Reviewer #1 (Public review):

Summary:

Praegel et al. explore the differences in learning an auditory discrimination task between adolescent and adult mice. Using freely-moving (Educage) and head-fixed paradigms, they compare behavioral performance and neuronal responses over the course of learning. The mice were initially trained for seven days on an easy pure frequency tone Go/No-go task (frequency difference of one octave), followed by seven days of a harder version (frequency difference of 0.25 octave). While adolescents and adults showed similar performance on the easy task, adults performed significantly better on the harder task. Quantifying the lick bias of both groups, the authors then argue that the difference in performance is not due to a difference in perception, but rather to a difference in cognitive control. The authors then used neuropixel recordings across 4 auditory cortical regions to quantify the neuronal activity related to the behavior. At the single cell level, the data shows earlier stimulus-related discrimination for adults compared to adolescents in both the easy and hard tasks. At the neuronal population level, adults displayed a higher decoding accuracy and lower onset latency in the hard task as compared to adolescents. Such differences were not only due to learning, but also to age as concluded from recordings in novice mice. After learning, neuronal tuning properties had changed in adults but not in adolescent. Overall, the differences between adolescent and adult neuronal data correlates with the behavior results in showing that learning a difficult task is more challenging for younger mice.

Strengths:

- The behavioral task is well designed, with the comparison of easy and difficult tasks allowing for a refined conclusion regarding learning across age. The experiments with optogenetics and novice mice are completing the research question in a convincing way.<br /> - The analysis, including the systematic comparison of task performance across the two age groups, is most interesting, and reveals differences in learning (or learning strategies?) that are compelling.<br /> - Neuronal recording during both behavioral training and passive sound exposure is particularly powerful, and allows interesting conclusions.

Weaknesses:<br /> - The presentation of the paper must be strengthened. Inconsistencies, missing information or confusing descriptions should be fixed.<br /> - The recording electrodes cover regions in the primary and secondary cortices. It is well known that these two regions process sounds quite differently (for example, one has tonotopy, the other not), and separating recordings from both regions is important to conclude anything about sound representations. The authors show that the conclusions are the same across regions for Figure 4, but is it also the case for the subsequent analysis? Comparing to the original manuscript, the authors have now done the analysis for AuDp and AUDv separately, and say that the differences are similar in both regions. The data however shows that this is not the case (Fig S7). And even if it were the case, how would it compatible with the published literature?

Reviewer #2 (Public review):

Summary:

The authors aimed to find out how and how well adult and adolescent mice discriminate tones of different frequencies and whether there are differences in processing at the level of the auditory cortex that might explain differences in behavior between the two groups. Adolescent mice were found to be worse at sound frequency discrimination than adult mice. The performance difference between the groups was most pronounced when the sounds are close in frequency and thus difficult to distinguish and could, at least in part, be attributed to the younger mice' inability to withhold licking in no-go trials. By recording the activity of individual neurons in the auditory cortex when mice performed the task or were passively listening as well as in untrained mice the authors identified differences in the way that the adult and adolescent brains encode sounds and the animals' choice that could potentially contribute to the differences in behavior.

Strengths:

The study combines behavioural testing in freely-moving and head-fixed mice, optogenetic manipulation and high density electrophysiological recordings in behaving mice to address important open questions about age differences in sound-guided behavior and sound representation in the auditory cortex.

Weaknesses:

For some of the analyses that the authors conducted it is unclear what the rationale behind them is and, consequently, what conclusion we can draw from them.

Reviewer #1 (Public review):

Summary:

Both flies and mammals have D1-like and D2-like dopamine receptors, yet the role of D2-like receptors in Drosophila learning and memory remains underexplored. This paper investigates the role of the D2-like dopamine receptor D2R in single pairs of dopaminergic neurons (DANs) during single-odor aversive learning in the Drosophila larva. First, confocal imaging is used to screen GAL4 driver strains that drive GFP expression in just single pairs of dopaminergic neurons. Next, thermogenetic manipulations of one pair of DANs (DAN-c1) suggest that DAN-c1 activity during larval aversive learning is important. Confocal imaging is then used to reveal expression of D2R in the DANs and mushroom body of the larval brain. Finally, optogenetic activation during training phenocopies D2R knockdown in these neurons: aversive learning is impaired when DAN-c1 is targeted, while appetitive and aversive learning are impaired when the mushroom body is manipulated. Finally, a model is proposed in which D2R limits excessive dopamine release to facilitate successful olfactory learning.

Strengths:

The paper convincingly reproduces prior findings that demonstrated D2R knockdown in DL1 DANs or the mushroom body impairs aversive olfactory learning in Drosophila larvae (Qi and Lee, 2014; doi:10.3390/biology3040831). These previous findings were built upon and extended with a comprehensive confocal imaging screen of 57 GAL4 drivers that identified tools driving GFP expression in individual DANs. One of the drivers, R76F02-AD; R55C10-DBD, was consistently shown to label DAN-c1 neurons and no other DANs in the larval brain. Confocal imaging is also used to demonstrate that GFP-tagged D2R is expressed in most DANs and the mushroom body. Behavioral experiments demonstrate that driving D2R knockdown in DAN-c1 neurons impairs aversive learning, as do other loss-of-function manipulations of DAN-c1 neurons.

Limitations:

(1) The single-odor paradigm used to train larvae does not have the advantages of a more conventional balanced or reciprocal training paradigm. The paper describes how the single-odor experimental design could be controlled for non-associative effects, but does not provide an independent validation of the control experiments performed by a different research group using different odors and genotypes 15 to 20 years ago (see Honjo and Furukubo-Tokunaga, 2005; doi:10.1523/jneurosci.2135-05.2005 and Honjo and Furukubo-Tokunaga, 2009; doi:10.1523/jneurosci.1315-08.2009). Whether the involvement of DAN-c1 for aversive learning generalizes to standard paradigms remains unclear (see Eschbach et al., 2020; doi:10.1038/s41593-020-0607-9 and Weber et al., 2023; doi:10.7554/elife.91387.1).

(2) In 11 of 22 larval brains examined in the paper, R76F02-AD; R55C10-DBD appears to drive GFP expression in 1 to 8 additional non-dopaminergic neurons (Figure S1P and Table S3). Of the remaining 11 brains, 4 of their corresponding ventral nerve cords also have expression in 2 to 4 neurons (Table S3). Therefore, experiments involving with the R76F02-AD; R55C10-DBD driver could be manipulating the activity of additional neurons in around 60% of larvae. The conclusions of the paper would be strengthened if key experiments were repeated with other GAL4 drivers that may label DAN-c1 with even greater specificity, such as SS03066 (Truman et al., 2023; doi:10.7554/elife.80594) or MB320C (Hige et al., 2015; doi:10.1016/j.neuron.2015.11.003).

(3) Successful immunostaining with an anti-D2R antibody (Draper et al., 2007; doi:10.1002/dneu.20355 and Love et al., 2023; doi:10.1111/gbb.12836) could validate GFP-tagged D2R expression (Figure 3) in the same way that TH immunostaining was used throughout the paper to determine whether neurons were dopaminergic.

(4) The paper proposes a model in which DAN-c1 activity conveys an aversive teaching signal (Figure 2f) but excessive artificial DAN-c1 activation causes excessive dopamine release that impairs aversive learning (Figures 2i and 5b). According to this model, thermogenetic DAN-c1 activation during training with water or sucrose conveys an aversive teaching signal that reduces performance (Figure 2i) whereas optogenetic DAN-c1 activation does not due to excessive dopamine release (Figures 5c and 5d). The model suggests that optogenetic DAN-c1 activation is strong enough to cause excessive dopamine release by itself whereas thermogenetic DAN-c1 activation can only achieve the same outcome when it occurs in conjunction with natural DAN-c1 activation evoked by quinine. Therefore, an experiment with weaker optogenetic DAN-c1 activation (with lower intensity light or pulsed at a lower frequency) during water or sucrose training would be expected to convey an aversive teaching signal rather than excessive dopamine release, reducing performance. Such an experiment could reconcile the differing thermogenetic and optogenetic results of the paper.

Reviewer #2 (Public review):

Summary:

The study wanted to functionally identify individual DANs that mediate larval olfactory learning. Then search for DAN-specific driver strains that mark single dopaminergic neurons, which subsequently can be used to target genetic manipulations of those neurons. 56 GAL4 drivers identifying dopaminergic neurons were found (Table 1) and three of them drive the expression of GFP to a single dopaminergic neuron in the third-instar larval brain hemisphere. The DAN driver R76F02-AD;R55C10-DBD appears to drive the expression to a dopaminergic neuron innervating the lower peduncle (LP), which would be DAN-c1.

Split-GFP reconstitution across synaptic partners (GRASP) technique was used to investigate the "direct" synaptic connections from DANs to the mushroom body. Potential synaptic contact between DAN-c1 and MB neurons (at the lower peduncle) were detected.

Then single odor associative learning was performed and thermogenetic tools were used (Shi-ts1 and TrpA1). When trained at 34{degree sign}C, the complete inactivation of dopamine release from DAN-c1 with Shibirets1 impaired aversive learning (Figure 2h), while Shibirets1 did not affect learning when trained at room temperature (22 {degree sign}C). When paired with a gustatory stimulus (QUI or SUC), activation of DAN-c1 during training impairs both aversive and appetitive learning (Figure 2k).<br /> Then examined the expression pattern of D2R in fly brains and were found in dopaminergic neurons and the mushroom body (Figure 3). To inspect whether the pattern of GFP signals indeed reflected the expression of D2R, three D2R enhancer driver strains (R72C04, R72C08, and R72D03-GAL4) were crossed with the GFP-tagged D2R strain.

D2R knockdown (UAS-RNAi) in dopaminergic neurons driven by TH-GAL4 impaired larval aversive learning. Using a microRNA strain (UAS-D2R-miR), a similar deficit was observed. Crossing the GFP-tagged D2R strain with a DAN-c1-mCherry strain demonstrated the expression of D2R in DAN-c1 (Figure 4a). Knockdown of D2R in DAN-c1 impaired aversive learning with the odorant pentyl acetate, while appetitive learning was unaffected (Figure 4e). Sensory and motor functions appear not affected by D2R suppression.

To exclude possible chronic effects of D2R knockdown during development, optogenetics was applied at distinct stages of the learning protocol. ChR2 was expressed in DAN-c1, and blue light was applied at distinct stages of the learning protocol. Optogenetic activation of DAN-c1 during training impaired aversive learning, not appetitive learning (Figure 5b-d).

Knockdown of D2Rs in MB neurons by D2R-miR impaired both appetitive and aversive learning (Figure 6a). Activation of MBNs during training impairs both larval aversive and appetitive learning.

Finally, based on the data the authors propose a model where the effective learning requires a balanced level of activity between D1R and D2R (Figure 7).

Strengths:

The work is well written, clear, and concise. They use well documented strategies to examine GAL4 drivers with expression in a single DAN, behavioral performance in larvae with distinct genetic tools including those to do thermo and optogenetics in behaving flies. Altogether, the study was able to expand our understanding of the role of D2R in DAN-c1 and MB neurons in the larva brain.

The study successfully examined the role of D2R in DAN-c1 and MB neurons in olfactory conditioning. The conclusions are well supported by the data and the model of adequate levels of cAMP (Figure 7b) appears to be able to explain a poor memory after insufficient or excessive cAMP signaling. The study provides insight into the role of D2R in associative learning expanding our understanding and might be a reference similarly to previous key findings (Qi and Lee, 2014, https://doi.org/10.3390/biology3040831).

Reviewer #1 (Public review):

Summary:

The topic of nanobody-based PET imaging is important, and holds great potential for real-world applications since nanobodies have many advantages over full sized immunoglobulins and small molecules.

Strengths:

The submitted manuscript contains quite a bit of interesting data from a collaborative team of well-respected researchers. The authors are to be congratulated for presenting results that may not have turned out the way they had hoped, and doing so in a transparent fashion.

Weaknesses:

However, the manuscript could be considered to be a collection of exploratory findings rather than a complete and mature scientific exposition. Most of the sample sizes were 3 per group, which is fine for exploratory work, but insufficient to draw strong, statistically robust conclusions for definitive results.

Overall, the following specific limitations are noted as suggestions for future work:

(1) The authors used DFO, which is well known to leak Zr, rather than the current standard for 89Zr PET which is DFO* (DFO-star)

(2) The brain tissues were not capillary depleted, which limits interpretation. Capillary depletion, with quantitative assessment of the completion of the depletion process, is the standard in the field.

(3) The authors have not experimentally tested the hypothesis that the PEG adduct reduced BBB transcytosis.

(4) The results in Fig. 7 involving the placenta are interesting, but need confirmation using constructs with 18F labeling and without the PEG adduct.

(5) If this line of investigation were to be translated to humans, an important consideration would be the relative safety of 89Zr and 64Cu. It is likely to be quite a bit worse than for 18F, since the 89Zr and 64Cu have longer half-lives, dissociate from their chelators, and lodge in off-target tissues.

(6) A surprising and somewhat disappointing finding was the modest amount of BBB transcytosis. Clearly additional work will be needed before nanobody-based brain PET becomes feasible.

Reviewer #2 (Public review):

Summary:

In this study the authors described a previously developed set of VHH-based PET tracers to track transplants (cancer cells, embryo's) in a murine immune-competent environment.

Strengths:

Unique set of PET tracer and mouse strain to track transplanted cells in vivo without genetic modification of the transplanted cells. This is a unique asset and a first-in-kind.

Weaknesses:

None

Reviewer #1 (Public review):

Summary:

The authors use analysis of existing data, mathematical modelling and new experiments to explore the relationship between protein expression noise, translation efficiency and transcriptional bursting.

Strengths:

The analysis of the old data and the new data presented is interesting and mostly convincing.

Weaknesses:

My main concern is the analysis presented in Figure 4. This is the core of mechanistic analysis that suggests ribosomal demand can explain the observed phenomenon. Revisions have improved clarity but I am both confused by the assumptions used here in the mathematical modelling of this section. I said before, the authors assumption that the fluctuations of a single gene mRNA levels will significantly affect ribosome demand is puzzling. The author's seem to dismiss this and maybe I am missing something. However, the specific forms used in equations of table S1 seem very phenomenological and I am not sure how these can be taken as good approximations for modelling ribosome demand. Why kc has this specific form, why such a sharp hill number is appropriate. how many total ribosomes per mRNA is assumed here (if this assumption is indeed needed). Again, my intuition is that on average the total level of mRNA across all genes would stay constant and therefore there are not big fluctuations in the ribosome demand due to the burstiness of transcription of individual genes (as this on average is compensated with drop in level of other transcripts). Should not one be considering all transcripts and total ribosomes to be able to model ribosome demand?

Reviewer #2 (Public review):

This work by Pal et al. studied the relationship between protein expression noise and translational efficiency. They proposed a model based on ribosome demand to explain the positive correlation between them, which is new as far as I realize. Nevertheless, I found the evidence of the main idea that it is the ribosome demand generating this correlation is weak. Below are my major and minor comments.

Major comments:

(1) Besides a hypothetical numerical model, I did not find any direct experimental evidence supporting the ribosome demand model. Therefore, I think the main conclusions of this work are a bit overstated.

(2) I found that the enhancement of protein noise due to high translational efficiency is quite mild, as shown in Figure 6A-B, which makes the biological significance of this effect unclear.

(3) The captions for most of the figures are short and do not provide much explanation, making the figures difficult to read.

(4) It would be helpful if the authors could define the meanings of noise (e.g., coefficient of variation?) and translational efficiency in the very beginning to avoid any confusion. It is also unclear to me whether the noise from the experimental data is defined according to protein numbers or concentrations, which is presumably important since budding yeasts are growing cells.

(5) The conclusions from Figure 1D and 1E are not new. For example, the constant protein noise as a function of mean protein expression is a known result of the two-state model of gene expression, e.g., see Eq. (4) in Paulsson, Physics of Life Reviews 2005.

(6) In Figure 4C-D, it is unclear to me how the authors changed the mean protein expression if the translation initiation rate is a function of variation in mRNA number and other random variables.

(7) If I understand correctly, the authors somehow changed the translation initiation rate to change the mean protein expression in Figure 4C-D. However, the authors changed the protein sequences in the experimental data of Figure 6. I am not sure if the comparison between simulations and experimental data is appropriate.

Comments on revisions:

Updated Review: The authors have satisfactorily answered all of my questions and comments. The current manuscript is much clearer and stronger than the previous one. I do not have any other questions.

Reviewer #1 (Public review):

Summary:

In this study, Floedder et al report that dopamine ramps in both Pavlovian and Instrumental conditions are shaped by reward interval statistics. Dopamine ramps are an interesting phenomenon because at first glance they do not represent the classical reward prediction errors associated with dopamine signaling. Instead, they seem somewhat to bridge the gap between tonic and phasic dopamine, with an intense discussion still being held in the field about what is their actual behavioral role. Here, in tests with head-fixed mice, and dopamine being recorded with a genetically encoded fluorescent sensor in the nucleus accumbens, the authors find that dopamine ramps were only present when intertrial intervals were relatively short and the structure of the task (Pavlovian cue or progression in a VR corridor) contained elements that indicated progression towards the reward (e.g., a dynamic cue). The authors propose that although these findings can be explained by classical theories of dopamine function, they are better explained by their model of Adjusted Net Contingency of Causal Relation (ANCCR). The results of this study provide constraints on future models of dopamine function, and are of high interest to the field.

Reviewer #2 (Public review):

In this manuscript by Floeder et al., the authors report a correlation between ITI duration and the strength of a dopamine ramp occurring in the time between a predictive conditioned stimulus and a subsequent reward. They found this relationship occurring within two different tasks with mice, during both a Pavlovian task as well as an instrumental virtual visual navigation task. Additionally, they observed this relationship only in conditions when using a dynamic predictive stimulus. The authors relate this finding to their previously published model ANCCR in which the time constant of the eligibility trace is proportionate to the reward rate within the task.

The relationship between ITI duration and the extent of a dopamine ramp which the authors have reported is very intriguing and certainly provides an important constraint for models for dopamine function. As such, these findings are potentially highly impactful to the field.

Reviewer #3 (Public review):

Summary:

Floeder and colleagues measure dopamine signaling in the nucleus accumbens core using fiber photometry of the dLight sensor, in Pavlovian and instrumental tasks in mice. They test some predictions from a recently proposed model (ANCCR) regarding the existence of "ramps" in dopamine that have been seen in some previous research, the characteristics of which remain poorly understood.

They find that cues signaling a progression toward rewards (akin to a countdown) specifically promote ramping dopamine signaling in the nucleus accumbens core, but only when the intertrial interval just experienced was short. This work is discussed in the context of ongoing theoretical conceptions of dopamine's role in learning.

This work is the clearest demonstration to date of concrete training factors that seem to directly impact whether or not dopamine ramps occur. The existence of ramping signals has long been a feature of debates in the dopamine literature and this work adds important context to that. Further, as a practical assessment of the impact of a relatively simple trial structure manipulation on dopamine patterns, this work will be important for guiding future studies. These studies are well done and thoughtfully presented. The additional data, analyses, and discussion in the revised version of the paper add strength and clarity to the conclusions.

The current results raise interesting questions regarding what, if any potential function cue-reward interval dopamine ramps serve. In the current data, licking behavior was similar on different trial types and was not related to ramping activity.

Reviewer #2 (Public review):

Summary:

In this manuscript, the authors recorded activity in the posterior parietal cortex (PPC) of monkeys performing a perceptual decision-making task. The monkeys were first shown two choice dots of two different colors. Then, they saw a random dot motion stimulus. They had to learn to categorize the direction of motion as referring to either the right or left dot. However, the rule was based on the color of the dot and not its location. So, the red dot could either be to the right or left, but the rule itself remained the same. It is known from past work that PPC neurons would code the learned categorization. Here, the authors showed that the categorization signal depended on whether the executed saccade was in the same hemifield as the recorded PPC neuron or in the opposite one. That is, if a neuron categorized the two motion directions such that it responded stronger for one than the other, then this differential motion direction coding effect was amplified if the subsequent choice saccade was in the same hemifield. The authors then built a computational RNN to replicate the results and make further tests by simulated "lesions".

Strengths:

Linking the results to RNN simulations and simulated lesions.

Weaknesses:

Potential interpretational issues due to a lack of explicit evidence on the sizes and locations of the response fields of the neurons. For example, is the contra/ipsi effect explained by the fact that in the contra condition, the response target and the saccade might have infringed on the outer edges of the response fields?

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 are based on sampling cerebrospinal fluid, and 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 (Fig. 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 (Fig. 4). Further, smallRNA-1 is detectable in the urine of experimentally infected mice as early as 24 hours post infection (Fig. 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 (Fig. 6B), and in whole blood from 2 out of 2 samples (Fig. 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 shows that whole blood could be tested for smallRNA-1 to diagnose N. fowleri infections. The potential for human blood or urine to be tested for N. fowleri could lead to critical early interventions.

Weaknesses:

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, serum, or human urine due to little to no sample material being available for testing. This limitation is examined thoroughly in the discussion section, and additional tests are beyond the scope of this work.

Reviewer #1 (Public review):

Summary

This paper summarises responses from a survey completed by around 5,000 academics on their manuscript submission behaviours. The authors find several interesting stylised facts, including (but not limited to):

- Women are less likely to submit their papers to highly influential journals (e.g., Nature, Science and PNAS).<br /> - Women are more likely to cite the demands of co-authors as a reason why they didn't submit to highly influential journals.<br /> - Women are also more likely to say that they were advised not to submit to highly influential journals.

The paper highlights an important point, namely that the submission behaviours of men and women scientists may not be the same (either due to preferences that vary by gender, selection effects that arise earlier in scientists' careers or social factors that affect men and women differently and also influence submission patterns). As a result, simply observing gender differences in acceptance rates - or a lack thereof - should not be automatically interpreted as as evidence for or against discrimination (broadly defined) in the peer review process.

Major comments

What do you mean by bias?

In the second paragraph of the introduction, it is claimed that "if no biases were present in the case of peer review, then we should expect the rate with which members of less powerful social groups enjoy successful peer review outcomes to be proportionate to their representation in submission rates." There are a couple of issues with this statement.

First, the authors are implicitly making a normative assumption that manuscript submission and acceptance rates *should* be equalised across groups. This may very well be the case, but there can also be valid reasons - even when women are not intrinsically better at research than men - why a greater fraction of female-authored submissions are accepted relative to male-authored submissions (or vice versa). For example, if men are more likely to submit their less ground-breaking work, then one might reasonably expect that they experience higher rejection rates compared to women, conditional on submission.

Second, I assume by "bias", the authors are taking a broad definition, i.e., they are not only including factors that specifically relate to gender but also factors that are themselves independent of gender but nevertheless disproportionately are associated with one gender or another (e.g., perhaps women are more likely to write on certain topics and those topics are rated more poorly by (more prevalent) male referees; alternatively, referees may be more likely to accept articles by authors they've met before, most referees are men and men are more likely to have met a given author if he's male instead of female). If that is the case, I would define more clearly what you mean by bias. (And if that isn't the case, then I would encourage the authors to consider a broader definition of "bias"!)

Identifying policy interventions is not a major contribution of this paper

I would take out the final sentence in the abstract. In my opinion, your survey evidence isn't really strong enough to support definitive policy interventions to address the issue and, indeed, providing policy advice is not a major - or even minor - contribution of your paper. (Basically, I would hope that someone interested in policy interventions would consult another paper that much more thoughtfully and comprehensively discusses the costs and benefits of various interventions!) While it's fine to briefly discuss them at the end of your paper - as you currently do - I wouldn't highlight that in the abstract as being an important contribution of your paper.

Minor comments

- What is the rationale for conditioning on academic rank and does this have explanatory power on its own - i.e., does it at least superficially potentially explain part of the gender gap in intention to submit?

Reviewer #2 (Public review):

Basson et al. present compelling evidence supporting a gender disparity in article submission to "elite" journals. Most notably, they found that women were more likely to avoid submitting to one of these journals based on advice from a colleague/mentor. Overall, this work is an important addition to the study of gender disparities in the publishing process.

I thank the authors for addressing my concerns.

Reviewer #4 (Public review):

Main strengths

The topic of the MS is very relevant given that across the sciences/academia, genders are unevenly represented, which has a range of potential negative consequences. To change this, we need to have the evidence on what mechanisms cause this pattern. Given that promotion and merit in academia are still largely based on the number of publications and the impact factor, one part of the gap likely originates from differences in publication rates of women compared to men.

Women are underrepresented compared to men in journals with a high impact factor. While previous work has detected this gap and identified some potential mechanisms, the current MS provides strong evidence that this gap might be due to a lower submission rate of women compared to men, rather than the rejection rates. These results are based on a survey of close to 5000 authors. The survey seems to be conducted well (though I am not an expert in surveys), and data analysis is appropriate to address the main research aims. It was impossible to check the original data because of the privacy concerns.

Interestingly, the results show no gender bias in rejection rates (desk rejection or overall) in three high-impact journals (Science, Nature, PNAS). However, submission rates are lower for women compared to men, indicating that gender biases might act through this pathway. The survey also showed that women are more likely to rate their work as not groundbreaking and are advised not to submit to prestigious journals, indicating that both intrinsic and extrinsic factors shape women's submission behaviour.

With these results, the MS has the potential to inform actions to reduce gender bias in publishing, but also to inform assessment reform at a larger scale.

I do not find any major weaknesses in the revised manuscript.

Reviewer #1 (Public review):

Summary:

The paper describes the cryoEM structure of RAD51 filament on the recombination intermediate. In the RAD51 filament, the insertion of a DNA-binding loop called the L2 loop stabilizes the separation of the complementary strand for the base-pairing with an incoming ssDNA and the non-complementary strand, which is captured by the second DNA-binding channel called the site II. The molecular structure of the RAD51 filament with a recombination intermediate provides a new insight into the mechanism of homology search and strand exchange between ssDNA and dsDNA.

Strong points:

This is the first human RAD51 filament structure with a recombination intermediate called the D-loop. The work has been done with great care, and the results shown in the paper are compelling based on cryo-EM and biochemical analyses. The paper is really nice and important for researchers in the field of homologous recombination, which gives a new view on the molecular mechanism of RAD51-mediated homology search and strand exchange.

Comments on revisions:

The authors nicely address most of the previous points.

Reviewer #2 (Public review):

Homologous recombination is essential for DNA double-strand break repair, with RAD51-catalyzed strand exchange at its core. This study presents a 2.64 Å resolution cryogenic electron microscopy structure of the RAD51 D-loop complex, achieved through reconstitution of a RAD51 mini-filament. The structure uncovers how specific RAD51 residues drive strand exchange, offering atomic-level insight into the mechanics of eukaryotic HR and DNA repair.

Comments on revisions:

Authors acknowledged:

"We acknowledge that there exists an extensive body of literature that has investigated the polarity of strand exchange by RecA and RAD51 under a variety of experimental conditions, and we have added a brief comment to the text to reflect this, as well as some of the key citations. Undoubtedly, and as we also mention in our reply to the public reviews, further experimental work will be needed for a full reconciliation of the available evidence."

In the revised manuscript, this is reflected in the statement:

"Our mechanistic interpretation of static D-loop structures awaits full reconciliation with earlier efforts to determine strand-exchange polarity for RecA and RAD51 measured under a variety of experimental conditions."

Among the four cited studies, my understanding (as a person who has never studied this subject of polarity) is as follows:<br /> •References 50 (EMBO J. 1997), 51 (Cell. 1995), and 52 (Nature. 2008) suggest that the strand exchange by human RAD51 occurs with a polarity opposite to that of RecA-that is, in the 5′→3′ direction relative to the complementary strand, or 3′→5′ relative to the initiating single-stranded DNA (isDNA).<br /> • In contrast, reference 49 (PNAS 1998) proposed that 5′→3′ polarity (relative to isDNA) is conserved across RecA, human RAD51, and yeast RAD51.

Given the substantial structural analysis provided in the current manuscript, it would strengthen the work to include a concise description of these earlier biochemical findings, rather than citing them without context. This would benefit readers who are not familiar with the longstanding studies in the field and allow for a more informed interpretation of how the structural observations may reconcile or contrast with previous work.

Reviewer #3 (Public review):

Summary:

Built on their previous pioneer expertise in studying RAD51 biology, in this paper, the authors aim to capture and investigate the structural mechanism of human RAD51 filament bound with a displacement loop (D-loop), which occurs during the dynamic synaptic state of the homologous recombination (HR) strand-exchange step. As the structures of both pre- and post-synaptic RAD51 filaments were previously determined, a complex structure of RAD51 filament during strand exchange is one of the key missing pieces of information for a complete understanding of how RAD51 functions in HR pathway. This paper aims to determine the high-resolution cryo-EM structure of RAD51 filament bound with D-loop. Combined with mutagenesis analysis and biophysical assays, the authors aim to investigate the D-loop DNA structure, RAD51 mediated strand separation and polarity, and a working model of RAD51 during HR strand invasion in comparison with RecA.

Strengths:

(1) The structural work and associated biophysical assays in this paper are solid, elegantly designed and interpreted.  These results provide novel insights into RAD51's function in HR.

(2) The DNA substrate used was well designed, taking into consideration of the nucleotide number requirement of RAD51 for stable capture of donor DNA. This DNA substrate choice lays the foundation for successfully determining the structure of the RAD51 filament on D-loop DNA using single-partial cryo-EM.

(3) The authors utilised their previous expertise in capping DNA ends using monometric streptavidin and combined their careful data collection and processing to determine the cryo-EM structure of full-length human RAD51 bound at D-loop in high resolution. This interesting structure forms the core part of this work and allows detailed mapping of DNA-DNA and DNA-protein interaction among RAD51, invading strands, and donor DNA arms (Figures 1, 2, 3, 4). The geometric analysis of D-loop DNA bound with RAD51 and EM density for homologous DNA pairing are also impressive (Figure S5). The previously disordered RAD51's L2-loop is now ordered and traceable in the density map and functions as a physical spacer when bound with D-loop DNA. Interestingly, the authors identified that the side chain position of F279 in the L2_loop of RAD51_H differs from other F279 residues in L2-loops of E, F and G protomers. This asymmetric binding of L2 loops and RAD51_NTD binding with donor DNA arms forms the basis of the proposed working model about the polarity on csDNA during RAD51-mediated strand exchange.

(4) This work also includes mutagenesis analysis and biophysical experiments, especially EMSA, single-molecule fluorescence imaging using an optical tweezer, and DNA strand exchange assay, which are all suitable methods to study the key residues of RAD51 for strand exchange and D-loop formation (Figure 5).

Weaknesses:

(1) The proposed model for the 3'-5' polarity of RAD51-mediated strand invasion is based on the structural observations in the cryo-EM structure. This study lacks follow-up biochemical/biophysical experiments to validate the proposed model compared to RecA or developing methods to capture structures of any intermediate states with different polarity models.

(2) The functional impact of key mutants designed based on structure has not been tested in cells to evaluate how these mutants impact the HR pathway.

The significance of the work for the DNA repair field and beyond:

Homologous recombination (HR) is a key pathway for repairing DNA double-strand breaks and involves multiple steps. RAD51 forms nucleoprotein filaments first with 3' overhang single-strand DNA (ssDNA), followed by a search and exchange with a homology strand. This function serves as the basis of an accurate template-based DNA repair during HR. This research addressed a long-standing challenge of capturing RAD51 bound with the dynamic synaptic DNA and provided the first structural insight into how RAD51 performs this function. The significance of this work extends beyond the discovery biology for the DNA repair field, into its medical relevance. RAD51 is a potential drug target for inhibiting DNA repair in cancer cells to overcome drug resistance. This work offers a structural understanding of RAD51's function with D-loop and provides new strategies for targeting RAD51 to improve cancer therapies.

Reviewer #2 (Public review):

In this manuscript, the authors investigated how partial loss of SynGap1 affects inhibitory neurons derived from the MGE in the auditory cortex, focusing on their synaptic inputs and excitability. While haplo-insufficiently of SynGap1 is known to lead to intellectual disabilities, the underlying mechanisms remain unclear.

This is the third revision of the manuscript that has improved further, and the main issues were addressed. Specifically, the Authors addressed the contradiction of mEPSC and sEPSC data of the previous version by new experiments and revision of the manuscript text. While alternative explanations are still possible, the new control experiments provide necessary background for reproducibility and the manuscript text puts the observations in the right context. Furthermore, the manuscript now appropriately emphasizes that anatomical analysis was restricted to somatic excitatory synapses. Thus, the readers will be aware of the potential limitations of these measurements.

Strengths:

The questions are novel and relevant. Most of the issues in the experimental design are solved or answered.

Weaknesses:

Despite the interesting and novel questions, there are potential alternative interpretations of the observations, but these cannot be addressed within the breadth of a single paper.

Reviewer #1 (Public review):

Summary:

The authors have developed self-amplifying RNAs (saRNAs) encoding additional genes to suppress dsRNA-related inflammatory responses and cytokine release. Their results demonstrate that saRNA constructs encoding anti-inflammatory genes effectively reduce cytotoxicity and cytokine production, enhancing the potential of saRNAs. This work is significant for advancing saRNA therapeutics by mitigating unintended immune activation.

Strengths:

This study successfully demonstrates the concept of enhancing saRNA applications by encoding immune-suppressive genes. A key challenge for saRNA-based therapeutics, particularly for non-vaccine applications, is the innate immune response triggered by dsRNA recognition. By leveraging viral protein properties to suppress immunity, the authors provide a novel strategy to overcome this limitation. The study presents a well-designed approach with potential implications for improving saRNA stability and minimizing inflammatory side effects.

Comments on revisions:

All comments have been thoroughly addressed, and the manuscript has been significantly improved.

Reviewer #3 (Public review):

Summary:

Context - this is the 2nd review, of a manuscript that has already undergone some revisions.<br /> The manuscript explores ways to make self-amplifying RNA (saRNA) more silent through the inclusion of genes to inhibit the innate immune response. The readouts are predominantly expression and cell viability. They take a layered approach, adding multiple genes, as well as altering the capping of the anti-immune genes.

Strengths:

As described by the other reviewers, the authors take a stepwise approach to demonstrate that they can lead to sustained expression of the transgene.

Weaknesses:

The following weaknesses need some consideration

(1) The data show sustained expression, but do not directly show amplification. The amount of RFP is constantly decreasing over the time course. There is some evidence for the srIκBα-Smad7-SOCS1 construct. But measuring the RNA itself would be beneficial<br /> (2) The end construct is very large - it has 12 genes, this may have manufacturing considerations, affecting the translatability.

Joint Public Review:

Summary:

For many years, there has been extensive electrophysiological research investigating the relationship between local field potential patterns and individual cell spike patterns in the hippocampus. In this study, using innovative imaging techniques, they examined spike synchrony of hippocampal cells during locomotion and immobility states. The authors demonstrated that hippocampal place cells exhibit prominent synchronous spikes locked to theta oscillations.

Strengths:

The single cell voltage imaging used in this study is a highly novel method that may allow recordings that were not previously possible using existing methods.

Weaknesses:

The strength of evidence remains incomplete because of the main claim that synchronous events are not associated with ripples. As was mentioned in previous rounds of review, ripples emerge locally and independently in the two hemispheres. Thus, obtaining ripple recordings from the contralateral hemisphere does not provide solid evidence for this claim. The papers the authors are citing to make the claim that "Additionally, we implanted electrodes in the contralateral CA1 region to monitor theta and ripple oscillations, which are known to co-occur across hemispheres (29-31)" do not support this claim. For example, reference 29 contains the following statement: "These findings suggest that ripples emerge locally and independently in the two hemispheres".

Reviewer #1 (Public review):

The authors of this study use electron microscopy and 3D reconstruction techniques to study the morphology of distinct classes of Drosophila sensory neurons *across many neurons of the same class.* This is a comprehensive study attempting to look at nearly all the sensory neurons across multiple sensilla in the same animal to determine a) how much morphological variability exists between and within neurons of different and similar sensory classes and b) identify dendritic features that may have evolved to support particular sensory functions. This study builds upon the authors' previous work which allowed them to identify and distinguish sensory neuron subtypes in the EM volumes without additional staining so that reconstructed neurons could reliably be placed in the appropriate class. This work is unique in looking at a large number of individual neurons of the same class to determine what is consistent and what is variable about their class-specific morphologies.

This means that in addition to providing specific structural information about these particular cells, the authors explore broader questions of how much morphological diversity exists between sensory neurons of the same class. This then informs our conceptualization about how different dendritic morphologies might affect specific sensory and physiological properties of neurons.

The authors found that CO2 sensing neurons have an unusual, sheet-like morphology in contrast to the thin branches of odor-sensing neurons. They show that this morphology greatly increases the surface area to volume ratio above what could be achieved by modest branching of thin dendrites, and posit that this might be important for their sensory function, though this was not directly tested in their study due to technical limitations. The study is mainly descriptive in nature, but thorough, and provides a nice jumping off point for future functional studies. One interesting future analysis could be to examine all four cell types within a single sensilla together to see if there are any general correlations that could reveal insights about how morphology is determined and relative contributions of intrinsic mechanisms vs interactions with neighboring cells. For example, if higher-than-average branching in one cell type correlated with higher-than-average branching in another type when within the same sensilla, it might suggest differential amounts of extracellular growth or branching cues within a given sensillum drive any heterogeneity observed within a class across sensilla. Conversely, if higher branching in one cell type consistently leads to reduced length or branching of the other neurons within its sensillum, this might point to dendrite-dendrite interactions between cells undergoing competitive or repulsive interactions to define territories within each sensillum as a major determinant of the variability.

Strengths:

This work provides a thorough morphometric analysis of the neurons of the *majority of all ab1 sensilla* across a single antenna. The authors use this analysis to 1) characterize the unique dendritic architecture of ab1C neurons relative to other ORNs including ab1D and 2) provide evidence of substantial morphological diversity even within a single subclass of neuron.

Weaknesses:

This is primarily a descriptive paper due to technical limitations since it is not currently technically feasible to determine individual ORN response properties and tie them to identified neurons with detailed EM-based ultrastructural analyses, nor to predictably alter dendritic morphology of these cells to directly test how different morphologies affect sensory function. However, the quantitative descriptive findings presented here will shape these future questions and are necessary for any such future work.

Reviewer #2 (Public review):

Summary:

The manuscript employs serial block‐face electron microscopy (SBEM) and cryofixation to obtain high‐resolution, three‐dimensional reconstructions of Drosophila antennal sensilla containing olfactory receptor neurons (ORNs) that detect CO2. This method has been used previously by the same lab in Gonzales et. al, 2021. (https://elifesciences.org/articles/69896), and Zhang et. al, 2019 Nature Communications. The previous study by Zhang also correlated morphometric measurements from SBEM with asymmetric ephaptic activity for paired neurons using electrophysiology across multiple olfactory sensilla. This manuscript applies the same SBEM method to now characterize the ab1 sensillum which houses the ab1C, CO2 detecting neuron, but stops short of integration neuronal activity with structural variability.

The SBEM-based morphometric studies do however significantly advance preliminary observations from older two-dimensional TEM-based reports. Previous images of the putative CO2 neuron in Drosophila (Shanbhag et al., 1999) and in mosquitoes (McIver and Siemicki, 1975; Lu et al, 2007) reported that the dendritic architecture of the CO2 neuron was somewhat different (circular and flattened, lamellated) from other olfactory neurons in the antenna of insects. In this study, the authors confirm this different morphology but also classify it into distinct subtypes (loosely curled, fully curled, split, and mixed).

