Reviewer #1 (Public review):

Summary:

The authors performed experimental evolution of MreB mutants that have a slow growing round phenotype and studied the subsequent evolutionary trajectory using analysis tool from molecular biology. It was remarkable and interesting that they found that the original phenotype was not restored (most common in these studies) but that the round phenotype was maintained.

Strengths:

The finding that the round phenotype was maintained during evolution rather than that the original phenotype, rod shape cells, was recovered is interesting. The paper extensively investigates what happens during adaptation with various different techniques. Also the extensive discussion of the findings at the end of the paper is well thought through and insightful.

Weaknesses:

I find there are three general weaknesses<br /> (1) Although the paper states in the abstract that it emphasizes "new knowledge to be gained" it remains unclear what this concretely is. At page 4 they state 3 three research questions, these could be more extensively discussed in the abstract. Also these questions read more like genetics questions while the paper is a lot about cell biological findings.<br /> (2) It is not clear to me from the text what we already know about restoration of MreB loss from suppressors studies (in the literature). Are there supressor screens in the literature and which part of the findings is consistent with suppressor screens and which parts are new knowledge?<br /> (3) The clarity of the figures, captions and data quantification need to be improved.

Reviewer #3 (Public review):

This paper addresses a long-standing problem in microbiology: the evolution of bacterial cell shape. Bacterial cells can take a range of forms, among the most common being rods and spheres. The consensus view is that rods are the ancestral form and spheres the derived form. The molecular machinery governing these different shapes is fairly well understood but the evolutionary drivers responsible for the transition between rods and spheres is not. Enter Yulo et al.'s work. The authors start by noting that deletion of a highly conserved gene called MreB in the Gram-negative bacterium Pseudomonas fluorescens reduces fitness but does not kill the cell (as happens in other species like E. coli and B. subtilis) and causes cells to become spherical rather than their normal rod shape. They then ask whether evolution for 1000 generations restores the rod shape of these cells when propagated in a rich, benign medium.

The answer is no. The evolved lineages recovered fitness by the end of the experiment, growing just as well as the unevolved rod-shaped ancestor, but remained spherical. The authors provide an impressively detailed investigation of the genetic and molecular changes that evolved. Their leading results are:

(1) the loss of fitness associated with MreB deletion causes high variation in cell volume among sibling cells after cell division;<br /> (2) fitness recovery is largely driven by a single, loss-of-function point mutation that evolves within the first ~250 generations that reduces the variability in cell volume among siblings;<br /> (3) the main route to restoring fitness and reducing variability involves loss of function mutations causing a reduction of TPase and peptidoglycan cross-linking, leading to a disorganized cell wall architecture characteristic of spherical cells.

The inferences made in this paper are on the whole well supported by the data. The authors provide a uniquely comprehensive account of how a key genetic change leads to gains in fitness and the spectrum of phenotypes that are impacted and provide insight into the molecular mechanisms underlying models of cell shape.

Suggested improvements and clarifications include:<br /> (1) A schematic of the molecular interactions governing cell wall formation could be useful in the introduction to help orient readers less familiar with the current state of knowledge and key molecular players;<br /> (2) It remains unclear whether corrections for multiple comparisons are needed when more than one construct or strain is compared to the common ancestor, as in Supp Fig 19A (relative PG density of different constructs versus the SBW25 ancestor). The author's response did not clarify matters: was data for the WT obtained independently alongside each each strain/construct (justifying a paired t-test) or was a single set of data for the WT obtained and used to compare against all other strains/constructs (which would demand a correction for multiple comparisons)?<br /> (3) The authors refrain from making strong claims about the nature of selection on cell shape, perhaps because their main interest is the molecular mechanisms responsible. They identify sources of stabilizing selection favouring an intermediate cell size (lack of DNA in small cells and disorganized DNA in large cells). Their interpretation of stabilizing selection in the review is correct and entirely consistent with the mechanistic causes identified here. I think this is valuable and interesting, although I recognize it is not the focus of the paper.

Comments on revisions:

Please further clarify the experimental design and replication for the contrast between mutants and WT to address the issue of multiple comparisons.

Reviewer #1 (Public review):

Summary:

In this study, Avila et al. tested the hypothesis that chronic pain states are associated with changes in excitability of the medial prefrontal cortex (mPFC). The authors used the slope of the aperiodic component of the EEG power spectrum (= the aperiodic exponent) as a novel, non-invasive proxy for the cortical excitation-inhibition ratio. They performed source localization to estimate the EEG signals generated specifically by the mPFC. By pooling resting-state EEG recordings from three existing datasets, the authors were able to compare the aperiodic exponent in the mPFC and across the whole brain (at all modeled cortical sources) between 149 chronic pain patients and 115 healthy controls. Additionally, they assessed the relationship between the aperiodic exponent and pain intensity reported by the patients. To account for heterogeneity in pain etiology, the analysis was also performed separately for two patient subgroups with different chronic pain conditions (chronic back pain and chronic widespread pain). The study found robust evidence against differences in the aperiodic exponent in the mPFC between people with chronic pain and healthy participants, and no correlation was observed between the aperiodic exponent and pain intensity. These findings were consistent across different patient subgroups and were corroborated by the whole-brain analysis.

Strengths:

The study is based on sound scientific reasoning and rigorously employs suitable methods to test the hypothesis. It follows a pre-registered protocol, which greatly increases the transparency and, consequently, the credibility of the reported results. In addition to the planned steps, the authors used a multiverse analysis to ensure the robustness of the results across different methodological choices. I find this particularly interesting, as the EEG aperiodic exponent has only recently been linked to network excitability, and the most appropriate methods for its extraction and analysis are still being determined. The methods are clearly and comprehensively described, making this paper very useful for researchers planning similar studies. The results are convincing, supported by informative figures, and the lack of the expected difference in mPFC excitability between the tested groups is thoroughly and constructively discussed.

Weaknesses:

Firstly, to augment the sample size, the authors pooled data recorded by different researchers using different experimental protocols. This inevitably increases sample variability and may limit the availability of certain measures, as was the case here with the reports of pain intensity in the patient group. Secondly, the analysis heavily relies on the estimation of cortical sources, an approach that may yield imprecise results, especially when default conduction models, source models, and electrode coordinates are used (as was the case here).

Comments on revisions:

The authors satisfactorily revised the manuscript and responded to previous questions and suggestions. I have no further comments.

Reviewer #2 (Public review):

Summary:

This study evaluated the aperiodic component in the medial prefrontal cortex (mPFC) using resting-state EEG recordings from 149 individuals with chronic pain and 115 healthy participants. The findings showed no significant differences in the aperiodic component of the mPFC between the two groups, nor was there any correlation between the aperiodic component and pain intensity. These results were consistent across various chronic pain subtypes and were corroborated by whole-brain analyses. The study's robustness was further reinforced by preregistration and multiverse analyses, which accounted for a wide range of methodological choices.

Strengths:

This study was rigorously conducted, yielding clear and conclusive results. Furthermore, it adhered to stringent open and reproducible science practices, including preregistration, blinded data analysis, and Bayesian hypothesis testing. All data and code have been made openly available, underscoring the study's commitment to transparency and reproducibility.

Weaknesses:

The aperiodic exponent of the EEG power spectrum is often regarded as an indicator of the excitatory/inhibitory (E/I) balance. However, this measure may not be the most accurate or optimal for quantifying E/I balance, a limitation that the authors might consider addressing in the future.

Comments on revisions:

All my comments have been well addressed.

Reviewer #1 (Public review):

This study tests whether Little Swifts exhibit optimal foraging, which the data seem to indicate is the case. This is unsurprising as most animals would be expected to optimize the energy income : expenditure ratio, however it hasn't been explicitly quantified before the way it was in this manuscript.

The major strength of this work is the sheer volume of tracking data and the accuracy of those data. The ATLAS tracking system really enhanced this study and allowed for pinpoint monitoring of the tracked birds. These data could be used to ask and answer many questions beyond just the one tested here.

The major weakness of this work lies in the sampling of insect prey abundance at a single point on the landscape, 6.5 km from the colony. This sampling then requires the authors to work under the assumption that prey abundance is simultaneously even across the study region. It may be fair to say that prey populations might be correlated over space but are not equal. It is uncertain whether other aspects of the prey data are problematic. For example, the radar only samples insects at 50m or higher from the ground - how often do Little Swifts forage under 50m high?

The finding that Little Swifts forage optimally is indeed supported by the data, notwithstanding some of the shortcomings in the prey abundance data. The authors achieved their aims and the results support their conclusions.

At its centre, this work adds to our understanding of Little Swift foraging and extends to a greater understanding of aerial insectivores in general. While unsurprising that Little Swifts act as optimal foragers, it is good to have quantified this and show that the population declines observed in so many aerial insectivores are not necessarily a function of inflexible foraging habits. Further, the methods used in this research have great potential for other work. For example, the ATLAS system poses some real advantages and an exciting challenge to existing systems, like MOTUS. The radar that was used to quantify prey abundance also presents exciting possibilities if multiple units could be deployed to get a more spatially-explicit view.

To improve the context of this work, it is worth noting that this research goes into much further depth than any previous studies on a similar topic in several flycatcher and swallow species. A further justification is posited that this research is needed due to dramatic insect population declines, however, the magnitude and extent of such declines are fiercely debated in the literature.

Reviewer #2 (Public review):

Summary:

Bloch et al. studied the relationships between aerial foragers (lesser swifts) tracked using an automated radio telemetry system (Atlas) and their prey (flying insects) monitored using a small vertical-looking radar (BirdScan MR1). The aim of the study was to check whether swifts optimise their foraging according to the abundance of their prey. The results provide evidence that small swifts can increase their foraging rate when aerial insect abundance is high, but found no correlation between insect abundance and flight energy expenditure.

Key points:

This study fills gaps in fundamental knowledge of prey-predator dynamics in the air. It describes the coincidence between the abundance of flying insects and the characteristics derived from monitoring individual swifts.

Weaknesses:

The paper uses assumptions largely derived from optimal foraging theory, but mixes up the form of natural selection: parental energy, parental survival (predation risk), nestling foraging and reproductive success. The results are partly inconsistent, and confounding factors (e.g., the brooding phase versus the nestling phase) remained ignored. In conclusion, the analyses performed are insufficient to rigorously assess whether lesser swifts are optimising their foraging beyond making shorter foraging trips.<br /> The filters applied to the monitoring data are necessary but may strongly influence the characteristics derived based on maximum or mean values. Sensitivity tests or the use of characteristics that are less dependent on extreme values could provide more robust results.

Reviewer #1 (Public review):

Summary:

In the first half of this study, Pham et al. investigate the regulation of TEAD via ubiquitination and PARylation, identifying an E3 ubiquitin ligase, RNF146, as a negative regulator of TEAD activity through an siRNA screen of ubiquitin-related genes in MCF7 cells. The study also finds that depletion of PARP1 reduced TEAD4 ubiquitination levels, suggesting a certain relationship between TEAD4 PARylation and ubiquitination which was also explored through an interesting D70A mutation. Pham et al. subsequently tested this regulation in D. melanogaster by introducing Hpo loss-of-function mutations and rescuing the overgrowth phenotype through RNF146 overexpression.

In the second half of this study, Pham et al. designed and assayed several potential TEAD degraders with a heterobifunctional design, which they term TEAD-CIDE. Compounds D and E were found to effectively degrade pan-TEAD, an effect which could be disrupted by treatment with TEAD lipid pocket binders, proteasome inhibitors, or E1 inhibitors, demonstrating that the TEAD-CIDEs operate in a proteasome-dependent manner. These TEAD-CIDEs could reduce cell proliferation in OVCAR-8, a YAP deficient cell line, but not SK-N-FI, a Hippo pathway independent cell line. Finally, this study also utilizes ATAC-seq on Compound D to identify reductions in chromatin accessibility at the regions enriched for TEAD DNA binding motifs.

Strengths:

The study provides compelling evidence that the E3 ubiquitin ligase RNF146 is a novel negative regulator of TEAD activity. The authors convincingly delineate the mechanism through multiple techniques and approaches. The authors also describe the development of heterobifunctional pan-degraders of TEAD, that could serve as valuable reagents to more deeply study TEAD biology.

Weaknesses:

The scope of this study is extremely broad. The first half of the paper highlights the mechanisms underlying TEAD degradation; however, the connection to the second half of the paper on small molecule degraders of TEAD is jarring, and it seems as though two separate stories were combined into this single massive study. In my opinion, the study would be stronger if it chose to focus on only one of these topics and instead went deeper.

Additionally, the figure clarity needs to be substantially improved, as readability and interpretation was difficult in many panels. Lastly, there are numerous typos and poor grammar throughout the text that need to be addressed.

Comments on revisions:

The authors have addressed most of our critiques. The manuscript has improved significantly, particularly in the clarity of the figures and the flow of the text. The findings of this study contribute valuable insights into TEAD biology in cancer and provide useful resources for further research into TEAD.

However, as noted by other reviewers, the manuscript still feels somewhat disjointed, despite the attempt to connect the two parts on RNF146-mediated TEAD degradation and the development of TEAD degraders. Certain data inconsistencies and technical limitations may have made some aspects of the data hard to interpret accurately and could benefit from further clarification.

Reviewer #1 (Public review):

The revision by Ruan et al clarifies several aspects of the original manuscript that were difficult to understand, and I think it presents some useful and interesting ideas. I understand that the authors are distinguishing their model from the standard Wright-Fisher model in that the population size is not imposed externally, but is instead a consequence of the stochastic reproduction scheme. Here, the authors chose a branching process but in principle any Markov chain can probably be used. Within this framework, the authors are particularly interested in cases where the variance in reproductive success changes through time, as explored by the DDH model, for example. They argue with some experimental results that there is a reason to believe that the variance in reproductive success does change over time.

One of the key aspects of the original manuscript that I want to engage with is the DDH model. As the authors point out, their equations 5 and 6 are assumptions, and not derived from any principles. In essence, the authors are positing that that the variance in reproductive success, given by 6, changes as a function of the current population size. There is nothing "inherent" to a negative binomial branching mechanism that results in this: in fact, the the variance in offspring number could in principle be the same for all time. As relates to models that exist in the literature, I believe that this is the key difference: unlike Cannings models, the authors allow for a changing variance in reproduction through time.

This is, of course, an interesting thing to consider, and I think that the situation the authors point out, in which drift is lower at small population sizes and larger at large population sizes, is not appreciated in the literature. However, I am not so sure that there is anything that needs to be resolved in Paradox 1. A very strong prediction of that model is that Ne and N could be inversely related, as shown by the blue line in Fig 3b. This suggests that you could see something very strange if you, for example, infer a population size history using a Wright-Fisher framework, because you would infer a population *decline* when there is in fact a population *expansion*. However, as far as I know there are very few "surprising population declines" found in empirical data. An obvious case where we know there is very rapid population growth is human populations; I don't think I've ever seen an inference of recent human demographic history from genetic data that suggests anything other than a massive population expansion. While I appreciate the authors empirical data supporting their claim of Paradox 1 (more on the empirical data later), it's not clear to me that there's a "paradox" in the literature that needs explaining so much as this is a "words of caution about interpreting inferred effective population sizes". To be clear, I think those words of caution are important, and I had never considered that you might be so fundamentally misled as to infer decline when there is growth, but calling it a "paradox" seems to suggest that this is an outstanding problem in the literature, when in fact I think the authors are raising a *new* and important problem. Perhaps an interesting thing for the authors to do to raise the salience of this point would be to perform simulations under this model and then infer effective population sizes using e.g. dadi or psmc and show that you could identify a situation in which the true history is one of growth, but the best fit would be one of decline

The authors also highlight that their approach reflects a case where the population size is determined by the population dynamics themselves, as opposed to being imposed externally as is typical in Cannings models. I agree with the authors that this aspect of population regulation is understudied. Nonetheless, several manuscripts have dealt with the case of population genetic dynamics in populations of stochastically fluctuating size. For example, Kaj and Krone (2003) show that under pretty general conditions you get something very much like a standard coalescent; for example, combining their theorem 1 with their arguments on page 36 and 37, they find that exchangeable populations with stochastic population dynamics where the variance does not change with time still converge to exactly the coalescent you would expect from Cannings models. This is strongly suggestive that the authors key result isn't about stochastic population dynamics per se, but instead related to arguing that variance in reproductive success could change through time. In fact, I believe that the result of Kaj and Krone (2003) is substantially more general than the models considered in this manuscript. That being said, I believe that the authors of this manuscript do a much better job of making the implications for evolutionary processes clear than Kaj and Krone, which is important---it's very difficult to understand from Kaj and Krone the conditions under which effective population sizes will be substantially impacted by stochastic population dynamics.

I also find the authors exposition on Paradox 3 to be somewhat strange. First of all, I'm not sure there's a paradox there at all? The authors claim that the lack of dependence of the fixation probability on Ne is a paradox, but this is ultimately not surprising---fixation of a positively selected allele depends mostly on escaping the boundary layer, which doesn't really depend on the population size (see Gillespie's book "The Causes of Molecular Evolution" for great exposition on boundary layer effects). Moreover, the authors *use a Cannings-style argument* to get gain a good approximation of how the fixation probability changes when there is non-Poisson reproduction. So it's not clear that the WFH model is really doing a lot of work here. I suppose they raise the interesting point that the particularly simple form of p(fix) = 2s is due to the assumption that variance in offspring is equal to 1.

In addition, I raised some concerns about the analysis of empirical results on reproductive variance in my original review, and I don't believe that the authors responded to it at all. I'm not super worried about that analysis, but I think that the authors should probably respond to me.

Overall, I feel like I now have a better understanding of this manuscript. However, I think it still presents its results too strongly: Paradox 1 contains important words of caution that reflect what I am confident is an under appreciated possibility, and Paradox 3 is, as far as I'm concerned, not a paradox at all. I have not addressed Paradox 2 very much because I think that another reviewer had solid and interesting comments on that front and I am leaving it to them. That being said, I do think Paradox 2 actually presents a deep problem in the literature and that the authors' argument may actually represent a path toward a solution.

This manuscript can be a useful contribution to the literature, but as it's presented at the moment, I think most of it is worded too strongly and it continues to not engage appropriately with the literature. Theoretical advances are undoubtedly important, and I think the manuscript presents some interesting things to think about but ultimately needs to be better situated and several of the claims strongly toned down.

References:<br /> Kaj, I., & Krone, S. M. (2003). The coalescent process in a population with stochastically varying size. Journal of Applied Probability, 40(1), 33-48.

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 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.

Reviewer #3 (Public review):

Summary:

Ruan and colleagues consider a branching process model (in their terminology the "Haldane model") and the most basic Wright-Fisher model. They convincingly show that offspring distributions are usually non-Poissonian (as opposed to what's assumed in the Wright-Fisher model), and can depend on short-term ecological dynamics (e.g., variance in offspring number may be smaller during exponential growth). The authors discuss branching processes and the Wright-Fisher model in the context of 3 "paradoxes" --- 1) how Ne depends on N might depend on population dynamics; 2) how Ne is different on the X chromosome, the Y chromosome, and the autosomes, and these differences do match the expectations base on simple counts of the number of chromosomes in the populations; 3) how genetic drift interacts with selection. The authors provide some theoretical explanations for the role of variance in the offspring distribution in each of these three paradoxes. They also perform some experiments to directly measure the variance in offspring number, as well as perform some analyses of published data.

Strengths:

- The theoretical results are well-described and easy to follow.<br /> - The analyses of different variances in offspring number (both experimentally and analyzing public data) are convincing that non-Poissonian offspring distributions are the norm.<br /> - The point that this variance can change as the population size (or population dynamics) change is also very interesting and important to keep in mind.<br /> - I enjoyed the Density-Dependent Haldane model. It was a nice example of the decoupling of census size and effective size.<br /> - Equation (10) is a nice result (but see below)

Weaknesses:

- I am not convinced that these types of effects cannot just be absorbed into some time-varying Ne and still be well-modeled by the Wright-Fisher process. As a concrete example, Mohle and Sagitov 2001 show that a "coalescent Ne" for the WF model should be (N-1)/Var(K). This resolves the exponentially growing bacteria "paradox" raised in the present paper --- when the bacteria are growing Var(K) ~ 0, and hence there should be very little drift. This exactly resolves the "paradox" raised by the authors. Instead, it merely underscores that Ne does not need to be equal to (or even positively correlated!) with N. I absolutely do not see this as a failure of the WF model. Whether one finds branching processes or the WF model more biologically intuitive is a matter of taste, but to say that WF models cannot explain this "paradox" is false, when a well-known paper from more than 20 years ago does just that.<br /> - Along these lines, the result that Ne in the Wright-Fisher process might not be related to N in any straightforward (or even positively correlated) way are well-known (e.g., Neher and Hallatschek 2012; Spence, Kamm, and Song 2016; Matuszewski, Hildebrandt, Achaz, and Jensen 2018; Rice, Novembre, and Desai 2018; the work of Lounès Chikhi on how Ne can be affected by population structure; etc...)<br /> - I was also missing some discussion of the relationship between the branching process and the Wright-Fisher model (or more generally Cannings' Exchangeable Models) when conditioning on the total population size. In particular, if the offspring distribution is Poisson, then conditioned on the total population size, the branching process is identical to the Wright-Fisher model.<br /> - Given that Cannings' exchangeable models decouple N and Ne, it would not surprise me if something like equation (10) could be derived under such a model. I have not seen such a derivation, and the authors' result is nice, but I do not see it as proof that WF-type models (i.e., Cannings' models) are irreparably broken.

Reviewer #1 (Public review):

Summary:

The authors used multiple approaches to study salt effects in liquid-liquid phase separation (LLPS). Results on both wild-type Caprin1 and mutants and on different types of salts contribute to a comprehensive understanding.

Strengths:

The main strength of this work is the thoroughness of investigation. This aspect is highlighted by the multiple approaches used in the study, and reinforced by the multiple protein variants and different salts studied.

Weaknesses:

(1) The multiple computational approaches are a strength, but they're cruder than explicit-solvent all-atom molecular dynamics (MD) simulations and may miss subtle effects of salts. In particular, all-atom MD simulations demonstrate that high salt strengthens pi-types of interactions (ref. 42 and MacAinsh et al, https://www.biorxiv.org/content/10.1101/2024.05.26.596000v3).<br /> (2) The paper can be improved by distilling the various results into a simple set of conclusions. By example, based on salt effects revealed by all-atom MD simulations, MacAinsh et al. presented a sequence-based predictor for classes of salt dependence. Wild-type Caprin1 fits right into the "high net charge" class, with a high net charge and a high aromatic content, showing no LLPS at 0 NaCl and an increasing tendency of LLPS with increasing NaCl. In contrast, pY-Caprin1 belongs to the "screening" class, with a high level of charged residues and showing a decreasing tendency of LLLPS.<br /> (3) Mechanistic interpretations can be further simplified or clarified. (i) Reentrant salt effects (e.g., Fig. 4a) are reported but no simple explanation seems to have been provided. Fig. 4a,b look very similar to what has been reported as strong-attraction promotor and weak-attraction suppressor, respectively (ref. 50; see also PMC5928213 Fig. 2d,b). According to the latter two studies, the "reentrant" behavior of a strong-attraction promotor, CL- in the present case, is due to Cl-mediated attraction at low to medium [NaCl] and repulsion between Cl- ions at high salt. Do the authors agree with this explanation? If not, could they provide another simple physical explanation? (ii) The authors attributed the promotional effect of Cl- to counterion-bridged interchain contacts, based on a single instance. There is another simple explanation, i.e., neutralization of the net charge on Caprin1. The authors should analyze their simulation results to distinguish net charge neutralization and interchain bridging; see MacAinsh et al.<br /> (4) The authors presented ATP-Mg both as a single ion and as two separate ions; there is no explanation of which of the two versions reflects reality. When presenting ATP-Mg as a single ion, it's as though it forms a salt with Na+. I assume NaCl, ATP, and MgCl2 were used in the experiment. Why is Cl- not considered? Related to this point, it looks ATP is just another salt ion studied and much of the Results section is on NaCl, so the emphasis of ATP ("Diverse Roles of ATP" in the title is somewhat misleading.

Comments on revisions:

This revision addressed all my previous comments.

Reviewer #2 (Public review):

Summary:

In this paper, Lin and colleagues aim to understand the role of different salts on the phase behavior of a model protein of significant biological interest, Caprin1, and its phosphorylated variant, pY-Caprin1. To achieve this, the authors employed a variety of methods to complement experimental studies and obtain a molecular-level understanding of ion partitioning inside biomolecular condensates. A simple theory based on rG-RPA is shown to capture the different salt dependencies of Caprin1 and pY-Caprin1 phase separation, demonstrating excellent agreement with experimental results. The application of this theory to multivalent ions reveals many interesting features with the help of multicomponent phase diagrams. Additionally, the use of CG model-based MD simulations and FTS provides further clarity on how counterions can stabilize condensed phases.

Strengths:

The greatest strength of this study lies in the integration of various methods to obtain complementary information on thermodynamic phase diagrams and the molecular details of the phase separation process. The authors have also extended their previously proposed theoretical approaches, which should be of significant interest to other researchers. Some of the findings reported in this paper, such as bridging interactions, are likely to inspire new studies using higher-resolution atomistic MD simulations.

Reviewer #3 (Public review):

Authors first use rG-RPA to reproduce two observed trends. Caprin1 does not phase separate at very low salt but then undergoes LLPS with added salt while further addition of salt reduces its propensity to LLPS. On the other hand pY-Caprin1 exhibits a monotonic trend where the propensity to phase separate decreases with the addition of salt. This distinction is captured by a two component model and also when salt ions are explicitly modeled as a separate species with a ternary phase diagram. The predicted ternary diagrams (when co and counter ions are explicitly accounted for) also predict the tendency of ions to co-condense or exclude proteins in the dense phase. Predicted trends are generally in line with the measurement for Cparin1. Next, the authors seek to explain the observed difference in phase separation when Arginines are replaced by Lysines creating different variants. In the current rG-RPA type models both Arginine (R) and Lysine (K) are treated equally since non-electrostatic effects are only modeled in a mean-field manner that can be fitted but not predicted. For this reason, coarse grain MD simulation is suitable. Moreover, MD simulation affords structural features of the condensates. They used a force field that is capable of discriminating R and K. The MD predicted degrees of LLPS of these variants again is consistent with the measurement. One additional insight emerges from MD simulations that a negative ion can form a bridge between two positively charged residues on the chain. These insights are not possible to derive from rG-RPA. Both rG-RPA and MD simulation become cumbersome when considering multiple types of ions such as Na, Cl, [ATP] and [ATP-Mg] all present at the same time. FTS is well suited to handle this complexity. FTS also provides insights into the co-localization of ions and proteins that is consistent with NMR. By using different combinations of ions they confirm the robustness of the prediction that Caprin1 shows salt-dependent reentrant behavior, adding further support that the differential behavior of Caprin1, and pY-Caprin1 is likely to be mediated by charge-charge interactions.

Comments on revisions:

The authors addressed my comments and it is ready for publication.

Reviewer #1 (Public review):

Summary:

This manuscript explores the multiple cell types present in the wall of murine collecting lymphatic vessels with the goal of identifying cells that initiate the autonomous action potentials and contractions needed to drive lymphatic pumping. Through the use of genetic models to delete individual genes or detect cytosolic calcium in specific cell types, the authors convincingly determine that lymphatic muscle cells are the origin of the action potential that triggers lymphatic contraction.

Strengths:

The experiments are rigorously performed, the data justify the conclusions and the limitations of the study are appropriately discussed.

There is a need to identify therapeutic targets to improve lymphatic contraction and this work helps identify lymphatic muscle cells as potential cellular targets for intervention.

Reviewer #2 (Public review):

Summary:

This is a well written manuscript describing studies directed at identifying the cell type responsible for pacemaking in murine collecting lymphatics. Using state-of-the-art approaches, the authors identified a number of different cell types in the wall of these lymphatics and then using targeted expression of Channel Rhodopsin and GCaMP, the authors convincingly demonstrate that only activation of lymphatic muscle cells produces coordinated lymphatic contraction and that only lymphatic muscle cells display pressure-dependent Ca2+ transients as would be expected of a pacemaker in these lymphatics.

Strengths:

The use of targeted expression of channel rhodopsin and GCaMP to test the hypothesis that lymphatic muscle cells serve as the pacemakers in musing lymphatic collecting vessels.

Weaknesses:

The only significant weakness was the lack of quantitative analysis of most of the imaging data shown in Figures 1-11. In particular, the colonization analysis should be extended to show cells not expected to demonstrate colocalization as a negative control for the colocalization analysis that the authors present. These weaknesses have been resolved by revision and addition of new and novel RNAseq data, additional colocalization data and membrane potential measurements.

Reviewer #3 (Public review):

Summary:

Zawieja et al. aimed to identify the pacemaker cells in the lymphatic collecting vessels. Authors have used various Cre-based expression systems and optogentic tools to identify these cells. Their findings suggest these cells are lymphatic muscle cells that drive the pacemaker activity in the lymphatic collecting vessels.

Strengths:

The authors have used multiple approaches to test their hypothesis. Some findings are presented as qualitative images, while some quantitative measurements are provided.

Weaknesses:

- More quantitative measurements.<br /> - Possible mechanisms associated with the pacemaker activity.<br /> - Membrane potential measurements.

Comments on revisions:

The authors have answered my comments with additional experiments, data and manuscript edits.

Reviewer #1 (Public Review):

This study presents valuable observations of white matter organisation from diffusion MRI and two types of synchrotron imaging in both monkeys and mice. Cross-modality comparisons are interesting as the different methods are able to probe anatomical structures at different length scales, from single axons in high-resolution synchrotron (ESRF) imaging, to clusters of axons in lower-resolution synchrotron (DEXY) data, to axon populations at the mm-scale in diffusion MRI. By acquiring all modalities in monkey and mouse ex vivo samples, the authors can observe principles of fibre organisation, and characterise how fibre characteristics, such as tortuosity and micro-dispersion, vary across select brain regions and in healthy tissue versus a demyelination model.

One very interesting result is the observation of apparent laminar organisation of fibres in ex vivo monkey white matter samples. DESY data from the corpus callosum shows fibres with two dominant orientations (one L-R, one slightly inclined), clustered in laminar structures within this major fibre bundle. Thanks to the authors providing open data, I was able to look through the raw DESY volume and observe regions with different "textures" (different orientations) in the described laminar arrangement. That this organisation can be observed by eye, as well as by structure tensor, is fairly convincing.

Reviewer #2 (Public Review):

Summary:

In this work, the authors combine diffusion MRI and high-resolution x-ray synchrotron phase-contrast imaging in monkey and mouse brains to investigate the 3D organization of brain white matter across different scales and species. The work is at the forefront of the anatomical investigation of the human connectome and aligns with several current efforts to bridge the resolution gap between what we can see in vivo at the millimeter scale and the complexity of the human brain at the sub-micron scale. The authors compare the 3D white matter organization across modalities within 2 small regions in one monkey brain (body of the corpus callosum, centrum semiovale) and within one region (splenium of the corpus callosum) in healthy mice and in one murine model of focal demyelination. The study compares measures of tissue anisotropy and fiber orientations across modalities, performs a qualitative comparison of fasciculi trajectories across brain regions and tissue conditions using streamlined tractography based on the structure tensor, and attempts to quantify the shape of fasciculi trajectories by measuring the tortuosity index and the maximum deviation for each reconstructed streamline. Results show measures of anisotropy and fiber orientations largely agree across modalities, especially for larger FOV data. The high-resolution data allows us to explore the fiber trajectories in relation to tissue complexity and pathology. The authors claim the study reveals new common organization principles of white matter fibers across species and scales, for which axonal fasciculi arrange into sheet-like laminar structures.

Strengths:

The aim of the study is of central importance within present efforts to bridge the gap between macroscopic structures observable in vivo in humans using conventional diffusion MRI and the microscopic organization of white matter tissue. Results obtained from this type of study are important to interpret data obtained in vivo, inform the development of novel methodologies, and expand our knowledge of the structural and thus functional organization of brain circuits.

Multi-scale data acquired across modalities within the same sample constitute extremely valuable data that is often hard to acquire and represent a precious resource for validation of both diffusion MRI tractography and microstructure methods.

The inclusion of multi-species data adds value to the study, allowing the exploration of common organization principles across species.

The addition of data from a murine cuprizone model of focal demyelination adds interesting opportunities to study the underlying biological changes that follow demyelination and how these impact tissue anisotropy and fiber trajectories. These data can inform the interpretation and development of diffusion MRI microstructure models.

[Editors' note: The Reviewing Editor considers that the authors addressed the reviewers' questions adequately. The original reviews are here: https://elifesciences.org/reviewed-preprints/94917/reviews]

Reviewer #1 (Public review):

This study extends the previous interesting work of this group to address the potentially differential control of movement and posture. Their earlier work explored a broad range of data to make the case for a downstream neural integrator hypothesized to convert descending velocity movement commands into postural holding commands. Included in that data were observations from people with hemiparesis due to stroke. The current study uses similar data, but pushes into a different, but closely related direction, suggesting that these data may address the independence of these two fundamental components of motor control. I find the logic laid out in the second sentence of the abstract ("The paretic arm after stroke is notable for abnormalities both at rest and during movement, thus it provides an opportunity to address the relationships between control of reaching, stopping, and stabilizing") less then compelling, but the study does make some interesting observations. Foremost among them, is the relation between the resting force postural bias and the effect of force perturbations during the target hold periods, but not during movement. While this interesting observation is consistent with the central mechanism the authors suggest, it seems hard to me to rule out other mechanisms, including peripheral ones. These limitations should should be discussed.

Reviewer #2 (Public review):

Summary:

Here the authors address the idea that postural and movement control are differentially impacted with stroke. Specifically, they examined whether resting postural forces influenced several metrics of sensorimotor control (e.g., initial reach angle, maximum lateral hand deviation following a perturbation, etc.) during movement or posture. The authors found that resting postural forces influenced control only following the posture perturbation for the paretic arm of stroke patients, but not during movement. They also found that resting postural forces were greater when the arm was unsupported, which correlated with abnormal synergies (as assessed by the Fugl-Meyer). The authors suggest that these findings can be explained by the idea that the neural circuitry associated with posture is relatively more impacted by stroke than the neural circuitry associated with movement. They also propose a conceptual model that differentially weights the reticulospinal tract (RST) and corticospinal tract (CST) to explain greater relative impairments with posture control relative to movement control, due to abnormal synergies, in those with stroke.

Comments on revisions:

The authors should be commended for being very responsive to comments and providing several further requested analyses, which have improved the paper. However, there is still some outstanding issues that make it difficult to fully support the provided interpretation.

The authors say within the response, "We would also like to stress that these perturbations were not designed so that responses are directly compared to each other ***(though of course there is an *indirect* comparison in the sense that we show influence of biases in one type of perturbation but not the other)***." They then state in the first paragraph of the discussion that "Remarkably, these resting postural force biases did not seem to have a detectable effect upon any component of active reaching but only emerged during the control of holding still after the movement ended. The results suggest a dissociation between the control of movement and posture." The main issue here is relying on indirect comparisons (i.e., significant in one situation but not the other), instead of relying on direct comparisons. Using well-known example, just because one group / condition might display a significant linear relationship (i.e., slope_1 > 0) and another group / condition does not (slope_2 = 0), does not necessarily mean that the two groups / conditions are statistically different from one another [see Figure 1 in Makin, T. R., & Orban de Xivry, J. J. (2019). Ten common statistical mistakes to watch out for when writing or reviewing a manuscript. eLife, 8, e48175.].

The authors have provided reasonable rationale of why they chose certain perturbation waveforms for different. Yet it still holds that these different waveforms would likely yield very different muscular responses making it difficult to interpret the results and this remains a limitation. From the paper it is unknown how these different perturbations would differentially influence a variety of classic neuromuscular responses, including short-range stiffness and stretch reflexes, which would be at play here.

Much of the results can be interpreted when one considers classic neuromuscular physiology. In Experiment 1, differences in resting postural bias in supported versus unsupported conditions can readily be explained since there is greater muscle activity in the unsupported condition that leads to greater muscle stiffness to resist mechanical perturbations (Rack, P. M., & Westbury, D. R. (1974). The short-range stiffness of active mammalian muscle and its effect on mechanical properties. The Journal of physiology, 240(2), 331-350.). Likewise muscle stiffness would scale with changes in muscle contraction with synergies. Importantly for experiment 2, muscle stiffness is reduced during movement (Rack and Westbury, 1974) which may explain why resting postural biases do not seem to be impacting movement. Likewise, muscle spindle activity is shown to scale with extrafusal muscle fiber activity and forces acting through the tendon (Blum, K. P., Campbell, K. S., Horslen, B. C., Nardelli, P., Housley, S. N., Cope, T. C., & Ting, L. H. (2020). Diverse and complex muscle spindle afferent firing properties emerge from multiscale muscle mechanics. eLife, 9, e55177.). The concern here is that the authors have not sufficiently considered muscle neurophysiology, how that might relate to their findings, and how that might impact their interpretation. Given the differences in perturbations and muscle states at different phases, the concern is that it is not possible to disentangle whether the results are due to classic neurophysiology, the hypothesis they propose, or both. Can the authors please comment.

The authors should provide a limitations paragraph. They should address 1) how they used different perturbation force profiles, 2) the muscles were in different states which would change neuromuscular responses between trial phase / condition, 3) discuss a lack of direct statistical comparisons that support their hypothesis, and 4) provide a couple of paragraphs on classic neurophysiology, such as muscle stiffness and stretch reflexes, and how these various factors could influence the findings (i.e., whether they can disentangle whether the reported results are due to classic neurophysiology, the hypothesis they propose, or both).

Reviewer #1 (Public review):

Summary:

Govindan and Conrad use a genome-wide CRISPR screen to identify genes regulating retention of intron 4 in OGT, leveraging an intron retention reporter system previously described (PMID: 35895270). Their OGT intron 4 reporter reliably responds to O-GlcNAc levels, mirroring the endogenous splicing event. Through a genome-wide CRISPR knockout library, they uncover a range of splicing-related genes, including multiple core spliceosome components, acting as negative regulators of OGT intron 4 retention. They choose to follow up on SFSWAP, a largely understudied splicing regulator shown to undergo rapid phosphorylation in response to O-GlcNAc level changes (PMID: 32329777). RNA-sequencing reveals that SFSWAP depletion not only promotes OGT intron 4 splicing but also broadly induces exon inclusion and intron splicing, affecting decoy exon usage. While this study offers interesting insights into intron retention and O-GlcNAc signaling regulation, the RNA sequencing experiments lack the essential controls needed to provide full confidence to the authors' conclusions.

Strengths:

(1) This study presents an elegant genetic screening approach to identify regulators of intron retention, uncovering core spliceosome genes as unexpected positive regulators of intron retention.

(2) The work proposes a novel functional role for SFSWAP in splicing regulation, suggesting that it acts as a negative regulator of splicing and cassette exon inclusion, which contrasts with expected SR-related protein functions.

(3) The authors suggest an intriguing model where SFSWAP, along with other spliceosome proteins, promotes intron retention by associating with decoy exons.

Weaknesses:

(1) The conclusions on SFSWAP impact on alternative splicing are based on cells treated with two pooled siRNAs for five days. This extended incubation time without independent siRNA treatments raises concerns about off-target effects and indirect effects from secondary gene expression changes, potentially limiting confidence in direct SFSWAP-dependent splicing regulation. Rescue experiments and shorter siRNA-treatment incubation times could address these issues.

(2) The mechanistic role of SFSWAP in splicing would benefit from further exploration. Key questions remain, such as whether SFSWAP directly binds RNA, specifically the introns and exons (including the decoy exons) it appears to regulate. Furthermore, given that SFSWAP phosphorylation is influenced by changes in O-GlcNAc signaling, it would be interesting to investigate this relationship further. While generating specific phosphomutants may not yield definitive insights due to redundancy and also beyond the scope of the study, the authors could examine whether distinct SFSWAP domains, such as the SR and SURP domains, which likely overlap with phosphorylation sites, are necessary for regulating OGT intron 4 splicing.

(3) Data presentation could be improved (specific suggestions are included in the recommendations section). Furthermore, Excel tables with gene expression and splicing analysis results should be provided as supplementary datasheets. Finally, a more detailed explanation of statistical analyses is necessary in certain sections.

Reviewer #2 (Public review):

Summary:

The paper describes an effort to identify the factors responsible for intron retention and alternate exon splicing in a complex system known to be regulated by the O-GlcNAc cycling system. The CRISPR/Cas9 system was used to identify potential factors. The bioinformatic analysis is sophisticated and compelling. The conclusions are of general interest and advance the field significantly.

Strengths:

(1) Exhaustive analysis of potential splicing factors in an unbiased screen.

(2) Extensive genome wide bioinformatic analysis.

(3) Thoughtful discussion and literature survey.

Weaknesses:

(1) No firm evidence linking SFSWA to an O-GlcNAc specific mechanism.

(2) Resulting model leaves many unanswered questions.

Reviewer #3 (Public review):

Summary:

The major novel finding in this study is that SFSWAP, a splicing factor containing an RS domain but no canonical RNA binding domain, functions as a negative regulator of splicing. More specifically, it promotes retention of specific introns in a wide variety of transcripts including transcripts from the OGT gene previously studied by the Conrad lab. The balance between OGT intron retention and OGT complete splicing is an important regulator of O-GlcNAc expression levels in cells.

Strengths:

An elegant CRISPR knockout screen employed a GFP reporter, in which GFP is efficiently expressed only when the OGT retained intron is removed (so that the transcript will be exported from the nucleus to allow for translation of GFP). Factors whose CRISPR knockdown causes decreased intron retention therefore increase GFP, and can be identified by sequencing RNA of GFP-sorted cells. SFSWAP was thus convincingly identified as a negative regulator of OGT retained intron splicing. More focused studies of OGT intron retention indicate that it may function by regulating a decoy exon previously identified in the intron, and that this may extend to other transcripts with decoy exons.

Weaknesses:

The mechanism by which SFSWAP represses retained introns is unclear, although some data suggests it can operate (in OGT) at the level of a recently reported decoy exon within that intron. Interesting/appropriate speculation about possible mechanisms are provided and will likely be the subject of future studies.

Overall the study is well done and carefully described but some figures and some experiments should be described in more detail.

Reviewer #1 (Public review):

Summary:

This study explores how heterozygosity for specific neurodevelopmental disorder-associated Trio variants affects mouse behavior, brain structure, and synaptic function, revealing distinct impacts on motor, social, and cognitive behaviors linked to clinical phenotypes. Findings demonstrate that Trio variants yield unique changes in synaptic plasticity and glutamate release, highlighting Trio's critical role in presynaptic function and the importance of examining variant heterozygosity in vivo.

Strengths:

This study generated multiple mouse lines to model each Trio variant, reflecting point mutations observed in human patients with developmental disorders. The authors employed various approaches to evaluate the resulting behavioral, neuronal morphology, synaptic function, and proteomic phenotypes.

