Reviewer #2 (Public Review):

In this manuscript, He et al. have found that delayed anesthesia induction and early anesthesia emergence were observed in microglia-depleted mice. They also showed that neuronal activities were differentially regulated by microglia depletion, possibly via suppressing the neuronal network of anesthesia-activated brain regions and activating emergence-activated brain regions. Mechanistically, this influence was found to be dependent on the activation of microglial P2Y12 receptors and subsequent calcium influx. These findings contribute to a better understanding of the role microglia play in regulating anesthesia and shed light on the underlying mechanisms involved. Nonetheless, there are still some aspects that require further investigation and clarification.

1. In Figure 3A the authors used IBA1 to represent microglia, and the corresponding description is 'brain microglia were not influenced'. However, IBA1 is not a specific biomarker for brain resident microglia. It's recommended to use other biomarkers, such as TMEM119 and P2RY12 to better examine the efficiency of microglial depletion.<br /> 2. In Figure 7, 8 and 9 the authors stated that they aim to investigate the impacts microglia exert on neuronal activity. However, using only c-Fos is not sufficient to represent neuron. The authors are supposed to combine c-Fos with other specific biomarkers for neuron to better validate their conclusions.<br /> 3. In Figure 11 the authors use C1qa-/- transgenic mice and draw the conclusion 'microglia mediated anesthesia modulation does not result from spine pruning'. However, as C1q contains multiple subtypes, I have some reservations regarding whether the authors' conclusion is entirely warranted based solely on the knockout of a single subtype of C1q.<br /> 4. In Figure 14E the authors showed that expression levels of Stim1 is significantly down-regulated in CX3CR1CreER::STIM1fl/fl mouse brains. While this is not incorrect, I would suggest the authors sort microglia with FACS or MACS to perform q-RT-PCR and examine the expression levels of Stim1 since the Cre-LoxP system here is microglia specific.<br /> 5. The flow of the manuscript should have been improved. For instance, the results of repopulated microglia in Figure 1B was described even after Figure 2 and 3, which makes the manuscript a little confusing. Additionally, in Figure 14, it would be beneficial to provide a more comprehensive introduction to molecules such as hM3Dq and Stim1 to improve the clarity and readability of the result descriptions.

Reviewer #2 (Public Review):

Summary:<br /> A bidirectional occasion-setting design is used to examine sex differences in the contextual modulation of reward-related behaviour. It is shown that females are slower to acquire contextual control over cue-evoked reward seeking. However, once established, the contextual control over behaviour was more robust in female rats (i.e., less within-session variability and greater resistance to stress) and this was also associated with increased OFC activation.

Strengths:<br /> The authors use sophisticated behavioural paradigms to study the hierarchical contextual modulation of behaviour. The behavioural controls are particularly impressive and do, to some extent, support the specificity of the conclusions. The analyses of the behavioural data are also elegant, thoughtful, and rigorous.

Weaknesses:<br /> My primary concern is that the authors' claim of sex differences in context-dependent discrimination behaviour is not fully supported by their data.

First, the basic behavioural effect does not seem to replicate across experiments. The authors first show sex differences in the % time in food port and the discrimination ratio (Figures 1 and 2) such that males show better context-dependent discrimination than females (group ctx-dep O1). However, this difference is not observed in the baseline condition group in the next experiment, which investigates the effect of acute stress on context-gated reward seeking: "In Figure 4, we observe no difference between males versus females in group "ctx-dep O1".

Second, I am not fully convinced by the authors' assertion that the results are specific to the contextual modulation process. The authors' main conclusions are derived from comparing a group trained with the differential outcome procedure (group cxt-dep O1/O2) and a group with the non-differential outcome procedure (group cxt-dep O1). However, importantly, a different number of training sessions was used for ctx-dep O1/O2 and ctx-dep O1. Is it not possible that sex differences could have emerged with additional training in the cxt-dep O1/O2 group? Moreover, the authors also seem to assume that rats are not using a contextual strategy in the context-dep O1/O2 condition (i.e., rats use instead distinct context-outcome associations) but what is the evidence for this? Also, the authors argue that the impact of stress is specific to the hierarchical contextual modulation of behaviour however inspection of Figure 4A suggests that there may also be an effect of stress on the context-dependent O1/O2 group.

I also had some minor issues with how the authors interpreted some of the findings. First, it is shown that recent rewards disrupt contextual control of reward seeking in male, but not female, rats. That is, in males, prior reward increased the probability of responding on subsequent non-rewarded trials but trial history had no effect in females. How do the authors reconcile this finding with the quicker acquisition and better discrimination that is observed in males? It is not evident to me how males can have difficulty inhibiting responding to non-rewarded cues following recent reward yet still show better discrimination throughout training.

Finally, the authors argue that the contextual control over behaviour was more robust in female rats as females show less within-session variability and greater resistance to stress. What evidence is there that the restraint stress procedure causes a similar stress response in both sexes?

Reviewer #2 (Public Review):

This work introduces PLMGraph-Inter, a new deep-learning approach for predicting inter-protein contacts, which is crucial for understanding protein-protein interactions. Despite advancements in this field, especially driven by AlphaFold, prediction accuracy and efficiency in terms of computational cost) still remains an area for improvement. PLMGraph-Inter utilizes invariant geometric graphs to integrate the features from multiple protein language models into the structural information of each subunit. When compared against other inter-protein contact prediction methods, PLMGraph-Inter shows better performance which indicates that utilizing both sequence embeddings and structural embeddings is important to achieve high-accuracy predictions with relatively smaller computational costs for the model training.

The conclusions of this paper are mostly well supported by data, but test examples should be revisited with a more strict sequence identity cutoff to avoid any potential information leakage from the training data. The main figures should be improved to make them easier to understand.

1) The sequence identity cutoff to remove redundancies between training and test set was set to 40%, which is a bit high to remove test examples having homology to training examples. For example, CDPred uses a sequence identity cutoff of 30% to strictly remove redundancies between training and test set examples. To make their results more solid, the authors should have curated test examples with lower sequence identity cutoffs, or have provided the performance changes against sequence identities to the closest training examples.

2) Figures with head-to-head comparison scatter plots are hard to understand as scatter plots because too many different methods are abstracted into a single plot with multiple colors. It would be better to provide individual head-to-head scatter plots as supplementary figures, not in the main figure.

3) The authors claim that PLMGraph-Inter is complementary to AlphaFold-multimer as it shows better precision for the cases where AlphaFold-multimer fails. To strengthen the point, the qualities of predicted complex structures via protein-protein docking with predicted contacts as restraints should have been compared to those of AlphaFold-multimer structures.

4) It would be interesting to further analyze whether there is a difference in prediction performance depending on the depth of multiple sequence alignment or the type of complex (antigen-antibody, enzyme-substrates, single species PPI, multiple species PPI, etc).

Reviewer #2 (Public Review):

In this work, Urtecho et al. use genome-integrated massively parallel reporter assays (MPRAs) to catalog the locations of promoters throughout the E. coli genome. Their study uses four different MPRA libraries. First, they assayed a library containing 17,635 promoter regions having transcription start sites (TSSs) previously reported by three different sources. They found that 2,760 of these regions exhibited transcription above an experimentally determined threshold. Second, they assayed a library using sheared E. coli genome fragments. This library allowed the authors to systematically identify candidate promoter regions throughout the genome, some of which had not been identified before. Additionally, by performing experiments with this library under different growth conditions, the authors were able to identify promoters with condition-dependent activity. Third, to improve the resolution at which they were able to identify transcription start sites, the authors assayed a library that tiled all candidate promoter regions identified using the genomic fragments library. Data from the tiled library allowed the authors to identify minimal promoter regions. Fourth, the authors assayed a scanning mutagenesis library in which they systematically scrambled individual 10 bp windows within 2,057 previously identified active promoters at 5 bp intervals. After validation with known promoters, this approach allowed the authors to identify novel functional elements within regulatory regions. Finally, the authors fit multiple machine learning models to their data with the goal of predicting promoter activity from DNA sequences.

The work by Urtecho et al. provides an important resource for researchers studying bacterial transcriptional regulation. Despite decades of study, a comprehensive catalogue of E. coli promoters is still lacking. The results of Urtecho et al. provide a state-of-the-art atlas of promoters in the E. coli genome that is readily accessible through the website, http://ecolipromoterdb.com. The authors' work also provides an important demonstration of the power of genome-integrated MPRAs. Unlike many MPRA-based studies, the authors use the results of their initial MPRAs to design follow-up MPRAs, which they then carry out. Finally, the scanning mutagenesis MPRAs the authors perform provide valuable data that could lead to the discovery of novel transcription factor binding sites and other functional regulatory sequence elements.

Below I provide two major critiques and some minor critiques of the paper. The purpose of these critiques is simply to help the authors improve the quality of the manuscript.

Major points:<br /> 1. Ultimately, a comprehensive atlas of E. coli promoters should include nucleotide resolution TSS data, which is not present in the MPRA datasets reported by Urtecho et al.. The authors do use some methods to narrow down the positions of TSSs, but these methods do not provide the resolution one would ideally like to see in a TSS atlas. I understand that acquiring single-nucleotide-resolution data is beyond the scope of this manuscript, but it still might make sense for the authors to discuss this limitation in the Discussion section.

2. The authors should clarify which points in the Results section are novel conclusions or observations, and which points are simply statements that prior conclusions or observations were confirmed. This distinction can be unclear at times.

Minor points:<br /> 1. Line 200-203: "We conclude that inactive TSS-associated promoters lack -35 elements but may become active in growth conditions where additional transcription factors mobilize and facilitate RNAP positioning in the absence of a -35 motif." Making this type of mechanistic observations from the slight difference observed in the enrichment analysis seems too speculative to me. Also, I do not understand how the discrepancies can be explained in terms of transcription factor differences. If the previous studies from which the annotated TSS were extracted were also performed during the log phase in rich media, why would the transcription factors present be different?

2. Line 224-226: "Active TSSs not overlapping a candidate promoter region generally exhibited weak activity, which may indicate that greater sensitivity is achieved through testing of oligo-array synthesized regions (Figure S3)." The authors should clarify this statement. In particular, it is mechanistically unclear why one library would be more sensitive than another if they contain similar sequences.

3. Figure 2B. The authors should clarify that the heights of the arrows correspond to TSS activity as assayed by one library and that the pile-up plots represent promoter activity as assayed by a different library.

4. Line 255-257: "We also observed an enrichment for 150 bp minimal promoter regions, although these were generally weak indicating that our resolution is limited when tiling weaker promoters." The authors should clarify whether the peak at 150 bp is an artifact of using oligos containing 150 bp tiles to construct the library. Also, the authors should clarify why there are some minimal promoters with lengths > 150 bp when the length of the tiles was 150 bp.

5. Line 262 refers to "Supplementary Table 1", but I was not able to find this table in the supplement.

6. Line 324-325: "We used a σ70 PWM to identify the highest-scoring σ70 motifs within intragenic promoters and determined their relative coding frames". I find the term "relative coding frame" here to be unclear; the authors should clarify what they mean.

7. Figure 3 C , D: The authors should use the same terminology in the plots and the methods section describing them. They should also clarify how the values plotted in C and D were computed.

