Reviewer #2 (Public review):

Summary:

The work seeks to improve the detection of RNA m6A modifications using Nanopore sequencing through improvements in raw data analysis. These improvements are said to be in the segmentation of the raw data, although the work appears to position the alignment of raw data to the reference sequence and some further processing as part of the segmentation, and result statistics are mostly shown on the 'data-assigned-to-kmer' level.

As such, the title, abstract, and introduction stating the improvement of just the 'segmentation' does not seem to match the work the manuscript actually presents, as the wording seems a bit too limited for the work involved.

The work itself shows minor improvements in m6Anet when replacing Nanopolish eventalign with this new approach, but clear improvements in the distributions of data assigned per kmer. However, these assignments were improved well enough to enable m6A calling from them directly, both at site-level and at read-level.

Strengths:

A large part of the improvements shown appear to stem from the addition of extra, non-base/kmer specific, states in the segmentation/assignment of the raw data, removing a significant portion of what can be considered technical noise for further analysis. Previous methods enforced the assignment of all raw data, forcing a technically optimal alignment that may lead to suboptimal results in downstream processing as data points could be assigned to neighbouring kmers instead, while random noise that is assigned to the correct kmer may also lead to errors in modification detection.

For an optimal alignment between the raw signal and the reference sequence, this approach may yield improvements for downstream processing using other tools.<br /> Additionally, the GMM used for calling the m6A modifications provides a useful, simple, and understandable logic to explain the reason a modification was called, as opposed to the black models that are nowadays often employed for these types of tasks.

Weaknesses:

The work seems limited in applicability largely due to the focus on the R9's 5mer models. The R9 flow cells are phased out and not available to buy anymore. Instead, the R10 flow cells with larger kmer models are the new standard, and the applicability of this tool on such data is not shown. We may expect similar behaviour from the raw sequencing data where the noise and transition states are still helpful, but the increased kmer size introduces a large amount of extra computing required to process data and without knowledge of how SegPore scales, it is difficult to tell how useful it will really be. The discussion suggests possible accuracy improvements moving to 7mers or 9mers, but no reason why this was not attempted.

The manuscript suggests the eventalign results are improved compared to Nanopolish. While this is believably shown to be true (Table 1), the effect on the use case presented, downstream differentiation between modified and unmodified status on a base/kmer, is likely limited as during actual modification calling the noisy distributions are usually 'good enough', and not skewed significantly in one direction to really affect the results too terribly.

Furthermore, looking at alternative approaches where this kind of segmentation could be applied, Nanopolish uses the main segmentation+alignment for a first alignment and follows up with a form of targeted local realignment/HMM test for modification calling (and for training too), decreasing the need for the near-perfect segmentation+alignment this work attempts to provide. Any tool applying a similar strategy probably largely negates the problems this manuscript aims to improve upon.

Finally, in the segmentation/alignment comparison to Nanopolish, the latter was not fitted(/trained) on the same data but appears to use the pre-trained model it comes with. For the sake of comparing segmentation/alignment quality directly, fitting Nanopolish on the same data used for SegPore could remove the influences of using different training datasets and focus on differences stemming from the algorithm itself.

Appraisal:

The authors have shown their method's ability to identify noise in the raw signal and remove their values from the segmentation and alignment, reducing its influences for further analyses. Figures directly comparing the values per kmer do show a visibly improved assignment of raw data per kmer. As a replacement for Nanopolish eventalign it seems to have a rather limited, but improved effect, on m6Anet results. At the single read level modification modification calling this work does appear to improve upon CHEUI.

Impact:

With the current developments for Nanopore-based modification largely focusing on Artificial Intelligence, Neural Networks, and the like, improvements made in interpretable approaches provide an important alternative that enables a deeper understanding of the data rather than providing a tool that plainly answers the question of whether a base is modified or not, without further explanation. The work presented is best viewed in the context of a workflow where one aims to get an optimal alignment between raw signal data and the reference base sequence for further processing. For example, as presented, as a possible replacement for Nanopolish eventalign. Here it might enable data exploration and downstream modification calling without the need for local realignments or other approaches that re-consider the distribution of raw data around the target motif, such as a 'local' Hidden Markov Model or Neural Networks. These possibilities are useful for a deeper understanding of the data and further tool development for modification detection works beyond m6A calling.

Reviewer #2 (Public review):

The authors address the question of differences in the development of the central complex (Cx), a brain structure mainly controlling spatial orientation and locomotion in insects, which can be traced back to the neuroblast lineages that produce the Cx structure. The lineages are called type-II neuroblast (NB) lineages and assumed to be conserved in insects. While Tribolium castaneum produces a functional larval Cx that only consists of one part of the adult Cx structure, the fan-shaped body, in Drosophila melanogaster a non-functional neuropile primordium is formed by neurons produced by the embryonic type-II NBs which then enter a dormant state and continue development in late larval and pupal stages.

The authors present a meticulous study demonstrating that type-II neuroblast (NB) lineages are indeed present in the developing brain of Tribolium castaneum. In contrast to type-I NB lineages, type-II NBs produce additional intermediate progenitors. The authors generate a fluorescent enhancer trap line called fez/earmuff which prominently labels the mushroom bodies but also the intermediate progenitors (INPs) of the type-II NB lineages. This is convincingly demonstrated by high resolution images that show cellular staining next to large pointed labelled cells, a marker for type-II NBs in Drosophila melanogaster. Using these and other markers (e.g. deadpan, asense), the authors show that the cell type composition and embryonic development of the type-II NB lineages are similar to their counterparts in Drosophila melanogaster. Furthermore, the expression of the Drosophila type-II NB lineage markers six3 and six4 in subsets of the Tribolium type-II NB lineages (anterior 1-4 and 1-6 type-II NB lineages) and the expression of the Cx marker skh in the distal part of most of the lineages provide further evidence that the identified NB lineages are equivalent to the Drosophila lineages that establish the central complex. However, in contrast to Drosophila, there are 9 instead of 8 embryonic type-II NB lineages per brain hemisphere and the lineages contain more progenitor cells compared to the Drosophila lineages. The authors argue that the higher number of dividing progenitor cells supports the earlier development of a functional Cx in Tribolium.

While the manuscript clearly shows that type-II NB lineages similar to Drosophila exist in Tribolium, it does not establish a direct link between the characteristics of these lineages and a functional larval Cx in Tribolium, i.e., it does not identify the cause of the heterochronic development of the Cx in these insects. However, the detailed study lays the foundation for lineage tracing and gene function experiments that will elucidate if the higher number of Tribolium type-II NB lineage progenitors, the additional lineage and the timing of developmental progression of the progenitors can indeed be linked with the earlier function of the Cx and/or if other components are required for establishing the functional larval neural circuits in Tribolium such as e.g. larval born neurons as is the case in Drosophila.

Reviewer #3 (Public review):

Summary:

This study employs an optogenetics approach aimed at activating oncogene (KRASG12V) expression in a single somatic cell, with a focus on following the progression of activated cell to examine tumourigenesis probabilities under altered tissue environments. The research explores the role of stemness factors (VENTX/NANOG/OCT4) in facilitating oncogenic RAS (KRASG12V)-driven malignant transformations. Although the evidence provided is incomplete, the authors propose an important mechanism whereby reactivation of re-programming factors correlates with the increased likelihood of a mutant cell undergoing malignant transformation.

Strengths:

· Innovative Use of Optogenetics: The application of optogenetics for precise activation of KRAS in a single cell is valuable to the field of cancer biology, offering an opportunity to uncover insight into cellular responses to oncogenic mutations.<br /> · Important Observations: The findings concerning stemness factors' role in promoting oncogenic transformation are important, contributing data to the field of cancer biology.

Weaknesses:

Lack of Methodological Clarity: The manuscript lacks detailed descriptions of methodologies, making it difficult to fully evaluate the experimental design and reproducibility, rendering incomplete evidence to support the conclusion. Improving methodological transparency and data presentation will crucially strengthen the paper's contributions to understanding the complex processes of tumorigenesis.

Sub-optimal Data Presentation and Quality:<br /> The resolution of images through-out the manuscript are too low. Images presented in Figure 2 and Figure 4 are of very low resolution. It is very hard to distinguish individual cells and in which tissue they might reside.<br /> Lack of quantitative data and control condition data obtained from images of higher magnification limits the ability to robustly support the conclusions.

Here are some details:<br /> · Tissue specificity of the cells express KRASG12V oncogene: In this study, the ubiquitin promoter was used to drive oncogenic KRASG12V expression. Despite this, the authors claim to activate KRAS in a single brain cell based on their localized photo-activation strategy. However, upon reviewing the methods section, the description was provided that 'Localized uncaging was performed by illumination for 7 minutes on a Nikon Ti microscope equipped with a light source peaking at 405 nm, Figure 1. The size of the uncaging region was controlled by an iris that defines a circular illumination with a diameter of approximately 80 μm.' It is surprising that an epi-fluorescent microscope with an illumination diameter of around 80μm can induce activation in a single brain cell beneath skin tissue. Additionally, given that the half-life for mTFP maturation is around 60 minutes, it is likely that more cells from a variety of different lineages could be activated, but the fluorescence would not be visible until more than 1-hour post-illumination. Authors might want to provide more evidence to support their claim on the single cell KRAS activation.<br /> · Stability of cCYC: The manuscript does not provide information on the half-life and stability of cCYC. Understanding these properties is crucial for evaluating the system's reliability and the likelihood of leakiness, which could significantly influence the study's outcomes.<br /> · Metastatic Dissemination claim: Typically, metastatic cancer cells migrate to and proliferate within specific niches that are conducive to outgrowth, such as the caudal hematopoietic tissue (CHT) or liver. In Figure 3 A, an image showing the presence of mTFP expressing cells in both the head and tail regions of the larva, with additional positive dots located at the fin fold. This is interpreted as "metastasis" by the authors. However, the absence of supportive cellular compartment within the fin-fold tissue makes the presence of mTFP-positive metastatic cells there particularly puzzling. This distribution raises concerns about the spatial specificity of the optogenetic activation protocol.<br /> The unexpected locations of these signals suggest potential ectopic activation of the KRAS oncogene, which could be occurring alongside or instead of targeted activation. This issue is critical as it could affect the interpretation of whether the observed mTFP signal expansion over time is due to actual cell proliferation and infiltration, or merely a result of ectopic RAS transgene activation.<br /> · Image Resolution Concerns: The cells depicted in Figure 3C β, which appear to be near the surface of the yolk sac and not within the digestive system as suggested in the MS, underscore the necessity for higher-resolution imaging. Without clearer images, it is challenging to ascertain the exact locations and states of these cells, thus complicating the assessment of experimental results.<br /> · The cell transplantation experiment is lacking protocol details: The manuscript does not adequately describe the experimental protocols used for cell transplantation, particularly concerning the origin and selection of cells used for injection into individual larvae. This omission makes it difficult to evaluate the reliability and reproducibility of the results. Such as the source of transplanted cells:<br /> • If the cells are derived from hyperplastic growths in larvae where RAS and VX (presumably VENTX) were locally activated, the manuscript fails to mention any use of fluorescence-activated cell sorting (FACS) to enrich mTFP-positive cells. Such a method would be crucial for ensuring the specificity of the cells being studied and the validity of the results.<br /> • If the cells are obtained from whole larvae with induced RAS + VX expression, it is notable and somewhat surprising that the larvae survived up to six days post-induction (6dpi) before cells were harvested for transplantation. This survival rate and the subsequent ability to obtain single cell suspensions raise questions about the heterogeneity of the RAS + VX expressing cells that transplanted.<br /> · Unclear Experimental Conditions in Figure S3B: The images in Figure S3B lack crucial details about the experimental conditions. It is not specified whether the activation of KRAS was targeted to specific cells or involved whole-body exposure. This information is essential for interpreting the scope and implications of the results accurately.<br /> · Contrasting Data in Figure S3C compared to literatures: The graph in Figure S3C indicates that KRAS or KRAS + DEX induction did not result in any form of hyperplastic growth. This observation starkly contrasts with previous literature where oncogenic KRAS expression in zebrafish led to significant hyper-proliferation and abnormal growth, as evidenced by studies such as those published in and Neoplasia (2018), DOI: 10.1016/j.neo.2018.10.002; Molecular Cancer (2015), DOI: 10.1186/s12943-015-0288-2; Disease Models & Mechanisms (2014) DOI: 10.1242/dmm.007831. The lack of expected hyperplasia raises questions about the experimental setup or the specific conditions under which KRAS was expressed. The authors should provide detailed descriptions of the conditions under which the experiments were conducted in Figure S3B and clarifying the reasons for the discrepancies observed in Figure S3C are crucial. The authors should discuss potential reasons for the deviation from previous reports.<br /> Further comments:<br /> Throughout the study, KRAS-activated cell expansion and metastasis are two key phenotypes discussed that Ventx is promoting. However, the authors did not perform any experiments to directly show that KRAS+ cells proliferate only in Ventx-activated conditions. The authors also did not show any morphological features or time-lapse videos demonstrating that KRAS+ cells are motile, even though zebrafish is an excellent model for in vivo live imaging. This seems to be a missed opportunity for providing convincing evidence to support the authors' conclusions.<br /> There were minimal experimental details provided for the qPCR data presented in the supplementary figures S5 and S6, therefore, it is hard to evaluate results obtained.

Reviewer #2 (Public review):

Summary:

Lai and collaborators use a previously published RNAseq dataset derived from an experimental evolution set up to compare the pleiotropic properties of genes which expression evolved in response to fluctuating temperature for over 100 generations. The authors correlate gene pleiotropy with the degree of parallelisms in the experimental evolution set up to ask: are genes that evolved in multiple replicates more or less pleiotropic?

They find that, maybe counter to expectation, highly pleiotropic genes show more replicated evolution. And such effect seems to be driven by direct effects (which the authors can only speculate on) and indirect effect through low variance in pleiotropic genes (which the authors indirectly link to genetic variation underlying gene expression variance).

Weaknesses:

The results offer new insights into the evolution of gene expression and into the parameters that constrain such evolution, i.e., pleiotropy. Although the conclusions are supported by the data, I find the interpretation of the results a little bit complicated.

Major comment:

The major point I ask the authors to address is whether the connection between polygenic adaptation and parallelism can indeed be used to interpret gene expression parallelism. If the answer is not, please rephrase the introduction and discussion, if the answer is yes, please make it explicit in the text why it is so.

The authors argument: parallelism in gene expression is the same as parallelism in SNP allele frequency (AFC) (see L389-383 here they don't mention that this explanation is derived from SNP parallelism and not trait parallelism, and see Fig1 b). In previous publications the authors have explained the low level of AFC parallelism using a polygenic argument. Polygenic traits can reach a new trait optimum via multiple SNPs and therefore although the trait is parallel across replicates, the SNPs are not necessarily so.

In the current paper, they seem to be exchanging SNP AFC by gene expression, and to me, those are two levels that cannot be interchanged. Gene expression is a trait, not a SNP, and therefore the fact that a gene expression doesn't replicate cannot be explained by polygenic basis, because again the trait is gene expression itself. And, actually the results of the simulations show that high polygenicity = less trait parallelism (Fig4).

Now, if the authors focus on high parallel genes (present in e.g. 7 or more replicates) and they show that the eQTLs for those genes are many (highly polygenic) and the AFC of those eQTL are not parallel, then I would agree with the interpretation. But, given that here they just assess gene expression and not eQTL AFC, I do not think they can use the 'highly polygenic = low parallelism' explanation.

The interpretation of the results to me, should be limited to: genes with low variance and high pleiotropy tend to be more parallel, and the explanation might be synergistic pleiotropy.

Comments on revisions: The authors didn't really address any of the comments made by any of the reviewers - basically nothing was changed in the main text. Therefore, I leave my original review unchanged.

Reviewer #2 (Public review):

Summary:

The present manuscript addresses a longstanding challenge in neuroscience: how the brain assigns credit for delayed outcomes, especially in real-world learning scenarios where decisions and outcomes are separated by time. The authors focus on the lateral orbitofrontal cortex and hippocampus, key regions involved in contingent learning. By integrating fMRI data and behavioral tasks, the authors examined how neural circuits maintain a causal link between past decisions and delayed outcomes. Their findings offer insights into mechanisms that could have critical implications for understanding human decision-making.

Strengths:

- The experimental designs were extremely well thought-out. The authors successfully coupled behavioral data and neural measures (through fMRI) to explore the neural mechanisms of contingent learning. This integration adds robustness to the findings and strengthens their relevance.<br /> - The emphasis on the interaction between the lateral orbitofrontal cortex (lOFC) and hippocampus (HC) in this study is very well-targeted. The reported findings regarding their dynamic interactions provide valuable insights into contingent learning in humans.<br /> - The use of advanced modeling framework and analytical techniques allowed the authors to uncover new mechanistic insights regarding a complex case of decision-making process. The methods developed will also benefit analyses of future neuroimaging data on a range of decision-making tasks as well.

Weaknesses:

- Given the limited temporal resolution of fMRI and that the measured signal is an indirect measure of neural activity, it is unclear the extent to which the reported causality reflects the true relationship/interactions between neurons in different regions. That said, I believe this concern is minimized by a series of well-thought-out and robust analyses which consistently point to compelling results.

Comments on revisions:

Thank you for your thorough point-by-point responses to my comments and questions. After carefully reviewing the responses and additional analyses/results provided, I do not have further comments. Importantly, I believe the authors have done a great job addressing inevitable limitations that are inherent to fMRI signals. The thoughtful analyses used in the study combined with the timely questions the manuscript is able to address make the study an important contribution to the field.

Reviewer #2 (Public review):

Summary:

The authors aimed to characterize the cellular phenotype and spatial relationship of cell types infiltrating the islets of Langerhans in human T1D using CODEX, a multiplexed examination of cellular markers

Strengths:

Major strengths of this study are the use of pancreas tissue from well-characterized tissue donors, the use of CODEX, a state-of-the-art detection technique of extensive characterization and spatial characterization of cell types and cellular interactions. The authors have achieved their aims with the identification of the heterogeneity of the CD8+ T cell populations in insulitis, the identification of a vasculature phenotype and other markers that may mark insulitis-prone islets, and characterization of tertiary lymphoid structures in the acinar tissue of the pancreas. These findings are very likely to have a positive impact on our understanding (conceptual advance) of the cellular factors involved in T1D pathogenesis which the field requires to make progress in therapeutics.

Weaknesses:

A major limitation of the study is the cohort size, which the authors directly state. However, this study provides avenues of inquiry for researchers to gain further understanding of the pathological process in human T1D.

Comments on revisions:

The authors have responded well to the 3 critiques. They have addressed my specific comments in their revised text.<br /> I have no further comments.

Reviewer #2 (Public review):

This revision has further improved the clarity of the paper, better articulating assumptions of the model and data analysis. I particularly appreciate the authors' thorough response to eLife assessment. However, the authors did not provide point-by-point response to the specific comments I had from last round of review and didn't revise the manuscript accordingly, so my major concerns remain.

At conceptual level, my biggest concern with the model is the lack of constraint on V*(K), which makes the null neutral model too "liberal". On the one hand, the number of descendants of each gene copy must be non-negative; on the other hand, even homogenizing process within an individual is extremely strong, it cannot "spread" gene copies across individuals, so the maximum number of descendants of one gene copy cannot exceed the number of offspring that individual has times C. For these reasons, I believe there must be a theoretical upper bound of the value of V*(K), and the actual V*(K) is likely much smaller under realistic strength of the homogenizing process. When I asked about modeling of the underlying homogenizing process, I did not mean the authors need to include specific molecular process in the model; instead, I am asking the authors to provide some realistic scenarios that can give rise to very large V*(K) values. As a result of the very "liberal" neutral model, although I do agree that rejection of null provides stronger evidence for selection in human, it is unclear whether there is no evidence of selection in mouse. Please see below for my specific comments regarding the definition and assumptions of V*(K) (copied from last review).

Regarding the data analysis, although I understand the authors' methodology and rationale behind, I am not convinced that high sequence similarity between rDNA copies guarantees no biases in alignment and variant calling. Furthermore, given divergence between species, I am particularly concerned about the practice of aligning reads of different species to human and mus musculus reference sequences. A separate issue is the calculation of divergence level. Instead of using Fst>0.8 as the criterion of calling fixed sites, the authors could calculate the pairwise average divergence between a random copy from one species and a random copy from another species. Mathematically, this could be calculated as p1(1-p2)+p2(1-p1). The observation that the estimated substitution rates for rDNA with and without CpG sites are so close seems to be an indication of technical error. Please also see below for my specific questions about data analysis (copied from last round of review).

Specific comments from last round of review:

Questions regarding V*(K)<br /> (1) Another key parameter V*(K) was still not defined within the paper. In response 9, the authors explained that V*(K) refers to "the number of progeny to whom the gene copy of interest is transmitted (K) over a specific time interval". However, the meaning of "progeny" remains unclear. Are the authors referring to the descendent copies of a gene copy, or the offspring individuals (i.e., the living organisms)? For example, if a variant spreads horizontally through homogenizing processes and transmits vertically to multiple offspring individuals, the number of descent gene copies could differ substantially from the number of descendent individuals to whom a gene copy is transmitted to. This distinction needs to be clarified and clearly stated in the paper.

(2) The authors state that V*(K)>=1 for rDNA genes because of the homogenizing processes (lines 139-141) without providing justification. It is unclear, at least to me, whether homogenizing processes are expected increase or decrease the variance in "reproductive success" across gene copies. Moreover, the authors claim that V*(K) "can potentially reach values in the hundreds and may even exceed C, resulting in C*=C/V*(K)<1" (Response 7). This claim is unlikely to be true, as the minimum value of K is bounded by zero and E(K) is assumed to be 1. Even in the extreme case that 1% gene copies leave large numbers of descends while the others leave none, V*(K) would still be less than 100. Such extreme case seems highly improbable, given realistic rates of the homogenizing processes.

(3) Regardless of how the authors define V*(K), it is not immediately clear why Equation 1 (N*=NC/V*(K)) holds. Both sides of the equation have their independent meanings, so the authors need to provide a step-by-step derivation demonstrating that they are equal. Only by doing this will the implicit underlying assumptions become clearer. I also strongly recommend that the authors conduct forward-in-time simulations with fixed N, C, V*(K) (however they define it) and μ to confirm that the right side of Equation 1 actually predicts the N* as calculated from the polymorphism level using the equation in line 165.

Questions about Ne* for multi-copy system

(1) While Ne is clearly defined in the standard single-copy gene model as the reciprocal of genetic drift (i.e., the decay in heterozygosity), its meaning for multiple-copy genes is unclear. Based on the context, it appears that the authors define Ne as the parameter that fits the population polymorphism level (Hs) using the equation in line 165. This definition is reasonable, but it should be explicitly clarified in the text."

(2) Without providing justification, the authors assumed that a certain number N* exists for rRNA such that it fits both the polymorphism level (line 156) in recent timescales and divergence level in longer timescales (i.e., in the comparison between Tf and Td). However, if N, C or any other relevant parameters have varied substantially throughout evolution, N* is expected to vary with time, and the same value may not fit both polymorphism and divergence data simultaneously.

Questions about data analysis

(1) A significant issue with aligning reads to a single reference genome is reference bias, referring to the phenomenon that reads carrying the reference alleles tend to align more easily than those with one or more non-reference alleles, thus creating a bias in genotype calling or variant allele frequency quantification. As a result, there may be an underrepresentation of non-reference alleles in called variants or an underestimate of non-reference allele frequency, particularly in regions with high genetic diversity. Simply focusing on bi-allelic SNVs is insufficient to minimize reference bias. Given the fourfold increase in diversity within rDNA, the authors must either provide evidence that reference bias is not a significant concern or adopt graph-based reference genomes or more sophisticated alignment algorithms to address this issue.

(2) The potential for reference bias also renders the analysis of divergence sites unreliable, as aligning reads from one species (e.g. chimpanzee) to the reference of another species (e.g., human) is likely to introduce biases in variant calling between the two. One commonly adopted approach to address this imbalance is to align reads from both species to a third reference genome that is expected to be equidistantly related to both.

(3) Although it is somewhat reassuring that the estimated divergence rate of rDNA between human and macaque is comparable to that of the rest of the genome, there still remains concern of a under-estimation of divergence in rDNA regions due to reference bias issue. Note that while the "third genome" approach reduces imbalance between two genomes in comparison, it may still under-estimate overall divergence level due to under-calling of non-reference variants.<br /> (4) In response to my question about the similarity in rDNA substitution rates estimated with or without CpG sites, the authors suggest that this "may be due to strong homogenizing forces, which can rapidly fix or eliminate variants" (response17). However, this explanation is insufficient, because the observed substitution rate depends on the mutation rate multiplied by the fixation probability, and accelerated fixation or loss does not alter either. Unless the authors can provide more convincing explanation, technical errors in calling of fixed sites still remain a concern.

Minor points:

Line 157: The statement "where μ is the mutation rate of the entire gene" must be wrong, as the heterozygosity calculated with such μ would correspond to the chance of seeing two different haplotypes at gene level, which is incompatible with the empirical calculation specified in Equation 2. Instead, μ must represent the mutation rate per site averaged over the entire gene.

In response 22, the authors explained that the allele frequency spectrum shown in Fig 3 is folded, because the ancestral allele was not determined. However, this is inconsistent with x-axis Fig 3 ranging between 0 and 1. I suspect the x-axis represents the frequency of the alternative (i.e., non-reference) allele. If so, the reported correlation is inflated, as the reference allele is somewhat random, and a variant at joint ALT allele frequencies of (0.9, 0.9) is no different from a variant at (0.1, 0.1). The proper way of calculate this correlation is to first determine the minor allele frequency across individuals and then calculate the correlation between minor allele frequencies.

Similarly, in response 14, it is unclear what the x-axis represents. Is it the ALT allele frequency or derived allele frequency? If the former, why are only variants with AF>0.8 defined as fixed variants, while those with AF<0.2 excluded? If it is the latter, please describe how ancestral state is determined.

Reviewer #2 (Public review):

Summary:

This theoretical paper examines genetic drift in scenarios deviating from the standard Wright-Fisher model. The authors discuss Haldane's branching process model, highlighting that the variance in reproductive success equates to genetic drift. By integrating the Wright-Fisher model with the Haldane model, the authors derive theoretical results that resolve paradoxes related to effective population size.

Strengths:

The most significant and compelling result from this paper is perhaps that the probability of fixing a new beneficial mutation is 2s/V(K). This is an intriguing and potentially generalizable discovery that could be applied to many different study systems.

The authors also made a lot of effort to connect theory with various real-world examples, such as genetic diversity in sex chromosomes and reproductive variance across different species.

Comments on previous revisions:

The author has addressed some of the concerns in my review, and I think the revised manuscript is more clear. I like the discussion about the caveats of the WFH model.

I hope the authors could also discuss the conditions needed for V(K)/Ne to be a reasonable approximation. It is currently unclear how the framework should be adopted in general.

The idea about estimating male-female V(K) ratios from population genetic data is interesting. Unfortunately, the results fell short. The accuracy of their estimators (derived using approximation Ne/V(K) approximation, and certain choice of theta, and then theta estimated with Watterson's estimator) should be tested with simulated results before applying to real data. The reliability of their estimator and their results from real data are unclear.

Arguments made in this paper sometimes lack precision (perhaps the authors want to emphasize intuition, but it seems more confusing than otherwise). For example: The authors stated that "This independence from N seems intuitively obvious: when an advantageous mutation increases to say, 100 copies in determining a population (depending mainly on s), its fixation would be almost certain, regardless of N.". Assuming large Ne, and with approximation, one could assume the probability of loss is e^(-2sn), but the writing about "100 copies" and "almost certain" is very imprecise, in fact, a mutation with s=0.001 segregating at 100 copies in a large Ne population is most probably lost. Whereas in a small population, it will be fixed. Yet the following sentence states "regardless of N. This may be a most direct argument against equating genetic drift, certainly no less important than 1/ N . with N, or Ne (which is supposed to be a function of N's)." I find this new paragraph misleading.

Some of the statements/wordings in this paper still seem too strong to me.

Comments on revisions:

The authors toned down. I am a bit confused because I do not seem to find any point-to-point response to my review.

Reviewer #2 (Public review):

Summary:

The authors used a large panel of hepatocellular carcinoma patient-derived xenograft models to test the hypothesis that the developmental dependence of the liver on Jagged1-Notch2 signaling is retained in at least a subset of hepatocellular carcinomas. This led to the identification of two models that were extraordinarily sensitive to well-characterized, specific inhibitory antibodies against Jagged1 or Notch2. Based on additional analyses in these in vivo models, the authors provide compelling evidence that the response is due to the inhibition of human Notch2 and human Jagged1 on tumor cells and that this inhibition leads to a change in gene expression from a progenitor-like state to a hepatocyte-like state accompanied by cell cycle arrest. This change in cell state is associated with up-regulation of HNF4a and CEBPB and increased accessibility of predicted HNF4a and CEBPB genomic binding sites, accompanied by loss of accessibility to sequences predicted to bind TFs linked to multipotent liver progenitors. The authors put forth a plausible model in which inhibition of Notch2 downregulates transcriptional repressors of the Hairy/Enhancer of Split family, leading to increased expression of CEBPB and changes in gene expression that drive hepatocyte differentiation.

Strengths:

The strengths of the paper include the breadth of the preclinical screen in PDX models (which may be of an unprecedented size as preclinical trials go), the high quality of the well-characterized antibodies used as therapeutics and as biological perturbagens, the quality of the data and data analysis, and the authors balanced discussion of the strengths and weaknesses of their findings.

Weaknesses:

The principal weakness is the inability to clearly demonstrate the "translatability" of the PDX findings to primary human hepatocellular carcinoma.