Weaknesses:

While the authors present extensive results, the flow of experiments is challenging to follow, raising concerns about the strength of the experimental conclusions. Additionally, the connection between sex, age, behavioral data, brain regions, synaptic transmission, and plasticity lacks clarity, making it difficult to understand the rationale behind each experiment. Clearer explanations of the purpose and connections between experiments are recommended. Furthermore, the methodology requires more detail, particularly regarding mouse breeding strategies, timelines for behavioral tests, electrophysiology conditions, and data analysis procedures.

Reviewer #2 (Public review):

Summary:

The authors generated three mouse lines harboring ASD, Schizophrenia, and Bipolar-associated variants in the TRIO gene. Anatomical, behavioral, physiological, and biochemical assays were deployed to compare and contrast the impact of these mutations in these animals. In this undertaking, the authors sought to identify and characterize the cellular and molecular mechanisms responsible for ASD, Schizophrenia, and Bipolar disorder development.

Strengths:

The establishment of TRIO dysfunction in the development of ASD, Schizophrenia, and Bipolar disorder is very recent and of great interest. Disorder-specific variants have been identified in the TRIO gene, and this study is the first to compare and contrast the impact of these variants in vivo in preclinical models. The impact of these mutations was carefully examined using an impressive host of methods. The authors achieved their goal of identifying behavioral, physiological, and molecular alterations that are disorder/variant specific. The impact of this work is extremely high given the growing appreciation of TRIO dysfunction in a large number of brain-related disorders. This work is very interesting in that it begins to identify the unique and subtle ways brain function is altered in ASD, Schizophrenia, and Bipolar disorder.

Weaknesses:

(1) Most assays were performed in older animals and perhaps only capture alterations that result from homeostatic changes resulting from prodromal pathology that may look very different.

(2) Identification of upregulated (potentially compensating) genes in response to these disorder-specific Trio variants is extremely interesting. However, a functional demonstration of compensation is not provided.

(3) There are instances where data is not shown in the manuscript. See "data not shown". All data collected should be provided even if significant differences are not observed.

I consider weaknesses 1 and 2 minor. While they would very interesting to explore, these experiments might be more appropriate for a follow-up study. I would recommend that the missing data in 3 should be provided in the supplemental material.

Reviewer #1 (Public review):

Summary:<br /> This study addresses the roles of polyunsaturated fatty acids (PUFAs) in animal physiology and membrane function. A C. elegans strain carrying the fat-2(wa17) mutation possess a very limited ability to synthesize PUFAs and there is no dietary input because the E. coli diet consumed by lab grown C. elegans does not contain any PUFAs. The fat-2 mutant strain was characterized to confirm that the worms grow slowly, have rigid membranes, and have a constitutive mitochondrial stress response. The authors showed that chemical treatments or mutations known to increase membrane fluidity did not rescue growth defects. A thorough genetic screen was performed to identify genetic changes to compensate for the lack of PUFAs. The newly isolated suppressor mutations that compensated for FAT-2 growth defects included intergenic suppressors in the fat-2 gene, as well as constitutive mutations in the hypoxia sensing pathway components EGL-9 and HIF-1, and loss of function mutations in ftn-2, a gene encoding the iron storage protein ferritin. Taken together, these mutations lead to the model that increased intracellular iron, an essential cofactor for fatty acid desaturases, allows the minimally functional FAT-2(wa17) enzyme to be more active, resulting in increased desaturation and increased PUFA synthesis.

Strengths:<br /> (1) This study provides new information further characterizing fat-2 mutants. The authors measured increased rigidity of membranes compared to wild type worms, however this rigidity is not able to be rescued with other fluidity treatments such as detergent or mutants. Rescue was only achieved with polyunsaturated fatty acid supplementation.<br /> (2) A very thorough genetic suppressor screen was performed. In addition to some internal fat-2 compensatory mutations, the only changes in pathways identified that are capable of compensating for deficient PUFA synthesis was the hypoxia pathway and the iron storage protein ferritin. Suppressor mutations included an egl-9 mutation that constitutively activates HIF-1, and Gain of function mutations in hif-1 that are dominant. This increased activity of HIF conferred by specific egl-9 and hif-1 mutations lead to decreased expression of ftn-2. Indeed, loss of ftn-2 leads to higher intracellular iron. The increased iron apparently makes the FAT-2 fatty acid desaturase enzyme more active, allowing for the production of more PUFAs.<br /> (3) The mutations isolated in the suppressor screen show that the only mutations able to compensate for lack of PUFAs were ones that increased PUFA synthesis by the defective FAT-2 desaturase, thus demonstrating the essential need for PUFAs that cannot be overcome by changes in other pathways. This is a very novel study, taking advantage of genetic analysis of C. elegans, and it confirms the observations in humans that certain essential PUFAs are required for growth and development.<br /> (4) Overall, the paper is well written, and the experiments were carried out carefully and thoroughly. The conclusions are well supported by the results.

Weaknesses:<br /> Overall, there are not many weaknesses. The main one I noticed is that the lipidomic analysis shown in Figs 3C, 7C, S1 and S3. Whie these data are an essential part of the analysis and provide strong evidence for the conclusions of the study, it is unfortunate that the methods used did not enable the distinction between two 18:1 isomers. These two isomers of 18:1 are important in C. elegans biology, because one is a substrate for FAT-2 (18:1n-9, oleic acid) and the other is not (18:1n-7, cis vaccenic acid). Although rarer in mammals, cis-vaccenic acid is the most abundant fatty acid in C. elegans and is likely the most important structural MUFA. The measurement of these two isomers is not essential for the conclusions of the study, but the manuscript should include a comment about the abundance of oleic vs vaccenic acid in C. elegans (authors can find this information, even in the fat-2 mutant, in other publications of C. elegans fatty acid composition). Otherwise, readers who are not familiar with C. elegans might assume the 18:1 that is reported is likely to be mainly oleic acid, as is common in mammals.

Other suggestions to authors to improve the paper:<br /> (1) The title could be less specific; it might be confusing to readers to include the allele name in the title.<br /> (2) There are two errors in the pathway depicted in Figure 1A. The16:0-16:1 desaturation can be performed by FAT-5, FAT-6, and FAT-7. The 18:0-18:1 desaturation can only be performed by FAT-6 and FAT-7

Reviewer #2 (Public review):

Summary:<br /> The authors use a genetic screen in C. elegans to investigate the physiological roles of polyunsaturated fatty acids (PUFAs). They screen for mutations that rescue fat-2 mutants, which have strong reductions in PUFAs. As a result, either mutations in fat-2 itself, or mutations in genes involved in the HIF-1 pathway, were found to rescue fat-2 mutants.

Strengths:<br /> As C. elegans can produce PUFAs de novo as essential lipids, the genetic model is well suited to study the fundamental roles of PUFAs, and the results are very interesting. The genetic screen finds mutations in convergent pathways, suggesting that it has reached near-saturation. The link between the HIF-1 pathway and lipid unsaturation is very interesting. As many of the mutations found to rescue fat-2 mutants are of gain-of-function, it is unlikely that similar discoveries could have been made with other approaches like genome-wide CRISPR screenings, making the current study distinctive.

Weaknesses:<br /> The authors make very important statements, but some are not sufficiently supported by data. In page 5, they conclude that membrane rigidity is a minor cause of fat-2 mutant defects, which is a relevant observation regarding why PUFAs are important. However, they use treatments that have rescued fluidity in another mutant (paqr-2), but do not test if they have the same fluidifying effects in fat-2 mutants.

The screening results seem to converge into the HIF-1 pathway, which is hypothetically correct according to the literature. However, the authors do not validate this hypothesis, which is a critical limitation, especially because many of the mutations they obtained seem to be of gain-of-function. Therefore, without experimental testing, it cannot be concluded that the mutations have the expected effect on the HIF-1 pathway.

In some of the mutants, the rescues in lipid compositions seem to be weak, and it is arguable whether phenotypic rescues are really via a restoration in lipid compositions.

The hypothesis linking iron homeostasis and the rescue of fat-2 mutants is interesting, but the data of rescue by iron repletion seem to be against it. The results might be due to the inefficiency in iron repletion, as the authors suggest, but this has not been formally addressed.

Therefore, the authors propose multiple very interesting and important hypotheses, but experimental validations remain limited.

Reviewer #1 (Public review):

Summary:

In this article, Nedbalova et al. investigate the biochemical pathway that acts in circulating immune cells to generate adenosine, a systemic signal that directs nutrients toward the immune response, and S-adenosylmethionine (SAM), a methyl donor for lipid, DNA, RNA, and protein synthetic reactions. They find that SAM is largely generated through the uptake of extracellular methionine, but that recycling of adenosine to form ATP contributes a small but important quantity of SAM in immune cells during the immune response. The authors propose that adenosine serves as a sensor of cell activity and nutrient supply, with adenosine secretion dominating in response to increased cellular activity. Their findings of impaired immune action but rescued larval developmental delay when the enzyme Ahcy is knocked down in hemocytes are interpreted as due to effects on methylation processes in hemocytes and reduced production of adenosine to regulate systemic metabolism and development, respectively. Overall this is a strong paper that uses sophisticated metabolic techniques to map the biochemical regulation of an important systemic mediator, highlighting the importance of maintaining appropriate metabolite levels in driving immune cell biology.

Strengths:

The authors deploy metabolic tracing - no easy feat in Drosophila hemocytes - to assess flux into pools of the SAM cycle. This is complemented by mass spectrometry analysis of total levels of SAM cycle metabolites to provide a clear picture of this metabolic pathway in resting and activated immune cells.

The experiments show that the recycling of adenosine to ATP, and ultimately SAM, contributes meaningfully to the ability of immune cells to control infection with wasp eggs.

This is a well-written paper, with very nice figures showing metabolic pathways under investigation. In particular, the italicized annotations, for example, "must be kept low", in Figure 1 illustrate a key point in metabolism - that cells must control levels of various intermediates to keep metabolic pathways moving in a beneficial direction.

Experiments are conducted and controlled well, reagents are tested, and findings are robust and support most of the authors' claims.

Weaknesses:

The authors posit that adenosine acts as a sensor of cellular activity, with increased release indicating active cellular metabolism and insufficient nutrient supply. It is unclear how generalizable they think this may be across different cell types or organs.

The authors extrapolate the findings in Figure 3 of decreased extracellular adenosine in ex vivo cultures of hemocytes with knockdown of Ahcy (panel B) to the in vivo findings of a rescue of larval developmental delay in wasp egg-infected larvae with hemocyte-specific Ahcy RNAi (panel C). This conclusion (discussed in lines 545-547) should be somewhat tempered, as a number of additional metabolic abnormalities characterize Ahcy-knockdown hemocytes, and the in vivo situation may not mimic the ex vivo situation. If adenosine (or inosine) measurements were possible in hemolymph, this would help bolster this idea. However, adenosine at least has a very short half-life.

Reviewer #2 (Public review):

Summary:

In this work, the authors wish to explore the metabolic support mechanisms enabling lamellocyte encapsulation, a critical antiparasitic immune response of insects. They show that S-adenosylmethionine metabolism is specifically important in this process through a combination of measurements of metabolite levels and genetic manipulations of this metabolic process.

Strengths:

The metabolite measurements and the functional analyses are generally very strong and clearly show that the metabolic process under study is important in lamellocyte immune function.

Weaknesses:

The gene expression data are a potential weakness. Not enough is explained about how the RNAseq experiments in Figures 2 and 4 were done, and the representation of the data is unclear. The paper would also be strengthened by the inclusion of some measure of encapsulation effectiveness: the authors show that manipulation of the S-adenosylmethionine pathway in lamellocytes affects the ability of the host to survive infection, but they do not show direct effects on the ability of the host to encapsulate wasp eggs.

Reviewer #3 (Public review):

Summary:

The authors of this study provide evidence that Drosophila immune cells show upregulated SAM transmethylation pathway and adenosine recycling upon wasp infection. Blocking this pathway compromises the lamellocyte formation, developmental delay, and host survival, suggesting its physiological relevance.

Strengths:

Snapshot quantification of the metabolite pool does not provide evidence that the metabolic pathway is active or not. The authors use an ex vivo isotope labelling to precisely monitor the SAM and adenosine metabolism. During infection, the methionine metabolism and adenosine recycling are upregulated, which is necessary to support the immune reaction. By combining the genetic experiment, they successfully show that the pathway is activated in immune cells.

Weaknesses:

The authors knocked down Ahcy to prove the importance of SAM methylation pathway. However, Ahcy-RNAi produces a massive accumulation of SAH, in addition to blocking adenosine production. To further validate the phenotypic causality, it is necessary to manipulate other enzymes in the pathway, such as Sam-S, Cbs, SamDC, etc. The authors do not demonstrate how infection stimulates the metabolic pathway given the gene expression of metabolic enzymes is not upregulated by infection stimulus.

Reviewer #1 (Public review):

Summary:

In this study, the authors aim to understand the neural basis of implicit causal inference, specifically how people infer causes of illness. They use fMRI to explore whether these inferences rely on content-specific semantic networks or broader, domain-general neurocognitive mechanisms. The study explores two key hypotheses: first, that causal inferences about illness rely on semantic networks specific to living things, such as the 'animacy network,' given that illnesses affect only animate beings; and second, that there might be a common brain network supporting causal inferences across various domains, including illness, mental states, and mechanical failures. By examining these hypotheses, the authors aim to determine whether causal inferences are supported by specialized or generalized neural systems.

The authors observed that inferring illness causes selectively engaged a portion of the precuneus (PC) associated with the semantic representation of animate entities, such as people and animals. They found no cortical areas that responded to causal inferences across different domains, including illness and mechanical failures. Based on these findings, the authors concluded that implicit causal inferences are supported by content-specific semantic networks, rather than a domain-general neural system, indicating that the neural basis of causal inference is closely tied to the semantic representation of the specific content involved.

Strengths:

(1) The inclusion of the four conditions in the design is well thought out, allowing for the examination of the unique contribution of causal inference of illness compared to either a different type of causal inference (mechanical) or non-causal conditions. This design also has the potential to identify regions involved in a shared representation of inference across general domains.

(2) The presence of the three localizers for language, logic, and mentalizing, along with the selection of specific regions of interest (ROIs), such as the precuneus and anterior ventral occipitotemporal cortex (antVOTC), is a strong feature that supports a hypothesis-driven approach (although see below for a critical point related to the ROI selection).

(3) The univariate analysis pipeline is solid and well-developed.

(4) The statistical analyses are a particularly strong aspect of the paper.

Weaknesses:

Based on the current analyses, it is not yet possible to rule out the hypothesis that inferring illness causes relies on neurocognitive mechanisms that support causal inferences irrespective of their content, neither in the precuneus nor in other parts of the brain.

(1) The authors, particularly in the multivariate analyses, do not thoroughly examine the similarity between the two conditions (illness-causal and mechanical-causal), as they are more focused on highlighting the differences between them. For instance, in the searchlight MVPA analysis, an interesting decoding analysis is conducted to identify brain regions that represent illness-causal and mechanical-causal conditions differently, yielding results consistent with the univariate analyses. However, to test for the presence of a shared network, the authors only perform the Causal vs. Non-causal analysis. This analysis is not very informative because it includes all conditions mixed together and does not clarify whether both the illness-causal and mechanical-causal conditions contribute to these results.

(2) To address this limitation, a useful additional step would be to use as ROIs the different regions that emerged in the Causal vs. Non-causal decoding analysis and to conduct four separate decoding analyses within these specific clusters:<br /> (a) Illness-Causal vs. Non-causal - Illness First;<br /> (b) Illness-Causal vs. Non-causal - Mechanical First;<br /> (c) Mechanical-Causal vs. Non-causal - Illness First;<br /> (d) Mechanical-Causal vs. Non-causal - Mechanical First.<br /> This approach would allow the authors to determine whether any of these ROIs can decode both the illness-causal and mechanical-causal conditions against at least one non-causal condition.

(3) Another possible analysis to investigate the existence of a shared network would be to run the searchlight analysis for the mechanical-causal condition versus the two non-causal conditions, as was done for the illness-causal versus non-causal conditions, and then examine the conjunction between the two. Specifically, the goal would be to identify ROIs that show significant decoding accuracy in both analyses.

(4) Along the same lines, for the ROI MVPA analysis, it would be useful not only to include the illness-causal vs. mechanical-causal decoding but also to examine the illness-causal vs. non-causal conditions and the mechanical-causal vs. non-causal conditions. Additionally, it would be beneficial to report these data not just in a table (where only the mean accuracy is shown) but also using dot plots, allowing the readers to see not only the mean values but also the accuracy for each individual subject.

(5) The selection of Regions of Interest (ROIs) is not entirely straightforward:<br /> In the introduction, the authors mention that recent literature identifies the precuneus (PC) as a region that responds preferentially to images and words related to living things across various tasks. While this may be accurate, we can all agree that other regions within the ventral occipital-temporal cortex also exhibit such preferences, particularly areas like the fusiform face area, the occipital face area, and the extrastriate body area. I believe that at least some parts of this network (e.g., the fusiform gyrus) should be included as ROIs in this study. This inclusion would make sense, especially because a complementary portion of the ventral stream known to prefer non-living items (i.e., anterior medial VOTC) has been selected as a control ROI to process information about the mechanical-causal condition. Given the main hypothesis of the study - that causal inferences about illness might depend on content-specific semantic representations in the 'animacy network' - it would be worthwhile to investigate these ROIs alongside the precuneus, as they may also yield interesting results.

(6) Visual representation of results:<br /> In all the figures related to ROI analyses, only mean group values are reported (e.g., Figure 1A, Figure 3, Figure 4A, Supplementary Figure 6, Figure 7, Figure 8). To better capture the complexity of fMRI data and provide readers with a more comprehensive view of the results, it would be beneficial to include a dot plot for a specific time point in each graph. This could be a fixed time point (e.g., a certain number of seconds after stimulus presentation) or the time point showing the maximum difference between the conditions of interest. Adding this would allow for a clearer understanding of how the effect is distributed across the full sample, such as whether it is consistently present in every subject or if there is greater variability across individuals.

(7) Task selection:<br /> (a) To improve the clarity of the paper, it would be helpful to explain the rationale behind the choice of the selected task, specifically addressing: (i) why an implicit inference task was chosen instead of an explicit inference task, and (ii) why the "magic detection" task was used, as it might shift participants' attention more towards coherence, surprise, or unexpected elements rather than the inference process itself.<br /> (b) Additionally, the choice to include a large number of catch trials is unusual, especially since they are modeled as regressors of non-interest in the GLM. It would be beneficial to provide an explanation for this decision.

Reviewer #2 (Public review):

Summary:

In this study, the authors hypothesize that "causal inferences about illness depend on content-specific semantic representations in the animacy network". They test this hypothesis in an fMRI task, by comparing brain activity elicited by participants' exposure to written situations suggesting a plausible cause of illness with brain activity in linguistically equivalent situations suggesting a plausible cause of mechanical failure or damage and non-causal situations. These contrasts identify PC as the main "culprit" in a whole-brain univariate analysis. Then the question arises of whether the content-specificity has to do with inferences about animates in general, or if there are some distinctions between reasoning about people's bodies versus mental states. To answer this question, the authors localize the mentalizing network and study the relation between brain activity elicited by Illness-Causal > Mech-Causal and Mentalizing > Physical stories. They conclude that inferring about the causes of illness partially differentiates from reasoning about people's states of mind. The authors finally test the alternative yet non-mutually exclusive hypothesis that both types of causal inferences (illness and mechanical) depend on shared neural machinery. Good candidates are language and logic, which justifies the use of a language/logic localizer. No evidence of commonalities across causal inferences versus non-causal situations is found.

Strengths:

(1) This study introduces a useful paradigm and well-designed set of stimuli to test for implicit causal inferences.

(2) Another important methodological advance is the addition of physical stories to the original mentalizing protocol.

(3) With these tools, or a variant of these tools, this study has the potential to pave the way for further investigation of naïve biology and causal inference.

Weaknesses:

(1) This study is missing a big-picture question. It is not clear whether the authors investigate the neural correlates of causal reasoning or of naïve biology. If the former, the choice of an orthogonal task, making causal reasoning implicit, is questionable. If the latter, the choice of mechanical and physical controls can be seen as reductive and problematic.

(2) The rationale for focusing mostly on the precuneus is not clear and this choice could almost be seen as a post-hoc hypothesis.

(3) The choice of an orthogonal 'magic detection' task has three problematic consequences in this study:<br /> (a) It differs in nature from the 'mentalizing' task that consists of evaluating a character's beliefs explicitly from the corresponding story, which complicates the study of the relation between both tasks. While the authors do not compare both tasks directly, it is unclear to what extent this intrinsic difference between implicit versus explicit judgments of people's body versus mental states could influence the results.<br /> (b) The extent to which the failure to find shared neural machinery between both types of inferences (illness and mechanical) can be attributed to the implicit character of the task is not clear.<br /> (c) The introduction of a category of non-interest that contains only 36 trials compared to 38 trials for all four categories of interest creates a design imbalance.

(4) Another imbalance is present in the design of this study: the number of trials per category is not the same in each run of the main task. This imbalance does not seem to be accounted for in the 1st-level GLM and renders a bit problematic the subsequent use of MVPA.

(5) The main claim of the authors, encapsulated by the title of the present manuscript, is not tested directly. While the authors included in their protocol independent localizers for mentalizing, language, and logic, they did not include an independent localizer for "animacy". As such, they cannot provide a within-subject evaluation of their claim, which is entirely based on the presence of a partial overlap in PC (which is also involved in a wide range of tasks) with previous results on animacy.

Reviewer #3 (Public review):

Summary:

This study employed an implicit task, showing vignettes to participants while a bold signal was acquired. The aim was to capture automatic causal inferences that emerge during language processing and comprehension. In particular, the authors compared causal inferences about illness with two control conditions, causal inferences about mechanical failures and non-causal phrases related to illnesses. All phrases that were employed described contexts with people, to avoid animacy/inanimate confound in the results. The authors had a specific hypothesis concerning the role of the precuneus (PC) in being sensitive to causal inferences about illnesses.

These findings indicate that implicit causal inferences are facilitated by semantic networks specialized for encoding causal knowledge.

Strengths:

The major strength of the study is the clever design of the stimuli (which are nicely matched for a number of features) which can tease apart the role of the type of causal inference (illness-causal or mechanical-causal) and the use of two localizers (logic/language and mentalizing) to investigate the hypothesis that the language and/or logical reasoning networks preferentially respond to causal inference regardless of the content domain being tested (illnesses or mechanical).

Weaknesses:

I have identified the following main weaknesses:

(1) Precuneus (PC) and Temporo-Parietal junction (TPJ) show very similar patterns of results, and the manuscript is mostly focused on PC (also the abstract). To what extent does the fact that PC and TPJ show similar trends affect the inferences we can derive from the results of the paper? I wonder whether additional analyses (connectivity?) would help provide information about this network.

(2) Results are mainly supported by an univariate ROI approach, and the MVPA ROI approach is performed on a subregion of one of the ROI regions (left precuneus). Results could then have a limited impact on our understanding of brain functioning.

(3) In all figures: there are no measures of dispersion of the data across participants. The reader can only see aggregated (mean) data. E.g., percentage signal changes (PSC) do not report measures of dispersion of the data, nor do we have bold maps showing the overlap of the response across participants. Only in Figure 2, we see the data of 6 selected participants out of 20.

(4) Sometimes acronyms are defined in the text after they appear for the first time.

Reviewer #1 (Public review):

Summary:

Horizontal gene transfer is the transmission of genetic material between organisms through ways other than reproduction. Frequent in prokaryotes, this mode of genetic exchange is scarcer in eukaryotes, especially in multicellular eukaryotes. Furthermore, the mechanisms involved in eukaryotic HGT are unknown. This article by Banerjee et al. claims that HGT occurs massively between cells of multicellular organisms. According to this study, the cell free chromatin particles (cfChPs) that are massively released by dying cells are incorporated in the nucleus of neighboring cells. These cfChPs are frequently rearranged and amplified to form concatemers, they are made of open chromatin, expressed, and capable of producing proteins. Furthermore, the study also suggests that cfChPs transmit transposable elements (TEs) between cells on a regular basis, and that these TEs can transpose, multiply, and invade receiving cells. These conclusions are based on a series of experiments consisting in releasing cfChPs isolated from various human sera into the culture medium of mouse cells, and using FISH and immunofluorescence to monitor the state and fate of cfChPs after several passages of the mouse cell line.

Strengths:

The results presented in this study are interesting because they may reveal unsuspected properties of some cell types that may be able to internalize free-circulating chromatin, leading to its chromosomal incorporation, expression, and unleashing of TEs. The authors propose that this phenomenon may have profound impacts in terms of diseases and genome evolution. They even suggest that this could occur in germ cells, leading to within-organism HGT with long-term consequences.

Weaknesses:

The claims of massive HGT between cells through internalization of cfChPs are not well supported because they are only based on evidence from one type of methodological approach: immunofluorescence and fluorescent in situ hybridization (FISH) using protein antibodies and DNA probes. Yet, such strong claims require validation by at least one, but preferably multiple, additional orthogonal approaches. This includes, for example, whole genome sequencing (to validate concatemerization, integration in receiving cells, transposition in receiving cells), RNA-seq (to validate expression), ChiP-seq (to validate chromatin state).

Another weakness of this study is that it is performed only in one receiving cell type (NIH3T3 mouse cells). Thus, rather than a general phenomenon occurring on a massive scale in every multicellular organism, it could merely reflect aberrant properties of a cell line that for some reason became permeable to exogenous cfChPs. This begs the question of the relevance of this study for living organisms.

Should HGT through internalization of circulating chromatin occur on a massive scale, as claimed in this study, and as illustrated by the many FISH foci observed in Fig 3 for example, one would expect that the level of somatic mosaicism may be so high that it would prevent assembling a contiguous genome for a given organism. Yet, telomere-to-telomere genomes have been produced for many eukaryote species, calling into question the conclusions of this study.

Reviewer #2 (Public review):

I must note that my comments pertain to the evolutionary interpretations rather than the study's technical results. The techniques appear to be appropriately applied and interpreted, but I do not feel sufficiently qualified to assess this aspect of the work in detail.

I was repeatedly puzzled by the use of the term "function." Part of the issue may stem from slightly different interpretations of this word in different fields. In my understanding, "function" should denote not just what a structure does, but what it has been selected for. In this context, where it is unclear if cfChPs have been selected for in any way, the use of this term seems questionable.

Similarly, the term "predatory genome," used in the title and throughout the paper, appears ambiguous and unjustified. At this stage, I am unconvinced that cfChPs provide any evolutionary advantage to the genome. It is entirely possible that these structures have no function whatsoever and could simply be byproducts of other processes. The findings presented in this study do not rule out this neutral hypothesis. Alternatively, some particular components of the genome could be driving the process and may have been selected to do so. This brings us to the hypothesis that cfChPs could serve as vehicles for transposable elements. While speculative, this idea seems to be compatible with the study's findings and merits further exploration.

I also found some elements of the discussion unclear and speculative, particularly the final section on the evolution of mammals. If the intention is simply to highlight the evolutionary impact of horizontal transfer of transposable elements (e.g., as a source of new mutations), this should be explicitly stated. In any case, this part of the discussion requires further clarification and justification.

In summary, this study presents important new findings on the behavior of cfChPs when introduced into a foreign cellular context. However, it overextends its evolutionary interpretations, often in an unclear and speculative manner. The concept of the "predatory genome" should be better defined and justified or removed altogether. Conversely, the suggestion that cfChPs may function at the level of transposable elements (rather than the entire genome or organism) could be given more emphasis.

Reviewer #1 (Public review):

Summary:

Formins are complex proteins with multiple effects on actin filament assembly, including nucleation, capping with processive elongation, and bundling. Determining which of these activities is important for a given biological process and normal cellular function is a major challenge.

Here, the authors study the formin FHOD3L, which is essential for normal sarcomere assembly in muscle cells. They identify point mutants of FHOD3L in which formin nucleation and elongation/bundling activities are functionally separated. Expression of these mutants in neonatal rat ventricular myocytes shows that the control of actin filament elongation by formin is the major activity required for the normal assembly of functional sarcomeres.

Strengths:

The strength of this work is to combine sensitive biochemical assays with excellent work in neonatal rat ventricular myocytes. This combination of approaches is highly effective for analyzing the function of proteins with multiple activities in vitro.

Weaknesses:

FHOD3L does not seem to be the easiest formin to study because of its relatively weak nucleation activity and the short duration of capping events. This difficulty imposes rigorous biochemical analysis and careful interpretation of the data, which should be improved in this work.

Reviewer #2 (Public review):

This article elucidates the biochemical and cellular mechanisms by which the FHOD-family of formins, particularly FHOD3, contributes to sarcomere formation and contractility in cardiomyocytes. Formins are mainly known to nucleate and elongate actin filaments, with certain family members also exhibiting capping, severing, and bundling activities. Although FHOD3 has been well-established as essential for sarcomere assembly in cardiomyocytes, its precise biochemical functions and contributions to actin dynamics remain poorly understood.

In this study, the authors combine in vitro biochemical assays with cellular experiments to dissect FHOD3's roles in actin assembly and sarcomere formation. They demonstrate that FHOD3 nucleates actin filaments and acts as a transient elongator, pausing elongation after an initial burst of filament growth. Using separation-of-function mutants, they show that FHOD3's elongation activity - rather than its nucleation, capping, or bundling capabilities - is key for its sarcomeric function.

The experiments have been conducted rigorously and well-analyzed, and the paper is clearly written. The data presented support the authors' conclusions. I appreciate the detailed description and rationale behind the FHOD3 constructs used in this study.

However, I was somewhat surprised and a bit disappointed that while the authors conducted single-color TIRF experiments to observe the effects of FHOD3 on single filaments, they did not use fluorescently labeled FHOD3 to directly visualize its behavior. Incorporating such experiments would significantly strengthen their conclusions regarding FHOD3's bursts of elongation interspersed with capping activity. While I understand this might require a few additional weeks of experiments, these data would add considerable value by directly testing the proposed mechanism.

There is a typo in the word "required" in line number 30. The authors also use fit data to extract parameters in several panels (e.g., Figures 2b, 2d, 3a, and 3b). While these fit functions may be intuitive to actin experts, explicitly describing the fit functions in the figure legends or methods would greatly benefit the broader readership.

Reviewer #3 (Public review):

Valencia et al. aim to elucidate the biochemical and cellular mechanisms through which the human formin FHOD3 drives sarcomere assembly in cardiomyocytes. To do so, they combined rigorous in vitro biochemical assays with comprehensive in vivo characterizations, evaluating two wild-type FHOD3 isoforms and two function-separating mutants. Surprisingly, they found that both wild-type FHOD3 isoforms can nucleate new actin filaments, as well as elongate existing actin filaments in conjunction with profilin following barbed-end capping. This is in addition to FHOD3's proposed role as an actin bundler. Next, the authors asked whether FHOD3L promotes sarcomere assembly in cardiomyocytes through its activity in actin nucleation or rather elongation. With two function-separating mutants, the authors evaluated the numbers and morphology of sarcomeres, as well as their ability to beat and generate cardiac rhythm. The authors found that while the wild-type FHOD3L and the K1193L mutant can rescue sarcomere morphology and physiology, the GS-FH1 mutant fails to do so. Given that in GS-FH1 mainly elongation activity is compromised, the authors concluded that the elongation activity of FHOD3 is essential for its role in sarcomere assembly in cardiomyocytes, while its nucleator activity is dispensable. Overall, this important study provided a broadened view on the biochemical activities of FHOD3, and a pioneering view on a possible cellular mechanism of how FHOD3L drives sarcomere assembly. If further validated, this can lead to new mechanistic models of sarcomere assembly and potentially new therapeutic targets of cardiomyopathy.

The conclusions of this paper are mostly well supported by the comprehensive biochemical analyses performed by the authors. However, the sarcomere assembly defect phenotype in the GS-FH1 rescue condition requires further investigation, as the extremely low level of GS-FH1 signal in transfected cells in Figure 6A may reflect a failure of actin-binding by this construct in vivo, rather than its inability to drive elongation. Though the authors do show in Figure 6 that GS-FH1 can bind to normal-looking sarcomeres when they are present, this may be due to a lack of siRNA activity in these cells, such that endogenous FHOD3L is still present. In this possible scenario, GS-FH1 may dimerize with endogenous FHOD3L. The authors should demonstrate that GS-FH1 alone can indeed interact with existing actin filaments in vivo. While this has been clearly demonstrated in vitro, given the more complex biochemical environment in vivo where additional unknown binding partners may present, cautions should be made when extrapolating findings from the former to the latter.

Reviewer #1 (Public review):

Summary:

The authors seek to establish whether triadic interaction can promote affiliative relationships in the context of strict dominance hierarchies, and whether the vasopressinergic system is involved in such affiliations. To address this, they experimentally examine how male same-sex affiliations form by testing triadic cohabitation in large-billed crows, a species where males are known to develop and maintain same-sex affiliative relationships within a strict linear social hierarchy. They show a reduction in aggressive behavior over time with cohabitation and the formation of affiliative relationships, as measured by reciprocal allopreening, between two members (dyad) of the triad. The authors then administer a V1aR antagonist to each member of the triad, finding that allopreening decreases and dominance/submissive behaviors reemerge only in the dyad that developed an affiliated relationship ("affiliated dyad") with blockade of V1aR, demonstrating that V1aR mediates maintenance of affiliative peer relationships. The questions of how peer affiliations form, particularly in the context of dominance hierarchies, and the role of V1aR in regulating these behaviors are impactful for the field of social behavior. While the experimental paradigm provides a new way of approaching these questions, we have outlined below our concerns regarding the collection and interpretation of the data that limit the impact of this particular study.

Strengths:

(1) The authors develop a behavioral paradigm and experimental sequence using large-billed crows that allows them to identify the formation of stable, affiliated dyads within triadic groups that are robust to subsequent testing and are sensitive to pharmacological manipulation.

(2) The effects of V1aR antagonism on allopreening and respective dominance or submissive behaviors appear significant and specific to the affiliated dyad, which supports the view that V1aR plays a role in context-dependent, flexible regulation of aggressive behaviors across species. However, these results are difficult to interpret with respect to the authors' main claims given the weaknesses outlined below.

Weaknesses:

(1) The authors claim that the data demonstrates that a triadic social group facilitates the formation of affiliative dyads and go further to claim that these relationships have relevance to understanding coalition formation. It is difficult to say whether the triadic structure actually facilitates or promotes the formation of these affiliative interactions as stated without direct comparisons to alternately sized groupings. Further, the relevance to coalitions is weak without expanded behavioral testing.

(2) Aspects of the experimental design introduce confounding factors that make it difficult to interpret the resulting data. In experiment 1, 6 of the 18 animals that are used for testing are part of multiple triads. This is not accounted for in either the experimental design (wash-out period prior to reuse of animals) or statistical analysis (including repeated testing as a factor in the model) or is not described. Further, while the authors do randomize and counterbalance the two dose trials for the antagonist, vehicle vs drug exposure is not randomized.

(3) The re-emergence of dominance-related agonistic behaviors with V1aR antagonism specifically in the affiliated dyads is interesting, but difficult to interpret without further description and analysis of the dyadic behavior, particularly given the absence of dominance-related behaviors in either affiliated or unaffiliated dyads during the cohabitation period. In addition, the current data does not support the hypothesis that V1aR is also required to form affiliative relationships, as stated in the discussion (Lines 464-5, 472, 494), since the authors did not administer V1aR antagonist during the initial period of triadic cohabitation.

(4) Sentences are often repetitive or duplicated (lines 424-426), and paragraphs should be condensed for easier reading, especially in the discussion. Further, some of the discussion might be better presented in an "Ideas and Speculation" subsection, which would help readers appropriately assess the validity of the conclusions based on the data vs the larger implications suggested by the authors.

Reviewer #2 (Public review):

Seguchi and Izawa provide robust evidence for the role of vasopressin in modulating same-sex affiliative relationships. Especially striking is that these effects appear to be selective to key relationships within a triadic social context. Overall, this is an interesting and rich dataset with compelling results. I largely have some clarifying questions.

Experiment 1 Comments:

(1) The primary argument/finding in this experiment is that a triadic situation/environment facilitates the development of male-male reciprocal social relationships. Overall, this effect appears striking in that male-male affiliative bonds (defined as reciprocal allopreening) formed in 6 of the 8 triads tested. However, there is no comparison group of dyads to determine whether co-housing for 2 weeks could also support the formation of male-male social bonds. This lack of a comparison group makes it unclear to what extent the triad is the key aspect of the environment that supports social bonding.

(2) More specifically, the authors argue that it is not just that triads support affiliative male-male bonds, but that bonds form between the second "middle" (dominant/subordinate) and third "low" (subordinate/subordinate) individuals in each triad. However, it was difficult to assess this from the results.<br /> a) For example, in Figure 3B is each data point the average of two individuals, since in each triad there are two dominant and two subordinate individuals?<br /> b) For me, using more precise language beyond dominant and subordinate (e.g. middle and low), and more clearly displaying the results of allopreening for each pairwise dyad within a triad would improve the impact of the results and support the authors' argument.

(3) Experiment 2 Comments:<br /> The results here are quite striking, despite the low sample size. In Figure 4, it appears that in every instance of administration V1aRA low and high administration decreased allopreening for both dominant and subordinate individuals.

(4) Some methodological questions:<br /> a) Can you clarify whether the duration of the post-test was also 30 min?<br /> b) As in Experiment 1, how are individual birds represented in the triad? Was the second "Middle" bird (dominant/subordinate) tested as both a dominant and subordinate bird? My understanding is that the dominant and subordinate birds in Figure 4 are different individuals but that they are the same individuals represented between the affiliated dyad and unaffiliated dyad.

(5) Throughout the manuscript (Lines 57-67; 557-566) the authors argue that the role of VP in regulating gregariousness can be extrapolated to understand the role of same-sex affiliative bonding. Importantly, gregariousness does not necessarily reflect affiliative bonding. While allopreening is specifically associated with social bonding (e.g. monogamous pair bonds) independent of broader social systems, gregariousness in general, and specifically as defined in many of the references cited, is independent of social bonds - in fact, it is assessed primarily in novel social contexts.

(6) To clarify, adult prairie voles in the wild do not engage in same-sex affiliative behavior commonly. In fact one of the primary components of opposite-sex pair bonding is same-sex aggression. Thus, while mechanistic studies on the neurobiology of same-sex peer bonds are relevant for this work, I am less convinced that you can make comparisons between the ultimate function of same-sex affiliative relationships in prairie voles.

(17) The results here are consistent with VP having an anxiolytic effect, as has been suggested in birds, with the consequences on social behaviors being directly or indirectly related. This may be a useful point to draw on in the discussion when considering your findings.

Reviewer #3 (Public review):

Summary:

In this study, Seguchi & Izawa investigate the formation of male-male affiliative relationships within triads of large-billed crows. They then administered a vasopressin 1a receptor (V1aR) antagonist to either the dominant or subordinate individual within affiliative dyads, to examine whether blocking V1aR disrupts affiliative behavior. They discovered that affiliative dyads can be induced in large-billed crows by housing them in triads. They also found that blocking V1aRs significantly decreased allopreening (an affiliative behavior) within dyads. In addition, it increased aggression by dominant individuals and submissive calls by subordinate individuals.

Strengths:

This manuscript uses an especially interesting species - a highly intelligent and highly social corvid, with complex dominance hierarchies - to extend previous work into the effects of the oxytocin and vasopressin peptides hormones on social behaviors. The results are surprisingly clear, despite a small sample size. The authors use the correct statistical approaches to account for a complex, nested design. The introduction and discussion both reflect a strong understanding of the relevant literature, including the limitations of extrapolating from peripheral (intramuscular) versus central (into the brain) injections of the V1aR antagonist. In addition, the authors appear to have been transparent about the data and results, accounting for some of the challenges and limitations of the data and study.

Weaknesses:

There are two major concerns. First, the study has a very low sample size (8 triads for Experiment 1, and only 5 triads for Experiment 2). Despite the surprisingly convincing findings, the sample size is too small to support the claim that the vasopressin system "universally mediates same sex relationships. Secondly, the study does not account for the effects of V1aR on non-social behaviors. This is especially true because vasopressin/V1aR (and the particular antagonist used in this study) is known to have effects on osmotic balance, food intake, and stress, including in birds. My concern is that the behavioral effects could be accounted before by differences in general stress or activity levels. Allopreening is usually an activity performed in periods of relative inactivity with aggression being more characterized by high activity levels. The authors discuss these different effects of vasopressin/V1aR in the Discussion, but they do not account for these effects in the study design.

Reviewer #1 (Public review):

Summary:

In this manuscript, the authors investigate the role of microtubule dynamics and its effects on neuronal aging. Using C. elegans as a model, the authors investigate the role of evolutionarily conserved Hippo pathway in microtubule dynamics of touch receptor neurons (TRNs) in an age-dependent manner. Using genetic, molecular, behavioral, and pharmacological approaches, the authors show that age-dependent loss of microtubule dynamics might underlie structural and functional aging of TRNs. Further, the authors show that the Hippo pathway specifically functions in these neurons to regulate microtubule dynamics. Specifically, authors show that hyperactivation of YAP-1, a downstream component of the Hippo pathway that is usually inhibited by the kinase activity of the upstream components of the pathway, results in microtubule stabilization and that might underlie the structural and functional decline of TRNs with age. However, how the Hippo pathway regulates microtubule dynamics and neuronal aging was not investigated by the authors.

Strengths:

This is a well-conducted and well-controlled study, and the authors have used multiple approaches to address different questions.

Weaknesses:

There are no major weaknesses identified, except that the effect of the Hippo pathway seems to be specific to only a subset of neurons. I would like the authors to address the specificity of the effect of the Hippo pathway in TRNs, in their resubmission.

Reviewer #2 (Public review):

Summary:

This study examines a novel role of the Hpo signaling pathway, specifically of wts-1/LATS and the downstream regulator of gene expression, yap, in age-related neurodegeneration in C. elegans touch-responsive mechanosensory neurons, ALM and PLM. The study shows that knockdown or deletion of wts-1/LATS causes age-associated morphological abnormalities of these neurons, accompanied by functional loss of touch responsiveness. This is further associated with enhanced, abnormal, microtubule stabilization in these neurons.

Strengths:

This study examines a novel role of the Hpo signaling pathway, specifically of wts-1/LATS and the downstream regulator of gene expression, yap, in age-related neurodegeneration in C. elegans touch-responsive mechanosensory neurons, ALM and PLM. The study shows that knockdown or deletion of wts-1/LATS causes age-associated morphological abnormalities of these neurons, accompanied by functional loss of touch responsiveness. This is further associated with enhanced, abnormal, microtubule stabilization in these neurons. Strong pharmacological and especially genetic manipulations of MT-stabilizing or severing proteins show a strong genetic link between yap and regulation of MTs stability. The study is strong and uses robust approaches, especially strong genetics. The demonstrations on the aging-related roles of the Hpo signaling pathway, and the link to MTs, are novel and compelling. Nevertheless, the study also has mechanistic weaknesses (see below).