8. Line 329-332: "The observed depletion of -35 motifs positioned in the +2 reading frame and -10 motifs in the +1 reading frame is likely due to the fact that the canonical sequences for these motifs would create stop codons within the protein if placed at these positions." The definition of the reading frame here is unclear. Do the authors mean that the 0 frame is defined as occurring when the hexamer exactly overlaps 2 codons, the +1 frame is when the hexamer is shifted 1 nt downstream of that position, and the +2 frame is when the hexamer is shifted 2 nt downstream of that position?

9. Line 538-539: "We performed hyperparameter tuning for a three-layer CNN and achieved an AUPRC =0.44." The authors should explicitly describe the architecture used for the CNN, and perhaps include a diagram of this architecture. In addition, the authors should clarify the mathematical forms of the other methods tested.

10. Line 1204-1205: "We standardized all datasets as detailed above in 'Universal Promoter Expression Quantification and Activity Thresholding'". That title does not appear before in the text. I believe the appropriate subsection is called "Standardizing Promoter Expression Quantification and Activity Thresholding".

11. Line 1265-1266: "We include a k-mer if the absolute correlation with expression is greater than the 'random' k-mer frequency, resulting in 4800/5440 filtered k-mers." It is unclear to me which two correlations are being compared. Please clarify. For example, would this be accurate: "We include a k-mer if the absolute correlation of its frequency with expression is greater than the absolute correlation of its 'random' frequency with expression"?

Reviewer #2 (Public Review):

In this manuscript, Xie et al presented a new method derived from PORE-C, SCA-seq, for simultaneously measuring chromatin accessibility, genome 3D and CpG DNA methylation. SCA-seq provides a useful tool to the scientific communities to interrogate the genome structure-function relationship.

The revised manuscript has clarified almost of the concerns raised in the previous round of review, though I still have two minor concerns,

1) In fig 2a, there is no number presented in the Venn diagram (although the left panel indeed showed the numbers of the different categories, including the numbers in the right panel would be more straightforward).

2) The authors clarified the discrepancy between sfig 7a and sfig 7g. However, the remaining question is, why is there a big difference in the percentage of the cardinality count of concatemers of the different groups between the chr7 and the whole genome?

Reviewer #2 Public Review

The authors wish to apply established psychophysical methods to the study of number. Specifically, they wish to test the hypothesis - supported by their previous work - that human sensorimotor processes are tuned to specific number ranges. In a novel set of tasks, they ask participants to tap a button N times (either fast or slow), where N varies between 8 and 32 across trials. As I understood it, they then computed the Weber fraction (WF) for each participant for each number and correlated those values across participants and numbers. They find stronger correlations for nearby numbers than for distant numbers and interpret this as evidence of sensorimotor tuning functions. Two other analyses - cluster analyses and principal component analyses (PCA) - suggest that participants' performance relied on at least 2 mechanisms, one for encoding low numbers of taps (around 10) and another for encoding larger numbers (around 27).

Strengths

Individual differences can be a rich source of scientific insight and I applaud the authors for taking them seriously, and for exploring new avenues in the study of numerical cognition.

Weaknesses

Inter-subject-correlation<br /> The experiment "is based on the idea that interindividual variability conveys information that can reveal common sensory processes (Peterzell & Kennedy, 2016)" but I struggled to understand the logic of this technique. The authors explain it most clearly when they write "Regions of high intercorrelation between neighbouring stimuli intensity can be interpreted to imply that sets of stimuli are processed by the same (shared) underlying channel. This channel, while responding relatively more to its preferred stimulus, will also be activated by neighbouring stimuli that although slightly different from the preferred intensity, are nevertheless included in the same response distribution." As I understood it, the correlations are performed "between participants, for all targets values" - meaning that they are measuring the extent to which different participants' WFs vary together. But why is this a good measure of channels? This analysis seems to assume that if people have channels for numerical estimation, they will have the same channels, tuned to the same numerical ranges. But this is an empirical question - individual participants could have wildly different channels, and perhaps different numbers of channels (even in the tested range). If they do, then this between-subject analysis would mask these individual differences (despite the subtitle).

Different channels<br /> I had trouble understanding much of the analyses, and this may account for at least some of my confusion. That said, as I understand it, the results are meant to provide "evidence that tuned mechanisms exist in the human brain, with at least two different tunings" because of the results of the clustering analysis and PCA. However, as the authors acknowledge, "PCA aims to summarize the dataset with the minimal number of components (channels). We can therefore not exclude the possible existence of more than two (perhaps not fully independent) channels." So I believe this technique does not provide more evidence for the existence of 2 channels as for the existence of 4 or 8 or 11 channels, the upper bound for a task testing 11 different numbers. If we can conclude that people may have one channel per number, what does "channel" mean?

Several other questions arose for me when thinking through this technique. If people did have two channels (at least in this range), why would they be so broad? Why would they be centered so near the ends of the tested range? Can such effects be explained by binning on the part of the participants, who might have categorized each number (knowingly or not) as either "small" or "large"? Whereas the experiment tested numbers 8-32, numbers are infinite - How could a small number of channels cover an infinite set? Or even the set 8-10,000? More broadly, I was unsure what advantages channels would have - that is - how in principle would having distinct channels for processing similar stimuli improve (rather than impede) discrimination abilities?

No number perception<br /> I was uncertain about the analogy to studies of other continuous dimensions like spatial frequency, motion, and color. In those studies, participants view images with different spatial frequency, motion, or color - the analogy would be to see dot arrays containing different numbers of dots. Instead, here participants read written numerals (like "19"), symbols which themselves do not have any numerical properties to perceive. How does that difference change the interpretation of the effects? One disadvantage of using numerals is that they introduce a clear discontinuity: Our base-10 numerical system artificially chunks integers into decades, potentially causing category-boundary effects in people's reproductions.

Sensorimotor<br /> The authors wished to test for "sensorimotor mechanisms selective to numerosity" but it's not clear what makes their effects sensorimotor (or selective to numerosity, see below). It's true they found effects using a tapping task (which like all behavior is sensorimotor), but it's not clear that this effect is specific to sensorimotor number reproduction. They might find similar effects for numerical comparison or estimation tasks. Such findings would suggest the effect may be a general feature of numerical cognition across modalities.

Specific to numbers<br /> The authors argue that their effects are "number selective" but they do not provide compelling evidence for this selectivity. In principle, their main findings could be explained by the duration of tapping rather than the number of taps. They argue this is unlikely for two reasons. The first reason is that the overall pattern of results was unchanged across the fast and slow tapping conditions, but differences in duration were confounded with numerosity in both conditions, so the comparison is uninformative. (Given this, I am not sure what we stand to learn by comparing the two tapping speeds.) The second reason is that temporal reproduction was less precise in their control condition than numerical reproduction, but this logic is unclear: Participants could still use duration (or some combination of speed and duration) as a helpful cue to numerosity, even if their duration reproductions were imperfect.

If the authors wish to test the role of duration, they might consider applying the same analytical techniques they use for numbers to their duration data. Perhaps participants show similar evidence for duration-selective channels, in the absence of number, as they do for other non-numerical domains (like spatial frequency).

Theories of numerical cognition. An expansive literature on numerical cognition suggests that many animals, human children, and adults across cultures have two systems for representing numerosity without counting - one that can represent the exact cardinality of sets smaller than about 4 and another that represents the approximate number of larger sets (but see Cheyette & Piantadosi, 2020). The current paper would benefit from better relating its findings to this long lineage of theories and findings in numerical approximation across cultures, ages, and species.

Reviewer #2 (Public Review):

Summary:<br /> The interplay between the medial prefrontal cortex and ventral hippocampal system is critical for many cognitive processes, including memory and its consolidation over time. A prominent idea in recent research is that this relationship is mediated at least in part by the midline nucleus reuniens with respect to consolidation in particular. Whereas the bulk of evidence has focused on neuroanatomy and the effects of temproary or permanent lesions of the nucleus reuniens, the current work examined the electrophysiology of these three structures and how they inter-relate, especially during sleep, which is anticipated to be critical for consolidation. They provide evidence from intercellular recordings of the bi-directional functional connectivity among these structures. There is an emphasis on the interactions between these regions during sleep, especially slow-wave sleep. They provide evidence, in cats, that cortical slow waves precede reuniens slow waves and hippocampal sharp-wave ripples, which may reflect prefrontal control of the timing of thalamic and hippocampal events, They also find evidence that hippocampal sharp wave ripples trigger thalamic firing and precede the onset of reuniens and medial prefrontal cortex spindles. The authors suggest that the effectiveness of bidirectional connections between the reuniens and the (ventral) CA1 is particularly strong during non-rapid eye movement sleep in the cat. This is a very interesting, complex study on a highly topical subject.

Strengths:<br /> An excellent array of different electrophysiological techniques and analyses are conducted. The temporal relationships described are novel findings that suggest mechanisms behind the interactions between the key regions of interest. These may be of value for future experimental studies to test more directly their association with memory consolidation.

Weaknesses:<br /> Given the complexity and number of findings provided, clearer explanation(s) and organisation that directed the specific value and importance of different findings would improve the paper. Most readers may then find it easier to follow the specific relevance of key approaches and findings and their emphasis. For example, the fact that bidirectional connections exist in the model system is not new per se. How and why the specific findings add to existing literature would have more impact if this information was addressed more directly in the written text and in the figure legends.

Reviewer #2 (Public Review):

Summary:<br /> Silva et al. describe an experimental study conducted on cerebellar parallel fiber-to-molecular interneuron synapses to investigate the size of the readily releasable pool (RRP) of synaptic vesicles (SVs) per docking site in response to trains of action potentials. The study aims to determine whether there are multiple binding sites for SVs at each docking site, which could lead to a higher RRP size than previously thought.

The researchers used this glutamatergic synapse to conduct their experiments. They employed various techniques and manipulations to enhance release probability, docking site occupancy, and synaptic depression. By counting the number of released SVs in response to action potential trains and normalizing the results based on the number of docking sites, they estimated the RRP size per docking site.

The key findings and observations in the manuscript are as follows:

Docking Site Occupancy and Release Probability Enhancement: The researchers used 4-amidopyridine (4-AP) and post-tetanic potentiation (PTP) protocols to enhance the release probability of docked SVs and the occupancy of docking sites, respectively.

Synchronous and Asynchronous Release: Synchronous release refers to SVs released in response to individual action potentials, while asynchronous release involves SVs released after the initial release response due to calcium elevation. The study observed changes in the balance between synchronous and asynchronous release under different conditions, revealing the degree of filling of the RRP.

Modeling of Release Dynamics: The researchers employed a modeling approach based on the "replacement site/docking site" (RS/DS) model, where SVs bind to a replacement site before moving to a docking site and eventually undergoing release. The model was adjusted to experimental conditions to estimate parameters like docking site occupancy and release probabilities.

Comparison of Different Models: The study compared the RS/DS model with an alternative model known as the "loosely docked/tightly docked" (LS/TS) model. The LS/TS model assumes that a docking site can only accommodate one SV at a time, while the RS/DS model considers the possibility of accommodating multiple SVs.

Maximum RRP Size: Through a combination of experimental results and model simulations, the study revealed that the maximum RRP size per docking site reached close to two SVs under certain conditions, supporting the idea that each docking site can accommodate multiple SVs.

Strengths:<br /> The study is rigorously conducted and takes into consideration previous work of RRP size and SV docking site estimation. The study addresses a long-standing question in synaptic physiology.

