChIP-seq, supporting the mechanism implicating Cdk9 in the Rtf1 dependent mechanism of RNA Pol II pausing. 

      We thank the reviewer for the summary and for recognizing many strengths of our work. 

      Weaknesses: 

      While most of the basic conclusions are supported by the data, there are a number of analyses that are confusing as to why they chose to perform the experiments the way they did and some places where the interpretations presently do not support the interpretations. One of the conclusions is that the phenotype aUects the maturation of the cardiomyocytes and they are arresting in an immature state. However, this seems to be mostly derived from picking a few candidates from the single cell data in Fig. 6. If that were the case, wouldn't the expectation be to observe relatively normal expression of earlier marker genes required for specification, such as Nkx2.5 and Gata5/6? The in situ expression analysis from fish and mice (Fig. 2 and Fig. 3) and bulk RNA-seq (Fig. 5) seems to suggest that there are pretty early specification and diUerentiation defects. While some genes associated with cardiac development are not changed, many of these are not specific to cardiomyocyte progenitors and expressed broadly throughout the ALPM. Similarly, it is not clear why a consistent set of cardiac progenitor genes (for instance mef2ca, nkx2.5, and tbx20) was analyzed for all the experiments, in particular with the single cell analysis. 

      A major conclusion of our study is that Rtf1 deficiency impairs myocardial lineage differentiation from mesoderm, as suggested by the reviewer. Thus, the main goal of this study is to understand how Rtf1 drives cardiac differentiation from the LPM, rather than the maturation of cardiomyocytes.  Multiple lines of evidence support this conclusion:

      (a) In situ hybridization showed that Rtf1 mutant embryos do not have nkx2.5+ cardiac progenitor cells and subsequently fail to produce cardiomyocytes (Figs. 2, 3).

      (b) RT-PCR analysis showed that knockdown of Rtf1 in mouse embryonic stem cells causes a dramatic reduction of cardiac gene expression and production of significantly fewer beating patches (Fig.4).

      (c) Bulk RNA sequencing revealed significant downregulation of cardiac lineage genes, including nkx2.5 (Fig. 5).

      (d) Single cell RNA sequencing clearly showed that lateral plate mesoderm (LPM) cells are significantly more abundant in Rtf1 morphant,s whereas cardiac progenitors are less abundant (Fig. 6 and Fig.6 Supplement 1-5). 

      When feasible, we used cardiac lineage restricted markers in our assays. Nkx2.5 and tbx5a are not highlighted in the single cell analysis because their expression in our sc-seq dataset was too low to examine in the clustering/trajectory analysis.  In this revised manuscript, we provide violin plots showing the low expression levels of these genes in single cells from Rtf1 deficient embryos (Figure 6 Supplement 5).

      The point of the multiomic analysis is confusing. RNA- and ATAC-seq were apparently done at the same time. Yet, the focus of the analysis that is presented is on a small part of the RNA-seq data. This data set could have been more thoroughly analyzed, particularly in light of how chromatin changes may be associated with the transcriptional pausing. This seems to be a lost opportunity. Additionally, how the single cell data is covered in Supplemental Fig. 2 and 3 is confusing. There is no indication of what the diUerent clusters are in the Figure or the legend. 

      In this study, we performed single cell multiome analysis and used both scRNAseq and scATACseq datasets to generate reliable clustering.  The scRNAseq analysis reveals how Rtf1 deficiency impacts cardiac differentiation from mesoderm, which inspired us to investigate the underlying mechanism and led to the discovery of defects in Rtf1-dependent transcriptional pause release.

      We agree with the reviewer that deep examination of Rtf1-dependent chromatin changes would provide additional insights into how Rtf1 influences early development and careful examination of the scATACseq dataset is certainly a good future direction.  

      In this revised manuscript, we have revised Fig.6 Supplement 1 to include the predicted cell types and provide an additional excel file showing the annotation of all 39 clusters (Supplementary Table 2). 

      While the effect of Rtf1 loss on cardiomyocyte markers is certainly dramatic, it is not clear how well the mutant fish have been analyzed and how specific the eUect is to this population. It is interpreted that the eUects on cardiomyocytes are not due to "transfating" of other cell fates, yet supplemental Fig. 4 shows numerous eUects on potentially adjacent cell populations. Minimally, additional data needs to be provided showing the live fish at these stages and marker analysis to support these statements. In some images, it is not clear the embryos are the same stage (one can see pigmentation in the eyes of controls that is not in the mutants/morphants), causing some concern about developmental delay in the mutants. 

      Single cell RNA sequencing showed an increased abundance of LPM cells and a reduced abundance of cardiac progenitors in Rtf1 morphants (Fig. 6 and Fig.6 Supplement 1-5). The reclustering of anterior lateral plate mesoderm (ALPM) cells and their derivatives further showed that cells representing undifferentiated ALPM were increased whereas cells representing all three ALPM derivatives were reduced. These findings indicate a defect in ALPM differentiation. 

      The reviewer questioned whether we examined stage-matched embryos. In our assay, Rtf1 mutant embryos were collected from crosses of Rtf1 heterozygotes. Each clutch from these crosses consists of ¼ embryos showing rtf1 mutant phenotypes and ¾ embryos showing wild type phenotypes which were used as control. Mutants and their wild type siblings were fixed or analyzed at the same time.

      The reviewer questioned the specificity of the Rtf1 deficient cardiac phenotype and pointed out that Rtf1 mutant embryos do not have pigment cells around the eye.  Rtf1 is a ubiquitously expressed transcriptional regulator.  Previous studies in zebrafish have shown that Rtf1 deficiency significantly impacts embryonic development. Rtf1 deficiency causes severe defects in cardiac lineage and neural crest cell development; consequently, Rtf1 deficient embryos do not have cardiomyocytes and pigmentation (Langenbacher et al., 2011, Akanuma et al., 2007, and Jurynec et al., 2019).  We now provide an image showing a 2-day-old Rtf1 mutant embryo and their wild type sibling to illustrate the cardiac, neural crest, and somitogenesis defects caused by loss of Rtf1 activity (Fig. 2 Supplement 1).

      With respect to the transcriptional pausing defects in the Rtf1 deficient embryos, it is not clear from the data how this eUect relates to the expression of the cardiac markers. This could have been directly analyzed with some additional sequencing, such as PRO-seq, which would provide a direct analysis of transcriptional elongation. 

      We showed that Rtf1 deficiency results in a nearly genome-wide decrease in promoterproximal pausing and downregulation of cardiac makers. Attenuating transcriptional pause release could restore cardiomyocyte formation in Rtf1 deficient embryos. In this revised manuscript, we provide additional RNAseq data showing that the expression levels of critical cardiac development genes such as nkx2.5, tbx5a, tbx20, mef2ca, mef2cb, ttn.2, and ryr2b are significantly rescued.  We agree with the reviewer that further analyses using the PRO-seq approach could provide additional insights, but it is beyond the scope of this manuscript. 

      Some additional minor issues include the rationale that sequence conservation suggests an important requirement of a gene (line 137), which there are many examples this isn't the case, referencing figures panels out of order in Figs. 4, 7, and 8) as described in the text, and using the morphants for some experiments, such as the rescue, that could have been done in a blinded manner with the mutants. 

      We have clarified the rationale in this revised manuscript and made the eRort to reference figures in order. 

      The reviewer commented that rescue experiments “could have been done in a blinded manner with the mutants”. This was indeed how the flavopiridol rescue and cdk9 knockdown experiments were carried out. Embryos from crosses of Rtf1 heterozygotes were collected, fixed after treatment and subjected to in situ hybridization. Embryos were then scored for cardiac phenotype and genotyped (Fig.8 d-g). Morpholino knockdown was used in genomic experiments because our characterization of rtf1 morphants showed that they faithfully recapitulate the rtf1 mutant phenotype during the timeframe of interest (Fig. 2).

      Recommendations for the authors:

      Reviewer #1 (Recommendations For The Authors): 

      This reviewer has a few suggestions below, aimed at improving the clarity and impact of the current study. Once these items are addressed, the manuscript should be of interest to the Elife reader. 

      Item 1. Strengthening the interaction between Rfh1 and CDK9 on Pol2 pausing. 

      The authors have convincingly shown that the chemical inhibition of CDK9 by flavopiridol can partially rescue the expression of cardiac genes in the zebrafish model. Although flavopiridol is FDA approved and has been a classical inhibitor for the dissection of CDK9 function, it also inhibits related CDKs (such as Flavopiridol (Alvocidib) competes with ATP to inhibit CDKs including CDK1, CDK2, CDK4, CDK6, and CDK9 with IC50 values in the 20-100 nM range) Therefore, this study could be more impactful if the authors can provide evidence on which of these CDKs may be most relevant during Rtf1-dependent cardiogenesis. To determine whether the observed cardiac defect indicates a preferential role for CDK9, or that other CDKs may also be able to provide partial rescue may be clarified using additional, more selective small molecules (e.g., BAY1251152, LDC000067 are commercially available). 

      The reviewer raised a reasonable concern about the specificity of flavopiridol. We thank the reviewer for the insightful suggestion and share the concern about specificity. To address this question, we have used an orthogonal testing through morpholino inhibition where we directly targeted CDK9 and observed the same level of rescue, supporting a critical role of transcription pausing in cardiogenesis.

      Item 2. Differences between CRISPR lines and morphants 

      Much of the work presented used Rtf1 morphants while the authors have already generated 2 CRISPR lines. What is the diUerence between morphants and mutants? The authors should comment on the similarities and/or differences between using morphants or mutants in their study and whether the same Rtf1- CDK9 connection also occurs in the CRISPR lines. 

      The morphology of our mutants (rtf1<sup>LA2678</sup> and rtf1<sup>LA2679</sup>) resembles the morphants and the previously reported ENU-induced rtf1<sup>KT641</sup> allele. Extensive in situ hybridization analysis showed that the morphants faithfully recapitulate the mutant phenotypes (Fig.2). We have performed rescue experiments (flavopiridol and CDK9 morpholino) using Rtf1 mutant embryos and found that inhibiting Cdk9 restores cardiomyocyte formation (Fig.8). 

      Item 3. Discuss the therapeutic relevance of study 

      The authors have already generated a mouse model of Rtf1 Mesp1-Cre knockout where cardiac muscle development is severely derailed (Fig 3B). Thus, a demonstration of a conserved role for CDK9 inhibitor in rescuing cardiogenesis using mouse cells or the mouse model will provide important information on a conserved pathway function relevant to mammalian heart development. In the Discussion, how this underlying mechanistic role may be useful in the treatment of congenital heart disease should be provided.  

      Thank you for the insight. We have incorporated your comments in the discussion. 

      Item 4. Insights into the role of CDK9-Rtf1 in response to stress versus in cardiogenesis. 

      In the Discussion, the authors commented on the role of additional stress-related stimuli such as heat shock and inflammation that have been linked to CDK9 activity. However, the current ms provides the first, endogenous role of Pol2 pausing in a critical developmental step during normal cardiogenesis. The authors should emphasize the novelty and significance of their work by providing a paragraph on the state of knowledge on the molecular mechanisms governing cardiogenesis, then placing their discovery within this framework. This minor addition will also clarify the significance of this work to the broad readership of eLife. 

      Thank you for the suggestion. We have incorporated your comments and elaborate on the novelty and significance of our work in the discussion. 

      Reviewer #2 (Recommendations For The Authors): 

      (1) It is diUicult to assess what the overt defects are in the embryos at any stages. Images of live images were not included in the supplement. Do these have a small, malformed heart tube later or are the embryos just deteriorating due to broad defects? 

      The Rtf1 deficient embryos do not produce nkx2.5+ cardiac progenitors. Consequently, we never observed a heart tube or detected cells expressing cardiomyocyte marker genes such as myl7. This finding is consistent with previous reports using rtf1 morphants and rtf<sup>1KT64</sup>, an ENU-induced point mutation allele (Langenbacher et al., 2011 and Akanuma, 2007). In this revised manuscript, we provide a live image of 2-day-old wild type and rtf1<sup>LA2679/LA2679</sup> embryos (Fig. 2 Supplement 1). After two days, rtf1 mutant embryos undergo broad cell death. 

      (2) Fig. 2, although the in situs are convincing, there is not a quantitative assessment of expression changes for these genes. This could have been done for the bulk or single cell RNA-seq experiments, but was not and these genes weren't not included in the heat maps. A quantitative assessment of these genes would benefit the study. 

      The top 40 most significantly differentially expressed genes are displayed in the heatmap presented in Fig.5d. The complete differential gene expression analysis results for our hand2 FACS-based comparison of rtf1 morphants and controls is presented in Supplementary Data File 1.  In this revised manuscript, we provide a new supplemental figure with violin plots showing the expression levels of genes of interest in our single cell sequencing dataset (Fig.6 Supplement 5).

      (3) It doesn't not appear that any statistical tests were used for the comparisons in Fig. 2.

      We now provide the statistical data in the legend and Fig.2 b, d, f, h and i.

      (4) It's not clear the magnifications and orientations of the embryos in Fig. 3b are the same. 

      Embryos shown in Fig.3b are at the same magnification. However, because Rtf1 mutant embryos display severe morphological defects, the orientation of mutant embryos was adjusted to examine the cardiac tissue.

      (5) The n's for analysis of MLC2v in WT Rtf1 CKO embryos in Fig. 3b are only 1. At least a few more embryos should be analyzed to confirm that the phenotype is consistent. 

      We have revised the figure and present the number of embryos analyzed and statistics in Fig.3c. 

      (6) A number of figure panels are referred to out of order in the text. Fig. 4E-G are before Fig. 4C, D, Fig. 7C  before 7B, Fig. 8D-I before 8A ,B. In general, it is easier for the reader if the figures panels are presented in the order they are referred to in the text. 

      Revised as suggested.

      (7) While additional genes can be included, it is not clear why the same sets of genes are not examined in the bulk or single-cell RNA-seq as with the in situs or expression was analyzed in embryos. I suggest including the genes like nkx2.5, tbx20, myl7, in all the sequencing analysis. 

      We used the same set of genes in all analyses when possible. However, the low expression of genes such as nkx2.5 and myl7 in our sc-seq dataset preclude them from the clustering/trajectory analysis. In this revised manuscript, we present violin plots showing their expression in wild type and rtf1 morphants (Fig. 6 Supplement 5).

      (8) If a multiomic approach was used, why wasn't its analysis incorporated more into the manuscript? In general, a clearer presentation and deeper analysis of the single cell data would benefit the study. The integration of the RNA and ATAC would benefit the analysis.

      As addressed in our response to the reviewer’s public review, both datasets were used in clustering. Examining changes in chromatin accessibility is certainly interesting, but beyond the scope of this study. 

      (9) Many of the markers analyzed are not cardiac specific or it is not clear they are expressed in cardiac progenitors at the stage of the analysis. Hand2 has broader expression. Additional confirmation of some of the genes through in situ would help the interpretations. 

      Markers used for the in situ hybridization analysis (myl7, mef2ca, nkx2.5, tbx5a, and tbx20) are known for their critical role in heart development. For sc-seq trajectory analyses, most displayed genes (sema3e, bmp6, ttn.2, mef2cb, tnnt2a, ryr2b, and myh7bb) were identified based on their differential expression along the LPM-cardiac progenitor pseudotime trajectory. Rather than selecting genes based on their cardiac specificity, our goal was to examine the progressive gene expression changes associated with cardiac progenitor formation and compare gene expression of wild type and rtf1 deficient embryos.

      (10) Additional labels of the cell clusters are needed for Supplemental Figs. 2 and 3. 

      The cluster IDs were presented on Supplementary Figures 2 and 3. In this revised version, we added predicted cell types to the UMAP (revised Fig.6 Supplement 1) and provided an excel file with this information (revised Supplementary Table 2). 

      (11) On lines 101-102, the interpretation from the previous data is that diUerentiation of the LPM requires Rtf1. However, later from the single cell data the interpretation based on the markers is that Rtf1 loss aUects maturation. However, it is not clear this interpretation is correct or what changed from the single cell data. If that were the case, one would expect to see maintenance of more early marks and subsequent loss of maturation markers, which does not appear to the be the case from the presented data.

      Our data suggests that cardiac progenitor formation is not accomplished by simultaneously switching on all cardiac marker genes. Our pseudotime trajectory analysis highlights tnnt2a, ryr2b, and myh7bb as genes that increase in expression in a lagged manner compared to mef2cb (Fig. 6). Thus, the abnormal activation of mef2cb without subsequent upregulation of tnnt2a, ryr2b, and myh7bb in rtf1 morphants suggests a requirement for rtf1 in the progressive gene expression changes required for proper cardiac progenitor differentiation. Our single cell experiment focuses on the process of cardiac progenitor differentiation and does not provide insights into cardiomyocyte maturation. We have edited the text to clarify these interpretations. 

      (12) The interpretation that there is not "transfating" is not supported by the shown data. Analysis of markers in other tissues, again with in situ, to show spatially would benefit the study. 

      As stated in our response to the reviewer’s public review, we observed a dramatic increase of ALPM cells, but a decrease of ALPM derivatives including the cardiac lineage. We did not observe the expansion of one ALPM-derived subpopulation at the expense of the others. These observations suggest a defect in ALPM differentiation and argue against the notion that the region of the ALPM that would normally give rise to cardiac progenitors is instead differentiating into another cell type.

