Reviewer #1 (Public review):

Although the use of antimony has been discontinued in India, the observation that Leishmania parasites resistant to antimony are in circulation has been cited as evidence that these resistant parasites are now a distinct strain with properties that ensure their transmission and persistence. It is of interest to determine the properties that favor the retention of their drug resistance phenotype even in the absence of the selective pressure that the drug would otherwise exert. The hypothesis that these authors set out to test is that these parasites have developed a new capacity to acquire and utilize lipids, especially cholesterol, which enables them to grow robustly in infected hosts. The authors present compelling evidence that supports their hypothesis. However, the genetic basis for the parasite's gluttony for lipids remains unresolved.

An issue raised in the initial review was the insufficient detail in the discussion of experiments in which parasitophorous vacuoles were isolated from infected cells and their molecular content was investigated. In this new version, the authors have provided more details of those experiments, including the relative enrichment of the preparations.

A puzzling observation for which they provide compelling evidence is the capacity of LD-R parasites to undergo logarithmic growth between 4 and 24 hours in infected cells. Interestingly, after logarithmic growth within the macrophages at those early times, parasite growth slows down inexplicably after 24 hours. One is left to imagine what the consequences of such growth within an infected host will be.

They made the novel observation that Lamp1 expression increases as early as 4 hours after infection with LD-R and by 12 hours after infection with both LD-S and LD-R. Interestingly, transcription analysis did not provide evidence for increased Lamp1 transcripts, leaving open the possibility that parasite infection may exert control over host cell biology at the translational level. How this might be achieved and what genes would be targets for such controls are open questions.

The dynamic changes in lipid biosynthesis pathways, in comparison to lipid uptake and the formation of lipid droplets in infected cells, are tracked. The basis for the beneficial effect of aspirin to stifle parasite resistance to antimony is explored.

Reviewer #2 (Public review):

Summary:

Idiopathic scoliosis (IS) is a common spinal deformity. Various studies have linked genes to IS, but underlying mechanisms are unclear such that we still lack understanding of the causes of IS. The current manuscript analyzes IS patient populations and identified EPHA4 as a novel associated gene, finding three rare variants in EPHA4 from three patients (one disrupting splicing and two missense variants) as well as a large deletion (encompassing EPHA4) in a Waardenburg syndrome patient with scoliosis. EPHA4 is a member of the Eph receptor family. Drawing on data from zebrafish experiments, the authors argue that EPHA4 loss of function disrupts central pattern generator (CPG) function necessary for motor coordination.

Strengths:

The main strength of this manuscript is the human genetic data, which provide convincing evidence linking EPHA4 variants to IS. The loss of function experiments in zebrafish strongly support the conclusion that EPHA4 variants that reduce function lead to IS.

Weaknesses:

The conclusion that disruption of CPG function causes spinal curves in the zebrafish model is not fully supported. The authors' final model is that a disrupted CPG leads to asymmetric mechanical loading on the spine and, over time, the development of curves. This is a reasonable idea, but currently not strongly backed up by data in the manuscript. Potentially, the impaired larval movements simply coincide with, but do not cause, juvenile-onset scoliosis. Support for the authors' conclusion would require independent methods of disrupting CPG function and determining if this is accompanied by spine curvature. Nevertheless, the data showing correlations between spine curvature and abnormal neural patterning, neuronal firing, and swimming in eph4a loss-of-function mutant larvae are sound.

Comments on revisions:

I think the authors misunderstood my point about genetic nomenclature for the zebrafish alleles. The nomenclature guidelines are described at ZFIN, and ZFIN will ask for appropriate allele designations.

Reviewer #1 (Public review):

Public Review

The authors investigated the role of the C. elegans Flower protein, FLWR-1, in synaptic transmission, vesicle recycling, and neuronal excitability. They confirmed that FLWR-1 localizes to synaptic vesicles and the plasma membrane and facilitates synaptic vesicle recycling at neuromuscular junctions. They observed that hyperstimulation results in endosome accumulation in flwr-1 mutant synapses, suggesting that FLWR-1 facilitates the breakdown of endocytic endosomes. Using tissue-specific rescue experiments, the authors showed that expressing FLWR-1 in GABAergic neurons restored the aldicarb-resistant phenotype of flwr-1 mutants to wild-type levels. By contrast, cholinergic neuron expression did not rescue aldicarb sensitivity at all. They also showed that FLWR-1 removal leads to increased Ca2+ signaling in motor neurons upon photo-stimulation. From these findings, the authors conclude that FLWR-1 helps maintain the balance between excitation and inhibition (E/I) by preferentially regulating GABAergic neuronal excitability in a cell-autonomous manner.

Overall, the work presents solid data and interesting findings, however the proposed cell-autonomous model of GABAergic FLWR-1 function may be overly simplified in my opinion.

Most of my previous comments have been addressed; however, two issues remain.

(1) I appreciate the authors' efforts conducting additional aldicarb sensitivity assays that combine muscle-specific rescue with either cholinergic or GABergic neuron-specific expression of FLWR-1. In the revised manuscript, they conclude, "This did not show any additive effects to the pure neuronal rescues, thus FLWR-1 effects on muscle cell responses to cholinergic agonists must be cell-autonomous." However, I find this interpretation confusing for the reasons outlined below.

Figure 1 - Figure Supplement 3B shows that muscle-specific FLWR-1 expression in flwr-1 mutants significantly restores aldicarb sensitivity. However, when FLWR-1 is co-expressed in both cholinergic neurons and muscle, the worms behave like flwr-1 mutants and no rescue is observed. Similarly, cholinergic FLWR-1 alone fails to restore aldicarb sensitivity (shown in the previous manuscript). These observations indicate a non-cell-autonomous interaction between cholinergic neurons and muscle, rather than a strictly muscle cell-autonomous mechanism. In other words, FLWR-1 expressed in cholinergic neurons appears to negate or block the rescue effect of muscle-expressed FLWR-1. Therefore, FLWR-1 could play a more complex role in coordinating physiology across different tissues. This complexity may affect interpretations of Ca2+ dynamics and/or functional data, particularly in relation to E/I balance, and thus warrants careful discussion or further investigation.

(2) The revised manuscript includes new GCaMP analyses restricted to synaptic puncta. The authors mention that "we compared Ca2+ signals in synaptic puncta versus axon shafts, and did not find any differences," concluding that "FLWR-1's impact is local, in synaptic boutons." This is puzzling: the similarity of Ca2+ signals in synaptic regions and axon shafts seems to indicate a more global effect on Ca2+ dynamics or may simply reflect limited temporal resolution in distinguishing local from global signals due to rapid Ca2+ diffusion. The authors should clarify how they reached the conclusion that FLWR-1 has a localized impact at synaptic boutons, given that synaptic and axonal signals appear similar. Based on the presented data, the evidence supporting a local effect of FLWR-1 on Ca2+ dynamics appears limited.

Reviewer #1 (Public review):

Summary:

In this study from Belato, Knight and co-workers, the authors investigated the Rec domain of a thermophilic Cas9 from Geobacillus stearothermophilus (GeoCas9). The authors investigated three constructs, two individual subdomains of Rec (Rec1 and Rec2) and the full Rec domain. This domain is involved in binding to the guide RNA of Cas9, as well as the RNA-DNA duplex that is formed upon target binding. The authors performed RNA binding and relaxation experiments using NMR for the wild-type domain as well as two-point mutants. They observed differences in RNA binding activities as well as the flexibility of the domain. The authors also performed molecular dynamics and functional experiments on full-length GeoCas9 to determine whether these biophysical differences affect the RNA binding or cleavage activity. Although the authors observed some changes in the thermal stability of the mutant GeoCas9-gRNA complex, they did not observe substantial differences in the guide RNA binding or cleavage activities of the mutant GeoCas9 variants.

Overall, this manuscript provides a detailed biophysical analysis of the GeoCas9 Rec domain. The NMR assignments for this construct should prove very useful, and can serve as the basis for future similar studies of GeoCas9 Rec domain mutants. While the two mutants tested in the study did not produce significant differences from wild-type GeoCas9, the study rules out the possibility that analogous mutations can be translated between type II-A and II-C Cas9 orthologs. Together, these findings may provide the grounds for future engineering of higher fidelity variants of GeoCas9

Reviewer #1 (Public review):

Summary.

The authors goal was to map the neural circuitry underlying cold sensitive contraction in Drosophila. The circuitry underlying most sensory modalities has been characterized but noxious cold sensory circuitry has not been well studied. Importantly, they analyze all downstream partner neurons connected to the Class III sensory neurons. The authors achieve their goal and map out sensory and post-sensory neurons involved in this behavior.

Strengths.

The manuscript provides compelling evidence for sensory and post sensory neurons involved in noxious cold sensitive behavior. They use both connectivity data and functional data to identify these neurons. This work is a clear advance in our understanding of noxious cold behavior. The experiments are done with a high degree of experimental rigor.

Weaknesses.

I find no major weaknesses in this work. It is a massive amount of data that clearly shows the role of the Class III neurons in cold-induced larval body contraction.

Reviewer #1 (Public review):

Summary:

In this study, Nakagawa and colleagues report the observation that YAP is differentially localized, and thus differentially transcriptionally active, in spheroid cultures versus monolayer cultures. YAP is known to play a critical role in the survival of drug-tolerant cancer cells, and as such, the higher levels of basally activated YAP in monolayer cultures lead to higher fractions of surviving drug-tolerant cells relative to spheroid culture (or in vivo culture). The findings of this study, revealed through convincing experiments, are elegantly simple and straightforward, yet they add significantly to the literature in this field by revealing that monolayer cultures may actually be a preferential system for studying residual cell biology simply because the abundance of residual cells in this format is much greater than in spheroid or xenograft models. The potential linkage between matrix density and stiffness and YAP activation, while only speculated upon in this manuscript, is intriguing and a rich starting point for future studies.

Although this work, like any important study, inspires many interesting follow-on questions, I am limiting my questions to only a few minor ones, which may potentially be explored either in the context of the current study or in separate, follow-on studies.

Strengths:

The major strengths of the work are described above.

Weaknesses:

Rather than considering the following points as weaknesses, I instead prefer to think of them as areas for future study:

(1) Given the field's intense interest in the biology and therapeutic vulnerabilities of residual disease cells, I suspect that one major practical implication of this work could be that it inspires scientists interested in working in the residual disease space to model it in monolayer culture. However, this relies upon the assumption that drug-tolerant cells isolated in monolayer culture are at least reasonably similar in nature to drug-tolerant cells isolated from spheroid or xenograft systems. Is this true? An intriguing experiment that could help answer this question would be to perform gene expression profiling on a cell line model in the following conditions: monolayer growth, drug tolerant cells isolated from monolayer growth conditions, spheroid growth, drug tolerant cells isolated from spheroid growth conditions, xenograft tumors, and drug tolerant cells isolated from xenograft tumors. What are the genes and programs shared between drug-tolerant cells cultured in the three conditions above? Which genes and programs differ between these conditions? Data from this exercise could help provide additional, useful context with which to understand the benefits and pitfalls of modeling residual tumor cell growth in monolayer culture.

(2) In relation to the point above, there is an interesting and established connection between mesenchymal gene expression and YAP/TAZ signaling. For example, analyses of gene expression data from human tumors and cell lines demonstrate an extremely strong correlation between these two gene expression programs. Further, residual persister cancer cells have often been characterized as having undergone an EMT-like transition. From the analysis above, is there evidence that residual tumor cells with increased YAP signaling also exhibit increased mesenchymal gene expression?

Reviewer #1 (Public review):

Summary

Olfactory sensory neurons (OSNs) in the olfactory epithelium detect myriads of environmental odors that signal essential cues for survival. OSNs are born throughout life and thus represent one of the few neurons that undergo life-long neurogenesis. Until recently, it was assumed that OSN neurogenesis is strictly stochastic with respect to subtype (i.e. the receptor the OSN chooses to express). However, a recent study showed that olfactory deprivation via naris occlusion selectively reduced birthrates of only a fraction of OSN subtypes and indicated that these subtypes appear to have a special capacity to undergo changes in birthrates in accordance with the level of olfactory stimulation. These previous findings raised the interesting question of what type of stimulation influences neurogenesis, since naris occlusion does not only reduce the exposure to potentially thousands of odors, but also to more generalized mechanical stimuli via preventing airflow.

In this study, the authors set out to identify the stimuli that are required to promote the neurogenesis of specific OSN subtypes. Specifically, they aim to test the hypothesis if discrete odorants selectively stimulate the same OSN subtypes whose birthrates are affected. This would imply a highly specific mechanism in which exposure to certain odors can "amplify" OSN subtypes responsive to those odors suggesting that OE neurogenesis serves, in part, an adaptive function.

To address this question, the authors focused on a family of OSN subtypes that had previously been identified to respond to musk-related odors and that exhibit higher transcript levels in the olfactory epithelium of mice exposed to males compared to mice isolated from males. First, the authors confirm via a previously established cell birth dating assay in unilateral naris occluded mice that this increase in transcript levels actually reflects a stimulus-dependent birthrate acceleration of this OSN subtype family. In a series of experiments (in unilateral occluded and non-occluded mice) using the same birth dating assay, they show that several subtypes of this OSN family, but not other "control" subtypes exhibit increased birthrates in response to adolescent male exposure, but not to female exposure.

In the core experiment of the study, they expose unilaterally naris occluded and non-occluded mice to two musk-related odors and two "control" odors (that do not activate musk-responsive OSN subtypes) to test if these odors specifically accelerate the birth rates of OSN types that are responsive to these odors. This experiment reveals that (for the tested odors and OSN subtypes) indeed birthrates are only affected by discrete odorants that stimulate these OSN subtypes (with a complex relationship between birth rate acceleration and odor concentrations) suggesting that OE neurogenesis may serve, in part, as an adaptive function

Strength:

The scientific question is valid and opens an interesting direction. The previously established cell birth dating assay in naris occluded and non-occluded mice is well performed and accompanied by several control experiments addressing potential other interpretations of the data.

In this revised version, the authors added several new experiments addressing the previous concern that only the effect of one specific odor (muscone) on musk-responsive OSN subtypes had been tested to make the general claim that discrete odors specifically accelerate the birth rate of OSN subtypes they stimulate. Now the authors demonstrate that another musk-related odor (ambretone) also induces this effect and that other non-musk odors do not. In addition, they show that two other OSN subtypes that do not respond to musk-related odors are not affected. These experiments further substantiate the above claim.

Weakness:

(1) The main research question of this study was to test if discrete odors specifically accelerate the birth rate of OSN subtypes they stimulate, i.e. does muscone only accelerate the birth rate of OSNs that express muscone-responsive ORs, or vice versa is the birthrate of muscone-responsive OSNs only accelerated by odors they respond to?<br /> As mentioned under "strength" the authors added several experiments to further substantiate their claim. While these controls are very important to show that the observed effect is indeed specific for musk-related odors on musk-responsive OSN subtypes, these experiments still only focus on one closely related family of musk-responsive OSN subtypes. To understand if this phenomenon is a more generalized mechanism and plays a role for other OSN subtypes beyond this small family of related receptors, further experiments showing this effect for other OSN subtypes are critical.

(2) Previous concerns (#2, #4, #5 and #6) about a lack of increase in UNO effect size for olfr1440 under any muscone concentrations, strong fluctuations of newborn neurons on the closed side as well as a seemingly contradicting statement that overstimulation possibly reflects reduced survival have been addressed by adding potential explanations to the text.

In addition, the previous remark (#3) that certain phrases gave the misleading impression that musk-related odors are indeed excreted into male mouse urine at certain concentrations was addressed not only by re-phrasing, but by performing additional experiments. Although these did not deliver clear results (because of technical difficulties), interesting possibilities are discussed.

Reviewer #1 (Public review):

Summary:

In this study, Le et al.. aimed to explore whether AAV-mediated overexpression of Oct4 could induce neurogenic competence in adult murine Müller glia, a cell type that, unlike its counterparts in cold-blooded vertebrates, lacks regenerative potential in mammals. The primary goal was to determine whether Oct4 alone, or in combination with Notch signaling inhibition, could drive Müller glia to transdifferentiate into bipolar neurons, offering a potential strategy for retinal regeneration.

The authors demonstrated that Oct4 overexpression alone resulted in the conversion of 5.1% of Müller glia into Otx2+ bipolar-like neurons by five weeks post-injury, compared to 1.1% at two weeks. To further enhance the efficiency of this conversion, they investigated the synergistic effect of Notch signaling inhibition by genetically disrupting Rbpj, a key Notch effector. Under these conditions, the percentage of Müller glia-derived bipolar cells increased significantly to 24.3%, compared to 4.5% in Rbpj-deficient controls without Oct4 overexpression. Similarly, in Notch1/2 double-knockout Müller glia, Oct4 overexpression increased the proportion of GFP+ bipolar cells from 6.6% to 15.8%.

To elucidate the molecular mechanisms driving this reprogramming, the authors performed single-cell RNA sequencing (scRNA-seq) and ATAC-seq, revealing that Oct4 overexpression significantly altered gene regulatory networks. They identified Rfx4, Sox2, and Klf4 as potential mediators of Oct4-induced neurogenic competence, suggesting that Oct4 cooperates with endogenously expressed neurogenic factors to reshape Müller glia identity.

Overall, this study aimed to establish Oct4 overexpression as a novel and efficient strategy to reprogram mammalian Müller glia into retinal neurons, demonstrating both its independent and synergistic effects with Notch pathway inhibition. The findings have important implications for regenerative therapies as they suggest that manipulating pluripotency factors in vivo could unlock the neurogenic potential of Müller glia for treating retinal degenerative diseases.

Strengths:

(1) Novelty: The study provides compelling evidence that Oct4 overexpression alone can induce Müller glia-to-bipolar neuron conversion, challenging the conventional view that mammalian Müller glia lacks neurogenic potential.<br /> (2) Technological Advances: The combination of Muller glia-specific labeling and modifying mouse line, AAV-GFAP promoter-mediated gene expression, single-cell RNA-seq, and ATAC-seq provides a comprehensive mechanistic dissection of glial reprogramming.<br /> (3) Synergistic Effects: The finding that Oct4 overexpression enhances neurogenesis in the absence of Notch signaling introduces a new avenue for retinal repair strategies.

Weaknesses:

(1) In this study, the authors did not perform a comprehensive functional assessment of the bipolar cells derived from Müller glia to confirm their neuronal identity and functionality.<br /> (2) Demonstrating visual recovery in a bipolar cell-deficiency disease model would significantly enhance the translational impact of this work and further validate its therapeutic potential.

Comments on revisions:

The author answered all my questions and corrected the minor comments, so I have no more comments on the manuscript.

Reviewer #2 (Public review):

This study by Yu and coworkers investigates the potential role of Secretory leukocyte protease inhibitor (SLPI) in Lyme arthritis. They show that, after needle inoculation of the Lyme disease agent, B. burgdorferi, compared to wild type mice, a SLPI-deficient mouse suffers elevated bacterial burden, joint swelling and inflammation, pro-inflammatory cytokines in the joint, and levels of serum neutrophil elastase (NE). They suggest that SLPI levels of Lyme disease patients are diminished relative to healthy controls. Finally, using a powerful screen of secreted mammalian proteins, they find that SLPI interacts directly B. burgdorferi.

The known role of SLPI in dampening inflammation and inflammatory damage by inhibition of NE makes the enhanced inflammation in the joint of B. burgdorferi-infected mice a predicted result but it has not previously been demonstrated and could spur further study. A limitation that is unaddressed experimentally is potential contribution of the greater bacterial burden to the enhanced inflammation, leaving open the question of whether greater immunologic stimulus or a defect in the regulation of inflammation is responsible for the observed enhanced disease. Answering this question would better justify the statement in the abstract that "These data demonstrate the importance of SLPI in suppressing periarticular joint inflammation in Lyme disease."

Although the finding of SLPI binding to bacteria is potentially quite interesting the biological relevance of this interaction is not addressed. Readers of only the abstract, which describes the direct interaction of SLPI with bacteria, may mistakenly conclude that the authors demonstrate that recruitment of this immunoregulatory factor to the bacterial surface enhances inflammation of infected tissues. This attractive possibility has not been demonstrated in this study; such assertion would require comparison of bacteria that either bind or do not bind SLPI in a mouse infection model.

Finally, the investigators take advantage of clinical samples to ask if serum SLPI levels a diminished in Lyme disease patients relative to healthy controls. The assessment of human samples is interesting and generally to be lauded, but here the comparison is limited by: (a) a small sample number, with only 5 healthy control samples (which should not be difficult to obtain); and (b) the inclusion of samples from 4 patients with erythema migrans rather than Lyme arthritis, which was the manifestation tracked in the mouse studies. Moreover, of the 3 Lyme arthritis patients, serum samples from multiple blood draws were included, resulting in 5 data points; similarly, of the 4 erythema migrans patients, 13 separate samples were included. The multiple samplings from some but not all subjects could result in differential "weighting" of samples. Therefore, although the investigators provide a statistical analysis of these data, it is difficult to evaluate the validity of this apparent difference.

In summary, this is an interesting study that provides new information regarding infection in a host deficient in SLPI and, using a state-of-the-art screen of the mammalian secretome to show that B. burgdorferi binds SLPI, raising the attractive possibility that this pathogen utilizes a host immune regulator to enhance inflammation. The conclusions that SLPI enhances inflammation directly due to its immunoregulatory activity and that SLPI levels are diminished in human Lyme disease patients, as well as the implication that SLPI binding by the bacterium has pathogenic significance, each require further study.

Reviewer #1 (Public review):

The paper proposes an interesting perspective on the spatio-temporal relationship between FC in fMRI and electrophysiology. The study found that while similar networks configurations are found in both modalities, there is a tendency for the networks to spatially converge more commonly at synchronous than asynchronous timepoints.

My confidence in the findings and their interpretation has been improved by the addition of some basic simulations. It helps give confidence in the measure being used to distinguish between scenarios.

Of course, there may be other scenarios that are problematic that are not covered by the current simulations - this highlights the difficulty of making a claim based on a heuristic measure.

That said, with the simulations included and if the caveat above is acknowledged, then I think the paper is in good shape.

Instructions on how to add the facilitator as an editor/commenter might help.

Reviewer #1 (Public review):

Summary:

Huntington's disease (HD) is characterized by the expansion of polyglutamine repeats in huntingtin protein (HTT), leading to the formation of aggresomes composed of mutant huntingtin (mHTT). This study investigates the potential therapeutic strategy of enhancing autophagy to clear mHTT. The authors' evaluation of the autophagic-lysosomal pathway (ALP) in human HD brains shows that, in early stages, there is upregulated lysosomal biogenesis and relatively normal autophagy flux, while late-stage brains exhibit impaired autolysosome clearance, suggesting that early intervention may be beneficial. The authors cross the Q175 HD knock-in model with the TRGL autophagy reporter mouse to investigate ALP dynamics in vivo. In these models, mHTT is detected in autophagic vacuoles and colocalizes with autophagy receptors p62/SQSTM1 and ubiquitin. Although ALP alterations in the Q175 model are milder and later onset compared to human HD, they do show lysosome depletion and impaired autophagic flux. Treatment with an mTOR inhibitor in 6-month-old TRGL/Q175 mice normalized lysosome numbers, alleviated aggresome pathology, and reduced mHTT, p62, and ubiquitin levels. These findings suggest that autophagy modulation during the early stages of disease progression may offer potential therapeutic interventions for HD pathology.

Strengths:

Provide supportive animal evidence for mTOR inhibition in enhancing autophagy and reducing toxicity in HD animal models.

Weaknesses:

Lacks animal behavior and survival rate data, particularly regarding whether the extent of motor dysfunction in TRGL/Q175 mice is comparable to that in Q175 mice and whether the administration of mTORi INK improves these symptoms.

Reviewer #1 (Public review):

This report addresses a compelling topic. However, I have significant concerns, which necessitate a reassessment of the report's overall value.

Anatomical Specificity and Stimulation Site:<br /> While the authors clarify that the ventral MGB (MGv) was the intended stimulation target, the electrode track (Fig. 1A) and viral spread (Fig. 2E) suggest possible involvement of the dorsal MGB (MGd) and broader area. Given that MGv-AI and MGd-AC pathways have distinct-and sometimes opposing-effects on plasticity, the reported LTP values (with unusually small standard deviations) raise concerns about the specificity of the findings. Additional anatomical verification would help resolve this issue.

Statistical Rigor and Data Variability:<br /> The remarkably low standard deviations in LTP measurements are unexpected based on established variability in thalamocortical plasticity. The authors' response confirms these values are accurate, but further justification, such as methodological controls or replication-would bolster confidence in these results. Additionally, the comparison of in vivo vs. in vitro LTP variability requires more substantive support.

Viral Targeting and Specificity:<br /> The manuscript does not clearly address whether cortical neurons were inadvertently infected by AAV9. Given the potential for off-target effects, explicit confirmation (e.g., microphotograph of stimulation site) would strengthen the study's conclusions.

Integration of Prior Literature:<br /> The discussion of existing work is adequate but could be more comprehensive. A deeper engagement with contrasting findings would provide better context for the study's contributions.

Therapeutic Implications:<br /> The authors' discussion of therapeutic potential is now appropriately cautious and well-reasoned.

Conclusion:<br /> While the study presents intriguing findings, the concerns outlined above must be addressed to fully establish the validity and impact of the results. I appreciate the authors' efforts thus far and hope they can provide additional data or clarification to resolve these issues. With these revisions, the manuscript could make a valuable contribution to the field.

Reviewer #1 (Public review):

Summary:

The manuscript provides a novel method for the automated detection of scent marks from urine and feces in rodents. Given the importance of scent communication in these animals and their role as model organisms, this is a welcome tool.

Strengths:

The method uses a single video stream to allow for the distinction between urine and feces. It is automated.

Weaknesses:

The accuracy is decent but not perfect and may be too low to detect some effects that are biologically real but subtle (e.g. less than 10% differences). For many assays, however, this tools will be useful.