Strengths:

The study makes a convincing case that ab1C neurons exhibit a unique, dendritic morphology unlike the canonical cylindrical dendrites found in ab1D neurons. This observation extends previous qualitative TEM findings by not only confirming the presence of flattened lamellae in CO₂ neurons but also quantifying key morphometrics such as dendritic length, surface area, and volume, and calculating surface area-to-volume ratios. The enhanced ratios observed in the flattened segments are speculated to be linked to potential advantages in receptor distribution (e.g., Gr21a/Gr63a) and efficient signal propagation.

Weaknesses:

Although this quantitative approach is very robust compared to earlier reports, interpretations are somewhat limited by the absence of direct electrophysiological data to confirm whether ultrastructural differences translate into altered neuronal function. The biggest question remains unanswered: whether structural variation observed in the ab1C dendrites by SBEM have an electrophysiological functional relevance?

Surveys of ab1 sensillum with single-sensillum recordings (even a few from multiple Drosophila antenna) as they have done for ab2s and others in the past, would have measured spontaneous activity, spike amplitude, and response to CO2. This could have allowed for comparison of frequency of functional variation, if any, to structural variation and a discussion would therefore have strengthened the overall characterization. In the case of ab2 sensilla the authors find very little variance, could the ab1 also be the same? In the absence of this data, it becomes hard to speculate whether structural variation observed in the ab1C dendrites by SBEM have any functional relevance or whether they are simply random variations in dendrite development.

Additionally, artifacts could be a consideration, even though Cryofixation is superior to chemical fixation. Although this is hard to address, all types of fixations in TEMs cause some artifacts, as does serial sectioning. An understanding of the error rates for the SBEM method would have increased the confidence in the conclusions drawn. For example, what is the structural variation of SBEMs in the ab2 population, which shows very little electrophysiological variation? Can a comparison be done?

Reviewer #3 (Public review):

Summary:

In the current manuscript entitled "Population-level morphological analysis of paired CO2- and odor-sensing olfactory neurons in D. melanogaster via volume electron microscopy", Choy, Charara et al. use volume electron microscopy and neuron reconstruction to compare the dendritic morphology of ab1C and ab1D neurons of the Drosophila basiconic ab1 sensillum. They aim to investigate the degree of dendritic heterogenity within a functional class of neurons using ab1C and ab1D, which they can identify due to the unique feature of ab1 sensilla to house four neurons and the stereotypic location on the third antennal segment. This is a great use of volumetric electron imaging and neuron reconstruction to sample a population of neurons of the same type. Their data convincingly shows that there is dendritic heterogenity in both investigated populations and their sample size is sufficient to strongly support this observation. This data proposes that the phenomenon of dendritic heterogenity is common in the Drosophila olfactory system and will stimulate future investigations into the developmental origin, functional implications and potential adaptive advantage of this feature.

Moreover, the authors discovered that there is a difference between CO2- and odour sensing neurons of which the first show a characteristic flattened and sheet-like structure not observed in other sensory neurons sampled in this and previous studies. They hypothesize that this unique dendritic organization which increases the surface area to volume ratio, might allow more efficient Co2 sensing by housing higher numbers of Co2 receptors. This is supported by previous attempts to express Co2 sensors in olfactory sensory neurons which lack this dendritic morphology, resulting in lower Co2 sensitivity compared to endogenous neurons.

Overall, this detailed morphological description of olfactory sensory neurons' dendrites convincingly shows heterogeneity in two neuron classes with potential functional impacts for odour sensing.

Strength:

The volumetric EM imaging and reconstruction approach offers unpreceeded details in single cell morphology and compares dendrite heterogenity across a great fraction of ab1 sensilla.<br /> The authors identify specific shapes for ab1C sensilla potentially linked to their unique function in CO2 sensing.

Weaknesses:

While the morphological description is highly detailed, current methods prevent linking morphology to odour sensitivity or other properties of the neurons. Therefore, this study remains mainly descriptive and will require future work to link neuron structure and function.

Reviewer #1 (Public Review):

Summary:

Here, Millet et al. consider whether the nematode C. elegans 'discounts' the value of reward due to effort in a manner similar to that shown in other species, including rodents and humans. They designed a T-maze effort choice paradigm inspired by previous literature, but manipulated how effortful the food is to consume. C. elegans worms were sensitive to this novel manipulation, exhibiting effort-discounting-like behaviour that could be shaped by varying the density of food at each alternative in order to calculate an indifference point. This discounting-like behaviour was related to worms' rates of patch leaving, which differed between the low and high effort patches in isolation. The authors also found a potential relationship to dopamine signalling, and also that this discounting behaviour was not specific to lab-based strains of C. elegans.

Strengths:

The question is well-motivated, and the approach taken here is novel. The authors are careful in their approach to altering and testing the properties of the effortful, elongated bacteria. Similarly, they go to some effort to understand what exactly is driving behavioural choices in this context, both through the application of simple standard models of effort discounting and a kinetic analysis of patch leaving. The comparisons to various dopamine mutants further extend the translational potential of their findings. I also appreciate the comparison to natural isolate strains, as the question of whether this behaviour may be driven by some sort of strain-specific adaptation to the environment is not regularly addressed in mammalian counterparts. The manuscript is well-written, and the figures are clear and comprehensible.

Weaknesses:

Discounting is typically defined as the alteration of a subjective value by effort (or time, risk, etc.), which is then used to guide future decision-making. By adapting the standard t-maze task for C. elegans as a patch-leaving paradigm, the authors observe behaviour strongly consistent with discounting models, but that is likely driven by a different process, in particular by an online estimate of the type of food in the current patch, which then influences patch-leaving dynamics (Figure 3). This is fundamentally different from decision-making strategies relating to effort that have been described in the rodent and human literatures. Similarly, the calculation of indifference points at the group instead of at the individual level also suggests a different underlying process and limits the translational potential of their findings. The authors do not discuss the implications of these differences or why they chose not to attempt a more analogous trial-based experiment.

In the case of both the dopamine and natural isolate experiments, the data are very noisy despite large (relative to other C. elegans experiments) sample sizes. In the dopamine experiment, disruption of dop-1, dop-2, and cat-2 had no statistically significant effect. There do not appear to be any corrections for multiple comparisons, and the single significant comparison, for dop-3, had a small effect size. More detailed behavioural analyses on both these and the wild isolate strains, for example by applying their kinetic analysis, would likely give greater insight as to what is driving these inconsistent effects.

Reviewer #2 (Public Review):

Summary:

Millet et al. show that C. elegans systematically prefers easy-to-eat bacteria but will switch its choice when harder-to-eat bacteria are offered at higher densities, producing indifference points that fit standard economic discounting models. Detailed kinetic analysis reveals that this bias arises from unchanged patch-entry rates but significantly elevated exit rates on effortful food, and dop-3 mutants lose the preference altogether, implicating dopamine in effort sensitivity. These findings extend effort-discounting behavior to a simple nematode, pushing the phylogenetic boundary of economic cost-benefit decision-making.

Strengths:

(1) Extends the well-characterized concept of effort discounting into _C. elegans_, setting a new phylogenetic boundary and opening invertebrate genetics to economic-behavior studies.

(2) Elegant use of cephalexin-elongated bacteria to manipulate "effort" without altering nutritional or olfactory cues, yielding clear preference reversals and reproducible indifference points.

(3) Application of standard discounting models to predict novel indifference points is both rigorous and quantitatively satisfying, reinforcing the interpretation of worm behavior in economic terms.

(4) The three-state patch-model cleanly separates entry and exit dynamics, showing that increased leaving rates-rather than altered re-entry-drive choice biases.

(5) Investigates the role of dopamine in this behavior to try to establish shared mechanisms with vertebrates.

(6) Demonstration of discounting in wild strain (solid evidence).

Weaknesses:

(1) The kinetic model omits rich trajectory details-such as turning angles or hazard functions-that could distinguish a bona fide roaming transition from other exit behaviors.

(2) Only _dop-3_ shows an effect, and the statistical validity of this result is questionable. It is not clear if the authors corrected for multiple comparisons, and the effect size is quite small and noisy, given the large number of worms tested. Other mutants do not show effects. Given these two concerns, the role of dopamine in c. elegans effort discounting was unconvincing.

(3) With only five wild isolates tested (and variable data quality), it's hard to conclude that effort discounting isn't a lab-strain artifact or how broadly it varies in natural populations.

(4) Detailed analysis of behavior beyond preference indices would strengthen the dopamine link and the claim of effort discounting in wild strains.

(5) A few mechanistic statements (e.g., tying satiety exclusively to nutrient signals) would benefit from explicit citations or brief clarifications for non-worm specialists.

Reviewer #3 (Public Review):

Summary:

The authors establish a behavioral task to explore effort discounting in C. elegans. By using bacterial food that takes longer to consume, the authors show that, for equivalent effort, as measured by pumping rate, they obtain less food, as measured by fat deposition.

The authors formalize the task by applying a formal neuroeconomic decision-making model that includes value, effort, and discounting. They use this to estimate the discounting that C. elegans applies based on ingestion effort by using a population-level 2-choice T-maze.

They then analyze the behavioral dynamics of individual animals transitioning between on-food and off-food states. Harder to ingest bacteria led to increased food patch leaving.

Finally, they examined a set of mutants defective in different aspects of dopamine signaling, as dopamine plays a key role in discounting in vertebrates and regulates certain aspects of C. elegans foraging.

Strengths:

The behavioral experiments and neuroeconomic analysis framework are compelling and interesting, and make a significant contribution to the field. While these foraging behaviors have been extensively studied, few include clearly articulated theoretical models to be tested.

Demonstrating that C. elegans effort discounting fits model predictions and has stable indifference points is important for establishing these tasks as a model for decision making.

Weaknesses:

The dopamine experiments are harder to interpret. The authors point out the perplexing lack of an effect of dat-1 and cat-2. dop-3 leads to general indifference. I am not sure this is the expected result if the argument is a parallel functional role to discounting in vertebrates. dop-3 causes a range of locomotor phenotypes and may affect feeding (reduced fat storage), and thus, there may be a general defect in the ability to perform the task rather than anything specific to discounting.

That said, some of the other DA mutants also have locomotor defects and do not differ from N2. But there is no clear result here - my concern is that global mutants in such a critical pathway exhibit such pleiotropy that it's difficult to conclude there is a clear and specific role for DA in effort discounting. This would require more targeted or cell-specific approaches.

Meanwhile, there are other pathways known to affect responses to food and patch leaving decisions: serotonin, pigment-dispersing factor, tyramine, etc. The paper would have benefited from a clarification about why these were not considered as promising candidates to test (in addition to or instead of dopamine).

Reviewer #1 (Public review):

Summary:

Ritzau-Jost et al. investigate the potential contribution of AP broadening in homeostatic upregulation of neuronal network activity with a specific focus on dissociated neuronal cultures. In cultures obtained from a few brain regions from mice or rats using different culture conditions and examined by different laboratories, AP half-width remained stable despite chronic activity block with TTX. The finding suggests that AP width is not significantly modulated by changes in sodium channel activity.

Strengths:

The collaborative nature of the study amongst the neuronal culture experts and the rigorous electrophysiological assessments provides for a compelling support of the main conclusion.

Weaknesses:

Given the negative nature of the results, a couple of remaining issues (such as the cell density of cultures and the presentation of imaging experiments with a voltage sensor) warrant further consideration. In addition, a discussion of the reasons for the seeming stability of AP half-width to sodium channel modulation might help extend the scope of the study beyond the presentation of a negative conclusion.

Reviewer #2 (Public review):

Summary:

This study reexamined the idea that action potential broadening serves as a homeostatic mechanism to compensate for changes in network activity. The key finding was that, while action potential broadening does occur in certain neurons - such as CA3 pyramidal cells-it is far from a universal response. This is important because it helps resolve longstanding discrepancies in the field, thereby contributing to a better understanding of network dynamics. The replication of these findings across multiple laboratories further strengthened the study's rigor.

Strengths:

Mechanisms of network homeostasis are essential to understand network dynamics.

Weaknesses:

No weaknesses were noted by this reviewer.

Reviewer #3 (Public review):

Summary:

The manuscript "Unreliable homeostatic action potential broadening in cultured dissociated neurons" by Ritzau-Jost et al. investigates action potential (AP) broadening as a mechanism underlying homeostatic synaptic plasticity. Given the existing variability in the literature concerning AP broadening, the authors address an important and timely research question of considerable interest to the field.

The study systematically demonstrates cell-type- and model-specific AP broadening in hippocampal neurons after chronic treatment with either tetrodotoxin (TTX) or glutamatergic transmission blockers. The findings indicate AP broadening in CA3 pyramidal neurons in organotypic cultures after TTX treatment, but notably not in dissociated hippocampal neurons under identical conditions. However, blocking glutamatergic neurotransmission caused AP broadening in dissociated hippocampal neurons. Moreover, extensive evaluations in neocortical dissociated cultures robustly challenge previous findings by revealing a lack of AP broadening following TTX treatment. Additionally, the proposed role of BK-type potassium channels in mediating AP broadening is convincingly questioned through complementary electrophysiological and voltage-imaging experiments.

Strengths:

The manuscript exhibits an outstanding experimental design, employing state-of-the-art techniques and a rigorous multi-lab validation approach that greatly enhances scientific reliability. The experimental results are meticulously illustrated, and the conclusions drawn are justified and supported by the presented data. Furthermore, the manuscript is comprehensively and clearly written.

Weaknesses:

Concerning the statistical analyses employed, it is advisable to consider the Kruskal-Wallis test with corrections for multiple comparisons when evaluating more than two experimental groups.

Reviewer #1 (Public review):

Summary:

Wu and colleagues aimed to explain previous findings that adolescents, compared to adults, show reduced cooperation following cooperative behaviour from a partner in several social scenarios. The authors analysed behavioural data from adolescents and adults performing a zero-sum Prisoner's Dilemma task and compared a range of social and non-social reinforcement learning models to identify potential algorithmic differences. Their findings suggest that adolescents' lower cooperation is best explained by a reduced learning rate for cooperative outcomes, rather than differences in prior expectations about the cooperativeness of a partner. The authors situate their results within the broader literature, proposing that adolescents' behaviour reflects a stronger preference for self-interest rather than a deficit in mentalising.

Strengths:

The work as a whole suggests that, in line with past work, adolescents prioritise value accumulation, and this can be, in part, explained by algorithmic differences in weighted value learning. The authors situate their work very clearly in past literature, and make it obvious the gap they are testing and trying to explain. The work also includes social contexts that move the field beyond non-social value accumulation in adolescents. The authors compare a series of formal approaches that might explain the results and establish generative and model-comparison procedures to demonstrate the validity of their winning model and individual parameters. The writing was clear, and the presentation of the results was logical and well-structured.

Weaknesses:

I also have some concerns about the methods used to fit and approximate parameters of interest. Namely, the use of maximum likelihood versus hierarchical methods to fit models on an individual level, which may reduce some of the outliers noted in the supplement, and also may improve model identifiability.

There was also little discussion given the structure of the Prisoner's Dilemma, and the strategy of the game (that defection is always dominant), meaning that the preferences of the adolescents cannot necessarily be distinguished from the incentives of the game, i.e. they may seem less cooperative simply because they want to play the dominant strategy, rather than a lower preferences for cooperation if all else was the same.

Appraisal & Discussion:

The authors have partially achieved their aims, but I believe the manuscript would benefit from additional methodological clarification, specifically regarding the use of hierarchical model fitting and the inclusion of Bayes Factors, to more robustly support their conclusions. It would also be important to investigate the source of the model confusion observed in two of their models.

I am unconvinced by the claim that failures in mentalising have been empirically ruled out, even though I am theoretically inclined to believe that adolescents can mentalise using the same procedures as adults. While reinforcement learning models are useful for identifying biases in learning weights, they do not directly capture formal representations of others' mental states. Greater clarity on this point is needed in the discussion, or a toning down of this language.

Additionally, a more detailed discussion of the incentives embedded in the Prisoner's Dilemma task would be valuable. In particular, the authors' interpretation of reduced adolescent cooperativeness might be reconsidered in light of the zero-sum nature of the game, which differs from broader conceptualisations of cooperation in contexts where defection is not structurally incentivised.

Overall, I believe this work has the potential to make a meaningful contribution to the field. Its impact would be strengthened by more rigorous modelling checks and fitting procedures, as well as by framing the findings in terms of the specific game-theoretic context, rather than general cooperation.

Reviewer #2 (Public review):

Summary:

This manuscript investigates age-related differences in cooperative behavior by comparing adolescents and adults in a repeated Prisoner's Dilemma Game (rPDG). The authors find that adolescents exhibit lower levels of cooperation than adults. Specifically, adolescents reciprocate partners' cooperation to a lesser degree than adults do. Through computational modeling, they show that this relatively low cooperation rate is not due to impaired expectations or mentalizing deficits, but rather a diminished intrinsic reward for reciprocity. A social reinforcement learning model with asymmetric learning rate best captured these dynamics, revealing age-related differences in how positive and negative outcomes drive behavioral updates. These findings contribute to understanding the developmental trajectory of cooperation and highlight adolescence as a period marked by heightened sensitivity to immediate rewards at the expense of long-term prosocial gains.

Strengths:

(1) Rigid model comparison and parameter recovery procedure.

(2) Conceptually comprehensive model space.

(3) Well-powered samples.

Weaknesses:

(1) A key conceptual distinction between learning from non-human agents (e.g., bandit machines) and human partners is that the latter are typically assumed to possess stable behavioral dispositions or moral traits. When a non-human source abruptly shifts behavior (e.g., from 80% to 20% reward), learners may simply update their expectations. In contrast, a sudden behavioral shift by a previously cooperative human partner can prompt higher-order inferences about the partner's trustworthiness or the integrity of the experimental setup (e.g., whether the partner is truly interactive or human). The authors may consider whether their modeling framework captures such higher-order social inferences. Specifically, trait-based models-such as those explored in Hackel et al. (2015, Nature Neuroscience)-suggest that learners form enduring beliefs about others' moral dispositions, which then modulate trial-by-trial learning. A learner who believes their partner is inherently cooperative may update less in response to a surprising defection, effectively showing a trait-based dampening of learning rate.

(2) This asymmetry in belief updating has been observed in prior work (e.g., Siegel et al., 2018, Nature Human Behaviour) and could be captured using a dynamic or belief-weighted learning rate. Models incorporating such mechanisms (e.g., dynamic learning rate models as in Jian Li et al., 2011, Nature Neuroscience) could better account for flexible adjustments in response to surprising behavior, particularly in the social domain.

(3) Second, the developmental interpretation of the observed effects would be strengthened by considering possible non-linear relationships between age and model parameters. For instance, certain cognitive or affective traits relevant to social learning-such as sensitivity to reciprocity or reward updating-may follow non-monotonic trajectories, peaking in late adolescence or early adulthood. Fitting age as a continuous variable, possibly with quadratic or spline terms, may yield more nuanced developmental insights.

(4) Finally, the two age groups compared - adolescents (high school students) and adults (university students) - differ not only in age but also in sociocultural and economic backgrounds. High school students are likely more homogenous in regional background (e.g., Beijing locals), while university students may be drawn from a broader geographic and socioeconomic pool. Additionally, differences in financial independence, family structure (e.g., single-child status), and social network complexity may systematically affect cooperative behavior and valuation of rewards. Although these factors are difficult to control fully, the authors should more explicitly address the extent to which their findings reflect biological development versus social and contextual influences.

Reviewer #3 (Public review):

Summary:

Wu and colleagues find that in a repeated Prisoner's Dilemma, adolescents, compared to adults, are less likely to increase their cooperation behavior in response to repeated cooperation from a simulated partner. In contrast, after repeated defection by the partner, both age groups show comparable behavior.

To uncover the mechanisms underlying these patterns, the authors compare eight different models. They report that a social reward learning model, which includes separate learning rates for positive and negative prediction errors, best fits the behavior of both groups. Key parameters in this winning model vary with age: notably, the intrinsic value of cooperating is lower in adolescents. Adults and adolescents also differ in learning rates for positive and negative prediction errors, as well as in the inverse temperature parameter.

Strengths:

The modeling results are compelling in their ability to distinguish between learned expectations and the intrinsic value of cooperation. The authors skillfully compare relevant models to demonstrate which mechanisms drive cooperation behavior in the two age groups.

Weaknesses:

Some of the claims made are not fully supported by the data:

The central parameter reflecting preference for cooperation is positive in both groups. Thus, framing the results as self-interest versus other-interest may be misleading.

It is unclear why the authors assume adolescents and adults have the same expectations about the partner's cooperation, yet simultaneously demonstrate age-related differences in learning about the partner. To support their claim mechanistically, simulations showing that differences in cooperation preference (i.e., the w parameter), rather than differences in learning, drive behavioral differences would be helpful.

Two different schedules of 120 trials were used: one with stable partner behavior and one with behavior changing after 20 trials. While results for order effects are reported, the results for the stable vs. changing phases within each schedule are not. Since learning is influenced by reward structure, it is important to test whether key findings hold across both phases.

The division of participants at the legal threshold of 18 years should be more explicitly justified. The age distribution appears continuous rather than clearly split. Providing rationale and including continuous analyses would clarify how groupings were determined.

Claims of null effects (e.g., in the abstract: "adults increased their intrinsic reward for reciprocating... a pattern absent in adolescents") should be supported with appropriate statistics, such as Bayesian regression.

Once claims are more closely aligned with the data, the study will offer a valuable contribution to the field, given its use of relevant models and a well-established paradigm.

Reviewer #1 (Public review):

Summary:

The authors investigated the potential role of IgG N-glycosylation in Haemorrhagic Fever with Renal Syndrome (HFRS), which may offer significant insights for understanding molecular mechanisms and for the development of therapeutic strategies for this infectious disease. However, several issues need to be addressed.

Major Points:

(1) The authors should provide a detailed description of the pathogenesis of Haemorrhagic Fever with Renal Syndrome (HFRS) and elaborate on the crucial role of IgG proteins in the disease's progression (line 65).

(2) An additional discussion on the significance of glycosylation, particularly IgG N-glycosylation, in viral infections should be included in the Introduction section.

(3) In the Abstract section, the authors state that HTNV-specific IgG antibody titers were detected and IgG N-glycosylation was analyzed. However, the analysis of plasma IgG N-glycans is described in the Methods section. Therefore, the authors should clarify the glycome analysis process. Was the specific IgG glycome profile similar to the total IgG N-glycome? Given the biological relevance of specific IgG in immunological diseases, characterizing the specific IgG N-glycome profile would be more significant than analyzing the total plasma IgG.

(4) Further details regarding the N-glycome analysis should be provided, including the quantity of IgG protein used and the methodology employed for analyzing IgG N-glycans (lines 286-287).

(5) Additional statistical analyses should be performed, including multiple comparisons with p-value adjustment, false discovery rate (FDR) control, and Pearson correlation (line 291).

(6) Quality control should be conducted prior to the IgG N-glycome analysis. Additionally, both biological and technical replicates are essential to assess the reproducibility and robustness of the methods.

(7) Multiple regression analysis should be conducted to evaluate the influence of genetic and environmental factors on the IgG N-glycome.

(8) Line 196. Additional discussions should be included, focusing on the underlying correlation between the differential expression of B-cell glycogenes and the dysregulated IgG N-glycome profile, as well as the potential molecular mechanisms of IgG N-glycosylation in the development of HFRS.

Reviewer #2 (Public review):

Summary:

This work sought to explore antibody responses in the context of hemorrhagic fever with renal syndrome (HFRS) - a severe disease caused by Hantaan virus infection. Little is known about the characteristics or functional relevance of IgG Fc glycosylation in HFRS. To address this gap, the authors analyzed samples from 65 patients with HFRS spanning the acute and convalescent phases of disease via IgG Fc glycan analysis, scRNAseq, and flow cytometry. The authors observed changes in Fc glycosylation (increased fucosylation and decreased bisection) coinciding with a 4-fold or greater increase in Haantan virus-specific antibody titer. They suggest that these shifts contribute to disease recovery. The study also includes exploratory analyses linking IgG glycan profiles to glycosylation-related gene expression in distinct B cell subsets, using single-cell transcriptomics. Overall, this is an interesting study that combines serological profiling with transcriptomic data to shed light on humoral immune responses in an underexplored infectious disease. The integration of Fc glycosylation data with single-cell transcriptomic data is a strength. However, some improvements could be made in the clarity of both the Results and Materials and Methods sections, and some conclusions would benefit from greater caution, particularly in avoiding overinterpretation of correlative findings.

Comments:

(1) While it is great to reference prior publications in the Materials and Methods section, the current level of detail is insufficient to clearly understand the study design and experimental procedures performed. Readers should not be expected to consult multiple previous papers to grasp the core methodological aspects of the present paper. For instance, the categorization of HFRS patients into different clinical subtypes/courses, and the methods for measuring Fc glycosylation should be explicitly described in the Materials and Methods section of this manuscript.

(2) The authors should explain the nature of their cohort in a bit more detail. While it appears that HFRS cases were identified based on IgM ELISA and/or PCR, these are indicators of the Haantan virus infection. My understanding is that not all Haantan virus infections progress to HFRS. Thus, it is unclear whether all patients in the HFRS group actually had hemorrhagic fever. This distinction is critical for interpreting how the results observed relate to disease severity.

(3) The authors state that: "A 4-fold or greater increase in HTNV-NP-specific antibody titers usually indicates a protective humoral immune response during the acute phase", but they do not cite any references or provide any context that supports this claim. Given that in their own words, one of the most significant findings in the study is changes in glycosylation coinciding with this 4-fold increase, it is important to ground this claim in evidence. Without this, the use of a 4-fold threshold appears arbitrary and weakens the rationale for using this immune state as a proxy for protective immunity.

(4) The authors also claim that changes in Fc glycosylation influence recovery from HFRS - a point even emphasized in the manuscript title. However, this conclusion is not well supported by the data for two main reasons. First, the authors appear to measure bulk IgG Fc glycans, not Fc glycans of Hantaan virus-specific antibodies. While reasonable, this is something that should be communicated in the manuscript. Hantaan virus-specific antibodies are likely a very small fraction of total circulating IgG antibodies (perhaps ~1%), even during acute infection. As a result, changes in bulk Fc glycosylation may (or may not) accurately reflect the glycosylation state of Hantaan virus-specific antibodies. Second, even if the bulk Fc glycan shifts do mirror those of Hantaan virus-specific antibodies, it remains unclear whether these changes causally drive recovery or are merely a consequence of the infection being resolved. Thus, while the differences in Fc glycosylation observed are interesting - and it is tempting to speculate on their functional significance - the manuscript treats the observed correlations as causal mechanistic insight without sufficient data or justification.

(5) Fc glycosylation is known to be influenced by covariates such as age and sex. While it is helpful that the authors stratified the patients by age group and looked for significant differences in glycosylation across them, a more robust approach would be to directly control for these covariates in the statistical analysis - such as by using a linear mixed effects model, in which disease state (e.g., acute vs. convalescent), age, and sex are treated as fixed effects, and subject ID is included as a random effect to account for repeated measures. This would allow the authors to assess whether observed differences in Fc glycosylation remain significant after accounting for potential confounders. This could be important given that some of the reported differences are quite small, for example, 94.29% vs. 94.89% fucosylation.

(6) The manuscript states that there are limited studies on antibody glycosylation in the context of HFRS, but does not cite any relevant literature. If prior work exists, it should be cited to contextualize the current study. If no prior studies have been conducted/reported, to the author's knowledge, that should be stated explicitly to show the novelty of the work.

Reviewer #1 (Public review):

Building upon their previous work, the authors present an enhanced method for confocal live imaging of leg regeneration in the crustacean Parhyale hawaiensis. Parhyale is an emerging and tractable model system that offers insights into the evolution and mechanisms of development and regeneration. Çevrim et al. demonstrate the ability to image the complete leg regeneration process, spanning several days, with 10-20 minute time intervals and cellular resolution. They have concurrently optimized imaging conditions to enable cell tracking while minimizing phototoxicity. Additionally, they report successfully implementing HCR in situ hybridization in Parhyale, allowing for specific gene transcript staining at the endpoint of live imaging. This opens the possibility of assigning molecular identities to tracked cells.

A key challenge in many regeneration models is achieving continuous imaging throughout the entire regenerative process, as many organisms are difficult to immobilize or cannot tolerate extended imaging without stress. This manuscript's major strength lies in providing practical solutions to these challenges in Parhyale, a compelling and accessible arthropod model for limb regeneration. The authors also employ complementary tools to analyze time-lapse movies and correlate them with endpoint staining. Together, these advances will serve as a useful resource for researchers studying regeneration in Parhyale or in other systems where parts of this workflow can be adapted.

While the data demonstrating the methodological advancement and technical feasibility are solid, much of the benchmarking and regeneration characterization remains qualitative. This does not undermine the validity of the proof-of-principle, but limits the study's broader appeal.

Reviewer #2 (Public review):

The manuscript by Çevrim et al. presents a live-imaging workflow that captures the complete leg regeneration process in the crustacean Parhyale hawaiensis, at a resolution suitable for cell tracking and gene expression analysis. Building on earlier work describing selective stages of leg regeneration (Alwes et al., 2016), the authors recorded 22 confocal time-lapse movies, starting from amputation to full regeneration. They defined three distinct phases of regeneration (wound closure, cell proliferation and morphogenesis, and differentiation) based on cellular and morphological features.

One movie was used to assess how imaging parameters (z-spacing, time intervals, and image quality) influence tracking reliability and the time required for manual proofreading, with an effort to minimize phototoxicity. Tracking was performed in the upper tissue layers using an improved version of the Mastodon plugin Elephant in Fiji. The same sample was fixed post-imaging for in situ hybridization using an HCR protocol adapted for adult legs, targeting the gene spineless. This enabled the alignment of gene expression with specific cell lineages and the identification of progenitor cells present at the time of amputation.

In summary, the study provides a proof-of-principle for combining long-term live imaging, cell tracking, and gene expression analysis during regeneration. Given the labor-intensive nature of tracking over a 5-10 day time-lapse movie, the use of a single movie for this study is well justified. The workflow, from imaging to lineage reconstruction and molecular annotation, is successfully demonstrated and well documented with this dataset.

Although the biological insights from the cell lineage and molecular mapping are still limited, the methodology offers significant potential in regenerative biology to uncover the cellular and molecular contributions to tissue and cell type re-formation.

Confocal microscopy was used for live imaging, which restricted imaging to the upper 30 µm tissue layer. Light-sheet microscopy could have provided gentler imaging and enabled imaging from multiple angles to image the whole leg. While the authors acknowledge this possibility in the manuscript, they discarded it due to incompatibility between their mounting strategy and available light-sheet microscopes. As a future direction, optimizing the mounting approach for compatibility with light-sheet microscopes could enable more comprehensive tissue imaging.

Reviewer #1 (Public review):

Functional lateralization between the right and left hemispheres is reported widely in animal taxa, including humans. However, it remains largely speculative as to whether the lateralized brains have a cognitive gain or a sort of fitness advantage. In the present study, by making use of the advantages of domestic chicks as a model, the authors are successful in revealing that the lateralized brain is advantageous in the number sense, in which numerosity is associated with spatial arrangements of items. Behavioral evidence is strong enough to support their arguments. Brain lateralization was manipulated by light exposure during the terminal phase of incubation, and the left-to-right numerical representation appeared when the distance between items gave a reliable spatial cue. The light-exposure induced lateralization, though quite unique in avian species, together with the lack of intense inter-hemispheric direct connections (such as the corpus callosum in the mammalian cerebrum), was critical for the successful analysis in this study. Specification of the responsible neural substrates in the presumed right hemisphere is expected in future research. Comparable experimental manipulation in the mammalian brain must be developed to address this general question (functional significance of brain laterality) is also expected.

Reviewer #2 (Public review):

Summary:

This is the first study to show how a L-R bias in the relationship between numerical magnitude and space depends on brain lateralisation, and moreover, how this is modulated by in ovo conditions.

Strengths:

Novel methodology for investigating the innateness and neural basis of a L-R bias in the relationship between number and space.

Weaknesses:

I would query the way the experiment was contextualised. They ask whether culture or innate pre-wiring determines the 'left-to-right orientation of the MNL [mental number line]'.<br /> The term, 'Mental Number Line' is an inference from experimental tasks. One of the first experimental demonstrations of a preference or bias for small numbers in the left of space and larger numbers in the right of space, was more carefully described as the spatial-numerical association of response codes - the SNARC effect (Dehaene, S., Bossini, S., & Giraux, P. (1993). The mental representation of parity and numerical magnitude. Journal of Experimental Psychology: General, 122, 371-396).<br /> This has meant that the background to the study is confusing. First, they note correctly that many other creatures, including insects can show this bias, though in none of these has neural lateralisation been shown to be a cause. Second, their clever experiment shows that an experimental manipulation creates the bias. If it were innate and common to other species, the experimental manipulation shouldn't matter. There would always be a L-R bias. Third, they seem to be asserting that humans have a left-to-right (L-R) MNL. This is highly contentious, and in some studies, reading direction affects it, as the original study by Dehaene et al showed; and in others, task affects direction (e.g. Bachtold, D., Baumüller, M., & Brugger, P. (1998). Stimulus-response compatibility in representational space. Neuropsychologia, 36, 731-735, not cited). Moreover, a very careful study of adult humans, found no L-R bias (Karolis, V., Iuculano, T., & Butterworth, B. (2011), not cited). Mapping numerical magnitudes along the right lines: Differentiating between scale and bias. Journal of Experimental Psychology: General, 140(4), 693-706). Indeed, Rugani et al claim, incorrectly, that the L-R bias was first reported by Galton in 1880. There are two errors here: first, Galton was reporting what he called 'visualised numerals' and are typically referred to now as 'number forms' - spontaneous and habitual conscious visual representations - not an inference from a number line task. Second, Galton reported right-to-left, circular, and vertical visualised numerals, and no simple left-to-right examples (Galton, F. (1880). Visualised numerals. Nature, 21, 252-256.). So in fact did Bertillon, J. (1880). De la vision des nombres. La Nature, 378, 196-198, and more recently Seron, X., Pesenti, M., Noël, M.-P., Deloche, G., & Cornet, J.-A. (1992). Images of numbers, or "When 98 is upper left and 6 sky blue". Cognition, 44, 159-196, and Tang, J., Ward, J., & Butterworth, B. (2008). Number forms in the brain. Journal of Cognitive Neuroscience, 20(9), 1547-1556.

If the authors are committed to chicks' MN Line they should test a series of numbers showing that the bias to left is greater for 2 and 3 than for 4 etc.

What does all this mean? I think that the experiment should absolutely be published in eLife, but the paper should be shorn of its misleading contextualisation, including the term 'Mental Number Line'. The authors also speculate, usefully, on why chicks and other species might have a L-R bias. I don't think the speculations are convincing, but at least if there is an evolutionary basis for the bias, it should at least be discussed.

In fact, I think it would make a very interesting special issue to bring up to date how and why the L-R bias exists, and where and why it does not.

Karolis, V., Iuculano, T., & Butterworth, B. (2011). Mapping numerical magnitudes along the right lines: Differentiating between scale and bias. Journal of Experimental Psychology: General, 140(4), 693-706. doi:10.1037/a0024255

Review of the revised version:

The background and terminology in the text have been significantly altered and clarified: Spatial Numerical Association (SNA) instead of Mental Number Line (MNL) in the text, but with a discussion about how SNA might be the basis of MNL. This entails a link from SNA - a bias - to mental representation of a sequence of numerical magnitudes, which will need to be spelt out in subsequent work with a sequence of numbers rather than a single number, in this case 4. Could the effect be generalised to much larger numbers?

Although the relationship between number and space seems fundamental, the key question is why the L-R SNA bias should exist at all. The authors take on this challenge and make important arguments for the evolutionary advantage of the bias is (see lines 138ff, 375ff, 444ff), though this is likely still to be controversial.

Subsequent work may clarify its interaction of brain lateralisation with culture, notably reading and writing direction (e.g. Dehaene, S., Bossini, S., & Giraux, P. (1993). The mental representation of parity and numerical magnitude. Journal of Experimental Psychology: General, 122, 371-396), though this relationship has exceptions and challenges (e.g. Karolis, V., Iuculano, T., & Butterworth, B. (2011). Mapping numerical magnitudes along the right lines: Differentiating between scale and bias. Journal of Experimental Psychology: General, 140(4), 693-706).

For example, would humans with more lateralised brains show a stronger bias? Would humans with reverse lateralisation show a R-L SNA?

Reviewer #1 (Public review):

Summary:

This study provides a comprehensive single-cell and multiomic characterization of trabecular meshwork (TM) cells in the mouse eye, a structure critical to intraocular pressure (IOP) regulation and glaucoma pathogenesis. Using scRNA-seq, snATAC-seq, immunofluorescence, and in situ hybridization, the authors identify three transcriptionally and spatially distinct TM cell subtypes. The study further demonstrates that mitochondrial dysfunction, specifically in one subtype (TM3), contributes to elevated IOP in a genetic mouse model of glaucoma carrying a mutation in the transcription factor Lmx1b. Importantly, treatment with nicotinamide (vitamin B3), known to support mitochondrial health, prevents IOP elevation in this model. The authors also link their findings to human datasets, suggesting the existence of analogous TM3-like cells with potential relevance to human glaucoma.

Strengths:

The study is methodologically rigorous, integrating single-cell transcriptomic and chromatin accessibility profiling with spatial validation and in vivo functional testing. The identification of TM subtypes is consistent across mouse strains and institutions, providing robust evidence of conserved TM cell heterogeneity. The use of a glaucoma model to show subtype-specific vulnerability, combined with a therapeutic intervention-gives the study strong mechanistic and translational significance. The inclusion of chromatin accessibility data adds further depth by implicating active transcription factors such as LMX1B, a gene known to be associated with glaucoma risk. The integration with human single-cell datasets enhances the potential relevance of the findings to human disease.

Weaknesses:

Although the LMX1B transcription factor is implicated as a key regulator in TM3 cells, its role in directly controlling mitochondrial gene expression is not fully explored. Additional analysis of motif accessibility or binding enrichment near relevant target genes could substantiate this mechanistic link. The therapeutic effect of vitamin B3 is clearly demonstrated phenotypically, but the underlying cellular and molecular mechanisms remain somewhat underdeveloped - for instance, changes in mitochondrial function, oxidative stress markers, or NAD+ levels are not directly measured. While the human relevance of TM3 cells is suggested through marker overlap, more quantitative approaches, such as cell identity mapping or gene signature scoring in human datasets, would strengthen the translational connection.

Overall, this is a compelling and carefully executed study that offers significant advances in our understanding of TM cell biology and its role in glaucoma. The integration of multimodal data, disease modeling, and therapeutic testing represents a valuable contribution to the field. With additional mechanistic depth, the study has the potential to become a foundational resource for future research into IOP regulation and glaucoma treatment.