Additional Comments:

Hepatocellular carcinoma is increasing in frequency and is difficult to treat; cure is only possible through early diagnosis and surgery, often in the form of liver transplantation. It is also a common cancer, and so even if only 5% of tumors (a value based on the frequency of super-responders in this preclinical trial) fall into the Jagged1-Notch2 group defined by Seidel et al., the development of an effective therapy for this subgroup would be a very important advance. The chief limitation of their work is that it stops short of identifying primary human hepatocellular carcinomas that correspond to the super-responder PDX models. It can be hoped that their intriguing observations will spur work aimed at filling this gap

There are several other loose ends. An unusual feature of this model is that both Jagged 1 and Notch2 are expressed in the same cells, and even in the same individual cells. In developmental systems, the expression of ligands and receptors in the same cell generally produces receptor inhibition rather than activation, a phenomenon described as cis inhibition. Their super-responder tumor models appear to break this rule, and how and why this is so remains to be understood. A follow-up question is what explains the observed heterogeneity in tumor cells, both at the level of Notch2 activation and scRNAseq clustering, and whether these different cell states are static or interchangeable.

Another unanswered issue pertains to the nature of the tumor response to Notch signaling blockade, which appears to be mainly cell cycle arrest. There are a number of human tumors with cell autonomous Notch signaling due to gain of function Notch receptor mutations that also respond to Notch blockade with cell cycle arrest, such as T cell acute lymphoblastic leukemia (T-ALL). In general, clinical trials of pan-Notch inhibitors such as gamma-secretase inhibitors have been disappointing in such tumors, perhaps reflecting a limitation of treatments with significant toxicity that do not kill tumor cells directly. It could be argued that this limitation will be mitigated by the apparently excellent safety profile of Notch2 blocking antibody, which perhaps could be administered for a sustained period, akin to the use of tyrosine kinase inhibitors in chronic myeloid leukemia---but this remains to be determined.

A minor comment is reserved for the statement in the discussion that "In chronic myelomonocytic leukemia, which results from an inactivating mutation in the y-secretase complex component nicastrin, Notch signaling has a tumor suppressive function, that is mediated through direct repression of CEBPA and PU.1 by HES1 (Klinakis et al., 2011)". Thousands of cases of CMML and related myeloid tumors have been subjected to whole exome and even whole genome sequencing without the identification of Notch signaling pathway mutations. Thus, an important tumor suppressive role for Notch-mediated through HES1 in myeloid tumors is not proven.

Reviewer #2 (Public review):

Summary/Significance of the findings:

The authors have done a great job by extensively carrying out transcriptomic and epigenomic analyses in the primary human/mouse monocytes/macrophages to investigate TNF-PGE2 (TP) crosstalk and their regulation by IFN-γ in the Rheumatoid arthritis (RA) synovial macrophages. They proposed that TP induces inflammatory genes via a novel regulatory axis whereby IFN-γ and PGE2 oppose each other to determine the balance between two distinct TNF-induced inflammatory gene expression programs relevant to RA and ICI-arthritis.

Strengths:

The authors have done a great job on RT-qPCR analysis of gene expression in primary human monocytes stimulated with TNF and showing the selective agonists of PGE2 receptors EP2 and EP4 22 that signal predominantly via cAMP. They have beautifully shown IFN-γ opposes the effects of PGE2 on TNF-induced gene expression. They found that TP signature genes are activated by cooperation of PGE2-induced AP-1, CEBP, and NR4A with TNF-induced NF-κB activity. On the other hand, they found that IFN-γ suppressed induction of AP-1, CEBP, and NR4A activity to ablate induction of IL-1, Notch, and neutrophil chemokine genes but promoted expression of distinct inflammatory genes such as TNF and T cell chemokines like CXCL10 indicating that TP induces inflammatory genes via IFN-γ in the RA and ICI-arthritis.

Weaknesses:

(1) The authors carried out most of the assays in the monocytes/macrophages. How do APC-cells like Dendritic cells behave with respect to this TP treatment similar dosing?

(2) The authors studied 3h and 24h post-treatment transcriptomic and epigenomic. What happens to TP induce inflammatory genes post-treatment 12h, 36h, 48h, 72h. It is critical to see the upregulated/downregulated genes get normalised or stay the same throughout the innate immune response.

(3) The authors showed IL1-axis in response to the TP-treatment. Do other cytokine axes get modulated? If yes, then how do they cooperate to reduce/induce inflammatory responses along this proposed axis?

Overall, the data looks good and acceptable but I need to confirm the above-mentioned criticisms.

Reviewer #3 (Public review):

Summary:

Using a mouse model of Staphylococcus aureus gut colonization Lejeune et al demonstrate that the microbiome, immune system, and sex are important contributing factors for whether this important human pathogen persists in the gut. The work begins by describing differential gut clearance of S. aureus in female B6 mice bred at NYU compared to those from Jackson Laboratories (JAX). NYU female mice cleared S. aureus from the gut but NYU male mice and mice of both sexes from JAX exhibited persistent gut colonization. Further experimentation demonstrated that differences between staphylococcal gut clearance in NYU and JAX female mice were attributed to the microbiome. However, NYU male and female mice harbor similar microbiomes, supporting the conclusion that the microbiome cannot account for the observed sex-dependent clearance of S. aureus gut colonization. To identify factors responsible for female clearance of S. aureus, the authors performed RNAseq on intestinal epithelia cells and cells enriched within the lamina propria. This analysis revealed sex-dependent transcriptional responses in both tissues. Genes associated with immune cell function and migration were distinctly expressed between the sexes. To determine which immune cell types contribute to S. aureus clearance Lejeune et al employed genetic and antibody-mediated immune cell depletion. This experiment demonstrated that CD4+ IL17+ cells and neutrophils promote elimination of S. aureus from the gut. Subsequent experiments, including the use of the 'four core genotype model' were conducted to discern between the roles of sex chromosomes and sex hormones. This work demonstrated that sex-chromosome linked genes are not responsible for clearance, increasing the likelihood that hormones play a dominant role in controlling S. aureus gut colonization.

Strengths:

A strength of the work is the rigorous experimental design. Appropriate controls were executed and, in most cases, multiple approaches were conducted to strengthen the authors' conclusions. The conclusions are supported by the data.<br /> The following suggestions are offered to improve an already strong piece of scholarship.

Weaknesses:

The correlation between female sex hormones and elimination of S. aureus from the gut could be further validated by quantifying sex hormones produced in the four core genotype mice in response to colonization. Additionally, and this may not be feasible, but according to the proposed model administering female sex hormones to male mice should decrease colonization. Finally, knowing whether the quantity of IL-17a CD4+ cells change in the OVX mice has the potential to discern whether the abundance/migration of the cells or their activation is promoted by female sex hormones.

In the Discussion the authors highlight previous work establishing a link between immune cells and sex hormone receptors, but whether the estrogen (and progesterone) receptor is differentially expressed in response to S. aureus colonization could be assessed in the RNAseq dataset. Differential expression of known X and Y chromosome linked genes were discussed but specific sex hormones or sex hormone receptors, like the estrogen receptor were not. This potential result could be highlighted.

Comments on revisions:

The authors have adequately addressed my comments. I have only one minor adjustment: the Esr1 mice should be included the Materials and Methods.

Reviewer #2 (Public review):

Summary:

The study by Cao et al. highlights an interesting and important aspect of heat- and thermal biology: the effect of repetitive, long-term heat exposure and its impact on brain function.<br /> Even though peripheral, sensory temperature sensors and afferent neuronal pathways conveying acute temperature information to the CNS have been well established, it is largely unknown how persistent, long-term temperature stimuli interact with and shape CNS function, and how these thermally-induced CNS alterations modulate efferent pathways to change physiology and behavior. This study is therefore not only novel but, given global warming, also timely.

The authors provide compelling evidence that neurons of the paraventricular thalamus change plastically over three weeks of episodic heat stimulation and they convincingly show that these changes affect behavioral outputs such as social interactions, and anxiety related behaviors.

Strengths:

• It is impressive that the assessed behaviors can be (i) recruited by optogenetic fiber activation and (ii) inhibited by optogenetic fiber inhibition when mice are exposed to heat. Technically, when/how long is the fiber inhibition performed? It says in the text "3 min on and 3 min off". Is this only during the 20 minutes heat stimulation or also at other times?<br /> • It is interesting that the frequency of activity in pPVT neurons, as assessed by fiber photometry, stays increased after long-term heat exposure (day 22) when mice are back at normal room temperature. This appears similar to a previous study that found long-term heat exposure to transform POA neurons plastically to become tonically active (https://www.biorxiv.org/content/10.1101/2024.08.06.606929v1 ). Interestingly, the POA neurons that become tonically active by persistent heat exposure described in the above study are largely excitatory and thus these could drive the activity of the pPVT neurons analyzed in this study.<br /> How can it be reconciled that the majority of the inputs from the POA are found to be largely inhibitory (Fig. 2H)? Is it possible that this result stems from the fact that non-selective POA-to-pPVT projections are labelled by the approach used in this study and not only those pathways activated by heat? These points would be nice to discuss.<br /> • It is very interesting that no LTP can be induced after chronic heat exposure (Fig. K-M); the authors suggest that "the pathway in these mice were already saturated" (line 375). Could this hypothesis be tested in slices by employing a protocol to extinguish pre-existing (chronic heat exposure-induced) LTP? This would provide further strength to the findings/suggestion that an important synaptic plasticity mechanism is at play that conveys behavioral changes upon chronic heat stimulation.<br /> • It is interesting that long-term heat does not increase parameters associated with depression (Fig. 1N-Q), how is it with acute heat stress, are those depression parameters increased acutely? It would be interesting to learn if "depression indicators" increase acutely but then adapt (as a consequence of heat acclimation) or if they are not changed at all and are also low during acute heat exposure.

Reviewer #2 (Public review):

Gaertner and colleagues present a study examining the transcriptomic diversity and spatial location of dopaminergic neurons from mice and examine the changes in gene expression resulting from knock in of the Parkinson's LRRK G2019S risk variant. Overall, I found the manuscript presented their study very clearly, well written with very clear figures for the most part. I am not an expert on mouse neuroanatomy but found their classification reasonably well justified and spatial orientation of dopaminergic neurons within the mouse brain informative and clear. While trends were clear and well presented, the apparent spatial heterogeneity suggests that knowledge of the functional connections and roles of these neurons will be required to better interpret the results presented but nonetheless their findings exposed significant detail that is required for further understanding.

The study of the transcriptional effects of the LRRK2 KI was also informative and clearly framed in terms of a focused analyses on the effects of the KI only on dopaminergic neurons.

I thank the authors for addressing my previous concerns and comments, and feel they have done so well. I agree that as GSEA only includes ranked genes from the specific study, the gene set is already limited to the relevant background.

Reviewer #2 (Public review):

Summary:

The authors combined inhibitory neurostimulation (continuous theta-burst stimulation, cTBS) with subsequent MRI measurements to investigate the impact of inhibition of the left anterior temporal lobe (ATL) on task-related activity and performance during a semantic task and link stimulation-induced changes to the neurochemical level by including MR spectroscopy (MRS). cTBS effects in the ATL were compared with a control site in the vertex. The authors found that relative to stimulation of the vertex, cTBS significantly increased the local GABA concentration in the ATL. cTBS also decreased task-related semantic activity in the ATL and potentially delayed semantic task performance by hindering a practice effect from pre to post. Finally, pooled data with their previous MRS study suggest an inverted u-shape between GABA concentration and behavioral performance. These results help to better understand the neuromodulatory effects of non-invasive brain stimulation on task performance.

Strengths:

Multimodal assessment of neurostimulation effects on the behavioral, neurochemical, and neural levels. In particular, the link between GABA modulation and behavior is timely and potentially interesting.

Weaknesses:

The analyses are not sound. Some of the effects are very weak and not all conclusions are supported by the data since some of the comparisons are not justified. There is some redundancy with a previous paper by the same authors, so the novelty and contribution to the field are overall limited. A network approach might help here.

Reviewer #2 (Public review):

Summary:

Fei, Lu, Shi, et al. present a thorough evaluation of the immune cell landscape in pre-eclamptic human placentas by single-cell multi-omics methodologies compared to normal control placentas. Based on their findings of elevated frequencies of inflammatory macrophages and memory-like Th17 cells, they employ adoptive cell transfer mouse models to interrogate the coordination and function of these cell types in pre-eclampsia immunopathology. They demonstrate the putative role of the IGF1-IGF1R axis as the key pathway by which inflammatory macrophages in the placenta skew CD4+ T cells towards an inflammatory IL-17A-secreting phenotype that may drive tissue damage, vascular dysfunction, and elevated blood pressure in pre-eclampsia, leaving researchers with potential translational opportunities to pursue this pathway in this indication.

They present a major advance to the field in their profiling of human placental immune cells from pre-eclampsia patients where most extant single-cell atlases focus on term versus preterm placenta, or largely examine trophoblast biology with a much rarer subset of immune cells. While the authors present vast amounts of data at both the protein and RNA transcript level, we, the reviewers, feel this manuscript is still in need of much more clarity in its main messaging, and more discretion in including only key data that supports this main message most effectively.

Strengths:

(1) This study combines human and mouse analyses and allows for some amount of mechanistic insight into the role of pro-inflammatory and anti-inflammatory macrophages in the pathogenesis of pre-eclampsia (PE), and their interaction with Th17 cells.

(2) Importantly, they do this using matched cohorts across normal pregnancy and common PE comorbidities like gestation diabetes (GDM).

(3) The authors have developed clear translational opportunities from these "big data" studies by moving to pursue potential IGF1-based interventions.

[Editors' note: the authors have provided responses to the previously identified weaknesses]

Reviewer #2 (Public review):

Summary:

In this paper, the authors test whether controllability beliefs and associated actions/resource allocation are modulated by things like time, effort, and monetary costs (what they call "elastic" as opposed to "inelastic" controllability). Using a novel behavioral task and computational modeling, they find that participants do indeed modulate their resources depending on whether they are in an "elastic," "inelastic," or "low controllability" environment. The authors also find evidence that psychopathology is related to specific biases in controllability.

Strengths:

This research investigates how people might value different factors that contribute to controllability in a creative and thorough way. The authors use computational modeling to try to dissociate "elasticity" from "overall controllability," and find some differential associations with psychopathology. This was a convincing justification for using modeling above and beyond behavioral output and yielded interesting results. Interestingly, the authors conclude that these findings suggest that biased elasticity could distort agency beliefs via maladaptive resource allocation. Overall, this paper reveals some important findings about how people consider components of controllability.

Weaknesses:

The primary weakness of this research is that it is not entirely clear what is meant by "elastic" and "inelastic" and how these constructs differ from existing considerations of various factors/calculations that contribute to perceptions of and decisions about controllability. I think this weakness is primarily an issue of framing, where it's not clear whether elasticity is, in fact, theoretically dissociable from controllability. Instead, it seems that the elements that make up "elasticity" are simply some of the many calculations that contribute to controllability. In other words, an "elastic" environment is inherently more controllable than an "inelastic" one, since both environments might have the same level of predictability, but in an "elastic" environment, one can also partake in additional actions to have additional control over achieving the goal (i.e., expend effort, money, time).

Reviewer #2 (Public review):

Summary:

Sugimoto et al. explore the relationship between glucose dynamics - specifically value, variability, and autocorrelation - and coronary plaque vulnerability in patients with varying glucose tolerance levels. The study identifies three independent predictive factors for %NC and emphasizes the use of continuous glucose monitoring (CGM)-derived indices for coronary artery disease (CAD) risk assessment. By employing robust statistical methods and validating findings across datasets from Japan, America, and China, the authors highlight the limitations of conventional markers while proposing CGM as a novel approach for risk prediction. The study has the potential to reshape CAD risk assessment by emphasizing CGM-derived indices, aligning well with personalized medicine trends.

Strengths:

(1) The introduction of autocorrelation as a predictive factor for plaque vulnerability adds a novel dimension to glucose dynamic analysis.

(2) Inclusion of datasets from diverse regions enhances generalizability.

(3) The use of a well-characterized cohort with controlled cholesterol and blood pressure levels strengthens the findings.

(4) The focus on CGM-derived indices aligns with personalized medicine trends, showcasing the potential for CAD risk stratification.

Weaknesses:

(1) The link between autocorrelation and plaque vulnerability remains speculative without a proposed biological explanation.

(2) The relatively small sample size (n=270) limits statistical power, especially when stratified by glucose tolerance levels.

(3) Strict participant selection criteria may reduce applicability to broader populations.

(4) CGM-derived indices like AC_Var and ADRR may be too complex for routine clinical use without simplified models or guidelines.

(5) The study does not compare CGM-derived indices to existing advanced CAD risk models, limiting the ability to assess their true predictive superiority.

(6) Varying CGM sampling intervals (5-minute vs. 15-minute) were not thoroughly analyzed for impact on results.

Reviewer #2 (Public review):

The authors have demonstrated the use of adenine base editors delivered via adeno-associated viruses to introduce edits in the mitochondrial genome. The manuscript describes the methodology well, and the conclusions are aptly supported by the results. It highlights the potential of these base editors to model mtDNA variations in somatic tissues in animal models.

However, there are a few comments that need to be addressed:

(1) Limitations of the small sample size need to be explained clearly for the results described.

(2) It will be beneficial for the readers if some light is shed on the possible reasons why the efficiencies of adenine base editing are lower than those reported for published cytosine base editors to introduce edits in the mitochondrial DNA.

(3) The conclusion should more explicitly address the limitations and future directions on low editing efficiency and what can be possible optimization steps.

(4) In Figure 1, A-to-G editing for the genes Mt-Cytb, Mt-CoII, and Mt-Atp6 appears to be strand-specific for the different architectures of adenine base editors. Do authors have a possible hypothesis if one of the strands is more favorable to editing depending on where the TadA8 binds or is it random?

Reviewer #2 (Public review):

Summary:

The study expands previous knowledge on the dual ribosome system in zebrafish by demonstrating the expression of maternal ribosomes in the primordial germ cells as well as the formation of hybrid ribosomes combining subunits of maternal and somatic ribosomes. Although the distinction between the two types is clear at the rRNA level, this is not paralleled at the protein level. An attempt to associate the expression of germ-line-specific transcripts to maternal ribosomes remains inconclusive. Thus, evidence for the functional specialisation of ribosomes in this system is still lacking.

Strengths:

The experiments are well-conducted and the main conclusions are well-supported.

Weaknesses:

The attempt to take advantage of the system to provide an example of functional ribosome specialisation is justified and the expression of maternal-type ribosomes in the germ line may still be key to understanding the expression of classes of mRNA. However, an alternative possibility related to genome evolution and sex determination is equally relevant.

Assessment following the structure of the manuscript:

Shah et al.: "A dual ribosomal system in zebrafish soma and germline"

The zebrafish dual ribosome system is attractive because it offers a favourable setting to look for ribosome specialization and my impression is that this is exactly what the authors set out to do rather than to try to understand why zebrafish have this unusual setup. If this is correct, the title and the abstract should better reflect the authors' aim and main results. The title suggests to the non-specialist that the dual ribosome system is a novel find which obviously is not the case.

I was a bit confused when reading the introduction. In the first paragraph, it was unclear to me if the degradation of maternal ribosomes is an active process different from normal turnover. I also found the third paragraph slightly out of tune with the discussion section. The dual ribosome setting at the level of ribosomal RNA genes represents an extreme case of sequence heterogeneity and appears to be sporadic in nature in that it only is reported from Plasmodium and zebrafish. The Xenopus example is 5S rRNA (as also mentioned in the discussion section), and the Drosophila example is protein composition, only. If a broader view of ribosome types is intended, there will be more examples, e.g. Trypanosomes that express different stage-dependent ribosomes at the level of rRNA modifications. The occurrence of dual ribosomes in fish should be placed in context with insight from other fish genomes, e.g. Medaka, which has only one type of ribosomes. Also, the duality in zebrafish is not restricted to ribosomes, but also comprises two types of spliceosomes. These observations suggest that the phenomenon should be investigated in the context of genome evolution. This is appropriately brought up in the discussion section, but I believe it would serve the reading of the manuscript if this was made clear from the beginning. With respect to the structural aspects, I am puzzled why one of the few other papers studying this system, Ramachandran et al. RNA 2020 (PMID: 32912962) is not referenced. This paper is focused on ribose methylation of the two types of ribosomal RNA and should be relevant to several aspects of the present study.

The manuscript reports three novel and important findings. First, the maternal-type ribosomes are expressed in PGCs, where they furthermore are shown to translate germ line-specific transcripts, and in the male germ line. Regardless, the authors wisely decide to maintain the classical terminology of maternal and somatic ribosomes. Second, both types of ribosomes are polysome-associated and thus translationally active at 24 hpf when they are found in equal amounts. An elaborate experiment shows that hybrid ribosomes are formed at this stage. Finally, a RIP experiment fails to show selectivity in ribosomal recruitment of a germ line-specific mRNA based on the nanos3 3´-UTR. There are several other results, but these are mainly confirmatory or negative, albeit of good quality and important to communicate.

The part of the study that describes differences in protein composition is a bit difficult to follow, partly because of the complexity of the results, and partly because of the disappointment that no parallel changes in proteins to the clear differences in rRNA were observed. Except for the discussion of eS8 in relation to subunit bridging, it is purely descriptive. There is quite a literature on paralog expression (e.g. in yeast and humans) and perhaps it would be possible to relate to the literature in a way that could provide more meaning to the observations. From the M&M section, it appears that the proteomics data were already published in the Leesch and Lorenzo-Orts et al. paper (Nature 2023). They are here found in Table S1 which is presented in a minimal fashion, from which it is time-consuming to extract meaningful information, e.g. on how stringently the ribosomes were prepared.

The hybrid-ribosome observation is convincing, but additional information on the choice of cycloheximide concentration would be helpful to rule out other interpretations.

The experiment on translation of primordial germ cell-specific transcripts by maternal ribosomes is a key experiment. Unfortunately, the experiment failed to show selectivity compared to somatic ribosomes, and in my reading, the promise in the abstract of "preferential association" is not quite justified. More importantly, this experiment is not exhaustive, and a more elaborate discussion on the limitations of the experiment and other approaches would be helpful.

The discussion section is interesting. Importantly, the authors make the non-specialist aware of the peculiarities of laboratory strains of zebrafish with respect to the lack of sex chromosomes and a possible connection between the rDNA locus and sex determination. This information is critical to include in a journal that has a broad readership. I was unable to follow the argument about the 3´half of 5.8S "to play a role" in ribosome degradation based on Locati et al., 2018 (which is missing from the reference list) and "serve as a target for degradation of maternal ribosomes". Kinetic effects on the degradation pattern of rRNA are frequently observed and difficult to interpret.

Reviewer #2 (Public review):

Summary:

The analyses of long-time malaria series to investigate the complex relationship between malaria incidence and climate is hampered by the non-stationarity introduced by both changing control interventions and irregular climate events such as the el nino Southern Oscillation (ENSO).

Strengths:

By applying wavelets the authors were able to investigate the effect of the major climate factors such as rainfall, air and land temperature, and sea surface temperature (as a measure for ENSO) while at the same time taking into account changing bednet coverage. The wavelet approach is both flexible and powerful and was able to demonstrate well that shorter term. seasonal fluctuation in malaria incidence in Western Kenya is driven by rainfall patterns, while providing some evidence for temperature and SST may predict fluctuations at longer timescales.

Weaknesses:

While flexible and able to deal with non-stationarity, the wavelet approach does not really allow investigation of multiple factors at the same time but is limited to uni- and bivariate analyses. This limits the interpretability of the effect of complex climate patterns while also 'adjusting' for the changing control environment. There is also some concern that the choice of the wavelet and transforms used for different analyses (Morelet, Coiflet, maximal overlap discreet transform) may affect the results. The reasons for choosing these particular wavelets and transforms are not always evident.

The attempt to investigate the effect of longer terms / irregular period climate events is laudable. However, why were the analyses restricted to only ENSO (measured as SST)? Other climate factors such as e.g. the Indian Ocean Dipole (i.e. the difference in SST between the western and eastern Indian Ocean) are also known to affect climate and rainfall patterns in Eastern Africa.

Nevertheless, this work is a compelling demonstration of the utility of wavelets for the analyses of (non-stationary) epidemiological time series data.

Reviewer #2 (Public review):

Summary:

Using the theory of efficient coding, the authors study how neural gains may be adjusted to optimize coding by noisy neural populations while minimizing metabolic costs. The manuscript first presents mathematical results for the general case where the computational goals of the neural population are not specified (the computation is implicit in the assumed tuning curves) and then develops the theory for a specific probabilistic coding scheme. The general theory provides an explanation for firing rate homeostasis at the level of neural clusters with firing rate heterogeneity within clusters, and the specific application further captures stimulus-specific and neuron-specific adaptation in the visual cortex.

The mathematical derivations, simulations, and application to visual cortex data are solid as far as I can tell.

In the current format, the significance is difficult to assess fully: the manuscript is a bit sprawling, in the first half the general theory is lengthy and technical, and then in the second half a few phenomena are addressed without a clear relation between them (rate homeostasis, rate heterogeneity, synaptic homeostasis, V1 adaptation, divisive normalization), requiring several ad-hoc choices and assumptions.

Strengths:

The problem of efficient coding is a long-standing and important one. This manuscript contributes to that field by proposing a theory of efficient coding through gain adjustments, independent of the computational goals of the system. The main result is a normative explanation for firing rate homeostasis at the level of neural clusters (groups of neurons that perform a similar computation) with firing rate heterogeneity within each cluster. Both phenomena are widely observed, and reconciling them under one theory is important.

The mathematical derivations are thorough as far as I can tell. Although the model of neural activity is artificial, the authors make sure to include many aspects of cortical physiology, while also keeping the models quite general.

Section 2.5 derives the conditions in which homeostasis would be near-optimal in the cortex, which appear to be consistent with many empirical observations in V1. This indicates that homeostasis in V1 might be indeed close to the optimal solution to code efficiently in the face of noise.

The application to the data of Benucci et al 2013 is the first to offer a normative explanation of stimulus-specific and neuron-specific adaptation in V1.

Weaknesses:

The novelty and significance of the work are not presented clearly. The relation to other theoretical work, particularly Ganguli and Simoncelli and other efficient coding theories, is explained in the Discussion but perhaps would be better placed in the Introduction, to motivate some of the many choices of the mathematical models used here.

The manuscript is very hard to read as is, it almost feels like this could be two different papers. The first half seems like a standalone document, detailing the general theory with interesting results on homeostasis and optimal coding. The second half, from Section 2.7 on, presents a series of specific applications that appear somewhat disconnected, are not very clearly motivated nor pursued in-depth, and require ad-hoc assumptions.

For instance, it is unclear if the main significant finding is the role of homeostasis in the general theory or the demonstration that homeostatic DDC with Bayes Ratio coding captures V1 adaptation phenomena. It would be helpful to clarify if this is being proposed as a new/better computational model of V1 compared to other existing models.

Early on in the manuscript (Section 2.1), the theory is presented as general in terms of the stimulus dimensionality and brain area, but then it is only demonstrated for orientation coding in V1.

The manuscript relies on a specific response noise model, with arbitrary tuning curves. Using a population model with arbitrary tuning curves and noise covariance matrix, as the basis for a study of coding optimality, is problematic because not all combinations of tuning curves and covariances are achievable by neural circuits (e.g. https://pubmed.ncbi.nlm.nih.gov/27145916/ )

The paper Benucci et al 2013 shows that homeostasis holds for some stimulus distributions, but not others i.e. when the 'adapter' is present too often. This manuscript, like the Benucci paper, discards those datasets. But from a theoretical standpoint, it seems important to consider why that would be the case, and if it can be predicted by the theory proposed here.

Reviewer #2 (Public review):

The metastasis poses a significant challenge in cancer treatment. During the transition from non-invasive cells to invasive metastasis cells, cancer cells usually experience mechanical stress due to a crowded cellular environment. The molecular mechanisms underlying mechanical signaling during this transition remain largely elusive. In this work, the authors utilize an in vitro cell culture system and advanced imaging techniques to investigate how non-invasive and invasive cells respond to cell crowding, respectively.

The results clearly show that pre-malignant cells exhibit a more pronounced reduction in cell volume and are more prone to spreading compared to non-invasive cells. Furthermore, the study identifies that TRPV4, a calcium channel, relocates to the plasma membrane both in vitro and in vivo (patient's samples). Activation and inhibition of TRPV4 channel can modulate the cell volume and cell mobility. These results unveil a novel mechanism of mechanical sensing in cancer cells, potentially offering new avenues for therapeutic intervention targeting cancer metastasis by modulating TRPV4 activity. This is a very comprehensive study, and the data presented in the paper are clear and convincing. The study represents a very important advance in our understanding of the mechanical biology of cancer.

Reviewer #3 (Public review):

Summary:

This is an important paper that investigates the relationship between proteolytic stability of an antibiotic target enzyme and the evolution of antibiotic resistance via increased gene copy number. The target of the antibiotic trimethoprim is dihydrofolate reductase (DHFR). In Escherichia coli, DHFR is encoded by folA and the major proteolysis housekeeping protease is Lon (lon). In this manuscript, the authors report the result of the experimental evolution of a lon mutant strain of E. coli in response to sub-inhibitory concentrations of the antibiotic trimethoprim then investigate the relationship between proteolytic stability of DHFR mutants and the evolution of folA gene duplication. After 25 generations of serial passaging in a fixed concentration of trimethoprim, the authors found that folA duplication events were more common during evolution of the lon strain, than the wt strain. However, with continued passaging, some folA duplications were replaced by a single copy of folA containing a trimethoprim resistance-conferring point mutation. Interestingly, evolution of the lon strain in the setting of increasing concentrations of trimethoprim resulted in evolved strains with different levels of DHFR expression. In particular, some strains maintained two copies of a mutant folA that encoded an unstable DHFR. In a lon+ background, this mutant folA did not express well and did not confer trimethoprim resistance. However, in the lon- background, it displayed higher expression and conferred high-level trimethoprim resistance. The authors concluded that maintenance of the gene duplication event (and the absence of Lon) compensated for the proteolytic instability of this mutant DHFR. In summary, they provide evidence that the proteolytic stability of an antibiotic target protein is an important determinant of the evolution of target gene copy number in the setting of antibiotic selection.

