Reviewer #1 (Public review):

Summary:

The authors introduce the Training Village (TV), an open-source and modular system that allows group-housed rodents to live in enriched home cages while individually accessing a single shared operant box for automated cognitive training. The paper reported the animals' activity both in the operant box and in the home cages, which is novel.

Strengths:

A major strength of the work is that it moves beyond a proof-of-concept and demonstrates sustained box usage, long-term trial accumulation, and compatibility with different task designs.

(1) The platform provided a technical contribution in rodent cognitive neuroscience: obtaining large amounts of behavioral data from complex tasks while reducing experimenter intervention and preserving social housing.

(2) The authors demonstrate that the system can sustain prolonged task engagement (up to 12 months), maintain efficient use of a single operant box.

(3) The manuscript opens interesting opportunities for studying behavior outside standard session-based training. Because animals self-initiate training while remaining in a group-housed setting, the platform has the potential to illuminate relationships among motivation, spontaneous activity, and task engagement that are hard to access in conventional paradigms.

Weaknesses:

(1) One area that would benefit from further clarification is the manuscript's core advance relative to prior automated group-housed training systems, particularly Mouse Academy (Qiao et al., 2018). The authors listed some advantages in the Discussion section; however, those were some minor engineering improvements, and what is more interesting is the scientific question or results that can be asked or obtained from this study. The current study clearly presents a functional and carefully documented platform, but it would help the reader if the authors more explicitly distinguished the present system from earlier related approaches, both in terms of system design and in terms of experimental validation.

(2) At the system level, several of the claimed advantages could be supported more directly with quantitative data. For example, if the double-detection corridor and alarm system are important distinguishing features, it would be valuable to report measures such as detection accuracy, missed detections, co-entry failures, alarm frequency, and the degree of manual intervention required in practice. Similarly, the welfare-related arguments are plausible and important, but would be strengthened by more direct evidence, such as longitudinal body weight data, water intake, or comparison with group-housed no-task controls.

(3) At the experimental level, the manuscript would also benefit from a more detailed characterization of training performance. Although three behavioral paradigms are presented, the data currently shown provide a stronger demonstration of feasibility than of training optimization. For a study focused on automated cognitive training, it would be critical to include more information on learning speed, progression across stages, success and failure rates, and variability across animals. Along the same lines, the comparison with manual training is a useful addition, but a broader benchmark including learning curves, time to criterion, and between-animal variability would make the practical value of the system easier to assess.

(4) The authors claimed that they conducted 3 complex cognitive tasks (3AFC, 2AFC, 2AB) in their setup. However, those 3 tasks are quite basic for rodents and have been demonstrated in many studies, especially comparing tasks implemented in Yu et al., eLife 2025. Therefore, lowering this 'complex' statement is necessary.

(5) The authors claimed that they have successfully implemented the so-called hybrid mode, but it is only briefly described and not supported by citations or data. Since this may be one of the most broadly applicable use cases of the platform, a more detailed explanation of how the system can be integrated with recording workflows would strengthen the manuscript.

(6) The manuscript highlights the opportunity to relate task behavior to home-cage activity and to study individualized behavioral patterns. To better support these aspects, it would be helpful to include more subject-level analyses, rather than relying predominantly on population averages, or alternatively to discuss in more concrete terms which features of the dataset may be especially informative for studying individuality. More generally, the manuscript would benefit from clarifying whether different parameter settings within this group-housed framework may be better suited for maximizing training efficiency versus preserving more naturalistic or socially modulated behavior, and what the implications of these choices may be for interpretation.

(7) In Table S1, 'Touch screen' is task-specific and is not necessarily a metric. 'Testing outside home cage' is also not necessarily an advantage (please clarify if it is). Many other systems implemented different levels of 'Alarm system', which is not reflected in the table.

(8) Table S3 shows important data that help the reader to evaluate the paper's work, thus is deserved to move to the main text.

Reviewer #1 (Public review):

Summary:

This paper examines whether humans use protracted temporal integration in a noise-free, deferred-response contrast discrimination task, using a covert evidence-duration manipulation combined with EEG (SSVEP, CPP, Mu/Beta). The key finding is that evidence for protracted sampling is behaviorally and neurally supported, but even joint CPP + behaviour fitting cannot fully discriminate a standard integration (DDM) model from a novel "extremum-flagging" non-integration model. The paper is transparent about this outcome.

Strengths:

This is a well-conducted and well-written study that makes a genuine contribution to the perceptual decision-making literature by introducing a clean experimental design for probing temporal integration without participants adapting their strategy and demonstrating for the first time that a non-integration model (extremum-flagging) can replicate CPP waveform dynamics that have long been considered hallmarks of evidence accumulation. The transparent treatment of equivocal modelling outcomes is commendable.

Weaknesses:

My main concerns relate to statistical power, the under-specification of the and the extremum-flagging mechanism. Addressing these would greatly strengthen the paper.

(1) The sample of 16 participants (15, after the exclusion of one participant) is described as "close to similar EEG studies" with no formal power analysis. Given that the paper's core claim rests on subtle quantitative differences between two model classes - differences that are, by the authors' own admission, not sufficient to declare a winner - even a modest increase in sample size might yield a more decisive outcome. At a minimum, the authors should report a sensitivity analysis or post-hoc power calculation to indicate what effect sizes the current N could reliably detect, particularly for the rmANOVA comparisons and the neural constraint fitting.

(2) The Extremum-flagging model is the paper's most novel contribution, yet its physiological basis is underspecified. The model posits that each decision-terminating bound-crossing triggers a stereotyped, half-sine-shaped centroparietal signal, but no neural circuit or computational mechanism is proposed for how the brain could detect the first bound-crossing event in a non-accumulating evidence stream or generate a temporally precise, fixed-amplitude signal in response. Possible connections to P3b theories of context updating and response facilitation are acknowledged, but these are vague functional descriptions rather than mechanistic accounts. I think the discussion should engage more directly with potential neural substrates that could generate this flagging signal, and whether these are consistent with the known generators of the CPP/P3b. Without this, the extremum-flagging model risks being viewed as a mathematical convenience rather than a biologically plausible alternative.

(3) The Integration model at the preferred neural weighting estimates a high-to-low contrast drift rate ratio of 8.7, whereas the empirical Mu/Beta lateralization slopes suggest a ratio of approximately 3.5. The authors attribute this discrepancy to the nonlinear contrast response function of early visual cortex and the salience of the high-contrast evidence onset, but these explanations are speculative. These outcomes are arguably the most quantitatively damaging result for the integration model, so they deserve more than a brief discussion. I would recommend that the authors (a) estimate what range of contrast response nonlinearities would be required to close this gap, (b) test whether an alternative drift rate parameterization (e.g., scaling drift rates directly by SSVEP amplitude rather than contrast) reduces the discrepancy, or (c) be more explicit about treating this as a point against the Integration account.

(4) The sensitivity analysis over neural constraint weightings (w = 0.1 to 1000) is thoughtful, but the paper ultimately acknowledges that the preferred weighting is w=10, chosen because it achieves "a good fit to CPP dynamics without substantively sacrificing behavioral fit" - a qualitative criterion. No principled statistical framework is used to select the optimal weighting or to compare models at a given weighting. A Bayesian model comparison could provide a more formal framework for combining behavioral and neural fit components, and would allow a clearer statement about the relative posterior probability of each model.

Reviewer #1 (Public review):

Vasilevskaya and Keller test different models of cortical function through the lens of predictive processing, a powerful framework for the brain to learn and predict the statistics of the world via generative internal models. The authors use a clever combination of behavioral perturbations in closed-loop and open-loop visuomotor virtual reality assays, a paradigm the Keller lab pioneered and used effectively in the past decade, in conjunction with two-photon imaging of neuronal calcium responses and targeted optogenetic perturbations of activity. They specifically put to test proposed hierarchical vs. non-hierarchical circuit implementations of predictive processing by analyzing the logic of inter-lamina interactions (superficial vs. deep; L2/3 vs. L5/6).

The authors conclude that both versions of predictive processing architectures they analyze are likely invalid, and instead formulate an alternative novel model of cortical function based on a recently developed machine learning algorithm for self-supervised learning (joint embeddings of predictive architectures, JEPA) and its further refinements. JEPA borrows elements from predictive processing, engaging two encoder networks and training the output of one network to predict the output of the other. In their new model of cortical computations, prediction error neurons in L2/3 compare the deep layers (L5/6) activity, which is taken as a teaching signal, to a local, L2/3 prediction of this latent representation.

Specifically, the authors build on their previous work and reports from other groups that different sets of L2/3 neurons compute positive prediction errors (fire when sensory stimuli appear unexpectedly with respect to the movements of the animal; e.g., grating onsets in the absence of locomotion) and respectively negative prediction errors (fire when sensory stimuli are absent, while the brain expected them to be present; e.g. mice locomote but visual flow is suddenly halted - visuomotor mismatches). These L2/3 positive and negative prediction error neurons exchange messages with neurons in the deeper cortical layers that, the authors propose, build an internal representation (R) of the sensory stimuli given the animals' movements.

In the hierarchical model, internal representation neurons (R) are supposed to act as a teaching signal for both types of prediction error neurons; the output of the positive prediction error neurons is assumed to suppress activity of R such that the error between the teaching signal and the prediction is minimized; similarly, in the non-hierarchical version, R serves as a prediction for the prediction error neurons, and in turn it receives excitatory drive from the positive prediction error neurons and negative input from the negative prediction error neurons.

The authors find that the functional impact of L5 neurons on L2/3 neurons is not compatible with the non-hierarchical architecture they and other groups proposed, but rather in accordance with the hierarchical model. At the same time, the functional impact of L2/3 neurons (positive vs. negative prediction error neurons) on L5 neurons (internal representation) appears not compatible with the hierarchical model, but rather in accordance with the non-hierarchical implementation.

They further hypothesize that L2/3 prediction error neurons don't use sensory input, but rather the L5 activity as a teaching signal, and test it using perturbations (halts) of optogenetic stimulation of L5 neurons coupled with locomotion (Figure 7).

All in all, the question is topical, and the new model addresses a decades-long quest to develop a unifying model of cortical function. The findings reported here transform our understanding of cortical computations, opening new, exciting avenues for future investigation. The experimental design and execution are rigorous; the arguments are clearly laid out (in spite of ample potential for confusion given the numerous loops and sign flips). These include a discussion of why the non-hierarchical model proposed by the same group does not hold, as well as potential caveats in interpreting the results and novel testable proposed experiments emerging from the JEPA-like model.

I have several questions about the interpretations of some of the claims and suggestions for potential additional experiments and analyses.

(1) Some of the pieces of the puzzle remain to be identified and demonstrated: the existence of internal representation neurons in L2/3 and ascertaining that the L5/6 neurons analyzed function indeed as internal representation neurons. The authors find that stimulation of L2/3 positive prediction error neurons enhances activity of L5 neurons...If L5 neurons hold a latent representation that serves as a teaching signal for L2/3 neurons (as the authors posit), wouldn't one expect that the input they receive from the positive prediction neurons be suppressive, such that the error is further minimized?

(2) Do the authors envision any specific differences between the representations of the two encoder networks posited to exist in L2/3 and L5 in the JEPA-like implementation? Are they synchronous/offset in their temporal representations, or any other features?

(3) Where is the prediction coming from onto L2/3 neurons? Is it emerging locally in L2/3 from the putative internal representation neurons, or is it long-range - as work from the authors previously proposed? Or a mix of both?

(4) What is the role of the indiscriminate L4 input that appears to enhance activity of both positive and negative prediction error neurons in L2/3?

(5) Does Figure 7D change in a meaningful manner if the authors plot the correlation between optomotor mismatch response and visuomotor mismatch response specifically for the negative prediction error neurons in L2/3 (Adamts-2) rather than for all L2/3 cells sampled?

(6) Do the optomotor mismatch responses in L2/3 neurons depend on how long the closed-loop coupling of optogenetic stimulation of Tlx3 L5 neurons and locomotion speed has been in place for?

Reviewer #1 (Public review):

Summary:

This manuscript investigates mutations and expression patterns of zinc finger proteins in Kenyan breast cancer patients. Whole-exome sequencing and RNA-seq were performed on 23 breast cancer samples alongside matched normal tissues.

Strengths:

Whole-exome sequencing and RNA-seq were performed on 23 breast cancer samples alongside matched normal tissues in Kenyan breast cancer patients. The authors identified mutations in ZNF217, ZNF703, and ZNF750.

Weaknesses:

(1) Research scope:

The results primarily focus on mutations in ZNF217, ZNF703, and ZNF750, with limited correlation analyses between mutations and gene expression. The rationale for focusing only on these genes is unclear. Given the availability of large breast cancer cohorts such as TCGA and METABRIC, the authors should compare their mutation profiles with these datasets. Beyond European and U.S. cohorts, sequencing data from multiple countries, including a recent Nigerian breast cancer study (doi: 10.1038/s41467-021-27079-w), should also be considered. Since whole-exome sequencing was performed, it is unclear why only four genes were highlighted, and why comparisons to previous literature were not included.

(2) Language and Style Issues

There are many typos and clear errors in the main text (e.g. (ref)).

Additionally, several statements read unnaturally. For example:

"Investigators uncovered 170 mutations ..." should instead be phrased as "We identified 170 mutations ...."

"The research team ..." should be rephrased as "Our team ...."

(3) Methods and Data Analysis Details

The methods section is vague, with general descriptions rather than specific details of data processing and analysis. The authors should provide:

(a) Parameters used for trimming, mapping, and variant calling (rather than referencing another paper such as Tang et al. 2023).

(b) Statistical methods for somatic mutation/SNP detection.

(c) Details of RNA purification and RNA-seq library preparation.

Without these details, the reproducibility of the study is limited.

(4) Data Reporting

This study has the potential to provide a valuable resource for the field. However, data-sharing plans are unclear. The authors should:

a) Deposit sequencing data in a public repository.

b) Provide supplementary tables listing all detected mutations and all differentially expressed genes (DEGs).

c) Clarify whether raw or adjusted p-values were used for DEG analysis.

d) Perform DEG analyses stratified by breast cancer subtypes, since differential expression was observed by HER2 status, and some zinc finger proteins are known to be enriched in luminal subtypes.

(5) Mutation Analysis

Visualizations of mutation distribution across protein domains would greatly strengthen interpretation. Comparing mutation distribution and frequency with published datasets would also contextualize the findings.

Comments on revisions:

The revised manuscript hasn't addressed any of these concerns. Careful proofreading is recommended, even if the authors do not intend to make further modifications to the manuscript.

Reviewer #1 (Public review):

[Editors' note: this version has been assessed by the Reviewing Editor without further input from the original reviewers. The authors have addressed the comments raised in the previous round of review.]

Summary:

Here, the authors have addressed the recruitment and firing patterns of motor units (MUs) from the long and lateral heads of triceps in the mouse. They used their newly developed Myomatrix arrays to record from these muscles during treadmill locomotion at different speeds, and they used template-based spike sorting (Kilosort) to extract units. Between MUs from the two heads, the authors observe differences in their firing rates, recruitment probability, phase of activation within the locomotor cycle and interspike interval patterning. Examining different walking speeds, the authors find increases in both recruitment probability and firing rates as speed increases. The authors also observed differences in the relation between recruitment and the angle of elbow extension between motor units from each head. These differences indicate meaningful variation between motor units within and across motor pools, and may reflect the somewhat distinct joint actions of the two heads of triceps.

Strengths:

The extraction of MU spike timing for many individual units is an exciting new method that has great promise for exposing the fine detail in muscle activation and its control by the motor system. In particular, the methods developed by the authors for this purpose seem to be the only way to reliably resolve single MUs in the mouse, as the methods used previously in humans and in monkeys (e.g. Marshall et al. Nature Neuroscience, 2022) do not seem readily adaptable for use in rodents.

The paper provides a number of interesting observations. There are signs of interesting differences in MU activation profiles for individual muscles here, consistent with those shown by Marshall et al. It is also nice to see fine scale differences in the activation of different muscle heads, which could relate to their partially distinct functions. The mouse offers greater opportunities for understanding the control of these distinct functions, compared to the other organisms in which functional differences between heads have previously been described.

The Discussion is very thorough, providing a very nice recounting of a great deal of relevant previous results.

Reviewer #1 (Public review):

Summary:

The manuscript by Bohra et al. describes the indirect effects of ligand-dependent gene activation on neighboring non-target genes. The authors utilized single-molecule RNA-FISH (targeting both mature and intronic regions), 4C-seq, and enhancer deletions to demonstrate that the non-enhancer-targeted gene TFF3, located in the same TAD as the target gene TFF1, alters its expression when TFF1 expression declines at the end of the estrogen signaling peak. Since the enhancer does not loop with TFF3, the authors conclude that mechanisms other than estrogen receptor or enhancer-driven induction are responsible for TFF3 expression. Moreover, ERα intensity correlations show that both high and low levels of ERα are unfavorable for TFF1 expression. The ERa level correlations are further supported by overexpression of GFP-ERa. The authors conclude that transcriptional machinery used by TFF1 for its acute activation can negatively impact the TFF3 at peak of signaling but once, the condensate dissolves, TFF3 benefits from it for its low expression.

Strengths:

The findings are indeed intriguing. The authors have maintained appropriate experimental controls, and their conclusions are well-supported by the data.

Weaknesses:

There are some major and minor concerns that related to approach, data presentation and discussion. But the authors have greatly improved the manuscript during the revision work.

Comments on latest version:

The authors have done a lot of work for the revision. The manuscript has been greatly improved.

Reviewer #1 (Public review):

Summary:

In this manuscript, the authors present comprehensive experimental observations and a theoretical framework to explain the heterogeneous behaviour of sarcomeres in cardiomyocytes. They show that a stochastic component exists in their contractile activity, which may act as a feedback mechanism regulating physiological function.

Strengths:

Experiments and data analysis are robust and valid. The rigorous statistical analysis and unbiased methods enable the authors to draw well-supported conclusions that go beyond the existing literature. Their outcomes inform about cellular activity at the individual level and the authors explain how the transient dynamics of single sarcomeres are governed by a force-velocity relationship and lead to the complex contractile patterns. The similarity of the results to the study cited in [24] demonstrates the validity of the in vitro setup for answering these questions and the feasibility of such in-vitro systems to extend our knowledge of out-of-equilibrium dynamics in cardiac cells.

Very interesting the suggestion that the interplay between intrinsic fluctuations and the dynamic instability are part of a feedback mechanism for maintaining structural and functional homeostasis.

The addition of the theoretical model and the new text of the manuscript improves the clarity of the study.

Reviewer #1 (Public review):

Actin filaments and their kinetics have been the subject of extensive research, with several models for filament length control already existing in the literature. The work by Rosario et al. focuses instead on bundle length dynamics and how their fluctuations can inform us on the underlying kinetics. Surprisingly, the authors show that irrespective of the details, typical "balance point" models for filament kinetics give the wrong scaling of bundle length variance with mean length compared to experiments. Instead, the authors show that if one considers a bundle made of several individual filaments, length control for the bundle naturally emerges even in the absence of such a mechanism at the individual filament level. Furthermore, the authors show that the fluctuations of the bundle length display the same scaling with respect to the average as experimental measurements from different systems. This work constitutes a simple yet nuanced and powerful theoretical result that challenges our current understanding of actin filament kinetics and helps relate accessible experimental measurements such as actin bundle length fluctuations to their underlying kinetics. Finally, I found the manuscript to be very well written, with a particularly clear structure and development, which made it very accessible.

Comments on revisions:

I maintain my original favorable assessment of this manuscript.

I thank the authors for considering my comments and for their thoughtful replies. It would have been helpful to see some of the comments reflected in the text and discussion. I leave this to the authors.

I appreciate that the authors replaced the figures with higher-resolution versions, but I maintain my assessment that the graphical and aesthetic quality of the figures, especially the size of the legends (which are often tiny and difficult to read), labels, colors, etc., could be improved. Again, I leave this to the authors.

Reviewer #1 (Public review):

Summary:

The factors that create and maintain diversity in host-associated microbiomes remain poorly understood. A better understanding of these factors will help in the efforts to leverage the adaptive potential of the microbiome to help solve pressing problems in health and agriculture.

Experimental evolution provides a promising path forward as we can track the causes and consequences in the emergence of novel variants, but experimental evolution remains underutilized in host-microbiome interactions. Here, Gracia-Alvira utilizes a long-term experimental evolution study in Drosophila simulans under hot and cold temperature regimes to identify strain-level variation in an important fly bacterium, Lactiplantibacillus plantarum. They identify three strains of L. plantarum, which are most prevalent in their respective three temperature regimes, suggesting that these are locally adapted bacteria. Then, using a combination of genomics, in vitro, and in vivo, Gracia-Alvira et al attempt to understand the factors that led to the differentiation of the hot and cold L. plantarum and their impacts on the fly host.

Strengths:

This is an excellent use of experimental evolution to track the emergence of novelty in the microbiome. The genomic analyses are all solid and appropriate for the data sets. It is especially striking that the comparisons with the other, independent experimental evolution studies in different labs (and across continents between Portugal and South Africa) show a consistent response to temperature. Many have disregarded the microbiome as it is something that is too sensitive to seemingly innocuous variables (particularly in the fly microbiome), such that we cannot find generalities. However, this finding highlights the potential for experimental evolution to uncover these dynamics. The question of how strains emerge and are maintained is timely and is one of the key open questions in host-microbiome evolution currently.

Weaknesses:

(1) The framing in the title and throughout the discussion about "subspecies competition" does not match the data that was collected. The subspecies competition requires actually tracking the competitive outcomes between the hot, cold, and unevolved L. plantarum. In the in vivo work, I can see that mixes of the strains were made, but they did not track whether the cold strain outcompeted the hot strain in vivo under cold conditions, for example. While Figure 4 is suggestive that there is ongoing competition in the hot temperature regime, this is not necessarily shown in the cold, which is dominated by the C clade. It could also be that the bacteria cannot survive in the flies at the different temperatures. The growth curve assays hint that the bacteria can grow, but the plate reader couldn't actually maintain the 18 {degree sign}C temperature (line 455). So all of this evidence is very indirect and insufficient to say that strain competition is driving these patterns.

(2) The in vivo results are interesting in that there appears to be a fitness cost of clade C, but the explanation is underdeveloped. I say under-developed because in Figure 4, the cold L. plantarum remains much higher throughout adaptation to the hot temperature regime than the hot L. plantarum in the cold regime. The hot L. plantarum is low abundance throughout the cold regime. I felt like this observation was not explained, but it seems relevant to understanding the strain dynamics.

I will also note that this is not the first time that L. plantarum or other Lactobacillus have been shown to exert fitness costs to Drosophila. Gould, PNAS, 2018, shows that both Lactobacillus plantarum and Lactobacillus brevis in mono-association have lower fitness (measured through Leslie matrix projections using lifespan and fecundity) than axenic flies. Many studies of wild Drosophila fail to find Lactobacillus, or it is low abundance (e.g., Chandler, PLoS Genetics, 2014; Wang, Environmental Microbiology Reports, 2018; Henry & Ayroles, Molecular Ecology, 2022; Gale, AEM, 2025). This might help provide useful context for the in vivo results.

(3) The data in Figure 4 are compelling to focus on the L. plantarum variants. However, I can see from the methods that the competitive mapping included only other strains of Wolbachia. It is not clear how other members of the microbiome changed in response to the temperature regimes. As I note in point #2, given that Lactobacillus is often rare, it is not clear what the rest of the microbiome looks like over the course of adaptation. Indeed, it seems like Mazzucco & Schlotterer, PRSB, 2021 did a broader analysis of the microbiome and found that Acetobacter is by far the most common bacterium (I think this data is also part of the data shown here?). Expanding on why or why not in this context is important and will improve this study, particularly if the focus is on connecting these evolutionary dynamics to ecological competition to explain the emergence of strain diversity.

Reviewer #1 (Public review):

Giordano et al. demonstrate that yeast cells expressing separated N- and C-terminal regions of Tfb3 are viable and grow well. Using this creative and powerful tool, the authors effectively uncouple CTD Ser5 phosphorylation at promoters and assess its impact on transcription. This strategy is complementary to previous approaches, such as Kin28 depletion or the use of CDK7 inhibitors. The results are largely consistent with earlier studies, reinforcing the importance of the Tfb3 linkage in mediating CTD Ser5 phosphorylation at promoters and subsequent transcription.

Notably, the authors also observe effects attributable to the Tfb3 linker itself, beyond its role as a simple physical connection between the N- and C-terminal domains. These findings provide functional insight into the Tfb3 linker, which had previously been observed in structural studies but lacked clear functional relevance. Overall, I am very positive about the publication of this manuscript and offer a few minor comments below that may help to further strengthen the study.

Page 4 PIC structures show the linker emerging from the N-terminal domain as a long alpha-helix running along the interface between the two ATPase subunits, followed by a turn and a short stretch of helix just N-terminal to a disordered region that connects to the C-terminal region (see schematic in Fig. 1A).

The linker helix was only observed in the poised PIC (Abril-Garrido et al., 2023), not other fully-engaged PIC structures.

Page 8 Recent structures (reviewed in (Yu et al., 2023)) show that the Kinase Module would block interactions between the Core Module and other NER factors. Therefore, TFIIH either enters into the NER complex as free Core Module, or the Kinase Module must dissociate soon after.

To my knowledge, this is still controversial in the NER field. I note the potential function on the kinase module is likely attributed to the N-terminal region of Tfb3 through its binding to Rad3. Because the yeast strains used in Fig. 6 retain the N-terminal region of Tfb3, the UV sensitivity assay presented here is unlikely to directly address the contribution of the kinase module to NER.

Page 11. Notably, release of the Tfb3 Linker contact also results in the long alpha-helix becoming disordered (Abril-Garrido et al., 2023), which could allow the kinase access to a far larger radius of area. This flexibility could help the kinase reach both proximal and distal repeats within the CTD, which can theoretically extend quite far from the RNApII body.

Although the kinase module was resolved at low resolution in all PIC-Mediator structures, these structural studies consistently reveal the same overall positioning of the kinase module on Mediator, indicating that its localization is constrained rather than variable. This observation suggests that the linker region may help position the kinase module at this specific site, likely through direct interactions with the PIC or Mediator. This idea is further supported by numerous cross-links between the linker region and Mediator (Robinson et al., 2016).

Comments on revisions:

Revised ms clarified all my points, including those I previously misunderstood.

Reviewer #1 (Public review):

Summary:

The authors address whether theta/beta ratio /TBR) can be used as a clinical biomarker for ADHD.

Strengths:

The data were acquired independently from 2 separate datasets, and there are sufficient subjects for adequate statistical power. The authors applied up-to-date EEG data preprocessing, state-of-the-art feature extraction, and statistical analyses, using a multiverse approach. By testing and comparing all meaningful approaches, defined a priori in the previous meta-analysis, the author convincingly demonstrates that TBR cannot be used as a clinical biomarker, and previous positive results can be explained by interactions between different factors (alpha peak frequency, aperiodic component, age).

Weaknesses:

There are no apparent issues with data, separate datasets, large sample sizes, and state-of-the-art data analysis.

Reviewer #1 (Public review):

Summary:

The authors set out to conduct a behavioral comparison of macaque and human vision across a wide range of visual properties. Such a comparison is critical for evaluating the use of macaques as a model system for understanding human vision and the underlying neural mechanisms. This goal represents a unique endeavour since prior studies have typically focused on only highly specific tasks. While the authors found consistent coarse representational structure for objects, evidence for Weber's Law and amodal completion, there was divergence for mirror image confusion and the use of global or local image properties.

Strengths:

There are three major strengths of the study. First, the authors employed a behavioral paradigm (oddball search) that allowed them to test multiple perceptual phenomena without having to train the macaques on the specific type of stimuli tested. Second, humans and macaques could be tested in an identical manner. Third, the authors tested a range of different visual properties and phenomena, allowing a broader comparison between species.

There are also some weaknesses to the study (described below), but that doesn't change the fact that the authors have demonstrated and validated a novel approach for systematic and comprehensive comparisons of vision across species.

Weaknesses:

The weaknesses of the study arise in part because of the breadth of the work. In cases where there are divergences between the two species, it would be helpful to know what might account for such divergence, to have more depth. Is it really a species difference, or could there be a different account? For example, does the difference in mirror image confusion arise because the stimuli were objects that would have been highly familiar to the humans but not the macaques? Further, the authors often used small sets of stimuli (e.g. 8 objects only in the test of object similarity; a small set of highly specific occlusion stimuli), and how well the findings will generalize beyond those stimuli is unclear.

The authors discuss the implications of training macaques to perform specific tasks on specific stimuli in comparing across species. While I agree that extensive training in monkeys could change perception, it is important to also consider that humans have been extensively trained through the types of visual tasks we conduct throughout our lives, so I'm not sure it is universally true that the best comparison is between humans and untrained monkeys. But this just consideration just highlights the general problem of comparing across species.

Reviewer #1 (Public review):

Summary:

This paper describes a complex series of studies that measure and explain object recognition in mice. The authors demonstrate that mice are capable of solving an object recognition task, that object identity is decodable in different regions of cortex, and the decodability, to some extent, can be captured by extant theory on object manifolds in deep neural networks. The authors further add some correlational analysis of the time courses of object discriminability to bolster their claim of an object processing hierarchy in the mouse cortex.

