Reviewer #1 (Public Review):

This manuscript by Xu and colleagues addresses the important question of how multi-modal associations are encoded in the rodent brain. They use behavioral protocols to link stimuli to whisker movement and discover that the barrel cortex can be a hub for associations. Based on anatomical correlations, they suggest that structural plasticity between different areas can be linked to training. Moreover, they provide electrophysiological correlates that link to behavior and structure. Knock-down of nlg3 abolishes plasticity and learning.

This study provides an important contribution as to how multi-modal associations can be formed across cortical regions.

Reviewer #1 (Public Review):

Soudi, Jahani et al. provide a valuable comparative study of local adaptation in four species of sunflowers, and investigate the repeatability of observed genomic signals of adaptation and their link to haploblocks, known to be numerous and important in this system. The study builds on previous work in sunflowers that have investigated haploblocks in those species and on methodologies developed to look at repeated signals of local adaptations. The authors provide solid evidence of both genotype-environment associations (GEA) and genome-wide association study (GWAS), as well as phenotypic correlations with the environment, to show that part of the local adaptation signal is repeatable and significantly co-occur in regions harboring haploblocks. Results also show that part of the signal is species specific and points to high genetic redundancy. This work will be of interest to evolutionary biologists in general and population geneticists in particular, and constitutes a good example of comparative local adaptation. Importantly, this study helps in advancing our understanding of the genetic architecture implicated in the adaptation process.

Strenghts: The authors take great care in acknowledging and investigating the multiple biases inherent to the used methods (GEA and GWAS) and use conservative and well thought statistical approaches to draw their conclusions. Additionally, I appreciated the nuanced discussion and can only agree with the authors that the adaptation process is complex and does not fully fit the classic simplified genetics models of either few large effect genes or only infinitesimal quantitative traits. I find the added Summary figure of this revised version (S1) extremely helpful in better understanding the different analysis steps and how they relate to the different questions.

Weaknesses: After those revisions, I did not find any major weakness and am satisfied with the authors responses.

Reviewer #1 (Public Review):

Summary:<br /> The manuscript of Davidsen and Sullivan describes an improved tRNA-seq protocol to determine aminoacyl-tRNA levels. The improvements include: (i) optimizing the Whitfeld or oxidation reaction to select aminoacyl-tRNAs from oxidation-sensitive non-acylated tRNAs; (ii) using a splint-assisted ligation to modify the tRNAs' ends for the following RT-PCR reaction; (iii) using an error-tolerating mapping algorithm to map the tRNA sequencing reads that contain mismatches at modified nucleotides.

Strengths:<br /> The two steps, the oxidation, and the splint-assisted ligation are yield-diminishing steps, thus the protocol of Davidsen and Sullivan is an important improvement of the current protocols to enhance the quantification of aminocyl-tRNAs.

Weaknesses:<br /> The oxidation and the selection of aminoacyl-tRNA is the first step in all protocols. Thereafter they differ on whether blunt ligation, hairpin (DM-tRNA-seq, YAMAT-seq, QuantM-seq, mim tRNA-seq, LOTTE tRNA-seq), or splint ligation is used and finally what detection method is applied (i-tRAP, tRNA microarrays). What is the correlation to those alternative approaches (e.g. i-tRAP (PMID 36283829), tRNA microarrays (PMID: 31263264) etc.)? What is the correlation with other approaches with which this improved protocol shares some steps (DM-tRNA-seq, mim-tRNA-seq)?

Reviewer #1 (Public Review):

Summary:<br /> The authors present a neural network (NN)-based approach to computationally cheaper emulation of simulations of biophysically relatively detailed cardiac cell models based on systems of ordinary differential equations. Relevant case studies are used to demonstrate the performance in the prediction of standard action potentials, as well as action potentials manifesting early depolarizations. Application to the "reverse problem" (inferring the effect of pharmacological compounds on ion channels based on action potential data before and after drug treatment) is also explored, which is a task of generally high interest.

Strengths:<br /> This is a well-designed study, which explores an area that many in the cardiac simulation community will be interested in. The article is well written and I particularly commend the authors on transparency of methods description, code sharing, etc. - it feels rather exemplary in this regard and I only wish more authors of cardiac simulation studies took such an approach. The training speed of the network is encouraging and the technique is accessible to anyone with a reasonably strong GPU, not needing specialized equipment.

Weaknesses:<br /> Below are several points that I consider to be weaknesses and/or uncertainties of the work:

1. I am not convinced by the authors' premise that there is a great need for further acceleration of cellular cardiac simulations - it is easy to simulate tens of thousands of cells per day on a workstation computer, using simulation conditions similar to those of the authors. I do not really see an unsolved task in the field that would require further speedup of single-cell simulations.

At the same time, simulations offer multiple advantages, such as the possibility to dissect mechanisms of the model behaviour, and the capability to test its behaviour in a wide array of protocols - whereas a NN is trained for a single purpose/protocol, and does not enable a deep investigation of mechanisms. Therefore, I am not sure the cost/benefit ratio is that strong for single-cell emulation currently.

An area that is definitely in need of acceleration is simulations of whole ventricles or hearts, but it is not clear how much potential for speedup the presented technology would bring there. I can imagine interesting applications of rapid emulation in such a setting, some of which could be hybrid in nature (e.g. using simulation for the region around the wavefront of propagating electrical waves, while emulating the rest of the tissue, which is behaving more regularly/predictable, and is likely to be emulated well), but this is definitely beyond of the scope of this article.

2. The authors run a cell simulation for 1000 beats, training the NN emulator to mimic the last beat. It is reported that the simulation of a single cell takes 293 seconds, while emulation takes only milliseconds, implying a massive speedup. However, I consider the claimed speedup achieved by emulation to be highly context-dependent, and somewhat too flattering to the presented method of emulation. Two specific points below:

First, it appears that a not overly efficient (fixed-step) numerical solver scheme is used for the simulation. On my (comparable, also a Threadripper) CPU, using the same model ("ToR-ORd-dyncl"), but a variable step solver ode15s in Matlab, a simulation of a cell for 1000 beats takes ca. 50 seconds, rather than 293 of the authors. This can be further sped up by parallelization when more cells than available cores are simulated: on 32 cores, this translates into ca. 2 seconds amortized time per cell simulation (I suspect that the NN-based approach cannot be parallelized in a similar way?). By amortization, I mean that if 32 models can be simulated at once, a simulation of X cells will not take X*50 seconds, but (X/32)*50. (with only minor overhead, as this task scales well across cores).

Second, and this is perhaps more important - the reported speed-up critically depends on the number of beats in the simulation - if I am reading the article correctly, the runtime compares a simulation of 1000 beats versus the emulation of a single beat. If I run a simulation of a single beat across multiple simulated cells (on a 32-core machine), the amortized runtime is around 20 ms per cell, which is only marginally slower than the NN emulation. On the other hand, if the model was simulated for aeons, comparing this to a fixed runtime of the NN, one can get an arbitrarily high speedup.

Therefore, I'd probably emphasize the concrete speedup less in an abstract and I'd provide some background on the speedup calculation such as above, so that the readers understand the context-dependence. That said, I do think that a simulation for anywhere between 250 and 1000 beats is among the most reasonable points of comparison (long enough for reasonable stability, but not too long to beat an already stable horse; pun with stables was actually completely unintended, but here it is...). I.e., the speedup observed is still valuable and valid, albeit in (I believe) a somewhat limited sense.

3. It appears that the accuracy of emulation drops off relatively sharply with increasing real-world applicability/relevance of the tasks it is applied to. That said, the authors are to be commended on declaring this transparently, rather than withholding such analyses. I particularly enjoyed the discussion of the not-always-amazing results of the inverse problem on the experimental data. The point on low parameter identifiability is an important one and serves as a warning against overconfidence in our ability to infer cellular parameters from action potentials alone. On the other hand, I'm not that sure the difference between small tissue preps and single cells which authors propose as another source of the discrepancy will be that vast beyond the AP peak potential (probably much of the tissue prep is affected by the pacing electrode?), but that is a subjective view only. The influence of coupling could be checked if the simulated data were generated from 2D tissue samples/fibres, e.g. using the Myokit software.

Given the points above (particularly the uncertain need for further speedup compared to running single-cell simulations), I am not sure that the technology generated will be that broadly adopted in the near future. However, this does not make the study uninteresting in the slightest - on the contrary, it explores something that many of us are thinking about, and it is likely to stimulate further development in the direction of computationally efficient emulation of relatively complex simulations.

Reviewer #1 (Public Review):

In this study, the authors demonstrated a new model that B cell contraction after antigen encountering was dependent on N-WASP-branched actin polymerization. This statement is achieved by a systemic comparison of genetic modified mice vs wild type mice or inhibitor treated cells vs control cells. By imaging how B cells interact with antigen-coated planar lipid bilayer, the authors further suggested that the contraction event may provide B cells a channel to dismiss downstream kinase for a purpose to attenuate B cell activation signaling.

In this revised version, the authors have fully addressed my concerns raised against the initial submission of their studies.

Reviewer #1 (Public Review):

Summary:

The investigators sought to determine whether Marco regulates the levels of aldosterone by limiting uptake of its parent molecule cholesterol in the adrenal gland. Instead, they identify an unexpected role for Marco on alveolar macrophages in lowering the levels of angiotensin-converting enzyme in the lung. This suggests an unexpected role of alveolar macrophages and lung ACE in the production of aldosterone.

Strengths:

The investigators suggest an unexpected role for ACE in the lung in the regulation of systemic aldosterone levels.<br /> The investigators suggest important sex-related differences in the regulation of aldosterone by alveolar macrophages and ACE in the lung.<br /> Studies to exclude a role for Marco in the adrenal gland are strong, suggesting an extra-adrenal source for the excess Marco observed in male Marco knockout mice.

Weaknesses:

While the investigators have identified important sex differences in the regulation of extrapulmonary ACE in the regulation of aldosterone levels, the mechanisms underlying these differences are not explored.<br /> The physiologic impact of the increased aldosterone levels observed in Marco -/- male mice on blood pressure or response to injury is not clear.<br /> The intracellular signaling mechanism linking lung macrophage levels with the expression of ACE in the lung is not supported by direct evidence.

Joint Public Review:

This paper aimed to assess the link between genetic and environmental factors on psychotic-like experiences and the potential mediation through cognitive ability. This study was based on data from the ABCD cohort, including 6,602 children aged 9-10 years. The authors report a mediating effect, suggesting that cognitive ability is a key mediating pathway in linking several genetic and environmental (risk and protective) factors to psychotic-like experiences.

Strengths of the methods: The authors use a wide range of validated (genetic, self- and parent-reported, and cognitive) measures in a large dataset with a 2-year follow-up period. The statistical methods have the potential to address key limitations of previous research.

Weaknesses of the methods: Not the largest or most recent GWASes were used to generate PGSes.

Strengths of the results: The authors included a comprehensive array of analyses.

Weaknesses of the results: Results are only sometimes clearly described and presented.

Appraisal: The authors suggest that their findings provide evidence for policy reforms (e.g., targeting residential environments, family SES, parenting, and schooling).

Impact: Immediate impact is limited given the short follow-up period (2 years), possibly concerns for selection bias and attrition in the data, and some methodological concerns. The authors are transparent about most of these limitations.

Reviewer #1 (Public Review):

Summary:

The study conducted on mice establishes a noteworthy connection between dietary protein intake and resistance exercise impact on metabolic health and muscle development. In sedentary mice, a diet rich in protein resulted in excessive fat accumulation and compromised blood sugar regulation in comparison to a diet low in protein. Intriguingly, when mice followed the high protein diet alongside progressive resistance training, they exhibited protection against surplus fat gain, though blood glucose regulation remained impaired. The research also revealed that resistance training notably enhanced muscle hypertrophy induced by exercise, particularly in mice on the high protein diet. Although the maximum strength achieved was similar across diets, this highlights the potential synergy between high protein consumption and resistance exercise in promoting skeletal muscle growth.

Strengths:

The study possesses several significant strengths. Firstly, it combines controlled dietary manipulations with resistance exercise, providing a comprehensive understanding of their combined effects on metabolic health and muscle growth. The use of mouse models, while not directly translatable to humans, offers a controlled experimental environment, enabling precise measurements and observations. Moreover, the study reveals nuanced outcomes such as the differential impact of high protein intake on adiposity and muscle hypertrophy. The emphasis on both positive and negative findings lends balance to the conclusions, enhancing the overall credibility of the study. Additionally, the clear delineation of diet-exercise interactions contributes to the broader understanding of dietary and exercise recommendations for metabolic health and muscle development.

Weaknesses:

Certain limitations warrant consideration. Firstly, the study's exclusive reliance on mice might limit the generalizability of the findings to humans due to inherent physiological differences. Additionally, the absence of direct investigation into the underlying molecular mechanisms responsible for the observed outcomes leaves room for speculation. Moreover, the research's concentration on male and young mice raises questions about the applicability of these findings to female and older subjects. Lastly, the study's duration and the specific resistance exercise protocol utilized might not fully reflect long-term human scenarios, underscoring the need for further research in more diverse populations and over extended timeframes.

Reviewer #1 (Public Review):

The paper from Hsu and co-workers describes a new automated method for analyzing the cell wall peptidoglycan composition of bacteria using liquid chromatography and mass spectrometry (LC/MS) combined with newly developed analysis software. The work has great potential for determining the composition of bacterial cell walls from diverse bacteria in high-throughput, allowing new connections between cell wall structure and other important biological functions like cell morphology or host-microbe interactions to be discovered. A downside to the method is that it does require some prior knowledge of an organisms peptidoglycan composition to generate the database for automated analysis. Nevertheless, the automation will allow rapid analysis of peptidoglycan composition under a variety of conditions and/or between closely related organisms once the general peptidoglycan structure is known. The methodology described will therefore be useful for the field.

The potential connection between the structure of different cell walls from bifidobacteria and cell stiffness proposed in the report is weak. The cells analyzed are from different strains such that there are many possible reasons for the change in physical measurements made by AFM. Conclusions relating cell wall composition to stiffness would be best drawn from a single strain of bacteria genetically modified to have an altered content of 3-3 crosslinks.

Reviewer #1 (Public Review):

The manuscript describes that cultured mammalian cells adapt to chronic stress by increasing their size and protein translation through Hsp90. The authors extensively use Hsp90 knockout cells and mass spectrometry to provide solid evidence that chronic heat shock response is accompanied by cell size changes and stress resistance in large cells. The major strength of the work is the authors ability to document the heat shock response in detail. The increased stress resistance of large cells is conceptually important and provides one potential explanation why cells need to control their size. This work adds to our understanding of how cellular stress is managed, and while stress responses have been observed previously in relation to cell size, this work provides evidence for increased stress resistance in larger cells.

Reviewer #1 (Public Review):

The manuscript by Sejour et al. is testing "translational ramp" model described previously by Tuller et al. in S. cerevisiae. Authors are using bioinformatics and reporter based experimental approaches to test whether "rare codons" in the first 40 codons of the gene coding sequences increase translation efficiency and regulate abundance of translation products in yeast cells. Authors conclude that "translation ramp" model does not have support using a new set of reporters and bioinformatics analyses. The strength of bioinformatic evidence and experimental analyses (even very limited) of the rare codons insertion in the reporter make a compelling case for the authors claims. However the major weakness of the manuscript is that authors do not take into account other models that previously disputed "rare or slow codon" model of Tuller et al. and overstate their own results that are rather limited. This maintains to be the weak part of the manuscript even in the revised form.

The studies that authors do not mention argue with "translation ramp" model and show more thorough analyses of translation initiation to elongation transition as well as early elongation "slow down" in ribosome profiling data. Moreover several studies have used bioinformatical analyses to point out the evolution of N-terminal sequences in multiple model organisms including yeast, focusing on either upstream ORFs (uORFs) or already annotated ORFs. The authors did not mention multiple of these studies in their revised manuscript and did not comment on their own results in the context of these previous studies. As such the authors approach to data presentation, writing and data discussion makes the manuscript rather biased, focused on criticizing Tuller et al. study and short on discussing multiple other possible reasons for slow translation elongation at the beginning of the protein synthesis. This all together makes the manuscript at the end very limited.

Reviewer #1 (Public Review):

Zhang et al. investigate the hypothesis that tRNA methyl transferase 1 (TRMT1) is cleaved by NSP5 (nonstructural protein 5 or MPro), the SARS-CoV-2 main protease, during SARS-CoV-2 infection. They provide solid evidence that TRMT1 is a substrate of Nsp5, revealing an Nsp5 target consensus sequence and evidence of TRMT1 cleavage in cells. Their conclusions are exceptionally strong given the co-submission by D'Oliveira et al showing cleavage of TRMT1 in vitro by Nsp5. Separately, the authors convincingly demonstrate widespread downregulation of RNA modifications during CoV-2 infection, including a requirement for TRMT1 in efficient viral replication. This finding is congruent with the authors' previous work defining the impact of TRMT1 and m2,2g on global translation, which is most likely necessary to support infection and virion production. What still remains unclear is the functional relevance of TRMT1 cleavage by Nsp5 during infection. Based on the data provided here, TRMT1 cleavage may be an act by CoV-2 to self-limit replication, as the expression of a non-cleavable TRMT1 (versus wild-type TRMT1) supports enhanced viral RNA expression at certain MOIs. Theoretically, TRMT1 cleavage should inactivate the modification activity of TRMT1, which the authors thoroughly and elegantly investigate with rigorous biochemical assays. However, only a minority of TRMT1 undergoes cleavage during infection in this study and thus whether TRMT1 cleavage serves an important functional role during CoV-2 replication will be an important topic for future work. The authors fairly assess their work in this regard. This study pushes forward the idea that control of tRNA expression and functionality is an important and understudied area of host-pathogen interaction.

Weaknesses noted:<br /> The detection of the N-terminal TRMT1 fragment by western blot is not robust. The polyclonal antibody used to detect TRMT1 in this work cross-reacts with a non-specific protein product. Unfortunately, this obstructs the visualization of the predicted N-terminal TRMT1 fragment. It is unclear how the authors were able to perform densitometry, given the interference of the non-specific band. Additionally, the replicates in the source data make it clear that the appearance of the N-terminal fragment "wisp" under the non-specific band is not seen in every replicate. Though the disappearance of this wisp with mutant Nsp5 and uncleavable TRMT1 is reassuring, the detection of the N-terminal fragment with the TRMT1 antibody should be assessed critically. Considering this group has strong research interests in TRMT1, I assume that attempts to make other antibodies have proved unfruitful. Additionally, N-terminal tagging of TRMT1 is predicted to disrupt the mitochondrial targeting signal, eliminating the potential for using alternative antibodies to see the N-terminal fragment. These technical issues reiterate the fact that the functional significance of TRMT1 cleavage during CoV-2 infection remains unclear. However, this study demonstrates an important finding that the tRNA modification landscape is altered during CoV-2 infection and that TRMT1 is an important host factor supporting CoV-2 replication.

Reviewer #1 (Public Review):

In this study, the structural characteristics of plant AlaDC and SerDC were analyzed to understand the mechanism of functional differentiation, deepen the understanding of substrate specificity and catalytic activity evolution, and explore effective ways to improve the initial efficiency of theanine synthesis.

On the basis of previous solid work, the authors successfully obtained the X-ray crystal structures of the precursors of theanine synthesis-CsAlaDC and AtSerDC, which are key proteins related to ethylamine synthesis, and found a unique zinc finger structure on these two crystal structures that are not found in other Group II PLP- dependent amino acid decarboxylases. Through a series of experiments, it is pointed out that this characteristic zinc finger motif may be the key to the folding of CsAlaDC and AtSerDC proteins, and this discovery is novel and prospective in the study of theine synthesis.

In addition, the authors identified Phe106 of CsAlaDC and Tyr111 of AtSerDC as key sites of substrate specificity by comparing substrate binding regions and identified amino acids that inhibit catalytic activity through mutation screening based on protein structure. It was found that the catalytic activity of CsAlaDCL110F/P114A was 2.3 times higher than that of CsAlaDC. At the same time, CsAlaDC and AtSerDC substrate recognition key motifs were used to carry out evolutionary analysis of the protein sequences that are highly homologous to CsAlaDC in embryos, and 13 potential alanine decarboxylases were found, which laid a solid foundation for subsequent studies related to theanine synthesis.

In general, this study has a solid foundation, the whole research idea is clear, the experimental design is reasonable, and the experimental results provide strong evidence for the author's point of view. Through a large number of experiments, the key links in the theanine synthesis pathway are deeply studied, and an effective way to improve the initial efficiency of theanine synthesis is found, and the molecular mechanism of this way is expounded. The whole study has good novelty and prospectivity, and sheds light on a new direction for the efficient industrial synthesis of theanine.

Reviewer #1 (Public Review):

D'Oliviera et al. have demonstrated cleavage of human TRMT1 by the SARS-CoV-2 main protease in vitro. Following this, they solved the structure of Mpro-C145A bound to TRMT1 substrate peptide, revealing binding conformation distinct from most viral substrates. Overall, this work enhances our understanding of substrate specificity for a key drug target of CoV2. The paper is well-written and the data is clearly presented. It complements the companion article by demonstrating the interaction between Mpro and TRMT1 and TRMT1 cleavage under isolated conditions in vitro. Importantly, the revelation of flexible substrate binding of Nsp5 is fundamental for understanding Nsp5 as a drug target. Trmt1 cleavage assays revealed similar kinetics for TRMT1 cleavage as compared to the nsp8/9 viral polyprotein cleavage site, however, it would have been more rigorous for the authors to independently reproduce the kinetics reported for nsp8/9 using their specific experimental conditions. The finding that murine TRMT1 lacks a conserved consensus sequence is interesting, but is not experimentally tested here and is reported elsewhere. I am unable to comment critically on the structural analyses as it is outside of my expertise. Overall, I think that these findings are important for confirming TRMT1 as a substrate of Mpro and defining substrate binding and cleavage parameters for an important drug target of SARS-CoV-2.

Joint Public Review:

This study investigates the role of Ikaros, a zinc finger family transcription factor related to Helios and Eos, in T-regulatory (Treg) cell functionality in mice. Through genome-wide association studies and chromatin accessibility studies, the authors find that Ikaros shares similar binding sites to Foxp3. Ikaros cooperates with Foxp3 to establish a major portion of the Treg epigenome and transcriptome. Ikaros-deficient Treg exhibits Th1-like gene expression with abnormal expression of IL-2, IFNg, TNFa, and factors involved in Wnt and Notch signalling. Further, two models of inflammatory/ autoimmune diseases - Inflammatory Bowel Disease (IBD) and organ transplantation - are employed to examine the functional role of Ikaros in Treg-mediated immune suppression. The authors provide a detailed analysis of the epigenome and transcriptome of Ikaros-deficient Treg cells.

These studies establish Ikaros as a factor required in Treg for tolerance and the control of inflammatory immune responses. The data are of high quality. Overall, the study is well organized, and reports new data consolidating mechanistic aspects of Foxp3 mediated gene expression program in Treg cells.

Strengths:<br /> The authors have performed biochemical studies focusing on mechanistic aspects of molecular functions of the Foxp3-mediated gene expression program and complemented these with functional experiments using two models of autoimmune diseases, thereby strengthening the study. The studies are comprehensive at both the cellular and molecular levels. The manuscript is well organized and presents a plethora of data regarding the transcriptomic landscape of these cells.

Weakness:<br /> The authors claim that the mice have no pathologic signs of autoimmune disease even at a relatively old age, yet mice have an increased number of activated CD4+ T cells and T-follicular helper cells (even at the age of 6 weeks) as well as reduced naïve T-cells. Thus, immune homeostasis is perturbed in these mice even at a young age and the effect of inflammatory microenvironments on cellular functions cannot be ruled out. Further, clear conclusions from the genome-wide studies are lacking.

Reviewer #1 (Public Review):

Summary:<br /> The Notch signaling pathway plays an important role in many developmental and disease processes. Although well-studied there remain many puzzling aspects. One is the fact that as well as activating the receptor through trans-activation, the transmembrane ligands can interact with receptors present in the same cell. These cis-interactions are usually inhibitory, but in some cases, as in the assays used here, they may also be activating. With a total of 6 ligands and 4 receptors, there is potentially a wide array of possible outcomes when different combinations are co-expressed in vivo. Here the authors set out to make a systematic analysis of the qualitative and quantitative differences in the signaling output from different receptor-ligand combinations, generating sets of "signaling" (ligand expressing) and "receiving" (receptor +/- ligand expressing cells).

The readout of pathway activity is transcriptional, relying on the fusion of GAL4 in the intracellular part of the receptor. Positive ligand interactions result in the proteolytic release of Gal4 that turns on the expression of H2B-citrine. As an indicator of ligand and receptor expression levels, they are linked via TA to H2B mCherry and H2B mTurq expression respectively. The authors also manipulate the expression of the glycosyltransferase Lunatic-Fringe (LFng) that modifies the EGF repeats in the extracellular domains impacting their interactions. The testing of multiple ligand-receptor combinations at varying expression levels is a tour de force, with over 50 stable cell lines generated, and yields valuable insights although as a whole, the results are quite complex.

Strengths:<br /> Taking a reductionist approach to testing systematically differences in the signaling strength, binding strength, and cis-interactions from the different ligands in the context of the Notch1 and Notch 2 receptors (they justify well the choice of players to test via this approach) produces a baseline understanding of the different properties and leads to some unexpected and interesting findings. Notably:

- Jag1 ligand expressing cells failed to activate Notch1 receptor although were capable of activating Notch2. Conversely, Jag2 cells elicited the strongest activation of both receptors. The results with Jag1 are surprising also because it exhibits some of the strongest binding to plate-bound ligands. The failure to activate Notch1 has major functional significance and it will be important in the future to understand the mechanistic basis.

- Jagged ligands have the strongest ciis-inhibitory effects and the receptors differ in their sensitivity to cis-inhibition by Dll ligands. These observations are in keeping with earlier in vivo and cell culture studies. More referencing of those would better place the work in context but it nicely supports and extends previous studies that were conducted in different ways.

- Responses to most trans-activating ligands showed a degree of ultrasensitivity but this was not the case for cis-interactions where effects were more linear. This has implications for the way the two mechanisms operate and for how the signaling levels will be impacted by ligand expression levels.

- Qualitatively similar results are obtained in a second cell line, suggesting they reflect fundamental properties of the ligands/receptors.

Weaknesses:<br /> One weakness is that the methods used to quantify the expression of ligands and receptors rely on the co-translation of tagged nuclear H2B proteins. These may not accurately capture surface levels/correctly modified transmembrane proteins. In general, the multiple conditions tested partly compensate for the concerns - for example, as Jag1 cells do activate Notch2 even if they do not activate Notch1 some Jag1 must be getting to the surface. But even with Notch2, Jag1 activities are on the lower side, making it important to clarify, especially given the different outcomes with the plated ligands. Similarly, is the fact that all ligands "signalled strongest to Notch2" an inherent property or due to differences in surface levels of Notch 2 compared to Notch1? The results would be considerably strengthened by calibration of the ligand/receptor levels (and ideally their sub-cellular localizations). Assessing the membrane protein levels would be relatively straightforward to perform on some of the basic conditions because their ligand constructs contain Flag tags, making it plausible to relate surface protein to H2B, and there are antibodies available for Notch1 and Notch2.

Cis-activation as a mode of signaling has only emerged from these synthetic cell culture assays raising questions about its physiological relevance. Cis-activation is only seen at the higher ligand (Dll1, Dll4) levels, how physiological are the expression levels of the ligands/receptors in these assays? Is it likely that this would make a major contribution in vivo? Is it possible that the cells convert themselves into "signaling" and "receiving" sub-populations within the culture by post-translational mechanism? Again some analysis of the ligand/receptors in the cultures would be a valuable addition to show whether or not there are major heterogeneities.

It is hard to appreciate how much cell-to-cell variability in the "output" there is. For example, low "outputs" could arise from fewer cells becoming activated or from all cells being activated less. As presented, only the latter is considered. That may be already evident in their data, but not easy for the reader to distinguish from the way they are presented. For example, in many of the graphs, data have been processed through multiple steps of normalization. Some discussion/consideration of this point is needed.

Impact:<br /> Overall, cataloguing the outcomes from the different ligand-receptor combinations, both in cis and trans, yields a valuable baseline for those investigating their functional roles in different contexts. There is still a long way to go before it will be possible to make a predictive model for outcomes based on expression levels, but this work gives an idea about the landscape and the complexities. This is especially important now that signaling relationships are frequently hypothesised based on single-cell transcriptomic data. The results presented here demonstrate that the relationships are not straightforward when multiple players are involved.