Strengths:

The major strength of this paper is identifying an example of antibiotic resistance evolution that illustrates the interplay between the proteolytic stability and copy number of an antibiotic target in the setting of antibiotic selection. The results are rigorous and convincingly support the conclusions. This paper will be of interest to any biologist that studies the evolution of resistance mechanisms or gene duplication.

Weaknesses:

The impact of this finding is somewhat limited given that it is a single example that occurred in a lon strain of E. coli. Although the specific mechanism is unlikely to occur naturally, this study represents an important and convincing proof of the principle that gene duplication can provide increased expression demand for an unstable resistance determinant in the setting of antibiotic selection.

Reviewer #2 (Public review):

Summary:

This is a timely and original study on the geometry of macroscopic (2.5 mm) brain representations of multiple cues and contexts in Pavlovian fear conditioning. The authors report that these representations differ between initial learning, and reversal learning, and remain stable during extinction.

Strengths:

The authors address an important question and use a rigorous experimental methodology.

Weaknesses:

The findings are limited (a) by the chosen spatial resolution (2.5 mm) which is far away from what modern fMRI can achieve, and (b) by the statistical analysis method. While transparently reported, their voxel-wise correction for multiple comparisons rests on a false discovery rate (i.e. 5% of the reported findings should be considered false positives) and there is no correction for the number of hypothesis tests (with an exception in some post hoc tests). Furthermore, there are some minor presentation issues that the authors could address to improve clarity.

Reviewer #2 (Public review):

Summary:

Alizadeh et al. investigate how varying cellular E/I (excitatory/inhibitory) composition impacts coding across cortical layers. They build on findings from a recent study (Huang et al., 2022) that demonstrated a decrease in the fraction of inhibitory neurons from L2/3 to L4. Using a network of excitatory and inhibitory leaky integrate-and-fire neurons, they systematically assess how these anatomical features influence the dimensionality of network activity and coding capacity. Their key finding is that increasing the proportion of inhibitory neurons enhances the dimensionality of activity and improves the encoding of time-varying stimuli.

Strengths:

The authors use a clear methodology and well-established model of network activity that allows them to relate network parameters to the coding properties. They systematically evaluate the impact of the key features of the inhibitory population. Thus, in addition to changing the fraction of inhibitory cells, they control for the inhibitory firing threshold of inhibitory neurons and connection strength between inhibitory and excitatory cells. Furthermore, they show their modeling results are aligned with the analysis of the spiking activity in L2/3 vs. L4 from the Allen Institute data.

Weaknesses:

One general shortcoming of this approach is that it focuses on a small preselected number of network features. For example, it is unclear to what extent the results would be affected by other aspects of the organization of cortical columns, such as subclasses of inhibitory cells (SOM, VIP, PV), specific differences in synapses, realistic population sizes, or even connectivity between layers. Similarly, the models of L2/3 and L4 are constrained based on a limited set of observations, and it has not been demonstrated whether the same findings hold true for V1 recordings analyzed by the authors.

The modeling relies on anatomical data from the barrel cortex, but the decoding comparison is based on V1 data. This raises questions about how anatomical differences between regions may influence the conclusions.

The coding capacity appears inversely correlated with the firing rate, which in this study is largely influenced by the properties of the inhibitory population. It would be important to confirm that the observed changes in coding capacity and participation ratio are not solely driven by firing rate changes.

Reviewer #2 (Public review):

Summary:

This study marks a noteworthy advance in the targeted design of AMPs, leveraging a pioneering deep learning framework to generate potent bifunctional peptides with specificity against both bacteria and viruses. The introduction of a GAN for generation and a GCN-based AMPredictor for MIC predictions is methodologically robust and a major stride in computational biology. Experimental validation in vitro and in animal models, notably with the highly potent P076 against a multidrug-resistant bacterium and P002's broad-spectrum viral inhibition, underpins the strength of their evidence. The findings are significant, showcasing not just promising therapeutic candidates, but also demonstrating a replicable means to rapidly develop new antimicrobials against the threat of drug-resistant pathogens.

Strengths:

The de novo AMP design framework combines a generative adversarial network (GAN) with an AMP predictor (AMPredictor), which is a novel approach in the field. The integration of deep generative models and graph-encoding activity regressors for discovering bifunctional AMPs is cutting-edge and addresses the need for new antimicrobial agents against drug-resistant pathogens. The in vitro and in vivo experimental validations of the AMPs provide strong evidence to support the computational predictions. The successful inhibition of a spectrum of pathogens in vitro and in animal models gives credibility to the claims. The discovery of effective peptides, such as P076, which demonstrates potent bactericidal activity against multidrug-resistant A. baumannii with low cytotoxicity, is noteworthy. This could have far-reaching implications for addressing antibiotic resistance. The demonstrated activity of the peptides against both bacterial and viral pathogens suggests that the discovered AMPs have a wide therapeutic potential and could be effective against a range of pathogens.

Comments on revisions: I have no further comments on revisions.

Reviewer #2 (Public review):

Summary

This revised manuscript investigates the role and the mechanism by which PDE1 impacts NSCLC progression. They provide evidence to demonstrate that PDE1 binds to m6A reader YTHDF2, in turn, regulating STAT3 signaling pathway through its interaction, promoting metastasis and angiogenesis.

Strength:

The study uncovers a novel PDE1A/YTHDF2/SOCS2/STAT3 pathway in NSCLC progression and the findings provide a potential treatment strategy for NSCLC patients with metastasis.

Weakness:

In discussion, it is stated in the revised version that "the role of YTHDF2 in PDE1A-driven tumor metastasis should be elucidated in future studies", however, given that physical interaction of PDE1A and YTHDF2 plays a critical role in PDE1A-mediated NSCLC metastasis, whether YTHDF2 mimicking the effect of PDE1A in metastasis will strength the manuscript.

Reviewer #3 (Public review):

Summary:

This paper aims to investigate how the human brain represents different forms of value and uncertainty that participate in active inference within a free-energy framework, in a two-stage decision task involving contextual information sampling, and choices between safe and risky rewards, which promotes shifting between exploration and exploitation. They examine neural correlates by recording EEG and comparing activity in the first vs second half of trials and between trials in which subjects did and did not sample contextual information, and perform a regression with free-energy-related regressors against data "mapped to source space."

Strengths:

This two-stage paradigm is cleverly designed to incorporate several important processes of learning, exploration/exploitation and information sampling that pertain to active inference. Although scalp/brain regions showing sensitivity to the active-inference related quantities do not necessarily suggest what role they play, they are illuminating and useful as candidate regions for further investigation. The aims are ambitious, and the methodologies are impressive. The paper lays out an extensive introduction to the free energy principle and active inference to make the findings accessible to a broad readership.

Weaknesses:

It is worth noting that the high lower-cutoff of 1 Hz in the bandpass filter, included to reduce the impact of EEG noise, would remove from the EEG any sustained, iteratively updated representation that evolves with learning across trials, or choice-related processes that unfold slowly over the course of the 2-second task windows. It is thus possible there are additional processes related to the active inference quantities that are missed here. This is not a flaw as one must always try to balance noise removal against signal removal in filter settings - it is just a caveat. As the authors also note, the regions showing up as correlated with model parameters change depending on source modelling method and correction for multiple comparisons, warranting some caution around the localisation aspect.

Reviewer #2 (Public review):

Summary:

Juvenile hormone (JH) is a pleiotropic terpenoid hormone in insects that mainly regulates their development and reproduction. In particular, its developmental functions are described as the "status quo" action, as its presence in the hemolymph (the insect blood) prevents metamorphosis-initiating effects of ecdysone, another important hormone in insect development, and maintains the juvenile status of insects.

While such canonical functions of JH are known to be mediated by its intracellular receptor complex composed of Met and Tai, there have been multiple reports suggesting the presence of cell membrane receptor(s) for JH, which mediate non-genomic effects of this terpenoid hormone. In particular, the presence of receptor tyrosine kinase(s) that phosphorylate Met/Tai in response to JH and thus indirectly affect the canonical JH signaling pathway has been strongly suggested. Given the importance of JH in insect physiology and the fact that the JH signaling pathway is a major target of insect growth regulators, elucidating the identify and functions of putative JH membrane receptors is of great significance from both basic and applied perspectives.

In the present study, the authors identified candidate receptors for such cell membrane JH receptors, CAD96CA and FGFR1, in the cotton bollworm Helicoverpa armigera.

Strengths:

Their in vitro analyses are conducted thoroughly using multiple methods, which overall supports their claim that these receptors can bind to JH and mediate their non-genomic effects.

Weaknesses:

Results of their in vivo experiments, particularly those of their loss-of-function analyses using CRISPR mutants are still preliminary, and the results rather indicate that these membrane receptors do not have any physiologically significant roles in vivo. More specifically, previous studies in lepidopteran species have clearly and repeatedly shown that precocious metamorphosis is the hallmark phenotype for all JH signaling-deficient larvae. In contrast, the present study showed that Cad96ca and Fgfr1 G0 mutants only showed slight acceleration in their pupation timing, which is not a typical phenotype one would expect from JH signaling deficiency. This is inconsistent with their working model provided in Figure 6, which indicates that these cell membrane JH receptors promote the canonical JH signaling by phosphorylating Met/Tai.

If the authors argue that this slight acceleration of pupation is indeed a major JH signaling-deficient phenotype in Helicoverpa, they need to provide more data to support their claim by analyzing CRISPR mutants of other genes involved in JH signaling, such as Jhamt and Met. An alternative explanation is that there is functional redundancy between CAD96CA and FGFR1 in mediating phosphorylation of Met/Tai. This possibility can be tested by analyzing double knockouts of these two receptors.

Currently, the validity of their calcium imaging analysis in Figure 5 is also questionable. When performing calcium imaging in cultured cells, it is critically important to treat all the cells at the end of each experiment with a hormone or other chemical reagents that universally induce calcium increase in each particular cell line. Without such positive control, the validity of calcium imaging data remains unknown, and readers cannot properly evaluate their results.

> for - stats - addiction - rehab relapse - 2 to 10 times - addiction - rehab - revolving door

Reviewer #2 (Public review):

Summary:

In this paper, Wolff et al. describe an impressive collection of newly created split-GAL4 lines targeting specific cell types within the central complex (CX) of Drosophila. The CX is an important area in the brain that has been involved in the regulation of many behaviors including navigation and sleep/wake. The authors advocate that to fully understand how the CX functions, cell-specific driver lines need to be created. In that respect, this manuscript will be of very important value to all neuroscientists trying to elucidate complex behaviors using the fly model. In addition, and providing a further very important finding, the authors went on to assess neurotransmitter/neuropeptides and their receptors expression in different cells of the CX. These findings will also be of great interest to many and will help further studies aimed at understanding the CX circuitries. The authors then investigated how different CX cell types influence sleep and wake. While the description of the new lines and their neurochemical identity is excellent, the behavioral screen seems to be unfinished and could have been more matured.

Strengths:

(1) The description of dozens of cell-specific split-GAL4 lines is extremely valuable to the fly community. The strength of the fly system relies on the ability to manipulate specific neurons to investigate their involvement in a specific behavior. Recently, the need to use extremely specific tools has been highlighted by the identification of sleep-promoting neurons located in the VNC of the fly as part of the expression pattern of the most widely used dorsal-Fan Shaped Body (dFB) GAL4 driver. These findings should serve as a warning to every neurobiologist, make sure that your tool is clean. In that respect, the novel lines described in this manuscript are fantastic tools that will help the fly community.<br /> (2) The description of neurotransmitter/neuropeptides expression pattern in the CX is of remarkable importance and will help design experiments aimed at understanding how the CX functions.

Weaknesses:

(1) I find the behavioral (sleep) screen of this manuscript to be incomplete. It appears to me that this part of the paper is not as developed as it could be. The authors have performed neuronal activation using thermogenetic and/or optogenetic approaches. For some cell types, only thermogenetic activation is shown. There is no silencing data and/or assessment of sleep homeostasis or arousal threshold. The authors find that many CX cell types modulate sleep and wake but it's difficult to understand how these findings fit one with the other. It seems that each CX cell type is worthy of its own independent study and paper. I am fully aware that a thorough investigation of every CX neuronal type in sleep and wake regulation is a herculean task. So, altogether I think that this manuscript will pave the way for further studies on the role of CX neurons in sleep regulation.<br /> (2) Linked to point 1, it is possible that the activation protocols used in this study are insufficient for some neuronal types. The authors have used 29{degree sign} for thermogenetic activation (instead of the most widely used 31{degree sign}) and a 2Hz optogenetic activation protocol. The authors should comment on the fact that they may have missed some phenotypes by using these mild activation protocols.<br /> (3) There are multiple spelling errors in the manuscript that need to be addressed.

Comments on revisions:

I am satisfied with the authors response. This paper provides excellent starting points for additional studies into the role of different CX cell types in sleep and wake.

Reviewer #2 (Public review):

Summary:

Wethington et al. investigated the mechanistic principles underlying antigen-specific proliferation and memory formation in mouse natural killer (NK) cells following exposure to mouse cytomegalovirus (MCMV), a phenomenon predominantly associated with CD8+ T cells. Using a rigorous stochastic modeling approach, the authors aimed to develop a quantitative model of NK cell clonal dynamics during MCMV infection.

Initially, they proposed a two-state linear model to explain the composition of NK cell clones originating from a single immature Ly49+CD27+ NK cell at 8 days post-infection (dpi). Through stochastic simulations and analytical investigations, they demonstrated that a variant of the two-state model incorporating NK cell death could explain the observed negative correlation between NK clone sizes at 8 dpi and the percentage of immature (CD27+) NK cells (Page 8, Figure 1e, Supplementary Text 1). However, this two-state model failed to accurately reproduce the first (mean) and second (variance and covariance) moments of the measured CD27+ and CD27- NK cell populations within clones at 8 dpi (Figure 1g).

To address this limitation, the authors increased the model's complexity by introducing an intermediate maturation state, resulting in a three-stage model with the transition scheme: CD27+Ly6C- → CD27-Ly6C- → CD27-Ly6C+. This three-stage model quantitatively fits the first and second moments under two key constraints: (i) immature CD27+ NK cells exhibit faster proliferation than CD27- NK cells, and (ii) there is a negative correlation (upper bound: -0.2) between clone size and the fraction of CD27+ cells. The model predicted a high proliferation rate for the intermediate stage and a high death rate for the mature CD27-Ly6C+ cells.

Using NK cell reporter mice data from Adams et al. (2021), which tracked CD27+/- cell population dynamics following tamoxifen treatment, the authors validated the three-stage model. This dataset allowed discrimination between NK cells originating from the bone marrow and those pre-existing in peripheral blood at the onset of infection. To test the prediction that mature CD27- NK cells have a higher death rate, the authors measured Ly49H+ NK cell viability in the mice spleen at different time points post-MCMV infection. Experimental data confirmed that mature (CD27-) NK cells exhibited lower viability compared to immature (CD27+) NK cells during the expansion phase (days 4-8 post-infection).

Further mathematical analyses using a variant of the three-stage model supported the hypothesis that the higher death rate of mature CD27- cells contributes to a larger proportion of CD27- cells in the dead cell compartment, as introduced in the new variant model.

Altogether, the authors proposed a three-stage quantitative model of antigen-specific expansion and maturation of naïve Ly49H+ NK cells in mice. This model delineates a maturation trajectory: (i) CD27+Ly6C- (immature) → (ii) CD27-Ly6C- (mature I) → (iii) CD27-Ly6C+ (mature II). The findings highlight the highly proliferative nature of the mature I (CD27-Ly6C-) phenotype and the increased cell death rate characteristic of the mature II (CD27-Ly6C+) phenotype.

Strengths:

By designing models capable of explaining correlations, first and second moments, and employing analytical investigations, stochastic simulations, and model selection, the authors identified the key processes underlying antigen-specific expansion and maturation of NK cells. This model distinguishes the processes of antigen-specific expansion, contraction, and memory formation in NK cells from those observed in CD8+ T cells. Understanding these differences is crucial not only for elucidating the distinct biology of NK cells compared to CD8+ T cells but also for advancing the development of NK cell therapies currently under investigation.

Weaknesses:

The conclusions of this paper are largely supported by the available data. However, a comparative analysis of model predictions with more recent works in the field would be desirable. Moreover, certain aspects of the simulations, parameter inference, and modeling require further clarification and expansion, as outlined below:

(1) Initial Conditions and Grassmann Data: The Grassmann data is used solely as a constraint, while the simulated values of CD27+/CD27- cells could have been directly fitted to the Grassmann data, which assumes a 1:1 ratio of CD27+/CD27- at t = 0. This approach would allow for an alternative initial condition rather than starting from a single CD27+ cell, potentially improving model applicability.

(2) Correlation Coefficients in the Three-State Model: Although the parameter scan of the three-state model (Figure 2) demonstrates the potential for achieving negative correlations between colony size and the fraction of CD27+ cells, the authors did not present the calculated correlation coefficients using the estimated parameter values from fitting the three-state model to the data. Including these simulations would provide additional insight into the parameter space that supports negative correlations and further validate the model.

(3) Viability Dynamics and Adaptive Response: The authors measured the time evolution of CD27+/- dynamics and viability over 30 days post-infection (Figure 4). It would be valuable to test whether the three-state model can reproduce the adaptive response of CD27- cells to MCMV infection, particularly the observed drop in CD27- viability at 5 dpi (prior to the 8 dpi used in the study) and its subsequent rebound at 8 dpi. Reproducing this aspect of the experiment is critical to determine whether the model can simultaneously explain viability dynamics and moment dynamics. Furthermore, this analysis could enable sensitivity analysis of CD27- viability with respect to various model parameters.

Reviewer #2 (Public review):

Summary:

Salt stress is a significant and growing concern for agriculture in some parts of the world. While the effects of sodium excess have been studied in Arabidopsis and (many) crop species, most studies have focused on Na uptake, toxicity and overall effects on yield, rather than on developmental responses to excess Na, per se. The work by Ishka and colleagues aims to fill this gap.

Working from an existing dataset that exposed a diverse panel of A. thaliana accessions to control, moderate, and severe salt stress, the authors identify candidate loci associated with altering the root:shoot ratio under salt stress. Following a series of molecular assays, they characterize a DUF247 protein which they dub SR3G, which appears to be a negative regulator of root growth under salt stress.

Overall, this is a well-executed study which demonstrates the functional role played by a single gene in plant response to salt stress in Arabidopsis.

Comments on latest version:

All of the issues that I raised in previous reviews have been addressed by the authors. That said, there are several points that I see have come up in subsequent reviews that remain unresolved.

In response to Reviewer 1, comment 2, regarding changes in expression differences, the authors are misinterpreting simple statistical results. They say that they performed Tukey tests for differences of means, finding, for example, that two means have the same group assignments (in this case, both "c,d") but then argue that "we still observed a clear reduction in WRKY75 transcript abundance." This is not how statistical tests work - we cannot perform a formal test for means and then just do an eyeball test. They also misinterpret the result in which one mean is assigned "b,c,d" results and a second "c,d" - these are statistically overlapping means.

Having said this, I do think that the subtle differences in expression between these different alleles is not critical to the central message of the study. It can be difficult to recapitulate results between labs, much less between different synthetic alleles. I think, in this case, we can let readers decide for themselves whether the reported differences - or lack thereof - is important for follow-up work.

Reviewer #2 (Public review):

Summary:

In their manuscript, Fang and colleagues make a notable contribution to the field of oncology, particularly in advancing our understanding of triple-negative breast cancer (TNBC). The research delineates the role of STAMBPL1 in promoting angiogenesis in TNBC through its interaction with FOXO1 and the subsequent activation of the GRHL3/HIF1A/VEGFA axis. The evidence presented is robust, with a combination of in vitro experiments, RNA sequencing, and in vivo studies providing a comprehensive view of the molecular mechanisms at play. The strength of the evidence is anchored in the systematic approach and the utilization of multiple methodologies to substantiate the findings.

Strengths:

The manuscript presents a methodologically robust framework, incorporating RNA-sequencing, chromatin immunoprecipitation (ChIP) assays, and a suite of in vitro and in vivo model systems, which collectively substantiate the claims regarding the pro-angiogenic role of STAMBPL1 in TNBC. The employment of multiple cellular models, conditioned media to assess HUVEC functional responses, and xenograft tumor models in murine hosts offers a comprehensive evaluation of STAMBPL1's impact on angiogenic processes.A salient strength of this work is the identification of GRHL3 as a transcriptional target of STAMBPL1 and the demonstration of a physical interaction between STAMBPL1 and FOXO1, which modulates GRHL3-driven HIF1A transcription. The study further suggests a potential therapeutic strategy by revealing the synergistic inhibitory effects of combined VEGFR and FOXO1 inhibitor treatment on TNBC tumor growth.

Weaknesses:

A potential limitation of the study is the reliance on specific cellular and animal models, which may constrain the extrapolation of these findings to the broader spectrum of human TNBC biology. Furthermore, while the study provides evidence for a novel regulatory axis involving STAMBPL1, FOXO1, and GRHL3, the multifaceted nature of angiogenesis may implicate additional regulatory factors not exhaustively addressed in this research.

Appraisal of Achievement and Conclusion Support:

The authors have successfully demonstrated that STAMBPL1 promotes HIF1A transcription and activates the HIF1α/VEGFA axis in a non-enzymatic manner, leading to increased angiogenesis in TNBC. The results are generally supportive of their conclusions, with clear evidence that STAMBPL1 upregulates HIF1α expression and enhances the activity of HUVECs. The study also shows that STAMBPL1 interacts with FOXO1 to promote GRHL3 transcription, which in turn activates HIF1A.

Impact on the Field and Utility:

This research is poised to exert a substantial impact on the oncological research community by uncovering the role of STAMBPL1 in TNBC angiogenesis and by identifying the STAMBPL1/FOXO1/GRHL3/HIF1α/VEGFA axis as a potential therapeutic target. The findings could pave the way for the development of novel therapeutic strategies for TNBC, a subtype characterized by a paucity of effective treatment options. The methodologies utilized in this study are likely to be valuable to the research community, offering a paradigm for investigating the role of deubiquitinating enzymes in oncogenic processes.

Additional Context:

It would be beneficial for readers to understand the broader context of TNBC research and the current challenges in treating this aggressive cancer subtype. The significance of this work is heightened by the lack of effective treatments for TNBC, making the identification of new therapeutic targets particularly important. Furthermore, understanding the specific mechanisms by which STAMBPL1 regulates HIF1α expression could provide insights into hypoxia signaling in other cancer types as well.

Reviewer #2 (Public review):

Summary:

This study introduces a valuable methodological innovation for detecting Trypanosoma cruzi, the causative agent of Chagas disease, using "deep-sampling PCR" which combines DNA fragmentation with multiple qPCR replications (>300 in some cases) on each sample. The authors aim to overcome the limitations of current qPCR methods by increasing the sensitivity of detection, which is fundamental for evaluating treatment responses in chronic Chagas disease patients. The work also evaluates the approach in multiple host species (macaques, humans, and dogs), at different times and across different sample types, including whole blood, blood cell pellets, plasma, and tissues.

Strengths:

The primary strength of this study lies in its methodological novelty, particularly the combination of multiple parallel PCR reactions and DNA fragmentation to enhance sensitivity. It is a sort of brute-force method for detecting the parasite. This approach promises the detection of parasitic DNA at levels significantly lower than those achievable with standard qPCR methods. Additionally, the authors demonstrate the utility of this method in tracking parasitemia dynamics and post-treatment responses in macaques and dogs, providing valuable insights for both research and clinical applications.

Weaknesses:

(1) Methodological Concerns on detection and quantification limits

Some methodological inconsistencies and limitations were observed that merit consideration. In Figure 1, there is a clear lack of consistency with theoretical expectations and with the trends observed in Figure 4A. Based on approximate calculations, having 10^-7 parasite equivalents with 100,000 target copies per parasite implies an average of 0.01 target copies per reaction. This would suggest an amplification rate of approximately 1 in 100 reactions, yet the observed 30% amplification appears disproportionately high. In addition, Figure 4A (not fragmented) shows lower values of positivity than Figure 1 for 10^-5 and 10^-6 dilutions showing this inconsistency among experiments. Some possible explanations could account for this inconsistency: (1) an inaccurate quantification of the starting number of parasites used for serial dilutions, or (2) random contamination not detected by negative controls, potentially due to a low number of template molecules.

Similarly, Figure 5B presents another inconsistency in theoretical expectations for amplification. The authors report detecting amplification in reactions containing 10^-9 parasites after DNA fragmentation. Based on the figure, at least 3 positives (as I can see because raw data is not available) out of 388 PCRs are observed at this dilution. Assuming 100,000 copies of satellite DNA per parasite, the probability of a single copy being present in a 10^-9 dilution is approximately 1/10,000. If we assume this as the probability of amplification of a PCR (an approximation), by using a simple binomial calculation, the probability of at least 3 positive reactions out of 388 is approximately 9.39 x 10^-6 (in ideal conditions, likely lower in real-world scenarios). This translates to a probability of about 1 in 100,000 to observe such frequency of positives, which is highly improbable and suggests either inaccuracies in the initial parasite quantification or issues with contamination. In addition, at 10^-6 PE/reactions (the proposed limit of quantification) it is observed that 40% of repetitions are amplified. The number of repetitions is not specified but probably more than 50 according to the graph. Such dilution implies 0.1 targets per reaction (assuming 100.000 copies divided by 10^6), which means a total of 5 target molecules to distribute among the reactions (0.1 targets multiplied by 50 reactions). It seems highly improbable that 40% of the reactions (20/50) would amplify under the described conditions. Even considering 200.000 target copies per parasite implies 0.2 targets per reaction and an average of 10 molecules to distribute among 50 reactions. The approximate probability of the observation of at least 20/50 positives can be calculated by determining the probability of a reaction to receive targets by assuming a random distribution of the targets among the tubes, p= 1 - (1 - 1/50)^10, and then by using a binomial distribution to determine the probability that at least 20 reactions receive at least one target copy. The probability of at least 20/50 positive reactions in a dilution of 10^-6 parasites (200.000 target copies per parasite) is 0.00028. Consequently, the observed result is highly unlikely.

2) Lack of details on contamination detection

Additionally, the manuscript does not provide enough details on how cross-contamination was detected or managed. It is unclear how the negative controls (NTCs) and no-template controls were distributed across plates, in terms of both quantity and placement. This omission is critical, as the low detection thresholds targeted in this study increase the risk of false positives by contamination. To ensure reliability and reproducibility, future uses of the technique would benefit from more standardized and clearly documented protocols for control placement and handling.

3) Unclear relevance for treatment monitoring in Humans

In Figure 7A, the results suggest that the deep-sampling PCR method does not provide a clearly significant improvement over conventional qPCR in humans. Of the 9 samples tested, 6 (56%) were consistently amplified in all or nearly all reactions, indicating these samples could also be reliably detected with standard PCR protocols. Two additional samples were detected only with the deep-sampling approach, increasing sensitivity to 78%; however, these detections might be attributable to random chance given the limited sample size. While the authors acknowledge the small sample size in the discussion, they do not address the fact that a similar increase in sensitivity was reported in citation 5, where only 3 samples were tested with 3 replicates each. This raises an important question: how many PCR reactions are needed in human samples to reach a plateau in detection rates? This issue should be further discussed to contextualize the results and their implications.

Despite these limitations, this work represents a promising step forward in the development of highly sensitive diagnostic tools for T. cruzi. It offers a novel foundation for advancing the detection and monitoring of parasitemia, which could significantly benefit Chagas disease research community and clinicians focused on neglected tropical diseases. While addressing the methodological inconsistencies and improving robustness will be critical, this study provides valuable insights and data that could lead to future innovations in parasitological research and diagnostics.

Reviewer #2 (Public review):

Summary:

The authors suggest that ECM abundance and composition change depending on the aetiology of liver fibrosis. To understand this they have investigated the proteome in two models of animal fibrosis and resolution. They suggest their findings could provide a foundation for future anti-fibrotic therapies.

The revised version has been improved. Although some areas remain (described below), it is perhaps the dataset that will be most valuable.

Strengths:

The dataset appears well supported and will be valuable.

Weaknesses:

The manuscript is still fairly descriptive but on balance this is a useful dataset and appears to have broad support in that regard.

There are no conclusions that can be drawn from their rebuttal regarding the human data they included as it is one patient per group and will most likely change dramatically with more patients. As such this area is still an issue but they have improved some of the data elsewhere.

Reviewer #2 (Public review):

Summary:

In this paper the authors wanted to show that capsaicin can disrupt the interaction between Keap1 and Nrf2 by directly binding to Keap1 at an allosteric site. The resulting stabilization of Nrf2 would protect CAP-treated gastric cells from alcohol- induced redox stress and damage as well as inflammation (both in vitro and in vivo)

Strengths:

One major strength of the study is the use of multiple methods (CoIP, SPR, BLI, deuterium exchange MS, CETSA, MS simulations, target gene expression) that consistently show for the first time that capsaicin can disrupt the Nrf2/Keap1 interaction at an allosteric site and lead to stabilization and nuclear translocation of Nrf2.<br /> Moreover, efforts to show causal involvement of the Keap/Nrf2 axis for the made cellular observations as well as addressing potential off target effects of the polypharmacological CAP appreciated.