Reviewer #2 (Public review):

Summary:

This elegant study by Tolman and colleagues provides fundamental findings that substantially advance our knowledge of the major cell types within the limbus of the mouse eye, focusing on the aqueous humor outflow pathway. The authors used single-cell and single-nuclei RNAseq to very clearly identify 3 subtypes of the trabecular meshwork (TM) cells in the mouse eye, with each subtype having unique markers and proposed functions. The U. Columbia results are strengthened by an independent replication in a different mouse strain at a separate laboratory (Duke). Bioinformatics analyses of these expression data were used to identify cellular compartments, molecular functions, and biological processes. Although there were some common pathways among the 3 subtypes of TM cells (e.g., ECM metabolism), there also were distinct functions. For example:

• TM1 cell expression supports heavy engagement in ECM metabolism and structure, as well as TGF2 signaling.

• TM2 cells were enriched in laminin and pathways involved in phagocytosis, lysosomal function, and antigen expression, as well as End3/VEGF/angiopoietin signaling.

• TM3 cells were enriched in actin binding and mitochondrial metabolism.

They used high-resolution immunostaining and in situ hybridization to show that these 3 TM subtypes express distinct markers and occupy distinct locations within the TM tissue. The authors compared their expression data with other published scRNAseq studies of the mouse as well as the human aqueous outflow pathway. They used ATAC-seq to map open chromatin regions in order to predict transcription factor binding sites. Their results were also evaluated in the context of human IOP and glaucoma risk alleles from published GWAS data, with interesting and meaningful correlations. Although not discussed in their manuscript, their expression data support other signaling pathways/ proteins/ genes that have been implicated in glaucoma, including: TGF2, BMP signaling (including involvement of ID proteins), MYOC, actin cytoskeleton (CLANs), WNT signaling, etc.

In addition to these very impressive data, the authors used scRNAseq to examine changes in TM cell gene expression in the mouse glaucoma model of mutant Lmxb1-induced ocular hypertension. In man, LMX1B is associated with Nail-Patella syndrome, which can include the development of glaucoma, demonstrating the clinical relevance of this mouse model. Among the gene expression changes detected, TM3 cells had altered expression of genes associated with mitochondrial metabolism. The authors used their previous experience using nicotinamide to metabolically protect DBA2/J mice from glaucomatous damage, and they hypothesized that nicotinamide supplementation of mutant Lmx1b mice would help restore normal mitochondrial metabolism in the TM and prevent Lmx1b-mediated ocular hypertension. Adding nicotinamide to the drinking water significantly prevented Lmxb1 mutant mice from developing high intraocular pressure. This is a laudable example of dissecting the molecular pathogenic mechanisms responsible for a disease (glaucoma) and then discovering and testing a potential therapy that directly intervenes in the disease process and thereby protects from the disease.

Strengths:<br /> There are numerous strengths in this comprehensive study including:<br /> • Deep scRNA sequencing that was confirmed by an independent dataset in another mouse strain at another university.<br /> • Identification and validation of molecular markers for each mouse TM cell subset along with localization of these subsets within the mouse aqueous outflow pathway.<br /> • Rigorous bioinformatics analysis of these data as well as comparison of the current data with previously published mouse and human scRNAseq data.<br /> • Correlating their current data with GWAS glaucoma and IOP "hits".<br /> • Discovering gene expression changes in the 3 TM subgroups in the mouse mutant Lmx1b model of glaucoma.<br /> • Further pursuing the indication of dysfunctional mitochondrial metabolism in TM3 cells from Lmx1b mutant mice to test the efficacy of dietary supplementation with nicotinamide. The authors nicely demonstrate the disease modifying efficacy of nicotinamide in preventing IOP elevation in these Lmx1b mutant mice, preventing the development of glaucoma. These results have clinical implications for new glaucoma therapies.

Weaknesses:<br /> • Occasional over-interpretation of data. The authors have used changes in gene expression (RNAseq) to implicate functions and signaling pathways. For example: they have not directly measured "changes in metabolism", "mitochondrial dysfunction" or "activity of Lmx1b".<br /> • In their very thorough data set, there is enrichment of or changes in gene expression that support other pathways that have been previously reported to be associated with glaucoma (such as TGF2, BMP signaling, actin cytoskeletal organization (CLANs), WNT signaling, ossification, etc. that appears to be a lost opportunity to further enhance the significance of this work.

Reviewer #3 (Public review):

Summary:In this study, the authors perform multimodal single-cell transcriptomic and epigenomic profiling of 9,394 mouse TM cells, identifying three transcriptionally distinct TM subtypes with validated molecular signatures. TM1 cells are enriched for extracellular matrix genes, TM2 for secreted ligands supporting Schlemm's canal, and TM3 for contractile and mitochondrial/metabolic functions. The transcription factor LMX1B, previously linked to glaucoma, shows the highest expression in TM3 cells and appears to regulate mitochondrial pathways. In Lmx1bV265D mutant mice, TM3 cells exhibit transcriptional signs of mitochondrial dysfunction associated with elevated IOP. Notably, vitamin B3 treatment significantly mitigates IOP elevation, suggesting a potential therapeutic avenue.

This is an excellent and collaborative study involving investigators from two institutions, offering the most detailed single-cell transcriptomic and epigenetic profiling of the mouse limbal tissues-including both TM and Schlemm's canal (SC), from wild-type and Lmx1bV265D mutant mice. The study defines three TM subtypes and characterizes their distinct molecular signatures, associated pathways, and transcriptional regulators. The authors also compare their dataset with previously published murine and human studies, including those by Van Zyl et al., providing valuable cross-species insights.

Strengths:

(1) Comprehensive dataset with high single-cell resolution<br /> (2) Use of multiple bioinformatic and cross-comparative approaches<br /> (3) Integration of 3D imaging of TM and SC for anatomical context<br /> (4) Convincing identification and validation of three TM subtypes using molecular markers.

Weaknesses:

(1) Insufficient evidence linking mitochondrial dysfunction to TM3 cells in Lmx1bV265D mice: While the identification of TM3 cells as metabolically specialized and Lmx1b-enriched is compelling, the proposed link between Lmx1b mutation and mitochondrial dysfunction remains underdeveloped. It is unclear whether mitochondrial defects are a primary consequence of Lmx1b-mediated transcriptional dysregulation or a secondary response to elevated IOP. Additional evidence is needed to clarify whether Lmx1b directly regulates mitochondrial genes (e.g., via ChIP-seq, motif analysis, or ATAC-seq), or whether mitochondrial changes are downstream effects.<br /> Furthermore, the protective effects of nicotinamide (NAM) are interpreted as evidence of mitochondrial involvement, but no direct mitochondrial measurements (e.g., immunostaining, electron microscopy, OCR assays) are provided. It is essential to validate mitochondrial dysfunction in TM3 cells using in vivo functional assays to support the central conclusion of the paper. Without this, the claim that mitochondrial dysfunction drives IOP elevation in Lmx1bV265D mice remains speculative. Alternatively, authors should consider revising their claims that mitochondrial dysfunction in these mice is a central driver of TM dysfunction.

(2) Mechanism of NAM-mediated protection is unclear: The manuscript states that NAM treatment prevents IOP elevation in Lmx1bV265D mice via metabolic support, yet no data are shown to confirm that NAM specifically rescues mitochondrial function. Do NAM-treated TM3 cells show improved mitochondrial integrity? Are reactive oxygen species (ROS) reduced? Does NAM also protect RGCs from glaucomatous damage? Addressing these points would clarify whether the therapeutic effects of NAM are indeed mitochondrial.

(3) Lack of direct evidence that LMX1B regulates mitochondrial genes: While transcriptomic and motif accessibility analyses suggest that LMX1B is enriched in TM3 cells and may influence mitochondrial function, no mechanistic data are provided to demonstrate direct regulation of mitochondrial genes. Including ChIP-seq data, motif enrichment at mitochondrial gene loci, or perturbation studies (e.g., Lmx1b knockout or overexpression in TM3 cells) would greatly strengthen this central claim.

(4)Focus on LMX1B in Fig. 5F lacks broader context: Figure 5F shows that several transcription factors (TFs)-including Tcf21, Foxs1, Arid3b, Myc, Gli2, Patz1, Plag1, Npas2, Nr1h4, and Nfatc2-exhibit stronger positive correlations or motif accessibility changes than LMX1B. Yet the manuscript focuses almost exclusively on LMX1B. The rationale for this focus should be clarified, especially given LMX1B's relatively lower ranking in the correlation analysis. Were the functions of these other highly ranked TFs examined or considered in the context of TM biology or glaucoma? Discussing their potential roles would enhance the interpretation of the transcriptional regulatory landscape and demonstrate the broader relevance of the findings.

Other weaknesses:

(1) In abstract, they say a number of 9,394 wild-type TM cell transcriptomes. The number of Lmx1bV265D/+ TM cell transcriptomes analyzed is not provided. This information is essential for evaluating the comparative analysis and should be clearly stated in the Abstract and again in the main text (e.g., lines 121-123). Including both wild-type and mutant cell counts will help readers assess the balance and robustness of the dataset.

(2) Did the authors monitor mouse weight or other health parameters to assess potential systemic effects of treatment? It is known that the taste of compounds in drinking water can alter fluid or food intake, which may influence general health. Also, does Lmx1bV265D/+ have mice exhibit non-ocular phenotypes, and if so, does nicotinamide confer protection in those tissues as well? Additionally, starting the dose of the nicotinamide at postnatal day 2, how long the mice were treated with water containing nicotinamide, and after how many days or weeks IOP was reduced, and how long the decrease in the IOP was sustained.<br /> (3) While the IOP reduction observed in NAM-treated Lmx1bV265D/+ mice appears statistically significant, it is unclear whether this reflects meaningful biological protection. Several untreated mice exhibit very high IOP values, which may skew the analysis. The authors should report the mean values for IOP in both untreated and NAM-treated groups to clarify the magnitude and variability of the response.<br /> (4) Additionally, since NAM has been shown to protect RGCs in other glaucoma models directly, the authors should assess whether RGCs are preserved in NAM-treated Lmx1b V265D/+ mice. Demonstrating RGC protection would support a synergistic effect of NAM through both IOP reduction and direct neuroprotection, strengthening the translational relevance of the treatment.<br /> (5) Can the authors add any other functional validation studies to explore to understand the pathways enriched in all the subtypes of TM1, TM2, and TM3 cells, in addition to the ICH/IF/RNAscope validation?<br /> (6) The authors should include a representative image of the limbal dissection. While Figure S1 provides a schematic, mouse eyes are very small, and dissecting unfixed limbal tissue is technically challenging. It is also difficult to reconcile the claim that the majority of cells in the limbal region are TM and endothelium. As shown in Figure S6, DAPI staining suggests a much higher abundance of scleral cells compared to TM cells within the limbal strip. Additional clarification or visual evidence would help validate the dissection strategy and cellular composition of the captured region.

Reviewer #3 (Public review):

Summary

The paper presents an imaging and analysis pipeline for whole-mount gastruloid imaging with two-photon microscopy. The presented pipeline includes spectral unmixing, registration, segmentation, and a wavelength-dependent intensity normalization step, followed by quantitative analysis of spatial gene expression patterns and nuclear morphometry on a tissue level. The utility of the approach is demonstrated by several experimental findings, such as establishing spatial correlations between local nuclear deformation and tissue density changes, as well as the radial distribution pattern of mesoderm markers. The pipeline is distributed as a Python package, notebooks, and multiple napari plugins.

Strengths

The paper is well-written with detailed methodological descriptions, which I think would make it a valuable reference for researchers performing similar volumetric tissue imaging experiments (gastruloids/organoids). The pipeline itself addresses many practical challenges, including resolution loss within tissue, registration of large volumes, nuclear segmentation, and intensity normalization. Especially the intensity decay measurements and wavelength-dependent intensity normalization approach using nuclear (Hoechst) signal as reference are very interesting and should be applicable to other imaging contexts. The morphometric analysis is equally well done, with the correlation between nuclear shape deformation and tissue density changes being an interesting finding. The paper is quite thorough in its technical description of the methods (which are a lot), and their experimental validation is appropriate. Finally, the provided code and napari plugins seem to be well done (I installed a selected list of the plugins and they ran without issues) and should be very helpful for the community.

Weaknesses

I don't see any major weaknesses, and I would only have two issues that I think should be addressed in a revision:

(1) The demonstration notebooks lack accompanying sample datasets, preventing users from running them immediately and limiting the pipeline's accessibility. I would suggest to include (selective) demo data set that can be used to run the notebooks (e.g. for spectral unmixing) and or provide easily accessible demo input sample data for the napari plugins (I saw that there is some sample data for the processing plugin, so this maybe could already be used for the notebooks?).

(2) The results for the morphometric analysis (Figure 4) seem to be only shown in lateral (xy) views without the corresponding axial (z) views. I would suggest adding this to the figure and showing the density/strain/angle distributions for those axial views as well.

Reviewer #2 (Public review):

Summary:

This study presents an integrated experimental and computational pipeline for high-resolution, quantitative imaging and analysis of gastruloids. The experimental module employs dual-view two-photon spectral imaging combined with optimized clearing and mounting techniques to image whole-mount immunostained gastruloids. This approach enables the acquisition of comprehensive 3D images that capture both tissue-scale and single-cell level information.

The computational module encompasses both pre-processing of acquired images and downstream analysis, providing quantitative insights into the structural and molecular characteristics of gastruloids. The pre-processing pipeline, tailored for dual-view two-photon microscopy, includes spectral unmixing of fluorescence signals using depth-dependent spectral profiles, as well as image fusion via rigid 3D transformation based on content-based block-matching algorithms. Nuclei segmentation was performed using a custom-trained StarDist3D model, validated against 2D manual annotations, and achieving an F1 score of 85+/-3% at a 50% intersection-over-union (IoU) threshold. Another custom-trained StarDist3D model enabled accurate detection of proliferating cells and the generation of 3D spatial maps of nuclear density and proliferation probability. Moreover, the pipeline facilitates detailed morphometric analysis of cell density and nuclear deformation, revealing pronounced spatial heterogeneities during early gastruloid morphogenesis.

All computational tools developed in this study are released as open-source, Python-based software.

Strengths:

The authors applied two-photon microscopy to whole-mount deep imaging of gastruloids, achieving in toto visualization at single-cell resolution. By combining spectral imaging with an unmixing algorithm, they successfully separated four fluorescent signals, enabling spatial analysis of gene expression patterns.

The entire computational workflow, from image pre-processing to segmentation with a custom-trained StarDist3D model and subsequent quantitative analysis, is made available as open-source software. In addition, user-friendly interfaces are provided through the open-source, community-driven Napari platform, facilitating interactive exploration and analysis.

Weaknesses:

The computational module appears promising. However, the analysis pipeline has not been validated on datasets beyond those generated by the authors, making it difficult to assess its general applicability.<br /> Besides, the nuclei segmentation component lacks benchmarking against existing methods.

Appraisal:

The authors set out to establish a quantitative imaging and analysis pipeline for gastruloids using dual-view two-photon microscopy, spectral unmixing, and a custom computational framework for 3D segmentation and gene expression analysis. This aim is largely achieved. The integration of experimental and computational modules enables high-resolution in toto imaging and robust quantitative analysis at the single-cell level. The data presented support the authors' conclusions regarding the ability to capture spatial patterns of gene expression and cellular morphology across developmental stages.

Impact and utility:

This work presents a compelling and broadly applicable methodological advance. The approach is particularly impactful for the developmental biology community, as it allows researchers to extract quantitative information from high-resolution images to better understand morphogenetic processes. The data are publicly available on Zenodo, and the software is released on GitHub, making them highly valuable resources for the community.

Reviewer #1 (Public review):

Summary:

The image analysis pipeline is tested in analysing microscopy imaging data of gastruloids of varying sizes, for which an optimised protocol for in toto image acquisition is established based on whole mount sample preparation using an optimal refractive index matched mounting media, opposing dual side imaging with two-photon microscopy for enhanced laser penetration, dual view registration, and weighted fusion for improved in toto sample data representation. For enhanced imaging speed in a two-photon microscope, parallel imaging was used, and the authors performed spectral unmixing analysis to avoid issues of signal cross-talk.

In the image analysis pipeline, different pre-treatments are done depending on the analysis to be performed (for nuclear segmentation - contrast enhancement and normalisation; for quantitative analysis of gene expression - corrections for optical artifacts inducing signal intensity variations). Stardist3D was used for the nuclear segmentation. The study analyses into properties of gastruloid nuclear density, patterns of cell division, morphology, deformation, and gene expression.

Strengths:

The methods developed are sound, well described, and well-validated, using a sample challenging for microscopy, gastruloids. Many of the established methods are very useful (e.g. registration, corrections, signal normalisation, lazy loading bioimage visualisation, spectral decomposition analysis), facilitate the development of quantitative research, and would be of interest to the wider scientific community.

Weaknesses:

A recommendation should be added on when or under which conditions to use this pipeline.

Reviewer #1 (Public review):

Summary:

In this manuscript, Rainey et al investigated the effects of transcription factors, ATOH1, POU4F3, GFI1, and SIX1 on the induction of hair cells from human pluripotent stem cells. The authors used a doxycycline-inducible system to control transgene expression and demonstrated significant improvement in the efficiency of MYO7A+ hair cell differentiation compared to the retrovirus-mediated approach. Next, they characterized differentiated cells using single-cell RNA-seq and identified a population of hair cell-like cells with gene expression profiles similar to the fetal human vestibular hair cells. Finally, they revealed the electrophysiological properties of induced cells consistent with those of mechanosensitive hair cells.

Strengths:

A key finding in this study is the rapid induction of cells expressing multiple hair cell markers that takes place within 21 days after overexpression of the four transcription factors. Additionally, the authors demonstrate that doxycycline-mediated gene overexpression outperforms retroviral-mediated gene transfer in terms of both the efficiency and reproducibility of hair cell induction. Furthermore, the authors demonstrate that these induced hair cells can be used to study hair cell protection from cisplatin ototoxicity.

Weaknesses:

The authors conclude that the induced cells lack distinct hair cell subtypes. However, the characterization of generated hair cells in single-cell RNA-seq data is insufficient. Additional vestibular or cochlear hair cell-enriched marker gene and protein expression should be analyzed. Moreover, the morphological features and mechanotransduction channel activity of the induced hair cells have not been analyzed.

Reviewer #2 (Public review):

Summary:

The study employs a specific set of transcription factors to promote lineage conversion of pluripotent stem cells into fetal hair cells. In pluripotent stem cells, an inducible expression system containing SIX1, ATOH1, POU4F3, and GFI1 (SAPG) was inserted into a safe harbor site. The stable cell line allows for doxycycline-inducible expression of transcription factors to generate induced hair cells (iHCs). These changes were observed in gene expression and electrophysiological properties. Comparing the transcriptome with iHCs derived from fibroblasts or primary human inner ear tissue suggested that it is similar to human hair cells. Although the iHCs did not have hair bundles - a key morphological feature of hair cells - the cellular system has immense potential for the field. The defined transcription factors allow for the dissection of gene regulatory networks and provide a molecular handle for the lineage conversion process. The results also suggest that the pluripotent stem cells were not directly converted into iHCs. Instead, there are several transitional cell states. These observations indicate that lineage conversion may still be hampered by yet undefined molecular obstacles and may help identify and overcome these in future work. The stable cell line allows for repeatable and large-scale screening studies, which is not feasible using primary human cells.

Strengths:

The cellular system is well-designed, with clearly described expression of the defined factors. Transient expression of the exogenous transcription factors SIX1, ATOH1, POU4F3, and GFI1 (SAPG) upon doxycycline induction is well-documented. Increased expression of endogenous SAPG factors suggests activation of self-regulatory feedback pathways during conversion. The stable iPS cell line provides a tool for the field to study lineage conversion or generate large numbers of iHCs.

Single-nuclear RNA-seq distinguishes distinct cell clusters and cellular transition states, validating the system's utility. A comparison of previously published data from iHCs and human fetal hair cells also suggested that iHCs are similar to developing human hair cells at the transcriptome level. Whole-cell patch clamp recordings show the generation of excitable cells with heterogeneous ion channel properties, which suggests a change in the cell type.

Weaknesses:

The interpretation of the snRNA-seq results could be strengthened by explaining the three distinct clusters for uninduced cells and how they transition into the iHC trajectory.

Although the analysis focuses on the cell cluster that represents iHCs (R5), a short discussion on what clusters R1-R4 (Figure 3B) represent would be useful. These cells do not express high levels of the SAPG factors even after 21 days of continuous doxycycline induction and may provide insight into hurdles that hamper lineage conversion.

RNA velocity analysis on single-nuclear RNA-seq is impressive but requires clarification on inferring the pseudotime trajectory. Some rationale and explanation on how the ratio of unspliced to spliced mRNA in the nucleus can be used to infer the differentiation trajectory would strengthen the discussion.

Reviewer #3 (Public review):

Summary:

In this manuscript, Robert N. Rainey et. al. reported a new approach to induce hair cell-like cells from a human induced pluripotent stem cell line. Based on the previously identified key transcription factors SIX1, ATOH1, POU4F3, and GFI1 (SAPG), which are essential for the conversion into induced hair cell-like cells in mice. The manuscript represents an advance over the authors' previous published work, which used the same transcription factors but viral gene delivery.

Strengths:

The manuscript is clear and well-written. The background is easy to follow for people outside of the field. The data are well-organized and well-described. The evidence is strong.

Weaknesses:

General comments:

(1) The manuscript generated multiple valuable datasets for the field. However, the data are not deposited in the hearing field central resource for gene expression (umgear.org), and links are not provided in the figure legends to datasets or dataset collections in the gEAR. This is a major comment as it significantly decreases the utility of the datasets generated in the manuscript and decreases the ease of reuse of the data. This is a flaw that could be easily addressed by uploading the data and generating links to datasets in the body of the manuscript.

(2) If a pulse of Dox induces the SAPG and starts the conversion process, it is not clear why the analyzed cells were treated for 21 days - a duration that can negatively affect the fate of converting hair cells.

(3) Foxj1 is listed as a supporting cell-specific gene; however, it is expressed in the cochlear hair cells until the end of the first postnatal week.

(4) It is not clear why cells were sorted for analysis of the retrovirally induced cells but not in the stable cell line, which also expressed tdTomato.

(5) Figure 1D and Supplementary Figure 2: the authors state that the endogenous ATOH1 and POU4F3 expressions decrease after 7d. Should the authors have stats on the graphs?

(6) Supplementary Figure 4: OCT4 should be replaced by POU5F1 (or vice versa) for consistency.

(7) The authors show the induction or decrease of the exogenous transcription factor expressions by RT-qPCR. It would be nice, if possible, to also see either WB or immuno with antibodies directed against the tags.

Bioinformatic comments:

(1) In the previous study (Menendez et al. 2020), ATAC-seq and regulatory elements are employed in the analysis, while a similar analysis is missing in this study. It will be informative to show the motif enrichment analysis at promoter regions of differentially expressed genes (DEGs) in the most hair cell-like cluster 3 (RV-R3).

(2) In the previous study (Menendez et al. 2020), it was stated that SAPG can convert supporting cells to hair cells, while in this study, the authors stated that "reprogramming with SAPG does not activate supporting cell networks in the stable cell line". Can the authors provide more analysis/comments on this difference?

(3) The approach in this study tends to generate a very similar level of expression for the SAPG factors, while the real levels of expression might be different for actual transcriptional regulation, eg, Figure 1C. How will this very close expression level of SAPG affect the features of the induced hair cell?

(4) Figure 5B, missing color bar to show the DEG strength in the heatmap. Why are Six1 and Gfi1 not shown in this heatmap?

Reviewer #1 (Public review):

Summary:

This work integrates two timepoints from the Adolescent Brain Cognitive Development Study to understand how neuroimaging, genetic and environmental data contribute to the predictive power of mental health variables in predicting cognition in a large early adolescent sample. Their multimodal and multivariate prediction framework involves a novel opportunistic stacking model to handle complex types of information to predict variables that are important in understanding mental health-cognitive performance associations.

Strengths:

The authors are commended for incorporating and directly comparing the contribution of multiple imaging modalities (task fMRI, resting state fMRI, diffusion MRI, structural MRI), neurodevelopmental markers, environmental factors and polygenic risk scores in a novel multivariate framework (via opportunistic stacking), as well as interpreting mental health-cognition associations with latent factors derived from Partial Least Squares. The authors also use a large well-characterized and diverse cohort of adolescents from the Adolescent Brain Cognitive Development (ABCD) Study. The paper is also strengthened by commonality analyses to understand the shared and unique contribution of different categories of factors (e.g., neuroimaging vs mental health vs polygenic scores vs sociodemographic and adverse developmental events) in explaining variance in cognitive performance

Weaknesses:

The paper is framed with an over-reliance on the RDoC framework in the introduction, despite deviations from the RDoC framework in the methods. The field is also learning more about RDoC's limitations when mapping cognitive performance to biology. The authors also focus on a single general factor of cognition as the core outcome of interest as opposed to different domains of cognition. The authors could consider predicting mental health rather than cognition. Using mental health as a predictor could be limited by the included 9-11 year age range at baseline (where mental health concerns are likely to be low or not well captured), as well as the nature of how the data was collected, i.e., either by self-report or from parent/caregiver report.

Comments on revisions:

The authors have done an excellent job of addressing my comments. I have no other suggestions to add. Great work!

Reviewer #2 (Public review):

Summary:

This paper by Wang et al. uses rich brain, behaviour, and genetics data from the ABCD cohort to ask how well cognitive abilities can be predicted from mental health related measures, and how brain and genetics influence that prediction. They obtain an out of sample correlation of 0.4, with neuroimaging (in particular task fMRI) proving the key mediator. Polygenic scores contributed less.

Strengths:

This paper is characterized by the intelligent use of a superb sample (ABCD) alongside strong statistical learning methods and a clear set of questions. The outcome - the moderate level of prediction between brain, cognition, genetics and mental health - is interesting, and particularly important is the dissection of which features best mediate that prediction and how developmental and lifestyle factors play a role.

Weaknesses:

There are relatively few weaknesses to this paper. It has already undergone review at a different journal, and the authors clearly took the original set of comments into account in revising their paper. Overall, while the ABCD sample is superb for the questions asked, it would have been highly informative to extend the analyses to datasets containing more participants with neurological/psychiatric diagnoses (e.g. HBN, POND) or extending it into adolescent/early adult onset psychopathology cohorts. But it is fair enough that the authors want to leave that for future work.

Reviewer #1 (Public review):

Summary:

In this work, Wang et al. use a combination of genetic tools, novel experimental approaches and biomechanical models to quantify the contribution of passive leg forces in Drosophila. They also deduce that passive forces are not sufficient to support the body weight of the animal. Overall, the contribution of passive forces reported in this work is much less than what one would expect based on the size of the organism and previous literature from larger insects and mammals. This is an interesting finding, but some major caveats in their approach remain unanswered.

Strengths:

(1) The authors combine experimental measurements and modeling to quantify the contributions of passive forces at limb joints in Drosophila.

(2) The authors replicate a previous experimental strategy (Hooper et al 2009, J. Neuro) to suspend animals in air for measuring passive forces and, as in previous studies, find that passive forces are much stronger than gravitational forces acting on the limbs. While in these previous studies using large insects, a lot of invasive approaches for accurately quantifying passive forces are possible (e.g., physically cutting of nerves, directly measuring muscle forces in isolated preparations, etc), the small size of Drosophila makes this difficult. The authors overcome this using a novel approach where they attach additional weight to the leg (changes gravitational force) and inactivate motor neurons (remove active forces). With a few approximations and assumptions, the authors then deduce the contribution of passive forces at each joint for each leg.

(3) The authors find interesting differences in passive forces across different legs. This could have behavioral implications.

(4) Finally, the authors compare experimental results of how a free-standing Drosophila is lowered ("falls down") on silencing motor neurons, to a biomechanical "OpenSim" model for deducing the role of passive forces in supporting the body weight of the fly. Using this approach, they conclude that passive forces are not sufficient to support the body weight of the fly.

Weaknesses:

(1) Line 65 "(Figure 1A). Inactivation causes a change in the leg's rest position; however, in preliminary experiments, the body rotation did not have a large effect on the rest positions of the leg following inactivation. This result is consistent with the one already reported for stick insects and shows that passive forces within the leg are much larger than the gravitational force on a leg and dominate limb position [1]." This is the direct replication of the previous work by Hooper et al 2009 and therefore authors should ideally show the data for this condition (no weight attached).

(2) The authors use vglut-gal4, a very broad driver for inactivating motor neurons. The driver labels all glutamatergic neurons, including brain descending neurons and nerve cord interneurons, in addition to motor neurons. Additionally, the strength of inactivation might differ in different neurons (including motor neurons) depending on the expression levels of the opsins. As a result, in this condition, the authors might not be removing all active forces. This is a major caveat that authors do not address. They explore that they are not potentially silencing all inputs to muscles by using an additional octopaminergic driver, but this doesn't address the points mentioned above. At the very least, the authors should try using other motor neuron drivers, as well as other neuronal silencers. This driver is so broad that authors couldn't even use it for physiology experiments. Additionally, the authors could silence VGlut-labeled motor neurons and record muscle activity (potentially using GCaMP as has been done in several recent papers cited by the authors, Azevedo et al, 2020) as a much more direct readout.

(3) Figure 4 uses an extremely simplified OpenSim model that makes several assumptions that are known to be false. For example, the Thorax-Coxa joint is assumed to be a ball and socket joint, which it is not. Tibia-tarsus joint is completely ignored and likely makes a major contribution in supporting overall posture, given the importance of the leg "claw" for adhering to substrates. Moreover, there are a couple of recent open-source neuromechanical models that include all these details (NeuromechFly by Lobato-Rios et al, 2022, Nat. Methods, and the fly body model by Vaxenburg et al, 2025, Nature). Leveraging these models to rule in or rule out contributions at other joints that are ignored in the authors' OpenSim model would be very helpful to make their case.

(4) Figure 5 shows the experimental validation of Figure 4 simulations; however, it suffers from several caveats.

a) The authors track a single point on the head of the fly to estimate the height of the fly. This has several issues. Firstly, it is not clear how accurate the tracking would be. Secondly, it is not clear how the fly actually "falls" on VGlut silencing; do all flies fall in a similar manner in every trial? Almost certainly, there will be some "pitch" and "role" in the way the fly falls. These will affect the location of this single-tracked point that doesn't reflect the authors' expectations. Unless the authors track multiple points on the fly and show examples of tracked videos, it is hard to believe this dataset and, hence, any of the resulting interpretations.

b) As described in the previous point, the "reason" the fly falls on silencing all glutamatergic neurons could be due to silencing all sorts of premotor/interneurons in addition to the silencing of motor neurons.

c) (line 175) "The first finding is that there was a large variation in the initial height of the fly (Figure 5C), consistent with a recent study of flies walking on a treadmill[20]." The cited paper refers to how height varies during "walking". However, in the current study, the authors are only looking at "standing" (i.e. non-walking) flies. So it is not the correct reference. In my opinion, this could simply reflect poor estimation of the fly's height based on poor tracking or other factors like pitch and role.

d) "The rate at which the fly fell to the ground was much smaller in the experimental flies than it was in the simulated flies (Figure 5E). The median rate of falling was 1.3 mm/s compared to 37 mm/s for the simulated flies (Figure 5F). (Line 190) The most likely reason for the longer than expected time for the fly to fall is delays associated with motor neuron inactivation and muscle inactivation." I don't believe this reasoning. There are so many caveats (which I described in the above points) in the model and the experiment, that any of those could be responsible for this massive difference between experiment and modeling. Simply not getting rid of all active forces (inadequate silencing) could be one obvious reason. Other reasons could be that the model is using underestimates of passive forces, as alluded to in point 3.

(5) Final figure (Figure 6) focuses on understanding the time course of neuronal silencing. First of all, I'm not entirely sure how relevant this is for the story. It could be an interesting supplemental data. But it seems a bit tangential. Additionally, it also suffers from major caveats.

a) The authors now use a new genetic driver for which they don't have any behavioral data in any previous figures. So we do not know if any of this data holds true for the previous experiments. The authors perform whole-cell recordings from random unidentified motor neurons labeled by E49-Gal4>GtACR1 to deduce a time constant for behavioral results obtained in the VGlut-Gal4>GtACR1 experiments.

b) The DMD setup is useful for focal inactivation, however, the appropriate controls and data are not presented. Line 200 "A spot of light on the cell body produces as much of the hyperpolarization as stimulating the entire fly (mean of 11.3 mV vs 13.1 mV across 9 neurons). Conversely, excluding the cell body produces only a small effect on the MN (mean of 2.6 mV)." First of all, the control experiment for showing that DMD is indeed causing focal inactivation would be to gradually move the spot of light away from the labeled soma, i.e. to the neighboring "labelled" soma and show that there is indeed focal inactivation. Instead authors move it quite a long distance into unlabeled neuropil. Secondly, I still don't get why the authors are doing this experiment. Even if we believe the DMD is functioning perfectly, all this really tells us is that a random subset motor neurons (maybe 5 or 6 cells, legend is missing this info) labeled by E49-Gal4 is strongly hyperpolarized by its own GtACR1 channel opening, rather than being impacted because of hyperpolarizations in other E49-Gal4 labeled neurons. This has no relevance to the interpretation of any of the VGlut-Gal4 behavioral data. VGLut-Gal4 is much broader and also labels all glutamatergic neurons, most of which are inhibitory interneurons whose silencing could lead to disinhibition of downstream networks.

Reviewer #2 (Public review):

Summary:

The authors aim to quantify passive muscle forces in the legs of Drosophila, and test the hypothesis that these forces would be sufficient to support body weight in small insects. They take advantage of the genetic tools available in Drosophila, and use a combination of genetic silencing (optogenetic inactivation of motor neurons), kinematic measurements, and simulations using OpenSim. This integrative toolkit is used to examine the role of passive torques across multiple leg joints. They find that passive forces are weaker than expected - in particular, passive forces were found to be too weak to support the body weight of the fly. This challenges previous scaling assumptions derived from studies in larger insects and has potential implications for our understanding of motor control in small animals.

Strengths:

The primary strength of this work lies in its integration of multiple analyses. By pulling together simulations, kinematic measurements from high-resolution videos, and genetic manipulation, they are able to overcome limitations of past studies. In particular, optogenetic manipulation allowed for measurements to be made in whole animals, and the modeling component is valuable because it both validates experimental findings and elucidates the mechanism behind some of the observed dynamic consequences (e.g., the rapid fall after motor inactivation). The conclusions made in the study are well-supported by the data and could have an impact on a number of fields, including invertebrate neurobiology and bioinspired design.

Weaknesses:

While (as mentioned above) the study's conclusions are well-supported by the results and modeling, limitations arise because of the assumptions made. For instance, using a linear approximation may not hold at larger joint angles, and future studies would benefit from accounting for nonlinearities. Future studies could also delve into the source of passive forces, which is important for more deeply understanding the anatomical and physical basis of the results in this study. For instance, assessments of muscle or joint properties to correlate stiffness values with physical structure might be an area of future consideration

Reviewer #3 (Public review):

Summary:

The authors present a novel method to measure passive joint torques - torques due to internal forces other than active muscle contraction - in the fruit fly: genetically inactivating all motor neurons in intact limb acted upon by a gravitational load results in a change in limb configuration; evaluating the moment equilibrium condition about the limb joints then yields a direct estimate of the passive joint torques. Deactivating all motor neurons in an intact standing fly provided two further conclusions: First, because deactivation causes the fly to drop to the floor, the passive joint torques are deemed insufficient to maintain rotational equilibrium against the body weight; using a multi-body-dynamics simulation, the authors estimate that the passive torques would need to be about 40-80 times higher to maintain a typical posture without active muscle action. Second, a delay between the motor neuron inactivation and the onset of the "free fall" motivates the authors to invoke a simple exponential decay model, which is then used to derive a time constant for muscle deactivation, in robust agreement with direct electro-physiological recordings.

Strengths:

The experimental design that permits determination of passive joint torques is elegant, effective, novel, and altogether excellent; it permits measurements previously impossible. A careful error analysis is presented, and a spectrum of technically challenging methods, including multi-body dynamics and e-phys, is deployed to further interpret and contextualise the results.

Weaknesses:

(1) Passive torques are measured, but only some short speculative statements, largely based on previous work, are offered on their functional significance; some of these claims are not well supported by experimental evidence or theoretical arguments. Passive forces are judged as "large" compared to the weight force of the limb, but the arguably more relevant force is the force limb muscles can generate, which, even in equilibrium conditions, is already about two orders of magnitude larger. The conclusion that passive forces are dynamically irrelevant seems natural, but contrasts with the assertion that "passive forces [...] will have a strong influence on limb kinematics". As a result, the functional significance of passive joint torques in the fruit fly, if any, remains unclear, and this ambiguity represents a missed opportunity. We now know the magnitude of passive joint torques - do they matter and for what? Are they helpful, for example, to maintain robust neuronal control, or a mechanical constraint that negatively impacts performance, e.g., because they present a sink for muscle work?

(2) The work is framed with a scaling argument, but the assumptions that underpin the associated claims are not explicit and can thus not be evaluated. This is problematic because at least some arguments appear to contradict textbook scaling theory or everyday experience. For example, active forces are assumed to scale with limb volume, when every textbook would have them scale with area instead; and the asserted scaling of passive forces involves some hidden assumptions that demand more explicit discussion to alert the reader to associated limitations. Passive forces are said to be important only in small animals, but a quick self-experiment confirms that they are sufficient to stabilize human fingers or ankles against gravity, systems orders of magnitude larger than an insect limb, in seeming contradiction with the alleged dominance of scale. Throughout the manuscript, there are such and similar inaccuracies or ambiguities in the mechanical framing and interpretation, making it hard to fairly evaluate some claims, and rendering others likely incorrect.

Reviewer #1 (Public review):

Summary:

Perlee et al. sought to generate a zebrafish line where CRISPR-based gene editing is exclusively limited to the melanocyte lineage, allowing assessment of cell-type restricted gene knockouts. To achieve this, they knocked in Cas9 to the endogenous mitfa locus, as mitfa is a master regulator of melanocyte development. The authors use multiple candidate genes - albino, sox10, tuba1a, ptena/ptenb, tp53 - to demonstrate that their system induces lineage-restricted gene editing. This method allows researchers to bypass embryonic lethal and non-cell autonomous phenotypes emerging from whole body knockout (sox10, tuba1a), drive directed phenotypes, such as depigmentation (albino), and induce lineage-specific tumors, such as melanomas (ptena/ptenb, tp53, when accompanied with expression of BRAFV600E). The main weakness of the manuscript is that the mechanistic explanations proposed to underlie the presented phenotypes are minimally interrogated, but nonetheless interesting and motivating for future experimentation. Overall, there is a clear use for this genetic methodology, and its implementation will be of value to many in vivo researchers.

Strengths:

The strongest component of this manuscript is the genetic control offered by the mitfa:Cas9 system and the ability to make stable, lineage-specific knockouts in zebrafish. This is exemplified by the studies of tuba1a, where the authors nicely show non-cell autonomous mechanisms have obfuscated the role of this gene in melanocyte development. In addition, the mitfa:Cas9 system is elegantly straightforward and can be easily implemented in many labs. Mostly, the figures are clean, controls are appropriate, and phenotypes are reproducible. The invented method is a welcome addition to the arsenal of genetic tools used in zebrafish. The authors kindly and honestly responded to reviewer criticism, which has led to an improved manuscript and a pleasant review process.