Reviewer #1 (Public review):

About R squared in the plots:<br /> The authors have used a z-scored R squared in the main ridge regression plots. While this may be interpretable, it seems non-standard and overly complicated. The authors could use a simple Pearson r to be most direct and informative (and in line with similar work, including Goldstein et al. 2022 which they mentioned). This way the sign of the relationships is preserved.

About the new TRF analysis:<br /> The new TRF analysis is a necessary addition and much appreciated. However, it is missing the results for the acoustic regressors, which should be there analogous to the HM-LSTM ridge analysis. The authors should also specify which software they have utilized to conduct the new TRF analysis. It also seems that the linguistic predictors/regressors have been newly constructed in a way more consistent with previous literature (instead of using the HM-LSTM features); these specifics should also be included in the manuscript (did it come from Montreal Forced Aligner, etc.?). Now that the original HM-LSTM can be compared to a more standard TRF analysis, it is apparent that the results are similar.

The authors' wording about this suggests that these new regressors have a nonzero sample at each linguistic event's offset, not onset. This should also be clarified. As the authors know, the onset would be more standard, and using the offset has implications for understanding the timing of the TRFs, as a phoneme has a different duration than a word, which has a different duration from a sentence, etc.

About offsets:<br /> TRFs can still be interpretable using the offset timings though; however, the main original analysis seems to be utilizing the offset times in a different, more confusing way. The authors still seem to be saying that only the peri-offset time of the EEG was analyzed at all, meaning the vast majority of the EEG trial durations do not factor into the main HM-LSTM response results whatsoever. The way the authors describe this does not seem to be present in any other literature, including the papers that they cite. Therefore, much more clarification on this issue is needed. If the authors mean that the regressors are simply time-locked to the EEG by aligning their offsets (rather than their onsets, because they have varying onsets or some such experimental design complexity), then this would be fine. But it does not seem to be what the authors want to say. This may be a miscommunication about the methods, or the authors may have actually only analyzed a small portion of the data. Either way, this should be clarified to be able to be interpretable.

Reviewer #1 (Public review):

I want to reiterate my comment from the first round of reviews: that I am insufficiently familiar with the intricacies of Maxwell's equations to assess the validity of the assumptions and the equations being used by WETCOW. The work ideally needs assessing by someone more versed in that area, especially given the potential impact of this method if valid.

Effort has been made in these revisions to improve explanations of the proposed approach (a lot of new text has been added) and to add new simulations.

However, the authors have still not compared their method on real data with existing standard approaches for reconstructing data from sensor to physical space. Refusing to do so because existing approaches are deemed inappropriate (i.e. they "are solving a different problem") is illogical.

Similarly, refusing to compare their method with existing standard approaches for spatio-temporally describing brain activity, just because existing approaches are deemed inappropriate, is illogical.

For example, the authors say that "it's not even clear what one would compare [between the new method and standard approaches]". How about:

(1) Qualitatively: compare EEG activation maps. I.e. compare what you would report to a researcher about the brain activity found in a standard experimental task dataset (e.g. their gambling task). People simply want to be able to judge, at least qualitatively on the same data, what the most equivalent output would be from the two approaches. Note, both approaches do not need to be done at the same spatial resolution if there are constraints on this for the comparison to be useful.

and

(2) Quantitatively: compare the correlation scores between EEG activation maps and fMRI activation maps

The abstract claims that there is a "direct comparison with standard state-of-the-art EEG analysis in a well-established attention paradigm", but no actual comparison appears to have been completed in the paper.

Reviewer #2 (Public review):

Summary:

In this present Mendelian randomization-phenome-wide association study, the authors found BMI to be positively associated with many health-related conditions, such as heart disease, heart failure, and hypertensive heart disease. They also found sex differences in some traits, such as cancer, psychological disorders, and ApoB.

Strengths:

The use of the UK-biobank study with detailed phenotype and genotype information.

Comments on revisions:

I believe the authors have presented convincing arguments for the novelty and interpretation of their study. I have no additional comments.

DOI: 10.1038/s41556-025-01658-1

Resource: bcl2fastq (RRID:SCR_015058)

Curator: @dhovakimyan1

SciCrunch record: RRID:SCR_015058

What is this?

DOI: 10.1038/s41467-025-58821-3

Resource: None

Curator: @dhovakimyan1

SciCrunch record: RRID:ZFIN_ZDB-ALT-131212-1

What is this?

DOI: 10.1038/s41467-025-58821-3

Resource: (ZFIN Cat# ZDB-ALT-150904-1,RRID:ZFIN_ZDB-ALT-150904-1)

Curator: @scibot

SciCrunch record: RRID:ZFIN_ZDB-ALT-150904-1

What is this?

Reviewer #1 (Public review):

Summary:

The study identifies two types of activation: one that is cue-triggered and non-specific to motion directions, and another that is specific to the exposed motion directions but occurs in a reversed manner. The finding that activity in the medial temporal lobe (MTL) preceded that in the visual cortex suggests that the visual cortex may serve as a platform for the manifestation of replay events, which potentially enhance visual sequence learning.

Evaluations:

Identifying the two types of activation after exposure to a sequence of motion directions is very interesting. The experimental design, procedures and analyses are solid. The findings are interesting and novel.

In the original submission, it was not immediately clear to me why the second type of activation was suggested to occur spontaneously. The procedural differences in the analyses that distinguished between the two types of activation need to be a little better clarified. However, this concern has been satisfactorily addressed in the revision.

Reviewer #1 (Public review):

Summary:

The submitted article reports the development of an unsupervised learning method that enables quantification of behaviour and poses of C. elegans from 15 minute long videos and presents a spatial map of both. The entire pipeline is a two part process, with the first part based on contrastive learning that represents spatial poses onto an embedded space, while the second part uses a transformer encoder to enable estimation of masked parts in a spatiotemporal sequence.

Strengths:

This analysis approach will prove to be useful for the C. elegans community. The application of the method on various age-related videos on various strains presents a good use-case for the approach. The manuscript is well written and presented.

Specific comments:

(1) One of the main motivations as mentioned in the introduction as well as emphasized in the discussion section is that this approach does not require key-point estimation for skeletonization and is also not dependent on the eigenworm approach for pose estimation. However, the eigenworm data has been estimated using the Tierpsy tracker in videos used in this work and stored as metadata. This is subsequently used for interpretation. It is not clear at this point, how else the spatial embedded map may be interpreted without using this kind of pose estimates obtained from other approaches. Please elaborate and comment.

(2) As per the manuscript, the second part of the pipeline is used to estimate the masked sequences of the spatiotemporal behavioral feature. However, it is not clear what the numbers listed in Fig. 2.3 represent?

(3) It is not clear how motion speed is linked to individual poses as mentioned in Figs. 4 (b) and (c).

Reviewer #1 (Public review):

Summary:

Using a combination of EEG and behavioural measurements, the authors investigate the degree to which processing of spatially-overlapping targets (coherent motion) and distractors (affective images) are sampled rhythmically and how this affects behaviour. They found that both target processing (via measurement of amplitude modulations of SSVEP amplitude to target frequency) and distractor processing (via MVPA decoding accuracy of bandpassed EEG relative to distractor SSVEP frequency) displayed a pronounced rhythm at ~1Hz, time-locked to stimulus onset. Furthermore, the relative phase of this target/distractor sampling predicted the accuracy of coherent motion detection across participants.

Strengths:

(1) The authors are addressing a very interesting question with respect to sampling of targets and distractors, using neurophysiological measurements to their advantage in order to parse out target and distractor processing.

(2) The general EEG analysis pipeline is sensible and well-described.

(3) The main result of rhythmic sampling of targets and distractors is striking and very clear even on a participant level.

(4) The authors have gone to quite a lot of effort to ensure the validity of their analyses, especially in the Supplementary Material.

(5) It is incredibly striking how the phases of both target and distractor processing are so aligned across trials for a given participant. I would have thought that any endogenous fluctuation in attention or stimulus processing like that would not be so phase aligned. I know there is literature on phase resetting in this context, the results seem very strong here and it is worth noting. The authors have performed many analyses to rule out signal processing artifacts, e.g., the sideband and beating frequency analyses.

Weaknesses:

(1) In general, the representation of target and distractor processing is a bit of a reach. Target processing is represented by SSVEP amplitude, which is most likely going to be related to the contrast of the dots, as opposed to representing coherent motion energy, which is the actual target. These may well be linked (e.g., greater attention to the coherent motion task might increase SSVEP amplitude), but I would call it a limitation of the interpretation. Decoding accuracy of emotional content makes sense as a measure of distractor processing, and the supplementary analysis comparing target SSVEP amplitude to distractor decoding accuracy is duly noted.

(2) Comparing SSVEP amplitude to emotional category decoding accuracy feels a bit like comparing apples with oranges. They have different units and scales and probably reflect different neural processes. Is the result the authors find not a little surprising in this context? This relationship does predict performance and is thus intriguing, but I think this methodological aspect needs to be discussed further. For example, is the phase relationship with behaviour a result of a complex interaction between different levels of processing (fundamental contrast vs higher order emotional processing)?

Reviewer #1 (Public review):

Summary:

Some years ago, Brookshire proposed a method to identify oscillations in behavioural data that controls for effects of aperiodic trends. Such trends can produce false positive results if not controlled for. Although this method successfully controlled for this issue, it was also relatively insensitive to true effects, and it remained unclear whether it was unable to replicate published evidence for behavioural oscillations because they were false positives or the method could not detect them. In simulated data, Harris & Beale show that their revised version of the method proposed by Brookshire is more sensitive to effects and equally unsusceptible to false positives. When applied to available data, this new version indeed revealed evidence for behavioural oscillations. This paper is therefore an important piece in the puzzle of the ongoing debate on behavioural oscillations.

Strengths:

(1) The paper is well written and compact.

(2) The new method proposed is tested thoroughly, and its application in simulated data shows its properties.

(3) It is very important that the code is made publicly available.

(4) The fact that this new version identifies behavioural oscillations in available datasets can resolve the current debate on the existence of such oscillations.

Weaknesses:

I see the following weaknesses as minor.

(1) I wonder whether the frequency-dependent results (e.g., Figures 7 and 8) need to be seen in light of the sampling rate used in the simulations. For example, a lower sampling rate might be sufficient if only low frequencies are of interest in the data and lead to higher sensitivity as the number of trials (per time point) can be increased. Conversely, a higher sampling rate might lead to a higher sensitivity for the detection of effects at higher frequencies.

(2) The behavioural oscillations from individual participants do not need to have common phases for this analysis to reveal an effect. However, this also means that in a scenario where they do have common phases, this similarity remains "unused" by the analysis (e.g., due to similar phases, the oscillation could be easier to identify on the group level as signals that are not phase locked are averaged out). In such a scenario, it remains unclear whether the analysis proposed is the most sensitive one.

Reviewer #1 (Public review):

The authors note that very premature infants experience the visual world early and, as a consequence, sustain lasting deficits including compromised motion processing. Here they investigate the effects of early eye opening in ferret, choosing a time point after birth when both retinal waves and light traveling through closed lids drive sensory responses. The laboratory has long experience in quantitative studies of visual response properties across development and this study reflects their expertise.

The investigators find little or no difference in mean orientation and direction selectivity, or in spatial frequency tuning, as a result of early eye opening but marked differences in temporal frequency tuning. These changes are especially interesting as they relate to deficits seen in prematurely delivered children. Temporal frequency bandwidth for responses evoked from early-opened contralateral eyes were broader than for controls; this is the case for animals in which either one or both eyes were opened prematurely. Further, when only one eye was opened early, responses to low temporal frequencies were relatively stronger.

The investigators also found changes in firing rate and signs of response to visual stimuli. Premature eye-opening increased spontaneous rates in all test configurations. When only one eye was opened early, firing rates recorded from the ipsilateral cortex were strongly suppressed, with more modest effects in other test cases.

As the authors' discussion notes, these observations are just a starting point for studies underlying mechanism. The experiments are so difficult to perform and so carefully described that the results will be foundational for future studies of how premature birth influences cortical development.

Reviewer #1 (Public review):

Summary:

This computational modeling study builds on multiple previous lines of experimental and theoretical research to investigate how a single neuron can solve a nonlinear pattern classification task. The authors construct a detailed biophysical and morphological model of a single striatal medium spiny neuron, and endow excitatory and inhibitory synapses with dynamic synaptic plasticity mechanisms that are sensitive to (1) the presence or absence of a dopamine reward signal, and (2) spatiotemporal coincidence of synaptic activity in single dendritic branches. The latter coincidence is detected by voltage-dependent NMDA-type glutamate receptors, which can generate a type of dendritic spike referred to as a "plateau potential." In the absence of inhibitory plasticity, the proposed mechanisms result in good performance on a nonlinear classification task when specific input features are segregated and clustered onto individual branches, but reduced performance when input features are randomly distributed across branches. Interestingly, adding inhibitory plasticity improves classification performance even when input features are randomly distributed.

Strengths:

The integrative aspect of this study is its major strength. It is challenging to relate low-level details such as electrical spine compartmentalization, extrasynaptic neurotransmitter concentrations, dendritic nonlinearities, spatial clustering of correlated inputs, and plasticity of excitatory and inhibitory synapses to high-level computations such as nonlinear feature classification. Due to high simulation costs, it is rare to see highly biophysical and morphological models used for learning studies that require repeated stimulus presentations over the course of a training procedure. The study aspires to prove the principle that experimentally-supported biological mechanisms can explain complex learning.

Weaknesses:

The high level of complexity of each component of the model makes it difficult to gain an intuition for which aspects of the model are essential for its performance, or responsible for its poor performance under certain conditions. Stripping down some of the biophysical detail and comparing it to a simpler model may help better understand each component in isolation.

Reviewer #1 (Public review):

Summary:

In this study, Jeong and Choi examine neural correlates of behavior during a naturalistic foraging task in which rats must dynamically balance resource acquisition (foraging) with the risk of threat. Rats first learn to forage for sucrose reward from a spout, and when a threat is introduced (an attack-like movement from a "LobsterBot"), they adjust their behavior to continue foraging while balancing exposure to the threat, adopting anticipatory withdraw behaviors to avoid encounter with the LobsterBot. Using electrode recordings targeting the medial prefrontal cortex (PFC), they identify heterogenous encoding of task variables across prelimbic and infralimbic cortex neurons, including correlates of distance to the reward/threat zone and correlates of both anticipatory and reactionary avoidance behavior. Based on analysis of population responses, they show that prefrontal cortex switches between different regimes of population activity to process spatial information or behavioral responses to threat in a context-dependent manner. Characterization of the heterogenous coding scheme by which frontal cortex represents information in different goal states is an important contribution to our understanding of brain mechanisms underlying flexible behavior in ecological settings.

Strengths:

As many behavioral neuroscience studies employ highly controlled task designs, relatively less is generally known about how the brain organizes navigation and behavioral selection in naturalistic settings, where environment states and goals are more fluid. Here, the authors take advantage of a natural challenge faced by many animals - how to forage for resources in an unpredictable environment - to investigate neural correlates of behavior when goal states are dynamic. Related to his, they also investigate prefrontal cortex (PFC) activity is structured to support different functional "modes" (here, between a navigational mode and a threat-sensitive foraging mode) for flexible behavior. Overall, an important strength and real value of this study is the design of the behavioral experiment, which is trial-structured, permitting strong statistical methods for neural data analysis, yet still rich enough to encourage natural behavior structured by the animal's volitional goals. The experiment is also phased to measure behavioral changes as animals first encounter a threat, and then learn to adapt their foraging strategy to its presence. Characterization of this adaptation process is itself quite interesting and sets a foundation for further study of threat learning and risk management in the foraging context. Finally, the characterization of single-neuron and population dynamics in PFC in this naturalistic setting with fluid goal states is an important contribution to the field. Previous studies have identified neural correlates of spatial and behavioral variables in frontal cortex, but how these representations are structured, or how they are dynamically adjusted when animals shift their goals, has been less clear. The authors synthesize their main conclusions into a conceptual model for how PFC activity can support mode switching, which can be tested in future studies with other task designed and functional manipulations.

Weaknesses:

While the task design in this study is intentionally stimulus-rich and places minimal constraint on the animal to preserve naturalistic behavior, this also introduces confounds that limit interpretability of the neural analysis. For example, some variables which are the target of neural correlation analysis, such as spatial/proximity coding and coding of threat and threat-related behaviors, are naturally entwined. To their credit, the authors have included careful analyses and control conditions to disambiguate these variables and significantly improve clarity.

The authors also claim that the heterogenous coding of spatial and behavioral variables in PFC is structured in a particular way that depends on the animal's goals or context. As the authors themselves discuss, the different "zones" contain distinct behaviors and stimuli, and since some neurons are modulated by these events (e.g., licking sucrose water, withdrawing from the LobsterBot, etc.), differences in population activity may to some extent reflect behavior/event coding. The authors have included a control analysis, removing timepoints corresponding to salient events, to substantiate the claim that PFC neurons switch between different coding "modes." While this significantly strengthens evidence for their conclusion, this analysis still depends on relatively coarse labeling of only very salient events. Future experiment designs, which intentionally separate task contexts (e.g. navigation vs. foraging), could serve to further clarify the structure of coding across contexts and/or goal states.

Finally, while the study includes many careful, in-depth neural and behavioral analyses to support the notion that modal coding of task variables in PFC may play a role in organizing flexible, dynamic behavior, the study still lacks functional manipulations to establish any form of causality. This limitation is acknowledged in the text, and the report is careful not to over interpret suggestions of causal contribution, instead setting a foundation for future investigations.

Joint Public Review:

Editors’ note: This is the third version of this article, and it addresses the points made during the peer review of the second version by performing additional analyses and clarifying some of the limitations of the study.

Comments made during the peer review of the first version, along with author's responses to these comments, are available with previous versions of the article.

The following summary of the article is taken from comments made by Reviewer #1 about version 2 of the article:

In this manuscript, the authors use a large dataset of neuroscience publications to elucidate the nature of self-citation within the neuroscience literature. The authors initially present descriptive measures of self-citation across time and author characteristics; they then produce an inclusive model to tease apart the potential role of various article and author features in shaping self-citation behavior. This is a valuable area of study, and the authors approach it with a rich dataset and solid methodology.

Reviewer #1 (Public review):

Summary:

This study seeks to investigate the role of the transcription factor Bcl11b/Ctip2 in regulating subcerebral projection neuron (SCPN) axon development through both cell-autonomous and non-cell-autonomous mechanisms. The authors demonstrate that Bcl11b is required within SCPNs for axonal outgrowth and proper entry into the internal capsule, while its expression in medium spiny neurons (MSNs) influences SCPN axon fasciculation and pathfinding in a non-cell-autonomous manner. Notably, through transcriptomic analysis, immunocytochemistry, and in vivo growth cone purification, the study identifies Cdh13 as a downstream mediator of Bcl11b function, localizing along axons and at growth cone surfaces to regulate SCPN axonal outgrowth.

Strengths:

To me the most interesting aspect of this study is how common transcriptional programs across neuronal cell types cooperate to facilitate axon pathfinding, this is a very interesting concept.

Overall, it could be of interest to the brain development field.

Weaknesses:

My main concern is that, as presented in the figures, many phenotypes are too subtle to be convincing and would require quantitative analyses to corroborate the claims of the study.

I also think that the growth cones transcription data needs additional validation to be incorporated into the manuscript. In fact, I am not even sure that it really brings anything to the story.

I also think that the CRISPR in utero electroporation experiments lack appropriate controls.

Reviewer #1 (Public review):

Summary:

Nysten et al. use in vivo 2-photon calcium imaging in behaving mice learning a visual associative memory task to understand how neural dynamics in the postrhinal cortex and medial entorhinal cortex evolve over task learning and through reversal learning. Using a combination of analyses to measure trial-averaged neural responses, regression models, and population decoding methods, the authors argue that both POR and MEC dynamics evolve over learning, with relatively more neurons in MEC becoming responsive. The impact of this study comes from comparing neural dynamics across multiple medial temporal lobe circuits to show how different aspects of task structure are differentially encoded. Below, I have listed several major concerns that need to be addressed to ensure the findings are robust.

Strengths:

(1) The study employs a well-controlled behavioral paradigm alongside powerful cellular-resolution two-photon imaging, enabling high-throughput recordings of hundreds of neurons simultaneously in deep brain structures.

(2) The simplicity of the task allows for a detailed examination of learning dynamics across multiple stages, including early and late learning in the main task, as well as during reversal learning.

(3) The use of sophisticated analysis methods to compare and contrast learning dynamics in large neuronal populations strengthens the study, though additional steps are needed to ensure their robustness (detailed below).

(4) Two-photon imaging enables the investigation of functional topography, further supporting previous findings of functional clustering in MEC across different task and behavioral domains.

Weaknesses:

(1) GLM Robustness & Behavioral Attribution: The current GLM design may misattribute neural activity by lacking appropriate time lags for velocity and not accounting for distinct neural states (e.g., rest vs. run). Given MEC's known speed-invariant coding, the observed decrease in speed-modulated neurons may be an artifact rather than a true learning effect. Additionally, gradual behavioral stabilization over training could influence neural dynamics in ways not fully accounted for.

(2) Licking vs. Movement Encoding: The increase in lick-modulated neurons raises questions about whether these neurons encode reward anticipation or motor execution. Without a detailed analysis of error trials and the timing of licking vs. movement adjustments, it remains unclear whether MEC activity reflects predictive coding of reward or simply motor feedback.

(3) Clustering Interpretation Issues: The functional clustering approach does not control for correlations between behavioral features, making it difficult to determine whether speed modulation plays a role in cluster assignments. The anatomical analysis in Figure 6 relies heavily on clusters that may be predominantly defined by a single regressor, requiring further clarification.

(4) Data Presentation & Statistical Support: Some key claims, particularly the increase in task-modulated neurons with learning (Figure 3), lack statistical quantification.

Reviewer #1 (Public review):

Summary:

The manuscript reports that expression of the E. coli operon topAI/yjhQ/yjhP is controlled by the translation status of a small open reading frame, that authors have discovered and named toiL, located in the leader region upstream of the operon. Authors propose the following model for topAI activation: Under normal conditions, toiL is translated but topAI is not expressed because of Rho-dependent transcription termination within the topAI ORF and because its ribosome binding site and start codon are trapped in an mRNA hairpin. Ribosome stalling at various codons of the toiL ORF, prompted in this work by some ribosome-targeting antibiotics, triggers an mRNA conformational switch which allows translation of topAI and, in addition, activation of the operon's transcription because presence of translating ribosomes at the topAI ORF blocks Rho from terminating transcription. The model is appealing and several of the experimental data mainly support it. However, it remains unanswered what is the true trigger of the translation arrest at toiL and what is the physiological role of the induced expression of the topAI/yjhQ/yjhP operon.

Reviewer #1 (Public review):

The manuscript consists of two separate but interlinked investigations: genomic epidemiology and virulence assessment of Salmonella Dublin. ST10 dominates the epidemiological landscape of S. Dublin, while ST74 was uncommonly isolated. Detailed genomic epidemiology of ST10 unfolded the evolutionary history of this common genotype, highlighting clonal expansions linked to each distinct geography. Notably, North American ST10 was associated with more antimicrobial resistance compared to others. The authors also performed long read sequencing on a subset of isolates (ST10 and ST74), and uncovered a novel recombinant virulence plasmid in ST10 (IncX1/IncFII/IncN). Separately, the authors performed cell invasion and cytotoxicity assays on the two S. Dublin genotypes, showing differential responses between the two STs. ST74 replicates better intracellularly in macrophage compared to ST10, but both STs induced comparable cytotoxicity levels. Comparative genomic analyses between the two genotypes showed certain genetic content unique to each genotype, but no further analyses were conducted to investigate which genetic factors likely associated with the observed differences. The study provides a comprehensive and novel understanding on the evolution and adaptation of two S. Dublin genotypes, which can inform public health measures. The methodology included in both approaches were sound and written in sufficient detail, and data analysis were performed with rigour. Source data were fully presented and accessible to readers.

Comments on revised version:

The authors have addressed all the points raised by the reviewer. The manuscript is now much enhanced in clarity and accuracy. The rewritten Discussion is more relevant and brings in comparison with other invasive Salmonella serotypes.

Reviewer #1 (Public review):

Summary:

This work uses a novel, ethologically relevant behavioral task to explore decision-making paradigms in C. elegans foraging behavior. By rigorously quantifying multiple features of animal behavior as they navigate in a patch food environment, the authors provide strong evidence that worms exhibit one of three qualitatively distinct behavioral responses upon encountering a patch: (1) "search", in which the encountered patch is below the detection threshold; (2) "sample", in which animals detect a patch encounter and reduce their motor speed, but do not stay to exploit the resource and are therefore considered to have "rejected" it; and (3) "exploit", in which animals "accept" the patch and exploit the resource for tens of minutes. Interestingly, the probability of these outcomes varies with the density of the patch as well as the prior experience of the animal. Together, these experiments provide an interesting new framework for understanding the ability of the C. elegans nervous system to use sensory information and internal state to implement behavioral state decisions.

Strengths:

-The work uses a novel, neuroethologically-inspired approach to studying foraging behavior<br /> -The studies are carried out with an exceptional level of quantitative rigor and attention to detail<br /> -Powerful quantitative modeling approaches including GLMs are used to study the behavioral states that worms enter upon encountering food, and the parameters that govern the decision about which state to enter<br /> -The work provides strong evidence that C. elegans can make 'accept-reject' decisions upon encountering a food resource<br /> -Accept-reject decisions depend on the quality of the food resource encountered as well as on internally represented features that provide measurements of multiple dimensions of internal state, including feeding status and time

Reviewer #1 (Public review):

Summary:

The use of a multi-omics approach to elucidate the regulatory mechanism underlying parturition and myometrial quiescence adds novelty to the study. The identification of myometrial cis-acting elements and their association with gene expression, particularly the regulation of the PLCL2 gene by PGR opens the door to further investigate the impact of PGR and other regulators.