      (13) The rationale that sequence conservation means a gene is important (lines 137-139) is not really true. There are examples a lot of highly conserved genes whose mutants don't have defects. 

      We have revised the text to avoid confusion. 

      (14) The data showing that the 8 bp mutations do not aUect the RNA transcript is not shown or at least indicated in Fig. 7. It would seem that this experiment could have been done in the mutant embryos, in which case the experiment would have been semi-blinded as the genotyping would occur after imaging. 

      The modified Rtf1 wt RNA (Rtf1 wt* in revised Fig. 7) robustly rescued nkx2.5 expression in rtf1 deficient embryos, demonstrating that the 8 bp modifications do not negatively impact the activity of the injected RNA. As stated previously, morpholino knockdown was used in some experiments because our characterization of rtf1 morphants showed that they faithfully recapitulate the rtf1 mutant phenotype during the timeframe of interest.

      (15) Using a technique like PRO-seq at the same stage as the ChIP-seq would complement the ChIP-seq and allow a more detailed analysis of the transcriptional pausing on specific genes observed in WT and mutant embryos. 

      As stated in our response to the reviewer’s public review, we appreciate the suggestion but PRO-seq is beyond the scope of this study.

    1. Reviewer #3 (Public review):

      Summary:

      In this study, Miyatake et al. present the interesting finding that ectopic expression of miR-195 in EBF1-deficient hematopoietic progenitor cells can partially rescue their developmental block and allows B cells to progress to a B220+ CD19+ cells stage. Notably, this is accompanied by an upregulation of B cell specific genes and, correspondingly, a downregulation of T, myeloid and NK lineage-related genes, suggesting that miR-195 expression is at least in part equivalent to EBF1 activity in orchestrating the complex gene regulatory network underlying B cell development. Strengthening this point, ATAC sequencing of miR-195-expressing EBF1-deficient B220+CD19+ cells and a comparison of these data to public datasets of EBF1-deficient and -proficient cells suggest that miR-195 indirectly regulates gene expression and chromatin accessibility of some, but not all regions regulated by EBF1.

      Mechanistically, the authors identify a subset of potential target genes of miR-195 involved in MAPK and PI3K signalling. Dampening of these pathways has previously been demonstrated to activate FOXO1, a key transcription factor for early B cells downstream of EBF1. Accordingly, the authors hypothesize that miR-195 exerts its function through FOXO1. Supporting this claim, also exogenous FOXO1 expression is able to promote the development of EBF1-deficient cells to the B220+CD19+ stage and thus recapitulates the miR-195 phenotype.

      Strengths:

      The strength of the presented study is the detailed assessment of the altered chromatin accessibility in response to ectopic miR-195 expression. This provides insight into how miR-195 impacts on the gene regulatory network that governs B cell development and allows the formation of mechanistic hypotheses.

      Weaknesses:

      The key weakness of this study is that its findings are based on the artificial and ectopic expression of a miRNA out of its normal context, which in my opinion strongly limits the biological relevance of the presented work.

      While the authors performed qPCRs for miR-195 on different B cell populations and show that its relative expression peaks in early B cells, it remains unclear whether the absolute miR-195 expression is sufficiently high to have any meaningful biological activity. In fact, other miRNA expression data from immune cells (e.g. DOI 10.1182/blood-2010-10-316034 and DOI 10.1016/j.immuni.2010.05.009) suggest that miR-195 is only weakly, if at all, expressed in the hematopoietic system.<br /> Update to this part after revision: The authors now state in the discussion that their study does not aim to uncover and characterize a physiological role of miR-195 in lymphocytes development, but rather reveals "the potential of miR-195 to compensate for EBF1 deficiency". However, in my opinion, the absence of any physiological context still limits this study's relevance.

      The authors support their finding by a CRISPR-derived miR-195 knockout mouse model which displays mild but significant differences in the hematopoietic stem cell compartment and in B cell development. However, they fail to acknowledge and discuss a lymphocyte-specific miR-195 knockout mouse that does not show any B cell defects in the bone marrow or spleen and thus contradicts the authors' findings (DOI 10.1111/febs.15493). Of note, B-1 B cells in particular have been shown to be elevated upon loss of miR-15-16-1 and/or miR-15b-16-2, which contradicts the data presented here for loss of the family member miR-195.

      A second weakness is that some claims by the authors appear overstated or at least not fully backed up by the presented data. In particular, the findings that miR-195-expressing cells can undergo VDJ recombination, express the pre-BCR/BCR and can class switch need to be strengthened. It would be beneficial to include additional controls to these experiments, e.g. a RAG-deficient mouse as a reference/negative control for the ddPCR and the surface IgM staining, and cells deficient in class switching for the IgG1 flow cytometric staining.

      Moreover, the manuscript would be strengthened by a more thorough investigation of the hypothesis that miR-195 promotes the stabilization and activity of FOXO1, e.g. by comparing the authors' ATACseq data to the FOXO1 signature.

    2. Author response:

      The following is the authors’ response to the original reviews.

      eLife assessment 

      This useful study reports that the exogenous expression of the microRNA miR-195 can partially compensate in early B cell development for the loss of EBF1, one of the key transcription factors in B cells. While this finding will be of interest to those studying lymphocyte development, the evidence, particularly with regard to the molecular mechanisms that underpin the effect of miR-195, is currently incomplete. 

      Public Reviews: 

      Reviewer #1 (Public review):

      Summary: 

      Here, the authors are proposing a role for miR-196, a microRNA that has been shown to bind and enhance the degradation of mRNA targets in the regulation of cell processes, and has a novel role in allowing the emergence of CD19+ cells in cells in which Ebf1, a critical B-cell transcription factor, has been genetically removed. 

      Strengths: 

      That over-expression of mR-195 can allow the emergence of CD19+ cells missing Ebf1 is somewhat novel. 

      Their data does perhaps support to a degree the emergence of a transcriptional network that may bypass the absence of Ebf1, including the FOXO1 transcription factor, but this data is not strong or definitive. 

      Weaknesses: 

      It is unclear whether this observation is in fact physiological. When the authors analyse a knockout model of miR-195, there is not much of a change in the B-cell phenotype. Their findings may therefore be an artefact of an overexpression system. 

      The authors have provided insufficient data to allow a thorough appraisal of the stepwise molecular changes that could account for their observed phenotype. 

      Reviewer #2 (Public review): 

      Summary: 

      The authors investigate miRNA miR-195 in the context of B-cell development. They demonstrate that ectopic expression of miR-195 in hematopoietic progenitor cells can, to a considerable extent, override the consequences of deletion of Ebf1, a central Blineage defining transcription factor, in vitro and upon short-term transplantation into immunodeficient mice in vivo. In addition, the authors demonstrate that the reverse experiment, genetic deletion of miR-195, has virtually no effect on B-cell development. Mechanistically, the authors identify Foxo1 phosphorylation as one pathway partially contributing to the rescue effect of miR-195. An additional analysis of epigenetics by ATACseq adds potential additional factors that might also contribute to the effect of ectopic expression of miR-195. 

      Strengths: 

      The authors employ a robust assay system, Ebf1-KO HPC, to test for B-lineage promoting factors. The manuscript overall takes on an interesting perspective rarely employed for the analysis of miRNA by overexpressing the miRNA of interest. Ideally, this approach may reveal, if not the physiological function of this miRNA, the role of distinct pathways in developmental processes. 

      Weaknesses: 

      At the same time, this approach constitutes a major weakness: It does not reveal information on the physiological role of miR-195. In fact, the authors themselves demonstrate in their KO approach, that miR-195 has virtually no role in B-cell development, as has been demonstrated already in 2020 by Hutter and colleagues. While the authors cite this paper, unfortunately, they do so in a different context, hence omitting that their findings are not original. 

      Conceptually, the authors stress that a predominant function of miRNA (in contrast to transcription factors, as the authors suggest) lies in fine-tuning. However, there appears to be a misconception. Misregulation of fine-tuning of gene expression may result in substantial biological effects, especially in developmental processes. The authors want to highlight that miR-195 is somewhat of an exception in that regard, but this is clearly not the case. In addition to miR-150, as referenced by the authors, also the miR-17-92 or miR-221/222 families play a significant role in B-cell development, their absence resulting in stage-specific developmental blocks, and other miRNAs, such as miR-155, miR-142, miR-181, and miR-223 are critical regulators of leukocyte development and function. Thus, while in many instances a single miRNA moderately affects gene expression at the level of an individual target, quite frequently targets converge in common pathways, hence controlling critical biological processes. 

      The paper has some methodological weaknesses as well: For the most part, it lacks thorough statistical analysis, and only representative FACS plots are provided. Many bar graphs are based on heavy normalization making the T-tests employed inapplicable. No details are provided regarding the statistical analysis of microarrays. Generation of the miR-195-KO mice is insufficiently described and no validation of deletion is provided. Important controls are missing as well, the most important one being a direct rescue of Ebf1-KO cells by re-expression of Ebf1. This control is critical to quantify the extent of override of Ebf1-deficiency elicited by miR-195 and should essentially be included in all experiments. A quantitative comparison is essential to support the authors' main conclusion highlighted in the title of the manuscript. As the manuscript currently stands, only negative controls are provided, which, given the profound role of Ebf1, are insufficient, because many experiments, such as assessment of V(D)J recombination, IgM surface expression, or class-switch recombination, are completely negative in controls. In addition, the authors should also perform long-term reconstitution experiments. While it is somewhat surprising that the authors obtained splenic IgM+ B cells after just 10 days, these experiments would be certainly much more informative after longer periods of time. Using "classical" mixed bone marrow chimeras using a combination of B-cell defective (such as mb1/mb1) bone marrow and reconstituted Ebf1-KO progenitors would permit much more refined analyses. 

      With regard to mechanism, the authors show that the Foxo1 phosphorylation pathway accounts for the rescue of CD19 expression, but not for other factors, as mentioned in the discussion. The authors then resort to epigenetics analysis, but their rationale remains somewhat vague. It remains unclear how miR-195 is linked to epigenetic changes. 

      Reviewer #3 (Public review): 

      Summary: 

      In this study, Miyatake et al. present the interesting finding that ectopic expression of miR-195 in EBF1-deficient hematopoietic progenitor cells can partially rescue their developmental block and allow B cells to progress to a B220+ CD19+ cells stage. Notably, this is accompanied by an upregulation of B-cell-specific genes and, correspondingly, a downregulation of T, myeloid, and NK lineage-related genes, suggesting that miR-195 expression is at least in part equivalent to EBF1 activity in orchestrating the complex gene regulatory network underlying B cell development. Strengthening this point, ATAC sequencing of miR-195-expressing EBF1-deficient B220+CD19+ cells and a comparison of these data to public datasets of EBF1-deficient and -proficient cells suggest that miR-195 indirectly regulates gene expression and chromatin accessibility of some, but not all regions regulated by EBF1. 

      Mechanistically, the authors identify a subset of potential target genes of miR-195 involved in MAPK and PI3K signaling. Dampening of these pathways has previously been demonstrated to activate FOXO1, a key transcription factor for early B cells downstream of EBF1. Accordingly, the authors hypothesize that miR-195 exerts its function through FOXO1. Supporting this claim, also exogenous FOXO1 expression is able to promote the development of EBF1-deficient cells to the B220+CD19+ stage and thus recapitulates the miR-195 phenotype. 

      Strengths: 

      The strength of the presented study is the detailed assessment of the altered chromatin accessibility in response to ectopic miR-195 expression. This provides insight into how miR-195 impacts the gene regulatory network that governs B-cell development and allows the formation of mechanistic hypotheses. 

      Weaknesses: 

      The key weakness of this study is that its findings are based on the artificial and ectopic expression of a miRNA out of its normal context, which in my opinion strongly limits the biological relevance of the presented work. 

      While the authors performed qPCRs for miR-195 on different B cell populations and show that its relative expression peaks in early B cells, it remains unclear whether the absolute miR-195 expression is sufficiently high to have any meaningful biological activity. In fact, other miRNA expression data from immune cells (e.g. DOI

      10.1182/blood-2010-10-316034 and DOI 10.1016/j.immuni.2010.05.009) suggest that miR-195 is only weakly, if at all, expressed in the hematopoietic system. 

      The authors support their finding by a CRISPR-derived miR-195 knockout mouse model which displays mild, but significant differences in the hematopoietic stem cell compartment and in B cell development. However, they fail to acknowledge and discuss a lymphocyte-specific miR-195 knockout mouse that does not show any B cell defects in the bone marrow or spleen and thus contradicts the authors' findings (DOI

      10.1111/febs.15493). Of note, B-1 B cells in particular have been shown to be elevated upon loss of miR-15-16-1 and/or miR-15b-16-2, which contradicts the data presented here for loss of the family member miR-195. 

      A second weakness is that some claims by the authors appear overstated or at least not fully backed up by the presented data. In particular, the findings that miR-195expressing cells can undergo VDJ recombination, express the pre-BCR/BCR and class switch needs to be strengthened. It would be beneficial to include additional controls to these experiments, e.g. a RAG-deficient mouse as a reference/negative control for the ddPCR and the surface IgM staining, and cells deficient in class switching for the IgG1 flow cytometric staining. 

      Moreover, the manuscript would be strengthened by a more thorough investigation of the hypothesis that miR-195 promotes the stabilization and activity of FOXO1, e.g. by comparing the authors' ATACseq data to the FOXO1 signature. 

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors): 

      Miyatake et al., present a manuscript that explores the role of miR-195 in B cell development. 

      Their data suggests a role for this microRNA: 

      Using an Ebf1 fetal liver knockout of B-cell differentiation that a small population of CD19 expressing with some evidence of V(D)J recombination capable of class switch can be derived by transduction of miR-195. 

      In the emergent CD19+ Ebf1-/- cells, the authors provide some evidence that Mapk and Akt3 may be miR-195 targets that are downregulated allowing FOXO1 transcription factor pathway may be involved in the emergent CD19+ cells arising from miR-195 transduction. 

      Perhaps less compelling data is provided with regards to a role for miR-195 in normal Bcell development through analysis of a miR-195 knockout model. 

      While there are some interesting preliminary data presented for a role for miR-195 in the context of Ebf1-/- cells, there are some questions I think the authors could consider. 

      Comments: 

      (1-1) It is difficult to ascertain the potential role of miR-195 transduction in allowing the emergence of CD19+ cells from the data provided. miR-195 has been generally shown to destabilize mRNA transcripts by 3' UTR binding that targets mRNA transcripts for degradation. The effect of transduction of miR-195 would therefore be expected to be related to the degradation of factors opposing aspects of B-lineage specification or maintenance. I would be particularly interested in transcriptional or epigenetic regulators that may be modified in this way, at an mRNA as well as protein level.

      We appreciate the reviewerʼs thoughtful comments and agree that miRNAs often exert their effects through the degradation or translational repression of mRNAs encoding regulatory factors. In our study, we attempted to address this point by combining predictive analysis (using TargetScan and starBase) with luciferase reporter assays and qPCR to validate several potential targets of miR-195, including Mapk3 and Akt3. We acknowledge that this is not a comprehensive mechanistic analysis. We agree that a broader and systematic identification of direct targets of miR-195, particularly those involved in transcriptional and epigenetic regulation, would further clarify the mechanisms involved. However, due to limitations in resources and time, we are currently unable to perform global proteomic or ChIP-based validations. Nevertheless, our ATAC-seq and microarray data indicate that miR-195 overexpression leads to increased accessibility and expression of several key B-lineage transcription factors (Pax5, Runx1, Irf8), suggesting that miR-195 indirectly activates transcriptional programs relevant to B cell commitment. We have now clarified this limitation in the revised Discussion section (lines 505‒524), and we emphasize that our current findings represent the potential of miR-195 rather than its physiological role. We hope that this clarification addresses the concern.

      (1-2) While I acknowledge the authors have undertaken TargetScan and starBase analysis to try and predict miR-195 interactions, they do not provide a comprehensive list of putative targets that can be referenced against their cDNA data. Though they postulate Mapk3 and Akt3 as putative miR-195 targets and assay these in luciferase reporter systems (Figure 4), these were not clearly differentially regulated in the microarray data they provided (Figure 1E) as being downregulated on miR-195 transduction in Ebf1-/- cells.

      We thank the reviewer for pointing out the need for a more comprehensive list of predicted miR-195 targets. In response, we have now included a supplementary table 4 (human) and 5 (mouse) listing all putative miR-195 targets predicted by TargetScan and starBase. As noted, Mapk3 expression was indeed downregulated upon miR-195 transduction, consistent with our luciferase reporter and qPCR results. For Akt3, we observed variability in the microarray data depending on the probe used, resulting in inconsistent expression levels. We acknowledge this and have added a clarification in the revised manuscript (lines 335‒339), noting that the regulation of Akt3 by miR-195 is potentially probe-dependent and may require further validation. We hope this clarification resolves the concern.