Weaknesses:<br /> It remains unclear how generalizable the findings are to other types of synapses.

Reviewer #2 (Public Review):

SUMMARY: In this study, the authors use the tractable Drosophila embryonic/larval motor circuit to determine how manipulations to activity during a critical period (CP) modify the circuit in ways that persist into later developmental stages. Previously, this group demonstrated that manipulations to the aCC/MN-Ib neuron in embryonic stages enhance (or can rescue) susceptibility to seizures at later larval stages. Here, the authors demonstrate that following enhanced excitatory drive (by PTX feeding), the aCC neuron acquires increased sensitivity to cholinergic excitatory transmission, presumably due to increased postsynaptic receptor abundance and/or sensitivity, although this is not clarified. Although locomotion is not altered at later developmental larval stages, the authors suggest there is reduced "robustness" to induced seizures. The second part of the study then goes on to enhance inhibition during the CP in an attempt to counteract the enhanced excitation, and show that many aspects of the CP plasticity are rescued. The author conclude that "average" E/I activity is integrated during the CP to determine excitability of the mature locomotor network.

Overall, this study provides compelling mechanistic insight into how a final motor output neuron changes in response to enhanced excitatory drive during a CP to change functionality of the circuit at later mature developmental stages. The first part of this study is strong, clearly showing the changes in the aCC neuron that result from enhanced excitatory input. This includes very nice electrophysiology and imaging data that assess synaptic function and structure onto aCC neurons from pre-motor inputs resulting from PTX exposure during development. However, the later experiments in Figures 6 and 7 designed to counteract the CP plasticity are somewhat difficult to interpret. In particular, the specificity of the manipulations of the ch neuron intended to counteract the CP plasticity is unclear, given the complexities of how these changes impact excitability all neurons during development. It is clear that CP plasticity is largely rescued in later stages, but it is hard to know if downstream or secondary adaptations may be masking the PTX-induced plasticity normally observed. Nonetheless, this study provides an important advance in our understanding of what parameters change during CPs to calibrate network dynamics at later developmental stages.

Reviewer #2 (Public Review):

Summary:<br /> Golov et al performed the capture of MChIP-C using the H3K4me3 antibody. The new method significantly increases the resolution of Micro-C and can detect clear interactions which are not well described in the previous HiChIP/PLAC-seq method. Overall, the paper represents a significant technological advance that can be valuable to the 3D genomic field in the future.

Strengths:<br /> 1. The authors established a novel method to profile the promoter center genomic interactions based on the Micro-C method. Such a method could be very useful to dissect the enhancer promoter interaction which has long been an issue for the popular HiC method.

2. With the MChIP-C method the authors are able to find new genomic interactions with promoter regions enriched in CTCF. The author has significantly increased the detection sensitivity of such methods as PLAC-seq, Micro-C, and HiChIP.

3. The authors identified a new type of interaction between the CTCF-less promoter and the CTCF binding site. This particular type of interaction could explain the CTCF's function in regulating gene transcription activity as observed in many studies. I personally think the second stripe model of P-CTCF interaction is more likely as this has been proposed for the super-enhancer stripe model before. The author should also discuss this part of the story more.

Weaknesses:<br /> 1. The data presentation should include the contact heat map. The current data presentation makes it hard for the readers to have a comprehensive view of pair-wise interactions between promoters and the PIR. In particular, these maps may directly give answers to the proposed model of promoter-CTCF interactions by the authors in Figure 3a.

2. In Fig 3D, there seems a very limited increase of power predicting MChIP-C signal for DHS-promoter pairs beyond the addition of CTCF. This figure could be simplified with fewer factors.

3. The current method seems to have a big fraction of unusable reads. How the authors process the data should be included to allow for future reproduction. Ideally, the authors should generate a package on R or Bioconda for this processing.

Reviewer #2 (Public Review):

Summary:<br /> The manuscript by Kang et al investigates how the consideration of pairwise encounters (consumer-resource chasing, intraspecific consumer pair, and interspecific consumer pair) influences the community assembly results. To explore this, they presented a new model that considers pairwise encounters and intraspecific interference among consumer individuals, which is an extension of the classical Beddington-DeAngelis (B-D) phenomenological model, incorporating detailed considerations of pairwise encounters and intraspecific interference among consumer individuals. Later, they connected with several experimental datasets.

Strengths:<br /> They found that the negative feedback loop created by the intraspecific interference allows a diverse range of consumer species to coexist with only one or a few types of resources. Additionally, they showed that some patterns of their model agree with experimental data, including time-series trajectories of two small in-lab community experiments and the rank-abundance curves from several natural communities. The presented results here are interesting and present another way to explain how the community overcomes the competitive exclusion principle.

Weaknesses:<br /> The authors only explore the case with interspecific interference or intraspecific interference exists. I believe they need to systematically investigate the case when both interspecific and intraspecific interference exists. In addition, the text description, figures, and mathematical notations have to be improved to enhance the article's readability. I believe this manuscript can be improved by addressing my comments, which I describe in more detail below.

1. In nature, it is really hard for me to believe that only interspecific interference or intraspecific interference exists. I think a hybrid between interspecific interference and intraspecific interference is very likely. What would happen if both the interspecific and intraspecific interference existed at the same time but with different encounter rates? Maybe the authors can systematically explore the hybrid between the two mechanisms by changing their encounter rates. I would appreciate it if the authors could explore this route.

2. In the first two paragraphs of the introduction, the authors describe the competitive exclusion principle (CEP) and past attempts to overcome the CEP. Moving on from the first two paragraphs to the third paragraph, I think there is a gap that needs to be filled to make the transition smoother and help readers understand the motivations. More specifically, I think the authors need to add one more paragraph dedicated to explaining why predator interference is important, how considering the mechanism of predator interference may help overcome the CEP, and whether predator interference has been investigated or under-investigated in the past. Then building upon the more detailed introduction and movement of predator interference, the authors may briefly introduce the classical B-D phenomenological model and what are the conventional results derived from the classical B-D model as well as how they intend to extend the B-D model to consider the pairwise encounters.

3. The notations for the species abundances are not very informative. I believe some improvements can be made to make them more meaningful. For example, I think using Greek letters for consumers and English letters for resources might improve readability. Some sub-scripts are not necessary. For instance, R^(l)_0 can be simplified to g_l to denote the intrinsic growth rate of resource l. Similarly, K^(l)_0 can be simplified to K_l. Another example is R^(l)_a, which can be simplified to s_l to denote the supply rate. In addition, right now, it is hard to find all definitions across the text. I would suggest adding a separate illustrative box with all mathematical equations and explanations of symbols.

4. What is the f_i(R^(F)) on line 131? Does it refer to the growth rate of C_i? I noticed that f_i(R^(F)) is defined in the supplementary information. But please ensure that readers can understand it even without reading the supplementary information. Otherwise, please directly refer to the supplementary information when f_i(R^(F)) occurs for the first time. Similarly, I don't think the readers can understand \Omega^\prime_i and G^\prime_i on lines 135-136.

Reviewer #2 (Public Review):

Summary:<br /> The authors developed a tool-set Photo-SynthSeg for the software FreeSurfer which performs 3D reconstruction and high-resolution 3D segmentation on a stack of dissection photographs of brain tissues. The tool-set consists of three modules: the pre-processing module, which performs dissection photography correction; the registration module, which registers corrected dissection photographs based on 3D surface scan, ex vivo MRI or probabilistic atlas; the segmentation module based on U-Net. To prove the performance of the tools, three experiments were conducted, including a volumetric comparison of brain tissues on AD and HC groups from MADRC, a quantitative evaluation of segmentation on UW-ADRC and a quantitative evaluation of 3D reconstruction on HCP digitally sliced MRI data.

Strengths:<br /> The quantitative evaluation of segmentation and reconstruction on synthetic and real data demonstrates the accuracy of the methodology. Also, the successful application of this toolset on two brain banks with different slice thicknesses, tissue processing, and photograph settings demonstrates its robustness. The toolset also benefits from its adaptability of different 3D references, such as surface scans, ex vivo MRI, and even probabilistic atlas, suiting the needs of different brain banks.

Weaknesses:<br /> 1) The current method could only perform accurate segmentation on subcortical tissues. It is of more interest to accurately segment cortical tissues, whose morphometrics are more predictive of neuropathology. The authors also mentioned that they would extend the toolset to allow for cortical tissue segmentation in the future.

2) Brain tissues are not rigid bodies, so dissected slices could be stretched or squeezed to some extent. Also, dissected slices that contain temporal poles may have several disjoined tissues. Therefore, each pixel in dissected photographs may go through slightly different transformations. The authors constrain that all pixels in each dissected photograph go through the same affine transform in the reconstruction step probably due to concerns of computational complexity. But ideally, dissected photographs should be transformed with some non-linear warping or locally linear transformations. Or maybe the authors could advise how to place different parts of dissected slices when taking dissection photographs to reduce such non-linearity of transforms.

3) For the quantitative evaluation of the segmentation on UW-ARDC, the authors calculated 2D Dice scores on a single slice for each subject. Could the authors specify how this single slice is chosen for each subject? Is it randomly chosen or determined by some landmarks? It's possible that the chosen slice is between dissected slices so SAMSEG cannot segment accurately. Also from Figure 3, it seems that SAMSEG outperforms Photo-SynthSeg on large tissues, WM/Cortex/Ventricle. Is there an explanation for this observation?

4) In the third experiment, quantitative evaluation of 3D reconstruction, each digital slice went through random affine transformations and illumination fields only. However, it's better to deform digital slices using random non-linear warping due to the non-rigidity of the brain as mentioned in 2). So, the reconstruction errors estimated here are quite optimistic. It would be more realistic if digital slices were deformed using random non-linear warping.

Overall, this is quite useful a toolset that could be widely used in many brain banks without MRI scanners.

Reviewer #2 (Public Review):

The study from Gumaste et al investigates whether mice can use changes of intermittency, a temporal odor feature, to locate an odor source. First, the study tries to demonstrate that mice can discriminate between low and high intermittency and that their performance is not affected by the odor used or the frequency of odor whiffs. Then, they show that there is a correlation between glomerular responses (OSNs and mitral cells) and intermittency. Finally, they conclude that sniffing frequency impacts the behavioral discrimination of intermittency as well as its neural representation. Overall, the authors seek to demonstrate that intermittency is an odor-plume property that can inform olfactory navigation.

The paper explored an interesting question, the use of intermittency of an odor plume as a behavioral cue, which is a new and intriguing hypothesis. However, it falls short in demonstrating that the animal is actually sensitive to intermittency but not other flow parameters, and is missing some important details.

Major concerns

1) One of the cornerstones of this paper consists in showing that mice are behaviorally able to distinguish among different intermittency values (high or low), across a variety of different stimuli and without confounds such as the number of whiffs or concentration. However, I could not find in the paper a convincing explanation of how these confounds were tested. It is clear that the authors repeat their measurements in different conditions (low or high concentration, and different whiff numbers) but it is not specified how: do the authors mix all stimuli in the same session, and so the animals simply generalize across all the stimuli and only consider intermittency for the behavioral choices? Or do authors repeat different sessions for different parameters? For example: do they perform two separate sessions with low concentration and high concentration? If this last one is the case, I would argue that this is not enough proof that animals generalize across concentrations, as the animals might simply use concentration as a cue and change the decision criteria at each session. Please clarify.