One point that still hampers a bit of full appreciation of the capsaicin effect in cells is that capsaicin is not investigated alone, but mostly in combination with alcohol only.<br /> Moreover, the true add-on value of the developed nanoparticles remains obscure.<br /> The partly relatively high levels of NRF2 in putatively unstressed cells question the validity of used models.

The rationale for switching between different CAP concentrations is unclear /not entirely convincing.

The language and introduction could be improved.

Overall, the authors are convinced that capsaicin (although weakly) can bind to Keap1 and releases Nrf2 from degradation, with relevance for biological settings. With this, the authors provide a significant finding with marked relevance for the redox/Nrf2 as well as natural products /hit discovery communities.

- Figure 2C: It is still not clear why naïve (unstressed /untreated cells) already show rather high nuclear abundance of Nrf2 (shouldn´t Nrf2 be continuously tagged for degradation by Keap1)<br /> - Figure 2G-H: Why switch to rather high concentrations?<br /> - Figure 2I: in the pics of mitochondria the control mitochondria look way more punctuated (likely fissed) than the ones treated with EtOH or EtOH + CAP. Wouldn´t one expect that EtOH leads to mitochondrial fission and CAP can prevent it?<br /> - Figure 3H: High basal Nrf2 levels in unstressed/untreated HEK WT cells, why?<br /> - Figure 4a: Inclusion of an additional Keap1 binding protein (one with a ETGE motif) would have been desirable (to get information on specificity/risks of off-target (unwanted) effects of CAP)<br /> - Figure 4D: Why is there no stabilization of Nrf2 by CAP in lane 2 ?<br /> - Figure 4f: 5% DMSO is a rather high solvent concentration , why so high (the solvent alone seems to have quite marked effects !)<br /> - Figure 6/7: not expert enough to judge formulations and histology scores. However, the benefit of the encapsulated capsaicin does not become entirely clear to me, as CAP and IRHSA@CAP mostly do not significantly differ in their elicited response.<br /> - Figure 7: Rebamipide was introduced as positive control in the text with an activating effect on Nrf2, but there is no induction of hmox and nqo in Figure 7f, why? It does not look as the positive control was wisely chosen.

Reviewer #2 (Public review):

In this article, Schmidt et al use iPSC-derived human cortical neurons to test the effects the psychedelic psilocin in different models of neuroplasticity.

Using human iPSC-derived cortical neurons, the authors test the expression of 5-HT2A and subcellular distribution, as well as the effect of different times of exposure to psilocin on 5-HT2A expression. The authors evaluated the effect of the 5-HT2 antagonist ketanserin, as well as the inhibition of dynamin-dependent endocytic pathways with dynasore. Gene expression and plasticity (structural and functional) was also evaluated after different times of exposure to psilocin.

In general, results are interesting since they use the iPSC to evaluate the potentially translationally relevant effects of psilocin (the active metabolite of the psychedelic psilocybin). However, there are a few concerns that need to be addressed:

(1) My main critique is the lack of experimental validation of selectivity and/or specificity of the anti-5-HT2A antibody targeting the extracellular loop of the 5-HT2A receptor (Alomone labs, cat # ASR-033). Most of the primary antibodies targeting class A GPCRs (including the 5-HT2A receptor) have very limited selectivity. Without validation (using for example knockdown techniques to decrease expression of 5-HT2A in their iPSC-derived human cortical neurons), the experiments using this antibody should be excluded from the manuscript.

(2) Did the author evaluate whether 5-HT is present in the cell media? If it is, this may affect the functional outcomes evaluated throughout, since as the endogenous ligand it would in principle activate the 5-HT2A receptor.

(3) Some of the datasets are not statistically analyzed (or quantified), such as Figure S1F.

(4) Another important concern is the experimental design used to evaluate the effect of psilocin at different time points (24h, 4 days and 10 days). One of the unique and translationally interesting effects of psychedelics including psilocybin is that the in vivo plasticity-related effects (increased structural or synaptic plasticity for example) are observed post-acutely, or once the active compound psilocin is fully metabolized, or not present in the CNS directly targeting the 5-HT2A. Using the iPSC, it seems that the authors continuously exposed cells to psilocin (for hours or even days) at least for some of the experimental techniques. Since this is not the model of what occurs using an in vivo model (such as a single dose of psilocybin to mice, collecting frontal cortex samples 24-h after drug administration, once the active compound is fully metabolized), the authors' findings lack translational validity. Can the authors comment on this?

(5) In Figure 2E, it seems that ketamine by itself is reducing BDNF density. How then the authors conclude that ketamine blocks psi-induced effects? Using a more selective 5-HT2A antagonist such as M100907 could also improve the outcome (in terms of selectivity) of this experiment.

(6) To evaluate neurite complexity, the authors used the AAV-CamKII-mCherry viral vector, but mCherry (Fig 4A) seems to be retained in the nucleus.

(7) Minor: Reference 36- this is a review article that does not mention the psychedelic psilocin

Reviewer #3 (Public review):

Summary:

The authors sought to understand social interactions both within and between groups of feral pigs, with the intent of applying their findings to models of disease transmission. The authors analyzed GPS tracking data from across various populations to determine patterns of contact that could support the transmission of a range of zoonotic and livestock diseases.<br /> The analysis then focused on the effects of sex, group dynamics, and seasonal changes on contact rates that could be used to base targeted disease control strategies which would prioritize the removal of adult males for reducing intergroup disease transmission.

Strengths:

It utilized GPS tracking data from 146 feral pigs over several years, effectively capturing seasonal and spatial variation in the social behaviors of interest. Using proximity-based social network analysis, this work provides a highly resolved snapshot of contact rates and interactions both within and between groups, substantially improving research in wildlife disease transmission.<br /> Results were highly useful and provided practical guidance for disease management, showing that control targeted at adult males could reduce intergroup disease transmission, hence providing an approach for the control of zoonotic and livestock diseases.

Weaknesses:

None, as the authors have already addressed the identified weaknesses.

Reviewer #3 (Public review):

Summary:

This study investigates the cellular and molecular events leading to hyposmia, an early dysfunction in Parkinson's disease (PD), which develops up to 10 years prior to motor symptoms. The authors use five Drosophila knock-in models of familial PD genes (LRRK2, RAB39B, PINK1, DNAJC6 (Aux), and SYNJ1 (Synj)), three expressing human genes and two Drosophila genes with equivalent mutations.

The authors carry out single-cell RNA sequencing of young fly brains and single-nucleus RNA sequencing of human brain samples. The authors found that cholinergic olfactory projection neurons (OPN) were consistently affected across the fly models, showing synaptic dysfunction before the onset of motor deficits, known to be associated with dopaminergic neuron (DAN) dysfunction.

Single-cell RNA sequencing revealed significant transcriptional deregulation of synaptic genes in OPNs across all five fly PD models. This synaptic dysfunction was confirmed by impaired calcium signalling and morphological changes in synaptic OPN terminals. Furthermore, these young PD flies exhibited olfactory behavioural deficits that were rescued by selective expression of wild-type genes in OPNs.

Single-nucleus RNA sequencing of post-mortem brain samples from PD patients with LRRK2 risk mutations revealed similar synaptic gene deregulation in cholinergic neurons, particularly in the nucleus basalis of Meynert (NBM). Gene ontology analysis highlighted enrichment for processes related to presynaptic function, protein homeostasis, RNA regulation, and mitochondrial function.

This study provides compelling evidence for the early and primary involvement of cholinergic dysfunction in PD pathogenesis, preceding the canonical DAN degeneration. The convergence of familial PD mutations on synaptic dysfunction in cholinergic projection neurons suggests a common mechanism contributing to early non-motor symptoms like hyposmia. The authors also emphasise the potential of targeting cholinergic neurons for early diagnosis and intervention in PD.

Strengths:

This study presents a novel approach, combining multiple mutants to identify salient disease mechanisms. The quality of the data and analysis is of a high standard, providing compelling evidence for the role of OPN neurons in olfactory dysfunction in PD. The authors also provide evidence to show that early olfactory defects lead to later dopaminergic neuron dysfunction. The comprehensive single-cell RNA sequencing data from both flies and humans is a valuable resource for the research community. The identification of consistent impairments in cholinergic olfactory neurons, at early disease stages, is a powerful finding that highlights the convergent nature of PD progression. The comparison between fly models and human patients' brains provides strong evidence of the conservation of molecular mechanisms of disease, which can be built upon in further studies using flies to prove causal relationships between the defects described here and neurodegeneration.

The identification of specific neurons involved in olfactory dysfunction opens up potential avenues for diagnostic and therapeutic interventions.

SEXUALITY

LGBTQ+ individuals: (lesbian, gay, bisexual, transgender, and queer, plus other identities such as two-spirit, asexual, pansexual, and so on). The term was historically used in a derogatory way but was reclaimed as an affirmative and self-referential term in the 1990s United States.

chapter 2 (DOS)

GENDER chapter 2: identities and other terms

Reviewer #2 (Public review):

Summary:

Tóth and Bazeli et al. find rapamycin activates heterologously-expressed TRPM8 and dissociated sensory neurons in a TRPM8-dependent way with Ca2+-imaging. With electrophysiology and STTD-NMR, they confirmed the activation is through direct interaction with TRPM8. Using mutants and computational modeling, the authored localized the binding site to the groove between S4 and S5, different than the binding pocket of cooling agents such as menthol. The hydroxyl group on carbon 40 within the cyclohexane ring in rapamycin is indispensable for activation, while other rapalogs with its replacement, such as everolimus, still bind but cannot activate TRPM8. Overall, the findings provide new insights into TRPM8 functions and may indicate previously-unknown physiological effects or therapeutic mechanisms of rapamycin.

Strengths:

The authors spent extensive effort on demonstration that the interaction between TRPM8 and rapamycin is direct. The evidence is solid. In probing the binding site and the structural-function relationship, the authors combined computational simulation and functional experiments. It is very impressive to see that "within" a rapamycin molecule, the portion shared with everolimus is for "binding", while the hydroxyl group in the cyclohexane ring is for activation. Such detailed dissection represents a successful trial in computational biology-facilitated, functional experiment-validated study of TRP channel structural-activity relationship. The research draws the attention of scientists, including those outside the TRP channel field, to previously-neglected effects of rapamycin, and therefore the manuscript deserves broad readership.

Weaknesses:

The significance of the research could be improved by showing or discussing whether a similar binding pocket is present in other TRP channels, and hence rapalogs might bind to or activate these TRP channels. Additionally, while the finding on TRPM8 is novel, it is worthwhile to perform more comprehensive pharmacological characterization, including single-channel recording and a few more mutant studies to offer further insight into the mechanism of rapamycin binding to S4~S5 pocket driving channel opening. It is also necessary to know if rapalogs have independent or synergistic effects on top of other activators, including cooling agents and lower temperature, and its dependence on regulators such as PIP2.

Additional discussion that might be helpful:

The authors did confirm that rapamycin does not activate TRPV1, TRPA1 and TRPM3. But other TRP channels, particularly other structurally-similar TRPM channels, should be discussed or tested. Alignment of the amino acid sequences or structures at the predicted binding pocket might predict some possible outcomes. In particular, rapamycin is known to activate TRPML1 in a PI(3,5)P2-dependent manner, which should be highlighted in comparison among TRP channels (PMID: 35131932, 31112550).

After revision:

I acknowledge that the authors have addressed some of the questions in their revised version. They have explained that additional experiments might be beyond the scope of the current study. I appreciate their effort in doing their best to improve the manuscript and to leave the rest in discussion.

Reviewer #2 (Public review):

Summary:

In this preprint, De Sancho and López use alchemical molecular dynamics simulations and quantum mechanical calculations to elucidate the origin of the observed preference of Tyr over Phe in phase separation. The paper is well written, and the simulations conducted are rigorous and provide good insight into the origin of the differences between the two aromatic amino acids considered.

Strengths:

The study addresses a fundamental discrepancy in the field of phase separation where the predicted ranking of aromatic amino acids observed experimentally is different from their anticipated rankings when considering contact statistics of folded proteins. While the hypothesis that the difference in the microenvironment of the condensed phase and hydrophobic core of folded proteins underlies the different observations, this study provides a quantification of this effect. Further, the demonstration of the crossover between Phe and Tyr as a function of the dielectric is interesting and provides further support for the hypothesis that the differing microenvironments within the condensed phase and the core of folded proteins is the origin of the difference between contact statistics and experimental observations in phase separation literature. The simulations performed in this work systematically investigate several possible explanations and therefore provide depth to the paper.

Weaknesses:

While the study is quite comprehensive and the paper well written, there are a few instances that would benefit from additional details. In the methods section, it is unclear as to whether the GGXGG peptides upon which the alchemical transforms are conducted are positioned restrained within the condensed/dilute phase or not. If they are not, how would the position of the peptides within the condensate alter the calculated free energies reported? It would also be interesting to see what the variation in the transfer of free energy is across multiple independent replicates of the transform to assess the convergence of the simulations. Additionally, since the authors use a slab for the calculation of these free energies, are the transfer free energies from the dilute phase to the interface significantly different from those calculated from the dilute phase to the interior of the condensate? The authors mention that the contact statistics of Phe and Tyr do not show significant difference and thereby conclude that the more favorable transfer of Tyr primarily originates from the dielectric of the condensate. However, the calculation of contacts neglects the differences in the strength of interactions involving Phe vs. Tyr. Though the authors consider the calculation of energy contact formation later in the manuscript, the scope of these interactions are quite limited (Phe-Phe, Tyr-Tyr, Tyr-Amide, Phe-Amide) which is not sufficient to make a universal conclusion regarding the underlying driving forces. A more appropriate statement would be that in the context of the minimal peptide investigated the driving force seems to be the difference in dielectric. However, it is worth mentioning that the authors do a good job of mentioning some of these caveats in the discussion section.

Reviewer #2 (Public review):

Summary:

The authors present a very interesting collection of methods and results using brain ultrasound localization microscopy (ULM) in awake mice. They emphasize the effect of the level of anesthesia on the quantifiable elements assessable with this technique (i.e. vessel diameter, flow speed, in veins and arteries, area perfused, in capillaries) and demonstrate the possibility of achieving longitudinal cerebrovascular assessment in one animal during several weeks with their protocol.<br /> The authors made a good rewriting of the article based on the reviewers' comments. One of the message of the first version of the manuscript was that variability in measurements (vessel diameter, flow velocity, vascularity) were much more pronounced under changes of anesthesia than when considering longitudinal imaging across several weeks. This message is now not quite mitigated, as longitudinal imaging seems to show a certain variability close to the order of magnitude observed under anesthesia. In that sense, the review process was useful in avoiding hasty conclusion and calls for further caution in ULM awake longitudinal imaging, in particular regarding precision of positioning and cancellation of tissue motion.

Strengths:

Even if the methods elements considered separately are not new (brain ULM in rodents, setup for longitudinal awake imaging similar to those used in fUS imaging, quantification of vessel diameters/bubble flow/vessel area), when masterfully combined as it is done in this paper, they answer two questions that have been long-running in the community: what is the impact of anesthesia on the parameters measured by ULM (and indirectly in fUS and other techniques)? Is it possible to achieve ULM in awake rodents for longitudinal imaging? The manuscript is well constructed, well written, and graphics are appealing.<br /> The manuscript has been much strengthened by the round of review, with more animals for the longitudinal imaging study.

Weaknesses:

Some weaknesses remain, not hindering the quality of the work, that the authors might want to answer or explain.<br /> - When considering fig 4e and fig 4j together: it seems that in fig 4e the vascularity reduction in the cortical ROI is around 30% for downward flow, and around 55% for upward flow; but when grouping both cortical flows in fig 4j, the reduction is much smaller (~5%), even at the individual level (only mouse 1 is used in fig 4e). Can you comment on that?<br /> - When considering fig4e, fig 4j, fig6e and fig6i altogether, it seems that vascularity can be highly variable, whether it be under anesthesia or vascular imaging, with changes between 5 to 40%. Is this vascularity quantification worth it (namely, reliable for example to quantify changes in a pathological model requiring longitudinal imaging)?

Reviewer #2 (Public review):

This paper tests the hypothesis that perceptual switches during the presentation of ambiguous stimuli are accompanied by changes in neuromodulation that alter neural gain and trigger abrupt changes in brain activity. To test this hypothesis, the study combines pupillometry, artificial recurrent network (RNN) analysis and fMRI recording. In particular, the study uses methods of energy landscape analysis inspired by physics, which is particularly interesting.

Strengths

- The authors should be commended for combining different methods (pupillometry, RNNs, fMRI) to test their hypothesis. This combination provides a mechanistic insight into perceptual switches in the brain and artificial neural networks.<br /> - The study combines different viewpoints and fields of scientific literature, including neuroscience, psychology, physics, and dynamical systems. In order to make this combination more accessible to the reader, the different aspects are presented in a pedagogical way to be accessible to all fields.<br /> - This combination of methods and viewpoints is rarely done, so it is very useful.<br /> - The authors introduce dynamic gain modulation in their recurrent neural network, which is novel. They devote a section of the paper to studying the dynamics, fixed points and convergence of this type of network.

Weaknesses

- The study may not be specific to perceptual switches. This is because the study relies on a paradigm in which participants report when they identify a switch in the item category. Therefore, it is unclear whether the effects reported in the paper are related to the perceptual switch itself, to attention, or to the detection of behaviourally relevant events. The authors are cautious and explicitly acknowledge this point in their study.<br /> - The demonstration of the causal role of gain modulation in perceptual switches is partial. This causality is clearly demonstrated in the simulation work with the RNN. However, it is not fully demonstrated in the pupil analysis and the fMRI analysis. One reason is that this work is correlative (which is already very informative). An analysis of the timing of the effect might have overcome this limitation. For example, in a previous study, the same group showed that fMRI activity in the LC region precedes changes in the energy landscape of fMRI dynamics, which is a step towards investigating causal links between gain modulation, changes in the energy landscape and perceptual switches.<br /> - Some effects may reflect the expectation of a perceptual switch rather than the perceptual switch itself. To mitigate this risk, the design of the fMRI task included catch trials, in which no switch occurs, to reduce the expectation of a switch. The pupil study, however, did not include such catch trials.<br /> - The paper uses RNN-based modelling to provide mechanistic insight into the role of gain modulation in perceptual switches. However, the RNN solves a task that differs markedly from that performed by human participants, which may limit the explanatory value of the model. The RNN is provided with two inputs characterising the sensory evidence supporting the first and last image category in the sequence (e.g. plane and shark). In contrast, observers in the task were naïve as to the identity of the last image at the beginning of the sequence. The brain first receives sensory evidence about the image category (e.g. plane) with which the sequence begins, which is very easy to recognise, then it sees a sequence of morphed images and has to discover what the final image category will be. To discover the final image category, the brain has to search a vast space of possible second images (it is a shark?, a frog?, a bird?, etc.), rather than comparing the likelihood of just two categories. This search process and the perceptual switch in the task appear to be mechanistically different from the competition between two inputs in the RNN.<br /> - Another aspect of the motivation for the RNN model remains unclear. The authors introduce dynamic gain modulation in the RNN, but it is not clear what the added value of dynamic gain modulation is. Both static (Fig. S1) and dynamic (Fig. 2F) gain modulation lead to the predicted effect: faster switching when the gain is larger.<br /> - The authors are to be commended for addressing their research questions with multiple tools and approaches. There are links between the different parts of the study. The RNN and the pupil are linked by the notion of gain modulation, the RNN and the fMRI analysis are linked by the study of the energy landscape, the fMRI study and the pupil study are indirectly linked by previous work for this group showing that the peak in LC fMRI activity precedes a flattening of the energy landscape. These links are very interesting but could have been stronger and more complete.

Reviewer #2 (Public Review):

Summary:

This paper aimed to examine the spatial frequency selectivity of macaque inferotemporal (IT) neurons and its relation to category selectivity. The authors suggest in the present study that some IT neurons show a sensitivity for the spatial frequency of scrambled images. Their report suggests a shift in preferred spatial frequency during the response, from low to high spatial frequencies. This agrees with a coarse-to-fine processing strategy, which is in line with multiple studies in the early visual cortex. In addition, they report that the selectivity for faces and objects, relative to scrambled stimuli, depends on the spatial frequency tuning of the neurons.

Strengths:

Previous studies using human fMRI and psychophysics studied the contribution of different spatial frequency bands to object recognition, but as pointed out by the authors little is known about the spatial frequency selectivity of single IT neurons. This study addresses this gap and shows spatial frequency selectivity in IT for scrambled stimuli that drive the neurons poorly. They related this weak spatial frequency selectivity to category selectivity, but these findings are premature given the low number of stimuli they employed to assess category selectivity.

The authors revised their manuscript and provided some clarifications regarding their experimental design and data analysis. They responded to most of my comments but I find that some issues were not fully or poorly addressed. The new data they provided confirmed my concern about low responses to their scrambled stimuli. Thus, this paper shows spatial frequency selectivity in IT for scrambled stimuli that drive the neurons poorly (see main comments below). They related this (weak) spatial frequency selectivity to category selectivity, but these findings are premature given the low number of stimuli to assess category selectivity.

Reviewer #2 (Public review):

Summary:

The authors report several interesting species and sex differences in cell type expression that may relate to species differences in behavior. The differential cell type abundance findings build on previously observed species/sex differences in behavior and brain anatomy. These data will be a valuable resource for behavioral neuroscientists. These findings are important but the manuscript goes too far in attributing causal influences to differences in behavior. A second important problem is that dissections used for the sequencing data include other neuropeptide-rich areas of the hypothalamus like the PVN. Although histology is included, the results into the main manuscript often do not include the mPOA making it hard to know if species/sex differences are consistent across different hypothalamic regions. The manuscript would benefit from more precise language.

Strengths:

The data are novel because cell-type atlases are available for only a few species.

The authors have clearly defined appropriate steps taken to obtain trustworthy estimations of cell type abundance. Furthermore, the criteria for each cell type assignment was described in a way for readers to easily replicate. The rigor in comparing cell abundance provides convincing evidence that these species have differences in MPOA cellular composition.

The authors have a good explanation for why 19 of the 53 neuron clusters were not classified (possible Mus/Peromyscus anatomical differences, some cell types don't have well-defined transcriptional profiles)

Validated findings with histology.

Reviewer #2 (Public review):

The authors developed a strategy to image inferior olive somata via viral GCaMP6s expression, an implanted GRIN lens, and a one-photon head-mounted microscope, providing the first in vivo somatic recordings from these neurons. The main new findings relate to the activation of the nucleoolivary pathway, specifically that: this manipulation does not produce a spiking rebound in the IO; it exerts a larger effect on spontaneous IO spiking than stimulus (airpuff)-evoked spiking. In addition, several findings previously demonstrated in vivo in Purkinje cell complex spikes or inferior olivary axons are confirmed here in olivary somata: differences in event sizes from single cells versus co-activated cells; reduced coactivation when activating the NO pathway; more coactivation within a single zebrin compartment.

The study presents some interesting findings, and for the most part, the analyses are appropriate. My two principal critiques are that the study does not acknowledge major technical limitations and their impact on the claims; and the study does not accurately represent prior work with respect to the current findings.

Several significant technical limitations necessarily impact the veracity of several of the claims:

(1) The authors use GCaMP6s, which has a tau_1/2 of >1 s for a normal spike, and probably closer to 2 s (10.1038/nature12354) for the unique and long type of olivary spikes that give rise to axonal bursts (10.1016/j.neuron.2009.03.023). Indeed, the authors demonstrate as much (Fig. 2B1). This affects at least several claims:

a. The authors report spontaneous spike rates of 0.1 Hz. They attribute this to anesthesia, yet other studies under anesthesia recording Purkinje complex spikes via either imaging or electrophysiology report spike rates as high as 1.5 Hz (10.1523/JNEUROSCI.2525-10.2011). This discrepancy is not acknowledged and a plausible explanation is not given. Citations are not provided that demonstrate such low anesthetized spike rates, nor are citations provided for the claim that spike rates drop increasingly with increasing levels of anesthesia when compared to awake resting conditions. More likely, this discrepancy reflects spikes that are missed due to a combination of the indicator kinetics and low imaging sensitivity (see (2)), neither of which are presented as possible plausible alternative explanations.

b. Many claims are made throughout about co-activation ("clustering"), but with the GCaMP6s rise time to peak (0.5 s), there is little technical possibility to resolve co-activation. This limitation is not acknowledged as a caveat and the implications for the claims are not engaged with in the text.

c. The study reports an ultralong "refractory period" (L422-etc) in the IO, but this again must be tempered by the possibility that spikes are simply being missed due to very slow indicator kinetics and limited sensitivity. Indeed, the headline numeric estimate of 1.5 s (L445) is suspiciously close to the underlying indicator kinetic limitation of ~1-2 s.

(2) The study uses endoscopic one-photon miniaturized microscope imaging. Realistically, this is expected to permit an axial point spread function (z-PSF) on the order of ~40um, which must substantially reduce resolution and sensitivity. This means that if there *is* local coactivation, the data in this study will very likely have individual ROIs that integrate signals from multiple neighboring cells. The study reports relationships between event magnitude and clustering, etc; but a fluorescence signal that contains photons contributed by multiple neighboring neurons will be larger than a single neuron, regardless of the underlying physiology - the text does not acknowledge this possibility or limitation.

Second, the text makes several claims for the first multicellular in vivo olivary recordings. (L11; L324, etc). I am aware of at least two studies that have recorded populations of single olivary axons using two-photon Ca2+ imaging up to 6 years ago (10.1016/j.neuron.2019.03.010; 10.7554/eLife.61593). This technique is not acknowledged or discussed, and one of these studies is not cited. No argument is presented for why axonal imaging should not "count" as multicellular in vivo olivary recording: axonal Ca2+ reflects somatic spiking.

Reviewer #2 (Public review):

Summary:

The manuscript by Kawadkar et al investigates the role of Nup107 in developmental progression via the regulation of ecdysone signaling. The authors identify an interesting phenotype of Nup107 whole-body RNAi depletion in Drosophila development - developmental arrest at the late larval stage. Nup107-depleted larvae exhibit mislocalization of the Ecdysone receptor (EcR) from the nucleus to the cytoplasm and reduced expression of EcR target genes in salivary glands, indicative of compromised ecdysone signaling. This mis-localization of EcR in salivary glands was phenocopied when Nup107 was depleted only in the prothoracic gland (PG), suggesting that it is not nuclear transport of EcR but the presence of ecdysone (normally secreted from PG) that is affected. Consistently, whole-body levels of ecdysone were shown to be reduced in Nup107 KD, particularly at the late third instar stage when a spike in ecdysone normally occurs. Importantly, the authors could rescue the developmental arrest and EcR mislocalization phenotypes of Nup107 KD by adding exogenous ecdysone, supporting the notion that Nup107 depletion disrupts biosynthesis of ecdysone, which arrests normal development. Additionally, they found that rescue of the Nup107 KD phenotype can also be achieved by over-expression of the receptor tyrosine kinase torso, which is thought to be the upstream regulator of ecdysone synthesis in the PG. Transcript levels of the torso are also shown to be downregulated in the Nup107KD, as are transcript levels of multiple ecdysone biosynthesis genes. Together, these experiments reveal a new role of Nup107 or nuclear pore levels in hormone-driven developmental progression, likely via regulation of levels of torso and torso-stimulated ecdysone biosynthesis.

Strengths:

The developmental phenotypes of an NPC component presented in the manuscript are striking and novel, and the data appears to be of high quality. The rescue experiments are particularly significant, providing strong evidence that Nup107 functions upstream of torso and ecdysone levels in the regulation of developmental timing and progression.

Weaknesses:

The underlying mechanism is however not clear, and any insight into how Nup107 may regulate these pathways would greatly strengthen the manuscript. Some suggestions to address this are detailed below.

Major questions:

(1) Determining how specific this phenotype is to Nup107 vs. to reduced NPC levels overall would give some mechanistic insight. Does knocking down other components of the Nup107 subcomplex (the Y-complex) lead to similar phenotypes? Given the published gene regulatory function of Nup107, do other gene regulatory Nups such as Nup98 or Nup153 produce these phenotypes?

(2) In a related issue, does this level of Nup107 KD produce lower NPC levels? It is expected to, but actual quantification of nuclear pores in Nup107-depleted tissues should be added. These and the above experiments would help address a key mechanistic question - is this phenotype the result of lower numbers of nuclear pores or specifically of Nup107?

(3) Additional experiments on how Nup107 regulates the torso would provide further insight. Does Nup107 regulate transcription of the torso or perhaps its mRNA export? Looking at nascent levels of the torso transcript and the localization of its mRNA can help answer this question. Or alternatively, does Nup107 physically bind the torso?

(4) The depletion level of Nup107 RNAi specifically in the salivary gland vs. the prothoracic gland should be compared by RT-qPCR or western blotting.

(5) The UAS-torso rescue experiment should also include the control of an additional UAS construct - so Nup107; UAS-control vs Nup107; UAS-torso should be compared in the context of rescue to make sure the Gal4 driver is functioning at similar levels in the rescue experiment.

Minor:

(6) Figures and figure legends can stand to be more explicit and detailed, respectively.

Reviewer #2 (Public review):

Summary:

In this work, the authors investigated the extent of shared variability in cortical population activity in the visual cortex in mice and macaques under conditions of spontaneous activity and visual stimulation. They argue that by studying the average response to repeated presentations of sensory stimuli, investigators are discounting the contribution of variable population responses that can have a significant impact at the single trial level. They hypothesized that, because these fluctuations are to some degree shared across cortical populations depending on the sources of these fluctuations and the relative connectivity between cortical populations within a network, one should be able to predict the response in one cortical population given the response of another cortical population on a single trial, and the degree of predictability should vary with factors such as retinotopic overlap, visual stimulation, and the directionality of canonical cortical circuits.