The behavioral and neural data described in this paper are likely to be of interest to the general neuroscience community. That said, I have some issues with the analyses, modeling, and image dataset that I'll detail below.

Strengths:

(1) The behavioral work is incredibly cool. Getting mice to solve this task is a real achievement and opens up new avenues for mice as a model for complex visual tasks.

(2) Similarly, the neural recordings are astounding in their scale.

(3) This could be the most complete demonstration of a primate-analogous object processing network in the mouse.

Weaknesses:

No new weaknesses were noted by this reviewer.

Reviewer #1 (Public review):

Summary:

Liao et al. performed a large-scale integrative analysis to explore the function of two cancer genes (BRCA1 and BRCA2) in lung cancer, which is one of the cancers with an extremely high mortality rate. The detailed genetic analysis demonstrated new roles of BRCA1/2 in causing the tumor microenvironment in lung cancer. In particular, the discovery of different mechanisms of BRCA1 and BRCA2 provides an essential foundation for developing drugs that target BRCA1 or BRCA2 in lung cancer therapy.

Strengths:

(1) This study leveraged large-scale genomic and transcriptomic datasets to investigate the prognostic implications of BRCA1/2 mutations in LUAD patients (~2,000 samples). The datasets range from genomics to single-cell RNA-seq to scTCR-seq.

(2) In particular, the scTCR-seq offers a powerful approach for understanding T cell diversity, clonal expansion, and antigen-specific immune responses. Leveraging these data, this study found that BRCA1 mutations were associated with CD8+ Trm expansion, whereas BRCA2 mutations were linked to tumor CD4+ Trm expansion and peripheral T/NK cell cytotoxicity.

(3) This study also performed a comprehensive analysis of genomic variation, gene expression, and clinical data from the TCGA program, which provides an independent validation of the findings from LUAD patients newly collected in this study.

(4) This study provides an exemplary integration analysis using both computational biology and wet bench experiments. The experimental testing in the A549 cell line further supports the robustness of the computational analysis.

(5) The findings of this study offer a comprehensive view of the molecular mechanisms underlying BRCA1 and BRCA2 mutations in LUAD. BRCA1 and BRCA2 are two well-known cancer-related genes in multiple cancers. However, their role in shaping the tumor microenvironment, particularly in lung cancer, is largely unknown.

(6) By focusing on PD-L1-negative LUAD patients, this study demonstrated the molecular mechanisms underlying resistance to immune therapy. These new insights highlight new opportunities for personalized therapeutic strategies to BRCA-driven tumors. For example, they found histone deacetylase (HDAC) inhibitors consistently downregulated 4-R genes in A549 cells.

(7) The deposition of raw single-cell sequencing (including scRNA-seq and scTCR-seq) data will provide an essential data resource for further discovery in this field.

Comments on revisions:

The author has revised accordingly. I have no further comments.

Reviewer #1 (Public review):

[Editors' note: this version has been assessed by the Reviewing Editor without further input from the original reviewers. The authors have addressed most of the comments raised in the previous round of review.]

Summary:

This study addresses the emerging role of fungal pathogens in colorectal cancer and provides mechanistic insights into how Candida albicans may influence tumor-promoting pathways. While the work is potentially impactful and the experiments are carefully executed, the strength of evidence is limited by reliance on in vitro models, small patient sample size, and the absence of in vivo validation, which reduces the translational significance of the findings.

Strengths:

(1) Comprehensive mechanistic dissection of intracellular signaling pathways.

(2) Broad use of pharmacological inhibitors and cell line models.

(3) Inclusion of patient-derived organoids, which increases relevance to human disease.

(4) Focus on an emerging and underexplored aspect of the tumor microenvironment, namely fungal pathogens.

Reviewer #1 (Public review):

In this revision the authors address some of the points, but they also make some technical errors. My overall view of the manuscript hasn't changed since the original evaluation.

Previously I noted that SC sparsity presents an issue when comparing to full FC matrices. They authors misinterpreted the Honey et al paper. They resampled ALL entries of the SC matrix (including zeros) from a Gaussian distribution. In effect, this assigns zeros small (but uniform) weights. In Honey et al, the authors resampled only existing edge weights from a gaussian distribution (the rationale at the time was that there might be pushback against the extremely heavy-tailed edge weight distribution). In other words, the zeros are still zeros following this resampling procedure.

That said, I agree that the log transform is likely useful or necessary given edge weight distributions.

In short, I still think that the approach is interesting and meritorious, I just don't think the execution is correct.

Reviewer #1 (Public review):

In this manuscript, the authors aim to determine the ligand on Plasmodium falciparum infected erythrocytes for the NK cell integrin, LFA-1, following up on previous evidence that LFA-1 is important for immune cell-mediated recognition of iRBCs.

They start by incubating LFA-1 with iRBCs and show by flow analysis that a substantial population of these iRBCs binds to the LFA-1 (Fig 1C). They do conduct the control with uninfected RBCs, but put this in the supplementary material. As this is a critical control, I think that it should be moved to Figure 1C as it is essential to allow interpretation of the iRBC data. The authors also do not state which strain of P. falciparum they used (line 144). This is critical information, as different strains have different variant surface antigens and should be included. With these changes, this data seems convincing.

They next incubated LFA-1 with the iRBCs, cross-linked and conducted a pulldown, identifying GP130 as a binding partner. Using cross-linkers is a dangerous strategy as it risks non-specific cross-linking. Did they try without cross-linking and find an interaction?

They raised antibodies to PfGBP and showed IFA, which reveals that these antibodies stain iRBCs (Figure 2Ciii). This experiment lacks a critical control of uninfected RBCs, which needs to be included to show that the staining is specific. Without this, it is not possible to conclude that there is iRBC-specific staining with PfGBP.

They then conduct a pulldown using LFA-Fc, which does show GP130 only in the presence of the LFA-Fc, but not when empty beads are used. This is convincing. BLI measurements are also used to study this interaction (Figure 2Ci). The BLI data is presented in such a way that any association phase is obscured by the y-axis, which makes it impossible to know whether there is binding here. I think that the data needs to be shown with some baseline before the addition of the ligand so that association can be seen. The data is also a bit messy with a downward drift and the curves showing different shapes, for example, with the 1.0uM curve seeming to have a different association rate. As this is the only data which shows a direct interaction between LFA1 and GBP, as pulldowns are done with lysates, which might mean bridging components. I think that it is important to repeat the BLI, or use additional biophysical methods to assess binding, to obtain more convincing data.

The authors next do some modelling of the putative complex. This is done by homology modelling and docking, which is not the most up-to-date method and is overinterpreted. Personally, I would remove this data as I did not find it convincing and it is not important for the story. If the authors wish to include it, then I think that they should validate the modelling by mutagenesis to show that the residues which the models indicate might bind are involved in the interaction.

They next made GP130 and tested the binding of this to THP-1 cells, which are often used as a model for macrophages. They observe greater binding of PfGBP-Fc to these cells when compared with hIgG and show that LFA-1 siRNA reduces this binding. I was a little confused about how the flow plots related to the graph in the bottom right corner of Figure 3Bii. In the flow plots, hIgG control shows 12.8% of cells in the gated region, while the unstained cells has 5.63%, but the MFI data shows a decrease in binding for hIgG vs unstained cells. How is this consistent? Also the siRNA reduces the number of cells in gated region from 66.6% to 25.9%, which is still substantially more that 5.63% in the unstained control. This also doesn't seem quite consistent with the MFI data. Could the authors explain this? Also perhaps an additional experiment would be to add soluble LFA-1 into this assay as an additional control to determine whether this blocks PfGBP binding to the THP-1 cells? It could. Be that there are additional mechanisms of binding which indicate why the siRNA has a partial effect. The same is true for the NK cell experiments in Figure 3Ci in which the siRNA has a partial effect. The authors also test binding to HEK, HepG2 and 'stem' cells and claim 'only background levels of binding', but in each case, there is more binding to these cells by PfGBP-Fc than by hIgG, albeit less than in THP-1 and NK cells. Why have the authors decided that these increases are not significant? All in all, these experiments do indicate a role for the GBP-LFA1 interaction in the binding of immune cells to iRBCs, but perhaps not as absolutely as is suggested.

The authors next produce CHO cells with PfGBP on the surface. These cells bind to LFA-1 specifically. When these cells were incubated with primary NK cells, they did see increases in activation markers, which were reduced by addition of antiCD11a, suggesting these to be specific. They also conduct the same experiment with anti-GBP with iRBCs but this is in a different figure. It would be easier for the reader if Figure 5B were in the same figure as Figure 4B as it is related data using the same method. I found this data convincing, showing that the LFA1:GBP interaction does contribute to immune cell recognition and activation.

The authors next conduct an experiment in which they assess parasite growth in the presence of NK cells and in the presence of anti-GBP. They use Heochst staining as a measure of parasite growth and claim that NK cells reduce the number of parasites, but that anti-GBP abolishes this effect (Figure 5A). I found this experiment very unconvincing as there are small effects and no demonstration of significance. More commonly used approaches to study parasite growth are lactate dehydrogenase GIA assays or calcein-AM labelling. I did not find this experiment convincing and would either remove or supplement with additional data using a more robust assay, with repeats and tests of statistical significance.

In summary, the authors present a set of data which comes together to indicate an interaction between LFA1 and PfGBP on the Plasmodium infected erythrocyte surface. Pulldown studies show convincingly that these two proteins co-precipitate and BLI data suggest that this is direct. Also convincing is that NK cell activation can be reduced using antibodies against either LFA1 or PfGBP, indicating that this interaction does play a role in immune cell recognition of iRBCs.

Comments on revised version:

The authors made some minor changes in response to my review, but did not present any substantial new data to demonstrate a direct interaction between PfGBP and LFA1 or to convincingly show differences in NK cell-mediated killing.

Reviewer #1 (Public review):

In this study, the authors investigate responses to methionine in the olfactory system of the Xenopus tadpole. They show that the LFP response is local to the glomerular layer, arises ipsilaterally, and is blocked by pharmacological blockade of AMPA and NMDA receptors, with little modulation during blockade of GABA-A receptors. They then show that this response is translently enlarged following transection of the contralateral olfactory nerve, but not the optic lobe nerve. Measurement of ROS- a marker of inflammation- was not affected by contralateral nerve transection, and LFP expansion was not affected by pharmacological blockade of ROS production. Imaging biased towards presynaptic terminals suggests that the enlargement of the LFP has a presynaptic component. A D2 antagonist increases the LFP size and variability in intact tadpoles, while a GABA-B antagonist does not. Finally, the authors provide anatomical and physiological evidence that the contralateral dopamine signal may arise from the lateral pallium. Overall, I found the array of techniques and approaches applied in this study to be creatively and effectively employed.

Reviewer #1 (Public review):

Summary:

The authors convincingly demonstrate that when PKMzeta is genetically deleted from the hippocampus, the related atypical PKC, PKClambda is upregulated and compensates both neurophysiologically and behaviorally for the missing PKMzeta. Specifically, the upregulatiion of PKClambda supports late-phase hippocampal long-term potentiation (L-LTP) and long-term spatial memory in the PKMzeta knockout mice.

Strengths:

The study uses up-to-date transgenic techniques to alter the expression of the two atypical PKCs. The synaptic and behavioral experiments are well-controlled and appear to have been carefully executed.

Weaknesses:

None

Reviewer #1 (Public review):

The manuscript by Tang et al. characterizes the expression dynamics and functional roles of aldehyde dehydrogenase 1 activity in uterine physiology. Using a combination of in vivo lineage tracing and cell ablation coupled with organoid culture, the authors propose that Aldh1a1 lineage-marked cells contribute to uterine gland development and epithelial regeneration. The descriptive data will be of interest to reproductive biologists and clinicians and will build on established hypotheses in the field. The manuscript is well written and scientifically sound; however, several experimental limitations and interpretation caveats should be addressed.

The methods surrounding the passage number and duration of culture following sorting prior to transcriptomic profiling should be clarified in the figure legends. Related to this, the representative images in Figures 1D and 1E do not appear consistent with the quantification presented in Figures 1F-H and should be reconciled.

The conclusion that ALDH1A1+ cells are enriched in populations with stem cell characteristics relies primarily on transcriptomic analysis. Protein-level co-localization should be performed to strengthen this claim.

The overlap of 19 genes between the data set here and AXIN2 HI data is presented as evidence of shared stemness identity, but no statistical assessment of this overlap is provided. A hypergeometric test should be performed to determine whether this overlap is greater than expected by chance.

The impact of tamoxifen injection on Aldh1a1 expression should be characterized in the neonatal uterus, as tamoxifen itself has known estrogenic activity that could confound interpretation of the lineage tracing results at early postnatal timepoints. Related to this, while low-dose tamoxifen is shown to label individual cells within 24 hours of injection, the translation dynamics of the label following Cre-mediated recombination can require up to 72 hours. The presence of only a few labeled clones at PND8 but multiple separate clones per cross-section at later timepoints warrants discussion and may reflect labeling kinetics rather than clonal expansion.

It would strengthen the in vivo ablation data to validate the degree of cell death following diphtheria toxin treatment directly. It is possible that a general decrease in cell number rather than specific loss of a stem cell population is responsible for the observed reduction in gland number and FOXA2 expression (Tongtong et al 2017).

The lineage tracing data in the postpartum endometrium demonstrate that Aldh1a1-marked cells are present during regeneration, but it remains unclear whether these cells are preferentially activated or expanded in response to tissue injury. Coupling these studies with diphtheria toxin-mediated ablation during active regeneration would more directly test the proposed regenerative role of this population.

The contribution of stromal Aldh1a1 lineage-positive cells is underexplored in the discussion, given the lineage tracing data showing stromal labeling across multiple timepoints and its potential relevance to mesenchymal-to-epithelial transition.

Finally, the word 'control' may overstate the functional evidence presented. 'Contribute' may be more accurate given the partial and context-dependent nature of the phenotypes observed.

Reviewer #1 (Public review):

Summary:

The authors investigate how methicillin-resistant (MRSA) and sensitive (MSSA) Staphylococcus aureus adapt to a new host (C. elegans) in the presence or absence of a low dose of the antibiotic oxacillin. Using an "Evolve and Resequence" design with 48 independently evolving populations, they track changes in virulence, antibiotic resistance, and other fitness-related traits over 12 passages. Their key finding is that selection from both the host and the antibiotic together, rather than either pressure alone, synergistically results in the evolution of the most virulent pathogens. Genomically, they find that this adaptation repeatedly involves parallel mutations in a small number of key regulatory genes, most notably codY, agr, and saeRS.

Strengths:

The main advantage of the research lies in its strong and thoroughly replicated experimental framework, enabling significant conclusions to be drawn based on the concept of parallel evolution. The study successfully integrates various phenotypic assays (virulence, growth, hemolysis, biofilm formation) with whole-genome sequencing, offering an extensive perspective on the adaptive landscape. The identification of certain regulatory genes as common targets of selection across distinct lineages is an important result that indicates a level of predictability in how pathogens adapt. Furthermore, the detailed mapping of specific parallel mutations provides a highly useful genomic resource for the microbiology community.

Revisions and Re-Appraisal:

In the initial version of the manuscript, a primary limitation was the use of causal language to link specific mutations to phenotypes, despite the evidence from the evolution experiment being correlational. In this revised version, the authors have excellently addressed this limitation. They have meticulously revised the text to accurately reflect these relationships as strong, statistically significant genetic associations rather than confirmed facts. Furthermore, they explicitly acknowledge that future ancestral reconstruction experiments will be required to confirm direct causality. The authors have also appropriately clarified the visual interpretations of their data (such as the PCA clustering) and refined their discussion of mutation rates. With these revisions, the claims made are fully supported by the data presented.

Impact and Context:

The authors successfully achieve their aims, demonstrating that the combined effects of host and antibiotic pressures collaboratively propel the evolution of heightened virulence. While the nematode model does not perfectly mimic human or mammalian infection, the evolutionary principles uncovered here are highly relevant to both evolutionary biology and infectious disease management. The evidence presented is compelling, and the strong correlational hypotheses generated by this study offer a robust and significant basis for upcoming mechanistic research into pathogen adaptation.

Comments on revisions:

I commend the authors for their thorough, thoughtful, and highly constructive revision. You have successfully addressed all of my major and minor comments. The addition of Table S2 and the careful revisions to the causal language have significantly strengthened the manuscript and clarified the data interpretation. I have no further recommendations. Great work!

Reviewer #1 (Public review):

Summary:

This paper examines whether action potentials (APs) reliably propagate to the distal axon in neocortical parvalbumin-expressing interneurons (PV-Ins) during prolonged high-frequency activity, as occurring during epileptiform activity. The authors use dual soma and axon-attached patch-clamp recordings from mouse and human PV-INs and show that axon AP amplitude declines when the firing frequency exceeds ~200 Hz and fails during seizure-like bursts. Finally, they show that elevation of external K+ to 10 mM also reduces AP amplitude. Taken together, these data strongly suggest that the reduction in transmitter release observed during intense PV-INs activity or during seizure-like events is mainly mediated by the reduction in the presynaptic AP amplitude in PV-INs.

Strengths:

This paper is very interesting, well-written and technically impressive. It provides new and important results. The paper will have a great impact in the field of both axon physiology and epilepsy.

Weaknesses:

I did not find any significant weakness in the methods, data analysis and results.

Reviewer #1 (Public review):

This study investigates how astrocyte metabolic state influences astrocyte-synapse interactions and the organization of the dopaminergic circuit in the Drosophila CNS. Using a creative split-GFP-based contact reporter ("PEAPOD"), combined with genetic perturbations of glycolytic enzymes, synaptic labeling, EM, transsynaptic tracing, single-cell transcriptomics, and behavioral assays, the authors propose that disruption of astrocyte glycolysis enhances astrocyte-dopamine neuron contacts, promotes synaptogenesis, and biases dopaminergic-motor circuit connectivity through a mechanism involving altered Neuroligin 2 trafficking.

The work is conceptually ambitious and technically broad. The development and application of a contact reporter for astrocyte-neuronal interfaces is potentially valuable to the field, and the convergence of multiple glycolytic perturbations on similar phenotypes is a notable strength. However, several central conclusions currently extend beyond the direct evidence presented. Clarification and calibration of these claims would substantially strengthen the manuscript.

Major Points:

(1) Astrocyte glycolytic impairment is inferred rather than directly demonstrated

The central premise of the manuscript is that reduced astrocyte glycolysis drives the observed phenotypes. While multiple glycolytic enzymes (e.g., pfk, eno, pyk) are genetically perturbed and produce similar increases in PEAPOD signal, the manuscript does not directly demonstrate altered glycolytic flux or metabolic state in astrocytes under these conditions. Reduced enzyme levels or genetic mutation do not necessarily establish functional metabolic deficiency, particularly given potential compensatory mechanisms.

Because glycolytic impairment is foundational to the proposed mechanism, the conclusions should either be supported by direct metabolic readouts in astrocytes or framed more cautiously as perturbations of glycolytic enzymes rather than confirmed metabolic deficiency.

(2) Interpretation of the PEAPOD signal requires clearer calibration

The PEAPOD system is an innovative tool to detect membrane proximity between astrocytes and dopamine neurons. However, the manuscript frequently interprets increased PEAPOD intensity and volume as increased "ensheathment" or increased synaptic contact. A split-GFP-based reporter measures membrane apposition within a defined spatial range but does not directly quantify structural ensheathment, synapse number, or functional synaptic engagement.

Although the authors show an association of the PEAPOD signal with presynaptic markers in some regions, the distinction between increased membrane contact, altered membrane organization, and true changes in perisynaptic coverage should be more explicitly discussed. Several conclusions would benefit from clearer wording that distinguishes contact proximity from ultrastructural or functional synapse remodeling.

(3) Evidence for biased dopaminergic-motor circuit wiring is indirect

The manuscript proposes that disruption of astrocyte glycolysis biases dopaminergic-motor connectivity. This conclusion relies heavily on trans-Tango labeling intensity and downstream cell-type composition analysis via FACS and single-cell RNA sequencing.

Transsynaptic labeling approaches can be influenced by expression levels, reporter trafficking, labeling efficiency, and differential recovery during dissociation and FACS. Changes in labeled cell abundance or reporter intensity do not necessarily equate to altered synaptic wiring. Given that this conclusion represents a major conceptual advance of the study, the manuscript should either provide additional orthogonal support or temper the claim to reflect that altered labeling efficiency or synaptic engagement, rather than definitive rewiring, has been demonstrated.

(4) Mechanistic claims regarding Neuroligin 2 trafficking are suggestive but not definitive

The authors propose that astrocyte glycolytic disruption alters Neuroligin 2 (Nlg2) trafficking, leading to ER retention and downstream synaptogenic effects. The observation of Nlg2-positive intracellular bodies colocalizing with ER markers is intriguing. However, quantitative analysis, additional compartment markers, and/or biochemical support would be necessary to firmly establish altered ER exit or glycosylation status.

At present, the mechanistic model is plausible but should be presented more explicitly as a working model supported by suggestive evidence rather than a fully established trafficking defect.

(5) Behavioral phenotypes are not yet causally linked to dopaminergic circuit changes

The locomotor phenotypes observed upon astrocyte glycolytic perturbation are clear. However, the manuscript attributes these changes to altered dopaminergic-motor connectivity. A direct causal linkage between astrocyte metabolic state, dopaminergic circuit remodeling, and behavior is not conclusively demonstrated. The discussion should either clarify the inferential nature of this link or provide additional evidence supporting dopamine-specific dependence.

Minor Points:

(1) Statistical analyses across multi-group comparisons should be more clearly justified, particularly where multiple pairwise tests are performed. A clarification of the multiple-comparison correction and the exact comparison strategy would improve rigor.

(2) The temporal interpretation of activity-dependent remodeling experiments would benefit from a clearer explanation of what timescale is being tested.

(3) Developmental compensation versus the acute effects of glycolytic perturbation are not fully distinguished and should be discussed.

(4) The orthology and functional equivalence of Drosophila Nlg2 should be described with greater precision to avoid potential confusion.

Reviewer #1 (Public review):

Summary:

In this manuscript, Kong et al. conduct a systematic analysis of the multi-cancer risk locus at 2q33. The authors start with a careful analysis of co-localization between the melanoma risk SNPs and several other cancers and conclude that a subset of credible causal SNPs is shared among different cancers, including breast cancer. Next, they define a starting list of 27 SNPs as potential credible causal SNPs and analysis of TADs (topologically associating domains) to zoom in on CASP8 and FLA CC1 as potential target genes. They then systematically rule out coding and splicing variants in the set and focus on a smaller set of three SNPs constituting a melanocyte enhancer element. Using a combination of mass spectrometry, reporter assays, and electrophoretic mobility shift assays, the authors define a role for transcription factors IRF2 and E4F1 in the regulatory network driving risk at the locus.

This work represents a high-quality tour de force, using multiple tools, to zoom in on a gene expression regulatory network associated with risk for multiple cancers. It provides a detailed framework for analyses of other multi-cancer risk loci. Limitations of the work, which is rather a current limitation of the field, is the lack of a model to study how the identified network of regulatory elements, transcription factors, and target genes mechanistically drive risk at the organismal level. Advances such as those described in this manuscript contribute significantly to our knowledge of how common risk variants drive risk.

Reviewer #1 (Public review):

[Editors' note: this version has been assessed by the Reviewing Editor without further input from the original reviewers. The authors have addressed the major comments raised in the previous round of review. Public Reviews below refer to the version submitted to Review Commons.]

Summary:

Gosselin et al., develop a method to target protein activity using synthetic single-domain nanobodies (sybodies). They screen a library of sybodies using ribosome/ phage display generated against bacillus Smc-ScpAB complex. Specifically, they use an ATP hydrolysis deficient mutant of SMC so as to identify sybodies that will potentially disrupt Smc-ScpAB activity. They next screen their library in vivo, using growth defects in rich media as a read-out for Smc activity perturbation. They identify 14 sybodies that mirror smc deletion phenotype including defective growth in fast-growth conditions, as well as chromosome segregation defects. The authors use a clever approach by making chimeras between bacillus and S. pnuemoniae Smc to narrow-down to specific regions within the bacillus Smc coiled-coil that are likely targets of the sybodies. Using ATPase assays, they find that the sybodies either impede DNA-stimulated ATP hydrolysis or hyperactivate ATP hydrolysis (even in the absence of DNA). The authors propose that the sybodies may likely be locking Smc-ScpAB in the "closed" or "open" state via interaction with the specific coiled-coil region on Smc. I have a few comments that the authors should consider:

Major comments:

(1) Lack of direct in vitro binding measurements:

The authors do not provide measurements of sybody affinities, binding/ unbinding kinetics, stoichiometries with respect to Smc-ScpAB. Additionally, do the sybodies preferentially interact with Smc in ATP/ DNA-bound state? And do the sybodies affect the interaction of ScpAB with SMC?

It is understandable that such measurements for 14 sybodies is challenging, and not essential for this study. Nonetheless, it is informative to have biochemical characterization of sybody interaction with the Smc-ScpAB complex for at least 1-2 candidate sybodies described here.

(2) Many modes of sybody binding to Smc are plausible

The authors provide an elaborate discussion of sybodies locking the Smc-ScpAB complex in open/ closed states. However, in the absence of structural support, the mechanistic inferences may need to be tempered. For example, is it also not possible for the sybodies to bind the inner interface of the coiled-coil, resulting in steric hinderance to coiled-coil interactions. It is also possible that sybody interaction disrupts ScpAB interaction (as data ruling this possibility out has not been provided). Thus, other potential mechanisms would be worth considering/ discussing. In this direction, did AlphaFold reveal any potential insights into putative binding locations?

(3) Sybody expression in vivo

Have the authors estimated sybody expression in vivo? Are they all expressed to similar levels?

(4) Sybodies should phenocopy ATP hydrolysis mutant of Smc

The sybodies were screened against an ATP hydrolysis deficient mutant of Smc, with the rationale that these sybodies would interfere this step of the Smc duty cycle. Does the expression of the sybodies in vivo phenocopy the ATP hydrolysis deficient mutant of Smc? Could the authors consider any phenotypic read-outs that can indicate whether the sybody action results in an smc-null effect or specifically an ATP hydrolysis deficient effect?

Significance:

Overall, this is an impressive study that uses an elegant strategy to find inhibitors of protein activity in vivo. The manuscript is clearly written and the experiments are logical and well-designed. The findings from the study will be significant to the broad field of genome biology, synthetic biology and also SMC biology. Specifically, the coiled coil domain of SMC proteins has been proposed to be of high functional value. The authors have elegantly identified key coiled-coil regions that may be important for function, and parallelly exhibited potential of the use of synthetic sybody/designed binders for inhibition of protein activity.

Reviewer #1 (Public review):

[Editors' note: this version has been assessed by the Reviewing Editor without further input from the original reviewers. The authors have addressed the comments raised in the previous round of review.]

Original review:

Summary:

Lumen formation is a fundamental morphogenetic event essential for the function of all tubular organs, notably the vertebrate vascular network, where continuous and patent conduits ensure blood flow and tissue perfusion. The mechanisms by which endothelial cells organize to create and maintain luminal space have historically been categorized into two broad strategies: cell shape changes, which involve alterations in apical-basal polarity and cytoskeletal architecture, and cell rearrangements, wherein intercellular junctions and positional relationships are remodeled to form uninterrupted conduits. The study presented here focuses on the latter process, highlighting a unique morphogenetic module, junction-based lamellipodia (JBL), as the driver for endothelial rearrangements.

Strengths:

The key mechanistic insight from this work is the requirement of the Arp2/3 complex, the classical nucleator of branched actin filament networks, for JBL protrusion. This implicates Arp2/3-mediated actin polymerization in pushing force generation, enabling plasma membrane advancement at junctional sites. The dependence on Arp2/3 positions JBL within the family of lamellipodia-like structures, but the junctional origin and function distinguish them from canonical, leading-edge lamellipodia seen in cell migration.

Weaknesses:

The study primarily presents descriptive observations and includes limited quantitative analyses or genetic modifications. Molecular mechanisms are typically interrogated through the use of pharmacological inhibitors rather than genetic approaches. Furthermore, the precise semantic distinction between JAIL and JBL requires additional clarification, as current evidence suggests their biological relevance may substantially overlap.

Reviewer #1 (Public review):

Summary:

In their paper, Shimizu and Baron describe the signaling potential of cancer gain-of-function Notch alleles using the Drosophila Notch transfected in S2 cells. These cells do not express Notch or the ligand Dl or Dx, which are all transfected. With this simple cellular system, the authors have previously shown that it is possible to measure Notch signaling levels by using a reporter for the 3 main types of signaling outputs, basal signaling, ligand-induced signaling and ligand-independent signaling regulated by deltex. The authors proceed to test 22 cancer mutations for the above-mentioned 3 outputs. The mutation is considered a cluster in the negative regulatory region (NRR) that is composed of 3 LNR repeats wrapping around the HD domain. This arrangement shields the S2 cleavage site that starts the activation reaction.