2) It looks to me that the measure of intermittency strongly depends on the set. What is the logic of setting a specific threshold? Do the results hold when this threshold changes within a reasonable range? The same questions (maybe even more important) go for the measure of glomerular intermittence. Unfortunately, a sensitivity analysis for both measures is missing, which makes it hard to interpret the results.

3) The logic of choosing the decision boundary for the discrimination task is not clear: low intermittency is considered to be below 0.15 and high intermittency is considered to be between 0.2 and 0.8. Do these values correspond to natural intermittency distribution? How were these values chosen?

4) Only 2 odors were used in the whole study and some results were in disagreement between the two odors. By looking at only two odors it is very difficult to make a general conclusion about intermittency encoding in the OB.

5) Assuming that all the above issues are resolved, one can conclude that intermittency can be perceived by an animal. The study puts a strong accent on the fact that this feature could be used for navigation. I understand that it is extremely hard to demonstrate that this feature is actually used for navigation, however, the analysis of relevance of this measure is missing. Even if it is used in navigation, most probably this would be in combination with other features, thus its relative importance needs to be discussed, or even better, established.

Reviewer #2 (Public Review):

Investigating the relationship between transcriptomic profiles, their axonal projection and collateralization patterns will help define neuronal cell types in the mammalian central nervous system. The study by Xu et al. combined multiple retrograde viruses with barcodes and single-cell RNA-sequencing (MERGE-seq) to determine the projection and collateralization patterns of transcriptomically defined ventral medial prefrontal cortex (vmPFC) projection neurons. They found a complex relationship: the same transcriptomically defined cell types project to multiple target regions, and the same target region receives input from multiple transcriptomic types of vmPFC neurons. Further, collateralization patterns of vmPFC to the five target regions they investigated are highly non-random.

While many of the biological conclusions are not surprising given recent studies on the collateralization patterns of vmPFC neurons using single neuron tracing and other methods that integrate transcriptomics and projections, MERGE-seq provides validation, at the single cell level, collateralization patterns of individual vmPFC neurons, and thus offer new and valuable information over what has been published. The method can also be used to study collateralization patterns of other neuron types.

Some of the conclusions the authors draw depend on the efficiency of retrograde labeling, which was not determined. Without quantitative information on retrograde labeling efficiency, and unless such efficiency is close to 100%, these conclusions are likely misleading.

Reviewer #2 (Public Review):

Here, Brown and colleagues report a valuable finding on the function and evolution of the seminal odorant-binding protein Obp56g in Drosophila melanogaster. Previous studies have shown that this family of proteins is highly expressed in olfactory tissues like the antennae and maxillary palps. Some of these proteins have been shown to mediate behavioural responses to specific odorants-hence the general moniker odorant binding proteins. This slightly misleading historical naming convention implies an exclusive role in olfaction-however, many of these proteins are expressed in other tissues of the animal, including the male reproductive system. In addition, seminal fluid proteins exhibit a fascinating evolutionary history, with rapid evolution and turnover across taxa.

The authors suggest that the Obp56g protein may have been co-opted for a reproductive role in Drosophila melanogaster during evolution. The authors show that Obp56g is required for male fertility and the induction of the post-mating response in females. Mutant males lacking Obp56g fail to form a mating plug in the female reproductive tract-leading to ejaculate loss and reduced sperm storage. The experimental evidence supporting the claims of the authors is solid and compelling. The data were collected and analyzed using solid and validated methodologies. The author's findings can be used as a starting point for understanding the mechanistic roles of this family of proteins in mating plug coagulation. The work will interest biologists studying non-sperm seminal fluid protein function and evolution.

Reviewer #2 (Public Review):

This paper argues for an explanation of sequential effects in prediction based on the computational cost of representing probability distributions. This argument is made by contrasting two cost-based models with several other models in accounting for first- and second-order dependencies in people's choices. The empirical and modeling work is well done, and the results are compelling.

The main weaknesses of the paper are as follows:

1. The main argument is against accounts of dependency based on sensitivity to statistics (ie. modeling the timeseries as having dependencies it doesn't have). However, such models are not included in the model comparison, which makes it difficult to compare these hypotheses.

2. The task is not incentivized in any way. Since incentives are known to affect probability-matching behaviors, this seems important. In particular, we might expect incentives would trade off against computational costs - people should increase the precision of their representations if it generates more reward.

3. The sample size is relatively small (20 participants). Even though a relatively large amount of data is collected from each participant, this does make it more difficult to evaluate the second-order dependencies in particular (Figure 6), where there are large error bars and the current analysis uses a threshold of p < .05 across a large number of tests hence creating a high false-discovery risk.

4. In the key analyses in Figure 4, we see model predictions averaged across participants. This can be misleading, as the average of many models can produce behavior outside the class of functions the models themselves can generate. It would be helpful to see the distribution of raw model predictions (ideally compared against individual data from humans). Minimally, showing predictions from representative models in each class would provide insight into where specific models are getting things right and wrong, which is not apparent from the model comparison.

Reviewer #2 (Public Review)

DNA adenine methylation (6mA) is a rediscovered modification that has been described in a wide range of eukaryotes. However, 6mA presence in eukaryote remains controversial due to low abundance of its modification in eukaryotic genome. In this manuscript, Boulet et al. re-investigate 6mA presence in drosophila using axenic or conventional fly to avoid contaminant from feeding bacteria. By using these flies, they find that 6mA is rare but present in drosophila genome by performing LC/MS/MS. They also find that the loss of TET (also known as DMAD) does not impact on 6mA levels in drosophila, contrary to previous studies. In addition, the authors find that TET is required for fly development in its enzymatic activity-independent manner.

The strength of this study is, compared to previous studies of 6mA in drosophila, the authors employ axenic or conventional fly for 6mA analysis. These fly strains make it possible to analyze 6mA presence in drosophila without bacterial contaminant. This established method is valuable in this field.

Reviewer #2 (Public Review):

Summary:

Complexin (Cplx) is expressed at nearly all chemical synapses. Mammalian Cplx comes in four different paralogs which are differentially expressed in different neuron types, either selectively or in combination with one or two other Cplx isoforms. Cplx binds with high affinity to assembled SNARE complexes and promotes AP-evoked release by increasing vesicle fusogenicity. Cplx is assumed to preclude premature SV fusion by preventing full SNARE assembly, thereby arresting subsequent SNARE-driven fusion ("fusion-clamp" theory). The protein has multiple domains, the functions of which are controversially discussed. Cplx's function has been studied in a variety of model organisms including mice, flies, worms, and fish with seemingly conflicting results which led to partly contradicting conclusions.

Makee et al. study the function of mammalian Cplx2 by making use of chromaffin cells derived from Cplx2 ko mice as a system to overexpress and functionally characterize mutant Cplx2 forms. This work is an important extension of previous studies of the same lab using similar techniques. The main conclusion of the present study are:

The hydrophobic character of the amphipathic helix in Cplx's C-terminal domain is essential for inhibiting premature vesicle fusion at a [Ca2+]i of several hundreds of nM (pre-flash [Ca2+]i). The Cplx-mediated inhibition of fusion under these conditions does not rely on the expression of either Syt1 or Syt7.

Slow-down of exocytosis by N-terminally truncated Cplx mutants in response to a [Ca2+]i of several µM (peak flash [Ca2+]i) occurs regardless of the presence or absence of Syt7 demonstrating that Cplx2 does not act as a switch favoring preferential assembly of the release machinery with Syt1,2 rather than the "slow" sensor Syt7.

Cplx's N-terminal domain is required for the Cplx2-mediated increase in the speed of exocytosis and faster onset of exocytosis which likely reflect an increased apparent Ca2+ sensitivity and faster Ca2+ binding of the release machinery.

Strengths:

The authors perform systematic truncation/mutational analyses of Cplx2 by making use of chromaffin cells derived from Cplx2 ko mice. They analyze the impact of single and combined deficiencies for Cplx2 and Syt1 to establish interactions of both proteins.

State-of-the-art methods are employed: Vesicle exocytosis is assayed directly and with high resolution using capacitance measurements. Intracellular [Ca2+] is controlled by loading via the patch-pipette and by UV-light-induced flash-photolysis of caged [Ca2+]. The achieved [Ca2+ ] is measured with Ca2+ -sensitive dyes.

The data is of high quality and the results are convincing.

Weaknesses:

The authors provide a "chromaffin cell-centric" view of the function of mammalian Cplx in vesicle fusion. With the exception of mammalian retinal ribbon synapses (and some earlier RNAi knockdown studies that had off-target effects), there is very little evidence for a "fusion-clamp"-like function of Cplxs in mammalian synapses. At conventional mammalian synapses, genetic loss of Cplx (i.e. KO) consistently decreases AP-evoked release, and generally either also decreases spontaneous release rates or does not affect spontaneous release, which is inconsistent with a "fusion-clamp" theory. This is in stark contrast to invertebrate (D. m. and C. e.) synapses where genetic Cplx loss is generally associated with strong upregulation of spontaneous release, providing support for Cplx acting as a "fusion-clamp".

The authors use a Semliki Forest virus-based approach to express mutant proteins in chromaffin cells. This strategy leads to a strong protein overexpression (~7-8fold, Figure 3 Suppl. 1). Therefore, experimental findings under these conditions may not necessarily be identical to findings with normal protein expression levels.

Measurements of delta Cm in response to Ca2+ uncaging by ramping [Ca2+ ] from resting levels up to several µM over a time period of several seconds were used to establish changes in the release rate vs [Ca2+ ]i relationship. It is not clear to this reviewer if and how concurrently occurring vesicle endocytosis together with a possibly Ca2+-dependent kinetics of endocytosis may affect these measurements.

It should be pointed out that an altered "apparent Ca2+ affinity" or "apparent Ca2+ binding rate" does not necessarily reflect changes at Ca2+-binding sites (e.g. Syt1).

There are alternative models on how Cplx may "clamp" vesicle fusion (see Bera et al. 2022, eLife) or how Cplx may achieve its regulation of transmitter release without mechanistically "clamping" fusion (Neher 2010, Neuron). Since the data presented here cannot rule out such alternative models (in this reviewer's opinion), the authors may want to mention and briefly discuss such alternative models.

Some parts of the Discussion are quite general and not specifically related to the results of the present study. The authors may want to consider shortening those parts.

Last but not least, the presentation of the results could be improved to make the data more accessible to non-specialists, this concerns providing necessary background information, choice of colors, and labeling of diagrams.

Reviewer #2 (Public Review):

Summary:<br /> Yang et al. recorded the activity of D1- and D2-MSNs in the dorsal striatum and analyzed their firing activity in relation to single-limb gait in normal and 6-OHDA lesioned mice. Although some of the observations of striatal encoding are interesting, the novelty and implications of this firing activity in relation to gait behavior remain unclear. More specifically, the authors made two major claims. First, the striatal D1- and D2-MSNs were phase-locked to the walking gait cycles of individual limbs. Second, dopamine lesions led to enhanced phase-locking between D2-MSN activity and walking gait cycles. The second claim was supported by the increase of vector length in D2-MSNs after unilateral 6-OHDA administration to the medial forebrain bundle. However, for the first claim, the authors failed to convincingly demonstrate that striatal MSNs were more phase-locked to gait with single-limb and step resolution than to the global gait cycles.