Weaknesses:

Specific comments:

(1) The study demonstrates age-specific roles of the Hpo pathway, specifically of wts-1/LATS and yap, specifically in TRN mechanosensory neurons, without observing developmental defects in these neurons, or effects in other neurons. This is a strong demonstration. Nevertheless, the study does not address whether there is a correlation of Hpo signaling pathway activity decline specifically in these neurons, and not other neurons, and at the observed L4 stage and onwards (including the first day of adulthood, 1DA stage). Such demonstrations of spatio-temporal regulation of the Hpo signaling pathway and its activation seem important for linking the Hpo pathway with the observed age-related neurodegeneration. Can this age-related response be correlated to indeed a decline in Hpo signaling during adulthood? Especially at L4 and onwards? It will be informative to measure this by examining the decline in wts1 as well as yap levels and yap nuclear localization.

(2) The Hpo pathway eventually activates gene expression via yap. Although the study uses robust genetic manipulations of yap and wts-1/LATS, it is not clear whether the observed effects are attributed to yap-mediated regulation of gene expression (see 3).

(3) The observations on the abnormal MT stabilization, and the subsequent genetic examinations of MT-stability/severing genes, are a significant strength of the study. Nevertheless, despite the strong genetic links to yap and wts-1/LATS, it is not clear whether MT-regulatory genes are regulated by transcription downstream of the Hpo pathway, thus not enabling a strong causal link between MT regulation and Hpo-mediated gene expression, making this strong part of the study mechanistically circumstantial. Specifically, it will be good to examine whether the genes addressed herein, for example, Spastin, are transcriptionally regulated downstream of the Hpo pathway. This comment is augmented by the finding that in the wts-1/ yap-1 double mutants, MT abnormality, and subsequent neuronal morphology and touch responses are restored, clearly indicating that there is an associated transcriptional regulation

Other comments:

(1) The TRN-specific knockdown of wts-1 and yap-1 is a clear strength. Nevertheless, these do not necessarily show cell-autonomous effects, as the yap transcription factor may regulate the expression of external cues, secreted or otherwise, thus generating non-cell autonomous effects. For example, it is known that yap regulates TGF-beat expression and signaling.

(2) Continuing from comment (3) above, it seems that many of the MT-regulators chosen here for genetic examinations were chosen based on demonstrated roles in neurodegeneration in other studies. It would be good to show whether these MT-associated genes are directly regulated by transcription by the Hpo pathway.

(3) The impairment of the touch response may not be robust: it is only a 30-40% reduction at L4, and even less reduction at 1DA. It would be good to offer possible explanations for this finding.

Reviewer #1 (Public Review):

Summary

The authors asked if parabrachial CGRP neurons were only necessary for a threat alarm to promote freezing or were necessary for a threat alarm to promote a wider range of defensive behaviors, most prominently flight.

Major Strengths of Methods and Results

The authors performed careful single-unit recording and applied rigorous methodologies to optogenetically tag CGRP neurons within the PBN. Careful analyses show that single-units and the wider CGRP neuron population increases firing to a range of unconditioned stimuli. The optogenetic stimulation of experiment 2 was comparatively simpler but achieved its aim of determining the consequence of activating CGRP neurons in the absence of other stimuli. Experiment 3 used a very clever behavioral approach to reveal a setting in which both cue-evoked freezing and flight could be observed. This was done by having the unconditioned stimulus be a "robot" traveling along a circular path at a given speed. Subsequent cue presentation elicited mild flight in controls and optogenetic activation of CGRP neurons significantly boosted this flight response. This demonstrated for the first time that CGRP neuron activation does more than promote freezing. The authors conclude by demonstrating that bidirectional modulation of CGRP neuron activity bidirectionally affects freezing in a traditional fear conditioning setting and affects both freezing and flight in a setting in which the robot served as the unconditioned stimulus. Altogether, this is a very strong set of experiments that greatly expand the role of parabrachial CGRP neurons in threat alarm.

Weaknesses

In all of their conditioning studies the authors did not include a control cue. For example, a sound presented the same number of times but unrelated to US (shock or robot) presentation. This does not detract from their behavioral findings. However, it means the authors do not know if the observed behavior is a consequence of pairing. Or is a behavior that would be observed to any cue played in the setting? This is particularly important for the experiments using the robot US.

The authors make claims about the contribution of CGRP neurons to freezing and fleeing behavior, however, all of the optogenetic manipulations are centered on the US presentation period. Presently, the experiments show a role for these neurons in processing aversive outcomes but show little role for these neurons in cue responding or behavior organizing. Claims of contributions to behavior should be substantiated by manipulations targeting the cue period.

Appraisal

The authors achieved their aims and have revealed a much greater role for parabrachial CGRP neurons in threat alarm.

Discussion

Understanding neural circuits for threat requires us (as a field) to examine diverse threat settings and behavioral outcomes. A commendable and rigorous aspect of this manuscript was the authors decision to use a new behavioral paradigm and measure multiple behavioral outcomes. Indeed, this manuscript would not have been nearly as impactful had they not done that. This novel behavior was combined with excellent recording and optogenetic manipulations - a standard the field should aspire to. Studies like this are the only way that we as a field will map complete neural circuits for threat.

Reviewer #2 (Public Review):

-Summary of the Authors' Aims:<br /> The authors aimed to investigate the role of calcitonin gene-related peptide (CGRP) neurons in the parabrachial nucleus (PBN) in modulating defensive behaviors in response to threats. They sought to determine whether these neurons, previously shown to be involved in passive freezing behavior, also play a role in active defensive behaviors, such as fleeing, when faced with imminent threats.

-Major Strengths and Weaknesses of the Methods and Results:<br /> The authors utilized an innovative approach by employing a predator-like robot to create a naturalistic threat scenario. This method allowed for a detailed observation of both passive and active defensive behaviors in mice. The combination of electrophysiology, optogenetics, and behavioral analysis provided a comprehensive examination of CGRP neuron activity and its influence on defensive behaviors. The study's strengths lie in its robust methodology, clear results, and the multi-faceted approach that enhances the validity of the findings.

No notable weakness found.

-Appraisal of Aims and Results:<br /> The authors successfully achieved their aims by demonstrating that CGRP neurons in the PBN modulate both passive and active defensive behaviors. The results clearly show that activation of these neurons enhances fear memory and promotes conditioned fleeing behavior, while inhibition reduces these responses. The study provides strong evidence supporting the hypothesis that CGRP neurons act as a comprehensive alarm system in the brain.

-Impact on the Field and Utility of Methods and Data:<br /> This work has significant implications for the field of neuroscience, particularly in understanding the neural mechanisms underlying adaptive defensive behaviors. The innovative use of a predator-like robot to simulate naturalistic threats adds ecological validity to the findings and may inspire future studies to adopt similar approaches. The comprehensive analysis of CGRP neuron activity and its role in defensive behaviors provides valuable data that could be useful for researchers studying fear conditioning, neural circuitry, and behavior modulation.

-Additional Context:<br /> The study builds on previous research that primarily focused on the role of CGRP neurons in passive defensive responses, such as freezing. By extending this research to include active responses, the authors have provided a more complete picture of the role of these neurons in threat detection and response. The findings highlight the versatility of CGRP neurons in modulating different types of defensive behaviors based on the perceived intensity and immediacy of threats.

Overall, this manuscript makes a significant contribution to our understanding of the neural basis of defensive behaviors and offers valuable methodological insights for future research in the field.

Reviewer #3 (Public Review):

Strengths:<br /> The study used optogenetics together with in vivo electrophysiology to monitor CGRP neuron activity in response to various aversive stimuli including robot chasing to determine whether they encode noxious stimuli differentially. The study used an interesting conditioning paradigm to investigate the role of CGRP neurons in the PBN in both freezing and flight behaviors.

Weakness:<br /> The major weakness of this study is that the chasing robot threat conditioning model elicits weak unconditioned and conditioned flight responses, making it difficult to interpret the robustness of the findings. Furthermore, the conclusion that the CGRP neurons are capable of inducing flight is not substantiated by the data. No manipulations are made to influence the flight behavior of the mouse. Instead, the manipulations are designed to alter the intensity of the unconditioned stimulus.

Reviewer #1 (Public review):

Summary:

This study investigates the potential of targeting specific regions within the RNA genome of the Porcine Epidemic Diarrhea Virus (PEDV) for antiviral drug development. The authors used SHAPE-MaP to analyze the structure of the PEDV RNA genome in infected cells. They categorized different regions of the genome based on their structural characteristics, focusing on those that might be good targets for drugs or small interfering RNAs (siRNAs).

They found that dynamic single-stranded regions can be stabilized by compounds (e.g., to form G-quadruplexes), which inhibit viral proliferation. They demonstrated this by targeting a specific G4-forming sequence with a compound called Braco-19. The authors also describe stable (structured) single-stranded regions that they used to design siRNAs showing that they effectively inhibited viral replication.

Strengths:

There are a number of strengths to highlight in this manuscript.

(1) The study uses a sophisticated technique (SHAPE-MaP) to analyze the PEDV RNA genome in situ, providing valuable insights into its structural features.

(2) The authors provide a strong rationale for targeting specific RNA structures for antiviral development.

(3) The study includes a range of experiments, including structural analysis, compound screening, siRNA design, and viral proliferation assays, to support their conclusions.

(4) Finally, the findings have potential implications for the development of new antiviral therapies against PEDV and other RNA viruses.

Overall, this interesting study highlights the importance of considering RNA structure when designing antiviral therapies and provides a compelling strategy for identifying promising RNA targets in viral genomes.

Weaknesses:

I have some concerns about the utility of the 3D analyses, the effects of their synonymous mutants on expression/proliferation, a potentially missed control for studies of mutants, and the therapeutic utility of the compound they tested vs. G-quadruplexes.

Reviewer #2 (Public review):

Summary:

Luo et. al. use SHAPE-MaP to find suitable RNA targets in Porcine Epidemic Diarrhoea Virus. Results show that dynamic and transient structures are good targets for small molecules, and that exposed strand regions are adequate targets for siRNA. This work is important to segment the RNA targeting.

Strengths:

This work is well done and the data supports its findings and conclusions. When possible, more than one technique was used to confirm some of the findings.

Weaknesses:

The study uses a cell line that is not porcine (not the natural target of the virus).

Reviewer #3 (Public review):

Summary:

This manuscript by Luo et al. applied SHAPE-Map to analyze the secondary structure of the Porcine Epidemic Diarrhoea Virus (PEDV) RNA genome in infected cells. By combining SHAPE reactivity and Shannon entropy, the study indicated that the folding of the PEDV genomic RNA was nonuniform, with the 5' and 3' untranslated regions being more compactly structured, which revealed potentially antiviral targetable RNA regions. Interestingly, the study also suggested that compounds bound to well-folded RNA structures in vitro did not necessarily exhibit antiviral activity in cells, because the binding of these compounds did not necessarily alter the functions of the well-folded RNA regions. Later in the manuscript, the authors focus on guanine-rich regions, which may form G-quadruplexes and be potential targets for small interfering RNA (siRNA). The manuscript shows the binding effect of Braco-19 (a G-quadruplex-binding ligand) to a predicted G4 region in vitro, along with the inhibition of PEDV proliferation in cells. This suggests that targeting high SHAPE-high Shannon G4 regions could be a promising approach against RNA viruses. Lastly, the manuscript identifies 73 single-stranded regions with high SHAPE and low Shannon entropy, which demonstrated high success in antiviral siRNA targeting.

Strengths:

The paper presents valuable data for the community. Additionally, the experimental design and data analysis are well documented.

Weakness:

The manuscript presents the effect of Braco-19 on PQS1, a single G4 region with high SHAPE and high Shannon entropy, to suggest that "the compound can selectively target the PQS1 of the high SHAPE-high Shannon region in cells" (lines 625-626). While the effect of Braco-19 on PQS1 is supported by strong evidence in the manuscript, the conclusion regarding the G4 region with high SHAPE and high Shannon entropy is based on a single target, PQS1.

Reviewer #1 (Public review):

Summary:<br /> In the manuscript "Intergenerational transport of double-stranded RNA limits heritable epigenetic changes," Shugarts and colleagues investigate intergenerational dsRNA transport in the nematode C. elegans. By inducing oxidative damage, they block dsRNA import into cells, which affects heritable gene regulation in the adult germline (Fig. 2). They identify a novel gene, sid-1-dependent gene-1 (sdg-1), upregulated upon SID-1 inhibition (Fig. 3). Both transient and genetic depletion of SID-1 lead to the upregulation of sdg-1 and a second gene, sdg-2 (Fig. 5). Interestingly, while sdg-1 expression suggests a potential role in dsRNA transport, neither its overexpression nor loss-of-function impacts dsRNA-mediated silencing in the germline (Fig. 7).

Strengths:<br /> • The authors employ a robust neuronal stress model to systematically explore SID-1 dependent intergenerational dsRNA transport in C. elegans.<br /> • They discover two novel SID-1-dependent genes, sdg-1 and sdg-2.<br /> • The manuscript is well-written and addresses the compelling topic of dsRNA signaling in C. elegans.

Weaknesses:<br /> • The molecular mechanism downstream of SDG-1 remains unclear. Testing whether sdg-2 functions redundantly with sdg-1could provide further insights.<br /> • SDG-1 dependent genes in other nematodes remain unknown.

Reviewer #2 (Public review):

Summary:

RNAs can function across cell borders and animal generations as sources of epigenetic information for development and immunity. The specific mechanistic pathways how RNA travels between cells and progeny remains an open question. Here, Shugarts, et al. use molecular genetics, imaging, and genomics methods to dissect specific RNA transport and regulatory pathways in the C. elegans model system. Larvae ingesting double-stranded RNA is noted to not cause continuous gene silencing throughout adulthood. Damage of neuronal cells expressing double-stranded target RNA is observed to repress target gene expression in the germline. Exogenous short or long double-stranded RNA required different genes for entry into progeny. It was observed that the SID-1 double-stranded RNA transporter showed different expression over animal development. Removal of the sid-1 gene caused upregulation of two genes, the newly described sid-1-dependent gene sdg-1 and sdg-2. Both genes were observed to be negatively regulated by other small RNA regulatory pathways. Strikingly, loss then gain of sid-1 through breeding still caused variability of sdg-1 expression for many, many generations. SDG-2 protein co-localizes with germ granules, intracellular sites for heritable RNA silencing machinery. Collectively, sdg-1 presents a model to study how extracellular RNAs can buffer gene expression in germ cells and other tissues.

Strengths:

(1) Very cleaver molecular genetic methods and genomic analyses, paired with thorough genetics, were employed to discover insights into RNA transport, sdg-1 and sdg-2 as sid-1-dependent genes, and sdg-1's molecular phenotype.

(2) The manuscript is well cited, and figures reasonably designed.

(3) The discovery of the sdg genes being responsive to the extracellular RNA cell import machinery provides a model to study how exogenous somatic RNA is used to regulate gene expression in progeny. The discovery of genes within retrotransposons stimulates tantalizing models how regulatory loops may actually permit the genetic survival of harmful elements.

Weaknesses:

(1) The manuscript is broad, making it challenging to read and consider the data presented. Of note, since the original submission, the authors have improved the clarity of the writing and presentation.

Comments on revised version:

This reviewer thanks the authors for their efforts in revising the manuscript. In their rebuttal, the authors acknowledged the broad scope of their manuscript. I concur. While I still think the manuscript is a challenge to read due to its expansive nature, the current draft is substantially improved when compared to the previous one. This work will contribute to our general knowledge of RNA biology, small RNA regulatory pathways, and RNA inheritance.

Reviewer #1 (Public review):

Summary:

Recommendations for the authors In this study, Liu, Jiang, Diao et.al. investigated the role of GSDMD in psoriasis-like skin inflammation in mice. The authors have used full-body GSDMD knock-out mice and Gsdm floxed mice crossed with the S100A8- Cre. In both mice, the deficiency of GSDMD ameliorated the skin phenotype induced by the imiquimod. The authors also analyzed RNA sequencing data from the psoriatic patients to show an elevated expression of GSDMD in the psoriatic skin.

Strengths:

It has the potential to unravel the new role of neutrophils.

Comments on revisions:

The authors have addressed the majority of comments and concerns and highlighted the potential limitations wherever not possible.

Reviewer #2 (Public review):

Summary:

The authors describe elevated GSDMD expression in psoriatic skin, and knock-out of GSDMD abrogates psoriasis-like inflammation.

Strengths:

The study is well conducted with transgenic mouse models. Using mouse-models with GSDMD knock-out showing abrogating inflammation, as well as GSDMD fl/fl mice without neutrophils having a reduced phenotype.

My major concern would be the involvement of other inflammasome and GSDMD bearing cell types, esp. Keratinocytes (KC), which could be an explanation why the experiments in Fig 4 still show inflammation.

Comments on revisions:

The authors have sufficiently addressed my questions.

Reviewer #1 (Public review):

Fuchs describes a novel method of enzymatic protein-protein conjugation using the enzyme Connectase. The author is able to make this process irreversible by screening different Connectase recognition sites to find an alternative sequence that is also accepted by the enzyme. They are then able to selectively render the byproduct of the reaction inactive, preventing the reverse reaction, and add the desired conjugate with the alternative recognition sequence to achieve near-complete conversion. I agree with the authors that this novel enzymatic protein fusion method has several applications in the field of bioconjugation, ranging from biophysical assay conduction to therapeutic development. Previously the author has published on the discovery of the Connectase enzymes and has shown its utility in tagging proteins and detecting them by in-gel fluorescence. They now extend their work to include the application of Connectase in creating protein-protein fusions, antibody-protein conjugates, and cyclic/polymerized proteins. As mentioned by the author, enzymatic protein conjugation methods can provide several benefits over other non-specific and click chemistry labeling methods. Connectase specifically can provide some benefits over the more widely used Sortase, depending on the nature of the species that is desired to be conjugated. However, due to a similar lengthy sequence between conjugation partners, the method described in this paper does not provide clear benefits over the existing SpyTag-SpyCatcher conjugation system. Additionally, specific disadvantages of the method described are not thoroughly investigated, such as difficulty in purifying and separating the desired product from the multiple proteins used. Overall, this method provides a novel, reproducible way to enzymatically create protein-protein conjugates.

The manuscript is well-written and will be of interest to those who are specifically working on chemical protein modifications and bioconjugation.

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 #1 (Public review):

Summary:

This study by Lo et al. seeks to explain the cellular defects underlying the brain phenotypes of Lowe syndrome (LS). There have been limited studies on this topic and hence this is a timely study.

Strengths:

Studies such as these can contribute to an understanding of the cellular and developmental mechanisms of brain disorders.

Weaknesses:

This study by Lo et al. seeks to explain the cellular defects underlying the brain phenotypes of Lowe syndrome (LS). There have been limited studies on this topic and hence this is a timely study.

The study uses two models: (1) an LS IOB knockout mouse and (2) neurons derived from iPSC lines from LS patients. These two models are used to present three separate findings: (1) altered mitochondria function, (2) altered numbers of neurons and glia in both models, and (3) some evidence of altered Sonic Hedgehog signaling projected as a defect in cilia.

Conceptually, there are some problems of serious concern which must be carefully considered:<br /> (1) The IOB mouse was very extensively phenotyped when it was generated by Festa et.al HMM, 2019. It does not have any obvious phenotypes of brain deficits although the studies in this paper were very detailed indeed.<br /> (2) Reduced brain size is reported as a phenotype of the IOB mouse in this study. Yet over the many clinical studies of LS published over the years, altered brain size has not been noted, either in clinical examination or in the many MRI reports of LS patients.

While reading through these results it is striking that the link between the three reported phenotypes is at least tenuous, and in fact may not exist at all. The link between mitochondria and neurogenesis is based on a single paper that has been cited incorrectly and out of context. There is no evidence presented for a link between the Shh signaling defect reported and the mitochondrial phenotype.

General comments

(1) The preparation of the manuscript requires improvement. There are many errors in the presentation of data.<br /> (2) The use of references needs to be re-considered. Sometimes a reference is used when in fact the results included in that paper are the opposite of what the authors intend.<br /> (3) The authors conclude the paper by claiming that mitochondrial dysfunction and impairments of the ciliary SHH contribute to abnormal neuronal differentiation in LS, but the mechanism by which this sequence of events might happen hasn't been shown.

Final comments:

(1) Phenotype of increased astrocytes:<br /> The phenotype of increased astrocytes in both the IOB mouse brain or iPSC-derived cultures iN cells requires clarification as one of the markers used as an astrocyte marker, BRN2, is commonly used as a neuronal marker. As LS is a neurodevelopmental disorder, and the phenotype in question is related to differentiation, it is crucial to shed light on the developmental timeline in which this phenotype is seen in the mouse brain.

(2) Ciliary homeostasis:<br /> Mitochondrial dysfunction in astrocytes has been shown to induce a ciliogenic program. However, almost the opposite is shown in this paper, with regards to ciliation. Morphology of the cilia was not assessed either, which is an important feature of ciliary homeostasis. The improper ciliary homeostasis here appears to be the improper Shh signalling, which has not been shown to be related to mitochondrial dysfunction. This leaves one wondering how exactly the different phenotypes shown in this paper are connected.

(3) This paper lacks a clear mechanistic approach. While the data validates the 3 broad phenotypes mentioned, there is a lack of connection between these phenotypes or an answer to why these phenotypes appear. While the discussion attempts to shed light on this by referencing previous studies, some of the referenced studies show contradicting results. Hence, it would be beneficial to clarify these gaps with further experiments and address the larger question of the connection between the mitochondria, Shh signalling, and astrocyte formation.

(4) Most importantly, there is no mention of how the loss of OCRL, a 5-phosphatase enzyme, results in the appearance of the mentioned phenotypes. Since there are multiple studies in the field of Lowe Syndrome that shed light on the various functions of OCRL, both catalytic and non-catalytic, it is important to address the role of OCRL in resulting in these phenotypes.

(5) There are numerous errors in the qPCR experiments performed with regard to the genes that were assayed. The genes mentioned in the text section do not match those indicated in the graphs or legends. This takes away the confidence of the reader in this data.

Reviewer #2 (Public review):

Summary:

This manuscript investigates how neural cell development is affected in Lowe syndrome. Using neural cultures differentiated from human iPSCs carrying either an LS mutation or a genetically engineered mutation in OCRL, the authors show a depletion of mitochondrial DNA and a decrease in mitochondrial activities that correlate with an increased formation of astrocytes at the expense of neurons. Similar effects on mitochondria and on astrocyte development were observed in an LS mouse model. Moreover, these mutant brain cells are less likely to be ciliated and show a reduction in Sonic Hedgehog signalling.

Strengths/Weaknesses:

The study derives strength from the analyses of two different models of Lowe syndrome, both reaching similar conclusions. However, the observed changes in mitochondrial defects, neuronal/astrocytic development, and primary cilia are only correlated, with no attempt to investigate a causal relationship. Moreover, the mouse model is only analysed at the adult stage providing no insights into the development of the defects. Different brain regions are analysed with immunostainings and qRT-PCR making it challenging to draw clear correlations between these findings. The quality of the corresponding figures is often poor and the selection of markers is frequently inappropriate. Taken together, these limitations complicate the interpretations of the data and significantly limit the conclusions that can be drawn from the study.

Reviewer #1 (Public review):

Summary:

The authors develop a set of biophysical models to investigate whether a constant area hypothesis or a constant curvature hypothesis explains the mechanics of membrane vesiculation during clathrin-mediated endocytosis.

Strengths:

The models that the authors choose are fairly well-described in the field and the manuscript is well-written.

Weaknesses:

One thing that is unclear is what is new with this work. If the main finding is that the differences are in the early stages of endocytosis, then one wonders if that should be tested experimentally. Also, the role of clathrin assembly and adhesion are treated as mechanical equilibrium but perhaps the process should not be described as equilibria but rather a time-dependent process. Ultimately, there are so many models that address this question that without direct experimental comparison, it's hard to place value on the model prediction.<br /> While an attempt is made to do so with prior published EM images, there is excessive uncertainty in both the data itself as is usually the case but also in the methods that are used to symmetrize the data. This reviewer wonders about any goodness of fit when such uncertainty is taken into account.

Reviewer #2 (Public review):

Summary:

In this manuscript, the authors employ theoretical analysis of an elastic membrane model to explore membrane vesiculation pathways in clathrin-mediated endocytosis. A complete understanding of clathrin-mediated endocytosis requires detailed insight into the process of membrane remodeling, as the underlying mechanisms of membrane shape transformation remain controversial, particularly regarding membrane curvature generation. The authors compare constant area and constant membrane curvature as key scenarios by which clathrins induce membrane wrapping around the cargo to accomplish endocytosis. First, they characterize the geometrical aspects of the two scenarios and highlight their differences by imposing coating area and membrane spontaneous curvature. They then examine the energetics of the process to understand the driving mechanisms behind membrane shape transformations in each model. In the latter part, they introduce two energy terms: clathrin assembly or binding energy, and curvature generation energy, with two distinct approaches for the latter. Finally, they identify the energetically favorable pathway in the combined scenario and compare their results with experiments, showing that the constant-area pathway better fits the experimental data.

Strengths:

The manuscript is well-written, well-organized, and presents the details of the theoretical analysis with sufficient clarity.<br /> The calculations are valid, and the elastic membrane model is an appropriate choice for addressing the differences between the constant curvature and constant area models.<br /> The authors' approach of distinguishing two distinct free energy terms-clathrin assembly and curvature generation-and then combining them to identify the favorable pathway is both innovative and effective in addressing the problem.<br /> Notably, their identification of the energetically favorable pathways, and how these pathways either lead to full endocytosis or fail to proceed due to insufficient energetic drives, is particularly insightful.

Weaknesses:

Membrane remodeling in cellular processes is typically studied in either a constant area or constant tension ensemble. While total membrane area is preserved in the constant area ensemble, membrane area varies in the constant tension ensemble. In this manuscript, the authors use the constant tension ensemble with a fixed membrane tension, σe. However, they also use a constant area scenario, where 'area' refers to the surface area of the clathrin-coated membrane segment. This distinction between the constant membrane area ensemble and the constant area of the coated membrane segment may cause confusion.

As mentioned earlier, the theoretical analysis is performed in the constant membrane tension ensemble at a fixed membrane tension. The total free energy E_tot of the system consists of membrane bending energy E_b and tensile energy E_t, which depends on membrane tension, σe. Although the authors mention the importance of both E_b and E_t, they do not present their individual contributions to the total energy changes. Comparing these contributions would enable readers to cross-check the results with existing literature, which primarily focuses on the role of membrane bending rigidity and membrane tension.

The authors introduce two different models, (1,1) and (1,2), for generating membrane curvature. Model 1 assumes a constant curvature growth, corresponding to linear curvature growth, while Model 2 relates curvature growth to its current value, resembling exponential curvature growth. Although both models make physical sense in general, I am concerned that Model 2 may lead to artificial membrane bending at high curvatures. Normally, for intermediate bending, ψ > 90, the bending process is energetically downhill and thus proceeds rapidly. the bending process is energetically downhill and thus proceeds rapidly. However, Model 2's assumption would accelerate curvature growth even further. This is reflected in the endocytic pathways represented by the green curves in the two rightmost panels of Fig. 4a, where the energy steeply increases at large ψ. I believe a more realistic version of Model 2 would require a saturation mechanism to limit curvature growth at high curvatures.

Reviewer #1 (Public review):

Summary:

Al Asafen and colleagues apply a set of scanning fluorescence correlation spectroscopic approaches (Raster Image Correlation Spectroscopy (RICS), cross-correlation RICS, and pair-correlation function spectroscopy) to address the nuclear-cytoplasmic kinetics of the Dorsal (Dl) transcription factor in early Drosophila embryos. The Toll/Dl system has long been appreciated to establish dorsal-ventral polarity of the embryo through Toll-dependent control of Dl nuclear localization, and provides an example of a morphogen gradient produced with high enough precision to yield robust biophysical measurements of general transcription factor activity and function. By measuring GFP-tagged Dl protein, either in wild-type embryos or in mutant embryos with low/medium/high levels of Toll signaling, the authors report diffusivity of Dl in nuclear and cytoplasmic compartments of the embryo, as well as the fraction of mobile and immobile Dl, which can be correlated with DNA binding through cross-correlation RICS. A model is presented where Cactus/IkB is implicated in preventing Dl from binding to DNA.

Strengths:

The experiments on wild-type GFP-tagged Dorsal are performed well, are mostly reported well, and are interpreted fairly.

Weaknesses:

The discrepancy between experiment and theory as pertains to Michaelis-Menten kinetics is not fully motivated in the text, and could benefit from a more clear presentation. The experiments performed to distinguish between the contribution of Toll-dependent phosphorylation and Cactus interaction models for limiting Dorsal DNA binding are possibly confounded by the presence of wild-type, GFP-tagged Dorsal protein.

Reviewer #2 (Public review):

Summary:

In this manuscript, Al Asafen, Clark et al., use fluorescence correlation spectroscopy (FCS) to quantitatively analyze the mobility of Dl along the DV axis of the early Drosophila embryo. Dl is essential for dorsal-ventral (DV) patterning and its gradient initiates the activation of several genes and thereby orchestrates the formation of the Drosophila body plan. While the mechanisms underlying the formation of the Dl gradient have been extensively studied by this group and others, there are some observations for which there is not yet a mechanistic explanation. For example, the peak of the Dl gradient grows continuously during nuclear cycles 10-14. This is likely due to Cact-dependent Dl diffusion and Dl binding to DNA. However, the biophysical parameters governing Dl nuclear dynamics that would support these claims have not been previously measured. In this work, the authors provide evidence that GFP-tagged Dl may be separated into a mobile pool and an immobile pool. Interestingly, the fraction of immobile Dl is position-dependent along the DV axis, revealing more binding to DNA in the ventral than in the dorsal nuclei. This is either due to higher binding affinity in ventral locations (due to Toll-dependent Dl phosphorylation) or to higher Dl-Cact binding in dorsal nuclei that would prevent Dl from binding to DNA. Using dl-mutant alleles, the authors support the latter hypothesis.

Strengths:

The manuscript is well written and their conclusions are convincingly supported by their methodology and analysis. As a quantitative study, the biophysical analysis seems rigorous, in general.

Although this is not the first study that employs FSC to investigate the dynamics of a morphogen, it further exemplifies how these quantitative tools can be used to uncover mechanistic aspects of morphogen dynamics during development. In particular, the manuscript reports novel biophysical parameters of Dl dynamics that will be helpful in future hypotheses-driven modeling studies.

Weaknesses:

In my opinion, the main weakness of the manuscript is that the main biological implication of the study, namely that the asymmetry in the fraction of immobile Dl is a result of nuclear Dl-Cact binding which prevents Dl from binding DNA (Figure 5), occurs in a region of the embryo where there is very little Dl anyways (Figure 1A, 5A). While it is interesting that the fraction of immobile Dl increases (just a little, but significantly) in dorsal nuclei in mutants expressing a form of Dl with reduced Cact binding it is unclear what is the biological impact of this effect in a location where Dl is nearly absent. As can be seen in Figure 3F, the fraction of immobile is unaffected in Dl-mutant forms with reduced DNA binding, because it is already very low. It is unlikely that Dl binding to Cact in dorsal nuclei would affect shuttling as well since the fraction is very low anyway.

While the authors have a very clear understanding of the biology of the Dl gradient, I feel that the manuscript is more written as a 'tools' paper (i.e., to exemplify how FSC methods and analysis can be used for biological discovery). This is ok, but I think that the authors should discuss further what are the biological implications of these findings other than the contribution to uncovering the biophysical parameters. For example, I think that the implications of the rejected hypothesis (i.e., that Toll-dependent Dl phosphorylation does not seem to have an impact on Dl binding affinities to DNA) are important and should be further discussed (even if no additional experiments are performed). What is then the role of Dl phosphorylation? Perhaps it could have an impact on patterning robustness in lateral regions. The authors should report in Figure 5 also what happens to the fraction of Dl bound to DNA in lateral regions in the reduced Cact binding and reduced Toll phosphorylation mutants.

The way that position along the DV axis is reported using the nuclear-cytoplasmic-ratio (NCR) in Figures 1-3 is not incorrect, but I wonder if it is the best way of doing it. The reason is that it spreads out a relatively small region of the embryo (the ventral-most locations) and shrinks a relatively large region of the embryo (lateral and dorsal regions), see Figure 1A. Perhaps reporting the NCR in log_2 units would be more appropriate.

Reviewer #1 (Public review):

Summary:

This study presents useful insights into the in vivo dynamics of insulin-producing cells (IPCs), key cells regulating energy homeostasis across the animal kingdom. The authors further provide compelling evidence using adult Drosophila melanogaster that IPCs, unlike neighboring DH44 cells, do not respond to glucose directly, but that glucose can indirectly regulate IPC activity after ingestion supporting an incretin-like mechanism in flies similar to mammals. The authors link decreased activity of IPCs to hyperactivity observed in starved flies, a locomotive behavior aimed to increase food search. Furthermore, the authors provide evidence that IPCs receive inhibitory inputs from Dh44 neurons, which are linked to increased locomotor activity.

This paper is of outstanding interest to scientists aiming to understand metabolic control of circuit dynamics, in particular for internal state-linked behaviors competing with the feeding state.

Strengths:

(1) By using whole cell patch clamp recording, the authors convincingly showed the activity pattern and regulation of IPCs and neighboring DH44 neurons under different feeding states and in various refeeding paradigms.<br /> (2) The paper provides compelling evidence that IPCs are not directly and acutely activated by glucose, but rather through a post-ingestive incretin-like mechanism. In addition, the authors show that Dh44 neurons located adjacent to the IPCs respond to bath application of nutritive sugars contrary to the IPCs.<br /> (3) The paper also provides useful data on the regulation of IPC activity by Dh44 neurons, which is useful to understand their regulation in vivo.

No major weaknesses remain in the revised version of this work.

Reviewer #2 (Public review):

Summary

In this study, Bisen et al. characterized the state-dependency of insulin-producing cells in the brain of Drosophila melanogaster. They successfully established that IPC activity is modulated by the nutritional state and age of the animal. Interestingly, they demonstrate that IPCs respond to the ingestion of glucose, rather than to perfusion with it, an observation reminiscent of the incretin effect in mammals. The study is well conducted and presented and the experimental data convincingly support the claims made.

Strengths

The study makes great use of the tools available in *Drosophila* research, demonstrating the effect that starvation and subsequent refeeding have on the physiological activity of IPCs as well as on the behavior of flies to then establish causal links by making use of optogenetic tools.<br /> It is particularly nice to see how the authors put their findings in context to published research and use for example TDC2 neuron activation or DH44 activity to establish baselines to relate their data to.

Reviewer #3 (Public review):

Although insulin release is essential in the control of metabolism, adjusted to nutritional state, and plays major roles in normal brain function as well as in aging and disease, our knowledge about the activity of insulin-producing (and releasing) cells (IPCs) in vivo in limited.

In this technically demanding study, IPC activity is studied in the Drosophila model system by fine in vivo patch clamp recordings with parallel behavioral analyses and various optogenetic as well as feeding manipulations.

The data provide compelling evidence that IPC activity is increased with a slow time course after feeding a high glucose diet. By contrast, IPC activity is not directly affected by rising blood glucose levels. This is reminiscent of the incretin effect known from vertebrates and points to a conserved mechanism in insulin production and release upon sugar feeding.

Moreover, the data confirm earlier studies that nutritional state strongly affects locomotion. Surprisingly, strong evidence shows that IPC activity makes only a negligible contribution to this. Instead, other modulatory neurons that are directly sensitive to blood glucose levels strongly affect locomotion. Together, these data reveal a network of multiple parallel and interacting neuronal layers to orchestrate the physiological, metabolic, and behavioral responses to the nutritional state. Together with the data from a previous study, this work sets the stage to dissect the architecture and function of this network.

Strengths:

State-of-the-art current clamp in situ patch clamp recordings in behaving animals are a demanding but powerful method to provide novel insight into the interplay of nutritional state, IPC activity, and locomotion. The patch clamp recordings and the parallel behavioral analyses are of high quality, as are the optogenetic manipulations. The data showing that starvation silences IPC activity in young flies (younger than 1 week) are excellent. The evidence for the claim that locomotor activity is not increased upon IPC activity but upon the activity of other blood glucose sensitive modulatory neurons (Dh44) is compelling, too. The study provides a great system to experimentally dissect the interplay of insulin production and release with metabolism, physiology, nutritional state, and behavior. Demonstrating the incretin effect in Drosophila provides novel experimental routes to further study it. During the revision process, compelling evidence has been added to underscore the incretin effect, the finding that IPCs themselves do not sense sugars, and that feeding a high sugar diet does not cause unspecific stress responses.

I found no more weaknesses: The authors have carefully addressed all of my previous critiques by adding compelling new data and carefully revising the text. This paper provides a prime example of how responsible authors can utilize this constructive (but relatively new) reviewing procedure to make a very good manuscript even better.

Reviewer #1 (Public review):

Summary:

The authors test the "OHC-fluid-pump" hypothesis by assaying the rates of kainic acid dispersal both in quiet and in cochleae stimulated by sounds of different levels and spectral content. The main result is that sound (and thus, presumably, OHC contractions and expansions) result in faster transport along the duct. OHC involvement is corroborated using salicylate, which yielded results similar to silence. Especially interesting is the fact that some stimuli (e.g., tones) seem to provide better/faster pumping than others (e.g., noise), ostensibly due to the phase profile of the resulting cochlear traveling-wave response.

Strengths:

The experiments appear well controlled and the results are novel and interesting. Some elegant cochlear modeling that includes coupling between the organ of Corti and the surrounding fluid as well as advective flow supports the proposed mechanism.

The current limitations and future directions of the study, including possible experimental tests, extensions of the modeling work, and practical applications to drug delivery, are thoughtfully discussed.

Reviewer #2 (Public review):

Although recent cochlear micromechanical measurements in living animals have shown that outer hair cells drive broadband vibration of the reticular lamina, the role of this vibration in cochlear fluid circulation remains unclear. The authors hypothesized that motile outer hair cells facilitate cochlear fluid circulation. To test this, they investigated the effects of acoustic stimuli and salicylate on kainic acid-induced changes in the cochlear nucleus activities. The results reveal that low-frequency tones accelerate the effect of kainic acid, while salicylate reduces the impact of acoustic stimuli, indicating that outer hair cells actively drive cochlear fluid circulation.

The major strengths of this study lie in its high significance and the synergistic use of both electrophysiological recording and computational modeling. Recent in vivo observations of the broadband reticular lamina vibration challenge the traditional view of frequency-specific cochlear amplification. Furthermore, there is currently no effective noninvasive method to deliver the drugs or genes to the cochlea. This study addresses these important questions by observing outer hair cells' roles in the cochlear transport of kainic acid. The author utilized a well-established electrophysiological method to produce valuable new data and a custom-developed computational model to enhanced the interpretation of their experimental results.

The authors successfully validated their hypothesis, showing through the experimental and modeling results that active outer hair cells enhance cochlear fluid circulation in the living cochlea.

These findings have significant implications for advancing our understanding of cochlear amplification and offer promising clinical applications for treating hearing loss by accelerating cochlear drug delivery.

Reviewer #3 (Public review):

Summary:

This study reveals that sound exposure enhances drug delivery to the cochlea through the non-selective action of outer hair cells. The efficiency of sound-facilitated drug delivery is reduced when outer hair cell motility is inhibited. Additionally, low-frequency tones were found to be more effective than broadband noise for targeting substances to the cochlear apex. Computational model simulations support these findings.

Strengths:

The study provides compelling evidence that the broad action of outer hair cells is crucial for cochlear fluid circulation, offering a novel perspective on their function beyond frequency-selective amplification. Furthermore, these results could offer potential strategies for targeting and optimizing drug delivery throughout the cochlear spiral.

Weaknesses:

The primary weakness of this paper lies in the surgical procedure used for drug administration through the round window. Opening the cochlea can alter intracochlear pressure and disrupt the traveling wave from sound, a key factor influencing outer hair cell activity. However, the authors do not provide sufficient details on how they managed this issue during surgery. Additionally, the introduction section needs further development to better explain the background and emphasize the significance of the work.

Reviewer #1 (Public review):

I have reviewed the manuscript "Psychological stress disturbs bone metabolism via miR-335-3p/Fos signaling in osteoclast" with interest. The described findings are relevant and useful for daily practice in periodontology. The paper is concise, professionally written, and easy to read. In this study, Jiayao et al. revealed the role of miR-335-3p in psychological stress-induced osteoporosis. CUMS mice were constructed to observe the femur phenotype, osteoclasts were identified as the main research object, and miRNA-seq was used to find the key miRNAs linking the brain and peripheral tissues. This study showed that miR-335-3p expression was simultaneously reduced in murine NAC, serum, and bone under psychological stress. The miR-335-3p/Fos/NFATC1 signaling pathway was validated in osteoclasts to reveal the potential mechanism of enhanced osteoclast activity under psychological stress. This study, from a new perspective of miRNAs, indicates a possible cause of disturbed bone metabolism due to psychological stress and may suggest a new approach to treating osteoporosis.

Reviewer #2 (Public review):

Zhang et al. established chronic unpredictable mild stress (CUMS) mouse model, which displayed osteoporosis phenotype, suggesting a potential correlation between psychological stress and bone metabolism. They found that miRNA candidate miR-335-3p is downregulated in the long bone of CUMS mice through microRNA sequencing experiments and qRT-PCR. They further demonstrated that miR-335-3p attenuates osteoclast activity via inhibiting Fos signaling, which can induce NFATC1 expression and regulate osteoclast activity.

My concerns have been addressed. And the quality of the manuscript is improved significantly.

Reviewer #1 (Public review):

Batra, Cabrera and Spence et al. present a model which integrates histone posttranslational modification (PTM) data across cell models to predict gene expression with the goal of using this model to better understand epigenetic editing. This gene expression prediction model approach is useful if a) it predicts gene expression in specific cell lines b) it predicts expression values rather than a rank or bin, c) if it helps us to better understand the biology of gene expression or d) it helps us to understand epigenome editing activity. Problematically for point a) and b) it is easier to directly measure gene expression than to measure multiple PTMs and so the real usefulness of this approach mostly relates to c) and d).

Other approaches have been published that use histone PTM to predict expression (e.g. PMID 27587684, 36588793). Is this model better in some way? No comparisons are made although a claim is made that direct comparisons are difficult. I appreciate that the authors have not used the histone PTM data to predict gene expression levels of an "average cell" but rather that they are predicting expression within specific cell types or for unseen cell types. Approaches that predict expression levels are much more useful whereas some previous approaches have only predicted expressed or not expressed or a rank order or bin-based ranking. The paper does not seem to have substantial novel insights into understanding the biology of gene expression.