Reviewer #1 (Public Review):

In this work the authors propose a new regulatory role for one the most abundant circRNAs, circHIPK3, by showing that it interacts with an RNA binding protein (IGF2BP2) and, by sequestering it, it regulates the expression of hundreds of genes containing a sequence (11-mer motif) in their untranslated regions (3'-UTR). This sequence is also present in circHIPK3, precisely where IGF2BP2 binds. The study further focuses on one specific case, the STAT3 gene, whose mRNA product is downregulated upon circHIPK3 depletion apparently through sequestering IGF2BP2, which otherwise binds to and stabilizes STAT3 mRNA. The study presents mechanistic insight into the interactions, sequence motifs, and stoichiometries of the molecules involved in this new mode of regulation. Altogether, this new mechanism seems to underlie the effects of circHIPK3 in cancer progression.

Strengths:<br /> The authors show mechanistic insight into a proposed novel "sponging" function of circHIPK3 which is not mediated by sequestering miRNAs but rather by a specific RNA binding protein (IGF2BP2). They address the stoichiometry of the molecules involved in the interaction, which is a critical aspect that is frequently overlooked in this type of study. They provide both genome-wide analysis and a specific case (STAT3) that is relevant for cancer progression.

Weaknesses:<br /> One of the central conclusions of the manuscript, namely that circHIPK3 sequesters IGF2BP2 and thereby regulates target mRNAs, lacks more direct experimental evidence such as rescue experiments where both species are simultaneously knocked down. CircRNA overexpression lacks a demonstration of circularization efficiencies. There seem to be contradictory effects of circHIPK3 and STAT3 depletion in cancer progression, namely that while circHIPK3 is frequently downregulated in cancer, circHIPK3 downregulation in this study leads to downregulation of STAT3. This does not seem to fit the fact that STAT3 is normally activated in a wide diversity of cancers and is positively associated with cell proliferation. The result is neither consistent with the fact that circHIPK3 expression positively correlates with good clinical outcomes. Overall, the authors have achieved some of their aims but additional controls would be advisable to fully support their conclusions.

Reviewer #1 (Public Review):

Summary:<br /> The authors describe the dynamic distribution of laminin in the olfactory system and forebrain. Using immunohistochemistry and transgenic lines, they found that the olfactory system and adjacent brain tissues are enveloped by BMs from the earliest stages of olfactory system assembly. They also found that laminin deposits follow the axonal trajectory of axons. They performed a functional analysis of the sly mutant to analyse the function of laminin γ1 in the development of the zebrafish olfactory system. Their study revealed that laminin enables the shape and position of placodes to be maintained late in the face of major morphogenetic movements in the brain, and its absence promotes the local entry of sensory axons into the brain and their navigation towards the olfactory bulb.

Strengths:<br /> -They showed that in the sly mutants, no BM staining of laminin and Nidogen could be detected around the OP and the brain. The authors then elegantly used electron microscopy to analyse the ultrastructure of the border between the OP and the brain in control and sly mutant conditions.<br /> -To analyse the role of laminin γ1-dependent BMs in OP coalescence, the authors used the cluster size of Tg(neurog1:GFP)+ OP cells at 22 hpf as a marker. They found that the mediolateral dimension increased specifically in the mutants. However, proliferation did not seem to be affected, although apoptosis appeared to increase slightly at a later stage. This increase could therefore be due to a dispersal of cells in the OP. To test this hypothesis, the authors then analysed the cell trajectories and extracted 3D mean square displacements (MSD), a measure of the volume explored by a cell in a given period of time. Their conclusion indicates that although brain cell movements are increased in the absence of BM during coalescence phases, overall OP cell movements occur within normal parameters and allow OPs to condense into compact neuronal clusters in sly mutants. The authors also analysed the dimensions of the clusters composed of OMP+ neurons. Their results show an increase in cluster size along the dorso-ventral axis. These results were to be expected since, compared with BM, early neurog1+ neurons should compact along the medio-lateral axis, and those that are OMP+ essentially along the dorso-ventral axis. In addition to the DV elongation of OP tissue, the authors show the existence of isolated and ectopic (misplaced) YFP+ cells in sly mutants.<br /> -To understand the origin of these phenotypes, the authors analysed the dynamic behaviour of brain cells and OPs during forebrain flexion. The authors then quantitatively measured brain versus OPs in the sly mutant and found that the OP-brain boundary was poorly defined in the sly mutant compared with the control. Once again, the methods (cell tracks, brain size, and proliferation/apoptosis, and the shape of the brain/OP boundary) are elegant but the results were expected.<br /> -They then analysed the dynamic behaviour of the axon using live imaging. Thus, olfactory axon migration is drastically impaired in sly mutants, demonstrating that Laminin γ1-dependent BMs are essential for the growth and navigation of axons from the OP to the olfactory bulb.<br /> -The authors therefore performed a quantitative analysis of the loss of function of Laminin γ1. They propose that the BM of the OP prevents its deformation in response to mechanical forces generated by morphogenetic movements of the neighbouring brain.

Weaknesses:<br /> - The authors did not analyse neurog1 + axonal migration at the level of the single cell and instead made a global analysis. An analysis at the cell level would strengthen their hypotheses.<br /> - Rescue experiments by locally inducing Laminin expression would have strengthened the paper.<br /> -The paper lacks clarity between the two neuronal populations described (early EONs and late OSNs).<br /> -The authors quantitatively measured brain versus OPs in the sly mutant and found that the OP-brain boundary was poorly defined in the sly mutant compared with the control. Once again, the methods (cell tracks, brain size, proliferation/apoptosis, and the shape of the brain/OP boundary) are elegant but the results were expected.<br /> - A missing point in the paper is the effect of Laminin γ1 on the migration of cranial NCCs that interact with OP cells. The authors could have analysed the dynamic distribution of neural crest cells in the sly mutant.

Reviewer #1 (Public Review):

Most amino acids are stereoisomers in the L-enantiomer, but natural D-serine has also been detected in mammals and its levels shown to be connected to a number of different pathologies. Here, the authors convincingly show that D-serine is transported in the kidney by the neutral amino acid transporter ASCT2 and as a non-canonical substrate for the sodium-coupled monocarboxylate transporter SMCTs. Although both transport D-serine, this important study further shows in a mouse model for acute kidney injury that ASCT2 has the dominant role.

Strengths:<br /> The paper combines proteomics, animal models, ex vivo transport analyses, and in vitro transport assays using purified components. The exhaustive methods employed provide compelling evidence that both transporters can translocate D-serine in the kidney.

Weakness:<br /> In the model for acute kidney injury, the SMCTs proteins were not showing a significant change in expression levels and were rather analysed based on other, circumstantial evidence. Although its clear SMCTs can transport D-serine its physiological role is less obvious compared to ASCT2.

Reviewer #1 (Public Review):

Summary. The authors goal was to map the neural circuitry underlying cold sensitive contraction in Drosophila. The circuitry underlying most sensory modalities has been characterized but noxious cold sensory circuitry has not been well studied. The authors achieve their goal and map out sensory and post-sensory neurons involved in this behavior.

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

Positive comments

-Campari is nicely done to map cold responsive neurons, although it doesn't give data on individual neurons.

-Chrimson and TNT experiments are nicely done.

-Cold temperature activates basin neurons, it's a solid and convincing result.

Weaknesses. Among the few weaknesses in this manuscript is the failure to trace the circuit from sensory neuron to motor neuron; and to ignore analysis of the muscles driving, cold induced contraction. Authors also need to elaborate more on the novel aspects of their work in the introduction or abstract.

Major comments.

-Class three sensory neuron connectivity is known, and role in cold response is known (turner 16, 18). Need to make it clearer what the novelty of the experiments are.

-Why focus on premotor neurons in mechano nociceptive pathways? Why not focus on PMNs innervating longitudinal muscles, likely involved in longitudinal larval contraction? Especially since chosen premotor neurons have only weak effects on cold induced contraction?

https://www.legifrance.gouv.fr/codes/article_lc/LEGIARTI000028160058

https://www.legifrance.gouv.fr/codes/article_lc/LEGIARTI000027682737

https://www.legifrance.gouv.fr/codes/article_lc/LEGIARTI000044541942

Reviewer #1 (Public Review):

Rai1 encodes the transcription factor retinoic acid-induced 1 (RAI1), which regulates expression of factors involved in neuronal development and synaptic transmission. Rai1 haploinsufficiency leads to the monogenic disorder Smith-Magenis syndrome (SMS), which is associated with excessive feeding, obesity and intellectual disability. Consistent with findings in human subjects, Rai1+/- mice and mice with conditional deletion of Rai1 in Sim+ neurons, which are abundant in the paraventricular nucleus (PVN), exhibit hyperphagia, obesity and increased adiposity. Furthermore, RAI1-deficient mice exhibit reduced expression of brain-derived neurotrophic factor (BDNF), a satiety factor essential for the central control of energy balance. Notably, overexpression of BDNF in PVN of RAI1-deficient mice mitigated their obesity, implicating this neurotrophin in the metabolic dysfunction these animals exhibit. In this follow up study, Javed et al. interrogated the necessity of RAI1 in BDNF+ neurons promoting metabolic health.

Consistent with previous reports, the authors observed reduced BDNF expression in hypothalamus of Rai1+/- mice. Moreover, proteomics analysis indicated impairment in neurotrophin signaling in the mutants. Selective deletion of Rai1 in BDNF+ neurons in the brain during development resulted in increased body weight, fat mass and reduced locomotor activity and energy expenditure without changes in food intake. There was also a robust effect on glycemic control, with mutants exhibiting glucose intolerance. Selective depletion of RAI1 in BDNF+ neurons in PVN in adult mice also resulted in increased body weight, reduced locomotor activity and glucose intolerance without affecting food intake. Blunting RAI1 activity also leads to increases and decreases the inhibitory tone and intrinsic excitability, respectively, of BDNF+ neurons in the PVN.

Overall, the experiments are well designed and multidisciplinary approaches are employed to demonstrate that RAI1 deficits in BDNF+ neurons diminish hypothalamic BDNF signaling and produce metabolic dysfunction. The most significant advance relative to previous reports is the finding from electrophysiological studies showing that blunting RAI1 activity leads to increases and decreases the inhibitory tone and intrinsic excitability, respectively, of BDNF+ neurons in the PVN. Furthermore, that intact RAI1 function is required in BDNF+ neurons for the regulation of glucose homeostasis.

Depleting RAI1 in BDNF+ neurons had a robust effect compromising glycemic control while playing a lesser part driving deficits in energy balance regulation. Accordingly, both global central depletion of Rai1 in BDNF+ neurons during development and deletion of Rai1 in BDNF+ neurons in the adult PVN elicited modest effects on body weight (less than 18% increase) and did not affect food intake. This contrasts with mice with selective Bdnf deletion in the adult PVN, which are hyperphagic and dramatically obese (90% heavier than controls). Therefore, the results suggest that deficits in RAI1 in PVN or the whole brain only moderately affect BDNF actions influencing energy homeostasis and that other signaling cascades and neuronal populations play a more prominent role driving the phenotypes observed in Rai1+/- mice, which are hyperphagic and 95% heavier than controls. The results from the proteomic analysis of hypothalamic tissue of Rai1 mutant mice and controls could be useful in generating alternative hypotheses.

Reviewer #1 (Public Review):

Summary:

The paper by Majeed et al has a valuable and worthwhile aim: to provide a set of tools to standardize the quantification of synapses using fluorescent markers in the nematode C. elegans. Using current approaches, the identification of synapses using fluorescent markers is tedious and subject to significant inter-experimenter variability. Majeed et al successfully developed and validated a computational pipeline called "WormPsyQi" that overcomes some of these obstacles and will be a powerful resource for many C. elegans neurobiologists.

Strengths:

The computational pipeline is rigorously validated and shown to accurately quantitate fluorescent puncta, at least as well as human experimenters. The inclusion of a mask - a region of interest defined by a cytoplasmic marker - is a powerful and useful approach. Users can take advantage of one of four pre-trained neural networks, or train their own. The software is freely available and appears to be user-friendly. A series of rigorous experiments demonstrate the utility of the pipeline for measuring differences in the number of synaptic puncta between sexes and across developmental stages. Neuron-to-neuron heterogeneity in patterns of synaptic growth during development is convincingly demonstrated. Weaknesses and caveats are realistically discussed.

Reviewer #1 (Public Review):

The paper "Quantifying gliding forces of filamentous cyanobacteria by self-buckling" combines experiments on freely gliding cyanobacteria, buckling experiments using two-dimensional V-shaped corners, and micropipette force measurements with theoretical models to study gliding forces in these organisms. The aim is to quantify these forces and use the results to perhaps discriminate between competing mechanisms by which these cells move. A large data set of possible collision events are analyzed, bucking events evaluated, and critical buckling lengths estimated. A line elasticity model is used to analyze the onset of buckling and estimate the effective (viscous type) friction/drag that controls the dynamics of the rotation that ensues post-buckling. This value of the friction/drag is compared to a second estimate obtained by consideration of the active forces and speeds in freely gliding filaments. The authors find that these two independent estimates of friction/drag correlate with each other and are comparable in magnitude. The experiments are conducted carefully, the device fabrication is novel, the data set is interesting, and the analysis is solid. The authors conclude that the experiments are consistent with the propulsion being generated by adhesion forces rather than slime extrusion. While consistent with the data, this conclusion is inferred.

Summary:

The paper addresses important questions on the mechanisms driving the gliding motility of filamentous cyanobacteria. The authors aim to understand these by estimating the elastic properties of the filaments, and by comparing the resistance to gliding under a) freely gliding conditions, and b) in post-buckled rotational states. Experiments are used to estimate the propulsion force density on freely gliding filaments (assuming over-damped conditions). Experiments are combined with a theoretical model based on Euler beam theory to extract friction (viscous) coefficients for filaments that buckle and begin to rotate about the pinned end. The main results are estimates for the bending stiffness of the bacteria, the propulsive tangential force density, the buckling threshold in terms of the length, and estimates of the resistive friction (viscous drag) providing the dissipation in the system and balancing the active force. It is found that experiments on the two bacterial species yield nearly identical values of 𝑓 (albeit with rather large variations). The authors conclude that the experiments are consistent with the propulsion being generated by adhesion forces rather than slime extrusion.

Strengths of the paper:

The strengths of the paper lie in the novel experimental setup and measurements that allow for the estimation of the propulsive force density, critical buckling length, and effective viscous drag forces for movement of the filament along its contour - the axial (parallel) drag coefficient, and the normal (perpendicular) drag coefficient (I assume this is the case, since the post-buckling analysis assumes the bent filament rotates at a constant frequency). These direct measurements are important for serious analysis and discrimination between motility mechanisms.

Weaknesses:

There are aspects of the analysis and discussion that may be improved. I suggest that the authors take the following comments into consideration while revising their manuscript.

The conclusion that adhesion via focal adhesions is the cause for propulsion rather than slime protrusion is consistent with the experimental results that the frictional drag correlates with propulsion force. At the same time, it is hard to rule out other factors that may result in this (friction) viscous drag - (active) force relationship while still being consistent with slime production. More detailed analysis aiming to discriminate between adhesion vs slime protrusion may be outside the scope of the study, but the authors may still want to elaborate on their inference. It would help if there was a detailed discussion on the differences in terms of the active force term for the focal adhesion-based motility vs the slime motility.

Can the authors comment on possible mechanisms (perhaps from the literature) that indicate how isotropic friction may be generated in settings where focal adhesions drive motility? A key aspect here would probably be estimating the extent of this adhesion patch and comparing it to a characteristic contact area. Can lubrication theory be used to estimate characteristic areas of contact (knowing the radius of the filament, and assuming a height above the substrate)? If the focal adhesions typically cover areas smaller than this lubrication area, it may suggest the possibility that bacteria essentially present a flat surface insofar as adhesion is concerned, leading to a transversely isotropic response in terms of the drag. Of course, we will still require the effective propulsive force to act along the tangent.

I am not sure why the authors mention that the power of the gliding apparatus is not rate-limiting. The only way to verify this would be to put these in highly viscous fluids where the drag of the external fluid comes into the picture as well (if focal adhesions are on the substrate-facing side, and the upper side is subject to ambient fluid drag). Also, the friction referred to here has the form of a viscous drag (no memory effect, and thus not viscoelastic or gel-like), and it is not clear if forces generated by adhesion involve other forms of drag such as chemical friction via temporary bonds forming and breaking. In quasi-static settings and under certain conditions such as the separation of chemical and elastic time scales, bond friction may yield overall force proportional to local sliding velocities.

For readers from a non-fluids background, some additional discussion of the drag forces, and the forms of friction would help. For a freely gliding filament if 𝑓 is the force density (per unit length), then steady gliding with a viscous frictional drag would suggest (as mentioned in the paper) 𝑓 ∼ 𝑣! 𝐿 𝜂∥. The critical buckling length is then dependent on 𝑓 and on 𝐵 the bending modulus. Here the effective drag is defined per length. I can see from this that if the active force is fixed, and the viscous component resulting from the frictional mechanism is fixed, the critical buckling length will not depend on the velocity (unless I am missing something in their argument), since the velocity is not a primitive variable, and is itself an emergent quantity.

Reviewer #1 (Public Review):

Summary:<br /> The authors have made a novel and important effort to distinguish and include different sources of active deformations for fitting C elegans embryo development: cyclic muscle contractions and actomyosion circumferential stresses. The combination and synchronisation of both contributions are, according to the model, responsible for different elongation rates, and can induce bending and torsion deformations, which are a priori not expected from purely contractile forces. The model can be applied to other growth processes in initially cylindrical shapes.

Strengths:<br /> The model allows us to fit and deduce specific growth patterns, frequencies, and locations of contractions that yield the observed axial elongation during the 240 min of the studied process.

The deformation gradient is decomposed according to muscle and actomyosin activity, which can be distinguished and quantified. An energy-transferring process allows for the retrieval of the necessary permanent deformations that embryo development requires.

Weaknesses:<br /> Despite the completeness of the model, the explanation of the methodology needs to be improved. Parameters and quantities are not always explained in the main text and are introduced on some occasions in an ordered manner. This makes the comprehension and deduction of methodology difficult. There are some minor comments that are listed below. The most important points are:

-How are the authors sure that there is a torsional deformation? Without tracking the muscle fibers, bending with respect to different angles for different Zs may yield a shape similar to the one in Figure 6E. Furthermore, it is unclear why the model yields torsion deformation. If material points of actomyosin rings do not change in reference configuration, no helicoidal growth should be happening.

-The triple decomposition F=F_e*G_i*G_0 seems to complicate the expressions of growth and requires the use of angles alpha and beta due to the initial deformation G_0. Why not use a simpler decomposition F=F_e*G, where G contains all contributions from actomyosin and muscle contractions in a material frame? This would avoid considering angles alpha and beta.

The section "Energy transformation and Elongation" is unclear. Indeed, stresses need to relax, otherwise, the removal of muscle and actin activity would send the embryo back to its initial state. However, the rationale behind the energy transfer is not explained. Authors seem to impose W_c=W_r, and from this deduce the necessary actin contraction after muscle relaxation. Why should energy be maintained when muscle relaxes? Which mechanism physically imposes this energy transfer? Muscle contraction could indeed induce elongation if traction forces at the opposite side of the contracting muscle relax. In fact, an alternative approach for obtaining stress relaxation and axial elongation would be converting part of the elastic deformation F_e to a permanent deformation F_p.

-Self contact is ignored. This may well be a shape generator and responsible for bending deformations. The convoluted shape of the embryo in the confined space deserves at least commenting on this limitation of the model.

Reviewer #1 (Public Review):

This work continues a series of recent publications from the Grigorieff lab (https://doi.org/10.7554/eLife.25648, https://doi.org/10.7554/eLife.68946, https://doi.org/10.7554/eLife.79272, https://doi.org/10.1073/pnas.2301852120) showcasing the development of high-resolution 2D template matching (2DTM) for detection and reconstruction of macromolecules in cryo-electron microscopy (cryo-EM) images of crowded cellular environments. It is well known in the field of cryo-EM that searching noisy images with a template can result in retrieval of the template itself when averaging the candidate particles detected, an effect known as "Einstein-from-noise" (https://doi.org/10.1073/pnas.1314449110). Briefly, this occurs because it is statistically likely to find a match to an arbitrary motif over a large noisy dataset just by chance. The effect can be mitigated for example by limiting the resolution of the template, but this prevents the accurate detection of macromolecules in a crowded environment, as their "fingerprint" lies in the high-resolution range (https://doi.org/10.7554/eLife.25648). Here, the authors show through several experiments on in vitro and in situ data that features as small as drug compounds and water molecules can be reliably retrieved by 2DTM if they are searched by a template (the "bait") that contains expected neighboring features but not the targets themselves.

The ideas are generally clearly presented with appropriate references to related work, and claims are well supported by the data. In particular, the experiments for verifying the density of the ribosomal protein L7A as well as the systematic removal of residuals from the template model to assess bias are particularly clever.

The revised version of the manuscript addresses essentially all of the concerns raised previously by this reviewer, with the addition of figures and extended discussion of the key concepts.

Joint Public Review:

Summary:

In this paper, the authors point out that the standard approach of estimating LD is inefficient for datasets with large numbers of SNPs, with a computational cost of O(nm^2), where n is the number of individuals and m is the number of SNPs. Using the known relationship between the LD matrix and the genomic-relatedness matrix, they can calculate the mean level of LD within the genome or across genomic segments with a computational cost of O(n^2m). Since in most datasets, n<<br /> Strengths:

Generally, for computational papers like this, the proof is in the pudding, and the authors have been successful at their aim of producing an efficient computational tool. The most compelling evidence of this in the paper are Figure 2 and Supplementary Figure S2. In Figure 2, they report how well their X-LD estimates of LD compare to estimates based on the standard approach using PLINK. They appear to have very good agreement. In Figure S2, they report the computational runtime of X-LD vs PLINK, and as expected X-LD is faster than PLINK as long as it is evaluating LD for more than 8000 SNPs.

Weakness:

This method seems to be limited to calculating average levels of LD in broad regions of the genome. While it would be possible to make the regions more fine-grained, doing so appears to make this approach much less efficient. As such, applications of this method may be limited to those proposed in the paper, for questions where average LD of large chromosomal segments is informative.

Impact:

This approach seems to produce real gains for settings where broad average levels of LD are useful to know, but it will likely have less of an impact in settings where fine-grained levels are LD are necessary (e.g., accounting for LD in GWAS summary statistics).

Reviewer #1 (Public Review):

The manuscript by Hariani et al. presents experiments designed to improve our understanding of the connectivity and computational role of Unipolar Brush Cells (UBCs) within the cerebellar cortex, primarily lobes IX and X. The authors develop and cross several genetic lines of mice that express distinct fluorophores in subsets of UBCs, combined with immunocytochemistry that also distinguishes subtypes of UBCs, and they use confocal microscopy and electrophysiology to characterize the electrical and synaptic properties of subsets of so-labelled cells, and their synaptic connectivity within the cerebellar cortex. The authors then generate a computer model to test possible computational functions of such interconnected UBCs.

Using these approaches, the authors report that:<br /> 1) GRP-driven TDtomato is expressed exclusively in a subset (20%) of ON-UBCs, defined electrophysiologically (excited by mossy fiber afferent stimulation via activation of UBC AMPA and mGluR1 receptors) and immunocytochemically by their expression of mGluR1.

2) UBCs ID'd/tagged by mCitrine expression in Brainbow mouse line P079 is expressed in a similar minority subset of OFF-UBCs defined electrophysiologically (inhibited by mossy fiber afferent stimulation via activation of UBC mGluR2 receptors) and immunocytochemically by their expression of Calretinin. However, such mCitrine expression was also detected in some mGluR1 positive UBCs, which may not have shown up electrophysiologically because of the weaker fluorophore expression without antibody amplification.

3) Confocal analysis of crossed lines of mice (GRP X P079) stained with antibodies to mGluR1 and calretinin documented the existence of all possible permutations of interconnectivity between cells (ON-ON, ON-OFF, OFF-OFF, OFF-ON), but their overall abundance was low, and neither their absolute or relative abundance was quantified.

4) A computational model (NEURON ) indicated that the presence of an intermediary UBC (in a polysynaptic circuit from MF to UBC to UBC) could prolong bursts (MF-ON-ON), prolong pauses (MF-ON-OFF), cause a delayed burst (MF-OFF-OFF), cause a delayed pause (MF-OFF-ON) relative to solely MF to UBC synapses which would simply exhibit long bursts (MF-ON) or long pauses (MF-OFF).

The authors thus conclude that the pattern of interconnected UBCs provides an extended and more nuanced pattern of firing within the cerebellar cortex that could mediate longer lasting sensorimotor responses.

The cerebellum's long known role in motor skills and reflexes, and associated disorders, combined with our nascent understanding of its role in cognitive, emotional, and appetitive processing, makes understanding its circuitry and processing functions of broad interest to the neuroscience and biomedical community. The focus on UBCs, which are largely restricted to vestibular lobes of the cerebellum reduces the breadth of likely interest somewhat. The overall design of specific experiments is rigorous and the use of fluorophore expressing mouse lines is creative. The data that is presented and the writing are clear. However, despite some additional analysis in response to the initial review, the overall experimental design still has issues that reduce overall interpretation (please see specific issues for details), which combined with a lack of thorough analysis of the experimental outcomes undermines the value of the NEURON model results and the advance in our understanding of cerebellar processing in situ (again, please see specific issues for details).

Specific issues:<br /> 1) All data gathered with inhibition blocked. All of the UBC response data (Fig. 1) was gathered in the presence of GABAAR and Glycine R blockers. While such an approach is appropriate generally for isolating glutamatergic synaptic currents, and specifically for examining and characterizing monosynaptic responses to single stimuli, it becomes problematic in the context of assaying synaptic and action potential response durations for long lasting responses, and in particular for trains of stimuli, when feed-forward and feed-back inhibition modulates responses to afferent stimulation. I.e. even for single MF stimuli, given the >500ms duration of UBC synaptic currents, there is plenty of time for feedback inhibition from Golgi cells (or feedforward, from MF to Golgi cell excitation) to interrupt AP firing driven by the direct glutamatergic synaptic excitation. This issue is compounded further for all of the experiments examining trains of MF stimuli. Beyond the impact of feedback inhibition on the AP firing of any given UBC, it would also obviously reduce/alter/interrupt that UBC's synaptic drive of downstream UBCs. This issue fundamentally undermines our ability to interpret the simulation data of Vm and AP firing of both the modeled intermediate and downstream UBC, in terms of applying it to possible cerebellar cortical processing in situ.

The authors' response to the initial concern is (to paraphrase), "its not possible to do and its not important", neither of which are soundly justified.

As stated in the original review, it is fully understandable and appropriate to use GABAAR/GlycineR antagonists to isolate glutamatergic currents, to characterize their conductance kinetics. That was not the issue raised. The issue raised was that then using only such information to generate a model of in situ behavior becomes problematic, given that feedback and lateral inhibition will sculpt action potential output, which of course will then fundamentally shape their synaptic drive of secondary UBCs, which will be further sculpted by their own inhibitory inputs. This issue undermines interpretation of the NEURON model.

The argument that taking inhibition into account is not possible because of assumed or possible direct electrical excitation of Golgi cells is confusing for two interacting reasons. First, one can certainly stimulate the mossy fiber bundle to get afferent excitation of UBCs (and polysynaptic feedback/lateral inhibitory inputs) without directly stimulating the Golgi cells that innervate any recorded UBC. Yes, one might be stimulating some Golgi cells near the stimulating electrode, but one can position the stimulating electrode far enough down the white matter track (away from the recorded UBC), such that mossy fiber inputs to the recorded UBC can be stimulated without affecting Golgi cells near or synaptically connected to the recorded UBC. Moreover, if the argument were true, then presumably the stimulation protocol would be just as likely to directly stimulate neighboring UBCs, which then drove the recorded UBC's responses. Thus, it is both doable and should be ensured that stimulation of the white matter is distant enough to not be directly activating relevant, connected neurons within the granule cell layer.