Strengths:

(1) Multi-Omic Approach: The paper employs a comprehensive multi-omic approach, combining ChIP-Seq, RNA-Seq, and CRISPRa-based Perturb-Seq assays, which allow for a thorough investigation of the regulatory mechanisms underlying myometrial gene expression.<br /> (2) Clinical Relevance: Investigating human myometrial specimens provides direct clinical relevance, as understanding the molecular mechanisms governing parturition and myometrial quiescence can have significant implications for the management of pregnancy-related disorders.<br /> (3) Functional work: For functional screening, They have used CRISPRa-based screening of PLCL2 gene regulation using immortalized human cell-line hTERT-HM and T-hESC to add more dimension to the work which strengthens their finding of PGR-dependent regulation of the PLCL2 gene in the human myometrial cells.

Weaknesses:

(1) Variability in epigenomic mapping: The significant variations in the number and location of H3K27ac-positive intervals across different samples and studies suggest potential challenges in accurately mapping the myometrial epigenome. This variability may introduce uncertainty and complicate the interpretation of results.<br /> (2) Sample specificity: The study focuses on term pregnant nonlabor myometrial specimens, limiting the generalizability of the findings to other stages of pregnancy or labor.<br /> (3) Limited Understanding of Regulatory Mechanisms: While the study identifies potential regulatory programs within super-enhancers, the exact mechanisms by which these enhancers regulate gene expression and cellular functions in the myometrium remain unclear. Further mechanistic studies are needed to elucidate these processes.<br /> (4) Discordant analysis: Why regular enhancers are being understood in terms of motif enrichment of transcription factors and super-enhancers in terms of pathways enriched for active genes? This needs a clear reason.

Reviewer #2 (Public review):

Summary:

This study investigates the molecular function of the N-glycan-dependent endoplasmic reticulum protein quality control system (ERQC) in Cryptococcus neoformans and correlates this pathway with key features of C. neoformans virulence, especially those mediated by extracellular vesicle transport. The findings provide valuable insights into the connection between this pathway and the biogenesis of C. neoformans extracellular vesicles.

Strengths:

The strength of this study lies primarily in the careful selection of appropriate and current methodologies, which provide a solid foundation for the authors' results and conclusions across all presented data. All experiments are supported by well-designed and established controls in the study of C. neoformans, further strengthening the validity of the results and conclusions drawn from them. The study presents novel data on this important pathway in C. neoformans, establishing its connection with C. neoformans virulence. Interestingly, the findings led the authors to understand the relationship between this pathway and the transport of key fungal virulence factors via extracellular vesicles. This was demonstrated in the study, paving the way for a deeper understanding of extracellular vesicle biogenesis-a field still filled with gaps but one that this study contributes to with solid data, helping to clarify aspects of this process.

Reviewer #1 (Public review):

Summary:

This manuscript aims to explain the emergence of grid-like spatial firing patterns. Rather than taking the existence of grid cells as a given and asking what does their properties say about their function, the authors reverse the approach: they begin with a proposed computational function that the brain may need to perform-coding of 2D spatial trajectories using sequences of neural activity-and ask what type of neural code would optimally support this function. They show that, under a set of formal assumptions, such a code leads to the emergence of spatial periodicity and a hexagonal grid pattern. The aim is to provide a normative explanation for the existence of grid cells grounded in functional constraints.

Strengths:

The manuscript presents a mathematically well-defined framework that is internally consistent. The derivation is structured and leads to a hexagonal lattice as the most efficient solution for representing directional trajectories. The authors provide comparisons to experimental observations and extend the model to explain several findings in the grid cell literature. In the revised version, the discussion of foundational assumptions is expanded, and the manuscript better situates itself in relation to prior theoretical work. Overall, this work adds a very interesting view to the broader conversation about the role and origin of grid cells by offering a theoretical alternative grounded in trajectory coding.

Weaknesses:

The model depends on assumptions that, while plausible, should be treated as chosen assumptions. These include the premise that (1) grid function is trajectory coding, (2) that trajectory coding is implemented through sequences of neural activity, and (3) that such sequences are largely independent of spatial position. In the revised manuscript, the authors provide more literature to support these assumptions.

Joint Public Review:

Summary:

In this study, Daniel et al. used three cognitive tasks to investigate behavioural signatures of cerebellar degeneration. In the first two tasks, the authors found that if an equation was incorrect, reaction times slowed significantly more for cerebellar patients than for healthy controls. In comparison, the slowing in the reaction times when the task required more operations was comparable to normal controls. In the third task, the authors show increased errors in cerebellar patients when they had to judge whether a letter string corresponded to an artificial grammar.

Strengths:

Overall, the work is methodologically sound and the manuscript well written. The data do show some evidence for specific cognitive deficits in cerebellar degeneration patients.

Weaknesses:

The current version has some weaknesses in the visual presentation of results. Overall, the study lacks a more precise discussion on how the patterns of deficits relate to the hypothesized cerebellar function.

The reviewers and the editor agreed that the data are interesting and point to a specific cognitive deficit in cerebellar patients. However, in the discussion, we were somewhat confused about the interpretation of the result:

If the cerebellum (as proposed in the introduction) is involved in forming expectations in a cognitive task, should they not show problems both in the expected (1+3 =4) and unexpected (1+3=2) conditions? Without having formed the correct expectation, how can you correctly say "yes" in the expected condition? No increase in error rate is observed - just slowing in the unexpected condition. But this increase in error rate was not observed. If the patients make up for the lack of prediction by using some other strategy, why are they only slowing in the unexpected case?

If the cerebellum is NOT involved in making the prediction, but only involved in detecting the mismatch between predicted and real outcome, why would the patients not show specifically more errors in the unexpected condition?

Reviewer #1 (Public review):

Summary:

This study builds upon a major theoretical account of value-based choice, the 'attentional drift diffusion model' (aDDM), and examines whether and how this might be implemented in the human brain using functional magnetic resonance imaging (fMRI). The aDDM states that the process of internal evidence accumulation across time should be weighted by the decision maker's gaze, with more weight being assigned to the currently fixated item. The present study aims to test whether there are (a) regions of the brain where signals related to the currently presented value are affected by the participant's gaze; (b) regions of the brain where previously accumulated information is weighted by gaze.

To examine this, the authors developed a novel paradigm that allowed them to dissociate currently and previously presented evidence, at a timescale amenable to measuring neural responses with fMRI. They asked participants to choose between bundles or 'lotteries' of food times, which they revealed sequentially and slowly to the participant across time. This allowed modelling of the haemodynamic response to each new observation in the lottery, separately for previously accumulated and currently presented evidence.

Using this approach, they find that regions of the brain supporting valuation (vmPFC and ventral striatum) have responses reflecting gaze-weighted valuation of the currently presented item, whereas regions previously associated with evidence accumulation (preSMA and IPS) have responses reflecting gaze-weighted modulation of previously accumulated evidence.

Strengths:

A major strength of the current paper is the design of the task, nicely allowing the researchers to examine evidence accumulation across time despite using a technique with poor temporal resolution. The dissociation between currently presented and previously accumulated evidence in different brain regions in GLM1 (before gaze-weighting), as presented in Figure 5, is already compelling. The result that regions such as preSMA respond positively to |AV| (absolute difference in accumulated value) is particularly interesting, as it would seem that the 'decision conflict' account of this region's activity might predict the exact opposite result. Additionally, the behaviour has been well modelled at the end of the paper when examining temporal weighting functions across the multiple samples.

Weaknesses:

The results relating to gaze-weighting in the fMRI signal could do with some further explication to become more complete. A major concern with GLM2, which looks at the same effects as GLM1 but now with gaze-weighting, is that these gaze-weighted regressors may be (at least partially) correlated with their non-gaze-weighted counterparts (e.g., SVgaze will correlate with SV). But the non-gaze-weighted regressors have been excluded from this model. In other words, the authors are not testing for effects of gaze-weighting of value signals *over and above* the base effects of value in this model. In my mind, this means that the GLM2 results could simply be a replication of the findings from GLM1 at present. GLM3 is potentially a stronger test, as it includes the value signals and the interaction with gaze in the same model. But here, while the link to the currently attended item is quite clear (and a replication of Lim et al, 2011), the link to previously accumulated evidence is a bit contorted, depending upon the interpretation of a behavioural regression to interpret the fMRI evidence. The results from GLM3 are also, by the authors' own admission, marginal in places.

Reviewer #1 (Public review):

Summary:

This study builds on previous work demonstrating that several beta connexins (Cx26, Cx30, and Cx32) have a carbamylation motif which renders them sensitive to CO2. In response to CO2, hemichannels composed of these connexins open, enabling diffusion of small molecules (such as ATP) between the cytosol and extracellular environment. Here, the authors have identified that an alpha connexin, Cx43, also contains a carbamylation motif, and they demonstrate that CO2 opens Cx43 hemichannels. Most of the study involves using transfected cells expressing wild-type and mutant Cx43 to define amino acids required for CO2 sensitivity. Hippocampal tissue slices in culture were used to show that CO2-induced synaptic transmission was affected by Cx43 hemichannels, providing a physiological context. The authors point out that the Cx43 gene significantly diverges from the beta connexins that are CO2 sensitive, suggesting that the conserved carbamylation motif was present before the alpha and beta connexin genes diverged.

Strengths:

(1) The molecular analysis defining the amino acids that contribute to the CO2 sensitivity of Cx43 is a major strength of the study. The rigor of analysis was strengthened by using three independent assays for hemichannel opening: dye uptake, patch clamp channel measurements, and ATP secretion. The resulting analysis identified key lysines in Cx43 that were required for CO2-mediated hemichannel opening. A double K to E Cx43 mutant produced a construct that produced hemichannels that were constitutively open, which further strengthened the analysis.

(2) Using hippocampal tissue sections to demonstrate that CO2 can influence field excitatory postsynaptic potentials (fEPSPs) provides a native context for CO2 regulation of Cx43 hemichannels. Cx43 mutations associated with Oculodentodigital Dysplasia (ODDD) inhibited CO2-induced hemichannel opening, although the mechanism by which this occurs was not elucidated.

Weaknesses:

(1) Cx43 channels are sensitive to cytosolic pH, which will be affected by CO2. Cytosolic pH was not measured, and how this affects CO2-induced Cx43 hemichannel activity was not addressed.

(2) Cultured cells are typically grown in incubators containing 5% CO2, which is ~40 mmHg. It is unclear how cells would be viable if Cx43 hemichannels are open at this PCO2.

(3) Experiments using Gap26 to inhibit Cx43 hemichannels in fEPSP measurements used a scrambled peptide as a control. Analysis should also include Gap peptides specifically targeting Cx26, Cx30, and Cx32 as additional controls.

(4) The mechanism by which ODDD mutations impair CO2-mediated hemichannel opening was not addressed. Also, the potential roles for inhibiting Cx43 hemichannels in the pathology of ODDD are unclear.

(5) CO2 has no effect on Cx43-mediated gap junctional communication as opposed to Cx26 gap junctions, which are inhibited by CO2. The molecular basis for this difference was not determined.

(6) Whether there are other non-beta connexins that have a putative carbamylation motif was not addressed. Additional discussion/analysis of how the evolutionary trajectory for Cx43 maintaining a carbamylation motif is unique for non-beta connexins would strengthen the study.

Reviewer #1 (Public review):

Summary:

In this manuscript, Lau et al reported that KDM5 inhibition in luminal breast cancer cells results in R-loop-mediated DNA damage, reduced cell fitness and an increase in ISG and AP signatures as well as cell surface Major Histocompatibility Complex (MHC) class I, mediated by RNA:DNA hybrid activation of the CGAS/STING pathway.

Strengths:

More importantly, they have shown that KDM5 inhibition does not result in DNA damage or activation of the CGAS/STING pathway in normal breast epithelial cells. This suggests that KDM5 inhibitors may enable a wide therapeutic window in this setting, as compared to STING agonists or Type I Interferons. Their findings provide new insights into the interplay between epigenetic regulation of genomic repeats, R-loop formation, innate immunity, and cell fitness in the context of cancer evolution and therapeutic vulnerability.

Weaknesses:

More thorough analyses would be appreciated.

Reviewer #1 (Public review):

Summary:

In this study, the authors set out to define how arginine availability regulates lipid metabolism and to explore the implications of this relationship in pancreatic ductal adenocarcinoma (PDAC), a tumor type known to exist in an arginine-poor microenvironment. Using a combination of rigorous genetic and metabolomic approaches, they uncover a previously underappreciated role for arginine in maintaining lipid homeostasis. Importantly, they demonstrate that arginine deprivation sensitizes PDAC cells to ferroptosis through lipidome perturbations, which can be exploited therapeutically via co-treatment with aESA and ferroptosis inducers (FINs). These findings have meaningful implications for the field. They not only shed light on the metabolic vulnerabilities created by nutrient restriction in PDAC, but also suggest a practical avenue for combination therapies that exploit ferroptosis sensitivity. This is particularly relevant in the context of pancreatic cancer, which is notoriously resistant to conventional treatments. The methods employed are broadly applicable to other nutrient-stress contexts and may inspire similar investigations in other solid tumor types.

Strengths:

One of the major strengths of the study is the use of complementary and well-controlled approaches-including metabolomic profiling, genetic perturbations, and in vivo models-to support the central hypothesis. The experiments are thoughtfully designed and clearly presented, and the conclusions are, for the most part, well supported by the data. The findings provide mechanistic insight into nutrient-lipid crosstalk and identify a potential therapeutic strategy for targeting arginine-deprived tumors.

Weaknesses:

A key weakness of the study lies in the mechanistic connection between arginine levels and SREBP1 activation. While the authors show that arginine restriction leads to reduced SREBP1 expression, the magnitude of this effect appears modest relative to the substantial changes observed in the lipidome. The study would benefit from a deeper analysis of SREBP1 regulation-particularly whether nuclear translocation or activation is affected. This could be addressed by examining the nuclear pool of SREBP1, using either subcellular fractionation or improved immunofluorescence imaging in both cell lines and tissue samples.

Another area where additional context would strengthen the manuscript is in the transcriptomic profiling of PDAC cells cultured in a tumor interstitial fluid mimic (TIFM). While the study emphasizes lipid-related pathways, highlighting the most significantly upregulated and downregulated pathways in Figure 1B would give readers a broader perspective on how arginine restriction reprograms the PDAC transcriptome. For instance, because polyamines are downstream of arginine and are known to influence lipid metabolism, it would be worth discussing whether these metabolites contribute to the phenotypes observed. Similarly, an evaluation of whether Dgat1/2 expression is altered could help delineate the full scope of lipid metabolic rewiring.

Finally, it is worth noting that the KPC mouse model used in this study is based on conditional deletion of p53, which leads to faster-growing tumors and a distinct tumor microenvironment compared to models harboring the p53^R172H point mutation. Including a brief discussion of this distinction would help readers contextualize the translational relevance of the findings.

Reviewer #1 (Public review):

Summary:

The manuscript uses state-of-the-art analysis technology to document the spatio-temporal dynamics of brain activity during the processing of threats. The authors offer convincing evidence that complex spatio-temporal aspects of brain dynamics are essential to describe brain operations during threat processing.

Strengths:

Rigorous complex analyses well suited to the data.

Weaknesses:

Lack of a simple take-home message about discovery of a new brain operation.

Comments on revisions:

The authors have improved the presentation of the work. The overstatements about existing models of brain functions ignoring exogenous components remains largely unaddressed. The clarifications and improvements provided in revision confirm my assessment of the paper.

Reviewer #1 (Public review):

Summary:

A cortico-centric view is dominant in the study for the neural mechanisms of consciousness. This investigation represents the growing interest to understand how subcortical regions are involved in conscious perception. To achieve this, the authors engaged an ambitious and rare procedure in humans of directly recording from neurons in the subthalamic nucleus and thalamus. While participants were in surgery for the placement of deep brain stimulation devices for the treatment of essential tremor and Parkinson's disease, they were awakened and completed a perceptual-threshold tactile detection task. The authors identified individual neurons and analyzed single-unit activity corresponding with the task phases and tactile detection/perception. Among the neurons that were perception-responsive, the authors report changes in firing rate beginning ~150 milliseconds from the onset of the tactile stimulation. Curiously, the majority of the perception-responsive neurons had a higher firing rate for missed/not perceived trials. In summary, this investigation is a valuable addition to the growing literature on the role of subcortical regions in conscious perception.

Strengths:

The authors achieve the challenging task of recording human single-unit activity while participants performed a tactile perception task. The methods and statistics are clearly explained and rigorous, particularly for managing false positives and non-normal distributions. The results offer new detail at the level of individual neurons in the emerging recognition for the role of subcortical regions in conscious perception. Also, this study highlights the timing of neural activity linked to conscious perception (approximately 150 millisecond).

Weaknesses:

Due to constraints of testing with this patient population, a standard report-based detection task was administered. This type of task cannot fully exclude motor preparatory and post-perceptual processing as a factor that contributes to distinguishing between perceived versus not perceived stimuli. The authors show sensitivity to this issue by identifying task-selective neurons and their discussion of the results that refers to the confound of post-perceptual processing. Despite this limitation, the results are valuable for contributing to a growing body of literature on the subcortical neural mechanisms of consciousness.

Reviewer #1 (Public review):

This study examines the role of host blood meal source, temperature, and photoperiod on the reproductive traits of Cx. quinquefasciatus, an important vector of numerous pathogens of medical importance. The host use pattern of Cx. quinquefasciatus is interesting in that it feeds on birds during spring and shifts to feeding on mammals towards fall. Various hypotheses have been proposed to explain the seasonal shift in host use in this species but have provided limited evidence. This study examines whether the shifting of host classes from birds to mammals towards autumn offers any reproductive advantages to Cx. quinquefasciatus in terms of enhanced fecundity, fertility, and hatchability of the offspring. The authors found no evidence of this, suggesting that alternate mechanisms may drive the seasonal shift in host use in Cx. quinquefasciatus.

Reviewer #1 (Public review):

In this study, Tiang et al. explore the role of ubiquitination of non-structural protein 16 (nsp16) in the SARS-CoV-2 life cycle. nsp16, in conjunction with nsp10, performs the final step of viral mRNA capping through its 2'-O-methylase activity. This modification allows the virus to evade host immune responses and protects its mRNA from degradation. The authors demonstrate that nsp16 undergoes ubiquitination and subsequent degradation by the host E3 ubiquitin ligases UBR5 and MARCHF7 via the ubiquitin-proteasome system (UPS). Specifically, UBR5 and MARCHF7 mediate nsp16 degradation through K48- and K27-linked ubiquitination, respectively. Notably, degradation of nsp16 by either UBR5 or MARCHF7 operates independently, with both mechanisms effectively inhibiting SARS-CoV-2 replication in vitro and in vivo. Furthermore, UBR5 and MARCHF7 exhibit broad-spectrum antiviral activity by targeting nsp16 variants from various SARS-CoV-2 strains. This research advances our understanding of how nsp16 ubiquitination impacts viral replication and highlights potential targets for developing broadly effective antiviral therapies.

Strengths:

The proposed study is of significant interest to the virology community because it aims to elucidate the biological role of ubiquitination in coronavirus proteins and its impact on the viral life cycle. Understanding these mechanisms will address broadly applicable questions about coronavirus biology and enhance our overall knowledge of ubiquitination's diverse functions in cell biology. Employing in vivo studies is a strength.

Weaknesses:

Minor comments:<br /> Figure 5A- The authors should ensure that the figure is properly labeled to clearly distinguish between the IP (Immunoprecipitation) panel and the input panel.

Reviewer #1 (Public review):

Summary:

In this manuscript, the authors investigated the effect of chronic activation of dopamine neurons using chemogenetics. Using Gq-DREADDs, the authors chronically activated midbrain dopamine neurons and observed that these neurons, particularly their axons, exhibit increased vulnerability and degeneration, resembling the pathological symptoms of Parkinson's disease. Baseline calcium levels in midbrain dopamine neurons were also significantly elevated following the chronic activation. Lastly, to identify cellular and circuit-level changes in response to dopaminergic neuronal degeneration caused by chronic activation, the authors employed spatial genomics (Visium) and revealed comprehensive changes in gene expression in the mouse model subjected to chronic activation. In conclusion, this study presents novel data on the consequences of chronic hyperactivation of midbrain dopamine neurons.

Strengths:

This study provides direct evidence that the chronic activation of dopamine neurons is toxic and gives rise to neurodegeneration. In addition, the authors achieved the chronic activation of dopamine neurons using water application of clozapine-N-oxide (CNO), a method not commonly employed by researchers. This approach may offer new insights into pathophysiological alterations of dopamine neurons in Parkinson's disease. The authors also utilized state-of-the-art spatial gene expression analysis, which can provide valuable information for other researchers studying dopamine neurons. They also presented a substantial number of intriguing ideas in their discussion, which are worth further investigation.

Weaknesses:

Although not fully supported by data, the authors provided a well-explained rationale and proposed possible mechanisms for dopamine neuron degeneration due to chronic activation in their results and discussion.

Comments on revised version:

The authors have adequately addressed most of my comments, and I have no further concerns.

Reviewer #1 (Public Review):

Summary:

In this manuscript, the authors investigated the effect of chronic activation of dopamine neurons using chemogenetics. Using Gq-DREADDs, the authors chronically activated midbrain dopamine neurons and observed that these neurons, particularly their axons, exhibit increased vulnerability and degeneration, resembling the pathological symptoms of Parkinson's disease. Baseline calcium levels in midbrain dopamine neurons were also significantly elevated following the chronic activation. Lastly, to identify cellular and circuit-level changes in response to dopaminergic neuronal degeneration caused by chronic activation, the authors employed spatial genomics (Visium) and revealed comprehensive changes in gene expression in the mouse model subjected to chronic activation. In conclusion, this study presents novel data on the consequences of chronic hyperactivation of midbrain dopamine neurons.

Strengths:

This study provides direct evidence that the chronic activation of dopamine neurons is toxic and gives rise to neurodegeneration. In addition, the authors achieved the chronic activation of dopamine neurons using water application of clozapine-N-oxide (CNO), a method not commonly employed by researchers. This approach may offer new insights into pathophysiological alterations of dopamine neurons in Parkinson's disease. The authors also utilized state-of-the-art spatial gene expression analysis, which can provide valuable information for other researchers studying dopamine neurons. Although the authors did not elucidate the mechanisms underlying dopaminergic neuronal and axonal death, they presented a substantial number of intriguing ideas in their discussion, which are worth further investigation.

Weaknesses:

Many claims raised in this paper are only partially supported by the experimental results. So, additional data are necessary to strengthen the claims. The effects of chronic activation of dopamine neurons are intriguing; however, this paper does not go beyond reporting phenomena. It lacks a comprehensive explanation for the degeneration of dopamine neurons and their axons. While the authors proposed possible mechanisms for the degeneration in their discussion, such as differentially expressed genes, these remain experimentally unexplored.

Reviewer #2 (Public review):

The aim of the investigation was to find out more about the mechanism(s) by which the structural protein vimentin can facilitate the epithelial-mesenchymal transition in breast cancer cells.

The authors focused on a key amino acid of vimentin, C238, its role in the interaction between vimentin and actin microfilaments, and the downstream molecular and cellular consequences. They model the binding between vimentin and actin in silico to demonstrate the potential involvement of C238, due to its location in a rod domain known to bind beta-actin. The phenotype of a non-metastatic breast cancer cell line MCF7, which doesn't express vimentin, could be changed to a metastatic phenotype when mutant C238S vimentin, but not wild-type vimentin, was expressed in the cells. Expression of vimentin was confirmed at the level of mRNA, protein and microscopically. Patterns of expression of vimentin and actin reflected the distinct morphology of the two cell lines. Phenotypic changes were assessed through assay of cell adhesion, proliferation, migration and morphology and were consistent with greater metastatic potential in the C238S MCF7 cells. Changes in the transcriptome of MCF7 cells expressing wild-type and C238S vimentins were compared and expression of Xist long ncRNA was found to be the transcript most markedly increased in the metastatic cells expressing C238S vimentin. Moreover changes in expression of many other genes in the C238S cells are consistent with an epithelial mesenchymal transition. Tumourigenic potential of MCF7 cells carrying C238S but not wild-type, vimentin was confirmed by inoculation of cells into nude mice. This assay is a measure of stem-cell quality of the cells and not a measure of metastasis. It does demonstrate phenotypic changes that could be linked to metastasis.

shRNA was used to down-regulate vimentin or Xist in the MCF7 C238S cells. The description of the data is limited in parts and data sets require careful scrutiny to understand the full picture. Down-regulation of vimentin reversed the morphological changes to some degree, but down-regulation of Xist didn't. Conversely down-regulation of Xist inhibited cell growth, a sign of reversing metastatic potential, but down-regulation of vimentin had no effect on growth. Down-regulation of either did inhibit cell migration, another sign of metastatic reversal. Most of these findings are consistent with previous work based on ectopic expression of wild-type vimentin in MCF7 cells, but the mechanism of inhibition of cell migration by downregulation of Xist remains speculative. More complete knockdown of vimentin or Xist by CRISPR technology may be helpful.

Overall the study describes an intriguing model of metastasis that is worthy of further investigation, especially at the molecular level to unravel the connection between vimentin and metastasis. The identification of a potential role for Xist in metastasis, beyond its normal role in female cells to inactivate one of the X chromosomes, corroborates the work of others demonstrating increased levels in a variety of tumours in women and even in some tumours in men. It would be of great interest to see where in metastatic cells Xist is expressed and what it binds to.

Comments on revisions:

The revised manuscript incorporates changes in presentation of the data modelling interaction between the region of vimentin including C238 and F-actin. There is also inclusion of an extra citation supporting the role for Xist in cancer stem cell differentiation.

Reviewer #1 (Public review):

Summary:

Hua et al show how targeting amino acid metabolism can overcome Trastuzumab resistance in HER2+ breast cancer.

Strengths:

The authors used metabolomics, transcriptomics and epigenomics approaches in vitro and in preclinical models to demonstrate how trastuzumab resistant cells utilize cysteine metabolism.

Weaknesses:

However, there are some key aspects that needs to be addressed.

Major:

(1) Patient Samples for Transcriptomic Analysis: It is unclear from the text whether tumor tissues or blood samples were used for the transcriptomic analysis. This distinction is crucial, as these two sample types would yield vastly different inferences. The authors should clarify the source of these samples.