The approach of using this model to predict epigenetic editor activity on transcription is interesting and to my knowledge novel although only examined in the context of a p300 editor. As the author point out the interpretation of the epigenetic editing data is convoluted by things like sgRNA activity scoring and to fully understand the results likely would require histone PTM profiling and maybe dCas9 ChIP-seq for each sgRNA which would be a substantial amount of work.

Furthermore from the model evaluation of H3K9me3 is seems the model is performing modestly for other forms of epigenetic or transcriptional editing- e.g. we know for the best studied transcriptional editor which is CRISPRi (dCas9-KRAB) that recruitment to a locus is associated with robust gene repression across the genome and is associated with H3K9me3 deposition by recruitment of KAP1/HP1/SETDB1 (PMID: 35688146, 31980609, 27980086, 26501517).

One concern overall with this approach is that dCas9-p300 has been observed to induce sgRNA independent off target H3K27Ac (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8349887/ see Figure S5D) which could convolute interpretation of this type of experiment for the model.

Reviewer #2 (Public review):

Summary:

The authors build a gene expression model based on histone post-translational modifications, and find that H3K27ac is correlated with gene expression. They proceed to perturb H3K27ac at 13 gene promoters in two cell types, and measure gene expression changes to test their model.

Strengths:

The combination of multiple methods to model expression, along with utilizing 6 histone datasets in 13 cell types allowed the authors to build a model that correlates between 0.7-0.79 with gene expression. They use dCas9-p300 fusions to perturb H3K27ac and monitor gene expression to test their model. Ranked correlations of the HEK293 data showed some support for the predictions after perturbation of H3K27ac.

Weaknesses:

The perturbation of 5 genes in K562 with perturb-seq data shows a modest correlation of ~0.5 and isn't included in the main figures. The authors are then left to speculate reasons why the outcome of epigenome editing doesn't fit their predictions, which highlights the limited value in the current version of this method.

As mentioned before, testing genes that were not expressed being most activated by dCas9-p300 weaken the correlations vs. looking at a broad range of different gene expression as the original model was trained on.<br /> If the authors want this method to be used to predict outcomes of epigenome editing, expanding to dCas9-KRAB and other CRISPRa methods (SAM and VPR) would be useful. Those datasets are published and could be analyzed for this manuscript.<br /> The authors don't compare their method to other prediction methods.

Reviewer #1 (Public review):

Summary:

In this article, the authors set out to understand how people's food decisions change when they are hungry vs. sated. To do so, they used an eye-tracking experiment where participants chose between two food options, each presented as a picture of the food plus its "Nutri-Score". In both conditions, participants fasted overnight, but in the sated condition, participants received a protein shake before making their decisions. The authors find that participants in the hungry condition were more likely to choose the tastier option. Using variants of the attentional drift-diffusion model, they further find that the best-fitting model has different attentional discounts on the taste and health attributes and that the attentional discount on the health information was larger for the hungry participants.

Strengths:

The article has many strengths. It uses a food-choice paradigm that is established in neuroeconomics. The experiment uses real foods, with accurate nutrition information, and incentivized choices. The experimental manipulation is elegant in its simplicity - administering a high-calorie protein shake. It is also commendable that the study was within-participant. The experiment also includes hunger and mood ratings to confirm the effectiveness of the manipulation. The modeling work is impressive in its rigor - the authors test 9 different variants of the DDM, including recent models like the mtDDM and maaDDM, as well as some completely new variants (maaDDM2phi and 2phisp). The model fits decisively favor the maaDDM2phi.

Weaknesses:

First, in examining some of the model fits in the supplements, e.g. Figures S9, S10, S12, S13, it looks like the "taste weight" parameter is being constrained below 1. Theoretically, I understand why the authors imposed this constraint, but it might be unfairly penalizing these models. In theory, the taste weight could go above 1 if participants had a negative weight on health. This might occur if there is a negative correlation between attractiveness and health and the taste ratings do not completely account for attractiveness. I would recommend eliminating this constraint on the taste weight.

Second, I'm not sure about the mediation model. Why should hunger change the dwell time on the chosen item? Shouldn't this model instead focus on the dwell time on the tasty option?

Third, while I do appreciate the within-participant design, it does raise a small concern about potential demand effects. I think the authors' results would be more compelling if they replicated when only analyzing the first session from each participant. Along similar lines, it would be useful to know whether there was any effect of order.

Fourth, the authors report that tasty choices are faster. Is this a systematic effect, or simply due to the fact that tasty options were generally more attractive? To put this in the context of the DDM, was there a constant in the drift rate, and did this constant favor the tasty option?

Fifth, I wonder about the mtDDM. What are the units on the "starting time" parameters? Seconds? These seem like minuscule effects. Do they align with the eye-tracking data? In other words, which attributes did participants look at first? Was there a correlation between the first fixations and the relative starting times? If not, does that cast doubt on the mtDDM fits? Did the authors do any parameter recovery exercises on the mtDDM?

Reviewer #2 (Public review):

Summary:

This study investigates the effect of a fed vs hungry state on food decision-making.

70 participants performed a computerized food choice task with eye tracking. Food images came from a validated set with variability in food attributes. Foods ranged from low caloric density unprocessed (fruits) to high caloric density processed foods (chips and cookies).

Prior to the choice task participants rated images for taste, health, wanting, and calories. In the choice task participants simply selected one of two foods. They were told to pick the one they preferred. Screens consisted of two food pictures along with their "Nutri-Score". They were told that one preferred food would be available for consumption at the end.

A drift-diffusion model (DDM) was fit to the reaction time values. Eye tracking was used to measure dwell time on each part of the monitor.

Findings:

Participants tended to select the item they had rated as "tastier", however, health also contributed to decisions.

Strengths:

The most interesting and innovative aspect of the paper is the use of the DDM models to infer from reaction time and choice the relative weight of the attributes.

Were the ratings redone at each session? E.g. were all tastiness ratings for the sated session made while sated? This is relevant as one would expect the ratings of tastiness and wanting to be affected by the current fed state.

Weaknesses:

My main criticism, which doesn't affect the underlying results, is that the labeling of food choices as being taste- or health-driven is misleading. Participants were not cued to select health vs taste. Studies in which people were cued to select for taste vs health exist (and are cited here). Also, the label "healthy" is misleading, as here it seems to be strongly related to caloric density. A high-calorie food is not intrinsically unhealthy (even if people rate it as such). The suggestion that hunger impairs making healthy decisions is not quite the correct interpretation of the results here (even though everyone knows it to be true). Another interpretation is that hungry people in negative calorie balance simply prefer more calories.

Reviewer #3 (Public review):

Summary:

This well-powered study tested the effects of hunger on value-based dietary decision-making. The main hypothesis was that attentional mechanisms guide choices toward unhealthier and tastier options when participants are hungry and are in the fasted state compared to satiated states. Participants were tested twice - in a fasted state and in a satiated state after consuming a protein shake. Attentional mechanisms were measured during dietary decision-making by linking food choices and reaction times to eye-tracking data and mathematical drift-diffusion models. The results showed that hunger makes high-conflict food choices more taste-driven and less health-driven. This effect was formally mediated by relative dwell time, which approximates attention drawn to chosen relative to unchosen options. Computational modeling showed that a drift-diffusion model, which assumed that food choices result from a noisy accumulation of evidence from multiple attributes (i.e., taste and health) and discounted non-looked attributes and options, best explained observed choices and reaction times.

Strengths:

This study's findings are valuable for understanding how energy states affect decision-making and provide an answer to how hunger can lead to unhealthy choices. These insights are relevant to psychology, behavioral economics, and behavioral change intervention designs.

The study has a well-powered sample size and hypotheses were pre-registered. The analyses comprised classical linear models and non-linear computational modeling to offer insight into putative cognitive mechanisms.

In summary, the study advances the understanding of the links between energy states and value-based decision-making by showing that depleting is powerful for shaping the formation of food preferences. Moreover, the computational analysis part offers a plausible mechanistic explanation at the algorithmic level of observed effects.

Weaknesses:

Some parts of the positioning of the hunger state manipulation and the interpretation of its effects could be improved.

On the positioning side, it does not seem like a 'bad' decision to replenish energy states when hungry by preferring tastier, more often caloric options. In this sense, it is unclear whether the observed behavior in the fasted state is a fallacy or a response to signals from the body. The introduction does mention these two aspects of preferring more caloric food when hungry. However, some ambiguity remains about whether the study results indeed reflect suboptimal choice behavior or a healthy adaptive behavior to restore energy stores.

On the interpretation side, previous work has shown that beliefs about the nourishing and hunger-killing effectiveness of drinks or substances influence subjective and objective markers of hunger, including value-based dietary decision-making, and attentional mechanisms approximated by computational models and the activation of cognitive control regions in the brain. The present study shows differences between the protein shake and a natural history condition (fasted, state). This experimental design, however, cannot rule between alternative interpretations of observed effects. Notably, effects could be due to (a) the drink's active, nourishing ingredients, (b) consuming a drink versus nothing, or (c) both.

Reviewer #1 (Public review):

In this meta-analysis, Ng and colleagues review the association between slow-oscillation spindle coupling during sleep and overnight memory consolidation. The coupling of these oscillations (and also hippocampal sharp-wave ripples) have been central to theories and mechanistic models of active systems consolidation, that posit that the coupling between ripples, spindles, and slow oscillations (SOs) coordinate and drive the coordinated reactivation of memories in hippocampus and cortex, facilitating cross-regional information and ultimately memory strengthening and stabilisation.

Given the importance that these coupling mechanisms have been given in theory, this is a timely and important contribution to the literature in terms of determining whether these theoretical assumptions hold true in human data. The results show that the timing of sleep spindles relative to the SO phase, and the consistency of that timing, predicted overnight memory consolidation in meta-analytic models. The overall amount of coupling events did not show as strong a relationship. The coupling phase in particular was moderated by a number of variables including spindle type (fast, slow), channel location (frontal, central, posterior), age, and memory type. The main takeaway is that fast spindles that consistently couple close to the peak of the SO in frontal channel locations are optimal for memory consolidation, in line with theoretical predictions.

I did not follow the logic behind including spindle amplitude in the meta-analysis. This is not a measure of SO-spindle coupling (which is the focus of the review), unless the authors were restricting their analysis of the amplitude of coupled spindles only. It doesn't sound like this is the case though. The effect of spindle amplitude on memory consolidation has been reviewed in another recent meta-analysis (Kumral et al, 2023, Neuropsychologia). As this isn't a measure of coupling, it wasn't clear why this measure was included in the present meta-analysis. You could easily make the argument that other spindle measures (e.g., density, oscillatory frequency) could also have been included, but that seems to take away from the overall goal of the paper which was to assess coupling.

At the end of the first paragraph of section 3.1 (page 13), the authors suggest their results "... further emphasise the role of coupling compared to isolated oscillation events in memory consolidation". This had me wondering how many studies actually test this. For example, in a hierarchical regression model, would coupled spindles explain significantly more variance than uncoupled spindles? We already know that spindle activity, independent of whether they are coupled or not, predicts memory consolidation (e.g., Kumral meta-analysis). Is the variance in overnight memory consolidation fully explained by just the coupled events? If both overall spindle density and coupling measures show an equal association with consolidation, then we couldn't conclude that coupling compared to isolated events is more important.

It was very interesting to see that the relationship between the fast spindle coupling phase and overnight consolidation was strongest in the frontal electrodes. Given this, I wonder why memory promoting fast spindles shows a centro-parietal topography? Surely it would be more adaptive for fast spindles to be maximally expressed in frontal sites. Would a participant who shows a more frontal topography of fast spindles have better overnight consolidation than someone with a more canonical centro-parietal topography? Similarly, slow spindles would then be perfectly suited for memory consolidation given their frontal distribution, yet they seem less important for memory.

The authors rightly note the issues with multiple comparisons in sleep physiology and memory studies. Multiple comparison issues arise in two ways in this literature. First are comparisons across multiple electrodes (many studies now use high-density systems with 64+ channels). Second are multiple comparisons across different outcome variables (at least 3 ways to quantify coupling (phase, consistency, occurrence) x 2 spindle types (fast, slow). Can the authors make some recommendations here in terms of how to move the field forward, as this issue has been raised numerous times before (e.g., Mantua 2018, Sleep; Cox & Fell 2020, Sleep Medicine Reviews for just a couple of examples). Should researchers just be focusing on the coupling phase? Or should researchers always report all three metrics of coupling, and correct for multiple comparisons? I think the use of pre-registration would be beneficial here, and perhaps could be noted by the authors in the final paragraph of section 3.5, where they discuss open research practices.

Reviewer #2 (Public review):

Summary:

This article reviews the studies on the relationship between slow oscillation (SO)-spindle (SP) coupling and memory consolidation. It innovatively employs non-normal circular linear correlations through a Bayesian meta-analysis. A systematic analysis of the retrieved studies highlighted that co-coupling of SO and the fast SP's phase and amplitude at the frontal part better predicts memory consolidation performance. I only have a few comments that I recommend are addressed.

Major Comments:

Regarding the Moderator of Age: Although the authors discuss the limited studies on the analysis of children and elders regarding age as a moderator, the figure shows a significant gap between the ages of 40 and 60. Furthermore, there are only a few studies involving participants over the age of 60. Given the wide distribution of effect sizes from studies with participants younger than 40, did the authors test whether removing studies involving participants over 60 would still reveal a moderator effect?

Reviewer #3 (Public review):

This manuscript presents a meta-analysis of 23 studies, which report 297 effect sizes, on the effect of SO-spindle coupling on memory performance. The analysis has been done with great care, and the results are described in great detail. In particular, there are separate analyses for coupling phase, spindle amplitude, coupling strength (e.g., measured by vector length or modulation index), and coupling percentage (i.e., the percentage of SPs coupled with SOs). The authors conclude that the precision and strength of coupling showed significant correlations with memory retention.

There are two main points where I do not agree with the authors.

First, the authors conclude that "SO-SP coupling should be considered as a general physiological mechanism for memory consolidation". However, the reported effect sizes are smaller than what is typically considered a "small effect" (0.10<br /> Second, the study implements state-of-the-art Bayesian statistics. While some might see this as a strength, I would argue that it is the greatest weakness of the manuscript. A classical meta-analysis is relatively easy to understand, even for readers with only a limited background in statistics. A Bayesian analysis, on the other hand, introduces a number of subjective choices that render it much less transparent. This becomes obvious in the forest plots. It is not immediately apparent to the reader how the distributions for each study represent the reported effect sizes (gray dots). Presumably, they depend on the Bayesian priors used for the analysis. The use of these priors makes the analyses unnecessarily opaque, eventually leading the reader to question how much of the findings depend on subjective analysis choices (which might be answered by an additional analysis in the supplementary information). However, most of the methods are not described in sufficient detail for the reader to understand the proceedings. It might be evident for an expert in Bayesian statistics what a "prior sensitivity test" and a "posterior predictive check" are, but I suppose most readers would wish for a more detailed description. However, using a "Markov chain Monte Carlo (MCMC) method with the no-U-turn Hamiltonian Monte Carlo (HMC) sampler" and checking its convergence "through graphical posterior predictive checks, trace plots, and the Gelman and Rubin Diagnostic", which should then result in something resembling "a uniformly undulating wave with high overlap between chains" is surely something only rocket scientists understand. Whether this was done correctly in the present study cannot be ascertained because it is only mentioned in the methods and no corresponding results are provided. This kind of analysis seems not to be made to be intelligible to the average reader. It follows a recent trend of using more and more opaque methods. Where we had to trust published results a decade ago because the data were not openly available, today we must trust the results because the methods can no longer be understood with reasonable effort.

In one point the method might not be sufficiently justified. The method used to transform circular-linear r (actually, all references cited by the authors for circular statistics use r² because there can be no negative values) into "Z_r", seems partially plausible and might be correct under the H0. However, Figure 12.3 seems to show that under the alternative Hypothesis H1, the assumptions are not accurate (peak Z_r=~0.70 for r=0.65). I am therefore, based on the presented evidence, unsure whether this transformation is valid. Also, saying that Z_r=-1 represents the null hypothesis and Z_r=1 the alternative hypothesis can be misinterpreted, since Z_r=0 also represents the null hypothesis and is not half way between H0 and H1.

Joint Public Review:

Summary:

Hossain and coworkers investigate the mechanisms of recognition of xCas9, a variant of Cas9 with expanded targeting capability for DNA. They do so by using molecular simulations and combining different flavors of simulation techniques, ranging from long classical MD simulations, to enhanced sampling, to free energy calculations of affinity differences. Through this, the authors are able to develop a consistent model of expanded recognition based on the enhanced flexibility of the protein receptor.

Strengths:

The paper is solidly based on the ability of the authors to master molecular simulations of highly complex systems. In my opinion, this paper shows no major weaknesses. The simulations are carried out in a technically sound way. Comparative analyses of different systems provide valuable insights, even within the well-known limitations of MD. Plus, the authors further investigate why xCas9 exhibits improved recognition of the TGG PAM sequence compared to SpCas9 via well-tempered metadynamics simulations focusing on the binding of R1335 to the G3 nucleobase and the DNA backbone in both SpCas9 and xCas9. In this context, the authors provide a free-energy profiling that helps support their final model.

The implementation of FEP calculations to mimic directed evolution improvement of DNA binding is also interesting, original and well-conducted.

Overall, my assessment of this paper is that it represents a strong manuscript, competently designed and conducted, and highly valuable from a technical point of view.

Weaknesses:

To make their impact even more general, the authors may consider expanding their discussion on entropic binding to other recent cases that have been presented in the literature recently (such as e.g. the identification of small molecules for Abeta peptides, or the identification of "fuzzy" mechanisms of binding to protein HMGB1). The point on flexibility helping adaptability and expansion of functional properties is important, and should probably be given more evidence and more direct links with a wider picture.

Reviewer #1 (Public review):

Summary:

The work provides more evidence of the importance of data quality and representation for ligand-based virtual screening approaches. The authors have applied different machine learning (ML) algorithms and data representation using a new dataset of BRAF ligands. First, the authors evaluate the ML algorithms, and demonstrate that independently of the ML algorithm, predictive and robust models can be obtained in this BRAF dataset. Second, the authors investigate how the molecular representations can modify the prediction of the ML algorithm. They found that in this highly curated dataset the different molecule representations are adequate for the ML algorithms since almost all of them obtain high accuracy values, with Estate fingerprints obtaining the worst performing predictive models and ECFP6 fingerprints producing the best classificatory models. Third, the authors evaluate the performance of the models on subsets of different composition and size of the BRAF dataset. They found that given a finite number of active compounds, increasing the number of inactive compounds worsens the recall and accuracy. Finally, the authors analyze if the use of "less active" molecules affect the model's predictive performance using "less active" molecules taken from ChEMBl Database or using decoys from DUD-E. As results, they found that the accuracy of the model falls as the number of "less active" examples in the training dataset increases while the implementation of decoys in the training set generates results as good as the original models or even better in some cases. However, the use of decoys in the training set worsens the predictive power in the test sets that contain active and inactive molecules.

Strengths:

This is a highly relevant topic in medicinal chemistry and drug discovery. The manuscript is well-written, with a clear structure that facilitates easy reading, and it includes up-to-date references. The hypotheses are clearly presented and appropriately explored. The study provides valuable insights into the importance of deriving models from high-quality data, demonstrating that, when this condition is met, complex computational methods are not always necessary to achieve predictive models. Furthermore, the generated BRAF dataset offers a valuable resource for medicinal chemists working in ligand-based virtual screening.

Weaknesses:

While the work highlights the importance of using high-quality datasets to achieve better and more generalizable results, it does not present significant novelty, as the analysis of training data has been extensively studied in chemoinformatics and medicinal chemistry. Additionally, the inclusion of "AI" in the context of data-centric AI is somewhat unclear, given that the dataset curation is conducted manually, selecting active compounds based on IC50 values from ChEMBL and inactive compounds according to the authors' criteria.

Moreover, the conclusions are based on the analysis of only two high-quality datasets. To generalize these findings, it would be beneficial to extend the analysis to additional high-quality datasets (at least 10 datasets for a robust benchmarking exercise).

A key aspect that could be improved is the definition of an "inactive" compound, which remains unclear. In the manuscript, it is stated:

• "The inactives were carefully selected based on the fact that they have no known pharmacological activity against BRAF."<br /> Does the lack of BRAF activity data necessarily imply that these compounds are inactive?<br /> • "We define a compound as 'inactive' if there are no known pharmacological assays for the said compound on our target, BRAF."<br /> However, in the authors' response, they mention:<br /> • "We selected certain compounds that we felt could not possibly be active against BRAF, such as ligands for neurotransmitter receptors, as inactives."

Given that the definition of "inactive" is one of the most critical concepts in the study, I believe it should be clearly and consistently explained.

Lastly, while statistical comparison is not always common in machine learning, it would greatly enhance the value of this work, especially when comparing models with small differences in accuracy.

Reviewer #2 (Public review):

Summary:

The authors explored the importance of data quality and representation for ligand-based virtual screening approaches. I believe the results could be of potential benefit to the drug discovery community, especially to those scientists working in the field of machine learning applied to drug research. The in silico design is comprehensive and adequate for the proposed comparisons.

This manuscript by Chong A. et al describes that it is not necessary to resort to the use of sophisticated deep learning algorithms for virtual screening, since based on their results considering conventional ML may perform exceptionally well if feeded by the right data and molecular representations.

The article is interesting and well-written. The overview of the field and the warning about dataset composition are very well thought-out and should be of interest to a broad segment of the AI in drug discovery readership. This article further highlights some of the considerations that need to be taken into consideration for the implementation of data-centric AI for computer-aided drug design methods.

Strengths:

This study contributes significantly to the field of machine learning and data curation in drug discovery. The paper is, in general, well-written and structured. However, in my opinion, there are some suggestions regarding certain aspects of the data analyses.

Weaknesses:

The conclusions drawn in the study are based on the analysis of a two dataset. The authors chose BRAF as an example in this study, and expanded with BACE-1 dataset; however a benchmark with several targets would be suitable to evaluate reproducibility or transferability of the method. One concern could be the applicability of the method in other targets.

Reviewer #3 (Public review):

Summary:

The authors presented a data-centric ML approach for virtual ligand screening. They used BRAF as an example to demonstrate the predictive power of their approach.

Strengths:

The performance of predictive models in this study is superior (nearly perfect) with respect to exiting methods.

Comments on revisions:

In the revised manuscript, the presented approach has been robustly tested and can be very useful for ligand prediction.

Joint Public Review:

Riva et al uncovered the neural substrate underlying the oviposition rhythm in Drosophila melanogaster using a novel device that automates egg collection from individual mated females over the course of multiple days. By systematically knocking down the clock gene period in specific clock neurons the authors show that three cryptochrome (cry) positive dorso-lateral neurons (LNds) present in each hemisphere of the fly brain are critical to generating a female, sex-specific rhythm in oviposition. Interestingly, these neurons are not essential for freerunning locomotor activity. By contrast, the LNvs (lateral ventral neurons), which are essential for freerunning locomotor activity rhythmicity, were not involved in controlling the circadian rhythmicity of oviposition. Thus, this work has identified the first truly sex-specific circadian circuit in Drosophila. Using available Drosophila hemibrain connectome data they identify bidirectional connections between cry-expressing LNd and oviposition-related neurons.

Strengths:

This paper established a new semi-automatic device to register egg-laying activity, in Drosophila and found a specific role for a subset of clock neurons in the control of a female-specific circadian behavior. They also lay the groundwork for understanding how these neurons are connected to the neurons that control egg laying.

Weaknesses:

(1) Controls for the genetic background are incomplete, leaving open the possibility that the observed oviposition timing defects may be due to targeted knockdown of the period (per) gene but from the GAL4, Gal80, and UAS transgenes themselves. To resolve this issue the authors should determine the egg-laying rhythms of the relevant controls (GAL4/+, UAS-RNAi/+, etc); this only needs to be done for those genotypes that produced an arrhythmic egg-laying rhythm.

(2) Reliance on a single genetic tool to generate targeted disruption of clock function leaves the study vulnerable to associated false positive and false negative effects: a) The per RNAi transgene used may only cause partial knockdown of gene function, as suggested by the persistent rhythmicity observed when per RNAi was targeted to all clock neurons. This could indicate that the results in Fig 2C-H underestimate the phenotypes of targeted disruption of clock function. b) Use of a single per RNAi transgene makes it difficult to rule out that off-target effects contributed significantly to the observed phenotypes. We suggest that the authors repeat the critical experiments using a separate UAS-RNAi line (for period or for a different clock gene), or, better yet, use the dominant negative UAS-cycle transgene produced by the Hardin lab (https://doi.org/10.1038/22566).

(3) The egg-laying profiles obtained show clear damping/decaying trends which necessitates careful trend removal from the data to make any sense of the rhythm. Further, the detrending approach used by the authors is not tested for artefacts introduced by the 24h moving average used.

(4) According to the authors the oviposition device cannot sample at a resolution finer than 4 hours, which will compel any experimenter to record egg laying for longer durations to have a suitably long time series which could be useful for circadian analyses.

(5) Despite reducing the interference caused by manually measuring egg-laying, the rhythm does not improve the signal quality such that enough individual rhythmic flies could be included in the analysis methods used. The authors devise a workaround by combining both strongly and weakly rhythmic (LSpower > 0.2 but less than LSpower at p < 0.05) data series into an averaged time series, which is then tested for the presence of a 16-32h "circadian" rhythm. This approach loses valuable information about the phase and period present in the individual mated females, and instead assumes that all flies have a similar period and phase in their "signal" component while the distribution of the "noise" component varies amongst them. This assumption has not yet been tested rigorously and the evidence suggests a lot more variability in the inter-fly period for the egg-laying rhythm.

(6) This variability could also depend on the genotype being tested, as the authors themselves observe between their Canton-S and YW wild-type controls for which their egg-laying profiles show clearly different dynamics. Interestingly, the averaged records for these genotypes are not distinguishable but are reflected in the different proportions of rhythmic flies observed. Unfortunately, the authors also do not provide further data on these averaged profiles, as they did for the wild-type controls in Figure 1, when they discuss their clock circuit manipulations using perRNAi. These profiles could have been included in Supplementary figures, where they would have helped the reader decide for themselves what might have been the reason for the loss of power in the LS periodogram for some of these experimental lines.

(7) By selecting 'the best egg layers' for inclusion in the oviposition analyses an inadvertent bias may be introduced and the results of the assays may not be representative of the whole population.

(8) An approach that measures rhythmicity for groups of individual records rather than separate individual records is vulnerable to outliers in the data, such as the inclusion of a single anomalous individual record. Additionally, the number of individual records that are included in a group may become a somewhat arbitrary determinant for the observed level of rhythmicity. Therefore, the experimental data used to map the clock neurons responsible for oviposition rhythms would be more convincing if presented alongside individual fly statistics, in the same format as used for Figure 1.

(9) The features in the experimental periodogram data in Figures 3B and D are consistent with weakened complex rhythmicity rather than arrhythmicity. The inclusion of more individual records in the groups might have provided the added statistical power to demonstrate this. Graphs similar to those in 1G and 1I, might have better illustrated qualitative and quantitative aspects of the oviposition rhythms upon per knockdown via MB122B and Mai179; Pdf-Gal80.

Wider context:

The study of the neural basis of oviposition rhythms in Drosophila melanogaster can serve as a model for the analogous mechanisms in other animals. In particular, research in this area can have wider implications for the management of insects with societal impact such as pests, disease vectors, and pollinators. One key aspect of D. melanogaster oviposition that is not addressed here is its strong social modulation (see Bailly et al.. Curr Biol 33:2865-2877.e4. doi:10.1016/j.cub.2023.05.074). It is plausible that most natural oviposition events do not involve isolated individuals, but rather groups of flies. As oviposition is encouraged by aggregation pheromones (e.g., Dumenil et al., J Chem Ecol 2016 https://link.springer.com/article/10.1007/s10886-016-0681-3) its propensity changes upon the pre-conditioning of the oviposition substrates, which is a complication in assays of oviposition rhythms that periodically move the flies to fresh substrate.

Reviewer #1 (Public review):

Summary:

The authors demonstrate a fully unsupervised, high throughput (meaning very low human interaction required) approach to quantifying marmoset behavior in unconstrained environments.

Strengths:

The authors provide an approach that is scalable, easy to implement at face value, and highly robust. Currently, most behavioral quantification approaches do not work well on marmosets, or the published examples that do look promising do not scale towards high throughput as demonstrated by the authors.

While marmosets can certainly be a useful translational research model devoid of free behavior quantification, the authors make a compelling point about how this approach can be useful in the study of treatments of emerging marmoset disease models.

Overall this is a very exhaustive manuscript that overcomes significant shortcomings in previous work and speaks highly to the use of marmosets for unconstrained behavioral and neural assessment.

Weaknesses:

Recording marmoset behavior with a 60Hz frame rate is a significant limitation to the approach which is hopefully easily alleviated in the future through better cameras/reconstruction pipelines. Marmosets (in the reviewers' experience) have a lot of motion energy above the 30Hz nyquist limit imposed by this system and are agile to a degree requiring higher frame rates.

The manuscript neglects recent approaches to non-human primate behavioral quantification from other groups that should be included. Simians are simians after all.

As a minor weakness, this reviewer would have liked to see code shared for the reviewers to evaluate, especially pertaining to the high throughput and robustness of the approach.

Reviewer #2 (Public review):

In this manuscript, Menegas et al. classify the "control" behavior of captive marmosets. They combine behavioral screening from video recordings with audio and neural recordings (from the striatum) to better define what can be considered a typical behavioral repertoire for captive marmoset monkeys. A range of analyses is presented, investigating various aspects of behavior, such as social interactions and the detection of atypical individuals.

The manuscript is compelling in many respects, especially due to the richness of the dataset and the breadth of analyses presented. However, a significant issue with the manuscript lies in its writing: the results are conveyed in an overly succinct and superficial manner, and the "Methods" section is nearly absent. Key concepts are often undefined, and the mathematical details underlying the figures are not explained, leaving readers to guess the authors' approach.

Another issue is the vague use of the term "natural behavior." All data presented here appear to have been collected in small cages with limited climbing opportunities and enrichment. Thus, the authors should refrain from using "natural" to describe these conditions.

Below, we elaborate further on the lack of methodological detail. Based on these issues, we believe the manuscript, in its current form, does not meet the scientific standards necessary for proper review. We strongly encourage the authors to undertake an extensive revision.

Major Revision Points:

The methods and results require significantly more detail. A scientific publication should provide readers with enough information to reproduce the study. Here, the detail level is far too low to fully understand, or reproduce, the study, and in many instances, readers are left to guess how the figure panels were produced. Below is a non-exhaustive list of examples illustrating these issues:

(1) "we temporarily placed horizontal cage dividers to reduce the total cage size during data collection": What were the resulting (and initial) cage dimensions?

(2) "After training the network, we hierarchically clustered the latent space": What is the latent space? Based on Figure 2a, it appears related to the network's recurrent layer, but this is not clarified in the text.

(3) Alpha and perplexity parameters: Please define these terms. Since these concepts appear fundamental, readers should not have to consult external references.

(4) "We then traced cluster identities across hierarchical levels": What are hierarchical levels?

(5) "To understand how the input time series data was weighed in the bottleneck layer of the model": What is the bottleneck layer?

(6) "we measured the average attention allocation to previous time points": The authors should define "attention allocation."

(7) "we compared each neuron's firing rate distribution to shuffled data based on the overall frequency of each behavior during the session": This description is insufficient to understand the analysis.

(8) "we hierarchically clustered neurons according to their firing rate enrichment maps": No mathematical explanation is provided for neuron clustering, nor is the concept of a "firing rate enrichment map" clarified.

(9) "Cluster 4 showed higher activity when neurons were 'alone' or 'active'": This is vague and uses unclear jargon (e.g., "neurons alone"). Additionally, no mathematical explanation is provided for assigning neuronal activity to behavioral states.

(10) Figure 3f, right-side panels: The analysis seems to involve cage mate positioning, yet no description is provided.

(11) "we used motion watches to measure activity across all hours": Are these motion-sensitive watches physically attached to the animals? The methodology should be described, including data analysis details.

This list could continue, but we trust the authors understand the point. There is a wealth of analyses and information in this study, but the descriptions are too superficial. We understand that fully describing each analysis may require significant rewriting, including supplementary figures, and will likely make the manuscript longer. This is entirely acceptable, as the ideas presented here are worth the added rigor.

"Natural behavior": Typically, the term "natural" suggests that the dataset reflects the range of behaviors exhibited by animals in the wild. Here, however, recordings were made in a small cage with limited climbing opportunities and enrichment. Under these conditions, it's hard to justify describing the behavior as "natural". In a project aimed at classifying the behavioral repertoire of marmoset monkeys and making this dataset accessible to other laboratories, it would be helpful to include more detailed information about the animals' housing conditions. This might include cage sizes, temperature, humidity, and details on food quantities, quality, and feeding times.

Correlation versus causation: In the section titled "Large-scale data collection reveals variability across days and correlation between cagemates," the authors conclude: "Overall, these results indicate that measurements of animals' behavioral traits depend heavily on their social environment." This interpretation seems incorrect. We know that animal behavior varies throughout the day, with activity peaks typically occurring in the morning and afternoon. Such factors, or other external influences, could induce correlations between animals that are not caused by social interactions.

Figure 4g: What are we intended to conclude from this analysis?

Figure 5: Please specify the type of calls analyzed. For example, did you analyze only long-distance calls (aka 'loud phees' or 'shrills')? In "We split the audio data into 5-minute (non-continuous) segments and found that the average call rate in these segments varied from 0 calls per minute to 60 calls per minute (Fig. 5d-e)," does the call rate refer to individual animals or the entire cage?

"This implies that a high rate of calls in a room can interrupt animals during social resting states and cause them to preferentially exhibit more active/attentive states." Does it? This could simply indicate that more active animals produce more calls.

"We recorded neural activity in the striatum because it is known to contain diverse signals related to movement and social interactions." While I understand that the authors intend to publish neural data separately, a brief discussion of the striatum's role here would be helpful.

Reviewer #1 (Public review):

Summary:

Ren et al developed a novel computational method to investigate cell evolutionary trajectory for scRNA-seq samples. This method, MGPfact, estimates pseudotime and potential branches in the evolutionary path through explicitly modeling the bifurcations in a Gaussian process. They benchmarked this method using synthetic as well as real world samples and showed superior performance for some of the tasks in cell trajectory analysis. They further demonstrated the utilities of MGPfact using single cell RNA-seq samples derived from microglia or T cells and showed that it can accurately identify the differentiation timepoint and uncover biologically relevant gene signatures.

Strengths:

Overall I think this is a useful new tool that could deliver novel insights for the large body of scRNA-seq data generated in the public domain. The manuscript is written is a logical way and most parts of the method are well described.

Comments on revisions:

In this revision, the authors have sufficiently addressed all of my concerns. I don't have any follow-up comments.

Reviewer #2 (Public review):

Summary of the manuscript:

Authors present MGPfactXMBD, a novel model-based manifold-learning framework designed to address the challenges of interpreting complex cellular state spaces from single-cell RNA sequences. To overcome current limitations, MGPfactXMBD factorizes complex development trajectories into independent bifurcation processes of gene sets, enabling trajectory inference based on relevant features. As a result, it is expected that the method provides a deeper understanding of the biological processes underlying cellular trajectories and their potential determinants.

MGPfactXMBD was tested across 239 datasets, and the method demonstrated similar to slightly superior performance in key quality-control metrics to state-of-the-art methods. When applied to case studies, MGPfactXMBD successfully identified critical pathways and cell types in microglia development, validating experimentally identified regulons and markers. Additionally, it uncovered evolutionary trajectories of tumor-associated CD8+ T cells, revealing new subtypes with gene expression signatures that predict responses to immune checkpoint inhibitors in independent cohorts.

Overall, MGPfactXMBD represents a relevant tool in manifold-learning for scRNA-seq data, enabling feature selection for specific biological processes and enhancing our understanding of the biological determinants of cell fate.

Summary of the outcome:

The novel method addresses core state-of-the-art questions in biology related to trajectory identification. The design and the case studies are of relevance.

Comments on revisions:

The authors have addressed all my previous comments to satisfaction.

Reviewer #1 (Public review):

This study is focused on a population of neurons in the mouse parasubthalamic nucleus (pSTN) that express Tackhykinin1 (Tac1). This gene has been used before to target pSTN for functional circuit studies because it is fairly selective for pSTN in this region, though it targets only a subset of pSTN neurons. Prior work has shown that activity in these neurons can impact motivated behaviors, including feeding and drinking behaviors, and that their activity is associated with aversion or avoidance behaviors. While not breaking much new ground, this study adds to that work by making use of a 2-way active avoidance assay, where a CS predicts a US (footshock), that the mice can escape. Using fiber photometry the authors show convincing evidence that Tac1 neurons in pSTN increase their activity in response to a US footshock, and that after some pairings the neurons will start responding to the CS too, though to a lesser extent than the US. Their most important data shows that either ablation or optogenetic inhibition of these cells can hugely block the active avoidance (escape) behavior, suggesting these neurons are key for the performance of this task, which they interpret as key for learning the task (but see more below). They show that optogenetic stimulation is aversive in a real-time place assay, and when paired with footshock can enhance active avoidance behavior. Finally, they show that Tac1 pSTN axons in PVT recapitulate these effects while showing that axons in CEA or PBN may only recapitulate some of these effects (more below). Overall I think the data is solid and shows that the activity of Tac1 pSTN neurons in the 2 way active avoidance task is causally related to avoidance behavior in the direction that would be predicted by recent literature. However, I think the authors overstate the conclusions in the title, abstract, and text. I do not think the data make a strong case for a role for these cells in learning, at least in any classical sense, as used in the title and abstract and elsewhere. Also the statement in the abstract that the pSTN mediates its effects 'differentially' through its downstream targets is not convincingly supported by data.

Major concerns:

(1) The authors infer that the activity in the Tac1 pSTN neurons is necessary for aversive or avoidance 'learning'. But this is not well defined, what exactly does that mean and what types of evidence would support or falsify such a hypothesis? Moreover, the authors show convincingly, and in line with prior reports, that these cells are activated by aversive stimuli (here footshock), and that activation of these cells is sufficient to induce avoidance behavior. Because manipulation of these cells can serve as a primary negative reinforcer, it becomes even more challenging and important to explain how experiments that manipulate these cells while measuring behavior/performance can discriminate between changes in: (1) primary aversion, (2) motivation to avoid, (3) associative learning, or (4) memory/retrieval. The authors seem to favor #3, but they don't make a clear case for this point of view or else what they mean by 'avoidance learning'. In my opinion, the data do not well discriminate between possibilities 1 through 3. The authors should clarify their logic and temper their conclusions throughout.

(2) Abstract line 37 is not well supported. The authors focus mostly on pSTN projections to PVT and show that the measurements or manipulation of these axons recapitulates the effects seen with pSTN cell bodies. The authors do fewer studies of axons in CeA and PBN, but do find that they can recapitulate the effects with opsin inhibition, but detect no effects with opsin stimulation. However, the lack of effect with opsin stimulation in Figure S7a-e proves very little on its own. It could be technical, due to inadequate expression or functional efficacy. It is not supported by histological and functional evidence that the manipulation was effective. Overall I can only conclude that the projections to these regions might be very similar (based on the inhibition data), or might be a little different. The data are thus inadequate to support the authors' claim that the pSTN mediates learning differentially through its downstream targets.

Other concerns:

(3) Line 93 is not adequately supported by data in Figure 1b. Additional data is needed that shows expression across cases, including any spread that may be visible when zooming out from pSTN. Additional methods are needed to indicate what exclusion criteria were applied and how many mice were excluded. These data could help support the statement on line 93 that expression was largely restricted within pSTN.

(4) From the results and methods it is not clear where the GFP signal would come from in the mice expressing Casp3 for the ablation studies. It is therefore not clear if the absence of GFP should be taken as evidence of cell loss. For example, it is not clear if multiple vectors were used, if volumes and titers were carefully matched between control groups, or if competition/occlusion between AAVs could be ruled out. It is also not clear how this was quantified, that is how many sections/subjects and how counting was done. It is not clear how long was waited between the AAV infusion, behavior, and euthanasia, perhaps especially important for the ablation done after avoidance learning occurred.

(5) The authors should consider showing individual measurements and not just mean/sem wherever feasible, for example, to support the statement on line 141 that 'all ablated mice showed...'.

(6) S3 is an important control for interpreting data in Figure 2d-i. Something similar is needed to support the inferences made in 2j-u. The very strong effect showing a lack of active avoidance in response to CS or the US when pSTN Tac1 neurons are inhibited during CS or during US suggests that something gross may be going on, such as a gross motor or sensory response that supersedes the effect of footshock. The authors do not comment on whether there are any gross behavioral responses to the inhibition, but an experiment as in S3 is needed, for example, to show that behavior is intact during pSTN inhibition if delivered after the mice already learned to associate CS with US.

(7) The authors use 100 shocks of 0.8 mA for 7 days. I think this is quite strong and in the pSTN inhibition experiments it seems to be functionally 'inescapable' and could thus produce behaviors similar to 'learned helplessness'. Can the authors consider whether this might contribute to the striking findings they observed in their opsin inhibition assays?

(8) The description of the experiment in S5 is inadequate. What are the adjacent areas? Where do the authors see spread? The use of the word 'case' in figure S5 implies an individual case, but the legend says 5 mice were used for 'case 1' and 3 mice were used for 'case 2'. The use of the word 'off-target in the figure implies that the expression was of the intended target. But the text of results and methods implies it was intentional targeting of unnamed and unshown adjacent regions. This should be clarified.

(9) The authors suggest the CPA study is divergent from Serra et al 2023. Though I think this could be due to how the conditioning was done, it would be helpful for the authors to include less processed data. This would aid in possible interpretations for any divergences across studies. Can the authors include raw data (in seconds of time spent) in each compartment for each group across baseline and test days?

Reviewer #2 (Public review):

Summary:

The manuscript by Hu et. al presents a clearly-designed examination of the role of tachykinin1-expressing neurons in the parasubthalamic nucleus of the lateral posterior hypothalamus (PTSN) in active avoidance learning. These glutamatergic neurons have previously been implicated in responding to negative stimuli. This manuscript expands the current understanding of PTSNTac1 neurons in learned responses to threats by showing their role in encoding and mediating the active avoidance response. The authors first use bulk fiber photometry imaging to show the encoding of the active avoidance procedure, followed by cell-type specific manipulations of PTSNTac1 neurons during active avoidance. Finally, they show that encoding and mediation of active avoidance in a downstream target of PTSNTac1 neurons, the PVT/intermediodorsal nuclei of the dorsal thalamus (IMD), has the same effect as what was discovered in the cell body. This contrasts other output regions of the PTSN, such as the PBN and CeA, which were not found to promote active avoidance learning. The experiments presented were well-designed to support the conclusions of the authors, however, the manuscript is missing several key control experiments and supplemental information to support their main findings.