Weaknesses:

The authors argue that the benefit of their system is the maintenance of endogenous regulatory elements. However, no direct comparison is made with other tools that offer similar genetic control, such as MAZERATI. This is a missed opportunity to provide researchers the ability to evaluate these two similar genetic approaches. There is a slight concern that tumor onset with this system is hindered by the heterozygous state it imparts to the lineage master regulator (here, mitfa). The authors do a good job at addressing these issues in the Discussion, but experimentation would have been appreciated. Additionally, the authors claim 86% of mitfa+ cells express Cas9. The image shown in Figure 1C does not do a convincing job at showing this percentage.

Another weakness of the manuscript regards minimally investigated mechanistic explanations for each biological vignette. Detailed mechanistic information is indeed out-of-scope for this manuscript, which intends to prove the efficacy of a genetic tool. Readers are cautioned to use the mechanistic insights from these vignettes as inspiration rather than bona fide truth.

The authors performed the necessary experiments to address each of the reviewers' concerns and thereby quell any substantial issues raised during the first review. They have additionally edited their language appropriately to make their claims more accurate. Their efforts during the review process are appreciated.

Conclusion:

The authors were highly receptive to reviewer comments and improved their manuscript from the first submission. The authors were successful in their goal of creating a rapid genetic approach to study cell-type specific genetic insults in vivo. They have presented multiple interesting and convincing stories to support the power of their invented methodology. The refined mechanisms underlying their observed phenotypes may be lacking but this does not take away from the methodological benefit this manuscript provides to the large field of in vivo researchers.

Reviewer #3 (Public review):

Summary:

Perlee et al. present a method for generating cell-type restricted knockouts in zebrafish, focusing on melanocytes. For this method, the authors knock-in a Cas9 encoding sequence into the mitfa locus. This mitfaCas9 line has restricted Cas9 expression, allowing the authors to generate melanocyte-specific knockouts rapidly by follow-up injection of sgRNA expressing transposon vectors.

The paper presents some interesting vignettes to illustrate the utility of their approach. These include 1) a derivation of albino mutant fish as a demonstration of the method's efficiency, 2) an interrogation and novel description of tuba1a/tuba1c as a potential non-autonomous contributor to melanosome dispersion, and 3) the generation of sox10 deficient melanoma tumors that show "escape" of sox10 loss through upregulation of sox9. The latter two examples highlight the usefulness of cell-type targeted knockouts (Body-wide sox10 and tuba1a loss elicit developmental defects). Additionally, the tumor models involve highly multiplexed sgRNAs for tumor initiation which is nicely facilitated by the stable Cas9.

Strengths:

The approach is clever and could prove very useful for studying melanocytes and other cell types. As the authors hint at in their discussion, this approach would become even more powerful with the generation of other Cas9-restricted lineages so a single sgRNA construct can be screened across many lineages rapidly (or many sgRNA and fish lines screened combinatorially).

The biological findings used to demonstrate the power of the approach are interesting in their own right. The non-autonomous effect of tuba1a/tuba1c loss on melanosome dispersion are striking and demonstrates very nicely how one could use Perlee et al.'s approach to search for similar mechanisms systematically. The dual targeting nature of the tuba1a/tuba1c sgRNA also suggests similar approaches might be explored for knocking out paralogs. The observation of the sox9 escape mechanism with sox10 loss is a beautiful demonstration of the relevance of SOX10/SOX9's reciprocal regulation in vivo. This system would be a very nice model for further interrogating mechanisms/interventions surrounding Sox10 in melanoma.

Finally, the figure presentation is very nice. This work involves complex genetic approaches, including multiple fish generations and multiplexed construct injections. The vector diagrams and breeding schemes in the paper make everything very clear/"grok-able," and the paper was enjoyable to read.

Weaknesses:

The authors' claims are grounded and tested rigorously. The major weaknesses that we raised in the first round of reviews were either addressed experimentally or are now detailed as limitations in the text. Congrats on the beautiful paper!

Reviewer #1 (Public review):

Summary:

This manuscript by Garbelli et al. investigates the roles of excitatory amino acid transporters (EAATs) in retinal bipolar cells. The group previously identified that EAAT5b and EAAT7 are expressed at the dendritic tips of bipolar cells, where they connect with photoreceptor terminals. The previous study found that the light responses of bipolar cells, measured by electroretinogram (ERG) in response to white light, were reduced in double mutants, though there was little to no reduction in light responses in single mutants of either EAAT5b or EAAT7.

The current study further explores the roles of EAAT5b and EAAT7 in bipolar cells' chromatic responses. The authors found that bipolar cell responses to red light, but not to green or UV-blue light, were reduced in single mutants of both EAAT5b and EAAT7. In contrast, UV-blue light responses were reduced in double mutants. Additionally, the authors observed that EAAT5b, but not EAAT7, is strongly localized in the UV cone-enriched area of the eye, known as the "Strike Zone (SZ)." This led them to investigate the impact of the EAAT5b mutation on prey detection performance, which is mediated by UV cones in the SZ. Surprisingly, contrary to the predicted role of EAAT5b in prey detection, EAAT5b mutants did not show any changes in prey detection performance compared to wild-type fish. Interestingly, EAAT7 mutants exhibited enhanced prey detection performance, though the underlying mechanisms remain unclear.

The distribution of EAAT7 protein in the outer plexiform layer across the eye correlates with the distribution of red cones. Based on this, the authors tested the behavioral performance driven by red light in EAAT5b and EAAT7 mutants. The results here were again somewhat contrary to predictions based on ERG findings and protein localization: the optomotor response was reduced in EAAT5b mutants, but not in EAAT7 mutants.

Strengths:

Although the paper lacks cohesive conclusions, as many results contradict initial predictions as mentioned above, the authors discuss possible mechanisms for these contradictions and suggest future avenues for study. Nevertheless, this paper demonstrates a novel mechanism underlying chromatic information processing.<br /> The manuscript is well-written, the data are well-presented, and the analysis is thorough.

Weaknesses:

I have only a minor comment. The authors present preliminary data on mGluR6b distribution across the eye. Since this result is based on a single fish, I recommend either adding more samples or removing this data, as it does not significantly impact the paper's main conclusions.

Comments on revisions:

The authors addressed all of the concerns that I had in the original manuscript.

Reviewer #2 (Public review):

Garbelli et. al. set out to elucidate the function of two glutamate transporters, EAAT5b and EAAT7, in the functional and behavioral responses to different wavelengths of light. The question is an interesting one because these transporters are well-positioned to affect responses to light, and their distribution in the retina suggests that they could play differential roles in visual behaviors. However, the resolution of the functional and behavioral data presented here means that the conclusions are necessarily a bit vague.

In Figure 1, the authors show that the double KO has a decreased ERG response to UV/blue and red wavelengths. However, the individual mutations both only affect the response to red light, suggesting that they might affect behaviors such as OMR that typically rely on this part of the visual spectrum. However, there was no significant change in the response to UV/blue light of any intensity, making it unclear whether the mutations could individually play roles in detection of UV prey. Based on the later behavioral data, it seems likely that at least the EAAT7 KO should affect retinal responses to UV light, but it may be that the ERG does not have the spatial or temporal resolution to detect the difference, or that the presence of blue light overwhelmed any effect of the individual knockouts on the response to UV light.

In Figures 5 and 6, the authors compare the two knockouts to wild-type fish in terms of their sensitivity to UV prey in a hunting assay. The EAAT5b KO showed no significant impairment in UV sensitivity, while the EAAT7 KO fish actually had an increased hunting response to UV prey. However, there is no comparison of the KO and WT responses to different UV intensities, only in bulk, so we cannot conclude that the EAAT7 KO is allowing the fish to detect weaker prey-like stimuli.

In Figure 7, the EAAT5b KO seems to cause a decrease in OMR behavior to red grating stimuli, but only one stimulus is tested, so it is unclear whether this is due to a change in visual sensitivity or resolution.

The conclusions made in the manuscript are appropriately conservative; the abstract states that these transporters somehow influence prey detection and motion sensing, and this is likely true.

In terms of impact on the field, this work highlights the potential importance of these two transporters to visual processing, but further studies will be required to say how important they are and exactly what they are doing.

Reviewer #1 (Public review):

Summary

The authors present a new protocol to assess social dominance in pairs and triads of C57BL/6j mice, based on a competition to access a hidden food pellet. Using this new protocol, the authors have been able to identify stable ranking among male and female pairs, while reporting more fluctuant hierarchies among triads of males. Ranking readout identified with this new apparatus was compared to the outcome obtained with the same animals competing in the tube and in the warm spot tests, which have been both commonly used during the last decade to identify social ranks in rodents under laboratory conditions.

Strengths

FPCT allows for an easy and fast identification of a winner and loser in a context of food competition. The apparatus and the protocol are relatively easy and quick to implement in the lab and free from any complex post processing/analysis, which qualifies it for wide distribution, particularly within laboratories that do not have the resources to implement more sophisticated protocols. Hierarchical readout identified through the FPCT correlates with social ranks identified with the tube and the warm spot tests, which have been widely adopted during the last decade and allow for study comparison.

Weaknesses

While the FPCT is validated by the tube and the warm spot test, this paper would have gained strength by providing a more ethologically based validation. Tube and warm spot tests have been shown to provide conflicting results and might not be a sufficient measurement for social ranking (see Varholik et al, Scientific Reports, 2019; Battivelli et al, Biological Psychiatry, 2024). Instead, a general consensus pushing toward more ethological approaches for neuroscience studies is emerging.<br /> Other papers already successfully identified social ranks dyadic food competition, using relatively simple scoring protocol (see, for example, Merlot et al., 2006), within a more naturalistic set-up, allowing the 2 opponents to directly interact while competing for the food. A potential issue with the FPCT, is that the opponents being isolated from each other, the normal inhibition expected to appear in subordinates in presence of a dominant to access food, could be diminished, and usually avoiding subordinates could be more motivated to push for the access to the food pellet.

Comments on revisions:

We thank the authors for the significant improvement of the English in the revised version and for the replacement of some conceptual terms that now seem more relevant and appropriate. We only noticed that the term "society" remains in use, although it might not be appropriate to describe a mouse colony (see previous review).

Conclusive remarks

Although this protocol aims to provide a novel approach to evaluate social ranks in mice, it is not clear how it really brings a significant advance in neuroscience research. The FPCT dynamic is very similar to the one observed in the tube test, where mice compete to navigate forward in a narrow space, constraining the opponent to go backwards. The main difference between the FPCT and the tube test is the presence of food between the opponents. In the tube test, food reward was initially used to increase motivation to cross the tube and push the opponent upon the testing day. This component has been progressively abandoned, precisely because it was not necessary for the mice to compete in the tube.<br /> This paper would really bring a significant contribution to the field by providing a neuronal imaging or manipulation correlate to the behavioral outcome obtained by the application of the FPCT.

Reviewer #2 (Public review):

Summary:

In this study, the authors have devised a novel assay to measure relative social rank in mice that is aimed at incorporating multiple aspects of social competition while minimizing direct contact between animals. Forming a hierarchy often involves complex social dynamics related to competitive drives for different fundamental resources, including access to food, water, territory and sexual mates. This makes the study of social dominance and its neural underpinnings hard, warranting the development of new tools and methods that can help understand both social function as well as dysfunction.

Strengths:

This study showcases an assay called the Food Pellet Competition Test, where cagemate mice compete for food, without direct contact, by pushing a block in a tube from opposite directions. This task ran with stranger mice leads to more variable outcomes, suggesting co-housing helps stabilize outcomes. The authors have attempted to quantify motivation to obtain the food independent of other factors by running the assay under two conditions: one where the food is accessible and one where it isn't. This assay results in high outcome consistency across days for females and males paired housed and for male groups of three. Further, the determined social ranks correlate strongly with two common assays: the tube test and the warm spot test.

Weaknesses:

This new assay has limited ethological validity since mice do not compete for food without touching each other with a block in the middle. In addition, the assay may only be valid for a single trial per day, making its utility for recording neural recordings and manipulations limited to a single sample per mouse. The authors claim, as currently stated in results, for the new control experiment in 1H-J is not warranted given that 6/8 mice had majority winning or losing across all strangers.

Reviewer #3 (Public review):

Summary:

The laboratory mouse is an ideal animal to study the neural and psychological underpinnings of social dominance behavior because of its economic cost and the animals' readiness to display dominant and subordinate behaviors in simple and testable environments. Here, a new and novel method for measuring dominance and the individual social status of mice is presented using a food competition assay. Historically, food competition assays have been avoided because they occur in an open arena or the home cage, and it can be difficult to assess who gets priority access to the resource and to avoid aggressive interactions such as bite wounding. Now, the authors have designed a narrow rectangular arena separated in half by a sliding floor-to-ceiling obstacle, where the mice placed at opposite sides of the obstacle compete by pushing the obstacle to gain priority access to a food pellet resting on the arena floor under the obstacle. One can also place the food pellet within the obstacle to restrict priority access to the food and measure the time or effort spent pushing the obstacle back and forth. As hypothesized, the outcomes in the food competition test were significantly consistent with those of the more common tube test (space competition) and warm spot competition test. This suggests that these animals have a stereotypic dominance organization that exists across multiple resource domains (i.e., food, space, and temperature). Only male and female C57 mice in same-sex pairs or triads were tested.

Strengths:

The design of the apparatus and the inclusion of females are significant strengths within the study.

Weaknesses:

There are at least two major weaknesses of the study: the test with unfamiliar non-cagemates and not providing the mice time to recognize who they are competing with.

The authors conclude in the first section of the results that they "did not detect significant difference in winning/losing results between unfamiliar non-cagemate male mice." Given the data and analysis provided, I believe this statement is false. My understanding is that the authors would like to show that the establishment of social relationships (i.e., familiarity) is necessary for FPCT to distinguish social ranks of mice. There are many ways to test this. The simplest would be to randomly pair unfamiliar non-cagemates that are housed in isolation with one another and see if they perform at chance, individually. The more involved empirical way would be to measure the ranks of mice in a social group, then test them with unfamiliar non-cagemate mice to see if they maintain their outcomes regardless of social familiarity, or return to chance outcomes when paired with non-cagemates. Figure 1I clearly shows that they did not perform at chance. Since the outcome is win or lose, then the probability of getting all of one outcome 4 times in a row would be 1 in 16. The data shows that this occured twice, so 2 mice of 8 had the same outcome 4 times in a row (i.e., Mouse B3 and A1). So, they did not perform at chance. I am not even sure if there are enough animals here to test this question. One may need to consult a mathematician. Moreover, the original tube-test study by Lindzey et al. 1961 (https://www.nature.com/articles/191474a0) used unfamiliar non-cagemate male mice, and showed that 100% of the A/alb strain won more than half of their oppositions against C3H and DBA/8 mice. Thus, A/alb mice were more "dominant" mice relative to C3H or DBA/8. Taking into consideration the results, is mouse A1 naturally dominant? So maybe it doesn't matter what mouse you pair with it, it will always win? If this is true, is "individual identification of the partner" actually necessary to get this outcome? All they have to do is push to get the food reward, does it matter who is on the other side? If one wants to measure social dominance relationships, then it should matter who is on the other side. If one would like to measure attributes of dominant behavior (e.g., pushing), then one may do so and not insinuate a social link. Studying dominance relationships (i.e., social ranking) of animals is an extremely difficult task. We must ensure that we are not assigning something about a relationship that does not exist. Please read "Dominance: The baby and the bathwater" but Irwin Bernstein, https://annas-archive.org/scidb/10.1017/s0140525x00009614/

Unlike the tube test and warm spot test, the food competition test presented here provides no opportunity for the animals to identify their opponent. That is, they cannot sniff their opponent's fur or anogenital region, which would allow them an opportunity to identify them individually. Thus, as the authors state, the test only measures a psychological motivation to get a food reward. Notably, the outcome in the direct and indirect testing of food competition is in agreement, leaving many to wonder whether they are measuring the social relationship or the effort an individual puts forth in attaining a food reward regardless of the social opponent. Specifically, in the direct test, an individual can retrieve the food reward by pushing the obstacle out of the way first. In the indirect test, the animals cannot retrieve the reward and can only push the obstacle back and forth, which contains the reward inside. In Figure 2F, you can see that winners spent more time pushing the block in the indirect test--albeit not significantly. Thus, whether the test measures a social relationship or just the likelihood to gain priority access to food is unclear. To rectify this issue, the authors could provide an opportunity for the animals to interact before lowering the obstacle and raising(?) a food reward. They may also create a very long one-sided apparatus to measure the amount of effort an individual mouse puts forth in the indirect test with only one individual-or any situation with just one mouse where the moving obstacle is not pushed back, and the animal can just keep pushing until they stop. This would require another experiment. It also may not tell us much more since it remains unclear whether inbred mice can individually identify one another (see https://doi.org/10.1098/rspb.2000.1057 for more details).

Reviewer #2 (Public review):

Summary:

In this manuscript, Wang et al analyze ~17,000 transcriptomes from 35 human tissues from the GTEx database and address transcriptomic variations due to age and sex. They identified both gene expression changes as well as alternative splicing events that differ among sexes. Using breakpoint analysis, the authors find sex dimorphic shifts begin with declining sex hormone levels with males being affected more than females. This is an important pan-tissue transcriptomic study exploring age and sex-dependent changes although not the first one.

Strengths:

(1) The authors use sophisticated modeling and statistics for differential, correlational and predictive analysis.

(2) The authors consider important variables such as genetic background, ethnicity, sampling bias, sample sizes, detected genes etc.

(3) This is likely the first study to evaluate alternative splicing changes with age and sex at a pan-tissue scale.

(4) Sex dimorphism with age is an important topic and is thoroughly analyzed in this study.

Reviewer #3 (Public review):

Summary:

In this study, Wang et al utilized the available GTEx data to compile a comprehensive analysis that attempt to reveal aging-related sex-dimorphic gene expression as well as alternative splicing changes in human. The key conclusions based upon their analysis are that 1) extensive sex-dimorphisms during aging with distinct patterns of change in gene expression and alternative splicing (AS), and 2) the male-biased age-associated AS events have a stronger association with Alzheimer's disease, and 3) the females-biased events are often regulated by several sex-biased splicing factors that may be controlled by estrogen receptors. They further performed break-point analysis and reveal in males there are two main breakpoints around ages 35 and 50, while in female only one breakpoint at 45.

Strengths:

This study sets an ambitious goal, leveraging the extensive GTEx dataset to investigate aging-related, sex-dimorphic gene expression and alternative splicing changes in humans. The research addresses a significant question, as our understanding of sex-dimorphic gene expression in the context of human aging is still in its early stages. Advancing our knowledge of these molecular changes is vital for identifying therapeutic targets for age-related diseases and extending human healthspan. The study is highly comprehensive, and the authors are commendable for their attempted thorough analysis of both gene expression and alternative splicing-an area often overlooked in similar studies.

Reviewer #1 (Public review): <br /> The authors survey the ultrastructural organization of glutamatergic synapses by cryo-ET and image processing tools using two complementary experimental approaches. The first approach employs so-called "ultra-fresh" preparations of brain homogenates from a knock-in mouse expressing a GFP-tagged version of PSD-95, allowing Peukes and colleagues to specifically target excitatory glutamatergic synapses. In the second approach, direct in-tissue (using cortical and hippocampal regions) targeting of the glutamatergic synapses employing the same mouse model is presented. In order to ascertain whether the isolation procedure causes any significant changes in the ultrastructural organization (and possibly synaptic macromolecular organization) the authors compare their findings using both of these approaches. The quantitation of the synaptic cleft height reveals an unexpected variability, while the STA analysis of the ionotropic receptors provides insights into their distribution with respect to the synaptic cleft.

The main novelty of this study lies in the continuous claims by the authors that the sample preservation methods developed here are superior to any others previously used. This leads them as well to systematically downplay or directly ignore a substantial body of previous cryo-ET studies of synaptic structure. Without comparisons with the cryo-ET literature, it is very hard to judge the impact of this work in the field. Furthermore, the data does not show any better preservation in the so-called "ultra-fresh" preparation than in the literature, perhaps to the contrary as synapses with strangely elongated vesicles are often seen. Such synapses have been regularly discarded for further analysis in previous synaptosome studies (e.g. Martinez-Sanchez 2021). Whilst the targeting approach using a fluorescent PSD95 marker is novel and seems sufficiently precise, the authors use a somewhat outdated approach (cryo-sectioning) to generate in-tissue tomograms of poor quality. To what extent such tomograms can be interpreted in molecular terms is highly questionable. The authors also don't discuss the physiological influence of 20% dextran used for high-pressure freezing of these "very native" specimens.

Lastly, a large part of the paper is devoted to image analysis of the PSD which is not convincing (including a somewhat forced comparison with the fixed and heavy-metal staining room temperature approach). Despite being a technically challenging study, the results fall short of expectations.

Reviewer #2 (Public review):

Summary:

The authors set out to visualize the molecular architecture of the adult forebrain glutamatergic synapses in a near-native state. To this end, they use a rapid workflow to extract and plunge-freeze mouse synapses for cryo-electron tomography. In addition, the authors use knockin mice expression PSD95-GFP in order to perform correlated light and electron microscopy to clearly identify pre- and synaptic membranes. By thorough quantification of tomograms from plunge- and high-pressure frozen samples, the authors show that the previously reported 'post-synaptic density' does not occur at high frequency and therefore not a defining feature of a glutamatergic synapse.

Subsequently, the authors are able to reproduce the frequency of post-synaptic density when preparing conventional electron microscopy samples, thus indicating that density prevalence is an artifact of sample preparation. The authors go on to describe the arrangement of cytoskeletal components, membraneous compartments, and ionotropic receptor clusters across synapses.

Demonstrating that the frequency of the post-synaptic density in prior work is likely an artifact and not a defining feature of glutamatergic synapses is significant. The descriptions of distributions and morphologies of proteins and membranes in this work may serve as a basis for the future of investigation for readers interested in these features.

Strengths:

The authors perform a rigorous quantification of the molecular density profiles across synapses to determine the frequency of the post-synaptic density. They prepare samples using two cryogenic electron microscopy sample preparation methods, as well as one set of samples using conventional electron microscopy methods. The authors can reproduce previous reports of the frequency of the post-synaptic density by conventional sample preparation, but not by either of the cryogenic methods, thus strongly supporting their claim.

Reviewer #3 (Public review):

Summary:

The authors use cryo-electron tomography to thoroughly investigate the complexity of purified, excitatory synapses. They make several major interesting discoveries: polyhedral vesicles that have not been observed before in neurons; analysis of the intermembrane distance, and a link to potentiation, essentially updating distances reported from plastic-embedded specimen; and find that the postsynaptic density does not appear as a dense accumulation of proteins in all vitrified samples (less than half), a feature which served as a hallmark feature to identify excitatory plastic-embedded synapses.

Strengths:

(1) The presented work is thorough: the authors compare purified, endogenously labeled synapses to wild-type synapses to exclude artifacts that could arise through the homogenation step, and, in addition, analyse plastic embedded, stained synapses prepared using the same quick workflow, to ensure their findings have not been caused by way of purification of the synapses. Interestingly, the 'thick lines of PSD' are evident in most of their stained synapses.

(2) I commend the authors on the exceptional technical achievement of preparing frozen specimens from a mouse within two minutes.

(3) The approaches highlighted here can be used in other fields studying cell-cell junctions.

(4) The tomograms will be deposited upon publication which will enable neurobiologists and researchers from other fields to carry on data evaluation in their field of expertise since tomography is still a specialized skill and they collected and reconstructed over 100 excellent tomograms of synapses, which generates a wealth of information to be also used in future studies.

(5) The authors have identified ionotropic receptor positions and that they are linked to actin filaments, and appear to be associated with membrane and other cytosolic scaffolds, which is highly exciting.

(6) The authors achieved their aims to study neuronal excitatory synapses in great detail, were thorough in their experiments, and made multiple fascinating discoveries. They challenge dogmas that have been in place for decades and highlight the benefit of implementing and developing new methods to carefully understand the underlying molecular machines of synapses.

Impact on community:

The findings presented by Peukes et al. pertaining to synapse biology change dogmas about the fundamental understanding of synaptic ultrastructure. The work presented by the authors, particularly the associated change of intermembrane distance with potentiation and the distinct appearance of the PSD as an irregular amorphous 'cloud' will provide food for thought and an incentive for more analysis and additional studies, as will the discovery of large membranous and cytosolic protein complexes linked to ionotropic receptors within and outside of the synaptic cleft, which are ripe for investigation. The findings and tomograms available will carry far in the synapse fields and the approach and methods will move other fields outside of neurobiology forward. The method and impactful results of preparing cryogenic, unlabeled, unstained, near-native synapses may enable the study of how synapses function at high resolution in the future.

Reviewer #1 (Public review):

Summary:

This paper is a relevant overview of the currently published literature on low-intensity focused ultrasound stimulation (TUS) in humans, with a meta-analysis of this literature that explores which stimulation parameters might predict the directionality of the physiological stimulation effects.

The pool of papers to draw from is small, which is not surprising given the nascent technology. It seems nevertheless relevant to summarize the current field in the way done here, not least to mitigate and prevent some of the mistakes that other non-invasive brain stimulation techniques have suffered from, most notably the theory- and data-free permutation of the parameter space.

The meta-analysis concludes that there are, at best, weak trends toward specific parameters predicting the direction of the stimulation effects. The data have been incorporated into an open database that will ideally continue to be populated by the community and thereby become a helpful resource as the field moves forward.

Strengths:

The current state of human TUS is concisely and well summarized. The methods of the meta-analysis are appropriate. The database is a valuable resource.

Suggestions:<br /> - The paper remains lengthy and somewhat unfocused, to the detriment of readability. One can understand that the authors wish to include as much information as possible, but this reviewer is sceptical that this will aid the use of the databank, or help broaden the readership. For one, there is a good chunk of repetition throughout. The intro is also somewhat oscillating between TMS, tDCS and TUS. While the former two help contextualizing the issue, it doesn't seem necessary. In the section on clinical applications of TUs and possible outcomes of TUS, there's an imbalance of the content across examples. That's in part because of the difference in knowledge base but some sections could probably be shortened, eg stroke. In any case, the authors may want to consider whether it is worth making some additional effort in pruning the paper

- The terms or concept of enhancement and suppression warrant a clearer definition and usage. In most cases, the authors refer to E/S of neural activity. Perhaps using terms such as "neural enhancement" etc helps distinguish these from eg behavioural or clinical effects. Crucially, how one maps onto the other is not clear. But in any case, a clear statement that the changes outlined on lines 277ff do not

- Re tb-TUS (lines 382ff), it is worth acknowledging here that independent replication is very limited (eg Bao et al 2024; Fong et al bioRxiv 2024) and seems to indicate rather different effects

- The comparison with TPS is troublesome. For one, that original study was incredibly poorly controlled and designed. Cherry-picking individual (badly conducted) proof-of-principle studies doesn't seem a great way to go about as one can find a match for any desired use or outcome.

Moreover, other than the concept of "pulsed" stimulation, it is not clear why that original study would motivate the use of TUS in the way the authors propose; both types of stimulation act in very different ways (if TPS "acts" at all). But surely the cited TPS study does not "demonstrate the capability for TUS for pre-operative cognitive mapping". As an aside, why the authors feel the need to state the "potential for TPS... to enhance cognitive function" is unclear, but it is certainly a non-sequitur. This review feels quite strongly that simplistic analogies such as the one here are unnecessary and misleading, and don't reflect the thoughtful discussion of the rest of the paper. In the other clinical examples, the authors build their suggestions on other TUS studies, which seems more sensible.

Reviewer #1 (Public review):

Summary:

This manuscript presents a compelling and innovative approach that combines Track2p neuronal tracking with advanced analytical methods to investigate early postnatal brain development. The work provides a powerful framework for exploring complex developmental processes such as the emergence of sensory representations, cognitive functions, and activity-dependent circuit formation. By enabling the tracking of the same neurons over extended developmental periods, this methodology sets the stage for mechanistic insights that were previously inaccessible.

Strengths:

(1) Innovative Methodology:<br /> The integration of Track2p with longitudinal calcium imaging offers a unique capability to follow individual neurons across critical developmental windows.

(2) High Conceptual Impact:<br /> The manuscript outlines a clear path for using this approach to study foundational developmental questions, such as how early neuronal activity shapes later functional properties and network assembly.

(3) Future Experimental Potential:<br /> The authors convincingly argue for the feasibility of extending this tracking into adulthood and combining it with targeted manipulations, which could significantly advance our understanding of causality in developmental processes.

(4) Broad Applicability:<br /> The proposed framework can be adapted to a wide range of experimental designs and questions, making it a valuable resource for the field.

Weaknesses:

No major weaknesses were identified by this reviewer. The manuscript is conceptually strong and methodologically sound. Future studies will need to address potential technical limitations of long-term tracking, but this does not detract from the current work's significance and clarity of vision.

Reviewer #2 (Public review):

Summary:

The manuscript by Majnik and colleagues introduces "Track2p", a new tool designed to track neurons across imaging sessions of two-photon calcium imaging in developing mice. The method addresses the challenge of tracking cells in the growing brain of developing mice. The authors showed that "Track2p" successfully tracks hundreds of neurons in the barrel cortex across multiple days during the second postnatal week. This enabled the identification of the emergence of behavioral state modulation and desynchronization of spontaneous network activity around postnatal day 11.

Strengths:

The manuscript is well written, and the analysis pipeline is clearly described. Moreover, the dataset used for validation is of high quality, considering the technical challenges associated with longitudinal two-photon recordings in mouse pups. The authors provide a convincing comparison of both manual annotation and "CellReg" to demonstrate the tracking performance of "Track2p". Applying this tracking algorithm, Majnik and colleagues characterized hallmark developmental changes in spontaneous network activity, highlighting the impact of longitudinal imaging approaches in developmental neuroscience. Additionally, the code is available on GitHub, along with helpful documentation, which will facilitate accessibility and usability by other researchers.

Weaknesses:

(1) The main critique of the "Track2p" package is that, in its current implementation, it is dependent on the outputs of "Suite2p". This limits adoption by researchers who use alternative pipelines or custom code. One potential solution would be to generalize the accepted inputs beyond the fixed format of "Suite2p", for instance, by accepting NumPy arrays (e.g., ROIs, deltaF/F traces, images, etc.) from files generated by other software. Otherwise, the tool may remain more of a useful add-on to "Suite2p" (see https://github.com/MouseLand/suite2p/issues/933) rather than a fully standalone tool.

(2) Further benchmarking would strengthen the validation of "Track2p", particularly against "CaIMaN" (Giovannucci et al., eLife, 2019), which is widely used in the field and implements a distinct registration approach.

(3) The authors might also consider evaluating performance using non-consecutive recordings (e.g., alternate days or only three time points across the week) to demonstrate utility in other experimental designs.

Reviewer #3 (Public review):

Summary:

In this manuscript, Majnik et al. developed a computational algorithm to track individual developing interneurons in the rodent cortex at postnatal stages. Considerable development in cortical networks takes place during the first postnatal weeks; however, tools to study them longitudinally at a single-cell level are scarce. This paper provides a valuable approach to study both single-cell dynamics across days and state-driven network changes. The authors used Gad67Cre mice together with virally introduced TdTom to track interneurons based on their anatomical location in the FOV and AAVSynGCaMP8m to follow their activity across the second postnatal week, a period during which the cortex is known to undergo marked decorrelation in spontaneous activity. Using Track2P, the authors show the feasibility of tracking populations of neurons in the same mice, capturing with their analysis previously described developmental decorrelation and uncovering stable representations of neuronal activity, coincident with the onset of spontaneous active movement. The quality of the imaging data is compelling, and the computational analysis is thorough, providing a widely applicable tool for the analysis of emerging neuronal activity in the cortex. Below are some points for the authors to consider.

Major points:

(1) The authors used 20 neurons to generate a ground truth dataset. The rationale for this sample size is unclear. Figure 1 indicates the capability to track ~728 neurons. A larger ground truth data set will increase the robustness of the conclusions.

(2) It is unclear how movement was scored in the analysis shown in Figure 5A. Was the time that the mouse spent moving scored after visual inspection of the videos? Were whisker and muscle twitches scored as movement, or was movement quantified as the amount of time during which the treadmill was displaced?

(3) The rationale for binning the data analysis in early P11 is unclear. As the authors acknowledged, it is likely that the decoder captured active states from P11 onwards. Because active whisking begins around P14, it is unlikely to drive this change in network dynamics at P11. Does pupil dilation in the pups change during locomotor and resting states? Does the arousal state of the pups abruptly change at P11?

Reviewer #1 (Public review):

Summary:

In this manuscript, Mack and colleagues investigate the role of posttranslational modifications, including lysine acetylation and ubiquitination, in methyltransferase activity of SETD2 and show that this enzyme functions as a tumor suppressor in a KRASG12C-driven lung adenocarcinoma. In contrast to H3K36me2-specific oncogenic methyltransferases, the deletion of SETD2, which is capable of H3K36 trimethylation, increases lethality in a KRASG12C-driven lung adenocarcinoma mouse tumor model. In vitro, the authors demonstrate that polyacetylation of histone H3, particularly of H3K27, H3K14, and H3K23, promotes the catalytic activity of SETD2, whereas ubiquitination of H2A and H2B has no effect.

Strengths:

Overall, this is a well-designed study that addresses an important biological question regarding the functioning of the essential chromatin component. The manuscript contains excellent quality data, and the conclusions are convincing and justified. This work will be of interest to many biochemists working in the field of chromatin biology and epigenetics.

Weaknesses:

A minor comment: labels should be added in the Figures and should be uniform across all Figures (some are distorted).

Reviewer #2 (Public review):

Summary:

Human histone H3K36 methyltransferase Setd2 has been previously shown to be a tumor suppressor in lung and pancreatic cancer. In this manuscript by Mack et al., the authors first use a mouse KRASG12D-driven lung cancer model to confirm in vivo that Setd2 depletion exacerbates tumorigenesis. They then investigate the enzymatic regulation of the Setd2 SET domain in vitro, demonstrating that H2A, H3, or H4 acetylation stimulates Setd2-SET activity, with specific enhancement by mono-acetylation at H3K14ac or H3K27ac. In contrast, histone ubiquitination has no effect. The authors propose that H3K27ac may regulate Setd2-SET activity by facilitating its binding to nucleosomes. This work provides insight into how cross-talk between histone modifications regulates Setd2 function. However, the manuscript lacks a clear discussion on how Setd2's in vivo tumor suppressor role and the in vitro mechanistic regulation findings are connected. Additionally, some experiments require more controls and better data quality for proper interpretation.

Specific comments:

(1) As for Figure 2F, Setd2-SET activity on WT rNuc (H3) appears to be significantly lower compared to what is extensively reported in the literature. This is particularly puzzling given that Figure 2B suggests that using 3H-SAM, H3-nuc are much better substrates than K36me1, whereas in Figure 3F, rH3 is weaker than K36me1. It is recommended for the authors to perform additional experimental repeats and include a quantitative analysis to ensure the consistency and reliability of these findings.

(2) The additional bands observed in Figure 4B, which appear to be H4, should be accompanied by quantification of the intensity of the H3 bands to better assess K36me3 activity. Additionally, the quantification presented in Figure 4C for SAH does not seem accurate as it potentially includes non-specific methylation activity, likely from H4. This needs to be addressed for clarity and accuracy.

(3) In Figure 4E, the differences between bound and unbound substrates are not sufficiently pronounced. Given the modest differences observed, authors might want to consider repeating the assay with sufficient replicates to ensure the results are statistically robust.

(4) Regarding labeling, there are multiple issues that need correction: In the depiction of Epicypher's dNuc, it is crucial to clearly mark H2B as the upper band, rather than ambiguously labeling H2A/H2B together when two distinct bands are evident. In Figure 3B and D, the histones appear to be mislabeled, and the band corresponding to H4 has been cut off. It would be beneficial to refer to Figure 3E for correct labeling to maintain consistency and accuracy across figures.

(5) There are issues with the image quality in some blots; for instance, Figure 2EF and Figure 2D exhibit excessive contrast and pixelation, respectively. These issues could potentially obscure or misrepresent the data, and thus, adjustments in image processing are recommended to provide clearer, more accurate representations.

(6) The authors are recommended to provide detailed descriptions of the materials used, including catalog numbers and specific products, to allow for reproducibility and verification of experimental conditions.

(7) The identification of Setd2 as a tumor suppressor in KrasG12C-driven LUAD is a significant finding. However, the discussion on how this discovery could inspire future therapeutic approaches needs to be more balanced. The current discussion (Page 10) around the potential use of inhibitors is somewhat confusing and could benefit from a clearer explanation of how Setd2's role could be targeted therapeutically. It would be beneficial for the authors to explore both current and potential future strategies in a more structured manner, perhaps by delineating between direct inhibitors, pathway modulators, and other therapeutic modalities.

Reviewer #1 (Public review):

The small conductance calcium-activated potassium channel 2 (SK2) is an important drug target for treating neurological and cardiovascular diseases. However, structural information on this subtype of SK channels has been lacking, and it has been difficult to draw conclusions about activator and inhibitor binding and action in the absence of structural information.

Here the authors set out to (1) determine the structure of the transmembrane regions of a mammalian SK2 channel, (2) determine the binding site of apamin, a historically important SK2 inhibitor whose mode of action is unclear, and (3) use the structural information to generate a novel set of activators/inhibitors that selectively target SK2.

The authors largely achieved all the proposed goals, and they present their data clearly.

Unable to solve the structure of the human SK2 due to excessive heterogeneity in its cytoplasmic regions, the authors create a chimeric construct using SK4, whose structure was previously solved, and use it for structural studies. The data reveal a unique extracellular structure formed by the S2-S3 loop, which appears to directly interact with the selectivity filter and modulate its conductivity. Structures of SK2 in the absence and presence of the activating Ca2+ ions both possess non-K+-selective/conductive selectivity filters, where only sites 3 and 4 are preserved. The S6 gates are captured in closed and open states, respectively. Apamine binds to the S2-S3 loop, and unexpectedly, induces a K+ selective/conductive conformation of the selectivity filter while closing the S6 gate.

Through high-throughput screening of small compound libraries and compound optimization, the group identified a reasonably selective inhibitor and a related compound that acts as an activator. The characterization shows that these compounds bind in a novel binding site. Interestingly, the inhibitor, despite binding in a site different from that of apamine, also induces a K+ selective/conductive conformation of the selectivity filter while the activator induces a non-K+ selective/conductive conformation and an open S6 gate.

The data suggest that the selectivity filter and the S6 gate are rarely open at the same time, and the authors hypothesize that this might be the underlying reason for the small conductance of SK2. The data will be valuable for understanding the mechanism of SK2 channel (and other SK subtypes).

Overall, the data is of good quality and supports the claims made by the authors. However, a deeper analysis of the cryo-EM data sets might yield some important insights, i.e., about the relationship between the conformation of the selectivity filter and the opening of the S6 gate.

Some insight and discussion about the allosteric networks between the SF and the S6 gate would also be a valuable addition.

Reviewer #2 (Public review):

Summary:

The authors have used single-particle cryoEM imaging to determine how small-molecule regulators of the SK channel interact with it and modulate their function.

Strengths:

The reconstructions are of high quality, and the structural details are well described.

Weaknesses:

The electrophysiological data are poorly described. Several details of the structural observations require a mechanistic context, perhaps better relating them to what is known about SK channels or other K channel gating dynamics.

The most pressing point I have to make, which could help improve the manuscript, relates to the selectivity filter (SF) conformation. Whether the two ion-bound state of SK2-4 (Figure 4A) represents a non-selective, conductive SF occluded by F243 or represents a C-type inactivated SF, further occluded by F243, is unclear. It would be important to discuss this. Reconstructions of Kv1.3 channels also feature a similar configuration, which has been correlated to its accelerated C-type inactivation.