      (1-3) The authors should provide a more comprehensive analysis of transcriptional changes induced by miR-195 Ebf1-/- specifically in the preproB cell stage of development in Ebf1-/- and miR-195 Ebf1-/- cells. The differentially expressed gene list should be provided as a supplemental file. The gene expression data should be provided for the different B-cell differentiation stages, eg. Ebf1-/- preproB cells, and Ebf1-/- miR-195 preproB cells, CD19+ cells and more differentiated subsets induced by miR-195 transduction.

      We appreciate the reviewerʼs suggestion to provide a more comprehensive transcriptomic analysis at different B-cell differentiation stages. Unfortunately, due to the limited availability of cells and technical constraints, we were unable to perform RNA-seq on miR-195 transduced Ebf1<sup>−/−</sup> pre-pro-B or CD19+ cells. However, to address this point, we referenced publicly available RNA-seq data (GEO accession: GSE92434), which includes transcriptomic profiles of Ebf1<sup>−/−</sup> pro-B cells and wild-type controls. By comparing our microarray data from miR-195 transduced Ebf1<sup>−/−</sup> cells with this dataset, we found partial restoration of expression for several key B-lineage genes, such as Pax5, Runx1, and Irf8, which are normally downregulated in the absence of EBF1. This comparison supports the notion that miR-195 partially reactivates the transcriptional network essential for B cell development. We have added this interpretation to the Discussion section (lines 528‒533).

      (1-4) More replicates (at least 3 of each genotype) are required for their Western Blots for FOXO1 and pFOXO1 (Fig 4C, D). Western blots should also be provided for other known B-lineage transcriptional regulators such as PAX5 and ERG.

      We thank the reviewer for these valuable suggestions. In response, we have now quantified and added the relative band intensities of FOXO1 and pFOXO1 from three independent experiments in the revised Figure 4C, and we include statistical analysis to support the reproducibility of these results. Additionally, as requested, we performed western blotting for PAX5 and ERG using the same samples. The results showed no significant change in these protein levels between miR-195-transduced and control Ebf1<sup>−/−</sup> cells, consistent with the modest upregulation observed in our microarray data. We have included the PAX5 and ERG western blot images in Supplementary Figure S3 and have revised the text in the Results section (lines 351‒35)

      (1-5) The authors have not shown a transcriptional binding by ChIPseq or other methods such as cut and tag/ cut and run for FOXO1 binding to B-lineage genes in their Ebf1-/- miR-195 CD19+ cells to be able to definitively show this TF is critical for the emergence of the C19+ cell phenotype by demonstrating direct binding to "upregulated" genes cis-regulatory regions in the Ebf1-/- miR-195 CD19+ cells

      We appreciate the reviewerʼs suggestion regarding the use of ChIP-seq or related methods to demonstrate direct FOXO1 binding to cis-regulatory regions of B-lineage genes in Ebf1<sup>−/−</sup> miR-195 CD19⁺ cells. We agree that such data would provide definitive evidence of FOXO1's direct involvement in promoting the B cell-like transcriptional program. However, due to current technical limitations, including the scarcity of CD19⁺ cells derived from Ebf1<sup>−/−</sup> miR-195 transduction and the requirement for large cell numbers in ChIP-seq or CUT&RUN protocols, we were unable to perform these assays in this study. Nevertheless, our current data provide multiple lines of indirect evidence supporting the involvement of FOXO1:

      miR-195 transduction leads to reduced phosphorylation and increased accumulation of FOXO1 protein (Fig. 4C).

      Overexpression of FOXO1 in Ebf1<sup>−/−</sup> HPCs partially recapitulates the miR-195 phenotype (Fig. 4D).

      ATAC-seq data show increased chromatin accessibility at known FOXO1 target gene loci (e.g., Pax5, Runx1, Irf8) in miR-195-induced CD19⁺ cells, many of which overlap with FOXO1 motifs(Fig.5)

      These observations collectively suggest that FOXO1 activity is functionally important for the emergence of CD19⁺ cells, even though direct binding has not been confirmed. We have added this limitation to the Discussion (lines 531‒537), and we note that future studies using FOXO1 CUT&RUN in this system would be valuable to further define the underlying mechanism.

      (1-6) The authors have not shown significant upregulation of expression of other critical B-cell regulatory transcription factors in their Ebf1-/- miR-195 CD19+ cells that could account for the emergence of these cells such as Pax5 or Erg. The legend in Figure 1E suggests for example the change in expression of Pax5 is modest if anything at best as no LogFC or western blot data is presented. 

      We thank the reviewer for raising this point. In our microarray analysis (Figure 1D, original Figure 1E), we observed that both Pax5 and Erg mRNA levels were upregulated in Ebf1<sup>−/−</sup> cells upon miR-195 transduction. Specifically, Pax5 showed an increase of approximately log₂FC 1.2, and Erg was also consistently elevated across biological replicates. These changes, although modest, were statistically significant and consistent with the upregulation of other B-lineage-associated transcription factors, such as Runx1 and Irf8. We agree that the magnitude of Pax5 upregulation is not as high as typically seen during full B cell commitment, and therefore may not have been immediately apparent in Figure 1D (original Figure 1E). To clarify this point, we have now revised the text in the Results section (lines 170‒174) to highlight the observed changes in Pax5 and Erg expression. We believe that the upregulation of these transcription factors, together with increased FOXO1 activity and changes in chromatin accessibility (Figure 5), contributes to the partial reactivation of the B cell gene regulatory network in the absence of EBF1.

      (1-7) Which V(D)J transcripts have been produced? A more detailed analysis other than ddPCR is required to help understand the emergence of this population that can presumably proceed through the preBCR and BCR checkpoints.

      We appreciate the reviewerʼs interest in understanding the nature of the V(D)J rearrangements in Ebf1<sup>−/−</sup> miR-195 CD19⁺ cells. As noted, our current data rely on droplet digital PCR (ddPCR), which was used to detect rearranged VH-JH segments in the bone marrow of engrafted mice. While this approach does not allow for detailed mapping of specific V, D, or J gene usage, it provides a sensitive and quantitative measure of V(D)J recombination activity. The detection of rearranged VH-JH fragments in miR-195-transduced Ebf1<sup>−/−</sup> cells suggests that at least partial recombination of the immunoglobulin heavy chain locus is occurring̶an essential checkpoint for progression past the pro-B cell stage. Given the lack of such rearrangements in control-transduced Ebf1<sup>−/−</sup> cells, we interpret this as evidence that miR-195 enables cells to initiate the recombination process. We acknowledge the limitations of ddPCR and agree that a more detailed analysis using VDJ-seq or singlecell RNA-seq would be valuable in determining the diversity and completeness of the V(D)J transcripts produced. This is a direction we intend to pursue in future work. We have added this limitation to the Discussion section (lines 538‒543).

      (1-8) The authors reveal that the Foxo1 transduced Ebf1-/- cells (Fig. 4D) do not persist in vitro or be detected via transplant assay (line 256) and therefore does not represent a truly "rescued" B cell, suggesting that CD19+ cells Ebf1-/- miR-195 transduced cells have more B-cell potential. Further characterisation is therefore warranted of this cell population. For instance, can these cells be induced to undergo myeloid differentiation in myeloid cytokine conditions? What other B-lineage transcriptional regulators are expressed in this cell population that could account for VDJ recombination and expression of a B-lineage transcriptional program (see comments 1, 3, and 5) that allow transition through preBCR and BCR checkpoints as well as undergo class switching?

      We thank the reviewer for this insightful comment. We agree that the persistence and lineage potential of the CD19⁺ cells emerging from Ebf1<sup>−/−</sup> miR-195-transduced progenitors deserve further characterization. Although we were unable to perform additional lineage re-direction assays, our current data provide several lines of evidence suggesting that these cells are stably committed toward the B-lineage:

      Gene expression profiling revealed upregulation of multiple B cell transcriptional regulators, including Pax5, Runx1, and Irf8.

      ATAC-seq analysis showed increased chromatin accessibility at B cell‒specific loci and enrichment of motifs bound by key B-lineage factors such as FOXO1 and E2A.

      The cells express surface IgM and undergo class switch recombination to IgG1 upon stimulation, indicating successful transition through the pre-BCR and BCR checkpoints and acquisition of mature B cell functions.

      Importantly, no upregulation of myeloid- or T-lineage genes was detected in the microarray analysis, arguing against multipotency at this stage.We acknowledge that functional tests for lineage plasticity under altered cytokine conditions would provide important insights and plan to address this question in future studies. This limitation has now been noted in the revised Discussion (lines 544‒550).

      (1-9) In the original Ebf1-/- miR-195 CD19+ experiments, a wild-type control should be provided for each experiment. 

      We appreciate the reviewerʼs suggestion to include wild-type controls in all experiments. While we did not include wild-type samples side-by-side in every assay, we carefully designed our experiments to include biologically appropriate and informative comparisons. For example, in the bone marrow transplantation experiments (Figure 2), Ebf1<sup>−/−</sup> cells transduced with empty vector served as negative controls, clearly lacking CD19 expression, V(D)J recombination, IgM surface expression, and class switch capability. This allowed us to specifically assess the gain-of-function effects of miR-195 in the EBF1-deficient background. In several analyses̶such as the ATAC-seq and microarray comparisons̶we did incorporate or refer to existing wild-type datasets (e.g., GSE92434), providing context for the extent of recovery toward a WT-like profile. We agree, however, that including parallel WT controls across all experimental platforms would enhance interpretability.

      (1-10) For ATACseq data, a comparison between Ebf1-/- preproB cells and Ebf1-/- miR-195 CD19+ cells should be undertaken.

      We thank the reviewer for this important point. As suggested, we have performed a direct comparison of chromatin accessibility between Ebf1<sub>−/−</sub> pre-pro-B‒like cells (CD19<sub>-</sub>, control transduction) and Ebf1<sub>−/−</sub> miR-195‒transduced CD19⁺ cells. This comparison is shown in green in Figure 5B and represents the ATAC-seq peaks differentially accessible between these two populations.  

      (1-11) I cannot agree with the authors with some of their statements such as Line 242 - "therefore miR-195 considered to have similar function with EBF1 to some extent" - how can this be the case when miR-195 is a miRNA and EBF1 is a transcription factor with pioneering transcriptional activity? Surely the effects of miR-195 must be secondary.

      We thank the reviewer for pointing out the inappropriateness of comparing miR-195 to EBF1 in terms of functional similarity. We agree that miR-195, as a microRNA, operates through post-transcriptional regulation and does not possess the pioneering transcriptional activity characteristic of EBF1. To avoid confusion or overstatement, we have removed the sentence in line 242 ("therefore miR-195 is considered to have similar function with EBF1 to some extent").

      (1-12) It is unclear whether this observation is in fact physiological. When the authors analyse a knockout model of miR-195, there is not much of a change in the B-cell phenotype. Their findings may therefore be an artefact of an overexpression system. The authors should comment on this observation in their discussion.  

      We thank the reviewer for this important observation. We agree that the mild phenotype observed in our miR-195 knockout mice suggests that miR-195 is not essential for B cell development under steady-state physiological conditions. Accordingly, we do not claim a physiological requirement for miR-195. Rather, our study demonstrates that miR-195 possesses the potential to activate a B-lineage program in the absence of EBF1 when ectopically expressed. This functional potential̶rather than its endogenous necessity̶ is the main focus of our work. We have now clarified this distinction in the revised Discussion section (lines 551‒560), and we emphasize that our findings highlight an alternative regulatory pathway that can be artificially engaged under specific conditions.

      (1-13) I recommend the authors check spelling and grammar throughout their manuscript.

      We thank the reviewer for the suggestion. In response, we have carefully reviewed the manuscript for spelling, grammar, and clarity. Minor corrections have been made throughout the text to improve readability and ensure consistency. We hope that the revised version addresses any language-related concerns. In addition, the manuscript has been reviewed by professional editing service to improve the language quality.

      (1-14) In general, I recommend more comprehensive primary data be presented in the manuscript or supplementary files to add value to their submission.

      We thank the reviewer for this helpful suggestion. In response, we have revised the manuscript and supplementary materials to include additional primary data wherever possible. The bar graphs have been updated to include individual data points to show variability and replicate information. Uncropped western blot images are now provided in Supplementary Figure S2. We hope these additions provide greater transparency and value to the manuscript. 

      Reviewer #2 (Recommendations for the authors): 

      I have a number of suggestions with regard to inclusion of details and controls: 

      (2-1) The authors need to provide more details on in vitro differentiation, especially culture times. 

      Thank you for your comment. The culture conditions for in vitro differentiation of Ebf1<sup>−/−</sup> hematopoietic progenitor cells are described in the Methods section (lines 648‒ 649) under “Culture of lineage-negative (Lin‒) cells from the fetal liver.” As stated, cells were cultured more than 7 days under the specified conditions.

      (2-2) In Figure 1E, the authors need to provide information on statistics (FDR or similar). 

      I thank the reviewer for the suggestion. In Figure 1D (Original Figure 1E) (the microarray analysis), only two biological replicates were available for each condition (n = 2 per group). Due to this limited sample size, we did not perform statistical testing, as the power would be insufficient to produce reliable p-values or adjusted FDRs. Instead, we focused on genes with consistent and biologically meaningful changes in expression, and presented representative examples based on fold change values.

      (2-3) For in vivo experiments (Figure 2) the authors should comment on their use of two different recipient mouse strains despite very low n numbers. As described above, classical mixed BM chimeras would be much more informative. In these experiments, the authors should also show the formation of other lymphoid lineages. This would answer the question of whether miR-195 redirects cells to the B lineage. Most importantly, absolute numbers need to be provided, especially in conjunction with Ebf1 rescue as described above. 

      We thank the reviewer for the thoughtful and detailed suggestions regarding our in vivo experiments. Regarding the use of different recipient mouse strains, our initial intention was to perform the transplantations in BRG mice; however, due to facility restrictions and animal husbandry considerations, we had to switch to NOG mice. All in vivo experiments were performed with n = 3 per group, in accordance with ethical guidelines and efforts to minimize animal use while still ensuring reproducibility. With respect to the suggestion of mixed bone marrow chimeras, we agree that this approach can provide valuable information on lineage competitiveness. However, in our system, miR-195 confers only a very limited B cell developmental potential in Ebf1<sup>−/−</sup> progenitors. In such a setting, the inclusion of wild-type competitor cells would overwhelmingly dominate the B cell compartment, likely masking any measurable effect of miR-195. Therefore, we opted to assess the gain-of-function potential of miR-195 in a noncompetitive setting. Regarding the assessment of other lymphoid lineages, we focused our analysis on the emergence of B-lineage cells, as the frequency of CD19⁺ cells induced by miR-195 is quite low. Given this low efficiency, we consider it unlikely that miR-195 significantly alters the development of non-B lineages, and thus did not observe substantial lineage diversion effects. Our aim was not to demonstrate lineage redirection, but rather to show that miR-195 can confer partial B cell potential in the absence of EBF1.

      Finally, we acknowledge the importance of presenting absolute cell numbers. However, the cell number collected from the mice were so few that we did not get the reliable results, we described it in the manuscript. (lines 498-501)

      (2-4) The statistics in Figure 3 are inadequate. No S.D. is provided for WT. How then was normalization performed? Student's T-test cannot be applied to ratios. 

      We thank the reviewer for highlighting the need for more appropriate statistical analysis. Due to considerable inter-batch variability in absolute measurements, we normalized the KO values to their paired WT counterparts from the same experimental batch. Specifically, for each replicate, we calculated the KO/WT ratio to control for batch-specific variation. We then applied a one-sample t-test (against a null hypothesis of ratio = 1) to determine statistical significance. We have now revised the figure to show individual ratio values for each replicate and updated the legend and Methods to clearly explain the statistical approach. We hope this addresses the concern and improves the clarity and rigor of the analysis.

      (2-5) In Figure 4A, the authors should comment on the strong repression of the Akt3UTR. 

      We appreciate the reviewerʼs observation regarding the strong repression observed with the Akt3 3'UTR construct. Indeed, we also noted that luciferase activity was markedly reduced in the presence of the Akt3 3'UTR, even in cells transduced with a control vector. We hypothesize that the Akt3 3'UTR contains strong post-transcriptional regulatory elements̶such as AU-rich elements or binding sites for endogenous miRNAs or RNA-binding proteins̶which may suppress mRNA stability or translation independent of miR-195. Alternatively, the secondary structure or length of the UTR may inherently reduce luciferase expression. We have added this limitation to the Discussion section (lines 561‒569).

      (2-6) The Western blot in Figure 4C is of insufficient quality. The authors need to provide unspliced versions of the bands including markers. 

      We thank the reviewer for this important comment. In response, we have included the unprocessed, full-length Western blot images corresponding to Figure 4C as Fig. S2. This provides a transparent view of the original data and addresses the concern about image cropping.

      (2-7) The ATACseq experiment in Figure 5 is difficult to comprehend. A simpler design including Ebf1 rescue controls would clearly improve this part. 

      We thank the reviewer for this valuable feedback. We agree that the original presentation of the ATAC-seq data may have been difficult to interpret. To address this, we have included a clear interpretation of the overlapping regions in the revised figure legend (lines 1018-1022). We hope this improves the clarity of the data and facilitates understanding of the chromatin changes mediated by EBF1 and miR-195.

      (2-8) The miR-195 KO mouse lacks validation (RT-PCR, genomic PCR) as well as a clear description of the deleted region and whether miR-497 is affected. In addition, the genetic background and number of backcrosses for the removal of potential off-target effects need to be mentioned. 