Finally, the authors present three examples of UBC recordings with and without inhibitory inputs blocked, and state "Thus, these large conductances are unlikely to be significantly shaped by 1-10 ms IPSCs from feedforward and feedback GABA/glycine inhibition" and "GABA/glycinergic inhibition...has little to no effect on the slow inward current that develops after the end of stimulation". This response reflects on original concerns about lack of quantification or consideration of important parameters. In particular, while the traces with and without inhibition are qualitatively similar, quantitative considerations indicate otherwise. First, unquantified examples are not adequate to drive conclusions. Regardless, the main issue (how inhibition affects actual responses in situ) is actually highlighted by the authors current clamp recordings of UBC responses, before and after blocking inhibition. The output response is dramatically different, both at early and late time points, when inhibition is blocked. Again, a lack of quantification (of adequate n's) makes it hard to know exactly how important, but quick "eye ball" estimates of impact include: 1) a switch from only low frequency APs initially (without inhibition blocked) to immediate burst of high frequency APs (high enough to not discern individual APs with given figure resolution) when inhibition is blocked, 2) Slow rising to a peak EPSP, followed by symmetrical return to baseline (without inhibition blocked) versus immediate rise to peak, followed by prolonged decay to baseline (with inhibition blocked), 3) substantially shorter duration (~34% shorter) secondary high frequency burst (individual APs not discernible) of APs (with inhibition blocked versus without inhibition blocked), and 4) substantial reduction in number of long delayed APs (with inhibition blocked versus without inhibition blocked). Thus, clearly, feedback/lateral inhibition is actually sculpting AP output at all phases of the UBC response to trains of afferent stimulations. Importantly, the single voltage clamp trace showing little impact of transient IPSCs on the slow EPSC do not take into account likely IPSC influences on voltage-activated conductances that would not occur in voltage-clamp recordings but would be free to manifest in current clamp, and thereby influence AP output, as observed.

So again, our ability to understand how interconnected UBCs behave in the intact system is undermined by the lack of consideration and quantification of the impact of inhibition, and it not being incorporated into the model. At the very least a strong proviso about lack of inclusion of such information, given the authors' data showing its importance in the few examples shown, should be added to the discussion.

2) No consideration for involvement of polysynaptic UBCs driving UBC responses to MF stimulation in electrophysiology experiments. Given the established existence (in this manuscript and Dino et al. 2000 Neurosci, Dino et al. 2000 ProgBrainRes, Nunzi and Mugnaini 2000 JCompNeurol, Nunzi et al. 2001 JCompNeurol) of polysynaptic connections from MFs to UBCs to UBCs, the MF evoked UBC responses established in this manuscript, especially responses to trains of stimuli could be mediated by direct MF inputs, or to polysynaptic UBC inputs, or possibly both (to my awareness not established either way). Thus the response durations could already include extension of duration by polysynaptic inputs, and so would overestimate the duration of monosynaptic inputs, and thus polysynaptic amplification/modulation, observed in the NEURON model.

Author response: "UBCs receive a single mossy fiber input on their dendritic brush, and thus if our stimulation produces a reliable, short-latency response consistent with a monosynaptic input, then there is not likely to be a disynaptic input."

This statement is not congruent with the literature, with early work by Mugnaini and colleagues (Mugnaini et al. 1994 Synapse; Mugnaini and Flores 1994 J. Comp. Neurol.) indicating that UBCs are innervated by 1-2 mossy fibers, which are as likely other UBC terminals as MFs. This leaves open the possibility that so called monosynaptic responses do, as originally suggested, already include polysynaptic feedforward amplification of duration. While the authors also indicate that isolated disynaptic currents can be observed when they occur in isolation, a careful examination and objective documentation of "monosynaptic" responses would address this issue. Presumably, if potential disynaptic UBC inputs occur during a monosynaptic MF response, it would be detected as an abrupt biphasic inward/outward current, due to additional AMPA receptor activation but further desensitization of those already active (as observed by Kinney et al. 1997 J. Neurophysiol: "The delivery of a second MF stimulus at the peak of the slow EPSC evoked a fast EPSC of reduced amplitude followed by an undershoot of the subsequent slow current"). If such polysynaptic inputs are truly absent and are "rare" in isolation, some estimation of how common or not such synaptic amplification is, would improve our understanding of the overall significance of these inputs.

3) Lack of quantification of subtypes of UBC interconnectivity. Given that it is already established that UBCs synapse onto other UBCs (see refs above), the main potential advance of this manuscript in terms of connectivity is the establishment and quantification of ON-ON, ON-OFF, OFF-ON, and OFF-OFF subtypes of UBC interconnections. But, the authors only establish that each type exists, showing specific examples, but no quantification of the absolute or relative density was provided, and the authors' unquantified wording explicitly or implicitly states that they are not common. This lack of quantification and likely small number makes it difficult to know how important or what impact such synapses have on cerebellar processing, in the model and in situ.

To address this issue, the authors added the following text to the discussion section: "We did not estimate the density of these UBC to UBC connections, because the sparseness of labeling using these approaches made an accurate calculation impossible. Previous work using organotypic slice cultures from P8 mice estimated that 2/3 of the UBC population receives input from other UBCs (Nunzi & Mugnaini, 2000), although it is unclear whether this is the case in older mice."

While accurate, the addition doesn't really address the situation, which is that apparently the reported connections are rare. Adding the information about 2/3 of UBCs having UBC inputs in culture, implies the opposite might be true (i.e. that they might be quite common), which is in contrast to the authors' data, so should be reworded for clarity, which should also incorporate the considerations covered in point #2 above. I.e. if the authors do establish that none of their recordings have polysynaptic inputs, and if they determine that the number of cells that showed isolated di-synaptic inputs is indeed rare, then it suggests that these specific polysynaptic connections are in fact rare.

4) Lack of critical parameters in NEURON model.<br /> A) The model uses # of molecules of glutamate released as the presumed quantal content, and this factor is constant. However, no consideration of changes in # of vesicles released from single versus trains of APs from MFs or UBCs is included. At most simple synapses, two sequential APs alters release probability, either up or down, and release probability changes dynamically with trains of APs. It is therefore reasonable to imagine UBC axon release probability is at least as complicated, and given the large surface area of contact between two UBCs, the number of vesicles released for any given AP is also likely more complex.

B) the model does not include desensitization of AMPA receptors, which in the case of UBCs can paradoxically reduce response magnitude as vesicle release and consequent glutamate concentration in the cleft increases (Linney et al. 1997 JNeurophysiol, Lu et al. 2017 Neuron, Balmer et al. 2021 eLIFE), as would occur with trains of stimuli at MF to ON-UBCs.

While the authors have not added the suggested additional parameters, their clarifications regarding the implications of existing parameters, and demonstration of reasonable fits to experimental data, and lack of substantial effect of simulating reduced vesicle release probability, provided by the authors, adequately addresses this concern.

5) Lack of quantification of various electrophysiological responses. UBCs are defined (ON or OFF) based on inward or outward synaptic response, but no information is provided about the range of the key parameter of duration across cells, which seems most critical to the current considerations. There is a similar lack of quantification across cells of AP duration in response to stimulation or current injections, or during baseline. The latter lack is particularly problematic because in agreement with previous publications, the raw data in Fig. 1 shows ON UBCs as quiescent until MF stimulation and OFF UBCs firing spontaneously until MF stimulation, but, for example, at least one ON UBC in the NEURON model is firing spontaneously until synaptically activated by an OFF UBC (Fig. 11A), and an OFF UBC is silent until stimulated by a presynaptic OFF UBC (Fig. 11C). This may be expected/explainable theoretically, but then such cells should be observed in the raw data.

The authors have added additional analysis and discussion, which adequately addresses this concern.

Reviewer #1 (Public Review):

Summary: The authors apply a new approach to monitor widespread changes in sensory evoked hemodynamic activity after focal stroke in fully conscious rats. Using functional ultrasound (fUS), they report immediate and lasting (up to 5 days) depression of sensory evoked responses in somatosensory thalamic and cortical regions.

Strengths: This a technically challenging study that employs new methods to study more distributed changes in sensory evoked neural activity, inferred from changes in cerebral blood flow. The authors provide compelling images and rigorous analysis to support their conclusions.

The primary weakness of this paper was the small sample size used for drawing conclusions. The authors have added additional references that help support their preliminary findings.

Ultimately, it is a proof of concept paper showing the potential of this imaging approach for examining brain wide changes in activity before and after stroke in awake animals. In that sense, I think this paper will be well appreciated by researchers trying to understand how stroke leads to distributed changes in brain function.

Reviewer #1 (Public Review):

Summary:<br /> The authors were attempting to determine the extent that CIH altered swallowing motor function; specifically, the timing and probability of the activation of the larygneal and submental motor pools. The paper describes a variety of different motor patterns elicited by optogenetic activation of individual neuronal phenotypes within PiCo in a group of mice exposed to CIH. They show that there are a variety of motor patterns that emerge in CIH mice; this is apparently different than the more consistent motor patterns elicited by PiCo activation in normoxic mice (previously published).

Strengths:<br /> The preparation is technically challenging and gives valuable information related to the role of PiCo in the pattern of motor activation involved in swallowing and its timing with phrenic activity. Genetic manipulations allow for the independent activation of the individual neuronal phenotypes of PiCo (glutamatergic, cholinergic) which is a strength.

Weaknesses:<br /> 1. The data presented are largely descriptive in terms of the effect of PiCo activation on the probability of swallowing and the pattern of motor activation changes following CIH. Comparisons made between experimental data acquired currently and those obtained in a previous cohort of animals (possibly years before) are extremely problematic, with the potential confounding influence of changing environments, genetics, and litter effects. The statistical analyses (i.e. comparing CIH with normoxic) appear insufficiently robust. Exactly how the data were compared is not described.

2. There is limited mechanistic insight into how PiCo manipulation alters the pattern and probability of motor activation. For example, does CIH alter PiCo directly, or some other component of the circuit (NTS)? Techniques that silence or activation projections to/from PiCo should be interrogated. This is required to further delineate and define the swallowing circuit, which remains enigmatic.

3. The functional significance of the altered (non-classic) patterns is unclear.

Joint Public Review:

The authors aimed to contrast the effects of pharmacologically enhanced catecholamine and acetylcholine levels versus the effects of voluntary spatial attention on decision making in a standard spatial cuing paradigm. Meticulously reported, the authors show that atomoxetine, a norepinephrine reuptake inhibitor, and cue validity both enhance model-based evidence accumulation rate, but have several distinct effects on EEG signatures of pre-stimulus cortical excitability, evoked sensory EEG potentials and perceptual evidence accumulation. The results are based on a reasonable sample size (N=28) and state-of-the art modeling and EEG methods.

The authors' EEG findings provide solid evidence for the overall conclusion that selective attention and neuromodulatory systems shape perception in "similar, unique, and interactive" ways. This is an important conclusion because neuromodulatory systems and selective spatial attention are both known to regulate the neural gain of task-relevant single neurons and neural networks. Apparently, these effects on neural gain affect decision making in partly overlapping and partly dissociable ways.

The effects of donepezil, a cholinesterase inhibitor, were generally less strong than those of atomoxetine, and in various analyses went in the opposite direction. The authors fairly conclude that more work is necessary to determine the effects of cholinergic neuromodulation on perceptual decision making.

Joint Public Review:

Cook, Watt, and colleagues previously reported that a mouse model of Spinocerebellar ataxia type 6 (SCA6) displayed defects in BDNF and TrkB levels at an early disease stage. Moreover, they have shown that one month of exercise elevated cerebellar BDNF expression and improved ataxia and cerebellar Purkinje cell firing rate deficits. In the current work, they attempt to define the mechanism underlying the pathophysiological changes occurring in SCA6. For this, they carried out RNA sequencing of cerebellar vermis tissue in 12-month-old SCA6 mice, a time when the disease is already at an advanced stage, and identified widespread dysregulation of many genes involved in the endo-lysosomal system. Focusing on BDNF/TrkB expression, localization, and signaling they found that, in 7-8 month-old SCA6 mice early endosomes are enlarged and accumulate BDNF and TrkB in Purkinje cells. Curiously, TrkB appears to be reduced in the recycling endosomes compartment, despite the fact that recycling endosomes are morphologically normal in SCA6. In addition, the authors describe a reduction in the Late endosomes in SCA6 Purkinje cells associated with reduced BDNF levels and a probable deficit in late endosome maturation.

Strengths:<br /> The article is well written, and the findings are relevant for the neuropathology of different neurodegenerative diseases where dysfunction of early endosomes is observed. The authors have provided a detailed analysis of the endo-lysosomal system in SCA6 mice. They have shown that TrkB recycling to the cell membrane in recycling endosomes is reduced, and the late endosome transport of BDNF for degradation is impaired. The findings will be crucial in understanding underlying pathology. Lastly, the deficits in early endosomes are rescued by chronic administration of 7,8-DHF.

Weaknesses:<br /> The specificity of BDNF and TrkB immunostaining requires additional controls, as it has been very difficult to detect immunostaining of BDNF.<br /> The revised manuscript has included additional analysis using epitope retrieval and a negative liver control with the Abcam antibody against BDNF. An alternative antibody that may be considered for BDNF detection is from Icosagen AS. This antibody has been found to be effective for immunofluorescence and immunoblot purposes.

Two other issues were brought up in the initial review process--

1) One important concern about the conclusions is that the RNAseq experiment was conducted in 12-month-old SCA6 mice suggesting that the defects in the endo-lysosomal system may be caused by other pathophysiological events and, likewise, the impairment in BDNF signaling may also be indirect, as also noted by the authors. Indeed, Purkinje cells in SCA6 mice have an impaired ability to degrade other endocytosed cargo beyond BDNF and TrkB, most likely because of trafficking deficits that result in a disruption in the transport of cargo to the lysosomes and lysosomal dysfunction.<br /> This concern was acknowledged in the revision and will require further analysis.

2) Moreover, the beneficial effects of 7,8-DHF treatment on motor coordination may be caused by 7,8-DHF properties other than the putative agonist role on TrkB. Indeed, many reservations have been raised about using 7,8-DHF as an agonist of TrkB activity. Several studies have now debunked (Todd et al. PlosONE 2014, PMID: 24503862; Boltaev et al. Sci Signal 2017, PMID: 28831019) or at the very least questioned (Lowe D, Science 2017: see Discussion: https://www.science.org/content/blog-post/those-compounds-aren-t-what-you-think-they-are Wang et al. Cell 2022 PMID: 34963057). Another interpretation is that 7,8-DHF possesses antioxidant activity and neuroprotection against cytotoxicity in HT-22 and PC12 cells, both of which do not express TrkB (Chen et al. Neurosci Lett 201, PMID: 21651962; Han et al. Neurochem Int. 2014, PMID: 24220540). Thus, while this flavonoid may have a beneficial effect on the pathophysiology of SCA6, it is most unlikely that mechanistically this occurs through a TrkB agonistic effect considering the potent anti-oxidant and anti-inflammatory roles of flavonoids in neurodegenerative diseases (Jones et al. Trends Pharmacol Sci 2012, PMID: 22980637).<br /> The authors have acknowledged alternative explanations for the action of 7,8-DHF and have qualified the discussion of this issue.

Reviewer #1 (Public Review):

Cullinan et al. explore the hypothesis that the cytoplasmic N- and C-termini of ASIC1a, not resolved in x-ray or cryo-EM structures, form a dynamic complex that breaks apart at low pH, exposing a C-terminal binding site for RIPK1, a regulator of necrotic cell death. They expressed channels tagged at their N- and C-termini with the fluorescent, non-canonical amino acid ANAP in CHO cells using amber stop-codon suppression. Interaction between the termini was assessed by FRET between ANAP and colored transition metal ions bound either to a cysteine reactive chelator attached to the channel (TETAC) or metal-chelating lipids (C18-NTA). A key advantage to using metal ions is that they are very poor FRET acceptors, i.e. they must be very close to the donor for FRET to occur. This is ideal for measuring small distances/changes in distance on the scales expected from the initial hypothesis. In order to apply chelated metal ions, CHO cells were mechanically unroofed, providing access to the inner leaflet of the plasma membrane. At high pH, the N- and C- termini are close enough for FRET to be measured, but apparently too far apart to be explained by a direct binding interaction. At low pH, there was an apparent increase in FRET between the termini. FRET between ANAP on the N-and C-termini and metal ions bound to the plasma membrane suggests that both termini move away from the plasma membrane at low pH. The authors propose an alternative hypothesis whereby close association with the plasma membrane precludes RIPK1 biding to the C-terminus of ASIC1a.

The findings presented here are certainly valuable for the ion channel/signaling field and the technical approach only increases the significance of the work. The choice of techniques is appropriate for this study and the results are clear and high quality. Sufficient evidence is presented against the starting hypothesis. I have a few questions about certain controls and assumptions that I would like to see discussed more explicitly in the manuscript.

--As discussed by the authors, the C-terminal citrine could potentially disrupt the hypothesized interaction between the N- and C-termini.

--There is apparent read-through of some of the stop codons in the absence of ANAP, which could complicate interpretation of the experiments. The largest amount of read-through is for the E6TAG, L18TAG, and H515TAG constructs, which were not used for further experiments. However, some degree of read-through is evident from western blots for V10TAG, Q14TAG, L41TAG, and A44TAG as well.

Since the epitope used for western blots is on the C-terminus of the protein, the blots do not show the fraction of truncated protein. As discussed by the authors, N-terminally truncated constructs would be too small to assemble into channels. In constructs with the TAG codon towards the C-terminus, there is the potential for co-assembly of full-length and truncated subunits into trimers. Truncated subunits would not contribute directly to the fluorescence signal, but could potentially have allosteric effects on the position of the C-termini of full-length ANAP-tagged constructs in the context of a mixed channel.

Reviewer #1 (Public Review):

This nice study by Miyano combines slice electrophysiology and superresolution microscopy to address the role of RBP2 in Ca2+ channel clustering and neurotransmitter release at hippocampal mossy fiber terminals. While a number of studies demonstrated a critical role for RBPs in clustering Ca2+ channels at other synapses and some provided evidence for a role of the protein in molecular coupling of Ca2+ channels and release sites, the present study targets another key synapse that is an important model for presynaptic studies and offers access to a microdomain controlled synaptic vesicle (SV) release mechanism with low initial release probability.

Summarizing a large body of high-quality work, the authors demonstrate reduced Ca2+ currents and a reduced release probability. They attribute the latter to the reduced Ca2+ influx and can restore release by increasing Ca2+ influx. Moreover, they propose an altered fusion competence of the SVs, which is not so strongly supported by the data in my view.

The effects are relatively small, but I think the careful analysis of the RBP role at the mossy fiber synapse is an important contribution.

Reviewer #1 (Public Review):

Summary:<br /> The current study provided a follow-up analysis using published datasets focused on the individual variability of both the distraction effect (size and direction) and the attribute integration style, as well as the association between the two. The authors tried to answer the question of whether the multiplicative attribute integration style concurs with a more pronounced and positively oriented distraction effect.

Strengths:<br /> The analysis extensively examined the impacts of various factors on decision accuracy, with a particular focus on using two-option trials as control trials, following the approach established by Cao & Tsetsos (2022). The statistical significance results were clearly reported.

The authors meticulously conducted supplementary examinations, incorporating the additional term HV+LV into GLM3. Furthermore, they replaced the utility function from the expected value model with values from the composite model.

Weaknesses:<br /> There are several weaknesses in terms of theoretical arguments and statistical analyses.

First, the manuscript suggests in the abstract and at the beginning of the introduction that the study reconciled the "different claims" about "whether distraction effect operates at the level of options' component attributes rather than at the level of their overall value" (see line 13-14), but the analysis conducted was not for that purpose. Integrating choice attributes in either an additive or multiplicative way only reflects individual differences in combining attributes into the overall value. The authors seemed to assume that the multiplicative way generated the overall value ("Individuals who tended to use a multiplicative approach, and hence focused on overall value", line 20-21), but such implicit assumption is at odds with the statement in line 77-79 that people may use a simpler additive rule to combine attributes, which means overall value can come from the additive rule.

The second weakness is sort of related but is more about the lack of coherent conceptual understanding of the "additive rule", or "distractor effect operates at the attribute level". In an assertive tone (lines 77-80), the manuscript suggests that a weighted sum integration procedure of implementing an "additive rule" is equal to assuming that people compare pairs of attributes separately, without integration. But they are mechanistically distinct. The additive rule (implemented using the weighted sum rule to combine probability and magnitude within each option and then applying the softmax function) assumes value exists before comparing options. In contrast, if people compare pairs of attributes separately, preference forms based on the within-attribute comparisons. Mathematically these two might be equivalent only if no extra mechanisms (such as inhibition, fluctuating attention, evidence accumulation, etc) are included in the within-attribute comparison process, which is hardly true in the three-option decision.

Could the authors comment on the generalizability of the current result? The reward magnitude and probability information are displayed using rectangular bars of different colors and orientations. Would that bias subjects to choose an additive rule instead of the multiplicative rule? Also, could the conclusion be extended to other decision contexts such as quality and price, whether a multiplicative rule is hard to formulate?

The authors did careful analyses on quantifying the "distractor effect". While I fully agree that it is important to use the matched two-option trials and examine the interaction terms (DV-HV)T as a control, the interpretation of the results becomes tricky when looking at the effects in each trial type. Figure 2c shows a positive DV-HV effect in two-option trials whereas the DV-HV effect was not significantly stronger in three-option trials. Further in Figure 5b,c, in the Multiplicative group, the effect of DV-HV was absent in the two-option trials and present in the three-option trials. In the Additive group, however, the effect of DV-HV was significantly positive in the two-option trials but was significantly lowered in the three-option trials. Hence, it seems the different distractor effects were driven by the different effects of DV-HV in the two-option trials, rather than the three-option trials?

Note that the pattern described above was different in Supplementary Figure 2, where the effect of DV-HV on the two-option trials was negative for both Multiplicative and Additive groups. I would suggest considering using Supplementary Figure 2 as the main result instead of Figure 5, as it does not rely on multiplicative EV to measure the distraction effect, and it shows the same direction of DV-HV effect on two-option trials, providing a better basis to interpret the (DV-HV)T effect.

Reviewer #1 (Public Review):

Summary:<br /> The authors re-analysed the data of a previous study in order to investigate the relation between asymmetries of subcortical brain structures and the hemispheric lateralization of alpha oscillations during visual spatial attention. The visual spatial attention task crossed the factors of target load and distractor salience, which made it possible to also test the specificity of the relation of subcortical asymmetries to lateralized alpha oscillations for specific attentional load conditions. Asymmetry of globus pallidus, caudate nucleus, and thalamus explained inter-individual differences in attentional alpha modulation in the left versus right hemisphere. Multivariate regression analysis revealed that the explanatory potential of these regions' asymmetries varies as a function of target load and distractor salience.

Strengths:<br /> The analysis pipeline is straightforward and follows in large parts what the authors have previously used in Mazzetti et al (2019). The authors use an interesting study design, which allows for testing of effects specific to different dimensions of attentional load (target load/distractor salience). The results are largely convincing and in part replicate what has previously been shown. The article is well-written and easy to follow.

Weaknesses:<br /> While the article is interesting to read for researchers studying alpha oscillations in spatial attention, I am somewhat sceptical about whether this article is of high interest to a broader readership. Although I read the article with interest, the conceptual advance made here can be considered mostly incremental. As the authors describe, the present study's main advance is that it does not include reward associations (as in previous work) and includes different levels of attentional load. While these design features and the obtained results indeed improve our general understanding of how asymmetries of subcortical structures relate to lateralized alpha oscillations, the conceptual advance is somewhat limited.

While the analysis of the relation of individual subcortical structures to alpha lateralization in different attentional load conditions is interesting, I am not convinced that the present analysis is suited to draw strong conclusions about the subcortical regions' specificity. For example, the Thalamus (Fig. 5) shows a significant negative beta estimate only in one condition (low-load target, non-salient distractor) but not in the other conditions. However, the actual specificity of the relation of thalamus asymmetry to lateralized alpha oscillations would require that the beta estimate for this one condition is significantly higher than the beta estimates for the other three conditions, which has not been tested as far as I understand.

Reviewer #1 (Public Review):

Summary:<br /> In the present study, authors found the ternary complex formed by NCAN, TNC, and HA as an important factor facilitating the multipolar to bipolar transition in the intermediate zone (IZ) of the developing cortex. NCAM binds HA via the N-terminal Link modules, meanwhile, TNC cross-links NCAN through the CDL domain at the C-terminal. The expression and right localization of these three factors facilitate the multipolar-bipolar transition necessary for immature neurons to migrate radially. TNC and NCAM are also involved in neuronal morphology. The authors used a wide range of techniques to study the interaction between these three molecules in the developing cortex. In addition, single and double KO mice for NCAN and TNC were analyzed to decipher the role of these molecules in neuronal migration and morphology.

Strengths:<br /> The study of the formation of the cerebral cortex is crucial to understanding the pathophysiology of many neurodevelopmental disorders associated with malformation of the cerebral cortex. In this study, the authors showed, for the first time, that the ternary complex formed by NCAN, TNC, and HA promotes neuronal migration. The results regarding the interaction between the three factors forming the ternary complex are convincing.

Weaknesses:<br /> However, regarding the in vivo experiments, the authors should consider some points for the interpretation of the results:<br /> -The authors did not use the proper controls in their experiments. For embryonic analysis, such as cortical migration, neuronal morphology, and protein distribution (Fig. 6, 7, and 9), mutant mice should be compared with control littermates, since differences in the results could be due to differences in embryonic stages. For example, in Fig. 6 the dKO is more developed than the WT embryo.<br /> -The authors claim that NCAM and TNC are involved in neuronal migration from experiments using single KO embryos. This is a strong statement considering the mild results, with no significant difference in the case of TNC KO embryos, and once again, using embryos from different litters.<br /> -The measurement of immunofluorescence intensity is not the right method to compare the relative amount of protein between control and mutant embryos unless there is a right normalization.

Reviewer #1 (Public Review):

Summary:<br /> In this manuscript, the authors use anatomical tracing and slice physiology to investigate the integration of thalamic (ATN) and retrosplenial cortical (RSC) signals in the dorsal presubiculum (PrS). This work will be of interest to the field, as the postsubiculum is thought to be a key region for integrating internal head direction representations with external landmarks. The main result is that ATN and RSC inputs drive the same L3 PrS neurons, which exhibit superlinear summation to near-coincident inputs. Moreover, this activity can induce bursting in L4 PrS neurons, which can pass the signals LMN (perhaps gated by cholinergic input).

Strengths:<br /> The slice physiology experiments are carefully done. The analyses are clear and convincing, and the figures and results are well-composed. Overall, these results will be a welcome addition to the field.

Weaknesses:<br /> The conclusions about the circuit-level function of L3 PrS neurons sometimes outstrip the data, and their model of the integration of these inputs is unclear. I would recommend some revision of the introduction and discussion. I also had some minor comments about the experimental details and analysis.

Specific major comments:<br /> 1) I found that the authors' claims sometimes outstrip their data, given that there were no in vivo recordings during behavior. For example, in the abstract, their results indicate "that layer 3 neurons can transmit a visually matched HD signal to medial entorhinal cortex", and in the conclusion they state "[...] cortical RSC projections that carry visual landmark information converge on layer 3 pyramidal cells of the dorsal presubiculum". However, they never measured the nature of the signals coming from ATN and RSC to L3 PrS (or signals sent to downstream regions). Their claim is somewhat reasonable with respect to ATN, where the majority of neurons encode HD, but neurons in RSC encode a vast array of spatial and non-spatial variables other than landmark information (e.g., head direction, egocentric boundaries, allocentric position, spatial context, task history to name a few), so making strong claims about the nature of the incoming signals is unwarranted.

2) Related to the first point, the authors hint at, but never explain, how coincident firing of ATN and RSC inputs would help anchor HD signals to visual landmarks. Although the lesion data (Yoder et al. 2011 and 2015) support their claims, it would be helpful if the proposed circuit mechanism was stated explicitly (a schematic of their model would be helpful in understanding the logic). For example, how do neurons integrate the "right" sets of landmarks and HD signals to ensure stable anchoring? Moreover, it would be helpful to discuss alternative models of HD-to-landmark anchoring, including several studies that have proposed that the integration may (also?) occur in RSC (Page & Jeffrey, 2018; Yan, Burgess, Bicanski, 2021; Sit & Goard, 2023). Currently, much of the Discussion simply summarizes the results of the study, this space could be better used in mapping the findings to the existing literature on the overarching question of how HD signals are anchored to landmarks.

Reviewer #1 (Public Review):

Summary:<br /> These types of analyses use many underlying assumptions about the data, which are not easy to verify. Hence, one way to test how the algorithm is performing in a task is to study its performance on synthetic data in which the properties of the variable of interest can be apriori fixed. For example, for burst detection, synthetic data can be generated by injected bursts of known durations, and checking if the algorithm is able to pick it up. Burst detection is difficult in the spectral domain since direct spectral estimators have high variance (see Subhash Chandran et al., 2018, J Neurophysiol). Therefore, detected burst lengths are typically much lower than injected burst lengths (see Figure 3). This problem can be solved by doing burst estimation in the time domain itself, for example, using Matching Pursuit (MP). I think the approach presented in this paper would also work since this model is also trained on data in the time domain. Indeed, the synthetic data can be made more "challenging" by injecting multiple oscillatory bursts that are overlapping in time, for which a greedy approach like MP may fail. It would be very interesting to test whether this method can "keep up" as the data is made more challenging. While showing results from brain signals directly (e.g., Figure 7) is nice, it will be even more impactful if it is backed up with results obtained from synthetic data with known properties.