(2) The study only tested one trastuzumab-resistant and one trastuzumab-sensitive cell lines. It is unclear whether these findings are applicable to other HER2-positive tumor cell lines, such as HCC1954. The authors should validate their results in additional cell lines to strengthen their conclusions.

(3) Relevance to Metastatic Disease: Trastuzumab resistance often arises in patients during disease recurrence, which is frequently associated with metastasis. However, the mouse experiments described in this paper were conducted only in the primary tumors. This article will have more impact if the authors could demonstrate that the combination of Erastin or cysteine starvation with trastuzumab can also improve outcomes in metastasis models.

Minor:

(1) The figures lack information about the specific statistical tests used. Including this information is essential to show the robustness of the results.

(2) Figure 3K Interpretation: The significance asterisks in Figure 3K do not specify the comparison being made. Are they relative to the DMSO control? This should be clarified.

Comments on revisions:

While the authors acknowledge the limitation of using only a single trastuzumab resistant/sensitive pair, simply stating that additional cell lines will be tested in future work is simply inadequate. The biological heterogeneity of HER2-positive breast cancer demands validation in at least one independent resistant model (e.g., HCC1954 or BT 474R) alongside its parental counterpart. Without demonstrating that SLC7A11 upregulation, cysteine dependency, and sensitivity to Erastin plus trastuzumab extend beyond the original cell line pair, the generalizability and translational relevance of the findings remain uncertain. The authors need to perform and report key functional results (cell viability, apoptosis, and SLC7A11 expression) in an additional resistant and sensitive HER2-positive cell line before this manuscript can be considered robust.

Reviewer #1 (Public review):

Summary:

This study provides new insight into the non-canonical voltage-gating mechanism of BK channels through prolonged (10 μs) MD simulations of the Slo1 transmembrane domain conformation and K+ conduction in response to high imposed voltages (300, 750 mV). The results support previous conclusions based on functional and structural data and MD simulations that the voltage-sensor domain (VSD) of Slo1 undergoes limited conformational changes compared to Kv channels, and predicts gating charge movement comparable in magnitude to experimental results. The gating charge calculations further indicate that R213 and R210 in S4 are the main contributors owing to their large side chain movements and the presence of a locally focused electric field, consistent with recent experimental and MD simulation results by Carrasquel-Ursulaez et al.,2022. Most interestingly, changes in pore conformation and K+ conduction driven by VSD activation are resolved, providing information regarding changes in VSD/pore interaction through S4/S5/S6 segments proposed to underly electromechanical coupling.

Strengths:

Include that the prolonged timescale and high voltage of the simulation allow apparent equilibration in the voltage-sensor domain (VSD) conformational changes and at least partial opening of the pore. The study extends the results of previous MD simulations of VSD activation by providing quantitative estimates of gating charge movement, showing how the electric field distribution across the VSD is altered in resting and activated states, and testing the hypothesis that R213 and R210 are the primary gating charges by steered MD simulations. The ability to estimate gating charge contributions of individual residues in the WT channel is useful as a comparison to experimental studies based on mutagenesis which have yielded conflicting results that could reflect perturbations in structure. Use of dynamic community analysis to identify coupling pathways and information flow for VSD-pore (electromechanical) coupling, as well as analysis of state-dependent S4/S5/S6 interactions that could mediate coupling, provides useful predictions extending beyond what has been experimentally tested.

Weaknesses:

Include that a truncated channel (lacking the C-terminal gating ring) was used for simulations, which is known to have reduced single channel conductance and reduced electromechanical coupling compared to the full-length channel. In addition, as VSD activation in BK channels is much faster than opening, the timescale of simulations was likely insufficient to achieve a fully open state, as supported by differences in the degree of pore expansion in replicate simulations, which are also smaller than observed in Ca-bound open structures of the full-length channel. Taken together, these limitations suggest that the analysis regarding coupling pathways and interactions is incomplete. In addition, while the simulations convincingly demonstrate voltage-dependent channel opening as evidenced by pore expansion, and conduction of K+ and water through the pore, single channel conductance is underestimated by at least an order of magnitude, as in previous studies of other K+ channels. These quantitative discrepancies suggest that MD simulations may not yet be sufficiently advanced to provide insight into mechanisms underlying the extraordinarily large conductance of BK channels.

Reviewer #1 (Public review):

In this work, Ligneul and coauthors implemented diffusion-weighted MRS in young rats to follow longitudinally and in vivo the microstructural changes occurring during brain development. Diffusion-weighted MRS is here instrumental in assessing microstructure in a cell-specific manner, as opposed to the claimed gold-standard (manganese-enhanced MRI) that can only probe changes in brain volume. Differential microstructure and complexification of the cerebellum and the thalamus during rat brain development were observed non-invasively. In particular, lower metabolite ADC with increasing age were measured in both brain regions, reflecting increasing cellular restriction with brain maturation. Higher sphere (representing cell bodies) fraction for neuronal metabolites (total NAA, glutamate) and total creatine and taurine in the cerebellum compared to the thalamus were estimated, reflecting the unique structure of the cerebellar granular layer with a high density of cell bodies. Decreasing sphere fraction with age was observed in the cerebellum, reflecting the development of the dendritic tree of Purkinje cells and Bergmann glia. From morphometric analyses, the authors could probe non-monotonic branching evolution in the cerebellum, matching 3D representations of Purkinje cells expansion and complexification with age. Finally, the authors highlighted taurine as a potential new marker of cerebellar development.

From a technical standpoint, this work clearly demonstrates the potential of diffusion-weighted MRS at probing microstructure changes of the developing brain non-invasively, paving the way for its application in pathological cases. Ligneul and coauthors also show that diffusion-weighted MRS acquisitions in neonates are feasible, despite the known technical challenges of such measurements, even in adult rats. They also provide all necessary resources to reproduce and build upon their work, which is highly valuable for the community.

From a biological standpoint, claims are well supported by the microstructure parameters derived from advanced biophysical modelling of the diffusion MRS data.

Specific strengths:

(1) The interpretation of dMRS data in terms of cell-specific microstructure through advanced biophysical modelling (e.g. the sphere fraction, modelling the fraction of cell bodies versus neuronal or astrocytic processes) is a strong asset of the study, going beyond the more commonly used signal representation metrics such as the apparent diffusion coefficient, which lacks specificity to biological phenomena.<br /> (2) The fairly good data quality despite the complexity of the experimental framework should be praised: diffusion-weighted MRS was acquired in two brain regions (although not in the same animals) and longitudinally, in neonates, including data at high b-values and multiple diffusion times, which altogether constitutes a large-scale dataset of high value for the diffusion-weighted MRS community.<br /> (3) The authors have shared publicly data and codes used for processing and fitting, which will allow one to reproduce or extend the scope of this work to disease populations, and which goes in line with the current effort of the MR(S) community for data sharing.

Specific weaknesses:

Ligneul and coauthors have convincingly addressed and included my comments in their revised manuscript.

I believe the following conceptual concerns, which are inherent to the nature of the study and do not require further adjustments of the manuscript, remain:

(1) Metabolite compartmentation in one cell type or the other has often been challenged and is currently impossible to validate in vivo. Here, Ligneul and coauthors did not use this assumption a priori and supported their claims also with non-MR literature (eg. for Taurine), but the interpretation of results in that direction should be made with care.

(2) Longitudinal MR studies of the developing brain make it difficult to extract parameters with an "absolute" meaning. Indirect assumptions used to derive such parameters may change with age and become confounding factors (brain structure, cell distribution, concentrations normalizing metabolites (here macromolecules), relaxation times...). While findings of the manuscript are convincing and supported with literature, the true underlying nature of such changes might be difficult to access.

(3) Diffusion MRI in addition to diffusion MRS would have been complementary and beneficial to validate some of the signal contributions, but was unfeasible in the time constraints of experiments on young animals.

Reviewer #1 (Public review):

Summary:

This study by Torok et al. takes a creative approach to studying circuit perturbations in a sensorimotor region for vocalization control, in a songbird species, the zebra finch. By expressing the light chain of tetanus toxin in neurons in a sensorimotor region HVC, the authors constrain neural firing and study the resulting degradation and then recovery of song, after a protracted (> 70-day) period. Recording data suggest a form of synaptic homeostasis emergent in both HVC and RA as a result of the profound loss of (inhibitory?) tone in HVC. The methods to analyze changes in song are particularly strong here, using dimension reduction and visualization techniques. Single-cell sequencing data showed accompanying changes in microglia abundance, as well as several other markers that were not observed in control viral injections. LFP analyses in birds during the tetanus onset phase showed clear dysregulation of typical voltage deflections and spectral power, each of which showed recovery in parallel with song recovery. Lastly, the authors present data indicating that the anterior forebrain region LMAN is not critical for the song degradation process, pointing instead to the direct relationship between HVC and RA in song plasticity in adults. The methods are generally well established, but my main concerns regard the validation of the viral construct, the lack of direct confirmation of tetanus toxin on inhibitory neurons or E/I balance in HVC, and a missed opportunity to look at song syllable sequence degradation and recovery.

Strengths:

The species under investigation is the premier model for the neural basis of vocal learning, and the telencephalic brain regions investigated are well mapped out for their control of vocal learning behavior. The methods for electrophysiology recording and analysis, song analysis, scRNAseq, and in situ hybridization pose no concern as they are well established for this group of co-authors.

Weaknesses:

The introduction lays out a case for pursuing long-term E/I imbalances, vis-à-vis transient perturbations that have shown effects on the behavior. However, the rationale is not clearly stated. Why should the reader care that "prolonged E/I imbalances" may occur? Do they occur naturally or in some disease states (as alluded to in the first paragraph)? Without this rationale, the reader is left with an impression that the experiments were done because of a technical capability rather than a conceptual thrust.

The cited works for the statement the "AAV viral vector expressing TeNT undre the human dlx promoter, which is selective for HVC inhibitory interneurons" (reference 5 Kosche et al., 2016; and reference 10 Vallentin et al 2016) do not substantiate the targeting of this dlx5 promoter for interneurons in zebra finch HVC. Neither of these cited studies used viral vectors, and so this is a misattribution of the dlx5 promoter as targeting HVC inhibitory interneurons. However, the original development of this enhancer by Gord Fishell and others did have solid expression in HVC (Dimidschstein et al., 2016, Nature Neuroscience), and the enhancer was used to successfully target inhibitory neurons in nearby nidopallium NCM (Spool et al., 2022, Curr Biol). Citing these two studies would improve the standing of this viral approach. Nevertheless, the specific construct used here is not the same as the published studies mentioned above (AAV9-dlx-TeNT). The authors therefore need to show expression of the virus using some histological confirmation to cement the idea that they are indeed targeting inhibitory interneurons with this manipulation. The methods statement "a single injection (~100 nL) in the center of HVC was sufficient to label enough cells" is not convincing in the absence of quantified photomicrographs.

The authors present no physiological confirmation of TeNT on E/I balance directly, and so we don't have a clear picture of how/whether HVC interneurons are physiologically altered by this manipulation. That said, the Npix recordings show that there was a tremendous increase in gamma power following TeNT manipulation, which subsides as the protracted song recovery unfolds. This finding is somewhat counterintuitive, given that gamma oscillations are typically driven by inhibitory neurons in many systems (including songbird pallium) while the TeNT manipulation is purported to cause *reductions* in inhibitory neurotransmitter release within HVC. Some interpretation of these incongruent results would be useful in the Discussion.

The degradation and recovery of song is based mainly on the measures of duration of syllables and inter-syllable intervals, but HVC is also a key locus for song syllable sequence coding. The supplementary figures show some changes in sequences. It would improve the interpretation of both the degradation and recovery of the song to know whether syllable sequences (iiiABCCDDEF) truly recovered or were morphed in some way (e.g., iiiCDDDBEF). The PCA analyses (that the authors conducted) for these two potential outcomes would likely be very similar, but the actual songs would differ greatly under these two scenarios in terms of syllable sequence. From the representative spectrograms, it appears that the song syllable sequence does indeed recover well in these examples (perhaps less so in Supplementary Figure 3). A simple Markov-chain analysis of the syllable sequences across birds in the study would provide important confirmation of these insights.

Reviewer #1 (Public review):

Summary:

In this manuscript, the authors Eapen, et al. investigated the peptide inhibitors of Cdc20. They applied a rational design approach, substituting residues found in the D-box consensus sequences to better align the peptides with the Cdc20-degron interface. In the process, the authors designed and tested a series of more potent binders, including ones that contain unnatural amino acids, and verified binding modes by elucidating the Cdc-20-peptide structures. The authors further showed that these peptides can engage with Cdc20 in the cellular context, and can inhibit APC/CCdc20 ubiquitination activity. Finally, the authors demonstrated that these peptides could be used as portable degron motifs that drive the degradation of a fused fluorescent protein.

Strengths:

This manuscript is clear and straightforward to follow. The investigation of different peptide variations was comprehensive and well-executed. This work provided the groundwork for the development of peptide drug modalities to inhibit degradation or applying peptides as portable motifs to achieve targeted degradation. Both of which are impactful. The additional points provided by the authors in response to reviewers further strengthened the manuscript and enhanced its clarity.

Weaknesses:

None, the authors have addressed all my comments, and I have no additional suggestions.

Reviewer #1 (Public review):

Summary:

The study dissects distinct pools of diacylglycerol (DAG), continuing a line of research on the central concept that there is a major lipid metabolism DAG pool in cells, but also a smaller signaling DAG pool. It tests the hypothesis that the second pool is regulated by Dip2, which influences Pkc1 signaling. The group shows that stressed yeast increase specific DAG species C36:0 and 36:1, and propose this promotes Pkc1 activation via Pck1 binding 36:0. The study also examines how perturbing the lipid metabolism DAG pool via various deletions such as lro1, dga1, and pah1 deletion impacts DAG and stress signaling. Overall this is an interesting study that adds new data to how different DAG pools influence cellular signaling.

Strengths:

The study nicely combined lipidomic profiling with stress signaling biochemistry and yeast growth assays.

Weaknesses:

One suggestion to improve the study is to examine the spatial organization of Dip2 within cells, and how this impacts its ability to modulate DAG pools. Dip2 has previously been proposed to function at mitochondria-vacuole contacts (Mondal 2022). Examining how Dip2 localization is impacted when different DAG pools are manipulated such as by deletion Pah1 (also suggested to work at yeast contact sites such as the nucleus-vacuole junction), or with Lro1 or Dga1 deletion would broaden the scope of the study.

Comments on revisions:

The revision addresses several of the concerns raised previously. Most importantly, it softens several conclusions that more clearly delineates limitations of the study. The study has yet to address how Dip2 and Pkc1 crosstalk, but new text addresses this limitation. There is also more analysis of Dip2 localization in other conditions where cell DAG pools are elevated (ie a LRO1 and DGA1 double KO, as well as PAH1 KO). Loss of these proteins elevates ER DAG, but Dip2 remains mitochondrially associated. This may imply DAG specificity, or that changes to DAG pools globally does not impact Dip2 import into mitochondria.

Reviewer #1 (Public review):

This study uses MEG to test for a neural signature of the trial history effect known as 'serial dependence.' This is a behavioral phenomenon whereby stimuli are judged to be more similar than they really are, in feature space, to stimuli that were relevant in the recent past (i.e., the preceding trials). This attractive bias is prevalent across stimulus classes and modalities, but a neural source has been elusive. This topic has generated great interest in recent years, and I believe this study makes a unique contribution to the field.

Specifically, while previous neuroimaging studies have found apparent reactivations of previous information, or repulsive biases that may indirectly relate to serial dependence, here Fischer at al. find an attractive bias in neural activity patterns that aligns with the direction of the behavioral effect. Moreover, the data show that the bias emerges later in a trial, after perceptual encoding, which speaks to an ongoing debate about whether such biases are perceptual or decisional.

The revised preprint thoroughly addresses many of the initial concerns, but the results are still open to interpretation. For instance, the model training/testing regime allows that some training data timepoints may be inherently noisier than others (e.g., delay period more so than encoding), and potentially more (or differently) susceptible to bias. The S1 and S2 epochs show no attractive bias, but they may also be based on more high fidelity training sets (i.e., encoding), and therefore less susceptible to the bias that is evident in the retrocue epoch. So, the results could reflect that serial dependence is indeed a post-perceptual process, or it may instead be that the WM representations, as detected with these MEG analyses, become noisier and more subject to reveal the attractive bias over time.

The results are intriguing, but the study was not powered to examine whether there is any feature-specificity to the neural bias (e.g., whether it matches the behavioral pattern that biases are amplified within a particular range of feature distances between stimuli). Nor do analyses get at temporally precise information about when attractive and repulsive biases appear, which would help to better reconcile the work with previous findings. As in, the reconstructions average across coarse trial epochs. The S1 and S2 reconstructions show no attractive bias, and appear to show subtle repulsion, but if the timing were examined more precisely, we might see repulsion magnified at earlier timepoints that shift toward attraction at later time points, thereby counteracting the effect. That is to say that the averaging approach, across feature values and timepoints, still leaves these important theoretical questions unresolved.

Nonetheless, the work marks an important step in identifying the neurophysiological bases of serial dependence. Ideally, all of the data, including the eye-tracking, would be made available so that others might try to address some of these follow-up questions.

Reviewer #1 (Public review):

Summary:

This manuscript addresses the challenge of understanding and capturing the similarity among large numbers of visual images. The authors show that an automated approach using artificial neural networks that focuses upon the embedding of similarity through behaviorally relevant dimensions can predict human similarity data up to a certain level of granularity.

Strengths:

The manuscript starts with a very useful introduction that sets the stage with an insightful Figure 1. The methods are state of the art and well thought off, and the data are compelling. The authors demonstrate the added value of their approach in several directions, resulting in a manuscript that is highly relevant for different domains. The authors also explore its limitations (e.g., granularity).

Weaknesses:

Although this manuscript and the work it describes are already of high quality, I see several ways in which it could be further improved. Below I rank these suggestions tentatively in order of importance.

Predictions obtain correlations above 0.80, often close to correlations of 0.90. The performance of DimPred is not trivial, given how much better it performs relative to classic RSA and feature reweighting. Yet, the ceiling is not sufficiently characterized. What is the noise ceiling in the main and additional similarity sets that are used? If the noise ceiling is higher than the prediction correlations, then can the authors try to find the stimulus pairs for which the approach systematically fails to capture similarity? Or is the mismatch very distributed across the full stimulus set?

Also in the section on p. 8-p.9, it is crucial to provide information on the noise ceiling of the various datasets.

This consideration of noise ceiling brings me to another consideration. Arguments have been made that a focus on overall prediction accuracy might mask important differences in underlying processes that can be demonstrated in more specific, experimental situations (Bowers et al., 2023). Can the authors exclude the possibility that their automatic approach would fail dramatically in specifically engineered situations? Some examples can be found in the 2024 challenge of the BrainScore platform. How can future users of this approach know whether they are in such a situation or not?

The authors demonstrated one limitation of the DimPred approach to capture fine-grained similarity among highly similar stimuli. The implications of this finding were not clear to me from the Abstract etc, because it is not sufficiently highlighted in the summaries that in this case DimPred performs even worse, and much worse, than more simple approaches like feature reweighting and even than classic RSA. I would discuss this outcome more in detail. With hindsight, this problem might not be so surprising given that DimPred relies upon the embedding with a few tens dimensions that mostly capture between-category differences. To me, this seems like a more fundamental limitation than a mere problem of granularity or lack of data, as suggested in the abstract.

The DimPred approach is based on the dimensions of a similarity embedding derived from human behavior. What is important here is (i) that DimPred is based upon an approach that tries to capture latent dimensions; or (ii) that these dimensions are behaviorally relevant? There are a lot of dimension-focused approaches. Generic ones are PCA, MDS, etc. More domain-specific approaches in cogneuro include the following: (i) for two-dimensional shape representations, good results have been obtained with image-computable dimensions of various levels of complexity (Morgenstern et al., 2021, PLOS Comput. Biol.); (ii) another dimension-focused approach has focused upon identifying dimensions that are universal across networks & human representations (Chen & Bonner, 2024, arXiv). Would such generic or more specific approaches work as well as DimPred?

Joint Public Reviews:

In this study, the authors suggest that DuoHexaBody-CD37, a biparatopic CD37-targeting antibody, can induce direct cytotoxicity in diffuse large B-cell lymphoma (DLBCL) cells through antibody clustering and SHP-1 activation, independent of complement. They further propose that DuoHexaBody-CD37 inhibits cytokine-mediated pro-survival signalling, suggesting a broader role for CD37-directed therapy in disrupting tumour supportive signalling networks.

A strength of the study is the systematic in vitro characterisation of signalling responses to DuoHexaBody-CD37 across both malignant and normal B-cells. The inclusion of phosphoproteomic profiling and mutant constructs provides mechanistic detail, and the findings may be of interest to researchers working on antibody therapeutics in lymphoma.

However, the evidence supporting key mechanistic processes - particularly the role of SHP-1 in mediating cytotoxicity and the requirement for Fc receptor crosslinking - is incomplete and would benefit from further functional validation. While CD37 has been explored previously as a therapeutic target, this study does add mechanistic insight into direct cytotoxicity and cytokine modulation. Nevertheless, the exclusive reliance on in vitro systems makes the translational relevance unclear.

Overall, the study provides valuable insight into CD37-mediated signalling in lymphoma cells, but the evidence remains incomplete to support broader conclusions about therapeutic impact.

Reviewer #1 (Public review):

Summary:

The authors analyze transcription in single cells before and after 4000 rads of ionizing radiation. They use Seuratv5 for their analyses, which allows them to show that most of the genes cluster along the proximal-distal axis. Due to the high heterogeneity in the transcripts, they use the Herfindahl-Hirschman index (HHI) from Economics, which measures market concentration. Using the HHI, they find that genes involved in several processes (like cell death, response to ROS, DNA damage response (DDR)) are relatively similar across clusters. However, ligands activating the JAK/STAT, Pvr, and JNK pathways and transcription factors Ets21C and dysf are upregulated regionally. The JAK/STAT ligands Upd1,2,3 require p53 for their upregulation after irradiation, but the normal expression of Upd1 in unirradiated discs is p53-independent. This analysis also identified a cluster of cells that expressed tribbles, encoding a factor that downregulates mitosis-promoting String and Twine, that appears to be G2/M arrested and expressed numerous genes involved in apoptosis, DDR, the aforementioned ligands, and TFs. As such, the tribbles-high cluster contains much of the heterogeneity.

Strengths:

(1) The authors have used robust methods for rearing Drosophila larvae, irradiating wing discs, and analyzing the data with Seurat v5 and HHI.

(2) These data will be informative for the field.

(3) Most of the data is well-presented.

(4) The literature is appropriately cited.

Weaknesses:

(1) The data in Figure 1 are single-image representations. I assume that counting the number of nuclei that are positive for these markers is difficult, but it would be good to get a sense of how representative these images are and how many discs were analyzed for each condition in B-M.

(2) Some of the figures are unclear.

Reviewer #1 (Public review):

In the manuscript, Aldridge and colleagues investigate the role of IL-27 in regulating hematopoiesis during T. gondii infection. Using loss-of-function approaches, reporter mice, and the generation of serial chimeric mice, they elegantly demonstrate that IL-27 induction plays a critical role in modulating bone marrow myelopoiesis and monocyte generation to the infection site. The study is well-designed, with clear experimental approaches that effectively address the mechanisms by which IL-27 regulates bone marrow myelopoiesis and prevents HSC exhaustion.

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.

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.

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.

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.

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 #1 (Public review):

Summary

Lysine acetoacetylation (Kacac) is a recently discovered histone post-translational modification (PTM) connected to ketone body metabolism. This research outlines a chemo-immunological method for detecting Kacac, eliminating the requirement for creating new antibodies. The study demonstrates that acetoacetate acts as the precursor for Kacac, which is catalyzed by the acyltransferases GCN5, p300, and PCAF, and removed by the deacetylase HDAC3. Acetoacetyl-CoA synthetase (AACS) is identified as a central regulator of Kacac levels in cells. A proteomic analysis revealed 139 Kacac sites across 85 human proteins, showing the modification's extensive influence on various cellular functions. Additional bioinformatics and RNA sequencing data suggest a relationship between Kacac and other PTMs, such as lysine β-hydroxybutyrylation (Kbhb), in regulating biological pathways. The findings underscore Kacac's role in histone and non-histone protein regulation, providing a foundation for future research into the roles of ketone bodies in metabolic regulation and disease processes.

Strengths

(1) The study developed an innovative method by using a novel chemo-immunological approach to the detection of lysine acetoacetylation. This provides a reliable method for the detection of specific Kacac using commercially available antibodies.

(2) The research has done a comprehensive proteome analysis to identify unique Kacac sites on 85 human proteins by using proteomic profiling. This detailed landscape of lysine acetoacetylation provides a possible role in cellular processes.

(3) The functional characterization of enzymes explores the activity of acetoacetyltransferase of key enzymes like GCN5, p300, and PCAF. This provides a deeper understanding of their function in cellular regulation and histone modifications.

(4) The impact of acetyl-CoA and acetoacetyl-CoA on histone acetylation provides the differential regulation of acylations in mammalian cells, which contributes to the understanding of metabolic-epigenetic crosstalk.

(5) The study examined acetoacetylation levels and patterns, which involve experiments using treatment with acetohydroxamic acid or lovastatin in combination with lithium acetoacetate, providing insights into the regulation of SCOT and HMGCR activities.

Weakness

(1) There is a limitation to functional validation, related to the work on the biological relevance of identified acetoacetylation sites. Hence, the study requires certain functional validation experiments to provide robust conclusions regarding the functional implications of these modifications on cellular processes and protein function. For example, functional implications of the identified acetoacetylation sites on histone proteins would aid the interpretation of the results.

(2) The authors could have studied acetoacetylation patterns between healthy cells and disease models like cancer cells to investigate potential dysregulation of acetoacetylation in pathological conditions, which could provide insights into their PTM function in disease progression and pathogenesis.

(3) The time-course experiments could be performed following acetoacetate treatment to understand temporal dynamics, which can capture the acetoacetylation kinetic change, thereby providing a mechanistic understanding of the PTM changes and their regulatory mechanisms.