      We thank the reviewer for this important comment. The miR-195 knockout mouse was generated via CRISPR/Cas9, and Sanger sequencing confirmed a 628 bp deletion on chromosome 11 (GRCm38/mm10 chr11:70,234,425‒70,235,103). This deletion includes the entire miR-497 locus and part of the miR-195 precursor sequence. Although we do not show PCR gel images, the deletion was validated by sequencing, and the results are now clearly described in the revised Methods section (lines 607619). All transgenic mice in this study were backcrossed to the C57BL/6 background for at least eight generations.

      (2-9) The manuscript requires extensive editing for language. 

      We appreciate the reviewerʼs comment. The manuscript has now been revised and professionally edited for language by a native English-speaking editor. We believe clarity and readability have been significantly improved.

      Reviewer #3 (Recommendations for the authors): 

      (3-1) What is the expression level of miR-195 after viral overexpression? In Figure 4B, the authors show a 2.5-fold increase, but this appears very low for the experimental system (expression through the MDH1 retroviral construct) and the observed repressive effects (e.g. Figure 4A and B). 

      We thank the reviewer for this insightful comment. We agree that the apparent ~2.5fold increase in miR-195 levels (Figure 4B) may seem modest in the context of retroviral overexpression and the associated functional effects. However, due to the high sequence similarity within the miR-15/16/195/497 family, it is technically challenging to measure mature miR-195 levels with complete specificity. The baseline signal observed in control samples likely reflects cross-reactivity with endogenous miRNAs such as miR-497 or miR-16, which share similar seed sequences. Therefore, the reported fold-change may underestimate the true level of ectopic miR-195 expression. Despite this, we observed robust repression of validated targets (e.g., Mapk3, Akt3) in both qPCR and luciferase assays, indicating that functionally effective levels of miR-195 were achieved. We have now clarified this limitation and interpretation in the revised Results sections (lines 332‒335).

      (3-2) In alignment with the transparency of the data, I would encourage the authors to display the individual data points for all bar graphs. 

      We thank the reviewer for this helpful suggestion. In the revised manuscript, we have updated bar graphs to include individual data points to increase transparency and allow better visualization of data variability. In the ddPCR experiments, we provided the raw data in Fig. S1 for full transparency. In Fig. 1A, we have confirmed miR-195 expression profiles using the deposit data which the reviewer suggested, but miR-195 expression was very lower than we expected. We also performed scRNA-seq using hematopoietic lineage cells in 8-week-old C57BL/6 mice, but we could not get the reproducibility of miR-195 expression profiles. Therefore, we determined that this is an artifact caused by the miR-195 probe used for qPCR, and deleted Fig. 1A.

      (3-3) The references appear to be compromised. For example, the authors state that "The Ebf1−/+ mouse was originally generated by R. Grosschedl (39)" (line 297), but this is not the respective paper. Likewise, the knockout mouse was generated "based on the CRISPR/Cas9 system established by C. Gurumurthy (40)" (line 299), but he/she is not involved in the referenced study. 

      We thank the reviewer for pointing out the discrepancies in the reference citations. Upon revising the Methods section to integrate it with the main text, the reference numbering became misaligned. We have corrected the reference in the revised manuscript, and we thank the reviewer for bringing this to our attention.

      (3-4) Given that the miRNA Taqman assays the authors used here have difficulties to discriminate closely related miRNAs such as e.g. miR-16 (highly expressed in the hematopoietic system) and miR-195, I would suggest that the authors test their qPCR in an appropriate setup, e.g. in their knockout mouse model. In this context, did the authors use another small RNA as a reference for the qPCR analysis? In the methods, only GAPDH is mentioned, but in my opinion, another RNA that uses the same stemloop-based cDNA synthesis protocol would be better suited.

      We thank the reviewer for this valuable and technically insightful comment.

      As correctly pointed out, TaqMan-based qPCR assays for miRNAs such as miR-195 can show cross-reactivity with closely related family members, particularly miR-16, which is abundantly expressed in hematopoietic cells. Indeed, due to this limitation, we do not treat the qPCR results shown in the original Figures 1A and 4B as definitive quantification of miR-195 expression. Rather, these data are used to provide a suggestion and a rough estimate of overexpression efficiency, while our core functional analyses rely on phenotypic and molecular outcomes such as target gene repression and lineage emergence. With this in mind, although we acknowledge that a small RNA reference based on the same stem-loop cDNA synthesis would offer a more compatible normalization in principle, the inherent variability and lack of absolute specificity in such assays also limits their interpretive value. Therefore, we used GAPDH as a normalization control for consistency with other qPCR analyses in the manuscript. We have now clarified this rationale and limitation in the revised Methods sections (lines 712‒716), and we thank the reviewer again for highlighting this important technical consideration.

      (3-5) The Western blot data used to support the hypothesis that FOXO1 phosphorylation is reduced upon overexpression of miR-195 are not convincing. The authors should not crop everything but the band. 

      We thank the reviewer for the helpful comment. In response, we have now provided the full-length, uncropped Western blot images corresponding to Figure 4C, including both total FOXO1 and phospho-FOXO1 blots. These images are included in Fig. S2.

    1. Reviewer #1 (Public review):

      Summary:

      Rahmani et al. utilize the TurboID method to characterize global proteome changes in the worm's nervous system induced by a salt-based associative learning paradigm. Altogether, they uncover 706 proteins tagged by the TurboID method in worms that underwent the memory-inducing protocol. Next, the authors conduct a gene enrichment analysis that implicates specific molecular pathways in salt-associative learning, such as MAP kinase and cAMP-mediated pathways, as well as specific neuronal classes including pharyngeal neurons, and specific sensory neurons, interneurons, and motor neurons. The authors then screen a representative group of hits from the proteome analysis. They find that mutants of candidate genes from the MAP kinase pathway, namely dlk-1 and uev-3, do not affect performance in the learning paradigm. Instead, multiple acetylcholine signaling mutants, as well as a protein-kinase-A mutant, significantly affected performance in the associative memory assay (e.g., acc-1, acc-3, lgc-46, and kin-2). Finally, the authors demonstrate that protein-kinase-A mutants, as well as acetylcholine signaling mutants, do not exhibit a phenotype in a related but distinct conditioning paradigm-aversive salt conditioning-suggesting their effect is specific to appetitive salt conditioning.

      Overall, the authors addressed the concerns raised in the previous review round, including the statistics of the chemotaxis experiments and the systems-level analysis of the neuron class expression patterns of their hits. I also appreciate the further attempt to equalize the sample size of the chemotaxis experiments and the transparent reporting of the sample size and statistics in the figure captions and Table S9. The new results from the panneuronal overexpression of the kin-2 gain-of-function allele also contribute to the manuscript. Together, these make the paper more compelling.

    2. Reviewer #3 (Public review):

      Summary:

      In this manuscript, authors used a learning paradigm in C. elegans; when worms were fed in a saltless plate, its chemotaxis to salt is greatly reduced. To identify learning-related proteins, authors employed nervous system-specific transcriptome analysis to compare whole proteins in neurons between high-salt-fed animals and saltless-fed animals. Authors identified "learning-specific proteins" which are observed only after saltless feeding. They categorized these proteins by GO analyses, pathway analyses and expression site analyses, and further stepped forward to test mutants in selected genes identified by the proteome analysis. They find several mutants that are defective or hyper-proficient for learning, including acc-1/3 and lgc-46 acetylcholine receptors, F46H5.3 putative arginine kinase, and kin-2, a cAMP pathway gene. These mutants were not previously reported to have abnormality in the learning paradigm.

      Concerns:

      Upon revision, authors addressed all concerns of this reviewer, and the results are now presented in a way that facilitates objective evaluation. Authors' conclusions are supported by the results presented, and the strength of the proteomics approach is persuasively demonstrated.

      Significance:

      (1) Total neural proteome analysis has not been conducted before for learning-induced changes, though transcriptome analysis has been performed for odor learning (Lakhina et al., http://dx.doi.org/10.1016/j.neuron.2014.12.029). This warrants the novelty of this manuscript, because for some genes, protein levels may change even though mRNA levels remain the same. Although in a few reports TurboID has been used in C. elegans, this is the first report of a systematic analysis of tissue-specific differential proteomics.

      (2) Authors found five mutants that have abnormality in the salt learning. These genes have not been described to have the abnormality, providing novel knowledge to the readers, especially those who work on C. elegans behavioural plasticity. Especially, involvement of acetylcholine neurotransmission has not been addressed before. Although transgenic rescue experiments have not been performed except kin-2, and the site of action (neurons involved) has not been tested in this manuscript, it will open the venue to further determine the way in which acetylcholine receptors, cAMP pathway etc. influences the learning process.

      [Editors' note: this version has been assessed without input from the reviewers.]

    3. Author response:

      The following is the authors’ response to the original reviews

      Comment from the editors at eLife:

      You could consider further strengthening the manuscript with the incorporation of new relevant public datasets for network modeling, but that is entirely your choice.

      We thank the editors and reviewers for their thoughtful and positive feedback on our article. We are particularly appreciative of the eLife assessment describing our work as valuable with a convincing methodology.

      As suggested, we have expanded our neuron class analysis by incorporating transcriptomic data from young adult animals (Kaletsky et al., 2016 Nature; Ghaddar et al., 2023 Science Advances; St Ange et al., 2024 Cell Genomics) to complement our existing analysis of larval stage 4 (L4) animals.

      In addition, we have updated Table S1 to include the outcross status of all strains used in this study, providing clearer information on the genotypes tested. We have also corrected the typographical errors noted by the reviewers. Please note that page and line numbers below refer to the MS Word Document with tracked changes set to ‘simple markup’.

      We greatly appreciate the reviewers’ input and hope these revisions further enhance the value and clarity of our study.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      Rahmani et al. utilize the TurboID method to characterize global proteome changes in the worm's nervous system induced by a salt-based associative learning paradigm. Altogether, they uncover 706 proteins tagged by the TurboID method in worms that underwent the memory-inducing protocol. Next, the authors conduct a gene enrichment analysis that implicates specific molecular pathways in salt-associative learning, such as MAP kinase and cAMP-mediated pathways, as well as specific neuronal classes including pharyngeal neurons, and specific sensory neurons, interneurons, and motor neurons. The authors then screen a representative group of hits from the proteome analysis. They find that mutants of candidate genes from the MAP kinase pathway, namely dlk-1 and uev-3, do not affect performance in the learning paradigm. Instead, multiple acetylcholine signaling mutants, as well as a protein-kinase-A mutant, significantly affected performance in the associative memory assay (e.g., acc-1, acc-3, lgc-46, and kin-2). Finally, the authors demonstrate that protein-kinase-A mutants, as well as acetylcholine signaling mutants, do not exhibit a phenotype in a related but distinct conditioning paradigm-aversive salt conditioning-suggesting their effect is specific to appetitive salt conditioning.

      Overall, the authors addressed the concerns raised in the previous review round, including the statistics of the chemotaxis experiments and the systems-level analysis of the neuron class expression patterns of their hits. I also appreciate the further attempt to equalize the sample size of the chemotaxis experiments and the transparent reporting of the sample size and statistics in the figure captions and Table S9. The new results from the panneuronal overexpression of the kin-2 gain-of-function allele also contribute to the manuscript. Together, these make the paper more compelling. The additional tested hits provide a comprehensive analysis of the main molecular pathways that could have affected learning. However, the revised manuscript includes more information and analysis, raising additional concerns.

      Major comments:

      As reviewer 4 noted, and as also shown to be relevant for C30G12.6 presented in Figure 6, the backcrossing of the mutants is important, as background mutations may lead to the observed effects. Could the authors add to Table 1, sheet 1, the outcrossing status of the tested mutants?

      We appreciate this important point. A column has now been added to Table S1 to indicate the outcross status of all strains used in this study. Additionally, we have updated the table legend on page 77 to clarify how to interpret the information provided in this column.

      It is important to validate that the results of the positive hits (where learning was affected), such as acc-1, acc-3, and lgc-46, do not stem from background mutations.

      While we agree that confirming the absence of background mutations is important, we have taken alternative steps to address this concern:

      - The outcross status of each strain is now clearly indicated in Table S1.

      - Observed phenotypes were consistent across multiple biological replicates over extended periods (months, sometimes years), reducing the likelihood that results stem from background mutations.

      We believe these measures provide confidence in the validity of our findings.

      The fold change in the number of hits for different neurons in the CENGEN-based rank analysis requires a statistical test (discussed on pages 17-19 and summarized in Table S7). Similar to the other gene enrichment analyses presented in the manuscript, the new rank analysis also requires a statistical test. Since the authors extensively elaborate on the results from this analysis, I think a statistical analysis is especially important for its interpretation. For example, if considering the IL1 neurons, which ranked highest, and assuming random groups of genes-each having the same size as those of the ranked neurons (209 genes in total for IL1 in Table S7)-how common would it be to get the calculated fold change of 1.38 or higher? Such bootstrapping analysis is common for enrichment analysis. Perhaps the authors could consult with an institutional expert (Dr. Pawel Skuza, Flinders University) for the statistical aspects of this analysis.

      We appreciate the suggestion and agree that statistical testing can be valuable for enrichment analyses. However, implementing additional tests such as bootstrapping is beyond the scope of this study. Our aim was to provide a descriptive overview rather than inferential statistics. To ensure transparency and interpretability, we have:

      - Clearly reported fold changes and rankings in Table S7.

      - Discussed the limitations of this approach in the manuscript text (page 18, lines 17–20).

      - Clearly outlined the methods used to perform this analysis (pages 53–54).

      We believe this descriptive analysis provides sufficient context for interpreting these results.

      The learning phenotypes from Figure S8, concerning acc-1, acc-3, and lgc-46 mutants, are summarized in a scheme in Figure 4; however, the chemotaxis results are found in the supplemental Figure S8. Perhaps I missed the reasoning, but for transparency, I think the relevant Figure S8 results should be shown together with their summary scheme in Figure 4.

      Thank you for this suggestion to improve clarity. We have now moved the panels corresponding to cholinergic signalling components from Figure S8 into Figure 4 on page 21, so that the summary scheme and underlying data are presented together. The figure legends and main text have been updated accordingly to reflect the correct figure numbers.

      Reviewer #2 (Public review):

      Summary:

      In this study by Rahmani in colleagues, the authors sought to define the "learning proteome" for a gustatory associative learning paradigm in C. elegans. Using a cytoplasmic TurboID expressed under the control of a pan-neuronal promoter, the authors labeled proteins during the training portion of the paradigm, followed by proteomics analysis. This approach revealed hundreds of proteins potentially involved in learning, which the authors describe using gene ontology and pathway analysis. The authors performed functional characterization of over two dozen of these genes for their requirement in learning using the same paradigm. They also compared the requirement for these genes across various learning paradigms and found that most hits they characterized appear to be specifically required for the training paradigm used for generating the "learning proteome".

      Strengths:

      The authors have thoughtfully and transparently designed and reported the results of their study. Controls are carefully thought-out, and hits are ranked as strong and weak. By combining their proteomics with behavioral analysis, the authors also highlight the biological significance of their proteomics findings, and support that even weak hits are meaningful.

      The authors display a high degree of statistical rigor, incorporating normality tests into their behavioral data which is beyond the field standard.

      The authors include pathway analysis that generates interesting hypotheses about processes involved learning and memory

      The authors generally provide thoughtful interpretations for all of their results, both positive and negative, as well as any unexpected outcomes.

      Weaknesses:

      - The authors use the Cengen single cell-transcriptomic atlas to predict where the proteins in the "learning proteome" are likely to be expressed and use this data to identify neurons that are likely significant to learning, and building hypothetical circuit. This is an excellent idea; however, the Cengen dataset only contains transcriptomic data from juvenile L4 animals, while the authors performed their proteome experiments in Day 1 Adult animals. It is well documented that the C. elegans nervous system transcriptome is significant different between these two stages (Kaletsky et al., 2016, St. Ange et al., 2024), so the authors might be missing important expression data, resulting in inaccurate or incomplete networks. The adult neuronal single-cell atlas data (https://cestaan.princeton.edu/) would be better suited to incorporate into neuronal expression analysis.

      Thank you for highlighting this important point. We have now incorporated transcriptomic data from young adult animals to complement the L4-based CeNGEN dataset. Specifically, we integrated data from CeSTAAN (https://cestaan.princeton.edu/, including St. Ange et al., 2024) and WormSeq (https://wormseq.org/, including Ghaddar et al., 2023), as outlined below. Importantly, CeSTAAN and WormSeq provide data for 79 and 104 neuron classes, respectively (compared to 128 from CeNGEN); for this reason, the main analysis focuses on CeNGEN due to its broader coverage, with additional datasets noted in brackets for completeness. This is stated on page 18, lines 15–17 to ensure transparency regarding our rationale.

      The main text has been updated to describe these datasets and their integration into our analysis (pages 18–20), and further details on how these resources were used have been added to the Experimental Procedures (pages 53–54).