I was wondering about what kind of "synthetic data" could be used for the results shown in Figure 8-12 but could not come up with a good answer. Perhaps data in which different sensory systems are activated (visual versus auditory) or sensory versus movement epochs are compared to see if the activation maps change as expected. We see similarities between states across multiple runs (reproducibility analysis) and across tasks (e.g. Figure 8 vs 9) and even methods (Figure 8 vs 10), which is great. However, we should also expect the emergence of new modes specific to sensory activation (say auditory cortex for an auditory task). This will allow us to independently check the performance of this method.

The authors should explain the reproducibility results (variational free energy and best run analysis) in the Results section itself, to better orient the reader on what to look for.

Page 15: the comparison across subjects is interesting, but it is not clear why sensory-motor areas show a difference and the mean lifetime of the visual network decreases. Can you please explain this better? The promised discussion in section 3.5 can be expanded as well.

Reviewer #1 (Public Review):

Summary:<br /> In this manuscript, Ketaren, Mast, Fridy et al. assessed the ability of a previously generated llama nanobody library (Mast, Fridy et al. 2021) to bind and neutralize SARS-CoV-2 delta and omicron variants. The authors identified multiple nanobodies that retain neutralizing and/or binding capacity against delta, BA.1 and BA.4/5. Nanobody epitope mapping on spike proteins using structural modeling revealed possible mechanisms of immune evasion by viral variants as well as mechanisms of cross-variant neutralization by nanobodies. The authors additionally identified two nanobody pairs involving non-neutralizing nanobodies that exhibited synergy in neutralization against the delta variant. These results enabled the refinement of target epitopes of the nanobody repertoire and the discovery of several pan-variant nanobodies for further preclinical development.

Strengths:<br /> Overall, this study is well executed and provides a valuable framework for assessing the impact of emerging SARS-CoV-2 variants on nanobodies using a combination of in vitro biochemical and cellular assays as well as computational approaches. There are interesting insights generated from the epitope mapping analyses, which offer possible explanations for how delta and omicron variants escape nanobody responses, as well as how some nanobodies exhibit cross-variant neutralization capacity. These analyses laid out a clear path forward for optimizing these promising next-gen therapeutics, particularly in the face of rapidly emerging SARS-CoV-2 variants. This work will be of interest to researchers in the fields of antibody/nanobody engineering, SARS-CoV-2 therapeutics, and host-virus interaction.

Weaknesses:<br /> A main weakness of the study is that the efficacy statement is not thoroughly supported. While the authors comprehensively characterized the neutralizing ability of nanobodies in vitro, there is no animal data involving mice or hamsters to demonstrate the real protective efficacy in vivo. Yet, in the title and throughout the manuscript, the authors repeatedly used phrases like "retains efficacy" or "remains efficacious" to describe the nanobodies' neutralization or binding capacities. This claim is not well supported by the data and underestimates the impact of variants on the nanobodies, especially the omicron sublineages. For example, the authors showed that S1-RBD-15 had a ~100-fold reduction in neutralization titer against Omicron, with an IC50 at around 1 uM. This is much higher than the IC50 value of a typical anti-ancestral RBD nanobody reported in the previous study (Mast, Fridy et al. 2021). In fact, the authors themselves ascribe nanobodies with an IC50 above 1 uM as weak neutralizers. And there were many in the range of 0.1-1 uM. Furthermore, many nanobodies selected for affinity measurement against BA.4/5 had no detectable binding. Without providing in vivo protection data or including monoclonal antibodies that are known to be efficacious against variants in the in vitro assays as a benchmark, it is difficult to evaluate the efficacy just with the IC50 values.

Reviewer #1 (Public Review):

Papalamprou et al. established a methodology to differentiate iPSCs to the syndetome stage and validated it by marker gene expression and scRNA-seq analysis. They further found that inhibition of WNT signaling enhanced the homogeneity of the cell population after identifying a group of braching-off cells that overexpressed WNT. Their results will be helpful in developing cell therapy systems for tendon injuries. However, there are several issues to improve the manuscript:

IPA analysis was performed after scRNA-seq. Although it is knowledge-based software with convenient graphic utilities, it is questionable whether an unbiased genome-level analysis was performed. Therefore, it is not convincing if WNT is the only and best signal for the branching-off marker. Perhaps independent approaches, such as GO, pathway, or module analyses, should be performed to validate the finding.

According to the method section, two iPSC lines were used for the study. However, throughout the manuscript, it is not clearly described which line was used for which experiment. Did they show similar efficiency in differentiation and in responses to WNTi? It is also worrisome if using only two lines is the norm in the stem cell field. Please provide a rationale for using only two lines, which will restrict the observation of individual-specific differential responses throughout the study.

How similar are syndetome cells with or without WNTi? It would be interesting to check if there are major DEGs that differentiate these two groups of cells.

Please discuss the improvement of the current study compared to previous ones (e.g., PMID 36203346, 35083031, 35372337).

Reviewer #1 (Public Review):

Genetic, physiological, and environmental manipulations that increase roaming increase leaving rates. The connection between increased roaming and increased leaving is lost when tax4-expressing sensory neurons are inactivated. This study is conceptually important in its characterization of worm behaviors as time-series of discrete states, a promising framework for understanding behavioral decisions as algorithms that govern state transitions. This framework is well-established in other animals, but relatively new to worms.

A key discovery is that lawn leaving behavior is probabilistically favored in states of behavioral arousal. I like the use of response-triggered averages (triggered on leaving events) that illustrate a "state-dependent receptive field" of the behavioral response. Response-triggered averages are common in sensory neuroscience, used, for example, to characterize the diverse "stimulus-dependent receptive fields" of different retinal ganglion cell types. It's nice to adapt the idea to illustrate the state-dependence of behavioral state transitions.

The simplest metric of arousal state is crawling speed. When animals crawl faster, they are more likely to leave lawns. A more sophisticated metric of behavioral context is whether the animal is in a "roaming" or "dwelling" state, two-state HMM modeling from previous work (Flavell et al., 2013). Roaming animals are more likely to leave lawns than dwelling animals. Different autoregressive HMM tools can segment worm behavior into 4-states. Also with ARHMMs, the most aroused state is again the state that promotes lawn-leaving. HMM analysis disentangles effects that were lumped by the simpler metric of overall speed.

The authors use diverse environmental, genetic, and optogenetic perturbations to regulate the roaming state, thereby regulating the statistics of leaving in the expected manner. One surprise is that feeding inhibition evokes roaming and lawn-leaving in both pdfr-1 and tph-1 mutants, even though the tph-1-expressing NSM neurons have been shown to sense bacterial ingestion and food availability.

Another surprise is that evoking roaming does not evoke leaving in tax-4 mutants. Without sensory neuron activity, worms are only more likely to roam for a minute before leaving rather than roaming for several minutes before leaving like wild-type (Figure 6C). ASJ seems to be the most important sensory neuron in this coupling between roaming and leaving (which is uncoupled when sensory neurons are inactivated).

Reviewer #1 (Public Review):

This manuscript by Kelly et al. reports results from single-cell transcriptomic analysis of spinal neurons in zebrafish. The work builds on a strong foundation of literature and the objective, to discern gene expression patterns specializing functionally distinct motor circuits, is well rationalized. Specifically, they compared the transcriptomes in the escape and swimming circuits.

The authors discovered, in the motor neurons of the escape circuit, two functional groups or "cassettes" of genes related to excitability and vesicle release, respectively. Expression of these genes make sense for a "fast" circuit. This finding will be important to the field and form the basis for subsequent studies differentiating the escape circuit from others.

Reviewer #1 (Public Review):

Muller glia function as retinal stem cells in the adult zebrafish retina. Following retinal injury, Muller glia are reprogrammed (reactive Muller glia), and then divide to produce a progenitor that amplifies and differentiates into retinal neurons. Previous scRNAseq analysis used total retinal RNA from uninjured and injured retinas isolated at time points when Muller glia are quiescent, being reprogrammed, and proliferating to reveal genes and gene regulatory networks underlying these events (Hoang et al., 2020). The manuscript by Celotto et al., used double transgenic zebrafish that allow them to purify by FACS quiescent and reactive Muller glia, Muller glia-derived progenitors, and their differentiating progeny at different times post retinal damage. RNA from these cell populations was used in scRNAseq studies to identify the transcriptomes associated with these cell populations. Importantly, they report two quiescent and two reactive Muller glia populations. These results raise the interesting possibility that Muller glia are a heterogeneous population whose members may exhibit different regenerative responses to retinal injury. However, without further experimentation, the validity and significance of this result remain unclear. In addition to putative Muller cell heterogeneity, Celotto et al., identified multiple progenitor classes, some of which are specified to regenerate specific retinal neuron types. Because of its focus on Muller glia and Muller glia-derived progenitors at mid to late stages of retina regeneration, this new scRNAseq data will be a useful resource to the research community for further interrogation of gene expression changes underlying retina regeneration.

Reviewer #1 (Public Review):

Summary:

The process of taste perception is significantly more intricate and complex in Lepidopteran insects. This investigation provides valuable insights into the role of Gustatory receptors and their dynamics in the sensation of sucrose, which serves as a crucial feeding cue for insects. The article highlights the differential sensitivity of Grs to sucrose and their involvement in feeding and insect behavior.

Strengths:

To support the notion of the differential specificity of Gr to sucrose, this study employed electrophysiology, ectopic expression of Grs in Xenopus, genome editing, and behavioral studies on insects. This investigation offers a fundamental understanding of the gustation process in lepidopteran insects and its regulation of feeding and other gustation-related physiological responses. This study holds significant importance in advancing our comprehension of lepidopteran insect biology, gustation, and feeding behavior.

Weaknesses:

While this manuscript demonstrates technical proficiency, there exists an opportunity for additional refinement to optimize comprehensibility for the intended audience. Several crucial sugars have been overlooked in the context of electrophysiology studies and should be incorporated. Furthermore, it is imperative to consider the potential off-target effects of Gr knock-out on other Gr expressions. This investigation focuses exclusively on Gr6 and Gr10, while neglecting a comprehensive narrative regarding other Grs involved in sucrose sensation.

Reviewer #1 (Public Review):

Summary:

In this work authors are trying to satisfy a real need in MR safety, when concerns can rise about the thermal increase due to metallic materials in patients carrying orthopedic implants. The "MR conditional" labeling of the implant obtained by ASTM in-vitro tests may help to plan the MR scan, but it is normally limited to a single specific MR sequence and a B0 value, and it is not always available. The adoption of an in-silico simulation testbed overcomes this limitation, providing a fast and reliable prediction of temperature increase from RF, in real-life scan conditions on human-like digital models. The FDA is pushing this approach.

Strengths:

The presented in-silico testbed looks valuable and validated. It is based on the widely available Visible Human Project (VHP) datasets, and the testbed is available on-line. The approval of the testbed by the FDA as a medical device development tool (MDDT) is a good premise for the large-scale adoption of this kind of solution.

Weaknesses:

A couple of limitations of the study are now clearly highlighted to the readers in this revised version of the paper. The following aspects:<br /> - the lack of the equivalent modeling for the gradients-related heating;<br /> - the way the implant is embedded in the VHP model that should take in consideration how to manage the removed and stretched tissues;<br /> are now correctly taken in consideration in the discussion, providing additional literature.

Reviewer #1 (Public Review):

Summary:<br /> The manuscript by Hann et. al examines the role of survival motor neuron protein (SMN) in lateral plate mesoderm-derived cells using the Prrx1Cre to elucidate how changing cell-specific SMN levels coordinate aspects of the spinal muscular atrophy (SMA) pathology. SMN has generally been studied in neuronal cells, and this is one of the first insights into non-neuronal cells that may contribute to SMA disease. The authors generated 3 mouse lines: a Prrx1;Smnf/f conditional null mouse, as well as, single and double copy Prrx1;Smnf/f;SMN2 mice carrying either one or two copies of a human SMN2 transgene. First, the bone development and growth of all three were assessed; the conditional null Smn mutation was lethal shortly after birth, while the SMN2 2-copy mutant did not exhibit bone growth phenotypes. Meanwhile, single-copy SMN2 mutant mice showed reduced size and shorter limbs with shorter proliferative and hypertrophic chondrocyte zones. The authors suggested that this was cell autonomous by assessing the expression of extrinsic factors known to modulate proliferation/differentiation of growth plate chondrocytes. After assessing bone phenotypes, the authors transitioned to the assessments of neuromuscular junction (NMJ) phenotypes, since there are documented neuromuscular impairments in SMA and the Prrx1Cre transgene is expressed in muscle-associated fibro-adipogenic progenitors (FAPs). Neonatal NMJ development was unchanged in mutant mice with two copies of SMN2 , but adult single-copy SMN2 mutant mice had abnormal NMJ morphology, altered presynaptic neurotransmission, and problematic nerve terminal structure. Finally, the authors sought to assess the ability to rescue NMJ phenotypes via FAP cell transplantation and showed wild-type FAPs were able to reduce pre/postsynaptic fragmentation and neurofilament varicosities.

Strengths:<br /> The conditional genetic approaches are novel and interestingly demonstrate the potential for chondrocyte and fibro-adipogenic progenitor-specific contributions to the SMA pathology.

The characterizations of the neuromuscular and NMJ phenotypes are relatively strong.

The data strongly suggest a non-neuronal contribution to SMA, which indicates a need for further mechanistic (cellular and molecular) studies to better understand SMA.

Weaknesses:<br /> The skeletal analyses are not rigorous and likely do not get to the core of how SMN regulates bone development.

The overall work is descriptive and lacks convincing mechanisms.

Additional experimentation is likely needed to fully justify the conclusions.

Reviewer #1 (Public Review):

In 2019, Wilkinson and colleagues (PMID: 31142833) managed to break the veil in a 20-year open question on how to properly culture and expand Hematopoietic Stem Cells (HSCs). Although this study is revolutionizing the HSC biology field, several questions regarding the mechanisms of expansion remain open. Leveraging on this gap, Zhang et al.; embarked on a much-needed investigation regarding HSC self-renewal in this particular culturing setting.

The authors firstly tacked the known caveat that some HSC membrane markers are altered during in vitro cultures by functionally establishing EPCR (CD201) as a reliable and stable HSC marker (Figure 1), demonstrating that this compartment is also responsible for long-term hematopoietic reconstitution (Figure 3). Next in Figure 2, the authors performed single-cell omics to shed light on the potential mechanisms involved in HSC maintenance, and interestingly it was shown that several hematopoietic populations like monocytes and neutrophils are also present in this culture conditions, which has not been reported. The study goes on to functionally characterize these cultured HSCs (cHSC). The authors elegantly demonstrate using state-of-the-art barcoding strategies that these culturing conditions provoke heterogeneity in the expanding HSC pool (Figure 4). In the last experiment (Figure 5), it was demonstrated that cHSC not only retain their high EPCR expression levels but upon transplantation, these cells remain more quiescent than freshly-isolated controls.

Taken together, this study independently validates that the proposed culturing system works and provides new insights into the mechanisms whereby HSC expansion takes place.

Most of the conclusions of this study are well supported by the present manuscript, some aspects regarding experimental design and especially the data analysis should be clarified and possibly extended.

1. The first major point regards the single-cell (sc) omics performed on whole cultured cells (Figure 2):<br /> a. The authors claim that both RNA and ATAC were performed and indeed some ATAC-seq data is shown in Figure 2B, but this collected data seems to be highly underused.<br /> b. It's not entirely clear to this reviewer the nature of the so-called "HSC signatures"(SF2C) and why exactly these genes were selected. There are genes such as Mpl and Angpt1 which are used for Mk-biased HSCs. Maybe relying on other HSC molecular signatures (PMID: 12228721, for example) would not only bring this study more into the current field context but would also have a more favorable analysis outcome. Moreover reclustering based on a different signature can also clarify the emergence of relevant HSC clusters.<br /> c. The authors took the hard road to perform experiments with the elegant HSC-specific Fgd5-reporter, and they claim in lines 170-171 that it "failed to clearly demarcate in our single-cell multimodal data". This seems like a rather vague statement and leads to the idea that the scRNA-seq experiment is not reliable. It would be interesting to show a UMAP with this gene expression regardless and also potentially some other HSC markers.

2. During the discussion and in Figure 4, the authors ponder and demonstrate that this culturing system can provoke divert HSC close expansion, having also functional consequences. This a known caveat from the original system, but in more recent publications from the original group (PMID: 36809781 and PMID: 37385251) small alterations into the protocol seem to alleviate clone selection. It's intriguing why the authors have not included these parameters at least in some experiments to show reproducibility or why these studies are not mentioned during the discussion section.

3. In this reviewer's opinion, the finding that transplanted cHSC are more quiescent than freshly isolated controls is the most remarkable aspect of this manuscript. There is a point of concern and an intriguing thought that sprouts from this experiment. It is empirical that for this experiment the same HSC dose is transplanted between both groups. This however is technically difficult since the membrane markers from both groups are different. Although after 8 weeks chimerism levels seem to be the same (SF5D) for both groups, it would strengthen the evidence if the author could demonstrate that the same number of HSCs were transplanted in both groups, likely by limiting dose experiments. Finally, it's interesting that even though EE100 cells underwent multiple replication rounds (adding to their replicative aging), these cells remained more quiescent once they were in an in vivo setting. Since the last author of this manuscript has also expertise in HSC aging, it would be interesting to explore whether these cells have "aged" during the expansion process by assessing whether they display an aged phenotype (myeloid-skewed output in serial transplantations and/or assisting their transcriptional age).

Reviewer #1 (Public Review):

Summary:

HIV-associated nephropathy (HIVAN) is a rapidly progressing form of kidney disease that manifests secondary to untreated HIV infection, and is predominantly seen in individuals of African descent. Tg26 mice carrying an HIV transgene lacking gag and pol exhibit high levels of albuminuria and rapid decline in renal function that recapitulates many features of HIVAN in humans. HIVAN is seen predominantly in individuals carrying two copies of missense variants in the APOL1 gene, and the authors have previously shown that APOL1 risk variant mRNA induces activity of the double-strand RNA sensor kinase PKR. Because of the tight association between the APOL1 risk genotype and HIVAN, the authors hypothesized that PKR activation may mediate renal injury in Tg26 mice, and tested this hypothesis by treating mice with a commonly used PKR inhibitory compound called C16. Treatment with C16 substantially attenuated renal damage in the Tg26 model as measured by urinary albumin/creatinine ratio, urinary NGAL/creatinine ratio, and improvement in histology. The authors then performed bulk and single-nucleus RNAseq on kidneys from mice from different treatment groups to identify pathways and patterns of cell injury associated with HIV transgene expression as well as to determine the mechanistic basis for the effect of C16 treatment. They show that proximal tubule nuclei from Tg26 mice appear to have more mitochondrial transcripts which was reversed by C16 treatment and suggest that this may provide evidence of mitochondrial dysfunction in this model. They explore this hypothesis by showing there is a decrease in the expression of nuclear-encoded genes and proteins involved in oxidative phosphorylation as well as a decrease in respiratory capacity via functional assessment of respiration in tubule and glomerular preparations from these mouse kidneys. All of these changes were reversed by C16 treatment. The authors propose the existence of a novel injured proximal tubule cell-type characterized by the leak of mitochondrial transcripts into the nucleus (PT-Mito). Analysis of HIV transgene expression showed high level expression in podocytes, consistent with the pronounced albuminuria that characterizes this model and HIVAN, but transcripts were also detected in tubular and endothelial cells. Because of the absence of mitochondrial transcripts in the podocytes, the authors speculate that glomerular mitochondrial dysfunction in this model is driven by damage to glomerular endothelial cells.

Strengths:

The strengths of this study include the comprehensive transcriptional analysis of the Tg26 model, including an evaluation of HIV transgene expression, which has not been previously reported. This data highlights that HIV transcripts are expressed in a subset of podocytes, consistent with the highly proteinuric disease seen in mice and humans. However, transcripts were also seen in other tubular cells, notably intercalated cells, principal cells and injured proximal tubule cells. Though the podocyte expression makes sense, the relevance of the tubular expression to human disease is still an open question.

The data in support of mitochondrial dysfunction are also robust and rely on combined evidence from downregulation of transcripts involved in oxidative phosphorylation, decreases in complex I and II as determined by immunoblot, and assessments of respiratory capacity in tubular and glomerular preparations. These data are largely consistent with other preclinical renal injury models reported in the literature as well as previous, less thorough assessments in the Tg26 model.

Weaknesses:

The key weakness of the study lies in the use of a PKR inhibitor with questionable specificity. C16 has been reported to inhibit numerous other kinases including cyclin CDKs and GSK3α and -β, and this means that the conclusions of this study with respect to the role of PKR are highly questionable. The rationale for the dose used was not provided (and is lower than used in other publications with C16), and in the absence of drug exposure data and assessment of target engagement, it is difficult to ascertain whether substantial inhibition of PKR was achieved.

A second key weakness lies in the identification of the PT-Mito cell cluster. Though the authors provide some rationale for the identification of this specific cell type, it seems equally plausible the cells merely reflect a high background capture of mitochondria in a subset of droplets. The IHC analysis that was provided is not convincing enough to support the claim and more careful high resolution imaging and in situ hybridization (with appropriate quantitation) will be needed to provide substantive support for the presence of a proximal tubule cell type with mitochondrial transcript that are trafficked to the nucleus.

Reviewer #1 (Public Review):

Summary:<br /> NFKB mutations are thought to be one of the causes of pituitary dysfunction, but until now they could not be reproduced in mice and their pathomechanism was unknown. The authors used the differentiation of hypothalamic-pituitary organoids from human pluripotent stem cells to recapitulate the disease in human iPS cells carrying the NFKB mutation.

Strengths:<br /> The authors achieved their primary goal of recapitulating the disease in human cells. In particular, the differentiation of the pituitary gland is closely linked to the adjacent hypothalamus in embryology, and the authors have again shown that this method is useful when the hypothalamus is suspected to be involved in pituitary abnormalities caused by genetic mutations.

Weaknesses:<br /> On the other hand, the pathomechanism is still not fully understood. This study provides some clues to the pathomechanism, but further analysis of NFKB expression and experiments investigating the relevant factors in more detail may help to clarify it further.

Reviewer #1 (Public Review):

Summary:<br /> In this manuscript, Huang et al have investigated the exercise mimetic role of Eugenol (a natural product) in skeletal muscle and whole-body fitness. The authors report that Eugenol facilitates skeletal muscle remodeling to a slower/oxidative phenotype typically associated with endurance. Eugenol also remodels the fat driving browning the WAT. In both skeletal muscle and fat Eugenol promotes oxidative capacity and mitochondrial biogenesis markers. Eugenol also improves exercise tolerance in a swimming test. Through a series of in vitro studies the authors demonstrate that eugenol may function through the trpv1 channel, Ca mobilization, and activation of CaN/NFAT signaling in the skeletal muscle to regulate slow-twitch phenotype. In addition, Eugenol also induces several myokines but mainly IL-15 through which it may exert its exercise mimetic effects. Overall, the manuscript is well-written, but there are several mechanistic gaps, physiological characterization is limited, and some data are mostly co-relative without vigorous testing (e.g. link between Eugenol, IL15 induction, and endurance). Specific major concerns are listed below.

Strengths:<br /> A natural product activator of the TRPV1 channel that could elicit exercise-like effects through skeletal muscle remodeling. Potential for discovering other mechanisms of action of Eugenol.

Weaknesses:<br /> (1) Figure 1: Histomorphological analysis using immunostaining for type I, IIA, IIX, and IIB should be performed and quantified across different muscle groups and also in the soleus. Fiber type switch measured based on qPCR and Westerns does not sufficiently indicate the extent of fiber type switch. Better images for Fig. 1c should be provided.

(2) Figure 2: Histomorphological analysis for SDH and NADH-TR should be performed and quantified in different muscle groups. Seahorse or oroborous respirometry experiments should be performed to determine the actually increase in mitochondrial respiratory capacity either in isolated mitochondria or single fibers from vehicle and Eugenol-treated mice. Em for mitochondrial should be added to determine the extent of mitochondrial remodeling. The current data is insufficient to indicate the extent of mitochondrial or oxidative remodeling.

(3) Figure 2: Gene expression analysis is limited to a few transcriptional factors. A thorough analysis of gene expression through RNA-seq should be performed to get an unbiased effect of Eugenol on muscle transcriptome. This is especially important because eugenol is proposed to work through CaN/NFAT signaling, major transcriptional regulators of muscle phenotype.

(4) I suggest the inclusion of additional exercise or performance testing including treadmill running, wheel running, and tensiometry. Quantification with a swimming test and measurement of the exact intensity of exercise, etc. is limited.

(5) In addition to muscle performance, whole-body metabolic/energy homeostatic effects should also be measured to determine a potential increase in aerobic metabolism over anaerobic metabolism.

(6) For the swimming test and other measurements, only 4 weeks of vehicle vs. Eugenol treatment was used. For this type of pharmacological study, a time course should be performed to determine the saturation point of the effect. Does exercise tolerance progressively increase with time?

(7) The authors should also consider measuring adaptation to exercise training with or without Eugenol.

(8) Histomorphological analysis of Wat is also lacking. EchoMRI would give a better picture of lean and fat mass.

(9) The experiments performed to demonstrate that Eugenol functions through trpv1 are mostly correlational. Some experiments are needed with trpv1 KO or KD instead of inhibitor. Similarly, KD for other trpv channels should be tested (at least 1-4 that seem to be expressed in the muscle). Triple KO or trpv null cells should be considered to demonstrate that eugenol does not have another biological target.

(10) Eugenol + trpv1 inhibition studies are performed in c2c12 cells and only looks at myofiber genes expression. This is incomplete. Some studies in mitochondrial and oxsphos genes should be done.

(11) The experiments linking Eugenol to ca handling, and calcineurin/nfat activation are all performed in c2c12 cells. There seems to be a link between Eugenol activation and CaN/NFAT activation and fiber type regulation in cells, however, this needs to be tested in mouse studies at the functional level using some of the parameters measured in aims 1 and 2.

(12) The myokine studies are incomplete. The authors show a link between Eugenol treatment and myokines/IL-15 induction. However, this is purely co-relational, without any experiments performed to show whether IL-15 mediates any of the effects of eugenol in mice.

(13) An additional major concern is that it cannot be ruled out that Engenol is uniquely mediating its effects through trpv1. Ideally, muscle-specific trpv1 mice should be used to perform some experiments with Eugenol to confirm that this ion channel is involved in the physiological effects of eugenol.

Reviewer #1 (Public Review):

Summary:<br /> Zhang et al. described a warm autopsy case of a metastatic prostate cancer patient and the follow-up genomic and epigenomic analysis. The authors provided a thorough description of the warm autopsy procedure including consent process, patient evaluation, layout of operation room, specialties required to conduct a warm autopsy, and many other details. Following autopsy, they conducted a series of genomics and epigenomics experiments on selected primary tumors and metastasized tumors from different body sites. Genomic data analysis revealed several interesting results. For example, they discovered a putative metastasis driver event, CDKN1B truncation, and they provided functional relevance of this gene using cell cultures. They were able to piece together the evolutionary history and subclonal structures of the tumors in this patient, which also revealed extensive heterogeneity. They showed a strong correlation between the genetic and epigenetic distances across the tumors.

Strengths:<br /> Overall this is a very well-designed and nicely conducted study. According to the authors, warm autopsy procedures and systems are not yet well established in China. Therefore, this study represents the first warm autopsy in China, and will likely have a strong impact on similar future studies in China. The authors did a good job describing the rationale of a warm autopsy and provided a clear guideline. The genomics analyses were somewhat standard but provided interesting insights.

Weaknesses:<br /> There are several limitations that can be improved upon.

First, while this reviewer does not require the authors to increase the sample size, the authors should provide some discussion, especially on the limitation of generalizing their findings to other patients/cases/cancer types.

Second, the DNA methylation data was used to estimate clonal evolution, but the authors did not investigate whether there is any driver epigenetic events in metastasis. It seems that the authors did not generate WGBS on the primary tumors, which is another limitation.

Third, the authors generated RNA-seq data across many samples but did not provide any analysis beyond the expression level of CDKN1B. This seems to be a missed opportunity.

Fourth, the clonal relationship between the three primary tumors (PB1, PB2, and PB3) and the metastasized tumors is not very well described. Do the authors believe that the metastasis came from a subclone ancestral to the three primary tumors?

Reviewer #1 (Public Review):

Summary:<br /> Heitmann et al introduce a novel method for predicting the potential of drug candidates to cause Torsades de Pointes using simulations. Despite the fact that a multitude of such methods have been proposed in the past decade, this approach manages to provide novelty in a way that is potentially paradigm-shifting. The figures are beautiful and manage to convey difficult concepts intuitively.