Strengths:

The manuscript provides information on a brain region and downstream target that mediates active avoidance learning. The manuscript provides valuable information via necessity and sufficiency experiments to show the role of the population of interest (PTSNTac1 neurons) in active avoidance learning. The authors also performed most behavior experiments in male and female mice, with adequate power to address potential sex differences in the control of active avoidance by PTSNTac1 neurons. Finally, the manuscript provides valuable information about the specificity of the PTSNTac1 downstream target in regulating active avoidance learning, identifying the PVT/intermediodorsal nuclei of the dorsal thalamus as the key target and ruling out the PBN and CeA.

Weaknesses:

However, several main conclusions of the paper must be interpreted carefully due to missing or inadequate control experiments and histological verification.

(1) Inadequate presentation of viral localization. The authors state that expression was "largely restricted within PSTN" however there is no quantification of the amount of viral expression beyond the target region. Given that Tac1 is expressed in neighboring regions, it is critical to show the viral expression and fiber implant location data for all animals included in the figures. Furthermore, criteria for inclusion and exclusion based on mistargeting should be delineated. This should also be clearly outlined for the experiments in Figure S5, where "behavioral effects of activation of sparsely Tac1-expressing neurons in two adjacent areas of PSTN" was tested but the location of viral expression in those cases is unclear.

(2) Lack of motion artifact correction with isosbestic signal for GCamp recordings. It is appreciated that the authors included a separate EGFP-expressing group to compare to the GCamp-expressing group, however, additional explanation is required for the methods used to analyze the raw fluorescent signal. Namely, were fluorescent signals isosbestic-corrected prior to calculating ΔF/F? If no isosbestic signal was used to correct motion artifacts within a recording session, additional explanation is needed to explain how this was addressed. The lack of motion artifacts in the EGFP signal in a separate cohort is inadequate to answer this caveat as motion artifacts are within-animal.

(3) Missing control experiment demonstrating intact locomotor performance in caspase ablation experiments. The authors use caspase ablation of PTSNTac1 neurons prior to active avoidance learning to appraise the necessity of this cell population. However, a control experiment showing intact locomotor ability in ablated mice was not performed.

(4) Missing control experiment demonstrating [lack of] valence with PTSN silencing manipulations. The authors performed a real-time and conditioned place preference experiments for ChR2-expressing mice (Fig 3M) and found stimulation to be negatively-valenced and generate an aversive memory, respectively. Absent this control experiment with silencing, an alternative conclusion remains possible that optogenetic silencing via GtACR2 created nonspecific location preferences in the active avoidance apparatus, confounding the interpretation of those results.

(5) Incomplete analysis of sex differences. Data in female mice is conspicuously missing from inhibition experiments. The rationale for exclusion from this dataset would be useful for the interpretation of the other noted sex differences.

Reviewer #3 (Public review):

Summary:

This study by Hu et al. examined the role of tachykinin1 (Tac1)-expressing neurons in the para subthalamic nucleus (PSTH) in active avoidance of electric shocks. Bulk recording of PSTH Tac1 neurons or axons of these neurons in PVT showed activation of a shock-predicting tone and shock itself. Ablation of these neurons or optogenetic manipulation of these neurons or their projection to PVT suggests the causality of this pathway with the learning of active avoidance.

Strengths:

This work found an understudied pathway potentially important for active avoidance of electric shocks. Experiments were thoroughly done and the presentation is clear. The amount of discussion and references are appropriate.

Weaknesses:

Critical control experiments are missing for most experiments, and statistical tests are not clear or not appropriate in most parts. Details are shown below.

(1) There are some control experiments missing. Notably, optogenetic manipulation is not verified in any experiments. It is important to verify whether neural activation with optogenetic activation is at the physiological level or supra-physiological level, and whether optogenetic inhibition does not cause unwanted activity patterns such as rebound activation at the critical time window.

(2) Neural ablation with caspase was confirmed by GFP expression. However, from the present description, a different virus to express EITHER caspase or GFP was injected, and then the numbers of GFP-expressing neurons were compared. It is not clear how this can detect ablation.

(3) In many places, statistical approaches are not clear from the present figures, figure legends, and Methods. It seems that most statistics were performed by pooling trials, but it is not described, or multiple "n" are described. For example, it is explicitly mentioned in Figure 4H, "n = 3 mice, n = 213 avoidance trials and n = 87 failure trials". The authors should not pool trials, but should perform across-animal tests in this and other figures, and "n" for statistical tests should be clearly described in each plot.

(4) It is also unclear how the test types were selected. For example, in Figure 1K and O with similar datasets, one is examined by a paired test and the other is by an unpaired test. Since each animal has both early vs late trials, and avoidance vs failure trials, paired tests across animals should be performed for both.

(5) It is also strange to show violin plots for only 6 animals. They should instead show each dot for each animal, connected with a line to show consistent increases of activity in late vs early trials and avoidance vs failure trials.

(6) To tell specificity in avoidance learning, it is better to show escape in the current trials with optogenetic manipulation.

(7) For place aversion, % time decrease across days was tested. It is better to show the original number before normalization, as well.

(8) For anatomical results in Figure S6, it is important to show images with lower magnification, too.

(9) Inactivation of either pathway from PSTH to PBN or to CeA also inhibits active avoidance, but the authors conclude that these effects are "partial" compared to the inactivation of PSTH to PVT. It is not clear how the effects were compared since the effects of PSTH-CeA inactivation are quite strong, comparable to PSTH-PVT inactivation by eye. They should quantify the effects to conclude the difference.

(10) Supplementary table 1: as mentioned above, n for statistical tests should be clearer.

Reviewer #1 (Public review):

Summary:

The investigators in this study analyzed the dataset assembly from 540 Salmonella isolates, and those from 45 recent isolates from Zhejiang University of China. The analysis and comparison of the resistome and mobilome of these isolates identified a significantly higher rate of cross-region dissemination compared to localized propagation. This study highlights the key role of the resistome in driving the transition and evolutionary history of S. Gallinarum.

Strengths:

The isolates included in this study were from 16 countries in the past century (1920 to 2023). While the study uses S. Gallinarun as the prototype, the conclusion from this work will likely apply to other Salmonella serotypes and other pathogens.

Weaknesses:

While the isolates came from 16 countries, most strains in this study were originally from China.

Comments on revisions:

This reviewer is happy with the detailed responses from the authors regarding revising this manuscript. I do not have further comments.

Reviewer #2 (Public review):

Summary:

The authors sequence 45 new samples of S. Gallinarum, a commensal Salmonella found in chickens, which can sometimes cause disease. They combine these sequences with around 500 from public databases, determine the population structure of the pathogen, and coarse relationships of lineages with geography. The authors further investigate known anti-microbial genes found in these genomes, how they associate with each other, whether they have been horizontally transferred, and date the emergence of clades.

Strengths:

- It doesn't seem that much is known about this serovar, so publicly available new sequences from a high burden region are a valuable addition to the literature.<br /> - Combining these sequences with publicly available sequences is a good way to better contextualise any findings.<br /> - The genomic analyses have been greatly improved since the first version of the manuscript, and appropriately analyse the population and date emergence of clades.<br /> - The SNP thresholds are contextualised in terms of evolutionary time.<br /> - The importance and context of the findings are fairly well described.

Weaknesses:

- There are still a few issues with the genomic analyses, although they no longer undermine the main conclusions:

(1) Although the SNP distance is now considered in terms of time, the 5 SNP distance presented still represents ~7yrs evolution, so it is unlikely to be a transmission event, as described. It would be better to use a much lower threshold or describe the interpretation of these clusters more clearly. Bringing in epidemiological evidence or external references on the likely time interval between transmissions would be helpful.

(2) The HGT definition has not fundamentally been changed and therefore still has some issues, mainly that vertical evolution is still not systematically controlled for. Using a 5kb window is not sufficient, as LD may extend across the entire genome. As the authors have now run gubbins correctly, they could use the results from this existing analysis to find recent HGT. To definite mobilisation, perhaps a standard pipeline such (e.g. https://github.com/EBI-Metagenomics/mobilome-annotation-pipeline) would be more convincing.

(3) The invasiveness index is better described, but the authors still did not provide convincing evidence that the small difference is actually biologically meaningful (there was no statistical difference between the two strains provided in response Figure 6). What do other Salmonella papers using this approach find, and can their links be brought in? If there is still no good evidence, a better description of this difference would help make the conclusions better supported.

In summary, the analysis is broadly well described and feels appropriate. Some of the conclusions are still not fully supported, although the main points and context of the paper now appear sound.

Reviewer #1 (Public review):

Summary:

Cell metabolism exhibits a well-known behavior in fast-growing cells, which employ seemingly wasteful fermentation to generate energy even in the presence of sufficient environmental oxygen. This phenomenon is known as Overflow Metabolism or the Warburg effect in cancer. It is present in a wide range of organisms, from bacteria and fungi to mammalian cells.

In this work, starting with a metabolic network for Escherichia coli based on sets of carbon sources, and using a corresponding coarse-grained model, the author applies some well-based approximations from the literature and algebraic manipulations. These are used to successfully explain the origins of Overflow Metabolism, both qualitatively and quantitatively, by comparing the results with E. coli experimental data.

By modeling the proteome energy efficiencies for respiration and fermentation, the study shows that these parameters are dependent on the carbon source quality constants K_i (p.115 and 116). It is demonstrated that as the environment becomes richer, the optimal solution for proteome energy efficiency shifts from respiration to fermentation. This shift occurs at a critical parameter value K_A(C).<br /> This counter intuitive results qualitativelly explains Overflow Metabolism.

Quantitative agreement is achieved through the analysis of the heterogeneity of the metabolic status within a cell population. By introducing heterogeneity, the critical growth rate is assumed to follow a Gaussian distribution over the cell population, resulting in accordance with experimental data for E. coli. Overflow metabolism is explained by considering optimal protein allocation and cell heterogeneity.

The obtained model is extensively tested through perturbations: 1) Introduction of overexpression of useless proteins; 2) Studying energy dissipation; 3) Analysis of the impact of translation inhibition with different sub-lethal doses of chloramphenicol on Escherichia coli; 4) Alteration of nutrient categories of carbon sources using pyruvate. All model perturbations results are corroborated by E. coli experimental results.

Strengths:

In this work, the author effectively uses modeling techniques typical of Physics to address complex problems in Biology, demonstrating the potential of interdisciplinary approaches to yield novel insights. The use of Escherichia coli as a model organism ensures that the assumptions and approximations are well-supported in existing literature. The model is convincingly constructed and aligns well with experimental data, lending credibility to the findings. In this version, the extension of results from bacteria to yeast and cancer is substantiated by a literature base, suggesting that these findings may have broad implications for understanding diverse biological systems.

Weaknesses:

The author explores the generalization of their results from bacteria to cancer cells and yeast, adapting the metabolic network and coarse-grained model accordingly. In previous version this generalization was not completedly supported by references and data from the literature. This drawback, however, has been treated in this current version, where the authors discuss in much more detail and give references supporting this generalization.

Reviewer #2 (Public review):

In this version of manuscript, the author clarified many details and rewrote some sections. This substantially improved the readability of the paper. I also recognized that the author spent substantial efforts in the Appendix to answer the potential questions.

Unfortunately, I am not currently convinced by the theory proposed in this paper. In the next section, I will first recap the logic of the author and explain why I am not convinced. Although the theory fits many experimental results, other theories on overflow metabolism are also supported by experiments. Hence, I do not think based on experimental data we could rule in or rule out different theories.

Recap: To explain the origin of overflow metabolism, the author uses the following logic:

(1) There is a substantial variability of single-cell growth rate<br /> (2) The flux (J_r^E) and (J_f^E) are coupled with growth rate by Eq. 3<br /> (3) Since growth rate varies from cells to cells, flux (J_r^E) and (J_f^E) also varies<br /> (4) The variabilities of above fluxes in above create threshold-analog relation, and hence overflow metabolism.

My opinion:

The logic step (2) and (3) have caveats. The variability of growth rate has large components of cellular noise and external noise. Therefore, variability of growth rate is far from 100% correlated with variability of flux (J_r^E) and (J_f^E) at the single-cell level. Single-cell growth rate is a complex, multivariate functional, including (Jr^E) and (J_f^E) but also many other variables. My feeling is the correlation could be too low to support the logic here.

One example: ribosomal concentration is known to be an important factor of growth rate in bulk culture. However, the "growth law" from bulk culture cannot directly translate into the growth law at single-cell level [Ref1,2]. This is likely due to other factors (such as cell aging, other muti-stability of cellular states) are involved.

Therefore, I think using Eq.3 to invert the distribution of growth rate into the distribution of (Jr^E) and (J_f^E) is inapplicable, due to the potentially low correlation at single-cell level. It may show partial correlations, but may not be strong enough to support the claim and create fermentation at macroscopic scale.

Overall, if we track the logic flow, this theory implies overflow metabolism is originated from variability of k_cat of catalytic enzymes from cells to cells. That is, the author proposed that overflow metabolism happens macroscopically as if it is some "aberrant activation of fermentation pathway" at the single-cell level, due to some unknown partially correlation from growth rate variability.

Compared with other theories, this theory does not involve any regulatory mechanism and can be regarded as a "neutral theory". I am looking forward to seeing single cell experiments in the future to provide evidences about this theory.

[Ref1] https://www.biorxiv.org/content/10.1101/2024.04.19.590370v2<br /> [Ref2] https://www.biorxiv.org/content/10.1101/2024.10.08.617237v2

Reviewer #1 (Public review):

The authors sought to examine the associations between child age, reports of parent-child relationship quality, and neural activity patterns while children (and also their parents) watched a movie clip. Major methodological strengths include the sample of 3-8 year-old children in China (rare in fMRI research for both age range and non-Western samples), use of a movie clip previously demonstrated to capture theory of mind constructs at the neural level, measurement of caregiver-child neural synchrony, and assessment of neural maturity. Results provide important new information about parent-child neural synchronization during this movie and associations with reports of parent-child relationship quality. The work is a notable advance in understanding the link between the caregiving context and the neural construction of theory of mind networks in the developing brain.

There are several theoretical and methodological limitations of the manuscript in its current form:

(1) We appreciate that the authors wanted to show support for a mediational mechanism. However, we suggest that the authors drop the structural equation modeling because the data are cross-sectional so mediation is not appropriate. Other issues include the weak justification of including the parent-child neural synchronization as part of parenting.... it could just as easily be a mechanism of change or driven by the child rather than a component of parenting behavior. The paper would be strengthened by looking at associations between selected variables of interest that are MOST relevant to the imaging task in a regression type of model. Furthermore, the authors need to be more explicit about corrections for multiple comparisons throughout the manuscript; some of the associations are fairly weak so claims may need to be tempered if they don't survive correction.

(2) Reverse correlation analysis is sensible given what prior developmental fMRI studies have done. But reverse correlation analysis may be more prone to overfitting and noise, and lacks sensitivity to multivariate patterns. Might inter-subject correlation be useful for *within* the child group? This would minimize noise and allow for non-linear patterns to emerge.

(3) No learning effects or temporal lagged effects are tested in the current study, so the results do not support the authors' conclusions that the data speak to Bandura's social learning theory. The authors do mention theories of biobehavioral synchrony in the introduction but do not discuss this framework in the discussion (which is most directly relevant to the data). The data can also speak to other neurodevelopmental theories of development (e.g.,neuroconstructivist approaches), but the authors do not discuss them. The manuscript would benefit from significantly revising the framework to focus more on biobehavioral synchrony data and other neurodevelopmental approaches given the prior work done in this area rather than a social psychology framework that is not directly evaluated.

(4) The significance and impact of the findings would be clearer if the authors more clearly situated the findings in the context of (a) other movie and theory of mind fMRI task data during development; and (b) existing data on parent-child neural synchrony (often uses fNIRS or EEG). What principles of brain and social cognition development do these data speak to? What is new?

(5) There is little discussion about the study limitations, considerations about the generalizability of the findings, and important next steps and future directions. What can the data tell us, and what can it NOT tell us?

Reviewer #2 (Public review):

Summary:

This study investigates the impact of mother-child neural synchronization and the quality of parent-child relationships on the development of Theory of Mind (ToM) and social cognition. Utilizing a naturalistic fMRI movie-viewing paradigm, the authors analyzed inter-subject neural synchronization in mother-child dyads and explored the connections between neural maturity, parental caregiving, and social cognitive outcomes. The findings indicate age-related maturation in ToM and social pain networks, emphasizing the importance of dyadic interactions in shaping ToM performance and social skills, thereby enhancing our understanding of the environmental and intrinsic influences on social cognition.

Strengths:

This research addresses a significant question in developmental neuroscience, by linking social brain development with children's behaviors and parenting. It also uses a robust methodology by incorporating neural synchrony measures, naturalistic stimuli, and a substantial sample of mother-child dyads to enhance its ecological validity. Furthermore, the SEM approach provides a nuanced understanding of the developmental pathways associated with Theory of Mind (ToM).

Weaknesses:

(1) Upon reviewing the introduction, I feel that the first goal - developmental changes of the social brain and its relation to age - seems somewhat distinct from the other two goals and the main research question of the manuscript. The authors might consider revising this section to enhance the overall coherence of the manuscript. Additionally, the introduction lacks a clear background and rationale for the importance of examining age-related changes in the social brain.

(2) The manuscript uses both "mother-child" and "parent-child" terminology. Does this imply that only mothers participated in the fMRI scans while fathers completed the questionnaires? If so, have the authors considered the potential impact of parental roles (father vs. mother)?

(3) There is inconsistent usage of the terms ISC and ISS in the text and figures, both of which appear to refer to synchronization derived from correlation analysis. It would be beneficial to maintain consistency throughout the manuscript.

(4) Of the 50 dyads, 16 were excluded due to data quality issues, which constitutes a significant proportion. It would be helpful to know whether these excluded dyads exhibited any distinctive characteristics. Providing information on demographic or behavioral differences-such as Theory of Mind (ToM) performance and age range between the excluded and included dyads would enhance the assessment of the findings' generalizability.

(5) The article does not adhere to the standard practice of using a resting state as a baseline for subtracting from task synchronization. Is there a rationale for this approach? Not controlling for a baseline may lead to issues, such as whether resting state synchronization already differs between subjects with varying characteristics.

(6) The title of the manuscript suggests a direct influence of mother-child interactions on children's social brain and theory of mind. However, the use of structural equation modeling (SEM) may not fully establish causal relationships. It is possible that the development of children's social brain and ToM also enhances mother-child neural synchronization. The authors should address this alternative hypothesis of the potential bidirectional relationship in the discussion and exercise caution regarding terms that imply causality in the title and throughout the manuscript.

(7) I would appreciate more details about the 14 Theory of Mind (ToM) tasks, which could be included in supplemental materials. The authors score them on a scale from 0 to 14 (each task 1 point); however, the tasks likely vary in difficulty and should carry different weights in the total score (for example, the test and the control questions should have different weights). Many studies have utilized the seven tasks according to Wellman and Liu (2004), categorizing them into "basic ToM" and "advanced ToM." Different components of ToM could influence the findings of the current study, which should be further examined by a more in-depth analysis.

Reviewer #3 (Public review):

Summary:

The article explores the role of mother-child interactions in the development of children's social cognition, focusing on Theory of Mind (ToM) and Social Pain Matrix (SPM) networks. Using a naturalistic fMRI paradigm involving movie viewing, the study examines relationships among children's neural development, mother-child neural synchronization, and interaction quality. The authors identified a developmental pattern in these networks, showing that they become more functionally distinct with age. Additionally, they found stronger neural synchronization between child-mother pairs compared to child-stranger pairs, with this synchronization and neural maturation of the networks associated with the mother-child relationship and parenting quality.

Strengths:

This is a well-written paper, and using dyadic fMRI and naturalistic stimuli enhances its ecological validity, providing valuable insights into the dynamic interplay between brain development and social interactions. However, I have some concerns regarding the analysis and interpretation of the findings. I have outlined these concerns below in the order they appear in the manuscript, which I hope will be helpful for the revision.

Weaknesses:

(1) Given the importance of social cognition in this study, please cite a foundational empirical or review paper on social cognition to support its definition. The current first citation is primarily related to ASD research, which may not fully capture the broader context of social cognition development.

(2) It is standard practice to report the final sample size in the Abstract and Introduction, rather than the initial recruited sample, as high attrition rates are common in pediatric studies. For example, this study recruited 50 mother-child dyads, and only 34 remained after quality control. This information is crucial for interpreting the results and conclusions. I recommend reporting the final sample size in the abstract and introduction but specifying in the Methods that an additional 16 mother-child dyads were initially recruited or that 50 dyads were originally collected.

(3) In the "Neural maturity reflects the development of the social brain" section, the authors report the across-network correlation for adults, finding a negative correlation between ToM and SPM. However, the cross-network correlations for the three child groups are not reported. The statement that "the two networks were already functionally distinct in the youngest group of children we tested" is based solely on within-network positive correlations, which does not fully demonstrate functional distinctness. Including cross-network correlations for the child groups would strengthen this conclusion.

(4) The ROIs for the ToM and SPM networks are defined based on previous literature, applying the same ROIs across all age groups. While I understand this is a common approach, it's important to note that this assumption may not fully hold, as network architecture can evolve with age. The functional ROIs or components of a network might shift, with regions potentially joining or exiting a network or changing in size as children develop. For instance, Mark H. Johnson's interactive specialization theory suggests that network composition may adapt over developmental stages. Although the authors follow the approach of Richardson et al. (2018), it would be beneficial to discuss this limitation in the Discussion. An alternative approach would be to apply data-driven analysis to justify the selection of the ROIs for the two networks.

(5) The current sample size (N = 34 dyads) is a limitation, particularly given the use of SEM, which generally requires larger samples for stable results. Although the model fit appears adequate, this does not guarantee reliability with the current sample size. I suggest discussing this limitation in more detail in the Discussion.

(6) Based on the above comment, I believe that conclusions regarding the relationship between social network development, parenting, and support for Bandura's theory should be tempered. The current conclusions may be too strong given the study's limitations.

(7) The SPM (pain) network is associated with empathic abilities, also an important aspect of social skills. It would be relevant to explore whether (or explain why) SPM development and child-mother synchronization are (or are not) related to parenting and the parent-child relationship.

Reviewer #1 (Public review):

Summary:

The authors present NeuroSCAN, an accessible and interactive tool for visualizing and summarizing data from multiple previously annotated C. elegans connectomes. NeuroSCAN provides a useful entry point for streamlined observation of neuronal morphology, and the membrane contacts and synaptic connectivity between neurons across developmental stages and individual connectomes readily extracted from existing data.

Strengths:

Koonce et al. have generated a web-based visualization tool for exploring C. elegans neuronal morphology, contact area between neurons, and synaptic connectivity data. Here, the authors integrate volumetric segmentation of neurons and visualization of contact area patterns of individual neurons generated from Diffusion Condensation and C-PHATE embedding based on previous work from adult volumetric electron microscopy (vEM) data, extended to available vEM data for earlier developmental stages, which effectively summarizes modularity within the collated C. elegans contactomes to date. Overall, NeuroSCAN's relative ease of use for generating visualizations, its ability to quickly toggle between developmental stages, and its integration of a concise visualization of individual neurons' contact patterns strengthen its utility.

Weaknesses:

NeuroSCAN provides an accessible and convenient platform. However, many of the characteristics of NeuroSCAN overlap with that of an existing tool for visualizing connectomics data, Neuroglancer, which is a widely-used and shared platform with data from other organisms. The authors do not make clear their motivation for generating this new tool rather than building on a system that has already collated previous connectomics data. Although the field will benefit from any tool that collates connectomics data and makes it more accessible and user-friendly, such a tool is only useful if it is kept up-to-date, and if data formatting for submitting electron microscopy data to be added to the tool is made clear. It is unclear from this manuscript whether NeuroSCAN will be updated with recently published and future C. elegans connectomes, or how additional datasets can be submitted to be added in the future.

The interface for visualizing contacts and synapses would be improved with better user access to the quantitative underlying data. When contact areas or synapses are added to the viewer, adding statistics on the magnitude of the contact area, the number of synapses, and the rank of these values among the neuron's top connections, would make the viewer more useful for hypothesis generation. Furthermore, synapses are currently listed individually, with names that are not very legible to the web user. Grouping them by pre- and postsynaptic neurons and linking these groups across developmental stages would also be an improvement.

While the DC/C-PHATE visualizations are a useful tool for the user, it is difficult to understand when grouping or splitting of cell contact patterns is biologically significant. DC is a deterministic algorithm applied to a contactome from a single organism, and the authors do not provide quantitative metrics of distances between individual neurons or a number of DC iterations on the C-PHATE plot, nor is the selection process for the threshold for DC described in this manuscript. In the application of DC/C-PHATE to larval stage nerve ring strata organization shown by the authors, qualitative observations of C-PHATE plots colored based on adult data seem to be the only evidence shown for persistent strata during development (Figure 3) or changing architectural motifs across stages (Figure 4). Quantitation of differences in neuron position within the DC hierarchy, or differences in modularity across stages, is needed to support these conclusions. Furthermore, illustrating the quantitative differences in C-PHATE plots used to make these conclusions will provide a more instructive guide for users of NeuroSCAN in generating future hypotheses.

While the case studies presented by the authors help to highlight the utility of the different visualizations offered by the NeuroSCAN platform, the authors need to be more careful with the claims they make from these correlative observations. For example, in Figure 4, the authors use C-PHATE clustering patterns to make conclusions about changes in clustering patterns of individual neurons across development based on single animal datasets. In this and many other cases presented in this study with the limited existing datasets, it is difficult to differentiate between developmental changes and individual variability between the neurite positions, contacts, and synapse differences within these data. This caveat needs to be clearly addressed.

Reviewer #2 (Public review):

Summary:

The past five years have seen the publication of both new (Witvliet et al., 2021) and newly analyzed (Cook et al., 2019; Moyle et al., 2021; Brittin et al., 2021) data for the C. elegans connectome. The increase in data availability for a single species allows researchers to examine variability due to both stochastic events and changes over development. The quantity of these data is huge. To help the community make these data more accessible, the authors present a new online tool that allows the examination of 3D models for C. elegans neurons in the central neuropil across development. In addition to visualizing the overall structure of the neuronal processes and locations of synapses, the NeuroSCAN tool also allows users to probe into the C-PHATE visualization results, which this group previously pioneered to describe similarities in neuron adjacency (Moyle et al., 2021).

Strengths:

The ability to visualize the data from both a connectomics and contactomics perspective across developmental time has significant power. The original C. elegans connectome (White et al., 1986) presented their circuits as line drawings with chemical and electrical synapses indicated through arrows and bars. While these line drawings remain incredibly useful, they were also necessary simplifications for a 2D publication and they lack details of the complex architecture seen within each EM image. Koonce et al take advantage of segmented image data of each neuronal process within the nerve ring to create a web interface where users can visualize 3D models for their neuron of choice. The C-PHATE visualization allows users to explore similarities among different neurons in terms of adjacency and then go directly to the 3D model for these neurons. The 3D models it generates are beautiful and will likely be showing up in many future presentations and publications. The tool doesn't require any additional downloading and is open source.

Weaknesses:

While it's impossible to create one tool that will satisfy all potential users, I found myself wanting to have numbers associated with the data. For example, knowing the number of connections or the total surface area of contacts between individual neurons wasn't possible through the viewer, which limits the utility of taking deep analytical dives. While connectivity data are readily accessible through other interfaces such as Nemanode and WormWiring, a more thorough integration may be helpful to some users.

There were several issues with the user interface that made it a bit clunky to use. For example, as I added additional neurons to the filter search box, the loading time got longer and longer. I ran an experiment uploading all of the amphid neurons, one pair at a time. Each additional neuron pair added an additional 5-10 seconds to the loading. By the time I got to the last pair, it took over a minute to load. Issues like these, some of which may be unavoidable given the size of the data, could be conveyed through better documentation. I did not find the tutorial very helpful and the supplementary movies lacked any voiceover, so it wasn't always clear what they were trying to show.

Reviewer #3 (Public review):

Summary:

This work provides graphical tools for reconstructing the detailed anatomy of a nervous system from a series of sections imaged by electron microscopy. Contact between neuronal processes can direct outgrowth and is necessary for connectivity and, thus function. A bioinformatic approach is used to group neurons according to shared features (e.g., contact, synapses) in a hierarchy of "relatedness" that can be interrogated at each step. In this work, Koonze et al analyze vEM data sets for the C. elegans nerve ring (NR), a dense fascicle of processes from181 neurons. In a bioinformatic approach, the clustering algorithm Diffusion Condensation (DC) groups neurons according to similar cell biological features in iterations that remove chunks of differences in feature data with each step ultimately merging all NR neurons in one cluster. DC results are displayed with C-Phate a 3D visualization tool to produce a trajectory that can be interrogated for cell identities and other features at each iterative step. In previous work by these authors, this approach was utilized to identify subgroups of neuronal processes or "strata" in the NR that can be grouped by physical contact and connectivity. Here they expand their analysis to include a series of available vEM data sets across C. elegans larval development. This approach suggests that strata initially established during embryonic development are largely preserved in the adult. Importantly, exceptions involving stage-specific reorganization of neuronal placement in specific strata were also detected. A case study featured in the paper demonstrates the utility of this approach for visualizing the integration of newly generated neurons into the existing NR anatomy. Visualization tools used in this work are publicly available at NeuroSCAN.

Strengths:

A web-based app, NeuroSCAN, that individual researchers can use to interrogate the structure and organization of the C. elegans nerve ring across development

Weaknesses:

In the opinion of this reviewer, only minor revisions are required.

Reviewer #1 (Public review):

Summary:

In this lovely paper, McDermott and colleagues tackle an enduring puzzle in the cognitive neuroscience of perceptual prediction. Though many scientists agree that top-down predictions shape perception, previous studies have yielded incompatible results - with studies showing 'sharpened' representations of expected signals, and others showing a 'dampening' of predictable signals to relatively enhance surprising prediction errors. To deepen the paradox further, it seems like there are good reasons that we would want to see both influences on perception in different contexts.

Here, the authors aim to test one possible resolution to this 'paradox' - the opposing process theory (OPT). This theory makes distinct predictions about how the time course of 'sharpening' and 'dampening' effects should unfold. The researchers present a clever twist on a leading-trailing perceptual prediction paradigm, using AI to generate a large dataset of test and training stimuli so that it is possible to form expectations about certain categories without repeating any particular stimuli. This provides a powerful way of distinguishing expectation effects from repetition effects - a perennial problem in this line of work.

Using EEG decoding, the researchers find evidence to support the OPT. Namely, they find that neural encoding of expected events is superior in earlier time ranges (sharpening-like) followed by a relative advantage for unexpected events in later time ranges (dampening-like). On top of this, the authors also show that these two separate influences may emerge differently in different phases of learning - with superior decoding of surprising prediction errors being found more in early phases of the task, and enhanced decoding of predicted events being found in the later phases of the experiment.

Strengths:

As noted above, a major strength of this work lies in important experimental design choices. Alongside removing any possible influence of repetition suppression mechanisms in this task, the experiment also allows us to see how effects emerge in 'real-time' as agents learn to make predictions. This contrasts with many other studies in this area - where researchers 'over-train' expectations into observers to create the strongest possible effects or rely on prior knowledge that was likely to be crystallised outside the lab.

Weaknesses:

This study reveals a great deal about how certain neural representations are altered by expectation and learning on shorter and longer timescales, so I am loath to describe certain limitations as 'weaknesses'. But one limitation inherent in this experimental design is that, by focusing on implicit, task-irrelevant predictions, there is not much opportunity to connect the predictive influences seen at the neural level to the perceptual performance itself (e.g., how participants make perceptual decisions about expected or unexpected events, or how these events are detected or appear).

The behavioural data that is displayed (from a post-recording behavioural session) shows that these predictions do influence perceptual choice - leading to faster reaction times when expectations are valid. In broad strokes, we may think that such a result is broadly consistent with a 'sharpening' view of perceptual prediction, and the fact that sharpening effects are found in the study to be larger at the end of the task than at the beginning. But it strikes me that the strongest test of the relevance of these (very interesting) EEG findings would be some evidence that the neural effects relate to behavioural influences (e.g., are participants actually more behaviourally sensitive to invalid signals in earlier phases of the experiment, given that this is where the neural effects show the most 'dampening' a.k.a., prediction error advantage?)

Reviewer #2 (Public review):

Summary:

There are two accounts in the literature that propose that expectations suppress the activity of neurons that are (a) not tuned to the expected stimulus to increase the signal-to-noise ratio for expected stimuli (sharpening model) or (b) tuned to the expected stimulus to highlight novel information (dampening model). One recent account, the opposing process theory, brings the two models together and suggests that both processes occur, but at different time points: initial sharpening is followed by later dampening of the neural activity of the expected stimulus. In this study, the authors aim to test the opposing process theory in a statistical learning task by applying multivariate EEG analyses and finding evidence for the opposing process theory based on the within-trial dynamics.

Strengths:

This study addresses a very timely research question about the underlying mechanisms of expectation suppression. The applied EEG decoding approach offers an elegant way to investigate the temporal characteristics of expectation effects. A major strength of the study lies in the experimental design that aims to control for repetition effects, one of the common confounds in prediction suppression studies. The reported results are novel in the field and have the potential to substantially improve our understanding of expectation suppression in visual perception.

Weaknesses:

The strength in controlling for repetition effects by introducing a neutral (50% expectation) condition also adds a weakness to the current version of the manuscript, as this neutral condition is not integrated into the behavioral (reaction times) and EEG (ERP and decoding) analyses. This procedure remained unclear to me. The reported results would be strengthened by showing differences between the neutral and expected (valid) conditions on the behavioral and neural levels. This would also provide a more rigorous check that participants had implicitly learned the associations between the picture category pairings.

It is not entirely clear to me what is actually decoded in the prediction condition and why the authors did not perform decoding over trial bins in prediction decoding as potential differences across time could be hidden by averaging the data. The manuscript would generally benefit from a more detailed description of the analysis rationale and methods.

Finally, the scope of this study should be limited to expectation suppression in visual perception, as the generalization of these results to other sensory modalities or to the action domain remains open for future research.

Reviewer #3 (Public review):

Summary:

In their study, McDermott et al. investigate the neurocomputational mechanism underlying sensory prediction errors. They contrast two accounts: representational sharpening and dampening. Representational sharpening suggests that predictions increase the fidelity of the neural representations of expected inputs, while representational dampening suggests the opposite (decreased fidelity for expected stimuli). The authors performed decoding analyses on EEG data, showing that first expected stimuli could be better decoded (sharpening), followed by a reversal during later response windows where unexpected inputs could be better decoded (dampening). These results are interpreted in the context of opposing process theory (OPT), which suggests that such a reversal would support perception to be both veridical (i.e., initial sharpening to increase the accuracy of perception) and informative (i.e., later dampening to highlight surprising, but informative inputs).

Strengths:

The topic of the present study is of significant relevance to the field of predictive processing. The experimental paradigm used by McDermott et al. is well designed, allowing the authors to avoid several common confounds in investigating predictions, such as stimulus familiarity and adaptation. The introduction of the manuscript provides a well-written summary of the main arguments for the two accounts of interest (sharpening and dampening), as well as OPT. Overall, the manuscript serves as a good overview of the current state of the field.

Weaknesses:

In my opinion, several details of the methods, results, and manuscript raise doubts about the quality and reliability of the reported findings. Key concerns are:

(1) The results in Figure 2C seem to show that the leading image itself can only be decoded with ~33% accuracy (25% chance; i.e. ~8% above chance decoding). In contrast, Figure 2E suggests the prediction (surprisingly, valid or invalid) during the leading image presentation can be decoded with ~62% accuracy (50% chance; i.e. ~12% above chance decoding). Unless I am misinterpreting the analyses, it seems implausible to me that a prediction, but not actually shown image, can be better decoded using EEG than an image that is presented on-screen.

(2) The "prediction decoding" analysis is described by the authors as "decoding the predictable trailing images based on the leading images". How this was done is however unclear to me. For each leading image decoding the predictable trailing images should be equivalent to decoding validity (as there were only 2 possible trailing image categories: 1 valid, 1 invalid). How is it then possible that the analysis is performed separately for valid and invalid trials? If the authors simply decode which leading image category was shown, but combine L1+L2 and L4+L5 into one class respectively, the resulting decoder would in my opinion not decode prediction, but instead dissociate the representation of L1+L2 from L4+L5, which may also explain why the time-course of the prediction peaks during the leading image stimulus-response, which is rather different compared to previous studies decoding predictions (e.g. Kok et al. 2017). Instead for the prediction analysis to be informative about the prediction, the decoder ought to decode the representation of the trailing image during the leading image and inter-stimulus interval. Therefore I am at present not convinced that the utilized analysis approach is informative about predictions.

(3) I may be misunderstanding the reported statistics or analyses, but it seems unlikely that >10 of the reported contrasts have the exact same statistic of Tmax= 2.76. Similarly, it seems implausible, based on visual inspection of Figure 2, that the Tmax for the invalid condition decoding (reported as Tmax = 14.903) is substantially larger than for the valid condition decoding (reported as Tmax = 2.76), even though the valid condition appears to have superior peak decoding performance. Combined these details may raise concerns about the reliability of the reported statistics.

(4) The reported analyses and results do not seem to support the conclusion of early learning resulting in dampening and later stages in sharpening. Specifically, the authors appear to base this conclusion on the absence of a decoding effect in some time-bins, while in my opinion a contrast between time-bins, showing a difference in decoding accuracy, is required. Or better yet, a non-zero slope of decoding accuracy over time should be shown (not contingent on post-hoc and seemingly arbitrary binning).

(5) The present results both within and across trials are difficult to reconcile with previous studies using MEG (Kok et al., 2017; Han et al., 2019), single-unit and multi-unit recordings (Kumar et al., 2017; Meyer & Olson 2011), as well as fMRI (Richter et al., 2018), which investigated similar questions but yielded different results; i.e., no reversal within or across trials, as well as dampening effects with after more training. The authors do not provide a convincing explanation as to why their results should differ from previous studies, arguably further compounding doubts about the present results raised by the methods and results concerns noted above.

Impact:

At present, I find the potential impact of the study by McDermott et al. difficult to assess, given the concerns mentioned above. Should the authors convincingly answer these concerns, the study could provide meaningful insights into the mechanisms underlying perceptual prediction. However, at present, I am not entirely convinced by the quality and reliability of the results and manuscript. Moreover, the difficulty in reconciling some of the present results with previous studies highlights the need for more convincing explanations of these discrepancies and a stronger discussion of the present results in the context of the literature.

Reviewer #1 (Public review):

Summary:

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

Strengths:

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

Weaknesses:

Inferences rely heavily on the results of mixed effects models which may or may not be properly specified and are not supported by complementary analyses. Also, not all results hang together in a sensible way. For example, participants report feeling less subjective effort, but also more disliking of tasks when they were earning rewards for others versus self. Given that participants took longer to complete tasks when earning effort for others, it is conceivable that participants might have been working less hard for others versus themselves, and this may complicate the interpretation of results.

Reviewer #2 (Public review):

Summary:

Measurements of the reward positivity, an electrophysiological component elicited during reward evaluation, have previously been used to understand how self-benefitting effort expenditure influences the processing of rewards. The present study is the first to complement those measurements with electrophysiological reward after-effects of effort expenditure during prosocial acts. The results provide solid evidence that effort adds reward value when the recipient of the reward is the self but discounts reward value when the beneficiary is another individual.

Strengths:

An important strength of the study is that the amount of effort, the prospective reward, the recipient of the reward, and whether the reward was actually gained or not were parametrically and orthogonally varied. In addition, the researchers examined whether the pattern of results generalized to decisions about future efforts. The sample size (N=40) and mixed-effects regression models are also appropriate for addressing the key research questions. Those conclusions are plausible and adequately supported by statistical analyses.

Weaknesses:

Although the obtained results are highly plausible, I am concerned whether the reward positivity (RewP) and P3 were adequately measured. The RewP and P3 were defined as the average voltage values in the time intervals 300-400 ms and 300-440 ms after feedback onset, respectively. So they largely overlapped in time. Although the RewP measure was based on frontocentral electrodes (FC3, FCz, and FC4) and the P3 on posterior electrodes (P3, Pz, and P4), the scalp topographies in Figure 3 show that the RewP effects were larger at the posterior electrodes used for the P3 than at frontocentral electrodes. So there is a concern that the RewP and P3 were not independently measured. This type of problem can often be resolved using a spatiotemporal principal component analysis. My faith in the conclusions drawn would be further strengthened if the researchers extracted separate principal components for the RewP and P3 and performed their statistical analyses on the corresponding factor scores.

Reviewer #3 (Public review):

This study investigates how effort influences reward evaluation during prosocial behaviour using EEG and experimental tasks manipulating effort and rewards for self and others. Results reveal a dissociable effect: for self-benefitting effort, rewards are evaluated more positively as effort increases, while for other-benefitting effort, rewards are evaluated less positively with higher effort. This dissociation, driven by reward system activation and independent of performance, provides new insights into the neural mechanisms of effort and reward in prosocial contexts.

This work makes a valuable contribution to the prosocial behaviour literature by addressing areas that previous research has largely overlooked. It highlights the paradoxical effect of effort on reward evaluation and opens new avenues for investigating the mechanisms underlying this phenomenon. The study employs well-established tasks with robust replication in the literature and innovatively incorporates ERPs to examine effort-based prosocial decision-making - an area insufficiently explored in prior work. Moreover, the analyses are rigorous and grounded in established methodologies, further enhancing the study's credibility. These elements collectively underscore the study's significance in advancing our understanding of effort-based decision-making.

Despite these contributions, there are several gaps in the analysis that leave the conclusions incomplete and warrant further investigation. These issues can be summarized as follows:

(1) Incomplete EEG Reporting: The methods indicate that EEG activity was recorded for both tasks; however, the manuscript reports EEG results only for the first task, omitting the decision-making task. If the authors claim a paradoxical effect of effort on self versus other rewards, as revealed by the RewP component, this should also be confirmed with results from the decision-making task. Omitting these findings weakens the overall argument.

(2) Neural and Behavioural Integration: The neural results should be contrasted with behavioural data both within and between tasks. Specifically, the manuscript could examine whether neural responses predict performance within each task and whether neural and behavioural signals correlate across tasks. This integration would provide a more comprehensive understanding of the mechanisms at play.

(3) Success Rate and Model Structure: The manuscript does not clearly report the success rate in the prosocial effort task. If success rates are low, risk aversion could confound the results. Additionally, it is unclear whether the models accounted for successful versus unsuccessful trials or whether success was included as a covariate. If this information is present, it needs to be explicitly clarified. The exclusion criteria for unsuccessful trials in both tasks should also be detailed. Moreover, the decision to exclude electrodes as independent variables in the models warrants an explanation.