      We also incorporated data from Kaletsky et al. (2016) and St. Ange et al. (2024) into our neuron identity checks for all assigned and unassigned hits (page 16, lines 8–19). This analysis shows that the nervous system is highly represented in our proteome data: 75–87% of assigned hits and 75–83% of all hits correspond to neuron-enriched genes identified by St. Ange et al. and Kaletsky et al.

      In addition, we used several transcriptomic databases to confirm that learning regulators identified in this study through TurboID and validation experiments are expressed in the same neuron classes as suggested by CenGEN (page 36).

      - The authors offer many interpretations for why mutants in "learning proteome" hits have no detectable phenotype, which is commendable. They are however overlooking another important interpretation, it is possible that these changes to the proteome are important for memory, which is dependent upon translation and protein level changes, and is molecularly distinct from learning. It is well established in the field mutating or knocking down memory regulators in other paradigms will often have no detectable effect on learning. Incorporating this interpretation into the discussion and highlighting it as an area for future exploration would strengthen the manuscript.

      Thank you for this suggestion. We have incorporated this interpretation into the Results section (page 31, lines 17–23), specifying the potential role of these proteomic changes in memory encoding and retention, which are molecularly distinct from learning.

      - A minor weakness - In the discussion, the authors state that the Lakhina, et al 2015 used RNA-seq to assess memory transcriptome changes. This study used microarray analysis.

      This has been corrected on page 38, line 5.

      Significance:

      The approach used in this study is interesting and has the potential to further our knowledge about the molecular mechanisms of associative behaviors. There have been multiple transcriptomic studies in the worm looking at gene expression changes in the context of behavioral training. This study compliments and extends those studies, by examining how the proteome changes in a different training paradigm. This approach here could be employed for multiple different training paradigms, presenting a new technical advance for the field. This paper would be of interest to the broader field of behavioral and molecular neuroscience. Though it uses an invertebrate system, many findings in the worm regarding learning and memory translate to higher organisms, making this paper of interest and significant to the broader field of behavioral neuroscience.

      Reviewer #4 (Public review):

      Summary:

      In this manuscript, authors used a learning paradigm in C. elegans; when worms were fed in a saltless plate, its chemotaxis to salt is greatly reduced. To identify learning-related proteins, authors employed nervous system-specific transcriptome analysis to compare whole proteins in neurons between high-salt-fed animals and saltless-fed animals. Authors identified "learning-specific proteins" which are observed only after saltless feeding. They categorized these proteins by GO analyses, pathway analyses and expression site analyses, and further stepped forward to test mutants in selected genes identified by the proteome analysis. They find several mutants that are defective or hyper-proficient for learning, including acc-1/3 and lgc-46 acetylcholine receptors, F46H5.3 putative arginine kinase, and kin-2, a cAMP pathway gene. These mutants were not previously reported to have abnormality in the learning paradigm.

      Concerns:

      Upon revision, authors addressed all concerns of this reviewer, and the results are now presented in a way that facilitates objective evaluation. Authors' conclusions are supported by the results presented, and the strength of the proteomics approach is persuasively demonstrated.

      Thank you, we appreciate this positive feedback.

      Significance:

      (1) Total neural proteome analysis has not been conducted before for learning-induced changes, though transcriptome analysis has been performed for odor learning (Lakhina et al., http://dx.doi.org/10.1016/j.neuron.2014.12.029). This warrants the novelty of this manuscript, because for some genes, protein levels may change even though mRNA levels remain the same. Although in a few reports TurboID has been used in C. elegans, this is the first report of a systematic analysis of tissue-specific differential proteomics.

      (2) Authors found five mutants that have abnormality in the salt learning. These genes have not been described to have the abnormality, providing novel knowledge to the readers, especially those who work on C. elegans behavioural plasticity. Especially, involvement of acetylcholine neurotransmission has not been addressed before. Although transgenic rescue experiments have not been performed except kin-2, and the site of action (neurons involved) has not been tested in this manuscript, it will open the venue to further determine the way in which acetylcholine receptors, cAMP pathway etc. influences the learning process.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      The authors stated in their response to reviewers that "referring to a phenotype as both a trend and non-significant may confuse readers, which was originally stated in the manuscript in two locations," and that such sentences were removed. Unfortunately, in the new text (page 28, lines 18-19), the authors write: "uev-3 mutants showed a lower average CI after training compared with wild-type, but this did not reach statistical significance." As stated before, I find such sentences confusing and not interpretable. If the changes are not significant, then the lower average CI is not informative.

      Thank you for pointing this out. This has been corrected to improve clarity – we say instead that “trained phenotypes between wild-type and uev-3 mutants were not statistically significant” (page 29, lines 21–22).

      In response to reviewers' comments, the authors added more information about the biotinylation efficiency of the experiment, which is also described in the text:

      Page 8, line 27: "we found that biotin exposure increased the signal 1.3-fold for non-Tg and 1.7-fold for TurboID C. elegans."

      Page 10, line 4: "Quantification of the signal within entire lanes showed a 1.1-fold increase in the 'TurboID, control' lane compared with the 'non-Tg, control' lane, and a 1.9-fold increase in the 'TurboID, trained' lane compared with the 'non-Tg, trained' lane."

      Is it common in this field not to show the actual raw quantified numbers? I was expecting either a bar graph or instead that the measured values would appear in the text alongside the fold-change information.

      Table S2 (and its table legend on page 77) have been edited to include raw area values.

      Figure 5: Typo? - "pan neuronal expression of ..." The allele number is written as 139, but I believe it should be 179, as in the rest of the paper.

      The typo has been corrected on page 25.

      The results describing the absence of a learning phenotype in backcrossed C30G12.6 are presented in the main figure. If the authors believe this is an important result, I understand keeping it in the main figure; however, I find this uncommon.

      Thank you for your comment. We consider the absence of a learning phenotype in backcrossed C30G12.6 to be an important control for interpreting the original findings, which is why we have retained it in the main figure.

      Reviewer #4 (Recommendations for the authors):

      I noted a few typos.

      (1) In Fig 5B, the transgene is depicted kin-2(ce139) but it is probably kin-2(ce179).

      The typo has been corrected on page 25.

      (2) In text, R97C and ce179 are used interchangeably, but in fact there is no description that they are identical.

      We now state the following in the manuscript: “We tested worms with the ce179 mutant allele in kin-2, in which a conserved residue in the inhibitory domain (which normally functions to keep PKA turned off in the absence of cAMP) is mutated to cause an R92C amino acid change – this results in increased PKA activity (Schade et al., 2005).” (page 25, lines 1–3),

      (3) p31 line 7, Figure S7 -> Fig S9 C-E

      We apologise for this typographical error. This figure number is meant to correspond to salt associative learning assay data (Fig. S8), not salt aversive learning (Fig. S9). Since the data from Fig. S8 was moved to Fig. 4, the figure citation has been changed from Fig. S7 (which was incorrect) to Fig. 4 (page 32, line 17).

      (4) p45 line 11, Fig S9 -> Fig S6

      The typo has been corrected (page 47, line 12).

    1. Reviewer #1 (Public review):

      Summary:

      In this manuscript, Bisht et al. investigate the role of PPE2, a Mycobacterium tuberculosis (Mtb) secreted virulence factor, in adipose tissue physiology during tuberculosis (TB) infection. Previous work by this group established the significance of PPE proteins in Mtb virulence and their role in modulating the innate immune response. Here, the authors present compelling evidence that PPE2 regulates host cell adipogenesis and lipolysis, thereby establishing a link to the development of insulin resistance during TB infection. These fundamental findings demonstrate, for the first time, that a bacterial virulence factor is directly involved in the profound body fat loss, or "wasting," which is a long-established clinical symptom of active TB.

      Key Strengths:

      The confidence in the major findings of this study is significantly strengthened by the authors' comprehensive approach. They judiciously employ multiple experimental systems, including:

      (1) Purified PPE2 protein.

      (2) A non-pathogenic Mycobacterium strain engineered to express PPE2.

      (3) A pathogenic clinical Mtb strain (CDC1551) utilizing a targeted PPE2 deletion mutant.

      (4) While the presence of Mtb in adipose tissues in human and animal models is well-documented, this study is groundbreaking in demonstrating that an Mtb virulence-associated factor actively modulates host fatty acid metabolism within the adipose tissue.

      Key Weakness:

      Although the manuscript provides solid evidence associating the presence of PPE2 with transcriptional changes in host fatty acid machinery within the adipose tissue, the underlying mechanistic details remain elusive. A focused, deep mechanistic follow-up study will be essential to fully appreciate the complex biological implications of the findings reported here.

    2. Reviewer #2 (Public review):

      Summary:

      In the manuscript entitled "The PPE2 protein of Mycobacterium tuberculosis is responsible for the development of hyperglycemia and insulin resistance during tuberculosis" the authors identify PPE2, a secretory protein of Mycobacterium tuberculosis, as a modulator of adipose function. They show that PPE2 treatment in mice causes fat loss, immune cell infiltration into adipose, reduced gene expression of PPAR-γ, C/EBP-α, and adiponectin, and glucose intolerance. Overall, the authors link PPE2 with adipose tissue perturbation and insulin resistance following infection with M. tuberculosis. PPE2, a secretory protein of Mycobacterium tuberculosis, is a modulator of adipose function. They show that PPE2 treatment in mice causes fat loss, immune cell infiltration into adipose, reduced gene expression of PPAR-γ, C/EBP-α, and adiponectin, and glucose intolerance. Overall, the authors link PPE2 with adipose tissue perturbation and insulin resistance following infection with M. tuberculosis.

      Strengths:

      While it is known that M. tuberculosis persists in adipose, the mycobacterial factors contributing to adipose dysfunction are unknown. The study uses multiple mechanisms, including recombinant purified protein, non-pathogenic mycobacterium expressing PPE2, and a clinical strain of M. tuberculosis depleted of PPE2, to show that PPE2 may play an important role in causing fat loss, lipolysis, and insulin resistance following infection. The authors show that PPE2, through unknown mechanisms, decreases gene expression of proteins involved in adipogenesis. Although the mechanisms are unclear, this study advances the field as it is the first to identify a secreted factor (PPE2) from M. tuberculosis to play a role in disrupting adipose tissue.

      Weaknesses:

      There is a lack of completeness amongst the figures that greatly diminishes the claims and impact of the manuscript. For example, in Figures 2 and 5, the authors measure adipocyte area in H&E-stained adipose tissue to show adipose hypertrophy. However, this was not completed in Figures 3 and 4 despite the authors claiming that treatment with rPPE2 induces adipose hypertrophy. It is unclear why the adipocyte area was not measured in these figures, and having this included would support the author's claim and strengthen the manuscript. The same is true for immune cell infiltration, where the authors say there is increased immune cell infiltration following PPE2 treatment. This is based on H&E staining, but the data supporting this is limited. Although the authors measure CD3+ T cell infiltration in adipose tissue from mice infected with the clinical strain where PPE was depleted, staining was performed in only this experiment. Completing these experiments by showing data to support that PPE2 induces immune cell infiltration would greatly strengthen the manuscript.

      The authors state that a Student's t-test was performed to calculate the significance between two samples. However, there is no discussion of what statistical method was used when there were more than 2 groups, which occurs throughout the manuscript, such as in Figure 5, where 4 groups are analyzed. Having the appropriate statistical analysis is important for the impact of the manuscript.

    3. Reviewer #3 (Public review):

      Summary:

      In this manuscript titled "The PPE protein of Mycobacterium tuberculosis is responsible for the development of hyperglycemia and insulin resistance during tuberculosis", Bisht et al describe that PPE2 protein from Mtb is a key modulator of adipose tissue physiology that contributes to the development of insulin resistance. The authors have used 3T3-L1 preadipocyte cell lines, M. smegmatis overexpression strain, mice model, and genetically modified Mtb deletion strains to demonstrate that PPE promotes persistence in adipose tissue and regulates glucose homeostasis. Using qPCR and RNA-seq experiments, the authors demonstrate that PPE2 regulates the expression of key genes involved in adipogenesis.

      Strengths:

      Using purified protein, the authors show that PPE2 regulates adipose tissue physiology, and this effect was neutralised in the presence of anti-PPE2. The expression of several adipogenic markers was also reduced in 3TL-1 adipocytes treated with rPPE2 and in mice infected with M. smegmatis strains overexpressing PPE2. Using a mouse model of infection, the authors show that PPE2 contributes to enhanced mycobacterial survival within fat tissues. The authors also show infiltration of immune cells in the fat tissues of mice infected with wild-type and ppe2-complemented strains compared to the ppe2 KO strain. In order to gain a better mechanistic understanding of how PPE2 regulates adipogenesis, the authors employed an RNA-seq approach and identified 191 genes that were significantly differentially expressed in the fat tissues of mice infected with wild-type and ppe2 KO Mtb strains. The differentially expressed genes included transcripts encoding for proteins involved in chemokine/cytokine signalling, ER stress response. The expression of a few of these markers was also validated by qPCR and western blot analysis. Finally, the authors also show that PPE2 promotes lipolysis by reducing phosphodiesterase levels and activating PKA-HSL signalling. The experimental design is overall reasonable, and the methods used are reliable. Overall, the current study did provide some new information on the contribution of PPE2 in regulating adipose tissue physiology.

      Weaknesses:

      (1) The authors have used several methodologies to show that PPE2 regulates adipose tissue physiology and glucose homeostasis. But the exact mechanism is still not clear.

      (2) Mtb encodes several PE/PPE proteins? The authors have used PPE2 for their study. Will secretory PPE2 homologs also regulate similar cellular processes?

      (3) How do the authors rule out that the differences observed in the fat tissues of mice infected with wild-type and mutant strains are not associated with reduced bacterial burdens? Is it possible to include another Mtb attenuated strain as a control in mice experiments for few critical experiments?

    4. Author response:

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      In this manuscript, Bisht et al. investigate the role of PPE2, a Mycobacterium tuberculosis (Mtb) secreted virulence factor, in adipose tissue physiology during tuberculosis (TB) infection. Previous work by this group established the significance of PPE proteins in Mtb virulence and their role in modulating the innate immune response. Here, the authors present compelling evidence that PPE2 regulates host cell adipogenesis and lipolysis, thereby establishing a link to the development of insulin resistance during TB infection. These fundamental findings demonstrate, for the first time, that a bacterial virulence factor is directly involved in the profound body fat loss, or "wasting," which is a long-established clinical symptom of active TB.

      Key Strengths:

      The confidence in the major findings of this study is significantly strengthened by the authors' comprehensive approach. They judiciously employ multiple experimental systems, including:

      (1) Purified PPE2 protein.

      (2) A non-pathogenic Mycobacterium strain engineered to express PPE2.

      (3) A pathogenic clinical Mtb strain (CDC1551) utilizing a targeted PPE2 deletion mutant.

      (4) While the presence of Mtb in adipose tissues in human and animal models is well-documented, this study is groundbreaking in demonstrating that an Mtb virulence-associated factor actively modulates host fatty acid metabolism within the adipose tissue.

      We thank the reviewer for his appreciation that in this work we demonstrated for the first time that an Mtb virulent factor is directly linked to TB-associated wasting.

      Weakness:

      Although the manuscript provides solid evidence associating the presence of PPE2 with transcriptional changes in host fatty acid machinery within the adipose tissue, the underlying mechanistic details remain elusive. A focused, deep mechanistic follow-up study will be essential to fully appreciate the complex biological implications of the findings reported here.

      We agree with the reviewer that a deep-focused, mechanistic follow-up study is necessary to further elucidate the complex biological implications of PPE2 actions. However, we believe that we have uncovered at least one of the possible mechanisms by which PPE2 increases lipolysis and circulating free fatty acids during infection by targeting cAMP-PKA-HSL pathway (Figure 7). In future studies we will aim to dissect out the mechanisms by which PPE2 triggers hyperglycaemia and insulin resistance.

      Reviewer #2 (Public review):

      Summary:

      In the manuscript entitled "The PPE2 protein of Mycobacterium tuberculosis is respon,sible for the development of hyperglycemia and insulin resistance during tuberculosis" the authors identify PPE2, a secretory protein of Mycobacterium tuberculosis, as a modulator of adipose function. They show that PPE2 treatment in mice causes fat loss, immune cell infiltration into adipose, reduced gene expression of PPAR-γ, C/EBP-α, and adiponectin, and glucose intolerance. Overall, the authors link PPE2 with adipose tissue perturbation and insulin resistance following infection with M. tuberculosis. PPE2, a secretory protein of Mycobacterium tuberculosis, is a modulator of adipose function. They show that PPE2 treatment in mice causes fat loss, immune cell infiltration into adipose, reduced gene expression of PPAR-γ, C/EBP-α, and adiponectin, and glucose intolerance. Overall, the authors link PPE2 with adipose tissue perturbation and insulin resistance following infection with M. tuberculosis.

      Strengths:

      While it is known that M. tuberculosis persists in adipose, the mycobacterial factors contributing to adipose dysfunction are unknown. The study uses multiple mechanisms, including recombinant purified protein, non-pathogenic mycobacterium expressing PPE2, and a clinical strain of M. tuberculosis depleted of PPE2, to show that PPE2 may play an important role in causing fat loss, lipolysis, and insulin resistance following infection. The authors show that PPE2, through unknown mechanisms, decreases gene expression of proteins involved in adipogenesis. Although the mechanisms are unclear, this study advances the field as it is the first to identify a secreted factor (PPE2) from M. tuberculosis to play a role in disrupting adipose tissue.