Strengths:<br /> (1) Novel combination of detailed mechanistic simulations with rigorous statistical modeling

(2) A method for predicting drug safety that can be used during drug development

(3) A clear explication of difficult concepts.

Weaknesses:<br /> (1) In this reviewer's opinion, the most important scientific issue that can be addressed is the fact that when a drug blocks multiple channels, it is not only the IC50 but also the Hill coefficient that can differ. By the same token, two drugs that block the same channel may have identical IC50s but different Hill coefficients. This is important to consider since concentration-dependence is an important part of the results presented here. If the Hill coefficients were to be significantly different, the concentration-dependent curves shown in Figure 6 could look very different.

(2) The curved lines shown in Figure 6 can initially be difficult to comprehend, especially when all the previous presentations emphasized linearity. But a further issue is obscured in these plots, which is the fact that they show a two-dimensional projection of a 4-dimensional space. Some of the drugs might hit the channels that are not shown (INaL & IKs), whereas others will not. It is unclear, and unaddressed in the manuscript, how differences in the "hidden channels" will influence the shapes of these curves. An example, or at least some verbal description, could be very helpful.

Reviewer #1 (Public Review):

Summary:<br /> In this study, the authors set out to determine whether colorectal cancer surgery site (right, left, rectal) and chemotherapy impact the subsequent risk of developing T2DM in the Danish national health register.

Strengths:<br /> - The research question is conceptually interesting<br /> - The Danish national health register is a comprehensive health database<br /> - The data analysis was thorough and appropriate<br /> -The findings are interesting, and a little surprising that there was no impact of chemotherapy on the development of T2DM

Weaknesses:<br /> - This is not a weakness as such, but in the discussion, I would consider adding some brief comment on the international generalizability of the findings - e.g. demographic make up of the Danish population health register and background rates of DM and obesity in this population with CRC compared to countries on other continents.<br /> - A little more information would be helpful regarding how T2DM was diagnosed in the registry. If someone did develop transient hyperglycemia requiring DM medications during chemotherapy, would the investigators have been able to identify these people? Would they have been classified as T2DM based on filling a prescription for DM meds for a period of time? Also, did the authors have information regarding time to development of T2DM after surgery?<br /> - In the adjusted Models, the authors did not adjust for cancer stage, even though cancer stage appears to be very different between the chemo and no chemo groups. It would be interesting to know if it affects the results if the model adjusted for cancer stage<br /> - It would be worthwhile to report if mortality rates were different between the groups during follow up, and if the authors investigated whether perhaps differences in mortality rates led to specific groups living longer, and therefore having more time to develop DM

Overall, the authors achieved their aims, and the conclusions are supported by their results as reported.<br /> The results are unlikely to significantly change patient treatment or T2DM screening in this population. With some additional information, as described above, the results would be of interest to the community.

Reviewer #1 (Public Review):

Trypanosoma brucei undergoes antigenic variation to evade the mammalian host's immune response. To achieve this, T. brucei regularly expresses different VSGs as its major surface antigen. VSG expression sites are exclusively subtelomeric, and VSG transcription by RNA polymerase I is strictly monoallelic. It has been shown that T. brucei RAP1, a telomeric protein, and the phosphoinositol pathway are essential for VSG monoallelic expression. In previous studies, Cestari et al. (ref. 24) has shown that PIP5pase interacts with RAP1 and that RAP1 binds PI(3,4,5)P3. RNAseq and ChIPseq analyses have been performed previously in PIP5pase conditional knockout cells, too (ref. 24). In the current study, Touray et al. did similar analyses except that catalytic dead PIP5pase mutant was used and the DNA and PI(3,4,5)P3 binding activities of RAP1 fragments were examined. Specifically, the authors examined the transcriptome profile and did RAP1 ChIPseq in PIP5pase catalytic dead mutant. The authors also expressed several C-terminal His6-tagged RAP1 recombinant proteins (full-length, aa1-300, aa301-560, and aa 561-855). These fragments' DNA binding activities were examined by EMSA analysis and their phosphoinositides binding activities were examined by affinity pulldown of biotin-conjugated phosphoinositides. As a result, the authors confirmed that VSG silencing (both BES-linked and MES-linked VSGs) depends on PIP5pase catalytic activity, but the overall knowledge improvement is incremental. The most convincing data come from the phosphoinositide binding assay as it clearly shows that N-terminus of RAP1 binds PI(3,4,5)P3 but not PI(4,5)P2, although this is only assayed in vitro, while the in vivo binding of full-length RAP1 to PI(3,4,5)P3 has been previously published by Cestari et al (ref. 24) already. Considering that many phosphoinositides exert their regulatory role by modulating the subcellular localization of their bound proteins, it is reasonable to hypothesize that binding to PI(3,4,5)P3 can remove RAP1 from the chromatin.

Reviewer #1 (Public Review):

Summary:

What are the overarching principles by which prokaryotic genomes evolve? This fundamental question motivates the investigations in this excellent piece of work. While it is still very common in this field to simply assume that prokaryotic genome evolution can be described by a standard model from mathematical population genetics, and fit the genomic data to such a model, a smaller group of researchers rightly insists that we should not have such preconceived ideas and instead try to carefully look at what the genomic data tell us about how prokaryotic genomes evolve. This is the approach taken by the authors of this work. Lacking a tight theoretical framework, the challenge of such approaches is to devise analysis methods that are robust to all our uncertainties about what the underlying evolutionary dynamics might be.

The authors here focus on a collection of ~300 single-cell genomes from a relatively well-isolated habitat with relatively simple species composition, i.e. cyanobacteria living in hotsprings in Yellowstone National Park, and convincingly demonstrate that the relative simplicity of this habitat increases our ability to interpret what the genomic data tells us about the evolutionary dynamics.

Using a very thorough and multi-faceted analysis of these data, the authors convincingly show that there are three main species of Synechococcus cyanobacteria living in this habitat, and that apart from very frequent recombination within each species (which is in line with insights from other recent studies) there is also a remarkably frequent occurrence of hybridization events between the different species, and with as of yet unidentified other genomes. Moreover, these hybridization events drive much of the diversity within each species. The authors also show convincing evidence that these hybridization events are not neutral but are driven by selected by natural selection.

Strengths:

The great strength of this paper is that, by not making any preconceived assumptions about what the evolutionary dynamics is expected to look like, but instead devising careful analysis methods to tease apart what the data tells us about what has happened in the evolution in these genomes, highly novel and unexpected results are obtained, i.e. the major role of hybridization across the 3 main species living in this habitat.

The analysis is very thorough and reading the detailed supplementary material it is clear that these authors took a lot of care in devising these methods and avoiding the pitfalls that unfortunately affect many other studies in this research area.

The picture of the evolutionary dynamics of these three Synechococcus species that emerge from this analysis is highly novel and surprising. I think this study is a major stepping stone toward the development of more realistic quantitative theories of genome evolution in prokaryotes.

The analysis methods that the authors employ are also partially novel and will no doubt be very valuable for analysis of many other datasets.

Weaknesses:

I feel the main weakness of this paper is that the presentation is structured such that it is extremely difficult to read. I feel readers have essentially no chance to understand the main text without first fully reading the 50-page supplement with methods and 31 supplementary materials. I think this will unfortunately strongly narrow the audience for this paper and below in the recommendations for the authors I make some suggestions as to how this might be improved.

A very interesting observation is that a lot of hybridization events (i.e. about half) originate from species other than the alpha, beta, and gamma Synechococcus species from which the genomes that are analyzed here derive. For this to occur, these other species must presumably also be living in the same habitat and must be relatively abundant. But if they are, why are they not being captured by the sampling? I did not see a clear explanation for this very common occurrence of hybridization events from outside of these Synechococcus species. The authors raise the possibility that these other species used to live in these hot springs but are now extinct. I'm not sure how plausible this is and wonder if there would be some way to find support for this in the data (e.g that one does not observe recent events of import from one of these unknown other species). This was one major finding that I believe went without a clear interpretation.

The core entities in the paper are groups of orthologous genes that show clear evidence of hybridization. It is thus very frustating that exactly the methods for identifying and classifying these hybridization events were really difficult to understand (sections I and V of the supplement). Even after several readings, I was unsure of exactly how orthogroups were classified, i.e. what the difference between M and X clusters is, what a `simple hybrid' corresponds to (as opposed to complex hybrids?), what precisely the definitions of singlet and non-singlet hybrids are, etcetera. It also seems that some numbers reported in the main text do not match what is shown in the supplement. For example, the main text talks about "around 80 genes with more than three clusters (SM, Sec. V; fig. S17).", but there is no group with around 80 genes shown in Fig S17! And similarly, it says "We found several dozen (100 in α and 84 in β) simple hybrid loci" and I also cannot match those numbers to what is shown in the supplement. I am convinced that what the authors did probably made sense. But as a reader, it is frustrating that when one tries to understand the results in detail, it is very difficult to understand what exactly is going on. I mention this example in detail because the hybrid classification is the core of this paper, but I had similar problems in other sections.

Although I generally was quite convinced by the methods and it was clear that the authors were doing a very thorough job, there were some instances where I did not understand the analysis. For example, the way orthogroups were built is very much along the lines used by many in the field (i.e. orthoMCL on the graph of pairwise matchings, building phylogenies of connected components of the graph, splitting the phylogenies along long branches). But then to subdivide orthogroups into clusters of different species, the authors did not use the phylogenetic tree already built but instead used an ad hoc pairwise hierarchical average linkage clustering algorithm.

Reviewer #1 (Public Review):

Despite evidence suggesting the benefits of neutralizing mucosa-derived IgA in the upper airway in protection against the SARS-CoV-2 virus, all currently approved vaccines are administered intramuscularly, which mainly induces systemic IgG. Waki et al. aimed to characterize the benefits of intranasal vaccination at the molecular level by isolating B cell clones from nasal tissue. The authors found that Spike-specific plasma cells isolated from the spleen of vaccinated mice showed significant clonal overlap with Spike-specific plasma cells isolated from nasal tissue. Interestingly, they could not detect any spike-specific plasma cells in the bone marrow or Peyer's patches, indicating that these nose-derived cells did not necessarily home to and reside in these locations, although the Peyer's patch is not a typical plamsa cell niche - rather the lamina propria of the gut would have been a better place to look. Furthermore, they found that multimerization improves the antibody/antigen binding when the antibody is of low or intermediate affinity, but that high-affinity monomeric antibodies do not benefit from multimerization. Lastly, the authors used a competitive ELISA assay to show that multimerization could improve the neutralizing capacity of these antibodies.

The strength of this paper is the cloning of multiple IgA from the nasal mucosae (n=99) and the periphery (n=114) post-SARS-CoV-2 i.n. vaccination to examine the clonal relationship of this IgA with other sites, including the spleen. This analysis provides novel insights into the nature of the mucosal antibody response at the site where the host would encounter the virus, and whether this IgA response disseminates to other tissues.

There were also some weaknesses:

1. The finding that multimerization improves binding and neutralization is not surprising as this was observed before by Wang and Nussenzweig for anti-SARS-CoV-2 IgA (authors should cite Enhanced SARS-CoV-2 neutralization by dimeric IgA. Wang et al, Sci. Transl. Med 2021, 13:3abf1555). In addition, as far as I can tell we cannot ascertain the purity of fractions from the size exclusion chromatography thus I wasn't sure whether the input material used in Fig. 4 was a mixed population of dimer/trimer/tetramer?

2. The flow cytometric assessment of the IgA+ clones from the nasal mucosae was difficult to interpret (Fig. 1B). It was hard for me to tell what they were gating on and subsequently analysing without an IgA-negative population for reference.

3. While the i.n. study itself is large and challenging, it would have been interesting to compare an i.m. route and examine the breadth of SARS-CoV-2 variant S1 binding for IgGs as in Fig. 2A. Are the IgA responses derived from the mucosae of greater breadth than systemic IgG responses? Alternatively, and easier, authors could do some comparisons with well-characterized IgG mAb for affinity and cross-reactivity as a benchmark to compare with the IgAs they looked at.

Overall the authors did a good job of looking at a large range of systemic vs mucosal S1-specific antibodies in the context of an intra-nasal vaccination and this provides additional evidence for the utility of mucosal vaccination approaches for reducing person-to-person transmission.

Reviewer #1 (Public Review):

This is a well-designed study, with clear results that is also very well-written.<br /> The authors nicely demonstrate that previous contradictory results are largely due to the lack of the proper baseline condition (Exp 1 and Exp 2). The second experiment also replicates the previous study results that had found enhancement. However, the addition of the proper baseline allows for a completely different interpretation of the same results. In the final experiment, they further probe the role of prediction in attenuation of predicted touch and demonstrate that attenuation is due to the ability to predict the consequences of active touch.

Overall, I found the paper had many strengths including the pre-registered protocols, the replication of findings both in favor of attenuation and enhancements, the inclusion of a baseline condition to compare active touch manipulations, and lastly a rigorous analysis of the data.

While in part this confirms previous results on sensory attenuation, it also helps interpret previous results that suggest the contrary. Therefore the results will be of high value to the community.

Reviewer #1 (Public Review):

In this manuscript the authors perform a detailed analysis of the impact of food type on reproduction in C. elegans. They find that, in comparison with the standard OP50 strain of E. coli that is ubiquitously used to maintain C. elegans in the laboratory setting, the CS180 strain results in a reduction in the number of progeny that may be a consequence of an early transition from spermatogenesis to oogenesis that reduces total sperm number. They also find that the rate of oocyte fertilization is increased in animals fed CS180 vs. OP50. Using mutants and laser ablations, the authors show that, whereas the insulin-like peptide INS-6 acts in the ASJ sensory neurons to mediate the food type effect on total progeny and early oogenesis, the increased fertilization rate phenotype does not require ASJ or insulin-like signaling and instead requires the AWA olfactory neurons.

The major strengths of the manuscript are the establishment of INS-6 as a link between food type and reproduction and the detail and rigor with which the experiments were executed. The results presented generally support the authors' model. This role of insulin-like signaling in connecting food type and reproduction makes it a plausible target for evolutionary forces that may have shaped insulin-like signaling in invertebrates. As such, this work contributes broadly to our understanding of how insulin signaling may have evolved prior to the emergence of vertebrates.

A weakness of the work is the epistasis analysis of insulin-like pathway components, which is incomplete and at times difficult to interpret.

Reviewer #1 (Public Review):

The manuscript by Justynski et al., addresses an important question in the field of efferocytosis, namely how does the clearance of apoptotic cells promote wound healing. A major highlight of this work is the profiling of the transcriptional heterogeneity during the inflammatory phase of the wound healing program via single cell sequencing. Many of the genes analyzed in the manuscript are well-known players in efferocytosis and wound healing so the contribution of this work is the dynamic and high resolution temporal and cell type specific responses during injury mediated inflammation.

Overall the manuscript is technically sound and the conclusions are generally supported by the data. However, the authors are cautioned to tone down some of the sentences with the human diabetic samples as they rely heavily on extrapolation rather experimental tests. Other areas of improvement include the relatively simplistic approaches and interpretation of the results. For instance, the antibody inhibition of Axl had minimal effect on the clearance of apoptotic cells in the wound and this would be expected with the redundancy endowed by other TAM receptors.

There are also some inconsistencies between the quantifications and the representative images provided. For instance, in Figure 6, the number of TUNEL+ cells seem to be higher in the IgG samples compared to the anti-Timd4 treatment, but this is not the case in the quantification.

Reviewer #1 (Public Review):

Recently, chromatin-associated RNAs (caRNAs) were found to be involved in transcriptional regulation through multiple mechanisms, playing important roles in disease and development. Mitochondria has its own genome known as mtDNA, which codes crucial genes involved in oxidative phosphorylation. Additionally, mtDNA produces non-coding RNAs (ncRNAs), including small and long noncoding RNAs, the functions of which are still being explored. The communication between mitochondria and the nucleus is essential for coordinating gene expression and cellular function. Recent studies have identified the presence of mitochondrial RNAs (mtRNAs) in the nucleus, such as SncmtRNA, which can influence stress-induced transcription of genes related to cell adhesion.

In this manuscript, using the iMARI (in situ mapping of RNA-Genome Interactions) technology developed by the authors, they found that mitochondria-encoded lncRNA plays a role in regulating nuclear gene expressions. They then performed experimental confirmation, bulk-RNA-seq, snRNA, and scRNA-seq to demonstrate and verify the function of SncmtRNA in regulating nuclear gene expression in endothelial cells. This discovery is ground-breaking and the manuscript provides convincing evidence that mitochondrial RNAs can enter the cellular nucleus to regulate gene expression.

Reviewer #1 (Public Review):

In their work, Akuma and colleagues identify the autoprocessing in cis of casp11 as a key step that allows the aggregation of casp11, and its capacity to cleave GSDMD and induce pyroptosis. The authors utilize, for the first time, a fluorescent casp11 that allowed us to visualize its aggregation (formation of specks). This is a key event that was largely overlooked for casp11. Indeed, casp11 directly binds LPS and initiates pyroptosis in the absence of other NLR members and adaptors such as ASC. While NLRs and adaptors form the structure that allows the recruitment and cleavage of casp1, how casp11 specks are formed remained unknown so far. Using casp11 mutants that lack the catalytic activity or the autoprocessing site, as well as casp11 that can be cleaved by other proteases, the authors demonstrate that self-cleavage of casp11 is a pre-requisite for aggregation and speck formation. Also, by using their mutants the authors demonstrated that casp11 acts in cis, rather than in trans, to exert this function. So far, mostly based on casp1 biology, the main view was that aggregation is a prerequisite for cleaving. Here the authors changed this view for casp11, and found that casp11 autocleavage is upstream of its aggregation induced upon LPS sensing. They found that initial dimerization and subsequent oligomerization are two distinct events and that LPS binding of casp11 is insufficient to assemble the non-canonical inflammasome.

The paper makes use of elegant mutant caspases and is based on solid bases. Some experiments lack analyses of the functional consequences of non-canonical inflammasome formation, and the paper would benefit from this type of analysis.

Another key finding is that Cys-254 plays more roles than "simply" cleaving casp11 at D285. This finding needs to be better highlighted also in the abstract because it opens more future investigations.

Also, the separation between dimerization and oligomerization may open to future studies and may be briefly mentioned also in the abstract.

Reviewer #1 (Public Review):

This paper examines different signaling networks and attempts to give general results for when the network will exhibit biphasic behavior, which is the situation when the output of the network is a non-monotonic function of its inputs. The strength of the paper is in the approach it takes. It starts with the simplest network motifs that produce biphasic behavior and then asks too what happens when these motifs are parts of larger networks. Their approach is in contrast to the usual way in which this question is tackled, which tends to be within the confines of a specific signaling network, where general results like the ones that the authors are after, might be hard to spot.

The weakness of the paper, in my opinion, is the rather formal description of the results which I am afraid will be of rather limited utility to experimental groups seeking to make use of them. The paper attempts to provide general rules for when to expect biphasic behavior and it was hard to assess to what extent such rules exist as behaviors can change depending on the context of a larger network in which the smaller biphasic one is embedded. The other thing that made assessing the generality of the results difficult is that the input-output functions shown in all the figures are computed for a specific choice of parameters and I was left wondering how different choices of parameters might change the reported behaviors. The lack of specific proposals for how their results should guide future experiments on different signaling networks is another weakness.

While I appreciate that the authors adopted a style of presenting their results such that all the mathematics is buried in the figures, I found that it made reading the paper quite difficult, and contributed to my confusion about which results are general and insensitive to parameter choices and which are not. I believe a narrative that integrated the math with some simple intuition might have been more effective. For example, when the authors say in the text that model M0 is incapable of displaying biphasic response, how general is that result? Later on, when discussing model M2, they provide a criterion for biphasic response in terms of products of rate constants satisfying an inequality, but the meaning of this condition is not described. Such things make it hard to learn from the authors' work.

The text is sprinkled with statements like "this reveals the plurality of information processing behaviors..." where the meaning is quite opaque (for this example, there is no description of "information processing" and what it might mean in this context) and therefore it makes it hard to understand what are the lessons learned from these calculations. Another example is found in the description of Erk regulation where the authors speak of "significant robustness" but what is meant by "significant" is also unclear.

Overall, I think this is an interesting attempt to provide a general mathematical framework for analyzing biphasic response of signaling networks, but the authors fall short for the reasons described above. I think a lot can be fixed by improving the way the results are presented.

Reviewer #1 (Public Review):

This interesting manuscript sets out to develop for the mouse a series of important concepts and models that this group has previously developed for models of monkey brains, where they showed that in a large-scale model, anterior → posterior spatial gradients such as spine density (and thus inferred strength of local coupling) lead to a transition from transient stimulus responses to persistent responses, capable of supporting working memory (WM). No such spine density gradient is found in the mouse. Here, the authors propose and use modeling to explore the idea, that the corresponding gradient may be that of density of inhibitory PV cells in different regions of the brain.

The goal of the study - a large-scale, anatomically-constrained model of WM - is an extremely valuable one, and the authors' efforts in this direction should be supported. That said, some of the main claims in the manuscript were not, at least as currently written, clearly supported by the data, a number of important clarifications need to be made, and some claims of novelty are made in a way that, for a typical reader, may obscure the actual contribution being made.

The biggest issue is that one of the main claims, that together with cell-type specific long-range targeting, "density of cell classes define working memory representations" (abstract), is not terribly clear. For example, Figs. 2D and 2E show that a brain region's hierarchical location tightly predicts its persistent firing rate (2D), but that PV cell fraction has a far weaker correlation (2E). Is hierarchical location sufficient? If PV cell fraction were constant across model brain regions, would we still get persistent activity modes? It seems likely that the answer may be "yes", but the answer, easily within reach of the authors, is surprisingly not in the current version of the manuscript. Figure 3D, for the thalamocortical model, shows no significant correlation of firing rate with PV density.

Given the claim about PV density (in the abstract and the first main point of the discussion), this is a big concern. Yet it seems easily addressable: e.g. if indeed the authors found that hierarchy was sufficient and PV density immaterial, the model would be no less interesting. And if the authors demonstrated clearly that a PV density gradient is required, that would make the claim a solid one. If, within the model, such a causal demonstration is present, this reader at least missed it.

MAJOR CONCERNS:

(1) The model appears to be a model of a single side of the brain. Perhaps each brain region in the model could be considered an amalgam of that region across both sides of the brain. Yet given results like Li et al. Nature 2016, who show that persistent activity is robust to inhibition of one side, but not both sides of ALM, at the very least discussion of the issue is warranted.

(2) The authors make an interesting attempt to distinguish core WM regions from other regions such as "readout" regions, defined as showing persistent activity yet not having an effect on persistent activity elsewhere in the network.<br /> However, this definition seemed problematic: for example, consider a network that consists of 20 brain regions, all interconnected to each other, and all equivalent to each other, capable of displaying persistent activity thanks to mutual connectivity. Imagine that inhibition of any one of these regions is not sufficient to significantly perturb persistent activity in the other 19. Then they would all be labeled as "readout". Yet, by construction in this thought experiment, they are all equivalent to each other and are all core areas. Such redundancy may well be present in the brain. How would the authors address this redundancy issue?

(3) Also important to discuss would be the fact that every brain region in this model is set up as composed of two populations, and when long-range interactions are strong and the attractors strongly coupled, the entire brain is set up as a 1-bit working memory. How would results and the approach be impacted by considering WM for more flexible situations?

(4) Another concern that is important yet easily addressed is the authors' use of the term "novel cell-type specific graph theory measures". Describing in the abstract and elsewhere the fact that what they mean is to take into account the sign of connections, not just their magnitude, would transmit to readers the essence of the contribution in a manner very simple to understand. Most readers would fail to grasp the essential point of the current labeling, which sounds potentially very vague and complex.

(5) Finally, the overall significance of the study, and advances over previous work, were not entirely clear. In the discussion, the authors identify three major findings: (1) WM function is shaped by the PV cell density gradient. But as above, further work is required to make it clear that this claim is supported by the model. (2) if local recurrent excitation is insufficient to generate persistent activity, then long-range recurrent excitation is needed to generate it. I had trouble understanding why a model was needed to reach this conclusion - it seems as if it is simply a question of straightforward logic. The discussion states that in this regard, the work here "offers specific predictions to be tested experimentally", but I had trouble identifying what these specific predictions are. (3) Taking into account sign, not only magnitude, of connections, is important. This last point once again seemed a matter of straightforward logic, making its novelty difficult to assess.

Reviewer #1 (Public Review):

In this manuscript, Yadav and colleagues explore the metabolic changes associated with the regeneration of mechanosensory neurons in O-GlcNAc transferase (ogt-1) mutant worms. Using in vivo laser axotomy to assess the regeneration of individual mechanosensory neurons in C elegans, the authors discovered increased regeneration in ogt-1 mutant worms diverts enhanced glycolysis towards one-carbon metabolism and the downstream transsulfuration metabolic pathway. By genetically and pharmacologically disrupting one-carbon metabolism, they were able to abrogate this phenotype. Similar results were obtained by targeting the serine synthesis pathway. Furthermore, the authors tested downstream targets of this pathway and discovered that the vitamin B12 independent shunt pathway confers regeneration competence in these neurons. They also included RNA-Seq data to support the same conclusion. Ogt-1 mutants showed profound transcriptional changes in genes related to glycolysis and one-carbon metabolism. Perhaps more excitingly, supplementation of the methioninine in wild-type worms is sufficient to recapitulate the regenerative phenotype found in ogt-1 mutants.

I found these results convincing and novel. The experimental approach is elegant and the conclusions are robust. The supplemental data support the major points of the paper. The identification of specific metabolic pathways associated with axon growth and regeneration represents a significant contribution to the Neuroscience field. Interrogation of these data sets and pathways will certainly spark new exciting research in the years to come.

Reviewer #1 (Public Review):

Chaoming Wang and coauthors present a new framework for modeling neurons and networks of neurons, spanning a wide range of possible models from detailed (point-neuron) models with non-linear ion channel dynamics to more abstract rate neuron models. Models are defined in an object-oriented style, familiar to users of machine-learning frameworks like PyTorch, and are efficiently executed via the just-in-time compilation framework JAX/XLA. The programming paradigm naturally supports a hierarchical style, where e.g. a network is composed of neurons that contains ion channels; each of these components can be reused in different contexts and be simulated/analyzed individually.

Strengths:<br /> Brainpy's approach is an innovative application of state-of-the-art technology widely used in the machine learning community (auto-differentation, just-in-time compilation) to modeling in computational neuroscience and could provide a useful bridge between the two domains which overlap more and more. For researchers, describing, running, and optimizing their models in Python is very convenient. The use of Numba to write efficient operators for JAX/XLA is innovative and potentially very powerful.

The modeling framework is very flexible, where most types of models commonly used in computational neuroscience can be readily expressed.

The framework supports various integration algorithms for ODEs, SDEs, and FDEs, several additional convenience tools for model training, optimization, and analysis, as well as many pre-defined ion-channel, neuron, and synapse models. The wide range of included simulation and analysis tools and pre-defined models is impressive, and exceeds those offered by most competing software. The software comes with extensive documentation, tutorials, and examples, on par with that of existing simulators that have been around for much longer.

Weaknesses:<br /> While the article clearly outlines the strengths of the chosen approach, it lacks an equally clear exposition of its limitations and a more thorough comparison to established approaches. Two examples of limitations that should be stated more clearly, in my opinion: models need to be small enough to fit on a single machine (in contrast to e.g. NEURON and NEST which support distributed computation via MPI), and only single-compartment models are supported; both limitations are mentioned in passing in the discussion, but would merit a more upfront mention. Regarding the comparison to other approaches/simulators:<br /> 1) The study does not verify the accuracy of the presented framework. While its basic approach (time-step-based simulation, standard numerical integration algorithms) is sufficiently similar to other software to not expect major discrepancies, an explicit comparison would remove any doubt. Quantitative measures of accuracies are particularly important in the context of benchmarks (see below), since simulations can be made arbitrarily fast by sacrificing performance.<br /> 2) Benchmarking against other software is obviously important, but also full of potential pitfalls. The current article does not state clearly whether the results are strictly comparable. In particular: are the benchmarks on the different simulators calculating results to the same accuracy (use of single or double precision, same integration algorithm, etc.)? Does each simulator use the fastest possible execution mode (e.g. number of threads/processes for NEST, C++ standalone mode in Brian2, etc.)? What is exactly measured (compilation time, network generation time, simulation execution time, ...) - these components will scale differently with network size and simulation duration, so summing them up makes the results difficult to interpret. Details are also missing for the comparison between the XLA operator customization in C++ vs. Python: was the C++ variant written by the authors or by someone else? Does the NUMBA→XLA mechanism also support GPUs/TPUs? This comparison also seems to be missing from the GitHub repository provided for reproducing the paper results.<br /> 3) While the authors convincingly argue for the merits of their Python-based/object-oriented approach, in my opinion, they do not fully acknowledge the advantages of domain-specific languages (NMODL, NestML, equation syntax of ANNarchy and Brian2, ...). In particular, such languages aim at a strong decoupling of the mathematical model description from its implementation and other parts of the model. In contrast, models described with BrainPy's approach often need to refer to such details, e.g. be aware of differences between dense and sparse connectivity schemes, online, or batch mode, etc. It might also be worth mentioning descriptive approaches to synaptic connectivity as supported by other simulators (connection syntax in Brian2, Connection Set Algebra for NEST).