The main findings are:

(1) Figure 1: the cell system can recapture ectopic activation of 3 existing Drosophila alleles validated in vivo.

(2) Figure 2: Some of the HD mutants do show ectopic activation that is not induced by Dl or Dx, arguing that these mutations fully expose the S2 site. Some of the HD mutants do not show ectopic activation in this system, a fact that is suggested to be related to retention in the secretory pathway.

(3) Figure 3: Some of the LNR mutants do show ectopic activation that is induced by Dl or Dx, arguing that these might partially expose the S2 site.

(4) Figure 4-6: 3 sites of the LNR3 on the surface that are involved in receptor heterodimerization, if mutated to A, are found to cause ectopic activation that is induced by Dl or Dx. This is not due to changes in their dimerization ability, and these mutants are found to be expressed at a higher level than WT, possibly due to decreased levels of protein degradation.

Strengths and Weaknesses:

The paper is very clearly written, and the experiments are robust, complete, and controlled. It is somewhat limited in scope, considering that Figure 1 and 5 could be supplementary data (setup of the system and negative data). However, the comparative approach and the controlled and well-known system allow the extraction of meaningful information in a field that has struggled to find specific anticancer approaches. In this sense, the authors contribute limited but highly valuable information.

Comments on revised version:

I reviewed the changes and response to criticism, and it seems to me that all has been reasonably addressed.

Reviewer #1 (Public review):

Summary:

The authors have studied how a virus (EMCV) uses its RNA (Type 2 IRES) to hijack the host's protein-making machinery. They use cryo-EM to extract structural information about the recruitment of viral Type 2 IRES to ribosomal pre-IC. The authors propose a novel interaction mechanism in which the EMCV Type 2 IRES mimics 28S rRNA and interacts with ribosomal proteins and initiator tRNA (tRNAi).

Strengths:

(1) Getting structural insights about the Type 2 IRES-based initiation is novel.

(2) The study allows a good comparison of other IRES-based initiation systems.

(3) The manuscript is well-written and clearly explains the background, methods, and results.

Comments on revised version:

I have gone through the revised manuscript by Das and Hussain along with the rebuttal comments. While the poor resolution of the ribosomal complex limits detailed analysis of the molecular interactions, addition of the luciferase reporter assay in the supplementary has enriched the paper.

Reviewer #1 (Public review):

Summary:

The authors dissected the ears with some surrounding tissue from 600 embryos at 4 developmental time points of wild-type larvae, as well as from an lmx1bb mutant, performed scRNA-seq analyses, and subclustered the ear/neuromast clusters. They identified cluster markers and performed PAGA pseudotime analyses to build developmental timelines of lineages. They validated some of the cluster markers with HCRs. Many of the clusters are not annotated in detail, but the data sets are still valuable for the community.

Strengths:

Using scRNA-Seq, the authors identified cluster markers for tissues of the developing zebrafish ear and validated some of them with HCRs. The data they compiled and submitted to public databases is a valuable resource for the community.

Weaknesses:

Many of the clusters have not been annotated or rely on published data. For the ones for which no HCRs or UMAPs are shown, it is therefore difficult to estimate which of the markers are indeed the most cell type/state-specific ones.

Major comments:

(1) It would be very useful if the cluster numbers in the Excel files also had the associated cell type annotations as a second column (at least for the ones that are known). E.g., in Supplemental Table 2, the text states which clusters represent which neuromast and ear cell type, but these are not mentioned in the Excel table.

(2) Many of the clusters have not been annotated or rely on published data. For the ones for which no HCRs or UMAPs are shown, it is therefore difficult to estimate which of the markers are indeed the most cell-type/state-specific ones.

(3) Uploading the data to gEAR (https://umgear.org/dataset_explorer.html), a web-based, publicly available ear database, would further increase the usefulness of this study to the broader community.

Method:

The authors should provide the details about how many cells were sequenced for each ear developmental stage, how many cells were present per cluster (page 8), and how many cells were present in each subcluster of ear and lateral line clusters (page 10).

Reviewer #1 (Public review):

Summary:

In this work, the authors revisit a well-defined experimental system for studying temporal gene expression mechanisms in TNF-alpha-stimulated macrophages, bringing new tools to the process. Using a hybrid-capture approach, they are able to obtain deeper RNA sequencing of target genes, which allows them to identify potential differences in splicing kinetics of individual introns. Further implementing transcriptional blocks to measure intron half-lives, and predictive machine learning models to identify potential contributing cis-acting RNA elements, they define a group of 'bottleneck' introns whose delayed splicing is a rate-limiting step in mRNA maturation.

Strengths:

(1) The hybrid-capture approach enables deeper RNA sequencing of target transcripts.

(2) The neural network application to identify motifs outside of splice sites could be related to intron removal kinetics.

(3) The paper uses splicing reporters with modulation of 5' splice sites to test the effect on reporter gene expression in the context of 'bottleneck' introns.

Weaknesses:

(1) While evidence is provided that these introns are distinct from previously published splicing kinetics studies, 'bottleneck' introns are not adequately placed in context for assessment of how they are similar or different.

(2) Splicing reporters are a good approach, but the complexities of post-transcriptional gene expression regulation are not adequately addressed

(3) Deep learning models are a potentially powerful tool for identifying novel regulatory sequences; however, their use here is underdeveloped.

Reviewer #1 (Public review):

Summary:

In this manuscript, Matsuda and collaborators present a model of how tracheal tubulogenesis is controlled in Drosophila embryos. Some of the results backing the model are new, but others are based on information already published by the authors. However, the results in this manuscript present different molecular markers not published before, which agree with previous conclusions. The manuscript also analyses the requirement of the dpp and EGFR signalling pathways for trachealess (trh) maintenance, one of the main tracheal transcription factors.

Strengths:

The two most interesting novel points of the manuscript are:

(1) Its contribution to the analysis of how the dpp and EGFR pathways contribute to the maintenance of trh expression.

(2) The experimental evidence showing that mechanical invagination is not a requirement for trh maintenance in the tracheal cells, an intriguing hypothesis previously suggested by (Kondo Hayashi 2019 eLife 8:e45145) that can now be discarded by the data presented in this work.

Weaknesses:

Because of the mixture of new and already published data, this manuscript can be considered as a review/experimental paper.

Already known data:<br /> - The results showing that hh and vvl drive tracheal invaginaton independently of trh are reported in Figure 5 of (Matsuda et al. 2015 eLife 4:e09646).<br /> - The results showing dpp requirement for trh maintenance are partially reported in Figure 6 of (Matsuda 2015 eLife 4:e09646).

Reviewer #1 (Public review):

[Editors' note: this version has been assessed by the Reviewing Editor without further input from the original reviewers. The authors have addressed the comments raised in the previous round of review.]

Summary:

Zacharia and colleagues investigate the role of the C-terminus of IFT172 (IFT172c), a component of the IFT-B subcomplex. IFT172 is required for proper ciliary trafficking and mutations in its C-terminus are associated with skeletal ciliopathies. The authors begin by performing a pull-down to identify binding partners of His-tagged CrIFT172968-C in Chlamydomonas reinhardtii flagella. Interactions with three candidates (IFT140, IFT144, and a UBX-domain containing protein) are validated by AlphaFold Multimer with the IFT140 and IFT144 predictions in agreement with published cryo-ET structures of anterograde and retrograde IFT trains. They present a crystal structure of IFT172c and find that a part of the C-terminal domain of IFT172 resembles the fold of a non-canonical U-box domain. As U-box domains typically function to bind ubiquitin-loaded E2 enzymes, this discovery stimulates the authors to investigate the ubiquitin-binding and ubiquitination properties of IFT172c. Using in vitro ubiquitination assays with truncated IFT172c constructs, the authors demonstrate partial ubiquitination of IFT172c in the presence of the E2 enzyme UBCH5A. The authors also show a direct interaction of IFT172c with ubiquitin chains in vitro. Finally, the authors demonstrate that deletion of the U-box-like subdomain of IFT172 impairs ciliogenesis and TGFbeta signaling in RPE1 cells.

However, some of the conclusions of this paper are only partially supported by the data, and presented analyses are potentially governed by in vitro artifacts. In particular, the data supporting autoubiquitination and ubiquitin-binding are inconclusive. Without further evidence supporting a ubiquitin-binding role for the C-terminus, the title is potentially misleading.

Strengths:

(1) The pull-down with IFT172 C-terminus from C. reinhardtii cilia lysates is well performed and provides valuable insights into its potential roles.

(2) The crystal structure of the IFT172 C-terminus is of high quality.

(3) The presented AlphaFold-multimer predictions of IFT172c:IFT140 and IFT172c:IFT144 are convincing and agree with experimental cryo-ET data.

Reviewer #1 (Public review):

Summary:

This manuscript asks how the uterine lumen is remodeled across the peri-implantation window and whether this remodeling is functionally linked to embryo attachment and subsequent pregnancy establishment. The authors combine whole-organ three-dimensional imaging of optically cleared mouse uteri with single-cell and spatial transcriptomic profiling, conditional deletion of p38α at the uterine-wide versus epithelial-restricted level, and rescue experiments using progesterone and leukemia inhibitory factor. Based on these datasets, the authors propose that the luminal epithelium undergoes a previously underappreciated phase of organ-scale architectural reorganization before attachment, and that a p38α-dependent stress-responsive program coordinates epithelial remodeling together with epithelial-stromal communication required for implantation competence.

Strengths:

By moving beyond local attachment-site morphology to a horn-level representation of luminal topology, the work provides anatomical context that is difficult to reconstruct from conventional section-based approaches and should be broadly useful to the implantation community. The integration of organ-scale morphology with single-cell and spatial transcriptomic datasets, together with genetic perturbation and rescue experiments, adds breadth and increases the potential long-term utility of the dataset for investigators interested in uterine receptivity and embryo-uterine interactions.

Weaknesses:

(1) The whole-uterus analysis of luminal folds and creases requires stronger methodological support. Given the mechanical compliance of the uterine lumen, it is difficult to evaluate from the current description whether dissection, fixation, clearing, and/or mounting could influence the observed luminal topography. This issue is particularly important because several key conclusions depend on the spatial distribution of folds across the uterine horn. A fuller account of tissue handling and reconstruction, together with validation that the preparation preserves native morphology, would substantially strengthen confidence in the organ-scale conclusions.

(2) Several of the central morphological claims are supported primarily only by representative reconstructions. This includes the proposed flattening/creasing dynamics, alternating stretched and shrunken regions, persistence of abnormal folding in the mutant uterus, and the extent of structural rescue following progesterone supplementation. The authors could extract objective measures from the reconstructed luminal surface and provide more statistical analysis to demonstrate the reproducibility of the results.

(3) The manuscript appears to over-reach in concluding that luminal remodeling zones embryos before attachment from day 4 to 5. As presented, the data support a correlation between luminal architecture and embryo position, but do not discriminate between (i) luminal remodeling directing embryo positioning, (ii) embryos locally shaping the lumen, or (iii) parallel regulation of both. The evidence is based on observations of the uterus and the inside blastocysts at certain time points around implantation. Without the time-lapse analysis within the uterus, the dynamic interactions between embryos and the uterus couldn't be determined.

(4) The key conclusion of the manuscript is that uterine p38α regulates luminal epithelial remodeling required for embryo attachment, as shown in the title. Against this background, the finding that epithelial-restricted loss of p38α does not overtly impair fertility is notable, as it suggests that the major function of p38α may not be epithelial cell-autonomous but instead may arise through other uterine compartments that secondarily influence the epithelium. At present, however, this conclusion remains insufficiently supported: the epithelial-specific model is not characterized in sufficient depth during the peri-implantation period, and the transcriptomic evidence for altered epithelial-stromal communication does not by itself explain the phenotypic difference between uterine-wide and epithelial-specific deletion. If stromal p38α is proposed as the critical upstream regulator, more direct testing, such as stromal-specific deletion, would be needed.

Reviewer #1 (Public review):

Summary:

The authors provide high-resolution cryoEM structures to map and functionally characterize human antibodies against SARS-CoV-2 elicited by a standard mRNA vaccine. Here, they report high-resolution structural information on seven previously documented neutralizing antibodies from this response, which were produced from early plasmablasts and which engage diverse targets on the viral spike glycoprotein. This structural information is then integrated with functional assays to define how antibody epitope specificity, geometry, and conformational dynamics may shape neutralization outcomes.

Strengths:

A core strength of the study is a technically-well executed analysis of multiple 'ectopically balanced' mAbs elicited by early B cell plasmablast responses. These antibodies engage different neutralizing targets on the S-trimer of SARS-CoV-2, including the RBD and NTD domains. This has resolved a core distinction in terms of how nAbs engaging these features (and subfeatures, e.g., more conserved hydrophobic pocket within NTD) neutralize the virus.

Weaknesses:

A general weakness is that these antibody classes have been structurally characterized already (albeit individually), and much of this work has been done in the context of understanding susceptibility to escape mutations (delta, omicron, and subvariants therein; class I-IV antibody crossreactivity on Wuhan SARS-CoV-2 to present). It is exceptionally fine technical work presenting the antibodies in a collection like this, but perhaps the new predictive power of this analysis is somewhat overstated.

The early plasmablast angle seems like it could be better fleshed out. Many of the known SARS-CoV-2 nAbs are from the plasmablast pool, but how does this predict the antibody profile at latter stages, as per the stated goal and claim of the current study? Does the paratope pattern of plasmablast antibodies then change within the immune sera at later time points? New or existing cryoEMPEM data could shed light on this.

Reviewer #1 (Public review):

Summary:

The authors set out to evaluate how accurately direct sequencing of RNA can identify and quantify several chemical modifications on RNA molecules, focusing primarily on m6A. A central goal of the work is to compare this approach with an independent chemical-based method (glyoxal and nitrite-mediated deamination of unmethylated adenosines (GLORI), using the same RNA samples, in order to assess reproducibility, false-positive signals, and sensitivity across a range of detection strategies. The authors further aim to demonstrate the biological utility of this approach by applying it to two human cell types, primary human fibroblasts and HD10.6 neurons. While the manuscript also reports detection of additional RNA modifications (pseudouridine and m5C, the depth of analysis and strength of controls are greatest for m6A, which forms the primary focus of the study

Strengths:

A strength of this work is the direct comparison of two distinct measurement approaches performed on the same RNA input material; this has not been done in other recently published benchmarking studies evaluating the utility of the recent direct RNA sequencing for calling m6A. The authors systematically test multiple analysis models and show that, when appropriate filtering is applied, detection of modified sites is reproducible across software versions. The use of synthetic RNA standards and METTL3 inhibitors as negative controls helps to reinforce the overall results.

The data show good agreement between the two methods at higher m6A modification levels, supporting the conclusion that direct RNA sequencing can reliably detect high-confidence modification sites. The authors also demonstrate that this approach can, in principle, provide information at the level of individual RNA variants (although only one example was provided), which is difficult to achieve with short-read methods. The methodology described here is likely to be useful to others seeking to apply similar approaches to identify and quantify m6A. The study also explores the detection of other RNA modifications, which highlights the broader potential of the approach, although these analyses are necessarily more exploratory given the more limited controls and data available.

Weaknesses:

Despite these strengths, several issues limit the interpretation of the results and should be clarified for readers.

First, the authors appropriately address false-positive signals by estimating expected false-positive rates and by quantitatively comparing sequence motif enrichment before and after filtering. These analyses provide important support for the use of stoichiometry-based thresholds and demonstrate that filtering substantially improves specificity. However, even after filtering, a subset of detected sites remains outside the expected sequence context. It therefore remains unclear to what extent these non-canonical sites reflect genuine biology versus residual technical artifacts.

Second, claims regarding the ability of direct RNA sequencing to resolve modification patterns across different RNA variants are supported by very limited evidence. The conclusion that this approach provides superior isoform-level quantification relative to short-read methods is based largely on a single gene example. While this case is interesting, it does not establish how widespread or general this advantage is. A broader analysis indicating how many genes show isoform-specific modification patterns detectable by this method, and how often these are missed by the comparison approach, would be necessary to support a general claim.

Third, the biological interpretation of cell type-specific differences in modification levels remains underdeveloped. Although differences in modification stoichiometry are reported between fibroblasts and neuron-derived cells, the functional consequences of these differences are not addressed. It is unclear whether changes in modification levels are associated with differences in RNA abundance, stability, or translation. As a result, statements suggesting that these modifications fine-tune core cellular pathways are speculative and should either be supported with additional analyses or framed more cautiously.

Related to this point, differences in gene expression between the two cell types are a potential confounding factor. The pathway enrichment patterns presented appear biased toward particular functional categories, but without clear control for differential gene expression, it is difficult to determine whether the observed enrichment reflects cell type-specific regulation of RNA modification or simply differences in which genes are expressed. Clarifying how background gene sets were defined for these analyses would help readers interpret the results.

The manuscript also suggests broader differences in overall modification levels between cell types, but this is not validated using an independent global assay. An orthogonal measurement of total modification levels on polyadenylated RNA (for example, dot blot) would help place site-specific stoichiometry differences in a clearer biological context.

Finally, the effects of the METTL3 inhibitor on these cell types are not fully characterized. While changes in m6A modification patterns are reported following treatment, the manuscript does not address whether the treatment affects cell growth or viability.

Appraisal of conclusions and impact:

Overall, the study provides an informative technical assessment of direct RNA sequencing for modification detection and establishes clear conditions under which the method performs well. The evidence strongly supports conclusions related to technical benchmarking, reproducibility, and the importance of filtering and controls, particularly for m6A. In contrast, conclusions regarding isoform-specific regulation and cell type-specific biological roles of RNA modification are less well supported by the data currently presented, and would benefit from either additional analysis or more restrained interpretation.

The work is likely to have a meaningful impact as a practical reference for researchers using direct RNA sequencing, particularly by clarifying sources of false positives and the value of appropriate controls. With clearer limits placed on biological interpretation or more data presented in support of the biological interpretation, the study would serve as a valuable reference for users seeking to apply these technologies reliably.

Reviewer #1 (Public review):

Summary:

This study aims to investigate the development of infants' responses to music by examining neural activity via EEG and spontaneous body kinematics using video-based analysis. The authors also explore the role of musical pitch in eliciting neural and motor responses, comparing infants at 3, 6, and 12 months of age.

Strengths:

A key strength of the study lies in its analysis of body kinematics and modeling of stimulus-motor coupling, demonstrating how the amplitude envelope of music predicts infant movement, and how higher musical pitch may enhance auditory-motor synchronization.

EEG data provide evidence for enhanced neural responses to music compared to shuffled auditory sequences. These findings ecourage further investigation of the proposed developmental trajectory of neural responses to music and their link to musical behavior in infants.

Comments on revisions:

The authors have addressed my questions in their revision. I have no other questions. Thank you for the opportunity to read and evaluate this interesting study and also for all the work carried out in response to the comments.

Reviewer #1 (Public review):

Summary:

This preprint from Shaowei Zhao and colleagues presents results that suggest tumorous germline stem cells (GSCs) in the Drosophila ovary mimic the ovarian stem cell niche and inhibit the differentiation of neighboring non-mutant GSC-like cells. The authors use FRT-mediated clonal analysis driven by a germline-specific gene (nos-Gal4, UASp-flp) to induce GSC-like cells mutant for bam or bam's co-factor bgcn. Bam-mutant or bgcn-mutant germ cells produce tumors in the stem cell compartment (the germarium) of the ovary (Fig. 1). These tumors contain non-mutant cells - termed SGC for single-germ cells. 75% of SGCs do not exhibit signs of differentiation (as assessed by bamP-GFP) (Fig. 2). The authors demonstrate that block in differentiation in SGC is a result of suppression of bam expression (Fig. 2). They present data suggesting that in 73% of SGCs BMP signaling is low (assessed by dad-lacZ) (Fig. 3) and proliferation is less in SGCs vs GSCs. They present genetic evidence that mutations in BMP pathway receptors and transcription factors suppress some of the non-autonomous effects exhibited by SGCs within bam-mutant tumors (Fig. 4). They show data that bam-mutant cells secrete Dpp, but this data is not compelling (see below) (Fig. 5). They provide genetic data that loss of BMP ligands (dpp and gbb) suppresses the appearance of SGCs in bam-mutant tumors (Fig. 6). Taken together, their data support a model in which bam-mutant GSC-like cells produce BMPs that act on non-mutant cells (i.e., SGCs) to prevent their differentiation, similar to what in seen in the ovarian stem cell niche. This preprint from Shaowei Zhao and colleagues presents results that suggest tumorous germline stem cells (GSCs) in the Drosophila ovary mimic the ovarian stem cell niche and inhibit the differentiation of neighboring non-mutant GSC-like cells. The authors use FRT-mediated clonal analysis driven by a germline-specific gene (nos-Gal4, UASp-flp) to induce GSC-like cells mutant for bam or bam's co-factor bgcn. Bam-mutant or bgcn-mutant germ cells produce tumors in the stem cell compartment (the germarium) of the ovary (Fig. 1). These tumors contain non-mutant cells - termed SGC for single-germ cells. 75% of SGCs do not exhibit signs of differentiation (as assessed by bamP-GFP) (Fig. 2). The authors demonstrate that block in differentiation in SGC is a result of suppression of bam expression (Fig. 2). They present data suggesting that in 73% of SGCs BMP signaling is low (assessed by dad-lacZ) (Fig. 3) and proliferation is less in SGCs vs GSCs. They present genetic evidence that mutations in BMP pathway receptors and transcription factors suppress some of the non-autonomous effects exhibited by SGCs within bam-mutant tumors (Fig. 4). They show data that bam-mutant cells secrete Dpp, but this data is not compelling (see below) (Fig. 5). They provide genetic data that loss of BMP ligands (dpp and gbb) suppresses the appearance of SGCs in bam-mutant tumors (Fig. 6). Taken together, their data support a model in which bam-mutant GSC-like cells produce BMPs that act on non-mutant cells (i.e., SGCs) to prevent their differentiation, similar to what in seen in the ovarian stem cell niche.

Strengths:

(1) Use of an excellent and established model for tumorous cells in a stem cell microenvironment

(2) Powerful genetics allow them to test various factors in the tumorous vs non-tumorous cells

(3) Appropriate use of quantification and statistics

Weaknesses:

(1) What is the frequency of SGCs in nos>flp; bam-mutant tumors? For example, are they seen in every germarium, or in some germaria, etc or in a few germaria.

This concern was addressed in the rebuttal. The line number is 106, not line 103.

(2) Does the breakdown in clonality vary when they induce hs-flp clones in adults as opposed to in larvae/pupae?

This concern was addressed in the rebuttal. However, these statements are no on lines 331-335 but instead starting on line 339. Please be accurate about the line numbers cited in the rebuttal. They need to match the line numbers in the revised manuscript.

(3) Approximately 20-25% of SGCs are bam+, dad-LacZ+. Firstly, how do the authors explain this? Secondly, of the 70-75% of SGCs that have no/low BMP signaling, the authors should perform additional characterization using markers that are expressed in GSCs (i.e., Sex lethal and nanos).

The authors did not perform additional staining for GSC-enriched protein like Sex lethal and nanos.

(4) All experiments except Fig. 1I (where a single germarium with no quantification) were performed with nos-Gal4, UASp-flp. Have the authors performed any of the phenotypic characterizations (i.e., figures other than figure 1) with hs-flp?

In the rebuttal, the authors stated that they used nos>flp for all figures except for Fig. 1I. It would be more convincing for them to prove in Fig. 1 than there is not phenoytpic difference between the two methods and then switch to the nos>FLP method for the rest of the paper.

(5) Does the number of SGCs change with the age of the female? The experiments were all performed in 14-day old adult females. What happens when they look at young female (like 2-day old). I assume that the nos>flp is working in larval and pupal stages and so the phenotype should be present in young females. Why did the authors choose this later age? For example, is the phenotype more robust in older females? or do you see more SGCs at later time points?

The authors did not supply any data to prove that the clones were larger in 14-day-old flies than in younger flies. Additionally, the age of "younger" flies was not specified. Therefore, the authors did not satisfactorily answer my concern.

(6) Can the authors distinguish one copy of GFP versus 2 copies of GFP in germ cells of the ovary? This is not possible in the Drosophila testis. I ask because this could impact on the clonal analyses diagrammed in Fig. 4A and 4G and in 6A and B. Additionally, in most of the figures, the GFP is saturated so it is not possible to discern one vs two copies of GFP.

In the rebuttal, the authors stated that they cannot differential one vs two copies of GFP. They used other clone labeling methods in Fig. 4 and 6. I think that the authors should make a statement in the manuscript that they cannot distinguish one vs two copies of GFP for the record.

(7) More evidence is needed to support the claim of elevated Dpp levels in bam or bgcn mutant tumors. The current results with dpp-lacZ enhancer trap in Fig 5A,B are not convincing. First, why is the dpp-lacZ so much brighter in the mosaic analysis (A) than in the no-clone analysis (B); it is expected that the level of dpp-lacZ in cap cells should be invariant between ovaries and yet LacZ is very faint in Fig. 5B. I think that if the settings in A matched those in B, the apparent expression of dpp-lacZ in the tumor would be much lower and likely not statistically significantly. Second, they should use RNA in situ hybridization with a sensitive technique like hybridization chain reactions (HCR) - an approach that has worked well in numerous Drosophila tissues including the ovary.

The HCR FISH in Fig.5 of the revised manuscript needs an explanation for how the mRNA puncta were quantified. Currently, there is no information in the methods. What is meant but relative dpp levels. I think that the authors should report in and unbiased manner "number" of dpp or gbb puncta in TFs. For the germaria, I think that they should report the number of puncta of dpp or gbb divide by the total area in square pixels counted. Additionally, the background fluorescence is noticeably much higher in bamBG/delta86 germaria, which would (falsely) increase the relative intensity of dpp and gbb in bam mutants. Although, I commend the authors for performing HCR FISH, these data are still not convincing to me.

(8) In Fig 6, the authors report results obtained with the bamBG allele. Do they obtain similar data with another bam allele (i.e., bamdelta86)?

The authors did not try any experiments with the bamdelta86 allele, despite this allele being molecularly defined, where the bamBG allele is not defined.

Comments on second revision:

The authors have adequately addressed several points. However, there is still no information in the material and methods for how they measured and quantified the HCR-FISH probe signal. They have the same size region that they use for each genotype, but they do not control for the number of nuclei in each square. I would also be helpful if they provided a different image for the gbb probe stained in the mutant background. It is the only panel that does not have other germaria in very close proximity. I am still not fully convinced of the HCR data, esp for gbb.

Reviewer #1 (Public review):

This manuscript makes a significant contribution to the field by exploring the dichotomy between chemical synaptic and gap junctional contributions to extracellular potentials. While the study is comprehensive in its computational approach, adding experimental validation, network-level simulations, and expanded discussion on implications would elevate its impact further.

Strengths:

Novelty and Scope:

The manuscript provides a detailed investigation into the contrasting extracellular field potential (EFP) signatures arising from chemical synapses and gap junctions, an underexplored area in neuroscience.<br /> It highlights the critical role of active dendritic processes in shaping EFPs, pushing forward our understanding of how electrical and chemical synapses contribute differently to extracellular signals.

Methodological Rigor:

The use of morphologically and biophysically realistic computational models for CA1 pyramidal neurons ensures that the findings are grounded in physiological relevance.<br /> Systematic analysis of various factors, including the presence of sodium, leak, and HCN channels, offers a clear dissection of how transmembrane currents shape EFPs.

Biological Relevance:

The findings emphasize the importance of incorporating gap junctional inputs in analyses of extracellular signals, which have traditionally focused on chemical synapses.<br /> The observed polarity differences and spectral characteristics provide novel insights into how neural computations may differ based on the mode of synaptic input.

Clarity and Depth:

The manuscript is well-structured, with logical progression from synchronous input analyses to asynchronous and rhythmic inputs, ensuring comprehensive coverage of the topic.

Comments on revised version:

The authors have addressed all my concerns in the revised version of the manuscript.

Reviewer #1 (Public review):

Summary:

The authors Hall et al. establish a purification method for snake venom metalloproteinases (SVMPs). By generating a generic approach to purify this divergent class of recombinant proteins, they enhance the field's accessibility to larger quantity SVMPs with confirmed activity and, for some, characterized kinetics. In some cases, the recombinant protein displayed comparable substrate specificity and substrate recognition compared to the native enzyme, providing convincing evidence of the authors' successful recombinant expression strategy. Beyond describing their route towards protein purification, they further provide evidence for self-activation upon Zn2+ incubation. They further provide initial insights on how to design high throughput screening (HTS) methods for drug discovery and outline future perspectives for the in-depth characterization of these enzyme classes to enable the development of novel biomedical applications.

Strengths:

The study is well presented and structured in a compelling way and the universal applicability of the approach is nicely presented.<br /> The purification strategy results in highly pure protein products, well characterized by size exclusion chromatography, SDS page as well as confirmed by mass spectrometry analysis. Further, a significant portion of the manuscript focuses on enzyme activity, thereby validating function. Particularly convincing is the comparability between recombinant vs. native enzymes; this is successfully exemplified by insulin B digestion. By testing the fluorogenic substrate, the authors provide evidence that their production method of recombinant protein can open up possibilities in HTS. Since their purification method can be applied to three structurally variable SVMP classes, this demonstrates the robust nature of the approach.