      We thank the reviewer for his appreciation of our findings presented in the manuscript.

      Weaknesses:

      (1) There is a lack of completeness amongst the figures that greatly diminishes the claims and impact of the manuscript. For example, in Figures 2 and 5, the authors measure adipocyte area in H&E-stained adipose tissue to show adipose hypertrophy. However, this was not completed in Figures 3 and 4 despite the authors claiming that treatment with rPPE2 induces adipose hypertrophy. It is unclear why the adipocyte area was not measured in these figures, and having this included would support the author's claim and strengthen the manuscript. The same is true for immune cell infiltration, where the authors say there is increased immune cell infiltration following PPE2 treatment. This is based on H&E staining, but the data supporting this is limited. Although the authors measure CD3+ T cell infiltration in adipose tissue from mice infected with the clinical strain where PPE was depleted, staining was performed in only this experiment. Completing these experiments by showing data to support that PPE2 induces immune cell infiltration would greatly strengthen the manuscript.

      As per the suggestion of the esteemed reviewer, in the revised manuscript we will attempt to analyse adipocyte area in both Figures 3 and 4. In the original manuscript, immune cell infiltration analyses (H&E staining and CD3+ staining) was restricted to only M. tuberculosis-mouse infection model, which best reflects the human tuberculosis pathology.  In other experiments involving infection with M. smegmatis expressing PPE2, immune cell infiltration studies will be carried out.

      (2) The authors state that a Student's t-test was performed to calculate the significance between two samples. However, there is no discussion of what statistical method was used when there were more than 2 groups, which occurs throughout the manuscript, such as in Figure 5, where 4 groups are analyzed. Having the appropriate statistical analysis is important for the impact of the manuscript.

      We agree with the reviewer that we missed to include ANOVA in the statistical analyses. We will include one-way ANOVA analysis where more than two groups are present and mention the statistical methods in the figure legends as well in the text of the revised manuscript.

      Reviewer #3 (Public review):

      Summary:

      In this manuscript titled "The PPE protein of Mycobacterium tuberculosis is responsible for the development of hyperglycemia and insulin resistance during tuberculosis", Bisht et al describe that PPE2 protein from Mtb is a key modulator of adipose tissue physiology that contributes to the development of insulin resistance. The authors have used 3T3-L1 preadipocyte cell lines, M. smegmatis overexpression strain, mice model, and genetically modified Mtb deletion strains to demonstrate that PPE promotes persistence in adipose tissue and regulates glucose homeostasis. Using qPCR and RNA-seq experiments, the authors demonstrate that PPE2 regulates the expression of key genes involved in adipogenesis.

      Strengths:

      Using purified protein, the authors show that PPE2 regulates adipose tissue physiology, and this effect was neutralised in the presence of anti-PPE2. The expression of several adipogenic markers was also reduced in 3TL-1 adipocytes treated with rPPE2 and in mice infected with M. smegmatis strains overexpressing PPE2. Using a mouse model of infection, the authors show that PPE2 contributes to enhanced mycobacterial survival within fat tissues. The authors also show infiltration of immune cells in the fat tissues of mice infected with wild-type and ppe2-complemented strains compared to the ppe2 KO strain. In order to gain a better mechanistic understanding of how PPE2 regulates adipogenesis, the authors employed an RNA-seq approach and identified 191 genes that were significantly differentially expressed in the fat tissues of mice infected with wild-type and ppe2 KO Mtb strains. The differentially expressed genes included transcripts encoding for proteins involved in chemokine/cytokine signalling, ER stress response. The expression of a few of these markers was also validated by qPCR and western blot analysis. Finally, the authors also show that PPE2 promotes lipolysis by reducing phosphodiesterase levels and activating PKA-HSL signalling. The experimental design is overall reasonable, and the methods used are reliable. Overall, the current study did provide some new information on the contribution of PPE2 in regulating adipose tissue physiology.

      We thank the reviewer for encouraging comments about the manuscript.

      Weaknesses:

      (1) The authors have used several methodologies to show that PPE2 regulates adipose tissue physiology and glucose homeostasis. But the exact mechanism is still not clear.

      We have clearly demonstrated that PPE2 inhibit PPAR-γ and C/EBP-α expression to block adipogenic differentiation. Further, we demonstrated a possible mechanism by which PPE2 trigger lipolysis via activation of the ER stress and cAMP/PKA/HSL pathway which is responsible for increasing free fatty acids in circulation (Figure 7) as confirmed by our observation that PPE2KO (ppe2 knock-out) Mtb infected mice had lower NEFA as compared to the those infected with wild-type Mtb (Figure 7F). Crucially, we showed that this mechanism is clinically relevant since NEFA levels in the sera of TB patients were higher as compared to the healthy controls (Figure 7G) confirming presence of dyslipidemia in TB patients which is an established risk factor for insulin resistance (Karpe et al., 2011; Bhattacharya et al., 2007), As increased free fatty acids have been shown to be linked to development of insulin resistance in several studies, this mechanism links PPE2 with the regulation of glucose homeostasis.

      (2) Mtb encodes several PE/PPE proteins? The authors have used PPE2 for their study. Will secretory PPE2 homologs also regulate similar cellular processes?

      It is known that Mtb encodes several PE/PPE family proteins and some of these have been implicated to play a role in host–pathogen interactions (Mukhopadhyay and Balaji, 2011; Dahiya et al., 2025). However, so far only PPE2 is shown to be present in the circulation (Bisht et al., 2023) which is the main reason we chose it for this study. Presence of PPE2 homologues in the circulation is not known so far.

      (3) How do the authors rule out that the differences observed in the fat tissues of mice infected with wild-type and mutant strains are not associated with reduced bacterial burdens? Is it possible to include another Mtb attenuated strain as a control in mice experiments for few critical experiments?

      We agree with the reviewer that the differences in bacterial burden can influence host tissue responses.  Precisely for this reason, we did not rely on just one infection model alone. We used a multi-pronged approach to de-couple the effects of PPE2 from the effects of bacterial load, like;

      (1) In vitro Model using recombinantly purified PPE2 protein (rPPE2) (Figure 1): In cultured 3T3-L1 adipocytes, purified rPPE2 protein directly inhibited adipogenesis by downregulating important factors like PPAR-g,C/EBP-α and Fatty acid synthase (which play a critical role in triglyceride metabolism) demonstrating a direct effect of PPE2 in the complete absence of infection.

      (2) Recombinant Protein Injection (Figure 3): By injecting recombinantly purified PPE2 protein (rPPE2) into mice, we observed similar metabolic perturbations (fat loss, impaired glucose tolerance) in the complete absence of any bacteria, demonstrating that PPE2 can drive these phenotypes independent of bacterial burden. Further study of rescuing of PPE2 action in rPPE2-immunized mice strongly confirm the specific role of PPE2 in establishing hyperglycaemia and insulin resistance (Figure 4).

      While the Mtb aerosol model can be questioned for bacterial load effects, it provides crucial in vivo validation that PPE2 function is relevant in the context of mycobacterial infection.

      References

      Bhattacharya S, Dey D, Roy SS. Molecular mechanism of insulin resistance. J Biosci. 2007 Mar;32(2):405-13. doi: 10.1007/s12038-007-0038-8. PMID: 17435330.

      Bisht MK, Pal R, Dahiya P, Naz S, Sanyal P, Nandicoori VK, Ghosh S, Mukhopadhyay S. The PPE2 protein of Mycobacterium tuberculosis is secreted during infection and facilitates mycobacterial survival inside the host. Tuberculosis (Edinb). 2023 Dec;143:102421. doi: 10.1016/j.tube.2023.102421. Epub 2023 Oct 12. PMID: 37879126.

      Dahiya P, Bisht MK, Mukhopadhyay S. Role of PE family of proteins in mycobacterial virulence: Potential on anti-TB vaccine and drug design. Int Rev Immunol. 2025; 44(4):213-228. doi: 10.1080/08830185.2025.2455161. Epub 2025 Jan 31. PMID: 39889764.

      Karpe F, Dickmann JR, Frayn KN. Fatty acids, obesity, and insulin resistance: time for a reevaluation. Diabetes. 2011 Oct;60(10):2441-9. doi: 10.2337/db11-0425. PMID: 21948998; PMCID: PMC3178283.

      Mukhopadhyay S, Balaji KN. The PE and PPE proteins of Mycobacterium tuberculosis. Tuberculosis (Edinb). 2011 Sep;91(5):441-7. doi: 10.1016/j.tube.2011.04.004. Epub 2011 May 6. PMID: 21527209.

    1. C. 계약 관리

      당사 운영 구조상, 중개인이 계약서를 제출해야만 계약일 및 계약 성립 여부 확인이 가능합니다.


      이에 따라, 계약서 미제출 상태에서는 계약의 진행 여부 자체를 판단할 수 없으므로,

      계약서 미제출을 사유로 한 1차 시정 요구, 또는 3영업일 내 미제출 시 운영자가 계약을 중도 파기 절차로 이관하는 프로세스는 적용이 어렵습니다.

      이와 같은 사유로, 중개인이 계약 상태를 성실히 업로드할 수 있도록 유인 동기를 제공하기 위해 별도의 쿠폰을 지급하는 정책을 운영하고 있습니다.

    2. 사유 없는 잦은 지역 변경 요청은 반려할 수 있다.

      중개인의 활동지역 변경 정책은 아래 기준을 반영합니다.

      1. 중개인은 중개사무소 소재지 ‘구’ 외 1개의 ‘구’ 지역을 추가로 선택 가능합니다.

      2.추가 선택 지역에 대해 별도의 지역 제한은 적용하지 않습니다.

      3.추가 선택 지역은 월 1회에 한하여 변경 가능합니다.

      4.중개사무소 소재지 ‘구’는 사무소 이전 시에만 변경 가능하며, 사무소 주소 변경이 발생한 경우 시스템을 통해 변경 요청할 수 있습니다.

    1. monohybrid cross

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      English — monohybrid cross (thorough explanation)

      1) What a monohybrid cross is (core idea)

      A monohybrid cross is a genetic cross that examines inheritance of ONE trait only between two parents.

      Mono = one Hybrid = genetic cross

      So:

      Monohybrid cross = a cross involving one trait


      2) What kind of trait is studied

      The single trait must have two contrasting forms, such as:

      • Tall vs short plants
      • Round vs wrinkled seeds
      • Purple vs white flowers

      Each trait is controlled by one gene with two alleles.


      3) How a monohybrid cross is shown

      A monohybrid cross is usually shown using a 2 × 2 Punnett square.

      Example:

      • T = tall (dominant)
      • t = short (recessive)

      Parents: Tt × Tt

      Possible offspring genotypes:

      • TT
      • Tt
      • Tt
      • tt

      4) Genotype and phenotype ratios (exam favorite)

      Genotype ratio

      • 1 TT : 2 Tt : 1 tt

      Phenotype ratio

      • 3 tall : 1 short

      📌 This 3:1 phenotype ratio is a classic result of a monohybrid cross involving complete dominance.


      5) Why monohybrid crosses are important

      Monohybrid crosses help students:

      • Understand dominant and recessive alleles
      • Learn genotype vs phenotype
      • Practice Punnett squares
      • Predict inheritance patterns

      They were essential in Mendel’s experiments with pea plants.


      6) When to use a monohybrid cross

      Use a monohybrid cross when:

      • Only one trait is being studied
      • Each parent contributes one allele for that trait
      • The problem does not involve codominance or incomplete dominance (unless stated)

      One-sentence exam summary

      A monohybrid cross studies the inheritance of a single trait using one gene and two alleles.


      中文 — monohybrid cross(单性状杂交) 详细解释

      1) 什么是单性状杂交(核心概念)

      单性状杂交是指: 只研究一个性状遗传情况的杂交实验

      mono(单) + hybrid(杂交)


      2) 研究的性状特点

      该性状通常:

      • 一个基因控制
      • 两种对立表现 例如:
      • 高 / 矮
      • 圆 / 皱

      3) 单性状杂交如何表示

      通常使用 2×2 潘尼特方格

      例子:

      • T = 高(显性)
      • t = 矮(隐性)

      父母:Tt × Tt

      后代基因型:

      • TT
      • Tt
      • Tt
      • tt

      4) 常见比例(考试必背)

      基因型比例

      • 1 : 2 : 1

      表现型比例

      • 3 : 1

      📌 这是孟德尔单性状杂交的经典结果。


      5) 单性状杂交的重要性

      • 帮助理解显性与隐性
      • 区分基因型和表现型
      • 是学习遗传学的基础

      一句话考试版总结

      单性状杂交是研究一个性状遗传规律的杂交实验。

      如果你愿意,我可以把 monohybrid vs dihybrid cross 整理成 Science 10 中英对照对比表、练习题或互动 Punnett 方格,非常适合系统复习。

    2. gamete

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      English — gamete (thorough explanation)

      1) What a gamete is (core idea)

      A gamete is a sex cell used in sexual reproduction. Gametes carry half the normal number of chromosomes and combine during fertilization to form a new organism.

      Gamete = a reproductive cell with half the chromosomes


      2) Types of gametes

      There are two main types:

      • Sperm → male gamete
      • Egg (ovum) → female gamete

      Each parent contributes one gamete to the offspring.


      3) Chromosome number (very important)

      Gametes are haploid (n), meaning they contain half the usual chromosome number.

      Example (humans):

      • Body cells: 46 chromosomes (diploid, 2n)
      • Gametes: 23 chromosomes (haploid, n)

      📌 This ensures that when fertilization occurs, the offspring has the correct chromosome number.


      4) How gametes are made — meiosis

      Gametes are produced by meiosis, a special type of cell division.

      Meiosis:

      • Reduces chromosome number by half
      • Produces genetically unique gametes
      • Creates variation through crossing over and independent assortment

      5) Gametes and fertilization

      During fertilization:

      • One sperm gamete fuses with one egg gamete
      • Forms a zygote
      • The zygote is diploid (2n) again

      6) Why gametes are important

      Gametes:

      • Allow sexual reproduction
      • Maintain correct chromosome numbers
      • Increase genetic variation
      • Enable inheritance of traits from both parents

      One-sentence exam summary

      A gamete is a haploid sex cell (sperm or egg) that combines with another during fertilization.


      中文 — gamete(配子) 详细解释

      1) 什么是配子(核心概念)

      配子(gamete)是用于有性生殖的细胞,只含有一半的染色体数目

      配子 = 含一半染色体的生殖细胞


      2) 配子的类型

      • 精子 → 雄性配子
      • 卵子 → 雌性配子

      每个亲本提供 一个配子


      3) 染色体数量(必考)

      配子是 单倍体(n)

      • 人类体细胞:46 条染色体(2n)
      • 配子:23 条染色体(n)

      4) 配子如何形成 —— 减数分裂

      配子通过 减数分裂产生:

      • 染色体数减半
      • 形成遗传多样性
      • 后代基因组合不同

      5) 配子与受精

      • 精子 + 卵子 → 受精卵(zygote)
      • 受精卵恢复为 二倍体(2n)

      一句话考试版总结

      配子是含有一半染色体数的生殖细胞,用于有性生殖。

      如果你愿意,我可以把 gamete → meiosis → fertilization → zygote 整理成 Science 10 中英对照流程图或互动闪卡,非常适合系统复习与教学。

    3. self-pollinate.

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      English — self-pollinate / self-pollination (thorough explanation)

      1) What self-pollinate means (core idea)

      To self-pollinate means that a plant’s pollen fertilizes its own ovules. The pollen comes from the same flower or from another flower on the same plant.

      Self-pollinate = a plant fertilizes itself


      2) How self-pollination happens

      In flowering plants:

      • Pollen is produced in the anther
      • Ovules are located in the ovary
      • During self-pollination, pollen moves from the anther to the stigma of the same flower (or same plant)

      No wind, insects, or animals are required.


      3) Why some plants self-pollinate

      Self-pollination is useful because it:

      • Guarantees reproduction even if pollinators are absent
      • Preserves successful traits
      • Produces predictable offspring

      This is why self-pollinating plants are often used in genetics studies.


      4) Classic example (Science 10 context): peas

      Pea plants naturally self-pollinate because:

      • Their reproductive organs are enclosed
      • Pollen reaches the stigma before the flower opens

      This allows plants to produce offspring with very similar genotypes.


      5) Self-pollination vs cross-pollination (important comparison)

      | Feature | Self-pollination | Cross-pollination | | ---------------------- | ---------------- | ----------------- | | Pollen source | Same plant | Different plant | | Genetic variation | Low | High | | Offspring | Very similar | More diverse | | Depends on pollinators | No | Often yes |

      📌 Self-pollination increases genetic consistency, while cross-pollination increases variation.


      6) Advantages and disadvantages

      Advantages

      • Reliable reproduction
      • No need for pollinators
      • Stable traits

      Disadvantages

      • Less genetic diversity
      • Less ability to adapt to change

      One-sentence exam summary

      Self-pollination occurs when a plant’s pollen fertilizes ovules on the same plant, producing genetically similar offspring.