(4) Though the discussion section indeed provides critical analysis of the results in the context of existing literature, further providing insights into acetoacetylation's broader implications in histone modification. However, the study could provide a discussion on the impact of the overlap of other post-translational modifications with Kacac sites with their implications on protein functions.

Impact

The authors successfully identified novel acetoacetylation sites on proteins, expanding the understanding of this post-translational modification. The authors conducted experiments to validate the functional significance of acetoacetylation by studying its impact on histone modifications and cellular functions.

Reviewer #1 (Public review):

Summary:

In this paper, authors investigated the role of RUNT-related transcription factor 2 (RUNX2) in oral squamous carcinoma (OSCC) growth and resistance to ferroptosis. They found that RUNX2 suppresses ferroptosis through transcriptional regulation of peroxiredoxin-2. They further explored the upstream positive regulator of RUNX2, HOXA10 and found that HOXA1/RNUX2/PRDX2 axis protects OSCC from ferroptosis.

Strengths:

The study is well designed and provides a novel mechanism of HOXA1/RNUX2/PRDX2 control of ferroptosis in OSCC.

Weaknesses:

According to the data presented in (Figure 2F, Figure 3F and G, Figure 5D and Figure 6E and F), apoptosis seems to be affected in the same amount as ferroptosis by HOXA1/RNUX2/PRDX2 axis, which raises a question on the authors' specific focus on ferroptosis in this study. Reasonably, authors should adapt the title and the abstract in a way that it recapitulates the whole data, which is HOXA1/RNUX2/PRDX2 axis control of cell death, including ferroptosis and apoptosis in OSCC.

Comments on revisions:

The revised manuscript has been well improved, and I'm satisfied with the authors' response to my comments.

Reviewer #1 (Public review):

Summary:

Epiney et al. use single-nuclei RNA sequencing (snRNA-seq) to characterize the lineage of Type-2 (T2) neuroblasts (NBs) in the adult Drosophila brain. To isolate cells born from T2 NBs, the authors used a genetic tool that specifically allows the permanent labeling of T2-derived cell types, which are then FAC-sorted for snRNA-seq. This effective labeling approach also allows them to compare the isolated T2 lineage cells with T1-derived cell types by a simple exclusion method. The authors begin by describing a transcriptomic atlas for all T1 and T2-derived neuronal and glia clusters, reporting that the T2-derived lineage comprises 161 neuronal clusters, in contrast to the T1 lineage which comprises 114 of them. The authors then use the expression of VAChT, VGlut, Gad1, Tbh, Ple, SerT, and Tdc2 to show that T2 neuroblasts generate all major neuron classes of fast-acting neurotransmitters. Strikingly, they show that a subset of glia and neuronal clusters have disproportionate enrichment in males or females, suggesting that T2 neuroblasts generate sex-biased cell types. The authors then proceed to characterize neuropeptide expression across T2-derived neuronal clusters and argue that the same neuropeptide can be expressed across different cell types, while similar cell types can express distinct neuropeptides. The functional implication of both observations, however, remains to be tested. Furthermore, the authors describe combinatorial transcription factor (TF) codes that are correlated with neuropeptide expression for T2-derived neurons along with an overall TF code for all T2-derived cell types, both of which will serve as an important starting point for future investigations. Finally, the authors map well-studied neuronal types of the central complex to the clusters of their T2-derived snRNA-seq dataset. They use known marker combinations, bulk RNA-seq data and highly specific split-GAL4 driver lines to annotate their T2-derived atlas, establishing a comprehensive transcriptomic atlas that would guide future studies in this field.

Strengths:

This study provides an in-depth transcriptomic characterization of neurons and glia derived from Type-2 neuroblast lineages. The results of this manuscript offer several future directions to investigate the mechanisms of diversifying neuronal identity. The datasets of T1-derived and T2-derived cells will pave the way for studies focused on the functional analysis of combinatorial TF codes specifying cell identity, sex-based differences in neurogenesis and gliogenesis, the relationship between neuropeptide (co)expression and cell identity, and the differential contributions of distinct progenitor populations to the same cell type.

Weaknesses:

The study presents several important observations based on the characterization of Type II neuroblast-derived lineages. However, a mechanistic insight is missing for most observations. The idea that there is a sex-specific bias to certain T2-derived neurons and glial clusters is quite interesting, however, the functional significance of this observation is not tested or discussed extensively. Finally, the authors do not show whether the combinatorial TF code is indeed necessary for neuropeptide expression or if this is just a correlation due to cell identity being defined by TFs. Functional knockdown of some candidate TFs for a subset of neuropeptide-expressing cells would have been helpful in this case.

Comments on revisions:

The authors have addressed my recommendations.

Reviewer #2 (Public review):

Summary:

The authors developed a novel tool, SCellBOW, to perform cell clustering and infer survival risks on individual cancer cell clusters from the single cell RNA seq dataset. The key ideas/techniques used in the tool include transfer learning, bag of words (BOW), and phenotype algebra which is similar to word algebra from natural language processing (NLP). Comparisons with existing methods demonstrated that SCellBOW provides superior clustering results and exhibits robust performance across a wide range of datasets. Importantly, a distinguishing feature of SCellBOW compared to other tools is its ability to assign risk scores to specific cancer cell clusters. Using SCellBOW, the authors identified a new group of prostate cancer cells characterized by a highly aggressive and dedifferentiated phenotype.

Strengths:

The application of natural language processing (NLP) to single-cell RNA sequencing (scRNA-seq) datasets is both smart and insightful. Encoding gene expression levels as word frequencies is a creative way to apply text analysis techniques to biological data. When combined with transfer learning, this approach enhances our ability to describe the heterogeneity of different cells, offering a novel method for understanding the biological behavior of individual cells and surpassing the capabilities of existing cell clustering methods. Moreover, the ability of the package to predict risk, particularly within cancer datasets, significantly expands the potential applications.

Weaknesses:

Given the promising nature of this tool, it would be beneficial for the authors to test the risk-stratification functionality on other types of tumors with high heterogeneity, such as liver and pancreatic cancers, which currently lack clinically relevant and well-recognized stratification methods. Additionally, it would be worthwhile to investigate how the tool could be applied to spatial transcriptomics by analyzing cell embeddings from different layers within these tissues.

Reviewer #1 (Public review):

Summary:

The authors investigated the population structure of the invasive weed Lantana camara from 36 localities in India using 19,008 genome-wide SNPs obtained through ddRAD sequencing.

Strengths:<br /> The manuscript is well-written, the analyses are sound, and the figures are of great quality.

Weaknesses:

The narrative almost completely ignores the fact that this plant is popular in horticultural trade and the different color morphs that form genetic populations are most likely the result of artificial selection by humans for certain colors for trade, and not the result of natural selfing. Although it may be possible that the genetic clustering of color morphs is maintained in the wild through selfing, there is no evidence in this study to support that. The high levels of homozygosity are more likely explained as a result of artificial selection in horticulture and relatively recent introductions in India. Therefore, the claim of the title that "the population structure.. is shaped by its mating system" is in part moot, because any population structure is in large part shaped by the mating system of the organism, but further misleading because it is much more likely artificial selection that caused the patterns observed.

Reviewer #1 (Public review):

The authors present tviblindi, an algorithm to infer cell development trajectories from single-cell molecular data. The paper is well-written and the algorithm is conceptually interesting. However, the validation is incomplete as the comparison against existing trajectory inference methods is weak: although the lack of a proper benchmark was pointed out as the main weakness of the original version of the manuscript, the revised version still only contains qualitative comparisons against state-of-the-art methods.

Both me and Reviewer 2 pointed out that the lack of a proper benchmark against state-of-the-art methods on a wider variety of datasets (including scRNA-seq data) was a major weakness of the original version of the manuscript. In response to this criticism, the authors now did the following:

- They ran various competitor methods on the datasets that were used already for the previous version of the manuscript.<br /> - They ran tviblindi and two of the competitors on two public scRNA-seq datasets.<br /> - For all datasets, they qualitatively assessed the trajectories computed by tviblindi and its competitors and argued that tviblindi's trajectories better reflect the biological signal in the data.<br /> - The results of all of these additional analyses are reported in the supplement, which has now become very lengthy (88 pages).

In my opinion, this is insufficient to establish that tviblindi is comparable or even superior to the state of the art in the field. To show that this is the case, the authors would have to carry out a systematic benchmark study which relies on quantitative evaluation metrics rather than on qualitative intepretations of trajectories. As method developers, we are all susceptive to confirmation bias when comparing our new algorithms to the state of the art. To avoid this pitfall, reporting quantitative performance metrics is required. At the moment, the only quantitative metric reported by the authors is runtime, which is insufficient.

Moreover, the results of a benchmark study should be reported in the main manuscript, not in the supplement. When presenting a new algorithm in a field as crowded as trajectory inference, a benchmark against the state of the art serves to establish trust in the new algorithm and to provide the readers with a rationale to use it for their research. For this, the results of the benchmark have to be presented prominently and should not be hidden in the supplement.

A second major criticism raised in Reviewer 2's review of the original version of the manuscript is that tviblindi invites cherry picking due to its inherently interactive design. In response to this, the authors now argue at length that "the data-driven expert interpretation approach of tviblindi" (quote from Section 2.2.2) is a strength rather than a weakness. If we concede for the sake of the argument that tviblindi's "expert interpretation approach" is indeed a strength of the method (although I tend to agree with Reviewer 2 that it is rather a limitation), usability for biologists becomes critical. However, given the current implementation of tviblindi, its usability is far from optimal. The authors do not provide tviblindi as a web interface that is directly usable for domain experts without programming experience and not even as a package that is installable via some widely used package manager such as conda. Instead, they implemented tviblindi as an R package with a Shiny GUI that can either run in a Docker container or requires the installation of several dependencies. I therefore strongly doubt that many biologists will be able or willing to run tviblindi, which substantially limits the value of its "expert interpretation approach". Moreover, tviblindi does not support Apple silicon, which prevented also myself from testing the tool.

Reviewer #1 (Public review):

Summary:

In this work, Huang et al. revealed the complex regulatory functions and transcription network of 172 unknown transcriptional factors (TFs) in Pseudomonas aeruginosa PAO1. They have built a global TF-DNA binding landscape and elucidated binding preferences and functional roles of these TFs. More specifically, the authors established a hierarchical regulatory network and identified ternary regulatory motifs, and co-association modules. Since P. aeruginosa is a well known pathogen, the authors thus identified key TFs associated with virulence pathways (e.g., quorum sensing [QS], motility, biofilm formation), which could be potential drug targets for future development. The authors also explored the TF conservation and functional evolution through pan-genome and phylogenetic analyses. For the easy searching by other researchers, the authors developed a publicly accessible database (PATF_Net) integrating ChIP-seq and HT-SELEX data.

Strengths:

(1) The authors performed ChIP-seq analysis of 172 TFs (nearly half of the 373 predicted TFs in P. aeruginosa) and identified 81,009 significant binding peaks, representing one of the largest TF-DNA interaction studies in the field. Also, The integration of HT-SELEX, pan-genome, and phylogenetic analyses provided multi-dimensional insights into TF conservation and function.

(2) The authors provided informative analytical Framework for presenting the TFs, where a hierarchical network model based on the "hierarchy index (h)" classified TFs into top, middle, and bottom levels. They identified 13 ternary regulatory motifs and co-association clusters, which deepened our understanding of complex regulatory interactions.

(3) The PATF_Net database provides TF-target network visualization and data-sharing capabilities, offering practical utility for researchers especially for the P. aeruginosa field.

Weaknesses:

(1) There is very limited experimental validation for this study. Although 24 virulence-related master regulators (e.g., PA0815 regulating motility, biofilm, and QS) were identified, functional validation (e.g., gene knockout or phenotypic assays) is lacking, leaving some conclusions reliant on bioinformatic predictions. Another approach for validation is checking the mutations of these TFs from clinical strains of P. aeruginosa, where chronically adapted isolates often gain mutations in virulence regulators.

(2) ChIP-seq in bacteria may suffer from low-abundance TF signals and off-target effects. The functional implications of non-promoter binding peaks (e.g., coding regions) were not discussed.

(3) PATF_Net currently supports basic queries but lacks advanced tools (e.g., dynamic network modeling or cross-species comparisons). User experience and accessibility remain underevaluated. But this could be improved in the future.

Achievement of Aims and Support for Conclusions

(1) The authors successfully mapped global P. aeruginosa TF binding sites, constructed hierarchical networks and co-association modules, and identified virulence-related TFs, fulfilling the primary objectives. The database and pan-genome analysis provide foundational resources for future studies.

(2) The hierarchical model aligns with known virulence mechanisms (e.g., LasR and ExsA at the bottom level directly regulating virulence genes). Co-association findings (e.g., PA2417 and PA2718 co-regulating pqsH) resonate with prior studies, though experimental confirmation of synergy is needed.

Impact on the Field and Utility of Data/Methods

(1) This study fills critical gaps in TF functional annotation in P. aeruginosa, offering new insights into pathogenicity mechanisms (e.g., antibiotic resistance, host adaptation). The hierarchical and co-association frameworks are transferable to other pathogens, advancing comparative studies of bacterial regulatory networks.

(2) PATF_Net enables rapid exploration of TF-target interactions, accelerating candidate regulator discovery.

Reviewer #1 (Public review):

Summary:

In their manuscript, the authors provide compelling evidence that stimulus-frequency otoacoustic emission (SFOAE) phase-gradient delays predict the sharpness (quality factors) of auditory-nerve-fiber (ANF) frequency tuning curves in budgerigars. In contrast with mammals, neither SFOAE- nor ANF-based measures of cochlear tuning match the frequency dependence of behavioral tuning in this species of parakeet. Although the reason for the discrepant behavioral results (taken from previous studies) remains unexplained, the present data provide significant and important support for the utility of otoacoustic estimates of cochlear tuning, a methodology previously explored only in mammals.

Strengths:

* The OAE and ANF data appear solid and believable. (The behavioral data are taken from previous studies and the resulting limitations are discussed.)

* No other study in birds (and only a single previous study in mammals) has combined behavioral, auditory-nerve, and otoacoustic estimates of cochlear tuning in a single species.

* SFOAE-based estimates of cochlear tuning were obtained by assuming that the tuning ratio estimated in chicken applies also to the budgerigar. Possible complications arising from an avian apical-basal transition analogous to that found in mammals are discussed.

Reviewer #2 (Public review):

Summary:

By combining bioinformatical and experimental approaches, the authors address the question why several vertebrate lineages lack specific genes of the necroptosis pathway, or those that regulate the interplay between apoptosis and necroptosis. The lack of such genes was already known from previous publications, but the current manuscript provides a more in-depth analysis and also uses experiments in human cells to address the question of functionality of the remaining genes and pathways. A particular focus is placed on RIPK3/RIPK1 and their dual roles in inducing NFkB and/or necroptosis.

Strengths:

The well documented bioinformatical analyses provide a comprehensive data basis of the presence/absence of RIP-kinases, other RHIM proteins, apoptosis signaling proteins (FADD,CASP8,CASP10) and some other genes involved in these pathway. Several of these genes are known to be missing in certain animal lineages, which raises the question why their canonical binding partners are present in these species. By expressing several such proteins (both wildtype and mutants destroying particular interaction regions) in human cells, the authors succeed in establishing a general role of RIPK3 and RIPK1 in NFkB activation. This function appears to be better conserved and more universal than the necroptotic function of the RHIM proteins. The authors also scrutinize the importance of the kinase function and RHIM integrity for these separate functionalities.

Weaknesses:

A weakness of the presented study is the experimental restriction to human HEK293 cells. There are several situations where the functionality of proteins from distant organisms (like lampreys or even mussels) in human cells is not necessarily indicative of their function in native context. In some cases, these problems are addressed by co-expressing potential interaction partners, but not all of these experiments are really informative. However, I agree with the authors that it is not possible to perform all the experiments in native cells, and that comparing all proteins in the same (human) cell type allows for a better comparison.

The conclusions drawn by the authors are supported by convincing evidence. I have no doubts that this study will be very useful for future studies addressing the evolution of necroptosis and its regulation by NFkB and apoptosis.

Reviewer #1 (Public review):

Summary:

The authors have provided a mechanism by which how presence of truncated P53 can inactivate function of full length P53 protein. The authors proposed this happens by sequestration of full length P53 by truncated P53. In the study, the performed experiments are well described.

Significance:

The work in significant, since it points out more mechanistic insight how wild type full length P53 could be inactivated in the presence of truncated isoforms, this might offer new opportunity to recover P53 function as treatment strategies against cancer.

Comments on latest version:

The authors have made significant effort to address my concerns using the system available to them. I find the justifications provided in the rebuttal letter and the revised figures satisfactory. My initial concerns regarding the overexpression system have been largely addressed. However, the experimental system used by the authors lacks the means to measure the effect on endogenous p53, which remains a limitation.

Reviewer #1 (Public review):

Summary:

The concept that trained immunity, as defined, can be beneficial to subsequent immune challenges is important in the broad context of health and disease. The significance of this manuscript is the finding that trained immunity is actually a two-edged sword, herein, detrimental in the context of LPS-induced Acute Lung Injury that is mediated by AMs.

Strengths:

Several lines of evidence in different mouse models support this conclusion. The postulation that differences in immune responses in individuals is linked to differences in the mycobiome and consequent B-glucan makeup is provocative.

Weaknesses:

However, the findings that the authors state are relevant to sepsis are actually confined to a specific lung injury model and not classically-defined sepsis, the ontogeny of the reprogrammed AMs is uncertain, and links in the proposed signaling pathways need to be strengthened.

Comments on the latest version:

The manuscript is improved with further clarifications and additional experimentation. My prior concerns are addressed.

Reviewer #1 (Public review):

Summary:

This manuscript presents a study on expectation manipulation to induce placebo and nocebo effects in healthy participants. The study follows standard placebo experiment conventions with the use of TENS stimulation as the placebo manipulation. The authors were able to achieve their aims. A key finding is that placebo and nocebo effects were predicted by recent experience, which is a novel contribution to the literature. The findings provide insights into the differences between placebo and nocebo effects and the potential moderators of these effects.

Specifically, the study aimed to:

(1) assess the magnitude of placebo and nocebo effects immediately after induction through verbal instructions and conditioning<br /> (2) examine the persistence of these effects one week later, and<br /> (3) identify predictors of sustained placebo and nocebo responses over time.

Strengths:

An innovation was to use sham TENS stimulation as the expectation manipulation. This expectation manipulation was reinforced not only by the change in pain stimulus intensity, but also by delivery of non-painful electrical stimulation, labelled as TENS stimulation.

Questionnaire-based treatment expectation ratings were collected before conditioning and after conditioning, and after the test session, which provided an explicit measure of participants' expectations about the manipulation.

The finding that placebo and nocebo effects are influenced by recent experience provides a novel insight into a potential moderator of individual placebo effects.

Weaknesses:

There are a limited number of trials per test condition (10), which means that the trajectory of responses to the manipulation may not be adequately explored.

On day 8, one stimulus per stimulation intensity (i.e., VAS 40, 60, and 80) was applied before the start of the test session to re-familiarise participants with the thermal stimulation. There is a potential risk of revealing the manipulation to participants during the re-familiarization process, as they were not previously briefed to expect the painful stimulus intensity to vary without the application of sham TENS stimulation.

The differences between the nocebo and control conditions in pain ratings during conditioning could be explained by the differing physiological effects of the different stimulus intensities, so it is difficult to make any claims about expectation effects here.

A randomisation error meant that 25 participants received an unbalanced number of 448 trials per condition (i.e., 10 x VAS 40, 14 x VAS 60, 12 x VAS 80).

Reviewer #1 (Public review):

Summary:

Previous studies have shown that the MSH6 family of mismatch repair proteins contains an unstructured N-terminal domain that contains either a PWWP domain, a Tudor domain or neither and that the interaction of the histone reader domains with the appropriate histone H3 modification enhances mismatch repair, and hence reduces mutation rates in coding regions to some extent. However, the elimination of the MSH6-histone modification probably does not completely eliminate mismatch repair, although the published papers on this point do not seem definitive.

In this study, the authors perform a details phylogenetic analysis of the presence of the PWWP and Tudor domains in MSH6 proteins across the tree of life. They observe that there are basically three classes of organisms that contain either a PWWP domain, a Tudor domain, or neither. On the basis of their analysis, they suggest that this represents convergent evolution of the independent acquisition of histone reader domains and that key amino acid residues in the reader domains are selected for.

Strengths:

The phylogenetic aspects of the work seem well done and the basic evolutionary conclusions of the work are well supported. The basic evolutionary conclusions are interesting and there is little to criticize from my perspective.

Weaknesses:

A major concern about this paper is that the authors fail to put their work into the proper context of what is already known about the N-terminus of MSH6. Further, their structural studies, which are really structural illustrations, are misleading, often incorrect, and not always helpful in addition to having been published before.

Reviewer #1 (Public review):

Summary:

Is peristimulus alpha (8-14 Hz) frequency and/or phase involved in shaping the length of visual and audiovisual temporal binding windows, as posited by the discrete sampling hypothesis? If so, to what extent and perceptual scenario are they functionally relevant? The authors addressed such questions by collecting EEG data during the completion of the widely-known 2-flash fusion paradigm, administered both in a standard (i.e., visual only, F2) and audiovisual (i.e., 2 flashes and 1 beep, F2B1) fashion. Instantaneous frequency estimation performed over parieto-occipital sensors revealed slower alpha rhythms right after stimulus onset in the F2B1 condition, as compared to the F2, a pattern found to correlate with the difference between modality-specific ISIs (F2B1-F2). Of note, peristimulus alpha frequency differed also between 1 vs 2 flashes reports, although in the visual modality only (i.e., faster alpha oscillations in 2 flash percept vs 1 flash). This pattern of results was reinvigorated in a causal manner via occipital tACS, which was capable of, respectively, narrowing down vs enlarging the temporal binding window of individuals undergoing 13 Hz vs 8 Hz stimulation in the F2 modality alone. To elucidate what the oscillatory signatures of crossmodal integration might be, the authors further focused on the phase of posterior alpha rhythms. Accordingly, the Phase Opposition Sum proved to significantly differ between modalities (F2B1 vs F2) during the prestimulus time window, suggesting that audiovisual signals undergo finer processing based on the ongoing phase of occipital alpha oscillations, rather than the speed at which these rhythms cycle. As a last bit of information, a computational model factoring in the electrophysiological assumptions of both the discrete sampling hypothesis and auditory-induced phase-resetting was devised. Analyses run on such synthetic data were partially able to reproduce the patterns witnessed in the empirical dataset. While faster frequency rates broadly provide a higher probability to detect 2 flashes instead of 1, the occurrence of a concurrent auditory signal in cross-modal trials should cause a transient elongation (i.e. slower frequency rate) of the ongoing alpha cycle due to phase-reset dynamics (as revealed via inter-trial phase clustering), prompting larger ISIs during F2B1 trials. Conversely, the model provides that alpha oscillatory phase might predict how well an observer dissociates sensory information from noise (i.e., perceptual clarity), with the second flash clearly perceived as such as long as it falls within specific phase windows along the alpha cycle.

Strengths:

The authors leveraged complementary approaches (EEG, tACS, and computational modelling), the results thereof not only integrate, but depict an overarching mechanistic scenario elegantly framing phase-resetting dynamics into the broader theoretical architecture posited by the discrete sampling hypothesis. Analyses on brain oscillations (either via frequency sliding and phase opposition sum) mostly appear to be methodologically sound, and very-well supported by tACS results. Under this perspective, the modelling approach serves as a convenient tool to reconcile and shed more light on the pieces of evidence gathered on empirical data, returning an appealing account on how cross-modal stimuli interplay with ongoing alpha rhythms and differentially affect multisensory processing in humans.

Weaknesses:

Some information relative to the task and the analyses is missing. For instance, it is not entirely clear from the text what the number of flashes actually displayed in explicit short trials is (1 or 2?). We believe it is always two, but it should be explicitly stated.

Moreover, the sample size might be an issue. As highlighted by a recent meta-analysis on the matter (Samaha & Romei, 2024), an underpowered sample size may very well drive null-findings relative to tACS data in F2B1 trials, in interplay with broad and un-individualized frequency targets.

Some criticality arises regarding the actual "bistability" of bistable trials, as the statistics relative to the main task (i.e., the actual means and SEMs are missing) broadly point toward a higher proclivity to report 2 instead of 1 flash in both F2B1 and F2 trials. This makes sense to some extent, given that 2 flashes have always been displayed (at least in bistable trials), yet tells about something botched during the pretest titration procedure.

Coming to the analyses on brain waves, one main concern relates to the phase-reset-induced slow-down of posterior alpha rhythms being of true oscillatory nature, rather than a mere evoked response (i.e., not sustained over time). Another question calling for some further scrutiny regards the overlooked pattern linking the temporal extent of the IAF differences between F2 and F2B1 trials with the ISIs across experimental conditions (explicit short, bistable, and explicit long). That is, the wider the ISI, the longer the temporal extent of the IAF difference between sensory modalities. Although neglected by the authors, such a trend speaks in favour of a rather nuanced scenario stemming from not only auditory-induced phase-reset alpha cycle elongation, but also some non-linear and perhaps super-additive contribution of flash-induced phase-resetting. This consideration introduces some of the issues about the computational simulation, which was modelled around the assumption of phase-resetting being triggered by acoustic stimuli alone. Given how appealing the model already is, I wonder whether the authors might refine the model accordingly and integrate the phase-resetting impact of visual stimuli upon synthetic alpha rhythms. Relatedly, I would also suggest the authors to throw in a few more simulations to explore the parameter space and assay, to which quantitative extent the model still holds (e.g. allowing alpha frequency to randomly change within a range between 8 and 13 Hz, or pivoting the phase delay around 10 or 50 ms). As a last remark, I would avoid, or at least tone down, concluding that the results hereby presented might reconcile and/or explain the null effects in Buergers & Noppeney, 2022; as the relationship between IAFs and audiovisual abilities still holds when examining other cross-modal paradigms such as the Sound-Induced Flash-Illusion (Noguchi, 2022), and the aforementioned patterns might be due to other factors, such as a too small sample size (Samaha & Romei, 2024).