To test this, the authors analyzed previously collected and publicly available datasets. These include calcium imaging of the primary visual cortex in mice and electrophysiology recordings in V1 and V4 of macaques under different conditions of visual stimulation. The strength of this data is that it includes simultaneous recordings of hundreds of neurons across cortical layers or areas. However, the weaknesses of calcium dynamics (which has lower temporal resolution and misses some non-linear dynamics in cortical activity) and multi-unit envelope activity (which reflects fluctuations in population activity rather than the variance in individual unit spike trains), underestimate the variability of individual neurons. The authors deploy a regression model that is appropriate for addressing their hypothesis, and their analytic approach appears rigorous and well-controlled.

From their analysis, they found that there was significant predictability of activity between layer II/III and layer IV responses in mice and V1 and V4 activity in macaques, although the specific degree of predictability varied somewhat with the condition of the comparison with some minor differences between the datasets. The authors deployed a variety of analytic controls and explored a variety of comparisons that are both appropriate and convincing that there is a significant degree of predictability in population responses at the single trial level consistent with their hypothesis. This demonstrates that a significant fraction of cortical responses to stimuli is not due solely to the feedforward response to sensory input, and if we are to understand the computations that take place in the cortex, we must also understand how sensory responses interact with other sources of activity in cortical networks. However, the source of these predictive signals and their impact on function is only explored in a limited fashion, largely due to limitations in the datasets. Overall, this work highlights that, beyond the traditionally studied average evoked responses considered in systems neuroscience, there is a significant contribution of shared variability in cortical populations that may contextualize sensory representations depending on a host of factors that may be independent of the sensory signals being studied.

Strengths:

This work considers a variety of conditions that may influence the relative predictability between cortical populations, including receptive field overlap, latency that may reflect feed-forward or feedback delays, and stimulus type and sensory condition. Their analytic approach is well-designed and statistically rigorous. They acknowledge the limitations of the data and do not over-interpret their findings.

Weaknesses:

The different recording modalities and comparisons (within vs. across cortical areas) limit the interpretability of the inter-species comparisons. The mechanistic contribution of known sources or correlates of shared variability (eye movements, pupil fluctuations, locomotion, whisking behaviors) were not considered, and these could be driving or a reflection of much of the predictability observed and explain differences in spontaneous and visual activity predictions. Previous work has explored correlations in activity between areas on various timescales, but this work only considered a narrow scope of timescales. The observation that there is some degree of predictability is not surprising, and it is unclear whether changes in observed predictability with analysis conditions are informative of a particular mechanism or just due to differences in the variance of activity under those conditions. Some of these issues could be addressed with further analysis, but some may be due to limitations in the experimental scope of the datasets and would require new experiments to resolve.

Reviewer #2 (Public review):

In this manuscript, Epiney et al., present a single-nucleus sequencing analysis of Drosophila adult central brain neurons and glia. By employing an ingenious permanent labeling technique, they trace the progeny of T2 neuroblasts, which play a key role in the formation of the central complex. This transcriptomic dataset is poised to become a valuable resource for future research on neurogenesis, neuron morphology, and behavior.

The authors further delve into this dataset with several analyses, including the characterization of neurotransmitter expression profiles in T2-derived neurons. While some of the bioinformatic analyses are preliminary, they would benefit from additional experimental validation in future studies.

Reviewer #2 (Public review):

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

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

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

One concern I have with the first part is that they claim that:<br /> "In these experiments, the colony area on the plate, a proxy for colony size, followed exponential growth kinetics. The fitness of a mutant strain was determined as the rate of exponential growth normalized to the rate in wild type cells."

There are many works on "range expansions" showing that colonies expand at a constant velocity, the speed of which scales as the square root of the growth rate (these are called "Fisher waves", predicted in the 1940', and there are many experimental works on them, e.g. https://www.pnas.org/doi/epdf/10.1073/pnas.0710150104) If that's the case, the area of the colony should be proportional to growth_rate X time^2 , rather than exp(growth_rate*time), so the fitness they might be using here could be the log(growth_rate) rather than growth_rate itself? That could potentially have a big effect on the results.

Additional comments/questions:

(1) What is the motivation for the model where the effect of two genes is the minimum of the two?

(2) How seriously should we take the Scott-Hwa model? Should we view it as a toy model to explain the phenomenon or more than that? If the latter, then since the number of categories in the GO analysis is much more than two (47?) in many cases the analysis of the experimental data would take pairs of genes that both affect one process in the Scott-Hwa model - and then the product prediction should presumably fail? The same comment applies to the other coarse-grained model.

(3) There are many works in the literature discussing additive fitness contributions, including Kaufmann's famous NK model as well as spin-glass-type models (e.g. Guo and Amir, Science Advances 2019, Reddy and Desai, eLife 2021, Boffi et al., eLife 2023) These should be addressed in this context.

(4) The experimental data is for deletions, but it would be interesting to know the theoretical model's prediction for the expected effects of beneficial mutations and how they interact since that's relevant (as mentioned in the paper) for evolutionary experiments. Perhaps in this case the question of additive vs. multiplicative matters less since the fitness effects are much smaller.

Reviewer #2 (Public review):

Summary:

The molecular signature of tendon stem cells is not fully identified. The endogenous location of tendon stem cells within the native tendon is also not fully elucidated. Several molecular markers have been identified to isolate tendon stem cells but they lack tendon specificity. Using the declining tendon repair capacity of mature mice, the authors compared the transcriptome landscape and activity of juvenile (2 weeks) and mature (6 weeks) tendon cells of mouse Achilles tendons and identified CD55 and CD248 as novel surface markers for tendon stem cells. CD55+ CD248+ FACS-sorted cells display a preferential tendency to differentiate into tendon cells compared to CD55neg CD248neg cells.

Strengths:

The authors generated a lot of data on juvenile and mature Achilles tendons, using scRNAseq, snRNAseq, and ATACseq strategies. This constitutes a resource dataset.

Weaknesses:

The analyses and validation of identified genes are not complete and could be pushed further. The endogenous expression of newly identified genes in native tendons would be informative. The comparison of scRNAseq and snRNAseq datasets for tendon cell populations would strengthen the identification of tendon cell populations.

Reviewer #2 (Public review):

Summary:

The authors apply the recently developed VARX model, which explicitly models intrinsic dynamics and the effect of extrinsic inputs, to simulated data and intracranial EEG recordings. This method provides a directed method of 'intrinsic connectivity'. They argue this model is better suited to the analysis of task neuroimaging data because it separates the intrinsic and extrinsic activity. They show: that intrinsic connectivity is largely unaltered during a movie-watching task compared to eyes open rest; intrinsic noise is reduced in the task; and there is intrinsic directed connectivity from sensory to higher-order brain areas.

Strengths:

(1) The paper tackles an important issue with an appropriate method.

(2) The authors validated their method on data simulated with a neural mass model.

(3) They use intracranial EEG, which provides a direct measure of neuronal activity.

(4) Code is made publicly available and the paper is written well.

Weaknesses:

It is unclear whether a linear model is adequate to describe brain data. To the author's credit, they discuss this in the manuscript. Also, the model presented still provides a useful and computationally efficient method for studying brain data - no model is 'the truth'.

Appraisal of whether the authors achieve their aims:

As a methodological advancement highlighting a limitation of existing approaches and presenting a new model to overcome it, the authors achieve their aim. Generally, the claims/conclusions are supported by the results.

The wider neuroscience claims regarding the role of intrinsic dynamics and external inputs in affecting brain data could benefit from further replication with another independent dataset and in a variety of tasks - but I understand if the authors wanted to focus on the method rather than the neuroscientific claims in this manuscript.

Impact:

The authors propose a useful new approach that solves an important problem in the analysis of task neuroimaging data. I believe the work can have a significant impact on the field.

Reviewer #2 (Public review):

Summary:

In their study, Wang and co-workers aimed to identify sexual dimorphisms in the connectomes of male and hermaphrodite C. elegans, and link these to sex-related behaviors. To this end they analyzed and compared various network properties of simplified male and hermaphrodite connectome datasets, and then focused on the AVA premotor neurons, linking their distinctive connectivity with their differential influence on reversing behaviors between the two sexes.

Strengths:

The study employs a range of basic methods from network and computational neuroscience and provides experimental testing of one of the predictions of the analysis.

Weaknesses:

Various aspects of sexual dimorphism in the nervous system of C. elegans have already been described and discussed (reviewed, for example, in Emmons 2018, Walsh et al. 2021). In particular, Cook et al, (2019), who mapped the male connectome (which serves as the key data in the current study), included in their work an analysis of connectome-level differences between males and hermaphrodites. Unfortunately, the foundations of the current study are somewhat problematic, and the results it provides are rather rudimentary and do not provide substantial new insight.

My critique of the study can be organized around several major issues.

(1) Source data

A large portion of the work is based on the analysis of a single male and a single hermaphrodite connectome datasets from Cook et al. 2019. These original connectomes were simplified in the current study, merging most individual neurons into neuron class nodes. As a measure of edge weight, the authors used the number of synaptic contacts between each two nodes. Cook et al. 2019 estimated this number to be of high variance, and even when considering unweighted connectivity (whether two nodes are at all connected or not) substantial variability exists between independent connectome datasets (e.g., Birari and Rabinowitch, 2024). Therefore, basing the analysis on synaptic weights from a single connectome (for each sex) may be somewhat unreliable.

On top of this, a huge gap may exist between connectome structure and function, especially when overlooking: (1) the sign of the synapses (excitatory vs. inhibitory), (2) synaptic efficiency (a single strong synapse may be more efficient than multiple weak synapses), (3) the spatial distribution of the synapses (clusters of synapses, for example, may be stronger than scattered synapses). These should at the very least be acknowledged. Moreover, the pooling of electrical and chemical synapses done by the authors is problematic, as is assuming all electrical synapses are bidirectional. These and other factors may undermine the results of the analysis, and, again, at the very least should be considered and discussed.

A minimal validation of the analysis could be achieved by sensitivity analyses. For example, studying how consistent the results are when: separately analyzing the chemical and electrical networks; binarizing synaptic contacts to existing vs. non-existing connections regardless of weight; and comparing with additional connectome datasets (at least for hermaphrodites).

Another important approach for validation would be synaptic labeling of key pathways, in order to establish the extent to which they maintain sexual dimorphism across the population (as performed, for example, by Cook et al., 2019; Pechuk et al. 2022).

(2) Statistical analysis

Comparing any two connectomes will show differences in connectivity and other network properties. The question is to what degree the differences found in the current study between two particular male and hermaphrodite connectomes transcend such basic inconsistencies. This fundamental question is not addressed in the manuscript.

A second major concern is that a considerable portion of the results are based on improper comparisons between male and hermaphrodite connectome measures.

In Figure 1D,I,M,V, Figure 2D,H,L, Figure 4E,I there is no sense in statistically testing the differences between hermaphrodite sex-specific (N=2) and shared nodes. The sample size is way too small. Corresponding conclusions about male-specific neurons being different from hermaphrodite-specific neurons in terms of connectivity are thus improperly founded. Similarly, the analyses in Figure 1P,S, 2O,R contain more data points, because of connectivity, but could still be misleading, since all the edges there contain either HSN or VC (just two nodes).

More so, any claim comparing the differences between two measures in males vs. hermaphrodites should be based on a 2X2 (or 3X2) design (e.g., tested using 2-way ANOVA with an interaction term). It is erroneous to interpret comparisons between two effects without directly comparing them (Makin et al., 2019).

When more than one comparison is performed, a one-way ANOVA should precede post hoc analyses, and corrections for multiple comparisons should be carried out and reported.

The plots in Figure 1E,W and Figure 4F,J are illustrative but do not contain any statistical test to support the claims about which functions are emphasized in which sex. They also rely on a very superficial categorization of individual neuron class function, whereas in reality, in C. elegans many neurons serve multiple functions.

In Figures 5-7 individual data points should be plotted, and the error bars and boxes should be defined (in all figures).

Finally, Figure 3C,F,I,L,N,P and Figure 5A-C lack statistical analysis (e.g., via bootstrapping). In addition, the term 'significantly' in the text should be reserved for statistical significance.

(3) Testing network predictions

A key emphasis of the network analysis concerns the AVA premotor neurons. It is well established that reversing behavior is controlled by premotor neurons such as AVA (e.g., Maricq et al. 1995) and that AVA activity is spontaneous and coupled to reversing (e.g., Chronis et al. 2007). More so, it has already been shown that male reversal frequency is higher than that of hermaphrodites (e.g., Mah et al. 1992; Zhao et al. 2003). Similar findings in the current study are thus not very surprising. The current study does add some new detail. Namely, the higher frequency of AVA activity in adult males compared to hermaphrodites, and the presumably sex-specific roles of RIC and DVC as well as several AVA glutamate receptors, in modulating reversing. At the same time, PQR, for example, showed no such role, contrary to the predictions.

Incidentally, AVA is not a commander neuron, but rather a command or, preferably, a premotor neuron. Altogether, the major specific focus of the analysis, predicting a sexually dimorphic role for AVA, is not very novel.

(4) Further predictions

The discussion section presents several additional predictions stemming from the analysis. However, to me, they seem almost arbitrary.

The statement claiming that the authors found the male pharyngeal connectome to be more strongly wired to the main connectome as opposed to previous findings, is unclear. Sex-specific differences in connectivity between the pharyngeal and somatic networks are immediately evident from the connectomes and do not require graph theoretical tools to be discovered (page 4 and discussion of Figure 3N).

The prediction that the AIY→RIA→RMD_DV circuit may facilitate pheromone-guided olfactory steering behavior in males is not very strong. On the one hand, it is known that males respond to sex pheromones (notably, however, if these pheromone receptors are ectopically expressed in hermaphrodites then hermaphrodites also respond to the pheromones [Wan et al. 2019]). Since these pheromone-sensing neurons are also involved in other sensory processes, it is quite trivial that the circuits involved in general sensory-based steering should be shared with specific pheromone-based steering. The fact that the interneurons in the circuit may be more strongly connected (excitatory, inhibitory, electrical?) in males could imply many things but does not add much to the picture.

The authors also mention AFD as having more synaptic contacts with AIY in males, and link this somehow to the dimorphic expression of insulin-like peptides in AFD. However, neuropeptide-based transmission is largely independent of synaptic connections, so I don't see the relevance.

(5) Methods

The example provided in the Methods section for calculating graph measures is very helpful. I am not sure, however, why the length of a path was defined as the reciprocal sum of the edge weights of the connections within the path. Why the reciprocal? Is it the sum of the reciprocals? Do more synaptic contacts imply a shorter path?

The description in the text (as opposed to the Methods section) of node strength is not very clear: "The node strength measures how strongly a node directly possesses with other nodes in the network" - This should be clarified.

For the RC simulation, I assume the sodium and potassium conductances are fixed. If so, they are leak currents themselves. What does the extra leak current represent? Obviously the simulation includes multiple arbitrary assumptions and parameter values. It would be useful to discuss at least the considerations for choosing the model design and parameters. I also assume that the delayed responses in the bottom neurons in Figure 4A (that still respond) are due to indirect synaptic connections (path lengths > 1)?

Reviewer #2 (Public review):

Summary:

Unlike previous traditional protein fusion protocols, the author claims their proposed new method is fast, simple, specific, reversible, and results in a complete 1:1 fusion. A multi-disciplinary approach from cloning and purification, biochemical analyses, and proteomic mass spec confirmation revealed fusion products were achieved.

Strengths:

The author provides convincing evidence that an alternative to traditional protein fusion synthesis is more efficient with 100% yields using connectase. The author optimized the protocol's efficiency with assays replacing a single amino acid and identification of a proline aminopeptidase, Bacilius coagulans (BcPAP), as a usable enzyme to use in the fusion reaction. Multiple examples including Ubiquitin, GST, and antibody fusion/conjugations reveal how this method can be applied to a diverse range of biological processes.

Weaknesses:

Though the ~100% ligation efficiency is an advancement, the long recognition linker may be the biggest drawback. For large native proteins that are challenging/cannot be synthesized and require multiple connectase ligation reactions to yield a complete continuous product, the multiple interruptions with long linkers will likely interfere with protein folding, resulting in non-native protein structures. This method will be a good alternative to traditional approaches as the author mentioned but limited to generating epitope/peptide/protein tagged proteins, and not for synthetic protein biology aimed at examining native/endogenous protein function in vitro.

Reviewer #2 (Public review):

Summary:

The aim was to identify the mechanisms that underlie a form of long-term potentiation (LTP) that requires activation of dopamine (DA).

Strengths:

The authors have provided multiple lines of evidence that supports their conclusions; namely that this pathway involves activation of a cAMP / PKA pathway that leads to the insertion of calcium permeable AMPA receptors.

Weaknesses:

Some of the experiments could have been conducted in a more convincing manner.

Reviewer #2 (Public review):

Summary:

In this paper, the authors use numerical simulations to try to understand better a major experimental discovery in songbird neuroscience from 2002 by Richard Hahnloser and collaborators. The 2002 paper found that a certain class of projection neurons in the premotor nucleus HVC of adult male zebra finch songbirds, the neurons that project to another premotor nucleus RA, fired sparsely (once per song motif) and precisely (to about 1 ms accuracy) during singing.

The experimental discovery is important to understand since it initially suggested that the sparsely firing RA-projecting neurons acted as a simple clock that was localized to HVC and that controlled all details of the temporal hierarchy of singing: notes, syllables, gaps, and motifs. Later experiments suggested that the initial interpretation might be incomplete: that the temporal structure of adult male zebra finch songs instead emerged in a more complicated and distributed way, still not well understood, from the interaction of HVC with multiple other nuclei, including auditory and brainstem areas. So at least two major questions remain unanswered more than two decades after the 2002 experiment: What is the neurobiological mechanism that produces the sparse precise bursting: is it a local circuit in HVC or is it some combination of external input to HVC and local circuitry? And how is the sparse precise bursting in HVC related to a songbird's vocalizations?

The authors only investigate part of the first question, whether the mechanism for sparse precise bursts is local to HVC. They do so indirectly, by using conductance-based Hodgkin-Huxley-like equations to simulate the spiking dynamics of a simplified network that includes three known major classes of HVC neurons and such that all neurons within a class are assumed to be identical. A strength of the calculations is that the authors include known biophysically deduced details of the different conductances of the three major classes of HVC neurons, and they take into account what is known, based on sparse paired recordings in slices, about how the three classes connect to one another. One weakness of the paper is that the authors make arbitrary and not well-motivated assumptions about the network geometry, and they do not use the flexibility of their simulations to study how their results depend on their network assumptions. A second weakness is that they ignore many known experimental details such as projections into HVC from other nuclei, dendritic computations (the somas and dendrites are treated by the authors as point-like isopotential objects), the role of neuromodulators, and known heterogeneity of the interneurons. These weaknesses make it difficult for readers to know the relevance of the simulations for experiments and for advancing theoretical understanding.

Strengths:

The authors use conductance-based Hodgkin-Huxley-like equations to simulate spiking activity in a network of neurons intended to model more accurately songbird nucleus HVC of adult male zebra finches. Spiking models are much closer to experiments than models based on firing rates or on 2-state neurons.

The authors include information deduced from modeling experimental current-clamp data such as the types and properties of conductances. They also take into account how neurons in one class connect to neurons in other classes via excitatory or inhibitory synapses, based on sparse paired recordings in slices by other researchers.

The authors obtain some new results of modest interest such as how changes in the maximum conductances of four key channels (e.g., A-type K+ currents or Ca-dependent K+ currents) influence the structure and propagation of bursts, while simultaneously being able to mimic accurately current-clamp voltage measurements.

Weaknesses:

One weakness of this paper is the lack of a clearly stated, interesting, and relevant scientific question to try to answer. In the introduction, the authors do not discuss adequately which questions recent experimental and theoretical work have failed to explain adequately, concerning HVC neural dynamics and its role in producing vocalizations. The authors do not discuss adequately why they chose the approach of their paper and how their results address some of these questions.

For example, the authors need to explain in more detail how their calculations relate to the works of Daou et al, J. Neurophys. 2013 (which already fitted spiking models to neuronal data and identified certain conductances), to Jin et al J. Comput. Neurosci. 2007 (which already discussed how to get bursts using some experimental details), and to the rather similar paper by E. Armstrong and H. Abarbanel, J. Neurophys 2016, which already postulated and studied sequences of microcircuits in HVC. This last paper is not even cited by the authors.

The authors' main achievement is to show that simulations of a certain simplified and idealized network of spiking neurons, which includes some experimental details but ignores many others, match some experimental results like current-clamp-derived voltage time series for the three classes of HVC neurons (although this was already reported in earlier work by Daou and collaborators in 2013), and simultaneously the robust propagation of bursts with properties similar to those observed in experiments. The authors also present results about how certain neuronal details and burst propagation change when certain key maximum conductances are varied.

However, these are weak conclusions for two reasons. First, the authors did not do enough calculations to allow the reader to understand how many parameters were needed to obtain these fits and whether simpler circuits, say with fewer parameters and simpler network topology, could do just as well. Second, many previous researchers have demonstrated robust burst propagation in a variety of feed-forward models. So what is new and important about the authors' results compared to the previous computational papers?

Also missing is a discussion, or at least an acknowledgment, of the fact that not all of the fine experimental details of undershoots, latencies, spike structure, spike accommodation, etc may be relevant for understanding vocalization. While it is nice to know that some models can match these experimental details and produce realistic bursts, that does not mean that all of these details are relevant for the function of producing precise vocalizations. Scientific insights in biology often require exploring which of the many observed details can be ignored and especially identifying the few that are essential for answering some questions. As one example, if HVC-X neurons are completely removed from the authors' model, does one still get robust and reasonable burst propagation of HVC-RA neurons? While part of the nucleus HVC acts as a premotor circuit that drives the nucleus RA, part of HVC is also related to learning. It is not clear that HVC-X neurons, which carry out some unknown calculation and transmit information to area X in a learning pathway, are relevant for burst production and propagation of HVC-RA neurons, and so relevant for vocalization. Simulations provide a convenient and direct way to explore questions of this kind.

One key question to answer is whether the bursting of HVC-RA projection neurons is based on a mechanism local to HVC or is some combination of external driving (say from auditory nuclei) and local circuitry. The authors do not contribute to answering this question because they ignore external driving and assume that the mechanism is some kind of intrinsic feed-forward circuit, which they put in by hand in a rather arbitrary and poorly justified way, by assuming the existence of small microcircuits consisting of a few HVC-RA, HVC-X, and HVC-I neurons that somehow correspond to "sub-syllabic segments". To my knowledge, experiments do not suggest the existence of such microcircuits nor does theory suggest the need for such microcircuits.

Another weakness of this paper is an unsatisfactory discussion of how the model was obtained, validated, and simulated. The authors should state as clearly as possible, in one location such as an appendix, what is the total number of independent parameters for the entire network and how parameter values were deduced from data or assigned by hand. With enough parameters and variables, many details can be fit arbitrarily accurately so researchers have to be careful to avoid overfitting. If parameter values were obtained by fitting to data, the authors should state clearly what the fitting algorithm was (some iterative nonlinear method, whose results can depend on the initial choice of parameters), what the error function used for fitting (sum of least squares?) was, and what data were used for the fitting.

The authors should also state clearly the dynamical state of the network, the vector of quantities that evolve over time. (What is the dimension of that vector, which is also the number of ordinary differential equations that have to be integrated?) The authors do not mention what initial state was used to start the numerical integrations, whether transient dynamics were observed and what were their properties, or how the results depended on the choice of the initial state. The authors do not discuss how they determined that their model was programmed correctly (it is difficult to avoid typing errors when writing several pages or more of a code in any language) or how they determined the accuracy of the numerical integration method beyond fitting to experimental data, say by varying the time step size over some range or by comparing two different integration algorithms.

Also disappointing is that the authors do not make any predictions to test, except rather weak ones such as that varying a maximum conductance sufficiently (which might be possible by using dynamic clamps) might cause burst propagation to stop or change its properties. Based on their results, the authors do not make suggestions for further experiments or calculations, but they should.

Reviewer #2 (Public review):

Summary:

The authors constructed an in-frame deletion of moeA gene, which is involved in molybdopterin cofactor (MoCo) biosynthesis, and investigated its role in structural colors in Flavobacterium IR1. The deletion of moeA shifted colony color from green to blue, reduced colony spreading, and increased starch degradation, which was attributed to the upregulation of various proteins in polysaccharide utilization loci. This study lays the ground for developing new colorants by modifying genes involved in structural colors.

Major strengths and weaknesses:

The authors conducted well-designed experiments with appropriate controls and the results in the paper are presented in a logical manner, which supports their conclusions. Using statistical tests to compare the differences between the wild type and moeA mutant, and adding a significance bar in Figure 4B, would strengthen their claims on differences in cell motility regarding differences in cell motility. Additionally, in the result section (Figure 6), the authors suggest that the shift in blue color is "caused by cells which are still highly ordered but narrower", which to my knowledge is not backed up by any experimental evidence.

Overall, this is a well-written paper in which the authors effectively address their research questions through proper experimentation. This work will help us understand the genetic basis of structural colors in Flavobacterium and open new avenues to study the roles of additional genes and proteins in structural colors.

Reviewer #2 (Public review):

Summary:

Utilizing a combination of transcriptomic and proteomic profiling as well as cellular phenotyping from source-matched PASMC and PAAFs in IPAH, this<br /> study sought to explore a molecular comparison of these cells in order to track distinct cell fate trajectories and acquisition of their IPAH-associated cellular states. The authors also aimed to identify cell-cell communication axes in order to infer mechanisms by which these two cells interact and depend upon external cues. This study will be of interest to the scientific and clinical communities of those interested in pulmonary vascular biology and disease. It also will appeal to those interested in lung and vascular development as well as multi-omic analytic procedures.

Strengths:

(1) This is one of the first studies using orthogonal sequencing and phenotyping for characterization of source-matched neighoring mesenchymal PASMC and PAAF cells in healthy and diseased IPAH patients. This is a major strength which allows for direct comparison of neighboring cell types and the ability to address an unanswered question regarding the nature of these mesenchymal "mural" cells at a precise molecular level.

(2) Unlike a number of multi-omic sequencing papers that read more as an atlas of findings without structure, the inherent comparative organization of the study and presentation of the data were valuable in aiding the reader in understanding how to discern the distinct IPAH-associated cell states. As a result, the reader not only gleans greater insight into these two interacting cell types in disease but also now can leverage these datasets more easily for future research questions in this space.

(3) There are interesting and surprising findings in the cellular characterizations, including the low proliferative state of IPAH-PASMCs as compared to the hyperproliferative state in IPAH-PAAFs. Furthermore, the cell-cell communication axes involving ECM components and soluble ligands provided by PAAFs that direct cell state dynamics of PASMCs offer some of the first and foundational descriptions of what are likely complex cellular interactions that await discovery.

(4) Technical rigor is quite high in the -omics methodology and in vitro phenotyping tools used.

Weaknesses:

There are some weaknesses in the methodology that should temper the conclusions:

(1) The number of donors sampled for PAAF/PASMCs was relatively small for both healthy controls and IPAH patients. Thus, while the level of detail of -omics profiling was quite deep, the generalizability of their findings to all IPAH patients or Group 1 PAH patients is limited. In the revised manuscript, the authors addressed this concern with important text changes and additional data.

(2) While the study utilized early passage cells, these cells nonetheless were still cultured outside the in vivo milieu prior to analysis. Thus, while there is an assumption that these cells do not change fundamental behavior outside the body, that is not entirely proven for all transcriptional and proteomic signatures. As such, the major alterations that are noted would be more compelling if validated from tissue or cells derived directly from in vivo sources. Without such validation, the major limitation of the impact and conclusions of the paper is that the full extent of the relevance of these findings to human disease is not known. The authors addressed this concern appropriately with significant text changes to clarify these limitations for the reader.

(3) While the presentation of most of the manuscript was quite clear and convincing, the terminology and conclusions regarding "cell fate trajectories" throughout the manuscript did not seem to be fully justified. That is, all of the analyses were derived from cells originating from end-stage IPAH, and otherwise, the authors were not lineage tracing across disease initiation or development (which would be impossible currently in humans). So, while the description of distinct "IPAH-associated states" makes sense, any true cell fate trajectory was not clearly defined. The revised manuscript has removed this terminology and replaced it with more precise language.

Comments on revisions:

The authors were quite responsive to all of my concerns, offering both important revisions to the presentation of the work as well as new data. While some of the limitations were not fully resolved (and the authors provide appropriate justification for this), the revised manuscript is much improved. It will be of great interest to both the scientific and clinical communities.

Reviewer #3 (Public review):

Summary:

The goal of the paper is to examine the objective function of total reward rate in an environment to understand behavior of humans and animals in two types of decision-making tasks: 1) stay/forgo decisions and 2) simultaneous choice decisions. The main aims are to reframe the equation of optimizing this normative objective into forms that are used by other models in the literature like subjective value and temporally discounted reward. One important contribution of the paper is the use of this theoretical analysis to explain apparent behavioral inconsistencies between forgo and choice decisions observed in the literature.

Strengths:

The paper provides a nice way to mathematically derive different theories of human and animal behavior from a normative objective of global reward rate optimization. As such, this work has value in trying to provide a unifying framework for seemingly contradictory empirical observations in literature, such as differentially optimal behaviors in stay-forgo v/s choice decision tasks. The section about temporal discounting is particularly well motivated as it serves as another plank in the bridge between ecological and economic theories of decision-making. The derivation of the temporal discounting function from subjective reward rate is much appreciated as it provides further evidence for potential equivalence between reward rate optimization and hyperbolic discounting, which is known to explain a slew of decision-making behaviors in the economics literature.

Weaknesses:

(1) Readability and organization:<br /> While I appreciate the detailed analysis and authors' attempts to provide as many details as possible, the paper would have benefitted from a little selectivity on behalf of the authors so that the main contributions aren't buried by the extensive mathematical detail provided.<br /> For instance, in Figure 5, the authors could have kept the most important figures (A, B and G) to highlight the most relevant terms in the subjective value instead of providing all possible forms of the equation.