Strengths:<br /> It is a technically advanced study.

Weaknesses:<br /> 1. The authors focused on striatal encoding of gait information in current studies. However, it remains unclear whether the part of the striatum for which the authors performed neuronal recording is really responsible for or contributing to gait control. A lesion or manipulation experiment disrupting the part of the striatum recorded seems a necessary step to test or establish its relationship to gait control.

2. The authors attributed one of the major novelties to phase-locking of striatal neural activities with single-limb gait cycles. The claim was not clearly supported, as the authors did not demonstrate that phase-locking to single-limb gaits was more significant than phase-locking to global walking gait cycles. In rhythmic walking, the LR and RF limbs were roughly anti-phase with the LF and RR limbs (Fig. 1D, E). In line with this relationship, striatal neurons were mainly in-phase with LR and RF limbs and anti-phase with LF and RR limbs (Fig. 2J, K). One could instead interpret this as the striatal neurons spanned all the phases of the global walking gait cycles (Fig. 3D). To demonstrate phase-locking with individual limb movements, the authors need to show that neural activities were better correlated with a specific limb than to the global gait cycles.

3. The observation of the enhancement of coupling between D2 MSN firing and the gait cycles was interesting, but the physiological interpretation was not clear (as the authors also noted in the Discussion), which hampers the significance of the observation.

4. Due to the lack of causality experiments as mentioned in the first comment above, the observations of coupling between striatal neuronal activity and gait control might well result from a third brain region/factor serving as the common source to both, whether in normal or dopamine lesioned brain. If this is the case, the significance and implications of current findings will be greatly limited.

Reviewer #2 (Public Review):

The manuscript presents a method for tracking neurons recorded with neuropixels across days, based on the matching of cells' spatial layouts and spike waveforms at the population level. The method is tested on neuropixel recordings of the visual cortex carried over 47 days, with the similarity in visual receptive fields used to verify the matches in cell identity.

This is an important tool as electrophysiological recordings have been notoriously limited in terms of tracking individual neuron's fate over time, unlike imaging approaches. The method is generally sound and properly tested but I think some clarifications would be helpful regarding the implementation of the method and some of the results.

1) Page 6: I am not sure I understand the point of the imposed drift and how the value of 12µm is chosen.<br /> Is it that various values of imposed drift are tried, the EMDs computed to produce histograms as in Fig2c, values of rigid drifts estimated based on the histogram modes, and then the value associated with minimum cost selected? The corresponding manuscript section would need some clarification regarding this aspect.

2) The EMD is based on the linear sum, with identical weight, of cell distance and waveform similarity measures. How performance is affected by using a different weighting of the 2 measures (for instance, using only cell distance and no waveform similarity)? It is common that spike waveforms associated with a given neuron appear differently on different channels of silicon probes (i.e. the spike waveform changes depending on the position of recording sites relative to the neuron), so I wonder if that feature is helping or potentially impeding the tracking.

3) Fig.5: I assume the dots represent time gaps for which cell tracking is estimated. The 3 different groups of colors correspond to the 3 mice used. For a given mouse, I would expect to always see 3 dots (for ref, putative, and mixed) for a given tracking gap. However, for mouse AL036 for instance, at a tracking duration of 8 days, a dot is visible for mixed but not for ref and putative. How come this is happening?

4) Matched visual responses are measured by the sum of the correlation of visual fingerprints, which are vectors of cells' average firing rate across visual stimuli, and the correlation of PSTHs, which are implemented over all visual stimuli combined. I believe that some information is lost from combining all stimuli in the implementation of PSTHs (assuming that PSTHs show specificity to individual visual stimuli). The authors might consider, as an alternative measure of matched visual responses, a correlation of the vector concatenations of all stimulus PSTHs. Such a simpler measure would contain both visual fingerprint and PSTH information, and would not lose the information of PSTH specificity across visual stimuli.

Reviewer #2 (Public Review):

Summary:<br /> Watanabe et al establish a novel method for the activity-dependent labeling of neural circuits in flies. While activity mapping of neurons that are active during specific behaviors is widespread in rodents, the application of this method to fly circuit neuroscience is limited, mainly due to technological challenges. Thus, the present study addresses a timely problem. To do so, they apply the in situ hybridization amplification method called Hybridization Chain Reaction v. 3.0 (Choi et al. 2018) to the adult fly brain in order to visualize the expression changes of the immediate early gene (IEG) Hr38 under different types of social contexts. The conclusions of this paper are mostly very well supported by data but it would strongly benefit from additional methodological details as well as additional controls, in particular for the HI-catFISH experiments.

Strengths:<br /> The major strength of this method is its versatility and sensitivity. It can be applied to a wide variety of biological questions and assess the dynamic transcriptional regulation of an unlimited number of genes with a high signal-to-noise ratio. It will be therefore useful to many research labs working on different biological questions.

Weaknesses:<br /> Although the paper has great strengths in principle, the major weakness is the calibration of the temporal resolution of HI-CatFISH in Figure 4 and Figure Supplement 4. According to Figure Supplement 4C, close to 100% of the Hr38-positive cells are already labeled with the exonic probe 30min post-stimulation, which is not reflected in Figure 4B (there, the expression level of the exonic probe peaks 60min post-induction) and may have profound implications for the interpretation of the results. The present manuscript would strongly benefit from additional controls, such as the quantification of the intronic and exonic Hr38 probes after either only the 1st or 2nd social context but at the same timepoint than if two consecutive social contexts were tested.

Reviewer #2 (Public Review):

Summary:

The large-conductance Ca2+ activated K+ channel (BK) has been reported to promote breast cancer progression, but it is not clear how. The present study carried out in breast cancer cell lines, concludes that BK located in mitochondria reprograms cells towards the Warburg phenotype, one of the metabolic hallmarks of cancer.

Strengths:

The use of a wide array of modern complementary techniques, including metabolic imaging, respirometry, metabolomics, and electrophysiology. On the whole, experiments are astute and well-designed and appear carefully done. The use of BK knock-out cells to control for the specificity of the pharmacological tools is a major strength. The manuscript is clearly written. There are many interesting original observations that may give birth to new studies.

Weaknesses:

The main conclusion regarding the role of a BK channel located in mitochondria appears is not sufficiently supported. Other perfectible aspects are the interpretation of co-localization experiments and the calibration of Ca2+ dyes. These points are discussed in more detail in the following paragraphs:

1. May the metabolic effects be ascribed to a BK located in mitochondria? Unfortunately not, at least with the available evidence. While it is clear these cells have a BK in mitochondria (characteristic K+ currents detected in mitoplasts) and it is also well substantiated that the metabolic effects in intact cells are explained by an intracellular BK (paxilline effects absent in the BK KO), it does not follow that both observations are linked. Given that ectopic BK-DEC appeared at the surface, a confounding factor is the likely expression of BK in other intracellular locations such as ER, Golgi, endosomes, etc. To their credit, authors acknowledge this limitation several times throughout the text ("...presumably mitoBK...") but not in other important places, particularly in the title and abstract.

2. MitoBK subcellular location. Pearson correlations of 0.6 and about zero were obtained between the locations of mitoGREEN on one side, and mRFP or RFP-GPI on the other (Figs. 1G and S1E). These are nice positive and negative controls. For BK-DECRFP however, the Pearson correlation was about 0.2. What is the Z resolution of apotome imaging? Assuming an optimum optical section of 600 nm, as obtained by a 1.4 NA objective with a confocal, that mitochondria are typically 100 nm in diameter and that BK-DECRFP appears to stain more structures than mitoGREEN, the positive correlation of 0.2 may not reflect colocalization. For instance, it could be that BK-DECRFP is not just in mitochondria but in a close underlying organelle e.g. the ER. Along the same line, why did BK-RFP also give a positive Pearson? Isn´t that unexpected? Considering that BK-DEC was found by patch clamping at the plasma membrane, the subcellular targeting of the channel is suspect. Could it be that the endogenous BK-DEC does actually reside exclusively in mitochondria (a true mitoBK), but overflows to other membranes upon overexpression? Regarding immunodetection of BK in the mitochondrial Percoll preparation (Fig. S5), the absence of NKA demonstrates the absence of plasma membrane contamination but does not inform about contamination by other intracellular membranes.

3. Calibration of fluorescent probes. The conclusion that BK blockers or BK expression affects resting Ca2+ levels should be better supported. Fluorescent sensors and dyes provide signals or ratios that need to be calibrated if comparisons between different cell types or experimental conditions are to be made. This is implicitly acknowledged here when monitoring ER Ca2+, with an elaborate protocol to deplete the organelle in order to achieve a reading at zero Ca2+.

4. Line 203. "...solely by the expression of BKCa-DECRFP in MCF-7 cells". Granted, the effect of BKCa-DECRFP on the basal FRET ratio appears stronger than that of BK-RFP, but it appears that the latter had some effect. Please provide the statistics of the latter against the control group (after calibration, see above).

Reviewer #2 (Public Review):

Singh and colleagues employ a methodic approach to reveal the function of the transcription factors Rela and Stat3 in the regulation of the inflammatory response in the intestine.

Strengths of the manuscript include the focus on the function of these transcription factors in hepatocytes and the discovery of their role in the systemic response to experimental colitis. While the systemic response to induce colitis is appreciated, the cellular and molecular mechanisms that drive such systemic response, especially those involving other organs beyond the intestine are an active area of research. As such, this study contributes to this conceptual advance. Additional strengths are the complementary biochemical and metabolomics approaches to describe the activation of these transcription factors in the liver and their requirement - specifically in hepatocytes - for the production of bile acids in response to colitis.

Some weaknesses are noted in the presentation of the data, including a comprehensive representation of findings in all conditions and genotypes tested.

Reviewer #2 (Public Review):

Summary:

The authors of this manuscript address an important question regarding how macrophages respond to external stimuli to create different functional phenotypes, also known as macrophage polarization. Although this has been studied extensively, the authors argue that the transcription factors that mediate the change in state in response to a specific trigger remain unknown. They create a "master" human gene regulatory network and then analyze existing gene expression data consisting of PBMC-derived macrophage response to 28 stimuli, which they sort into thirteen different states defined by perturbed gene expression networks. They then identify the top transcription factors involved in each response that have the strongest predicted association with the perturbation patterns they identify. Finally, using S. aureus infection as one example of a stimulus that macrophages respond to, they infect THP-1 cells while perturbing regulatory factors that they have identified and show that these factors have a functional effect on the macrophage response.

Strengths:

- The computational work done to create a "master" hGRN, response networks for each of the 28 stimuli studied, and the clustering of stimuli into 13 macrophage states is useful. The data generated will be a helpful resource for researchers who want to determine the regulatory factors involved in response to a particular stimulus and could serve as a hypothesis generator for future studies.

- The streamlined system used here - macrophages in culture responding to a single stimulus - is useful for removing confounding factors and studying the elements involved in response to each stimulus.

- The use of a functional study with S. aureus infection is helpful to provide proof of principle that the authors' computational analysis generates data that is testable and valid for in vitro analysis.

Weaknesses:

- Although a streamlined system is helpful for interrogating responses to a stimulus without the confounding effects of other factors, the reality is that macrophages respond to these stimuli within a niche and while interacting with other cell types. The functional analysis shown is just the first step in testing a hypothesis generated from this data and should be followed with analysis in primary human cells or in an in vivo model system if possible.