Reviewer #1 (Public Review):

Due complicated and often unpredictable idiosyncratic differences, comparing fMRI topography between subjects typically would require extra expensive scan time and extra laborious analyzing steps to examine with specific functional localizer scan runs that contrast fMRI responses of every subject to different stimulus categories. To overcome this challenge, hyperaligning tools have recently been developed (e.g., Guntupalli et al., 2016; Haxby et al., 2011) based on aligning in a high-dimensional space of voxels of subjects' fMRI responses to watching a given movie. In the present study, Jiahui and colleagues propose a significantly improved version of hyperaligning functional brain topography between individuals. This new version, based on fMRI connectivity, works robustly on datasets when subjects watched different movies and were scanned with different parameters/scanners at different MRI centers.

Robustness is the major strength of this study. Despite the fact that datasets from different subjects watching different movies at different MRI centers with different scan parameters were used, the results of functional brain topography from between-subject hyperalignment based on fMRI connectivity were comparable to the golden standard of within-subject functional localizations, and significantly better than regular surface anatomical alignments. These results also support the claim that the present approach is a useful improvement from previous hyperalignments based on time-locked fMRI voxel responses, which would require normative samples of subjects watching a same movie.

Given the robustness, this new version of hyperalignment would provide much stronger statistical power for group-level comparisons with less costs of time and efforts to collect and analyze data from large sample size according to the current stringent standard, likely being useful to the whole research community of functional neuroimaging. That said, more discussions of the limit of the present hyperalignment approach would be helpful to potential readers. For example, to what extend the present hyperalignment approach would be applicable to individuals with atypical functional brain topography such as brain lesion patients with e.g., acquired prosopagnosia? Even in typical populations, while bilateral fusiform face areas can be identified in the majority through functional localizer scans, the left fusiform face area sometimes cannot be found. Moreover, many top-down factors are known to modulate functional brain topography. Due to these factors, brain responses and functional connectivity may be different even when a same subject watched a same movie twice (e.g., Cui et al., 2021).

Reviewer #1 (Public Review):

Summary:<br /> In this study, the authors generate a Drosophila model to assess disease-linked allelic variants in the UBA5 gene. In humans, variants in UBA5 have been associated with DEE44, characterized by developmental delay, seizures, and encephalopathy. Here, the authors set out to characterize the relationship between 12 disease-linked variants in UBA5 using a variety of assays in their Drosophila Uba5 model. They first show that human UBA5 can substitute all essential functions of the Drosophila Uba5 ortholog, and then assess phenotypes in flies expressing the various disease variants. Using these assays, the authors classify the alleles into mild, intermediate, and severe loss-of-function alleles. Further, the authors establish several important in vitro assays to determine the impacts of the disease alleles on Uba5 stability and function. Together, they find a relatively close correlation between in vivo and in vitro relationships between Uba5 alleles and establish a new Drosophila model to probe the etiology of Uba5-related disorders.

Strengths:<br /> Overall, this is a convincing and well-executed study. There is clearly a need to assess disease-associated allelic variants to better understand human disorders, particularly for rare diseases, and this humanized fly model of Uba5 is a powerful system to rapidly evaluate variants and relationships to various phenotypes. The manuscript is well written, and the experiments are appropriately controlled.

Reviewer #1 (Public Review):

The revised manuscript new presented 1) a permutation-based test for the significance of the overlap between DEGs and genes with positive selection signals in Tibetans, and 2) polygenic adaptation test for the eQTLs. I make my suggestions in detail as below:

Major Comments

1. My previous concern regarding the DEG analysis remains unresolved. Although the authors agreed in their response that the difference between the male- and female-specific DEGs are insufficient to the difference between sex-combined and sex-specific DEGs (Figure S6). However, the results section still states the opposite pattern between males and females as a decisive reason for the difference (p. 9, lines 236-239). Again, I would like to recommend the authors to test alternative ways of analysis to boost statistical power for DEG detection other than simply splitting data into males and females and performing analysis in each subset. For example, the authors may consider utilizing gene by environment interaction analysis schemes here biological sex as an environmental factor.

2. Multiple testing schemes are still sub-optimal in some cases. Most of all, the p-values in the WGCNA analysis (p. 11), the authors corrected for the number of traits (n=12) after adjusting for the correlation between them. However, they did not mention whether they counted for the number of modules they tested at all (n=136 and 161 for males and females, respectively). Whether they account for the number of modules will make a substantial difference in the significance threshold, please incorporate and describe a proper multiple testing scheme for this analysis.

3. Evidence for natural selection on the observed DEG pattern is still weak and not properly described.<br /> 1) For the overlap between DEGs and TSNGs, the authors introduced a permutation-based test, but used a total set of genes in the human genome as a comparison set (p. 25, lines 699-700). I believe that the authors should sample random sets of genes from those already expressed in each tissue to make a fair comparison.<br /> 2) The entire polygraph analysis for polygenic adaptation is poorly described. The current version of the Methods does not clarify i) for which genes the eQTLs are discovered, 2) how the authors performed the eQTL analysis, iii) how the authors polarized the effect, and iv) how they set up a comparison between the eQTLs and the others.

Reviewer #1 (Public Review):

Summary:<br /> Impairment in hand function is a challenge for stroke rehabilitation, and its neural underpinnings are of paramount importance for the field of biomedical science and neuroscience. The present study uses a novel finger force measurement device to measure individual fingers' force production in three dimensions when one finger is needed to produce an independent isometric force. Enslavement, i.e., the unwanted coactivation of non-intended fingers, is exaggerated in stroke survivors. The study started out by noting that the contribution of underlying factors (the loss of corticospinal drive, intrusion of flexor synergy due to a loss of regulation on subcortical pathways, and/or biomechanical changes) is not well understood. Detailed analysis for the inter-dependence between finger forces shows that the covariation between finger forces showed stroke-specific changes in shape and magnitudes, and these changes are not caused by biomechanical constraints. The important message that the study tries to convey is that the magnitude change in finger coactivation of the paretic hand is caused by the two dissociable factors, i.e., a loss of complexity in finger control and an intrusion of flexor bias. 

Strengths:<br /> The targeted topic of individual control of fingers for stroke survivors is of both theoretical and applied importance. The methodology of using isometric finger force to fulfill simple yet relevant motor tasks for stroke patients is also novel and sound. The paper is concisely written with excellent figures.

Weaknesses:<br /> I have three major concerns about the study: 1) the link between the analysis results and two of the study's main conclusions is weak, specifically for the conclusion that a loss of complexity in finger control and the intrusion of flexor bias is dissociable. 2) using hand posture measures to quantify the influence of biomechanical factors in stroke patients is not well justified. 3) only a limited number of stroke patients were recruited (n=13). <br /> <br /> First, the conclusion that the two factors contributing to the magnitude of finger covariation pattern are dissociable is not well reasoned. For example, the reasoning is clearly stated (Line 434) as: "Given the above converging evidence that Angular Distance is a measure of complexity of the geometric shape of finger coactivation, whereas Euclidean Distance is more sensitive to the magnitude change of these patterns across task goals if the two factors are dissociable, the intrusion of flexor bias would predict the magnitude (Euclidean Distances), but not the shape (Angular Distances) of the enslavement patterns. "

The logic behind this statement is unclear. Suppose the "two factors" are the complexity loss (shown by Angular Distance) and intrusion of flexor bias (shown by Bias). In that case, we cannot just use the predictability and the lack of predictability of the measure of intrusion of flexor bias (Bias) to reach the above conclusion, i.e., the Bias (for the intrusion of flexor bias) and changes in Angular Distance (for the loss of complex loss) is dissociable. Why not just test the association between Bias and Angular Distance directly?

Another conclusion is that the changes of Euclidian Distance and Angular Distance from the pattern similarity analysis of finger coactivation patterns inform us that the coactivation shape is preserved but its magnitude is increased in the paretic hand. However, the shape measure (Angular Distance) shows a decrease in paretic hands, indicating the coactivations for different task requirements become similar in the paretic hand. It becomes similar across task conditions, but this does not mean the coactivation shape for each task requirement is preserved in patients. In fact, one possible sign of reservation might be an unchanged function of distance measure (varied by intended fingers or directions) between groups (ideally shown in the format as Figure 5B). As we can see from the figure, the shape is preserved in the mild group but not so in the severe group if we compare the data between groups. Statistically, it is better to do ANOVA and use the group*fingers and group*directions interaction to show the reservation of "shape." The same logic applies to the Euclidean Distance measure (Figure 7B and 7D). Again, the connection between data analysis results and conclusions should be clarified. <br /> <br /> Second, the use of hand posture measures to quantify biomechanical factors for hand impairments is not validated.  

Based on two hand posture measures, the study rules out the contribution of biomechanical factors for enslavement in patients entirely (Line 390). However, the alternative explanation for the negative effect of posture variables is that these two specific variables (Mount Distance and Angle) might not reflect the postural changes (and biomechanical factors in hand function) in patients. Note these two measures are not about the resting hand posture of the patient, which is often affected. It is the posture when the hand is inserted into the apparatus, and the total force readings are minimal. The force readings would be quite small if people are good at relaxing their muscles and inhibiting unwanted reflexes in a specific posture. Healthy hands can remain a small force for rather different postures. Thus, healthy hands can produce a range of possible minimum-force postures, making the reliability of these "minimum" posture measures questionable. For patients, on the other hand, since a minimum-force posture is related to the ability to relax the muscles, it probably reflects both biomechanical changes (muscles and tendons, etc.) and subcortical influence. Thus, using these two measures to rule out the possibility of biomechanical factors needs further justification. <br /> <br /> Third, the number of stroke patients is limited (n=13), especially when one important test is to compare the mild group and the moderate-severe subgroups. The group comparison thus has small statistical power with a medium split. <br /> <br /> As the study aims to tease out the contributions of biomechanical, subcortical, and cortical input to the observed impairment of enslavement, we need to be careful about whether the selected behavioral variables are justified to reflect these factors and whether the data analysis results coherently support the conclusions. As it currently stands, the paper still has room to improve to achieve its aims.

Reviewer #1 (Public Review):

The author studies a family of models for heritable epigenetic information, with a focus on enumerating and classifying different possible architectures. The key aspects of the paper are:

- Enumerate all 'heritable' architectures for up to 4 constituents.<br /> - A study of whether permanent ("genetic") or transient ("epigenetic") perturbations lead to heritable changes.<br /> - Enumerated the connectivity of the "sequence space" formed by these heritable architectures.<br /> - Incorporating stochasticity, the authors explore stability to noise (transient perturbations).<br /> - A connection is made with experimental results on C elegans.

The study is timely, as there has been a renewed interest in the last decade in non-genetic, heritable heterogeneity (e.g., from single-cell transcriptomics). Consequently, there is a need for a theoretical understanding of the constraints on such systems. There are some excellent aspects of this study: for instance:

- the attention paid to how one architecture "mutates" into another, establishing the analogue of a "sequence space" for network motifs (Fig 3).<br /> - the distinction is drawn between permanent ("genetic") and transient ("epigenetic") perturbations that can lead to heritable changes.<br /> - the interplay between development, generational timescales, and physiological time (as in Fig. 5).

The manuscript would be very interesting if it focused on explaining and expanding these results. Unfortunately, as a whole, it does not succeed in formalising nor addressing any particular open questions in the field. Aside from issues in presentation and modelling choices (detailed below), it would benefit greatly from a more systematic approach rather than the vignettes presented.

## Terminology<br /> The author introduces a terminology for networks of interacting species in terms of "entities" and "sensors" -- the former being nodes of a graph, and the latter being those nodes that receive inputs from other nodes. In the language of directed graphs, "entities" would seem to correspond to vertices, and "sensors" those vertices with positive indegree and outdegree. Unfortunately, the added benefit of redefining accepted terminology from the study of graphs and networks is not clear.

## Heritability<br /> The primary goal of the paper is to analyse the properties of those networks that constitute "heritable regulatory architectures". The definition of heritability is not clearly stated anywhere in the paper, but it appears to be that the steady-state of the network must have a non-zero expression of every entity. As this is the heart of the paper, it would be good to have the definition of heritable laid out clearly in either the main text or the SI.

## Model<br /> As described in the supplementary, but not in the main text, the author first chooses to endow these networks with simple linear dynamics; something like $\partial_t \vec{x} = A x - T x$, where the vector $x$ is the expression level of each entity, $A$ has the structure of the adjacency matrix of the directed graph, and $T$ is a diagonal matrix with positive entries that determines the degradation or dilution rate of each entity. From a readability standpoint, it would greatly aid the reader if the long list of equations in the SI were replaced with the simple rule that takes one from a network diagram to a set of ODEs.

The implementation of negative regulation is manifestly unphysical if the "entities" represent the expression level of, say, gene products. For instance, in regulatory network E, the value of the variable z can go negative (for instance, if the system starts with z= and y=0, and x > 0).

The model seems to suddenly change from Figure 4 onwards. While the results presented here have at least some attempt at classification or statistical rigour (i.e. Fig 4 D), there are suddenly three values associated with each entity ("property step, active fraction, and number"). Furthermore, the system suddenly appears to be stochastic. The reader is left unsure of what has happened, especially after having made the effort to deduce the model as it was in Figs 1 through 3. No respite is to be found in the SI, either, where this new stochastic model should have been described in sufficient detail to allow one to reproduce the simulation.

## Perturbations<br /> Inspired especially by experimental manipulations such as RNAi or mutagenesis, the author studies whether such perturbations can lead to a heritable change in network output. While this is naturally the case for permanent changes (such as mutagenesis), the author gives convincing examples of cases in which transient perturbations lead to heritable changes. Presumably, this is due the the underlying mutlistability of many networks, in which a perturbation can pop the system from one attractor to another.

Unfortunately, there appears to be no attempt at a systematic study of outcomes, nor a classification of when a particular behaviour is to be expected. Instead, there is a long and difficult-to-read description of numerical results that appear to have been sampled at random (in terms of both the architecture and parameter regime chosen). The main result here appears to be that "genetic" (permanent) and "epigenetic" (transient) perturbations can differ from each other -- and that architectures that share a response to genetic perturbation need not behave the same under an epigenetic one. This is neither surprising (in which case even illustrative evidence would have sufficed) nor is it explored with statistical or combinatorial rigour (e.g. how easy is it to mistake one architecture for another? What fraction share a response to a particular perturbation?)

As an additional comment, many of the results here are presented as depending on the topology of the network. However, each network is specified by many kinetic constants, and there is no attempt to consider the robustness of results to changes in parameters.

## DNA analogy<br /> At two points, the author makes a comparison between genetic information (i.e. DNA) and epigenetic information as determined by these heritable regulatory architectures. The two claims the author makes are that (i) heritable architectures are capable of transmitting "more heritable information" than genetic sequences, and (ii) that, unlike DNA, the connectivity (in the sense of mutations) between heritable architectures is sparse and uneven (i.e. some architectures are better connected than others).

In both cases, the claim is somewhat tenuous -- in essence, it seems an unfair comparison to consider the basic epigenetic unit to be an "entity" (e.g., an entire transcription factor gene product, or an organelle), while the basic genetic unit is taken to be a single base-pair. The situation is somewhat different if the relevant comparison was the typical size of a gene (e.g., 1 kb).

Reviewer #1 (Public Review):

Summary:<br /> The study explores the mechanisms that preserve satellite cell function in extraocular muscles (EOMs) in a mouse model of familial Amyotrophic lateral sclerosis (ALS) that carries the G93A mutation in the Sod1 gene. ALS is a fatal neuromuscular disorder driven by motor neuron degeneration, leading to progressive wasting of most skeletal muscles but not EOM. The study first established that integrity of neuromuscular junction (NMJ) is preserved in EOM but not in limb and diaphragm muscles of G93A mice, and sodium butyrate (NaBu) treatment partially improves NMJ integrity in limb and diaphragm muscles of G93A mice. They also found a loss of synaptic satellite cells and renewability of cultured myoblasts in hindlimb and diaphragm muscles of G93A mice, but not in EOM, and NaBu treatment restores myoblast renewability. Using RNA-seq analysis, they identify that exon guidance molecules, particularly Cxcl12, are highly expressed in EOM myoblasts, along with more sustainable renewability. Using a neuromuscular co-culture model, they convincingly show that AAV-mediated Cxcl12 expression in G93A myotubes enhances motor axon extension and innervation. Strikingly, NaBu-mediated preservation of NMJ in limb muscles of G93A mice is associated with elevated expression of Cxcl12 in satellite cells and improved renewability of myoblasts. These results together offer molecular insights into genes critical for maintaining satellite cell function and revealing a mechanism through which NaBu ameliorates ALS.

Strengths:<br /> Combination of in vivo and cell culture models.<br /> Nice imaging of NMJ and associated satellite cells.<br /> Using motoneuron-myotube coculture to establish the mechanism.<br /> Tested and illustrated a mechanism through which a clinically used drug ameliorates ALS.

Weaknesses:<br /> Data presentation could be improved (see details in the Recommendation for Authors).<br /> It would have been nice to have included G93A motoneurons in the coculture study.

Reviewer #1 (Public Review):

This study is carefully designed and well executed, including a comprehensive suite of endpoint measures and large sample sizes that give confidence in the results. The authors have satisfactorily addressed my concerns. Specifically, the new graphical description of the experimental design along a timeline will be very helpful in guiding the reader through the paper. The narrative style is much improved and highly technical terminology is minimized. The authors now also address the question of sex differences, which will be important to study in future research. The additional analyses carried out by the authors are illuminating.

Joint Public Review:

The authors have greatly improved the manuscript after detailed revisions. I would like to discuss with the authors on how to make their findings more general across taxonomic groups. For example, whether it is possible for authors to conduct a more comprehensive analyses by including amphibians, birds, and mammals together to test the general role of the relationship between brain evolution and environmental resources, and what ecological factors determine the observed brain size variations among taxa except for their biological differences such as energetic demands. It is especially for population-level analyses when related data is available in the future, which may provide very helpful insights into the brain size biogeographic patterns and their determinants across taxa.

Reviewer #1 (Public Review):

In this manuscript, the authors are building on their previous work showing Delta-Notch regulates the entrance and exit from embryo-larval quiescence of neural stem cells of the central brain (called CB neuroblasts (NB) (PMID: 35112131)). Here they show that continuous depletion of Notch in NBs from early embryogenesis leads to cycling NBs in the adult. This - cycling NBs in the adult - is not seen in controls. The assumption here is that these Notch-RNAi NBs in adults are those that did not undergo terminal differentiation in pupal development. The authors show that Notch is activated by its ligand Delta which is expressed on the GMC daughter cell and on cortex glia. They determine that the temporal requirement for Notch activity is 0-72 hours after larval hatching (ALH) (i.e., 1st instar through mid-3rd instar at 25C). In NBs/GMCs depleted for Notch, early temporal markers were still expressed at time points when they should be off and late markers were delayed in expression. These effects were observed in ~20-40% of NBs (Figures 5 and 6). Through mining existing data sets, they found that the early temporal factor Imp - an RNA binding protein - can bind Delta mRNA. They show that Delta transcripts decrease over time, leading to the hypothesis that Delta mRNA is repressed by the late temporal factors. Over-expressing late factors Syp or E93 earlier in development leads to downregulation of a Delta::GFP protein trap. These results lead to a model in which Notch regulates expression of early temporal factors and early temporal factors regulate Notch activity through translation of Delta mRNA.

There are several strengths of this study and no major weaknesses. The authors report rigorous measurements and statistical analyses throughout the study. Their conclusions are appropriate for the results. Data mining revealed an important mechanism - that Imp binds Delta mRNA - supporting the model that that early temporal factors promote Delta expression, which in turn promotes Notch signaling.

An appraisal: The authors use temperature shifts with Gal80TS to show that Notch is required between 0-72 hours ALH. They show with the use of known markers of the temporal factors and Delta protein trap, that Imp promotes Delta protein expression and the later temporal factors reduce Delta, although the molecular mechanisms are not clearly delineated. Overall, these data support their model that the reduction of Delta expression during larval development leads to a loss of Notch activity.

As noted in the Discussion, this study raises many questions about what Notch does in larval CB NBs. For example, does it inhibit Castor or Imp? Is Notch required in certain neural lineages and not others. These studies will be of interest in the community of developmental neurobiologists.

Reviewer #1 (Public Review):

This study revealed that one of the mechanisms for iTreg (induced-Treg) lineage instability upon restimulation is through sustained store-operated calcium entry (SOCE), which activates transcription factor NFAT and promotes changes in chromatin accessibility to activated T cell-related genes. The authors revealed that, unlike thymus-derived Tregs (tTreg) with blunted calcium signaling and NFAT activation, iTregs respond to TCR restimulation with fully activated SOCE and NFAT similar to activated conventional T cells. Activated NFAT binds to open chromatin regions in genes related to T helper cells, increases their expression, and leads to the instability of iTreg cells. On the other hand, inhibition of the SOCE/NFAT pathway by chemical inhibitors could partially rescue the loss of Foxp3 expression in iTreg upon restimulation. The conclusion of the study is unexpected since previous studies showed that NFAT is required for Foxp3 induction and iTreg differentiation (Tone Y et al, Nat Immunol. 2008, PMID: 18157133; Vaeth M et al, PNAS, 2012, PMID: 22991461). Additionally, Foxp3 interacts with NFAT to control Treg function (Wu Y et al, Cell, 2006, PMID: 16873067). The data presented in this study demonstrated the complex role NFAT plays in the generation and stability of iTreg cells.

Several concerns are raised from the current study.<br /> 1. Previous studies showed that iTregs generated in vitro from culturing naïve T cells with TGF-b are intrinsically unstable, and prone to losing Foxp3 expression due to lack of DNA demethylation in the enhancer region of the Foxp3 locus (Polansky JK et al, Eur J Immunol., 2008, PMID: 18493985). It is known that removing TGF-b from the culture media leads to rapid loss of Foxp3 expression. In the current study, TGF-b was not added to the media during iTreg restimulation, therefore, the primary cause for iTreg instability should be the lack of the positive signal provided by TGF-b. NFAT signal is secondary at best in this culturing condition.

This point has been addressed in the revision. Figure Q1 could be added to the manuscript as a supplementary figure.

2. It is not clear whether the NFAT pathway is unique in accelerating the loss of Foxp3 expression upon iTreg restimulation. It is also possible that enhancing T cell activation in general could promote iTreg instability. The authors could explore blocking T cell activation by inhibiting other critical pathways, such as NF-kb and c-Jun/c-Fos, to see if a similar effect could be achieved compared to CsA treatment.

This point has been sufficiently addressed in the revision.

3. The authors linked chromatin accessibility and increased expression of T helper cell genes to the loss of Foxp3 expression and iTreg instability. However, it is not clear how the former can lead to the latter. It is also not clear whether NFAT binds directly to the Foxp3 locus in the restimulated iTregs and inhibits Foxp3 expression.

This point has been addressed in the rebuttal. Could the authors incorporate their comments in the rebuttal into the discussion section of the revised manuscript?

Reviewer #1 (Public Review):

The authors of this study seek to visualize NS1 purified from dengue virus infected cells. They infect vero cells with DV2-WT and DV2 NS1-T164S (a mutant virus previously characterized by the authors). The authors utilize an anti-NS1 antibody to immunoprecipitate NS1 from cell supernatants and then elute the antibody/NS1 complex with acid. The authors evaluate the eluted NS1 by SDS-PAGE, Native Page, mass spec, negative-stain EM, and eventually Cryo-EM. SDS-PAGE, mas spec, and native page reveal a >250 Kd species containing both NS1 and the proteinaceous component of HDL (ApoA1). The authors produce evidence to suggest that this population is predominantly NS1 in complex with ApoA1. This contrasts with recombinantly produced NS1 (obtained from a collaborator) which did not appear to be in complex with or contain ApoA1 (Figure 1C). The authors then visualize their NS1 stock in complex with their monoclonal antibody by CryoEM. For NS1-WT, the major species visualized by the authors was a ternary complex of an HDL particle in complex with an NS1 dimer bound to their mAB. For their mutant NS1-T164S, they find similar structures, but in contrast to NS1-WT, they visualize free NS1 dimers in complex with 2 Fabs (similar to what's been reported previously) as one of the major species. This highlights that different NS1 species have markedly divergent structural dynamics. It's important to note that the electron density maps for their structures do appear to be a bit overfitted since there are many regions with electron density that do not have a predicted fit and their HDL structure does not appear to have any predicted secondary structure for ApoA1. The authors then map the interaction between NS1 and ApoA1 using cross-linking mass spectrometry revealing numerous NS1-ApoA1 contact sites in the beta-roll and wing domain. The authors find that NS1 isolated from DENV infected mice is also present as a >250 kD species containing ApoA1. They further determine that immunoprecipitation of ApoA1 out of the sera from a single dengue patient correlates with levels of NS1 (presumably COIPed by ApoA1) in a dose-dependent manner.

In the end, the authors make some useful observations for the NS1 field (mostly confirmatory) providing additional insight into the propensity of NS1 to interact with HDL and ApoA1. The study does not provide any functional assays to demonstrate activity of their proteins or conduct mutagenesis (or any other assays) to support their interaction predications. The authors assertion that higher-order NS1 exists primarily as a NS1 dimer in complex with HDL is not well supported as their purification methodology of NS1 likely introduces bias as to what NS1 complexes are isolated. While their results clearly reveal NS1 in complex with ApoA1, the lack of other NS1 homo-oligomers may be explained by how they purify NS1 from virally infected supernatant. Because NS1 produced during viral infection is not tagged, the authors use an anti-NS1 monoclonal antibody to purify NS1. This introduces a source of bias since only NS1 oligomers with their mAb epitope exposed will be purified. Further, the use of acid to elute NS1 may denature or alter NS1 structure and the authors do not include controls to test functionality of their NS1 stocks (capacity to trigger endothelial dysfunction or immune cell activation). The acid elution may force NS1 homo-oligomers into dimers which then reassociate with ApoA1 in a manner that is not reflective of native conditions. Conducting CryoEM of NS1 stocks only in the presence of full-length mAbs or Fabs also severely biases what species of NS1 is visualized since any NS1 oligomers without the B-ladder domain exposed will not be visualized. If the residues obscured by their mAb are involved in formation of higher-order oligomers then this antibody would functionally inhibit these species from forming. The absence of critical controls, use of one mAb, and acid elution for protein purification severely limits the interpretation of these data and do not paint a clear picture of if NS1 produced during infection is structurally distinct from recombinant NS1. Certainly there is novelty in purifying NS1 from virally infected cells, but without using a few different NS1 antibodies to purify NS1 stocks (or better yet a polyclonal population of antibodies) it's unclear if the results of the authors are simply a consequence of the mAb they selected.

Data produced from numerous labs studying structure and function of flavivirus NS1 proteins provide diverse lines of evidence that the oligomeric state of NS1 is dynamic and can shift depending on context and environment. This means that the methodology used for NS1 production and purification will strongly impact the results of a study. The data in this manuscript certainly capture one of these dynamic states and overall support the general model of a dynamic NS1 oligomer that can associate with both host proteins as well as itself but the assertions of this manuscript are overall too strong given their data, as there is little evidence in this manuscript, and none available in the large body of existing literature, to support that NS1 exists only as a dimer associated with ApoA1. More likely the results of this paper are a result of their NS1 purification methodology.

Suggestions for the Authors:

Major:

1. Because of the methodology used for NS1 purification, it is not clear from the data provided if NS1 from viral infection differs from recombinant NS1. Isolating NS1 from viral infection using a polyclonal antibody population would be better to answer their questions. On this point, Vero cells are also not the best candidate for their NS1 production given these cells do not come from a human. A more relevant cell line like U937-DC-SIGN would be preferable.

2. The authors need to support their interaction predictions and models via orthogonal assays like mutagenesis followed by HDL/ApoA1 complexing and even NS1 functional assays. The authors should be able to mutate NS1 at regions predicted to be critical for ApoA1/HDL interaction. This is critical to support the central conclusions of this manuscript.