Further, in subfigure 5E, is there a reason that the outside reward r_out is shown to be zero? The text referencing 5E is also very unclear: "In so downscaling, the subjective value of a considered pursuit (green) is to the time it would take to traverse the world were the pursuit not taken, 𝑡_out, as its opportunity cost subtracted reward (cyan) is to the time to traverse the world were it to be taken (𝑡_in+ 𝑡_out) (Figure 5E)."

In the abstract, the malapportionment of time is mentioned as a possible explanation for reconciling observed empirical results between simultaneous and sequential decision-making. However, perhaps due to the density of mathematical detail presented, the discussion of the malapportionment hypothesis is pushed all the way to the end of the discussion section.

(2) Apportionment Cost definition and interpretation<br /> This additional cost arises in their analyses from redefining the opportunity cost in terms of just "outside" rewards so that the subjective value of the current pursuit and the opportunity cost are independent of each other. However, in doing so, an additional term arises in defining the subjective value of a pursuit, named here the "apportionment cost". The authors have worked hard to provide a definition to conceptualize the apportionment cost though it remains hard to intuit, especially in comparison to the opportunity cost. The additive form of apportionment cost (Equation 9) doesn't add much in way of intuition or their later analyses for the malapportionment hypothesis. It appears that the most important term is the apportionment scaling term so just focusing on this term will help the reader through the subsequent analyses.

(3) Malapportionment Hypothesis: From where does this malapportionment arise?<br /> The authors identify the range of values for t_in and t_out in Figure 18, the terms comprising the apportionment scaling term, that lead to optimal forgo behaviors despite suboptimally rejecting the larger-later (LL) choice in choice decisions. They therefore conclude that a lower apportionment scale, which arises from overestimating the time required outside the pursuit (t_out) or underestimating the time required at the current pursuit (t_in). What is not discussed though is whether and how the underestimation of t_out and overestimation of t_in can be dissociated, though it is understood that empirical demonstration of this dissociation is outside the scope of this work.

Reviewer #2 (Public review):

Summary:

In this study, Gao et al. use RNA-seq to identify Hspa2 as one of the earliest transcripts heterogeneously distributed between blastomeres. Functional studies are performed using siRNA knockdown showing Hspa2 may bias cells toward the ICM lineage via interaction with the known methyltransferase CARM1.

Strengths:

This study tackles an important question regarding the origins of the first cell fate decision in the preimplantation embryo. It provides novelty in its identification of Hspa2 as a heterogeneous transcript in the early embryo and proposes a plausible mechanism showing interactions with Carm1. Multiple approaches are used to validate their functional studies (FISH, WB, development rates, proteomics). Given only 4 other transcripts/RNA have been identified at or before the 4-cell stage (LincGET, CARM1, PRDM14, HMGA1), this would be an important addition to our understanding of how TE vs ICM fate is established.

Weaknesses:

The RNA-seq results leading the authors to focus on Hspa2 are not included in the manuscript. This dataset would serve as an important resource but is neither included nor discussed. Nor is it mentioned whether Hspa2 was identified in prior RNA-seq embryos studies (for example Deng Science 2014).

Furthermore, the authors show that Hspa2 knockdown at the 1-cell stage lowers total Carm1 levels at the 4-cell stage. However, it is unclear how total abundance within the embryo alters lineage specification within blastomeres. The authors go on to propose a plausible mechanism involving Hspa2 and Carm1 interaction, but do not discuss how expression levels may be involved.

Reviewer #2 (Public review):

Summary:

The work from You et al. elucidates the clonal contribution of ageing stem and progenitor cells to both native and perturbed hematopoiesis. The authors use a previously published in vivo lineage tracing system (Patel et al., 2022) that relies on the random integration of a transposon element in the mouse genome. They barcode all mouse cells and then look at lineage relationships between HSPC and mature populations after ~90 weeks.

Strengths:

This work offers very interesting insights into the clonal behaviour of HSPC in the native and perturbed setting during ageing. Experiments are well-planned and well-executed. Understanding the clonal output of HSPCs in aged mice in a native setting, after 5-FU treatment, and upon transplantation are important findings for the field.

Weaknesses:

We found appraising the graphs, interpreting the findings, and understanding those findings in the main text very difficult to follow. While we have made some suggestions below, we encourage the authors to think carefully about what the core messages are, and how best to visualise those, both in terms of data viz and in a schematic to summarise the key findings, and to use plain language in the text.

Reviewer #2 (Public review):

Summary:

The authors tested how ROS and PZA affected Mycobacterium survival to determine if ROS could have a role in the remarkable in vivo efficacy of PZA.

Strengths:

This is a well-written and clear manuscript convincingly demonstrating the synergy between PZA and reactive oxygen species in the inhibition of growth and survival of Mycobacterium tuberculosis.

Weaknesses:

The manuscript would benefit from a clear statement of the rationale for the protocols used to examine the synergy of PZA with ROS, the possible models their protocols could be testing, and then how their data supports or disproves the models being tested. The manuscript appears to propose, as stated in the title, that "Oxidative stress drives potent bactericidal activity of pyrazinamide...". However their experimental design more likely tests the effect of PZA on ROS sensitivity. Indeed, by the last figure, the authors begin the present their data as PZA sensitizing the bacteria to ROS. More clarity on these possible models and the different interpretations of the data should be considered.

Impact:

The data provide important insight to expand our understanding of the in vivo efficacy of PZA in the treatment of tuberculosis.

Reviewer #2 (Public review):

Summary:

Ueno et al. described substantial changes in the afadin knockout retina. These changes include decreased numbers of rods and cones, an increased number of bipolar cells, and disrupted somatic and synaptic organization of the outer limiting membrane, outer nuclear layer, and outer plexiform layer. In contrast, the number and organization of amacrine cells and retinal ganglion cells remain relatively intact. They also observed changes in ERG responses and RGC receptive fields and functions using MEA recordings.

Strengths:

The morphological characterization of retinal cell types and laminations is detailed and relatively comprehensive.

Weaknesses:

(1) The major weakness of this study, perhaps, is that its findings are predominantly descriptive and lack any mechanistic explanation. As afadin is key component of adherent junctions, its role in mediating retinal lamination has been reported previously (see PMCID: PMC6284407). Thus, a more detailed dissection of afadin's role in processes, such as progenitor generation, cell migration, or the formation of retinal lamination would provide greater insight into the defects caused by knocking out afadin.

(2) The authors observed striking changes in the numbers of rods, cones, and BCs, but not in ACs or RGCs. The causes of these distinct changes in specific cell classes remain unclear. Detailed characterizations, such as the expression of afadin in early developing retina, tracing cell numbers across various early developmental time points, and staining of apoptotic markers in developing retinal cells, could help to distinguish between defects in cell generation and survival, providing a better understand of the underlying causes of these phenotypes.

(3) Although the total number of ACs or RGCs remains unchanged, their localizations are somewhat altered (Figures 2E and 4E). Again, the cause of the altered somatic localization in ACs and RGCs is unclear.

(4) One conclusion that the authors emphasise is that the function of RGCs remains detectable despite a major disrupted outer plexiform layer. However, the organization of the inner plexiform layer remains largely intact, and the axonal innervation of BCs remains unchanged. This could explain the function integrity of RGCs. In addition, the resolution of detecting RGCs by MEA is low, as they only detected 5 clusters in heterozygous animals. This represents an incomplete clustering of RGC functional types and does not provide a full picture of how functional RGC types are altered in the afadin knockout.

Minor Comments:

(1) Line 56-67: "Overall, these findings provide the first evidence that retinal circuit function can be partially preserved even when there are significant disruptions in retinal lamination and photoreceptor synapses" There is existing evidence showing substantial adaption in retinal function when retinal lamination or photoreceptor synapses are disrupted, such as PMCID: PMC10133175.

(2) Line 114-115: "we focused on afadin, which is a scaffolding protein for nectin and has no ortholog in mice." The term "Ortholog" is misused here, as the mouse has an afadin gene. Should the intended meaning be that afadin has no other isoforms in mouse?

Reviewer #2 (Public review):

Summary:

In this paper, the authors want to test the hypothesis that frictional instabilities rather than friction are the main drivers for discriminating flat surfaces of different sub-nanometric roughness profiles.

They first produced flat surfaces with 6 different coatings giving them unique and various properties in terms of roughness (picometer scale), contact angles (from hydrophilic to hydrophobic), friction coefficient (as measured against a mock finger), and Hurst exponent.

Then, they used those surfaces in two different experiments. In the first experiment, they used a mock finger (PDMS of 100kPA molded into a fingertip shape) and slid it over the surfaces at different normal forces and speeds. They categorized the sliding behavior as steady sliding, sticking spikes, and slow frictional waves by visual inspection, and show that the surfaces have different behaviors depending on normal force and speed. In a second experiment, participants (10) were asked to discriminate pairs of those surfaces. It is found that each of those pairs could be reliably discriminated by most participants.

Finally, the participant's discrimination performance is correlated with differences in the physical attributes observed against the mock finger. The authors found a positive correlation between participants' performances and differences in the count of steady sliding against the mock finger and a negative correlation between participants' reaction time and differences in the count of stiction spikes against the mock finger. They interpret those correlations as evidence that participants use those differences to discriminate the surfaces.

Strengths:

The created surfaces are very interesting as they are flat at the nanometer scale, yet have different physical attributes and can be reliably discriminated.

Weaknesses:

In my opinion, the data presented in the paper do not support the conclusions. The conclusions are based on a correlation between results obtained on the mock finger and results obtained with human participants but there is no evidence that the human participants' fingertips will behave similarly to the mock finger during the experiment. Figure 3 gives a hint that the 3 sliding behaviors can be observed in a real finger, but does not prove that the human finger will behave as the mock finger, i.e., there is no evidence that the phase maps in Figure 1C are similar for human fingers and across different people that can have very different stiffness and moisture levels.

I believe that the authors collected the contact forces during the psychophysics experiments, so this shortcoming could be solved if the authors use the actual data, and show that the participant responses can be better predicted by the occurrence of frictional instabilities than by the usual metrics on a trial by trial basis, or at least on a subject by subject basis. I.e. Poor performers should show fewer signs of differences in the sliding behaviors than good performers.

The sample size (10) is very small.

Reviewer #2 (Public review):

Summary:

In this manuscript, the authors identify Leiomodin-1 (LMOD1) as a key regulator of early myogenic differentiation, demonstrating its interaction with SIRT1 to influence SIRT1's cellular localization and gene expression. The authors propose that LMOD1 translocates SIRT1 from the nucleus to the cytoplasm to permit the expression of myogenic differentiating genes such as MYOD or Myogenin.

Strengths:

A major strength of this work lies in the robust temporal resolution achieved through a time-course mass spectrometry analysis of in vitro muscle differentiation. This provides novel insights into the dynamic process of myogenic differentiation, often under-explored in terms of temporal progression. The authors provide a strong mechanistic case for how LMOD1 exerts its role in muscle differentiation which opens avenues to modulate.

Weaknesses:

One limitation of the study is the in vivo data. Although the authors do translate their findings in vivo for LMOD1 localization and expression, the cross-sectional imaging is not highly convincing. Longitudinal cuts or isolated fibers could have been more useful specimens to answer these questions. Moreover, the authors do not assess their in vitro SIRT1 findings in vivo. A few key experiments in regenerating or aged mice would strengthen the mechanistic insight of the findings.

Discussion:

Overall, the study emphasizes the importance of understanding the temporal dynamics of molecular players during myogenic differentiation and provides valuable proteomic data that will benefit the field. Future studies should explore whether LMOD1 modulates the nuclear-cytoplasmic shuttling of other transcription factors during muscle development and how these processes are mechanistically achieved. Investigating whether LMOD1 can be therapeutically targeted to enhance muscle regeneration in contexts such as exercise, aging, and disease will be critical for translational applications. Additionally, elucidating the interplay among LMOD1, LMOD2, and LMOD3 could uncover broader implications for actin cytoskeletal regulation in muscle biology.

Reviewer #2 (Public review):

Summary:

To design proteins and predict disease, we want to predict the effects of mutations on the function of a protein. To make these predictions, biologists have long turned to statistical models that learn patterns that are conserved across evolution. There is potential to improve our predictions however by incorporating structure. In this paper the authors build a denoising auto-encoder model that incorporates sequence and structure to predict mutation effects. The model is trained to predict the sequence of a protein given its perturbed sequence and structure. The authors demonstrate that this model is able to predict the effects of mutations better than sequence-only models.

As well, the authors curate a set of assays measuring the effect of mutations on thermostability. They demonstrate their model also predicts the effects of these mutations better than previous models and make this benchmark available for the community.

Strengths:

The authors describe a method that makes accurate mutation effect predictions by informing its predictions with structure.

The authors curate a new dataset of assays measuring thermostability. These can be used to validate and interpret mutation effect prediction methods in the future.

Weaknesses:

In the review period, the authors included a previous method, SaProt, that similarly uses protein structure to predict the effects of mutations, in their evaluations. They see that SaProt performs similarly to their method.

ProteinGym is largely made of deep mutational scans, which measure the effect of every mutation on a protein. These new benchmarks contain on average measurements of less than a percent of all possible point mutations of their respective proteins. It is unclear what sorts of protein regions these mutations are more likely to lie in; therefore it is challenging to make conclusions about what a model has necessarily learned based on its score on this benchmark. For example, several assays in this new benchmark seem to be similar to each other, such as four assays on ubiquitin performed in pH 2.25 to pH 3.0.

Comments on revisions:

I think the rounds of review have improved the paper and I've raised my score.

Reviewer #3 (Public review):

Arbués and colleagues describe the impact of mycobacterial genetic diversity on host-infection phenotypes. The authors evaluate Mtb infection and contextualize host-responses, bacterial growth and metabolic transitioning in vitro using their previously established model of blood-derived, primary-human-cells cultured within a collagen/fibronectin matrix. They seek to demonstrate the effectiveness of the model in determining mycobacterial strain specific granuloma-dependent host-pathogen interactions.

Understanding the way mycobacterial genetic diversity impacts granuloma biology in tuberculosis is an important goal. One of this works strengths is the use of primary human cells and two constituents of pulmonary extracellular matrix to model Mtb infection. The authors and others have previously shown that Mtb infected PBMC aggregates share important characteristics with early pulmonary TB granulomas. Use of multiple genetically distinct strains of Mtb defines this work and further bolsters it potential impact. However, the study is not comprehensive as lineages 6 and 7 are not tested. Experiments are primarily descriptive, and the methodologies are conventional. Correlative relationships are the manuscripts focus and effect sizes are generally small.

The main aim of this work is to extend an in vitro granuloma model to the study of a large collection of well characterized, genetically diverse representatives of the mycobacterium tuberculosis complex (MTBC). I believe that they accomplish that aim. The work does investigate MTBC infection of aggregated PBMCs using three strains each of Mtb lineages 1-5 and H37Rv, which is not a trivial undertaking. The experimental aims are to show that MTBC genetic diversity impacts growth and dormancy of granuloma bound bacteria and, the host responses of granulomatous aggregation as well as macrophage apoptosis, lymphocyte activation and soluble mediator release within granulomas. The methodologies employed are sufficient to test most of these aims. The authors conclusions regarding their results are mostly supported by the data. The conclusion that lineage impacts growth within granulomas is likely true and the data as presented reflect such a relationship. Their conclusions regarding lineage's impact on dormancy are partially supported, as their findings demonstrate that assays for dormancy identify strain-specific metabolic changes in the bacteria consistent with a dormancy-like state but also identify replicating bacteria as being dormant. The data strongly supports the impact of mycobacterial genetic diversity on a spectrum of granulomatous responses in their model system. Those findings are a highlight of the publication. The data further supports the idea that strain diversity impacts macrophage apoptosis but a relationship of apoptosis to the granulomatous response is not effectively evaluated. The association of lymphocyte activation with reduced mycobacterial growth as an aspect of granulomas is well documented in the literature and a negative correlation between T cell activation and growth is supported by the authors results. Their data also support the conclusion that soluble mediator production by PBMCs is different based on the infecting strain of mycobacteria and that IL1b modulates aggregate phenotypes in their model.

The authors contribute some valuable insights, particularly in Figure 3. Their model is higher echelon relative to others in the field, but I don't believe that it possesses all the components necessary to replicate formation of mycobacterial granulomas in vivo. That being said, their identification of donor-dependent aggregation phenotypes by mycobacterial strain has the potential to enable future investigations of human and mycobacterial genetic components that are involved in the formation of TB granulomas.

Reviewer #2 (Public review):

Summary:

NRDE-3 is a nuclear WAGO-clade Argonaute that, in somatic cells, binds small RNAs amplified in response to the ERGO-class 26G RNAs that target repetitive sequences. This manuscript reports that, in the germline and early embryos, NRDE-3 interacts with a different set of small RNAs that target mRNAs. This class of small RNAs were previously shown to bind to a different WAGO-clade Argonaute called CSR-1, which is cytoplasmic unlike nuclear NRDE-3. The switch in NRDE-3 specificity parallels recent findings in Ascaris where the Ascaris NRDE homolog was shown to switch from sRNAs that target repetitive sequences to CSR-class sRNAs that target mRNAs.

The manuscript also correlates the change in NRDE-3 specificity with the appearance in embryos of cytoplasmic condensates that accumulate SIMR-1, a scaffolding protein that the authors previously implicated in sRNA loading for a different nuclear Argonaute HRDE-1. By analogy, and through a set of corelative evidence, the authors argue that SIMR foci arise in embryogenesis to facilitate the change in NRDE-3 small RNA repertoire. The paper presents lots of data that beautifully documents the appearance and composition of the embryonic SIMR-1 foci, including evidence that a mutated NRDE-3 that cannot bind sRNAs accumulate in SIMR-1 foci in SIMR-1-dependent fashion.

Reviewer #2 (Public review):

Summary:

In this study, the authors aimed to delineate the antimicrobial activity of linalool and tried to investigate the mode of action on linalool against S. parasitica infection. One of the main focus of this work was to identify the in vitro and in vivo mechanisms associated with the protective role of linalool against S. parasitica infection.

Strengths:

(1) Authors have used a variety of techniques to prove their hypothesis.<br /> (2) Adequate number of replicates were used in their studies.<br /> (3) Their findings showed a protective role of linalool against oomycetes and makes it an attractive future antibiotic in the aquaculture industry.

Weaknesses: The revised version of the manuscript is more thoroughly written with clearer explanations, however there are a few weaknesses in this manuscript.

(1) Although the introduction section was rewritten with rationale, it's still lengthy and not very much to the point.<br /> (2) The claim of linalool regulating the gut microbiota is based on the correlation analysis only. It's not super convincing and requires experimental validation to strengthen the claim.

Overall, the conclusions drawn by the authors are justified by the data. Importantly, this paper has discovered the novelty of the compound linalool as a potent antimicrobial agent and might open up future possibilities to use this compound in the aquaculture industry.

Reviewer #2 (Public review):

Summary:

The manuscript by Nosaka et al is a comprehensive study exploring the involvement of IL1beta signaling in a 2-hit model of lung injury + ventilation, with a focus on modulation by hypothermia.

Strengths:

The authors demonstrate quite convincingly that interleukin 1 beta plays a role in the development of ventilator-induced lung injury in this model, and that this role includes the regulation of neutrophil extracellular trap formation. The authors use a variety of in vivo animal-based and in vitro cell culture work, and interventions including global gene knockout, cell-targeted knockout and pharmacological inhibition, which greatly strengthen the ability to make clear biological interpretations.

Weaknesses:

A primary point for open discussion is the translatability of the findings to patients. The main model used, one of intratracheal LPS plus mechanical ventilation is well accepted for research exploring the pathogenesis and potential treatments for acute respiratory distress syndrome (ARDS). However, the interpretation may still be open to question - in the model here, animals were exposed to LPS to induce inflammation for only 2 hours, and seemingly displayed no signs of sickness, before the start of ventilation. This would not be typical for the majority of ARDS patients, and whether hypothermia could be effective once substantial injury is already present remains an open question. The interaction between LPS/infection and temperature is also complicated - in humans, LPS (or infection) induces a febrile, hyperthermic response, whereas in mice LPS induces hypothermia (eg. Ganeshan K, Chawla A. Nat Rev Endocrinol. 2017;13:458-465). Given this difference in physiological response, it is therefore unclear whether hypothermia in mice and hypothermia in humans are easily comparable. Finally, the use of only young, male animals such as in the current study has been typical but may be criticised as limiting translatability to people.

Therefore while the conclusions of the paper are well supported by the data, and the biological pathways have been impressively explored, questions still remain regarding the ultimate interpretations.

Reviewer #2 (Public review):

Summary:<br /> In this manuscript Qiwang Xiang et al. investigated the role of the E3 ubiquitin ligase ITCH in the life cycle of SARS-CoV-2. They claim the following:<br /> i) ITCH promotes virion assembly by interacting with E and M proteins and enhancing their K63-linked ubiquitination<br /> ii) ITCH-mediated ubiquitination promotes autophagosome-dependent secretion of viral particles.<br /> iii) ITCH stabilizes the viral spike protein by impairing its processing by furin and catepsin L proteases.<br /> The manuscript provides an interesting exploration of ITCH's role in the SARS-CoV-2 life cycle but requires additional work to strengthen key claims and address potential confounding factors.

Strengths:

The experiments are sufficiently clear in documenting that ITCH activity is critical for efficient SARS-CoV-2 replication and for M and E proteins K63-linked ubiquitination

Weaknesses:

• The manuscript does not convincingly demonstrate how ITCH-mediated ubiquitination of E and M impacts virus assembly and release. Identifying the specific lysine residues in M and E targeted by ITCH, and generating mutant VLPs or recombinant viruses, would strengthen the conclusions.<br /> • Most of the conclusions rely on ITCH overexpression data, which may have off-target effects on Golgi integrity and vesicular trafficking. For instance, figure 4F provides evidence of altered Golgi morphology and TGN46 fragmentation raising concerns that ITCH overexpression could indirectly mislocalize furin, affecting S1/S2 cleavage of the spike protein. In addition, inhibition of furin activity may also lead to off-target effects, given its role in processing numerous host proteins.<br /> • Similarly, ITCH overexpression is likely to indirectly affect cathepsin-L maturation. In addition, the manuscript does not clarify how impaired cathepsin L activity would influence virus assembly or release.<br /> • A major concern is also the lack of quantification and statistical analysis of immunofluorescence images throughout the manuscript, which undermines the reliability of these observations.

Reviewer #2 (Public review):

The study by Xue et al. reports the structural basis for the regulation of the human cardiac sodium-calcium exchanger, NCX1, by the endogenous activator PIP2 and the small molecule inhibitor SEA400. This well-written study contextualizes the new data within the existing literature on NCX1 and the broader NCX family. This work builds upon the authors' previous study (Xue et al., 2023), which presented the cryo-EM structures of human cardiac NCX1 in both inactivated and activated states. The 2023 study highlighted key structural differences between the active and inactive states and proposed a mechanism where the activity of NCX1 is regulated by the interactions between the ion-transporting transmembrane domain and the cytosolic regulatory domain. Specifically, in the inward-facing state and at low cytosolic calcium levels, the transmembrane (TM) and cytosolic domains form a stable interaction that results in the inactivation of the exchanger. In contrast, calcium binding to the cytosolic domain at high cytosolic calcium levels disrupts the interaction with the TM domain, leading to active ion exchange.

In the current study, the authors present two mechanisms explaining how both PIP2 stimulates NCX1 activity by destabilizing the protein's inactive state (i.e., by disrupting the interaction between the TM domain and the cytosolic domain) and how SEA400 stabilizes this interaction, thereby acting as a specific inhibitor of the system.

The first part of the results section addresses the effect of PIP2 and PIP2 diC8 on NCX1 activity. This is pertinent as the authors use the diC8 version of this lipid (which has a shorter acyl chain) in their subsequent cryo-EM structure due to the instability of native PIP2. I am not an electrophysiology expert; however, my main comment would be to ask whether there is sufficient data here to characterise fully the differences between PIP2 and PIP2 diC8 on NCX1 function. It appears from the text that this study is the first to report these differences, so perhaps this data needs to be more robust. The spread of the data points in Figure 1B is possibly a little unconvincing given that only six measurements were taken. Why is there one outlier in Figure 1A? Were these results taken using the same batch of oocytes? Are these technical or biological replicates? Is the convention to use statistical significance for these types of experiments?

I am also somewhat skeptical about the modelling of the PIP2 diC8 molecule. The authors state, "The density of the IP3 head group from the bound PIP2 diC8 is well-defined in the EM map. The acyl chains, however, are flexible and could not be resolved in the structure (Fig. S2)."

However, the density appears rather ambiguous to me, and the ligand does not fit well within the density. Specifically, there is a large extension in the volume near the phosphate at the 5' position, with no corresponding volume near the 4' phosphate. Additionally, there is no bifurcation of the volume near the lipid tails. I attempted to model cholesterol hemisuccinate (PDB: Y01) into this density, and it fits reasonably well - at least as well as PIP2 diC8. I am also concerned that if this site is specific for PIP2, then why are there no specific interactions with the lipid phosphates? How can the authors explain the difference between PIP2 and PIP2 diC8 if the acyl chains don't make any direct interactions with the TM domain? In short, the structures do not explain the functional differences presented in Figure 1.

The side chain densities for Arg167 and Arg220 are also quite weak. While there is some density for the side chain of Lys164, it is also very weak. I would expect that if this site were truly specific for PIP2, it should exhibit greater structural rigidity - otherwise, how is this specific?

Given this observation, have the authors considered using other PIP2 variants to determine if the specificity lies with PI4,5P2 as opposed to PI3,5P2 or PI3,4P2? A lack of specificity may explain the observed poor density.

I also noticed many lipid-like densities in the maps for this complex. Is it possible that the authors overlooked something? For instance, there is a cholesterol-like density near Val51, as well as something intriguing near Trp763, where I could model PIP2 diC8 (though this leads to a clash with Trp763). I wonder if the authors are working with mixed populations in their dataset. The accompanying description of the structural changes is well-written (assuming it is accurate).

I would recommend that the authors update the figures associated with this section, as they are currently somewhat difficult to interpret without prior knowledge of NCX architecture. My suggestions include:

- Including the density for the PIP2 diC8 in Figure 2A.

- Adding membrane boundaries (cytosolic vs. extracellular) in Figure 2B.

- Labeling the cytosolic domains in Figure 2B.

- Adding hydrogen bond distances in Figure 2A.

- Detailing the domain movements in Figure 2B (what is the significance of the grey vs. blue structures?).

The section on the mechanism of SEA400-induced inactivation is strong. The maps are of better quality than those for the PIP2 diC8 complex, and the ligand fits well. However, I noticed a density peak below F02 on SEA400 that lies within the hydrogen bonding distance of Asp825. Is this a water molecule? If so, is this significant?

Furthermore, there are many unmodeled regions that are likely cholesterol hemisuccinate or detergent molecules, which may warrant further investigation.

The authors introduce SEA400 as a selective inhibitor of NCX1; however, there is little to no comparison between the binding sites of the different NCX proteins. This section could be expanded. Perhaps Fig. 4C could include sequence conservation data.

Additionally, is the fenestration in the membrane physiological, or is it merely a hole forced open by the binding of SEA400? I was unclear as to whether the authors were suggesting a physiological role for this feature, similar to those observed in sodium channels.

Reviewer #2 (Public review):

Summary:

Micronuclei are aberrant nuclear structures frequently seen following the missegregation of chromosomes. The authors present two image analysis methods, one robust and another rapid, to identify micronuclei (MN) bearing cells. To analyse their software efficacy, the authors study images of cells treated with MPS1 inhibitor to induce chromosome missegregation. Next, the authors use RNA-seq to assess the outcomes of their MN-identifying methods: they do not observe a transcriptomic signature specific to MN but find changes that correlate with aneuploidy status. Overall, this work offers new tools to identify MN-presenting cells, and it sets the stage with clear benchmarks for further software development.

Strengths:

Currently, there are no robust MN classifiers with a clear quantification of their efficiency across cell lines (mIoU score). The software presented here tries to address this gap. GitHub material (images, ground truth labels, tools, protocols, etc.) provided is a great asset to computational biologists. The method has been tested in more than one cell line. This method can help integrate cell biology and 'omics' data, making it suitable for multimodal studies.

Weaknesses:

Although the classifier outperforms available tools for MN segmentation by providing mIoU, it's not yet at a point where it can be reliably applied to functional genomics assays where we expect a range of phenotypic penetrance in most cell lines (e.g., misshapen, multinucleated, and lagging DNA in addition to micronucleated cells). The discussion considers the nature and proportion of MN in RPE1 cells, and how the classifier is well-suited for RPE1 that predominantly display MN structures. Whether the classifier can rigorously assign MN-presenting cells amidst drastic nuclear aberrancies following a spindle checkpoint loss needs to be tested in the future.

Reviewer #2 (Public review):

Summary:

This manuscript is about using different analytical approaches to allow ancestry adjustments to GWAS analyses amongst admixed populations. This work is a follow-on from the recently published ITHGC multi-population GWAS (https://doi.org/10.7554/eLife.84394), with the focus on the admixed South African populations. Ancestry adjustment models detected a peak of SNPs in the class II HLA DPB1, distinct from the class II HLA DQA1 loci signficant in the ITHGC analysis.

Strengths:

Excellent demonstration of GWAS analytical pipelines in highly admixed populations. Particularly the utility of ancestry adjustment to improve study power to detect novel associations. Further confirmation of the importance of the HLA class II locus in genetic susceptibility to TB.