(4) Prosocial Decision Computational Modelling: The prosocial decision task largely replicates prior behavioural findings but misses the opportunity to directly test the hypotheses derived from neural data in the prosocial effort task. If the authors propose a paradoxical effect of effort on self-rewards and an inverse effect for prosocial effort, this could be formalised in a computational model. A model comparison could evaluate the proposed mechanism against alternative theories, incorporating the complex interplay of effort and reward for self and others. Furthermore, these parameters should be correlated with neural signals, adding a critical layer of evidence to the claims. As it is, the inclusion of the prosocial decision task seems irrelevant.

(5) Contradiction Between Effort Perception and Neural Results: Participants reported effort as less effortful in the prosocial condition compared to the self condition, which seems contradictory to the neural findings and the authors' interpretation. If effort has a discounting effect on rewards for others, one might expect it to feel more effortful. How do the authors reconcile these results? Additionally, the relationship between behavioural data and neural responses should be examined to clarify these inconsistencies.

Necessary Revisions to Manuscript: If the authors address the issues above, corresponding updates to the introduction and discussion sections could strengthen the narrative and align the manuscript with the additional analyses.

Reviewer #1 (Public review):

The manuscript by Coquel et al. investigates the effects of BKC and IBC, two compounds found in Psoralea corylifolia in DNA replication and the response to DNA damage, and explores their potential use in cancer treatment. These compounds have been previously shown to affect different cellular pathways and the authors use transformed cancer cells of different origins and a non-transformed cell line to question if their combination is toxic in cancer versus non-cancer cells. They propose that BKC inhibits DNA polymerases while IBC targets CHK2. Their results show that both compounds do affect DNA replication, inducing replication stress and affecting double strand break repair. They also show that their combined use increases their toxicity in a synergistic manner.

Comments on current version:

The authors have addressed the main questions raised in the original manuscript. The new data provide stronger evidence supporting the inhibition of DNA polymerases by BKC and the effect of IBC on CHK2. In addition, the new data provides information about the potential mechanism of action of IBC in cells and xenograft models. Together, the revised manuscript has notably increased the relevance and impact of the results with stronger conclusions and better controlled experiments.

Reviewer #2 (Public review):

Summary:

The manuscript: "Synergistic effect of inhibiting CHK2 and DNA replication on cancer cell growth" successfully demonstrates that the compounds BKC and IBC found in Psoralea corylifolia act synergistically to inhibit cancer cell proliferation, using a wide range of well-chosen methodologies. Moreover, the authors characterized the mechanisms of action of both drugs, which result in inhibition of cell proliferation. The use of multiple cell lines and the mice models makes the study robust and complete.

Significance:

The manuscript presents a well written study that offers new insights and contributions to the field. Although the inhibitors described have been known in science, the authors present convincingly their mode of action, which is either better characterized (for BKC) or inhibiting a different than previously suggested enzyme (for IBC). Authors also nicely pinpoint and explain the narrow window of concentrations when these two compounds act synergistically rather than additively. The analyses in multiple cell lines, mouse models and in combination with other cancer treatments, make this study of interest not only for fundamental researchers but also for translational scientists and industry.

Reviewer #1 (Public review):

Summary:

Ngo et. al use several computational methods to determine and characterize structures defining the three major states sampled by the human voltage-gated potassium channel hERG: the open, closed, and inactivated state. Specifically, they use AlphaFold and Rosetta to generate conformations that likely represent key features of the open, closed, and inactivated states of this channel. Molecular dynamics simulations confirm that ion conduction for structure models of the open but not the inactivated state. Moreover, drug docking in silico experiments show differential binding of drugs to the conformation of the three states; the inactivated one being preferentially bound by many of them. Docking results are then combined with a Markov model to get state-weighted binding free energies that are compared with experimentally measured ones.

Strengths:

The study uses state-of-the art modeling methods to provide detailed insights into the structure-function relationship of an important human potassium channel. AlphaFold modeling, MD simulations, and Markov modeling are nicely combined to investigate the impact of structural changes in the hERG channel on potassium conduction and drug binding.

Weaknesses:

(1) The selection of inactivated conformations based on AlphaFold modeling seems a bit biased. The authors base their selection of the "most likely" inactivated conformation on the expected flipping of V625 and the constriction at G626 carbonyls. This follows a bit of the "Streetlight effect". It would be better to have selection criteria that are independent of what they expect to find for the inactivated state conformations. Using cues that favour sampling/modeling of the inactivated conformation, such as the deactivated conformation of the VSD used in the modeling of the closed state, would be more convincing. There may be other conformations that are more accurately representing the inactivated state. I see no objective criteria that justify the non-consideration of conformations from cluster 3 of the inactivated state modeling. I am not sure whether pLDDT is a good selection criterion. It reports on structural confidence, but that may not relate to functional relevance.

(2) The comparison of predicted and experimentally measured binding affinities lacks an appropriate control. Using binding data from open-state conformations only is not the best control. A much better control is the use of alternative structures predicted by AlphaFold for each state (e.g. from the outlier clusters or not considered clusters) in the docking and energy calculations. Using these docking results in the calculations would reveal whether the initially selected conformations (e.g. from cluster 2 for the inactivated state) are truly doing a better job in predicting binding affinities. Such a control would strengthen the overall findings significantly.

(3) Figures where multiple datapoints are compared across states generally lack assessment of the statistical significance of observed trends (e,g. Figure 3d).

(4) Figure 3 and Figures S1-S4 compare structural differences between states. However, these differences are inferred from the initial models. The collection of conformations generated via the MD runs allow for much more robust comparisons of structural differences.

Reviewer #2 (Public review):

Summary:

Ngo et al. use AlphaFold2 and Rosetta to model closed, open, and inactive states of the human ion channel hERG. Subsequent MD simulations and comparisons with experiments support the plausibility of their models.

Strengths:

This is thorough work studied from many different angles. It provides a self-consistent picture of how conformational changes in hERG may affect its function and binding to different targets.

Weaknesses:

Though this work claims the methodologies can be generalized to other systems, it is not obvious how. Many modeling choices seem arbitrary and also seem to have required extensive expert knowledge of the system. This limits the applicability of the modeling strategy.

Reviewer #3 (Public review):

Summary:

The authors use Alphafold2, Rosetta, and Molecular Dynamics to model structures of the hERG K channel in open, inactive, and closed states. Experimental CryoEM data for open hERG (Wang and Mackinnon 2017), and closed EAG (Mandala and Mackinnon, 2002) were used as the main templates for channel models presented here. Given the importance of hERG as a safety pharmacology target, the identification of a robust simulation method to assess drug block is an important addition to the field.

Strengths

The key findings here are new inactivated and closed hERG channel conformations and hERG channel conformations with drugs docked in the inner vestibule below the selectivity filter. Amino acid pathways and interaction networks for different states are also presented.

The inactive state and drug block models are carefully correlated with experimental data for the inactivated state of hERG (Lau et al, 2024) and with experimental free energy data for drug binding and have overall good agreement.

It is remarkable that using cytoplasmic domain structures of hERG as a starting point revealed inactivation state structures in the hERG selectivity filter in Figures 2,3.

Weaknesses

Figure 6, if each data point is for a different drug, then perhaps identify each point.

The PAS domain was not included in the models as stated in Methods page 14 but the PAS does appear in some of the templates used as starting points for models in Figure 1 a,b,c. Perhaps mentioning that the PAS was not included in some (all?) of the final models should be moved into the main text and discussed.

The drug block of 1b channels (which do not contain PAS) has been reported to be slightly different than that for 1a channels (which contain PAS) and for 1a/1b channels (see London et al., 1997; https://doi.org/10.1161/01.RES.81.5.870 and Abi-Gerges et. al., 2011; DOI: 10.1111/j.1476-5381.2011.01378.x) and this should be discussed since the models presented here appear to be performed in the absence of the PAS.

It also appears that the N-linker region (between PAS and the S1) and distal C region of hERG (post CNBHD-COOH) are not included in models, please state this if correct, and discuss.

Reviewer #1 (Public review):

Summary:

The study by Fang et al. reports a 3D MERFISH method that enable spatial transcriptomics for tissues up to 200um in thickness. MERFISH as well other spatial transcriptomics technologies have been mainly used for thin (e.g, 10um) tissue slices, which limits the dimension of spaital transcriptomics technique. Therefore, expanding the capacity of MERFISH to thick tissues represents a major technical advance to enable 3D spatial transcriptomics. Here the authors provide detailed technical descriptions of the new method, troubleshooting, optimization, and application examples to demonstrate its technical capacity, accuracy, sensitivity, and utility. The method will likely have major impact on future spatial transcriptomics studies to benefit diverse biomedical fields.

Strengths:

The study was well-designed, executed, and presented. Extensive protocol optimization and quality assessments were carried out and conclusions are well supported by the data. The methods were sufficiently detailed and the results are solid and compelling.

Weaknesses:

Thorough performance comparison with other existing technologies can be done in the future.

Comments on revisions:

The authors have sufficiently addressed the previous comments.

Reviewer #1 (Public review):

Summary:

In this study, Kume et al examined the role of the protein Semaphorin 4a in steady state skin homeostasis and how this relates to skin changes seen in human psoriasis and imiquimod-induced psoriasis-like disease in mice. The authors found that human psoriatic skin has reduced expression of Sema4a in the epidermis. While Sema4a has been shown to drive inflammatory activation in different immune populations, this finding suggested Sema4a might be important for negatively regulating Th17 inflammation in the skin. The authors go on to show that Sema4a knockout mice have skin changes in key keratinocyte genes, increased gdT cells, and increased IL-17 similar to differences seen in non-lesional psoriatic skin, and that bone marrow chimera mice with WT immune cells and Sema4a KO stromal cells develop worse IMQ-induced psoriasis-like disease, further linking expression of Sema4a in the skin to maintaining skin homeostasis. The authors next studied downstream pathways that might mediate the homeostatic effects of Sema4a, focusing on mTOR given its known role in keratinocyte function. Like for the immune phenotypes, Sema4a KO mice had increased mTOR activation in the epidermis in a similar pattern to mTOR activation noted in non-lesional psoriatic skin. The authors next targeted the mTOR pathway and showed rapamycin could reverse some of the psoriasis-like skin changes in Sema4a KO mice, confirming the role of increased mTOR in contributing to the observed skin phenotype.

In the revised manuscript, the authors expand on the potential relevance to psoriasis by demonstrating similar findings in an IL-23-diriven model of skin inflammation, which is an orthogonal model of psoriasis to their original IMQ model. They also show that in addition to reversing steady state differences in skin thickness between Sema4a KO mice and WT mice, rapamycin improves metrics of disease in the IMQ model of psoriasis. These additional studies further bolster their conclusions that Sema4a may play a protective role in by preventing over-activation of mTOR in the skin in psoriasis.

Strengths:

The most interesting finding is the tissue-specific role for Sema4a, where it has previously been considered to play a mostly pro-inflammatory role in immune cells, this study shows that when expressed by keratinocytes, Sema4a plays a homeostatic role that when missing leads to development of psoriasis-like skin changes. This has important implications in terms of targeting Sema4a pharmacologically. It also may yield a novel mouse model to study mechanisms of psoriasis development in mice separate from the commonly used IMQ model. The included experiments are well-controlled and executed rigorously.

The new experiments provide additional data to support the conclusions through an orthogonal model of psoriasis and demonstrating rapamycin-induced reversal of changes in the IMQ disease model.

Weaknesses:

While the main weakness of these studies, lack of tissue-specific Sema4a knockout mice (e.g. in keratinocytes only), remains, generating these mice and performing the necessary experiments is beyond the scope of completing these particular studies. Similarly, it is understandable that additional bone marrow chimeras would be costly and labor intensive without adding much more in the absence of tissue-specific knockouts.

Reviewer #2 (Public review):

Summary:

Kume et al. found for the first time that Semaphorin 4A (Sema4A) was downregulated in both mRNA and protein levels in L and NL keratinocytes of psoriasis patients compared to control keratinocytes. In peripheral blood, they found that Sema4A is not only expressed in keratinocytes but is also upregulated in hematopoietic cells such as lymphocytes and monocytes in the blood of psoriasis patients. They investigated how the down-regulation of Sema4A expression in psoriatic epidermal cells affects the immunological inflammation of psoriasis by using a psoriasis mice model in which Sema4A KO mice were treated with IMQ. Kume et al. hypothesized that down-regulation of Sema4A expression in keratinocytes might be responsible for the augmentation of psoriasis inflammation. Using bone marrow chimeric mice, Kume et al. showed that KO of Sema4A in non-hematopoietic cells was responsible for the enhanced inflammation in psoriasis. The expression of CCL20, TNF, IL-17, and mTOR was upregulated in the Sema4AKO epidermis compared to the WT epidermis, and the infiltration of IL-17-producing T cells was also enhanced.

Strengths:

Decreased Sema4A expression may be involved in psoriasis exacerbation through epidermal proliferation and enhanced infiltration of Th17 cells, which helps understand psoriasis immunopathogenesis.

Weaknesses:

The mechanism of decreased Sema4A expression in psoriasis is not clear, although this does not affect the strength of this research.

Reviewer #1 (Public review):

The authors focus on the molecular mechanisms by which EMT cells confer resistance to cancer cells. The authors use a wide range of methods to reveal that overexpression of Snail in EMT cells induces cholesterol/sphingomyelin imbalance via transcriptional repression of biosynthetic enzymes involved in sphingomyelin synthesis. The study also revealed that ABCA1 is important for cholesterol efflux and thus for counterbalancing the excess of intracellular free cholesterol in these snail-EMT cells. Inhibition of ACAT, an enzyme catalyzing cholesterol esterification, also seems essential to inhibit the growth of snail-expressing cancer cells.

However, It seems important to analyze the localization of ABCA1, as it is possible that in the event of cholesterol/sphingomyelin imbalance, for example, the intracellular trafficking of the pump may be altered.<br /> The authors should also analyze ACAT levels and/or activity in snail-EMT cells that should be increased. Overall, the provided data are important to better understand cancer biology.

Reviewer #2 (Public review):

Summary:

In this study, the authors discovered that the chemoresistance in RCC cell lines correlates with the expression levels of the drug transporter ABCA1 and the EMT-related transcription factor Snail. They demonstrate that Snail induces ABCA1 expression and chemoresistance, and that ABCA1 inhibitors can counteract this resistance. The study also suggests that Snail disrupts the cholesterol-sphingomyelin (Chol/SM) balance by repressing the expression of enzymes involved in very long-chain fatty acid-sphingomyelin synthesis, leading to excess free cholesterol. This imbalance activates the cholesterol-LXR pathway, inducing ABCA1 expression. Moreover, inhibiting cholesterol esterification suppresses Snail-positive cancer cell growth, providing potential lipid-targeting strategies for invasive cancer therapy.

Strengths:

This research presents a novel mechanism by which the EMT-related transcription factor Snail confers drug resistance by altering the Chol/SM balance, introducing a previously unrecognized role of lipid metabolism in the chemoresistance of cancer cells. The focus on lipid balance, rather than individual lipid levels, is a particularly insightful approach. The potential for targeting cholesterol detoxification pathways in Snail-positive cancer cells is also a significant therapeutic implication.

Weaknesses:

The study's claim that Snail-induced ABCA1 is crucial for chemoresistance relies only on pharmacological inhibition of ABCA1, lacking additional validation. The causal relationship between the disrupted Chol/SM balance and ABCA1 expression or chemoresistance is not directly supported by data. Some data lack quantitative analysis.

Reviewer #1 (Public review):

Summary:

Howard et al. performed deep mutational scanning on the MC4R gene, using a reporter assay to investigate two distinct downstream pathways across multiple experimental conditions. They validated their findings with ClinVar data and previous studies. Additionally, they provided insights into the application of DMS results for personalized drug therapy and differential ligand responses across variant types.

Strengths:

They captured over 99% of variants with robust signals and investigated subtle functionalities, such as pathway-specific activities and interactions with different ligands, by refining both the experimental design and analytical methods.

Weaknesses:

While the study generated informative results, it lacks a detailed explanation regarding the input library, replicate correlation, and sequencing depth for a given number of cells. Additionally, there are several questions that it would be helpful for authors to clarify.

(1) It would be helpful to clarify the information regarding the quality of the input library and experimental replicates. Are variants evenly represented in the library? Additionally, have the authors considered using long-read sequencing to confirm the presence of a single intended variant per construct? Finally, could the authors provide details on the correlation between experimental replicates under each condition?

(2) Since the functional readout of variants is conducted through RNA sequencing, it seems crucial to sequence a sufficient number of cells with adequate sequencing saturation. Could the authors clarify the coverage depth used for each RNA-seq experiment and how this depth was determined? Additionally, how many cells were sequenced in each experiment?

(3) It appears that the frequencies of individual RNA-seq barcode variants were used as a proxy for MR4C activity. Would it be important to also normalize for heterogeneity in RNA-seq coverage across different cells in the experiment? Variability in cell representation (i.e., the distribution of variants across cells) could lead to misinterpretation of variant effects. For example, suppose barcode_a1 represents variant A and barcode_b1 represents variant B. If the RNA-seq results show 6 reads for barcode_a1 and 7 reads for barcode_b1, it might initially appear that both variants have similar effect sizes. However, if these reads correspond to 6 separate cells each containing 1 copy of barcode_a1, and only 1 cell containing 7 copies of barcode_b1, the interpretation changes significantly. Additionally, if certain variants occupy a larger proportion of the cell population, they are more likely to be overrepresented in RNA sequencing.

(4) Although the assay system appears to effectively represent MC4R functionality at the molecular level, we are curious about the potential disparity between the DMS score system and physiological relevance. How do variants reported in gnomAD distribute within the DMS scoring system?

(5) To measure Gq signaling, the authors used the GAL4-VPR relay system. Is there additional experimental data to support that this relay system accurately represents Gq signaling?

(6) Identifying the variants responsive to the corrector was impressive. However, we are curious about how the authors confirmed that the restoration of MC4R activity was due to the correction of the MC4R protein itself. Is there a possibility that the observed effect could be influenced by other factors affected by the corrector? When the corrector was applied to the cells, were any expected or unexpected differential gene expression changes observed?

(7) As mentioned in the introduction, gain-of-function (GoF) variants are known to be protective against obesity. It would be interesting to see further studies on the observed GoF variants. Do the authors have any plans for additional research on these variants?

Reviewer #2 (Public review):

Overview

In this manuscript, the authors use deep mutational scanning to assess the effect of ~6,600 protein-coding variants in MC4R, a G protein-coupled receptor associated with obesity. Reasoning that current deep mutational scanning approaches are insufficiently precise for some drug development applications, they focus on articulating new, more precise approaches. These approaches, which include a new statistical model and innovative reporter assay, enable them to probe molecular phenotypes directly relevant to the development of drugs that target this receptor with high precision and statistical rigor.

They use the resulting data for a variety of purposes, including probing the relationship between MC4R's sequence and structure, analyzing the effect of clinically important variants, identifying variants that disrupt downstream MC4R signaling via one but not both pathways, identifying loss of function variants are amenable to a corrector drug and exploring how deep mutational scanning data could guide small molecule drug optimization.

Strengths

The analysis and statistical framework developed by the authors represent a significant advance. In particular, the study makes use of barcode-level internally replicated measurements to more accurately estimate measurement noise.

The framework allows variant effects to be compared across experimental conditions, a task that is currently hard to do with rigor. Thus, this framework will be applicable to a large number of existing and future deep mutational scanning experiments.

The authors refine their existing barcode transcription-based assay for GPCR signaling, and develop a clever "relay" new reporter system to boost signaling in a particular pathway. They show that these reporters can be used to measure both gain of function and loss of function effects, which many deep mutational scanning approaches cannot do.

The use of systematic approaches to integrate and then interrogate high-dimensional deep mutational scanning data is a big strength. For example, the authors applied PCA to the variant effect results from reporters for two different MC4R signaling pathways and were able to discover variants that biased signaling through one or the other pathway. This approach paves the way for analyses of higher dimensional deep mutational scans.

The authors use the deep mutational scanning data they collect to map how different variants impact small molecule agonists activate MC4R signaling. This is an exciting idea, because developing small-molecule protein-targeting therapeutics is difficult, and this manuscript suggests a new way to map small-molecule-protein interactions.

Weaknesses

The authors derive insights into the relationship between MC4R signaling through different pathways and its structure. While these make sense based on what is already known, the manuscript would be stronger if some of these insights were validated using methods other than deep mutational scanning.

Likewise, the authors use their data to identify positions where variants disrupt MC4R activation by one small molecule agonist but not another. They hypothesize these effects point to positions that are more or less important for the binding of different small molecule agonists. The manuscript would be stronger if some of these insights were explored further.

Impact

In this manuscript, the authors present new methods, including a statistical framework for analyzing deep mutational scanning data that will have a broad impact. They also generate MC4R variant effect data that is of interest to the GPCR community.

Reviewer #1 (Public review):

The authors, Zhang et al., demonstrate the beneficial effects of treating degenerate human primary intervertebral disc (IVD) cells with recombinant human PDGF-AB/BB on the senescence transcriptomic signatures. Utilizing a combination of degenerate cells from elderly humans and experimentally induced senescence in young, healthy IVD cells, the authors show the therapeutic effects on mRNA transcription as well as cellular processes through informatics approaches.

One notable strength of this study is the use of human primary cells and recombinant forms of human PDGF-AB/BB proteins, which increases the translational potential of these in vitro studies. The manuscript is well-written, and the informatics analyses are thorough and clearly presented.

However, in its current form, the study does not provide sufficient experimental details, and clarifications are needed. These are as follows:

(1) The source of PDGF-AB/BB proteins is not detailed.<br /> (2) The irradiation parameters are not adequately reported - the authors should consider (PMCID: PMC5495460) for the parameters that should be reported.<br /> (3) The criteria for young and old patient donors are not explicitly described - though from the table, one presumes the cut-off for young is 27 years old.<br /> (4) What is the rationale for using different concentrations of PDGF-AB/BB in the degenerate cell and irradiation experiments?

There are also a number of other issues the authors could consider. First, in the title and throughout the manuscript, the effects of PDGF-AB/BB are described as protective, yet in all the experiments, PDGF-AB/BB appears to be administered following either in vivo degeneration or in vitro irradiation, where protective effects (e.g., administration prior to insult) were not tested. Therefore, the effects of PDGF-AB/BB may be more accurately described as mitigating or therapeutic rather than protective.

The authors state that the focus on NP (nucleus pulposus) cell studies is due to NP being the first site impacted during degeneration. However, this reviewer believes that this is because changes in the NP are more clinically evident (by imaging methods), despite degeneration often initiating from the AF (annulus fibrosus), e,g. through tears/microtears.

A prior study has examined the effects of X-ray irradiation on NF-kB signaling in young and aged IVDs (PMCID: PMC5495460), and the authors may wish to consider this work.

Reviewer #2 (Public review):

Summary:

This work highlights a novel role for platelet-derived growth factor (PDGF) in mitigating cellular senescence associated with age-related and painful intervertebral disc degeneration. Prior literature has demonstrated the importance of the accumulation of senescent cells in mediating many of the pathological effects associated with the degenerate disc joint such as inflammation and tissue breakdown. In this study, the authors treat clinically relevant human nucleus pulposus and annulus fibrosus cells from patients undergoing discectomy with recombinant PDGF-AB/BB for 5 days and then deep phenotyped the outcomes using bulk RNA sequencing. In addition, they irradiated healthy human disc cells which they subsequently treated with PDGF-AB/BB examining the expression of SASP-related markers and also PDGFRA receptor gene expression. Overall PDGF was able to down-regulate many senescent-associated pathways and the degenerate phenotype in IVD cells. Altered pathways were associated with neurogenesis, mechanical stimuli, metabolism, cell cycle, reactive oxygen species, and mitochondrial dysfunction. Overall the authors achieved their aims and the results by and large support their conclusions although improvements could be made to enhance the rigor of the study and findings.

Strengths:

A major strength of this study is the use of human cells from patients undergoing discectomy for disc herniation as well as access to healthy human cells. Investigating the role of PDGF regarding cellular senescence in the degenerate disc joint is a novel and underexplored area of research which is a significant contribution to the field of spine. This study highlights a potential target for addressing cellular senescence where most of the prior focus has been on senolytic drugs. Such studies have broad implications for other age-related diseases where senescence plays a major role. The use of transcriptomics and therefore an unbiased approach to investigating the role of PDGF is also considered a strength as are the follow-up studies involving irradiating healthy human disc cells and treating these cells with PDGF. The combined assessment of both nucleus pulposus and annulus fibrosus cells in the context of these studies adds to the impact.

Weaknesses:

A weakness of these studies lies in the lack of experimental details provided in the methodology including the rationale for such methods/conditions. Many details such as the specific culture models utilized, substrates, cell density, and media components are missing which impacts rigor. Such details would strengthen the manuscript and the ability to replicate and build on such work/findings. An additional weakness relates to qualitative data presented such as the B-galactosidase assay and immunofluorescence of senescence-associated proteins such as P21 and P16. Quantification of such data sets would greatly strengthen the studies and lend further support to the hypotheses. The study in its current form could be strengthened by the inclusion of mechanistic studies probing the downstream PDGF receptor-associated pathways for example specifically targeting or modulating the activity of the PDGF receptor PDGFRA including validation of the gene data for PDGFRA with protein level data to determine if the transcripts are being translated to protein. The claim that in annulus fibrosus cells, PDGF do not mediate their effects via the PDGFRA does not appear to be supported by the current data as only gene expression for the receptor was assessed with no functional or mechanistic studies being performed. Further discussion, interpretation, and direct comparison of the nucleus pulposus and annulus fibrosus data sets would be helpful for the readers. The magnitude of changes related to the effects of PDGF-BB on the S-phase in irradiated NP and AF cells between control and treated groups seem small making interpretation of these findings challenging.

Reviewer #1 (Public review):

Summary:

In this manuscript, the authors discovered MYL3 of marine medaka (Oryzias melastigma) as a novel NNV entry receptor, elucidating its facilitation of RGNNV entry into host cells through macropinocytosis, mediated by the IGF1R-Rac1/Cdc42 pathway.

Strengths:

In this manuscript, the authors have performed in vitro and in vivo experiments to prove that MnMYL3 may serve as a receptor for NNV via macropinocytosis pathway. These experiments with different methods include Co-IP, RNAi, pulldown, SPR, flow cytometry, immunofluorescence assays, and so on. In general, the results are clearly presented in the manuscript.

Weaknesses:

For the writing in the introduction and discussion sections, the author Yao et al mainly focus on the viral pathogens and fish in Aquaculture, the meaning and novelty of results provided in this manuscript are limited, and not broad in biology. The authors should improve the likely impact of their work on the viral infection field, maybe also in the evolutionary field with the fish model.

(1) Myosin is a big family, why did authors choose MYL3 as a candidate receptor for NNV?

(2) What is the relationship between MmMYL3 and MmHSP90ab1 and other known NNV receptors? Why does NNV have so many receptors? Which one is supposed to serve as the key entry receptor?

(3) In vivo knockout of MYL3 using CRISPR-Cas9 should be conducted to verify whether the absence of MYL3 really inhibits NNV infection. Although it might be difficult to do it in marine medaka as stated by the authors, the introduction of zebrafish is highly recommended, since it has already been reported that zebrafish could serve as a vertebrate model to study NNV (doi: 10.3389/fimmu.2022.863096).

(4) The results shown in Figure 6 are not enough to support the conclusion that "RGNNV triggers macropinocytosis mediated by MmMYL3". Additional electron microscopy of macropinosomes (sizes, morphological characteristics, etc.) will be more direct evidence.

(5) MYL3 is "predominantly found in muscle tissues, particularly the heart and skeletal muscles". However, NNV is a virus that mainly causes necrosis of nervous tissues (brain and retina). If MYL3 really acts as a receptor for NNV, how does it balance this difference so that nervous tissues, rather than muscle tissues, have the highest viral titers?

Reviewer #2 (Public review):

Summary:

The manuscript offers an important contribution to the field of virology, especially concerning NNV entry mechanisms. The major strength of the study lies in the identification of MmMYL3 as a functional receptor for RGNNV and its role in macropinocytosis, mediated by the IGF1R-Rac1/Cdc42 signaling axis. This represents a significant advance in understanding NNV entry mechanisms beyond previously known receptors such as HSP90ab1 and HSC70. The data, supported by comprehensive in vitro and in vivo experiments, strongly justify the authors' claims about MYL3's role in NNV infection in marine medaka.

Strengths:

(1) The identification of MmMYL3 as a functional receptor for RGNNV is a significant contribution to the field. The study fills a crucial gap in understanding the molecular mechanisms governing NNV entry into host cells.

(2) The work highlights the involvement of IGF1R in macropinocytosis-mediated NNV entry and downstream Rac1/Cdc42 activation, thus providing a thorough mechanistic understanding of NNV internalization process. This could pave the way for further exploration of antiviral targets.

Reviewer #3 (Public review):

Summary:

The manuscript presents a detailed study on the role of MmMYL3 in the viral entry of NNV, focusing on its function as a receptor that mediates viral internalization through the macropinocytosis pathway. The use of both in vitro assays (e.g., Co-IP, SPR, and GST pull-down) and in vivo experiments (such as infection assays in marine medaka) adds robustness to the evidence for MmMYL3 as a novel receptor for RGNNV. The findings have important implications for understanding NNV infection mechanisms, which could pave the way for new antiviral strategies in aquaculture.

Strengths:

The authors show that MmMYL3 directly binds the viral capsid protein, facilitates NNV entry via the IGF1R-Rac1/Cdc42 pathway, and can render otherwise resistant cells susceptible to infection. This multifaceted approach effectively demonstrates the central role of MmMYL3 in NNV entry.

Reviewer #1 (Public review):

In this manuscript, Domingo et al. present a novel perturbation-based approach to experimentally modulate the dosage of genes in cell lines. Their approach is capable of gradually increasing and decreasing gene expression. The authors then use their approach to perturb three key transcription factors and measure the downstream effects on gene expression. Their analysis of the dosage response curve of downstream genes reveals marked non-linearity.

One of the strengths of this study is that many of the perturbations fall within the physiological range for each cis gene. This range is presumably between a single-copy state of heterozygous loss-of-function (log fold change of -1) and a three-copy state (log fold change of ~0.6). This is in contrast with CRISPRi or CRISPRa studies that attempt to maximize the effect of the perturbation, which may result in downstream effects that are not representative of physiological responses.

Another strength of the study is that various points along the dosage-response curve were assayed for each perturbed gene. This allowed the authors to effectively characterize the degree of linearity and monotonicity of each dosage-response relationship. Ultimately, the study revealed that many of these relationships are non-linear, and that the response to activation can be dramatically different than the response to inhibition.

To test their ability to gradually modulate dosage, the authors chose to measure three transcription factors and around 80 known downstream targets. As the authors themselves point out in their discussion about MYB, this biased sample of genes makes it unclear how this approach would generalize genome-wide. In addition, the data generated from this small sample of genes may not represent genome-wide patterns of dosage response. Nevertheless, this unique data set and approach represents a first step in understanding dosage-response relationships between genes.

Another point of general concern in such screens is the use of the immortalized K562 cell line. It is unclear how the biology of these cell lines translates to the in vivo biology of primary cells. However, the authors do follow up with cell-type-specific analyses (Figures 4B, 4C, and 5A) to draw a correspondence between their perturbation results and the relevant biology in primary cells and complex diseases.

The conclusions of the study are generally well supported with statistical analysis throughout the manuscript. As an example, the authors utilize well-known model selection methods to identify when there was evidence for non-linear dosage response relationships.

Gradual modulation of gene dosage is a useful approach to model physiological variation in dosage. Experimental perturbation screens that use CRISPR inhibition or activation often use guide RNAs targeting the transcription start site to maximize their effect on gene expression. Generating a physiological range of variation will allow others to better model physiological conditions.

There is broad interest in the field to identify gene regulatory networks using experimental perturbation approaches. The data from this study provides a good resource for such analytical approaches, especially since both inhibition and activation were tested. In addition, these data provide a nuanced, continuous representation of the relationship between effectors and downstream targets, which may play a role in the development of more rigorous regulatory networks.

Human geneticists often focus on loss-of-function variants, which represent natural knock-down experiments, to determine the role of a gene in the biology of a trait. This study demonstrates that dosage response relationships are often non-linear, meaning that the effect of a loss-of-function variant may not necessarily carry information about increases in gene dosage. For the field, this implies that others should continue to focus on both inhibition and activation to fully characterize the relationship between gene and trait.

Reviewer #2 (Public review):

Summary:

This work investigates transcriptional responses to varying levels of transcription factors (TFs). The authors aim for gradual up- and down-regulation of three transcription factors GFI1B, NFE2, and MYB in K562 cells, by using a CRISPRa- and a CRISPRi line, together with sgRNAs of varying potency. Targeted single-cell RNA sequencing is then used to measure gene expression of a set of 90 genes, which were previously shown to be downstream of GFI1B and NFE2 regulation. This is followed by an extensive computational analysis of the scRNA-seq dataset. By grouping cells with the same perturbations, the authors can obtain groups of cells with varying average TF expression levels. The achieved perturbations are generally subtle, not reaching half or double doses for most samples, and up-regulation is generally weak below 1.5-fold in most cases. Even in this small range, many target genes exhibit a non-linear response. Since this is rather unexpected, it is crucial to rule out technical reasons for these observations.

Strengths:

The work showcases how a single dataset of CRISPRi/a perturbations with scRNA-seq readout and an extended computational analysis can be used to estimate transcriptome dose responses, a general approach that likely can be built upon in the future.

Weaknesses:

(1) The experiment was only performed in a single replicate. In the absence of an independent validation of the main findings, the robustness of the observations remains unclear.

(2) The analysis is based on the calculation of log-fold changes between groups of single cells with non-targeting controls and those carrying a guide RNA driving a specific knockdown. How the fold changes were calculated exactly remains unclear, since it is only stated that the FindMarkers function from the Seurat package was used, which is likely not optimal for quantitative estimates. Furthermore, differential gene expression analysis of scRNA-seq data can suffer from data distortion and mis-estimations (Heumos et al. 2023 (https://doi.org/10.1038/s41576-023-00586-w), Nguyen et al. 2023 (https://doi.org/10.1038/s41467-023-37126-3)). In general, the pseudo-bulk approach used is suitable, but the correct treatment of drop-outs in the scRNA-seq analysis is essential.

(3) Two different cell lines are used to construct dose-response curves, where a CRISPRi line allows gene down-regulation and the CRISPRa line allows gene upregulation. Although both lines are derived from the same parental line (K562) the expression analysis of Tet2, which is absent in the CRISPRi line, but expressed in the CRISPRa line (Figure S3A) suggests substantial clonal differences between the two lines. Similarly, the PCA in S4A suggests strong batch effects between the two lines. These might confound this analysis.

(4) The study uses pseudo-bulk analysis to estimate the relationship between TF dose and target gene expression. This requires a system that allows quantitative changes in TF expression. The data provided does not convincingly show that this condition is met, which however is an essential prerequisite for the presented conclusions. Specifically, the data shown in Figure S3A shows that upon stronger knock-down, a subpopulation of cells appears, where the targeted TF is not detected anymore (drop-outs). Also Figure 3B (top) suggests that the knock-down is either subtle (similar to NTCs) or strong, but intermediate knock-down (log2-FC of 0.5-1) does not occur. Although the authors argue that this is a technical effect of the scRNA-seq protocol, it is also possible that this represents a binary behavior of the CRISPRi system. Previous work has shown that CRISPRi systems with the KRAB domain largely result in binary repression and not in gradual down-regulation as suggested in this study (Bintu et al. 2016 (https://doi.org/10.1126/science.aab2956), Noviello et al. 2023 (https://doi.org/10.1038/s41467-023-38909-4)).

(5) One of the major conclusions of the study is that non-linear behavior is common. This is not surprising for gene up-regulation, since gene expression will reach a plateau at some point, but it is surprising to be observed for many genes upon TF down-regulation. Specifically, here the target gene responds to a small reduction of TF dose but shows the same response to a stronger knock-down. It would be essential to show that his observation does not arise from the technical concerns described in the previous point and it would require independent experimental validations.

(6) One of the conclusions of the study is that guide tiling is superior to other methods such as sgRNA mismatches. However, the comparison is unfair, since different numbers of guides are used in the different approaches. Relatedly, the authors point out that tiling sometimes surpassed the effects of TSS-targeting sgRNAs, however, this was the least fair comparison (2 TSS vs 10 tiling guides) and additionally depends on the accurate annotation of TSS in the relevant cell line.

(7) Did the authors achieve their aims? Do the results support the conclusions?: Some of the most important conclusions are not well supported because they rely on accurately determining the quantitative responses of trans genes, which suffers from the previously mentioned concerns.

(8) Discussion of the likely impact of the work on the field, and the utility of the methods and data to the community:<br /> Together with other recent publications, this work emphasizes the need to study transcription factor function with quantitative perturbations. Missing documentation of the computational code repository reduces the utility of the methods and data significantly.

Reviewer #1 (Public review):

Summary:

In this paper, Blancke Soares and Stäcker et al serendipitously identify a domain of the Plasmodium falciparum protein MSRP6 that mediates both export from the parasite into the infected red blood cell and association with the Maurer's cleft organelles found in the infected cell. The authors use this domain to identify a putative complex of proteins at the Maurer's cleft via proximity biotinylation. Six members of the complex are confirmed to interact with MSRP6 by co-immunoprecipitation.

The functions of select proteins of this complex are further investigated with regard to the formation of Maurer's clefts. Disruption of PeMP2, PIESP2, and Pf332 resulted in morphological changes to the Maurer's clefts and prevented the anchoring of the Maurer's clefts to the infected red blood cell plasma membrane that normally occurs in the trophozoite stage. Curiously, disruption of MSRP6, the central member of the complex, did not affect Maurer's cleft anchoring. Mechanistically, how this complex affects Maurer's cleft structure and anchoring remains unclear.

Finally, the authors show that the loss of Maurer's cleft anchoring observed upon disruption of PIESP2 or Pf332 does not affect cytoadherence of infected red blood cells via PfEMP1, arguing against a prior assumption that cleft tethering is required for the presentation of parasite-exported proteins on the infected red blood cell surface.

Strengths:

Maurer's clefts are enigmatic organelles found in red blood cells infected by Plasmodium falciparum that are presumed to play a role in trafficking exported parasite proteins to the surface of the red blood cells, though little is known about their biogenesis and function. The authors here convincingly identify a protein complex present at the Maurer's clefts using multiple orthogonal tools, and carry out assays that indicate this protein complex has a role in shaping and anchoring the Maurer's clefts at their final location at the red blood cell membrane. The data indicating that Maurer's cleft anchoring is dispensable for trafficking of P. falciparum exported proteins to the infected red blood cell membrane has implications for understanding the function of this organelle.

Weaknesses:

In many instances, the data lack appropriate controls that would be desirable for the highest level of rigor. Many, if not most, fluorescence microscopy assays lack untagged/parental controls (prepared in parallel and captured with the same settings) that are necessary to determine the validity of the data - that the observed signal is specific to the protein of interest and not due to autofluorescence or bleed-through from other channels. In other cases, wild-type controls are missing where data from disruption mutants are presented. Additionally, while some phenotypes are quantified, others are only qualitatively described where a more thorough quantitative investigation would be valuable. Finally, where phenotypes have been quantified, in many instances it is not clear that the analyses have included biological replicates as would be expected.

Reviewer #2 (Public review):

Summary:

Soares et al characterize several P. falciparum exported proteins that localize to Maurer's Clefts (MCs), membrane structures formed in the host erythrocyte cytosol. MCs are thought to act as sorting stations that mediate the trafficking of effector proteins to the erythrocyte membrane, such as the surface adhesin and major virulence factor PfEMP1. While initially mobile within the host cytosol, MCs become anchored at the erythrocyte periphery around the time PfEMP1 appears on the RBC surface. While MC immobilization is thought to be important for the delivery of PfEMP1 onto the erythrocyte surface, this hypothesis has remained untested due to the lack of mutants that prevent anchoring. The study begins by determining the sequence features able to mediate the export of PF3D7_0830300 and MSRP6, both PEXEL-Negative Exported Proteins (PNEPs) with signal peptides. The authors show that in both proteins, a region downstream of the signal peptide is sufficient to mediate export, indicating the mature N-terminus is also important for the translocation of this type of PNEP, similar to other classes of exported proteins. Surprisingly, an additional C-terminal region of MSRP6 is also sufficient to mediate export when placed downstream of the signal peptide in the absence of other MSRP6 features. This region also mediates recruitment to MCs and was used as BioID bait to identify proximal MC proteins, several of which form a complex with MSRP6. Strikingly, disruption of certain MSRP6 interacting proteins (PeMP2, PIESP2, and Pf332) abolishes MC anchoring and in some cases also results in major changes in MC morphology. Surprisingly, neither PfEMP1 surface display nor cytoadhesion of infected RBCs is impacted in these mutants. This study features an impressive array of genetically modified parasites and will be of broad interest in providing the first functional analysis of MC anchoring, challenging the prevailing model for PfEMP1 trafficking within the infected RBC.

Strengths:

(1) The first section of the paper presents an in-depth dissection of the features that enable the export of signal peptide-containing PNEPs, confirming the mature N-terminus is sufficient for export across all known types of exported proteins. While it remains unknown how these features enable export, the results reinforce the universal importance of the mature N-terminus, whether generated by signal peptidase or Plasmepsin 5.

(2) The discovery that a C-terminal region of MSRP6 (MAD) is also sufficient for export is novel. The authors suggest this may be the result of piggybacking on another exported protein, although the discussion acknowledges there are challenges with this model since unfolding by PTEX would be expected to disrupt these interactions. An alternative might be considered: the related protein MSRP7 is also exported but consists essentially of a signal peptide and MSP7-like domain without the large N-terminal region found in MSRP6. Presumably, the mature N-terminus of MSRP7 mediates export. If MSRP6 is derived from an exported predecessor composed only of the MSP7-like domain (like MSRP7), the MAD domain might retain the ancestral export information near the beginning of the MSP7-like domain. If this were the case, then the MAD domain (3cd region) should only be sufficient to mediate export when positioned immediately after the signal peptide as in the experiment in Fig 3C (SP-3cd-GFP). It would be interesting to determine if an SP-GFP-3cd construct is exported.

(3) Disruption of PeMP2, PIESP2 or Pf332 is found to prevent MC anchoring. This is the most exciting part of the study as it provides the first set of mutants that interfere with anchoring, enabling the surprising observation that MC immobilization is not important for PfEMP1 surface display or cytoadhesion. The MC movement assay is a nice way to visualize anchoring and would be strengthened by a quantitative measure of colocalization between the time-lapse images (ie, Pearson correlation coefficient) to enable a statistical test. The use of SLI to specifically activate a var gene of choice is an exciting new approach that will be of great use to the PfEMP1 field together with the semi-automated binding assay that helps to increase throughput and reduce bias.

Weaknesses:

(1) At least two of the MSRP6 complex members were found to depend on other complex members for MC trafficking: PeMP3 depends on MSRP6 and Pf332 depends on PIESP2 (previously shown by Zhang et al 2018 and confirmed in the present study). While the authors disrupted all seven MSRP6 complex members, the impact on the trafficking of the other complex members was not systematically investigated. It would be particularly interesting to know which (if any) complex members are required for MC recruitment of PeMP2 since this protein is also needed for MC anchoring.