Furthermore, binding of a toxin derivative to Kv1.3 restores the SF into a conductive form, though occluded by the toxin. It appears that apamin binding to SK2-4 might be doing something similar. Although I am not sure whether SK channels undergo C-type inactivation like gating, classical MTS accessibility studies have suggested that dynamics of the SF might play a role in the gating of SK channels. It would be really useful (if not essential) to discuss the SF dynamics observed in the study and relate them better to aspects of gating reported in the literature.

The SF of K channels, in conductive states, are usually stabilized by an H-bond network involving water molecules bridged to residues behind the SF (D363 in the down-flipped conformation and Y361). Considering the high quality of the reconstructions, I would suspect that the authors might observe speckles of density (possibly in their sharpened map) at these sites, which overlap with water molecules identified in high-resolution X-ray structures of KcsA, MthK, NaK, NaK2K, etc. It could be useful to inspect this region of the density map.

Reviewer #3 (Public review):

This is a fundamentally important study presenting cryo-EM structures of a human small conductance calcium-activated potassium (SK2) channel in the absence and presence of calcium, or with interesting pharmacological probes bound, including the bee toxin apamin, a small molecule inhibitor, and a small molecule activator. As efforts to solve structures of the wild-type hSK2 channel were unsuccessful, the authors engineered a chimera containing the intracellular domain of the SK4 channel, the subtype of SK channel that was successfully solved in a previous study (reference 13). The authors present many new and exciting findings, including opening of an internal gate (similar to SK4), for the first time resolving the S3-S4 linker sitting atop the outer vestibule of the pore and unanticipated plasticity of the ion selectivity filter, and the binding sites for apamin, one new small molecule inhibitor and another small molecule activator. Appropriate functional data are provided to frame interpretations arising from the structures of the chimeric protein; the data are compelling, the interpretations are sound, and the writing is clear. This high-quality study will be of interest to membrane protein structural biologists, ion channel biophysicists, and chemical biologists, and will be valuable for future drug development targeting SK channels.

The following are suggestions for strengthening an already very strong and solid manuscript:

(1) It would be good to include some information in the text of the results section about the method and configuration used to obtain electrophysiological data and the limitations. It is not until later in the text that the Qube instrument is mentioned in the results section, and it is not until the methods section that the reader learns it was used to obtain all the electrophysiological data. Even there, it is not explicitly mentioned that a series of different internal solutions were used in each cell where the free calcium concentration was varied to obtain the data in Figure1C. Also, please state the concentration of free calcium for the data in Figure 1B.

(2) The authors do a nice job of discussing the conformations of the selectivity filter they observed here in SK as they relate to previous work on NaK and HCN, but from my perspective the authors are missing an opportunity to point out even more striking relationships with slow C-type inactivation of the selectivity filter in Shaker and Kv1 channels. C-type inactivation of the filter in Shaker was seen in 150 mM K using the W434F mutant (PMC8932672) or in 4 mM K for the WT channel (PMC8932672), and similar results have been reported for Kv1.2 (PMC9032944; PMC11825129) and for Kv1.3 (PMC9253088; PMC8812516) channels. For Kv1.3, C-type inactivation occurs even in 150 mM K (PMC9253088; PMC8812516). Not unlike what is seen here with apamin, binding of the sea anemone toxin (ShK) with a Fab attached (or the related dalazatide) inserts a Lys into the selectivity filter and stabilizes the conducting conformation of Kv1.3 even though the Lys depletes occupancy of S1 by potassium (PMC9253088; PMC8812516). What is known about how the functional properties of SK2 channels (where the filter changes conformation) differ from SK4, where the filter remains conducting (reference 13)? Is there any evidence that SK2 channels inactivate? Or might the conformation of the filter be controlled by regulatory processes in SK2 channels? I think connecting the dots here would enhance the impact of this study, even if it remains relatively speculative.

Reviewer #1 (Public Review):

Summary:

In this paper, Li and colleagues overcome solubility problems to determine the structure of FtsEX bound to EnvC from E. coli.

Strengths:

The structural work is well done, and the work is consistent with previous work on the structure of this complex from P. aerugionsa.

Weaknesses:

The model does not take into account all the information that the authors obtained, as well as known in vivo data.

The work lacks a clear comparison to the Pseudomonas structure highlighting new information that was obtained so that it is readily available to the reader.

The authors set out to obtain the structure of FtsEX-EnvC complex from E. coli. Previously, they were unable to do so but were able to determine the structure of the complex from P. aeruginosa. Here they persisted in attacking the E. coli complex since more is known about its involvement in cell division and there is a wealth of mutants in E. coli. The structural work is well done and recapitulates the results this lab obtained with this complex from P. aeruginosa. It would be helpful to compare more directly the results obtained here with the E. coli complex with the previously reported P. aeruginosa complex - are they largely the same or has some insight been obtained from the work that was not present in the previous complex from P. aeruginosa. This is particularly the case in discussing the symmetrical FtsX dimer binding to the asymmetrical EnvC, since this is emphasized in the paper. However, Figures 3C & D of this paper appear similar to Figures 2D & E of the P. aeruginosa structure. Presumably, the additional information obtained and presented in Figure 4 is due to the higher resolution, but this needs to be highlighted and discussed to make it clear to a general audience.

The main issue is the model (Figure 6). In the model ATP is shown to bind to FtsEX before EnvC, however, in Figure 1c, it is shown that ADP is sufficient to promote binding of FtsEX to EnvC.

The work here is all done in vitro, however, information from in vivo needs to be considered. In vivo results reveal that the ATP-binding mutant FtsE(D162N)X promotes the recruitment of EnvC (Proc Natl Acad Sci U S A 2011 108:E1052-60). Thus, even FtsEX in vivo can bind EnvC without ATP (not sure if this mutant can bind ADP).

Perhaps the FtsE protein from E. coli has to have bound nucleotides to maintain its 3D structure.

Comments after revision:

The most interesting aspect of this complex is that it has yet to be determined the order of events in the ATPase cycle as the authors acknowledge. Although the authors have responded quite well to the comments, I am still worried about the significance of the in vitro results compared to the in vivo results reported by others. In vivo ATP binding does not appear required for complex formation (of course it is possible that ADP is responsible in vivo). Have the authors tried to solve the complex with ADP since they suggested that it is sufficient to hold the complex together). If possible, it would confirm the role of ATP binding by comparing the structures. Also, it is not clear if ADP binds to any of the mutants made by the Bernhardt lab (D162N, K41M). If they do not bind ADP then FtsEX without nucleotide is able to bind EnvC as the authors indicate is the case in Pseudomonas. It is also unclear the significance of the ATPase activity of FtsEX in vitro with or without EnvC. Could the activity be some basal activity that is not relevant to the in vivo situation. If EnvC caused FtsEX to hydrolyze ATP it would be a futile cycle as FtsEX and EnvC are localized to the septum long before they are involved septal hydrolysis.

Reviewer #2 (Public Review):

Summary:

Peptidoglycan remodeling, particularly that carried out by enzymes known as amidases, is essential for the later stages of cell division including cell separation. In E. coli, amidases are generally activated by the periplasmic proteins EnvC (AmiA and AmiB) and NlpD (AmiC). The ABC family member, FtsEX, in turn, has been implicated as a modulator of amidase activity through interactions with EnvC. Specifically, how FtsEX regulates EnvC activity in the context of cell division remains unclear.

Strengths:

Li et al. make two primary contributions to the study of FtsEX. The first, the finding that ATP binding stabilizes FtsEX in vitro, enables the second, structural resolution of full-length FtsEX both alone (Figure 2) and in combination with EnvC (Figure 3). Leveraging these findings, the authors demonstrate that EnvC binding stimulates FtsEX-mediated ATP hydrolysis approximately two-fold. The authors present structural data suggesting EnvC binding leads to a conformational change in the complex. Biochemical reconstitution experiments (Figure 5) provide compelling support for this idea.

Weaknesses:

The potential impact of the study is curtailed by the lack of experiments testing the biochemical or physiological relevance of the model which is derived almost entirely from structural data.

Altogether the data support a model in which interaction with EnvC, results in a conformational change stimulating ATP hydrolysis by FtsEX and EnvC-mediated activation of the amidases, AmiA and AmiB. However, the study is limited in both approach and scope. The importance of interactions revealed in the structures to the function of FtsEX and its role in EnvC activation are not tested. Adding biochemical and/or in vivo experiments to fill in this gap would allow the authors to test the veracity of the model and increase the appeal of the study beyond the small number of researchers specifically interested in FtsEX.

Comments after revision:

Although I appreciate the authors' desire to save future biochemical experiments for a separate publication, the lack of in vitro data verifying their model makes it challenging to reconcile with published studies from other groups. The other reviewer's point about EnvC activating FtsEX ATPase activity resulting in a futile cycle since both are recruited to the septum well before constriction, is a good example of the disconnect between the model presented here and in vivo data.

Reviewer #1 (Public review):

Summary:

Melin et al. developed a quantitative assay to measure the fate of paternal mitochondria after fertilization. They combine this assay with C. elegans genetics to show that multiple genes contribute to paternal mitochondrial elimination. However, despite their claims, they unconvincingly place these genes into distinct pathways and fail to determine whether additional unknown genes are involved in the process.

Strengths:

Melin et al. develop a new assay to quantify the fate of paternal mitochondria during embryonic development in C. elegans. They use complex C. elegans genetics to disrupt 5 different genes and nicely measure their contributions to paternal mitochondrial elimination. In an attempt to place these genes into pathways, the authors interrupt genes in various combinations and measure paternal mitochondrial persistence. The authors discovered that disrupting 4 of the genes known to contribute to paternal mitochondrial elimination still resulted in paternal mitochondrial elimination, suggesting that more genes also contribute to this process. Finally, the authors discovered that pink-1, which had previously been discounted, indeed contributes to paternal mitochondrial elimination when the major pathway involving allo-1 is also disrupted.

Weaknesses:

In the introduction, the authors describe the importance of studying the maternal inheritance of mitochondrial DNA. However, the authors mostly study the inheritance of paternally-derived mitochondrial proteins (HSP6::GFP). While the authors do use a PCR approach to measure paternal mitochondrial DNA, their results are not as quantitative and thorough (applied to multiple mutant combinations) as their microscopy assay. Using their microscopy assay, the authors did not combine mutants for all 5 genes. Therefore, they cannot support or discount the possibility that undiscovered paternal mitochondrial elimination mechanisms exist. The author's genetic epistasis experiments are incomplete and occasionally improperly interpreted (as described below). Finally, the authors were unable to achieve paternal mitochondrial transmission to the F2 generation (which admittedly has not been achieved in any experimental system).

Reviewer #2 (Public review):

Summary:

Mitochondrial DNA (mtDNA) is exclusively maternally transmitted in almost all species. Paternal mitochondria, with their mtDNA, must be rapidly degraded after fertilisation to prevent their transmission to progeny, which could lead to subsequent detrimental mito-nuclear incompatibilities. Multiple layers of mechanisms contribute to blocking the transmission of paternal mitochondria and their mtDNA to progeny. Endonuclease activity and mitophagy form a part of these strategies. However, other key regulatory mechanisms remain to be elucidated, as inactivating endonuclease and mitophagy activity only delays the clearance of paternal mitochondria. In this study, the authors mainly focused on genes involved in endonuclease function (csp-6) and autophagy (allo-1) in C. elegans, demonstrating a synergic genetic interaction that potentialize their activity. They also revealed a contribution by pink-1/pink1, in the absence of allo-1.

Strengths:

The majority of data relies on confocal microscopy images and corresponding image analysis and quantification. Images are clear, and quantifications are supported by several biological replicates of >10 n and standard statistical tests. Mutants used were obtained from the Caenorhabditis Genetics Center (CGC) and were previously validated and confirmed by the C. elegans community. The scientific approach is solid and rigorous and in line with state-of-the-art C. elegans methods. Proper controls have been performed to rule out the effect of animal viability on observed results or to confirm the staining validity of TUBES on subcellular structures surrounding paternal mitochondria. Controls validating uaDf5 PCR specificity were conducted.

Weaknesses:

However, the embryonic expression of paternally contributing genes in feminised animals cannot be completely ruled out, as RNAi was used to alter gene expression levels. An issue inherent to RNAi approaches. Also, the impact of pink-1/pink1 is significant, but there is a lack of evidence demonstrating its mitophagic function.

Goal achievements and data supportive of conclusions:

In the first part of the study, the authors strongly and clearly demonstrate the synergistic interaction between the csp-6 and allo-1 in delaying paternal mitochondria degradation and associated mtDNA in the fertilised egg. In wild-type animals, paternal mitochondria are visible (using a mitochondrial HSP-::GFP marker) until the 4-cell stage embryo. In the csp-6; allo-1 double mutant genetic background, paternal mitochondria very significantly perdures until the 2-fold embryonic stage. The uaDf5 mitochondrial deletion, detectable by PCR, that was introduced by crossing with a male, followed the same trend. In addition, loss of fncd-1/fndc1 and phb-2 did not extend the perdurance of paternal mitochondria. In the second part of the study, the authors demonstrate a contribution of the loss of pink-1/pink1, in the absence of allo-1, in delaying paternal mitochondria degradation until the 100-cell stage. Overall, the conclusions are in accordance with the data shown.

Impact on the field:

Endonuclease activity and mitophagy aren't sufficient to prevent the transmission of paternal mitochondria and associated mtDNA to progeny, but they still contribute significantly to regulating the perdurance of paternal mitochondria in early embryos. Understanding how these two functions work in concert to potentialize their activity is important, as they could potentially be manipulated/enhanced to improve paternal mitochondrial degradation in the future. Here, the authors demonstrate a detailed synergistic genetic interaction between these functions. Also, they pointed out a new potential contribution of pink-1/pink1, which may underlie a potentially more complex mitophagic protective function.

Reviewer #3 (Public review):

Summary:

The present study examines the cooperation among four allophagy/mitophagy factors, ALLO-1, CPS-6, FNDC-1, and PHB-2, implicated in the elimination of the sperm-derived mitochondria in C. elegans embryos. The key finding of the cumulative effect of ALLO-1 and CPS-6 inactivation causing delayed sperm mitophagy is significant for the understanding of mitochondrial inheritance in the nematode model and in general. Below are some specific suggestions on how the impact of the article could be elevated:

Abstract:

The authors should shorten the description of previously identified mitophagy factors and provide more detail on the present study results. An impact statement should be added at the end, with significance for understanding mitochondrial inheritance across taxa, all the way to mammals/humans.

Introduction:

The authors should provide more details on ALLO-1 and its interaction with LC-3. Also, it should be specified which of those previously identified allophagy factors are unique to worms and which ones are conserved. See also my comment below about including a diagram and a table of pathways and determinants involved in allophagy/paternal mitophagy.

Results:

If I understand the mtDNA data correctly, paternal mtDNA is maintained throughout the lifespan of the F1 generation but absent from the F2 generation. This is reminiscent of past studies of interspecific Mus musculus/Mus spretus mouse crosses by Kaneda/Shitara in which the paternal mtDNA was maintained F1 generation, resulting in heteroplasmy, but was lost from the F2 generation after back-crossing. Are CPS-6 and ALLO-1 effectors, but not determinants of maternal mtDNA inheritance in the nematode?

The finding that PINK-1 inactivation stabilizes sperm-derived mitochondria in the embryos is interesting. Are the substrates of PINK1 known in C. elegans? This could provide a clue concerning the aforementioned mitophagy determinants acting independently of ALLO-1.

Discussion:

A summary-diagram compiling the intersecting allophagy pathways would be helpful to accompany discussion, in addition to or expanding on the simple diagram presented as Figure 5; also, a table listing all the factors implicated in nematode allophagy next to those implicated in human/mammalian sperm mitophagy, which would highlight the divergences and overlaps between vertebrates and invertebrates.

Is it known how CPC-6 enters/gets imported into the sperm mitochondria inside the embryo? This pathway could potentially be targeted to decipher the allophagy mechanism.

PINK/PARKIN/PACRG and FUNDC1/2 pathways have been implicated in mammalian neurodegeneration as well as in mitophagy, including but not limited to sperm mitophagy after fertilization. These pathways in mammals should be briefly reviewed as they may provide further clues to how the allophagy pathways intersect in C. elegans.

Reviewer #1 (Public review):

Summary:

This study provides new insight into the non-canonicial voltage-gating mechanism of BK channels through prolonged (10 us) 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 provide useful predictions extending beyond what has been experimentally tested.

Weaknesses:

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 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 inferences regarding coupling pathways and interactions in the fully open voltage-activated channel may be only partially supported and therefore incomplete. That said, adequate discussion regarding these limitations are provided together with dynamic community analysis based on the Ca-bound open structure. The latter supports the main conclusions based on simulations, while providing an indication of potential interaction differences between simulated and fully open conformations. Another limitation is that 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.

Comments on revisions:

My previous questions and concerns have been adequately addressed.

Reviewer #2 (Public review):

Summary:

The manuscript by Jia and Chen addresses the structural basis of voltage-activation of BK channels using computational approaches. Although a number of experimental studies using gating current and patch-clamp recording have analyzed voltage-activation in terms of observed charge movements and the apparent energetic coupling between voltage-sensor movement and channel opening, the structural changes that underlie this phenomenon have been unclear. The present studies use a reduced molecular system comprising the transmembrane portion of the BK channel (i.e. the cytosolic domain was deleted), embedded in a POPC membrane, with either 0 or 750 mV applied across the membrane. This system enabled acquisition of long simulations of 10 microseconds, to permit tracking of conformational changes of the channel. The authors principal findings were that the side chains of R210 and R213 rapidly moved toward the extracellular side of the membrane (by 8 - 10 Å), with greater displacements than any of the other charged transmembrane residues. These movements appeared tightly coupled to movement of the pore-lining helix, pore hydration, and ion permeation. The authors estimate that R210 and R213 contribute 0.25 and 0.19 elementary charges per residue to the gating current, which is roughly consistent with estimates based on electrophysiological measurements that used the full-length channel.

Strengths:

The methodologies used in this work are sound, and these studies certainly contribute to our understanding of voltage-gating of BK channels. An intriguing observation is the strongly coupled movement of the S4, S5, and S6 helices that appear to underlie voltage-dependent opening. Based on Fig 2a-d, the substantial movements of the R210 and R213 side chains occur nearly simultaneously to the S6 movement (between 4 - 5 usec of simulation time). This seems to provide support for a "helix-packing" mechanism of voltage gating in the so-called "non-domain-swapped" voltage-gated K channels.

Weaknesses:

The main limitation is that these studies used a truncated version of the BK channel, and there are likely to be differences in VSD-pore coupling in the context of the full-length channels that will not be resolved in the present work. Nonetheless, the authors provide a strong rationale for their use of the truncated channel, and the results presented will provide a good starting point for future computational studies of this channel.

Reviewer #1 (Public review):

Summary:

This study provides comprehensive instructions for using the chromatophore tracking software, Chromas, to track and analyse the dynamics of large numbers of cephalopod chromatophores across various spatiotemporal scales. This software addresses a long-standing challenge faced by many researchers who study these soft-bodied creatures, known for their remarkable ability to change colour rapidly. The updated software features a user-friendly interface that can be applied to a wide range of applications, making it an essential tool for biologists focused on animal dynamic signalling. It will also be of interest to professionals in the fields of computer vision and image analysis.

Strengths:

This work provides detailed instructions for this tool kit along with examples for potential users to try. The Gitlab inventory hosts the software package, installation documentation, and tutorials, further helping potential users with a less steep learning curve.

Weaknesses:

The evidence supporting the authors' claims is solid, particularly demonstrated through the use of cuttlefish and squid. However, it may not be applicable to all coleoid cephalopods yet, such as octopuses, which have an incredibly versatile ability to change their body forms.

Comments on revisions:

I am pleased to see the more detailed version of this useful tool along with tutorials designed for diverse users who are interested in animal dynamic colouration. This study provides detailed instructions for using the chromatophore tracking software Chromas to track and analyse the dynamics of large numbers of cephalopod chromatophores across various spatiotemporal scales. The software features a user-friendly interface that is highly compelling and can be applied to a wide range of applications.

Reviewer #2 (Public review):

Summary:

The authors developed a computational pipeline named CHROMAS to track and analyze chromatophore dynamics, which provides a wide range of biological analysis tools without requiring the user to write code.

Strengths:

(1) CHROMAS is an integrated toolbox that provides tools for different biological tasks such as: segment, classify, track and measure individual chromatophores, cluster small groups of chromatophores, analyze full-body patterns, etc.

(2) It could be used to investigate different species. The authors have already applied it to analyze the skin of the bobtail squid Euprymna berryi and the European cuttlefish Sepia officinalis.

(3) The tool is open-source and easy to install. The paper describes in detail the experiment requirements, command to complete each task and provides relevant sample figures, which are easy to follow.

Weaknesses:

(1) There are some known limitations for the current version. The users should read the "Discussion" chapter carefully before preparing their experiments and using CHROMAS.

Reviewer #2 (Public review):

Summary:

The authors show that a combination of arginine methyltransferase inhibitors synergize with PARP inhibitors to kill ovarian and triple negative cancer cell lines in vitro and in vivo using preclinical mouse models.

Strengths and weaknesses

The experiments are well-performed, convincing and have the appropriate controls (using inhibitors and genetic deletions) and use statistics.

They identify the DNA damage protein ERCC1 to be reduced in expression with PRMT inhibitors. As ERCC1 is known to be synthetic lethal with PARPi, this provides a mechanism for the synergy. They use cell lines only for their study in 2D as well as xenograph models.

Joint Public Review:

Summary:

How mechanical forces transmitted by blood flow contribute to cardiac development remains incompletely understood. Using the unique advantages of the zebrafish model, Chen et al make the fundamental discovery that endocardial expression of the transcriptional repressor, Id2b, is maintained in endocardial cells by blood flow. Id1b zebrafish mutants fail to form the valve in the atrioventricular canal (AVC) and show reduced myocardial contractility that they suggest is due to impaired calcium transients. Id2b mutants are largely viable during the first 6 months of life until ~20% display cardiomyopathy characterized by visible edema, structural abnormalities, retrograde blood flow, and reduced systolic function and calcium handling. Mechanistically, the authors suggest that flow-mediated expression of Id2b leads to neuregulin 1 (nrg1) upregulation by physically interacting with and sequestering the Tcf3b transcriptional repressor from conserved tcf3b binding sites upstream of nrg1. Overall, this study advances our understanding of flow-mediated endocardial-myocardial crosstalk during heart development.

Strengths:

The strengths of the study are the significance of the biological question being addressed, use of the zebrafish model, data quality, and use of genetic tools. The text is generally well-written and easy to understand.

Weaknesses:

The main weakness that remains is the lack of rigor surrounding the molecular mechanism where the authors suggest that blood flow induces endocardial expression of Id2b, which binds to Tcf3b and sequesters it from binding the Nrg1 promoter to repress transcription. Although good faith efforts were made to bolster their model, the physical interaction between Id2b and Tcf3b is limited to overexpression of tagged proteins in HEK293 cells. Moreover, no mutagenesis was performed on the tcf3b binding sites identified in the nrg1 promoter to learn their importance in vivo.

Reviewer #1 (Public review):

Summary:

This study uses a cell-based computational model to simulate and study T cell development in the thymus. They initially applied this model to assess the effect of the thymic epithelial cells (TECs) network on thymocyte proliferation and demonstrated that increasing TEC size, density, or protrusions increased the number of thymocytes. They postulated and confirmed that this was due to changes in IL7 signalling and then expanded this work to encompass various environmental and cell-based parameters, including Notch signalling, cell cycle duration, and cell motility. Critical outcomes from the computational model were tested in vivo using medaka fish, such as the role of IL-7 signalling and minimal effect of Notch signalling.

Strengths:

The strength of the paper is the use of computational modelling to obtain unique insights into the niche parameters that control T cell development, such as the role of TEC architecture, while anchoring those findings with in vivo experiments. I can't comment on the model itself, as I am not an expert in modelling, however, the conclusions of the paper seem to be well-supported by the model.

Reviewer #2 (Public review):

Summary:

The authors have worked up a ``virtual thymus' using EPISIM, which has already been published. Attractive features of the computational model are stochasticity, cell-to-cell variability, and spatial heterogeneiety. They seek to explore the role of TECs, that release IL-7 which is important in the process of thymocyte division.

In the model, ordinary clones have IL7R levels chosen from a distribution, while `lesioned' clones have an IL7R value set to the maximum. The observation is that the lesioned clones are larger families, but the difference is not dramatic. This might be called a cell-intrinsic mechanism. One promising cell-extrinsic mechanism is mentioned: if a lesioned clone happens to be near a source of IL-7 and begins to proliferate, the progeny can crowd out cells of other clones and monopolise the IL-7 source. The effect will be more noticeable if sources are rare, so is seen when the TEC network is sparse.

Strengths:

Thymic disfunctions are of interest, not least because of T-ALL. New cells are added, one at a time, to simulate the conveyor belt of thymocytes on a background of stationary cells. They are thus able to follow cell lineages, which is interesting because one progenitor can give rise to many progeny.

There are some experimental results in Figures 4,5 and 6. For example, il7 crispant embryos have fewer thymocytes and smaller thymii; but increasing IL-7 availability produces large thymii.

Reviewer #3 (Public review):

Summary:

Tsingos et al. seek to advance beyond the current paradigm that proliferation of malignant cells in T-cell acute lymphoblastic leukemia occurs in a cell-autonomous fashion. Using a computational agent-based model and experimental validation, they show instead that cell proliferation also depends on interaction with thymic epithelial cells (TEC) in the thymic niche. One key finding is that a dense TEC network inhibits the proliferation of malignant cells and favors the proliferation of normal cells, whereas a sparse TEC network leads to rapid expansion of malignant thymocytes.

Strengths:

A key strength of this study is that it combines computational modeling using an agent-based model with experimental work. The original modeling and novel experimental work strengthen each other well. In the agent-based model, the authors also tested the effects of varying a few key parameters of cell proliferation.

Reviewer #1 (Public review):

Summary:

This manuscript describes a series of lab and field experiments to understand the role of tadpole transport in shaping the microbiome of poison frogs in early life. The authors conducted a cross-foster experiment in which R. variabilis tadpoles were carried by adults of their own species, carried by adults of another frog species, or not carried at all. After being carried for 6 hours, tadpole microbiomes resembled those of their caregiving species. Next, the authors reported higher microbiome diversity in tadpoles of two species that engage in transport-based parental care compared to one species that does not. Finally, they collected tadpoles either from the backs of an adult (i.e., they had recently been transported) or from eggs (i.e., not transported) but did not find significant overlap in microbiome composition between transported tadpoles and their parents.

Strengths:

The cross-foster experiment and the field experiment that reared transported and non-transported tadpoles are creative ways to address an important question in animal microbiome research. Together, they imply a small role for parental care in the development of the tadpole microbiome. The manuscript is generally well-written and easy to understand. The authors make an effort (improved since the first version of the manuscript) to acknowledge the limitations of their experimental design.

Weaknesses:

Cross-foster experiment: The "heterospecific transport" tadpoles were manually brushed onto the back of the surrogate frog, while the "biological transport" tadpoles were picked up naturally by the parent. It is challenging to interpret the effect of caregiver species since it is conflated with the method of attachment to the parent.

Cross-species analysis: The authors attribute the difference in diversity to parental care behavior, but the comparison only includes n=2 transporting species and n=1 non-transporting species that differ in many other ways. I would also add that increased diversity is not necessarily an expectation of vertical transmission. Similarity between adults and tadpoles is likely a more relevant outcome for vertical transmission, but the authors did not find any evidence that tadpole-adult similarity was any higher in species with tadpole transport. In fact, tadpoles and adults were more similar in the non-transporting species than in one of the transporting species (lines 296-298), which seems to directly contradict the authors' hypothesis.

Reviewer #2 (Public review):

Summary:

Here, the Fischer et al. attempt to understand the role of parental care, specifically the transport of offspring, in the development of the amphibian microbiome. The amphibian microbiome is an important study system due to its association with host health and disease outcomes. This study provides vertical transfer of bacteria through parental transport of tadpoles as one mechanism, among others, influencing tadpole microbiome composition. This paper gives insight into the relative roles of the environment, species, and parental care in amphibian microbiome assembly.

The authors determine the time of bacterial colonization during tadpole development using PCR, observing that tadpoles were not colonized by bacteria prior to hatching from the vitelline membrane. This is an important finding for amphibian microbiome research and I would be curious to see if this is seen broadly across amphibian species. By doing this, the impact of transport can be more accurately assessed in their laboratory experiments. The authors found that caregiver species influenced community composition, with transported tadpoles sharing a greater proportion of their skin communities with the transporting species.

In a comparison of three sympatric amphibian species that vary in their reproductive strategies, the authors found that tadpole community diversity was not reflective of habitat diversity, but may be associated with the different reproductive strategies of each species. Parental care explained some of the variance of tadpole microbiomes between species, however, transportation by conspecific adults did not lead to more similar microbiomes between tadpoles and adults compared to species that do not exhibit parental transport. This finding is in agreement with the understanding that the amphibian microbiome is distinct between developmental stages (eggs/tadpoles/adults) and also that amphibian microbiome composition is generally species specific.

When investigating contributions of caretakers to transported offspring, the authors found that tadpole-adult pairs with a history of direct contact were not more similar than tadpole-adult pairs lacking that history. This conclusion was surprising when considering the direct contact between the adults and tadpoles, however if only certain taxa from the adults are capable of colonizing tadpoles, then one could expect that similar ASVs might be donated between tadpole-adult pairs.

I did not find any major weaknesses in my review of this paper. I think that the data and conclusions here are of value to other researchers looking into the assembly of the amphibian microbiome. This paper offers insight into how tadpole-transport could influence the microbiome and adds to our overall understanding of amphibian microbiome assembly across the varied life histories of frogs.

Reviewer #1 (Public review):

Petrovic et al. investigate CCR5 endocytosis via arrestin2, with a particular focus on clathrin and AP2 contributions. The study is thorough and methodologically diverse. The NMR titration data are particularly compelling, clearly demonstrating chemical shift changes at the canonical clathrin-binding site (LIELD), present in both the 2S and 2L arrestin splice variants.

To assess the effect of arrestin activation on clathrin binding, the authors compare: truncated arrestin (1-393), full-length arrestin, and 1-393 incubated with CCR5 phosphopeptides. All three bind clathrin comparably, whereas controls show no binding. These findings are consistent with prior crystal structures showing peptide-like binding of the LIELD motif, with disordered flanking regions. The manuscript also evaluates a non-canonical clathrin binding site specific to the 2L splice variant. Though this region has been shown to enhance beta2-adrenergic receptor binding, it appears not to affect CCR5 internalization.

Similar analyses applied to AP2 show a different result. AP2 binding is activation-dependent and influenced by the presence and level of phosphorylation of CCR5-derived phosphopeptides. These findings are reinforced by cellular internalization assays.

In sum, the results highlight splice-variant-dependent effects and phosphorylation-sensitive arrestin-partner interactions. The data argue against a (rapidly disappearing) one-size-fits-all model for GPCR-arrestin signaling and instead support a nuanced, receptor-specific view, with one example summarized effectively in the mechanistic figure.

Reviewer #2 (Public review):

Summary:

Based on extensive live cell assays, SEC, and NMR studies of reconstituted complexes, these authors explore the roles of clathrin and the AP2 protein in facilitating clathrin-mediated endocytosis via activated arrestin-2. NMR, SEC, proteolysis, and live cell tracking confirm a strong interaction between AP2 and activated arrestin using a phosphorylated C-terminus of CCR5. At the same time, a weak interaction between clathrin and arrestin-2 is observed, irrespective of activation.

These results contrast with previous observations of class A GPCRs and the more direct participation by clathrin. The results are discussed in terms of the importance of short and long phosphorylated bar codes in class A and class B endocytosis.

Strengths:

The 15N,1H, and 13C, methyl TROSY NMR and assignments represent a monumental amount of work on arrestin-2, clathrin, and AP2. Weak NMR interactions between arrestin-2 and clathrin are observed irrespective of the activation of arrestin. A second interface, proposed by crystallography, was suggested to be a possible crystal artifact. NMR establishes realistic information on the clathrin and AP2 affinities to activated arrestin, with both kD and description of the interfaces.

Weaknesses:

This reviewer has identified only minor weaknesses with the study.

(1) Arrestin-2 1-418 resonances all but disappear with CCR5pp6 addition. Are they recovered with Ap2Beta2 addition, and is this what is shown in Supplementary Figure 2D?

(2) I don't understand how methyl TROSY spectra of arrestin2 with phosphopeptide could look so broadened unless there are sample stability problems.

(3) At one point, the authors added an excess fully phosphorylated CCR5 phosphopeptide (CCR5pp6). Does the phosphopeptide rescue resolution of arrestin2 (NH or methyl) to the point where interaction dynamics with clathrin (CLTC NTD) are now more evident on the arrestin2 surface?

(4) Once phosphopeptide activates arrestin-2 and AP2 binds, can phosphopeptide be exchanged off? In this case, would it be possible for the activated arrestin-2 AP2 complex to re-engage a new (phosphorylated) receptor?

(5) Did the authors ever try SEC measurements of arrestin-2 + AP2beta2+CCR5pp6 with and without PIP2, and with and without clathrin (CLTC NTD? The question becomes what the active complex is and how PIP2 modulates this cascade of complexation events in class B receptors.

Reviewer #3 (Public review):

Summary:

Overall, this is a well-done study, and the conclusions are largely supported by the data, which will be of interest to the field.

Strengths:

(1) The strengths of this study include experiments with solution NMR that can resolve high-resolution interactions of the highly flexible C-terminal tail of arr2 with clathrin and AP2. Although mainly confirmatory in defining the arr2 CBL 376LIELD380 as the clathrin binding site, the use of the NMR is of high interest (Figure 1). The 15N-labeled CLTC-NTD experiment with arr2 titrations reveals a span from 39-108 that mediates an arr2 interaction, which corroborates previous crystal data, but does not reveal a second area in CLTC-NTD that in previous crystal structures was observed to interact with arr2.

(2) SEC and NMR data suggest that full-length arr2 (1-418) binding with the 2-adaptin subunit of AP2 is enhanced in the presence of CCR5 phospho-peptides (Figure 3). The pp6 peptide shows the highest degree of arr2 activation and 2-adaptin binding, compared to less phosphorylated peptides or not phosphorylated at all. It is interesting that the arr2 interaction with CLTC NTD and pp6 cannot be detected using the SEC approach, further suggesting that clathrin binding is not dependent on arrestin activation. Overall, the data suggest that receptor activation promotes arrestin binding to AP2, not clathrin, suggesting the AP2 interaction is necessary for CCR5 endocytosis.

(3) To validate the solid biophysical data, the authors pursue validation experiments in a HeLa cell model by confocal microscopy. This requires transient transfection of tagged receptor (CCR5-Flag) and arr2 (arr2-YFP). CCR5 displays a "class B"-like behavior in that arr2 is rapidly recruited to the receptor at the plasma membrane upon agonist activation, which forms a stable complex that internalizes into endosomes (Figure 4). The data suggest that complex internalization is dependent on AP2 binding, not clathrin (Figure 5).

Weaknesses:

The interaction of truncated arr2 (1-393) was not impacted by CCR5 phospho-peptide pp6, suggesting the interaction with clathrin is not dependent on arrestin activation (Figure 2). This raises some questions.

Overall, the data are solid, but for added rigor, can these experiments be repeated without tagged receptor and/or arr2? My concern stems from the fact that the stability of the interaction between arr2 and receptor may be related to the position of the tags.

Reviewer #1 (Public review):

Summary:

The study shows, perhaps surprisingly, that human fecal homogenates enhance the invasiveness of Salmonella typhimurium into cells of a swine colonic explant. This effect is only seen with chemotactic cells that express the chemoreceptor Tsr. However, two molecules sensed by Tsr that are present at significant concentrations in the fecal homogenates, the repellent indole and the attractant serine, do not, either by themselves or together at the concentrations in which they are present in the fecal homogenates, show this same effect. The authors then go on to study the conflicting repellent response to indole and attractant response to serine in a number of different in vitro assays.

Strengths:

The demonstration that homogenates of human feces enhance the invasiveness of chemotactic Salmonella Typhimurium in a colonic explant is unexpected and interesting. The authors then go on to document the conflicting responses to the repellent indole and the attractant serine, both sensed by the Tsr chemoreceptor, as a function of their relative concentration and the spatial distribution of gradients.

Weaknesses:

The authors do not identify what is the critical compound or combination of compounds in the fecal homogenate that gives the reported response of increased invasiveness. They show it is not indole alone, serine alone, or both in combination that have this effect, although both are sensed by Tsr and both are present in the fecal homogenates. Some of the responses to conflicting stimuli by indole and serine in the in vitro experiments yield interesting results, but they do little to explain the initial interesting observation that fecal homogenates enhance invasiveness.

Reviewer #3 (Public review):

Summary:

In this manuscript, Franco and colleagues describe careful analyses of Salmonella chemotactic behavior in the presence of conflicting environmental stimuli. By doing so, the authors describe that this human pathogen integrates signals from a chemoattractant and a chemorepellent into an intermediate "chemohalation" phenotype.

Strengths:

The study was clearly well-designed and well-executed. The methods used are appropriate and powerful. The manuscript is very well written, and the analyses are sound. This is an interesting area of research, and this work is a positive contribution to the field.

Weaknesses:

No significant weaknesses noted.

Reviewer #1 (Public review):

Summary:

The authors developed a tool for simulating multiplexed single-cell RNA-seq and ATAC-seq data with various adjustable settings like ambient RNA/DNA rate and sequencing depth. They used the simulated data with different settings to evaluate the performance of many demultiplexing methods. They also proposed a new metric at single-cell level that correlates with the RNA/DNA contamination level.

Strengths:

The simulation tool has a straightforward design and provides adjustability in multiple parameters that have practical relevance, such as sequencing depth and ambient contamination rate. With the growing use of multiplexing in single-cell RNAseq and ATACseq experiments, the tools and results in this paper can guide the experimental design and tool selection for many researchers. The simulation tool also provides a platform for benchmarking newly developed demultiplexing tools.

Weaknesses:

The usefulness of the proposed new metric of "variant consistency" and how it can guide users in selecting demultiplexing methods seems a little unclear. It correlates with the level of ambient RNA/DNA contamination, which makes it look like a metric on data quality. However, it does depend on the exact demultiplexing method, yet it's not clear how it directly connects to the "accuracy" of each demultiplexing method, which is the most important property that users of these methods care about. Since the simulated data has ground truth of donor identities available, I would suggest using the simulated data to show whether "variant consistency" directly indicates the accuracy of each method, especially the accuracy within those "C2" reads.

I also think the tool and analyses presented in this paper need some further clarification and documentation on the details, such as how the cell-type gene and peak probabilities are determined in the simulation, and how doublets from different cell types are handled in the simulation and analysis. A few analyses and figures also need a more detailed description of the exact methods used.