3. The authors need to show that the NS1 stocks produced using acid elution are functional compared to standard recombinantly produced NS1. Do acidic conditions impact structure/function of NS1?

4. Overall, the data obtained from the mutant NS1 (contrasted to WT NS1) reveals how dynamic the oligomeric state of NS1 proteins are but the authors do not provide any insight into how/why this is, some additional lines of evidence using either structural studies or mutagenesis to compare WT and their mutant and even NS1 from a different serotype of DENV would help the field to understand the dynamic nature of NS1.

Reviewer #1 (Public Review):

Summary:<br /> Transposable Elements (TEs) are exogenously acquired DNA regions that have played important roles in the evolutional acquisition of various biological functions. TEs may have been important in the evolution of the immune system, but their role in thymocytes has not been fully clarified.

Using the human thymus scRNA dataset, the authors suggest the existence of cell type-specific TE functions in the thymus. In particular, it is interesting to show that there is a unique pattern in the type and expression level of TEs in thymic antigen-presenting cells, such as mTECs and pDCs, and that they are associated with transcription factor activities. Furthermore, the authors suggested that TEs may be non-redundantly regulated in expression by Aire, Fezf2, and Chd4, and that some TE-derived products are translated and present as proteins in thymic antigen-presenting cells. These findings provide important insights into the evolution of the acquired immune system and the process by which the thymus acquires its function as a primary lymphoid tissue.

Strengths:<br /> 1. By performing single-cell level analysis using scRNA-seq datasets, the authors extracted essential information on heterogeneity within the cell population. It is noteworthy that this revealed the diversity of expression not only of known autoantigens but also of TEs in thymic antigen-presenting cells.

2. The attempt to use mass spectrometry to confirm the existence of TE-derived peptides is worthwhile, even if the authors did not obtain data on as many transcripts as expected.

3. The use of public data sets and the clearly stated methods of analysis improved the transparency of the results.

Weaknesses:<br /> 1. The authors sometimes made overstatements largely due to the lack or shortage of experimental evidence.

For example in figure 4, the authors concluded that thymic pDCs produced higher copies of TE-derived RNAs to support the constitutive expression of type-I interferons in thymic pDCs, unlike peripheral pDCs. However, the data was showing only the correlation between the distinct TE expression pattern in pDCs and the abundance of dsRNAs. We are compelled to say that the evidence is totally too weak to mention the function of TEs in the production of interferon. Even if pDCs express a distinct type and amount of TE-derived transcripts, it may be a negligible amount compared to the total cellular RNAs. How many TE-derived RNAs potentially form the dsRNAs? Are they over-expressed in pDCs?<br /> The data interpretation requires more caution to connect the distinct results of transcriptome data to the biological significance.

2. Lack of generality of specific examples. This manuscript discusses the whole genomic picture of TE expression. In addition, one good way is to focus on the specific example to clearly discuss the biological significance of the acquisition of TEs for the thymic APC functions and the thymic selection.

In figure 2, the authors focused on ETS-1 and its potential target genes ZNF26 and MTMR3, however, the significance of these genes in NK cell function or development is unclear. The authors should examine and discuss whether the distinct features of TEs can be found among the genomic loci that link to the fundamental function of the thymus, e.g., antigen processing/presentation.

3. Since the deep analysis of the dataset yielded many intriguing suggestions, why not add a discussion of the biological reasons and significance?<br /> For example, in Figure 1, why is TE expression negatively correlated with proliferation? cTEC-TE is mostly postnatal, while mTEC-TE is more embryonic. What does this mean?

4. To consolidate the experimental evidence about pDCs and TE-derived dsRNAs, one option is to show the amount of TE-derived RNA copies among total RNAs. The immunohistochemistry analysis in figure 4 requires additional data to demonstrate that overlapped staining was not caused by technical biases (e.g. uneven fixation may cause the non-specifically stained regions/cells). To show this, authors should have confirmed not only the positive stainings but also the negative staining (e.g. CD3, etc.). Another possible staining control was showing that non-pDC (CD303- cell fractions in this case) cells were less stained by the ds-RNA probe.

Reviewer #1 (Public Review):

Summary:

This work provides significant insight into freshwater cable bacteria (CB) and is an important contribution to the emerging CB literature. In this manuscript, Yang et al. describe current-voltage measurements on CB collected from two freshwater sources in Southern California. The studies use electrostatic and conductive atomic force microscopies, as well as four-probe measurements. These measurements are consistent with back-of-the-envelope calculations on conductivities needed to sustain CB function. The data shows that freshwater CB have a similar structure and function to the more studied marine cable bacteria.

Strengths:

Excellent measurements on a new class of cable bacteria.

Weaknesses:

The paper would benefit from additional analysis of the data.

Reviewer #1 (Public Review):

Summary:<br /> The authors are developing differences in the dynamics and allostery of the SARS-COV-2 spike protein for several of the variants. They consider mainly the delta, omicron, and Omicron XBB, and show major differences in the dynamics of the open forms. In the most compelling step, they go further and compare against experimental values of IC50 and KD.

Overall, this is an important application of methods that were developed in the senior author's lab.

Strengths:<br /> The paper presents a strong case for the difference in the dynamical behavior of these sequence variants and relates this to available experiments.

Weaknesses:<br /> The work does not drill down to the effects of individual mutations, which might be possible and would improve our understanding of the effects of single mutations and would dissect the contributions of each single difference in sequence.

Reviewer #1 (Public Review):

Recently the auxin-inducible gene expression system (AGES) has been frequently used for inducing target protein degradation acutely in Drosophila and other organisms. This study investigated the effects of auxin exposure on Drosophila adults, focusing on their feeding behavior, fatty acid metabolism, and oogenesis. The authors have provided strong evidence that high levels of auxin exposure perturb feeding behavior, survival rates, lipid metabolism, and gene expression patterns, providing a cautionary note for the field in using this technology.

This study documented the auxin feeding-induced effects in adult Drosophila, with a design with temporally controlled gene expression using a modified Gal4/Gal80 system. Due to the widespread usage of the auxin-mediated method, it is important to address whether the application of auxin itself causes any physiological changes.

Overall, the experiments were suitably designed with appropriate sample size and data analysis methods. The authors reported evidence of several auxin-induced effects, including strong evidence that high levels of auxin exposure perturb feeding behavior, survival rates, lipid metabolism, and gene expression patterns. For example, they found that auxin-fed flies have significantly lower triglyceride levels than the control flies using Ultra High-pressure Liquid Chromatography-Mass Spectrometry (UHPLC-MS)-based metabolomics assays. Further transcriptome analyses using the whole flies show changes in genes involved in fatty acid metabolism. However, female oogenesis and fecundity do not seem to be affected, at least using the current assays. These results indicate that auxin may not be used in experiments involving lipid-related metabolism, but could be appropriate to be applied for other biological processes.

However, this work can be improved based on the following recommendations:

1) Although authors showed that auxin causes gene expression changes including the possible alteration of Gal4 expression levels, no cell-type-specific data is provided. It would be informative to the Drosophila field if the authors could examine major Gal4 drivers in their expression levels, such as the ones used in studying metabolism and oogenesis.

2) Although the authors briefly mentioned aging research, feeding behavior, and lipid metabolism, RNA-seq data are provided only for short-term treatment (2 days). The ovary phenotype was examined with long-term treatment (15 days). It would be informative if the authors could also show other long-term treatment data.

3) The auxin used in this work is a more water-soluble version and at a high concentration (10 mM). In the C. elegans system, researchers are using a much lower concentration of auxin typically at 1 mM. Therefore, the discussion of their results in terms of potential impacts on other experimental systems should be done carefully. It would be helpful to know what impacts might be observed at a lower concentration of auxin. The recommendation would be that the authors add the 1 mM auxin data point to key elements of their analysis.

4) Another related question is whether these detected changes are reversible or not after exposure to auxin at different concentrations. This would be informative for researchers to better design their temporally controlled experiments.

5) It would also be helpful to know whether spermatogenesis is affected or not.

6) A few other points include changing the nomenclature and validating some of the key genes shown in Figure 3 using quantitative RT-PCR experiments with the tissues where the affected genes are known to be expressed and functional.

Reviewer #1 (Public Review):

In this manuscript, Butkovic et al. perform a genome-wide association (GWA) study on Arabidopsis thaliana inoculated with the natural pathogen turnip mosaic virus (TuMV) in laboratory conditions, with the aim to identify genetic associations with virus infection-related parameters. For this purpose, they use a large panel of A. thaliana inbred lines and two strains of TuMV, one naïve and one pre-adapted through experimental evolution. A strong association is found between a region in chromosome 2 (1.5 Mb) and the risk of systemic necrosis upon viral infection, although the causative gene remains to be pinpointed.

This project is a remarkable tour de force, but the conclusions that can be reached from the results obtained are unfortunately underwhelming. Some aspects of the work could be clarified, and presentation modified, to help the reader.

Reviewer #1 (Public Review):

Summary:

The authors' goal here was to explore how a non-hebbian form of plasticity, heterosynaptic LTP, could shape neuronal responses and learning. They used several conceptually and technically innovative approaches to answer this. First, they identified a behavioral paradigm that was a subthreshold training paradigm (stimulation of thalamic inputs with a footshock), which could be 'converted' to memory via homosynaptic LTP (HFS of thalamic inputs). They then found that stimulation of 'cortical' inputs could also convert the subthreshold stimulation to a lasting memory and that this was associated with a change in neuronal response, akin to LTP. Finally, they provided some slice work that demonstrated that stimulation of cortical inputs could stabilize LTP at thalamic inputs.

Strengths:

1) The approach was innovative and asked an important question in the field.

2) The studies are, for the most part, quite rigorous, using a novel dual opsin approach to probe multiple inputs in vivo.

3) The authors explore neural responses both in vivo and ex vivo, as well as leveraging a 'simple' behavior output of freezing.

Weaknesses:

1) There appears to be a flaw in the exploration of cortical inputs. the authors never show that HFS of cortical inputs has no effect in the absence of thalamic stimulation. It appears that there is a citation showing this, but I think it would be important to show this in this study as well.

2) It is somewhat confusing that the authors refer to the cortical input as driving heterosynaptic LTP, but this is not shown until Figure 4J, that after non-associative conditioning (unpaired shock and tone) HFS of the cortex can drive freezing and heterosynaptic LTP of thalamic inputs. Further, the authors are 'surprised' by this outcome, which appears to be what they predict.

3) 'Cortex' as a stimulation site is vague. The authors have coordinates they used, it is unclear why they are not using standard anatomical nomenclature.

4) The authors' repeated use of homoLTP and heteroLTP to define the input that is being stimulated makes it challenging to understand the experimental detail. While I appreciate this is part of the goal, more descriptive words such as 'thalamic' and 'cortical' would make this much easier to understand.

Reviewer #1 (Public Review):

Summary:

Information transfer between the hippocampus and prefrontal cortex is thought to be critical for spatial working memory, but most of the prior evidence for this hypothesis is correlational. This study attempts to test this causally by linking trial start times to theta-band coherence between these two structures. The authors find that trials initiated during periods of high coherence led to a dramatic improvement in performance. This applied not only to a spatial working memory task, but also to a cue-guided navigation task, suggesting that coherence in these regions may be a signature of a heightened attentional or preparatory state. The authors supplement this behavioral result with electrophysiological recordings to test whether the ventral midline thalamus is likely to mediate hippocampal-prefrontal coherence.

Strengths:

This study demonstrates a striking behavioral effect; by changing the moment at which a trial is initiated, performance on a spatial working memory task improves dramatically, from around 80% correct to over 90% correct. A smaller but nonetheless robust increase in accuracy was also seen in a texture discrimination task. Therefore, prefrontal-hippocampal synchronization in the theta band may not only be important for spatial navigation but may also be associated with improved performance in a range of tasks. If these results can be replicated using noninvasive EEG, it would open up a powerful avenue for modulating human behavior.

Weaknesses:

Ventral midline thalamic nuclei, such as reuniens, have reciprocal projections to both the prefrontal cortex and hippocampus and are therefore well-situated to mediate theta-band interactions between these structures. However, alternative mechanisms cannot be ruled out by the results of this study. For example, theta rhythms are globally coherent across the rodent hippocampus, and the ventral hippocampus projects directly to the prefrontal cortex. Theta propagation may depend on this pathway, and may only be passively inherited by VMT.

The optogenetic manipulations are intended to show that theta in VMT propagates to PFC and also affects HPC-PFC coherence. However, the "theta" induced by driving thalamic neurons at 7 Hz is extremely artificial. To demonstrate that VMT is causally involved in coordinating activity across HPC and PFC, it would have been better to optogenetically inhibit, rather than excite, these nuclei. If the authors were able to show that the natural occurrence of theta in PFC depends on activity in VMT, that would be a much more convincing test of their hypothesis.

Joint Public Review:

In the present manuscript, Abele et al use Salmonella strains modified to robustly induce one of two different types of regulated cell death, pyroptosis or apoptosis in all cell types to assess the role of pyroptosis versus apoptosis in systemic versus intestinal epithelial pathogen clearance. They demonstrate that in systemic spread, which requires growth in macrophages, pyroptosis is required to eliminate Salmonella, while in intestinal epithelial cells (IEC), extrusion of the infected cell into the intestinal lumen induced by apoptosis or pyroptosis is sufficient for early pathogen restriction. The methods used in these studies are thorough and well controlled and lead to robust results, that mostly support the conclusions. The impact on the field is considered minor as the observations are somewhat redundant with previous observations and and not generalizable due to cited evidence of different outcomes in other models of infection and a relatively artificial study system that does not permit the assessment of later timepoints in infection due to rapid clearance. This excludes the study of later effects of differences between pyroptosis and apoptosis in IEC such as i.e. IL-18 and eicosanoid release, which are only observed in the former and can have effects later in infection.

Joint Public Review:

In this manuscript, Kipfer et al describe a method for a fast and accurate SARS-CoV2 rescue and mutagenesis. This work is based on a published method termed ISA (infectious subgenomic amplicons), in which partially overlapping DNA fragments covering the entire viral genome and additional 5' and 3' sequences are transfected into mammalian cell lines. These DNA fragments recombine in the cells, express the full length viral genomic RNA and launch replication and rescue of infectious virus.

CLEVER, the method described here significantly improves on the ISA method to generate infectious SARS-CoV2, making it widely useful to the virology community.

Specifically, the strengths of this method are:<br /> 1) The successful use of various cell lines and transfection methods.<br /> 2) Generation of a four-fragment system, which significantly improves the method efficiency due to lower number of required recombination events.<br /> 3) Flexibility in choice of overlapping sequences, making this system more versatile.<br /> 4) The authors demonstrated how this system can be used to introduce point mutations as well as insertion of a tag and deletion of a viral gene.<br /> 5) Fast-tracking generation of infectious virus directly from RNA of clinical isolates by RT-PCR, without the need for cloning the fragments or using synthetic sequences.<br /> 6) The authors further expanded this method to work on additional plus-strand RNA viruses beyond SARS-CoV-2 (CHIKV, DENV)

The manuscript clearly presents the findings, and the proof-of-concept experiments are well designed.

Overall, this is a very useful method for SARS-CoV2 research. Importantly, it can be applicable to many other viruses, speeding up the response to newly emerging viruses than threaten the public health.

Reviewer #1 (Public Review):

This manuscript provides important evidence on the association between sleep regularity and mortality in the UK Biobank, which is a popular topic in recent sleep and circadian research in population-based studies. The analysis reported robust associations between sleep irregularity and increased total, CVD and cancer mortality, and provided evidence to support the role of sleep and circadian health in disease progression and longevity in human populations. The Sleep Regularity Index (SRI) used in this study is a novel metric that quantifies the consistency in rest-activity rhythms over consecutive 24 hour periods, thus providing objective assessment of potential circadian disruption. The study is based on a large accelerometer study with validated follow-up of incident diseases and deaths. The data quality and large sample size strengthen the credibility of the conclusion. Overall, the analyses are appropriately done and the manuscript is clearly written.

Joint Public Review:

In this study by Porter et al reports on outcomes from a small, open-label, pilot randomized clinical trial comparing dornase-alfa to the best available care in patients hospitalized with COVID-19 pneumonia. As the number of randomized participants is small, investigators describe also a contemporary cohort of controls and the study concludes about decrease of inflammation (reflected by CRP levels) after 7 days of treatment but no other statistically significant clinical benefit.

Suggestions to the authors:

• Please re-analyze findings by omitting from all Tables and Figures all data of comparators who were not randomized (BAC). I understand the difficulties of running this trial but the results of excess reduction of mortality do not allow the publication of a trial where comparators do not come from the randomized patient population.<br /> • The presentation remains confusing and the manuscript should be critically revised for clarity. There is a repetition of methods (e.g. lines 176-187 repeat 160-175) and redundant results (e.g. Figure S2, Table 3). At Table 4: the authors should select one method of illustration for lab results, either Table or figure, without repetitions<br /> • Regarding inclusion criteria, it is unclear whether high radiological suspicion is sufficient for inclusion or whether PCR based confirmation is required in all instances (differences in wording between lines 153 and 191), and under which oxygen requirements (lines 155 and 192)<br /> • Table 1 should be merged with Table S2 and a better description of cohort baseline severity (P/F, SOFA, APACHE, organ support, number of patients in each point of the WHO severity score) and treatments should be made available

Reviewer #1 (Public Review):

The manuscript by Hage et al. presents interesting results from a foraging behavior in Marmosets that explores the interactions of saccade and lick vigor with pupil dilation and performance as well as a marginal value theory and foraging theory-inspired value-based decision-making model thereof. The results are generally robust and carefully presented and analyses, particularly of vigor, are carefully executed.

Reviewer #1 (Public Review):

Summary:<br /> The authors study age-related changes in the excitability and firing properties of sympathetic neurons, which they ascribe to age-related changes in the expression of KCNQ (Kv7, "M-type") K+ currents in rodent sympathetic neurons, whose regulation by GPCRs has been most thoroughly studied for over 40 years. The authors suggest the ingestion of rapamycin may partially reverse the age-related decrease in M-channel expression. With the rapamycin part included, it is unclear how this work will impact the field of age-related neuronal dysfunction, as the mechanistic information is not strong.

Strengths:<br /> The strengths include the rigor of the current-clamp and voltage-clamp experiments, the lovely, crisp presentation of the data, and the expert statistics. The separation of neurons into tonic, phasic, and adapting classes is also interesting, and informative. The writing is also elegant, and crisp. The above is especially true of the manuscript up until the part dealing with the effects of rapamycin, which becomes less compelling.

Weaknesses:<br /> Where the manuscript becomes less compelling is in the rapamycin section, which does not provide much in the way of mechanistic insights. As such, the effect is more of an epi-phenomenon of unclear insight, and the authors cannot ascribe a signaling mechanism to it that is supported by data. Thus, this latter part rather undermines the overall impact and central advance of the manuscript. The problem is exacerbated by the controversial and anecdotal nature of the entire mTor/aging field, some of whose findings have very unfortunately had to be recently retracted.

I would strongly recommend to the authors that they end the manuscript with their analysis of the role of M current/KCNQ channels in the numerous age-related changes in sympathetic neuron function that they elegantly report, and save the rapamycin, and possible mTor action, for a separate line of inquiry that the authors could develop in a more thorough and scholarly way.

Reviewer #1 (Public Review):

Summary:<br /> In this research article, the authors utilized the zebrafish embryo to explore the idea that two different cell types emerge with different morphodynamics from the floor of the dorsal aorta based on their apicobasal polarity establishment. The hypothesis that the apical-luminal polarity of the membrane could be maintained after EHT and confer different functionality to the cell is exciting, however, this could not be established. There is a general lack of data supporting several of the main statements and conclusions. In addition, the manuscript is difficult to follow and needs refinement. We present below some questions and suggestions with the goal of guiding the authors to improve the manuscript and solidify their findings.

Strengths:<br /> New transgenic zebrafish lines developed. Challenging imaging.

Weaknesses:<br /> 1. The authors conclude that the truncated version of Podxl2 fused to a fluorophore is enriched within the apical site of the cell. However, based on the images provided, an alternative interpretation is that the portion of the membrane within the apical side is less stretched than in the luminal side, and therefore the fluorophore is more concentrated and easier to identify by confocal. This alternative interpretation is also supported by data presented later in the paper where the authors demonstrate that the early HE is not polarized (membranes are not under tension and stretched yet). Could the authors confirm their interpretation with a different technique/marker like TEM?

2. Could the authors confirm that the engulfed membranes are vacuoles as they claimed, using, for example, TEM? Why is it concluded that "these vacuoles appear to emanate from the abluminal membrane (facing the sub-aortic space) and not from the lumen?" This is not clear from the data presented.

3. It is unclear why the authors conclude that "their dynamics appears to depend on the activity of aquaporins and it is very possible that aquaporins are active in zebrafish too, although rather in EHT cells late in their emergence and/or in post-EHT cells, for water chase and vacuolar regression as proposed in our model (Figure 1 - figure supplement 1B)." In our opinion, these figures do not confirm this statement.

4. Could the authors prove and show data for their conclusions "We observed that both EHT pol+ and EHT pol- cells divide during the emergence"; "both EHT pol+ and EHT pol- cells express reporters driven by the hematopoietic marker CD41 (data not shown), which indicates that they are both endowed with hematopoietic potential"; and "the full recovery of their respective morphodynamic characteristics (not shown)?".

5. The authors do not demonstrate the conclusion traced from Fig. 2B. Is there a fusion of the vacuoles to the apical side in the EHT pol+ cells? Do the cells inheriting less vacuoles result in pol- EHT? It looks like the legend for Fig. 2-fig supp is missing.

6. The title of the paper "Tuning apico-basal polarity and junctional recycling in the hemogenic endothelium orchestrates pre-hematopoietic stem cell emergence complexity" could be interpreted as functional heterogeneity within the HSCs, which is not demonstrated in this work. A more conservative title denoting that there are two types of EHT from the DA could avoid misinterpretations and be more appropriate.

7. There are several conclusions not supported by data: "Finally, we have estimated that the ratio between EHT pol+ and EHT pol- cells is of approximately 2/1". "We observed that both EHT pol+ and EHT pol- cells divide during the emergence and remain with their respective morphological characteristics". "We also observed that both EHT pol+ and EHT pol- cells express reporters driven by the hematopoietic marker CD41 (data not shown), which indicates that they are both endowed with hematopoietic potential." These conclusions are key in the paper, and therefore they should be supported by data.

Reviewer #1 (Public Review):

In the revised manuscript presented by Chen, Wang, and coworkers, the authors examine two proteins, STEAP1 and STEAP2, which are transmembrane hemoproteins that are involved in Fe and Cu homeostasis and are implicated in certain cancer states. The authors produce recombinant forms of STEAP1 and STEAP2 and attempt to reconstruct the electron-transport chains of both; under certain conditions, the electron transport chain of STEAP2 consists of an internal reductase domain that binds NADPH and transfers electrons to an internal FAD molecule prior to the heme b, while STEAP1 can use an independent/external b5 reductase instead of an intrinsic reductase domain to accomplish the same electron transport pathway. A strong feature of this manuscript is the determination of the cryo-EM structure of the human STEAP2 protein resolved to 3.2 Å globally and bound to heme, FAD (in an extended conformation), and NADP+/NADPH.

This revised study aims to address the previous weaknesses that were noted, such as the unclear presentation of the kinetics data, the lack of determined redox couples, the lack of in vivo oligomerization verification, and some minor weaknesses such as the fit of the BLI data and the exact redox states of the bound coenzymes. In general, the authors have sought to rectify these weaknesses chiefly through textual edits. Through these revisions, the kinetics data are now better presented and may be more easily interpreted by the reader, how the samples for cryo-EM were prepared with the respective coenzymes is clearer, and a comparison between the oligomerization of STEAP2 and STEAP4 suggests conservation of oligomerization. The determination of the redox potentials of the hemes in both STEAP1 and STEAP2 would still be a strong addition to the data presented, but it is recognized that the limitations in the ability to prepare sufficient quantities of recombinant enzyme limits the ability to determine the measurements and may represent another publication outside of the scope of this publication.

Joint Public Review:

Summary:<br /> In this study, the authors seek to characterize the role of splicing factor SRSF1. Using a conditional deletion of Srsf1 in germ cells, they find that SRSF1 is required for male fertility. Via immunostaining and RNA-seq analysis of the Srsf1 conditional knockout (cKO) testes, combined with SRSF1 CLIP-seq and IP-MS data from the testis, they conclude that Srsf1 is required for homing of precursor spermatogonial stem cells (SCCs) due to alternative splicing of Tial1. They further show that spermatogonia-related genes (Plzf, Id4, Setdb1, Stra8, Tial1/Tiar, Bcas2, Ddx5, Srsf10, Uhrf1, and Bud31) were bound by SRSF1 in the mouse testes by CLIP-seq. They show that SRSF1 coordinates with other RNA splicing-related proteins to directly bind and regulate the expression of several spermatogonia-related genes, including Tial1/Tiar, via alternative splicing Ultimately, the study shows that SRSF1's effects on alternative splicing are required to establish spermatogenesis. In the absence of Srsf1, the postnatal gonocytes do not properly mature into spermatogonia and consequently never initiate spermatogenesis.

Strengths:<br /> This study shows a role of SRSF1-mediated alternative splicing in establishment and survival of precursor SSCs, which may provide a framework to elucidate the molecular mechanisms of the posttranscriptional network underlying the formation of SSC pools. The histological analysis of the Srsf1 cKO traces the origins of the fertility defect to the postnatal testis, and the authors have generated interesting CLIP-seq, IP-MS, and RNA-seq datasets characterizing SRSF1's RNA targets and interacting proteins specifically in the testis. Together, this study provides detailed phenotyping of the Srsf1 cKO, which convincingly supports the Sertoli Cell Only phenotype, establishes the timing of the first appearance of the spermatogonial defect, and provides new insight into the role of splicing factors and SRSF1 specifically in spermatogenesis. The experiments are well-designed and conducted, the overall methods and results are robust and convincing.

Weaknesses:<br /> This study does not provide a full mechanistic explanation connecting altered splicing with defects in SSC precursors. The claim that altered splicing of the Tial1 transcript mediates the effect of SRSF1 loss is not convincingly supported. In addition, some regions of the text suggest that misregulated splicing of Tial1 disrupts spermatogonial survival; while Tial1 is required for primordial germ cell survival in embryonic gonads (E11.5-13.5; Beck et al 1998), it is unclear if Tial1 is required for germline development beyond this embryonic stage.

Reviewer #1 (Public Review):

Summary:<br /> This is large-scale genomics and transcriptomics study of the epidemic community-acquired methicillin-resistant S. aureus clone USA300, designed to identify core genome mutations that drove the emergence of the clone. It used publicly available datasets and a combination of genome-wide association studies (GWAS) and independent principal-component analysis (ICA) of RNA-seq profiles to compare USA300 versus non-USA300 within clonal complex 8. By overlapping the analyses the authors identified a 38bp deletion upstream of the iron-scavenging surface-protein gene isdH that was both significantly associated with the USA300 lineage and with a decreased transcription of the gene.

Strengths:<br /> Several genomic studies have investigated genomic factors driving the emergence of successful S. aureus clones, in particular USA300. These studies have often focussed on acquisition of key accessory genes or have focussed on a small number of strains. This study makes a smart use of publicly available repositories to leverage the sample size of the analysis and identify new genomics markers of USA300 success.<br /> The approach of combining large-scale genomics and transcriptomics analysis is powerful, as it allows to make some inferences on the impact of the mutations. This is particularly important for mutations in intergenic regions, whose functional impact is often uncertain.<br /> The statistical genomics approaches are elegant and state-of-the-art and can be easily applied to other contexts or pathogens.

Weaknesses:<br /> The main weakness of this work is that these data don't allow a casual inference on the role of isdH in driving the emergence of USA300. It is of course impossible to prove which mutation or gene drove the success of the clone, however, experimental data would have strengthened the conclusions of the authors in my opinion.<br /> Another limitation of this approach is that the approach taken here doesn't allow to make any conclusions on the adaptive role of the isdH mutation. In other words, it is still possible that the mutation is just a marker of USA300 success, due to other factors such as PVL, ACMI or the SCCmecIVa. This is because by its nature this analysis is heavily influenced by population structure. Usually, GWAS is applied to find genetic loci that are associated with a phenotype and are independent of the underlying population structure. Here, authors are using GWAS to find loci that are associated with a lineage. In other words, they are simply running a univariate analysis (likely a logistic regression) between genetic loci and the lineage without any correction for population structure, since population structure is the outcome. Therefore, this approach can't be applied to most phenotype-genotype studies where correction for population structure is critical.<br /> Finally, the approach used is complex and not easily reproduced in another dataset. Although I like DBGWAS and find the network analysis elegant, I would be interested in seeing how a simpler GWAS tool like Pyseer would perform.