(2) Some images of exported puncta are interpreted as localization to the MCs without a co-marker. Since other compartments have been identified in the RBC cytosol in addition to MCs (ie, J dots), an MC co-marker would help to verify these actually correspond to MCs. For example, in Figure 5B, GEXP18 gives an exported punctate appearance but lack of co-localization with SBP1 in Fig S2B shows that this does not correspond to MCs.

(3) The authors show MAHRP2 localization is not impacted in their PIESP2 and Pf332 mutants and this is interpreted to indicate the tether structures are not disrupted. However, this conclusion requires actual analysis of the tether structures by electron microscopy since MAHRP2 association to MCs may not require tether integrity and could persist even if the tethers are altered or disrupted. Otherwise, this statement should be adjusted. Additionally, since T2A skipping efficiency can vary between constructs, it would be a good idea to perform a western blot to ensure that the SBP1-GFP and MAHRP2-mScarlet signals in Figure 8D,F reflect separated proteins.

(4) The trypsin assays to monitor PfEMP1 surface display would benefit from a more detailed explanation of how the results were interpreted. For instance, though perhaps less intense than in the PIESP2, Pf332, and MSRP6 mutants, a Var01-protected fragment is also seen in the SBP1 mutant. Additionally, a protected fragment is indicated for most of the SBP1N controls (asterisk). As per the author's experimental design (lines 956-957), does this indicate that the RBC membrane was partially compromised during the experiment? In line 505, the trypsin assay data in the mutants is interpreted relative to the parent IT4var01-HA line but no data is shown for the parent.

Reviewer #3 (Public review):

Summary:

Malaria is caused by Plasmodium falciparum parasites that infect, grow, and reproduce inside red blood cells. The parasites extensively modify the blood cells they infect, by exporting hundreds of proteins into the red blood cell compartment. One of the most important modifications made by the parasite is to display adhesive proteins on the blood cell surface which attach the infected cells to walls of small blood vessels. This can lead to organ damage resulting in serious disease complications and there is great interest in blocking the adhesive process to reduce disease. This study investigates the function of an atypical, exported protein that along with other proteins maintains the integrity of membranous sacs formed by the parasite in the blood cell compartment. These sacs are widely believed to help organise the display of the adhesive proteins on the infected blood cell surface. This study challenges this dogma by showing that disruption of the sacs does not prevent the display of the adhesive proteins suggesting alternative pathways are likely involved in adhesive protein display.

Strengths:

The conclusions are supported by a beautiful series of live parasite images.

Weaknesses:

No major weaknesses were identified by this reviewer.

Joint Public Review:

Previously, this group showed that Tgfbr1 regulates the reorganization of the epiblast and primitive streak into the chordo-neural hinge and tailbud during the trunk-to-tail transition. Gdf11 signaling plays a crucial role in orchestrating the transition from trunk to tail tissues in vertebrate embryos, including the reallocation of axial progenitors into the tailbud and Tgfbr1 plays a key role in mediating its signaling activity. Progenitors that contribute to the extension of the neural tube and paraxial mesoderm into the tail are located in this region. In this work, the authors show that Tgfbr1 also regulates the reorganization of the posterior primitive streak/base of allantois and the endoderm as well.

By analyzing the morphological phenotypes and marker gene expression in Tgfbr1 mutant mouse embryos, they show that it regulates the merger of somatic and splanchnic layers of the lateral plate mesoderm, the posterior streak derivative. They also present evidence suggesting that Tgfbr1 acts upstream of Isl1 (key effector of Gdf11 signaling for controlling differentiation of lateral mesoderm progenitors) and regulates the remodelling of the major blood vessels, the lateral plate mesoderm and endoderm associated with the trunk-to-tail transition. Through a detailed phenotypic analysis, the authors observed that, similarly to Isl1 mutants, the lack of Tgfbr1 in mouse embryos hinders the activation of hindlimb and external genitalia maker genes and results in a failure of lateral plate mesoderm layers to converge during tail development. As a result, they interpret that ventral lateral mesoderm, which generates the peri cloacal mesenchyme and genital tuberculum, fails to specify.

They also show defects in the morphogenesis of the dorsal aorta at the trunk/tail juncture, resulting in an aberrant embryonic/extraembryonic vascular connection. Endoderm reorganization defects following abnormal morphogenesis of the gut tube in the Tgfbr1 mutants cause failure of tailgut formation and cloacal enlargement. Thus, Tgfbr1 activity regulates the morphogenesis of the trunk/tail junction and the morphogenetic switch in all germ layers required for continuing post-anal tail development. Taken together with the previous studies, this work places Gdf11/8 - Tgfbr1 signaling at the pivot of trunk-to-tail transition and the authors speculate that critical signaling through Tgfbr1 occurs in the posterior-most part of the caudal epiblast, close to the allantois.

The data shown is solid with excellent embryology/developmental biology. This work demonstrates meticulous execution and is presented in a comprehensive and coherent manner. Although not completely novel, the results/conclusions add to the known function of Gdf11 signaling during the trunk-to-tail transition.

Reviewer #1 (Public review):

Summary:

The authors investigate ligand and protein-binding processes in GPCRs (including dimerization) by the multiple walker supervised molecular dynamics method. The paper is interesting and it is very well written.

Strengths:

The authors' method is a powerful tool to gain insight on the structural basis for the pharmacology of G protein-coupled receptors.

Reviewer #2 (Public review):

The study by Deganutti and co-workers is a methodological report on an adaptive sampling approach, multiple walker supervised molecular dynamics (mwSuMD), which represents an improved version of the previous SuMD.<br /> Case-studies concern complex conformational transitions in a number of G protein Coupled Receptors (GPCRs) involving long time-scale motions such as binding-unbinding and collective motions of domains or portions. GPCRs are specialized GEFs (guanine nucleotide exchange factors) of heterotrimeric Gα proteins of the Ras GTPase superfamily. They constitute the largest superfamily of membrane proteins and are of central biomedical relevance as privileged targets of currently marketed drugs.<br /> MwSuMD was exploited to address:

a) binding and unbinding of the arginine-vasopressin (AVP) cyclic peptide agonist to the V2 vasopressin receptor (V2R);<br /> b) molecular recognition of the β2-adrenergic receptor (β2-AR) and heterotrimeric GDP-bound Gs protein;<br /> c) molecular recognition of the A1-adenosine receptor (A1R) and palmotoylated and geranylgeranylated membrane-anchored heterotrimeric GDP-bound Gi protein;<br /> d) the whole process of GDP release from membrane-anchored heterotrimeric Gs following interaction with the glucagon-like peptide 1 receptor (GLP1R), converted to the active state following interaction with the orthosteric non-peptide agonist danuglipron.

The revised version has improved clarity and rigor compared to the original also thanks to the reduction in the number of complex case studies treated superficially.<br /> The mwSuMD method is solid and valuable, has wide applicability and is compatible with the most world-widely used MD engines. It may be of interest to the computational structural biology community.<br /> The huge amount of high-resolution data on GPCRs makes those systems suitable, although challenging, for method validation and development.<br /> While the approach is less energy-biased than other enhanced sampling methods, knowledge, at the atomic detail, of binding sites/interfaces and conformational states is needed to define the supervised metrics, the higher the resolution of such metrics is the more accurate the outcome is expected to be. Definition of the metrics is a user- and system-dependent process.

Reviewer #3 (Public review):

Summary:

In the present work Deganutti et al. report a structural study on GPCR functional dynamics using a computational approach called supervised molecular dynamics.

Strengths:

The study has potential to provide novel insight into GPCR functionality. Example is the interaction between D344 and R385 identified during the Gs coupling by GLP-1R. However, validation of the findings, even computationally through for instance in silico mutagenesis study, is advisable.

Weaknesses:

No significant advance of the existing structural data on GPCR and GPCR/G protein coupling is provided. Most of the results are reproductions of the previously reported structures.

Reviewer #1 (Public review):

Summary:

The authors describe that the endocytic pathway is crucial for ColI fibrillogenesis. ColI is endocytosed by fibroblasts, prior to exocytosis and formation of fibrils, which can include a mixture of endogenous/nascent ColI chains and exogenous ColI. ColI uptake and fibrillogenesis are regulated by circadian rhythm as described by the authors in 2020, thanks to the dependence of this pathway on circadian-clock-regulated protein VPS33B. Cells are capable of forming fibrils with recently endocytosed ColI along when nascent chains are not available. Previously identified VPS33B is demonstrated not to have a role in endocytosis of ColI, but to play a role in fibril formation, which the authors demonstrate by showing the loss of fibril formation in VPS33B KO, and an excess of insoluble fibrils - along-side a decrease in soluble ColI secretion - in VPS33B overexpression conditions. A VPS33B binding protein VIPAS39 is also shown to be required for fibrillogenesis and to colocalise with ColI. The authors thus conclude that ColI is internalised into endosomal structures within the cell, and that ColI, VPS33B and VIPA39 are co-trafficked to the site of fibrillogenesis, where along with ITGA11, which by mass spectrometric analysis is shown to be regulated by VPS33B levels, ColI fibrils are formed. Interestingly, in involved human skin sections from idiopathic pulmonary fibrosis (IPF) patients, ITGA11 and VPS33B expression is increased compared to healthy tissue, while in patient-derived fibroblasts, uptake of fluorescently-labelled ColI is also increased. This suggests that there may be a significant contribution of endocytosis-dependent fibrillogenesis in the formation of fibrotic and chronic wound-healing diseases in humans.

Strengths:

This is an interesting paper that contributes an exciting novel understanding of the formation of fibrotic disease, which despite its high occurrence, still has no robust therapeutic options. The precise mechanisms of fibrillogenesis are also not well understood, so a study devoted to this complex and key mechanism is well appreciated. The dependence of fibrillogenesis on VPS33B and VIPA39 is convincing and robust, while the distinction between soluble ColI secretion and insoluble fibrillar ColI is interesting and informative.

Weaknesses:

There are a number of limitations to this study in its current state. Inhibition of ColI uptake is performed using Dyngo4a, which although proposed as an inhibitor of Clathrin-dependent endocytosis is known to be quite un-specific. This may not be a problem however, as the endocytic mechanism for ColI also does not seem to be well defined in the literature, in fact, the principle mechanism described in the papers referred to by the authors is that of phagocytosis. It would be interesting to explore this important part of the mechanism further, especially in relation to the intracellular destination of ColI. The circadian regulation does not appear as robust as the authors last paper, however, there could be a larger lag between endocytosis of ColI and realisation of fibrils. The authors state that the endocytic pathway is the mechanism of trafficking and that they show ColI, VPS33B and VIPA39 are co-trafficked. However, the only link that is put forward to the endosomes is rather tenuously through VPS33B/VIPA39. There is no direct demonstration of ColI localisation to endosomes (ie. immunofluorescence), and this is overstated throughout the text. Demonstrating the intracellular trafficking and localisation of ColI, and its actual relationship to VPS33B and VIPA39, followed by ITGA11, would broaden the relevance of this paper significantly to incorporate the field of protein trafficking. Finally, the "self-formation" of ColI fibrils is discussed in relation to the literature and the concentration of fluorescently-tagged ColI, however as the key message of the paper is the fibrillogenesis from exocytosed colI, I do not feel like it is demonstrated to leave no doubt. Specific inhibition of intracellular trafficking steps, or following the progressive formation of ColI fibrils over time by immunofluorescence would demonstrate without any further doubt that ColI must be endocytosed first, to form fibrils as a secondary step, rather than externally-added ColI being incorporated directly to fibrils, independent of cellular uptake.

Reviewer #3 (Public review):

Summary:

Chang et al. investigated the mechanisms governing collagen fibrillogenesis, firstly demonstrating that cells within tail tendons are able to uptake exogenous collagen and use this to synthesize new collagen-1 fibrils. Using an endocytic inhibitor, the authors next showed that endocytosis was required for collagen fibrillogenesis and that this process occurs in a circadian rhythmic manner. Using knockdown and overexpression assays, it was then demonstrated that collagen fibril formation is controlled by vacuolar protein sorting 33b (VPS33b), and this VPS33b-dependent fibrillogenesis is mediated via Integrin alpha-11 (ITGA11). The authors also demonstrated increased expression of VPS33b and ITGA11 at the gene level in fibroblasts from patients with idiopathic pulmonary fibrosis (IPF), and greater expression of these proteins in both lung samples from IPF patients and in chronic skin wounds, indicating that endocytic recycling is disrupted in fibrotic diseases. Finally, the authors performed knockdown assays in patient derived IPF fibroblasts to confirm that silencing of VPS33b and ITGA11 results in a decrease in recycling of exogenous collagen-1

Strengths:

The authors have performed a comprehensive functional analysis of the regulators of endocytic recycling of collagen, providing compelling evidence that VPS33b and ITGA11 are crucial regulators of this process, and that this endocytic recycling becomes disrupted in fibrotic diseases.

Joint Public Review:

Summary:

This work provides a new general tool for predicting post-ERCP pancreatitis before the procedure depending on pancreatic calcification, female sex, intraductal papillary mucinous neoplasm, a native papilla of Vater, or the use of pancreatic duct procedures. Even though it is difficult for the endoscopist to predict before the procedure which case might have post-ERCP pancreatitis, this new model score can help with the maneuver and when the patient is at high risk of pancreatitis, sometimes can be deadly), so experienced endoscopists can do the procedure from the start. This paper provides a model for stratifying patients before the ERCP procedure into low, moderate, and high risk for pancreatitis. To be validated, this score should be done in many countries and on large numbers of patients. Risk factors can also be identified and added to the score to increase rank.

Strengths:

(1) One of the severe complications of endoscopic retrograde cholangiopancreatography procedure is pancreatitis, so investigators try all the time to find a score that can predict which patients will probably have pancreatitis after the procedure. Most scores depend on the intraprocedural maneuver. Some studies discuss the preprocedural score that can predict pancreatitis before the procure. This study discusses a new preprocedural score for post-ERCP pancreatitis.

(2) Depending on this score that identifies low, moderate, and high-risk patients for post-pancreatitis, so from the start, experienced and well-trained endoscopists can do the procedure or can refer patients to tertiary hospitals or use interventional radiology or endoscopic retrograde cholangiopancreatography.

(3) The number of patients in this study is sufficient to analyze data correctly.

Weaknesses:

(1) It is a single-country, retrospective study.

(2) Many cases were excluded, so the score cannot be applied to those patients.

Comments on revised version:

Depending on old references cannot help us know the current situation. What if there are better more recent predictive tools? It would be better to test the validity of that score against, if present, a proven score to check its validity.

Reviewer #1 (Public review):

Summary

The authors determine the phylogenetic relation of the roughly two dozen wtf elements of 21 S. pombe isolates and show that none of them in the original S. pombe are essential for robust mitotic growth. It would be interesting to test their meiotic function by simply crossing each deletion mutant with the parent and analyzing spores for non-Mendelian inheritance. If this has been reported already, that information should be added to the manuscript. If not, I suggest the authors do these simple experiments and add this information.

Strengths:

The most interesting data (Figure 4) show that one recombinant (wtfC4) between wtf18 and wtf23 produces in mitotic growth a poison counteracted by its own antidote but not by the parental antidotes. Again, it would be interesting to test this recombinant in a more natural setting - meiosis between it and each of the parents.

Weaknesses:

In the opinion of this reviewer, some minor rewriting is needed.

Reviewer #2 (Public review):

Summary:

This important study provides a mechanism that can explain the rapid diversification of poison-antidote pairs (wtf genes) in fission yeast: recombination between existing genes.

Strengths:

The authors analyzed the diversity of wtf in S. pombe strains, and found pervasive copy number variations. They further detected signals of recurrent recombination in wtf genes. To address whether recombination can generate novel wtf genes, the authors performed artificial recombination between existing wft genes, and showed that indeed a new wtf can be generated: the poison cannot be detoxified by the antidotes encoded by parental wtf genes but can be detoxified by own antidote.

Weaknesses:

The study can benefit from demonstrating that the novel poison-antidote constructed by the authors can serve as a meiotic driver.

Reviewer #3 (Public review):

Summary:

In this manuscript, Wang and colleagues explore factors contributing to the diversification of wtf meiotic drivers. wtf genes are autonomous, single-gene poison-antidote meiotic drivers that encode both a spore-killing poison (short isoform) and an antidote to the poison (long isoform) through alternative transcriptional initiation. There are dozens of wtf drivers present in the genomes of various yeast species, yet the evolutionary forces driving their diversification remain largely unknown. This manuscript is written in a straightforward and effective manner, and the analyses and experiments are easy to follow and interpret. While I find the research question interesting and the experiments persuasive, they do not provide any deeper mechanistic understanding of this gene family.

Strengths:

(1) The authors present a comprehensive compendium and analysis of the evolutionary relationships among wtf genes across 21 strains of S. pombe.

(2) The authors found that a synthetic chimeric wtf gene, combining exons 1-5 of wtf23 and exon 6 of wtf18, behaves like a meiotic driver that could only be rescued by the chimeric antidote but neither of the parental antidotes. This is a very interesting observation that could account for their inception and diversification.

Weaknesses:

(1) Deletion strains

The authors separately deleted all 25 Wtf genes in the S. pombe ference strain. Next, the authors performed a spot assay to evaluate the effect of wtf gene knockout on the yeast growth. They report no difference to the WT and conclude that the wtf genes might be largely neutral to the fitness of their carriers in the asexual life cycle at least in normal growth conditions.

The authors could have conducted additional quantitative growth assays in yeast, such as growth curves or competition assays, which would have allowed them to detect subtle fitness effects that cannot be quantified with a spot assay. Furthermore, the authors do not rule out simpler explanations, such as genetic redundancy. This could have been addressed by crossing mutants of closely related paralogs or editing multiple wtf genes in the same genetic background.

Another concern is the lack of detailed information about the 25 knockout strains used in the study. There is no information provided on how these strains were generated or, more importantly, validated. Many of these wtf genes have close paralogs and are flanked by repetitive regions, which could complicate the generation of such deletion strains. As currently presented, these results would be difficult to replicate in other labs due to insufficient methodological details

(2) Lack of controls

The authors found that a synthetic chimeric wtf gene, constructed by combining exons 1-5 of wtf23 and exon 6 of wtf18, behaves as a meiotic driver that can be rescued only by its corresponding chimeric antidote, but not by either of the parental antidotes (Figure 4F). In contrast, three other chimeric wtf genes did not display this property (Figure 4C-E). No additional experiments were conducted to explain these differences, and basic control experiments, such as verifying the expression of the chimeric constructs, were not performed to rule out trivial explanations. This should be at the very least discussed. Also, it would have been better to test additional chimeras.

3. Statistical analyses

In line 130 the authors state that: "Given complex phylogenetic mixing observed among wtf genes (Figure 1E), we tested whether recombination occurred. We detected signals of recombination in the 25 wtf genes of the S. pombe reference genome (p = 0) and in the wtf genes of the 21 S. pombe strains (p = 0) using pairwise homoplasy index (HPI) test. ". Reporting a p-value of 0 is not appropriate. Exact P-values should be reported.

Reviewer #1 (Public review):

In the manuscript Cyclin-dependent kinase 5 (Cdk5) activity is modulated by light and gates rapid phase shifts of the circadian clock Brenna et al., study the role of Cdk5 on circadian rhythms, the authors aim to elucidate the role of Cyclin-Dependent Kinase 5 (Cdk5) in modulating circadian rhythms, particularly in response to light cues. They hypothesized that Cdk5 acts as a gatekeeper, regulating the sensitivity of the circadian clock to light-induced phase shifts.

Strengths:

• Novelty: The study presents a novel mechanism by which Cdk5 influences circadian rhythms, particularly its role in modulating the light-induced phase-shifting response.<br /> • Experiments: The authors have employed a combination of molecular, cellular, and behavioural techniques, including genetic manipulations, biochemical assays, and electrophysiology, to investigate the role of Cdk5. The set of experiments performed in this work is non-trivial, done to a high standard and the additional experiments, data and textual alterations presented following the 1st round of review needs to be lauded.<br /> • Data: The data is well-presented in clear figures and appropriately described in the text.

Weaknesses:

• Although I found the data on Cdk5 gating light responses highly convincing there could be additional mechanisms which the authors have duly acknowledged and discussed in their text.<br /> In my assessment, the authors have convincingly demonstrated that Cdk5 plays a critical role in gating the light-induced phase-shifting response of the circadian clock. Their results strongly support their conclusions, as evidenced by their findings:<br /> This study provides valuable insights into the molecular mechanisms underlying circadian rhythm regulation and the impact of light on the circadian clock. The findings have the potential to influence future research in the field of chronobiology and may have implications for understanding and treating circadian rhythm disorders.<br /> The methods and data presented in this study are valuable to the field and can be used to further investigate the role of Cdk5 and other signalling pathways in circadian rhythm regulation.<br /> Broader context<br /> The circadian clock is a fundamental biological process that regulates various physiological functions, including sleep-wake cycles, hormone secretion, and metabolism. Disruptions to the circadian clock have been linked to a variety of health problems, such as sleep disorders, metabolic disorders, and cancer. Understanding the molecular mechanisms that underlie circadian rhythm regulation is essential for developing effective treatments for these disorders.

All in all, I have no reservations regarding the manuscript titled "Cyclin-dependent kinase 5 (Cdk5) activity is modulated by light and gates rapid phase shifts of the circadian clock by Brenna et al. After consideration of the authors' revisions, I believe the manuscript has been significantly improved. I commend the authors for their diligence in addressing the reviewers' comments and for the quality of their research.

Reviewer #2 (Public review):

Summary:

Definition of the role of CdK5 in circadian locator activity and light induced neural activity in the mouse SCN in-vivo revealing its mode of action through PKA-CaMK-CREB signaling pathway.

Strengths:

The experimental approaches are carried from in-vivo, to cellular and molecular level and provide first evidence for the specific involvement of CdK5 in light-induced phase advance of the free-running rhythm.

Weaknesses:

The behavioral analyses are limited to some selected parameters.

Downstream effects on circadian oscillation of gene expression and physiological functions in other brain regions, organs is missing.

Comments on revisions:

I am happy with the manuscript in its present form.

Reviewer #1 (Public review):

Summary:

In this manuscript, the authors train mice on a two-armed bandit task, in which the reward value associated with the arms suddenly switches in a pseudorandom fashion. Their first finding is that the mice are able to anticipate the reward value switch points after long blocks, evident both prior to the switch point with higher rates of switching to the less-rewarded arm, and after the switch point with faster transition to the more-rewarded arm. They next find that unilateral ACAd/MO lesion / optogenetic silencing (surprisingly) causes greater anticipation of reward switch points, both prior to and after the switch point. They use behavioral modeling to argue that the unilateral ACAd/MO lesion effects are due to an increase in the contralateral hazard rate. Finally, they found that bilateral lesions did not have any effect on the hazard rate, suggesting that the unilateral lesion effect is due to balancing between hemispheres. This manuscript employed a clever behavioral design and analysis approach, though the effects were somewhat difficult to interpret and the author's interpretation relies heavily on the accuracy of their underlying behavioral model.

Strengths:

This paper employs a well-designed task that allows the researchers to detect whether mice have noticed a change in reward value both before and after the change takes place. The use of unilateral and bilateral inactivation experiments allowed the authors to test the role of the ACAd/MO region in the change point estimation. They found that unilateral inactivation, but not bilateral inactivation, had a significant effect on behavior. They performed sophisticated behavioral analysis to determine how ACAd/MO perturbations affect decision-making variables. This topic is of interest to the field, and the results are presented clearly and generally convincing.

Weaknesses:

The observed effects of the lesions are somewhat counterintuitive, with lesions appearing to affect persistence within a block more than change point detection itself-the mice actually adjusted more quickly to changes in reward values. Moreover, they had no issue detecting change points after bilateral inactivation. As a result, I'm not sure if the main framing of the article (including the title) is supported by their findings. Finally, I was unsure how the differences between unilateral and bilateral inactivation could be explained by their behavioral model.

Reviewer #2 (Public review):

Summary:

The manuscript by Murphy et al. titled "Change point estimation by the mouse medial prefrontal cortex during probabilistic reward learning" investigated the role of the mPFC in the exploitation of task structure. Previous work had shown that monkeys and humans exploit predictable task structures (e.g., switching rapidly when heavily trained a reversal learning task), but whether this was also the case for mice was not known. To test this, Murphy et al. trained head-fixed mice on a two-armed bandit task in which the contingencies reversed when mice met a performance criterion (10 trials choosing the better option) plus an additional random number of trials (referred to as Lrandom). They found that as the length of Lrandom increased, mice began to exhibit pre-emptive switching in their choices as if they were expecting and/or anticipating the reversal to occur. They report that unilateral lesions of the mPFC (ACC + MO) led to earlier pre-emptive switching (although I found this part of the manuscript the most challenging to understand) and faster post-reversal switching that they argue reflects an impairment in the proper estimation of the reversal. They also report that this requires inter-hemispheric coordination because bilateral lesions did not further impair this estimation. Optogenetic inhibition just prior to the mouse making a choice recapitulated some of the behavioral metrics observed in the mPFC lesioned animals. Finally, the authors developed a novel hybrid belief-choice kernel model to provide a computational approach to quantifying these behavioral differences.

Strengths:

The paper is extremely well written and was an absolute pleasure to read. The results are novel and provide exciting (although not surprising) evidence that mice exploit task structures to earn rewards. Moreover, the experiments were well-designed and included appropriate controls and/or control conditions that support their findings.

Weaknesses:

Some of the results need to be clarified and/or language changed to ensure that readers will understand. Restricting analyses to expert mice that show the predicted effect is problematic.

Reviewer #3 (Public review):

Summary:

The authors examine the role of the medial frontal cortex of mice in exploiting statistical structure in tasks. They claim that mice are "proactive": they predict upcoming changes, rather than responding in a "model-free" way to environmental changes. Further, they speculate that the estimation of future change (i.e., prediction of upcoming events, based on learning temporal regularities) might be "a main ... function of dorsal medial frontal cortex (dmFC)." Unfortunately, the current manuscript contains flaws such that the evidence supporting these claims is inadequate.

Strengths:

Understanding the neural mechanisms by which we learn about statistical structure in the world is an important goal. The authors developed an interesting task and used model-based techniques to try to understand the mechanisms by which perturbation of dmFC influenced behavior. They demonstrate that lesions and optogenetic silencing of dmFC influence behavior, showing that this region has a causal influence on the task.

Weaknesses:

I was concerned that the main behavioral effects shown in Figure 1F were a statistical artifact. By requiring the Geometric block length to be preceded by a performance-based block, the authors introduce a dependence that can generate the phenomena they describe as anticipation.

To demonstrate this, I simulated their task with an agent that does not have any anticipation of the change point (Reviewer image 1). The agent repeats the previous action with probability `p(repeat)` (similar to the choice kernel in the author's models). If the agent doesn't repeat then the next choice depends on the previous outcome. If the previous choice was rewarded, it stays with `P(WS)` and chooses randomly with `1-P(WS)`. If the previous choice was unrewarded, it switches with `P(LS)` and chooses randomly with `1-P(LS)`.

Review image 1.

An agent with `P(WS)=P(LS)=P(repeat)=0.85` shows the same phenomena as the mice: a difference in performance before the block switch and "earlier" crossing of the midpoint after the switch. https://imgdrop.io/image/aHn6y. The phenomena go away in the simulations when a fixed block length of 20 trials is followed by a Geometric block length.

The authors did not completely rely on the phenomena of Figure 1F for their conclusions. They did a model comparison to provide evidence that animals are anticipating the switch. Unfortunately, the authors did not use state-of-the-art methods in this section of the paper. In particular, they failed to show that under a range of generative parameters for each model class, the model selection process chooses the correct model class (i.e. a confusion matrix). A more minor point, they used BIC instead of a more robust cross-validated metric for model selection. Finally, instead of comparing their "best" anticipating model to their 2nd best model (without anticipation), they compared their best to their 4th best (Supp Fig 3.5). This seems misleading.

Given all of the the above issues, it is hard to critically evaluate the model-based analysis of the effects of lesions/optogenetics.

Reviewer #1 (Public review):

Of course, there is always another layer of the onion, VAMP-seq measures contributions from isolated thermodynamic stability, stability conferred by binding partners (small molecule and protein), synthesis/degradation balance (especially important in "degron" motifs), etc. Here the authors' goal is to create simple models that can act as a baseline for two main reasons:<br /> (1) how to tell when adding more information would be helpful for a global model;<br /> (2) how to detect when a residue/mutation has an unusual profile indicative of an unbalanced contribution from one of the factors listed above.

As such, the authors state that this manuscript is not intended to be a state-of-the-art method in variant effect prediction, but rather a direction towards considering static structural information for the VAMP-seq effects. At its core, the method is a fairly traditional asymmetric substitution matrix (I was surprised not to see a comparison to BLOSUM in the manuscript) - and shows that a subdivision by burial makes the model much more predictive. Despite only having 6 datasets, they show predictive power even when the matrices are based on a smaller number. Another success is rationalizing the VAMPseq results on relevant oligomeric states.

Specific Feedback:

Major points:

The authors spend a good amount of space discussing how the six datasets have different distributions in abundance scores. After the development of their model is there more to say about why? Is there something that can be leveraged here to design maximally informative experiments?

They compare to one more "sophisticated model" - RosettaddG - which should be more correlated with thermodynamic stability than other factors measured by VAMP-seq. However, the direct head-to-head comparison between their matrices and ddG is underdeveloped. How can this be used to dissect cases where thermodynamics are not contributing to specific substitution patterns OR in specific residues/regions that are predicted by one method better than the other? This would naturally dovetail into whether there is orthogonal information between these two that could be leveraged to create better predictions.

Perhaps beyond the scope of this baseline method, there is also ThermoMPNN and the work from Gabe Rocklin to consider as other approaches that should be more correlated only with thermodynamics.

I find myself drawn to the hints of a larger idea that outliers to this model can be helpful in identifying specific aspects of proteostasis. The discussion of S109 is great in this respect, but I can't help but feel there is more to be mined from Figure S9 or other analyses of outlier higher than predicted abundance along linear or tertiary motifs.

Reviewer #2 (Public review):

Summary:

This study analyzes protein abundance data from six VAMP-seq experiments, comprising over 31,000 single amino acid substitutions, to understand how different amino acids contribute to maintaining cellular protein levels. The authors develop substitution matrices that capture the average effect of amino acid changes on protein abundance in different structural contexts (buried vs. exposed residues). Their key finding is that these simple structure-based matrices can predict mutational effects on abundance with accuracy comparable to more complex physics-based stability calculations (ΔΔG).

Major strengths:

(1) The analysis focuses on a single molecular phenotype (abundance) measured using the same experimental approach (VAMP-seq), avoiding confounding factors present when combining data from different phenotypes (e.g., mixing stability, activity, and fitness data) or different experimental methods.

(2) The demonstration that simple structural features (particularly solvent accessibility) can capture a significant portion of mutational effects on abundance.

(3) The practical utility of the matrices for analyzing protein interfaces and identifying functionally important surface residues.

Major weaknesses:

(1) The statistical rigor of the analysis could be improved. For example, when comparing exposed vs. buried classification of interface residues, or when assessing whether differences between prediction methods are significant.

(2) The mechanistic connection between stability and abundance is assumed rather than explained or investigated. For instance, destabilizing mutations might decrease abundance through protein quality control, but other mechanisms like degron exposure could also be at play.

(3) The similar performance of simple matrix-based and complex physics-based predictions calls for deeper analysis. A systematic comparison of where these approaches agree or differ could illuminate the relationship between stability and abundance. For instance, buried sites showing exposed-like behavior might indicate regions of structural plasticity, while the link between destabilization and degradation might involve partial unfolding exposing typically buried residues. The authors have all the necessary data for such analysis but don't fully exploit this opportunity.

(4) The pooling of data across proteins to construct the matrices needs better justification, given the observed differences in score distributions between proteins (for example, PTEN's distribution is shifted towards high abundance scores while ASPA and PRKN show more binary distributions).

(5) Some key methodological choices require better justification. For example, combining "to" and "from" mutation profiles for PCA despite their different behaviors, or using arbitrary thresholds (like 0.05) for residue classification.

The authors largely achieve their primary aim of showing that simple structural features can predict abundance changes. However, their secondary goal of using the matrices to identify functionally important residues would benefit from more rigorous statistical validation. While the matrices provide a useful baseline for abundance prediction, the paper could offer deeper biological insights by investigating cases where simple structure-based predictions differ from physics-based stability calculations.

This work provides a valuable resource for the protein science community in the form of easily applicable substitution matrices. The finding that such simple features can match more complex calculations is significant for the field. However, the work's impact would be enhanced by a deeper investigation of the mechanistic implications of the observed patterns, particularly in cases where abundance changes appear decoupled from stability effects.

Reviewer #3 (Public review):

"Effects of residue substitutions on the cellular abundance of proteins" by Schulze and Lindorff-Larsen revisits the classical concept of structure-aware protein substitution matrices through the scope of modern protein structure modelling approaches and comprehensive phenotypic readouts from multiplex assays of variant effects (MAVEs). The authors explore 6 unique protein MAVE datasets based on protein abundance (and thus stability) by utilizing structural information, specifically residue solvent accessibility and secondary structure type, to derive combinations of context-specific substitution matrices predicting variant abundance. They are clear to outline that the aim of the study is not to produce a new best abundance predictor but to showcase the degree of prediction afforded simply by utilizing information on residue accessibility. The performance of their matrices is robustly evaluated using a leave-one-out approach, where the abundance effects for a single protein are predicted using the remaining datasets. Using a simple classification of buried and solvent-exposed residues, and substitution matrices derived respectively for each residue group, the authors convincingly demonstrate that taking structural solvent accessibility contexts into account leads to more accurate performance than either a structure-unaware matrix, secondary structure-based matrix, or matrices combining both solvent accessibility or secondary structure. Interestingly, it is shown that the performance of the simple buried and exposed residue substitution matrices for predicting protein abundance is on par with Rosetta, an established and specialized protein variant stability predictor. More importantly, the authors finish off the paper by demonstrating the utility of the two matrices to identify surface residues that have buried-like substitution profiles, that are shown to correspond to protein interface residues, post-translational modification sites, functional residues, or putative degrons.

Strengths:

The paper makes a strong and well-supported main point, demonstrating the utility of the authors' approach through performance comparisons with alternative substitution matrices and specialized methods alike. The matrices are rigorously evaluated without introducing bias, exploring various combinations of protein datasets. Supplemental analyses are extremely comprehensive and detailed. The applicability of the substitution matrices is explored beyond abundance prediction and could have important implications in the future for identifying functionally relevant sites.

Comments:

(1) A wider discussion of the possible reasons why matrices for certain proteins seem to correlate better than others would be extremely interesting, touching upon possible points like differences or similarities in local environments, degradation pathways, post-translation modifications, and regulation. While the initial data structure differences provide a possible explanation, Figure S17A, B correlations show a more complicated picture.

(2) The performance analysis in Figure 2D seems to show that for particular proteins "less is more" when it comes to which datasets are best to derive the matrix from (CYP2C9, ASPA, PRKN). Are there any features (direct or proxy), that would allow to group proteins to maximize accuracy? Do the authors think on top of the buried vs exposed paradigm, another grouping dimension at the protein/domain level could improve performance?

(3) While the matrices and Rosetta seem to show similar degrees of correlation, do the methods both fail and succeed on the same variants? Or do they show a degree of orthogonality and could potentially be synergistic?

Overall, this work presents a valuable contribution by creatively utilizing a simple concept through cutting-edge datasets, which could be useful in various.

Reviewer #1 (Public review):

Summary:

In this manuscript, the authors investigate the cellular mechanism underlying suppression of adrenergic effects on excitatory transmission onto hypothalamic CRH neurons by stress. Experiments in ex-vivo slices show that this is a long-lasting effect that occurs through endocytosis of receptors. The authors then move into an immortalized hypothalamic cell line to enable investigation of the mechanism of changes in receptor trafficking. They use a series of immunohistochemistry, FRET, and biochemical experiments to show that application of corticosterone increases targeting of alpha1 adrenergic receptors to the late endosome and lysosome rather than the recycling endosome. Perhaps most interesting, they find that alpha1 receptors and glucocortioid receptors form a complex that is ultimately transferred to the nucleus.

Strengths:

Overall, the studies in this manuscript are rigorous and well-conducted. The data supports their conclusions, and they've shown convincingly that glucocorticoid signaling affects trafficking of alpha1 receptors in the culture system they are using. These findings are important for the field of stress research, both in understanding how two components of the stress system (norepinephrine and HPA axis) interact with each other and in neuromodulatory modulation of hypothalamic CRH neurons. Their finding that alpha1 receptors and glucocorticoid receptors form a complex is particularly interesting and maybe impactful outside of the immediate application in the hypothalamus.

Weaknesses:

The study has two primary weaknesses. First, the majority of the experiments were conducted in an immortalized hypothalamic cell line. This was necessary to conduct the type of experiments needed to test the author's hypothesis, but it remains unclear how closely these cells resemble CRH neurons, or how the same mechanism may be preserved or altered in an intact circuit. Further discussion of these points would strengthen the manuscript.<br /> Second, while experiments are generally well-designed, the authors do not show that the effects of corticosterone can be blocked with a glucocorticoid receptor antagonist. This is fairly standard pharmacology and would strengthen confidence in the findings presented in the study.

Reviewer #2 (Public review):

Summary:

In this manuscript, the authors report novel and exciting findings delineating a non-transcriptional mechanism whereby glucocorticoids desensitize CRH neurons to NE in response to somatic stress. The authors find that this desensitization induced by CORT 1. persists more than 18h, 2. reduces surface expression of AR1bR (NE receptors) by redirecting trafficking from rapid recycling to late endosomal pools and lysosomes, 3. is dependent on NE binding to the AR1bR, 4. involves cellular nitrosylation, 5. involves ubiquitination of beta-arrestin, and 5. involves interactions between glucocorticoid receptors and AR1bs, glucocorticoid receptors and ubiquitinated beta-arrestin, and AR1b and ubiquitinated beta-arrestin. While the authors do not directly provide evidence for a trimeric complex composed of these three proteins, their data that CORT causes translocation of these dimeric complexes to the cell nucleus suggests it is likely. Overall, these results are highly informative for understanding novel mechanisms mediating glucocorticoid regulation of GPCRs.

Strengths:<br /> - Good rationale for each experiment, which describes many parts of the CORT-NE desensitization mechanism<br /> - Great discussion of limitations of the approaches and the parts of the mechanism we do not fully understand yet<br /> - Appropriate approaches for questions being answered<br /> - Describes a highly novel CORT mechanism that non-transcriptionally switches GPCR trafficking dynamics, something that could have far reaching implications for other GPCRs involved in stress responses

Weaknesses:<br /> - Unclear how this mechanism would generalize to other stressor modalities. Restraint stress is a somatic stressor, but can also be considered a psychological stressor (model of depression-like behavior). A purely somatic stressor might increase the robustness of this phenomenon.<br /> - Remains unknown how nitrosylation plays into the mechanism in terms of specific proteins affected by CORT (GRK2, endophilin, clathrin possibilities)

Reviewer #3 (Public review):

Summary:

In this manuscript, Weiss et al describe a mechanism through which glucocorticoids desensitize CRH neurons in the PVN to norepinephrine. This follows on from previous work from this lab showing rapid glucocorticoid suppression of adrenergic signaling in CRH neurons specific to somatic stress activation, and modality-selective glucocorticoid negative feedback.

Specifically, their previous work shows that:<br /> (1) NE increases glutamate drive to CRH neurons<br /> (2) CORT blunts the effects of NE through a dynamin-dependent mechanism<br /> (3) This contributes to loss of NE signalling after stress (specifically when the second stressor is a physiological one)

Here they extend this line of interrogation by showing that CORT redistributes Ara1b receptors from rapid recycling endosomes to late endosomes and lysosomes. They show a time window of CORT actions and provide additional mechanistic details implicating nitric oxide-dependent nitrosylation in receptor trafficking.

Strengths:

Builds on existing work to provide additional mechanistic details.<br /> The experiments are well done and data are compelling.<br /> The link to nitrosylation is novel (but see below)

Weaknesses:

(1) The link to nitrosylation is interesting, but a bit confusing. If I understand correctly, inhibiting the production of NO or using NEM increases receptor internalization, suggesting that NO-dependent nitrosylation prevents ligand-dependent internalization. What is unclear to me is how CORT is linked to this step. I note the authors show a decrease in nitrosylation with CORT. So, does CORT decrease the activity of NOS and, thus, the production of NO? If so, then exogenously activating this system in the presence of CORT should result in a recovery of NE-dependent increase in glutamate release. Or is the GCR directly decreasing nitrosylation? Linking these elements is critical in terms of furthering our mechanistic understanding of this process.

(2) It's not clear why/how blockade of Ara1 after CORT-induced cytosolic accumulation results in a reversal of effect. Unless I misunderstood something, this requires further explanation.

Reviewer #1 (Public Review):

The authors were curious about the formation of the electrosensory lateral line, which is found in non-traditional model organisms. This issue has traditionally hampered studies because those organisms are not amenable to controlled experimental work.

The authors skillfully use CRIPR-based technologies to overcome this limitation. Together with exceptionally good whole-mount in situ hybridisation, they produced a well-supported conclusion that Bmp signalling has different roles in the development of electrosensory ampullary organs.

I would not entirely agree that Bmp signalling has "opposing" roles because the authors do not show evidence of opposition via gain-of-function experiments at different developmental times. Instead, they are simply different at different periods of organogenesis.

The study is important for understanding the development of a still-mysterious sensory system, and for its implications in evolutionary biology more generally.

Reviewer #2 (Public Review):

Campbell et al have described the dynamic pattern of two Bmps (Bmp5, Bmp4), one of their receptors (Acvr2a), putative joint inhibitors of the Bmp & Wnt pathways (sostdc1, apcdd1) and an effector of Bmp signaling phosph-Smad, in the experimentally tractable sterlet sturgeon to better understand the role of Bmp signaling in electroreceptor development. The role of Bmp signaling is poorly understood in the lateral line system. Furthermore, the development of electroreceptors in ampullary organs remains poorly understood as most recent analysis of lateral line development has focused on model organisms Xenopus and zebrafish, which the electroreceptors have been lost. They show that expression of these players is consistent with a role for Bmp signaling in electroreceptor development. Furthermore, they show that Bmp5 crispants have fewer ampullary organs. However, inhibition of Bmp signaling with the small molecule inhibitor DMH1 for 20 hours starting from stage 36 after hatching and before ampullary organ development results in supernumerary ampullary organ development. These strikingly different results lead the authors to conclude that Bmp signaling has opposing roles in ampullary organ development.