Reviewer #2 (Public review):

Li et al. describe ambisim, a tool with the goal of creating realistic synthetic single-nucleus RNA/ATAC sequencing datasets. It has become standard to pool multiple genetically distinct donors when using single-cell sequencing followed by genotype-based demultiplexing (i.e., using donor single-nucleotide variants to identify specific donor origin). A plethora of tools exist to accomplish this demultiplexing, but advanced tools to create synthetic datasets, and therefore provide definitive benchmarking, are lacking. Ambisim is a well-thought-out simulator that improves upon previous tools available by allowing for modeling of variable ambient contamination proportions and doing so in a genotype-aware fashion. This provides more realistic synthetic datasets that provide challenging scenarios for future demultiplexing tools. The authors use ambisim to benchmark a large number of available and commonly used genotype-free and -dependent demultiplexing tools. They identify the strengths and weaknesses of these tools. They also go on to define a new metric, variant consistency, to further assess demultiplexing performance across tools. Overall, this manuscript provides a useful framework to more thoroughly evaluate future demultiplexing tools, as well as provides rationale for tool selection depending on a user's experimental conditions.

The authors provide measured conclusions that are supported by their findings. There are some aspects that are unclear.

(1) Throughout the manuscript, the figure legends are difficult to understand, and this makes it difficult to interpret the graphs.

(2) Since this is both a new tool and a benchmark, it would be worthwhile in the Discussion to comment on which demultiplexing tools one may want to choose for their dataset, especially given the warning against ensemble methods. From this extensive benchmarking, one may want to choose a tool based on the number of donors one has pooled, the modalities present, and perhaps even the ambient RNA (if it has been estimated previously).

(3) What are the minimal computational requirements for running ambisim? What is the time cost?

Reviewer #1 (Public review):

Summary:

The authors had previously found that a brief social isolation could increase the activity of these neurons, and that manipulation of these neurons could alter social behavior in a social rank dependent fashion. This manuscript explored which of the outputs were responsible for this, identifying the central nucleus of the amygdala as the key output region. The authors identified some discrete behavior changes associated with these outputs, and found that during photostimulation of these outputs, neuronal activity appeared altered in 'social response' neurons. In the revised manuscript, the authors address the comments in a rigorous fashion.

Strengths:

Rigorous analysis of the anatomy. Careful examination of the hetergenous effects on cell activity due to stimulation, linking the physiology with the behavior via photostimulation during recording in vivo.

Weaknesses:

The authors have responded to all of my comments.

Reviewer #2 (Public review):

Summary:

The authors perform a series of studies to follow up on their previous work, which established a role for dorsal raphe dopamine neurons (DRN) in the regulation of social-isolation-induced rebound in mice. In the present study, Lee et. al, use a combination of modern circuit tools to investigate putatively distinct roles of DRN dopamine transporting containing (DAT) projections to the bed nucleus of the stria terminalis (BNST), central amygdala (CeA), and posterior basolateral amygdala (BLP). Notably, they reveal that optogenetic stimulation of distinct pathways confers specific behavioral states, with DRNDAT-BLP driving aversion, DRNDAT-BNST regulating non-social exploratory behavior, and DRNDAT-CeA promoting socialability. A combination of electrophysiological studies and in situ hybridization studies reveal heterogenous dopamine and neuropeptide expression and different firing properties, providing further evidence of pathway-specific neural properties. Lastly, the authors combine optogenetics and calcium imaging to resolve social encoding properties in the DRNDAT-CeA pathway, which correlates observed social behavior to socially engaged neural ensembles.

Collectively, these studies provide an interesting way of dissecting out separable features of a complex multifaceted social-emotional state that accompanies social isolation and the perception of 'loneliness.' The main conclusions of the paper provide an important and interesting set of findings that increase our understanding of these distinct DRN projections and their role in a range of social (e.g., prosocial, dominance), non-social, and emotional behaviors. However, as noted below, the examination of these circuits within a homeostatic framework is limited given that a number of the datasets did not include an isolated condition. The DRNDAT-CeA pathway was investigated with respect to social homeostatic states in the present study for some of the datasets.

Strengths:

(1) The authors perform a comprehensive and elegant dissection of the anatomical, behavioral, molecular, and physiological properties of distinct DRN projections relevant to social, non-social, and emotional behavior, to address multifaceted and complex features of social state.

(2) This work builds on prior findings of isolation-induced changes in DRN neurons and provides a working framework for broader circuit elements that can be addressed across social homeostatic state.

(3) This work characterizes a broader circuit implicated in social isolation and provides a number of downstream targets to explore, setting a nice foundation for future investigation.

(4) The studies account for social rank and anxiety-like behavior in several of the datasets, which are important consideration to the interpretation of social motivation states, especially in male mice with respect to dominance behavior.

Weaknesses:

(1) The conceptual framework of the study is based on the premise of social isolation and perceived 'loneliness' under the framework of social homeostasis, analogous to hunger. In this framework, social isolation should provoke an aversive state and compensatory social contact behavior. In the authors' prior work, they demonstrate synaptic changes in DRN neurons and social rebound following acute social isolation. Thus, the prediction would be that downstream projections also would show state dependent changes as a function of social isolation state (e.g., grouped/socially engaged vs. isolated). In the current paper, a social isolation condition was included for some but not all experiments, which should be considered in the interpretation of the data, specifically within the context of dynamic isolation states.

(2) Figure 1 confirms co-laterals in the BNST and CeA via anatomical tracing studies. The goal of the optogenetic studies is to dissociate functional/behavioral roles of distinct projections. One limitation of optogenetic projection targeting is the possibility of back-propagating action potentials (stimulation of terminals in one region may back-propagate to activate cell bodies, and then afferent projections to other regions), and/or stimulation of fibers of passage. However, this is addressed in the discussion and the present data are convincing, which minimizes the concern.

(3) Sex as a biological variable should be considered in the present data, as included in the discussion.

Reviewer #3 (Public review):

Summary:

The authors investigated the role of dopaminergic neurons (dopamine transporter expressing, DAT) in the dorsal raphe nucleus (DRN) in regulating social and affective behavior through projections to the central nucleus of the amygdala (CeA), bed nucleus of the stria terminalis (BNST), and the posterior subdivision of the basolateral amygdala. The largest effect observed was in the DRN-DAT projections to the CeA. Augmenting previously published results from this group (Matthews et al., 2016), the comprehensive behavioral analysis relative to social dominance, gene expression analysis, electrophysiological profiling, and in vivo imaging provides novel insights into how DRN-DAT projections to the CeA influence the engagement of social behavior in the contexts of group housed and socially isolated mice.

Strengths:

Correlational analysis with social dominance is a nice addition to the study. The overall computational analyses performed are well-designed and rigorous.

Weaknesses:

(1) Analysis of dopamine receptor expression did not include Drd3, Drd4, or Drd5 which may provide more insights into how dopamine modulates downstream targets. This is particularly relevant to the BNST projection in which the densest innervation did not robustly co-localize with the expression of either Drd1 or Drd2. It is also possible that dopamine release from DRN-DAT neurons in any or all of these structures in modulating neurotransmitter release from inputs to these regions that contain D2 receptors on their terminals.

(2) Although not the focus of this study, without pharmacological blockade of dopamine receptors, it is not possible to assess what the contribution of dopamine is to the behavioral outcomes. Given the co-release of glutamate and GABA from these neurons it is possible that dopamine plays only a marginal role in the functional connectivity of DRN-DAT neurons.

(3) Photostimulation parameters used during the behavioral studies (8 pulses of light delivered at 30 Hz for several minutes) could lead to confounding results limiting data interpretation. As shown in Figure 6J, 8 pulses of light delivered at 30 Hz results in a significant attenuation of the EPSC amplitude in the BLP and CeA projection. Thus, prolonged stimulation could lead to significant synaptic rundown resulting in an overall suppression of connectivity in the later stages of the behavioral analyses.

Comments on revisions:

No further issues have been identified.

Reviewer #1 (Public review):

Summary:

This paper reports an intracranial SEEG study of speech coordination, where participants synchronize their speech output with a virtual partner that is designed to vary its synchronization behavior. This allows the authors to identify electrodes throughout the left hemisphere of the brain that have activity (both power and phase) that correlates with the degree of synchronization behavior. They find that high-frequency activity in secondary auditory cortex (superior temporal gyrus) is correlated to synchronization, in contrast to primary auditory regions. Furthermore, activity in inferior frontal gyrus shows a significant phase-amplitude coupling relationship that is interpreted as compensation for deviation from synchronized behavior with the virtual partner.

Strengths:

(1) The development of a virtual partner model trained for each individual participant, which can dynamically vary its synchronization to the participant's behavior in real time, is novel and exciting.

(2) Understanding real-time temporal coordination for behaviors like speech is a critical and understudied area.

(3) The use of SEEG provides the spatial and temporal resolution necessary to address the complex dynamics associated with the behavior.

(4) The paper provides some results that suggest a role for regions like IFG and STG in the dynamic temporal coordination of behavior both within an individual speaker and across speakers performing a coordination task.

Reviewer #2 (Public review):

Summary:

This paper investigates the neural underpinnings of an interactive speech task requiring verbal coordination with another speaker. To achieve this, the authors recorded intracranial brain activity from the left (and to a lesser extent, the right) hemisphere in a group of drug-resistant epilepsy patients while they synchronised their speech with a 'virtual partner'. Crucially, the authors were able to manipulate the degree of success of this synchronisation by programming the virtual partner to either actively synchronise or desynchronise their speech with the participant, or else to not vary its speech in response to the participant (making the synchronisation task purely one-way). Using such a paradigm, the authors identified different brain regions that were either more sensitive to the speech of the virtual partner (primary auditory cortex), or more sensitive to the degree of verbal coordination (i.e. synchronisation success) with the virtual partner (left secondary auditory cortex and bilateral IFG). Such sensitivity was measured by (1) calculating the correlation between the index of verbal coordination and mean power within a range of frequency bands across trials, and (2) calculating the phase-amplitude coupling between the behavioural and brain signals within single trials (using the power of high-frequency neural activity only). Overall, the findings help to elucidate some of the brain areas involved in interactive speaking behaviours, particularly highlighting high-frequency activity of the bilateral IFG as a potential candidate supporting verbal coordination.

Strengths:

This study provides the field with a convincing demonstration of how to investigate speaking behaviours in more complex situations that share many features with real-world speaking contexts e.g. simultaneous engagement of speech perception and production processes, the presence of an interlocutor and the need for inter-speaker coordination. The findings thus go beyond previous work that has typically studied solo speech production in isolation, and represent a significant advance in our understanding of speech as a social and communicative behaviour. It is further an impressive feat to develop a paradigm in which the degree of cooperativity of the synchronisation partner can be so tightly controlled; in this way, this study combines the benefits of using pre-recorded stimuli (namely, the high degree of experimental control) with the benefits of using a live synchronisation partner (allowing the task to be truly two-way interactive, an important criticism of other work using pre-recorded stimuli). A further key strength of the study lies in its employment of stereotactic EEG to measure brain responses with both high temporal and spatial resolution, an ideal method for studying the unfolding relationship between neural processing and this dynamic coordination behaviour.

Weaknesses:

One limitation of the current study is the relatively sparse coverage of the right hemisphere by the implanted electrodes (91 electrodes in the right compared to 145 in the left). Of course, electrode location is solely clinically motivated, and so the authors did not have control over this. In a previous version of this article, the authors therefore chose not to include data from the right hemisphere in reported analyses. However, after highlighting previous literature suggesting that the right hemisphere likely has high relevance to verbal coordination behaviours such as those under investigation here, the authors have now added analyses of the right hemisphere data to the results. These confirm an involvement of the right hemisphere in this task, largely replicating left hemisphere results. Some hemispheric differences were found in responses within the STG; however, interpretation should be tempered by an awareness of the relatively sparse coverage of the right hemisphere meaning that some regions have very few electrodes, resulting in reduced statistical power.

Reviewer #3 (Public review):

Summary:

In microbiology, accurately characterizing microbial populations and communities is essential. One widely used approach is to measure the absolute or relative abundance of microbial species. Recent research in microbial ecology, for instance, has shown that even genetically identical hosts exposed to the same microbial pool can develop very different gut microbiota, largely due to random colonization events. This study builds on that idea but adds a valuable layer: it suggests that some of the observed variability might actually result from experimental noise, specifically the randomness introduced by dilution and plate counting techniques. To address this, the authors introduce REPOP, a new tool designed to improve the quantification of microbial populations by explicitly accounting for the inherent stochasticity in these methods. They test REPOP using both simulated and experimental datasets, showing how it can help recover meaningful trends.

Strengths:

Overall, this paper is a good contribution to the field. The motivation is clear: improving our ability to quantify microbial populations is crucial for many research areas. The authors make a strong case that ignoring experimental noise is no longer acceptable, and they offer a well-argued solution. The manuscript is well-written and easy to follow, and the logic behind REPOP is convincingly laid out. The use of simulated data is especially valuable, as it allows the authors to test whether the method can recover known inputs, an important validation step. Even with experimental data, where true values are unknown, the method seems to behave in a reasonable and expected way, which is reassuring. All in all, this is an important step forward in how we quantify microbial populations.

Weaknesses:

While the study is promising, there are a few areas where the paper could be strengthened to increase its impact and usability. First, the extent to which dilution and plating introduce noise is not fully explored. Could this noise significantly affect experimental conclusions? And under what conditions does it matter most? Does it depend on experimental design or specific parameter values? Clarifying this would help readers appreciate when and why REPOP should be used. Second, more practical details about the tool itself would be very helpful. Simply stating that it is available on GitHub may not be enough. Readers will want to know what programming language it uses, what the input data should look like, and ideally, see a step-by-step diagram of the workflow. Packaging the tool as an easy-to-use resource, perhaps even submitting it to CRAN or including example scripts, would go a long way, especially since microbiologists tend to favor user-friendly, recipe-like solutions. Third, it would be great to see the method tested on existing datasets, such as those from Nic Vega and Jeff Gore (2017), which explore how colonization frequency impacts abundance fluctuation distributions. Even if the general conclusions remain unchanged, showing that REPOP can better match observed patterns would strengthen the paper's real-world relevance. Lastly, it would be helpful for the authors to briefly discuss the limitations of their method, as no approach is without its constraints. Acknowledging these would provide a more balanced and transparent perspective.

Reviewer #2 (Public review):

Summary:

Microbial population abundances are regularly estimated by multiplying plate counts by dilution factors, with inferences made about sample heterogeneity without taking into account heterogeneity generated through dilution and plating methods. The authors have developed REPOP, a method for disentangling methodological stochasticity from ecological heterogeneity using a Bayesian framework. They present three models: a unimodal distribution, a multimodal distribution, and a multimodal distribution that incorporates a colony count cutoff. They use a combination of simulated and experimental data to show the effectiveness of the REPOP method in resolving true microbial population distributions.

Strengths:

Overall, this paper addresses a significant issue in microbial ecology and reliably demonstrates that the REPOP method improves upon current methods of estimating microbial population heterogeneity, particularly with simulation data. The three models presented build upon each other and are discussed in a way that is fairly accessible to a broad audience. The authors also show that leveraging the information provided by non-countable plates is important. Additionally, the authors address the potential for extending this method to other sources of methodological stochasticity that may occur in microbial plating. However, it does seem that they could extend this further by discussing ways that this method could be applied to non-microbial systems, allowing this work to appeal to a broader audience.

Weaknesses:

A more thorough discussion of when and by how much estimated microbial population abundance distributions differ from the ground truth would be helpful in determining the best practices for applying this method. Not only would this allow researchers to understand the sampling effort necessary to achieve the results presented here, but it would also contextualize the experimental results presented in the paper. Particularly, there is a disconnect between the discussion of the large sample sizes necessary to achieve accurate multimodal distribution estimates and the small sample sizes used in both experiments.

Reviewer #1 (Public review):

Summary:

The authors developed a novel theoretical/computational procedure to count bacterial populations without introducing artificial randomness effects due to dilution. Surprisingly, this very important aspect of studies of bacterial systems has been overlooked. The proposed method provides a simple and transparent approach to eliminate the randomness of bacterial accounting procedures, allowing now to fully concentrate on the intrinsic effects of the studied systems.

Strengths:

A very simple and clear procedure is introduced and explained in full detail. This elegant approach finds an excellent compromise between mathematical rigor and computational efficiency, which is important for practical applications. The provided examples are convincing beyond a doubt, clearly indicating the potential strong impact of the proposed framework. Various complications and possible issues are also discussed and analyzed. This seems to be a very powerful novel method that should significantly advance the analysis of complex biological systems.

Weaknesses:

The only minor weakness that I found is the assumption of independence of bacterial species, which is expressed as the well-stirred approximation. One could imagine that bacterial species might cooperate, leading to non-uniform distributions that are real. How to distinguish such situations?

I believe that this method can be extended to determine if this is the case or not before the application. For example, if the bacteria species are independent of each other and one can use the binomial distributions, then the Fano factor would be proportional to the overall relative fraction of bacterial species. Maybe a simple test can be added to test it before the application of REPOP. However, I believe that this is a minor issue.

Reviewer #1 (Public review):

The authors conducted an fMRI study to investigate the neural effects of sustaining attention to areas of different sizes. Participants were instructed to attend to alphanumeric characters arranged in a circular array. The size of attention field was manipulated in four levels, ranging from small (18 deg) to large (162 deg). They used a model-based method to visualize attentional modulation in early visual cortex V1 to V3, and found spatially congruent modulations of the BOLD response, i.e., as the attended area increased in size, the neural modulation also increased in size in the visual cortex. They suggest that this result is a neural manifestation of the zoom-lens model of attention and that the model-based method can effectively reconstruct the neural modulation in the cortical space.

The study is well-designed with sophisticated and comprehensive data analysis. The results are robust and show strong support for a well-known model of spatial attention, the zoom-lens model. Overall, I find the results interesting and useful for the field of visual attention research.

Comments on revisions:

The authors have addressed my previous comments satisfactorily. I would encourage the authors to make data and code publicly available, which appears to be the custom in this era.

Reviewer #2 (Public review):

Summary:

The study in question utilizes functional magnetic resonance imaging (fMRI) to dynamically estimate the locus and extent of covert spatial attention from visuocortical activity. The authors aim to address an important gap in our understanding of how the size of the attentional field is represented within the visual cortex. They present a novel paradigm that allows for the estimation of the spatial tuning of the attentional field and demonstrate the ability to reliably recover both the location and width of the attentional field based on BOLD responses.

Strengths:

(1) Innovative Paradigm: The development of a new approach to estimate the spatial tuning of the attentional field is a significant strength of this study. It provides a fresh perspective on how spatial attention modulates visual perception.

(2) Refined fMRI Analysis: The use of fMRI to track the spatial tuning of the attentional field across different visual regions is methodologically rigorous and provides valuable insights into the neural mechanisms underlying attentional modulation.

(3) Clear Presentation: The manuscript is well-organized, and the results are presented clearly, which aids in the reader's comprehension of the complex data and analyses involved.

Weaknesses:

(1) Lack of Neutral Cue Condition: The study does not include a neutral cue condition where the cue width spans 360{degree sign}, which could serve as a valuable baseline for assessing the BOLD response enhancements and diminishments in both attended and non-attended areas.

(2) Clarity on Task Difficulty Ratios: The explicit reasoning for the chosen letter-to-number ratios for various cue widths is not detailed. Ensuring clarity on these ratios is crucial, as it affects the task difficulty and the comparability of behavioral performance across different cue widths. It is essential that observed differences in behavior and BOLD signals are attributable solely to changes in cue width and not confounded by variations in task difficulty.

Comments on revisions:

(1) Please standardize the naming of error metrics across Figures 4-6 to improve clarity (e.g., "angular error" (Figure 4), "|angular error|" (Figure 5), and "absolute error" (Figure 6) appear to refer to the same measure). This inconsistency is also present in the main text.

(2) Consider briefly mentioning the baseline offset in Lines 179-186. It is included in Figures 4-7 and serves as a reference for interpreting attentional modulation alongside gain. Introducing it with other model parameters would improve clarity.

(3) It may be valuable to examine BOLD responses in unattended visual regions. As shown in Figure 2a, suppression patterns (e.g., the most negative responses) appear to vary in extent and distribution with attentional cue width. Analyzing these unattended regions may offer a more complete view of how attention shapes the spatial profile of cortical activity.

Reviewer #1 (Public review):

Henshall et al. delete the highly abundant merozoite surface protein PfMSP2 from two Plasmodium falciparum laboratory lines (3D7 and Dd2) using CRISPR-Cas9. Parasites lacking MSP2 replicate and invade red cells normally, opposing the experimental history that suggests MSP2 is essential. Unexpectedly, the knock-outs become more susceptible to several inhibitory antibodies - most strikingly those that target the apical antigen AMA1-while antibodies to other surface or secreted proteins are largely unaffected. Recombinant MSP2 added in vitro can dampen AMA1-antibody binding, supporting a "conformational masking" model. The reported data suggest that MSP2 helps shield key invasion ligands from host antibodies and may itself be a double-edged vaccine target.

Reviewer #2 (Public review):

Summary:

The authors were trying to establish the role of Plasmodium falciparum surface protein 2 in merozoite biology, specifically the process of erythrocyte invasion.

Strengths:

The major strengths of the manuscript are in the Plasmodium falciparum genetic and phenotyping approaches. PfMSP2 knockouts are made in two different strains, which is important as it is known that invasion pathways can vary between strains, but is a level of comprehensiveness that is not always delivered in P. falciparum genetic studies. The knockout strains are characterised very thoroughly using multiple different assays, and the authors should be commended for publishing a good deal of negative data, where no phenotype was detected. This is not always done, but is very helpful for the field and reduces the potential for experimental redundancy, i.e., others repeating work that has already been performed but never published. The quality of the writing, referencing, and figures is also generally strong, although a few minor typos and technical comments on presentation have been communicated to the authors.

Weaknesses:

There are, however, some areas that are weaker.

(1) The section describing Laverania and avian Plasmodium MSP2 comparison is a lengthy section and could be told much more concisely for clarity in delivering the key message, i.e., that conservation in distantly related Plasmodium species could indicate an important function. The identification of MSP2-like genes in avian Plasmodium species was highlighted previously in the referenced Escalante paper, so it is not entirely novel, although this paper goes into more detailed characterisation of the extent of conservation. Overall, this section takes up much more space in the manuscript than is merited by the novelty and significance of the findings.

(2) Characterisation of the knockout strains is generally thorough, though relatively few interactions were followed by live microscopy (Figures 3E-H). A minimum of 30 merozoites were followed in each assay (although the precise number is not specified in the figure or legend), but there are intriguing trends in the data that could potentially have become significant if n was increased.

(3) The comparative RNAseq data is interesting, but is not followed up to any significant degree. Multiple transcripts are up-regulated in the absence of PfMSP2, but they are largely dismissed because they are genes of unknown function, not previously linked to invasion, or lack an obvious membrane anchor. Having gone to the lengths of exploring potentially compensatory changes in gene expression, it is disappointing not to validate or explore the hits that result.

(4) Given the abundance of PfMSP2 on the merozoite surface, it would have been interesting to see whether the knockout lines have any noticeable difference in surface composition, as viewed by electron microscopy, although, of course, this experiment relies on access to the appropriate facilities.

(5) One of the key findings is that deletion of PfMSP2 increases inhibition by some antibodies/nanobodies (some anti-CSS2, some anti-AMA1) but not others (anti-EBA/RH, anti-EBA175, anti-Rh5, anti-TRAMP, some anti-CSS2, some anti-AMA1). The data supporting these changes in inhibition are solid, but the selectivity of the effect (only a few antibodies, and generally those targeting later stages in invasion) is not really discussed in any detail. Do the authors have a hypothesis for this selectivity? The authors make attempts to explore the mechanisms for this antibody-masking (Figure 7), but the data is less solid. Surface Plasmon Resonance was non-conclusive, while an ELISA approach co-incubating MSP2 and anti-AMA1 antibodies to wells coated with AMA1 lacks appropriate controls (eg, including other merozoite proteins in similar experiments).

Overall, the claim that PfMSP2 is non-essential for in vitro growth is well justified and is an important contribution to the field. The impact of PfMSP2 deletion on antibody inhibition (which is highlighted in the title of the manuscript) and the mechanism behind it is much less definitive, but does open up an interesting area for further investigation, with more work to be done.

Reviewer #3 (Public review):

The central issue for evaluating the overfilling hypothesis is the identity of the mechanism that causes the very potent (>80% when inter pulse is 20 ms), but very quickly reverting (< 50 ms) paired pulse depression (Fig 1G, I). To summarize: the logic for overfilling at local cortical L2/3 synapses depends critically on the premise that probability of release (pv) for docked and fully primed vesicles is already close to 100%. If so, the reasoning goes, the only way to account for the potent short-term enhancement seen when stimulation is extended beyond 2 pulses would be by concluding that the readily releasable pool overfills. However, the conclusion that pv is close to 100% depends on the premise that the quickly reverting depression is caused by exocytosis dependent depletion of release sites, and the evidence for this is not strong in my opinion. Caution is especially reasonable given that similarly quickly reverting depression at Schaffer collateral synapses, which are morphologically similar, was previously shown to NOT depend on exocytosis (Dobrunz and Stevens 1997). Note that the authors of the 1997 study speculated that Ca2+-channel inactivation might be the cause, but did not rule out a wide variety of other types of mechanisms that have been discovered since, including the transient vesicle undocking/re-docking (and subsequent re-priming) reported by Kusick et al (2020), which seems to have the correct timing.

In an earlier round of review, I suggested raising extracellular Ca2+, to see if this would increase synaptic strength. This is a strong test of the authors' model because there is essentially no room for an increase in synaptic strength. The authors have now done experiments along these lines, but the result is not clear cut. On one hand, the new results suggest an increase in synaptic strength that is not compatible with the authors' model; technically the increase does not reach statistical significance, but, likely, this is only because the data set is small and the variation between experiments is large. Moreover, a more granular analysis of the individual experiments seems to raise more serious problems, even supporting the depletion-independent counter hypothesis to some extent. On the other hand, the increase in synaptic strength that is seen in the newly added experiments does seem to be less at local L2/3 cortical synapses compared to other types of synapses, measured by other groups, which goes in the general direction of supporting the critical premise that pv is unusually high at L2/3 cortical synapses. Overall, I am left wishing that the new data set were larger, and that reversal experiments had been included as explained in the specific points below.

Specific Points:

(1) One of the standard methods for distinguishing between depletion-dependent and depletion-independent depression mechanisms is by analyzing failures during paired pulses of minimal stimulation. The current study includes experiments along these lines showing that pv would have to be extremely close to 1 when Ca2+ is 1.25 mM to preserve the authors' model (Section "High double failure rate ..."). Lower values for pv are not compatible with their model because the k1 parameter already had to be pushed a bit beyond boundaries established by other types of experiments. The authors now report a mean increase in synaptic strength of 23% after raising Ca to 2.5 mM. The mean increase is not quite statistically significant, but this is likely because of the small sample size. I extracted a 95% confidence interval of [-4%, +60%] from their numbers, with a 92% probability that the mean value of the increase in the full population is > 5%. I used the 5% value as the greatest increase that the model could bear because 5% implies pv < 0.9 using the equation from Dodge and Rahamimoff referenced in the rebuttal. My conclusion from this is that the mean result, rather than supporting the model, actually undermines it to some extent. It would have likely taken 1 or 2 more experiments to get above the 95% confidence threshold for statistical significance, but this is ultimately an arbitrary cut off.

(2) The variation between experiments seems to be even more problematic, at least as currently reported. The plot in Figure 3-figure supplement 3 (left) suggests that the variation reflects true variation between synapses, not measurement error. And yet, synaptic strength increased almost 2-fold in 2 of the 8 experiments, which back extrapolates to pv < 0.2. If all of the depression is caused by depletion as assumed, these individuals would exhibit paired pulse facilitation, not depression. And yet, from what I can tell, the individuals depressed, possibly as much as the synapses with low sensitivity to Ca2+, arguing against the critical premise that depression equals depletion, and even arguing - to some extent - for the counter hypothesis that a component of the depression is caused by a mechanism that is independent of depletion. I would strongly recommend adding an additional plot that documents the relationship between the amount of increase in synaptic strength after increasing extracellular Ca2+ and the paired pulse ratio as this seems central.

(3) Decrease in PPR. The authors recognize that the decrease in the paired-pulse ratio after increasing Ca2+ seems problematic for the overfilling hypothesis by stating: "Although a reduction in PPR is often interpreted as an increase in pv, under conditions where pv is already high, it more likely reflects a slight increase in pocc or in the number of TS vesicles, consistent with the previous estimates (Lin et al., 2025)." I looked quickly, but did not immediately find an explanation in Lin et al 2025 involving an increase in pocc or number of TS vesicles, much less a reason to prefer this over the standard explanation that reduced PPR indicates an increase in pv. The authors should explain why the most straightforward interpretation is not the correct one in this particular case to avoid the appearance of cherry picking explanations to fit the hypothesis.

(4) The authors concede in the rebuttal that mean pv must be < 0.7, but I couldn't find any mention of this within the manuscript itself, nor any explanation for how the new estimate could be compatible with the value of > 0.99 in the section about failures.

(5) Although not the main point, comparisons to synapses in other brain regions reported in other studies might not be accurate without directly matching experiments. As it is, 2 of 8 synapses got weaker instead of stronger, hinting at possible rundown, but this cannot be assessed because reversibility was not evaluated. In addition, comparing axons with and without channel rhodopsins might be problematic because the channel rhodopsins might widen action potentials.

(6) Perhaps authors could double check with Schotten et al about whether PDBu does/does not decrease the latency between osmotic shock and transmitter release. This might be an interesting discrepancy, but my understanding is that Schotten et al didn't acquire information about latency because of how the experiments were designed.

(7) The authors state: "These data are difficult to reconcile with a model in which facilitation is mediated by Ca2+-dependent increases in pv." However, I believe that discarding the premise that depression is always caused by depletion would open up wide range of viable possibilities.

Reviewer #1 (Public review):

Summary:

Authors benchmarked five IBD detection methods (hmmIBD, isoRelate, hap-IBD, phasedIBD, and Refined IBD) in Plasmodium falciparum using simulated and empirical data. Plasmodium falciparum has a mutation rate similar to that of humans but a much higher recombination rate and lower SNP density. Thus, the authors evaluated how recombination rate and marker density affect IBD segment detection. Next, they performed parameter optimization for Plasmodium falciparum and benchmarked the robustness of downstream analyses (selection detection and Ne inference) using IBD segments detected by each method. They also tracked the computational efficiency of these methods. The authors' work is valuable for the tested species, and the analyses presented support their claim that users should be cautious when calling IBD in contexts of low SNP density and high recombination rate.

Strengths:

The study design is convincing and well-structured. The authors chose to use P. falciparum, which presents an interesting case due to its high recombination rate and a mutation rate similar to that of humans. The authors note that despite the widespread use of IBD for genomic surveillance, comprehensive evaluation of these methods in high-recombination, low-marker-density contexts has been lacking. Furthermore, they also examined the performance of IBD detection methods developed specifically for P. falciparum, and evaluated it with phased data which broadened the applicability of the work.

Weaknesses:

The authors thoughtfully addressed our prior concerns by 1) expanding the simulations; 2) updating figures and methods for clarity; and 3) more clearly framing the broader utility of their benchmarking effort. These updates strengthen the manuscript and make the relevance of their findings beyond Plasmodium falciparum more apparent.

More specifically:

The authors added three full replicates per simulation scenario and updated figures to reflect uncertainty at relevant levels, which addresses earlier concerns about reproducibility. The limited number of replicates is due to computational intensity. In the future, broader generalizability and deeper exploration of variance in benchmarking accuracy across parameter space would further strengthen the conclusions/generalizability. The author's also emphasized that, while the study is centered on Plasmodium falciparum, the benchmarking framework, not the parameters, are broadly applicable to other sexually recombining species. Lastly, they extensively updated multiple figures to include simulation models, results from simulation replicates, and improved the figures from the previous version of the manuscript.

Reviewer #2 (Public review):

Summary:

Guo et al. benchmarked and optimized methods for detecting Identity-By-Descent (IBD) segments in Plasmodium falciparum (Pf) genomes, which are characterized by high recombination rates and low marker density. Their goal was to address the limitations of existing IBD detection tools, which were primarily developed for human genomes and do not perform well in the genomic context of highly recombinant genomes. They first analysed various existing IBD callers, such as hmmIBD, isoRelate, hap-IBD, phased-IBD, and refinedIBD. They focused on the impact of recombination on the accuracy, which was calculated based on two metrics, the false negative rate and the false positive rate. The results suggest that high recombination rates significantly reduce marker density, leading to higher false negative rates for short IBD segments. This effect compromises the reliability of IBD-based downstream analyses, such as effective population size (Ne) estimation.<br /> They showed that the best tool for IBD detection in Pf is hmmIBD, because it has relatively low FN/FP error rates and is less biased for relatedness estimates. However, this method is less computationally efficient.<br /> Their suggestion is to optimize human-oriented IBD methods and use hmmIBD only for the estimation of Ne.

Strengths:

Although I am not an expert on Plasmodium falciparum genetics, I believe the authors have developed a valuable benchmarking framework tailored to the unique genomic characteristics of this species. Their framework enables a thorough evaluation of various IBD detection tools for non-human data, such as high recombination rates and low marker density, addressing a key gap in the field.

This study provides a comparison of multiple IBD detection methods, including probabilistic approaches (hmmIBD, isoRelate) and IBS-based methods (hap-IBD, Refined IBD, phased IBD). This comprehensive analysis offers researchers valuable guidance on the strengths and limitations of each tool, allowing them to make informed choices based on specific use cases. I think this is important beyond the study of Pf.

The authors highlight how optimized IBD detection can help identify signals of positive selection, infer effective population size (Ne), and uncover population structure.

They demonstrate the critical importance of tailoring analytical tools to suit the unique characteristics of a species. Moreover, the authors provide practical recommendations, such as employing hmmIBD for quality-sensitive analyses and fine-tuning parameters for tools originally designed for non-P. falciparum datasets before applying them to malaria research.

Overall, this study represents a meaningful contribution to both computational biology and malaria genomics, with its findings and recommendations likely to have an impact on the field.

Weaknesses:

One weakness of the study is the lack of emphasis on the broader importance of studying Plasmodium falciparum as a critical malaria-causing organism. Malaria remains a significant global health challenge, causing hundreds of thousands of deaths annually.

While the study provides a thorough technical evaluation of IBD detection methods and their application to Pf, it does not adequately connect these findings to the broader implications for malaria research and control efforts. Additionally, the discussion on malaria and its global impact could have framed the study in a more accessible and compelling way, making the importance of these technical advances clearer to a broader audience, including researchers and policymakers in the fight against malaria. In the revised version, the authors have placed greater emphasis on this aspect, while still maintaining the methodological focus of the paper.

Reviewer #1 (Public review):

Summary:

Gekko, Nomura et al., show that Drp1 elimination in zygotes using the Trim-Away technique leads to mitochondrial clustering and uneven mitochondrial partitioning during the first embryonic cleavage, resulting in embryonic arrest. They monitor organellar localization and partitioning using specific targeted fluorophores. They also describe the effects of mitochondrial clustering in spindle formation and the detrimental effect of uneven mitochondrial partitioning to daughter cells.

Strengths:

The authors have gathered solid evidence for the uneven segregation of mitochondria upon Drp1 depletion through different means: mitochondrial labelling, ATP labelling and mtDNA copy number assessment in each daughter cell. Authors have also characterised the defects in cleavage mitotic spindles upon Drp1 loss

Weaknesses:

This study convincingly describes the phenotype seen upon Drp1 loss. Further studies should be conducted to elucidate the mechanism by which Drp1 ensures even mitochondrial partitioning during the first embryonic cleavage.

Reviewer #2 (Public review):

Gekko et al investigate the impact of perturbing mitochondrial during early embryo development, through modulation of the mitochondrial fission protein Drp1 using Trim-Away technology. They aimed to validate a role for mitochondrial dynamics in modulating chromosomal segregation, mitochondrial inheritance and embryo development and achieve this through the examination of mitochondrial and endoplasmic reticulum distribution, as well as actin filament involvement, using targeted plasmids, molecular probes and TEM in pronuclear stage embryos through the first cleavages divisions. Drp1 deletion perturbed mitochondrial distribution, leading to asymmetric partitioning of mitochondria to the 2-cell stage embryo, prevented appropriate chromosomal segregation and culminated in embryo arrest. Resultant 2-cell embryos displayed altered ATP, mtDNA and calcium levels. Microinjection of Drp1 mRNA partially rescued embryo development. A role for actin filaments in mitochondrial inheritance is described, however the actin-based motor Myo19 does not appear to contribute.

Overall, this study builds upon their previous work and provides further support for a role of mitochondrial dynamics in mediating chromosomal segregation and mitochondrial inheritance. In particular, Drp1 is required for the redistribution of mitochondria to support symmetric partitioning and ongoing development.

Strengths:

The study is well designed, the methods are appropriate and the results are clearly presented. The findings are nicely summarised in a schematic.

The addition of further quantification, including mitochondrial cluster size, elongation/aspect ratio and ROS, as requested by the reviewers, has provided further evidence for the impact of Drp1 depletion on mitochondrial morphology and function.

Understanding the role of mitochondria in binucleation and mitochondrial inheritance is of clinical relevance for patients undergoing infertility treatment, particularly those undergoing mitochondrial replacement therapy.

Weaknesses:

The only remaining weakness is that the authors have not undertaken additional experiments to clarify any role for mitochondrial transport following Drp1 depletion.

Reviewer #3 (Public review):

Why mitochondria are finely maintained in the female germ cell (oocyte), zygotes, and preimplantation embryos? Mitochondrial fusion seems beneficial in somatic cells to compensate for unhealthy mitochondria, for example, mitochondria with mutated mtDNA that potentially defuel the respiratory activity if accumulated above a certain threshold. However, in the germ cells, it may rather increase the risk of transmitting mutated mtDNA to the next generation. Also, finely maintained mitochondria would also be beneficial for efficient removal when damaged, as the authors briefly discussed. Due in part to the limited suitable model, physiological role of mitochondrial fission in embryos were obscure. In this study, authors demonstrated that mitochondrial fission prevents multiple adverse outcomes, especially including the aberrant demixing of parental genome (a clinical phenotype of human embryos) in zygotic stage. Thus, this study would be also of clinical importance that could contribute by proposing a novel mechanism.

The authors have adequately indicated the limitations at each of the specific points. The revisions the authors made have consolidated their conclusion, thus still, making this study an excellent one.

Reviewer #1 (Public review):

Summary:

In this manuscript, Chua, Daugherty, and Smith analyze a new set of archaeal 20S proteasomes obtained by cryo-EM that illustrate how the occupancy of the HbYX binding pocket induces gate opening. They do so primarily through a V24Y mutation in the α-subunit. These results are supported by a limited set of mutations in K66 in the α subunit, bringing new emphasis to this unit.

Strengths:

The new structure's analysis is comprehensive, occupying the entire manuscript. As such, the scope of this manuscript is very narrow, but the strength of the data are solid, and they offer an interesting and important new piece to the gate-opening literature.

Weaknesses:

Extrapolating from the core HbYX activating motif shared by Archae and Eukaryotes to the specific operations of gate opening, which is more elaborate in eukaryotes, may prove challenging.

Reviewer #2 (Public review):

Summary:

The manuscript by Chuah et al. reports the experimental results that suggest the occupancy of the HbYX pockets suffices for proteasome gate opening. The authors conducted cryo-EM reconstructions of two mutant archaeal proteasomes. The work is technically sound and may be of special interest in the field of structural biology of the proteasomes.