Weakness

The product obtained from the purification protocol appears to be a heterogenous mixture of self-activated and intact protein species. The protocol would benefit from improved control over the self-activation process. The authors explain well why they cannot deplete Zn2+ in cell culture or increase the pH to prevent autoactivation during the current purification steps. However, this leads me to the suggestion, if the His tag could be exchanged to a different tag that is less pH sensitive and not dependent on divalent ions (Strep-Tactin XT?) to allow for removal of divalent ions and low pH during purification steps. Another suggestion would be if they could replace the endogenous protease cleavage site in their expression construct design to a TEV protease recognition site, for example, to have more control over activation of the recombinant proteins.

The graphic to explain the universal applicability of the approach, Figure S1, has some mistakes, like duplication of text, an arrow without a meaning and should be revised.

Overall, the authors successfully purified active SVMP proteins of all three structurally diverse classes in high quality and provided convincing evidence throughout the manuscript to support their claims. The described method will be of use for a broader community working with self-activating and cytotoxic proteases.

Comment on the revised version:

I find that the clarity and overall structure of the manuscript have improved. However, the weakness I previously highlighted has neither been addressed experimentally nor convincingly explained. Therefore, the assessment stayed unchanged from my side.

Reviewer #1 (Public review):

Summary:

This study identifies HSD17B7 as a cholesterol biosynthesis gene enriched in sensory hair cells, with demonstrated importance for auditory behavior and potential involvement in mechanotransduction. Using zebrafish knockdown and rescue experiments, the authors show that loss of hsd17b7 reduces cholesterol levels and impairs hearing behavior. They also report a heterozygous nonsense variant in a patient with hearing loss. The gene mutation has a complex and somewhat inconsistent phenotype, appearing to mislocalize, reduce mRNA and protein levels, and alter cholesterol distribution, supporting HSD17B7 as a potential deafness gene.

The study presents an interesting deafness candidate with a complex mechanism, and highlights an underexplored role for cholesterol (and lipids) in hair cell function.

The authors were very responsive to the initial reviews, and the manuscript is now significantly stronger.

Strengths:

- HSD17B7 is a new candidate deafness gene with plausible biological relevance.

- Cross-species RNAseq convincingly shows hair-cell enrichment.

- Lipid metabolism, particularly cholesterol homeostasis, is an emerging area of interest in auditory function.

- The connection between cholesterol levels and MET is potentially impactful and, if substantiated, would represent a significant advance.

- The localization of HSD17B7 is reasonably convincing, despite the lack of a KO control: In HEI-OC1 cells, HSD17B7 localizes to the ER, as expected. In mouse hair cells, the staining pattern is cytosolic. The developmental increase between P1 and P4, and the higher expression in OHCs aligns nicely with RNAseq data.

Weaknesses:

- The pathogenic mechanism of the E182STOP variant is unclear: The mutant protein presumably does not affect WT protein localization, arguing against a dominant-negative effect. Yet, overexpression of HSD17B7-E182* alone causes toxicity in zebrafish and it binds and mislocalizes cholesterol in HEI-OC1 cells, suggesting some gain-of-function or toxic effect. In addition, the mRNA of the variant has low expression level, suggesting nonsense-mediated decay. The mechanistic conclusions of the study are therefore not as clear cut as one would had hoped, but it might just be a reflection of real biological complexity.

- The link to human deafness is based on a single heterozygous patient with no syndromic features. Given that nearly all known cholesterol metabolism disorders are syndromic, this raises concerns about causality or specificity. HSD17B7 is therefore, at this point, a candidate deafness gene, and not a fully established "novel deafness gene". This is acknowledged by the authors.

- This study does not directly investigate how reduced cholesterol levels affect MET. However, this is not a significant limitation given the study's scope, and it is reasonable that such detailed functional analyses are left to specialists in hair cell physiology.

Reviewer #1 (Public review):

Summary:

In this manuscript, the authors describe the use of BindCraft computational protein design to create a series of binders to the chemokine CCL25. This chemokine normally mediates CCR9-dependent trafficking of immune cells to the gut, making it a potential target for the treatment of inflammatory bowel disease and related conditions. Importantly, CCL25 also binds a scavenging receptor, ACKR4. The computational protein design approach used does not involve defining particular epitopes to be targeted, allowing a free search for any potential interaction surface.

Among four designs tested, three were predicted to interact at a similar site on the chemokine, while a fourth clone, VUP25111, was predicted to bind to a different site. All four designs showed binding to CCL25, with similar high-nM KD values in all cases. The first three clones showed evidence of direct competition with the receptor for CCL25 binding, while VUP25111 showed incomplete inhibition of binding. In functional assays, all clones acted as antagonists except for VUP25111, which inhibited arrestin recruitment by CCR9, but did not affect G protein activation by CCR9 or arrestin recruitment by ACKR4 (which signals exclusively through arrestin and not G protein).

Strengths:

The work is completed to a high technical standard, and the functional diversity of the clones is intriguing. It is exciting to see pathway-selective modulation of signaling, and this basic paradigm is likely to generalize to other chemokine/receptor systems. The exceptional complexity of chemokine signaling makes this an excellent area to explore the development of modulators that can restrict signaling to a specific subset of receptors.

Weaknesses:

No major weaknesses were noted by this reviewer.

Reviewer #1 (Public review):

This manuscript makes a significant contribution to the field by exploring the dichotomy between chemical synaptic and gap junctional contributions to extracellular potentials. While the study is comprehensive in its computational approach, adding experimental validation, network-level simulations, and expanded discussion on implications would elevate its impact further.

Strengths:

Novelty and Scope:<br /> The manuscript provides a detailed investigation into the contrasting extracellular field potential (EFP) signatures arising from chemical synapses and gap junctions, an underexplored area in neuroscience.<br /> It highlights the critical role of active dendritic processes in shaping EFPs, pushing forward our understanding of how electrical and chemical synapses contribute differently to extracellular signals.

Methodological Rigor:<br /> The use of morphologically and biophysically realistic computational models for CA1 pyramidal neurons ensures that the findings are grounded in physiological relevance.<br /> Systematic analysis of various factors, including the presence of sodium, leak, and HCN channels, offers a clear dissection of how transmembrane currents shape EFPs.

Biological Relevance:<br /> The findings emphasize the importance of incorporating gap junctional inputs in analyses of extracellular signals, which have traditionally focused on chemical synapses.<br /> The observed polarity differences and spectral characteristics provide novel insights into how neural computations may differ based on the mode of synaptic input.

Clarity and Depth:<br /> The manuscript is well-structured, with a logical progression from synchronous input analyses to asynchronous and rhythmic inputs, ensuring comprehensive coverage of the topic.

Weaknesses and Areas for Improvement:

Generality and Validation:<br /> The study focuses exclusively on CA1 pyramidal neurons. Expanding the analysis to other cell types, such as interneurons or glial cells, would enhance the generalizability of the findings.<br /> Experimental validation of the computational predictions is entirely absent. Empirical data correlating the modeled EFPs with actual recordings would strengthen the claims.

Role of Active Dendritic Currents:<br /> The paper emphasizes active dendritic currents, particularly the role of HCN channels in generating outward currents under certain conditions. However, further discussion of how this mechanism integrates into broader network dynamics is warranted.

Analysis of Plasticity:<br /> While the manuscript mentions plasticity in the discussion, there are no simulations that account for activity-dependent changes in synaptic or gap junctional properties. Including such analyses could significantly enhance the relevance of the findings.

Frequency-Dependent Effects:<br /> The study demonstrates that gap junctional inputs suppress high-frequency EFP power due to membrane filtering. However, it could delve deeper into the implications of this for different brain rhythms, such as gamma or ripple oscillations.

Visualization:<br /> Figures are dense and could benefit from more intuitive labeling and focused presentations. For example, isolating key differences between chemical and gap junctional inputs in distinct panels would improve clarity.

Contextual Relevance:<br /> The manuscript touches on how these findings relate to known physiological roles of gap junctions (e.g., in gamma rhythms) but does not explore this in depth. Stronger integration of the results into known neural network dynamics would enhance its impact.

Suggestions for Improvement:

Broader Application:<br /> Simulate EFPs in multi-neuron networks to assess how the findings extend to network-level interactions, particularly in regions with mixed synaptic connectivity.

Experimental Correlation:<br /> Collaborate with experimental groups to validate the computational predictions using in vivo or in vitro recordings.

Mechanistic Insights:<br /> Provide a more detailed mechanistic explanation of how specific ionic currents (e.g., HCN, sodium, leak) interact during gap junctional vs. chemical synaptic inputs.

Implications for Neural Coding:<br /> Discuss how the observed differences in EFP signatures might influence neural coding, especially in circuits with heavy gap junctional connectivity.

Reviewer #1 (Public review):

[Editors' note: this version has been assessed by the Reviewing Editor without further input from the original reviewers.]

Summary:

This study resolves a cryo-EM structure of the GPCR, GPR30, in the presence of bicarbonate, which the author's lab recently identified as the physiological ligand. Understanding the ligand and the mechanism of activation is of fundamental importance to the field of receptor signaling. This solid study provides important insight into the overall structure and suggests a possible bicarbonate binding site.

Strengths:

The overall structure, and proposed mechanism of G-protein coupling are solid. Based on the structure, the authors identify a binding pocket that might accommodate bicarbonate. Although assignment of the binding pocket is speculative, extensive mutagenesis of residues in this pocket identifies several that are important to G-protein signaling. The structure shows some conformational differences with a previous structure of this protein determined in the absence of bicarbonate (PMC11217264). To my knowledge, bicarbonate is the only physiological ligand that has been identified for GPR30, making this study an important contribution to the field. However, the current study provides novel and important circumstantial evidence for the bicarbonate binding site based on mutagenesis and functional assays.

Weaknesses:

Bicarbonate is a challenging ligand for structural and biochemical studies, and because of experimental limitations, this study does not elucidate the exact binding site. Higher resolution structures would be required for structural identification of bicarbonate. The functional assay monitors activation of GPR30, and thus reports on not only bicarbonate binding, but also the integrity of the allosteric network that transduces the binding signal across the membrane. However, biochemical binding assays are challenging because the binding constant is weak, in the mM range.

The authors appropriately acknowledge the limitations of these experimental approaches, and they build a solid circumstantial case for the bicarbonate binding pocket based on extensive mutagenesis and functional analysis. However, the study does fall short of establishing the bicarbonate binding site.

Reviewer #1 (Public review):

Summary:

This study identifies NK2R as an intestinal GPCR that tunes enterocyte lipid uptake, lipid droplet storage, and chylomicron output, with loss or antagonism enhancing post‑prandial triglyceridemia and epithelial lipid stores, and agonism reducing adiposity and improving glycemia in DIO mice. Through bulk RNA‑seq, deconvolution, DSS colitis, and 16S profiling, the authors link Tacr2 deletion to coordinated induction of epithelial lipid‑metabolic programs, dampened immune gene expression, sex‑specific remodeling of secretory lineages, and male‑biased protection from experimental colitis despite dysbiotic microbiota. This is an overall important and thorough paper on an emerging obesity drug target, but it should temper some interpretations, and the following points would be needed to strengthen the claims in the manuscript.

Strengths:


The study uses an impressive combination of genetic loss‑of‑function, pharmacological agonism/antagonism, transcriptomics, and in vivo physiology to establish NK2R as a bidirectional regulator of epithelial lipid handling. The integration of RNA‑seq, epithelial cell‑type deconvolution, DSS colitis, and microbiome profiling provides a rich, systems‑level view of how Tacr2 deletion reshapes epithelial metabolism, lineage allocation, and inflammatory responsiveness in a sex‑specific manner. The gain- and loss‑of‑function data particularly support a model in which NK2R acts as an epithelial metabolic rheostat that restrains lipid absorption and chylomicron export, with downstream consequences for barrier fitness and immune tone.

Weaknesses:

Major points

While the data convincingly establish NK2R's role in epithelial lipid handling, the manuscript arguably overstates a primary "pro‑inflammatory" function for NK2R, given that Tacr2‑/‑ mice show enhanced enterocyte lipid uptake and storage, higher post‑prandial triglycerides, and a dysbiotic microbiota yet reduced mucosal immune gene expression and, in males, protection from DSS colitis. It remains equally plausible that the apparent "protection" reflects a mucosa that is less reactive to unfavorable microbiota rather than genuinely protected, and that NK2R's main function is metabolic, with immune changes emerging secondarily. Such a model would actually help reconcile the long-standing question as to why NK2R antagonism has not translated into clear benefit in clinical trials for GI inflammation over the past several decades.

Without temporal resolution, it is equally plausible that antagonists primarily perturb epithelial lipid homeostasis rather than directly and beneficially modulating immune tone. To discriminate between these possibilities and strengthen the potential direct inflammatory claims, the authors should:

(1) generate epithelial‑specific, immune‑cell-specific, and nociceptor‑specific Tacr2 deletions in the DSS model

(2) test gut‑restricted NK2R agonism versus antagonism under controlled dietary fat conditions for effects on LD load, barrier integrity, and colitis severity

(3) perform ex vivo tachykinin/NK2R stimulation of isolated epithelial versus immune compartments with functional readouts

(4) assess whether microbiota transfer from Tacr2‑/‑ versus WT donors into germ‑free or antibiotic‑treated recipients can recapitulate protection or susceptibility independently of epithelial NK2R status.

Minor points

Additional clarifications on Tac1 and tachykinin receptor expression in male/female colitis models, and validation of the NK2R antibody in KO tissue (or in situ hybridization), would also be needed to strengthen key mechanistic and localization claims.

Reviewer #1 (Public review):

Summary:

The authors have attempted to establish a role for XAP5, a transcriptional regulator they have previously identified for flagellar biogenesis in Chlamydomonas and mice, in primary cilia differentiation.

Strengths:

Genetic and biochemical analysis using a cultured mouse cell line, NIH3T3.

Weaknesses:

(1) The authors have ignored established data that, like in C. elegans and Drosophila, there is in vivo genetic evidence that primary cilia formation is regulated by the RFX transcriptional module (for example, PMID 19887680, PMID 29510665).

(2) The analysis with one mammalian cell line, NIH3T3, while done quite rigorously, is not sufficient. Also, the effect on cilia differentiation is very modest - a shortening of cilia length on XAP5, NONO and SOX5 knockout - which can happen for a variety of reasons, especially in culture conditions. In my view, this relatively mild phenotype does not establish that the XAP5/NONO and SOX5 axis is an important regulator of primary cilia differentiation.

(3) The lack of any data that validates the findings in the model vertebrate is a major weakness of this paper. Validation using clean genetics (whole body knockouts or tissue-specific conditional knockouts) is absolutely essential for these data to be acceptable.

Reviewer #1 (Public review):

Summary:

Heller et al use a murine model of AIRE deficiency, a disease that leads to systemic autoimmune disease, to demonstrate differential effects of selective JAK inhibitors. This group and others have previously demonstrated the efficacy of the JAK1/2 inhibitor ruxolitinib in patients with AIRE deficiency. Here, they focus on the ability of ruxolitinib versus drugs inhibiting either JAK1, JAK2, or JAK3 to alter organ pathology and accumulation of interferon-gamma producing immune cells in the lungs, which are important mediators of inflammation in patients with this disease. The current study provides evidence that selective JAK2 or JAK1 both reduce disease in this mouse model. There is potentially a more beneficial effect of selective JAK2 inhibition, although these differences are minor, and it is uncertain whether this is clinically relevant for patients. They demonstrate that inhibition of JAK3 alone in the mouse was clearly not beneficial for disease. Overall, this study provides evidence for consideration of more selective JAK inhibition in patients with AIRE deficiency.

Strengths:

(1) Robust model for investigating AIRE deficiency.

(2) They combine cellular studies (immune cell production of IFN-g) and robust organ pathology scoring to evaluate the effects of the drugs tested here.

(3) Data clearly demonstrates that JAK3 inhibition, at least as used here, may increase IFN-g production and does not reduce organ pathology.

Weaknesses:

(1) There is no direct comparison of the effects of JAK2 vs. JAK1 inhibition to support that JAK2 inhibition is clearly superior.

(2) They were not able to perform pharmacokinetic studies or measure the efficacy of JAK inhibition in their model, and it is uncertain how the doses of drug used here will translate to the treatment of patients.

(3) It is uncertain whether this study, performed in a murine model, will correspond to tissue/cell specificity of JAK inhibition in patients.

Reviewer #1 (Public review):

Summary:

This study examines the role of the long non-coding RNA Dreg1 in regulating Gata3 expression and ILC2 development. Using Dreg1 deficient mice, the authors show a selective loss of ILC2s but not T or NK cells, suggesting a lineage-specific requirement for Dreg1. By integrating public chromatin and TF-binding datasets, they propose a Tcf1-Dreg1-Gata3 regulatory axis. The topic is relevant for understanding epigenetic regulation of ILC differentiation.

Strengths:

(1) Clear in vivo evidence for a lineage-specific role of Dreg1.

(2) Comprehensive integration of genomic datasets.

(3) Cross-species comparison linking mouse and human regulatory regions.

Weaknesses:

(1) Mechanistic conclusions remain correlative, relying on public data.

(2) Lack of direct chromatin or transcriptional validation of Tcf1-mediated regulation.

(3) Human enhancer function is not experimentally confirmed.

(4) Insufficient methodological detail and limited mechanistic discussion.

Comments on revisions:

The authors have provided clear evidence that Dreg1 is necessary for ILC2 development, but their refusal to perform any mechanistic experiment remains a significant weakness. While their appeal to the 3Rs and the use of public datasets is noted, re-analyzing external data from heterogeneous sources cannot substitute for direct, internal validation of the Tcf1-Dreg1-Gata3 axis in their specific knockout model. This is particularly problematic because ILC2 progenitors, though rare, can be isolated from bone marrow, especially since assays like CUT&Tag and others are specifically designed for low cell numbers. By relying on public T-cell CRISPR screens to justify human ILC2 functions, the authors are substituting cross-cell-type correlation for definitive functional proof. Consequently, the manuscript currently describes a discovery of necessity without providing a verified molecular mechanism, which should be more explicitly reflected in the title and conclusions.

Reviewer #1 (Public review):

In this manuscript, the authors combine single-nucleus RNA sequencing with spatial transcriptomics to generate a spatiotemporal atlas of mouse placental development and explore the role of glycogen trophoblast cells in fetal viability. The study integrates several computational approaches, including trajectory analysis, regulatory network inference, and spatial mapping, together with histology and glycogen measurements. Based on these analyses, the authors propose that glycogen trophoblast cells provide metabolic support that is important for maintaining placental function and fetal survival.

One of the main strengths of the study is the quality and scope of the dataset. The integration of snRNA-seq with Stereo-seq spatial transcriptomics provides a detailed view of placental organization across regions and developmental stages. This type of combined spatial and transcriptional analysis is still relatively rare in placental biology and represents an important contribution to the field. The atlas itself will likely be a valuable resource for future studies.

Another strength is the effort to connect transcriptional findings with tissue-level validation. The glycogen staining and biochemical measurements support the interpretation that glycogen trophoblast cells contribute to placental metabolic function. The spatial analyses identifying macrophage accumulation in the labyrinth region of mutant placentas are also interesting and illustrate how spatial approaches can reveal microenvironmental changes that are difficult to detect otherwise.

The main limitation of the study is that the conclusion that glycogen cells are essential mediators of metabolic support for fetal viability remains partly indirect. The transcriptomic and spatial data strongly suggest a role for these cells, but it is still difficult to determine whether glycogen cell dysfunction is the primary cause of fetal lethality or a consequence of broader placental abnormalities. Clarifying this point would strengthen the central message of the paper.

Similarly, the macrophage accumulation observed in the labyrinth appears consistent with a response to tissue stress or injury, but its relationship to glycogen cell function is not fully explained. A clearer discussion of whether this represents a primary mechanism or a secondary effect would improve the interpretation.

Overall, this is a strong dataset and a useful spatial atlas of placental development. The study provides convincing descriptive insight into glycogen trophoblast biology, and with some clarification of the mechanistic conclusions, the manuscript will be even stronger.

Reviewer #1 (Public review):

Summary:

The authors present a new autofocusing method, LUNA (Locking Under Nanoscale Accuracy), designed to overcome severe focus drift, a major challenge in long-term time-lapse microscopy. Using this method, they address a fundamental question in bacterial cold shock response: whether cells halt growth and division following an abrupt temperature downshift. Through single-cell analysis, the authors uncover a multi-phase adaptation process with distinct growth deceleration dynamics, and show that bacterial cells adapt to cold shock in a largely uniform manner across the population. Overall, this work provides new insights into the bacterial cold shock response at the single-cell level, extending beyond what can be inferred from population-level measurements.

Strengths:

(1) The LUNA method shows improved performance compared to existing autofocusing systems, achieving nanoscale precision over a large focusing range. Its focusing speed is sufficient for the experiments presented, with potential for further improvement through faster motors and optimized control algorithms, suggesting broad applicability. Theoretical simulations and experimental validation together provide strong support for the method's robustness.

(2) Using LUNA, the authors address a long-standing question in bacterial physiology: whether cells arrest growth and division during the acclimation phase following cold shock. Single-cell analyses across the full course of cold adaptation reveal features that are obscured in bulk-culture studies. Cells continue to grow and divide at reduced rates while maintaining cell size regulation, and exhibit a three-phase adaptation program with distinct growth dynamics. This response appears uniform across the population, with no evidence for bet-hedging. Overall, the experiments are well designed, and the analyses are solid and support the authors' conclusions.

(3) The authors further propose a model describing how population-level optical density (OD) depends on cell dry mass density, volume, and concentration. Following cold shock, cells grow more slowly and exhibit smaller sizes, explaining the apparently unchanged OD. This model provides a valuable conceptual framework for interpreting OD-based growth measurements, a widely used method in microbiology, and will be of broad interest to the field.

Weaknesses:

No major weaknesses identified.

Comments on revisions:

The authors have thoroughly addressed all of my questions. I thank them for their clear clarifications and thoughtful revisions, and I greatly appreciate their efforts in improving the manuscript.

Reviewer #1 (Public review):

Summary:

The manuscript, titled Hippocampal Single-Cell RNA Atlas of Chronic Methamphetamine Abuse-Induced Cognitive Decline in Mice, focuses on single-cell RNA sequencing (scRNA-seq) analysis following chronic methamphetamine (METH) treatment in mice. The authors propose two hypotheses: (1) METH induces neuroinflammation involving T and NKT cells, and (2) METH alters neuronal stem cell differentiation.

Strengths:

The authors provide a substantial dataset with numerous replicates, offering valuable resources to the research community.

Weaknesses:

Concerns remain regarding the interpretation of the data and the appropriateness of the statistical analyses.

Although the authors provided detailed responses to the reviewer's concerns, I am still concerned that several key issues have not yet been fully addressed in the revised manuscript.

First, in Figure 5, the authors state that neural stem cells (NSCs) preferentially differentiate into astrocytes rather than neuroblasts following METH treatment. However, based on the presented trajectories, it is difficult to visually confirm differences in the relative proportions of astrocyte versus neuroblast differentiation between the control and METH-treated conditions. The current figures do not provide a quantitative or clearly interpretable comparison of lineage allocation that would support this conclusion.

Moreover, in Figures 5C and 5F, the inferred pseudotime trajectories differ both the starting cell populations and the intermediate and terminal cell identities. As a result, the trajectories are not directly comparable between the control and METH conditions. Under these circumstances, it is inappropriate to interpret gene expression changes as occurring along equivalent differentiation paths, and the current analysis does not convincingly support the stated conclusions regarding altered NSC differentiation.

If the authors intend to claim differential gene expression associated with altered differentiation trajectories, the analysis should at minimum present the expression of the same set of genes (e.g., Bsg, Ccl4, Fos, Sox11, Flt1, Hspb1, Igfbp7, and Tmsb10) plotted along a matched trajectory (for example, NSC-to-astrocyte or NSC-to-neuroblast lineages) in both control and METH-treated samples, so that readers can directly compare expression dynamics across conditions.

In addition, several statements throughout the manuscript describing changes in cell-type proportions are not supported by corresponding statistical analyses. For example, in Figure 2C (around line 430), the authors report changes in cell proportions of ~0.1% or 2-3%. Without appropriate statistical testing, it is unclear whether such marginal differences are biologically meaningful or reproducible. The authors should either provide statistical testing (e.g., sample-level proportion analysis with p-values or confidence intervals) or revise the text to describe these findings as descriptive rather than significant changes.

Finally, the reported decrease in astrocyte proportion following METH exposure (from 6.6% to 5.5%), together with the lack of reported changes in neuroblast proportions, appears inconsistent with the trajectory-based conclusion that NSCs preferentially differentiate into astrocytes in METH-treated mice. This apparent discrepancy should be clarified or the conclusions appropriately tempered.

Reviewer #1 (Public review):

Summary:

This study combined high-field fMRI with computational modelling (including a Bayesian population receptive field [pRF] model and functional gradient analysis) in humans to demonstrate that the architecture of the corpus callosum (CC) and its interhemispheric connections is organized into parallel ipsilateral and contralateral streams, rather than functioning as a mixed integration of inputs from both hemispheres. The human findings were validated through preclinical experiments in mice using viral axonal tracing, which revealed a non-overlapping laminar arrangement of axons carrying left and right visual field information.

These results suggest that the CC operates as a set of parallel, segregated pathways, with each stream independently conveying information from one side of the visual field. This organization preserves the spatial origin of visual signals within the white matter. Although the overall concept of interhemispheric parallel pathways is not entirely unexpected, this refined understanding of callosal organization provides important scientific and clinical insights in relation to pathway-specific perturbations and in neurological disorders.

Strengths:

The manuscript is well written, the methodology is sound, and the analyses are carefully conducted. I particularly appreciate the effort to integrate functional and structural approaches and to validate the human neuroimaging findings with more sensitive preclinical techniques, such as viral tracing.

Weaknesses:

Several points require clarification to allow a more complete interpretation of the results. In addition, some further analyses are necessary to fully substantiate the claims made in the manuscript. These are detailed below

Comment 1:

BOLD signals in white matter remain a matter of debate, although this is not the central focus of the present study. Nevertheless, it is important to establish whether the underlying data have sufficient tSNR to support robust pRF estimation in white matter. In Figure 1, the EV appears relatively robust; however, it seems that only the best-fitting examples are shown. In contrast, the group-average EV reported in Figure 2, and the individual maps in the Supplementary Information indicate very low EV values, typically below 5%. In conventional fMRI analyses, thresholds of approximately 15-20% EV are often applied to exclude poor fits that may bias pRF parameter estimates. It appears that no such threshold was applied here. Interestingly, in Figure S6, the average EV for dual pRF models appears to be approximately 17%. Do dual and triple pRF models systematically produce higher EV compared to single pRF models? Additionally, Figure 2 suggests the presence of baseline activation that is captured by the model. Could this be related to a delayed or altered hemodynamic response function (HRF) in white matter? Clarification would be helpful. To better assess the robustness of the reported findings, the authors should provide quantitative measures of tSNR within the white matter tracts where the pRF model was fitted. Furthermore, a plot showing the average BOLD signal during visual stimulation versus baseline in those tracts would greatly strengthen confidence in the signal quality.

Although the reported linear relationship between pRF size and eccentricity, as well as the test-retest reliability analyses, suggest the presence of consistent receptive field estimates, these analyses are based on distributions and may lack the sensitivity required to differentiate single, dual, and triple pRF models. Moreover, the pRF estimates within the FMA appear noisy, particularly at the individual level (Figure S4), making it difficult to clearly dissociate information originating from the left and right hemifields.

Comment 2.1:

The Bayesian modelling approach is interesting and robust. However, as I understand it, the authors must specify a priori the number of pRFs to be estimated. This introduces a strong assumption about the expected underlying receptive field structure. An alternative Bayesian approach, such as micro-probing (Carvalho et al., 2020), does not require prior assumptions regarding the number or shape of pRFs. Instead, it estimates receptive field profiles in a more data-driven manner and provides a direct visualization of the pRF structure. Implementing such an approach, or at least comparing it with the current modelling strategy, could yield more reliable and potentially less biased estimates of multiple pRFs, particularly in white matter where signal quality is limited.

Comment 2.2:

Some clarifications regarding the pRF model are needed: in the Methods section, the authors mention the use of a Difference-of-Gaussians (DoG) model. However, it appears from the Results that the analyses were performed using a single-Gaussian model. Additionally, in Section 5.6, the authors state that six different pRF models were tested. Which specific models were included in this comparison? A clear description of each model, along with justification for the final model selection criteria, would help better understand the study

Comment 3:

Throughout the manuscript, the authors repeatedly refer to laminar-specific findings. However, the reported functional resolution of 1.6 mm isotropic is insufficient to reliably resolve cortical layers. Given this limitation, the laminar interpretations appear overstated. For example, in the Discussion section titled "Integrating White Matter with Laminar-Resolved Function", the authors state: "The combination of anatomically segregated white matter pathways with functionally specific cortical laminae presents a powerful synergy for human brain circuit research." Given the spatial resolution of the functional data, how are laminar-specific functional claims justified?