      中文 — self-pollinate(自花授粉) 详细解释

      1) 什么是自花授粉(核心概念)

      自花授粉是指: 花粉来自同一朵花或同一株植物,并完成受精过程

      自花授粉 = 植物自己给自己授粉


      2) 自花授粉如何发生

      • 花粉产生于花药
      • 受精发生在雌蕊
      • 花粉直接从花药传到同一朵花的柱头(或同株另一朵花)

      不需要昆虫或风的帮助。


      3) 自花授粉的优点

      • 保证繁殖成功
      • 保持优良性状
      • 后代性状稳定

      4) 与异花授粉的对比(考试重点)

      | 类型 | 特点 | | ---- | ------ | | 自花授粉 | 遗传多样性低 | | 异花授粉 | 遗传多样性高 |


      一句话考试版总结

      自花授粉是指植物利用自身花粉完成受精的过程。

      如果你愿意,我可以把 self-pollination → cross-pollination → genetic variation 整理成 Science 10 中英对照图解或互动练习题,非常适合课堂与考试复习。

    4. pea

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      English — pea (thorough explanation, genetics focus)

      1) What a pea is (core idea)

      A pea is the small, round seed found inside a pea pod, produced by the pea plant. Peas are both a food crop and a classic model organism in genetics.

      Pea = a seed from a pea plant; widely used to study inheritance


      2) Peas in genetics (Science 10 key context)

      Pea plants were used by Gregor Mendel to discover the basic laws of inheritance.

      Why peas were ideal:

      • Easy to grow
      • Short generation time
      • Clear, contrasting traits
      • Can self-pollinate or be cross-pollinated by hand

      3) Common pea traits studied (exam favorites)

      Mendel studied traits with two clear forms, such as:

      | Trait | One form | Other form | | ------------ | -------- | ----------- | | Seed shape | Round | Wrinkled | | Seed color | Yellow | Green | | Flower color | Purple | White | | Pod shape | Inflated | Constricted | | Plant height | Tall | Short |

      These traits made it easy to observe dominant and recessive patterns.


      4) Peas and Punnett squares

      Pea traits are often used in Punnett square problems.

      Example:

      • R = round seeds (dominant)
      • r = wrinkled seeds (recessive)

      Cross: Rr × Rr

      Results:

      • Genotypes: RR, Rr, Rr, rr
      • Phenotypes: 3 round : 1 wrinkled

      5) Why peas are still used today

      Peas helped scientists understand:

      • Alleles
      • Dominant vs recessive inheritance
      • Genotype vs phenotype
      • Predictable trait ratios

      These principles apply to all sexually reproducing organisms, including humans.


      One-sentence exam summary

      Peas are seed plants used by Mendel to discover inheritance patterns because they have clear, contrasting traits.


      中文 — pea(豌豆) 详细解释(遗传学重点)

      1) 什么是豌豆(核心概念)

      豌豆(pea)是豌豆植物果荚中的种子,既是食物,也是遗传学研究中的经典材料。

      豌豆 = 常用于研究遗传规律的植物种子


      2) 豌豆在遗传学中的重要性

      孟德尔用豌豆发现了遗传的基本规律。

      豌豆适合研究的原因:

      • 容易种植
      • 生长周期短
      • 性状对比明显
      • 可自花授粉或人工杂交

      3) 常见研究性状(考试重点)

      | 性状 | 表现一 | 表现二 | | ---- | --- | --- | | 种子形状 | 圆 | 皱 | | 种子颜色 | 黄 | 绿 | | 花的颜色 | 紫 | 白 | | 豆荚形状 | 饱满 | 收缩 | | 植株高度 | 高 | 矮 |


      4) 豌豆与潘尼特方格

      豌豆性状常用于潘尼特方格题目,帮助预测后代表现。


      一句话考试版总结

      豌豆因性状清晰、易繁殖,被用于发现显性和隐性等遗传规律。

      如果你愿意,我可以把 pea traits → alleles → Punnett squares 整理成 Science 10 中英对照练习题或互动闪卡,非常适合系统复习。

    5. incomplete dominance

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      English — incomplete dominance (thorough explanation)

      1) What incomplete dominance means (core idea)

      Incomplete dominance is an inheritance pattern in which neither allele is completely dominant, so the heterozygous phenotype is an intermediate (blended) form of the two homozygous phenotypes.

      Incomplete dominance = blending of traits in heterozygotes


      2) How incomplete dominance works

      • Two different alleles affect the trait
      • In a heterozygous individual, both alleles partially influence the outcome
      • The result looks like a mix, not one trait hiding the other

      3) Classic example (Science 10 favorite): flower color

      Let:

      • R = red flowers
      • W = white flowers

      Cross: RR × WW

      Offspring:

      • RWpink flowers

      📌 Pink is not a new allele; it’s the intermediate phenotype.


      4) Incomplete dominance in Punnett squares

      Parents: RW × RW

      Possible offspring:

      • RR → red
      • RW → pink
      • RW → pink
      • WW → white

      Phenotype ratio: 1 red : 2 pink : 1 white

      📌 Notice: phenotype ratio = genotype ratio in incomplete dominance.


      5) Incomplete dominance vs other patterns (very important)

      | Pattern | Heterozygous result | Example | | ------------------------ | ------------------------- | ------------------ | | Dominant–recessive | Dominant trait only | Brown eyes | | Incomplete dominance | Blended trait | Red × white → pink | | Codominance | Both traits fully visible | AB blood type |


      6) Why incomplete dominance matters

      Incomplete dominance:

      • Explains traits that don’t follow simple dominance
      • Increases visible variation in populations
      • Is common in plants, animals, and humans (for some traits)

      One-sentence exam summary

      Incomplete dominance occurs when heterozygous individuals show an intermediate, blended phenotype.


      中文 — incomplete dominance(不完全显性) 详细解释

      1) 什么是不完全显性(核心概念)

      不完全显性是指: 两个等位基因中没有一个完全显性,杂合体表现为中间型性状

      不完全显性 = 性状混合表现


      2) 不完全显性的表现特点

      • 显性不能完全压制另一等位基因
      • 杂合体表现为中间状态
      • 性状不是“要么这个,要么那个”

      3) 经典例子(考试常考)

      花的颜色:

      • 红花(RR)
      • 白花(WW)

      杂交后:

      • RW → 粉红色花

      📌 粉红不是新基因,而是红和白的中间表现


      4) 潘尼特方格中的不完全显性

      父母:RW × RW

      后代比例:

      • 1 红(RR)
      • 2 粉(RW)
      • 1 白(WW)

      👉 表现型比例 = 基因型比例


      5) 不完全显性 vs 共显性(重点区分)

      | 遗传方式 | 表现结果 | | ----- | ---------- | | 不完全显性 | 中间型(混合) | | 共显性 | 两种性状同时清楚出现 |


      一句话考试版总结

      不完全显性指杂合体表现为两种性状的中间型。

      如果你愿意,我可以把 dominant / recessive / incomplete dominance / codominance 整理成 Science 10 中英对照对比表、潘尼特方格练习或互动闪卡,非常适合系统复习与教学。

    6. heterozygous

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      English — heterozygous (thorough explanation)

      1) What heterozygous means (core idea)

      Heterozygous describes a genotype in which an organism has two different alleles for the same gene.

      Heterozygous = two different alleles (e.g., Aa)

      Each allele comes from a different parent.


      2) How heterozygous genotypes work

      • Genes come in pairs (alleles)
      • In a heterozygous genotype, one allele is different from the other
      • Often written as one capital letter and one lowercase letter

      Example:

      • A = dominant allele
      • a = recessive allele
      • Aa = heterozygous

      3) Trait expression in heterozygous individuals

      In simple dominance:

      • The dominant allele determines the phenotype
      • The recessive allele is present but not expressed

      Example:

      • Genotype: Aa
      • Phenotype: dominant trait

      📌 The recessive allele can still be passed to offspring.


      4) Heterozygous vs homozygous (important comparison)

      | Term | Alleles | Example | Trait shown | | ------------------------ | --------- | ------- | ------------------ | | Heterozygous | Different | Aa | Dominant (usually) | | Homozygous dominant | Same | AA | Dominant | | Homozygous recessive | Same | aa | Recessive |


      5) Heterozygous in Punnett squares (Science 10 focus)

      Punnett squares show how heterozygous parents pass on alleles.

      Example: Aa × Aa

      Possible offspring:

      • AA
      • Aa
      • Aa
      • aa

      Genotype ratio:

      • 1 AA : 2 Aa : 1 aa

      📌 Half the offspring are heterozygous (Aa).


      6) Why heterozygous matters

      Heterozygous individuals:

      • Increase genetic variation
      • Can be carriers of recessive traits
      • Help explain why traits may skip generations
      • Are important in evolution and population genetics

      One-sentence exam summary

      Heterozygous means having two different alleles for a gene.


      中文 — heterozygous(杂合子 / 杂合) 详细解释

      1) 什么是杂合(核心概念)

      Heterozygous(杂合)指的是: 同一性状的两个等位基因不相同

      杂合 = 两个不同的等位基因

      常见形式:

      • Aa

      2) 杂合基因型如何表现

      • 一个等位基因来自父亲
      • 一个来自母亲
      • 通常是 一个显性 + 一个隐性

      例子:

      • Aa → 显性性状表现
      • 隐性基因被“隐藏”,但仍可遗传

      3) 杂合 vs 纯合(重点对比)

      | 类型 | 等位基因 | 示例 | | ---- | ---- | -- | | 杂合 | 不同 | Aa | | 纯合显性 | 相同 | AA | | 纯合隐性 | 相同 | aa |


      4) 潘尼特方格中的杂合

      父母:Aa × Aa

      后代可能为:

      • AA(纯合显性)
      • Aa(杂合)
      • aa(纯合隐性)

      比例:1 : 2 : 1


      一句话考试版总结

      杂合指一个性状的两个等位基因不同。

      如果你愿意,我可以把 heterozygous / homozygous / dominant / recessive / Punnett squares 整理成 Science 10 中英对照闪卡或互动练习,直接用于复习或课堂教学。

    7. homozygous

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      English — homozygous (thorough explanation)

      1) What homozygous means (core idea)

      Homozygous describes a genotype in which an organism has two identical alleles for a particular gene.

      Homozygous = same alleles + same alleles

      Common examples:

      • AA → homozygous dominant
      • aa → homozygous recessive

      2) Types of homozygous genotypes (Science 10 focus)

      A) Homozygous dominant

      • Genotype: AA
      • Phenotype: dominant trait shows
      • Example: Tall plant (if tall = dominant)

      B) Homozygous recessive

      • Genotype: aa
      • Phenotype: recessive trait shows
      • Example: Short plant (if short = recessive)

      📌 Recessive traits only appear when the genotype is homozygous recessive.


      3) Homozygous vs heterozygous (important comparison)

      | Term | Alleles | Example | Trait shown | | ---------------- | --------- | -------- | ------------------------------- | | Homozygous | Same | AA or aa | Dominant (AA) or recessive (aa) | | Heterozygous | Different | Aa | Dominant |


      4) Homozygous in Punnett squares

      Punnett squares often show homozygous outcomes.

      Example: Aa × Aa

      Possible offspring genotypes:

      • AA → homozygous dominant
      • Aa → heterozygous
      • aa → homozygous recessive

      Genotype ratio:

      • 1 AA : 2 Aa : 1 aa

      5) Why homozygous matters

      Homozygous genotypes:

      • Explain why recessive traits appear
      • Help predict inheritance patterns
      • Are important in genetics, breeding, and evolution
      • Can be linked to genetic disorders (if recessive)

      One-sentence exam summary

      Homozygous means having two identical alleles for a gene.


      中文 — homozygous(纯合子 / 纯合) 详细解释

      1) 什么是纯合(核心概念)

      Homozygous(纯合)指的是: 某一性状的两个等位基因完全相同

      纯合 = 两个一样的等位基因

      常见形式:

      • AA(纯合显性)
      • aa(纯合隐性)

      2) 纯合的两种类型(考试重点)

      ① 纯合显性

      • 基因型:AA
      • 表现型:显性性状

      ② 纯合隐性

      • 基因型:aa
      • 表现型:隐性性状 📌 隐性性状只有在纯合隐性时才会出现

      3) 纯合 vs 杂合(对比)

      | 类型 | 等位基因 | 例子 | | -- | ---- | ----- | | 纯合 | 相同 | AA、aa | | 杂合 | 不同 | Aa |


      4) 潘尼特方格中的纯合

      父母:Aa × Aa

      后代可能为:

      • AA(纯合显性)
      • Aa(杂合)
      • aa(纯合隐性)

      比例:1 : 2 : 1


      一句话考试版总结

      纯合指一个性状的两个等位基因相同。

      如果你需要,我可以把 homozygous / heterozygous / dominant / recessive 整理成 Science 10 中英对照速记卡或互动练习,方便系统复习。

    8. genotype

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      English — genotype (thorough explanation)

      1) What genotype means (core idea)

      A genotype is an organism’s genetic makeup for a specific trait — the combination of alleles it has.

      Genotype = the alleles an organism carries

      Genotypes are usually written as letter pairs, such as:

      • AA
      • Aa
      • aa

      These letters represent genes, not physical appearance.


      2) Where genotypes come from

      • One allele comes from the mother
      • One allele comes from the father
      • Together, they form the genotype

      Genotypes are found on homologous chromosomes at the same gene location (locus).


      3) Common genotype types (Science 10 focus)

      Homozygous

      • Both alleles are the same
      • Examples: AA, aa

      Heterozygous

      • Alleles are different
      • Example: Aa

      4) Genotype vs phenotype (very important)

      | Term | What it means | Example | | ------------- | ---------------- | ---------- | | Genotype | Genetic makeup | Bb | | Phenotype | Observable trait | Brown eyes |

      📌 You inherit the genotype, but you observe the phenotype.


      5) Genotype in Punnett squares

      Punnett squares are used to predict possible genotypes of offspring.

      Example: Parents: Aa × Aa

      Possible genotypes:

      • AA
      • Aa
      • Aa
      • aa

      Genotype ratio:

      • 1 AA : 2 Aa : 1 aa

      6) Why genotype matters

      Genotype:

      • Determines which traits can appear
      • Explains why recessive traits can be hidden
      • Helps predict inheritance patterns
      • Is the basis of genetics and evolution

      One-sentence exam summary

      Genotype is the genetic makeup of an organism, represented by its allele combinations.


      中文 — genotype(基因型) 详细解释

      1) 什么是基因型(核心概念)

      基因型(genotype)是指生物体在某一性状上所拥有的等位基因组合

      基因型 = 拥有的基因组合

      常见表示方式:

      • AA
      • Aa
      • aa

      2) 基因型从哪里来

      • 一个等位基因来自母亲
      • 一个来自父亲
      • 位于同源染色体的相同位置

      3) 基因型的类型(考试重点)

      纯合(homozygous)

      • AA、aa

      杂合(heterozygous)

      • Aa

      4) 基因型 vs 表现型(必考)

      | 项目 | 含义 | | --- | ------- | | 基因型 | 基因组合 | | 表现型 | 实际表现的性状 |

      📌 基因型决定潜力,表现型是结果


      5) 潘尼特方格中的基因型

      父母:Aa × Aa

      后代可能的基因型:

      • AA(25%)
      • Aa(50%)
      • aa(25%)

      一句话考试版总结

      基因型是生物体所携带的等位基因组合。

      如果你愿意,我可以把 allele → genotype → phenotype → Punnett square 整理成 Science 10 中英对照速记卡 / 课堂练习 / HTML 互动内容,方便你系统复习。

    9. phenotype

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      English — phenotype (thorough explanation)

      1) What phenotype means (core idea)

      A phenotype is the observable characteristics of an organism—what you can see or measure.

      Phenotype = the physical expression of genes

      Examples include:

      • Eye color
      • Height
      • Blood type
      • Flower color
      • Ability to roll the tongue (in simple genetics examples)

      2) What determines phenotype

      A phenotype is shaped by two factors:

      1. Genotype (the genetic makeup)
      2. Environment (external conditions)

      Phenotype = genotype + environment

      📌 This is why people with the same genes can sometimes look different.


      3) Phenotype vs genotype (must-know distinction)

      | Term | Meaning | Example | | ------------- | --------------------------- | ---------- | | Genotype | The alleles an organism has | Bb | | Phenotype | The trait that appears | Brown eyes |

      You inherit the genotype, but you observe the phenotype.


      4) Phenotype in Punnett squares (Science 10 focus)

      Punnett squares predict possible phenotypes of offspring.

      Example:

      • B = brown eyes (dominant)
      • b = blue eyes (recessive)

      Possible genotypes → phenotypes:

      • BB → brown eyes
      • Bb → brown eyes
      • bb → blue eyes

      📌 Phenotype ratios often differ from genotype ratios.


      5) Environmental effects on phenotype

      Even with the same genotype, environment can change phenotype:

      • Height → genes + nutrition
      • Skin color → genes + sunlight
      • Muscle size → genes + exercise

      This shows phenotype is not fixed by genes alone.


      6) Why phenotype matters

      Phenotypes:

      • Explain variation among individuals
      • Are what natural selection acts on
      • Help scientists study inheritance patterns

      One-sentence exam summary

      Phenotype is the observable traits of an organism resulting from the interaction of genes and environment.