Reviewer #1 (Public Review):

Summary:

In this paper, the authors aimed to test the ability of bumblebees to use bird-view and ground-view for homing in cluttered landscapes. Using modelling and behavioural experiments, the authors showed that bumblebees rely most on ground-views for homing.

Strengths:

The behavioural experiments are well-designed, and the statistical analyses are appropriate for the data presented. 

Weaknesses:

Views of animals are from a rather small catchment area.

Missing a discussion on why image difference functions were sufficient to explain homing in wasps (Murray and Zeil 2017).

The artificial habitat is not really 'cluttered' since landmarks are quite uniform, making it difficult to infer ecological relevance.

DOI: 10.1007/s10495-025-02112-1

Resource: (DSMZ Cat# ACC-761, RRID:CVCL_8800)

Curator: @dhovakimyan1

SciCrunch record: RRID:CVCL_8800

What is this?

Reviewer #1 (Public review):

Summary:

This paper tackles an important question: What drives the predictability of pre-stimulus brain activity? The authors challenge the claim that "pre-onset" encoding effects in naturalistic language data have to reflect the brain predicting the upcoming word. They lay out an alternative explanation: because language has statistical structure and dependencies, the "pre-onset" effect might arise from these dependencies, instead of active prediction. The authors analyze two MEG datasets with naturalistic data.

Strengths:

The paper proposes a very reasonable alternative hypothesis for claims in prior work. Two independent datasets are analyzed. The analyses with the most and least predictive words are clever, and nicely complement the more naturalistic analyses.

Weaknesses:

I have to admit that I have a hard time understanding one conceptual aspect of the work, and a few technical aspects of the analyses are unclear to me. Conceptually, I am not clear on why stimulus dependencies need to be different from those of prediction. Yes, it is true that actively predicting an upcoming word is different from just letting the regression model pick up on stimulus dependencies, but given that humans are statistical learners, we also just pick up on stimulus dependencies, and is that different from prediction? Isn't that in some way, the definition of prediction (sensitivity to stimulus dependencies, and anticipating the most likely upcoming input(s))?

This brings me to some of the technical points: If the encoding regression model is learning one set of regression weights, how can those reflect stimulus dependencies (or am I misunderstanding which weights are learned)? Would it help to fit regression models on for instance, every second word or something (that should get rid of stimulus dependencies, but still allow to test whether the model predicts brain activity associated with words)? Or does that miss the point? I am a bit unclear as to what the actual "problem" with the encoding model analyses is, and how the stimulus dependency bias would be evident. It would be very helpful if the authors could spell out, more explicitly, the precise predictions of how the bias would be present in the encoding model.

Reviewer #1 (Public review):

Summary:

This fMRI study shows that two regions of the visual cortex (BA18 and BA19) of blind and sighted individuals carry information about the physical similarity of objects denoted by words. This effect was found for written words (Braille in blind, visual in sighted) but not spoken words. The evidence complements earlier studies reporting physical similarity effects in the occipitotemporal cortex of blind and sighted individuals (e.g., Peelen et al., 2014).

Strengths:

The study addresses an important question in the fields of neural plasticity and visual cortex organization. The study is generally well-conducted and the findings are clearly presented.

Weaknesses:

While the evidence is statistically strong, it is currently incomplete because of missing control analyses (see below). The framing of the results, as arguing against the pluripotent cortex account, is not entirely convincing as it was not clear that the study addressed the key predictions of that account.

Main comments:

(1) The study is framed as a test of Bedny's "cognitively pluripotent cortex" proposal (2017) that attributes the increased visual cortex response to linguistic stimuli in blind individuals to high-level cognitive functions. Key evidence for this account came from studies showing increased responses in blind visual cortex to certain grammatical manipulations and to solving mathematical equations. The current study did not include such manipulations. Instead, the current study focused on the representation of objects denoted by single words. Bedny's account did not make a strong argument that the physical similarity of word referents should be differently represented in blind and sighted individuals - if it did, please state this explicitly. Indeed, evidence that (some regions of) the visual cortex represent objects similarly in blind and sighted individuals does not seem incompatible with it.

(2) Throughout the manuscript (including the abstract) it was not clear what was meant with "visual cortex" or "visual areas"; whether this refers to early visual cortex (V1/BA17) or to visual cortex more generally (e.g., BA17-BA19, occipitotemporal cortex (MT, etc)). This is important for the theoretical arguments and for the interpretation of the results. If visual cortex = BA17, the current results point to potentially important differences between blind and sighted individuals, with the physical similarity of objects only observed in the visual cortex of the blind. If visual cortex is meant to include areas beyond BA17, the blind and sighted show similarities in the current study, although such similarities have been observed before using similar research approaches.

(3) Related to the point above, the abstract does not accurately describe the results, as it only describes the similarities between blind and sighted but not the differences. The study revealed differences between groups, particularly in BA17 - primary visual cortex. The differences between the groups are also illustrated by the strikingly different searchlight results in the two groups separately (Figure S6). These differences do not reach significance in a whole-brain-corrected contrast, but that likely reflects a lack of power (particularly for a between-group contrast).

(4) Results were found for written words but not spoken words (Figure S9). This is somewhat surprising considering that the visual cortex was more strongly activated for written words in the sighted, with this activation presumably not adding any information about the physical properties of word referents. Together with the widespread significance of clusters correlating with the physical similarity matrix (Figure 6), this raises the possibility of a confound. It would be good to ensure that this is not the case, e.g., you could create similarity matrices based on word length, word visual similarity (e.g., overlap in letters), and word frequency, and correlate these matrices with the physical similarity matrix to ensure that these correlations are not positive (or if they are, partial it out).

(5) The study included a task manipulation, with participants either judging physical or conceptual properties. This task manipulation is a central aspect of the design but does not feature anywhere in the results, and is also not discussed or introduced in the text. It would be interesting to know whether the results depend on the property (physical/conceptual) being task-relevant. But more importantly, a potential concern is that the responses in the task (given for each object using a two-response button box) correlate with physical or conceptual similarity and that this explains the fMRI findings. For example, two objects that are elongated would both receive a "yes" button press when participants answer the question "is this elongated"; these objects would also be rated as physically similar. This may apply more to physical than conceptual similarity. To exclude this possibility, the responses need to be analysed and included in the fMRI analyses, either as a regressor in the GLM or as another matrix to be partialed out at the final stage of analysis.

(4) Many of the blind participants had some residual vision (9/20 had light perception, 2/20 had contour perception); this could possibly have prevented the reorganization of visual cortex.

Reviewer #1 (Public review):

Summary:

It is known that the nrp operon is induced by copper deprivation and encodes the synthesis of chalkophores. The authors carried out a genetic analysis that revealed transcriptional differences for WT and Mtb∆nrp when exposed to the copper chelator tetrathiomolybdate (TTM). The authors found that copper chelation results in upregulation of genes in the chalkophore cluster as well as genes involved in the respiratory chain: including, components of the heme-dependent oxidase CytBD and subunits of the bcc:aa3 heme-copper oxidase. Utilizing several knockout variants and inhibitors, the authors showed that copper starvation survival requires chalkophore synthesis and that copper starvation results in dysfunctional bcc:aa3 oxidase. By monitoring oxygen consumption, they go on to show that copper deprivation inhibits respiration through the bcc:aa3 oxidase. Lastly, the authors compare virulence of WT Mtb, Mtb∆nrp and MtbΔnrpΔcydAB strains in mice spleen and lung. The Mtb∆nrp strain showed mild attenuation, but virulence in MtbΔnrpΔcydAB was severely attenuated and complementation with the chalkophore biosynthetic pathway restored Mtb virulence. These results suggest that chalkophore mediated protection of the respiratory chain is critical to Mtb virulence, and that redundant respiratory oxidases within Mtb provide respiratory chain flexibility that may promote host adaptation.

This new information about Mtb biology may be leveraged for drug discovery, highlighting that the Mtb respiratory pathway is a promising drug target, where one may target the Mtb chalkophore biosynthetic pathway in conjunction with CytBD, to obliterate Mtb.

Strengths: Overall, the paper is very clear and well written, with thorough and well-thought-out experimentation.

No weaknesses.

Comments on revisions:

The authors have addressed all the reviewers' comments.

Reviewer #1 (Public review):

In this paper, the authors had 2 aims:

(1) Measure macaques' aversion to sand and see if its' removal is intentional, as it likely in an unpleasurable sensation that causes tooth damage.

(2) Show that or see if monkeys engage in suboptimal behavior by cleaning foods beyond the point of diminishing returns, and see if this was related to individual traits such as sex and rank, and behavioral technique.

They attempted to achieve these aims through a combination of geochemical analysis of sand, field experiments, and comparing predictions to an analytical model.

The authors' conclusions were that they verified a long-standing assumption that monkeys have an aversion to sand as it contains many potentially damaging fine grained silicates, and that removing it via brushing or washing is intentional.

They also concluded that monkeys will clean food for longer than is necessary, i.e. beyond the point of diminishing returns, and that this is rank-dependent.

High and low-ranking monkeys tended not to wash their food, but instead over-brushed it, potentially to minimize handling time and maximize caloric intake, despite the long-term cumulative costs of sand.

This was interpreted through the *disposable soma hypothesis*, where dominants maximize immediate needs to maintain rank and increase reproductive success at the potential expense of long-term health and survival.

Strengths:

The field experiment seemed well designed, and their quantification of the physical and mineral properties of quartz particles (relative to human detection thresholds) seemed good relative to their feret diameter and particle circularity (to a reviewer that is not an expert in sand). The *Rank Determination* and *Measuring Sand* sections were clear.

In achieving Aim 1, the authors validated a commonly interpreted, but unmeasured function, of macaque and primate behavior-- a key study/finding in primate food processing and cultural transmission research.

I commend their approach in trying to develop a quantitative model to generate predictions to compare to empirical data for their second aim.<br /> This is something others should strive for.

I really appreciated the historical context of this paper in the introduction and found it very enjoyable and easy to read.

I do think that interpreting these results in the context of the *disposable soma hypothesis* and the potential implications in the *paleolithic matters* section about interpreting dental wear in the fossil record are worthwhile.

Reviewer #1 (Public review):

Summary:

In this manuscript, Muramoto and colleagues have examined a mechanism by which the executioner caspase Drice is activated in a non-lethal context in Drosophila. The authors have comprehensively examined this in the Drosophila olfactory receptor neurons using sophisticated techniques. In particular, they had to engineer a new reporter by which non-lethal caspase activation could be detected. The authors conducted a proximity labeling experiment and identified Fasciclin 3 as a key protein in this context. While removal of Fascilin 3 did not block non-lethal caspase activation (likely because of redundant mechanisms), its overexpression was sufficient to activate non-lethal caspase activation.

Strengths:

While non-lethal functions of caspases have been reported in several contexts, far less is known about the mechanisms by which caspases are activated in these non-lethal contexts. So, the topic is very timely. The overall detail of this work is impressive and the results, for the most part, are well controlled and justified.

Weaknesses:

The behavioral results shown in Fig. 6 need more explanation and clarification (more details below). As currently shown, the results of Fig. 6 seem uninterpretable. Also, overall presentation of the Figures and description in legends can be improved.

Comments on revisions:

The authors have adequately addressed my comments.

Reviewer #2 (Public review):

Summary:

In a 1.5m diameter, 0.8m high circular arena bumblebees were accustomed to exit the entrance to their nest on the floor surrounded by an array of identical cylindrical landmarks and to forage in an adjacent compartment which they could reach through an exit tube in the arena wall at a height of 28cm. The movements of one group of bees were restricted to a height of 30cm, the height of the landmark array, while the other group was able to move up to heights of 80cm, thus being able to see the landmark array from above.

During one series of tests, the flights of bees returning from the foraging compartment were recorded as they tried to reach the nest entrance on the floor of the arena with the landmark array shifted to various positions away from the true nest entrance location. The results of these tests showed that the bees searched for the net entrance in the location that was defined by the landmark array.

In a second series of tests, access to the landmark array was prevented from the side, but not from top, by a transparent screen surrounding the landmark array. These tests showed that the bees of both groups rarely entered the array from above, but kept trying to enter it from the side.

The authors express surprise at this result because modelling the navigational information supplied by panoramic snapshots in this arena had indicated that the most robust information to the location of the nest entrance within the landmark array was supplied by views of the array from above, leading to the following strong conclusions:

line 51: "Snapshot models perform best with bird's eye views";<br /> line 188: "Overall, our model analysis could show that snapshot models are not able to find home with views within a cluttered environment but only with views from above it.";<br /> line 231: "Our study underscores the limitations inherent in snapshot models, revealing their inability to provide precise positional estimates within densely cluttered environments, especially when compared to the navigational abilities of bees using frog's-eye views."

Strengths:

The experimental set-up allows to record the flight behaviour of bees in great spatial and temporal detail and in principle also to reconstruct the visual information available to the bees throughout the arena.

Modelling: The revised manuscript now presents the results of modelling that includes information potentially available to the bees from the arena wall and in particular from the top edge of the arena.

As I predicted, this increases the width of rotational image difference functions and therefore provides directional guidance over a larger range of misalignments. However, the authors dismiss the modelling results based on such reconstructed views which more realistically describe the information available to the bumblebees, because (line 291ff): 'Further simulations with a rendered arena wall led to worse results because the agent was mainly led to the centre of the arena (Fig. S17, Fig. S18-21)".

What the modelling in Fig. 17 actually shows is that the agent is led more or less exactly to the 'entry points' to the arena chosen by the real bees (Fig. 4). The authors ignore this and in their rebuttal state that 'We hypothesised that the arena wall and object location created ambiguity'. The problem here is that you don't remove potential 'ambiguity' for real bees by ignoring information they are unlikely to ignore.

Behavioural analysis: The full potential of the set-up was not used to understand how the bees' navigation behaviour develops over time in this arena and what opportunities the bees have had to learn the location of the nest entrance during repeated learning flights and return flights.

Without a detailed analysis of the bees' behaviour during 'training', including learning flights and return flights, it is very hard to follow the authors' conclusions. The behaviour that is observed in the tests may be the result of the bees' extended experience shuttling between the nest and the entry to the foraging arena at 28cm height in the arena wall. For instance, it would have been important to see the return flights of bees following the learning flights shown in Fig. 17.

Basically both groups of bees (constrained to fly below the height of landmarks (F) or throughout the height of the arena (B)) had ample opportunities to learn that the nest entrance lies on the floor of the landmark array. The only reason why B-bees may not have entered the array from above when access from the side was prevented may simply be that bumblebees, because they bumble, find it hard to perform a hovering descent into the array.

The revised manuscript does not address my concerns. The rebuttal states that a detailed analysis of learning and return flights was 'outside the scope of this particular study', that their experimental design 'does not require the entire history of the bee's trajectory to be tested', that 'the entire flight history...will require...effort...conceptually' and that it would be 'difficult to test a hypothesis'.

These responses clarify the frustrating problem with this study: The authors are more concerned with testing hypotheses than with trying to understand how bumblebees learn to cope with a situation which constrains their learning choreography and confronts them with the one fundamental problem view-based homing has: repetitive scene elements.

Homing is an experience-dependent process and to understand what cues the bees used to navigate this set-up requires an analysis of the whole learning process. For instance, it may well be that the B+G+ bees initially did enter the array from above, but subsequently learnt a more efficient route into the array, by simply entering it from the side, followed by 'unguided' searching.

General: The most serious weakness of the set-up is that it is spatially and visually constrained, in particular lacking a distant visual panorama, which under natural conditions is crucial for the range over which rotational image difference functions provide navigational guidance. In addition, the array of identical landmarks is not representative of natural clutter and, because it is visually repetitive, poses unnatural problems for view-based homing algorithms. This is the reason why the functions degrade so quickly from one position to the next (Fig. 9-12) when more distant scene elements are excluded.

In conclusion, I do not feel that I have learnt anything useful from this experiment; it does suggest, however, that to fully appreciate and understand the homing abilities of insects, there is no alternative but to investigate these abilities in the natural conditions in which they have evolved. A nice start would be to build camera-based 3D models of natural bumblebee nest entrance environments and analyse whether there are any particularly unusual challenges for the visual localization of the nest entrance.

Reviewer #1 (Public review):

Summary and Strengths:

The study focuses on PIM1 and 2 in CD8 T cell activation and differentiation. These two serine/threonine kinases belong to a large network of Serine/Threonine kinases that acts following engagement of the TCR and of cytokine receptors and phosphorylates proteins that control transcriptional, translational and metabolic programs that result in effector and memory T cell differentiation. The expression of PIM1 and PIM2 is induced by the T-cell receptor and several cytokine receptors. The present study capitalized on high-resolution quantitative analysis of the proteomes and transcriptomes of Pim1/Pim2-deficient CD8 T cells to decipher how the PIM1/2 kinases control TCR-driven activation and IL-2/IL-15-driven proliferation, and differentiation into effector T cells.

Quantitative mass spectrometry-based proteomics analysis of naïve OT1 CD8 T cell stimulated with their cognate peptide showed that the PIM1 protein was induced within 3 hours of TCR engagement and its expression was sustained at least up to 24 hours. The kinetics of PIM2 expression was protracted as compared to that of PIM1. Such TCR-dependent expression of PIM1/2 correlated with the analysis of both Pim1 and Pim2 mRNA. In contrast, Pim3 mRNA was only expressed at very low levels and the PIM3 protein not detected by mass spectrometry. Therefore, PIM1 and 2 are the major PIM kinases in recently activated T cells. Pim1/Pim2 double knockout (Pim dKO) mice were generated on a B6 background and found to express lower number of splenocytes. No difference in TCR/CD28-driven proliferation was observed between WT and Pim dKO T cells over 3 days in culture. Quantitative proteomics of >7000 proteins further revealed no substantial quantitative or qualitative differences in protein content or proteome composition. Therefore, other signaling pathways can compensate for the lack of PIM kinases downstream of TCR activation.

Considering that PIM1 and PIM2 kinase expression is regulated by IL-2 and IL-15, antigen-primed CD8 T cells were expanded in IL-15 to generate memory phenotype CD8 T cells or expanded in IL-2 to generate effector cytotoxic T lymphocytes (CTL). Analysis of the survival, proliferation, proteome, and transcriptome of Pim dKO CD8 T cells kept for 6 days in IL-15 showed that PIM1 and PIM2 are dispensable to drive the IL-15-mediated metabolic or differentiation programs of antigen-primed CD8 T cells. Moreover, Pim1/Pim2-deficiency had no impact on the ability of IL-2 to maintain CD8 T cell viability and proliferation. However, WT CTL downregulated expression of CD62L whereas the Pim dKO CTL sustained higher CD62L expression. Pim dKO CTL were also smaller and less granular than WT CTL. Comparison of the proteome of day 6 IL-2 cultured WT and Pim dKO CTL showed that the latter expressed lower levels of the glucose transporters, SLC2A1 and SLC2A3, of a number of proteins involved in fatty acid and cholesterol biosynthesis, and CTL effector proteins such as granzymes, perforin, IFNg and TNFa. Parallel transcriptomics analysis showed that the reduced expression of perforin and some granzymes correlated with a decrease in their mRNA whereas the decreased protein levels of granzymes B and A, and of the glucose transporters SLC2A1 and SLC2A3 did not correspond with decreased mRNA expression. Therefore, PIM kinases are likely required for IL-2 to maximally control protein synthesis in CD8 CTL. Along that line, the translational repressor PDCD4 was increased in Pim dKO CTL and pan-PIM kinase inhibitors caused a reduction in protein synthesis rates in IL-2 expanded CTL. Finally, the differences between Pim dKO and WT CTL in terms of CD62L expression resulted in that Pim dKO CTL but not WT CTL retained the capacity to home to secondary lymphoid organs. In conclusion, this thorough and solid study showed that the PIM1/2 kinases shape the effector CD8 T cell proteomes rather than transcriptomes and are important mediators of IL2-signalling and CD8 T cell trafficking.

Weaknesses: None

Comments on revisions:

The authors have been able to provide in their rebuttal letter fair answers to most of the queries primarily raised by Reviewer 2 and they have incorporated the corresponding results in the revised text. It makes the paper stronger.

Reviewer #2 (Public review):

Summary:

Malaria transmission in the Gambia is highly seasonal, whereby periods of intense transmission at the beginning of the rainy season are interspersed by long periods of low to no transmission. This raises several questions about how this transmission pattern impacts the spatiotemporal distribution of circulating parasite strains, how parasites persist during the dry season, and how asymptomatic infections contribute to maintaining transmission during the low/no transmission season.

Combining a molecular barcode genotyping using 101 bi-allelic SNPs and SNPs from Whole Genome Sequence (WGS) in a "consensus barcode", the authors aimed at measuring the relatedness between parasites at different spatial (i.e., individual, household, village, and region) and temporal (i.e., high, low, and the corresponding the transitions) levels by assessing the fraction of the genome having a common ancestry (i.e. Identity-by-Descent (IBD)).

By measuring the Complexity of Infection (COI) and parasite relatedness by IBD the authors show that a large fraction of infections is polygenomic and stable over time, resulting in a high recombinational diversity. Moreover, they show that transmission intensity increases during the transition from the dry to wet seasons. However, they find that there is a higher probability of finding similar genotypes within the same household, but this similarity rapidly disappears over time and is not observed between different villages. If there is no drug selection during the dry season, and if resistance results in a fitness cost, alleles associated with drug resistance may change in frequency. The authors looked at the frequencies of six drug-resistance haplotypes (aat1, crt, dhfr, dhps, kelch13, and mdr1), and found no evidence of changes in allele frequencies associated with seasonality. They also find chronic infections lasting from one month to one and a half years with no dependence on age or gender.

This work makes use of genomic information and IBD analytic tools to show parasite relatedness from asymptomatic infections at different spatial and temporal scales, thus providing a better understanding of the transmission dynamics of malaria in highly seasonal environments.

Strength:

The authors use a combination of high-quality barcodes (425 barcodes representing 101 bi-allelic SNPs) and 199 high-quality genome sequences to infer the fraction of the genome with shared Identity by Descent (IBD) (i.e. a metric of recombination rate) over several time points covering two years. The barcode and whole genome sequence combination allows full use of a large dataset, to confidently infer the relatedness of parasite isolates at various spatiotemporal scales and show the advantage of using genomic information for understanding malaria transmission dynamics.

The authors aimed to establish how seasonal transmission cycles shape the spatiotemporal parasite population structure using metrics such as parasite genetic diversity, genetic relatedness, and frequency of drug resistance alleles, as well as the contribution of asymptomatic chronic carriers to sustained transmission. The results support their conclusions.

Using a combination of molecular barcodes and available whole genome sequence datasets opens new opportunities to understand malaria transmission dynamics in different transmission settings. This allows for data analysis at different spatiotemporal granularities, having a practical utility for identifying malaria control targets and acquiring metrics to evaluate malaria control programs. The development of molecular barcodes using similar SNPs by different malaria control programs would be of great utility to compare and understand malaria transmission dynamics in different settings worldwide.

Reviewer #1 (Public review):

Summary:

This paper examines changes in relaxation time (T1 and T2) and magnetization transfer parameters that occur in a model system and in vivo when cells or tissue are depolarized using an equimolar extracellular solution with different concentrations of the depolarizing ion K+. The motivation has been revised to state that the results suggest a potential approach to non-invasively detect changes in membrane potential using MRI.

Strengths:

The authors argue that the use of various concentrations of KCL in the extracellular fluid depolarize or hyperpolarize the cell pellets used, and that this change in membrane potential is the driving force for the T2 (and T1-supplementary material) changes observed. In particular, they report an increase in T2 with increasing KCL concentration in the extracellular fluid (ECF) of pellets of SH-SY5Y cells. To offset the increasing osmolarity of the ECF due to the increase in KCL, the NaCL molarity of the ECF is proportionally reduced. The authors measure the intracellular voltage using patch clamp recordings, which is a gold standard. With 80 mM of KCL in the ECF, a change in T2 of the cell pellets of ~10 ms is observed with the intracellular potential recorded as about -6 mv. A very large T1 increase of ~90 ms is reported under the same conditions. The PSR (ratio of hydrogen protons on macromolecules to free water) decreases by about 10% at this 80 mM KCL concentration. Similar results are seen in a Jurkat cell line and similar, but far smaller changes are observed in vivo, for a variety of reasons discussed. As a final control, T1 and T2 values are measured in the various equimolar KCL solutions. As expected, no significant changes in T1 and T2 of the ECF were observed for these concentrations.

Weaknesses:

While the concepts presented are interesting, and the actual experimental methods seem to be nicely executed, the conclusions are not supported by the data for a number of reasons. This is not to say that the data isn't consistent with the conclusions, but there are other controls not included that would be necessary to draw the conclusion that it is membrane potential that is driving these T1 and T2 changes. The results are consistent with Stroman et al. Magn. Reson. in Med. 59:700-706 (increased T2 with KCL) as well as some other cited work. However all those authors emphasize that cell swelling is the mechanism, not cell membrane potentials.

It is well established that cells swell/shrink upon depolarization/hyperpolarization. Cell swelling is accompanied by increased light transmittance in vivo, and this should be true in the pellet system as well. In a beautiful series of experiments, Stroman et al. (2008) showed in perfused brain slices that the cells swell upon equimolar KCL depolarization and the light transmittance increases. The time course of these changes is quite slow, of the order of many minutes, both for the T2-weighted MRI signal and for the light transmittance. Stroman et al. also show that hypoosmotic changes produce the exact same timecourse as the KCL depolarization changes (and vice versa for the hyperosmotic changes - which cause cell shrinkage). Their conclusion therefore, was that cell swelling (not membrane potential) was the cause of the T2-weighted changes observed, and that these were relatively slow (on the scale of many minutes).