These observations are interesting and the conclusions are supported by the data presented and the study makes important contributions to our understanding of the role of Bmp signaling in electroreceptor development in lateral line development. However, the study opens and leaves unresolved a number of questions. While a definitive answer to these questions may be outside the scope of this paper, some additional experiments may help strengthen the paper.

Reviewer #1 (Public review):

Summary:

"Neural noise", here operationalized as an imbalance between excitatory and inhibitory neural activity, has been posited as a core cause of developmental dyslexia, a prevalent learning disability that impacts reading accuracy and fluency. This is study is the first to systematically evaluate the neural noise hypothesis of dyslexia. Neural noise was measured using neurophysiological (electroencephalography [EEG]) and neurochemical (magnetic resonance spectroscopy [MRS]) in adolescents and young adults with and without dyslexia. The authors did not find evidence of elevated neural noise in the dyslexia group from EEG or MRS measures, and Bayes factors generally informed against including the grouping factor in the models. Although the comparisons between groups with and without dyslexia did not support the neural noise hypothesis, a mediation model that quantified phonological processing and reading abilities continuously revealed that EEG beta power in the left superior temporal sulcus was positively associated with reading ability via phonological awareness. This finding lends support for analysis of associations between neural excitatory/inhibitory factors and reading ability along a continuum, rather than as with a case/control approach, and indicates the relevance of phonological awareness as an intermediate trait that may provide a more proximal link between neurobiology and reading ability. Further research is needed across developmental stages and over a broader set of brain regions to more comprehensively assess the neural noise hypothesis of dyslexia, and alternative neurobiological mechanisms of this disorder should be explored.

Strengths:

The inclusion of multiple methods of assessing neural noise (neurophysiological and neurochemical) is a major advantage of this paper. MRS at 7T confers an advantage of more accurately distinguishing and quantifying glutamate, which is a primary target of this study. In addition, the subject-specific functional localization of the MRS acquisition is an innovative approach. MRS acquisition and processing details are noted in the supplementary materials using according to the experts' consensus recommended checklist (https://doi.org/10.1002/nbm.4484). Commenting on rigor the EEG methods is beyond my expertise as a reviewer.<br /> Participants recruited for this study included those with a clinical diagnosis of dyslexia, which strengthens confidence in the accuracy of the diagnosis. The assessment of reading and language abilities during the study further confirms the persistently poorer performance of the dyslexia group compared to the control group.<br /> The correlational analysis and mediation analysis provide complementary information to the main case-control analyses, and the examination of associations between EEG and MRS measures of neural noise is novel and interesting.<br /> The authors follow good practice for open science, including data and code sharing. They also apply statistical rigor, using Bayes Factors to support conclusions of null evidence rather than relying only on non-significant findings. In the discussion, they acknowledge the limitations and generalizability of the evidence and provide directions for future research on this topic.

Weaknesses:

Though the methods employed in the paper are generally strong, the MRS acquisition was not optimized to quantify GABA, so the findings (or lack thereof) should be interpreted with caution. Specifically, while 7T MRS affords the benefit of quantifying metabolites, such as GABA, without spectral editing, this quantification is best achieved with echo times (TE) of 68 or 80 ms in order to minimize the spectral overlap between glutamate and GABA and reduce contamination from the macromolecular signal (Finkelman et al., 2022, https://doi.org/10.1016/j.neuroimage.2021.118810). The data in the present study were acquired at TE=28 ms, and are therefore likely affected by overlapping Glu and GABA peaks at 2.3 ppm that are much more difficult to resolve at this short TE, which could directly affect the measures that are meant to characterize the Glu/GABA+ ratio/imbalance. In future research, MRS acquisition schemes should be optimized for the acquisition of Glutamate, GABA, and their relative balance.

As the authors note in the discussion, additional factors such as MRS voxel location, participant age, and participant sex could influence associations between neural noise and reading abilities and should be considered in future studies.

Appraisal:

The authors present a thorough evaluation of the neural noise hypothesis of developmental dyslexia in a sample of adolescents and young adults using multiple methods of measuring excitatory/inhibitory imbalances as an indicator of neural noise. The authors concluded that there was not support for the neural noise hypothesis of dyslexia in their study based on null significance and Bayes factors. This conclusion is justified, and further research is called for to more broadly evaluate the neural noise hypothesis in developmental dyslexia.

Impact:

This study provides an exemplar foundation for the evaluation of the neural noise hypothesis of dyslexia. Other researcher may adopt the model applied in this paper to examine neural noise in various populations with/without dyslexia, or across a continuum of reading abilities, to more thoroughly examine evidence (or lack thereof) for this hypothesis. Notably, the lack of evidence here does not rule out the possibility for a role of neural noise in dyslexia, and the authors point out that presentation with co-occurring conditions, such as ADHD, may contribute to neural noise in dyslexia. Dyslexia remains a multi-faceted and heterogenous neurodevelopmental condition, and many genetic, neurobiological and environmental factors play a role. This study demonstrates one step toward evaluating neurobiological mechanisms that may contribute to reading difficulties.

Reviewer #2 (Public review):

Summary:

This study utilized two complimentary techniques (EEG and 7T MRI/MRS) to directly test a theory of dyslexia: the neural noise hypothesis. The authors report finding no evidence to support an excitatory/inhibitory balance, as quantified by beta in EEG and Glutamate/GABA ratio in MRS. This is important work and speaks to one potential mechanism by which increased neural noise may occur in dyslexia.

Strengths:

This is a well conceived study with in depth analyses and publicly available data for independent review. The authors provide transparency with their statistics and display the raw data points along with the averages in figures for review and interpretation. The data suggest that an E/I balance issue may not underlie deficits in dyslexia and is a meaningful and needed test of a possible mechanism for increased neural noise.

Weaknesses:

The researchers did not include a visual print task in the EEG task, which limits analysis of reading specific regions such as the visual word form area, which is a commonly hypoactivated region in dyslexia. This region is a common one of interest in dyslexia, yet the researchers measured the I/E balance in only one region of interest, specific to the language network.

Reviewer #3 (Public review):

Summary:

This study by Glica and colleagues utilized EEG (i.e., Beta power, Gamma power, and aperiodic activity) and 7T MRS (i.e., MRS IE ratio, IE balance) to reevaluating the neural noise hypothesis in Dyslexia. Supported by Bayesian statistics, their results show convincing evidence of no differences in EI balance between groups, challenging the neural noise hypothesis.

Strengths:

Combining EEG and 7T MRS, this study utilized both the indirect (i.e., Beta power, Gamma power, and aperiodic activity) and direct (i.e., MRS IE ratio, IE balance) measures to reevaluating the neural noise hypothesis in Dyslexia.

Reviewer #1 (Public review):

Summary:

This study focuses on metabolic changes in the paraventricular hypothalamic (PVH) region of the brain during acute periods of cold exposure. The authors point out that in comparison to the extensive literature on the effects of cold exposure in peripheral tissues, we know relatively little about its effects on the brain. They specifically focus on the hypothalamus, and identify the PVH as having changes in Atgl and Hsl gene expression changes during cold exposure. They then go on to show accumulation of lipid droplets, increased Fos expression, and increased lipid peroxidation during cold exposure. Further, they show that neuronal activation is required for the formation of lipid droplets and lipid peroxidation.

Strengths:

A strength of the study is trying to better understand how metabolism in the brain is a dynamic process, much like how it has been viewed in other organs. The authors also use a creative approach to measuring in vivo lipid peroxidation via delivery of BD-C11 sensor through a cannula to the region in conjunction with fiber photometry to measure fluorescence changes deep in the brain.

Comments on revised version:

The authors have attempted to address concerns brought to their attention in the initial review. They have performed one or two additional experiments to address concerns (e.g. adding fiber photometry of PVH neurons and trying to manipulate lipid peroxidation) though many of the concerns from the original review stand. The authors have also revised the text to limit the extent of their claims and to improve clarity, which is appreciated.

Reviewer #1 (Public review):

Summary:

This manuscript addresses the question of whether spontaneous activity contributes to the clustering of retinogeniculate synapses before eye opening. The authors re-analyze a previously published dataset to answer the question. The authors conclude that synaptic clustering is eye-specific and activity dependent during the first postnatal week. While there is useful information in this manuscript, I don't see how the data meaningfully supports the claims made about clustering.<br /> In adult retinogeniculate connections, functionally specificity is supported by select pairings of retinal ganglion cells and thalamocortical cells forming dozens of synaptic connections in subcellular microcircuits called glomeruli. In this manuscript, the authors measure whether the frequency of nearby synapses is higher in the observed data than in a model where synapses are randomly distributed throughout the volume. Any real anatomical data will deviate from such a model. The interesting biological question is not whether a developmental state deviates from random. The interesting question is how much of the adult clustering occurs before eye opening. In trying to decode the analysis in this manuscript, I can't tell if the answer is 99% or 0.001%.

Strengths:

The source dataset is high resolution data showing the colocalization of multiple synaptic proteins across development. Added to this data is labeling that distinguishes axons from the right eye from axons from the left eye. The first order analysis of this data showing changes in synapse density and in the occurrence of multi-active zone synapses is useful information about the development of an important model system.

Weaknesses:

I don't think the analysis of clustering within this dataset improves our understanding of how the system works. It is possible that the result is clear to the authors based on looking at the images. As a reader trying to interpret the analysis, I ran into the following problems:

• It is not possible to estimate biologically meaningful effect sizes from the data provided. Spontaneous activity in the post natal week could be responsible for 99% or 0.001% of RGC synapse clustering.<br /> • There is no clear biological interpretation of the core measure of the publication, the normalized clustering index. The normalized clustering index starts with counting the fraction of single active zone synapses within various distances to the edge of synapses. This frequency is compared to a randomization model in which the positions of synapses are randomized throughout a volume. The authors found that the biggest deviation between the observed and randomized proximity frequency using a distance threshold of 1.5 um. They consider the deviation from the random model to be a sign of clustering. However, two RGC synapses 1.5 um apart have a good chance of coming from the same RGC axon. At this scale, real observations will, therefore, always look more clustered than a model where synapses are randomly placed in a volume. If you randomly place synapses on an axon, they will be much closer together than if you randomly place synapses within a volume. The authors normalize their clustering measure by dividing by the frequency of clustering in the normalized model. That makes the measure of clustering an ambiguous mix of synapse clustering, axon morphology, and synaptic density.<br /> • Other measures are also very derived. For instance, one argument is based on determining that the cumulative distribution of the distance of dominant-eye multi-active zone synapses with nearby single-active zone synapses from dominant-eye multi-active zone synapses is statistically different from the cumulative distribution of the distance of dominant-eye multi-active zones without nearby single-active zone synapses from dominant-eye multi-active zones. Multiple permutations of this measure are compared.<br /> • The sample size is too small for the kinds of comparisons being made. The authors point out that many STORM studies use an n of 1 while the authors have n = 3 for each of their six experimental groups. However, the critical bit is what kinds of questions you are trying to answer with a given sample size. This study depends on determining whether the differences between groups are due to age, genotype, or individual variation. This study also makes multiple comparisons of many different noisy parameters that test the same or similar hypothesis. In this context, it is unlikely that n = 3 sufficiently controls for individual variation.<br /> • There are major biological differences between groups that are difficult to control for. Between P2, P4, and P8, there are changes in cell morphology and synaptic density. There are also large differences in synapse density between wild type and KO mice. It is difficult to be confident that these differences are not responsible for the relatively subtle changes in clustering indices.<br /> • Many claims are based on complicated comparisons between groups rather than the predominating effects within the data. It is noted that: "In KO mice, dominant eye projections showed increased clustering around mAZ synapses compared to sAC synapses suggesting partial maintenance of synaptic clustering despite retinal wave defects". In contrast, I did not notice any discussion of the fact that the most striking trend in those measures is that the clustering index decreases from P2 to P8.<br /> • Statistics are improperly applied. In my first review I tried to push the authors to calculate confidence intervals for two reasons. First, I believed the reader should be able to answer questions such as whether 99% or 0.01% of RGC synaptic clustering occurred in the first postnatal week. Second, I wanted the authors to deal with the fact that n=3 is underpowered for many of the questions they were asking. While many confidence intervals can now be found leading up to a claim, it is difficult to find claims that are directly supported by the correct confidence interval. Many claims are still incorrectly based on which combinations of comparisons produced statistically significant differences and which combinations did not.

Reviewer #2 (Public review):

Summary:

This study provides a valuable data set showing changes in the spatial organization of synaptic proteins at the retinogeniculate connection during a developmental period of active axonal and synaptic remodeling. The data collected by STORM microscopy is state-of-the-art in terms of the high-resolution view of the presynaptic components of a plastic synapse. The revision has addressed many, but not all, of the initial concerns about the authors interpretation of their data. However, with the revisions, the manuscript has become very dense and difficult to follow.

Strengths:

The data presented is of good quality and provides an unprecedented view at high resolution of the presynaptic components of the retinogeniculate synapse during active developmental remodeling. This approach offers an advance to the previous mouse EM studies of this synapse because the CTB label allows identification of the eye from which the presynaptic terminal arises.

Weaknesses:

From these data the authors conclude that eye-specific increase in mAZ synapse density occur over retinogeniculate refinement, that sAZ synapses cluster close to mAZ synapses over age, and that this process depends on spontaneous activity and proximity to eye-specific mAZ synapses. While the interpretation of this data set is much more grounded in this revised submission, some of the authors' conclusions/statements still lack convincing supporting evidence.<br /> This includes:

(1) The conclusion that multi-active zone synapses are loci for synaptic clustering. This statement, or similar ones (e.g., line 407) suggest that mAZ synapses actively or through some indirect way influence the clustering of sAZ synapses. There is no evidence for this. Clustering of retinal synapses are in part due to the fact that retinal inputs synapse on the proximal dendrites. With increased synaptogenesis, there will be increased density of retinal terminals that are closely localized. And with development, perhaps sAZ synapses mature into mAZ synapses. This scenario could also explain a large part of this data set.

(2) The conclusion that, "clustering depends on spontaneous retinal activity" could be misleading to the reader given that the authors acknowledge that their data is most consistent with a failure of synaptogenesis in the mutant mice (in the rebuttal). Additionally clustering does occur in CTB+ projections around mAZ synapses.

(3). Line 403: "Since mAZ synapses are expected to have a higher release probability, they likely play an important role in driving plasticity mechanisms reliant on neurotransmission.":What evidence do the authors have that mAZ are expected to have higher release probability?

Reviewer #3 (Public review):

This study is a follow-up to a recent study of synaptic development based on a powerful data set that combines anterograde labeling, immunofluorescence labeling of synaptic proteins, and STORM imaging (Cell Reports, 2023). Specifically, they use anti-Vglut2 label to determine the size of the presynaptic structure (which they describe as the vesicle pool size), anti-Bassoon to label active zones with the resolution to count them, and anti-Homer to identify postsynaptic densities. Their previous study compared the detailed synaptic structure across the development of synapses made with contra-projecting vs. ipsi-projecting RGCs and compared this developmental profile with a mouse model with reduced retinal waves. In this study, they produce a new detailed analysis on the same data set in which they classify synapses into "multi-active zone" vs. "single-active zone" synapses and assess the number and spacing of these synapses. The authors use measurements to make conclusions about the role of retinal waves in the generation of same-eye synaptic clusters, providing key insight into how neural activity drives synapse maturation.

Strengths:

This is a fantastic data set for describing the structural details of synapse development in a part of the brain undergoing activity-dependent synaptic rearrangements. The fact that they can differentiate eye of origin is what makes this data set unique over previous structural work. The addition of example images from EM data set provides confidence in their categorization scheme.

Weaknesses:

Though the descriptions of synaptic clusters are important and represent a significant advance, the authors conclusions regarding the biological processes driving these clusters are not testable by such a small sample. This limitation is expected given the massive effort that goes into generating this data set. Of course the authors are free to speculate, but many of the conclusions of the paper are not statistically supported.

Joint Public Review:

Though the Norrin protein is structurally unrelated to the Wnt ligands, it can activate the Wnt/β-catenin pathway by binding to the canonical Wnt receptors Fzd4 and Lrp5/6, as well as the tetraspanin Tspan12 co-receptor. Understanding the biochemical mechanisms by which Norrin engages Tspan12 to initiate signaling is important, as this pathway plays an important role in regulating retinal angiogenesis and maintaining the blood-retina-barrier. Numerous mutations in this signaling pathway have also been found in human patients with ocular diseases. The overarching goal of the study is to define the biochemical mechanisms by which Tspan12 mediates Norrin signaling. Using purified Tspan12 reconstituted in lipid nanodiscs, the authors conducted detailed binding experiments to document the direct, high-affinity interactions between purified Tspan12 and Norrin. To further model this binding event, they used AlphaFold to dock Norrin and Tspan12 and identified four putative binding sites. They went on to validate these sites through mutagenesis experiments. Using the information obtained from the AlphaFold modeling and through additional binding competition experiments, it was further demonstrated that Tspan12 and Fzd4 can bind Norrin simultaneously, but Tspan12 binding to Norrin is competitive with other known co-receptors, such as HSPGs and Lrp5/6. Collectively, the authors proposed that the main function of Tspan12 is to capture low concentrations of Norrin at the early stage of signaling, and then "hand over" Norrin to Fzd4 and Lrp5/6 for further signal propagation. Overall, the study is comprehensive and compelling, and the conclusions are well supported by the experimental and modeling data.

Reviewer #1 (Public review):

Summary:

In this study, Zhang et al., presented an electrophysiology method to identify the layers of macaque visual cortex with high density Neuropixels 1.0 electrode. They found several electrophysiology signal profiles for high-resolution laminar discrimination and described a set of signal metrics for fine cortical layer identification.

Strengths:

There are two major strengths. One is the use of high density electrodes. The Neuropixels 1.0 probe has 20 um spacing electrodes, which can provide high resolution for cortical laminar identification. The second strength is the analysis. They found multiple electrophysiology signal profiles which can be used for laminar discrimination. Using this new method, they could identify the most thin layer in macaque V1. The data support their conclusion.

Weaknesses:

While this electrophysiology strategy is much easier to perform even in awake animals compared to histological staining methods, it provides an indirect estimation of cortical layers. A parallel histological study can provide a direct matching between the electrode signal features and cortical laminar locations. However, there are technical challenges, for example the distortions in both electrode penetration and tissue preparation may prevent a precise matching between electrode locations and cortical layers. In this case, additional micro wires electrodes binding with Neuropixels probe can be used to inject current and mark the locations of different depths in cortical tissue after recording.

Reviewer #2 (Public review):

Summary:

This paper documents a compelling attempt to accurately determine the locations and boundaries of the anatomically and functionally defined layers in macaque primary visual cortex using voltage signals recorded from a high-density electrode array that spans the full depth of cortex with contacts at 20 um spacing. First, the authors attempt to use current source density (CSD) analysis to determine layer locations, but they report a striking failure because the results vary greatly from one electrode penetration to the next and because the spatial resolution of the underlying local field potential (LFP) signal is coarse compared to the electrical contact spacing. The authors therefore turn to examining higher frequency signals related to action potentials and provide evidence that these signals reflect changes in neuronal size and packing density, response latency and visual selectivity, which taken together can advance the state-of-the-art accuracy in making layer assignments from in vivo recordings.

Strengths:

There is a lot of nice data to look at in this paper that show interesting quantities as a function of depth in V1. Bringing all of these together offers the reader a rich data set: CSD, action potential shape, response power and coherence spectrum, and post-stimulus time response traces. Furthermore, data are displayed as a function of eye (dominant or non-dominant) and for achromatic and cone-isolating stimuli.

This paper takes a strong stand in pointing out weaknesses in the ability of CSD analysis to make consistent determinations about cortical layering in V1. Many researchers have found CSD to be problematic, and the observations here may be important to motivate other researchers to carry out rigorous comparisons and publish their results, even if they reflect negatively on the value of CSD analysis.

The paper provides a thoughtful, practical and comprehensive recipe for assigning traditional cortical layers based on easily-computed metrics from electophysiological recordings in V1, and this is likely to be useful for electrophysiologists who are now more frequently using high-density electrode arrays.

Weaknesses:

Considerable space is taken in pointing out features that are well known, for example, the latency difference associated with different retinogeniculate pathways, the activity level differences associated with input layers, and the action potential shape differences associated with white vs. gray matter. These have been used for decades as indicators of depth and location of recordings in visual cortex as electrodes were carefully advanced. High density electrodes allow this type of data to now be collected in parallel, but at discrete, regular sampling points. Perhaps more emphasis could be placed on developing a rigorous analysis of how variable vs. reproducible are quantitative metrics of these features across penetrations, as a function of distance or functional domain, and from animal to animal, but this paper certainly makes a substantial push in this direction.

Another important piece of information for assessing the ability to determine layers from spiking activity is to carry out post-mortem histological processing so that the layer determination made in vivo can be compared to anatomical layering. However, histological methods also suffer from distortion and noise, thus it remains to be seen how much can ultimately be gained by integrating histology with the physiological methods explored here.

Overall

Overall, this paper makes a compelling argument in favor of using action potentials and stimulus driven responses, instead of CSD measurements, to assign cortical layers to electrode contacts in V1. The rich presentation of data, combined with the authors' highly educated interpretation and speculation about how useful such measurements will be for layer assignment make this an important paper for many labs using high-density electrodes. It is easy to agree with much of what is postulated here and to hope that we will soon have reliable, quantitative methods to make layer assignments that will be meaningful in terms of the differentiated roles of single neurons in cortical computation. How much this will end up corresponding to the canonical layer numbering that has been used for many decades will be interesting to see.

Comments on revisions:

I found that the authors addressed my main concerns to the degree they were able. They improved the consistency of language and figures, and they added some useful quantification.

Reviewer #3 (Public review):

Summary:

Zhang et al. explored strategies for aligning electrophysiological recordings from high-density laminar electrode arrays (Neuropixels) with the pattern of lamination across cortical depth in macaque primary visual cortex (V1), with the goal of improving the spatial resolution of layer identification based on electrophysiological signals alone. The authors compare the current commonly used standard in the field - current source density (CSD) analysis - with a new set of measures largely derived from action potential (AP) frequency band signals. Individual AP band measures provide distinct cues about different landmarks or potential laminar boundaries, and together they are used to subdivide the spatial extent of array recordings into discrete layers, including the very thin layer 4A, at a level of resolution unavailable when relying on CSD analysis alone for laminar identification. The authors compare the widths of the resulting subdivisions with previously reported anatomical measurements as evidence that layers have been accurately identified. This is a bit circular, given that they also use these anatomical measurements as guidelines limiting the boundary assignments; however, the strategy is overall sensible and the electrophysiological signatures used to identify layers are generally convincing. Furthermore, by varying the pattern of visual stimulation to target chromatically sensitive inputs known to be partially segregated by layer in V1, they show localized response patterns that lend confidence to their identification of particular sublayers.

The authors compellingly demonstrate the insufficiency of CSD analysis for precisely identifying fine laminar structure, and in some cases its limited accuracy at identifying coarse structure. CSD analysis produced inconsistent results across array penetrations and across visual stimulus conditions and was not improved in spatial resolution by sampling at high density with Neuropixels probes. Instead, in order to generate a typical, informative pattern of current sources and sinks across layers, the LFP signals from the Neuropixels arrays required spatial smoothing or subsampling to approximately match the coarser (50-100 µm) spacing of other laminar arrays. Even with smoothing, the resulting CSDs in some cases predicted laminar boundaries that were inconsistent with boundaries estimated using other measures and/or unlikely given the typical sizes of individual layers in macaque V1. This point alone provides an important insight for others seeking to link their own laminar array recordings to cortical layers.

They next offer a set of measures based on analysis of AP band signals. These measures include analyses of the density, average signal spread, and spike waveforms of units identified through spike sorting, as well as analyses of AP band power spectra and local coherence profiles across recording depth. The power spectrum measures in particular yield compact peaks at particular depths, albeit with some variation across penetrations, whereas the waveform measures most convincingly identified the layer 6-white matter transition. In general, some of the new measures yield inconsistent patterns across penetrations, and some of the authors' explanations of these analyses draw intriguing but rather speculative connections to properties of anatomy and/or responsivity. However, taken as a group, the set of AP band analyses appear sufficient to determine the layer 6-white matter transition with precision and to delineate intermediate transition points likely to correspond to actual layer boundaries, and the strategy serves as a substantial advancement over consideration of CSD signals alone to match electrophysiological recordings with cortical layers.

Strengths:

The authors convincingly demonstrate the potential to resolve putative laminar boundaries using only electrophysiological recordings from Neuropixels arrays. This is particularly useful given that histological information is often unavailable for chronic recordings. They make a clear case that CSD analysis is insufficient to resolve the lamination pattern with the desired precision and offer a thoughtful set of alternative analyses, along with an order in which to consider multiple cues in order to facilitate others' adoption of the strategy. The suggested analyses can be used to reliably identify certain landmarks (the positions of layer 4c and the layer 6-white matter transition), which provide very useful constraints for specifying the remaining laminar boundaries, and consideration of average anatomical patterns makes it unlikely that the remaining laminar boundaries will be far from their true locations. Overall, the widths of the resulting layers bear a sensible resemblance to the expected widths identified by prior anatomical measurements, and at least in some cases there are satisfying signatures of chromatic visual sensitivity and latency differences across layers that are predicted by the known connectivity of the corresponding layers. Thus, the proposed analytical toolkit appears to work well for macaque V1 and has strong potential to generalize to use in other cortical regions, though area-targeted selection of stimuli may be required.

Weaknesses:

The waveform measures, in particular the unit density distribution, are likely to be sensitive to the methods and criteria used for spike sorting, which differ among experimenters/groups, and this may limit the usefulness of this particular measure for others in the community.<br /> More generally, although the sizes of identified layers comport with typical sizes identified anatomically, a more powerful confirmation would be a direct comparison with histologically identified boundaries along each penetration's trajectory. Ultimately, the absence of this type of independent confirmation limits the strength of the claim that veridical laminar boundaries can be precisely identified from electrophysiological signals alone.

Reviewer #1 (Public review):

Summary:

Numerous pathways have been proposed to elucidate the nongenomic actions of progesterone within both male and female reproductive tissues. The authors employed the Xenopus oocyte system to investigate the PLA2 activity of ABHD2 and the downstream lipid mediators in conjunction with mPRb and P4, on their significance in meiosis. The research has been conducted extensively and is presented clearly.

Strengths:

While the interaction between membranous PR and ABHD2 is not a novel concept, this present study exhibits several strengths:

(1) mPRbeta, a member of the PAQR family, has been elusive in terms of detailed signal transduction. Through mutation studies involving the Zn binding domain, the authors discovered that the hydrolase activity of mPRbeta is not essential for meiosis and oocyte maturation. Instead, they suggest that ABHD2, acting as a coreceptor of mPRbeta, demonstrates phospholipase activity, indicating that downstream lipid mediators may play a dominant role when stimulated by progesterone.<br /> (2) Extensive exploration of downstream signaling pathways and the identification of several potential meiotic activity-related lipid mediators make this aspect of the study novel and potentially significant.

Weaknesses:

However, there are some weaknesses and areas that need further clarification:

(1) The mechanism governing the molecular assembly of mPRbeta and ABHD2 remains unclear. Are they constitutively associated or is their association ligand-dependent? Does P4 bind not only to mPRbeta but also to ABHD2, as indicated in Figure 6J? In the latter case, the reviewer suggests that the authors conduct a binding experiment using labeled P4 with ABHD2 to confirm this interaction and assess any potential positive or negative cooperativity with a partner receptor.

(2) The authors have diligently determined the metabolite profile using numerous egg cells. However, the interpretation of the results appears incomplete, and inconsistencies were noted between Figure 2F and Supplementary Figure 2C. Furthermore, PGE2 and D2 serve distinct roles and have different elution patterns by LC-MS/MS, thus requiring separate measurements. In addition, the extremely short half-life of PGI2 necessitates the measurement of its stable metabolite, 6-keto-PGF1a, instead. The authors also need to clarify why they measured PGF1a but not PGF2a. Unfortunately, even in the revision, authors did not adequately address the last issue (differential measurements of PGD2 and E2, 6-keto-PG!alpha be determined instead of PGI2).

(3) Although they propose PGs, LPA and S1P are important downstream mediators, the exact roles of the identified lipid mediators have not been clearly demonstrated, as receptor expression and activation were not demonstrated. While the authors showed S1PR3 expression and its importance by genetic manipulation, there was no observed change in S1P levels following P4 treatment (Supplementary Figure 2D). It is essential to identify which receptors (subtypes) are expressed and how downstream signaling pathways (PKA, Ca, MAPK, etc.) relate to oocyte phenotypes.

These clarifications and further experiments would enhance the overall impact and comprehensiveness of the study.

Comments on revisions:

Need correction and addition for differential analyses of PGD2 and PGE2, and measurement of 6-keto-PGF1alpha instead of PGI2 (Figure 2F). PGI2 is extremely unstable (T1/2, 1 min in neutral buffer) and rapidly converted nonenzymically to 6-keto-PGF1a.

Reviewer #2 (Public review):

Summary:

This interesting paper examines the earliest steps in progesterone-induced frog oocyte maturation, an example of non-genomic steroid hormone signaling that has been studied for decades but is still very incompletely understood. In fish and frog oocytes it seems clear that mPR proteins are involved, but exactly how they relay signals is less clear. In human sperm, the lipid hydrolase ABHD2 has been identified as a receptor for progesterone, and so the authors here examine whether ABHD2 might contribute to progesterone-induced oocyte maturation as well. The main results are:

(1) Knocking down ABHD2 makes oocytes less responsive to progesterone, and ectopically expressing ABHD2.S (but not the shorter ABHD2.L gene product) partially rescues responsiveness. The rescue depends upon the presence of critical residues in the protein's conserved lipid hydrolase domain, but not upon the presence of critical residues in its acyltransferase domain.

(2) Treatment of oocytes with progesterone causes a decrease in sphingolipid and glycerophospholipid content within 5 min. This is accompanied by an increase in LPA content and arachidonic acid metabolites. These species may contribute to signaling through GPCRs. Perhaps surprisingly, there was no detectable increase in sphingosine-1-phosphate, which might have been expected given the apparent substantial hydrolysis of sphingolipids. The authors speculate that S1P is formed and contributes to signaling but diffuses away.

(3) Pharmacological inhibitors of lipid-metabolizing enzymes support, for the most part, the inferences from the lipidomics studies, although there are some puzzling findings. The puzzling findings may be due to uncertainty about whether the inhbitors are working as advertised.

(4) Pharmacological inhibitors of G-protein signaling support a role for G-proteins and GPCRs in this signaling, although again there are some puzzling findings.

(5) Reticulocyte expression supports the idea that mPRβ and ABHD2 function together to generate a progesterone-regulated PLA2 activity.

(6) Knocking down or inhibiting ABHD2 inhibited progesterone-induced mPRβ internalization, and knocking down ABHD2 inhibited SNAP25∆20-induced maturation.

Strengths:<br /> All in all, this could be a very interesting paper and a nice contribution. The data add a lot to our understanding of the process, and, given how ubiquitous mPR and AdipoQ receptor signaling appear to be, something like this may be happening in many other physiological contexts.

Weaknesses:

I have several suggestions for how to make the main points more convincing.

Main criticisms:

(1) The ABHD2 knockdown and rescue, presented in Fig 1, is one of the most important findings. It can and should be presented in more detail to allow the reader to understand the experiments better. E.g.: the antisense oligos hybridize to both ABHD2.S and ABHD2.L, and they knock down both (ectopically expressed) proteins. Do they hybridize to either or both of the rescue constructs? If so, wouldn't you expect that both rescue constructs would rescue the phenotype, since they both should sequester the AS oligo? Maybe I'm missing something here.

In addition, it is critical to know whether the partial rescue (Fig 1E, I, and K) is accomplished by expressing reasonable levels of the ABHD2 protein, or only by greatly overexpressing the protein. The author's antibodies do not appear to be sensitive enough to detect the endogenous levels of ABHD2.S or .L, but they do detect the overexpressed proteins (Fig 1D). The authors could thus start by microinjecting enough of the rescue mRNAs to get detectable protein levels, and then titer down, assessing how low one can go and still get rescue. And/or compare the mRNA levels achieved with the rescue construct to the endogenous mRNAs.

Finally, please make it clear what is meant by n = 7 or n = 3 for these experiments. Does n = 7 mean 7 independently lysed oocytes from the same frog? Or 7 groups of, say, 10 oocytes from the same frog? Or different frogs on different days? I could not tell from the figure legends, the methods, or the supplementary methods. Ideally one wants to be sure that the knockdown and rescue can be demonstrated in different batches of oocytes, and that the experimental variability is substantially smaller than the effect size.

(2) The lipidomics results should be presented more clearly. First, please drop the heat map presentations (Fig 2A-C) and instead show individual time course results, like those shown in Fig 2E, which make it easy to see the magnitude of the change and the experiment-to-experiment variability. As it stands, the lipidomics data really cannot be critically assessed.

[Even as heat map data go, panels A-C are hard to understand. The labels are too small, especially on the heat map on the right side of panel B. And the 25 rows in panel C are not defined (the legend makes me think the panel is data from 10 individual oocytes, so are the 25 rows 25 metabolites? If so, are the individual oocyte data being collapsed into an average? Doesn't that defeat the purpose of assessing individual oocytes?) And those readers with red-green colorblindness (8% of men) will not be able to tell an increase from a decrease. But please don't bother improving the heat maps; they should just be replaced with more-informative bar graphs or scatter plots.]

(3) The reticulocyte lysate co-expression data are quite important, and are both intriguing and puzzling. My impression had been that to express functional membrane proteins, one needed to add some membrane source, like microsomes, to the standard kits. Yet it seems like co-expression of mPR and ABHD2 proteins in a standard kit is sufficient to yield progesterone-regulated PLA2 activity. I could be wrong here-I'm not a protein expression expert-but I was surprised by this result, and I think it is critical that the authors make absolutely certain that it is correct. Do you get much greater activities if microsomes are added? Are the specific activities of the putative mPR-ABHD2 complexes reasonable?

Comments on revisions:

The authors have satisfied my concerns with their response letter and revisions.

Reviewer #3 (Public review):

Summary:

The authors report two P4 receptors, ABHD2 and mPRβ that function as co-receptors to induce PLA2 activity and thus drive meiosis. In their experimental studies, the authors knock down ABHD2 and demonstrated inhibition of oocyte maturation and inactivation of Plk1, MAPK, and MPF, which indicated that ABHD2 is required for P4-induced oocyte maturation. Next, they showed three residues (S207, D345, H376) in the lipase domain that are crucial for ABHD2 P4-mediated oocyte maturation in functional assays. They performed global lipidomics analysis on mPRβ or ABHD2 knockdown oocytes, among which the downregulation of GPL and sphingolipid species were observed and enrichment in LPA was also detected using their metabolomics method. Furthermore, they investigated pharmacological profiles of enzymes predicted to be important for maturation based on their metabolomic analyses and ascertained the central role for PLA2 in inducing oocyte maturation downstream of P4. They showed the modulation of S1P/S1PR3 pathway on oocyte maturation and potential role for or Gαs signaling and potentially Gβγ downstream of P4.

Strengths:

The authors make a very interesting finding that ABHD2 has PLA2 catalytic activity but only in the presence of mPRβ and P4. Finally, they provided supporting data for a relationship between ABHD2/PLA2 activity and mPRβ endocytosis and further downstream signaling. Collectively, this research report defines early steps in nongenomic P4 signaling, which is of broad physiological implications.

Weaknesses:

There were concerns with the pharmacological studies presented. Many of these inhibitors are used at high (double digit micromolar) concentrations that could result in non-specific pharmacological effects and the authors have provided very little data in support of target engagement and selectivity under the multiple experimental paradigms. In addition, the use of an available ABHD2 small molecule inhibitor was lacking in these studies.

Comments on revisions:

In the revised manuscript, the authors have addressed my major concerns.

Reviewer #1 (Public review):

Summary:

This study is focused an important aspect of axon guidance at the central nervous system (CNS) midline: how neurons extend axons that either do or do not cross the CNS midline. The authors here address contradictory work in the field relating to how cell surface expression of the slit receptor Robo1 is regulated so as to generate crossed and non-crossed axon trajectories during Drosophila neural development. They use fly genetics, cell lines, and biochemical assessments to define a complex consisting of the commissureless, Nedd4 and Robo1 proteins necessary for regulating Robo1 protein expression. This work resolves certain remaining questions in the field regarding midline axon guidance, with strengths out weighing weaknesses; however, addressing some of these weaknesses would strengthen this study.

Strengths:

Strengths include:<br /> - The use of well controlled genetic gain-of-function (over expression) approaches in vivo in Drosophila to show that phosphorylation sites (there are 2, and this study allows for assessment of the contributions made by each) in the commissureless (Comm) protein are indeed required for Comm function with respect to regulating axon midline guidance via their role in directing Comm-mediated Robo1 ubiquitination and degradation in the lysosome.<br /> - The demonstration that in vitro, and in a sensitized genetic background in vivo, the Nedd4 ubiquitin ligase regulates Robo1 protein cell surface distribution and also midline axon crossing in vivo.<br /> - Important evidence here that serves to resolve many questions raised by previous studies (not from these authors) regarding how Robo1 is regulated by Comm and Nedd4 family ubiquitin ligases. Further, these results are likely to have implications for thinking about the regulation of midline guidance in more complex nervous systems.

Weaknesses:

- A weakness beyond the purview of revision but important to mention is that the authors chose not to complement their GOF experiments with gene editing approaches to generate endogenous PY mutant alleles of Comm that might have been useful in genetic interaction experiments directed toward revealing roles for endogenous Comm in the regulation of Robo1.

Comments on revised version:

In this revised manuscript the authors provide new experiments and also reasonable explanations to address concerns raised in the initial review. I am satisfied that these efforts address satisfactorily the points raised in the initial review and that this study has been strengthened. This is an interesting body of work that adds to our understanding of CNS midline guidance molecular mechanisms.

Reviewer #2 (Public review):

Summary:

Sullivan and Bashaw delve into the mechanisms that drive neural circuit assembly, and specifically, into the regulation of cell surface proteins that mediate axon pathfinding. During nervous system development, axons must traverse a molecularly and physically complex extracellular milieu to reach their synaptic targets. A fundamental, conserved repulsive signaling pathway is initiated by the Slit-Robo ligand-receptor pair. Robo, expressed on axon growth cones, binds Slit, secreted by midline cells, to prevent "pre-crossing" and "re-crossing" of axons at the midline. To control this repulsion, Robo surface levels are tightly regulated. In Drosophila, Commissureless (Comm) downregulates Robo surface levels and is required for axon crossing at the midline. Several studies suggest that PY motifs in Comm are required to localize Robo to endosomes. PY motifs have been shown to bind WW-domain containing proteins including the ubiquitin ligase Nedd4 family, so the authors propose that Comm may regulate Robo through Nedd4 interactions. Previous studies have hinted at a role for Nedd4-mediated ubiquitination of Comm in regulation of Robo localization, but there have also been conflicting data. For example, Comm mutants that are unable to be ubiquitinated mimic wild-type Comm, suggesting that ubiquitination of Comm is not required for regulation of Robo. The current study utilizes a suite of genetic analyses in Drosophila to resolve discrepancies pertaining to the mode of Comm-dependent regulation of Robo1 and proposes that Comm acts as an adapter for the Nedd4 ubiquitin ligase to recognize Robo1 as a substrate. The authors also demonstrate that Nedd4 is indeed required for midline crossing.

Strengths:

While this work is more incremental rather than field-shifting, it is nonetheless an excellent example of a rigorous, thorough analysis that culminates in enriching our mechanistic understanding of how neurons regulate cell-surface receptors in a spatiotemporal manner to control fundamental steps of circuit wiring. The experimental approach is thorough, and the manuscript is extremely well-written.

Weaknesses:

Some key experiments (eg. complex formation) were performed in cell culture in an overexpression background. However, updated experiments demonstrated complex formation using immunoprecipitation in tissues overexpression the corresponding components. Also, there was a missed opportunity to bolster the model proposed by using Comm PY mutants in several experiments.

Comments on revised version:

The revised manuscript bolsters the authors' conclusions and now provides evidence for interactions in tissue. No additional experiments are needed.

Reviewer #1 (Public review):

This work addresses an important question in the field of Drosophila aggression and mating- prior social isolation is known to increase aggression in males by increased lunging, which is suppressed by group housing (GH). However, it is also known that single-housed (SH) males, despite their higher attempts to court females, are less successful. Here, Gao et al., developed a modified aggression assay, to address this issue by recording aggression in Drosophila males for 2 hours, over a virgin female which is immobilized by burying its head in the food. They found that while SH males frequently lunge in this assay, GH males switch to higher intensity but very low-frequency tussling. Constitutive neuronal silencing and activation experiments implicate cVA sensing Or67d neurons promoting high-frequency lunging, similar to earlier studies, whereas Or47b neurons promote low-frequency but higher intensity tussling. Using optogenetic activation they found that three pairs of pC1 neurons- pC1SS2 increase tussling. While P1a neurons, previously implicated in promoting aggression and courtship, did not increase tussling in optogenetic activation (in the dark), they could promote aggressive tussling in thermogenetic activation carried out in the presence of visible light. It was further suggested, using a further modified aggression assay that GH males use increased tussling and are able to maintain territorial control, providing them mating advantage over SI males and this may partially overcome the effect of aging in GH males.

Strengths:

Using a series of clever neurogenetic and behavioral approaches, subsets of ORNs and pC1 neurons were implicated in promoting tussling behaviors. The authors devised a new paradigm to assay for territory control which appears better than earlier paradigms that used a food cup (Chen et al, 2002), as this new assay is relatively clutter-free, and can be eventually automated using computer vision approaches. The manuscript is generally well-written, and the claims made are largely supported by the data.

Weaknesses:

I have a few concerns regarding some of the evidence presented and claims made as well as a description of the methodology, which needs to be clarified and extended further.

(1) Typical paradigms for assaying aggression in Drosophila males last for 20-30 minutes in the presence of nutritious food/yeast paste/females or all of these (Chen et al. 2002, Nilsen et al., 2004, Dierick et al. 2007, Dankert et al., 2009, Certel & Kravitz 2012). The paradigm described in Figure 1 A, while important and more amenable for video recording and computational analysis, seems a modification of the assay from Kravitz lab (Chen et al., 2002), which involved using a female over which males fight on a food cup. The modifications include a flat surface with a central food patch and a female with its head buried in the food, (fixed female) and much longer adaptation and recording times respectively (30 minutes, 2 hours), so in that sense, this is not a 'new' paradigm but a modification of an existing paradigm and its description as new should be appropriately toned down. It would also be important to cite these earlier studies appropriately while describing the assay.

(2) Lunging is described as a 'low intensity' aggression (line 111 and associated text), however, it is considered a mid to high-intensity aggressive behavior, as compared to other lower-intensity behaviors such as wing flicks, chase, and fencing. Lunging therefore is lower in intensity 'relative' to higher intensity tussling but not in absolute terms and it should be mentioned clearly.