- It would be helpful for the authors to determine whether the effects they see in the THP-1 immortalized cell line are reproduced in another macrophage cell line, or ideally in PBMC-derived macrophages.

- The paper would benefit from an expanded explanation of the network mining approach used, as well as the cluster stability analysis and the Epitracer analysis. Although these approaches may be published elsewhere, readers with a non-computational background would benefit from additional descriptions.

- Although the authors identify 13 different polarization states, they return to the M0/M1/M2 paradigm for their validation and functional assays. It would be useful to comment on the broader applications of a 13-state model.

- The relative contributions of each "switching factor" to the phenotype remain unclear, especially as knocking out each individual factor changes different aspects of the model (Fig. S5).

Reviewer #2 (Public Review):

Summary:<br /> In this study, Huang et al. employed optogenetic stimulation alongside paired whole-cell recordings in genetically defined neuron populations of the medial entorhinal cortex to examine the spatial distribution of synaptic inputs and the functional-anatomical structure of the MEC. They specifically studied the spatial distribution of synaptic inputs from parvalbumin-expressing interneurons to pairs of excitatory stellate cells. Additionally, they explored the spatial distribution of synaptic inputs to pairs of PV INs. Their results indicate that both pairs of SCs and PV INs generally receive common input when their relative somata are within 200-300 ums of each other. The research is intriguing, with controlled and systematic methodologies. There are interesting takeaways based on the implications of this work to grid cell network organization in MEC.

Major concerns<br /> 1) Results indicate that in brain slices, nearby cells typically share a higher degree of common input. However, some proximate cells lack this shared input. The authors interpret these findings as: "Many cells in close proximity don't seem to share common input, as illustrated in Figures 3, 5, and 7. This implies that these cells might belong to separate networks or exist in distinct regions of the connectivity space within the same network.".

Every slice orientation could have potentially shared inputs from an orthogonal direction that are unavoidably eliminated. For instance, in a horizontal section, shared inputs to two SCs might be situated either dorsally or ventrally from the horizontal cut, and thus removed during slicing. Given the synaptic connection distributions observed within each intact orientation, and considering these distributions appear symmetrically in both horizontal and sagittal sections, the authors should be equipped to estimate the potential number of inputs absent due to sectioning in the orthogonal direction. How might this estimate influence the findings, especially those indicating that many close neurons don't have shared inputs?

2) The study examines correlations during various light-intensity phases of the ramp stimuli. One wonders if the spatial distribution of shared (or correlated) versus independent inputs differs when juxtaposing the initial light stimulation phase, which begins to trigger spiking, against subsequent phases. This differentiation might be particularly pertinent to the PV to SC measurements. Here, the initial phase of stimulation, as depicted in Figure 7, reveals a relatively sparse temporal frequency of IPSCs. This might not represent the physiological conditions under which high-firing INs function.

While the authors seem to have addressed parts of this concern in their focal stim experiments by examining correlations during both high and low light intensities, they could potentially extract this metric from data acquired in their ramp conditions. This would be especially valuable for PV to SC measurements, given the absence of corresponding focal stimulation experiments.

3) Re results from Figure 2: Please fully describe the model in the methods section. Generally, I like using a modeling approach to explore the impact of convergent synaptic input to PVs from SCs that could effectively validate the experimental approach and enhance the interpretability of the experimental stim/recording outcomes. However, as currently detailed in the manuscript, the model description is inadequate for assessing the robustness of the simulation outcomes. If the IN model is simply integrate-and-fire with minimal biophysical attributes, then the findings in Fig 2F results shown in Fig 2F might be trivial. Conversely, if the model offers a more biophysically accurate representation (e.g., with conductance-based synaptic inputs, synapses appropriately dispersed across the model IN dendritic tree, and standard PV IN voltage-gated membrane conductances), then the model's results could serve as a meaningful method to both validate and interpret the experiments.

Reviewer #2 (Public Review):

Summary:<br /> The study describes differences in responses to sounds and whisker deflections as well as combinations of these stimuli in different neurochemically defined subsections of the lateral and dorsal cortex of the inferior colliculus in anesthetised and awake mice.

Strengths:<br /> The main achievement of the work lies in obtaining the data in the first place as this required establishing and refining a challenging surgical procedure to insert a prism that enabled the authors to visualise the lateral surface of the inferior colliculus. Using this approach, the authors were then able to provide the first functional comparison of neural responses inside and outside of the GABA-rich modules of the lateral cortex. The strongest and most interesting aspects of the results, in my opinion, concern the interactions of auditory and somatosensory stimulation. For instance, the authors find that a) somatosensory-responses are strongest inside the modules and b) somatosensory-auditory suppression is stronger in the matrix than in the modules. This suggests that, while somatosensory inputs preferentially target the GABA-rich modules, they do not exclusively target GABAergic neurons within the modules (given that the authors record exclusively from excitatory neurons we wouldn't expect to see somatosensory responses if they targeted exclusively GABAergic neurons), and that the GABAergic neurons of the modules (consistent with previous work) preferentially impact neurons outside the modules, i.e. via long-range connections.

Weaknesses:<br /> While the findings are of interest to the subfield they have only rather limited implications beyond it. The writing is not as precise as it could be. Consequently, the manuscript is unclear in some places. For instance, the text is somewhat confusing as to whether there is a difference in the pattern (modules vs matrix) of somatosensory-auditory suppression between anesthetized and awake animals. Furthermore, there are aspects of the results which are potentially very interesting but have not been explored. For example, there is a remarkable degree of clustering of response properties evident in many of the maps included in the paper. Taking Figure 7 for instance, rather than a salt and pepper organization we can see auditory responsive neurons clumped together and non-responsive neurons clumped together and in the panels below we can see off-responsive neurons forming clusters (although it is not easy to make out the magenta dots against the black background). This degree of clustering seems much stronger than expected and deserves further attention.

Reviewer #2 (Public Review):

I thank the authors for considering my comments and think the manuscript has been significantly improved with revision. However while I considered that the analysis employed for predicting tACS effects with linear models was convincing, I am still concerned by a multiple comparison issue for this analysis. An alternative option would be to report the results of a Partial Least Squares (PLS) analysis, with the stimulation properties as predictor variables and tACS effects as response variables. The authors could use PLS instead of multiple linear regression models to take into account the multicollinearity in the predictor variables, and also this can be done with only one PLS model. They could then extract the fitted responses values and estimate if the model can significantly fit the tACS effects.

Then, to determine which variables contribute more to the prediction, they can calculate the variable importance in projection (VIP) scores for the PLS regression model.<br /> An alternative option for the authors would be to temper their conclusions regarding how well field modeling/montage explains the variance observed across subjects.

Reviewer #2 (Public Review):

In this manuscript, the authors conducted a study in which they measured eye movements, pupil diameter, and neural activity in V4 in monkeys engaged in a visual attention task. The task required the monkeys to report changes in the orientation of Gabors' visual stimuli. The authors manipulated the difficulty of the trials by varying the degree of orientation change and focused their analysis on trials of intermediate difficulty where the monkeys' hit rate was approximately 50%. Their key findings include the following: 1) Hit trials were preceded by larger pupil diameter, reflecting higher arousal, and by more stable eye positions; 2) V4 neurons exhibit larger visual responses in hit trials; 3) Superficial and deep layers exhibited greater coherence in hit trials during both the pre-target stimulus period and the non-target stimulus presentation period. These findings have useful implications for the field, and the experiments and analyses presented in this manuscript validly support the authors' claims.

Strengths:<br /> The experiments were well-designed and executed with meticulous control. The analyses of both behavioural and electrophysiological data align with the standards in the field.

Weaknesses:<br /> Many of the findings appear to be incremental compared to previous literature, including the authors' own work. While incremental findings are not necessarily a problem, the manuscript lacks clear statements about the extent to which the dataset, analysis, and findings overlap with the authors' prior research. For example, one of the main findings, which suggests that V4 neurons exhibit larger visual responses in hit trials (as shown in Fig. 3), appears to have been previously reported in their 2017 paper. Additionally, it seems that the entire Fig1-S1 may have been reused from the 2017 paper. These overlaps should have been explicitly acknowledged and correctly referenced.

Previous studies have demonstrated that attention leads to decorrelation in V4 population activity. The authors should have discussed how and why the high coherence across layers observed in the current study can coexist with this decorrelation.

Furthermore, the manuscript does not explore potentially interesting aspects of the dataset. For instance, the authors could have investigated instances where monkeys made 'false' reports, such as executing saccades towards visual stimuli when no orientation change occurred. It would be valuable to provide the fraction of the monkeys' responses in a session, including false reports and correct rejections in catch trials, to allow for a broader analysis that considers the perceptual component of neural activity over pure sensory responses.

Reviewer #2 (Public Review):

The manuscript by Zhu has generated ChIP-seq and RNA-seq data from sizeable cohorts of SCZ patient samples and controls. The samples include 15 AF-SCZ samples and 15 controls, as well as 14 AT-SCZ samples and 14 controls. The genomics data was generated using techniques optimized for low-input samples: MOWChIP-seq and SMART-seq2 for histone profiles and transcriptome, respectively. The study has generated a significant data resource for the investigation of epigenomic alterations in SCZ. I am not convinced that the hierarchical pairwise design - first comparing AF-SCZ and AT-SCZ with their corresponding controls and secondarily contrasting the two comparisons is fully justified. The authors should repeat the statistical analysis by modeling all three groups simultaneously with an interaction effect for treatment or directly compare AF-SCZ to AT-SCZ groups and evaluate if the main conclusions remain supported.

Major comments

1. The manuscript did not discuss (mention) the quality control of RNA-seq data shown in Fig. 1B. The color scheme choice for the heatmap visualization did not provide a quantitative presentation of the specificity of the RNA-seq data. I would recommend using bar plots to present the results more quantitatively.

2. How does the specificity of this RNA-seq dataset compare to previous studies using a similar NeuN sorting strategy?

3. I appreciate the effort to assess the ChIP-seq data quality using phantompeakqualtools. However, prior knowledge/experience with this tool is required to fully understand the QC results. The authors should additionally provide browser shots at different scales for key neuronal/glial genes, so readers can have a more direct assessment of data quality, such as the enrichment of H3K4me3 at promoters (but not elsewhere), and H3K27ac at promoters and enhancers. Existing browser views, such as Fig. 2B are too zoomed out for assessing the data quality.

4. The pairwise regression model should be explicitly reported in methods.

5. The statistical strategy to compare AF-SCZ and AT-SCZ to their corresponding control groups was unjustified. Why not model all three groups simultaneously with an interaction effect for treatment or directly compare AF-SCZ to AT-SCZ groups? If the manuscript argues that the antipsychotic effect is the main novelty, why not directly compare AF-SCZ and AT-SCZ?

6. The method of pairwise comparison to corresponding control groups, then further comparing the pairwise results opens the study to a number of statistical vulnerabilities. For example, on page 12, the studies identified 166 DEGs between AF and control, and 1273 DEGs between AT and control. Instead of implicating a greater amount of difference between AT and control, such a result can often be driven by differences in between-group variance, rather than between-group means, that is, are the SCZ-AF and SCZ-treated effect size magnitudes and directionalities similar (but the treated group has lower variance) or are the two groups truly different in terms of means? The result in Fig. 5A suggests effect sizes for the two comparisons (AF-Ctrl and AT-Ctrl) are similar but have lower variability in the treated group.