What are the implications for the current study? Well, for one, the authors cannot exclude cell swelling as the mechanism for T2 changes, as they have not measured that. It is however well established that cell swelling occurs during depolarization, so this is not in question. Water in the pelletized cells is in slow/intermediate exchange with the ECF, and the solutions for the two compartment relaxation model for this are well established (see Menon and Allen, Magn. Reson. in Med. 20:214-227 (1991). The T2 relaxation times should be multiexponential (see point (3) further below). The current work cannot exclude cell swelling as the mechanism for T2 changes (it is mentioned in the paper, but not dealt with). Water entering cells dilutes the protein structures, changes rotational correlation times of the proteins in the cell and is known to increase T2. The PSR confirms that this is indeed happening, so the data in this work is completely consistent with the Stroman work and completely consistent with cell swelling associated with depolarization. The authors should have performed light scattering studies to demonstrate the degree cell swelling or shrinkage. Measuring intracellular potential is not enough to clarify the mechanism.

So why does it matter whether the mechanism is cell swelling or membrane potential? The reason is response time. Cell swelling due to depolarization is a slow process, slower than hemodynamic responses that characterize BOLD. And in fact, cell swelling under normal homeostatic conditions in vivo is virtually non-existent. Only sustained depolarization events typically associated with non-naturalistic stimuli or brain dysfunction produce cell swelling. Membrane potential changes associated with neural activity, on the other hand, are very fast. In this manuscript, the authors have convincingly shown a signal change that is virtually the same as what was seem in the Stroman publication, but they have not shown that there is a response that can be detected with anything approaching the timescale of an action potential. So one cannot definitely say that the changes observed are due to membrane potential. One can only say they are consistent with cell swelling, regardless of what causes the cell swelling. The First line of the discussion still claims that T2 relaxation time and pool size ratio (PSR) can detect responses to membrane potential changes modulated by ionic solutions. However, in the absence of cell swelling controls, this cannot be stated.

For this mechanism to be relevant to measuring neuronal activity directly or explaining techniques such DIANA, one needs to show that the cell swelling changes occur within a millisecond, which has never been reported. If one knows the populations of ECF and pellet, the T2s of the ECF and pellet and the volume change of the cells in the pellet, one can model any expected T2 changes due to neuronal activity. I think one would find that these are minuscule within the context of an action potential, or even bulk action potentials.

Comments on revisions:

The manuscript is well written and my previous methodological concerns have been clarified as well. There are no flaws in the experiments, but the interpretation really depends on simultaneous measurements of cell volume and membrane potential, which have yet to be done.

Reviewer #2 (Public review):

Summary:

The authors conduct a causal analysis of years of secondary education on brain structure in late life. They use a regression discontinuity anlaysis to measure the impact of a UK law change in 1972 that increased the years of mandatory education by 1 year. Using brain imaging data from the UK Biobank, they find essentially no evidence for 1 additional year of education altering brain structure in adulthood.

Strengths:

The authors pre-registered the study and the regression discontinuity was very carefully described and conducted. They completed a large number of diagnostic and alternate analyses to allow for different possible features in the data. (Unlike a positive finding, a negative finding is only bolstered by additional alternative anlayses).

Weaknesses:

While the work is of high quality for the precise question asked, ultimately the exposure (1 additional year of education) is a very modest manipulation and the outcome measured long after the intervention. Thus a null finding here is completely consistent educational attainement (EA) in fact having an impact on brain structure, where EA may reflect elements of training after second education (e.g. university, post-graduate qualifications, etc) and not just stopping education at 16 yrs yes/no.

Reviewer #2 (Public review):

Summary:

The goal of this work is to define the functions of T-box transcription factors Tbx3 and Tbx5 in the adult mouse ventricular cardiac conduction system (VCS) using a novel conditional mouse allele in which both genes are targeted in cis. A series of studies over the past 2 decades by this group and others have shown that Tbx3 is a transcriptional repressor that patterns the conduction system by repressing genes associated with working myocardium, while Tbx5 is a potent transcriptional activator of "fast" conduction system genes in the VCS. In a previous work, the authors of the present study further demonstrated that Tbx3 and Tbx5 exhibit an epistatic relationship whereby the relief of Tbx3-mediated repression through VCS conditional haploinsufficiency allows better toleration of Tbx5 VCS haploinsufficiency. Conversely, excess Tbx3-mediated repression through overexpression results in disruption of the fast-conduction gene network despite normal levels of Tbx5. Based on these data the authors proposed a model in which repressive functions of Tbx3 drive adoption of conduction system fate, followed by segregation into a fast-conducting VCS and slow-conduction AVN through modulation of the Tbx5/Tbx3 ratio in these respective tissue compartments.

The question motivating the present work is: If Tbx5/Tbx3 ratio is important for slow versus fast VCS identity, what happens when both genes are completely deleted from the VCS? Is conduction system identity completely lost without both factors and if so, does the VCS network transform into a working myocardium-like state? To address this question, the authors have generated a novel mouse line in which both Tbx5 and Tbx3 are floxed on the same allele, allowing complete conditional deletion of both factors using the VCS-specific MinK-CreERT2 line, convincingly validated in previous work. The goal is to use these double conditional knockout mice to further explore the model of Tbx3/Tbx5 co-dependent gene networks and VCS patterning. First the authors demonstrate that the double conditional knockout allele results in the expected loss of Tbx3 and Tbx5 specifically in the VCS when crossed with Mink-CreERT2 and induced with tamoxifen. The double conditional knockout also results in premature mortality. Detailed electrophysiological phenotyping demonstrated prolonged PR and QRS intervals, inducible ventricular tachycardia, and evidence of abnormal impulse propagation along the septal aspect of the right ventricle. In addition, the mutants exhibit downregulation of VCS genes responsible for both fast conduction AND slow conduction phenotypes with upregulation of 2 working myocardial genes including connexin-43. The authors conclude that loss of both Tbx3 and Tbx5 results in "reversion" or "transformation" of the VCS network to a working myocardial phenotype, which they further claim is a prediction of their model and establishes that Tbx3 and Tbx5 "coordinate" transcriptional control of VCS identity.

Overall Appraisal:

As noted above, the present study does not further explore the Tbx5/Tbx3 ratio concept since both genes are completely knocked out in the VCS. Instead, the main claims are that absence of both factors results in a transcriptional shift of conduction tissue towards a working myocardial phenotype, and that this shift indicates that Tbx5 and Tbx3 "coordinate" to control VCS identity and function. However, only limited data are presented to support the claim of transcriptional reprogramming since the knockout cells are not directly compared to working myocardial cells at the transcriptional level and only a small number of key genes are assessed (versus genome-wide assessment). In addition, the optical mapping dataset has alternative interpretations that are not excluded or thoroughly discussed.

In sum, while this study adds an elegantly constructed genetic model to the field, the data presented mostly fit within the existing paradigm of established functions of Tbx3 and Tbx5. The authors present some evidence to support the claim that VCS cells adopt a working myocardial phenotype in the absence of Tbx3 and Tbx5, but some key experiments that could more definitively test this model were not performed, reducing the degree to which the data support the conclusions.

Strengths:

(1) Successful generation of a novel Tbx3-Tbx5 double conditional mouse model<br /> (2) Successful VCS-specific deletion of Tbx3 and Tbx5 using a VCS-specific inducible Cre driver line<br /> (3) Well-powered and convincing assessments of mortality and physiological phenotypes<br /> (4) Isolation of genetically modified VCS cells using flow.

Weaknesses:

(1) In general, the data is consistent with a long-standing and well-supported model in which Tbx3 represses working myocardial genes and Tbx5 activates expression of VCS genes, which seem like distinct roles in VCS patterning.<br /> (2) More direct quantitative comparison of Tbx5 Adult VCS KO with Tbx5/Tbx3 Adult VCS double KO would be helpful to ascertain whether deletion of Tbx3 on top of Tbx5 deletion changes the underlying phenotype in some discernable way beyond mRNA expression of a few genes. Superficially, the phenotypes look quite similar at the EKG and arrhythmia inducibility level and no optical mapping data from single Tbx5 KO is presented for comparison to the double KO. I understand that single Tbx5 VCS KO mutants have been evaluated in previous publications but I think in order to evaluate the claims presented here, it would be important to do a direct comparison using the same assays and conditions.<br /> (3) The authors claim that double knockout VCS cells transform to working myocardial fate, but there is no comparison of gene expression levels between actual working myocardial cells and the Tbx3/Tbx5 DKO VCS cells so it's hard to know if the data reflect an actual cell state change or a more non-specific phenomenon with global dysregulation of gene expression or perhaps dedifferentiation. I understand that the upregulation of Gja1 and Smpx is intended to address this, but it's only two genes and it seems relevant to understand their degree of expression relative to actual working myocardium. In addition, the gene panel is somewhat limited and does not include other key transcriptional regulators in the VCS such as Irx3 and Nkx2-5. RNA-seq in these populations would provide a clearer comparison among the groups.<br /> (4) From the optical mapping data, it is difficult to distinguish between the presence of (1) a focal proximal right bundle branch block due to dysregulation of gene expression in the VCS but overall preservation of the right bundle and its distal ramifications; from (2) actual loss of the VCS with reversion of VCS cells to a working myocardial fate. Related to this, the authors claim that this experiment allows for direct visualization of His bundle activation, but can the authors confirm or provide evidence that the tissue penetration of their imaging modality allows for imaging of a deep structure like the AV bundle as opposed to the right bundle branch which is more superficial? Does the timing of the separation of the sharp deflection from the subsequent local activation suggest visualization of more distal components of the VCS rather than the AV bundle itself? Additional clarification would be helpful.

impact:

The present study contributes a novel and elegantly constructed mouse model to the field. The data presented generally corroborate existing models of transcriptional regulation in the VCS. Acknowledging that the present work is strong start, some additional studies not included in the present manuscript will be needed for this new mouse model to decisively advance the field of VCS transcriptional biology.

Joint Public Review:

In this manuscript, the authors aim to evaluate the robustness of stable asymmetric polarization patterns by analyzing both a minimal 2-node network and a more biologically realistic 5-node network based on the C. elegans polarization system. They introduce a computational pipeline for systematically exploring reaction-diffusion network dynamics. Their study highlights the limitations of the widely used 2-node antagonistic network, demonstrating its susceptibility to simple modifications that disrupt polarization. However, they show that polarization stability can be restored by combining multiple regulatory mechanisms, and that spatially varying kinetic parameters can fine-tune the interface position. The authors further investigate the 5-node network of C. elegans, identifying key parameters that enhance its robustness against perturbations. Their findings provide novel insights into the mechanisms that ensure stable polarization in biological systems.

The major strengths of this work lie in its rigorous computational approach and the clarity of its findings. The authors demonstrate that the widely used 2-node antagonistic network is highly sensitive to parameter changes, requiring precise fine-tuning to maintain stable polarization. However, they show that stability can be restored through compensatory modifications, which expand the range of parameter sets supporting polarization. By further exploring spatial parameter variations, the authors reveal how compensatory adjustments can stabilize polarization patterns, offering insights into potential biological mechanisms regulating interface localization.

Extending their analysis to the C. elegans polarization network, the authors construct a 5-node model grounded in an extensive literature review. Their computational pipeline identifies key parameters that enhance robustness, and their model successfully replicates experimental observations, even in mutant conditions. Notably, among 34 possible network structures, only the naturally evolved 5-node network with mutual inhibition between specific components maintains stable polarization, highlighting its evolutionary optimization. This work significantly advances our understanding of polarization maintenance and provides a valuable framework for future in silico experiments.

Despite its strengths, the study has some limitations related to simplifying assumptions. The model neglects cortical flows and the role of actomyosin dynamics, which are known to be crucial during the establishment phase of polarization in the C. elegans zygote. While the authors focus on the maintenance phase, the absence of these biomechanical effects may limit the model's applicability to the full polarization process. Additionally, the assumption of infinitely fast cytoplasmic diffusion disregards potential effects of cytoplasmic flows on the stability of molecular distributions. Experimental measurements suggest that cytoplasmic diffusion coefficients are only an order of magnitude higher than membrane diffusion coefficients, meaning that finite diffusion combined with cytoplasmic flows could influence polarization stability. Although the authors acknowledge and discuss these limitations, incorporating these effects in future models could provide a more complete picture of the polarization dynamics in C. elegans embryos.

Reviewer #1 (Public review):

Summary:

The manuscript by Egawa and colleagues investigates differences in nodal spacing in an avian auditory brain stem circuit. The results are clearly presented and data are of very high quality. The authors make two main conclusions:

(1) Node spacing, i.e. internodal length, is intrinsically specified by the oligodendrocytes in the region they are found in, rather than axonal properties (branching or diameter).

(2) Activity is necessary (we don't know what kind of signaling) for normal numbers of oligodendrocytes and therefore the extent of myelination.

These are interesting observations, albeit phenomenon. I have only a few criticisms that should be addressed:

(1) The use of the term 'distribution' when describing the location of nodes is confusing. I think the authors mean rather than the patterns of nodal distribution, the pattern of nodal spacing. They have investigated spacing along the axon. I encourage the authors to substitute node spacing or internodal length for node distribution.

(2) In Seidl et al. (J Neurosci 2010) it was reported that axon diameter and internodal length (nodal spacing) were different for regions of the circuit. Can the authors help me better understand the difference between the Seidl results and those presented here?

(3) The authors looked only in very young animals - are the results reported here applicable only to development, or does additional refinement take place with aging?

(4) The fact that internodal length is specified by the oligodendrocyte suggests that activity may not modify the location of nodes of Ranvier - although again, the authors have only looked during early development. This is quite different than this reviewer's original thoughts - that activity altered internodal length and axon diameter. Thus, the results here argue against node plasticity. The authors may choose to highlight this point or argue for or against it based on results in adult birds?:

Significance:

This paper may argue against node plasticity as a mechanism for tuning of neural circuits. Myelin plasticity is a very hot topic right now and node plasticity reflects myelin plasticity. this seems to be a circuit where perhaps plasticity is NOT occurring. That would be interesting to test directly. One limitation is that this is limited to development.

Reviewer #1 (Public review):

Summary:

Ma & Yang et al. report a new investigation aimed at elucidating one of the key nutrients S. Typhimurium (STM) utilizes with the nutrient-poor intracellular niche within macrophage, focusing on the amino acid beta-alanine. From these data, the authors report that beta-alanine plays important roles in mediating STM infection and virulence. The authors employ a multidisciplinary approach that includes some mouse studies, and ultimately propose a mechanism by which panD, involved in B-Ala synthesis, mediates regulation of zinc homeostatisis in Salmonella.

Strengths and weaknesses:

The results and model are adequately supported by the authors' data. Further work will need to be performed to learn whether the Zn2+ functions as proposed in their mechanism. By performing a small set of confirmatory experiments in S. Typhi, the authors provide some evidence of relevance to human infections.

Impact:

This work adds to the body of literature on the metabolic flexibility of Salmonella during infection that enable pathogenesis.

Reviewer #2 (Public Review):

Summary:

This paper describes a new approach to detecting directed causal interactions between two genes without directly perturbing either gene. To check whether gene X influences gene Z, a reporter gene (Y) is engineered into the cell in such a way that (1) Y is under the same transcriptional control as X, and (2) Y does not influence Z. Then, under the null hypothesis that X does not affect Z, the authors derive an equation that describes the relationship between the covariance of X and Z and the covariance of Y and Z. Violation of this relationship can then be used to detect causality.

The authors benchmark their approach experimentally in several synthetic circuits. In 4 positive control circuits, X is a TetR-YFP fusion protein that represses Z, which is an RFP reporter. The proposed approach detected the repression interaction in 2 of the 4 positive control circuits. The authors constructed 16 negative control circuit designs in which X was again TetR-YFP, but where Z was either a constitutively expressed reporter, or simply the cellular growth rate. The proposed method detected a causal effect in two of the 16 negative controls, which the authors argue is perhaps not a false positive, but due to an unexpected causal effect. Overall, the data support the potential value of the proposed approach.

Strengths:

The idea of a "no-causality control" in the context of detected directed gene interactions is a valuable conceptual advance that could potentially see play in a variety of settings where perturbation-based causality detection experiments are made difficult by practical considerations.

By proving their mathematical result in the context of a continuous-time Markov chain, the authors use a more realistic model of the cell than, for instance, a set of deterministic ordinary differential equations.

The authors have improved the clarity and completeness of their proof compared to a previous version of the manuscript.

Limitations:

The authors themselves clearly outline the primary limitations of the study: The experimental benchmark is a proof of principle, and limited to synthetic circuits involving a handful of genes expressed on plasmids in E. coli. As acknowledged in the Discussion, negative controls were chosen based on the absence of known interactions, rather than perturbation experiments. Further work is needed to establish that this technique applies to other organisms and to biological networks involving a wider variety of genes and cellular functions. It seems to me that this paper's objective is not to delineate the technique's practical domain of validity, but rather to motivate this future work, and I think it succeeds in that.

Might your new "Proposed additional tests" subsection be better housed under Discussion rather than Results?

I may have missed this, but it doesn't look like you ran simulation benchmarks of your bootstrap-based test for checking whether the normalized covariances are equal. It would be useful to see in simulations how the true and false positive rates of that test vary with the usual suspects like sample size and noise strengths.

It looks like you estimated the uncertainty for eta_xz and eta_yz separately. Can you get the joint distribution? If you can do that, my intuition is you might be able to improve the power of the test (and maybe detect positive control #3?). For instance, if you can get your bootstraps for eta_xz and eta_yz together, could you just use a paired t-test to check for equality of means?

The proof is a lot better, and it's great that you nailed down the requirement on the decay of beta, but the proof is still confusing in some places:

- On pg 29, it says "That is, dividing the right equation in Eq. 5.8 with alpha, we write the ..." but the next equation doesn't obviously have anything to do with Eq. 5.8, and instead (I think) it comes from Eq 5.5. This could be clarified.

- Later on page 29, you write "We now evoke the requirement that the averages xt and yt are stationary", but then you just repeat Eq. 5.11 and set it to zero. Clearly you needed the limit condition to set Eq. 5.11 to zero, but it's not clear what you're using stationarity for. I mean, if you needed stationarity for 5.11 presumably you would have referenced it at that step.

It could be helpful for readers if you could spell out the practical implications of the theorem's assumptions (other than the no-causality requirement) by discussing examples of setups where it would or wouldn't hold.

Reviewer #1 (Public review):

The manuscript by Rios et al. investigates the potential of GSK3 inhibition to reprogram human macrophages, exploring its therapeutic implications in conditions like severe COVID-19. The authors present convincing evidence that GSK3 inhibition shifts macrophage phenotypes from pro-inflammatory to anti-inflammatory states, thus highlighting the GSK3-MAFB axis as a potential therapeutic target. Using both GM-CSF- and M-CSF-dependent monocyte-derived macrophages as model systems, the study provides extensive transcriptional, phenotypic, and functional characterizations of these reprogrammed cells. The authors further extend their findings to human alveolar macrophages derived from patient samples, demonstrating the clinical relevance of GSK3 inhibition in macrophage biology.

The experimental design is sound, leveraging techniques such as RNA-seq, flow cytometry, and bioenergetic profiling to generate a comprehensive dataset. The study's integration of multiple model systems and human samples strengthens its impact and relevance. The findings not only offer insights into macrophage plasticity but also propose novel therapeutic strategies for macrophage reprogramming in inflammatory diseases.

Strengths:

(1) Robust Experimental Design: The use of both in vitro and ex vivo models adds depth to the findings, making the conclusions applicable to both experimental and clinical settings.

(2) Thorough Data Analysis: The extensive use of RNA-seq and gene set enrichment analysis (GSEA) provides a clear transcriptional signature of the reprogrammed macrophages.

(3) Relevance to Severe COVID-19: The study's focus on macrophage reprogramming in the context of severe COVID-19 adds clinical significance, especially given the relevance of macrophage-driven inflammation in this disease.

Weaknesses:

There are no significant weaknesses in the study.

Reviewer #1 (Public review):

Summary:

The topic of tumor-immune co-evolution is an important, understudied topic with, as the authors noted, a general dearth of good models in this space. The authors have made important progress on the topic by introducing a stochastic branching process model of antigenicity/immunogenicity and measuring the proportion of simulated tumors that go extinct. The model is extensively explored, and the authors provide some nice theoretical results in addition to simulated results.

Major comments

The text in lines 183-191 is intuitively and nicely explained. However, I am not sure all of it follows from the figure panels in Figure 2. For example, the authors refer to a mutation that has a large immunogenicity, but it's not shown how many mutations, or the relative size of the mutations in Figure 2. The same comment holds true for the claim that spikes also arise for mutations with low antigenicity.

Reviewer #1 (Public review):

Processing in the primary visual cortex (V1) of mice is not only based on sensory inputs but also strongly modulated by locomotion. In this study, Meier et al. ask whether neurons that are modulated by locomotion form clusters in V1. Their work is based on previous studies from their lab establishing a modularity in the organization of primary visual cortex based on M2-muscarinic-acetylcholine-receptor-positive patches and interpatches (Ji et al. 2015, D'Souza et al. 2019). In these studies, they have highlighted the clustering of specific visual pathways and inhibition. In the current study, they extend this modularity to motor inputs, confirming a clustering of locomotion modulated neurons but also show that these clusters overlap with the M2-negative interpatches of layer 1. Finally, they establish a blueprint for visual processing streams in V1, segregating projections to and from lateral visual areas (LM, AL, and RL) from projections to and from the lateral areas, including the visual area PM, the retrosplenial cortex (RSP), and the secondary motor area (MOs).

Conceptually, this study provides an important finding in the organization of locomotion-related signaling in primary visual cortex, which clearly has substantial implications for sensory processing in visual cortex. While the anatomical data are solid, the link to physiology is incomplete. In conclusion, there are numerous issues that leave the main findings in some doubt, so the authors have some work to do before I find this story convincing.

Major issues:

(1) The major results in this study rely on proper quantification of neuronal responses during resting and running. Recently, it has been reported that hemodynamic occlusion can strongly influence measurements of fluorescent changes using two-photon imaging (Yogesh et al. 2025, doi.org/10.1101/2024.10.29.620650). Since it is unclear whether there is an inherent bias in vasculature and hemodynamic occlusion in M2 patches and interpatches, a quantification of the effect of hemodynamic occlusion would be necessary. This control would ideally be done using mice with GFP expression to test if there is still a clustering of locomotion-modulated neurons that overlaps with M2-negative interpatches. Alternatively, the authors should at the very least quantify the vascularization in M2 patches and interpatches.

(2) To assess the effects, the authors use a correlation analysis for many of their findings (e.g., Figures 2b,c, 4j,k, ...). This, however, is inappropriate to assess the significance of the results. I suggest redoing all statistics with hierarchical bootstrap sampling (Saravanan et al. 2020, PMID: 33644783) or similar.

(3) The authors use two different measures to assess whether and to what extent a neuron is locomotion sensitive, the LMI and "locomotion-responsive". While the LMI is defined based on recording in the light and dark (Figure 2), the "locomotion-responsiveness" is defined only in the dark (Figure 3a,c,d). The link between the two measures should be clarified.

a) Additionally, Figure 2b shows higher average LMI for interpatches, but the locomotion-responsive fraction is similar in interpatches and patches (relative number of pairs in Figure 3c and Figure 3d). How do the authors explain this discrepancy?

b) How is the LMI calculated - based on the average or the maximum response over stimuli? One particular stimulus? If the LMI is defined for each stimulus separately, what is plotted in Figure 2b?

(4) In the last panels of Figures 4-7, the authors analyze the alignment of cell bodies with the M2 patches. While in superficial layers it might be straightforward to align the cell body locations with the M2 patches and interpatches in layer 1, this alignment does not appear to be trivial for deeper layers. The authors should provide additional material to convince the reader of the proper alignment.

(5) Related to point 4 above - Given the importance of a proper alignment of M2 patches with the in vivo imaging, the in vivo - ex vivo alignment should be more convincing than Figure 1 C-E. Measuring M2 patches in vivo (as the authors have tried to do) would have provided more solid evidence. Have the authors tried to remove the dura for their in vivo imaging to increase signal-to-noise? In any case, more examples of proper alignment are necessary.

(6) The authors state that locomotion selectively affects M2-/M2- pairs based on Figure 3c. However, to make this claim, there should be a significant difference between the correlation of stimulus-driven noise of M2-/M2- locomotion-responsive pairs and M2-/M2- locomotion-unresponsive pairs, AND no significant difference in the same analysis for M2+/M2+ pairs (i.e., testing the differences between the bars in Figure 3c and Figure 3d).

Reviewer #1 (Public review):

Summary:

The authors use a sophisticated task design and Bayesian computational modeling to test their hypothesis that information generalization (operationalized as a combination of self-insertion and social contagion) in social situations is disrupted in Borderline Personality Disorder. Their main finding relates to the observation that two different models best fit the two tested groups: While the model assuming both self-insertion and social contagion to be present when estimating others' social value preferences fit the control group best, a model assuming neither of these processes provided the best fit to BPD participants.

Strengths:

The revisions have substantially strengthened the paper and the manuscript is much clearer and easier to follow now. The strengths of the presented work lie in the sophisticated task design and the thorough investigation of their theory by use of mechanistic computational models to elucidate social decision-making and learning processes in BPD.

Weaknesses:

Some critical concerns remain after the first revision, particularly regarding the use of causal language and the clarity of the hypotheses and results, specified in the points below.

(1) The authors frequently refer to their predictions and theory as being causal, both in the manuscript and in their response to reviewers. However, causal inference requires careful experimental design, not just statistical prediction. For example, the claim that "algorithmic differences between those with BPD and matched healthy controls" are "causal" in my opinion is not warranted by the data, as the study does not employ experimental manipulations or interventions which might predictably affect parameter values. Even if model parameters can be seen as valid proxies to latent mechanisms, this does not automatically mean that such mechanisms cause the clinical distinction between BPD and CON, they could plausibly also refer to the effects of therapy or medication. I recommend that such causal language, also implicit to expressions like "parameter influences on explicit intentional attributions", is toned down throughout the manuscript.

(2) Although the authors have now much clearer outlined the stuy's aims, there still is a lack of clarity with respect to the authors' specific hypotheses. I understand that their primary predictions about disruptions to self-other generalisation processes underlying BPD are embedded in the four main models that are tested, but it is still unclear what specific hypotheses the authors had about group differences with respect to the tested models. I recommend the authors specify this in the introduction rather than refering to prior work where the same hypotheses may have been mentioned.