      中文 — phenotype(表现型) 详细解释

      1) 什么是表现型(核心概念)

      表现型(phenotype)是指生物能够被观察到的性状或特征

      表现型 = 基因表现出来的外在结果

      例如:

      • 眼睛颜色
      • 身高
      • 血型
      • 花的颜色

      2) 表现型由什么决定

      表现型由两部分共同决定:

      1. 基因型(genotype)
      2. 环境因素

      表现型 = 基因型 + 环境


      3) 基因型 vs 表现型(必考)

      | 概念 | 含义 | | --- | -------- | | 基因型 | 拥有的等位基因 | | 表现型 | 实际表现出的性状 |


      4) 潘尼特方格中的表现型

      潘尼特方格用来预测:

      • 后代可能出现的表现型
      • 各性状出现的概率

      5) 环境对表现型的影响

      • 营养影响身高
      • 阳光影响肤色
      • 训练影响肌肉

      一句话考试版总结

      表现型是基因与环境共同作用下表现出来的性状。

      如果你愿意,我可以把 genotype / phenotype / allele / Punnett square 整理成 Science 10 中英对照闪卡或互动练习,方便系统复习。

    10. recessive

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      English — recessive (thorough explanation)

      1) What recessive means (core idea)

      Recessive describes an allele whose effect is hidden when a dominant allele is present. A recessive trait is expressed only when both alleles are recessive.

      Recessive = shows only when two recessive alleles are present


      2) How recessive alleles work

      • Each individual has two alleles for a gene (one from each parent)
      • If at least one dominant allele is present, the dominant trait appears
      • The recessive trait appears only in homozygous recessive individuals

      📌 Genetics notation:

      • A = dominant allele
      • a = recessive allele

      | Genotype | Trait shown | | -------- | --------------------------- | | AA | Dominant | | Aa | Dominant (recessive hidden) | | aa | Recessive |


      3) Examples of recessive traits

      Common textbook examples:

      • Blue eyes (recessive to brown)
      • Attached earlobes
      • Certain genetic disorders (e.g., cystic fibrosis)

      📌 A person can carry a recessive allele without showing the trait.


      4) Recessive traits in Punnett squares (Science 10 focus)

      Punnett squares help predict recessive traits.

      Example: Parents: Aa × Aa

      Possible offspring:

      • AA
      • Aa
      • Aa
      • aa

      👉 25% chance of showing the recessive trait (aa)


      5) Recessive vs dominant (key contrast)

      | Feature | Dominant | Recessive | | ----------------------- | ------------------- | -------------------- | | Expression | Shows with 1 allele | Shows with 2 alleles | | Hidden by other allele? | No | Yes | | Written as | Capital letter | Lowercase letter |


      6) Why recessive traits matter

      Recessive traits:

      • Explain why traits can skip generations
      • Help identify carriers
      • Are important in genetic counseling
      • Increase genetic variation in populations

      One-sentence exam summary

      A recessive allele is expressed only when two copies are present and is hidden by a dominant allele.


      中文 — recessive(隐性) 详细解释

      1) 什么是隐性(核心概念)

      隐性(recessive)指的是一种等位基因,当与显性等位基因同时存在时,不会表现出来

      隐性 = 只有在两个隐性等位基因同时存在时才表现


      2) 隐性等位基因如何表现

      • 每个性状由 两个等位基因控制
      • 只要有一个显性等位基因,显性性状就出现
      • 隐性性状必须是纯合隐性(aa)才会表现

      3) 隐性性状的例子

      • 蓝色眼睛
      • 连着的耳垂
      • 某些遗传疾病(如囊性纤维化)

      📌 携带者:有隐性基因,但不表现性状。


      4) 潘尼特方格中的隐性(考试重点)

      父母:Aa × Aa

      结果:

      • 25% aa(表现隐性性状)
      • 50% Aa(携带者)
      • 25% AA

      5) 隐性 vs 显性(对比)

      | 项目 | 显性 | 隐性 | | ---- | ------ | ---- | | 表现条件 | 有一个就表现 | 必须两个 | | 书写方式 | 大写字母 | 小写字母 |


      一句话考试版总结

      隐性性状只有在两个隐性等位基因同时存在时才会表现。

      如果你需要,我可以把 dominant / recessive / codominance / incomplete dominance 整理成 Science 10 中英对照速记表或练习题,帮助你快速区分考点。

    11. codominance

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      English — codominance (thorough explanation)

      1) What codominance means (core idea)

      Codominance is a pattern of inheritance in which both alleles in a heterozygous individual are fully and equally expressed.

      Codominance = both alleles show at the same time

      Neither allele is dominant or recessive over the other.


      2) How codominance looks (key idea)

      In codominance:

      • You do not get a blend
      • You see both traits clearly and separately

      📌 This is different from incomplete dominance, where traits blend.


      3) Classic examples of codominance (Science 10 favorites)

      A) Roan cattle

      • Red allele + White allele
      • Result: Roan coat with both red hairs and white hairs
      • Not pink → red and white are both visible

      B) Human blood type (AB)

      • Alleles: IA and IB
      • Genotype: IAIB
      • Phenotype: AB blood type
      • Both A and B antigens appear on red blood cells

      4) Codominance vs incomplete dominance (very important)

      | Feature | Codominance | Incomplete Dominance | | ----------------- | -------------------- | -------------------------- | | Allele expression | Both fully expressed | Blended | | Appearance | Both traits visible | Mixed/intermediate | | Example | AB blood type | Pink flowers (red × white) |

      📌 AB blood type = codominance 📌 Pink flowers = incomplete dominance


      5) Codominance in Punnett squares

      Codominance still uses Punnett squares, but:

      • Heterozygous offspring show both traits
      • No allele “hides” the other

      Example:

      • Alleles: R (red), W (white)
      • RW → red + white hairs

      6) Why codominance matters

      Codominance:

      • Explains traits that don’t follow simple dominant/recessive rules
      • Increases visible genetic variation
      • Is important in medical genetics (blood transfusions)

      One-sentence exam summary

      Codominance occurs when both alleles in a heterozygous individual are fully expressed at the same time.


      中文 — codominance(共显性) 详细解释

      1) 什么是共显性(核心概念)

      共显性(codominance)指的是: 两个不同的等位基因在杂合体中都会完全表现出来

      共显性 = 两个等位基因同时、完整地表现


      2) 共显性的表现特点

      • 不会混合
      • 两种性状同时清楚可见

      📌 和不完全显性不同,共显性没有中间型


      3) 常见例子(考试常考)

      A) 花牛(roan cattle)

      • 红色等位基因 + 白色等位基因
      • 结果:红毛和白毛同时存在

      B) 人类 AB 血型

      • 等位基因:IA 和 IB
      • 基因型:IAIB
      • 表现型:AB 型血
      • A 抗原和 B 抗原同时存在

      4) 共显性 vs 不完全显性(重点对比)

      | 特点 | 共显性 | 不完全显性 | | -- | ------- | ----- | | 表现 | 两种性状都出现 | 性状混合 | | 结果 | 同时可见 | 中间型 | | 例子 | AB 血型 | 红×白→粉 |


      5) 共显性在潘尼特方格中的体现

      • 杂合体表现两种性状
      • 没有“显性压制隐性”

      一句话考试版总结

      共显性是指杂合体中两个等位基因同时完全表现的遗传方式。

      如果你愿意,我可以把 dominance / incomplete dominance / codominance 整理成 Science 10 中英对照表或互动练习题,非常适合考试快速区分。

    12. alleles

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      English — alleles (thorough explanation)

      1) What alleles are (core idea)

      Alleles are different versions of the same gene. They control variations of a trait, such as eye color or flower color.

      Allele = one version of a gene

      Each gene can have two or more alleles, but an individual organism usually carries two alleles per gene (one from each parent).


      2) Where alleles are found

      • Genes are located on chromosomes
      • Alleles sit at the same position (locus) on homologous chromosomes
      • One allele comes from the mother
      • One allele comes from the father

      📌 This is why offspring show traits from both parents.


      3) Example of alleles (simple)

      Trait: Seed color

      • Y = yellow
      • y = green

      Possible allele combinations:

      • YY
      • Yy
      • yy

      These combinations affect the trait that appears.


      4) Dominant vs recessive alleles (Science 10 focus)

      Dominant allele

      • Shown with a capital letter (A)
      • Expressed if at least one copy is present

      Recessive allele

      • Shown with a lowercase letter (a)
      • Expressed only if two copies are present

      📌 Example:

      • Aa → dominant trait shows
      • aa → recessive trait shows

      5) Alleles, genotype, and phenotype (key relationship)

      | Term | Meaning | Example | | --------- | ------------------ | ---------- | | Allele | Version of a gene | A or a | | Genotype | Allele combination | Aa | | Phenotype | Physical trait | Brown eyes |

      Alleles determine the genotype, which determines the phenotype.


      6) Alleles in Punnett squares

      Punnett squares:

      • Show how alleles from parents combine
      • Predict possible offspring genotypes
      • Estimate trait probabilities

      📌 Example: Parents: Aa × Aa

      • Possible offspring: AA, Aa, Aa, aa

      7) Why alleles are important

      Alleles:

      • Explain variation within a species
      • Help predict inheritance patterns
      • Are the basis of genetics and evolution
      • Allow populations to adapt over time

      One-sentence exam summary

      Alleles are different versions of the same gene that determine variations in traits.


      中文 — alleles(等位基因) 详细解释

      1) 什么是等位基因(核心概念)

      等位基因(alleles)是指同一基因的不同版本,决定同一性状的不同表现。

      等位基因 = 同一基因的不同形式


      2) 等位基因在哪里

      • 基因位于染色体
      • 等位基因位于同源染色体的相同位置
      • 一个来自母亲,一个来自父亲

      3) 等位基因举例

      性状:豌豆高度

      • T = 高
      • t = 矮

      组合可能是:

      • TT
      • Tt
      • tt

      4) 显性与隐性等位基因(必考)

      • 显性等位基因:只要有一个就会表现
      • 隐性等位基因:必须两个都有才表现

      📌 Tt → 显性性状 📌 tt → 隐性性状


      5) 等位基因与性状的关系

      • 等位基因 → 基因型
      • 基因型 → 表现型

      一句话考试版总结

      等位基因是控制同一性状的不同基因形式。

      如果你愿意,我可以把 alleles → genotype → phenotype → Punnett squares 整理成 Science 10 中英对照闪卡或互动练习,直接用于复习或教学。

    13. traits

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      English — traits (thorough explanation)

      1) What traits are (core idea)

      Traits are characteristics or features of an organism. They describe how an organism looks, behaves, or functions.

      Trait = a characteristic of a living thing

      Traits can be:

      • Inherited (passed down from parents)
      • Influenced by the environment
      • Or a combination of both

      2) Types of traits

      A) Inherited (genetic) traits

      These traits are controlled by genes and passed from parents to offspring.

      Examples:

      • Eye color
      • Hair color and texture
      • Blood type
      • Natural height potential

      📌 These traits are present from birth.


      B) Acquired (environmental) traits

      These traits develop due to life experiences or environment.

      Examples:

      • Suntan
      • Muscle strength from exercise
      • Scars
      • Language spoken

      📌 These traits are not inherited genetically.


      C) Traits influenced by both genes and environment

      Many traits result from both heredity and environment.

      Examples:

      • Height (genes + nutrition)
      • Intelligence (genes + education)
      • Athletic ability (genes + training)

      3) Traits in genetics (Science 10 focus)

      In genetics, traits are:

      • Controlled by genes
      • Each gene may have different alleles
      • Alleles can be dominant or recessive

      📌 Example:

      • Brown eyes (dominant)
      • Blue eyes (recessive)

      Punnett squares are used to predict traits in offspring.


      4) Genotype vs phenotype (important distinction)

      | Term | Meaning | Example | | --------- | ------------------- | ---------- | | Genotype | Genetic makeup | Bb | | Phenotype | Physical expression | Brown eyes |

      📌 Traits are what you see (phenotype), based on genes (genotype).


      5) Why traits matter

      Traits:

      • Explain similarities and differences between organisms
      • Help scientists study inheritance
      • Are the basis of natural selection and evolution

      One-sentence exam summary

      Traits are characteristics of organisms that can be inherited, acquired, or influenced by both genes and environment.


      中文 — traits(性状 / 特征) 详细解释

      1) 什么是性状(核心概念)

      性状(traits)是指生物表现出来的特征或特点

      性状 = 生物的特征


      2) 性状的类型

      ① 遗传性状

      基因决定,从父母传给子女。

      例子:

      • 眼睛颜色
      • 头发颜色
      • 血型

      ② 获得性状

      环境或经历造成。

      例子:

      • 晒黑
      • 肌肉增强
      • 疤痕

      ③ 遗传 + 环境共同影响

      • 身高
      • 学习能力
      • 运动能力

      3) 遗传学中的性状(考试重点)

      • 性状由基因控制
      • 基因有不同等位基因
      • 等位基因有显性隐性

      4) 基因型 vs 表现型

      | 概念 | 含义 | | --- | ---- | | 基因型 | 基因组合 | | 表现型 | 外在性状 |


      一句话考试版总结

      性状是生物的特征,由遗传和环境共同决定。

      如果你需要,我可以把 traits / inherited traits / acquired traits / Punnett squares 做成 Science 10 中英对照闪卡或课堂练习题,直接用于教学或复习。

    14. Punnett squares

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      English — Punnett squares (thorough explanation)

      1) What Punnett squares are (core idea)

      Punnett squares are simple diagrams used in genetics to predict the possible genetic outcomes of offspring from two parents.

      Punnett square = a tool to predict inherited traits

      They help scientists and students see:

      • Possible genotypes (gene combinations)
      • Possible phenotypes (physical traits)
      • Probability of each outcome

      2) Why Punnett squares are used

      Punnett squares are used to:

      • Understand hereditary inheritance
      • Predict offspring traits
      • Explain why siblings can look different
      • Show how dominant and recessive genes work

      They do not guarantee results — they show likelihood.


      3) Key terms you must know (Science 10)

      | Term | Meaning | | --------- | -------------------------------------------- | | Gene | Section of DNA that controls a trait | | Allele | Different forms of a gene (e.g., A or a) | | Dominant | Masks another allele (A) | | Recessive | Only shows if both alleles are recessive (a) | | Genotype | Genetic makeup (AA, Aa, aa) | | Phenotype | Physical appearance (tall, short, etc.) |


      4) How a Punnett square works (step by step)

      Example: One trait (monohybrid cross)

      Trait: Plant height

      • T = tall (dominant)
      • t = short (recessive)

      Parents: Tt × Tt

      Step 1: Draw a 2×2 square Step 2: Put one parent’s alleles across the top (T, t) Step 3: Put the other parent’s alleles down the side (T, t) Step 4: Fill in the boxes

      Resulting genotypes:

      • TT
      • Tt
      • Tt
      • tt

      5) Reading the results

      Genotype ratio

      • 1 TT : 2 Tt : 1 tt

      Phenotype ratio

      • 3 tall : 1 short

      📌 Even though only 1 box is tt, that still means a 25% chance of short offspring.


      6) Types of Punnett squares

      A) Monohybrid cross

      • One trait
      • 2×2 square
      • Most common in Science 10

      B) Dihybrid cross (advanced)

      • Two traits at once
      • 4×4 square
      • Shows independent assortment

      7) Limits of Punnett squares

      Punnett squares:

      • Assume genes assort randomly
      • Do not account for environment
      • Work best for simple traits

      One-sentence exam summary

      Punnett squares are diagrams used to predict the probability of genetic traits in offspring.


      中文 — Punnett squares(潘尼特方格) 详细解释

      1) 什么是潘尼特方格(核心概念)

      潘尼特方格是一种遗传学工具,用来预测父母基因组合在后代中可能出现的结果

      潘尼特方格 = 预测遗传结果的表格


      2) 为什么要用潘尼特方格

      潘尼特方格可以帮助我们:

      • 理解遗传规律
      • 预测后代性状
      • 解释兄弟姐妹的差异
      • 学习显性与隐性

      3) 必须掌握的词汇(考试重点)

      | 英文 | 中文 | | --------- | ---- | | Gene | 基因 | | Allele | 等位基因 | | Dominant | 显性 | | Recessive | 隐性 | | Genotype | 基因型 | | Phenotype | 表现型 |


      4) 潘尼特方格如何使用(一步一步)

      例子:豌豆高度

      • T = 高(显性)
      • t = 矮(隐性)

      父母:Tt × Tt

      填表后得到:

      • TT
      • Tt
      • Tt
      • tt

      5) 结果解读

      基因型比例

      • 1 TT : 2 Tt : 1 tt

      表现型比例

      • 3 高 : 1 矮

      📌 这表示: 25% 矮,75% 高(概率,不是保证)


      6) 潘尼特方格的类型

      • 单性状杂交(2×2)
      • 双性状杂交(4×4,高阶内容)

      一句话考试版总结

      潘尼特方格用于预测遗传性状在后代中出现的概率。

      如果你愿意,我可以把 Punnett square → allele → genotype → phenotype 整理成 Science 10 中英对照闪卡 / 课堂练习 / HTML 互动方格,直接给学生用。

  3. pressbooks.library.torontomu.ca pressbooks.library.torontomu.ca