Strengths:

Overall, the work incrementally deepens our understanding of the proteasome activation and expands the structural foundation for therapeutic intervention of proteasome function. The evidence presented appears to be well aligned with the existing literature, which adds confidence in the presentation.

Comments on revisions:

The authors have addressed all my questions.

Reviewer #1 (Public review):

N'Guessan et al have improved the report of their study of expression QTL (eQTL) mapping in yeast using single cells. The authors make use of advances in single cell RNAseq (scRNAseq) in yeast to increase the efficiency with which this type of analysis can be undertaken. Building on prior research led by the senior author that entailed genotyping and fitness profiling of almost 100,000 cells derived from a cross between two yeast strains (BY and RM) they performed scRNAseq on a subset of ~5% (n = 4,489) individual cells. To address the sparsity of genotype data in the expression profiling they used a Hidden Markov Model (HMM) to infer genotypes and then identify the most likely known lineage genotype from the original dataset. To address the relationship between variance in fitness and gene expression the authors partition the variance to investigate the sources of variation. They then perform eQTL mapping and study the relationship between eQTL and fitness QTL identified in the earlier study.

This paper seeks to address the question of how quantitative trait variation and expression variation are related. scRNAseq represents an appealing approach to eQTL mapping as it is possible to simultaneously genotype individual cells and measure expression in the same cell. As eQTL mapping requires large sample sizes to identify statistical relationships, the use of scRNAseq is likely to dramatically increase the statistical power of such studies. However, there are several technical challenges associated with scRNAseq and the authors' study is focused on addressing those challenges. The authors have successfully demonstrated their stated goal of developing, and illustrating the benefit of, a one-pot scRNA-seq experiment and analysis for eQTL mapping.

Reviewer #2 (Public review):

This work describes the single-cell expression profiling of thousands of cells of recombinant genotypes from a model natural-variation system, a cross between two divergent yeast strains.

I appreciate the addition of lines 282-291, which now makes the authors' point about one advantage of the single-cell technique for eQTL mapping clearly: the authors don't need to normalize for culture-to-culture variation the way standard bulk methods do (e.g. in Albert et al., 2018 for the current yeast cross), and without this normalization, they can integrate analyses of expression with those of estimates of growth behaviors from the abundance of a genotype in the pool. The main question the manuscript addresses with the latter, in Figure 3, is how much variation in growth appears to have nothing to do with expression, for which the answer the authors given is 30%. I agree that this represents a novel finding. The caveats are (1) the particular point will perhaps only be interesting to a small slice of the eQTL research community; (2) the authors provide no statistical controls/error estimate or independent validation of the variance partitioning analysis in Figure 3, and (3) the authors don't seem to use the single-cell growth/fitness estimates for anything else, as Figure 4 uses loci mapped to growth from a previously published, standard culture-by-culture approach.

Reviewer #1 (Public review):

Summary:

This is an interesting follow-up to a paper published in Human Molecular Genetics reporting novel roles in corticogenesis of the Kif7 motor protein that can regulate the activator as well as the repressor functions of the Gli transcription factors in Shh signalling. This new work investigates how a null mutation in the Kif7 gene affects the formation of corticofugal and thalamocortical axon tracts and the migration of cortical interneurons. It demonstrates that Kif7 null mutant embryos present with ventriculomegaly and heterotopias as observed in patients carrying KIF7 mutations. The Kif7 mutation also disrupts the connectivity between cortex and thalamus and leads to an abnormal projection of thalamocortical axons. Moreover, cortical interneurons show migratory defects that are mirrored in cortical slices treated with the Shh inhibitor cyclopamine suggesting that the Kif7 mutation results in a down-regulation of Shh signalling. Interestingly, these defects are much less severe at later stages of corticogenesis.

Strengths/weaknesses:

The findings of this manuscript are clearly presented and are based on detailed analyses. Using a compelling set of experiments, especially the live imaging to monitor interneuron migration, the authors convincingly investigate Kif7's roles and their results support their major claims. The migratory defects in interneurons and the potential role of Shh signalling present novel findings and provide some mechanistic insights but rescue experiments would further support Kif7's role in interneuron migration. Similarly, the mechanism underlying the misprojection which has previously been reported in other cilia mutants remains unexplored. Taken together, this manuscript makes novel contributions to our understanding of the role of primary cilia in forebrain development and to the aetiology of the neural symptons in ciliopathy patients.

Comments on revisions:

The authors addressed most of the points I raised in my original review. However, I am not convinced by the figures the authors present on Shh protein expression. The "bright tiny dots" of Shh protein in the cortex are not visible on the images in Figure 7. I wonder whether the authors could present higher magnification and/or black and white images with increased contrast.

Reviewer #2 (Public review):

Summary:

This study investigates the role of KIF7, a ciliary kinesin involved in the Sonic Hedgehog (SHH) signaling pathway, in cortical development using Kif7 knockout mice. The researchers examined embryonic cortex development (mainly at E14.5), focusing on structural changes and neuronal migration abnormalities.

Strengths:

(1) The phenotype observed is interesting, and the findings provide neurodevelopmental insight into some of the symptoms and malformations seen in patients with KIF7 mutations.

(2) The authors assess several features of cortical development, including structural changes in layers of the developing cortex, connectivity of the cortex with thalamus, as well as migration of cINs from CGE and MGE to cortex.

Weaknesses:

(1) The Kif7 null does have phenotype differences from individual mutations seen in patients. It would be interesting to add more thoughts about how the null differs from these mutants in ciliary structure and SHH signaling via the cilium.

(2) The description of altered cortex development at E14.5 is perhaps rather descriptive. It would be useful to assess more closely the changes occurring in different cell types and stages. For this it seems very important to have a time course of cortical development and how the structural organization changes over time. This would be easy to assess with the addition of serial sections from the same mice. It might also be interesting to see how SHH signaling is altered in different cortical cell types over time with a SHH signaling reporter mouse.

(3) Abnormal neurodevelopmental phenotypes have been widely reported in the absence of other key genes affecting primary cilia function (Willaredt et al., J Neurosci 2008; Guo et al., Nat Commun 2015). It would be interesting to have more discussion of how the Kif7 null phenotype compares to some of these other mutants.

(4) The authors see alterations in cIN migration to the cortex and observe distinct differences in the pattern of expression of Cxcl12 as well as suggest cell intrinsic differences within cIN in their ability to migrate. The slice culture experiments though make it a little difficult to interpret the cell intrinsic effects on cIN of loss of Kif7, as the differences in Cxcl12 patterns still exist presumably in the slice cultures. It would be useful to assess their motility in an assay where they were isolated, as well as assess transcriptional changes in cINs in vivo lacking KIF7 for expression patterns that may affect motility or other aspects of migration.

Comments on revisions:

The authors have made significant and thoughtful responses as well as experimental additions to the authors comments. Their efforts are appreciated and the manuscript is much improved.

Reviewer #1 (Public review):

Summary:

In this study by Li et al., the authors re-investigated the role of cDC1 for atherosclerosis progression using the ApoE model. First, the authors confirmed the accumulation of cDC1 in atherosclerotic lesions in mice and humans. Then, in order to examine the functional relevance of this cell type, the authors developed a new mouse model to selectively target cDC1. Specifically, they inserted the Cre recombinase directly after the start codon of the endogenous XCR1 gene, thereby avoiding off-target activity. Following validation of this model, the authors crossed it with ApoE-deficient mice and found a striking reduction of aortic lesions (numbers and size) following a high-fat diet. The authors further characterized the impact of cDC1 depletion on lesional T cells and their activation state. Also, they provide in-depth transcriptomic analyses of lesional in comparison to splenic and nodal cDC1. These results imply cellular interactions between lesion T cells and cDC1. Finally, the authors show that the chemokine XCL1, which is produced by activated CD8 T cells (and NK cells), plays a key role in the interaction with XCR1-expressing cDC1 and particularly in the atherosclerotic disease progression.

Strengths:

The surprising results on XCL1 represent a very important gain in knowledge. The role of cDC1 is clarified with a new genetic mouse model.

Weaknesses:

My criticism is limited to the analysis of the scRNAseq data of the cDC1. I think it would be important to match these data with published data sets on cDC1. In particular, the data set by Sophie Janssen's group on splenic cDC1 might be helpful here (PMID: 37172103; https://www.single-cell.be/spleen_cDC_homeostatic_maturation/datasets/cdc1). It would be good to assign a cluster based on the categories used there (early/late, immature/mature, at least for splenic DC).

Reviewer #2 (Public review):

This study investigates the role of cDC1 in atherosclerosis progression using Xcr1Cre-Gfp Rosa26LSL-DTA ApoE-/- mice. The authors demonstrate that selective depletion of cDC1 reduces atherosclerotic lesions in hyperlipidemic mice. While cDC1 depletion did not alter macrophage populations, it suppressed T cell activation (both CD4+ and CD8+ subsets) within aortic plaques. Further, targeting the chemokine Xcl1 (ligand of Xcr1) effectively inhibits atherosclerosis. The manuscript is well-written, and the data are clearly presented. However, several points require clarification:

(1) In Figure 1C (upper plot), it is not clear what the Xcr1 single-positive region in the aortic root represents, or whether this is caused by unspecific staining. So I wonder whether Xcr1 single-positive staining can reliably represent cDC1. For accurate cDC1 gating in Figure 1E, Xcr1+CD11c+ co-staining should be used instead.

(2) Figure 4D suggests that cDC1 depletion does not affect CD4+/CD8+ T cells. However, only the proportion of these subsets within total T cells is shown. To fully interpret effects, the authors should provide:<br /> a) Absolute numbers of total T cells in aortas.<br /> b) Absolute counts of CD4+ and CD8+ T cells.

(3) How does T cell activation mechanistically influence atherosclerosis progression? Why was CD69 selected as the sole activation marker? Were other markers (e.g., KLRG1, ICOS, CD44) examined to confirm activation status?

(4) Figure 7B: Beyond cDC1/2 proportions within cDCs, please report absolute counts of: Total cDCs,cDC1, and cDC2 subsets. Figure 7D: In addition to CD4+/CD8+ T cell proportions, the following should be included:<br /> a) Total T cell numbers in aortas<br /> b) Absolute counts of CD4+ and CD8+ T cells.

(5) cDC1 depletion reduced CD69+CD4+ and CD69+CD8+ T cells, whereas Xcl1 depletion decreased Xcr1+ cDC1 cells without altering activated T cells. How do the authors explain these different results? This discrepancy needs explanation.

Reviewer #1 (Public review):

Summary:

This study presents a compelling strategy for ultrasound-mediated immunomodulation in HCC, supported by robust scRNA-Seq data. While the mechanistic depth and translational validation require further refinement, the work significantly advances the field of noninvasive cancer immunotherapy. Addressing the major concerns, particularly regarding calcium signaling specificity and STNDs@Ca²⁺ safety, will strengthen the manuscript's impact.

Strengths:

(1) Innovative Approach:<br /> The integration of noninvasive ultrasound with calcium-targeted nanotechnology (STNDs@Ca²⁺) represents a significant advancement in cancer immunotherapy. The dual mechanism - direct immunomodulation via FUS and calcium delivery via nanoparticles - is both novel and promising.

(2) Comprehensive Mechanistic Insights:<br /> The use of scRNA-seq and flow cytometry provides a detailed map of immune cell dynamics, highlighting key pathways (TNF, NFκB, MAPK) and cellular transitions (e.g., MDSC suppression, CD8⁺/NK cell activation).

(3) Robust Preclinical Validation:<br /> The study validates findings in two distinct HCC models (H22 and Hepal-6), demonstrating consistent tumor suppression (>70-90%) and prolonged survival, which strengthens translational relevance.

Weaknesses:

Major Issues:

(1) Mechanistic Specificity of Calcium Influx:<br /> While the study attributes immunomodulation to ultrasound-induced calcium influx, the exact mechanism (e.g., involvement of mechanosensitive channels like Piezo1 or TRP families) remains underdiscussed. The qRT-PCR data shows no changes in TRP channels, but the upregulation of Piezo1 warrants deeper exploration.

Suggestion: The authors should include experiments to inhibit Piezo1 or other calcium channels to confirm their role in FUS-mediated effects.

(2) STNDs@Ca²⁺ Biodistribution and Safety:<br /> Although biodistribution data show splenic accumulation, potential off-target effects (e.g., liver/lung uptake) and long-term toxicity are not fully addressed. The serum biochemical analysis (Table 2) lacks critical markers like inflammatory cytokines or immune cell counts.

Suggestion: The authors should provide longitudinal toxicity data (e.g., histopathology beyond 3 hours) and assess systemic immune activation/inflammation.

(3) Statistical and Technical Clarifications:<br /> The statistical methods for multi-group comparisons (e.g., ANOVA vs. t-test) are inconsistently described. For instance, Figure 1 labels significance without specifying correction for multiple comparisons.

Suggestion: the authors should clarify statistical methods in figure legends and the Methods section; apply Bonferroni or FDR correction where appropriate.

(4) Interpretation of scRNA-seq Data:<br /> The clustering of MDSCs using surface markers (Itgam/Ly6c2/Ly6g) overlaps with conventional myeloid populations (Supplementary Figure 16), raising questions about subset specificity.

Suggestion: The authors should validate MDSC identity using functional assays (e.g., T cell suppression) or additional markers (e.g., Arg1, iNOS).

Reviewer #2 (Public review):

Summary:

Wang et al. studied the therapeutic potential of focused ultrasound noninvasively stimulating the spleen (FUS sti. spleen) to modulate the splenic immunity, with an aim to exert anti-tumor effect. They found that the treatment enhanced antitumor capability in CD8 T/ NK cells and reduced the immunosuppression, facilitating the inhibition of HCC growth in vivo.

Strengths:

They have utilized bulk RNA sequencing, single cell RNA sequencing, and flow cytometry to investigate the immune and tumor cell profiling in the mouse models upon FUS sti. spleen. Moreover, they highlighted the importance of combining FUS with spleen-targeted nanodroplets encapsulating bioavailable calcium ions (STND@Ca2+), which facilitated the calcium influx into the murine spleen and further enhanced the therapeutic efficacy of FUS.

Weaknesses:

While the study is interesting and potentially clinically impactful, the mechanism of action of the therapy is not fully elucidated. It would benefit from more rigorous approaches. With the theoretical part strengthened, this paper would be of interest to cancer cell biologists and clinician scientists working on the oncology field.

Reviewer #1 (Public review):

Summary:

In this fMRI study, the authors wished to assess neural mechanisms supporting flexible "temporal construals". For this, human participants learned a story consisting of fifteen events. During fMRI, events were shown to them and they were instructed to consider the event from "an internal" or from "an external" perspective. The authors found opposite patterns of brain activity in the posterior parietal cortex and the anterior hippocampus for the internal and the external viewpoint. They conclude that allocentric sequences are stored in the hippocampus, whereas egocentric sequences are used in the parietal cortex. The claims align with previous fMRI work addressing this question.

Strengths:

The research topic is fascinating, and very few labs in the world are asking the question of how time is represented in the human brain. Working hypotheses have been recently formulated, and this work seems to want to tackle some of them.

Weaknesses:

The current writing is fuzzy both conceptually and experimentally. I cannot provide a sufficiently well-informed assessment of the quality of the experimental work because there is a paucity of details provided in the report. Any future revisions will likely improve transparency.

(1) Improving writing and presentation:

The abstract and the introduction make use of loaded terms such as "construals", "mental timeline", "panoramic views" in very metaphoric and unexplained ways. The authors do not provide a comprehensive and scholarly overview of these terms, which results in verbiage and keywords/name-dropping without a clear general framework being presented. Some of these terms are not metaphors. They do refer to computational concepts that the authors should didactically explain to their readership. This is all the more important that some statements in the Introduction are misattributed or factually incorrect; some statements lack attributions (uncited published work).

Once the theory, the question, and the working hypothesis are clarified, the authors should carefully explain the task.

(2) The experimental approach lacks sufficient details to be comprehensible to a general audience. In my opinion, the results are thus currently uninterpretable. I highlight only a couple of specific points (out of many). I recommend revision and clarification.

a) No explanation of the narrative is being provided. The authors report a distribution of durations with no clear description of the actual sequence of events. The authors should provide the text that was used, how they controlled for low-level and high-level linguistic confounds.

b) The authors state, "we randomly assigned 15 phrases to the events twice". It is impossible to comprehend what this means. Were these considered stimuli? Controls? IT is also not clear which event or stimulus is part of the "learning set" and whether these were indicated to be such to participants.

c) The left/right counterbalancing is not being clearly explained. The authors state that there is counterbalancing, but do not sufficiently explain what it means concretely in the experiment. If a weak correlation exists between sequential position and distance, it also means that the position and the distance have not been equated within. How do the authors control for these?

d) The authors used two tasks. In the "external perspective" one, the authors asked participants to report whether events were part of the same or a different part of the day. In the "internal perspective one", the authors asked participants to project themselves to the reference event and to determine whether the target event occurred before or after the projected viewpoint. The first task is a same/different recognition task. The second task is a temporal order task (e.g., Arzy et al. 2009). These two asks are radically different and do not require the same operationalization. The authors should minimally provide a comprehensive comparison of task requirements, their operationalization, and, more importantly, assess the behavioral biases inherent to each of these tasks that may confound brain activity observed with fMRI.

e) The authors systematically report interpreted results, not factual data. For instance, while not showing the results on behavioral outcomes, the authors directly interpret them as symbolic distance effects.

Crucially, the authors do not comment on the obvious differences in task difficulty in these two tasks, which demonstrates a substantial lack of control in the experimental design. The same/different task (task 1 called "external perspective") comes with known biases in psychophysics that are not present in the temporal order task (task 2 called " internal perspective"). The authors also did not discuss or try to match the performance level in these two tasks. Accordingly, the authors claim that participants had greater accuracy in the external (same/different) task than in the internal task, although no data are shown and provided to support this report. Further, the behavioral effect is trivialized by the report of a performance accuracy trade-off that further illustrates that there is a difference in the task requirements, preventing accurate comparison of the two tasks.

All fMRI contrasts are also confounded by this experimental shortcoming, seeing as they are all reported at the interaction level across a task. For instance, in Figure 4, the authors report a significant beta difference between internal and external tasks. It is impossible to disentangle whether this effect is simply due to task difference or to an actual processing of the duration that differs across tasks, or to the nature of the representation (the most difficult to tackle, and the one chosen by the authors).

Conclusion:

In conclusion, the current experimental work is confounded and lacks controls. Any behavioral or fMRI contrasts between the two proposed tasks can be parsimoniously accounted for by difficulty or attentional differences, not the claim of representational differences being argued for here.

Reviewer #2 (Public review):

Summary:

Xu et al. used fMRI to examine the neural correlates associated with retrieving temporal information from an external compared to internal perspective ('mental time watching' vs. 'mental time travel'). Participants first learned a fictional religious ritual composed of 15 sequential events of varying durations. They were then scanned while they either (1) judged whether a target event happened in the same part of the day as a reference event (external condition); or (2) imagined themselves carrying out the reference event and judged whether the target event occurred in the past or will occur in the future (internal condition). Behavioural data suggested that the perspective manipulation was successful: RT was positively correlated with sequential distance in the external perspective task, while a negative correlation was observed between RT and sequential distance for the internal perspective task. Neurally, the two tasks activated different regions, with the external task associated with greater activity in the supplementary motor area and supramarginal gyrus, and the internal condition with greater activity in default mode network regions. Of particular interest, only a cluster in the posterior parietal cortex demonstrated a significant interaction between perspective and sequential distance, with increased activity in this region for longer sequential distances in the external task, but increased activity for shorter sequential distances in the internal task. Only a main effect of sequential distance was observed in the hippocampus head, with activity being positively correlated with sequential distance in both tasks. No regions exhibited a significant interaction between perspective and duration, although there was a main effect of duration in the hippocampus body with greater activity for longer durations, which appeared to be driven by the internal perspective condition. On the basis of these findings, the authors suggest that the hippocampus may represent event sequences allocentrically, whereas the posterior parietal cortex may process event sequences egocentrically.

Strengths:

The topic of egocentric vs. allocentric processing has been relatively under-investigated with respect to time, having traditionally been studied in the domain of space. As such, the current study is timely and has the potential to be important for our understanding of how time is represented in the brain in the service of memory. The study is well thought out, and the behavioural paradigm is, in my opinion, a creative approach to tackling the authors' research question. A particular strength is the implementation of an imagination phase for the participants while learning the fictional religious ritual. This moves the paradigm beyond semantic/schema learning and is probably the best approach besides asking the participants to arduously enact and learn the different events with their exact timings in person. Importantly, the behavioural data point towards successful manipulation of internal vs. external perspective in participants, which is critical for the interpretation of the fMRI data. The use of syllable length as a sanity check for RT analyses, as well as neuroimaging analyses, is also much appreciated.

Weaknesses/Suggestions:

Although the design and analysis choices are generally solid, there are a few finer details/nuances that merit further clarification or consideration in order to strengthen the readers' confidence in the authors' interpretation of their data.

(1) Given the known behavioural and neural effects of boundaries in sequence memory, I was wondering whether the number of traversed context boundaries (i.e., between morning-afternoon, and afternoon-evening) was controlled for across sequential length in the internal perspective condition? Or, was it the case that reference-target event pairs with higher sequential numbers were more likely to span across two parts of the day compared to lower sequential numbers? Similarly, did the authors examine any potential differences, whether behaviourally or neurally, for day part same vs. day part different external task trials?

(2) I would appreciate further insight into the authors' decision to model their task trials as stick functions with duration 0 in their GLMs, as opposed to boxcar functions with varying durations, given the potential benefits of the latter (e.g., Grinband et al., 2008). I concur that in certain paradigms, RT is considered a potential confound and is taken into account as a nuisance covariate (as the authors have done here). However, given that RTs appear to be critical to the authors' interpretation of participant behavioural performance, it would imply that variations in RT actually reflect variations in cognitive processes of interest, and hence, it may be worth modelling trials as boxcar functions with varying durations.

(3) The activity pattern across tasks and sequential distance in the posterior parietal cortex appears to parallel the RT data. Have the authors examined potential relationships between the two (e.g., individual participant slopes for RT across sequential distance vs. activity betas in the posterior parietal cortex)?

(4) There were a few places in the manuscript where the writing/discussion of the wider literature could perhaps be tightened or expanded. For instance:

i) On page 16, the authors state 'The negative correlation between the activation level in the right PPC and sequential distance has already been observed in a previous fMRI study (Gauthier & van Wassenhove, 2016b). The authors found a similar region (the reported MNI coordinate of the peak voxel was 42, -70, 40, and the MNI coordinate of the peak voxel in the present study was 39, -70, 35), of which the activation level went up when the target event got closer to the self-positioned event. This finding aligns with the evidence suggesting that the posterior parietal cortex implements egocentric representations.' Without providing a little more detail here about the Gauthier & van Wassenhove study and what participants were required to do (i.e., mentally position themselves at a temporal location and make 'occurred before' vs. 'occurred after' judgements of a target event), it could be a little tricky for readers to follow why this convergence in finding supports a role for the posterior parietal cortex in egocentric representations.

ii) Although the authors discuss the Lee et al. (2020) review and related studies with respect to retrospective memory, it is critical to note that this work has also often used prospective paradigms, pointing towards sequential processing being the critical determinant of hippocampal involvement, rather than the distinction between retrospective vs. prospective processing.

iii) The authors make an interesting suggestion with respect to hippocampal longitudinal differences in the representation of event sequences, and may wish to relate this to Montagrin et al. (2024), who make an argument for the representation of distant goals in the anterior hippocampus and immediate goals in the posterior hippocampus.

Reviewer #1 (Public review):

Summary:

This is a rigorous data-driven modeling study, extending the authors' previous model of spinal locomotor central pattern generator (CPG) circuits developed for the mouse spinal cord and adapted here to the rat to explore potential circuit-level changes underlying altered speed-dependent gaits, due to asymmetric (lateral) thoracic spinal hemisection and symmetric midline contusion. The model reproduces key features of the rat speed-dependent gait-related experimental data before injury and after recovery from these two different thoracic spinal cord injuries and suggests injury-specific mechanisms of circuit reorganization underlying functional recovery. There is much interest in the mechanisms of locomotor behavior recovery after spinal cord injury, and data-driven behaviorally relevant circuit modeling is an important approach. This study represents an important advance in the authors' previous experimental and modeling work on locomotor circuitry and in the motor control field.

Strengths:

(1) The authors use an advanced computational model of spinal locomotor circuitry to investigate potential reorganization of neural connectivity underlying locomotor control following recovery from symmetrical midline thoracic contusion and asymmetrical (lateral) hemisection injuries, based on an extensive dataset for the rat model of spinal cord injury.

(2) The rat dataset used is from an in vivo experimental paradigm involving challenging animals to perform overground locomotion across the full range of speeds before and after the two distinct spinal cord injury models, enabling the authors to more completely reveal injury-specific deficits in speed-dependent interlimb coordination and locomotor gaits.

(3) The model reproduces the rat gait-related experimental data before injury and after recovery from these two different thoracic spinal cord injuries, which exhibit roughly comparable functional recovery, and suggests injury-specific, compensatory mechanisms of circuit reorganization underlying recovery.

(4) The model simulations suggest that recovery after lateral hemisection mechanistically involves partial functional restoration of descending drive and long propriospinal pathways. In contrast, recovery following midline contusion relies on reorganization of sublesional lumbar circuitry combined with altered descending control of cervical networks.

(5) These observations suggest that symmetrical (contusion) and asymmetrical (lateral hemisection) injuries induce distinct types of plasticity in different spinal cord regions, suggesting that injury symmetry partly dictates the location and type of neural plasticity supporting recovery.

(6) The authors suggest that therapeutic strategies may be more effective by targeting specific circuits according to injury symmetry.

Weaknesses:

The recovery mechanisms implemented in the model involve circuit connectivity/connection weights adjustment based on assumptions about the structures involved and compensatory responses to the injury. As the authors acknowledge, other factors affecting locomotor patterns and compensation, such as somatosensory afferent feedback, neurochemical modulator influences, and limb/body biomechanics, are not considered in the model.

Reviewer #2 (Public review):

Summary:

In this paper, the authors present a detailed computational model and experimental data concerning overground locomotion in rats before and after recovery from spinal cord injury. They are able to manually tune the parameters of this physiologically based, detailed model to reproduce many aspects of the observed animals' locomotion in the naive case and in two distinct injury cases.

Strengths:

The strengths are that the model is driven to closely match clean experimental data, and the model itself has detailed correspondence to proposed anatomical reality. As such, this makes the model more readily applicable to future experimental work. It can make useful suggestions. The model reproduces a large number of conditions across frequencies, and with the model structure changed by injury and recovery. The model is extensive and is driven by known structures, with links to genetic identities, and has been extensively validated across multiple experiments and manipulations over the years. It models a system of critical importance to the field, and the tight coupling to experimental data is a real strength.

Weaknesses:

A downside is that, scientifically, here, the only question tackled is one of sufficiency. By manually tuning parameters in a manner that aligns with the field's understanding from experimental work, the detailed model can accurately reproduce the experimental findings. One of the benefits of computational models is that the counterfactual can be tested to provide evidence against alternative hypotheses. That isn't really done here. I'm fairly certain that there are competing theories regarding what happens during recovery from a hemi-section injury and a contusion injury. The model could be used to make predictions for some alternative hypotheses, supporting or rejecting theories of recovery. This may be part of future plans. Here, the focus is on showing that the model is capable of reproducing the experimental results at all, for any set of parameters, however tuned.

Reviewer #3 (Public review):

Summary:

This study describes a computational model of the rat spinal locomotor circuit and how it could be reconfigured after lateral hemisection or contusion injuries to replicate gaits observed experimentally.

The model suggests the emergence of detour circuits after lateral hemisection, whereas after a midline contusion, the model suggests plasticity of left-right and sensory inputs below the injury.

Strengths:

The model accurately models many known connections within and between forelimb and hindlimb spinal locomotor circuits.

The simulation results mirror closely gait parameters observed experimentally. Many gait parameters were studied, as well as variability in these parameters in intact versus injured conditions.

Weaknesses:

The study could provide some sense of the relative importance of the various modified connectivities after injury in setting the changes in gait seen after the two types of injuries.

Overall, the authors achieved their aims, and the model provides solid support for the changes in connectivity after the two types of injuries were modelled. This work emphasizes specific changes in connectivity after lateral hemisection or after contusion that could be investigated experimentally. The model is available for public use and could serve as a tool to analyze the relative importance of various highlighted or previously undiscovered changes in connectivity that may underlie the recovery of locomotor function in spinalized rats.

Reviewer #1 (Public review):

In this manuscript, Saeb et al reported the mechanistic roles of the flexible stalk domain in sTREM2 function using molecular dynamics simulations. They have reported some interesting molecular bases explaining why sTREM2 shows protective effects during AD, such as partial extracellular stalk domain promoting binding preference and stabilities of sTREM2 with its ligand even in the presence of known AD-risk mutation, R47H. Furthermore, they found that the stalk domain itself acts as the site for ligand binding by providing an "expanded surface", known as 'Expanded Surface 2' together with the Ig-like domain. Also, they observed no difference in the binding free energy of phosphatidyl-serine with wild TREM2-Ig and mutant TREM2-Ig, which is a bit inconsistent with the previous report with experiment studies by Journal of Biological Chemistry 293, (2018), Alzheimer's and Dementia 17, 475-488 (2021), Cell 160, 1061-1071 (2015).

Reviewer #2 (Public review):

Significance:

TREM2 is an immunomodulatory receptor expressed on myeloid cells and microglia in the brain. TREM2 consists of a single immunoglobular (Ig) domain that leads into a flexible stalk, transmembrane helix, and short cytoplasmic tail. Extracellular proteases can cleave TREM2 in its stalk and produce a soluble TREM2 (sTREM2). TREM2 is genetically linked to Alzheimer's disease (AD), with the strongest association coming from an R47H variant in the Ig domain. Despite intense interest, the full TREM2 ligand repertoire remains elusive, and it is unclear what function sTREM2 may play in the brain. The central goal of this paper is to assess the ligand-binding role of the flexible stalk that is generated during the shedding of TREM2. To do this, the authors simulate the behavior of constructs with and without stalk. However, it is not clear why the authors chose to use the isolated Ig domain as a surrogate for full-length TREM2. Additionally, experimental binding evidence that is misrepresented by the authors contradicts the proposed role of the stalk.

Summary and strengths:

The authors carry out MD simulations of WT and R47H TREM2 with and without the flexible stalk. Simulations are carried out for apo TREM2 and for TREM2 in complex with various lipids. They compare results using just the Ig domain to results including the flexible stalk that is retained following cleavage to generate sTREM2. The computational methods are well-described and should be reproducible. The long simulations are a strength, as exemplified in Figure 2A where a CDR2 transition happens at ~400-600 ns. The stalk has not been resolved in structural studies, but the simulations suggest the intriguing and readily testable hypothesis that the stalk interacts with the Ig domain and thereby contributes to the stability of the Ig domain and to ligand binding. I suspect biochemists interested in TREM2 will make testing this hypothesis a high priority.

Comments on latest version:

The authors have addressed my critiques and carried out additional simulations, as requested. I would upgrade my assessment of the evidence to "solid."

Reviewer #1 (Public review):

Summary:

Odor- and taste-sensing are mediated by two different systems, the olfactory and gustatory systems, and have different behavioral roles. In this study, Wei et al. challenge this dichotomy by showing that odors can activate gustatory receptor neurons (GRNs) in Drosophila to promote feeding responses, including the proboscis extension response (PER) that was previously thought to be driven only by taste. While previous studies suggested that odors can promote PER to appetitive tastants, Wei et al. go further to show that odors alone cause PER, this effect is mediated through sweet-sensing GRNs, and sugar receptors are required. The study also shows that odor detection by bitter-sensing GRNs suppresses PER. The authors' conclusions are supported by behavioral assays, calcium imaging, electrophysiological recordings, and genetic manipulations. The observation that both attractive and aversive odors promote PER leaves an open question as to why this effect is adaptive. Overall, the study sheds new light on chemosensation and multimodal integration by showing that odor and taste detection converge at the level of sensory neurons, a finding that is interesting and surprising while also being supported by another recent study (Dweck & Carlson, Sci Advances 2023).

Strengths:

(1) The main finding that odors alone can promote PER by activating sweet-sensing GRNs is interesting and novel.

(2) The study uses video tracking of the proboscis to quantify PER rather than manual scoring, which is typically used in the field. The tracking method is less subjective and provides a higher-resolution readout of the behavior.

(3) The study uses calcium imaging and electrophysiology to show that odors activate GRNs. These represent complementary techniques that measure activity at different parts of the GRN (axons versus dendrites, respectively) and strengthen the evidence for this conclusion.

(4) Genetic manipulations show that odor-evoked PER is primarily driven by sugar GRNs and sugar receptors rather than olfactory neurons. This is a major finding that distinguishes this work from previous studies of odor effects on PER and feeding (e.g., Reisenman & Scott, 2019; Shiraiwa, 2008) that assumed or demonstrated that odors were acting through olfactory neurons.

Weaknesses/Limitations:

(1) Many of the odor effects on behavior or neuronal responses were only observed at very high concentrations. Most effects seemed to require concentrations of at least 10^-2 (0.01 v/v), which is at the high end of the concentration range used in olfactory studies (e.g., Hallem et al., 2004), and most experiments in the paper used a far higher concentration of 0.5 v/v. It is unclear whether these are concentrations that would be naturally encountered by flies. In addition, it is difficult to compare the concentrations used for electrophysiology and behavior given that they are presented in solution versus volatile form.

(2) The timecourse of GRN activation by odors seems quite prolonged (and possibly delayed, depending on the exact timing of odor onset to the fly), and this timecourse is not directly compared with activation by tastes to determine whether it is a property of the calcium sensor or a real difference.

(3) While the overall effect of different conditions is tested using appropriate statistical methods, post-hoc tests are not always used to determine which specific groups are different from each other (e.g., which odors and concentrations elicit significant PER compared to air or mineral oil controls in Fig. 1; which odors show impaired responses without olfactory organs in Fig. 2A).

Discrepancies with previous studies:

These discrepancies are important to note but should not necessarily be considered "weaknesses" of the present study.

(1) It is not entirely clear why PER to odors alone has not been previously reported, especially as this study shows that it is a broad effect evoked by many different odors. Previous studies (Oh et al., 2021; Reisenman & Scott, 2019; Shiraiwa, 2008) tested the effect of odors on PER and only observed enhancement of PER to sugar rather than odor-evoked PER; some of these studies explicitly show no effect of odor alone or odor with low sugar concentration. In the Response to Reviewers, the authors propose that genetic background may explain discrepancies, but this is not discussed much in the paper itself. Differences in behavioral quantification (automated vs. manual scoring, quantification of PER duration versus probability) may also contribute.

(2) The calcium imaging data showing that sugar GRNs respond to a broad set of odors contrasts with results from Dweck & Carlson (Sci Adv, 2023) who recorded sugar neurons with electrophysiology and observed responses to organic acids, but not other odors. This discrepancy is mentioned in the Discussion but the underlying reason is not clear.

Reviewer #3 (Public review):

Summary:

Using flies, Kazama et al. combined behavioral analysis, electrophysiological recordings, and calcium imaging experiments to elucidate how odors activate gustatory receptor neurons (GRNs) and elicit a proboscis extension response, which is interpreted as a feeding response.

The authors used DeepLabCut v2.0 to estimate the extension of the proboscis, which represents an unbiased and more precise method for describing this behavior compared to manual scoring.

They demonstrated that the probability of eliciting a proboscis extension increases with higher odor concentrations. The most robust response occurs at a 0.5 v/v concentration, which, despite being diluted in the air stream, remains a relatively high concentration. Although the probability of response is not particularly high it is higher than control stimuli. Notably, flies respond with a proboscis extension to both odors that are considered positive and those regarded as negative.

The authors used various transgenic lines to show that the response is mediated by GRNs. Specifically, inhibiting Gr5a reduces the response, while inhibiting Gr66a increases it in fed flies. Additionally, they find that odors induce a strong positive response in both types of GRNs, which is abolished when the labella of the proboscis are covered. This response was also confirmed through electrophysiological tip recordings.

Finally, the authors demonstrated that the response increases when two stimuli of different modalities, such as sucrose and odors, are presented together, suggesting clear multimodal integration

Strengths:

The integration of various techniques, which collectively supports the robustness of the results.<br /> The assessment of electrophysiological recordings in intact animals, preserving natural physiological conditions.

Weaknesses:

Only highly concentrated odours are capable of evoking positive responses and, even then, the proportion remains relatively low.

The authors have incorporated my suggestions.

Reviewer #1 (Public review):

Summary:

The authors attempted to dissect the function of a long non-coding RNA, lnc-FANCI-2, in cervical cancer. They profiled lnc-FANCI-2 in different cell lines and tissues, generated knockout cell lines, and characterized the gene using multiple assays.

Strengths:

A large body of experimental data has been presented and can serve as a useful resource for the scientific community, including transcriptomics and proteomics datasets. The reported results also span different parts of the regulatory network and open up multiple avenues for future research.

Weaknesses:

The write-up is somewhat unfocused and lacks deep mechanistic insights in some places.

Comments on revisions:

The manuscript is much improved. I am satisfied with the authors' responses.

Reviewer #3 (Public review):

Summary:

A long noncoding RNA, lnc-FANCI-2, was reported to be regulated by HPV E7 oncoprotein and a cell transcription factor, YY1 by this group. The current study focuses on the function of lnc-FANCI-2 in HPV-16 positive cervical cancer is to intrinsically regulate RAS signaling, thereby facilitating our further understanding additional cellular alterations during HPV oncogenesis. Authors used the advanced technical approaches such as KO, transcriptome and (IRPCRP) and LC- MS/MS analyses in the current study and concluded that KO Inc-FANCI-2 significantly increase RAS signaling, especially phosphorylation of Akt and Erk1/2.

Strengths:

(1) HPV E6E7 are required for full immortalization and maintenance of malignant phenotype of cervical cancer, but they are NOT sufficient for full transformation and tumorigenesis. This study helps further the understanding of other cellular alterations in HPV oncogenesis.<br /> (2) lnc-FANCI-2 is upregulated in cervical lesion progression from CIN1, CIN2-3 to cervical cancer, cancer cell lines and HPV transduced cell lines.<br /> (3) Viral E7 of high-risk HPVs and host transcription factor YY1 are two major factors promoting lnc-FANCI-2 expression.<br /> (4) Proteomic profiling of cytosolic and secreted proteins showed inhibition of MCAM, PODXL2 and ECM1 and increased levels of ADAM8 and TIMP2 in KO cells.<br /> (5) RNA-seq analyses revealed that KO cells exhibited significantly increased RAS signaling but decreased IFN pathways.<br /> (6) Increased phosphorylated Akt and Erk1/2, IGFBP3, MCAM, VIM, and CCND2 (cyclin D2) and decreased RAC3 were observed in KO cells.

Comments on revisions:

The revised manuscript has been significantly improved. The authors addressed all my concerns.