Similarly, the authors suggest that: "It becomes possible to assess not just if the CC is damaged, but precisely which directional pathways are compromised-either the pathways projecting from the lesioned hemisphere, or those projecting to the other, or both." It is unclear to me how the current methodology uniquely enables this level of directional specificity, and whether this was not already feasible using existing structural and diffusion-based approaches. The authors should clarify what is genuinely novel in this study.

Comment 4:

In the Discussion, the authors state: "These findings fundamentally reframe our understanding of interhemispheric communication, moving beyond static connectivity to reveal a dynamic, directionally specific highway where spatial location encodes the origin of information. This framework provides a novel blueprint for decoding directional information flow in the living human brain." Based on the analyses presented, it is unclear how the findings of this study demonstrate dynamic connectivity or true directional specificity. The reported results appear to characterize spatial organization and segregation of callosal pathways, but they do not measure the directionality of information flow, temporal dynamics, or causal directionality between hemispheres. To substantiate claims regarding dynamic or directional communication, additional analyses, such as connective field model (Haak et al.2013), effective connectivity modelling, time-resolved approaches, or perturbation-based methods (neuromodulation) would be required. As currently presented, the findings seem to support structural and functional segregation rather than dynamic or directionally resolved interhemispheric information transfer. The authors should either provide stronger evidence for these claims or moderate them.

Comment 5:

I agree with the authors that pooling of information across hemispheres represents a plausible explanation for the presence of dual pRFs. As discussed in the manuscript, such an effect would be expected to predominantly affect pRFs located near the vertical meridian. However, Figures S6C and S6D do not appear to demonstrate that bilateral pRFs are preferentially located along the vertical meridian.

Reviewer #1 (Public review):

Summary:

The manuscript entitled "Autonomic reflex plasticity associates with time-dependent SUDEP susceptibility in a murine model with hyperactive stress circuits" by Dr. Saunders and colleagues combined a traditional mouse model of SUDEP, ventral intrahippocampal kainite (vIHKA) injection, with a genetic model of chronic hyperactivity of central corticotropin-releasing hormone (CRH) neurons (Kcc2/Crh) that further increases the risk of SUDEP in the weeks following seizure.

Strengths:

Their results show during spontaneous seizures Kcc2/Crh mice had more pronounced reflex-like ictal bradycardias compared to WT controls that notably occurred prior (~10 sec) to seizure termination and had greater autonomic disturbances compared to WT controls, including a pronounced serotonin-mediated Bezold Jarisch reflex. These results show chronic hyperactivity of central corticotropin-releasing hormone (CRH) neurons (Kcc2/Crh) increased autonomic disturbances and risk of SUDEP in a kainic acid model of epilepsy.

Weaknesses:

This study could be improved with a more thorough assessment of heart rate, blood pressure and breathing during and following the seizures, and in particular the fatal event. It is unclear if the bradycardias were spontaneous or a result of preceding central or obstructive apneas, oxygen desaturations, hypercapnia, arrhythmias, or other possible triggers.

Considerable prior work in the literature suggests SUDEP could be mediated, in some patients, by a burst of parasympathetic activity to the heart. Were the heart rate changes in these animals during seizures inhibited or blocked by atropine or atenolol?<br /> The injection of the 5HT agonist phenylbiguanide into the right jugular is not a selective approach for activating the Bezold Jarisch Reflex (BJR), which is caused by increased activity of intracardiac sensory neurons (generally activated with ischemia or a combination of low preload with high contractility). The results should be interpreted more cautiously, as a response to systemic administration of phenylbiguanide only.

Reviewer #1 (Public review):

In this study, Szinte et al. measured the spatial selectivity of fMRI BOLD responses while subjects viewed dynamic noise stimuli vignetted by a moving bar aperture. Subjects viewed these moving bar stimuli as they fixated at one of three screen locations. This design enabled the authors to test whether fMRI responses are better explained by a model in which stimulus location is encoded relative to the retina or relative to the screen (in other words, 'retintopic' vs. 'spatiotopic' encoding). In retinotopic encoding, the pRFs should move with the eyes. In spatiotopic encoding, the pRFs should be locked to particular screen locations, regardless of eye position. The results are unambiguous: the retinotopic model wins.

A number of prior human fMRI studies have addressed this issue, and there is an overwhelming consensus in the field that spatial encoding throughout human visual cortex (and high-level cortex) is retinotopic (during fixation). All of the results shown in the present manuscript are consistent with these earlier observations. Szinte et al. also find that the degree of retinotopic selectivity is not affected by the task or locus of spatial attention. This too has been observed in multiple prior studies.

So, while this manuscript is primarily confirmatory, the study does nonetheless provide valuable measurements at 7T with a higher signal-to-noise ratio and high spatial resolution than previous studies. The authors also apply an innovative Bayesian decoding analysis (which is beautifully documented on their webpage, with a step-by-step tutorial and ample examples). So, a major strength of this paper is the methods; this study does set a high standard and is an ideal example for a rigorous, replicable analysis pipeline and cutting-edge statistical inference.

The results focus on the spatial profile of pRFs with different eye positions. However, the main idea behind eye-position gain fields is that the amplitude of the visual responses changes with eye position. I could not find any analysis testing response amplitude as a function of eye position. In the Discussion, the authors assert: "We did not find an influence of gaze position at the level of individual voxels nor at the level of visual areas." The authors speculate that this might be because gain fields have a salt-and-pepper organization in the cortex that cancel out when pooled across a voxel. While the salt-and-pepper explanation seems like perfectly fine speculation, here they are discussing a result that isn't shown in the Results!

Several prior human fMRI studies have reported eye position gain fields in humans, suggesting that the salt-and-pepper explanation is not correct. Rather, it is likely the case that the authors did not test a sufficiently wide range of eye positions to detect a gain modulation. For example, a study from Merriam et al. (J. Neurosci, 2013), which is mysteriously not cited here, measured both the spatial selectivity of visual receptive fields AND the response amplitude at 8 different eye positions that were spaced by as much as 24 degrees of visual angle (including both vertical and horizontal changes in eye position). Under these conditions, Merriam et al. did find reliable modulation in response amplitude with changes in eye position, even though the spatial selectivity of the responses did not change. Importantly, Merriam et al. found that visual response selectivity was consistent with a retinotopic reference frame (not a spatiotopic reference frame) and that this selectivity was invariant to the attention task. Consideration of these issues suggests that the experimental design used in the current experiment may have precluded the detection of eye position gain fields. The current manuscript would be much improved by a careful consideration of this prior literature, which is so closely related to what the authors report here.

Reviewer #1 (Public review):

Summary:

This manuscript investigates whether newborns can use speaker identity to separate verbal memories, aiming to shed light on the earliest mechanisms of language learning and memory formation. The authors employ a well-designed experimental paradigm using functional near-infrared spectroscopy (fNIRS) to measure neural responses in newborns exposed to familiar and novel words, with careful counterbalancing and acoustic controls. Their main finding is that newborns show differential neural activation to novel versus familiar words, particularly when speaker identity changes, suggesting that even at birth, infants can use indexical cues to support memory.

Strengths:

Major strengths of the work include its innovative approach to a longstanding question in developmental science, the use of appropriate and state-of-the-art neuroimaging methods for this age group, and a thoughtful experimental design that attempts to control for order and acoustic confounds. The study addresses a significant gap in our understanding of how infants process and remember speech, and the data are presented transparently, with clear reporting of both significant and non-significant results.

A previous concern was that the recognition effect appeared restricted to a subgroup of participants. The authors clarify that the bilateral STG and left IFG effects were present in both groups - it was only the right IFG modulation that was group-dependent. This is an important distinction and is now clearer in the revised manuscript. The timing of the effect emerging in a specific testing window also appears less arbitrary given the authors' explanation that prior work guided the analytical approach, and that task difficulty was expected to determine whether recognition would appear in earlier or later test blocks.

The sample size question is handled honestly. A power analysis based on a related ANOVA study produced an implausibly small estimate of N=5-7, which the authors rightly set aside. Aligning with fNIRS neonate studies - where mean sample sizes around N=24 are standard - is defensible, and the within-subject design with mixed-model analysis does improve sensitivity relative to simpler approaches. This is now explained in the manuscript.

The episodic memory framing has been scaled back appropriately. The revised discussion is clear that the study demonstrates what-who binding - an early component of episodic-like processing - rather than mature episodic memory in the Tulvingian sense. This is a more honest characterization of what the paradigm can show, and it opens a reasonable developmental question about how the remaining components (where, when) come online over the first months and years of life.

Weaknesses

The weaknesses are largely interpretive rather than fatal to the core findings. The absence of a same-speaker interference control within the current paradigm means the causal role of speaker change cannot be established entirely from internal evidence alone - the inference relies partly on comparison with Benavides-Varela et al. (2011), which used a somewhat different design. This is a reasonable approach given the ethical and practical constraints of testing newborns, and the authors are transparent about it, but readers should keep in mind that the conclusion about speaker change as the critical variable is supported by converging evidence across studies rather than a direct within-study manipulation.

Overall, the study contributes new and meaningful data on an underexplored aspect of early speech processing: the role of the speaker as a contextual dimension in word memory. The findings, taken together with the prior literature, tell a coherent story and have real implications for theories of early language acquisition and the developmental origins of episodic-like memory. The paradigm is sound and the results are worth pursuing in larger and more controlled follow-up studies.

Reviewer #1 (Public review):

Summary

The manuscript by K.H. Lee et al. presents Spyglass, a new open-source framework for building reproducible pipelines in systems neuroscience. The framework integrates the NWB (Neurodata Without Borders) data standard with the DataJoint relational database system to organize and manage analysis workflows. It enables the construction of complete pipelines, from raw data acquisition to final figures. The authors demonstrate their capabilities through examples, including spike sorting, LFP filtering, and sharp-wave ripple (SWR) detection. Additionally, the framework supports interactive visualizations via integration with Figurl, a platform for sharing neuroscience figures online.

Strengths:

Reproducibility in data analysis remains a significant challenge within the neuroscience community, posing a barrier to scientific progress. While many journals now require authors to share their data and code upon publication, this alone does not ensure that the code will execute properly or reproduce the original results. Recognizing this gap, the authors aim to address the community's need for a robust tool to build reproducible pipelines in systems neuroscience.

Comments on revisions:

In this revised version, the authors have addressed the majority of the concerns raised in the initial review. The manuscript is clearer, the documentation and explanations have been strengthened, and several important practical issues-particularly regarding usability, terminology, and deployment-have been meaningfully improved. While the framework continues to position itself both as a flexible analysis environment and as a mechanism for freezing and preserving reproducible pipelines, the authors have clarified their rationale for maintaining this dual role. I have no additional comments at this stage.

Reviewer #1 (Public review):

Summary:

The authors wanted to determine whether the set-19 gene, one of 38 SET-domain containing genes in C elegans, has a clear function in vivo with respect to lysine methylation. The question is not only whether it can modify this histone tail residue, but also what the impact of a loss of this locus is on the inheritance of repressive chromatin states.

Strengths:

The authors clearly achieved their goal, and it is convincingly shown that SET_19 is indeed a somatic cell histone methyltransferase with a striking specificity for H3K23. There is both recombinant protein work, quantitative mapping in vivo, of histone marks and transcriptional changes, and the authors rule out some other hypotheses that have been in the literature. Overall, this provides a compelling argument that SET-19 is indeed the major somatic cell HMT for this residue. Interestingly, the phenotypes are rather minimal, consistent with redundancy in the physiological roles of histone methylation, and redundancy as well in HMT function. For the most part, the data are not over-interpreted. The genetic alleles used, assuming they are confirmed, were revealing and well-documented.

Weaknesses:

The major weaknesses are easily fixed. The major weaknesses mainly reflect a slight overstatement of certain data (claiming insignificance, when it is not clear how that was determined) and claiming a bit too much about SET-32, which was independently claimed to be an H3K23 HMT. Clearly, the two SET domain enzymes are not redundant, nor is the claim that SET-32 has no role in H3K23 methylation completely convincing. Especially in germline or embryonic conditions. Finally, the imaging is not of very high quality, nor are the images fully quantitated. These points can be easily remedied.

Reviewer #2 (Public review):

Summary:

This study aims to examine the effects of the subcellular localization of the mammalian clock protein PER2 and its dedicated binding partners CRY1 and the kinase CK1. Using a combination of transient transfection and a Dox-inducible expression system, they show that CRY1 promotes nuclear retention of PER2, and that phosphorylation of PER2 by CK1 promotes cytoplasmic localization and release of CRY1. Changes in complex assembly and subcellular localization could impact the transcriptional repressive function of the CK1-PER2-CRY1 complex in the molecular clock.

Strengths:

The study establishes a system of transient transfection and Dox-inducible expression that allows for strict temporal control of the presence of fluorescently-tagged clock proteins. This is essential to conduct time-lapse microscopy studies that determine changes in the apparent subcellular localization and stability of associated clock proteins. With the potential caveats of overexpression set aside, the authors make use of good controls and supplement cell-based work with in vitro experiments where possible. The discovery that phosphorylation of PER2 by CK1 in the nucleus leads to cytoplasmic localization of PER2 and PER2-CRY1 complexes is a new finding. Moreover, the apparent dissociation of CRY1 from PER2 after CK1 phosphorylation provides a potentially new mechanism by which the repressive activity of this complex could be regulated.

Weaknesses:

Overexpression of circadian clock components, normally expressed at low levels, could disrupt the stoichiometry of native interactions, Although the authors provide a reasonable rationale for the Dox-inducible approach and use appropriate controls throughout the experiments, there is still concern that overexpression of the components of this transcriptional repressive complex far exceed the concentration of the transcription factor they regulate, and this has not been taken into consideration here. In addition, the interesting discovery that CK1 phosphorylation of PER2 leads to dissociation of CRY1 has not identified the phosphorylation site(s) responsible for this, so the mechanism by which this occurs is still unknown. Still, this study provides some interesting hypotheses regarding CK1 regulation of PER2 and CRY1 that could drive future work in the field.

Comments on latest version:

This manuscript has already undergone two rounds of review at a reputable journal, and we have been provided with the previous reviewers' comments and the authors' responses. I am satisfied with the responses and changes to the manuscript made in these previous rounds of review and don't have any further experiments to suggest that wouldn't represent significant additional work.

Reviewer #2 (Public review):

In this study, the authors investigate how increasing cognitive demand shapes activity patterns in the dorsal dentate gyrus (DG). Using a touchscreen-based TUNL task combined with TRAP/c-Fos tagging, birth-dating of adult-born granule cells (abDGCs), and chemogenetic inhibition, they show that higher task demand increases mature granule cell (mGC) recruitment and enhances suprapyramidal (SB) versus infrapyramidal (IB) blade bias. Functionally, mGC inhibition reduces overall activity and impairs performance without disrupting blade bias, whereas inhibition of {less than or equal to}7-week-old abDGCs increases mGC activity, abolishes blade bias, and impairs discrimination under high-demand conditions. These findings suggest that effective pattern separation depends not only on overall DG activity levels but also on the spatial organization of recruited ensembles.

The integration of touchscreen TUNL with temporally controlled activity tagging and birth-dated cohorts is technically strong. Quantification of SB-IB bias and radial/apical distributions adds anatomical precision beyond bulk activity measures. The comparison between mGC and abDGC inhibition is conceptually compelling and supports dissociable functional roles. Overall, the data convincingly demonstrate that increasing cognitive demand amplifies blade-biased DG recruitment and that mGCs and abDGCs differentially contribute to both behavioral performance and network organization.

However, how abDGCs are integrated into the mGC network under high cognitive demand remains unresolved. Additional experiments are needed to clarify how abDGCs shape spatial recruitment patterns and whether they directly inhibit or indirectly regulate mGC activity to maintain high performance.

Furthermore, the authors frame "high cognitive demand" as a multidimensional construct encompassing broad behavioral challenge. It would strengthen the work to delineate how local abDGC-mGC circuit interactions regulate specific task components in real time. This will require higher temporal resolution approaches, as TRAP and c-Fos labeling integrate activity over prolonged windows and primarily reflect sustained engagement rather than moment-to-moment computations.<br /> The central conclusion that dentate function depends on coordinated spatial recruitment rather than total activity magnitude is supported by the data, although mechanistic interpretations are tempered given methodological limitations.<br /> Overall, this work advances models of adult neurogenesis by emphasizing a critical-period modulatory role of abDGCs in organizing DG network activity during high-demand discrimination. The combined behavioral and circuit-level framework is likely to be influential in the field.

Comments on revisions:

None remaining.

Reviewer #1 (Public review):

The manuscript presents a compelling new in vitro system based on isogenic co-cultures of human iPSC-derived hepatocytes and macrophages, enabling the modelling of hepatic immune responses with unprecedented physiological relevance. The authors show that co-culture leads to enhanced maturation of hepatocytes and tissue-resident macrophage identity, which cannot be achieved through conditioned media alone. Using this system, they functionally validate immune-driven hepatotoxic responses to a panel of drugs and compare the system's predictive power to that of monocyte-derived macrophages. The results underscore the necessity of macrophage-hepatocyte crosstalk for accurate modelling of liver inflammation and drug toxicity in vitro. The manuscript is clearly written and addresses a key limitation in liver organoid systems: the lack of immune complexity and tissue-specific macrophage imprinting.

Strengths:

• Novelty and Relevance: The study presents a highly innovative co-culture system based on isogenic human iPSCs, addressing an unmet need in modelling immune-mediated hepatotoxicity.

• Mechanistic Insight: The reciprocal reprogramming between iHeps and iMacs, including induction of KC-specific pathways and hepatocyte maturation markers, is convincingly demonstrated.

• Functional Readouts: The application of the model to detect IL-6 responses to hepatotoxic compounds enhances its translational relevance.

Weaknesses:

The co-culture model with monocyte-derived macrophages is not fully characterised, making comparisons less informative.

Reviewer #1 (Public review):

The authors previously reported that Heliconius, one genus of the Heliconiini butterflies, evolved to be efficient foragers to feed pollen of specific plants and have massively expanded mushroom bodies. Using the same image dataset, the authors segmented the central complex and associated brain regions and found that the volume of the central complex relative to the rest of brain are largely conserved across the Heliconiini butterflies. By performing immunostaining to label specific subset of neurons, the authors found several potential sites of evolutional divergence in the central complex neural circuits, including the numbers of GABAergic ellipsoid body ring neurons and the innervation patterns of Allatostatin A expressing neurons in the noduli. These neuroanatomical data will be helpful to guide the future studies to understand the evolution of the neural circuits for vector-based navigations.

Strength

The authors used sufficiently large scale of dataset from 307 individuals of 41 specifies of Heliconiini butterflies to solidify the quantitative conclusions, and present new microscopy data for fine neuroanatomical comparison of the central complex.

Weakness

(1) Although the figures display a concise summary of anatomical findings, it would be difficult for non-experts to learn from this manuscript to identify the same neuronal processes in the raw confocal stacks. It would be helpful to have instructive movies to show step by step guide for identifications of neurons of interests, segmentations and 3D visualizations (rotation) for several examples including ER neurons (to supplement texts in line 347-353) and Allatostatin A neurons.

(2) Related to (1), it was difficult for me to access if the data in Fig 7 support the author's conclusions that ER neuron number increased in Heliconius Melpomene. By my understanding, the resolution of this dataset isn't high enough to trace individual axons and therefore authors do not rule out that the portion of "ER ring neurons" in Heliconius may not innervate the ER, as stated in Line 635 "Importantly, we also found that some ER neurons bypass the ellipsoid body and give rise to dense branches within distinct layers in the fan-shaped body (ER-FB)". If they don't innervate the ellipsoid body, why are they named as "ER neurons"?

(3) Discussions around the line 577-584 requires the assumption that each ellipsoid body (EB) ring neuron typically arborise in a single microglomerulus to form largely one-to-one connection with TuBu neurons within the bulb (BU), and therefore the number of BU microglomeruli should provide an estimation of the number of ER neurons. Explain this key assumption or provide an alternative explanation.

(4) The details of antibody information are missing in the Key resource table. Instead of citing papers, list the catalogue numbers and identifier for commercially available antibodies, and describe the antigen and if they are monoclonal or polyclonal. Are antigens conserved across species?

(5) I did not understand why authors assume that foraging to feed on pollens is more difficult cognitive task than foraging to feed on nectars. Would it be possible that they are equality demanding tasks but pollen feeding allows Heliconius to pass more proteins and nucleic acids to their offsprings and therefore they can develop larger mushroom bodies?

Comments on revisions:

The authors fully addressed my concerns and significantly improved the accessibility of the manuscript.

Reviewer #1 (Public review):

The author presents a new method for microRNA target prediction based on (1) a publicly available pretrained Sentence-BERT language model that the author fine-tunes using MeSH information and (2) downstream classification analysis for microRNA target prediction. In particular, the author's approach, named "miRTarDS", attempts to solve the microRNA target prediction problem by utilizing disease information (i.e., semantic similarity scores) from their language model. The author then compares the prediction performance with other sequence- and disease-based methods and attempts to show that miRTarDS is superior or at least comparable to existing methods. The author's general approach to this microRNA target prediction problem seems promising, but fails to demonstrate concrete computational evidence that miRTarDS outperforms other existing methods. The author's claim that disease information-based language models are sufficient is unfounded. The manuscript requires substantial rewriting and reorganization for readers with a strong background in biomedical research.

A major issue related to the author's claim of computational advance of miRTarDS: The author does not introduce existing biomedical-specific language models, and does not compare them against miRTarDS's fine-tuned model. The performance of miRTarDS is largely dependent on the semantic embedding of disease terms. The author shows in Figure 5 that MeSH-based fine-tuning leads to a substantial improvement in MeSH-based correlation compared to the publicly available pretrained SBERT model "multi-qa-MiniLM-L6-cos-v1" without sacrificing a large amount of BIOSSES-based correlation. However, the author does not compare the performance of MeSH- and BIOSSES-based correlation with existing language models such as ChatGPT, BioBERT, PubMedBERT, and more. Also, the substantial improvement in MeSH-based correlation is a mere indication that the MeSH-based fine-tuning strategy was reasonable and not that it's superior to the publicly available pretrained SBERT model "multi-qa-MiniLM-L6-cos-v1".

Another major issue is in the author's claim that disease-information from miRTarDS's language model is "sufficient" for accurate microRNA target prediction. Available microRNA targets with experimental evidence are largely biased for those with disease implications that have been reported in the biomedical literature. It's possible that their language model is biased by existing literature that has also been used to build microRNA target databases. Therefore, it is important that the author provides strong evidence that excludes the possibility of data leakage circularity. Similar concerns are prevalent across the manuscript, and so I highly recommend that the author reassess the evaluation frameworks and account for inflated performance, biased conclusions, and self-confirming results.

Last but not least, the manuscript requires a deeper and careful description and computational encoding of microRNA biology. I'd advise the author to include an expert in microRNA biology to improve the quality of this manuscript. For example, the author uses the pre-miRNA notation and replaces the mature miRNA notation to maintain computational encoding consistency across databases. However, the mature microRNA notation "the '-3p' or '-5p' is critical as the 3p and 5p mature microRNAs have different seed sequences and thus different mRNA targets. The 3p mature microRNA would most likely not target an mRNA targeted by the 5p mature microRNA.

Reviewer #1 (Public review):

Summary:

This study examines how traumatic brain injury (TBI) alters hippocampal network dynamics and single-unit activity in awake, behaving rats. Using laminar recordings, the authors report reductions in theta power, theta-gamma phase-amplitude coupling, and spike-field entrainment, alongside impairments in spatial memory performance.

Strengths of the study include the use of high-density laminar electrodes to localize activity across hippocampal layers and the integration of electrophysiological and behavioral measures. Analyses that consider behavioral state and account for broadband power changes improve confidence in the interpretation of oscillatory effects. Additional controls suggest that the observed differences are unlikely to be explained by gross motor or motivational deficits. The reported relationships between theta amplitude, phase-amplitude coupling, and spike entrainment provide useful insight into how network coordination is disrupted following injury.

There are a few minor weaknesses. The analyses of single-unit activity across environments are relatively limited, and more comprehensive approaches to characterizing spatial coding would strengthen conclusions about how TBI impacts hippocampal representations. The behavioral assessment relies primarily on a single task, which constrains the interpretation of the cognitive deficits. In addition, the relatively small number of animals is a limitation, although this is partially mitigated by the number of recorded units and the consistency of effects across measures.

Overall, this work provides a careful characterization of hippocampal circuit dysfunction following TBI and contributes to understanding how disruptions in oscillatory coordination and spike timing may relate to cognitive impairment.

Comments on revisions:

The authors have adequately addressed all of my concerns.

Reviewer #1 (Public review):

Summary:

This study utilizes fNIRS to investigate the effects of undernutrition on functional connectivity patterns in infants from a rural population in Gambia. fNIRS resting-state data recording spanned ages 5 to 24 months, while growth measures were collected from birth to 24 months. Additionally, executive functioning tasks were administered at 3 or 5 years of age. The results show an increase in left and right frontal-middle and right frontal-posterior connections with age and, contrary to previous findings in high-income countries, a decrease in frontal interhemispheric connectivity. Restricted growth during the first months of life was associated with stronger frontal interhemispheric connectivity and weaker right frontal-posterior connectivity at 24 months of age. Additionally, the study describes some connectivity patterns, including stronger frontal interhemispheric connectivity, which is associated with better cognitive flexibility at preschool age.

Strengths:

- The study analyses longitudinal data from a large cohort (n = 204) of infants living in a rural area of Gambia. This already represents a large sample for most infant studies, and it is impressive, considering it was collected outside the lab in a population that is underrepresented in the literature. The research question regarding the effect of early nutritional deficiency on brain development is highly relevant and may highlight the importance of early interventions. The study may also encourage further research on different underrepresented infant populations (i.e., infants not residing in Western high-income countries) or in settings where fMRI is not feasible.

- The preprocessing and analysis steps are carefully described, which is very welcome in the fNIRS field, where well-defined standards for preprocessing and analysis are still lacking.

Weaknesses:

- The study provides a solid description of the functional connectivity changes in the first two years of life at the group level and investigates how restricted growth influences connectivity patterns at 24 months. However, it does not explore the links between adverse situations and developmental trajectories for functional connectivity. Given the longitudinal nature of the dataset, future work should expand the analysis using more sophisticated tools to link undernutrition to specific developmental trajectories in functional connectivity, and eventually incorporate additional data to increase statistical power.

- Connectivity was assessed in 6 big ROIs to reduce variability due to head size and optode placement. Nevertheless, this also implies a significant reduction in spatial resolution. Individual digitalisation and co-registration of the optodes to a head model, followed by image reconstruction, could provide better spatial resolution. This is not a weakness specific to this study but rather a limitation common to most fNIRS studies, which typically analyse data at the channel level since digitalisation and co-registration can be challenging, especially in complex setups like this. The authors made an important effort to identify subjects with major optode displacement; however, future work might use tools to digitally record the positions of optodes and head markers.

Reviewer #1 (Public review):

Summary:

Hoverflies are renowned for their striking sexual dimorphism in eye morphology and early visual system physiology, as well as in sexually dimorphic behaviors. Surprisingly, male and female flight behaviors in response to optic flow exhibit only subtle differences. Nicholas et al. investigate the sensorimotor transformation of sexually dimorphic visual information into flight steering commands via descending neurons. Using a combination of intracellular and extracellular recordings, neuroanatomical analysis, and behavioral assays, the authors convincingly demonstrate that descending neurons-particularly at high optic flow velocities-exhibit pronounced sexual dimorphisms, while wing steering responses remain largely monomorphic. The study highlights a very interesting discrepancy between neuronal and behavioral response properties.

More specifically, the authors focused on two types of descending neurons that receive inputs from well-characterized wide-field sensitive tangential cells: OFS DN1 and OFS DN2. Their likely counterparts in Drosophila connect to neck, wing and haltere neuropils. The authors characterized the visual response properties of these two neuronal classes in both male and female hoverflies and identified several interesting differences. They then presented the same set of stimuli, tracked wing beat amplitude and analyzed the sum and the difference of right and left wing beat amplitude as a readout of lift or thrust, and yaw turning, respectively. Behavioral responses showed little to no sexual dimorphism, despite the observed neuronal differences.

Strengths:

I find the question very interesting and the results both convincing and intriguing. A fundamental goal in neuroscience is to link neuronal responses and behavior. The current study highlights that the transformations - even at the level of descending neurons to motoneurons - is complex and less straightforward than one might expect.

Weaknesses:

The authors investigated two types of descending neurons, but it was not clear to me how many other descending neurons are thought to be involved in wing steering responses to wide-field motion. I would suggest providing a more in-depth overview of what is known in hoverflies and Drosophila, since the conclusions drawn from the study would be different if these two types were the only descending neurons involved, as opposed to representing a subset of the neurons conveying visual information to the wing neuropil.

Both neuronal classes have counterparts in Drosophila that also innervate neck motor regions. The authors filled hoverfly DNs in intracellular recordings to characterize their arborization in the ventral nerve cord. In my opinion, these anatomical data could be further exploited and discussed a bit more: is the innervation in hoverflies also consistent with connecting to the neck and haltere motor regions? Are there any obvious differences and similarities to the Drosophila neurons mentioned by the authors? If the arborization also supports a role in neck movements, the authors could discuss whether they would expect any sexual dimorphism in head movements.