7. The pairwise comparison further raised the possibility the results were driven by the difference in the two control cohorts rather than the two SCZ cohorts.

Reviewer #2 (Public Review):

The paper follows a recent study by the same team (Jaroenlak et al Plos Pathogens 2020), which documented the dramatic ejection dynamics of the polar tube (PT) in microsporidia using live-imaging and scanning electron microscopy. Although several key observations were reported in this paper (the 3D architecture of the PT within the spore, the speed and extent of the ejection process, the translocation dynamics of the nucleus during germination), the precise geometry of the PT during ejection remain inaccessible to imaging, making it difficult to physically understand the phenomenon.

This paper aims to fill this gap with an indirect "data-driven" approach. By modeling the hydrodynamic dissipation for different unfolding mechanisms identified in the literature and by comparing the predictions with experiments of ejection in media of various viscosities, authors shows that data are compatible with an eversion (caterpillar-like) mechanism but not compatible with a "jack-in-the-box" scenario. In addition, the authors observe that most germinated spores exhibit an inward bulge, which they attribute to buckling due to negative pressure difference. They suggest that this buckling may be a mean of pushing the nucleus out of the PT during the final stage of ejection.

Major strengths:

The most compelling aspect of the study is the experimental analysis of the ejection dynamics (velocity, ejection length) in medium of various viscosities over 3 orders of magnitudes, which, combined with a modeling of the viscous drag of the PT tube, provides very convincing evidence that the unfolding geometry is not a global displacement of the tube but rather an apical extension, where the motion is localized at the end of the tube.

The systematic classification of the different unfolding scenarios, consistent with the previous literature, and their confrontation with data in terms of energy, pressure and velocity also constitute an original approach in microbiology, where in-situ and real time geometry is often difficult to access.

Major weaknesses:

The revised version has clarified some details of the model, adding a paragraph and a figure in the Sup Mat. However, in my opinion, it remains difficult to understand the precise topology and ejection mechanism from the various sketches presented in the article.

The article does not address the mechanical driver (force) of ejection, and the role of pressure is unclear. The revised version replaced the term "negative pressure" with "negative pressure difference", arguing that a positive or negative pressure difference could not be differentiated. However, it is not clear how a lower pressure in the spore than in the bath could eject the tube outside.

Reviewer #2 (Public Review):

In this study, the authors examined how maintenance of mitochondrial-associated endoplasmic reticulum membranes (MAM) are critical for the prevention of muscle atrophy under microgravity conditions. They observed, a reduction in MAM in myotubes placed in a microgravity condition; in addition, MFN2-deficient human iPS cells showed a decrease in the number of MAM, similar to in myotubes differentiated under microgravity conditions, in addition to the activation of the Notch signaling pathway. The authors, morover, obsreved that by treatment with the gamma-secretase inhibitor with DAPT preserved from the atrophic phenotype of differentiated myotubes in microgravity and improve the regenerative capacity of Mfn2-deficient muscle stem cells in dystrophic mice.

The entire study was well conducted, bringing an interesting analysis in vitro and in vivo of aging condition. In my opinion it is necessary to implement the analysis of both genes and proteins for better supporting the conclusions

The study can contribute to better understand one of the major problems of aging, such as muscle atrophy and inhibition of muscle regeneration, emphasizing the importance of NOTCH patway in these pathological situations. The work will be of interest to all scientist working on aging.

Reviewer #2 (Public Review):

Summary:<br /> Bestry et al. investigated the effects of prenatal alcohol exposure (PAE) and high methyl donor diet (HMD) on offspring DNA methylation and behavioral outcomes using a mouse model that mimics common patterns of alcohol consumption in pregnancy in humans. The researchers employed whole-genome bisulfite sequencing (WGBS) for unbiased assessment of the epigenome in the newborn brain and liver, two organs affected by ethanol, to explore tissue-specific effects and to determine any "tissue-agnostic" effects that may have arisen prior to the germ-layer commitment during early gastrulation. The authors found that PAE induces measurable changes in offspring DNA methylation. DNA methylation changes induced by PAE coincide with non-coding regions, including enhancers and promoters, with the potential to regulate gene expression. Though the majority of the alcohol-sensitive differentially methylated regions (DMRs) were not conserved in humans, the ones that were conserved were associated with clinically relevant traits such as facial morphology, educational attainment, intelligence, autism, and schizophrenia. Finally, the study provides evidence that maternal dietary support with methyl donors alleviates the effects of PAE on DNA methylation, suggesting a potential prenatal care option.

Strengths:<br /> The strengths of the study include the use of a mouse model where confounding factors such as genetic background and diet can be well controlled. The study performed whole-genome bisulfite sequencing which allows a comprehensive analysis of the effects of PAE on DNA methylation. However, some weaknesses and limitations of the study are detected.

Weaknesses:<br /> 1. The low generalizability between mouse and human data alerts the validity of the mouse model designed in the study. On the same note, the authors failed to detect any significant effect on PAE-induced behavioral outcomes. I recognize that it is difficult to model all possible conditions of PAE in mice because the amount, frequency, and duration of alcohol consumption in humans vary significantly. Therefore, if the authors only focus on moderate PAE, it should be emphasized in the title and throughout the paper to avoid misinterpretation. In addition, is it possible to stratify the human data based on the level of PAE and compare it to the mouse data?<br /> 2. A major finding of the study is that PAE affects non-coding genomic regions in mice including enhancers and promoters. To improve the significance of the study, the authors need to back up this finding with transcriptome analysis and determine if these DMRs indeed affect gene expression.<br /> 3. The low generalizability between mouse and human data suggests that the regions affected by PAE may be species-specific. It is critical to analyze if PAE-induced DMRs in humans are also enriched in non-coding genomic regions. Considering the huge difference between mouse and human development, particularly in the brain, it is not surprising that different genomic loci are affected, but the affected loci may share similar features.<br /> 4. The specific brain regions and the lobes of the liver where the samples were taken should be clearly indicated.<br /> 5. I don't fully agree with the authors' interpretation that the two shared genomic regions affected in the brain and the liver "must have arisen before the germ layers separated". To claim so, the authors need to exclude the possibility that the two regions are just a coincidence due to the stochastic effect of PAE on DNA methylation.

Reviewer #2 (Public Review):

Summary:<br /> The authors investigate the role of MafB in regulating podocyte genes. Mafb is required for podocyte differentiation and maintenance. Mutations of this gene cause FSGS in mice and humans. They profiled MafB binding genome-wide in isolated glomeruli and defined overlap with Wt1. They provide evidence that Mafb is required for Wt1 binding and H3K4me3 methylation at the promoters of two essential podocyte genes, Nphs1 and Nphs2. Understanding how the action of different transcription factors is coordinated to control gene expression - the main goal of this paper - is an important line of investigation.

While the main conclusion of the paper is supported by their data, the scope is limited. Additional ChIP-seq experiments and data analysis are needed to solidify and extend their conclusions.

Strengths:<br /> 1) Performing ChIP-seq for histone modifications on isolated podocytes provides valuable cell-type-specific information. Similarly, profiling Mafb and Wt1 in isolated glomeruli provides podocyte-specific binding patterns because these transcription factors (TFs) are not expressed in other cell types in glomeruli. The significant overlap of their Wt1 binding genome-wide with that of prior published work is reassuring. RNA-seq on isolated podocytes provides the appropriate cell-type specific gene expression data to integrate with ChIP-seq data. Together, the RNA-seq and ChIP-seq data are valuable resources for other investigators examining gene regulation in mouse podocytes.

2) The phenotype analysis of their FSGS model is convincing and well done.

3) Testing how Wt1 binding is affected by loss of Mafb provides insight into how these key podocyte TFs may cooperate to regulate genes.

Weaknesses:<br /> 1) The conclusion that Mafb is required for Wt1 binding and H3K4me3 methylation is based solely on ChIP-PCR at two gene promoters (Nphs1, Nphs2). This result should be validated and extended by ChIP-seq. Mafb and Wt1 binding overlap at more than 200 sites. If their model is correct, it is likely that Wt1 binding would be affected at other genomic sites. This result would add strong support to their model of how Wt1 and Mafb cooperate to regulate genes in podocytes. Moreover, ChIP-seq would define whether the dependence of Wt1 on Mafb is also evident at distal regulatory regions (defined H3K4me1, which is typically found at predicted enhancers).

2) The FSGS model generated by the authors involved conditional deletion of Mafb in podocytes at 8 weeks of age. They found that this resulted in reduced expression of Nphs1 and Nphs2 within 48 hours post-deletion. However, they investigated Wt1 binding and H3K4me3 genomic binding in Mafb homozygous null embryos. While this result provides information about podocyte differentiation, it does not address the maintenance of expression of these essential podocyte genes in the adult kidney. Because post-natal deletion of Mafb led to FSGS and reduced expression of Nphs1/2, ChIP-seq should be performed on the adult conditional mutants in order to provide mechanistic information about the disease.

3) H3K4me1 binds enhancer regions. The authors performed ChIP-seq to profile H3K4me1 in isolated podocytes. However, there was no analysis reported of these results. It would be valuable to determine if Wt1 and Mafb co-localize at predicted enhancers in podocytes and if Wt1 binding is lost at these regions in Mafb mutant glomeruli.

Reviewer #2 (Public Review):

Summary:<br /> The authors address an important outstanding question: what forces are the primary drivers of evolutionary rate covariation? Exploration of this topic is important because it is currently difficult to interpret the functional/mechanistic implications of evolutionary covariation. These analyses also speak to the predictive power (and limits) of evolutionary rate covariation. This study reinforces the existing paradigm that covariation is driven by a varied/mixed set of interaction types that all fall under the umbrella explanation of 'co-functional interactions'.

Strengths:<br /> Very smart experimental design that leverages individual protein domains for increased resolution.

Weaknesses:<br /> Nuanced and sometimes inconclusive results that are difficult to capture in a short title/abstract statement.

Reviewer #2 (Public Review):

In this manuscript, the authors present a novel interactome focused on human and fly alpha-arrestin family proteins and demonstrate its application in understanding the functions of these proteins. Initially, the authors employed AP/MS analysis, a popular method for mapping protein-protein interactions (PPIs) by isolating protein complexes. Through rigorous statistical and manual quality control procedures, they established two robust interactomes, consisting of 6 baits and 307 prey proteins for humans, and 12 baits and 467 prey proteins for flies. To gain insights into the gene function, the authors investigated the interactors of alpha-arrestin proteins through various functional analyses, such as gene set enrichment. Furthermore, by comparing the interactors between humans and flies, the authors described both conserved and species-specific functions of the alpha-arrestin proteins. To validate their findings, the authors performed several experimental validations for TXNIP and ARRDC5 using ATAC-seq, siRNA knockdown, and tissue staining assays. The experimental results strongly support the predicted functions of the alpha-arrestin proteins and underscore their importance.