(3) Caveats should also be added about the exploratory nature of the many parameter group comparisons. If there are any predictions about group differences that can be made based on prior literature, the authors should make such links clear.

(4) I'm not sure I understand why the authors, after adding multiple comparison correction, now list two kinds of p-values. To me, this is misleading and precludes the point of multiple comparison corrections, I therefore recommend they report the FDR-adjusted p-values only. Likewise, if a corrected p-value is greater than 0.05 this should not be interpreted as a result.

(5) Can the authors please elaborate why the algorithm proposed to be employed by BPD is more 'entropic', especially given both their self-priors and posteriors about partners' preferences tended to be more precise than the ones used by CON? As far as I understand, there's nothing in the data to suggest BPD predictions should be more uncertain. In fact, this leads me to wonder, similarly to what another reviewer has already suggested, whether BPD participants generate self-referential priors over others in the same way CON participants do, they are just less favourable (i.e., in relation to oneself, but always less prosocial) - I think there is currently no model that would incorporate this possibility? It should at least be possible to explore this by checking if there is any statistical relationship between the estimated θ_ppt^m and 〖p(θ〗_par |D^0).

"To note, social contagion under M3 was highly correlated with contagion under M1 (see Fig S11). This provides some preliminary evidence that trauma impacts beliefs about individualism directly, whereas trauma and persecutory beliefs impact beliefs about prosociality through impaired trait mentalising" - I don't understand what the authors mean by this, can they please elaborate and add some explanation to the main text?

Reviewer #2 (Public review):

Summary:

Demonstrate the breadth of IgA response as determined by isolating individual antigen-specific B cells and generating mAbs in mice following intranasal immunization of mice with SARS-CoV2 Spike protein. The findings show that some IgA mAb can neutralize the virus, but many do not. Notable immunization with Wuhan S protein generates a weak response to the omicron variant.

Strengths:

Detailed analysis characterizing individual B cells with the generation of mAbs demonstrates the response's breadth and diversity of IgA responses and the ability to generate systemic immune responses.

Comments on Revision:

I have re-reviewed the paper and responses to my and other reviewers' comments. I feel the authors have adequately addressed my and other reviewer's comments.

Reviewer #1 (Public review):

Summary:

Goal: Find downstream targets of cmk-1 phosphorylation, identify one that also seems to act in thermosensory habituation, test for genetic interactions between cmk-1 and this gene and assess where these genes are acting in the thermosensory circuit during thermosensory habituation.

Methods: Two in vitro analyses of cmk-1 phosphorylation of C. elegans proteins. Thermosensory habituation of cmk-1 and tax-6 mutants and double mutants was assessed by measuring rate of heat evoked reversals (reversal probability) of C. elegans before and after 20s ISI repeated heat pulses over 60 minutes.

Conclusions: cmk-1 and tax-6 act in separate habituation processes primarily in AFD, that interact complexly, but both serve to habituate the thermosensory reversal response. They found that cmk-1 primarily acts in AFD and tax-6 primarily acts in RIM (and FLP for naïve responses). They also identified hundreds of potential cmk-1 phosphorylation substrates in vitro.

Strengths:

The effects size in the genetic data is quite strong and a large number of genetic interaction experiments between cmk-1 and tax-1 demonstrate a complex interaction.

A major concern concerning this manuscript was the assumption that the process they are observing is habituation. The two previously cited papers using this (or a very similar) protocol, Lia and Glauser 2020 and Jordan and Glauser 2023, both use the word 'adaptation' to describe the observed behavioral decrement. Jordan and Glauser 2023 does occasionally use the words 'habituation' or 'habituation-like' 10 times, however it uses 'adaptation' over 100 times. It is critical to distinguish habituation from sensory adaptation (or fatigue) in this thermal reversal protocol. These processes are often confused/conflated, however they are very different; sensory adaptation is a process that decreases how much the nervous system is activated by a repeated stimulus, therefore it can even occur outside of the nervous system. Habituation is a learning process where the nervous system responds less to a repeated stimulus, despite (at least part of the nervous system) the nervous system still being similarly activated by the stimulus. Habituation is considered an attentional process, while adaptation is due to fatigue of sensory transduction machinery. Control experiments such as tests for dishabituation (where application of a different stimulus causes recovery of the decremented response) or rate of spontaneous recovery (more rapid recovery after short inter-stimulus intervals) are required to determine if habituation or sensory adaptation are occurring. These experiments will allow the results to be interpreted with clarity; without them, it isn't actually clear what biological process is actually being studied. The authors have accepted this distinction and now correctly call the process adaptation.

While there was originally some discrepancy between the two in vitro phosphorylation experiments and the in silico predictions, the revision has cleared up the issues.<br /> Figure 3 -S1: This model has been adjusted to more closely fit the data.

The authors have expanded the discussion about the significance of the sites of cmk-1 and tax-6 function in the neural circuit.

Reviewer #1 (Public review):

Summary:

This manuscript described a structure-guided approach to graft important antigenic loops of the neuraminidase to a homotypic but heterologous NA. This approach allows the generation of well-expressed and thermostable recombinant proteins with antigenic epitopes of choice to some extent. The loop-grafted NA was designated hybrid.

Strengths:

The hybrid NA appeared to be more structurally stable than the loop-donor protein while acquiring its antigenicity. This approach is of value when developing a subunit NA vaccine which is difficult to express. So that antigenic loops could be potentially grafted to a stable NA scaffold to transfer strain-specific antigenicity.

Reviewer #1 (Public review):

Summary:

This manuscript by Kremer et al. characterizes the tissue-specific responses to changes in TFAM levels and mtDNA copy number in prematurely aging mice (polg mutator model). The authors find that overexpression of TFAM can have beneficial or detrimental effects depending on the tissue type. For instance, increased TFAM levels increase mtDNA copy number in the spleen and improve spleen homeostasis but do not elevate mtDNA copy number in the liver and impair mtDNA expression. Similarly, the consequences of reduced TFAM expression are tissue-specific. Reduced TFAM levels improve brown adipocyte tissue function while other tissues are unaffected. The authors conclude that these tissue-specific responses to altered TFAM levels demonstrate that there are tissue-specific endogenous compensatory mechanisms in response to the continuous mutagenesis produced in the prematurely aging mice model, including upregulation of TFAM expression, elevated mtDNA copy number, and altered mtDNA gene expression. Thus, the impact of genetically manipulating global TFAM expression is limited and there must be other determinants of mtDNA copy number under pathological conditions beyond TFAM.

Strengths:

Overall, this is an interesting study. It does a good job of demonstrating that given the multi-functional role of TFAM, the outcome of manipulating its activity is complex.

Weaknesses:

No major weaknesses noted. The authors have adopted all our suggestions to improve the clarity of the manuscript.

Reviewer #1 (Public review):

Summary:

In this paper Kawasaki et al describe a regulatory role for the PIWI/piRNA pathway in rRNA regulation in Zebrafish. This regulatory role was uncovered through a screen for gonadogenesis defective mutants, which identified a mutation in the meioc gene, a coiled-coil germ granule protein. Loss of this gene leads to redistribution of Piwil1 from germ granules to the nucleolus, resulting in silencing of rRNA transcription.

Strengths:

Most of the experimental data provided in this paper is compelling. It is clear that in the absence of meioc, PiwiL1 translocates in to the nucleolus and results in down regulation of rRNA transcription. the genetic compensation of meioc mutant phenotypes (both organismal and molecular) through reduction in PiwiL1 levels are evidence for a direct role for PiwiL1 in mediating the phenotypes of meioc mutant.

Weaknesses:

Questions remain on the mechanistic details by which PiwiL1 mediated rRNA down regulation, and whether this is a function of Piwi in an unperturbed/wildtype setting. There is certainly some evidence provided in support of the a natural function for piwi in regulating rRNA transcription (figure 5A+5B). However, the de-enrichment of H3K9me3 in the heterozygous (Figure 6F) is very modest and in my opinion not convincingly different relative to the control provided. It is certainly possible that PiwiL1 is regulating levels through cleavage of nascent transcripts. Another aspect I found confounding here is the reduction in rRNA small RNAs in the meioc mutant; I would have assumed that the interaction of PiwiL1 with the rRNA is mediated through small RNAs but the reduction in numbers do not support this model. But perhaps it is simply a redistribution of small RNAs that is occurring. Finally, the ability to reduce PiwiL1 in the nucleolus through polI inhibition with actD and BMH-21 is surprising. What drives the accumulation of PiwiL1 in the nucleolus then if in the meioc mutant there is less transcription anyway?

Despite the weaknesses outlined, overall I find this paper to be solid and valuable, providing evidence for a consistent link between PIWI systems and ribosomal biogenesis. Their results are likely to be of interest to people in the community, and provide tools for further elucidating the reasons for this link.

Reviewer #1 (Public Review):

The study starts with the notion that in an AD-like disease model, ILC2s in the Rag1 knock-out were expanded and contained relatively more IL-5+ and IL-13+ ILC2s. This was confirmed in the Rag2 knock-out mouse model.

By using a chimeric mouse model in which wild-type knock-out splenocytes were injected into irradiated Rag1 knock-out mice, it was shown that even though the adaptive lymphocyte compartment was restored, there were increased AD-like symptoms and increased ILC2 expansion and activity. Moreover, in the reverse chimeric model, i.e. injecting a mix of wild-type and Rag1 knock-out splenocytes into irradiated wild-type animals, it was shown that the Rag1 knock-out ILC2s expanded more and were more active. Therefore, the authors could conclude that the RAG1 mediated effects were ILC2 cell-intrinsic.

Subsequent fate-mapping experiments using the Rag1Cre;reporter mouse model showed that there were indeed RAGnaïve and RAGexp ILC2 populations within naïve mice. Lastly, the authors performed multi-omic profiling, using single-cell RNA sequencing and ATAC-sequencing, in which a specific gene expression profile was associated with ILC2. These included well-known genes but the authors notably also found expression of Ccl1 and Ccr8 within the ILC2. The authors confirmed their earlier observations that in the RAGexp ILC2 population, the Th2 regulome was more suppressed, i.e. more closed, compared to the RAGnaïve population, indicative of the suppressive function of RAG on ILC2 activity. I do agree with the authors' notion that the main weakness was that this study lacks the mechanism by which RAG regulates these changes in ILC2s.

The manuscript is very well written and easy to follow, and the compelling conclusions are well supported by the data. The experiments are meticulously designed and presented. I wish to commend the authors for the study's quality.

Reviewer #1 (Public review):

Summary:

The authors aimed to classify hepatocellular carcinoma (HCC) patients into distinct subtypes using a comprehensive multi-omics approach. They employed an innovative consensus clustering method that integrates multiple omics data types, including mRNA, lncRNA, miRNA, DNA methylation, and somatic mutations. The study further sought to validate these subtypes by developing prognostic models using machine learning algorithms and extending the findings through single-cell RNA sequencing (scRNA-seq) to explore the cellular mechanisms driving subtype-specific prognostic differences.

Strengths:

(1) Comprehensive Data Integration: The study's integration of various omics data provides a well-rounded view of the molecular characteristics underlying HCC. This multi-omics approach is a significant strength, as it allows for a more accurate and detailed classification of cancer subtypes.

(2) Innovative Methodology: The use of a consensus clustering approach that combines results from 10 different clustering algorithms is a notable methodological advancement. This approach reduces the bias that can result from relying on a single clustering method, enhancing the robustness of the findings.

(3) Machine Learning-Based Prognostic Modeling: The authors rigorously apply a wide array of machine learning algorithms to develop and validate prognostic models, testing 101 different algorithm combinations. This comprehensive approach underscores the study's commitment to identifying the most predictive models, which is a considerable strength.

(4) Validation Across Multiple Cohorts: The external validation of findings in independent cohorts is a critical strength, as it increases the generalizability and reliability of the results. This step is essential for demonstrating the clinical relevance of the proposed subtypes and prognostic models.

Weaknesses:

(1) Inconsistent Storyline:<br /> Despite the extensive data mining and rigorous methodologies, the manuscript suffers from a lack of a coherent and consistent narrative. The transition between different sections, particularly from multi-omics data integration to single-cell validation, feels disjointed. A clearer articulation of how each analysis ties into the overall research question would improve the manuscript.

(2) Questionable Relevance of Immune Cell Activity Analysis:<br /> The evaluation of immune cell activities within the cancer cell model raises concerns about its meaningfulness. The methods used to assess immune function in the tumor microenvironment may not be fully appropriate, potentially limiting the insights gained from this part of the study.

(3) Incomplete Single-Cell RNA-Seq Validation:<br /> The validation of the findings using single-cell RNA-seq data appears insufficient to fully support the study's claims. While the authors make an effort to extend their findings to the single-cell level, the analysis lacks depth. A more comprehensive validation is necessary to substantiate the robustness of the identified subtypes.

(4) Figures and Visualizations:<br /> Several figures in the manuscript are missing necessary information, which affects the clarity of the results. For instance, the pathways in Figure 3A could be clustered to enhance interpretability, the blue bar in Figure 4A is unexplained, and Figure 4B is not discussed in the text. Additionally, the figure legend in Figure 7C lacks detail, and many figure descriptions merely repeat the captions without providing deeper insights.

(5) Appraisal of the Study's Aims and Results<br /> The authors have set out to achieve an ambitious goal of classifying HCC patients into distinct prognostic subtypes and validating these findings through both bulk and single-cell analyses. While the methodologies employed are innovative and the data integration comprehensive, the study falls short in fully achieving its aims due to inconsistencies in the narrative and incomplete validation. The results partially support the conclusions, but the lack of coherence and depth in certain areas limits the overall<br /> impact of the study.

(6) Impact on the Field<br /> If the identified weaknesses are addressed, this study has the potential to significantly impact the field of HCC research. The multi-omics approach combined with machine learning is a powerful framework that could set a new standard for cancer subtype classification. However, the current state of the manuscript leaves some uncertainty regarding the practical applicability of the findings, particularly in clinical settings.

(7) Additional Context<br /> For readers and researchers, this study offers a valuable look into the potential of integrating multi-omics data with machine learning to improve cancer classification and prognostication. However, readers should be aware of the noted weaknesses, particularly the need for more consistent narrative development and comprehensive validation of the methods. Addressing these issues could greatly enhance the study's utility and relevance to the community.

Comments on revisions:

The authors have addressed the reviewers' concerns effectively.

Reviewer #1 (Public review):

Summary:

The authors propose a new method to quantitatively assess morphogenetic processes during organismal development. They apply their method to ascidian morphogenesis and thus find that gastrulation is a two-step process.

The method applies to morphogenetic changes of surfaces. It consists of the following steps: first, surface deformations are quantified based on microscopy images without requiring cellular segmentation and tracking. This is achieved by mapping, at each time point, a polygonal mesh initially defined on a sphere to the surface of the embryo. The mapped vertices of this polygonal mesh then serve as (Lagrangian) markers for the embryonic surface. From these, one can infer the deformation of the surface, which can be expressed in terms of the strain tensor at each point of the surface. Changes in the strain tensor give the strain rate, which captures the morphogenetic processes. Second, at each time point, the strain rate field is decomposed in terms of spherical harmonics. Finally, the evolution of the weights of the various spherical harmonics in the decomposition is analysed via a wavelet analysis. The authors apply their workflow to ascidian development between 4 and 8.7 hpf. From their analysis they find clear indications for gastrulation and neurulation and identify two sub-phases of gastrulation, namely, endoderm invagination and 'blastophore closure'.

Strengths:

The combination of various tools allows the authors to obtain a quantitative description of the developing embryo without the necessity of identifying fiducial markers. Visual inspection shows that their method works well. Furthermore, this quantification then allows for an unbiased identification of different morphogenetic phases.

Weaknesses:

At times, the explanation of the method is hard to follow, unless the reader is already familiar with concepts like level-set methods or wavelet transforms. Furthermore, the software for performing the determination of Lagrangian markers or the subsequent spectral analysis does not seem to be available to the readers.

Reviewer #2 (Public review):

The revised manuscript by Genzoni et al. reports the striking discovery of a regulatory role for trophic eggs. Prior to this study, trophic eggs were widely assumed to play a nutritional role in the colony, but this study shows that trophic eggs can suppress queen development, and therefore, can play a role in regulating caste determination in specific social contexts. In this revised version of the manuscript, the authors have addressed many of the concerns raised in the first version regarding the lack of sufficient information and context in the Introduction and Discussion. I have several (mostly minor) comments I would like the authors to address:

Comments:

(1) The authors' experimental design is based on the comparison of a larva-only (control) versus larva+3 trophic eggs (treatment). The authors convincingly show that the larva plus 3 trophic eggs treatment has an inhibitory effect versus larva-only control. However, the authors should have also done a treatment composed of larva + 3 viable eggs to determine if the inhibitory effect observed on queens is specific to trophic eggs or whether it is an inhibitory effect of all eggs. This has had important mechanistic consequences, because if the inhibitory effect is specific to trophic eggs, it means there are specific inhibitory factors deposited in trophic eggs during oogenesis and the differences observed between trophic versus viable eggs are meaningful beyond just nutritional differences. If the inhibitory effect is a property of all eggs, then the inhibitory factor is dumped into all eggs and the differences observed between trophic and viable eggs are related to something else. In all cases, this reviewer is not necessarily asking that they perform this additional treatment, but the authors have to be clear in the text that they cannot claim that the inhibitory effect is specific to trophic eggs alone without doing this experiment.

(2) The other untested assumption the authors are making is that queen-laid trophic eggs would behave the same as worker-laid trophic eggs. This is apparent in the Discussion (line 422). They should instead highlight the interesting question of whether worker-laid trophic eggs would be similar in composition and have the same effect on caste as queen-laid eggs.

(3) To this reviewer, they are missing a crucial explanation in the discussion. As far as this reviewer knows, young queens produce a higher proportion of trophic eggs than older queens, meaning that trophic egg production decreases with age of the queen. This raises the possibility that trophic eggs may, in part, function to prevent the production of more virgin queens in young and immature colonies with small colony sizes. This would allow colonies to invest in producing more workers at a time when rapidly expanding the colony is crucial in young colonies' life. Production of trophic eggs, therefore, may have a dual function: one for nutrition and larval survival, and one in suppressing queen development in immature young colonies. It can be said then that trophic eggs can regulate / influence caste determination in specific social / life history contexts of the colony, rather than only proposing that trophic eggs are a constant attempt by the queen to manipulate her offspring. I prefer the superorganism explanation, but readers should at least hear explanations at the individual and superorganism scales as a way of explaining the authors' discovery that trophic eggs suppress further queen development.

(4) Why did the authors change the wording from caste "determination" to caste "differentiation." Determination is more appropriate because the trophic eggs do not affect morphogenesis of queens or workers, but rather the developmental switch between queens and workers.

(5) Khila and Abouheif (2008) is listed in the References but not cited in the text.

(6) On Line 70-81: "...may play a role in the regulation of body size" - I think the authors are trying to be broad in their language here since one study showed trophic eggs increased worker size but didn't induce queens, but this statement implies that the hypothesis is that trophic eggs act via body size to affect caste. Since the authors don't measure body size changes, only binary caste outcome, this is not the best way to set up the question. Could instead just conclude that previous work shows an effect on both caste and body size.

(7) Paragraph beginning line 432: this paragraph seems out of place, not well connected to previous parts of discussion. It introduces the term "egg cannibalism" without defining it - not clear if this is meant as a synonym for eating of trophic eggs, or broader (i.e., eating viable eggs also). Could either remove the paragraph, or better set up the context that egg-eating behaviour is common in ants, could have evolved for worker policing reasons and/or for nutritional exchange, trophic eggs (and potentially co-option of trophic eggs for caste determination functions) presumably evolved in this context of existing egg-eating behaviour.

(8) Line 41: Should read 'play an important part.

(9) Line 51: The food that was given is listed, but there is no information about the quantity of food given.

(10) Line 74: The paragraph states that queens were isolated for 16 hours per day. However, it lacks a clear reason for this specific duration. Why 16 hours? Could this isolation period have impacted egg quality or larval development?

(11) Line 76: The eggs were collected every 8 hours and then held for 10 days until hatching. This is a very long time for eggs to be held outside of the normal colony environment. This could have a large impact on the viability of the eggs, and the resulting larvae.

(12) Line 78: twice "that" in "suggested that that the larger castes"

(13) Lines 96-97: the following sentence is unclear: "The question mark indicates that it is unclear whether about the evidence for the production trophic eggs by queens and workers"

(14) Line 209: By simply stating "binomial GLMM," the authors are leaving out a crucial piece of information. Readers cannot fully understand how the model was fitted or how the coefficients should be interpreted without knowing the link function. Therefore, the critique is that for complete and replicable science, the link function must be reported.

Reviewer #1 (Public review):

Summary:

The authors' stated aim is to introduce so-called Minkowski tensors to characterize and quantify the shape of cells in tissues. The authors introduce Minkowski tensors and then define the p-atic order q_p, where p is an integer, as a cell shape measure. They also introduce a previously defined measure of p-atic order in the form of the parameter γ_p. The authors compute q_pp for data obtained by simulating an active vertex model and a multiphase field model, where they focus on p=2 and p=6 - nematic and hexatic order - as the two values of highest biological relevance. Based on their analysis, the authors claim that q₂ and q₆ are independent, that there is no crossover for the coarse-grained quantities, that the comparison of q_p for different values of p is not meaningful, and determine the dependence of the mean value of q₂ and q₆q₆ on cell activity and deformability. They then apply their method to data from MDCK monolayers and argue that the γ_p "fail to capture the nuances of irregular cell shapes".

Strength:

The work presents a set of parameters that are useful for analyzing cell shape.

Weaknesses:

The main weakness of the manuscript is that the points that the authors make are not sufficiently elaborated or supported by the data. Although they start out with Minkowski tensors, they eventually only consider the parameters q_p, which can be defined without any recourse to Minkowski tensors. Also, I dare to doubt that the average reader will benefit from the introduction to Minkowski tensors as it remains abstract and does not really go beyond repeating definitions. Eventually, for me, the work boils down to the statement that when you want to characterize (2d) cell shape, then it is better to take the whole cell contour instead of only the positions of the vertices of a polygon that approximates the full cell shape. By the way, for polygons, the q_p and γ_p should convey the same information as the vertex positions contain the whole geometric information.

Some statements made about the values of q_p are not supported by the data. For example, an independence of values of q₂ and q₆ cannot be inferred from Figure 7. Actually, Figure 8 points to some dependence between these values as the peaks of the pdfs move in the opposite direction as deformability and activity are changed. Figure 1 suggests that in general, larger cells have lower values of q_p for all p. Some more serious quantification should be obtained here.

The presented experimental data on MDCK cells is anecdotal.

Reviewer #1 (Public review):

Summary:

In recent years, it has become increasingly evident how beautifully intricate IAC are at the nanoscale. Studies like the one presented here that shed light on the precise inner organisation of IAC are thus quite important and relevant in order to obtain a better in-depth understanding of IAC functioning and the contribution of different integrin subtypes to cell adhesive and mechanotransductive processes.

Interestingly, the authors found a distinct localisation of α5β1 and αVβ3 integrin nanoclusters within focal adhesion of human fibroblasts, with α5β1 integrin nanoclusters being at the periphery of IAC and αVβ3 integrin nanoclusters randomly distributed. Furthermore, a surprisingly high percentage of inactive integrins within IAC and relatively low spatial integrin colocalisation with adaptor proteins has been shown.

Strengths:

This is a very thoroughly performed STORM-based assessment of the nanodistribution of α5β1 and αVβ3 nanoclusters within IAC (and outside). The image quality is outstanding, and the authors have meticulously executed the experiments and the image analyses.

Weaknesses:

The only weakness is maybe that the manuscript remains descriptive. However, the high quality of the "description" of the nano-organisation of IAC by this scrupulous study is really important to better understand the inner workings of IAC. It provides a very solid foundation to look deeper into the (patho)physiological implications of this organisation, see recommendations (which are rather suggestions in this case).

Reviewer #1 (Public review):

Summary:

Early and accurate diagnosis is critical to treating N. fowleri infections, which often lead to death within 2 weeks of exposure. Current methods-sampling cerebrospinal fluid are invasive, slow, and sometimes unreliable. Therefore, there is a need for a new diagnostic method. Russell et al. address this need by identifying small RNAs secreted by Naegleria fowleri (Figure 1) that are detectable by RT-qPCR in multiple biological fluids including blood and urine. SmallRNA-1 and smallRNA-2 were detectable in plasma samples of mice experimentally infected with 6 different N. fowleri strains, and were not detected in uninfected mouse or human samples (Figure 4). Further, smallRNA-1 is detectable in the urine of experimentally infected mice as early as 24 hours post-infection (Figure 5). The study culminates with testing human samples (obtained from the CDC) from patients with confirmed N. fowleri infections; smallRNA-1 was detectable in cerebrospinal fluid in 6 out of 6 samples (Figure 6B), and in whole blood from 2 out of 2 samples (Figure 6C). These results suggest that smallRNA-1 could be a valuable diagnostic marker for N. fowleri infection, detectable in cerebrospinal fluid, blood, or potentially urine.

Strengths:

This study investigates an important problem, and comes to a potential solution with a new diagnostic test for N. fowleri infection that is fast, less invasive than current methods, and seems robust to multiple N. fowleri strains. The work in mice is convincing that smallRNA1 is detectable in blood and urine early in infection. Analysis of patient blood samples suggest that whole blood (but not plasma) could be tested for smallRNA-1 to diagnose N. fowleri infections.

Weaknesses:

(1) There are not many N. fowleri cases, so the authors were limited in the human samples available for testing. It is difficult to know how robust this biomarker is in whole blood (only 2 samples were tested, both had detectable smallRNA-1), serum (1 out of 1 sample tested negative), or human urine (presumably there is no material available for testing). This limitation is openly discussed in the last paragraph of the discussion section.

(2) There seems to be some noise in the data for uninfected samples (Figures 4B-C, 5B, and 6C), especially for those with serum (2E). While this is often orders of magnitude lower than the positive results, it does raise questions about false positives, especially early in infection when diagnosis would be the most useful. A few additional uninfected human samples may be helpful.