Revision comment:

I thank the authors for their detailed replies to my questions and the additional clarifications and analysis included in the paper. All my concerns have been addressed.

Reviewer #1 (Public review):

[Editors' note: this version has been assessed by the Reviewing Editor without further input from the original reviewers. The editors have determined that the authors adequately addressed the prior reviewer comments.]

Summary:

The author's goal was to arrest PsV capsids on the extracellular matrix using cytochalasin D. The cohort was then released and interaction with the cell surface, specifically with CD151 was assessed.

Note on previous revisions:

The authors did an excellent job in their revision to include data from the effect of proteolytic priming on their observed virion transfer to the cell body. All other minor issues were addressed adequately.

The work could be especially critical to understanding the process of in vivo infection.

Reviewer #1 (Public review):

Summary:

Using comprehensive profiling of normal and cancerous tissue via bulk and single-cell RNA sequencing, the authors identified that high-grade serous ovarian cancer is likely to originate from the epithelial progenitor cells from the distal fimbrial region of the fallopian tube, where it has been previously shown to be most prone to ovulatory stress and other microenvironmental influences. The authors also included a CNV analysis to identify hotspots in HGSOCs.

The findings are preliminary, but the resource on its own has great potential and can be used for developing methods for early detection, stratification and treatment.

The main limitation of this study is that the lineage is purely inferred from bioinformatics analysis. More validation work is required, perhaps using cell models / other model organisms.

Strengths and weaknesses:

The authors investigated the origin of high-grade serous ovarian cancer, which is one of the deadliest. They performed comparative analysis using both bulk and single-nucleus RNA sequencing between cancerous and normal tissues (fallopian tube and ovaries) and identified a population of epithelial progenitor cells from the distal fimbrial region that are exposed to ovulatory stress, as the most plausible cells of origin. The extensive profiling of the molecular signatures can also be used for early detection and stratification for treating the disease.

Previous studies have shown that HGSOCs likely originated from the epithelial lining of the fallopian tubes (PMID 32349388). The bulk RNAseq data is confusing in that neither the overall correlation of the transcriptome nor the sample clustering (Figure 1) supports the idea that the HGSOCs are close to the fallopian tube. The authors could perform a more comprehensive marker gene-based analysis to demonstrate their relationship.

The authors also performed a comprehensive analysis of single-cell datasets on both normal and cancerous tissue in humans. From there, they performed a combination of RNA velocity, PAGA and pseudotime, etc, to try and delineate the relationship amongst related cell populations. It would be helpful if the authors could clarify why they applied this particular suite of tools (explaining the differences between tools and bioinformatic approaches) to assist the broader readership who may not be familiar with this type of single-cell bioinformatic analysis.

It also seems to me that the authors did not account for patient effect when they performed the data integration (this point is discussed in the text). This may explain at least partially why the clusters are segregated by patient samples. Another explanation is that it could be due to uneven sampling, as only very few cells (1000s) were captured from each of the tumour samples, and this is clear when a dramatic difference can be seen in their cellular composition.

The trajectory analysis of normal and cancer single-cell data should also include other cells to prevent confirmation bias, as these analyses would only consider relationships amongst the cells available in the model.

As the authors indicated in the limitations, the cell lineage in the studies is largely inferred from the bioinformatics analysis. Experimental lineage tracing via other experimental models (organoids/animal models) would be required.

Despite these limitations, this study will serve as an important resource for the scientific community. I would also suggest that the authors should share this resource via additional portals in addition to the GEO data deposit (e.g. the HCA, or single-cell portals such as at the Broad Institute or CellXGene Discover).

Reviewer #1 (Public review):

This work demonstrates that MORC2 undergoes phase separation (PS) in cells to form nuclear condensates, and the authors demonstrate convincingly the interactions responsible for this phase separation. Specifically, the authors make good use of crystallography and NMR to identify multiple protein:protein interactions and use EMSA to confirm protein:DNA interactions. These interactions work together to promote in vitro and in cell phase separation and boosted ATPase activity by the catalytic domain of MORC2.

Moreover, the authors show solid evidence supporting their important claim that MORC2 PS is important for MORC2-mediated gene regulation. Exploring causal links between PS and function is an important need in the phase separation field, particularly as regards the role of condensates in gene regulation, and is a non-trivial matter. It is crucial and challenging to properly explore the alternative possibility that soluble complexes, existing in the same conditions as phase-separated condensates, are the functional species. The authors have attempted to address this concern by manipulating the physical nature of the MORC2 condensates using a killswitch (KS) peptide (MORC2 +KS), finding that reducing condensates dynamics results in a cellular phenotype very similar to that of the phase separation-deficient MORC2 condensates. While not fully ruling out the alternative, soluble-complex hypothesis, this experiment suggests that function is indeed localized inside the MORC2 condensates, and that perturbing the condensate can be functionally equivalent to removing condensate formation.

The authors also look at several disease related mutants of MORC2. While most of these do not seem to have an obvious connection to the phase separation data, it is quite interesting that one mutant, E236G, displays similar intra-condensate dynamics compared to MORC2 +KS, strengthening the claim that MORC2 phase separation is important for function and suggesting that the observations in this paper may indeed have some disease relevance.

Strengths

Static light scattering and crystallography are nicely used to demonstrate the dimerization of MORC2FL and to discover the structure of the CC3 domain dimer, presumably responsible for the dimerization of MORC2FL (Figure 1).

Extensive use of deletion mutants in multiple cell lines is used to identify regions of MORC2 that are important for forming condensates in the nucleus: the IBD, IDR, and CC3 domains are found to both be essential for condensate formation, while the CW domain plays an unknown role in condensate morphology (Figure 3). The authors use NMR to further identify that the IBD domain seems to interact with the first third of the centrally located IDR, termed IDRa, but not with the latter two thirds of the IDR domain (Figure 4). This leads them to propose that phase separation is the product of IDB:IDRa interaction, CC3 dimerization, and an unknown but important role for the CW domain.

Based on the observation that removal of the NLS resulted in diffuse cytoplasmic localization, they hypothesized that DNA may play an important role in MORC2 PS. EMSA was used to demonstrate interaction between DNA and several MORC2 domains: CC1, CC2, IDR, and TCD-CC3-IBD. Further in vitro microscopy with purified MORC2 showed that DNA addition significantly reduces MORC2 saturation concentration (Figure 5).

These assays convincingly demonstrate that MORC2 phase separates in cells and identifies the protein domains and interactions responsible for this phenomenon.

Weaknesses

The connection between condensates and function, while improved from the original manuscript, still has some weak points.

The central experiment demonstrating that MORC2 condensates mediate function takes the form of RNA-Seq in MORC2 KO HeLa cells (Figure 6), rescued with WT, condensate-deficient mutants, and a KS peptide mutant that reduces dynamics by increasing homotypic protein interactions. The observation that rescuing with MORC2 +KS is ineffective, in a manner similar to rescue with condensate-deficient MORC2 mutants, suggests that unperturbed condensates are important for function. An alternative possibility, however, is that condensates are non-functional bystanders, and that the increased homotypic interactions present in MORC2 +KS result in stronger MORC2 +KS recruitment to condensates, reducing the pool of functional, dilute phase MORC2 +KS and squashing function via sequestration. Similar ideas have been explored by others for transcription factors (e.g. Chong et al, Mol Cell, 2022). This possibility is neither discussed nor ruled out. The absence of microscopy data showing similar localization of MORC2 and MORC2 +KS (particularly the amount of diffuse MORC2 outside condensates) amplifies this concern.

The RNA-Seq data presented in Figure 6h also has some concerning qualities. Inter-replicate variability is higher than ideal, particularly for MORC2 deltaCC3. This may be a product of the transient transfection system used for these experiments, which inherently results in stochasticity. Specific sets of genes regulated by MORC2 are consistent with the main conclusion (Figure 6i, individual genes in 6h, showing that all mutants are more similar to one another than to WT MORC2), but global transcription shifts seem quite different between MORC2 condensate-deficient mutants and MORC2 +KS (Figure 6h heatmap), suggesting much more than simple condensate disruption is taking place. Together, this weakens the conclusion that MORC2 condensates are the functional form of MORC2.

Reviewer #1 (Public review):

Summary:

This study investigates how ingestive behaviors are reflected in muscle activity and how these behaviors relate to neural dynamics in the brain. By combining muscle recordings with computational analysis, the authors identify patterns of mouth movements and show that these change over time and align with changes in brain activity. The work suggests that ingestion is not defined by a single action but by coordinated changes across multiple behaviors.

Strengths:

(1) Addresses an important and underexplored question about how ingestive behavior is organized.

(2) Combines behavioral, physiological, and computational approaches creatively.

(3) Provides a novel framework for quantifying complex ingestive movements.

(4) Demonstrates a clear temporal relationship between behavior and brain activity.

Weaknesses

(1) Behavioral labels rely on video-based scoring, which may not fully capture subtle or hidden movements.

(2) The relationship between brain activity and behavior is correlational, but sometimes interpreted more strongly.

(3) The manuscript could be clearer and more accessible to readers outside the field.

Reviewer #1 (Public review):

Summary:

The authors have used a macaque (two animals only) to follow the migration of 'seeded' TDP43 protein in neuronal pathways - thus mimicking the spread of ALS in the human CNS. Previous experiments in rodents failed to demonstrate this, posing interesting and important biological differences, possibly related to the UMN-LMN system in higher order apes and humans.

Strengths:

An important step forward.

Weaknesses:

No weaknesses were identified by this reviewer. Only 2 animals were used, but that is appropriate given the sensate status of the macaque. In the opinion of this reviewer, the results are entirely convincing.

Reviewer #1 (Public review):

Summary:

The question of how or whether "extensive memory training affects neocortical memory engrams" (to use the words of the authors) is an interesting question and an area where I think there is room for advancing current knowledge. That said, I do not think the current paper succeeds in meaningfully addressing this question. At a conceptual level, I really struggled with the predictions and interpretations of the findings. There are also several elements of the experimental paradigm and analysis decisions that feel incompatible with the claims that are made. While the manuscript does demonstrate that several measures of neural pattern similarity differ between the various groups of individuals, the issue is that it is difficult to draw clear conclusions from these findings.

Strengths:

(1) This is a very unique dataset. Being able to recruit and enroll high-level memory athletes is impressive.

(2) In principle, comparing memory athletes to control subjects, active control subjects (who received working memory training), and trained subjects (who received method of loci training) is very appealing.

(3) In several ways, the authors were rigorous in their analyses.

(4) In principle, the question of how memory training influences neural similarity vs. dissimilarity is of potential interest.

Weaknesses:

(1) As far as I can tell, the training manipulation is fully confounded with instructions. That is, subjects were only instructed to use the method of loci if they had completed method of loci training (or if they were the memory athletes). For the training group, in the pre-training session, there was no strategy instruction (subjects could do whatever they wanted), but post-training, they were told to use the method of loci. I understand the argument, of course, that naïve subjects might not be very good at using the method of loci if they had no experience with it. But, it does seem entirely possible that some (or even many) of the observed fMRI results that are attributed to "extensive training" are better explained by strategy use. That is, maybe the effects can be explained by TRYING to use the method of loci as opposed to actual proficiency with the method of loci. It seems impossible to address this, given the design of the experiments. As such, any claims about the effects of memory training, per se, feel inappropriate. It feels equally plausible that the effects are due to the strategy instruction. If the same results could be obtained through a simple strategy manipulation without ANY training at all, that would radically alter the interpretation of the effects. I think the strategy use account is, in fact, quite viable because it is very easy to improve subjects' memories with a method of loci instruction (relative to no strategy instruction) without ANY practice at all. Obviously, practice does improve memory performance with the method of loci, but my point is that even without any meaningful practice, there is likely to be SOME immediate benefit to adopting the method of loci as a strategy. There is also the question of why the effects for the memory athletes weren't obviously stronger than for the trained group, given that the memory athletes have much more experience with the method of loci. Ultimately, the problem with the current design is that I don't see how one can tease apart the role of training, per se, vs. strategy use.

(2) There is no clear theoretical framework for the predictions or interpretations. The Results section is mostly a list of lots of different permutations of analyses (similarity within a group, between groups, between trials, across trials between subjects, during encoding vs. retrieval, frontal vs. hippocampal vs. parietal ROIs, etc). For each analysis, I did not have an intuition for what the prediction should be (e.g., should athletes have higher or lower pattern similarity?), and even after seeing all the results, I still do not have an intuition for how to interpret them. For the main results related to dissimilarity in prefrontal cortex, I would have, if anything, predicted the opposite: that when individuals are trained to use a common strategy, there would be MORE similarity between them. The Discussion acknowledges a very wide range of possible factors that might contribute to measures of similarity/dissimilarity, but I am ultimately left feeling that I have no idea how to interpret the results because the design and analyses were not structured such that any of these interpretations could be teased apart.

(3) Same theme: the analyses shift from frontal regions (when looking at encoding) to hippocampus and precuneus (when looking at temporal recency). This shift in ROIs is confusing. The analyses (encoding vs. recognition) are essentially confounded with the ROIs (frontal vs. hippocampal/precuneus), so it's hard to know whether different analyses yielded different patterns or different ROIs yielded different patterns. Why were the frontal regions that were important for encoding ignored for the temporal recency judgments? And the fact that medial temporal lobe regions showed opposite effects to the frontal regions during encoding did not get much attention. Given that there were opposing patterns (dissimilarity vs. similarity) across different brain regions, the framing of the paper (that "the method of loci may bolster uniqueness") feels like a very selective representation of the data.

(4) One of the more surprising aspects of the analyses (or at least one of the analyses) is that representational similarity analyses (RSA) are used to compare the average activity pattern (averaged across all trials) between different individuals. At a conceptual level, this really just reduces to a univariate analysis. It is not standard (or intuitive) to think about RSA that is essentially blind to the actual representational content. In other words, averaging across trials obviously washes out the content, and what is left are process-level effects. For process-level analyses, univariate analyses are far more common and seem more straightforward. However, these 'RSA' analyses are described as reflecting the "uniqueness of each word-location association" (an account which strongly implies content-level effects). This feels like an inappropriate description of what the analyses actually reflect.

(5) I think the analysis looking at trial-by-trial similarity during word encoding (showing greater dissimilarity among the experienced individuals) is a somewhat interesting result, but again, I think the interpretation is very difficult. It is hard (or, impossible, I think) to get a clear sense of what is driving those differences. Is it the association of a unique spatial context? Is it somehow a product of better encoding, per se (as opposed to distinct spatial contexts)? These things could be tested by actually manipulating the spatial contexts in a more controlled way. For example, the paper by Liu et al. that is cited several times - and also a just-published paper by Christopher Baldassano (Nature Human Behaviour) - each used a very controlled paradigm where the (imagined) spatial location associated with each item was known/manipulated. However, the design of the current study does not allow for these things to be teased apart.

(6) Relatedly, the training group seemed to receive instruction on a common spatial route, but, surprisingly, "Participants were free to choose which route and how many they would use to anchor the 72 items." Thus, if I understand correctly, we don't know whether the trained individuals were using common or distinct locations. And the fact that they learned a 50-location route but then studied a 72-word list is also a bit strange. Not having control or knowledge of the location that was associated with each word (sequence position) is a major limitation and also a major difference between the current study and other recent studies. For that matter, the word order was also randomized, so there was no control over whether the words and/or locations matched. These issues really complicate interpretation.

(7) Again, same theme: for the result showing lower trial-by-trial similarity (within-subject similarity), the question is why, exactly, training/experience is associated with lower trial-by-trial similarity. Does training specifically or preferentially lead to greater differentiation between temporally-adjacent trials (as in Liu et al)? Does it lead to greater differentiation IF subjects associate each word with a unique location? Or maybe there is a more abstract effect of sequence/position that is independent of spatial location? Importantly, each of these three possibilities that I mention here has a precedent in prior studies that were more tightly controlled. But here, there is no way to tease these apart because of the experimental design, limiting the conclusions.

(8) The ISC analysis described on p. 9 (line 328) is confusing. If I understand correctly, correlations between different trials were not computed (e.g., subject 1 trial 1 was not correlated with subject 2 trial 2). Rather, trial 1 was always correlated with trial 1 (in other subjects). Thus, it is not clear whether trial-level alignment matters at all. Maybe the same results would be obtained if there were no correspondence across subjects in trial number. Or if the trial order was shuffled within the subject. Given this, I simply don't know how to think about the data. And why did memory athletes show higher pattern similarity in this analysis as opposed to lower pattern similarity (as in some other analyses)? And why was this analysis performed by comparing memory athletes to each other as opposed to memory athletes to non-athletes? And, conceptually, why was this selective to the memory athletes or to the precuneus? And why was it selective to the temporal order test and not encoding? I am not asking the authors to answer each of these questions; rather, the point I am trying to make is that this analysis, and many of the analyses, seem to raise more questions than they answer.

(9) The ISC analyses are interpreted in terms of scene construction and context reinstatement, but these conclusions go (very) far beyond what the data actually shows. Again, I don't see how this analysis lends itself to a meaningful conclusion. And this general critique applies to many of the analyses reported in this paper.

(10) The fact that words were in random order per subject also makes the ISC analysis even more confusing to think about. The memory athletes had unique spatial routes (that they used for the method of loci) and unique word lists. So, why would it make sense to look at trial-level ISC? At a conceptual level, I simply don't understand what this is intended to capture.

(11) Differences in the pattern of results between the encoding and temporal memory recognition task are hard to make sense of and are not addressed in much detail. Why would it make more sense to have across-trial similarity during recognition than during encoding? I think any account of this is very speculative.

Reviewer #2 (Public review):

In this revised version of the manuscript, the authors have addressed many of my concerns. The representative confocal images now provided, allow for a much better assessment of the claims being made and hence the data to be understood, for example the level of protein expression of Chi3l1 in the macrophages.

There is just 1 concern remaining, which is a main claim of the manuscript, that loss of Chi3l1 drives KC death in MASLD. This claim is made based on gene expression profiles and the presence of Tunel staining in liver sections. However the KC numbers are not altered compared with WT when assessed by flow cytometry. This discrepancy is not really addressed. If the cells are not actually dying this would explain the lack of moKCs (a concern raised by reviewer 1) and would indeed suggest that the loss of these cells is, as suggested by that reviewer, trivial in this timeframe. The authors propose in their rebuttal that the KCs are in a prolonged state of stress, explaining the Tunel staining, but to make the claim that they die, the authors need to show their eventual loss from the liver. Otherwise the claims of death should be revised.

Reviewer #1 (Public review):

Ma et al. use human-chimpanzee tetraploid cells across different cell types to identify the genetic causes and then transcriptomic consequences of divergence in DNA methylation. They conclude that the evolution of DNA methylation is driven primarily by cis-regulatory changes, and that the evolution of CpG sites contributes to cis-regulation, while transcription factor expression underlies some trans changes. They then argue that divergence in DNA methylation is associated with changes in gene expression and may contribute to human phenotypes.

The tetraploid model is able to provide compelling evidence that most regulatory evolution occurs due to cis-regulatory changes. My only concern is that the extent of trans-changes may be overstated, as almost all are eliminated by changing from a nominal p-value criterion to even a 25% false discovery rate. The follow-up analyses are incomplete with major gaps. The authors focus on single potential mechanisms for cis- and trans-changes, but it is not clear to what degree these mechanisms explain the extent of cis and trans changes. There are also other mechanisms which are not investigated, such as the importance of TF binding sites for cis-regulatory evolution. While likely beyond the scope of this work, communicating these areas for future work would have helped define the niche for this manuscript.

Next, the authors seek to show that differences in DNA methylation are functionally relevant. Consistent with previous results, they show that differences in DNA methylation are (weakly) associated with changes in gene expression. They hypothesize that genes with concordant regulatory elements should exhibit greater methylation-expression coupling than other genes and show that cis-expression/cis-methylation pairs are more strongly correlated than trans/trans pairs. However, I worry that this result could be confounded by larger effect sizes for cis-changes than trans effects. I also think that looking at cis/trans or trans/cis changes would have been useful to directly test the driving hypothesis. Another limitation is that this analysis is limited to promoter regions. It is not clear how many divergent DMRs are included and how many of those genes have differences in expression. The key question is whether differences in DNA methylation are functionally important, and the answer provided by these analyses is "sometimes".

Finally, the authors make a case for lineage-specific selection on DNA methylation that is connected to human traits. This evidence was not convincing. In fact, it is even said that these tests cannot be interpreted as evidence of lineage-specific selection (lines 399-401), so I am confused why these results are framed as testing for selection. The evidence better supports an argument connecting DNA methylation to human phenotypes.

In conclusion, I think this study provides a valuable resource for differences in DNA methylation between humans and chimpanzees across tissues, and provides important insight into the relative abundance of cis and trans regulatory evolution. Additional research is necessary to investigate the underlying regulatory mechanisms, and more care needs to be taken in exploring the functional consequences.

Reviewer #1 (Public review):

[Editor's note: this version has been assessed by the Reviewing Editor without further input from the original reviewers. The authors have satisfactorily addressed the previous concerns raised by the reviewers.]

Summary:

This study presents convincing findings that oligodendrocytes play a regulatory role in spontaneous neural activity synchronization during early postnatal development, with implications for adult brain function. Utilizing targeted genetic approaches, the authors demonstrate how oligodendrocyte depletion impacts Purkinje cell activity and behaviors dependent on cerebellar function. Delayed myelination during critical developmental windows is linked to persistent alterations in neural circuit function, underscoring the lasting impact of oligodendrocyte activity.

Strengths:

(1) The research leverages the anatomically distinct olivocerebellar circuit, a well-characterized system with known developmental timelines and inputs, strengthening the link between oligodendrocyte function and neural synchronization.

(2) Functional assessments, supported by behavioral tests, validate the findings of in vivo calcium imaging, enhancing the study's credibility.

(3) Extending the study to assess long-term effects of early life myelination disruptions adds depth to the implications for both circuit function and behavior.

Weaknesses:

(1) The study would benefit from a closer analysis of myelination during the periods when synchrony is recorded. Direct correlations between myelination and synchronized activity would substantiate the mechanistic link and clarify if observed behavioral deficits stem from altered myelination timing.

(2) Although the study focuses on Purkinje cells in the cerebellum, neural synchrony typically involves cross-regional interactions. Expanding the discussion on how localized Purkinje synchrony affects broader behaviors-such as anxiety, motor function, and sociality - would enhance the findings' functional significance.

(3) The authors discuss the possibility of oligodendrocyte-mediated synapse elimination as a possible mechanism behind their findings, drawing from relevant recent literature on oligodendrocyte precursor cells. However, there are no data presented supporting these assumptions. The authors should explain why they think the mechanism behind their observation extends beyond the contribution of myelination or remove this point from the discussion entirely.

Comment for resubmission: Although the argument on synaptic elimination has been removed, it has been replaced with similarly unclear speculation about roles for oligodendrocytes outside of conventional myelination or metabolic support, again without clear evidence. The authors measured MBP area but have not performed detailed analysis of oligodendrocyte biology to support the claims made in the discussion. Please consider removing this section or rephrasing it to align with the data presented.

(4) It would be valuable to investigate secondary effects of oligodendrocyte depletion on other glial cells, particularly astrocytes or microglia, which could influence long-term behavioral outcomes. Identifying whether the lasting effects stem from developmental oligodendrocyte function alone or also involve myelination could deepen the study's insights.

(5) The authors should explore the use of different methods to disturb myelin production for a longer time, in order to further determine if the observed effects are transient or if they could have longer-lasting effects.

(6) Throughout the paper, there are concerns about statistical analyses, particularly on the use of the Mann-Whitney test or using fields of view as biological replicates.

Reviewer #1 (Public review):

Summary:

The manuscript by Seraj et al. introduces a transformative structural biology methodology termed "in extracto cryo-EM." This approach circumvents the traditional, often destructive, purification processes by performing single-particle cryo-EM directly on crude cellular lysates. By utilizing high-resolution 2D template matching (2DTM), the authors localize ribosomal particles within a complex molecular "crowd," achieving near-atomic resolution (~2.2 Å). The biological centerpiece of the study is the characterization of the mammalian translational apparatus under varying physiological states. The authors identify elongation factor 2 (eEF2) as a nearly universal hibernation factor, remarkably present not only on non-translating 80S ribosomes but also on 60S subunits. The study provides a detailed structural atlas of how eEF2, alongside factors like SERBP1, LARP1, and IFRD2, protects the ribosome's most sensitive functional centers (the PTC, DC, and SRL) during cellular stress.

Strengths:

The "in extracto" approach is a significant leap forward. It offers the high resolution typically reserved for purified samples while maintaining the "molecular context" found in in situ studies. This addresses a major bottleneck in structural biology: the loss of transiently bound or labile factors during biochemical purification.

The finding that eEF2 binds and sequesters 60S subunits is a major biological insight. This suggests a "pre-assembly" hibernation state that allows for rapid mobilization of the translation machinery once stress is relieved, which was previously uncharacterized in mammalian cells.

The authors successfully captured eIF5A and various hibernation factors in states that are traditionally disrupted. The identification of eIF5A across nearly all translating and non-translating states highlights the power of this method to detect ubiquitous but weakly bound regulators.

The manuscript beautifully illustrates the "shielding" mechanism of the ribosome. By mapping the binding sites of eEF2 and its co-factors, the authors provide a clear chemical basis for how the cell prevents nucleolytic cleavage of ribosomal RNA during nutrient deprivation.

Weaknesses:

While 2DTM is a powerful search tool, it inherently relies on a known structural "template." There is a risk that this methodology may be "blind" to highly divergent or novel macromolecular complexes that do not share sufficient structural similarity with the search model. The authors should discuss the limitations of using a vacant 60S/80S template in identifying highly remodeled stress-induced complexes. For instance, what happens if an empty 40S subunit is used as template? In the current work, while 60S and 80S particles are picked, none are 40S. The authors should comment on this.

In the GTPase center, the authors identify density for "DRG-like" proteins. However, due to limited local resolution in that specific region, they are unable to definitively distinguish between DRG1 and DRG2. While the structural similarity is high, the functional implications differ, and the identification remains somewhat speculative. The authors should acknowledge this in the text.

While "in extracto" is superior to purified SPA, the act of cell lysis (even rapid permeabilization) still involves a change in the chemical environment (pH, ion concentration, and dilution of metabolites). The authors could strengthen the manuscript by discussing how post-lysis changes might affect the occupancy of factors like GTP vs. GDP states.

The study provides excellent snapshots of stationary states (translating vs. hibernating), but the kinetic transition-specifically how the 60S-eEF2 complex is recruited back into active translation-is not well discussed. On page 13, the authors present eEF2 bound to 60S but do not mention anything regarding which nucleotide is bound to the factor. It only becomes clear that it is GDP after looking at Figure S9. This should be clarified in the text. Similarly, the observations that eEF2 is bound to GDP in the 60S and 80S raises the questions as to how the factor dissociates from the ribosome. This could also be discussed.

Overall Assessment:

This work reported in this manuscript likely represents the future of structural proteomics. The combination of high-resolution structural biology with minimal sample perturbation provides a new standard for investigating the cellular machines that govern life. After addressing minor points regarding template bias, protein identification, and transition dynamics, this work may become a landmark in the field of translation.

Comments on revisions:

In the revised version of the manuscript, the authors have addressed my prior concerns.

Reviewer #1 (Public review):

Summary:

Rolland and colleagues investigated the interaction between Vibrio bacteria and Alexandrium algae. The authors found a correlation between the abundance of the two in the Thau Lagoon and observed in the laboratory that Vibrio grows to higher numbers in the presence of the algae than in monoculture. Timelapse imaging of Alexandrium in coculture with Vibrio enabled the authors to observe Vibrio bacteria in proximity to the algae and subsequent algae death. The authors further determine the mechanism of the interaction between the two and point out similarities between the observed phenotypes and predator prey behaviours across organisms.

Strengths:

The study combines field work with mechanistic studies in the laboratory and uses a wide array of techniques ranging from co-cultivation experiments to genetic engineering, microscopy and proteomics. Further, the authors test multiple Vibrio and Alexandria species and claim a wide spread of the observed phenotypes.

Comments on revisions:

I thank the authors for their additional work on the manuscript. My comments were addressed to my satisfaction.

Reviewer #1 (Public review):

Summary:

The main goal of this manuscript is to develop a mathematical model of the regulation of cortical dynamics by Cdk1 activity to explain why, in some embryos (e.g., Xenopus), surface contraction waves are believed to move in the same direction as Cdk1, while in other embryos (e.g., starfish) they are believed to move in the opposite direction.

Strengths:

(1) The paper addresses a very important question.

(2) The mathematical model is sensible and suggests that the different relationship between Cdk1 and surface contraction waves might arise from the different behavior of the mitotic entry wave and the mitotic exit wave.

(3) The authors propose a mechanism by which the wave observed at mitotic exit might not passively follow the trigger wave observed at mitotic entry'

(4) The proposed mechanism is a potential explanation of the observed differences.