Reviewer #1 (Public Review):

This manuscript by Martinez-Ara et al investigates how combinations of cis-regulatory elements combine to influence gene expression. Using a clever iteration on massively parallel reporter assays (MPRAs), the authors measure the combinatorial effects of pairs of enhancers on specific promoters. Specifically, they assayed the activity of 59x59 different enhancer-enhancer (E-E) combinations on 8 different promoters in mouse embryonic stem cells. The main claims of the paper are that E-E pairs combine nearly additively, and that supra-additive E-E pairs are rare and often promoter-dependent. The data in this study generally support these claims.

This paper makes a good contribution to the ongoing discussions about the selectivity of gene regulatory elements. Recent works, such as those by Martinez-Ara et al. and Burgman et al., have indicated limited selectivity between E-P pairs on plasmid-based assays; this paper adds another layer to that by suggesting a similar lack of selectivity between E-E pairs.

An interesting result in this manuscript is the observation that weak promoters allow more supra-additive E-E interactions than strong promoters (Figure 4b). This nonlinear promoter response to enhancers aligns with the model previously proposed in Hong et al. (from my own group), which posited that core promoter activities are nonlinearly scaled by the genomic environment, and that (similar to the trend observed in Figure 5b) the steepness of the scaling is negatively correlated with promoter strength.

My only suggestion for the authors is that they include more plots showing how much the intrinsic strengths of the promoters and enhancers they are working with explain the trends in their data.

Specific Suggestions<br /> Supplementary Figure 4 is presented as evidence for selectivity between single enhancers and promoters. Could the authors inspect the relationship between enhancer/promoter strength and this selectivity? Generating plots similar to Figure 4B and Figure 5B, but for single enhancers, should show if the ability of an enhancer to boost a promoter is inversely correlated to that promoter's intrinsic strength. Also, in Supplementary Figure 4, coloring each point by promoter type would clarify if certain promoters (the weak ones) consistently show higher boost indices across all enhancers. If they do not, the authors may want to speculate how single enhancers can show selectivity for promoters while the effect of adding a second enhancer to an existing E-P has little selectivity. An alternate explanation, based solely on the strength of the elements, would be that when the expression of a gene is low the addition of enhancer(s) has large effects, but when the expression of a gene is high (closer to saturation) the addition of enhancer(s) have small effects.

Can anything more be said about the enhancers in E-E-P combinations that exhibit supra-additivity? Specifically, it would be interesting to know if certain enhancers, e.g. strong enhancers or enhancers with certain motifs, are more likely to show supra-additivity with a given promoter.

Reviewer #1 (Public Review):

Summary:<br /> The authors identify a mechanical model of activation of Abelson kinase involving the modification of stability of an alpha helix by mutations and different classes of inhibitors. They use NMR chemical shifts of mutant sequences of the alpha helix in a model of Abelson kinase including the regulatory and kinase domains.

Strengths:<br /> The mechanism of inhibition of this important drug target is highly complex involving multiple domains' interactions, While crystal structures can establish end states well, the details of more dynamic interactions among the components can be assessed by NMR studies, The authors previously established {Sonti, 2018, PMID29319304} that different inhibitors and assembled states result from changes of stabilisation of the assembly involving the kinase and the SH3 domain. This is extended here to<br /> illuminate the role of the kinase C terminal alpha helic I' to the domains' interface, expanding the previous identification of this area of the protein as key to agonist/antagonist action at the allosteric myristlylation binding site.

Weaknesses:<br /> The conclusions are based on the relationship with prior observations of classes of chemical shift perturbation, with a set of deletion mutants limited by expression issues. The origin of the force involving the straight or bent helix is not readily apparent. The deletion mutants are treated as solely limiting the helix length irrespective of residue type, and their interactions may be more subtle, beyond the helix stabilization, in other interactions, and in the indirect nature of NMR chemical shift perturbations.

Reviewer #1 (Public Review):

The study provides a complete comparative interactome analysis of α-arrestin in both humans and drosophila. The authors have presented interactomes of six humans and twelve Drosophila α-arrestins using affinity purification/mass spectrometry (AP/MS). The constructed interactomes helped to find α-arrestins binding partners through common protein motifs. The authors have used bioinformatic tools and experimental data in human cells to identify the roles of TXNIP and ARRDC5: TXNIP-HADC2 interaction and ARRDC5-V-type ATPase interaction. The study reveals the PPI network for α-arrestins and examines the functions of α-arrestins in both humans and Drosophila. The authors have carried out the necessary changes that were suggested, and the manuscript can now be accepted.

Comments: I would like to congratulate the authors and the corresponding authors of this manuscript for bringing together such an elaborate study on α-arrestin and conducting a comparative study in drosophila and humans.

Introduction: The introduction provides a rationale behind why the comparison between humans and Drosophila is performed.

Results: The results cover all the necessary points concluded from the experiments and computational analysis. The images are elaborate and well-made. The authors have a rigorous amount of work added together for the success of this manuscript. The authors have provided a database of network of α-arrestins in both humans and Drosophila which can be used by other researchers working in the same subject to study the interacting genes.

Discussion: the authors have utilized and discussed the conclusion they draw from their study. But could highlight more on ARRDCs and why it was selected out of the other arrestins.

References: the authors have considered the suggestion and added the necessary references.

The authors have provided future work directions associated with their work.

Reviewer #1 (Public Review):

Summary:<br /> This study investigates how the neural representation of a stimulus transitions from that evoked by the presence of the stimulus (sensory) to one that exists only as a memory trace once the stimulus disappears (mnemonic). In simple terms, it explores the transition from so-called "iconic memory" (akin to residual sensory-driven neural activity) to working memory proper (self-sustained activity). The authors build a computational model for this transition and test it against data from two new psychophysical experiments plus two datasets from prior experiments.

Strengths and weaknesses:<br /> I really liked this work. It considers a fairly complex process but builds a mechanistically comprehensive scheme that is intuitive and testable. This is a hefty paper; the full model built by the authors has a lot of moving parts. But these are all carefully justified, and in fact, many of them are specifically tested by fitting customized variants of the model to the experimental data (which are rich enough to distinguish all of these variants, not only quantitatively but also qualitatively). Said differently, both the assumptions used to build the model and the conclusions drawn after comparison with the experimental data are well justified. In the end, although it takes some effort to put the whole scheme together, I think the reader learns a lot about memory mechanisms. The Discussion is rich, as beyond working memory per se, the work relates to numerous issues (e.g., perception, attention, neural dynamics, population coding). Importantly, although part of the value of the study lies in the way it integrates many prior results into a cohesive framework, it also makes an important novel point: that iconic and working memory are not qualitatively different things, but rather just different extreme manifestations of the one, continuous process whereby perceptual information is stored (as a pattern of neural activation) and made accessible to other cognitive functions. In this conceptualization, working memory corresponds to a readout of activity a significant time (typically > 1 s) after stimulus offset, whereas iconic memory is consistent with a readout from the same neural population but immediately or very shortly after stimulus offset. This account not only is parsimonious but also provides a specific hypothesis (or a set of hypotheses) that can be tested further.

I did not find any major weaknesses. The paper does require some time and effort in order to appreciate all that it contains, but this is inevitable, as it aims to (1) build a compact but mechanistically detailed account of a process that is somewhat complex, and (2) test key predictions through psychophysical experiments that must be sufficiently rich. In the end, I found the effort quite rewarding.

Reviewer #1 (Public Review):

Summary:<br /> In this work, the authors provide evidence to show that an increase in Kv7 channels in hilar mossy cells of Fmr1 knock out mice results in a marked decrease in their excitability. The reduction in excitatory drive onto local hilar interneurons produces an increased excitation/inhibition ratio in granule cells. Inhibiting Kv7 channels can help normalize the excitatory drive in this circuit, suggesting that they may represent a viable target for targeted therapeutics for fragile-x syndrome.

Strengths:<br /> The work is supported by a compelling and thorough set of electrophysiological studies. The authors do an excellent job of analysing their data and present a very complete data set.

Weaknesses:<br /> There are no significant weaknesses in the experimental work, however the complexity of the data presentation and the lack of a schematic showing the organizational framework of this circuit make the data less accessible to non-experts in the field. I highly encourage a graphical abstract and network diagram to help individuals understand the implications of this work.

The work is important as it identifies a unique regional and cell-specific abnormality in Fmr1 KO mice, showing how the loss of one gene can result in region-specific changes in brain circuits.

Reviewer #1 (Public Review):

Summary:<br /> Costantino et al report on data from thousands of participants from the UK Biobank whereby they assessed relationships between menopausal status, menopause type (surgical or natural), and age at menopause with cognition, neuroanatomical measures derived from magnetic resonance imaging and Alzheimer's disease (AD) risk.

Strengths:<br /> This is a really important field of research. Alzheimer's disease is a leading cause of death in women and better understanding whether hormonal and brain changes associated with the menopause transition are contributing to this risk is a crucial research question. Access to such a large database, with cognitive assessment alongside structural MRI data, is a strength of this study. The authors report a positive association between earlier age of menopause as well as surgical menopause and a higher risk of developing AD. The authors also report associations between age at natural menopause and performances on various cognitive tests. Positive associations were found between the age of menopause and fluid intelligence, numeric memory, and pair matching.

Weaknesses:<br /> The manuscript would benefit from further clarification about the sample and descriptions of analyses. At the moment, it is difficult to determine whether the conclusions align with the results. In terms of the method, this is a cross-sectional analysis, with different subgroups selected depending on the research question and model. Some further clarification on the full sample and the participants selected for each analysis would be helpful. Some clarification on how menopause status and AD diagnosis were determined would be helpful. The results and discussion refer to menopause having an impact on specific cognitive tasks - the domains that these tasks assess would be worthy of some discussion.

Reviewer #1 (Public Review):

Summary:<br /> In this manuscript, the role of orexin receptors in dopamine neurons is studied. Considering the importance of both orexin and dopamine signalling in the brain, with critical roles in arousal and drug seeking, this study is important to understand the anatomical and functional interaction between these two neuromodulators. This work suggests that such interaction is direct and occurs at the level of SN and VTA, via the expression of OX1R-type orexin receptors by dopaminergic neurons.

Strengths:<br /> The use of a transgenic line that lacks OX1R in dopamine-transporter-expressing neurons is a strong approach to dissecting the direct role of orexin in modulating dopamine signalling in the brain. The battery of behavioural assays to study this line provides a valuable source of information for researchers interested in the role of orexin-A in animal physiology.

Weaknesses:<br /> The choice of methods to demonstrate the role of orexin in the activation of dopamine neurons is not justified and the quantification methods are not described with enough detail. The representation of results can be dramatically improved and the data can be statistically analysed with more appropriate methods.

Reviewer #1 (Public Review):

This manuscript represents an elegant bioinformatics approach to addressing causal pathways in vascular and liver tissue related to atherosclerosis/coronary artery disease, including those shared by humans and mice and those that are specific to only one of these species. The authors constructed co-expression networks using bulk transcriptome data from human (aorta, coronary) and mouse (aorta) vascular and liver tissue. They mapped human CAD GWAS data onto these modules, mapped GWAS SNPs to putatively causal genes, identified pathways and modules enriched in CAD GWAS hits, assessed those shared between vascular and liver tissues and between humans and mice, determined key driver genes in CAD-associated supersets, and used mouse single-cell transcriptome data to infer the roles of specific vascular and liver cell types. The overall approach used by the authors is rigorous and provides new insights into potentially causal pathways in vascular tissue and liver involved in atherosclerosis/CAD that are shared between humans and mice as well as those that are species-specific. This approach could be applied to a variety of other common complex conditions.

Reviewer #1 (Public Review):

Summary:<br /> This study examines the context-dependent modulation of auditory cortical neurons in response to expected sensory input, either self-generated sounds or expected perturbations of self-generated sounds. Specifically, using songbirds, the authors ask whether social context (the presence of a female conspecific) affects 1) the response of auditory cortical neurons to the bird's own song when he is singing; and 2) the response of neurons to perturbations of auditory feedback that the bird has been trained to expect.

Strengths:<br /> First, the authors report that across the population, the responses of the neurons does not differ when a male bird sings alone or if he sings to a female. A fraction of auditory cortical neurons, however, do show significant differences in the firing rate, precision, and/or degree of burst firing when males sing alone vs. when they sing to females. This finding is broadly consistent with the literature showing that sensory neurons (visual, auditory, somatosensory, etc.) can be rapidly reconfigured into different "information processing modes" depending on behavioral state (e.g, quiescence vs vigilance).

For the perturbation experiments, the authors trained birds to expect distorted auditory feedback during a particular syllable. They found that some neurons showed greater responses during perturbation when a female was present (compared to when males were alone) while other neurons had smaller responses during perturbation when a female was present. In addition, the response of a small number of auditory cortical neurons were not affected by behavioral state. These results contrast with their prior report that the responses of midbrain dopaminergic neurons that project to the basal ganglia are "uniformly reduced" in the presence of a female, raising a question of how an evaluation signal is transformed in the circuit from the primary sensory region to the midbrain.

Weaknesses:<br /> While the experiments and analysis are solid, the finding that social context can alter responses of auditory cortical neurons in a multitude of ways (increase, decrease or no change) raises several questions that can be examined with additional analysis. For example, do context-dependent differences in auditory responses derive from context-dependent differences in the songs? Are context-dependent differences present in all classes of neurons and throughout the auditory system?

The observed heterogeneity in the firing properties of auditory cortical neurons, both in response to self-generated sounds and during perturbations of auditory feedback, raises the question of which neurons are sensitive to social context (which likely can be addressed by the authors in a revision). The authors should provide additional details about the recordings:

a) What are the locations of the recording sites?<br /> Prior work has shown that there is an organized map of spectrotemporal features of sounds in the auditory cortex of songbirds; spectral tuning widths change along the medial-lateral axis and temporal tuning widths differ between the input and output layers of Field L. Were the recordings primarily in Field L2 (thalamo-recipient region), L1 or L3? Were some recordings lateral to Field L in secondary auditory regions? Were the neurons that showed context-dependent changes in firing properties localized or distributed throughout Field L (i.e., were the context-dependent differences in neural responses truly brain-wide)? At a minimum, the authors should include a schematic showing the different regions of Field L and a summary of the location of the recording sites. Images of the processed tissue with electrolytic lesions would also be helpful.

b) Was the context-dependent modulation limited to a particular class of neurons (distinguished by spike waveform shape, spontaneous firing rate, or other feature)?

While the authors attribute differences in the responses of single auditory cortical neurons to the presence of a female, other potential explanations for the observed differences should be examined (and potentially ruled out):

a) Prior work has shown that songs of zebra finches differ slightly when males sing alone compared to when they sing to females: songs are faster; pitch is less variable; and the number of introductory elements is greater when males sing to females. Do some of the observed social context-dependent differences in the responses of auditory neurons reflect differences in the songs in the two conditions? This idea is supported in part by a prior study in juvenile zebra finches (Keller & Hahnloser, 2009) showing that ~20% of the neurons they recorded in Field L and a secondary auditory region (CLM) showed anticipatory activity even before the onset of a song bout, suggesting a source of premotor (or at least non-auditory drive) to neurons in the auditory cortex. Did the authors of this study also find premotor activity in Field L, and if so, did it differ between the two social contexts? Might differences in Field L responses reflect motor/song differences?

b) For the perturbation experiments, the authors report heterogeneous responses to playback, with some neurons firing more and other firing less when a female is present compared to when the male is alone. Keller and Hahnloser (2009) found that in juvenile birds, responses of Field L to perturbations of auditory feedback were sensitive to sound amplitude; perturbation responses increased with relative perturbation amplitude. This raises a question of whether perturbation amplitude is different when a male is alone and when a female is present (i.e., the male may move towards the female when she is present and if the speaker is close to the female, the perturbation may be louder than when the male is alone; alternatively, the male be more active when he is alone so the loudness of the perturbation may be more variable across song bouts). It would be useful to know if (and how much) perturbation amplitude varied depending on the location inside the cage as well as whether the sound pressure level of the underlying song was higher (e.g., Lombard effect). Addition of details of the experimental setup/procedure would help to allay concerns that the amplitude of the white noise varied significantly depending on behavioral context.

Finally, I am still trying to make sense of the differences in the context-dependent modulation of responses of auditory cortical neurons vs. midbrain dopaminergic neurons. Given the heterogeneity of responses in Field L, both to self-generated sounds and to expected perturbations during singing, how are the signals decoded downstream of Field L? At the population level, neither the mean firing rate nor the timing of firing of Field L neurons changed with courtship. Similarly, across the population, the responses to perturbations of auditory feedback were not affected by courtship state (error signal attenuated in 11 neurons, increased in 22 neurons and not affected in 10 neurons). Yet, the courtship state "uniformly" reduces the response of midbrain dopaminergic neurons to auditory perturbation. It would be helpful if the authors could include a model and/or more discussion of how this change may arise.

Reviewer #1 (Public Review):

Summary:<br /> Through an unbiased genomewide KO screen, the authors identified loss of DBT to suppress MG132-mediated death of cultured RPE cells. Further analyses suggested that DBT reduces ubiquitinated proteins by promoting autophagy. Mechanistic studies indicated that DBT loss promotes autophagy via AMPK and its downstream ULK and mTOR signaling. Furthermore, loss of DBT suppresses polyglutamine- or TDP-43-mediated cytotoxicity and/or neurodegeneration in fly models. Finally, the authors showed that DBT proteins are increased in ALS patient tissues, compared to non-neurological controls.

Strengths:<br /> The idea is novel, the evidence is mostly convincing, and the data are clean. The findings have implications for human diseases.

Weaknesses:<br /> More experiments are needed to establish the connections between DBT and autophagy. The mechanistic studies are somewhat biased, and it's unclear whether the same mechanism (i.e., AMPK-->mTOR) can be applied to TDP-43-mediated neurodegeneration. Also, some data interpretation has to be more accurate.

Reviewer #1 (Public Review):

Summary:<br /> In this work, Xie, Prescott, and colleagues have reevaluated the role of Nav1.7 in nociceptive sensory neuron excitability. They find that nociceptors can make use of different sodium channel subtypes to reach equivalent excitability. The existence of this degeneracy is critical to understanding neuronal physiology under normal and pathological conditions and could explain why Nav subtype-selective drugs have failed in clinical trials. More concretely, nociceptor repetitive spiking relies on Nav1.8 at DIV0 (and probably under normal conditions in vivo), but on Nav1.7 and Nav1.3 at DIV4-7 (and after inflammation in vivo).

The conclusions of this paper are mostly well supported by data, and these findings should be of broad interest to scientists working on pain, drug development, neuronal excitability, and ion channels.

Strengths:<br /> The authors have employed elegant electrophysiology experiments (including specific pharmacology and dynamic clamp) and computational simulations to study the excitability of a subpopulation of DRGs that would very likely match with nociceptors (they take advantage of using transgenic mice to detect Nav1.8-expressing neurons). They make a strong point showing the degeneracy that occurs at the ion channel expression level in nociceptors, adding this new data to previous observations in other neuronal types. They also demonstrate that the different Nav subtypes functionally overlap and are able to interchange their "typical" roles in action potential generation. As Xie, Prescott, and colleagues argue, the functional implications of the degenerate character of nociceptive sensory neuron excitability need to be seriously taken into account regarding drug development and clinical trials with Nav subtype-selective inhibitors.

Weaknesses:<br /> The next comments are minor criticisms, as the major conclusions of the paper are well substantiated. Most of the results presented in the article have been obtained from experiments with DRG neuron cultures, and surely there is a greater degree of complexity and heterogeneity about the degeneracy of nociceptors excitability in the "in vivo" condition. Indeed, the authors show in Figures 7 and 8 data that support their hypothesis and an increased Nav1.7's influence on nociceptor excitability after inflammation, but also a higher variability in the nociceptors spiking responses. On the other hand, DRG neurons targeted in this study (YFP (+) after crossing with Nav1.8-Cre mice) are >90% nociceptors, but not all nociceptors express Nav1.8 in vivo. As shown by Li et al., 2016 ("Somatosensory neuron types identified by high-coverage single-cell RNA-sequencing and functional heterogeneity"), there is a high heterogeneity of neuron subtypes within sensory neurons. Therefore, some caution should be taken when translating the results obtained with the DRG neuron cultures to the more complex "in vivo" panorama.

Although the authors have focused their attention on Nav channels, it should be noted that degeneracy concerning other ion channels (such as potassium ion channels) could also impact the nociceptor excitability. The action potential AHP in Figure 1, panel A is very different comparing the DIV0 (blue) and DIV4-7 examples. Indeed, the conductance density values for the AHP current are higher at DIV0 than at DIV7 in the computational model (supplementary table 5). The role of other ion channels in order to obtain equivalent excitability should not be underestimated.

Reviewer #1 (Public Review):

Summary:<br /> This study aimed to investigate the effects of optically stimulating the A13 region in healthy mice and a unilateral 6-OHDA mouse model of Parkinson's disease (PD). The primary objectives were to assess changes in locomotion, motor behaviors, and the neural connectome. For this, the authors examined the dopaminergic loss induced by 6-OHDA lesioning. They found a significant loss of tyrosine hydroxylase (TH+) neurons in the substantia nigra pars compacta (SNc) while the dopaminergic cells in the A13 region were largely preserved. Then, they optically stimulated the A13 region using a viral vector to deliver the channelrhodopsine (CamKII promoter). In both sham and PD model mice, optogenetic stimulation of the A13 region induced pro-locomotor effects, including increased locomotion, more locomotion bouts, longer durations of locomotion, and higher movement speeds. Additionally, PD model mice exhibited increased ipsilesional turning during A13 region photoactivation. Lastly, the authors used whole-brain imaging to explore changes in the A13 region's connectome after 6-OHDA lesions. These alterations involved a complex rewiring of neural circuits, impacting both afferent and efferent projections. In summary, this study unveiled the pro-locomotor effects of A13 region photoactivation in both healthy and PD model mice. The study also indicates the preservation of A13 dopaminergic cells and the anatomical changes in neural circuitry following PD-like lesions that represent the anatomical substrate for a parallel motor pathway.

Strengths:<br /> These findings hold significant relevance for the field of motor control, providing valuable insights into the organization of the motor system in mammals. Additionally, they offer potential avenues for addressing motor deficits in Parkinson's disease (PD). The study fills a crucial knowledge gap, underscoring its importance, and the results bolster its clinical relevance and overall strength.

The authors adeptly set the stage for their research by framing the central questions in the introduction, and they provide thoughtful interpretations of the data in the discussion section. The results section, while straightforward, effectively supports the study's primary conclusion - the pro-locomotor effects of A13 region stimulation, both in normal motor control and in the 6-OHDA model of brain damage.

Weaknesses:<br /> 1) Anatomical investigation. I have a major concern regarding the anatomical investigation of plastic changes in the A13 connectome (Figures 4 and 5). While the methodology employed to assess the connectome is technically advanced and powerful, the results lack mechanistic insight at the cell or circuit level into the pro-locomotor effects of A13 region stimulation in both physiological and pathological conditions. This concern is exacerbated by a textual description of results that doesn't pinpoint precise brain areas or subareas but instead references large brain portions like the cortical plate, making it challenging to discern the implications for A13 stimulation. Lastly, the study is generally well-written with a smooth and straightforward style, but the connectome section presents challenges in readability and comprehension. The presentation of results, particularly the correlation matrices and correlation strength, doesn't facilitate biological understanding. It would be beneficial to explore specific pathways responsible for driving the locomotor effects of A13 stimulation, including examining the strength of connections to well-known locomotor-associated regions like the Pedunculopontine nucleus, Cuneiformis nucleus, LPGi, and others in the diencephalon, midbrain, pons, and medulla. Additionally, identifying the primary inputs to A13 associated with motor function would enhance the study's clarity and relevance.

The study raises intriguing questions about compensatory mechanisms in Parkinson's disease and a new perspective on the preservation of dopaminergic cells in A13, despite the SNc degeneration, and the plastic changes to input/output matrices. To gain inspiration for a more straightforward reanalysis and discussion of the results, I recommend the authors refer to the paper titled "Specific populations of basal ganglia output neurons target distinct brain stem areas while collateralizing throughout the diencephalon from the David Kleinfeld laboratory." This could guide the authors in investigating motor pathways across different brain regions.

2) Description of locomotor performance. Figure 3 provides valuable data on the locomotor effects of A13 region photoactivation in both control and 6-OHDA mice. However, a more detailed analysis of the changes in locomotion during stimulation would enhance our understanding of the pro-locomotor effects, especially in the context of 6-OHDA lesions. For example, it would be informative to explore whether the probability of locomotion changes during stimulation in the control and 6-OHDA groups. Investigating reaction time, speed, total distance, and even kinematic aspects during stimulation could reveal how A13 is influencing locomotion, particularly after 6-OHDA lesions. The laboratory of Whelan has a deep knowledge of locomotion and the neural circuits driving it so these features may be instructive to infer insights on the neural circuits driving movement. On the same line, examining features like the frequency or power of stimulation related to walking patterns may help elucidate whether A13 is engaging with the Mesencephalic Locomotor Region (MLR) to drive the pro-locomotor effects. These insights would provide a more comprehensive understanding of the mechanisms underlying A13-mediated locomotor changes in both healthy and pathological conditions.

Reviewer #1 (Public Review):

This is an interesting study of the nature of representations across the visual field. The question of how peripheral vision differs from foveal vision is a fascinating and important one. The majority of our visual field is extra-foveal yet our sensory and perceptual capabilities decline in pronounced and well-documented ways away from the fovea. Part of the decline is thought to be due to spatial averaging ('pooling') of features. Here, the authors contrast two models of such feature pooling with human judgments of image content. They use much larger visual stimuli than in most previous studies, and some sophisticated image synthesis methods to tease apart the prediction of the distinct models.

More importantly, in so doing, the researchers thoroughly explore the general approach of probing visual representations through metamers-stimuli that are physically distinct but perceptually indistinguishable. The work is embedded within a rigorous and general mathematical framework for expressing equivalence classes of images and how visual representations influence these. They describe how image-computable models can be used to make predictions about metamers, which can then be compared to make inferences about the underlying sensory representations. The main merit of the work lies in providing a formal framework for reasoning about metamers and their implications, for comparing models of sensory processing in terms of the metamers that they predict, and for mapping such models onto physiology. Importantly, they also consider the limits of what can be inferred about sensory processing from metamers derived from different models.

Overall, the work is of a very high standard and represents a significant advance over our current understanding of perceptual representations of image structure at different locations across the visual field. The authors do a good job of capturing the limits of their approach and I particularly appreciated the detailed and thoughtful Discussion section and the suggestion to extend the metamer-based approach described in the MS with observer models. The work will have an impact on researchers studying many different aspects of visual function including texture perception, crowding, natural image statistics, and the physiology of low- and mid-level vision.

The main weaknesses of the original submission relate to the writing. A clearer motivation could have been provided for the specific models that they consider, and the text could have been written in a more didactic and easy-to-follow manner. The authors could also have been more explicit about the assumptions that they make.

Reviewer #1 (Public Review):

In the manuscript by Urban et al., the authors attempt to further delineate the role with which non-neuronal CNS cells play in the development of ALS. Towards this goal, the transmembrane signaling molecule ephrinB2 was studied. It was found that there is an increased expression of ephrinB2 in astrocytes within the cervical ventral horn of the spinal cord in a rodent model of ALS. Moreover, reduction of ephrinB2 reduced motoneuron loss and prevented respiratory dysfunction at the NMJ. Further driving the importance of ephrinB2 is an increased expression in the spinal cords of human ALS individuals. Collectively, these findings present compelling evidence implicating ephrinB2 as a contributing factor towards the development of ALS.

Reviewer #1 (Public Review):

To further understand the plasticity of vestibular compensation, Schenberg et al. sought to characterize the response of the vestibular system to short-term and partial impairment using gaze stabilization behaviors. A transient ototoxic protocol affected type I hair cells and produced gain changes in the vestibulo-ocular reflex and optokinetic response. Interestingly, decreases in vestibular function occurred in coordination with an increase in ocular reflex gain at frequencies where vestibular information is more highly weighted over visual. Moreover, computational approaches revealed unexpected detriment from low reproducibility on combined gaze responses. These results inform the current understanding of visual-vestibular integration especially in the face of dysfunction.

Strengths<br /> The manuscript takes advantage of VOR measurements that can be activated by targeted organs, are used in many species including clinically, and indicate additional adverse effects of vestibular dysfunction.

The authors use a variety of experimental procedures and analysis methods to verify results and consider individual performance effects on the population data.

The conclusions are well-justified by current data and supported by previous research and theories of visuo-vestibular function and plasticity.