Reviewer #1 (Public review):

Summary

Detecting unexpected epistatic interactions between multiple mutations requires a robust null expectation-or neutral function-that predicts the combined effects of multiple mutations on phenotype based on the individual effects of single mutations. This study evaluated the relevance of the product neutrality function, where double-mutant fitness is represented as a multiplicative combination of single-mutant fitness in the absence of epistatic interactions. The authors used a recent large dataset on fitness, specifically yeast colony size, to analyze epistatic interactions.

The study confirmed that the product function outperformed other neutral functions in predicting double-mutant fitness, showing no bias between negative and positive epistatic interactions. Additionally, in the theoretical portion of the study, the authors employed a previously established theoretical model of bacterial cell growth to simulate growth rates of both single- and double-mutants under multiple parameters. The simulations similarly demonstrated that the product function was superior to other functions in predicting the fitness of hypothetical double-mutants. Based on these findings, the authors concluded that the product function is a robust tool for analyzing epistatic interactions in growth fitness and effectively reflects how growth rates depend on the combination of multiple biochemical pathways.

Strength

By leveraging a previously published large dataset of yeast colony sizes for single- and double-knockout mutants, this study validated the relevance of the product function, which has frequently been used in genetics to analyze epistatic interactions. The confirmation that the product function provides a more reliable prediction of double-mutant fitness compared to other neutral functions is valuable for researchers analyzing epistatic interactions, particularly those working with the same dataset.<br /> Notably, this dataset has been previously used in studies exploring epistatic interactions with the product neutrality function. This study's findings affirm the validity of using the product function, which could enhance confidence in the conclusions drawn by those earlier studies. Consequently, both researchers utilizing this dataset and readers of prior research will benefit from the confirmation provided by this study.

Weakness

This study contains several serious problems, primarily stemming from the following issues: ignoring the substantial differences in the mechanisms regulating cell growth between prokaryotes and eukaryotes and adopting an overly specific and unrealistic set of assumptions in the mutation model. Below, the details are discussed.

(1) Misapplication of prokaryotic growth models

The mechanistic origin of the multiplicative model observed in yeast colony fitness is explained using a bacterial cell growth model. However, there is no valid justification for linking these two systems. The bacterial growth model, the Scott-Hwa model, heavily rely on specific molecular mechanisms, such as ppGpp-mediated regulation, which adjusts ribosome expression and activity during translation. In particular, this mechanism is critical to ensure growth-dependency of the fraction of ribosome in proteome in the Scott-Hwa model [https://doi.org/10.1111/j.1462-2920.2010.02357.x; https://doi.org/10.1073/pnas.2201585119]. Yeast cells lack this regulatory mechanism, making it inappropriate to directly apply bacterial growth models to yeast.<br /> The Weiße model is based on a larger set of underlying equations and involves more parameters than the Scott-Hwa model. In the original paper by Weiße et al. (PNAS, 2015), however, the model parameters were fitted solely to experimental data from E. coli, and the model's applicability to yeast was never assessed. In summary, for neither the Scott-Hwa model nor the Weiße model has it been demonstrated that the entire model quantitatively fits experimental data from yeast. A positive correlation between growth rate and RNA/protein ratio, often observed in yeast, supports only a limited portion of either model, and does not constitute validation of the models as a whole.

(2) Overly specific assumptions in the theoretical model

The theoretical model assumes that two mutations affect only independent parameters of specific biochemical processes. However, this overly restrictive assumption weakens the model's validity in explaining the general occurrence of the multiplicative model in mutations. Furthermore, experimental evidence suggests limitations of this approach. For example, in most viable yeast deletion mutants with reduced growth rates, the expression of ribosomal proteins remained largely unchanged, contrary to the predictions of the Scott-Hwa model [https://doi.org/10.7554/eLife.28034]. This discrepancy highlights that the Scott-Hwa model and its derivatives cannot reliably explain mutants' growth rates based on current experimental evidence.

(3) Limited reliability of the mechanistic origin of the multiplicative model

The authors seem to regard growth-optimizing feedback as the mechanistic origin of the multiplicative model. However, the importance of growth-optimizing feedback in explaining product neutrality heavily depends on the very specific framework of the Scott-Hwa model. As I pointed out above, the Scott-Hwa model is a bacterial growth model that considers only a narrowly defined set of biochemical reactions. Using such a narrow model to explore the mechanistic origin of product neutrality observed on a genome-wide scale appears to be inappropriate. Arguments based on either the Scott-Hwa model or the Weiße model fail to account for the generality of product neutrality across diverse genetic perturbations. These models, in their current form, do not explain the broader patterns of product neutrality observed experimentally.

Reviewer #2 (Public review):

The paper deals with the important question of gene epistasis, focusing on asking what is the correct null model for which we should declare no epistasis.

In the first part, they use the Synthetic Genetic Array dataset to claim that the effects of a double mutation on growth rate is well predicted by the product of the individual effects (much more than e.g. the additive model). The second (main) part shows this is also the prediction of two simple, coarse-grained models for cell growth.

I find the topic interesting, the paper well written, and the approach innovative.

Comments on revisions:

The authors have adequately addressed the comments raised in the review below, and I find that the paper has improved.

Reviewer #1 (Public review):

Summary:

This work provides a new potential tool to manipulate Tregs function for therapeutic use. It focuses on the role of PGAM in Tregs differentiation and function. The authors, interrogating publicly available transcriptomic and proteomic data of human regulatory T cells and CD4 T cells, state that Tregs express higher levels of PGAM (at both message and protein levels) compared to CD4 T cells. They then inhibit PGAM by using a known inhibitor ECGC and show that this inhibition affects Tregs differentiation. This result was also observed when they used antisense oligonucleotides (ASOs) to knockdown PGAM1.

PGAM1 catalyzes the conversion of 3PG to 2PG in the glycolysis cascade. However, the authors focused their attention on the additional role of 3PG: acting as starting material for the de novo synthesis of serine.

They hypothesized that PGAM1 regulates Tregs differentiation by regulating the levels of 3PG that are available for de novo synthesis of serine, which has a negative impact on Tregs differentiation. Indeed, they tested whether the effect on Tregs differentiation observed by reducing PGAM1 levels was reverted by inhibiting the enzyme that catalyzes the synthesis of serine from 3PG.

The authors continued by testing whether both synthesized and exogenous serine affect Tregs differentiation and continued with in vivo experiments to examine the effects of dietary serine restriction on Tregs function.

In order to understand the mechanism by which serine impacts Tregs function, the authors assessed whether this depends on the contribution of serine to one-carbon metabolism and to DNA methylation.

The authors therefore propose that extracellular serine and serine whose synthesis is regulated by PGAM1 induce methylation of genes Tregs associated, downregulating their expression and overall impacting Tregs differentiation and suppressive functions.

Strengths:

The strength of this paper is the number of approaches taken by the authors to verify their hypothesis. Indeed, by using both pharmacological and genetic tools in in vitro and in vivo systems they identified a potential new metabolic regulation of Tregs differentiation and function.

Reviewer #2 (Public review):

Summary:

The authors have tried to determine the regulatory role of Phosphoglycerate mutate (PGAM), an enzyme involved in converting 3-phosphoglycerate to 2-phosphoglycerate in glycolysis, in differentiation and suppressive function of regulatory CD4 T cells through de novo serine synthesis. This is done by contributing one carbon metabolism and eventually epigenetic regulation of Treg differentiation.

Strengths:

The authors have rigorously used inhibitors and antisense RNA to verify the contribution of these pathways in Treg differentiation in-vitro. This has also been verified in an in-vivo murine model of autoimmune colitis. This has further clinical implications in autoimmune disorders and cancer.

[Editors' note: The authors addressed important comments by the reviewers.]

Reviewer #1 (Public review):

Summary:

The authors strived for an inventory of GPCRs and GPCR pathway component genes within the genomes of 23 choanoflagellates and other close relatives of metazoans.

Strengths:

The authors generated a solid phylogenetic overview of the GPCR superfamily in these species. Intriguingly, they discover novel GPCR families, novel assortments of domain combinations, and novel insights into the evolution of those groups within the Opisthokonta clade. A particular focus is laid on adhesion GPCRs, for which the authors discover many hitherto unknown subfamilies based on Hidden Markov Models of the 7TM domain sequences, which were also reflected by combinations of extracellular domains of the homologs. In addition, the authors provide bioinformatic evidence that aGPCRs of choanoflagellates also contain a GAIN domain, which is self-cleavable, thereby reflecting the most remarkable biochemical feat of aGPCRs.

Weaknesses:

The chosen classification scheme for aGPCRs may require reassessment and amendment by the authors in order to prevent confusion with previously issued classification attempts of this family.

Reviewer #2 (Public review):

Summary:

The authors set out to characterise the GPCR family in choanoflagellates (and other unicellular holozoans). GPCRs are the most abundant gene family in many animal genomes, playing crucial roles in a wide range of physiological processes. Although they are known to evolve rapidly, GPCRs are an ancient feature of eukaryotic biology. Identifying conserved elements across the animal-protist boundary is therefore a valuable goal, and the increasing availability of genomes from non-animal holozoans provides new opportunities to explore evolutionary patterns that were previously obscured by limited taxon sampling. This study presents a comprehensive re-examination of GPCRs in choanoflagellates, uncovering examples of differential gene retention and revealing the dynamic nature of the GPCR repertoire in this group. As GPCRs are typically involved in environmental sensing, understanding how these systems evolved may shed light on how our unicellular ancestors adapted their signalling networks in the transition to complex multicellularity.

Strengths:

The paper combines a broad taxonomic scope with the use of both established and recently developed tools (e.g., Foldseek, AlphaFold), enabling a deep and systematic exploration of GPCR diversity. Each family is carefully described, and the manuscript also functions as an up-to-date review of GPCR classification and evolution. Although similar attempts to understand GPCR evolution were made over the last decade, the authors build on this foundation by identifying new families and applying improved computational methods to better predict structure and function. Notably, the presence of Rhodopsin-like GPCRs in some choanoflagellates and ichthyosporeans is intriguing, even though they do not fall within known animal subfamilies. The computational framework presented here is broadly applicable, offering a blueprint for surveying GPCR diversity in other non-model eukaryotes (and even in animal lineages), potentially revealing novel families relevant to drug discovery or helping revise our understanding of GPCR evolution beyond model systems.

Weaknesses:

While the study contributes several interesting observations, it does not radically revise the evolutionary history of the GPCR family. However, in an era increasingly concerned with the reproducibility of scientific findings, this is arguably a strength rather than a weakness. It is encouraging to see that previously established patterns largely hold, and that with expanded sampling and improved methods, new insights can be gained, especially at the level of specific GPCR subfamilies. Then, no functional follow-ups are provided in the model system Salpingoeca rosetta, but I am sure functional work on GPCRs in choanoflagellates is set to reveal very interesting molecular adaptations in the future.

Reviewer #1 (Public review):

Summary:

This is an interesting theoretical study examining the viability of Virtual Circular Genome (VCG) model, a recently proposed scenario of prebiotic replication in which a relatively long sequence is stored as a collection of its shorter subsequences (and their compliments). It was previously pointed out that VCG model is prone to so-called sequence scrambling which limits the overall length of such a genome. In the present paper, additional limitations are identified. Specifically, it is shown that VCG is well replicated when the oligomers are elongated by sufficiently short chains from "feedstock" pool. However, ligation of oligomers from VCG itself results in a high error rate. I believe the research is of high quality and well written. However, the presentation could be improved and the key messages could be clarified.

(1) It is not clear from the paper whether the observed error has the same nature as sequence scrambling

(2) The authors introduce two important lengths LS1 and LS2 only in the conclusions and do not explain enough which each of them is important. It would make sense to discuss this early in the manuscript.

(3) It is not entirely clear why specific length distribution for VCG oligomers has to be assumed rather than emerged from simulations.

(4) Furthermore, the problem has another important length, L0 that is never introduced or discussed: a minimal hybridization length with a lifetime longer than the ligation time. From the parameters given, it appears that L0 is sufficiently long (~10 bases). In other words, it appears that the study is done is a somewhat suboptimal regime: most hybridization events do not lead to a ligation. Am I right in this assessment? If that is the case, the authors might want to explore another regime, L0<br /> Strengths:

High-quality theoretical modeling of an important problem is implemented.

Reviewer #2 (Public review):

Summary:

This important theoretical and computational study by Burger and Gerland attempts to set environmental, compositional, kinetic, and thermodynamic constraints on the proposed virtual circular genome (VCG) model for the early non-enzymatic replication of RNA. The authors create a solid kinetic model using published kinetic and thermodynamic parameters for non-enzymatic RNA ligation and (de)hybridization, which allows them to test a variety of hypotheses about the VCG. Prominently, the authors find that the length (longer is better) and concentration (intermediate is better) of the VCG oligos have an outsized impact on the fidelity and yield of VCG production with important implications for future VCG design. They also identify that activation of only RNA monomers, which can be achieved using environmental separation of the activation and replication, can relax the constraints on the concentration of long VCG component oligos by avoiding the error-prone oligo-oligo ligation. Finally, in a complex scenario with multiple VCG oligo lengths, the authors demonstrate a clear bias for the extension of shorter oligos compared to the longer ones. This effect has been observed experimentally (Ding et al., JACS 2023) but was unexplained rigorously until now. Overall, this manuscript will be of interest to scientists studying the origin of life and the behavior of complex nucleic acid systems.

Strengths:

- The kinetic model is carefully and realistically created, enabling the authors to probe the VCG thoroughly.<br /> - Fig. 6 outlines important constraints for scientists studying the origin of life. It supports the claim that the separation of activation and replication chemistry is required for efficient non-enzymatic replication. One could easily imagine a scenario where activation of molecules occurs, followed by their diffusion into another environment containing protocells that encapsulate a VCG. The selective diffusion of activated monomers across protocell membranes would then result in only activated monomers being available to the VCG, which is the constraint outlined in this work. The proposed exclusive replication by monomers also mirrors the modern biological systems, which nearly exclusively replicate by monomer extension.<br /> - Another strength of the work is that it explains why shorter oligos extend better compared to the long ones in complex VCG mixtures. This point is independent of the activation chemistry used (it simply depends on the kinetics and thermodynamics of RNA base-pairing) so it should be very generalizable.

Reviewer #1 (Public review):

Summary:

The authors have assembled a cohort of 10 SiNET, 1 SiAdeno, and 1 lung MiNEN samples to explore the biology of neuroendocrine neoplasms. They employ single-cell RNA sequencing to profile 5 samples (siAdeno, SiNETs 1-3, MiNEN) and single-nuclei RNA sequencing to profile seven frozen samples (SiNET 4-10).

They identify two subtypes of siNETs, characterized by either epithelial or neuronal NE cells, through a series of DE analyses. They also report findings of higher proliferation in non-malignant cell types across both subtypes. Additionally, they identify a potential progenitor cell population in a single lung MiNEN samples.

In the revised study, they have addressed my points and I have no further comments.

Reviewer #2 (Public review):

Summary:

The research identifies two main SiNET subtypes (epithelial-like and neuronal-like) and reveals heterogeneity in non-neuroendocrine cells within the tumor microenvironment. The study validates findings using external datasets and explores unexpected proliferation patterns. While it contributes to understanding SiNET oncogenic processes, the limited sample size and depth of analysis present challenges to the robustness of the conclusions.

Strengths:

The studies effectively identified two subtypes of SiNET based on epithelial and neuronal markers. Key findings include the low proliferation rates of neuroendocrine (NE) cells and the role of the tumor microenvironment (TME), such as the impact of Macrophage Migration Inhibitory Factor (MIF).

Weaknesses:

However, the analysis faces challenges such as a small sample size and lack of clear biological interpretation in some analyses.

Reviewer #3 (Public review):

This study profiles small intestine NETs and one mixed lung NET at single cell resolution and identifies two subtypes of neuroendocrine cells, as well as explores the proliferation patterns in malignant and nonmalignant cell types, identifying MIF as a potential factor that promotes proliferation of B and plasma cells in siNETs. Furthermore, they explore the single-cell landscape of a mixed LCNEC and squamous cell carcinoma, from which they identify a putative stem cell population with expression of features from both lineages.

Strengths:

This work showcases single-cell profiling of a rare tumor type, which is very informative for the field of NETs. The authors highlight very interesting observations, including the identification of the epithelial and neuronal subtype of siNETs, which they validated with an independent bulk RNA sequencing cohort. Furthermore, the observation of low cycling in malignant cells and high cycling in nonmalignant cells is an interesting one which may be applicable to other NETs.

Weaknesses:

• The authors do not connect their findings to clinical outcome. For example, is the epithelial or neuronal subtype enriched in tumors with worse or better prognosis or high grade vs. low grade siNETs or in patients who metastasize vs. who don't? As the authors show they can identify epithelial vs. neuronal subtypes in bulk RNA seq, perhaps they can take advantage of these other studies with larger sample sizes to investigate this. Additionally, the authors identify that the phenomenon of higher B/plasma cell proliferation is particular to epithelial siNETs and write that "The implications of high B/plasma cell turnover, and of other downstream effects of high MIF expression, are unclear, but raise the possibility that MIF-CD74 interaction may constitute a relevant target for the epithelial-like SiNET subtype." However, if this interaction contributes to survival in these patients, targeting this interaction may not be beneficial. Thus, it is important for the authors to try to connect their finding to clinical outcomes to enhance the translational relevance of this paper.

• The generalizability of this study would be enhanced if the authors analyzed other available single cell studies of NETs and found a similar phenomenon of high proliferating nonmalignant cell types. Although these studies are also very limited in sample size, seeing concordance in findings across independent cohorts and different experimental techniques would help to strengthen the findings. While the authors rationalize that these other studies are too distinct from their own due to enrichment for immune cells, this limitation should be noted but does not prevent such an analysis from being attempted.

• On page 3, the authors claim that "Technical effects (e.g. single cell analysis of fresh samples vs. single nuclei analysis of frozen samples) could also impact the capture of distinct cell types, although we did not observe a clear pattern of such bias." Can the authors show that cell type frequencies are not significantly different between the samples profiled with these two methods?

• Why did siNET3 and siNET9 have much lower recovery of neuroendocrine cells compared to other samples? It would be interesting to see how similar or different the transcriptional profiles are of the samples that were obtained from the same patient, considering that multifocal siNETs are found to derive from distinct clones, although this analysis is understandably not possible in this case due to the lack of neuroendocrine cells in one of two samples from the same patient.

• It should be more clearly stated in the text that these samples were previously treated with somatostatin analogues, as this impacts the interpretation of the findings.

• The identification of a potential progenitor subtype in the miNEN is very intriguing, albeit a case study and represents a distinct cancer from the lowly proliferating siNETs. While the authors mention this in the text, the case study feels rather tangential to the other parts of the paper.

• How the authors compared the DE genes to known signatures for the fibroblast and endothelial cells should be clarified and discussed in the Methods section.

Reviewer #2 (Public review):

Summary:

In this manuscript by Peto et al., the authors describe the impact of different antimicrobials on gut microbiota in a prospective observational study of 225 participants (healthy volunteers, inpatients and outpatients). Both cross-sectional data (all participants) and longitudinal data (subset of 79 haematopoietic cell transplant patients) were used. Using metagenomic sequencing, they estimated the impact of antibiotic exposure on gut microbiota composition and resistance genes. In their models, the authors aim to correct for potential confounders (e.g. demographics, non-antimicrobial exposures and physiological abnormalities), and for differences in the recency and total duration of antibiotic exposure. I consider these comprehensive models an important strength of this observational study. Yet, the underlying assumptions of such models may have impacted the study findings and residual confounding is likely. Other strengths include the presence of both cross-sectional and longitudinal exposure data and presence of both healthy volunteers and patients. Together, these observational findings expand on previous studies (both observational and RCTs) describing the impact of antimicrobials on gut microbiota.

Weaknesses:

(1) The main weaknesses result from the observational design. This hampers causal interpretation and makes correction for potential confounding necessary. While the authors have used comprehensive models to correct for potential confounders and for differences between participants in duration of antibiotic exposure and time between exposure and sample collection, I believe residual confounding is likely (which is mentioned as a limitation in the discussion).<br /> For their models, the authors found a disruption half-life of 6 days to be the best fit based on Shannon diversity. Yet, the disruption caused by antimicrobials may be longer than represented in this model - as highlighted in the discussion.

(2) Another consequence of the observational design of this study is the relatively small number of participants available for some comparisons (e.g. oral clindamycin was only used by 6 participants). Care should be taken when drawing any conclusions from such small numbers.

Comments on revisions:

The authors have adequately addressed all of my comments.

Reviewer #1 (Public review):

Summary:

The study by Cao et al. provides a compelling investigation into the role of mutational input in the rapid evolution of pesticide resistance, focusing on the two-spotted spider mite's response to the recent introduction of the acaricide cyetpyrafen. This well-documented introduction of the pesticide-and thus a clearly defined history of selection-offers a powerful framework for studying the temporal dynamics of rapid adaptation. The authors combine resistance phenotyping across multiple populations, extensive resequencing to track the frequency of resistance alleles, and genomic analyses of selection in both contemporary and historical samples. These approaches are further complemented by laboratory-based experimental evolution, which serves as a baseline for understanding the genetic architecture of resistance across mite populations in China. Their analyses identify two key resistance-associated genes, sdhB and sdhD, within which they detect 15 mutations in wild-collected samples. Protein modeling reveals that these mutations cluster around the pesticide's binding site, suggesting a direct functional role in resistance. The authors further examine signatures of selective sweeps and their distribution across populations to infer the mechanisms-such as de novo mutation or gene flow-driving the spread of resistance, a crucial consideration for predicting evolutionary responses to extreme selection pressure. Overall, this is a well-rounded, thoughtfully designed and well-written manuscript. It shows significant novelty, as it is relatively rare to integrate broad-scale evolutionary inference from natural populations with experimentally informed bioassays, however, follow up work will be needed to fully resolve haplotype structure and the functional effects of resistance mutations in the system.

Strengths:

One of the most compelling aspects of this study is its integration of genomic time-series data in natural populations with controlled experimental evolution. By coupling genome sequencing of resistant field populations with laboratory selection experiments, the authors tease apart the individual effects of resistance alleles along with regions of the genome where selection is expected to occur, and compare that to the observed frequency in the wild populations over space and time. Their temporal data clearly demonstrates the pace at which evolution can occur in response to extreme selection. This type of approach is a powerful roadmap for the rest of the field of rapid adaptation.

The study effectively links specific genetic changes to resistance phenotypes. The identification of sdhB and sdhD mutations as major drivers of cyetpyrafen resistance is well supported by allele frequency shifts in both field and experimental populations. The scope of their sampling clearly facilitated the remarkable number of observed mutations within these target genes, and the authors provide a careful discussion of the likelihood of these mutations from de novo or standing variation. Furthermore, the discovered cross-resistance that these mutations confer to other mitochondrial complex II inhibitors highlights the potential for broader resistance management and evolution.

Weaknesses:

(1) Pleiotropy without pesticide modes of action (cyflumetofen and cyetpyrafen) may also play a role in the rapid response to the focal pesticide in this study<br /> (2) Other aspects of the environment that might influence selection were not considered in the structure of resistance alleles (i.e. climate, elevation)<br /> (3) Very little data were used for haplotype reconstruction, only 8 SNPs, and this excluded all heterozygous alleles, which could dramatically influence the complexity of these inferred haplotype networks.<br /> (4) Single Mutations and Their Effects:<br /> - Allelic effects were not estimated in isogenic lines, so the effects presented also include heterogeneity from allelic interactions with the genomic background<br /> - The authors see populations that segregate for resistance mutations but that have no survival to pesticides. This suggests either not all of the resistance mutations studied here actually have functional effects or that dominance is playing a role in masking their effects in the heterozygous state.

Reviewer #2 (Public review):

Summary:

This paper investigates the evolution of pesticide resistance in the two-spotted spider mite following the introduction of an SDHI acaricide, cyatpyrafen, in China. The authors make use of cyatpyrafen-naive populations collected before that pesticide was first used, as well as more recent populations (both sensitive and resistant) to conduct comparative population genomics. They report 15 different mutations in the insecticide target site from resistant populations, many reported here for the first time, and look at the mutation and selection processes underlying the evolution of resistance, through GWAS, haplotype mapping, and testing for loss of diversity indicating selective sweeps. None of the target site mutations found in resistant populations was found in pre-exposure populations, suggesting that the mutations may have arisen de novo rather than being present as standing variation, unless initially present at very low frequencies; a de novo origin is also supported by evidence of selective sweeps in some resistant populations. Furthermore, there is no significant evidence of migration of resistant genotypes between the sampled field populations indicating multiple origins of common mutations. Overall, this indicates a very high mutation rate and a wide range of mutational pathways to resistance for this target site in this pest species. The series of population genomic analyses carried out here, in addition to the evolutionary processes that appear to underly resistance development in this case, could have implications for the study of resistance evolution more widely.

Strengths:

This paper combines phenotypic characterisation with extensive comparative population genomics, made possible by the availability of multiple population samples (each with hundreds of individuals) collected before as well as after then introduction of the pesticide cyatpyrafen, as well as lab-evolved lines. This resuts in findings of mutation and selection processes that can be related back to the pesticide resistance trait of concern. Large numbers of mites were tested phenotypically to show the levels of resistance present, and the authors also made near-isogenic lines to confirm the phenotypic effects of key mutations. The population genomic analyses consider a range of alternative hypotheses, including mutations arising by de novo mutation or selection from standing genetic variation; and mutations in different populations arising independently or arriving by migration. The claim that mutations most likley arose by multiple repeated de novo mutations is therefore supported by multiple lines of evidence: the direct evidence of none of the mutations being found in over 2000 individuals from naive populations, and the indirect evidence from population genomics showing evidence of selective sweeps but not of significant migration between the sampled populations.

Weaknesses:

As acknowledged within the discussion, whilst evidence supports a de novo origin of the resistance associated mutations, this cannot be proven definitively as mutations may have been present at a very low frequency and therefore not found within the tested pesticide-naive population samples.

Near-isofemale lines were made to confirm the resistance levels associated with five of the 15 mutations, but otherwise the genotype-phenotype associations are correlative as confirmation by functional genetics was beyond the scope of this study.

Comments on revisions:

My recommendations have all been addressed in the revised version.

Reviewer #1 (Public review):

In this manuscript, Azlan et al. identified a novel maternal factor called Sakura that is required for proper oogenesis in Drosophila. They showed that Sakura is specifically expressed in the female germline cells. Consistent with its expression pattern, Sakura functioned autonomously in germline cells to ensure proper oogenesis. In sakura KO flies, germline cells were lost during early oogenesis and often became tumorous before degenerating by apoptosis. In these tumorous germ cells, piRNA production was defective and many transposons were derepressed. Interestingly, Smad signaling, a critical signaling pathway for the GSC maintenance, was abolished in sakura KO germline stem cells, resulting in ectopic expression of Bam in whole germline cells in the tumorous germline. A recent study reported that Bam acts together with the deubiquitinase Otu to stabilize Cyc A. In the absence of sakura, Cyc A was upregulated in tumorous germline cells in the germarium. Furthermore, the authors showed that Sakura co-immunoprecipitated Otu in ovarian extracts. A series of in vitro assays suggested that the Otu (1-339 aa) and Sakura (1-49 aa) are sufficient for their direct interaction. Finally, the authors demonstrated that the loss of otu phenocopies the loss of sakura, supporting their idea that Sakura plays a role in germ cell maintenance and differentiation through interaction with Otu during oogenesis.

Latest comments:

The reviewer acknowledges the importance of sharing the observed defects in Sakura mutant ovaries and the possible physiological significance of the Sakura-Out interaction with the research community, as this information could lay the groundwork for future functional analysis research.

Reviewer #2 (Public review):

In this study, the authors identified CG14545 (named it sakura), as a key gene essential for Drosophila oogenesis. Genetic analyses revealed that Sakura is vital for both oogenesis progression and ultimate female fertility, playing a central role in the renewal and differentiation of germ stem cells (GSC).

The absence of Sakura disrupts the Dpp/BMP signaling pathway, resulting in abnormal bam gene expression, which impairs GSC differentiation and leads to GSC loss. Additionally, Sakura is critical for maintaining normal levels of piRNAs. Also, the authors convincingly demonstrate that Sakura physically interacts with Otu, identifying the specific domains necessary for this interaction, suggesting a cooperative role in germline regulation. Importantly, the loss of otu produces similar defects to those observed in sakura mutants, highlighting their functional collaboration.

The authors provide compelling evidence that Sakura is a critical regulator of germ cell fate, maintenance, and differentiation in Drosophila. This regulatory role is mediated through modulation of pMad and Bam expression. However, the phenotypes observed in the germarium appear to stem from reduced pMad levels, which subsequently trigger premature and ectopic expression of Bam. This aberrant Bam expression could lead to increased CycA levels and altered transcriptional regulation, impacting piRNA expression. In this revised manuscript, the authors further investigated whether Sakura affects the function of Orb, a binding partner they identified, in deubiquitinase activity when Orb interacts with Bam.

This elaborate study will be embraced by both germline-focused scientists and the developmental biology community.

Latest comments:

The authors answered all my persistent concerns and made changes according to the recommendations I incorporated for the revised version of the manuscript.

Reviewer #3 (Public review):

In this very thorough study, the authors characterize the function of a novel Drosophila gene, which they name Sakura. They start with the observation that sakura expression is predicted to be highly enriched in the ovary and they generate an anti-sakura antibody, a line with a GFP-tagged sakura transgene, and a sakura null allele to investigate sakura localization and function directly. They confirm the prediction that it is primarily expressed in the ovary and, specifically, that it is expressed in germ cells, and find that about 2/3 of the mutants lack germ cells completely and the remaining have tumorous ovaries. Further investigation reveals that Sakura is required for piRNA-mediated repression of transposons in germ cells. They also find evidence that sakura is important for germ cell specification during development and germline stem cell maintenance during adulthood. However, despite the role of sakura in maintaining germline stem cells, they find that sakura mutant germ cells also fail to differentiate properly such that mutant germline stem cell clones have an increased number of "GSC-like" cells. They attribute this phenotype to a failure in the repression of Bam by dpp signaling. Lastly, they demonstrate that sakura physically interacts with otu and that sakura and otu mutants have similar germ cell phenotypes. Overall, this study helps to advance the field by providing a characterization of a novel gene that is required for oogenesis. The data are generally high-quality and the new lines and reagents they generated will be useful for the field.

Latest comments:

As with my previous assessment, I remain supportive of publication of this manuscript. Though I agree with the other reviewers that additional experimentation would increase the value of this study even further, I feel it will also be a useful contribution to the field as is.

Reviewer #2 (Public review):

Summary:

The authors report the discovery of a population of gingival fibroblasts displaying the expression of cellular senescence markers P21 and P16 in human periodontitis samples and a murine ligature-induced periodontitis (LIP) model. They support this finding in the murine model through bulk RNA-sequencing and show that differentially expressed genes are significantly enriched in the SenMayo cellular senescence in aging dataset. They then show that Ligature-Induced Periodontitis (LIP) mice treated with the senomorphic drug metformin display overall diminished bone damage, reduced histomorphic alterations, and a reduction in P21 and P16 immunostaining signal. To explore the cell types expressing cellular senescence markers in periodontitis, the authors make use of a combination of bioinformatic analyses on publicly available scRNA-seq data, immunostainings on patient samples and their LIP model; as well as in vitro culture of healthy human gingival fibroblasts treated with LPS. They found that fibroblasts are a cell population expressing P16 in periodontitis which are also enriched for SenMayo genes, suggesting they have a senescent phenotype. They then point to a subgroup of fibroblasts expressing CD81+ with the highest enrichment for a SASP geneset in periodontitis. They also show that treatment of LIP mice and human LPS-treated gingival fibroblasts with metformin leads to a reduction of P21 and P16-positive cells, as well as the senescence-associated beta-galactosidase (SA-beta-gal) marker. Finally, they show evidence suggesting that CD81+ senescent fibroblasts are the source of C3 complement protein, which they stipulate signals through the C3AR1 receptor present in neutrophils in periodontitis. The authors observed that both CD81+ fibroblast and C3AR1+ neutrophil populations are expanded in periodontitis, that both populations appear to be in close contact, and that treatment with metformin reduced both C3 and the neutrophil marker MPO in their mouse LIP model.

After a round of revision, the authors have made significant improvements to their manuscript, such as improving the quality of the data/evidence and also included new data from experiments using a well-known senolytic and the senomorphic metformin, which all together provide a solid support to their main claims.

Strengths:

The study implements several different techniques and tools on human samples, mouse models, fibroblast cultures, and publicly available data to support their conclusions. In summary, they provide solid evidence showing that in the context of periodontitis, there is an expansion of cells expressing senescence markers P21, and P16, as well as members of the SASP, and that this includes CD81+ fibroblasts.

Weaknesses:

The fact that in this study the periodontitis samples belonged to patients with a significantly higher median age (all older than 50 years of age) and the healthy samples belonged to young adults (all younger than 35 years of age), raises the need for caution in interpretation due to a possible effect of aging in the accumulation of CD81+ senescent fibroblasts. However, the recruitment of similar age groups in this case is of course difficult due to the higher prevalence of periodontitis in older adults. In this regard it is important to note that the authors still support their findings using a mouse ligature model. Similar studies comparing healthy and periodontitic patients from similar age groups will be of great importance in the future.

Reviewer #1 (Public review):

Summary:

In this paper, Wang et al show that differentiated peridermal cells of the zebrafish epidermis extend cytoneme-like protrusions toward the less differentiated, intermediate layer below. They present evidence that expression of a dominant-negative cdc42, inhibits cytoneme formation and leads to elevated expression of a marker of undifferentiated keratinocytes, krtt1c19e, in the periderm layer. It is demonstrated that Delta-Notch signaling is involved in keratinocyte differentiation and that loss of cytonemes correlates with a loss of Notch signaling. Finally, changes in expression of the inflammatory cytokine IL-17 and its receptors is shown to affect cytoneme number and periderm structure in a manner similar to Notch and cdc42 perturbations.

Strengths:

Overall, the idea that differentiated cells signal to underlying undifferentiated cells via membrane protrusions in skin keratinocytes is interesting and novel, and it is clear that periderm cells send out thin membrane protrusions that contain a Notch ligand. Further, and perturbations that affect cytoneme number, Notch signaling and IL-17 expression clearly lead to changes in periderm structure and gene expression.

Weaknesses:

The mechanisms by which IL-17 affects cytoneme formation requires further investigation.

Reviewer #2 (Public review):

Summary:

The aim of the study was to understand how cells of the skin communicate across dermal layers. The research group has previously demonstrated that cellular connections called airinemes contribute to this communication. The current work builds upon this knowledge by showing that differentiated keratinocytes also use cytonemes, specialized signaling filopodia, to communicate with undifferentiated keratinocytes. They show that cytonemes are the more abundant type of cellular extension used for communication between the differentiated keratinocyte layer and the undifferentiated keratinocytes. Disruption of cytoneme formation led to expansion of the undifferentiated keratinocytes into the periderm, mimicking skin diseases like psoriasis. The authors go on to show that disruption of cytonemes results in perturbations in Notch signaling between the differentiated keratinocytes of the periderm and the underlying proliferating undifferentiated keratinocytes. Further the authors show that Interleukin-17, also known to drive psoriasis, can restrict formation of periderm cytonemes, possibly through the inhibition of Cdc42 expression. This work suggests that cytoneme mediated Notch signaling plays a central role in normal epidermal regulation. The authors propose that disruption of cytoneme function may be an underlying cause of various human skin diseases.

Strengths:

The authors provide strong evidence that periderm keratinocytes cytonemes contain the notch ligand DeltaC to promote Notch activation in the underlying intermediate layer to regulate accurate epidermal maintenance.

Weaknesses:

The impact of the study would be increased if the mechanism by which Interlukin-17 and Cdc42 collaborate to regulate cytonemes was defined. Experiments measuring Cdc42 activity, rather than just measuring expression, would strengthen the conclusions.

Comments on revisions:

The authors have sufficiently addressed my critiques from the initial round of evaluation. They have included useful representative images, clarified how they scored cytonemes and provided additional controls/experimental conditions that improve the rigor of the study. The results provided now support the key conclusions of the study.

Reviewer #1 (Public review):

Summary:

This fundamental study presents a practical modification of the orthogonal hybridization chain reaction (HCR) technique, a promising yet underutilized method with broad potential for future applications across various fields. The authors advance this technique by integrating peptide ligation technology and nanobody-based antibody mimetics-cost-effective and scalable alternatives to conventional antibodies-into a DNA-immunoassay framework that merges oligonucleotide-based detection with immunoassay methodologies. They demonstrate this with compelling evidence that this approach facilitates a modified ELISA platform capable of simultaneously quantifying multiple target protein expression levels within a single protein mixture sample.

Strengths:

The hybridization chain reaction (HCR) technique was initially developed to enable the simultaneous detection of multiple mRNA expression levels within the same tissue. This method has since evolved into immuno-HCR, which extends its application to protein detection by utilizing antibodies. A key requirement of immuno-HCR is the coupling of oligonucleotides to antibodies, a process that can be challenging due to the inherent difficulties in expressing and purifying conventional antibodies.<br /> In this study, the authors present an innovative approach that circumvents these limitations by employing nanobody-based antibody mimetics, which recognize antibodies, instead of directly coupling oligonucleotides to conventional antibodies. This strategy facilitates oligonucleotide conjugation-designed to target the initiator hairpin oligonucleotide of HCR-through peptide ligation and click chemistry.

Weaknesses:

The sandwich-format technique presented in this study, which employs a nanobody that recognizes primary IgG antibodies, may have limited scalability compared to existing methods that directly couple oligonucleotides to primary antibodies. This limitation arises because the C-region types of primary antibodies are relatively restricted, meaning that the use of nanobody-based detection may constrain the number of target proteins that can be analyzed simultaneously. In contrast, the conventional approach of directly conjugating oligonucleotides to primary antibodies allows for a broader range of protein targets to be analyzed in parallel.

Additionally, in the context of HCR-based protein detection, the number of proteins that can be analyzed simultaneously is inherently constrained by fluorescence wavelength overlap in microscopy, which limits its multiplexing capability. By comparison, direct coupling oligonucleotides to primary antibodies can facilitate the simultaneous measurement of a significantly greater number of protein targets than the sandwich-based nanobody approach in the barcode-ELISA/NGS-based technique.

Comments on revisions:

The previous suggestions were well incorporated in the revised manuscript.

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Reviewer #2 (Public review):

Summary:

This study explores how a simple sensorimotor circuit in the nematode C. elegans enables it to navigate salt gradients based on past experiences. Using computational simulations and previously described neural connections, the study demonstrates how a single neuron, ASER, can change its signaling behavior in response to different salt conditions, with which the worm is able to "remember" prior environments and adjust its navigation toward "preferred" salinity accordingly.

Strengths:

The key novelty and strength of this paper is the explicit demonstration of computational neurobehavioral modeling and evolutionary algorithms to elucidate the synaptic plasticity in a minimal neural circuit that is sufficient to replicate memory-based chemotaxis. In particular, with changes in ASER's glutamate release and sensitivity of downstream neurons, the ASER neuron adjusts its output to be either excitatory or inhibitory depending on ambient salt concentration, enabling the worm to navigate toward or away from salt gradients based on prior exposure to salt concentration.

Weaknesses:

While the model successfully replicates some behaviors observed in previous experiments, some key assumptions of the work still need to be verified by biological validation of further experiments.

Comments on revisions:

Thank you for the authors' response. The revision and their response have substantially addressed my concerns.