(5) The proposed mechanism is centered on different dynamics between the nucleus and the cytoplasm, highlighting the potential importance of the nucleus (and nuclear size) in organizing cortical dynamics.

Weaknesses:

(1) The proposed mechanism works if the activity in the nucleus is much higher than the high activity (high state of the bistable system) of the cytoplasm. So, as the wave propagates across the cytoplasm, the activity around the nucleus remains higher, which potentially causes a delay in the onset of Cyclin B-Cdk1 degradation in the region around the nucleus compared to the surrounding cytoplasm. This effect happens over a typical length scale, and if such a length scale is comparable to embryo size, this becomes the predominant mechanism. However, such a mechanism should exist near the nucleus independently of embryo size. So, it seems that for embryos where the wave back and wave front should travel together, nuclear activity must be adjusted not to be much higher than cytoplasmic activity. A better discussion of the discovered process and its implications would strengthen the paper. It requires careful reading to understand what, in hindsight, is a rather simple explanation. Is there any experimental evidence that the overall activity of Cdk1 is higher in the nucleus than in the cytoplasm?

(2) While the fact that Cdk1 can enslave cortical dynamics is clearly shown in the model, this is expected from the literature. There are systems where the enslavement of cortical and bulk actomyosin contractility to Cdk1 activity has been more clearly demonstrated (Drosophila and zebrafish embryos), as well as shown to have clear functions (nuclear positioning and ooplasmic segregation).

(3) The writing could be improved. The authors make some claims of originality that seem a stretch, e.g., in the abstract, they say: "we develop a reaction-diffusion model of Cyclin B-Cdk1 signaling in spherical cells with localized nuclear activation", but they essentially use a previous model with a few numerical tweaks. The figures are sometimes mislabelled or not explained, and some of the units seem wrong.

(4) The authors give the existence of trigger waves as a fact. While the predominant view is that such waves exist in the first cycle of the Xenopus embryos (however, this is from measurement of the cortical contractions, so a bit circular for this paper), it is unclear if waves exist in the starfish embryo, so the potential explanation that the starfish embryo simply has different Cdk1 dynamics cannot be ruled out.

Reviewer #1 (Public review):

Summary:

This study examines Müller glia (MG) reprogramming in the uninjured mouse retina through a combination of Notch signaling inhibition and AAV-induced proliferation. Building on their prior work showing that Cyclin D1 overexpression and p27^Kip1^ knockdown (CCA) promotes MG proliferation with very limited neurogenesis, the authors now demonstrate that Rbpj deletion alone induces a modest degree of MG-to-neuron conversion without proliferation, in agreement with recent work in the field. However, combining Rbpj deletion with CCA-mediated proliferation substantially enhances MG dedifferentiation and the generation of retinal neuron-like cells. Through genetic lineage tracing, histological analyses, and single-cell transcriptomics, the authors provide evidence that MG-derived cells acquire molecular features of bipolar (ON, OFF, and rod bipolar) and amacrine neurons. Most MG-derived cells appear to survive long-term (up to 9 months).

Strengths:

Overall, the study is carefully designed and executed, and the manuscript is clearly written with well-presented figures. While the work does not significantly expand the repertoire of neuronal types generated from mammalian MG beyond what has been previously reported in the field, it provides a valuable and improved strategy for inducing robust MG proliferation and neurogenesis in the mammalian retina.

Weaknesses:

(1) It would be better to include a negative control AAV when evaluating the effect of CCA AAV in the Rbpj KO background. This could help distinguish the specific contribution of the CCA construct from potential effects of intravitreal AAV injection itself, which can induce mild inflammation, known to influence MG reprogramming.

(2) The extent of MG transduction by the CCA AAV is not clear. As quantifications are normalized to total MG (GFP^+^ or TdTomato^+^) or retinal length, it would be useful to clarify whether near-complete transduction is assumed, or if additional information on transduction efficiency can be provided.

(3) In Figure S10, the reduced MG proliferation observed in the CCA + Rbpj deletion group could also potentially reflect decreased GFAP promoter activity in dedifferentiated MG following Rbpj deletion. Alternatively, MG-derived cells may be more fragile under these conditions.

(4) In the CCA + Rbpj deletion condition, do MG undergo single or multiple rounds of cell division?

(5) What fraction of neuron-like cells (bipolar- and amacrine-like) arises from proliferation versus direct transdifferentiation? Quantification of MG-derived cells expressing neuronal markers (e.g., Otx2, HuC/D), with and without EdU labeling, would help distinguish these mechanisms.

(6) In Figure S18a, the authors state that "while the neuron-like clusters were best classified as BC-like and AC-like based on their distinct marker gene expression, they also exhibited mixed expression of genes associated with other retinal neuronal types, including RGC markers (e.g., Tubb3, Myt1l, Grin1) and photoreceptor markers (e.g., Crx, Prom1, Epha10, Gucy2e, Scg3) (Fig. S18a), suggesting that the regenerated cells exist in a hybrid state" and "MG derived neuron like cells also expressed genes characteristic of RGCs and photoreceptors, indicating enhanced lineage". However, many of these genes are not specific to RGCs or photoreceptors and are instead broadly expressed in retinal neurons or enriched in bipolar/amacrine populations. Therefore, it is unclear whether these cells exhibit hybrid RGC or photoreceptor identity.

(7) The authors provide a thorough molecular characterization of MG-derived cells through immunostaining and single-cell sequencing. However, their morphological features, synaptic connectivity (e.g., synaptic marker expression), and electrophysiological properties remain largely uncharacterized. While these experiments may be technically challenging, this limitation should be discussed.

(8) The conclusion that CCA + Rbpj deletion induces neurogenesis without compromising MG supportive functions or retinal homeostasis appears somewhat oversold. This claim is primarily based on gross retinal morphology and ZO-1 staining. Given the extent of MG dedifferentiation and ectopic cell generation in the ONL and INL, it is likely that retinal function is affected. Functional assessments (e.g., ERG) would be required to support this conclusion. The authors should consider tempering this statement.

(9) Regarding the mechanism by which CCA-induced proliferation enhances MG reprogramming in the Rbpj knockout background, one plausible explanation is that chromatin states (e.g., histone modifications and DNA methylation) are transiently reset during DNA replication and cell division. While this alone may be insufficient to activate neurogenic programs, it could synergize with Rbpj deletion to allow neurogenic transcription factors (such as Ascl1, Otx2, NeuroD1, and NeuroD2) to access previously inaccessible chromatin regions, thereby promoting MG reprogramming.

Reviewer #1 (Public review):

Summary:

This interesting paper probes the problematic relationships between the classical "spiralian" taxa, i.e., annelids, molluscs, brachiopods, platyhelminths and nemerteans, and shows that the branches leading to them are so short as to be unreliable guides to their relationships. This, in turn, has important implications for how we view the origin of the animal phyla.

Strengths:

A very careful analysis of a famous old problem with quite significant results. The results seem to be robust and support their conclusions.

It often passes uncommented that many different trees are published about animal relationships, yet some parts of the tree seem extremely difficult to resolve; the spiralians are perhaps the most difficult case. More recently, problems about sponges or ctenophores as sister groups to the rest of the animals have alerted us to major areas of uncertainty in large-scale phylogenetic reconstruction; this paper is a welcome reminder that other, perhaps even harder, problems exist which may be difficult to ever resolve with the (molecular) data we have.

Weaknesses:

The paper could have perhaps drawn out some of the implications of its results in a clearer manner.

Reviewer #1 (Public review):

This study integrates Xenium spatial transcriptomics of paired inflamed and uninvolved Crohn's disease tissues with functional analyses in a csf2rb-/- larval zebrafish DSS intestinal injury model to investigate the spatial and cell-type-specific roles of GM-CSF. The work is limited mechanistically and adds little to an already disputed field: GM-CSF's role in intestinal inflammation is context-dependent and extensively studied in mice and humans, and this study does not resolve these controversies. The zebrafish appears to be a poor model for these questions: it lacks mammalian intestinal architecture, complex microbiota, and clearly validated functional ILC populations. Putative ILC1s are poorly defined based on stress-response gene modules, while ILC3s are somewhat better characterized, but overall, the system does not allow mechanistic insights into GM-CSF regulation of ILCs. The DSS experiments largely recapitulate the known protective effects of GM-CSF in epithelial injury without clarifying underlying mechanisms.

Figure 1

GM-CSF expression is extremely sparse, rarely exceeding 0.005 frequency even in inflamed regions. The authors should acknowledge this and discuss why. Xenium could be used to characterize the niche around GM-CSF-producing cells, but no new cellular circuit is revealed beyond known myeloid-lymphoid interactions.

Figure 2

Colon length in DSS colitis is not decreased in Csf2rb⁻/⁻ versus wild-type zebrafish under untreated conditions, suggesting endogenous GM-CSF has minimal impact. In Figure 2E, Tg(mpeg1:mCherry) larvae show staining in vessel- or epithelial-like structures expressing Csf2rb, which does not resemble macrophages and requires clarification. pSTAT5 is upregulated with GM-CSF treatment, but the responding cell types are unclear.

Figure 3

Putative ILC1s are defined by stress-response gene modules rather than canonical markers. Overlapping genes with human (HSP90AA1, UBB, MCL1, DOK2) do not indicate ILC1 identity, which is described by IL7R, KLRB1, or TBX21 expression in the human Xenium dataset. ILC2s were not detected, and Ifng expression is broadly distributed, making attribution to ILC1s uncertain. ILC3s are somewhat better defined, but overall, the data do not support mechanistic conclusions about GM-CSF regulation of ILC populations.

Reviewer #1 (Public review):

Summary:

The authors sought to define the molecular mechanism by which the adaptor protein Egalitarian (Egl) recognizes and binds specific mRNA localization signals -- in particular, the K10 transport and localization signal (TLS) -- to initiate dynein-based transport in Drosophila. In doing so, they identified the minimal Egl domains required for RNA binding, determined the atomistic structure of the Egl-RNA complex, and explored the recognition mechanism (shape vs. structure). They furthermore performed in vivo functional validation using CRISPR-mediated genome editing in Drosophila that showed that the identified binding residues are biologically essential.

Strengths:

The authors provided a detailed crystal structure of the Egl-RNA complex at high resolution. In particular, they used a MBP-fusion crystallization driver to be able to resolve the flexible C-terminal domain of Egl (EHD). The authors' use of an integrative approach combining X-ray crystallography with binding assays and in vivo functional validation provides compelling evidence for their claims.

The work provides a detailed interaction mapping that identifies the protein residues responsible for the electrostatic interaction with the RNA. In doing so, the work explains how Egl can recognize diverse RNA sequences by demonstrating that Egl binds primarily to the phosphate backbone and specific structural bulges, providing a plausible model for how one protein can recognize many different localization signals that share little sequence similarity.

Weaknesses:

Discrepancy in the stoichiometric Egl-to-RNA ratio (the structural data in the paper indicate a 1:1 ratio, whereas previous single-molecule transport studies suggest a 2:1 ratio) remains unanswered, with the likely explanation that the truncated version of the protein might not capture the full (native) assembly. While the authors acknowledge this in the Discussion, the paper would benefit from this issue being raised earlier, already in the Results section. Moreover, there is a notable omission of a recent preprint on a very similar topic [https://www.biorxiv.org/content/10.1101/2025.08.02.668268v1.full].

In vitro, Egl shows a relatively high affinity for non-target RNAs such as the MS2 loop, whereas it is highly selective in vivo. Is it possible that other cofactors are required for the high-fidelity sorting not present in the study? Testing binding in the presence of co-factors (BicD or Dlc) could indicate whether they increase the specificity for target RNAs over non-target ones.

Including a more diverse set of size-matched RNA controls would have significantly strengthened the paper's claims regarding specificity. Using RNAs that mimic K10 TLS would have provided a more rigorous test of the shape-recognition by Egl - using, for instance, decoy RNAs of the same length but with differently positioned bulges (or no bulges at all) or testing other known localization signals (like bicoid or hairy) of similar length.

Appraisal of aims:

The authors successfully determined the crystal structure of the Egl-RNA complex, identifying a modular binding surface composed of the EXO domain, a helical linker, and the EHD. They effectively demonstrated that Egl uses a combination of shape-specific recognition (targeting RNA bulges) and sequence-specific interactions (bonding with specific bases), and confirmed the biological necessity of these findings by showing that mutating the identified residues in living flies leads to infertility and oocyte differentiation defects. These results provide robust evidence for the authors' claims that they have defined a minimal RNA localization signal. In particular, the correlation between the L-Triple mutation's binding defect and its total sterility in flies provides proof that the identified binding surface is the functional one. While the 1:1 stoichiometry remains a point for further investigation, the authors transparently address that full-length transport may require a 2:1 assembly, suggesting their structure represents the fundamental building block of that larger complex.

Impact of the work on the field:

This study provides a high-resolution picture of how a dynein adaptor recognizes its cargo. It moves the field from predictive models to atomic-level certainty, setting a benchmark for studying other similar transport complexes. By proving that Egl recognizes RNA shape (bulges) as much as sequence, the work changes the outlook on the search for localization signals in other genomes, moving beyond simple sequence motifs to 3D structural signatures. The coordinates deposited in the EBI (IDs: 9UJU, 9UJY, 9UUG) provide a resource for the modelling of higher-order transport complexes. The identification of specific residues (e.g., the L-Triple) provides the community with tools to disrupt RNA transport in Drosophila without destroying the entire protein, allowing for more nuanced studies of development.

Reviewer #1 (Public review):

Summary:

Zare‑Eelanjegh et al. investigate how the endoplasmic reticulum, the nucleus, and the cell periphery are mechanically linked by indenting intact cells with specially shaped atomic‑force probes that double as drug injection devices. Fluorescence‑lifetime imaging of the membrane tension reporter Flipper‑TR reveals that these three compartments are mechanically linked and that the actin cytoskeleton, microtubules, and lamins modulate this coupling in complex ways.

Strengths:

* The study makes an important advance by applying FluidFM to probe organelle mechanics in living cells, a technically demanding but powerful approach.

* Experimental design is quantitative, the data are clearly presented, and the conclusions are broadly consistent with the measurements.

Weaknesses:

* Calcium‑dependent effects: Indentation can evoke cytoplasmic Ca²⁺ elevations that drive myosin contraction and reshape the internal membrane network (e.g., vesiculation: PMID : 9200614, 32179693) possibly confounding the Flipper-TR responses; without simultaneous/matching Ca²⁺ imaging, cell viability assays (e.g., Sytox), and intracellular Ca²⁺ sequestration or myosin inhibition experiments, a more complex mechanochemical coupling cannot be excluded, weakening conclusions.

* Baseline measurements: Flipper‑TR lifetime images acquired without indentation do not exclude potential light‑induced or time‑dependent changes, which weakens the conclusions.

* Indentation depth versus nuclear stiffness/tension: Because lamin‑A/C depletion softens nuclei, a given force may produce a deeper pit and thus greater membrane stretch. It is unclear how the cytoskeletal perturbations affect indentation depth, which weakens the conclusions.

Comments on revisions:

With their responses, the authors have relieved my initial concerns.

Reviewer #1 (Public review):

Summary:

In the manuscript entitled 'The Role of ATP Synthase Subunit e (ATP5I) in 1 Mediating the Metabolic and Antiproliferative 2 Effects of Biguanides', Lefrancois G et al. identifies ATP5I, a subunit of F1Fo-ATP synthase, as a key target of medicinal biguanides. ATP5I stabilizes F1Fo-ATP synthase dimers, essential for cristae morphology, but its role in cancer metabolism is understudied. The research shows ATP5I interacts with a biguanide analogue, and its knockout in pancreatic cancer cells mimics biguanide treatment effects, including altered mitochondria, reduced OXPHOS, and increased glycolysis. ATP5I knockout cells resist biguanide-induced antiproliferative effects, but reintroducing ATP5I restores the effects of metformin and phenformin. These findings highlight ATP5I as a promising mitochondrial target for cancer therapies. The manuscript is well written.

Strengths:

Demonstrated the experiments in a systematic and well accepted methods

Weaknesses:

Significance of the target molecule and mechanisms may help in understanding the molecular mechanisms of metformin.

Comments on revisions:

In the revised manuscript, the authors addressed all the queries.

Joint Public Review:

Summary

Riva et al. introduce a semi-automatic setup for measuring Drosophila melanogaster oviposition rhythms and use it to map the timekeeping function underlying egg laying rhythms to a subset of clock cells. Using a combination of neurogenetic manipulations and referencing the publicly available female hemi-brain connectome dataset, they narrow the critical circuit down to two of the three CRYPTOCHROME expressing lateral-dorsal neurons (CRY[+] LNds). Their findings suggest that different overlapping sets of clock neurons may control different behavioral rhythms in D. melanogaster.

This work will be of interest to researchers interested in the circadian regulation of oviposition in D. melanogaster (and possibly other insects), a phenomenon which has been left relatively under-explored. The construction of a semi-automated setup which can be made relatively cheaply using available motors and 3D printed molds provides a useful model for obtaining longer records of oviposition activity.

Strengths

The authors use a semi-automated monitoring system to detect circadian egg laying rhythms in spite of inherently noisy data. Using this approach they use a variety of different genetic tools to show that CRY+ LNds play a role in generating the circadian rhythm of oviposition, that PDF-expressing neurons seem to be important for maintaining the circadian period of egg laying, and that period locus function is required for the circadian rhythmicity of oviposition. The authors also point to some potentially interesting connectome data that suggest hypotheses regarding the neuronal circuit linking daily timekeeping to oviposition, which will require further validation in future studies.

Weaknesses:

The major weaknesses of this work result from the noisy nature of the data, and the need to average the individual records of many animals in order to extract significant rhythmicity values. The predicted neural output pathways will require validation in future studies.

Reviewer #2 (Public review):

Summary:

Shahbazi et al. trained recurrent neural networks (RNNs) to simulate human upper limb movement during adaptation to a force field perturbation. They demonstrated that throughout adaptation, the pattern of motor commands to the muscles of the simulated arm changed, allowing the perturbed movements to regain their typical, perturbation-free straight-line paths. After this initial learning block (FF1), the network encountered null-fields to wash out the adaptation, before re-experiencing the force in a second learning block (FF2). Upon re-exposure, the network learned faster than during initial learning, consistent with the savings observed in behavioral studies of adaptation. They also found that as the number of hidden units in the RNN increased, so did the probability of exhibiting savings. The authors concluded that these results propose a neural basis for savings that is independent of context and strategic processes.

Strengths:

The paper addresses an important and controversial topic in motor adaptation: the mechanism underlying motor memory. The RNN simulation reproduces behavioral hallmarks of adaptation, and it provides a useful illustration of the pattern of muscle activity underlying human-like movements under both normal and perturbing conditions. While the savings effect produced by the network, though significant, appears somewhat small, the simulation demonstrating an increase in savings with a greater number of hidden units is particularly intriguing.

Main weakness:

The introduction details the ongoing debate in the literature regarding the mechanisms underlying savings, particularly whether it stems from explicit or implicit learning processes. However, it remains unclear how the current work addresses this debate. There is already a considerable body of research, particularly in visuomotor adaptation, demonstrating that savings is predominantly driven by explicit strategies (e.g., Morehead et al. 2015, Haith et al., 2015; Huberdeau et al., 2019; Avraham et al., 2021). Furthermore, there have been multiple reports that implicit adaptation exhibits attenuation upon relearning (Avraham et al., 2021, Leow et al., 2020; Yin and Wei, 2020; Hamel et al., 2021; Hamel et al., 2022; Wang and Ivry, 2023; Hadjiosif et al., 2023). In the discussion, the authors acknowledge that their goal was not to model a complete explicit-implicit system, but rather to probe how savings may emerge from a purely implicit mechanism. Given the central debate introduced by the authors, the manuscript would benefit from a more detailed discussion explaining how their findings elucidate the specific conditions under which savings emerge from purely implicit mechanisms versus when cognitive strategies predominate.

Reviewer #1 (Public review):

[Editors' note: The Reviewing Editor has assessed the revised manuscript without seeking further input from the original reviewers. The authors have addressed the main points raised during peer review, including clarifying methodological differences with prior work, providing additional analysis, and expanding the discussion of potential mechanisms. These revisions strengthen the interpretation and presentation of the findings, and the conclusions remain supported by the data.]

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.

Reviewer #1 (Public review):

Summary:

The authors investigated the role of an E3 ubiquitin ligase ITCH in regulating the viral life cycle of SARS-CoV-2. The authors showed that ITCH mediates ubiquitination of the membrane (M) and envelope (E) proteins of SARS-CoV-2. Ubiquitination of E and M result in enhanced interactions between the structural proteins and redistribution of the structural proteins into autophagosomes. The authors claim that the enhanced interactions between structural proteins and trafficking of the structural proteins into autophagosomes contribute to SARS-CoV-2 replication and egress, prompting ITCH as a potential antiviral target. ITCH also alters the cellular distribution of host proteases important for spike cleavage which protect and stabilize spike with cleavage. The authors also demonstrated that SARS-CoV-2 replication is augmented by ITCH in which virus replication is significantly impaired in cells lacking ITCH expression.

Strengths:

The authors provided high quality data with appropriate experimental controls to justify their claims and conclusions. The mechanistic analyses are excellent and presented in a logical manner. The investigation of the role of ubiquitination in coronavirus assembly and egress is novel as most previous studies focused on its role in mediating innate immune responses.

Comments on revisions:

The authors have addressed my previous concerns.

Reviewer #1 (Public review):

Summary:

In this remarkable study, the authors use some of their recently-developed oxytocin receptor knockout voles (Oxtr1-/- KOs) to re-examine how oxytocin might influence partner preference. They show that shorter cohabitation times leads to decreased huddling time and partner preference in the KO voles, but with longer periods preference is still established, i.e., the KO animals have a slower rate of forming preference, or are less sensitive to whatever cues or experiences lead to the formation of the pair bond as measured by this assay. This helps relate the authors recent study to the rest of the literature on oxytocin and partner preference in prairie voles. To better understand what might lead to slower partner preference, they quantified changes to the durations and frequency of huddling. In separate assays they also found that Oxtr1-/- KOs interacted more with stranger males than wild-type females. In a partner choice assay they found that wild-type males prefer wild-type females more than Oxtr1-/- KO females. They then performed bulk RNA-Seq profiling of nucleus accumbens of both wild-type and Oxtr1-/- KO males and females, either housed with animals of the same sex or paired with a wild-type of opposite sex. 13 differentially expressed genes were identified, mostly due to downregulation in wild-type females. These genes were also identified in a module lost in the Oxtr1-/- voles by correlated expression profiling. They also compared results of transcriptional profiling in female and male wild-type vs Oxtr1-/- voles (independently of bonding state), and found hundreds of differentially expressed genes in nucleus accumbens, mostly in females and often with some relation to neural development and/or autism. Some of the reduction in transcript was confirmed with in situs, as well as compared to changes in transcription in the lateral septum and paraventricular nucleus (PVN) of the hypothalamus. Finally they find fewer oxytocin+ and AVP+ neurons in the anterior PVN.

Strengths:

This is an important study helping to reveal the effects of oxytocin receptor knockout on behavior and gene expression. The experiments are thorough and reveal a surprising number of genetic and anatomical differences, with some sexual dimorphism as well, and the authors have more carefully examined the behavioral changes after shorter and longer periods of partner preference formation.

Weaknesses:

It is surprising that given all the genetic changes identified by the authors, that the behavioral phenotypes are fairly mild. The extent of gene changes also might be under-reported given the variability in the behavior and relative low number of animals profiled.

Comments on revisions:

No further recommendations. I commend the authors for finding the typos in their first version and correcting the manuscript.

Reviewer #1 (Public review):

The authors investigated the response of worms to the odorant 1-octanol (1-oct) using a combination of microfluidics-based behavioral analysis and whole-network calcium imaging. They hypothesized that 1-oct may be encoded through two simultaneous, opposing afferent pathways: a repulsive pathway driven by ASH, and an attractive pathway driven by AWC. And the ultimate chemotactic outcome is likely determined by the balance between these two pathways.

It is not surprising that 1-octanol is encoded as attractive at low concentrations and repulsive at higher concentrations. However, the novel aspect of this study is the discovery of the combinatorial coding of 1-oct in the periphery, where it serves as both an attractant and a repellent. Furthermore, the study uses this dual encoding as a model to explore the neural basis of sensory-driven behaviors at a whole-network scale in this organism. The basic conclusions of this study are well supported by the behavioral and imaging experiments, though there are certain aspects of the manuscript that would benefit from further clarification.

A key issue is that several previous studies have demonstrated a combinatorial and concentration-dependent coding of odorant sensing in the nematode peripheral nervous system. Specifically, ASH and AWC are the primary receptors for repellent and attractive responses, respectively. However, other neurons such as AWB, AWA, and ADL are also involved in the coding process. These neurons likely communicate with different interneurons to contribute to 1-oct-induced outputs. The authors' conclusion that loss of tax-4 reduces attractive responses and that osm-9 mutants reduce repulsive responses is not entirely convincing. TAX-4 is required for both AWC (an attractive neuron) and AWB (a repulsive neuron), and osm-9 is essential for ASH, ADL, and AWA (attraction-associated). Therefore, the observed effects on the attractive and repulsive responses could be more complex. Additionally, the interpretation of results involving the use of IAA to reduce the contribution of AWC at lower concentrations lacks clarity.

The authors did not observe any increased correlation between motor command interneurons and sensory neurons, which is consistent with the absence of a consistent relationship between state transitions and 1-oct application. Furthermore, they did not observe significant entrainment of AIB activity with the 2.2 mM 1-oct application. This might be due to the animals being anesthetized with 1 mM tetramisole hydrochloride, which could affect neural activity and/or feedback from locomotion.

Comments on revisions:

The authors have addressed all my previously raised concerns.

Reviewer #1 (Public review):

[Editors' note: this version has been assessed by the Reviewing Editor without further input from the original reviewers. The authors have addressed the comments raised in the previous round of review.]

Summary:

The Authors test the hypotheses, using and effort-exertion and an effort-based decision-making task, while recording brain dynamics with EEG, that the brain processes reward outcomes for effort differentially when they earned for themselves versus others.

Strengths:

The strengths of this experiment include what appears to be a novel finding of opposite signed effects of effort on the processing of reward outcomes when the recipient is self versus others. Also, the experiment is well-designed, the study seems sufficiently powered, and the data and code are publicly available.

Weaknesses:

There is some concern about the fact that participants report feeling less subjective effort, but also more disliking of tasks when they were earning rewards for others versus self. The concern is that participants worked with less vigor during self-versus-others trials and this may partly account for a key two-way Recipient x Effort interaction on the size of the Reward Positivity EEG component. Of note, participants took longer to complete tasks when working for others. While it is true that, in all cases, participants met the requisite task demands (they pressed the required number of buttons) they did so more sluggishly when earning rewards for others. The Authors argue that this reflects less motivation when working for others, which is a plausible explanation. The Authors also try to rule out this diminished vigor as a confounding explanation by showing that the two way interaction remains even when including reaction times (and also self-reported task liking) as a covariate. Nevertheless, it is possible that covariates do not fully account for the effects of differential motivation levels which would otherwise explain the two-way interaction. As such, I think a caveat is warranted regarding this particular result.

Reviewer #1 (Public review):

Summary:

This is a wonderful and landmark study in the field of human embryo modeling that uses patterned human gastruloids and conducts a functional screen on neural tube closure and identified positive and negative regulators and defines the epistasis among them.

Strengths:

This was achieved following optimization of micro-pattern based gastruloid protocol to achieve high efficiency, and then optimize was to conduct and deliver CRISPRi without disrupting the protocol. This is a technical tour de force as well as one of the first studies to reveal new knowledge on human development through embryo models which has not been done before.

Weaknesses:

A minor one. One can never find out if findings in human embryo models can be in vitro revalidated in humans in vivo for obvious and justified ethical reasons. However, the authors indicate that in the "limitations of study" section.

Comments on revisions:

The authors have adequately addressed all comments raised.

Reviewer #1 (Public review):

Summary:

This study investigates the role of the medial prefrontal cortex (mPFC) in generating goal-directed actions under threat, using a progressive behavioral paradigm, neural recordings, and optogenetic inhibition in mice. The authors demonstrate that while mPFC GABAergic neurons strongly encode cues, actions, and errors, particularly under high cognitive demand, this neural activity is not causally required for executing avoidance behaviors. By rigorously controlling for movement and arousal, the researchers found that much of the observed mPFC signaling actually reflects baseline behavioral states rather than the generation of the actions themselves. This dissociation between encoding and causality challenges traditional views of mPFC as an executive controller of action and provides a nuanced understanding of its role in evaluative and contextual processing.

Strengths:

The behavioral paradigm employed in this study is one of its greatest strengths, offering a rigorous, progressive, and well-controlled framework to dissect the neural mechanisms underlying avoidance under threat. This three-phase task design is particularly well-suited to tease apart the contributions of learning, discrimination, and cognitive load to both behavior and neural activity.

By tracking movement (speed, rotations) and including it as a covariate in statistical models, the authors also underscore the need to control for movement and baseline activity when interpreting cortical signals, which is relevant for all studies of brain-behavior relationships, ensuring that behavioral changes are not due to general arousal or motor activity.