Weaknesses:

Limited novelty compared to the group's previous existing publications and the body of work linking HLA class II alleles with TB susceptibility in South Africa or other African populations. This work includes only ~100 new cases and controls from what has already been published. High resolution HLA typing has detected significant signals in both the DQA1 and DPB1 regions identified by the larger ITHGC and in this GWAS analysis respectively (Chihab L et al. HLA. 2023 Feb; 101(2): 124-137).<br /> Despite the availability of strong methods for imputing HLA from GWAS data (Karnes J et Plos One 2017), the authors did not confirm with HLA typing the importance of their SNP peak in the class II region. This would have supported the importance of this ancestry adjustment versus prior ITHGC analysis.<br /> The populations consider active TB and healthy controls (from high-burden presumed exposed communities) and do not provide QFT or other data to identify latent TB infection.

Important methodological points for clarification and for readers to be aware of when reading this paper:

(1) One of the reasons cited for the lack of African ancestry-specific associations or suggestive peaks in the ITHGC study was the small African sample size. The current association test includes a larger African cohort and yields a near-genome-wide significant threshold in the HLA-DPB1 gene originating from the KhoeSan ancestry. Investigation is needed as to whether the increase in power is due to increased African samples and not necessarily the use of the LAAA model as stated on lines 295 and 296?

Authors response - The Manhattan plot in Figure 3 includes the results for all four models: the traditional GWAS model (GAO), the admixture mapping model (LAO), the ancestry plus allelic (APA) model and the LAAA model. In this figure, it is evident that only the LAAA model identified the association peak on chromosome 6, which lends support the argument that the increase in power is due to the use of the LAAA model and not solely due to the increase in sample size.<br /> Reviewer comment - This data supports the authors conclusions that increase power is related to the LAAA model application rather than simply increase sample size.

(2) In line 256, the number of SNPs included in the LAAA analysis was 784,557 autosomal markers; the number of SNPs after quality control of the imputed dataset was 7,510,051 SNPs (line 142). It is not clear how or why ~90% of the SNPs were removed. This needs clarification.

Authors response:<br /> In our manuscript (line 194), we mention that "...variants with minor allele frequency (MAF) < 1% were removed to improve the stability of the association tests." A large proportion of imputed variants fell below this MAF threshold and were subsequently excluded from this analysis.

Reviewers additional comment: The authors should specify the number of SNPs in the dataset before imputation and indicate what proportion of the 784,557 remaining SNPs were imputed. Providing this information might help the reader better understand the rationale behind the imputation process.

(3) The authors have used the significance threshold estimated by the STEAM p-value < 2.5x10-6 in the LAAA analysis. Grinde et al. (2019 implemented their significance threshold estimation approach tailored to admixture mapping (local ancestry (LA) model), where there is a reduction in testing burden. The authors should justify why this threshold would apply to the LAAA model (a joint genotype and ancestry approach).

Authors response: We describe in the methods (line 189 onwards) that the LAAA model is an extension of the APA model. Since the APA model itself simultaneously performs the null global ancestry only model and the local ancestry model (utilised in admixture mapping), we thus considered the use of a threshold tailored to admixture mapping appropriate for the LAAA model.

Reviewers additional comment: While the LAAA model is an extension of the APA model, the authors describe the LAAA test as 'models the combination of the minor allele and the ancestry of the minor allele at a specific locus, along with the effect of this interaction,' thus a joint allele and ancestry effects model. Grinde et al. (2019) proposed the significance threshold estimation approach, STEAM, specifically for the LA approach, which tests for ancestry effects alone and benefits from the reduced testing burden. However, it remains unclear why the authors found it appropriate to apply STEAM to the LAAA model, a joint test for both allele and ancestry effects, which does not benefit from the same reduction in testing burden.

(4) Batch effect screening and correction (line 174) is a quality control check. This section is discussed after global and local ancestry inferences in the methods. Was this QC step conducted after the inferencing? If so, the authors should justify how the removed SNPs due to the batch effect did not affect the global and local ancestry inferences or should order the methods section correctly to avoid confusion.

Authors response: The batch effect correction method utilised a pseudo-case-control comparison which included global ancestry proportions. Thus, batch effect correction was conducted after ancestry inference. We excluded 36 627 SNPs that were believed to have been affected by the batch effect. We have amended line 186 to include the exact number of SNPs excluded due to batch effect.<br /> The ancestry inference by RFMix utilised the entire merged dataset of 7 510 051 SNPs. Thus, the SNPs removed due to the batch effect make up a very small proportion of the SNPs used to conduct global and local ancestry inferences (less than 0.5%). As a result, we do not believe that the removed SNPs would have significantly affected the global and local ancestry inferences. However, we did conduct global ancestry inference with RFMix on each separate dataset as a sanity check. In the Author response tables 1 and 2, we show the average global ancestry proportions inferred for each separate dataset, the average global ancestry proportions across all datasets and the average global ancestry proportions inferred using the merged dataset. The SAC and Xhosa cohorts are shown in two separate tables due to the different number of contributing ancestral populations to each cohort. The differences between the combined average global ancestry proportions across the separate cohorts does not differ significantly to the global ancestry proportions inferred using the merged dataset.

This is an excellent response and should remain accessible to readers to clarify this issue.

Reviewer #2 (Public review):

Summary:

The manuscript by Hadebe and colleagues describes a striking reduction in airway hyperresponsiveness in Igm-deficient mice in response to HDM, OVA and papain across the B6 and BALB-c backgrounds. The authors suggest that the deficit is not due to improper type 2 immune responses, nor an aberrant B cell response, despite a lack of class switching in these mice. Through RNA-Seq approaches, the authors identify few differences between the lungs of WT and Igm-deficient mice, but see that two genes involved in actin regulation are greatly reduced in IgM-deficient mice. The authors target these genes by CRISPR-Cas9 in in vitro assays of smooth muscle cells to show that these may regulate cell contraction. While the study is conceptually interesting, there are a number of limitations, which stop us from drawing meaningful conclusions.

Strengths:

Fig. 1. The authors clearly show that IgMKO mice have striking reduced AHR in the HDM model, despite the presence of a good cellular B cell response.

Weaknesses:

Due to several technical and experimental limitations, it is unclear what leads to the reduction in airway hyperresponsiveness in IGM-KO mice. The limitations as outlined previously remain.

Reviewer #2 (Public review):

Summary:

Wang et al. investigate the role of TseP, a Type VI secretion system (T6SS) effector molecule, revealing its dual enzymatic activities as both an amidase and a lysozyme. This discovery significantly enhances the understanding of T6SS effectors, which are known for their roles in interbacterial competition and survival in polymicrobial environments. TseP's dual function is proposed to play a crucial role in bacterial survival strategies, particularly in hostile environments where competition between bacterial species is prevalent.

Strengths:

(1) The dual enzymatic function of TseP is a significant contribution, expanding the understanding of T6SS effectors.<br /> (2) The study provides important insights into bacterial survival strategies, particularly in interbacterial competition.<br /> (3) The findings have implications for antimicrobial research and understanding bacterial interactions in complex environments.

Weaknesses:

(1) The manuscript assumes familiarity with previous work, making it difficult to follow. Mutants and strains need clearer definition and references.<br /> (2) Figures lack proper controls, quantification, and clarity in some areas, notably in Figures 1A and 1C.<br /> (3) The Materials and Methods section is poorly organized, hindering reproducibility. Biophysical validation of Zn²⁺ interaction and structural integrity of proteins need to be addressed.<br /> (4) Discrepancies in protein degradation patterns and activities across different figures raise concerns about data reliability.

Comments on revisions:

The authors have addressed most of the comments, significantly improving the manuscript. They provided clear details of mutant constructs and strains, including additional references and a revised strain. Individual data points and statistical analyses were added to key figures, ensuring transparency and reproducibility. Supplemental data, such as protein purification details and loading controls, were included to address concerns about experimental reliability. However, the authors did not perform new experiments, such as isothermal titration calorimetry (ITC) to demonstrate the interaction between Zn²⁺ and TsePN or stop-flow spectroscopy to examine enzymatic kinetics, which could have further strengthened the manuscript. I trust these aspects will be addressed in future studies.

The revised Materials and Methods section was significantly improved, providing detailed protocols for bioinformatics analyses, microscopic imaging, and enzymatic assays.

These revisions provide a clearer and more robust presentation of TseP's dual enzymatic functions and their implications in bacterial competition. The manuscript now represents a significant contribution to understanding T6SS effectors, and I recommend it for publication in its current form.

Reviewer #2 (Public review):

Summary:

In this work, the authors present a differentiable version of the widely-used Gillespie Algorithm. The Gillespie Algorithm has been used for decades to simulate the behavior of stochastic biochemical reaction networks. But while the Gillespie Algorithm is a powerful tool for the forward simulation of biochemical systems given some set of known reaction parameters, it cannot be used for reverse process, i.e. inferring reaction parameters given a set of measured system characteristics. The Differentiable Gillespie Algorithm ("DGA") overcomes this limitation by approximating two discontinuous steps in the Gillespie Algorithm with continuous functions. This makes it possible to calculate of gradients for each step in the simulation process which, in turn, allows the reaction parameters to be optimized via powerful backpropagation techniques. In addition to describing the theoretical underpinnings of DGA, the authors demonstrate different potential use-cases for the algorithm in the context of simple models of stochastic gene expression.

Overall, the DGA represents an important conceptual step forward for the field and should lay the groundwork for exciting innovations in the analysis and design of stochastic reaction networks. At the same time, significantly more work is needed to establish when the approximations made by DGA are valid and to demonstrate the viability of the algorithm in the context of complicated reaction networks.

Strengths:

This work makes an important conceptual leap by introducing a version of the Gillespie Algorithm that is end-to-end differentiable. This idea alone has the potential to drive a number of exciting innovations in the analysis, inference, and design of biochemical reaction networks. Beyond the theoretical adjustments, the authors also implement their algorithm in a Python-based codebase that combines DGA powerful optimization libraries like PyTorch. This codebase has the potential to be of interest to a wide range of researchers, even if the true scope of the method's applicability remains to be fully determined.

The authors also demonstrate how DGA can be used in practice both to infer reaction parameters from real experimental data (Figure 7) and to design networks with user-specified input-output characteristics (Figure 8). These illustrations should provide a nice roadmap for researchers interested in applying DGA to their own projects/systems.

Finally, although it does not stem directly from DGA, the exploration of pairwise parameter dependencies in different network architectures provides an interesting window into the design constraints (or lack thereof) that shape the architecture of biochemical reaction networks.

Weaknesses:

While it is clear that the DGA represents an important conceptual advancement, the authors do not do enough in the present manuscript to (i) validate the robustness of DGA inference and (ii) demonstrate that DGA inference works in the kinds of complex biochemical networks where it would actually be of legitimate use.

It is to the authors' credit that they are open and explicit about the potential limitations of DGA due to breakdowns in its continuous approximations. However they do not provide the reader with nearly enough empirical (i.e. simulation-based) or theoretical context to assess when, why, and to what extent DGA will fail in different situations. In Figure 2, they compare DGA to GA (i.e. ground-truth) in the context of a simple two state model of a stochastic transcription. Even in this minimal system, we see that DGA deviates notably from ground-truth both in the simulated mRNA distributions (Figure 2A) and in the ON/OFF state occupancy (Figure 2C). This begs the question of how DGA will scale to more complicated systems, or systems with non-steady state dynamics. Will the deviations become more severe? This is important because, in practice, there is really not much need for using DGA with a simple 2 state system-we have analytic solutions for this case. It is the more complex systems where DGA has the potential to move the needle.

A second concern is that the authors' present approach for parameter inference and error calculation does not seem to be reliable. For example, in Figure 5A, they show DGA inference results for the ON rate of a two-state system. We see substantial inference errors in this case, even though the inference problem should be non-degenerate in this case. One reason for this seems to be that the inference algorithm does not reliably find the global minimum of the loss function (Figure 2B). To turn DGA into a viable approach, it is paramount that the authors find some way to improve this behavior, perhaps by using multiple random initializations to better search the loss space.

Finally, the authors do a good job of illustrating how DGA might be used to infer biological parameters (Figure 7) and design reaction networks with desired input-output characteristics (Figure 8). However, analytic solutions exist for both of the systems they select for examples. This means that, in practice, there would be no need for DGA in these contexts, since one could directly optimize, e.g., the expressions for the mean and Fano Factor of the system in Figure 7A. I still believe that it is useful to have these examples, but it seems critical to add a use-case where DGA is the only option.

Comments on revisions:

I am concerned that the results in Figure 8D may not be correct, or that the authors may be mis-interpreting them. From my reading of the paper they cite (Lammers & Flamholz 2023), the equilibrium sharpness limit for the network they consider in Figure 8 should be 0.25. But both solutions shown in Figure 8D fall below this limit, which means that they have sharpness levels that could have been achieved with no energy expenditure. If this is the case, then it would imply that while both systems do dissipate energy, they are not doing so productively; meaning that the same results could be achieved while holding Phi=0.

I acknowledge that this could be due to a difference in how they measure sharpness, but wanted to raise it here in case it is, in fact, a genuine issue with the analysis.

There should be an easy fix for this: just set the sharper "desired response" curve in 8b to be such that it demands non-equilibrium sharpness levels (0.25)

Reviewer #2 (Public review):

Summary:

This paper presented a hypothesis testing procedure for the independence of two time-series that was potentially suitable for nonlinear dependence and for small-sample cases. This should bring potential benefits for biology data.

Strengths:

The test offers good flexibility for different kinds of dependence (through adjusting \rho), and seems to have good finite sample performance compared to the literature. The justification regarding the validity of the test procedure is clear.

Weaknesses:

(1) The size of the test is not guaranteed to (asymptotically) equal \alpha, which may damage the power.

(2) The computational time can be an issue for a moderately large sample size when calculating the X / Y-perfect match. It will be beneficial to include discussions on the implementations of the test.

Reviewer #2 (Public review):

Summary:

In this manuscript the authors describe their study on the role of meteorins in establishing the left-right organizer. The left-right organizer is a transient organ in vertebrate embryos in which rotating cilia cause a fluid flow that breaks the left-right symmetry and coordinates lateralization of internal organs such as gut and heart. In zebrafish, the left-right organizer (also named Kupffer's vesicle) is formed by dorsal forerunner cells, but very little is known about how dorsal forerunner cells coalles and form this ciliated vesicle in the embryo. The authors mutated the three meteorin-coding genes in zebrafish and observed that mutations in each one of these causes laterality defects with the strongest defects observed in the triple mutant. Loss of meteorins affects nodal gene expression, which play essential roles in establishing organ laterality. Meteorins are widely expressed in developing embryos and expression in lateral plate mesoderm and dorsal forerunner cells was observed. The meteorin triple mutant embryos display defects in the migration and clustering of the dorsal forerunner cells impairing kupffer's vesicle formation and cilia rotation. Finally, the authors show that meteorins genetically interact with integrins.

Strengths:

- These authors went through the lengthy process of generating triple mutants affecting all three meteorin genes. This provides robust genetic evidence on the role of meteorins in establishing organ laterality and circumvented that interpretation of the results would be hard due to redundant functions of meteorins.<br /> - The use of life imaging on triple mutants is appreciated<br /> - High-quality imaging of dorsal forerunner to quantify cell migrations and its relation to Kupffer's vesicle formation.

Weaknesses:

- Lack of a model how meteorins regulate dorsal forerunner cell migration.<br /> - Only genetic data to suggest a link between meteorins and integrins<br /> - Besides its role in DFC migration, meteorins may also play a more direct role in regulating Nodal signaling, which is not addressed here.

Reviewer #2 (Public review):

The authors aim to investigate the ability of evolution to create strong transcription factor binding sites (TFBSs) de novo in E. coli. They focus on three global transcriptional regulators: CRP, Fis, and IHF, using a massively parallel reporter assay to evaluate the regulatory effects of over 30,000 TFBS variants. By analyzing the resulting genotype-phenotype landscapes, they explore the ruggedness, accessibility, and evolutionary dynamics of regulatory landscapes, providing insights into the evolutionary feasibility of strong gene regulation. Their experiments show that de novo adaptive evolution of new gene regulation is feasible. It is also subject to a blend of chance, historical contingency, and evolutionary biases that favor some peaks and evolutionary paths.

(1) Strengths of the methods and results:

The authors successfully employed a well-designed sort-seq assay combined with high-throughput sequencing to map regulatory landscapes. The experimental design ensures reliable measurement of regulation strengths. Their system accounts for gene expression noise and normalizes measurements using appropriate controls.

Comprehensive Landscape Mapping:<br /> The study examines ~30,000 TFBS variants per transcription factor, providing statistically robust and thorough maps of the regulatory landscapes for CRP, Fis, and IHF. The landscapes are rigorously analyzed for ruggedness (e.g., number of peaks) and epistasis, revealing parallels with theoretical uncorrelated random landscapes.

Evolutionary Dynamics Simulations:<br /> Through simulations of adaptive walks under varying population dynamics, the authors demonstrate that high peaks in regulatory landscapes are accessible despite ruggedness. They identify key evolutionary phenomena, such as contingency (multiple paths to peaks) and biases toward specific evolutionary outcomes.

Biological Relevance and Novelty:<br /> The author's work is novel in focusing on global regulators, which differ from previously studied local regulators (e.g., TetR). They provide compelling evidence that rugged landscapes are navigable, facilitating de novo evolution of regulatory interactions. The comparison of landscapes for CRP, Fis, and IHF underscores shared topographical features, suggesting general principles of global transcriptional regulation in bacteria.

(2) Weaknesses of the methods and results:

Undersampling of Genotype Space:<br /> While the quality filtering of the data ensures robustness, ~40% of the TFBS space remains uncharacterized. The authors acknowledge this limitation but could improve the analysis by employing subsampling or predictive modeling.

Simplified Regulatory Architecture:<br /> The study considers a minimal system of a single TFBS upstream of a reporter gene. While this may have been necessary for clarity, this simplification may not reflect the combinatorial complexity of transcriptional regulation in vivo.

Lack of Experimental Validation of Simulations:<br /> The adaptive walks are based on simulated dynamics rather than experimental evolution. Incorporating in vivo experimental evolution studies would strengthen the conclusions. Although this is a large request for the paper, that would not prevent publication.

Impact on the Field:<br /> This study advances our understanding of adaptive landscapes in gene regulation and offers a critical step toward deciphering how global regulators evolve de novo binding sites. The findings provide foundational insights for synthetic biology, evolutionary genetics, and systems biology by highlighting the evolutionary accessibility of strong regulation in bacteria.

Utility of Methods and Data:<br /> The sort-seq approach, combined with landscape analysis, provides a robust framework that can be extended to other transcription factors and systems. If made publicly available, the study's data and code would be valuable for researchers modeling transcriptional regulation or studying evolutionary dynamics.

Additional Context:<br /> The study builds on a growing body of work exploring regulatory evolution. For instance, recent studies on local regulators like TetR and AraC have revealed high ruggedness and epistasis in TFBS landscapes. This study distinguishes itself by focusing on global regulators, which are more biologically complex and influential in bacterial gene networks. The observed evolutionary contingency aligns with findings in other biological systems, such as protein evolution and RNA folding landscapes, underscoring the generality of these evolutionary principles.

Conclusion:<br /> The authors successfully mapped the genotype-phenotype landscapes for three global regulators and simulated evolutionary dynamics to assess the feasibility of strong TFBS evolution. They convincingly demonstrate that ruggedness and epistasis, while prominent, do not preclude the evolution of strong regulation. Their results support the notion that gene regulation evolves through a blend of chance, contingency, and evolutionary biases.

This paper makes a significant contribution to the understanding of regulatory evolution in bacteria. While minor limitations exist, the authors' methods are robust, and their findings are well-supported. The work will likely be of broad interest to researchers in molecular evolution, synthetic biology, and gene regulation.

Reviewer #2 (Public review):

Summary:

Cupollilo et al. investigate the properties of hippocampal CA3 neurons that express the immediate early gene cFos in response to a single foot shock. They compare ex-vivo the electrophysiological properties of these "engram neurons" labeled with two different cFos promoter-driven green markers: Their new tool FLEN labels neurons 2-6 h after activity, while RAM contains additional enhancers and peaks considerably later (>24 h). Since the fraction of labeled CA3 cells is comparable with both constructs, it is assumed (but not tested) that they label the same population of activated neurons at different time points. Both FLEN+ and RAM+ neurons in CA3 receive more synaptic inputs compared to non-expressing control neurons, which could be a causal factor for cFos activation, or a very early consequence thereof. Frequency facilitation and E/I ratio of mossy fiber inputs were also tested, but are not different in both cFos+ groups of neurons. One day after foot shock, RAM+ neurons are more excitable than RAM- neurons, suggesting a slow increase in excitability as a major consequence of cFos activation.

Strengths:

The study is conducted to high standards and contributes significantly to our understanding of memory formation and consolidation in the hippocampus. Modifications of intrinsic neuronal properties seem to be more salient than overall changes in the total number of (excitatory and inhibitory) inputs, although a switch in the source of the synaptic inputs would not have been detected by the methods employed in this study

Weaknesses:

With regard to the new viral tool, a direct comparison between the new tool FLEN and existing cFos reporters is missing.

Reviewer #2 (Public review):

Summary:

The present study identifies how mating and pup experience are correlated with differences in inhibitory neurotransmission underlying the promotion of paternal behavior toward pups. The study builds on existing knowledge about the circuit between the medial amygdala, medial preoptic area, and the bed nucleus of stria terminalis to uncover synaptic changes correlated with behavior. The authors find that inhibition from the medial amygdala is decreased in the medial preoptic area and increased in the bed nucleus of stria terminalis to promote paternal behavior in mated males.

Strengths:

The authors use a combination of in vivo activity manipulation and slice electrophysiology to study the role of inhibition in this circuit in dynamic infant-directed behavior induced by mating.

Weaknesses:

(1) Some technical and methodological details are incomplete or missing for interpretation of the significance of the findings. Statistical details are also left out.

(2) The rationale for using Cartpt as a marker is not fully explained. This marker has activity-dependent expression and this possibility is not explored experimentally--for example, could exposure to objects or pups change expression (or the number of cells expressing) cartpt alone?

(3) The cfos experiment is quantified by exposing a male to a pup inside a tea ball. Therefore, it is unclear how the male was classified as infanticidal or parental based on the available criteria provided in the methods section.

(4) There is no information about inclusion/exclusion criteria for chemical and viral experiments. Specifically, there is no information provided about the validation of the lesion experiment--how large were the lesions? Is there concern about leakage of the chemical into the recorded region (MPOA and BNST are adjacent).

(5) The authors do not provide information about how long rAAV is allowed to express before quantifying retrograde transport.

(6) For statistics, the authors do not provide information distinguishing the main effects from multiple comparisons post hoc testing for the ANOVA analyses.

Reviewer #2 (Public review):

Summary:

In this paper, Oláh and colleagues introduce new research data on the cellular and biophysical elements involved in transmission within the pyramidal circuits of the human neocortex. They gathered a comprehensive set of patch-clamp recordings from human and rat pyramidal neurons to compare how the temporal aspect of neuronal processing is maintained in the larger human neocortex. A range of experimental techniques have been used, including two-photon guided dual whole-cell recordings, electron microscopy, complemented by theoretical and computational methods.

The authors find that synaptically connected pyramidal neurons within the human neocortex have longer intercellular path lengths. They go on to show that the short soma to soma latencies is not due to propagation velocity along the axon but instead reflects a higher propagation speed of synaptic potentials from dendrite to soma. Next, in a series of extensive computational modeling studies focusing on the synaptic potentials, the authors show that the shorter latency may be explained by larger diameters, affecting the cable properties and resulting is relatively faster propagation of EPSPs in the human neuron. The manuscript is well-written, and the physiological experiments and in-depth theoretical steps for the simulations are clear. Whether passive cable properties of the dendrites alone are responsible for higher velocities remains to be further investigated. Based on the present data the contribution of active membrane properties cannot be excluded.

Strengths:

The authors used complex 2P-guided dual whole-cell recordings in human neurons. In combination with detailed reconstructions, these approaches represent the next steps in unravelling the information processing in human circuits.

The computational modelling and cable theory application to the experimentally constrained simulations provides an integrated view of the passive membrane properties of human neurons.

Weaknesses:

Whether the cable properties alone are the main explanation for speeding the electrical signaling in human pyramidal neurons deserves further studies.

Reviewer #3 (Public review):

Summary:

The manuscript is evaluating changes in dopamine signaling in the nucleus accumbens following pair bonding and exposure to various stimuli in mandarin voles. In addition, the authors present chemogenetic data which demonstrates excitation and inhibition of D1 and D2 MSN affect pair bond formation.

Strengths:

The experimental designs are strong. The approaches are innovative and use cutting-edge methods. The manuscript is well written.

Comments on revised version:

I appreciate the efforts by the authors to address many of my previous comments. The issues that remain are those associated with the statistics. It seems that not all statistical analyses were performed with the correct test. For example, the photometry data comparing emissions during partner vs stranger investigation over time would be best performed as a two-way ANOVA with odor type and time being separate variables. Also, there are paired t-tests being performed by calculating an average deltaF/F during the 4 second window following the being of a behavioral event. I think an area-under-the-curve calculation of these events would better capture the fluorescent emissions of these events as an index. Details in the Result describing the data being analyzed via ANOVA vs t-tests when reporting the results would be useful for the reviewer to understand each analysis.

Reviewer #2 (Public review):

Summary:

The authors main goal is to understand the mechanism by which pyroptosis (through the formation of Gasdermin D (GSDMD) pores in the plasma membrane) contributes to increased release of procoagulant Tissue Factor-containing microvesicles (MV). Their previous data demonstrate that GSDMD is critical for the release of MV that contains Tissue Factor (TF), thus making a link between pyroptosis and hypercoagulation. Given the recent identification of NINJ1 being responsible for plasma membrane rupture (Kayagaki et al. Nature 2011), the authors wanted to determine if NINJ1 is responsible for TF-containing MV release. Given the constitutive ninj1 KO mouse leads to partial embryonic lethality, the authors decide to use a heterozygous ninj1 KO mouse (ninj1+/-), and demonstrate that Ninj1 plays a role in release of TF-containing MV.

Reviewer #2 (Public review):

Summary:

The authors provide a very thorough investigation on the role of UBR-1 in anthelmintic resistance using the non-parasitic nematode, C. elegans. Anthelmintic resistance to macrocyclic lactones is a major problem in veterinary medicine and likely just a matter of time until resistance emerges in human parasites too. Therefore, this study providing novel insight into the mechanisms of ivermectin resistance is particularly important and significant.

Strengths:

The authors use very diverse technologies (behavior, genetics, pharmacology, genetically encoded reporters) to dissect the role of UBR-1 in ivermectin resistance. Deploying such a comprehensive suite of tools and approaches provides exceptional insight into the mechanism of how UBR-1 functions in terms of ivermectin resistance.

Weaknesses:

I do not see any major weaknesses in this study. My only concern is whether the observations made by the authors would translate to any of the important parasitic helminths in which resistance has naturally emerged in the field. This is always a concern when leveraging a non-parasitic nematode to shed light on a potential mechanism of resistance of parasitic nematodes, and I understand that it is likely beyond the scope of this paper to test some of their results in parasitic nematodes.

Comments on revisions: The authors have now addressed all my concerns.

Reviewer #2 (Public review):

Summary:

This research offers a comprehensive analysis of the regenerative process in sea cucumbers and builds upon decades of previous research. The approach involves a detailed examination using single-cell sequencing, making it a crucial reference paper while shedding new light on regeneration in this organism.

Strengths:

Detailed analysis of single-cell sequencing data and high-quality RNA localization images provide significant new insights into regeneration in sea cucumbers and, more broadly, in animals. Identifying a proliferating cluster of cells is very interesting and may open avenues to identify the cell lineage history and deeper molecular properties of the cells that regenerate the intestine.

Weaknesses:

The spatial context of the RNA localization images is challenging to interpret in this spatially complex tissue organization. Although the authors have taken care to perform RNA localization staining, it is still challenging to relate these data to their schematic model. This is only a minor weakness that will almost certainly be clarified by future work from the authors as they follow up on findings.

Reviewer #3 (Public review):

This revised paper provides evidence that food washing and brushing in wild long-tailed macaques are deliberate behaviors to remove sand that can damage tooth enamel. The demonstration of the immediate functional importance of these behaviors is nicely done, and there is some interesting initial evidence that macaques differ systematically in their investment in food cleaning based on dominance rank.

The authors interpret this evidence as support for "disposable soma" effects: that reduced time and effort invested food washing in high-ranking individuals is attributable to prioritizing reproductive effort. Given that the analysis is on a single group with no longitudinal data, there are no fitness measures or fitness proxies, the energetic constraints faced by this population are not clear, and both sexes are combined into a single dominance hierarchy (trade-offs between different forms of investment are typically thought to differ between sexes), this conclusion is premature, although an interesting foundation for future studies.

More generally, the results directly supported by the data collection and analysis (grit on Koshima likely damages macaque teeth; processing food helps mitigate the damage; there is some interesting interindividual variation in food processing time, and that time is not always in line with what appears to be optimal) tend to be combined with interpretation that is much more speculative (e.g., the effect sizes observed are consequential for fitness; high-ranking animals are making choices that optimize their long-term fitness at the expense of their soma). This is in part a stylistic choice but can have the effect of drawing attention away from the stronger empirical findings and/or be misleading. Similarly, although I appreciate that the authors were trying to interpret and respond to previous feedback from reviewers, I found the addition of the box text on the raccoon nomenclature and on irrational behavior and the Concorde effect distracting (more intro-textbook style than journal article style).