Finally, the study combines multiple advanced techniques-fiber photometry, single-cell calcium imaging (miniscopes), and two distinct optogenetic inhibition methods-to provide a comprehensive look at both neural encoding and causal necessity.

Weaknesses:

The authors conclude that mPFC is not required for avoidance, based on the minimal behavioral effects of optogenetic inhibition. While this interpretation is supported by the data, the choice of viral constructs could lead to an underestimation of the mPFC's role for other reasons. First, the choice of viral constructs could lead to an underestimation of the mPFC's role for several reasons. Specifically, the efficacy of eArch3.0 inhibition was not verified beyond histology, and its non-cell-type-specific nature could lead to disinhibition or compensatory activity in downstream regions. Although the authors' use of visual cortex (VI) inhibition as a control suggests that broad cortical inhibition does not impair avoidance, subcortical compensation cannot be ruled out. Additionally, Vgat-ChR2 targets only GABAergic neurons, potentially missing glutamatergic contributions. Addressing these limitations in the Discussion section would strengthen the manuscript.

Reviewer #1 (Public review):

Summary:

Liao et al. present SCOPE (Spatial reConstruction via Oligonucleotide Proximity Encoding), a method for reconstructing spatial organization from diffusion-defined DNA barcode interactions without the use of optical imaging. In SCOPE, hydrogel beads bearing unique DNA barcodes contain both "sender" and "receiver" oligonucleotides. Upon enzymatic release, sender oligos diffuse locally and hybridize to receiver oligos on neighboring beads, forming chimeric molecules that encode spatial proximity. Sequencing these products yields an interaction matrix, which is then used to reconstruct a spatial coordinate map.<br /> The authors demonstrate reconstruction of synthetic two-dimensional shapes, a large multicolor Snellen eye chart, and the interior surface of three-dimensional molds. The work expands the conceptual and experimental landscape of optics-free spatial sequencing.

Strengths:

SCOPE employs bidirectional sender and receiver oligonucleotides on every bead, rather than using asymmetric transmitter-receiver architectures found in other diffusion-based methods. The symmetric design may improve detection sensitivity and reconstruction strategies, and represents a meaningful variation on optics-free spatial encoding.

A notable strength of this study is the physical scale achieved. The authors reconstruct a Snellen chart spanning approximately 704 mm² and demonstrate molded 3D structures on the order of 75-100 mm³. Although some larger-scale warping is evident, and is discussed as potentially due to non-uniform diffusion, the relative local positioning across these large areas appears impressively accurate.

The authors extend reconstruction beyond two-dimensional arrays to three-dimensional molded surfaces. This demonstrates that the assay and the computational methods for interpreting proximity graphs can support non-planar spatial relationships, expanding the scope of optics-free spatial inference.

Weaknesses:

Although the method is discussed in the context of spatial genomics and potential tissue applications, it is currently demonstrated only on engineered two-dimensional bead arrays and three-dimensional shapes fabricated in molds. It remains unclear how SCOPE would perform in heterogeneous biological environments, where diffusion may exhibit additional non-uniformities. A biological proof-of-concept, even limited in scope, would help define the method's strengths and limitations more clearly.

The reconstruction of three-dimensional structures lacks strong sampling from volume interiors. This is speculated to be due to several possible factors; however, this limitation constrains the method to reconstruction of volume surfaces rather than comprehensive three-dimensional profiling.

The reconstruction workflow involves multiple preprocessing steps and embedding choices. While these appear to work well for synthetic shapes with known geometry, it is less clear how parameter choices would be made in contexts where ground truth is unknown. Clarifying how reconstruction robustness is assessed without prior knowledge of spatial structure would help readers understand how the method could be practically deployed, particularly in more heterogeneous tissue contexts.

Reviewer #1 (Public review):

Summary:

This study demonstrates, through a series of EEG and MEG experiments, that the human brain automatically categorizes words from alphabetic and non-alphabetic languages, and it unpacks the neural mechanisms of this process from multiple angles. The work examines not only univariate repetition-suppression (RS) effects, but also how repeating or alternating languages influences the representational similarity of words within and across language categories.

Strengths:

The univariate RS effects across multiple experiments lend support to some of the main conclusions

Weaknesses:

I have reservations about the logic underlying the multivariate analyses, and I believe the implications of the control experiments merit fuller discussion.

(1) Question 1: Logic of the multivariate analyses

The original text states:

"The processing of intra-language similarity was quantified as correlation distances between neural responses to two words of the same language, which occurred more frequently and would be inhibited in the Rep-Cond (vs. Alt-Cond) due to habituation (Fig. 1c)...".

I argue that this passage conflates two levels. Building a representational dissimilarity matrix (RDM) is a data-analysis step; it cannot be equated with a cognitive computation. Hence, there is no sense in which this computation occurs "more frequently" in one condition. RDM construction rests on the pairwise similarity of activity patterns, so even if a task engaged no cognitive computation of representational similarity, we could still compute an RDM. Conversely, if a task factor alters the RDM, we must explain how that factor changes the underlying neural patterns, not claim that it triggers specific cognitive processing. Therefore, I neither understand what "more frequent processing" the authors refer to, nor accept their account of the multivariate results.

The multivariate result pattern, briefly, is that distances between words, both within and across languages, are larger under the repetition condition. One plausible interpretation is that a word representation comprises two parts: language-type (alphabetic vs. non-alphabetic) and fine-grained identity features (visual shape, orthography, semantics, phonology, etc.). Repetition of language type may, via RS, reduce the weight of the first component, thereby increasing the relative contribution of fine-grained features and amplifying inter-word differences. This could explain the multivariate findings.

(2) Question 2:

For unlearned languages, people cannot distinguish lexical from sub-lexical levels. What, then, determines (i) the RS-effect difference between letters and radicals in familiar languages and words in unlearned ones, and (ii) the similarity of repetition effects between words in unlearned and familiar languages? An explicit account is needed.

Reviewer #1 (Public review):

Summary:

The behaviour of cells expressing constitutively active HRas is examined in mosaic monolayers, both in MCF10a breast epithelial and Beas2b bronchial epithelial cell lines, mimicking the potential initial phase of development of carcinoma. Single HRas-positive cells are excluded from MCF10a but not Beas2b monolayers. Most interestingly, however, when in groups, these cells are not excluded, but rather sharply segregated within a MCF10a monolayer. In contrast, they freely mix with wt Beas2b cells. Biophysical analysis identifies high tension at heterotypic interfaces between HRas and wild-type cells as the likely reason for segregation of MCF10a cells. The hypothesis is supported experimentally, as myosin inhibition abolishes segregation. The probable reason for lack of segregation in the bronchial epithelium is to be found in the different intrinsic properties of these cells, which form a looser tissue with lower basal actomyosin activity. The behaviour of single cells and groups is recapitulated in a vortex model based on the principle of differential interfacial tension, under the condition of high heterotypic interfacial tension.

Strengths:

Despite being long recognized as a crucial event during cancer development, segregation of oncogenic cells has been a largely understudied question. This nice work addresses the mechanics of this phenomenon through a straightforward experimental design, applying the biophysical analytical approaches established in the field of morphogenesis. Comparison between two cell types provides some preliminary clues on the diversity of effects in various cancers.

Weaknesses:

Although not calling into question the main message of this study, there are a few issues that one may want to address:

(1) One may be careful in interpreting the comparison between MCF10a and Beas2b cells as used in this study. The conditions may not necessarily be representative of the actual properties of breast and bronchial epithelia. How much of the epithelial organization is reconstituted under these experimental conditions remains to be established. This is particularly obvious for bronchial cells, which would need quite specific culture conditions to build a proper bronchial layer. In this study, they seemed to be on the verge of a mesenchymal phenotype (large gaps, huge protrusions, cells growing on top of each other, as mentioned in the manuscript).

As an alternative to Beas2b, comparison of MCF10a with another cell line capable of more robust in vitro epithelial organization, but ideally with different adhesive and/or tensile properties, would be highly interesting, as it may narrow down the parameters involved in segregation of oncogenic cells.

(2) While the seminal description of tissue properties based on interfacial tensions (Brodland 2002) is clearly key to interpreting these data, the actual "Differential Interfacial Tension Hypothesis" poses that segregation results from global differences, i.e., juxtaposition of two tissues displaying different intrinsic tensions. On the contrary, the results of the present work support a different scenario, where what counts is the actual difference in tension ALONG the tissue boundary, in other words, that segregation is driven by high HETEROTYPIC interfacial tension. This is an important distinction that should be clarified.

(3) Related: The fact that actomyosin accumulates at the heterotypic interface is key here. It would be quite informative to better document the pattern of this accumulation, which is not clear enough from the images of the current manuscript: Are we talking about the actual interface between mutant and wt cells (membrane/cortex of heterotypic contacts)? Or is it more globally overactivated in the whole cell layer along the border? Some better images and some quantification would help.

(4) In the case of Beas2b cells, mutant cells show higher actin than wt cells, while actin is, on the contrary, lower in mutant MCF10a cells (Figure 2b). Has this been taken into account in the model? It may be in line with the idea that HRas may have a different action on the two cell types, a possibility that would certainly be worth considering and discussing.

Comments on revisions:

There is still one last point that should be made even clearer:

The system is being modelled based on the principle of INTERFACIAL TENSION, a description pioneered by the works of Steinberg and of Harris, and nicely conceptualized by Brodland (2002). Now the observed behaviour is a perfect case of sorting based on higher interfacial tension AT the boundary between cell types (with nice additional documentation of local actin and myosin enrichment in the revised manuscript). What needs to be made crystal clear it that this is NOT equivalent to the model of DITH ("DIFFERENTIAL INTERFACIAL TENSION HYPOTHESIS)" (Brodland 2002, Krieg et al 2008). It is important to stop using DITH in this context, as it leads to confusion and misinterpretations. Indeed, DITH predicts cell/tissue sorting based on differences in interfacial tension WITHIN the two cell types. While DITH accounts for relative POSITIONING (one tissue engulfing the other), it is now established that this is not the motor for cell sorting and tissue segregation, the key parameter is being heterotypic tension at the heterotypic interface. I thus invite the authors to avoid the terms "differential"/DITH, and rather use either "interfacial tension", or specifically to "HIGH HETEROTYPIC INTERFACIAL TENSION".

Related: the authors correctly cite Canty et al NatComm2017 when discussing this phenomenon. I suggest to add an additional key supporting reference "D.M. Sussman, J.M. Schwarz, M.C. Marchetti, M.L. Manning, Soft yet sharp interfaces in a vertex model of confluent tissue, Phys. Rev. Letters 120 (2018) 058001". One may also include another pioneer work in Drosophila is "M. Aliee, J.C. Roper, K.P. Landsberg, C. Pentzold, T.J. Widmann, F. Julicher, C. Dahmann, Physical mechanisms shaping the Drosophila dorsoventral compartment boundary, Curr. Biol. 22 (2012) 967-976."

Reviewer #1 (Public review):

Summary:

The aim of this work is to directly image collagen in tissue using a new MRI method with positive contrast. The work presents a new MRI method that allows very short, powerful radio frequency (RF) pulses and very short switching times between transmission and reception of radio frequency signals.

Strengths:

The experiments with and without removal of 1H hydrogen, which is not firmly bound to collagen, on tissue samples from tendons and bones are very well suited to prove the detection of direct hydrogen signals from collagen. The new method has great potential value in medicine, as it allows for better investigation of ageing processes and many degenerative diseases in which functional tissue is replaced by connective tissue (collagen).

Comments on revisions:

All points of criticism in the reviews were answered very well and led to further improvement of the article.

Reviewer #1 (Public review):

Summary:

In this study, Angla et al investigate the basis of observations made from previous studies where loss of Onecut (OC) transcription factors leads to changes in spinal interneuron populations that do not themselves normally express OC. The authors hypothesize that OC expression in spinal motor neurons has non-cell-autonomous effects on pre-motor interneuron (V1, V2a/b/c) population size and distribution. By knocking out OC in the motor neuron lineage (i.e., downstream of Olig2, a motor neuron progenitor marker gene), they indeed show that motor neuron-specific loss of OC expression decreases V2c interneuron number and alters the spatial distribution of V1, V2a, V2b, and V2c populations. Using bulk RNA-sequencing of WT and OC conditional knockout (cKO) motor neurons, the authors identify that the neurotrophic factor Ntf3 is downregulated by OC expression. They subsequently hypothesize that the non-cell-autonomous effects observed by loss of OC expression in motor neurons can be explained by de-repression of Ntf3. To test this, the authors conditionally knock out Ntf3 downstream of Olig2 and show that this leads to increased interneuron numbers and alters their spatial distribution, ultimately leading to dysregulation of spinal motor circuits and motor activity.

Strengths:

The authors use sophisticated genetic tools to precisely remove OC and Ntf3 expression in a lineage-specific manner and comprehensively assess the downstream effects across brachial, thoracic, lumbar levels of the spinal cord, as well as at two developmental timepoints, E12.5 and E14.5.

Weaknesses:

There are two main concerns that are not fully addressed:

(1) Based on the effects observed with OC vs. Ntf3 cKO, it is unclear whether OC is indeed exerting its non-cell-autonomous effects via Ntf3. Knocking out both Ntf3 and OC and comparing the effects to those seen with just OC cKO alone could provide more insight on this point. Also, a quantitative summary of the effects of Ntf3 overexpression in motor neurons in the chick is lacking.

(2) How the authors assess changes in the spatial distribution of interneurons is unclear. In Figures 2 and 4, the control distributions (despite reporting the same populations in the same regions) look different, suggesting large sample-to-sample variance in distribution. Although the authors report that several sections in each level were taken from at least three animals for each condition, it's unclear how variance within WT or cKO sections was accounted for in the final statistical evaluation. It seems at a glance that a comparison between control samples in Figure 2 and Figure 4 could report statistically significant differences, which would be problematic. A more rigorous report of sample-to-sample variance and a more in-depth explanation of the statistical methods are needed.

Reviewer #1 (Public review):

Summary:

In this manuscript, Zmojdzian et al. provide an analysis of ryanodine receptor (RyR) expression and function in Drosophila. They also use CRISPR to engineer into flies a RyR variant of unknown significance (VUS) found in a human myopathy patient and demonstrate that it is likely a pathogenic mutation. From studies of RyR expression in embryonic and larval stages, and effects of RyR knockdown or overexpression in various muscle groups, the authors show that, in addition to its known actions in calcium-dependent excitation-contraction coupling, RyR promotes myogenesis during development.

The key conclusions of the paper are convincing. I do not have suggestions for necessary additional experimental work, and my comments are minor. One conclusion, that RyR dysfunction may be involved in aging, is stated in multiple places, sometimes speculatively but once very forcefully. The latter is in the final paragraph of the Discussion, which states RyR "plays an instrumental anti-aging role in differentiated striated muscle". This conclusion must be tempered, as even if RyR knockdown phenotypes resemble some of those seen in aging flies, the study does not examine aged flies, and there is no mechanistic analysis that might link the two. I assume the authors would prefer to modify that sentence than initiate work with aging flies to prove the assertion. Finally, the use of CRISPR to test a VUS is excellent and suggests a good way for testing of additional RyR variants in the future.

Significance:

The paper is significant in that RyR is known to be a critical protein in calcium-dependent excitation-contraction coupling but its role in developmental myogenesis is poorly studied. This study demonstrates that it is expressed during, and is important for, embryonic and larval myogenesis in the fly. RyR is also understudied in this valuable model organism, even though a P element-based mutant has been available since 2000. The mechanistic basis for the functional observations is not explored here but the work is well performed and will be of interest to investigators studying muscle development (my own field) and diseases caused by RyR mutations.

Reviewer #1 (Public review):

This is a very interesting paper. The research question is intriguing, allowing the authors to address commonly observed comorbidities between depression and anxiety and their dissociable and opposite relationship to mood fluctuations and sensitivity to reward prediction errors. The computational analyses are very in-depth, including many state-of-the-art checks and validations. Another strength is the inclusion of several large or very large samples, including a patient sample in addition to the general population sample.

I have the following questions:

(1) Factor analysis I found the hierarchical organization of the factors interesting. While this is a very common procedure in, for example, the field of intelligence (producing sub-scores and a general g factor), it is not yet very commonly used in the field of computational psychiatry (though it has been validated before for anxiety/depression, so it is used here with good reason). I was also impressed by the methodological depth. In particular, it was of note how thoroughly done it was (for example, repeating the EFA on the second half of the data set). I have one question though: is the sample size too small for the exploratory analyses, given the number of items? Given the stability across the half-split, I imagine it is not. Perhaps the authors could spell out how many items, what would be the recommended standard for a subject-to-item ratio, and comment on this. A very technical point, the authors should specify how they extracted the factor scores from the other data sets (is it using the Thurstone or Bartlett method)? From experience (though not doing a hierarchical factor analysis), Bartlett can be somewhat better compared to the default (Thurstone) - better as in the resulting factors more closely recapitulating the factor correlations in the original sample (and independence of responses of other participants in a sample for computing a person's factor score). Could you also comment on similarities or divergences in this hierarchical factor analysis approach from another one recently used transdiagnostically in Wise et al. (2026, Translational Psychiatry)?

(2) Linking factors to task parameters As I understand it, the authors relate the orthogonalized depression/anxiety to task parameters (sensitivity to RPEs on mood and mood variations) using correlations. In order to have a better understanding of how this relates to other commonly used approaches, I would pose two questions:

(i) What are the correlations when the full (non-orthogonalized) factor scores for depression and anxiety are used? Are the signs the same? (ii) What are the results when, instead of the independent correlations, the authors perform b_RPE ~ anxiety + depression (again using the non-orthogonalized factors)?

I'm assuming all of these analyses should give the same results if the authors' hypothesis of opposing effects of anxiety and depression holds true.

Minor comments:

(1) The authors should write down when the data were collected for each study. This is because AI capabilities have massively increased since ~2020 in quite specific steps (with the public release of new AI models), meaning that AI is likely to have been able to do tasks and questionnaires without detection if data were collected recently.

(2) The authors should include a statement in the methods section that checks for AI were done. If none yet, could you do any? Recent papers (Westwood, PNAS 2025; van der Stigchel PNAS, 2026) point to the risk since at least the release of o4-mini (used in the cited paper to create very human-like behaviour).

(3) It would have been good to collect questionnaires of other, thought to be unrelated psychiatric traits, like compulsivity or schizophrenia symptoms, to check the specificity of the results, also under the assumption that higher scores on either of these skewed questionnaires can pick up individual differences in 'bad questionnaire completion'. The authors should comment on the absence of other questionnaires in the discussion in the limitations section.

(4) The authors could include a more explicit sentence in the abstract stating that the anxiety result did not hold up in the clinical population.

Reviewer #1 (Public review):

Summary:

This is a study utilizing several types of analyses (computational modeling, neuronal cultures, rodent epilepsy model, and human intracranial multi-scale recordings) to address a highly relevant conceptual question: Are fast ripples (FRs) distinct pathological entities or largely emergent products of stochastic spike clustering? The results can potentially reshape current approaches to incorporating fast ripples into the epilepsy surgery evaluation.

Strengths:

The conceptualization of fast ripples as potentially arising by chance is highly novel and builds effectively on questions raised in prior studies that have never been satisfactorily resolved.

The integration across biological scales and models is a major strength. The state dependency analysis provides additional, strong support. The methodology and statistical approaches used are thoughtfully presented and rigorously applied.

In particular, this paper provides a strong response to the findings from Gliske et al, Nat Commun 2018. This study utilized long-term data analysis to uncover low rates of FRs detected from most recording sites, suggesting spurious detections, although FRs were concentrated within seizure onset areas.

Weaknesses:

The authors clearly aimed to use a statistical rather than a mechanism-based approach in this work. However, the paper's framing of true fast ripples as oscillatory events with stochastic fast ripples considered as confounders does not take prior investigations into biological mechanisms, particularly prior studies that point to an important role for stochastic fast ripples in some contexts. Incorporating recognition of these mechanisms would strengthen the manuscript and provide a more complete and nuanced characterization.

Some examples from the literature:

Eissa et al, eNeuro 2016, a paper that closely parallels this manuscript but took a mechanistic rather than statistical approach, showed that fast ripples can arise from population paroxysmal depolarizations - a key feature of epileptiform discharges - as temporally clustered, jittered population firing, with FRs appearing in LFP or EEG due to summated postsynaptic potentials (which are slower than action potentials and can generate signals in the high gamma range).

Foffani et al., 2007, Neuron, and Ibarz et al., 2010, J Neurosci, argue that FRs are pseudo-oscillations created by jittered neuronal populations in the setting of altered spike timing.

Smith et al., 2020, Sci Rep, contrasts FR characteristics in different regimes, i.e., intact inhibition early in a seizure vs. implied collapse of inhibition after recruitment. Schlingloff et al., 2025, J Neurosci, reported analogous findings in an animal model.

The computational model and subtraction approach provide a strong case for the random emergence of clustered activity in the high gamma band, given its assumptions. However, any such modeling effort needs to account for inhibitory activity, including impaired inhibitory function that is expected in epileptic brain regions, which has a strong modulating effect on excitatory firing and is thought to play a significant role in FR generation.

The shuffling procedure aims to preserve the power spectrum but randomizes high frequency phase (>200 Hz). However, this procedure removes biologically meaningful spike timing correlations, as well as structured cross-frequency coupling. The subtraction method thus likely underestimates the incidence of structured "distinct" FRs, while perhaps overestimating "chance" FRs due to biologically infeasible activity, making the statement that most FRs are due to chance correlation too strong.

The kainate findings underscore this point: the increase in the number of FR detections could be, as the authors state, an increase in chance clustering due to increased network excitability generally. However, the likelihood of a parallel increase in pathological FRs cannot be ruled out, given likely pro-epileptic alterations in spike timing and circuit function.

Reviewer #1 (Public review):

Summary:

This study examines whether gaze direction actively shapes choice during food preference decisions or whether gaze and choice evolve largely independently until the moment of commitment. The established framework in this context, the aDDM, assumes that gaze causally biases the accumulation of evidence in favour of the fixated item. The authors show convincingly that this model fails to fit key behavioural patterns across several datasets, as do other published models that make the same assumption. The authors propose an alternative model (Post-Decision-Gaze or PDG) in which gaze and decision formation are decoupled: gaze does not influence the decision process, nor is it drawn toward the ultimately chosen item, until after the decision threshold is reached. Only during the motor execution period (after commitment) is gaze directed to the chosen option. They demonstrate that this model fits several observed patterns better than the aDDM and related variants.

Strengths:

The work thoroughly considers multiple models and datasets. It advances an interesting alternative perspective on gaze-decision interactions and highlights meaningful shortcomings in existing models. The authors take the time to explain how modelling assumptions produce specific patterns in the data, which is certainly insightful to readers interested in the modelling of value-based decision making.

Weaknesses:

It is unclear to what extent the model's success relies on the way non-decision time is formalised in the model. In the proposed PDG model, non-decision time is decomposed into separate visual encoding, saccadic execution, and manual execution components. Several values (assumed or recovered) do not match known physiological or behavioural ranges. This is a common issue in the literature, and the authors may want to address it in light of broader work discussing what non-decision time consists of in both manual and saccadic actions (e.g., Bompas et al., 2024, Non decision time: the Higgs boson of decision, Psychological Review).

In particular, the "saccadic execution" parameter appears far too long and too variable to reflect merely execution; instead, it likely includes decisional components. This would make more sense since manual and saccadic planning essentially rely on distinct brain areas, hence it seems unrealistic that crossing a single threshold would trigger both manual and saccadic execution. Similarly, recovered manual non-decision times are substantially longer (though not more variable) than expected motor execution durations for button presses. These patterns suggest that parts of what the model treats as non-decision time are likely decisional in nature, although perhaps related to "action decision" rather than the "value-based decision" of interest to the authors. To what extent these two processes neatly follow each other or overlap could be usefully considered.

Reviewer #1 (Public review):

Summary:

This study examines whether gaze direction actively shapes choice during food preference decisions or whether gaze and choice evolve largely independently until the moment of commitment. The established framework in this context, the aDDM, assumes that gaze causally biases the accumulation of evidence in favour of the fixated item. The authors show convincingly that this model fails to fit key behavioural patterns across several datasets, as do other published models that make the same assumption. The authors propose an alternative model (Post-Decision-Gaze or PDG) in which gaze and decision formation are decoupled: gaze does not influence the decision process, nor is it drawn toward the ultimately chosen item, until after the decision threshold is reached. Only during the motor execution period (after commitment) is gaze directed to the chosen option. They demonstrate that this model fits several observed patterns better than the aDDM and related variants.

Strengths:

The work thoroughly considers multiple models and datasets. It advances an interesting alternative perspective on gaze-decision interactions and highlights meaningful shortcomings in existing models. The authors take the time to explain how modelling assumptions produce specific patterns in the data, which is certainly insightful to readers interested in the modelling of value-based decision making.

Weaknesses:

It is unclear to what extent the model's success relies on the way non-decision time is formalised in the model. In the proposed PDG model, non-decision time is decomposed into separate visual encoding, saccadic execution, and manual execution components. Several values (assumed or recovered) do not match known physiological or behavioural ranges. This is a common issue in the literature, and the authors may want to address it in light of broader work discussing what non-decision time consists of in both manual and saccadic actions (e.g., Bompas et al., 2024, Non decision time: the Higgs boson of decision, Psychological Review).

In particular, the "saccadic execution" parameter appears far too long and too variable to reflect merely execution; instead, it likely includes decisional components. This would make more sense since manual and saccadic planning essentially rely on distinct brain areas, hence it seems unrealistic that crossing a single threshold would trigger both manual and saccadic execution. Similarly, recovered manual non-decision times are substantially longer (though not more variable) than expected motor execution durations for button presses. These patterns suggest that parts of what the model treats as non-decision time are likely decisional in nature, although perhaps related to "action decision" rather than the "value-based decision" of interest to the authors. To what extent these two processes neatly follow each other or overlap could be usefully considered.

Reviewer #1 (Public review):

This manuscript investigates how chemogenetic depolarization of medial entorhinal cortex layer II stellate cells reshapes spatial coding in downstream hippocampal CA1. Building on the authors' prior work (Kanter et al., Neuron 2017), the study examines changes in grid cell subfield firing rates and CA1 place cell firing patterns after CNO administration. A central advance of the present work is the use of the same manipulation on two consecutive days. The authors show that the induced grid subfield rate changes are highly similar across days and that CA1 place field reorganization is likewise reproducible across days. In addition, they report that CA1 remapping after CNO is not arbitrary. The new main place field often emerges at a location that can be anticipated from the baseline rate map of the same cell, typically corresponding to a weak secondary peak outside the primary field. Finally, the authors demonstrate that these experimental findings can be recapitulated in a feedforward grid to place cell model by selectively redistributing grid subfield firing rates, supporting the interpretation that grid subfield rate changes are sufficient to drive predictable and reproducible place field reorganization.

Overall, this study is positioned as a follow-up to the authors' previous report in which the main phenomenon (grid subfield rate remapping and accompanying CA1 place cell remapping following chemogenetic depolarization of MEC layer II neurons) was already established. While the conceptual novelty is therefore incremental, the present manuscript adds important and convincing evidence about two key properties of this phenomenon, including its reproducibility across days and the extent to which the direction of place field reorganization is predictable from baseline activity. The experimental approach and analyses appear generally appropriate and carefully executed, and the inclusion of modeling strengthens the mechanistic interpretation. These results provide useful new insight into stable input-output relationships within the entorhinal hippocampal system, and the work will be of interest to researchers studying remapping and the grid to place cell transformation.

Reviewer #1 (Public review):

This study by Riegman & George et al. investigates the roles of the chromatin remodeling factor CHD7 and the proneural transcription factor Atoh1 at enhancers in cerebellar granule cells (GCs). Enhancers were categorized based on epigenetic marks and cross-referenced with promoter capture-HiC, ATAC-seq, and expression datasets to identify their long-range target genes, which were found to be enriched for critical neurodevelopmental processes. Differential expression and chromatin accessibility analyses in CHD7 knockout (KO) conditions suggest that this factor regulates a significant number of enhancers. These same enhancers are enriched for proneural transcription factor motifs, with Atoh1 being the most frequently present and likely the most affected. Finally, the direct interaction between CHD7 and Atoh1 was assessed via co-immunoprecipitation in co-transfected cells.

While the paper presents an interesting aspect of enhancer regulation in neurodevelopment, several points warrant attention:

Major Strengths:

The use of chromatin marks increases the resolution of promoter-interacting enhancer regions when integrated with capture-HiC, refining the identification of distal enhancers. Additionally, performing promoter capture-HiC experiments for the first time in this cell type constitutes a valuable resource for the community working on 3D genome organization and neurodevelopment.

Major Weaknesses:

As noted by the authors, limited sequencing depth reduces confidence in the conclusions and may result in missed weaker long-range interactions. Furthermore, the absence of capture-HiC and Atoh1 ChIP-seq experiments in the KO condition prevents direct comparison, thereby limiting the strength of the conclusions.

Additional Consideration:

Caution should be exercised regarding the assumption that every enhancer must physically contact its target promoter. While true for many enhancers, some act in trans through eRNAs or lncRNAs without direct physical contact.