Reviewer #2 (Public review):

Summary:

Intrinsic primary afferent neurons are an interesting population of enteric neurons that transduce stimuli from the mucosa, initiate reflexive neurocircuitry involved in motor and secretory functions, and modulate gut immune responses. The morphology, neurochemical coding, and electrophysiological properties of these cells have been relatively well described in a long literature dating back to the late 1800's but questions remain regarding their roles in enteric neurocircuitry, potential subsets with unique functions, and contributions to disease. Here, the authors provide RNAscope, immunolabeling, electrophysiological, and organ function data characterizing IPANs in mice and suggest that Cdh6 is an additional marker of these cells.

Strengths:

This paper would likely be of interest to the enteric neuroscience community and increases information regarding the properties of IPANs in mice. These data are useful and suggest that prior data from studies of IPANs in other species are likely translatable to mice.

Weaknesses:

Major weaknesses:<br /> (1) The novelty of this study is relatively limited. The main point of novelty suggests an additional marker of IPANs (Cdh6) that would add to the known list of markers for these cells. How useful this would be is unclear. Other main findings basically confirm that IPANs in mice display the same classical characteristics that have been known for many years from studies in guinea pigs, rats, mice and humans.

(2) Critical controls are needed to support the optogenetic experiments. Control experiments are needed to show that ChR2 expression 1) does not change the baseline properties of the neurons, 2) that stimulation with the chosen intensity of light elicits physiologically relevant responses in those neurons, and 3) that stimulation via ChR2 elicits comparable responses in IPANs in the different gut regions focused on here. These essential controls remain absent in the study and limit confidence in the data derived from this model.

(3) The motor effects observed in optogenetic experiments are difficult to understand in the absence of good controls for optogenetic control of the proposed neuron population (discussed above). It remains unclear how stimulating IPANs in the distal colon would generate retrograde CMCs while stimulating IPANs in the proximal colon did nothing. Key controls confirming that the optogentic stimulus was adequate, specific, and relevant are needed. In addition, better characterization of the Cdh6+ population of cells in both regions would be needed to understand the mechanisms underlying these effects.

(4) From the data shown, it is clear that expression driven by the Cdh6CreERT2 driver is not confined to IPANs. There is obviously expression of GFP and ChR2 in smooth muscle cells. This is a major limitation for the physiological experiments that attempt to use this model to specifically stimulate IPANs and assess changes in gut motor function. Better characterization of this model is needed and control experiments are necessary to assess whether functional ChR2 is expressed in cells beyond the proposed subtype of enteric IPANs.

(5) Some of the main conclusions of this study are overstated and claims of priority are made that are not true. For example, the authors state on lines 27-28 of the abstract that their findings provide the "first demonstration of selective activation of a single neurochemical and functional class of enteric neurons". This is certainly not true since Gould et al (AJP-GIL 2019) expressed ChR2 in nitrergic enteric neurons and showed that activating those cells disrupted CMC activity. In fact, prior work by the authors themselves (Hibberd et al Gastro 2018) showed that activating calretinin neurons with ChR2 evoked motor responses. Work by other groups has used chemogenetics and optogenetics to show effects of activating multiple other classes of neurons in the gut.

(6) The electrophysiological characterization of mouse IPANs is useful but is limited to a small subset of Cdh6+ neurons in the distal colon myenteric plexus. Therefore, it remains unclear how well the properties reported here might reflect those of other Cdh6+ IPANs in the same or different regions. Similarly, blocking IH with ZD7288 affects all IPANs and does not add specific information regarding the role of the proposed Cdh6+ subtype.

(7) The submucosal plexus (SMP) also contains enteric IPANs and these were not included in the analysis of Cdh6 expression. Whether or not the proposed IPAN marker Cdh6 would be useful for identifying or targeting those cells remains unclear.

[Editor's note: The Reviewing Editor considers that further controls requested from the reviewers have largely been provided already in prior publications by other groups, as they concern specifically tools published years ago but in a different tissue context. Hence the methodology used to deliver the results reported here fall within the standard practices in the field. The comprehensive, multi-technique approach to the results is compelling in and of itself, and ought to suffice, rendering this work reproducible and therefore a basis for further research.]

Reviewer #2 (Public review):

Summary:

The manuscript investigates the role of ANKRD5 (ANKEF1) as a component of the N-DRC complex in sperm motility and male fertility. Using Ankrd5 knockout mice, the study demonstrates that ANKRD5 is essential for sperm motility and identifies its interaction with N-DRC components through IP-mass spectrometry and cryo-ET. The results provide insights into ANKRD5's function, highlighting its potential involvement in axoneme stability and sperm energy metabolism.

Strengths:

The authors employ a wide range of techniques, including gene knockout models, proteomics, cryo-ET, and immunoprecipitation, to explore ANKRD5's role in sperm biology.

Weaknesses:

(1) Limited Citations in Introduction: Key references on the role of N-DRC components (e.g., DRC1, DRC2, DRC3, DRC5) in male infertility are missing, which weakens the contextual background.

(2) Lack of Functional Insights: While interacting proteins outside the N-DRC complex were identified, their potential roles and interactions with ANKRD5 are not adequately explored or discussed.

(3) Mitochondrial Function Uncertainty: Immunofluorescence suggests possible mitochondrial localization for ANKRD5, but experiments on its role in energy metabolism (e.g., ATP production, ROS) are insufficient, especially given the observed sperm motility defects.

(4) Glycolysis Pathway Impact: Proteomic analysis indicates glycolysis pathway disruptions in Ankrd5-deficient sperm, but the link between these changes and impaired motility is not well explained.

(5) Cryo-ET Data Limitations: The structural analysis of the DMT lacks clarity on how ANKRD5 influences N-DRC or RS3. The low quality of RS3 data hinders the interpretation of ANKRD5's impact on axoneme structure.

(6) Discussion of Findings: The manuscript could benefit from a deeper discussion on the broader implications of ANKRD5's interactions and its role in sperm energy metabolism and motility mechanisms.

Reviewer #2 (Public review):

Summary:

This study by Lum and colleagues reports on the role of Afadin, a cytosolic adapter protein that organizes multiple cell adhesion molecule families, in the generation and maintenance of complex cellular layers in the mouse retina. They used a conditional deletion approach, removing Afadin in retinal progenitors, and allowing them to analyze broad effects on retinal neuron development.

The study presents high-quality and extensive characterization of the cellular phenotypes, supporting the main conclusions of the paper. They show that Afadin loss results in significant disorganization of the retinal cellular layers and the neuropil, producing rosettes and displacement of cells away from their resident layers. The major classes of neurons in the inner retina are affected, and some neurons are, remarkably, displaced to the other side of the inner plexiform layer. Nevertheless, they mostly target their synaptic partners, including the RGCs to distant retinorecipient targets in the brain. The main conclusions are as follows. Afadin is necessary for establishing and maintaining the retinal architecture. It is not necessary for the generation of the correct numbers/densities of retinal neuron subtypes. Moreover, Afadin loss preserves associations between known synaptic partners and preserves axonal targeting to retinorecipient layers. The consequences on photoreceptor viability and visual processing are also interesting, underscoring the essential function for maintaining retinal structure and function. Overall the main conclusions describing the consequences are supported by the results.

Strengths:

The study provides new knowledge on the requirement of Afadin in retinal development. The introduction and discussion effectively set up the rationale for this work, and place it in the context of previous studies of Afadin in other regions of the CNS.

The study presents high-quality and extensive characterizations of the cellular phenotypes resulting from Afadin loss. By analyzing various aspects of retinal organization - from cellular densities to axon targeting to brain - the study narrows down the role of a structure for promoting the establishment of the layers, or maintenance. The data are straightforward and convincing, and the interpretations are bounded by the data shown (though minor weakness re. survival). Another important finding is that the targeting of retinal neuron processes to synaptic partners, including retinorecipient targets in the brain, are intact.

The study is important as it establishes a focused requirement for Afadin to set up and preserve the overall cellular organizations within the retinal tissue. The demonstration that Afadin is needed for photoreceptor viability and overall visual function enhances impact by establishing its functional importance.

The manuscript is well well-written and presented. The images are attractive and compelling, and the figures are well organized.

Weaknesses:

(1) Expanding on the developmental mechanism is beyond the scope of the study, and would not add to the main conclusions. However, the manuscript would be improved by providing more clarity on the developmental emergence of the defects. The study left me questioning whether the rosettes and cell displacements occur during earlier stages of retina development, or are progressive. For instance, do the RGCs migrate and establish within the GCL correctly at first, and then are displaced with the progressive disorganization? Or are they disorganized and delaminate en route? Images of RGC staining at P0, or earlier during their migration, would be informative. Data in Figure 1 is limited to DAPI staining at P7. Figure 4 shows an image of rod photoreceptors at P7, with their displacement in the GCL layer (and not contained within a rosette). Are the progenitors mislocalized due to delamination?

A few additional thoughts on how these defects compare to other mutants with rosettes might give us more context for understanding the results.

(2) The manuscript reports that the densities of major inner retinal classes are unaffected. There are a few details missing for this point. How were the cell densities quantified (in terms of ROI size), and normalized? This information is lacking in the methods. There is a striking thickening of the GCL in the DAPI-labeled images shown in Figure 1. What are these cells?

Reviewer #2 (Public review):

Summary:

This paper provides a valuable addendum to the findings described in Hamilton et al. 2020 (https://doi.org/ 10.7554/eLife.56582). In the earlier paper, the authors reconstituted the budding yeast centromeric nucleosome together with parts of the budding yeast kinetochore and tested which elements are required and sufficient for force transmission from microtubules to the nucleosome. Although budding yeast centromeres are defined by specific DNA sequences, this earlier paper did not use centromeric DNA but instead the generic Widom 601 DNA. The reason is that it has so far been impossible to stably reconstitute a budding yeast centromeric nucleosome using centromeric DNA.

In this new study, the authors now report that they were able to replace part of the Widom 601 DNA with centromeric DNA from chromosome 3. This makes the assay more closely resemble the in vivo situation. Interestingly, the presence of the centromeric DNA fragment makes one type of minimal kinetochore assembly, but not the other, withstand stronger forces.

Which kinetochore assembly turned out to be affected was somewhat unexpected, and can currently not be reconciled with structural knowledge of the budding yeast centromere/kinetochore. This highlights that, despite recent advances (e.g. Guan et al., 2021; Dendooven et al., 2023), aspects of budding yeast kinetochore architecture and function remain to be understood and that it will be important to dissect the contributions of the centromeric DNA sequence.

Given the unexpected result, the study would become yet more informative if the authors were able to pinpoint which interactions contribute to the enhanced force resistance in the presence of centromeric DNA.

Strength:

The paper demonstrates that centromeric DNA can increase the attachment strength between budding yeast microtubules and centromeric nucleosomes.

Weakness:

How centromeric DNA exerts this effect remains unclear.

Reviewer #3 (Public review):

In this manuscript, Casas-Tintó et al. explore the role of glial cell in the response to a neurodegenerative injury in the adult brain. They used Drosophila melanogaster as a model organism, and found that glial cells are able to generate new neurons through the mechanism of transdifferentiation in response to injury. This paper provides a new mechanism in regeneration, and gives an understanding to the role of glial cells in the process.

The authors have now addressed all my concerns.

Reviewer #2 (Public review):

Summary:

In the present study, the authors, using a mouse model of Fragile X syndrome, explore the very interesting hypothesis that restricting food access over a daily schedule will improve sleep patterns and, subsequently, behavioral capacities. By restricting food access from 12h to 6h over the nocturnal period (active period for mice), they show, in these KO mice, an improvement of the sleep pattern accompanied by reduced systemic levels of inflammatory markers and improved behavior. Using a classical mouse model of neurodevelopmental disorder (NDD), these data suggest that eating patterns might improve sleep quality, reduce inflammation and improve cognitive/behavioral capacities in children with NDD.

Strengths:

Overall, the paper is very well-written and easy to follow. The rationale of the study is generally well-introduced. The data are globally sound. The provided data support the interpretation overall.

Weaknesses:

(1) The introduction part is quite long in the Abstract, leaving limited space for the data provided by the present study.

(2) A couple of points are not totally clear for a non-expert reader:<br /> - The Fmr1/Fxr2 double KO mice are not well described.<br /> - What is the rationale for performing both LD and DD measures?

(3) The data on cytokines and chemokines are interesting. However, the rationale for the selection of these molecules is not given. In addition, these measures have been performed in the systemic blood. Measures in the brain could be very informative.

(4) An important question is the potential impact of fasting vs the impact of the food availability restriction. Indeed fasting has several effects on brain functioning including cognitive functions.

(5) How do the authors envision the potential translation of the present study to human patients? How to translate the 12 to 6 hours of food access in mice to children with Fragile X syndrome?

Reviewer #2 (Public review):

Summary:

Soham Mukhopadhyay et al. investigated the protein folding of the secretome from gall-forming microbes using the AI-based structure modeling tool AlphaFold2. Their study analyzed six gall-forming species, including two Plasmodiophorid species and four others spanning different kingdoms, along with one non-gall-forming Plasmodiophorid species, Polymyxa betae. The authors found no effector fold specifically conserved among gall-forming pathogens, leading to the conclusion that their virulence strategies are likely achieved through diverse mechanisms. However, they identified an expansion of the Ankyrin repeat family in two gall-forming Plasmodiophorid species, with a less pronounced presence in the non-gall-forming Polymyxa betae. Additionally, the study revealed that known effectors such as CCG and AvrSen1 belong to sequence-unrelated but structurally similar (SUSS) effector clusters.

Strengths:

(1) The bioinformatics analyses presented in this study are robust, and the AlphaFold2-derived resources deposited in Zenodo provide valuable resources for researchers studying plant-microbe interactions. The manuscript is also logically organized and easy to follow.

(2) The inclusion of the non-gall-forming Polymyxa betae strengthens the conclusion that no effector fold is specifically conserved in gall-forming pathogens and highlights the specific expansion of the Ankyrin repeat family in gall-forming Plasmodiophorids.

(3) Figure 4a and 4b effectively illustrate the SUSS effector clusters, providing a clear visual representation of this finding.

(4) Figure 1 is a well-designed, comprehensive summary of the number and functional annotations of putative secretomes in gall-forming pathogens. Notably, it reveals that more than half of the analyzed effectors lack known protein domains in some pathogens, yet some were annotated based on their predicted structures, despite the absence of domain annotations.

Weaknesses:

(1) The effector families discussed in this paper remain hypothetical in terms of their functional roles, which is understandable given the challenges of demonstrating their functions experimentally. However, this highlights the need for experimental validation as a next step.

(2) Some analyses, such as those in Figure 4e, emphasize motifs derived from sequence alignments of SUSS effector clusters. Since these effectors are sequence-unrelated, sequence alignments might be unreliable. It would be more rigorous to perform structure-based alignments in addition to sequence-based ones for motif confirmation. For instance, methods described in Figure 3E of de Guillen et al. (2015, https://doi.org/10.1371/journal.ppat.1005228) or tools like Foldseek (https://search.foldseek.com/foldmason) could be useful for aligning structures of multiple sequences.

(3) When presenting AlphaFold-generated structures, it is essential to include confidence scores such as pLDDT and PAE. For example, in Figure 1D of Derbyshire and Raffaele (2023, https://doi.org/10.1038/s41467-023-40949-9), the structural representations were colored red due to their high pLDDT scores, emphasizing their reliability.

Reviewer #2 (Public review):

Although recent cryo-EM structures of the CFTR ion channel were reported in a putative open state (ATP-bound, NBD-dimerized), it remains unclear whether these structures explain the conductive properties of the open channel observed in functional experiments. To investigate this, the authors conducted extensive molecular dynamics simulations at different voltages. The simulations are started from snapshots of their prior work, based on the experimental putative open state and including conditions with high negative voltage. Their analysis reveals that the cryo-EM structure represents a near-open metastable state, with most trajectories transitioning to either more closed or more open conformations, leading to the identification of a potential new open state. Permeation rate analysis shows that, unlike the other states, the proposed open state exhibits functional conductive properties of the open channel, although a strong inward rectification, inconsistent with experimental data, is also noted. Further structural analysis and simulations of ATP-unbound closed states offer additional mechanistic insights.

Overall, this work tackles key questions about CFTR: What is the true open conductive state? Does the ATP-bound cryo-EM structure reflect an actual open state? What is the ion permeation mechanism, and what structural changes occur during the closed-to-open transition? Which residues are critical, particularly those linked to diseases like CF? The study, based on a comprehensive set of all-atom molecular dynamics simulations, including a range of physiologically relevant voltages, provides important insights in this regard. It identifies key structural states, permeation pathways, critical residues, and conductance properties that can be directly compared to functional data. Notably, the analysis identifies a new open state of the channel, which, systematic analysis convincingly demonstrates is a conductive conformation of the channel, in line with experimental data at negative voltages. The authors carefully address some of the limitations of their results, exploring and discussing discrepancies with functional experiments, such as inward rectification. The work is also very well written, with a clear and logical presentation of key findings.

The main weakness of this study is that the simulation data rely on the conventional CHARMM36 force field for Cl− ions, which has been shown to significantly underestimate the interaction between Cl− and proteins (J. Chem. Theory Comput. 2021, 17, 6240-6261). For example, the conventional CHARMM36 force field destabilizes the Cl-binding site in CLC-ec1. The latter ion unbinds irreversibly during microseconds-long simulations which is at odds with the experimental binding affinity.

This imbalance in Cl−/protein/water interactions could significantly impact the CFTR simulations, potentially altering state populations and Cl− permeability. Notably, recent work by Levring and Chen (Proc Natl Acad Sci U S A. 2024) identifies a likely Cl− binding site in the bottleneck region of the channel, which contradicts the simulation results showing low occupancy Cl− ions in this region (Fig. 1B and Fig. 6A). This discrepancy may be due to the underestimation of Cl−/protein interactions. Indeed, Orabi et al. have proposed corrections that specifically tune these interactions, including those with aromatic residues, in line with the binding site geometry suggested by Levring and Chen. This imbalance in interactions may also lead to an underestimation of the conductance in the experimental near-open state.<br /> Balanced Cl−/protein interactions could also influence voltage/current relationships, potentially affecting the degree of inward rectification. For example, higher Cl− occupancy in the bottleneck region may stabilize the down state of R334, along with other measured interactions, thereby increasing conductance as the authors have shown.

The experimental evidence reported and discussed by the authors in support of the proposed open state is largely qualitative. For instance, in Figure 4 Supplement 2 there is a significant overlap in the distances and SASA distributions of open and near-open states for the reported residues (are those residues water accessible in the simulations?).

Given the known limitations of the standard CHARMM36 Cl− force field and in the absence of robust experimental validation of the proposed open state, I recommend validating at least part of the results using an independent set of simulations (not started from the previous ones) with an updated Cl− force field. It would be especially important to reassess whether the experimental near-open state is truly metastable and less probable than the new open state, and confirm that the near-open state exhibits negligible conductance.

A minor point worth discussing is whether the observed inward rectification may be influenced by hysteresis or incomplete equilibration, as many simulations were started from prior trajectories at large negative voltages and may not have fully relaxed. For instance, is not uncommon that small structural changes in backbone and sidechains occur in several microseconds (Shaw et al., Science, 2010). That said, discrepancies in current-voltage relationships are not unexpected due to challenges in simulation sampling and force field accuracy (J Gen Physiol 2013 May;141(5):619-32) as the authors stated.

Another minor point to address is the preparation of the simulation setup for the ATP-free structure of the protein. It would be helpful to specify whether any particular controls or steps were taken, given that the structure is based on a relatively low resolution (3.87 Å) model.

Reviewer #2 (Public review):

Summary:

Rennert et al. developed a thermodynamic framework for the assembly of branched networks to calculate the entropy dissipation associated with this process. They base their model on the simplest possible experimental system consisting of four proteins: actin, Arp2/3, capping protein, and NPF. They decompose the network assembly into a linear model where the order of events (polymerization, capping, and nucleation) is recorded sequentially. Polymerization and capping are sensitive to load and affected by Brownian ratchet effects, while nucleation is not. This simplified model provides an analytical solution that describes the load sensitivity of actin networks and agrees well with experimental data for a given set of transition rates.

Strengths:

(1) These thermodynamic approaches are original and fundamental to our understanding of these non-equilibrium systems.

(2) The fact that the model fits experimental data is encouraging.

Weaknesses:

(1) The possibility of describing branched actin assembly as a Markov process is not well justified.

(2) The choice of parameters controlling the system is open to question. Some parameters are probably completely negligible, while other ignored effects are potentially significant.

(3) The main conclusion of the manuscript, linked to the existence of a dissipation gap, is quite expected. The manuscript would have been more valuable if the authors had been able to decompose dissipation into different components in order to prove that a particular fraction is associated with adaptation.

Reviewer #2 (Public review):

Summary:

The authors reconstructed the three-dimensional organization of melanosomes in fossilized feathers belonging to a spectacular specimen of a stem avialan from China. The authors then proceed to infer the original coloration and related ecological implications.

Strengths:

I believe the study is well executed and well explained. The methods are appropriate to support the main conclusions. I particularly appreciate how the authors went beyond the simple morphological inference and interrogated the structural implications of melanosome organization in three dimensions. I also appreciate how the authors were upfront with the reliability of their methods, results, and limitations of their study. I believe this will be a landmark study for the inference of coloration in extinct species and how to interrogate its significance in the future.

Weaknesses:

I have a few minor comments.<br /> Introduction: I would suggest the authors move the paragraph on coloration in modern birds (lines 75-97) before line 64, as this is part of the reasoning behind the study. I believe this change would improve the flow of the introduction for the general reader.<br /> Melanosome organization: I was surprised to find little information in the main text regarding this topic. As this is one of the major findings of the study, I would suggest the authors include more information regarding the general geometry/morphology of the single melanosomes and their arrangement in three dimensions.<br /> Keratin: the authors use such a term pretty often in the text, but how is this inference justified in the fossil? Can the authors extend on this? Previous studies suggested the presence of degradation products deriving from keratin, rather than immaculated keratin per se.<br /> Ontogenetic assessment: the authors infer a sub-adult stage for the specimen, but no evidence or discussion is reported in the SI. Can the authors describe and discuss their interpretations?<br /> CT scan data: these data should be made freely available upon publication of the study.

Reviewer #2 (Public review):

Summary:

For centuries, humans have been developing methods to see ever smaller objects, such as cells and their contents. This has included studies of viruses and their interactions with host cells during processes extending from virion structure to the complex interactions between viruses and their host cells: virion entry, virus replication and virion assembly, and release of newly constructed virions. Recent developments have enabled simultaneous application of fluorescence-based detection and intracellular localization of molecules of interest in the context of sub-micron resolution imaging of cellular structures by electron microscopy.

The submission by Nahas et al., extends the state-of-the-art for visualization of important aspects of herpesvirus (HSV-1 in this instance) virion morphogenesis, a complex process that involves virus genome replication, and capsid assembly and filling in the nucleus, transport of the nascent nucleocapsid and some associated tegument proteins through the inner and outer nuclear membranes to the cytoplasm, orderly association of several thousand mostly viral proteins with the capsid to form the virion's tegument, envelopment of the tegumented capsid at a virus-tweaked secretory vesicle or at the plasma membrane, and release of mature virions at the plasma membrane.

In this groundbreaking study, cells infected with HSV-1 mutants that express fluorescently tagged versions of capsid (eYFP-VP26) and tegument (gM-mCherry) proteins were visualized with 3D correlative structured illumination microscopy and X-ray tomography. The maturation and egress pathways thus illuminated were studied further in infections with fluorescently tagged viruses lacking one of nine viral proteins.

Strengths:

This outstanding paper meets the journal's definitions of Landmark, Fundamental, Important, Valuable, and Useful. The work is also Exceptional, Compelling, Convincing, and Solid. The work is a tour de force of classical and state-of-the-art molecular and cellular virology. Beautiful images accompanied by appropriate statistical analyses and excellent figures. The numerous complex issues addressed are explained in a clear and coordinated manner; the sum of what was learned is greater than the sum of the parts. Impacts go well beyond cytomegalovirus and the rest of the herpesviruses, to other viruses and cell biology in general.

Weaknesses:

I have a few suggestions for minor adjustments in the text.

Reviewer #2 (Public review):

Summary:

This well-written manuscript addresses an important but recalcitrant problem - molecular mechanism of protein misfolding in Ig light chain (LC) amyloidosis (AL), a major life-threatening form of systemic human amyloidosis. The authors use expertly recorded and analyzed small-angle X-ray scattering (SAXS) data as a restraint for molecular dynamics simulations (called M&M). Six patient-based LC proteins are explored, including four AL and two non-AL. The authors report a partially populated "H-state" determined computationally, wherein the two domains in an LC molecule acquire a straight rather than bent conformation, with an extended interdomain linker; this H-state distinguishes AL from non-AL LCs. H-D exchange mass spectrometry is used to support this conclusion. This is a novel and interesting finding with potentially important translational implications.

Strengths:

Expertly recorded and analyzed SAXS data combined with clever M&M simulations lead to a novel and interesting conclusion, which is supported by limited H-D exchange data.<br /> Stabilization of the CL-CL interface is a good idea that may help protect a subset of AL LCs from misfolding in amyloid.

Computational M&M evidence is convincing and is supported by SAXS data, which are used as restraints for simulations. Although Kratky plots reported in the main MS Fig. 1 show significant differences between the data and the structural model for only one AL protein, AL-55, H-state is also inferred for other AL proteins.

Apparent limitations:

HDX MS results show that residues 35-50 from VL-VL and VL-CL dimerization interface are less protected in AL vs. non-AL proteins, which is consistent with the H-state. However, the small number of proteins yielding useful HDX data (three AL and one non-AL) suggests that this conclusion should be treated with caution. It is unclear whether the conformational heterogeneity depicted in M&M simulations is consistent with HDX results, and whether prior HDX studies of AL and MM LCs are consistent with the conclusions that a particular domain-domain interface is weakened in AL vs. non-AL LCs. The butterfly plots in Fig. 5 could benefit from the X-axis labeling with the peptide fragments.

Reviewer #2 (Public review):

Summary:

This well-written manuscript addresses an important but recalcitrant problem - molecular mechanism of protein misfolding in Ig light chain (LC) amyloidosis (AL), a major life-threatening form of systemic human amyloidosis. The authors use expertly recorded and analyzed small-angle X-ray scattering (SAXS) data as a restraint for molecular dynamics simulations (called M&M). Six patient-based LC proteins are explored, including four AL and two non-AL. The authors report a partially populated "H-state" determined computationally, wherein the two domains in an LC molecule acquire a straight rather than bent conformation, with an extended interdomain linker; this H-state distinguishes AL from non-AL LCs. H-D exchange mass spectrometry is used to support this conclusion. This is a novel and interesting finding with potentially important translational implications.

Strengths:

Expertly recorded and analyzed SAXS data combined with clever M&M simulations lead to a novel and interesting conclusion, which is supported by limited H-D exchange data.<br /> Stabilization of the CL-CL interface is a good idea that may help protect a subset of AL LCs from misfolding in amyloid.

Computational M&M evidence is convincing and is supported by SAXS data, which are used as restraints for simulations. Although Kratky plots reported in the main MS Fig. 1 show significant differences between the data and the structural model for only one AL protein, AL-55, H-state is also inferred for other AL proteins.

Apparent limitations:

HDX MS results show that residues 35-50 from VL-VL and VL-CL dimerization interface are less protected in AL vs. non-AL proteins, which is consistent with the H-state. However, the small number of proteins yielding useful HDX data (three AL and one non-AL) suggests that this conclusion should be treated with caution. It is unclear whether the conformational heterogeneity depicted in M&M simulations is consistent with HDX results, and whether prior HDX studies of AL and MM LCs are consistent with the conclusions that a particular domain-domain interface is weakened in AL vs. non-AL LCs. The butterfly plots in Fig. 5 could benefit from the X-axis labeling with the peptide fragments.

Reviewer #3 (Public review):

Summary:

The authors were trying to show that a novel neuronal metallothionein of poorly defined function, GIF/MT3, is actually heavily persulfidated in both the Zn-bound and apo (metal-free) forms of the molecule as purified from a heterologous (bacterial) or native host. Evidence in support of this conclusion is strong, with both spectroscopic and mss spectrometry evidence strongly consistent with this general conclusion. The authors would appear to have achieved their aims.

Strengths:

The analytical data in support of the author's primary conclusions are strong. The authors also provide some modeling evidence that supports the contention that MT3 (and other MTs) can readily accommodate a sulfane sulfur on each of the 20 cysteines in the Zn-bound structure, with little perturbation of the overall structure. This is not the case with Cys trisulfides, which suggests that the persulfide-metallated state is clearly positioned at lower energy relative to the immediately adjacent thiolate- or trisulfidated metal coordination complexes.

Weaknesses:

The biological significance of the findings is not entirely clear. On the one hand, the analytical data are solid (albeit using a protein derived from a bacterial over-expression experiment), and yes, it's true that sulfane S can protect Cys from overoxidation, but everything shown in the summary figure (Fig. 9D) can be done with Zn release from a thiol by ROS, and subsequent reduction by the Trx/TR system. In addition, it's long been known that Zn itself can protect Cys from oxidation. I view this as a minor shortcoming that will motivate follow-up studies.

Impact:

The impact will be high since the finding is potentially disruptive to the MT field for sure. The sulfane sulfur counting experiment (the HPE-IAM electrophile trapping experiment) may well be widely adopted by the field. Those in the metals field always knew that this was a possibility, and it will interesting to see the extent to which metal binding thiolates broadly incorporate sulfane sulfur into their first coordination shells.

Comments on revisions:

The revised manuscript is only slightly changed from the original, with the inclusion of a supplementary figure (Fig. S2) and minor changes in the text. The authors did not choose to carry out the quantitative Zn binding experiment (which I really wanted to see), but given the complexities of the experiment, I'll let it go.

Fig. 9: the authors imply in the mechanistic "redox-switch" figure that Trx/TR can not reduce persulfide linkages. A number of groups have shown this to be the case. I recommend modifying the figure legend or text to make this clear to the reader,