Reviewer #2 (Public Review):

Summary:<br /> Zhou et al. have revised their previous manuscript, which has greatly improved the quality of the work. Zhou et al. use publicly available GTEx data of 18 metabolic tissues from 310 individuals to explore gene expression correlation patterns within-tissue and across-tissues. Furthermore, they have added an analysis of data from a diverse panel of inbred mouse strains, which allows them to also incorporate data on physiological phenotypes relevant to metabolic signaling between tissues. They now focus on validating their approach to exploring signal in gene co-expression rather than emphasizing unvalidated discoveries. They provide a webtool (GD-CAT) to allow users to explore these data. Focusing more on known biology does result in the study making stronger conclusions from its data. The webtool is also improved, expanded with the mouse data, and of value to the scientific community. Their revision has also corrected key misconceptions from the initial submission and provides greater clarification of the methodologies used.

Strengths:<br /> GTEx as well as the hybrid diversity mouse panel are powerful resource for many areas of biomedicine, and this study represents a valid use of gene co-expression network methodology. They have greatly improved its description and contextualization within the gene co-expression studies. The authors previously did a good job of providing examples confirming known signaling biology and have further improved these. They have largely removed the sections on discovery of novel biology, which is potentially for the better given a lack of follow-up validation, which could be beyond the scope of this manuscript anyway. The webtool, GD-CAT, is easy to use and allows researchers with genes and tissues of interest to perform the same analyses in the GTEx and HMDP data.

Weaknesses:<br /> With the previous version, the primary weaknesses for me were key misconceptions and lack of detail in the methods, which have all been greatly improved. The manuscript could be considered more of a "Resource" than "Research", though there is value in showing how the known biology is reflected in the correlation data and could presumably be paired with validation to discover new biology. Finally, there are sentences here and there that could be rephrased to improve clarity, but overall it is greatly improved.

Reviewer #2 (Public Review):

How the chromosomal passenger complex (CPC) and its subunit Aurora B kinase regulate kinetochore-microtubule attachment, and how the CPC relocates from kinetochores to the spindle midzone as a cell transitions from metaphase to anaphase are questions of great interest. In this study, Ballmer and Akiyoshi take a deep dive into the CPC in T. brucei, a kinetoplastid parasite with a kinetochore composition that varies greatly from other organisms.

Using a combination of approaches, most importantly in silico protein predictions using alphafold multimer and light microscopy in dividing T. brucei, the authors convincingly present and analyse the composition of the T. brucei CPC. This includes the identification of KIN-A and KIN-B, proteins of the kinesin family, as targeting subunits of the CPC. This is a clear advancement over earlier work, for example by Li and colleagues in 2008. The involvement of KIN-A and KIN-B is of particular interest, as it provides a clue for the (re)localization of the CPC during the cell cycle. The evolutionary perspective makes the paper potentially interesting for a wide audience of cell biologists, a point that the authors bring across properly in the title, the abstract, and their discussion.

The evolutionary twist of the paper would be strengthened 'experimentally' by predictions of the structure of the CPC beyond T. brucei. Depending on how far the authors can extend their in-silico analysis, it would be of interest to discuss a) available/predicted CPC structures in well-studied organisms and b) structural predictions in other euglenozoa. What are the general structural properties of the CPC (e.g. flexible linkers, overall dimensions, structural differences when subunits are missing etc.)? How common is the involvement of kinesin-like proteins? In line with this, it would be good to display the figure currently shown as S1D (or similar) as a main panel.

Reviewer #2 (Public Review):

Summary:<br /> The authors previously generated renal Glut2 knockout mice, which have high levels of glycosuria but normal fasting glucose. They use this as an opportunity to investigate how compensatory mechanisms are engaged in response to glycosuria. They show that renal and hepatic glucose production, but not metabolism, is elevated in renal Glut2 male mice. They show that renal Glut2 male mice have elevated Crh mRNA in the hypothalamus and elevated plasma levels of ACTH and corticosterone. They also show that temporary denervation of renal nerves leads to a decrease in fasting and fed blood glucose levels in female renal Glut2 mice, but not control mice. Finally, they perform plasma proteomics in male mice to identify plasma proteins with a greater than 25% (up or down) between the knockouts and controls.

Strengths:<br /> The question that is trying to be addressed is clinically important: enhancing glycosuria is a current treatment for diabetes, but is limited in efficacy because of compensatory increases in glucose production.<br /> Also, the mouse line used is an inducible knockout, thus minimizing the impact of compensatory mechanisms engaged in early development.

Weaknesses:<br /> 1) Though the Methods specify that both male and female mice were used, it appears each experiment was performed only on one sex, rather than each experiment being performed on both sexes. For example, renal denervation was performed only on females, whereas all other experiments were performed exclusively on males. This makes it impossible to examine whether there are sex differences in any measures.

2) This study appears to use an inducible Glut2 knockout with tamoxifen, yet nothing describes when the tamoxifen was delivered relative to the experimental manipulations. Was the knockout performed in young animals? In adult animals? This is important both for the ability of readers to repeat the experiment, but also to interpret the results in light of potential compensatory changes (if the knockout was performed at an early age, for example).

3) In Methods, please clarify whether littermate controls were WT, het, or both. If het mice were used as controls, this is potentially problematic.

4) Conclusions like "the HPA axis may contribute to the compensatory increase in glucose production in renal Glut2 knockout mice" (line 215) are premature. All that is shown is that renal Glut2 male mice have elevated HPA activity. There are no experiments establishing causation. For example, the authors could administer a CRF antagonist or a glucocorticoid receptor antagonist in this mouse line, and examine whether this impacts blood glucose. This was not done.

5) If elevated glycosuria drives HPA activity, one would expect to see elevated HPA activity in humans who take SGLT2 inhibitors. Yet, this does not seem to be the case (Higashikawa et al, 2021; see also Perry et al, 2021 for rodent example). This raises the question of whether the glycosuria observed in the mouse line here is relevant to any human conditions. The relevance of the mechanisms proposed here would be much more convincing if a second model of glycosuria was used here (for example, inducing diabetes in mice and treating with SGLT2 inhibitors). Without these types of experiments, any relevance to human conditions is highly speculative and should be reserved for the Discussion. What the authors are studying here is one mechanism for maintaining blood glucose when glycosuria is induced by a genetic knockout.

6) The experiment examining the impact of renal denervation is nice but incomplete. For example, what is the relevance to the hepatic glucose production that was reported? It is interesting that the renal denervation normalized the elevated HPA activity in Glut2 female mice, but it is not clear how this signaling would alter HPA activity.

7) The Methods need to describe the plasma collection procedure for both ELISA and plasma proteomic experiments. What time of day were samples collected? Were samples collected when animals were euthanized from other experiments after experimental manipulations, or in animals without other experimentation?

8) In general, the links between the disparate mechanisms (signals in the plasma, changes in renal activity, changes in HPA activity) are weak. There are more experiments needed to establish a direct kidney-hypothalamus axis. If renal activity elevates blood glucose in the face of glycosuria, why are there no differences in renal activity between control and Glut2 knockout mice? If the blood glucose levels are regulated by renal activity, it must be the sensitivity to the renal activity that differs between control and knockout mice - perhaps this should be investigated. If one stimulates afferent renal nerves, can one drive HPA activation and elevate blood glucose? How are these measures related to the plasma proteins identified? Without these links, this study is descriptive and correlational.

Reviewer #2 (Public Review):

Summary:<br /> In this manuscript, Petersen et al. aimed for a comprehensive assessment of the relationship between cardiometabolic risk factors and cortical thickness. They found that a latent variable reflecting higher obesity, hypertension, LDL cholesterol, triglyerides, glucose, and lower HDL cholesterol was associated with lower cortical thickness in orbitofrontal, lateral prefrontal, insular, anterior cingulate, and temporal areas. In sensitivity analyses, they showed that this pattern replicated across cohorts and was also consistent with a clinical definition of the metabolic syndrome.

Further, when including cognition in the multivariate analysis, the pattern remained unchanged and indicated that cardiometabolic risk factors were associated with worse cognitive performance across different tests. The authors investigated the cell types implicated in the regions associated with cardiometabolic risk using the Allen brain atlas and found that the density of excitatory neurons type 8, endothelial cells, and microglia reliably co-located with the pattern of cortical thickness. Furthermore, they showed that cortical regions more strongly associated with MetS were more closely structurally & functionally connected than others.

Strengths:<br /> This study performed a comprehensive assessment of the combined association of cardiometabolic risk factors and brain structure and investigated micro- and macroscopic underpinnings. A major strength of the study is the methodological approach of Partial Least Squares which allows the authors to not single out risk factors but to take them into account simultaneously. The large sample size from two cohorts allowed for different sensitivity analyses and convincing evidence for the stability of the first latent variable. The authors demonstrated that the component was also reliably related to cognitive performance, replicating multiple previous studies that evidenced associations of different components of the MetS with worse cognitive performance.

The novel contribution of the study lies in the virtual histology and brain topology investigation of the cortical pattern related to MetS. The virtual histology provided clear evidence of the co-localization of endothelial, glial, and excitatory neuronal cells with the regions of MetS-associated cortical thinning while the brain topology analysis highlighted the disproportionate structural and functional connectivity between associated regions. This analysis provides insights into the role of inflammatory processes and the intricate link between gray matter morphology and microvasculature, both locally and in relation to long-range connectivity. This information is valuable to inform future mechanistic studies.

Weaknesses:<br /> The study is exclusively cross-sectional which does not allow to the authors to disentangle causes from consequences. While studies indicate that most of the differences seen in middle age are probably consequences of the MetS on the vasculature, blood-brain barrier, or inflammatory processes, differences in cortical morphology might also represent a risk factor for weight gain.

Another limitation is the omission of subcortical structures and the cerebellum which might have provided additional information on the pattern of GM differences associated with MetS.

The study is exploratory in nature and for the contextualization analyses it is difficult to judge whether those were selected from a larger pool of analyses. The analysis approach taken to relate the cardiometabolic risk, brain structure, and cognition does not allow the reader to determine whether brain regions most strongly related to the MetS are the ones also most strongly associated with cognitive performance. The cortical pattern arising from the models including cognition is not thoroughly compared to the MetS-only pattern and therefore, it is difficult to estimate to which extent the MetS-related cortical patterns explain variance in cognitive performance.

Reviewer #2 (Public Review):

Smirnova et al. present a cryo-EM structure of human SIRT6 bound to a nucleosome as well as the results from molecular dynamics simulations. The results show that the combined conformational flexibilities of SIRT6 and the N-terminal tail of histone H3 limit the residues with access to the active site, partially explaining the substrate specificity of this sirtuin-class histone deacetylase. Two other groups have recently published cryo-EM structures of SIRT6:nucleosome complexes; this manuscript confirms and complements these previous findings, with the addition of some novel insights into the role of structural flexibility in substrate selection.

Reviewer #2 (Public Review):

In this study, Nguyen et al. showed that cat saliva can robustly induce freezing behavior in mice. This effect is mediated through the accessory olfactory system as it requires physical contact and is abolished in Trp2 KO mice. The authors further showed that V2R-A4 cluster is responsive to cat saliva. Lastly, they demonstrated c-Fos induction in AOB and VMHdm/c by the cat saliva. The c-Fos level in the VMHdm/c is correlated with the freezing response.

Strength:<br /> The study opens an interesting direction. It reveals the potential neural circuit for detecting cat saliva and driving defense behavior in mice. The behavior results and the critical role of the accessory olfactory system in detecting cat saliva are clear and convincing.

Weakness:<br /> The findings are relatively preliminary. The identities of the receptor and the ligand in the cat saliva that induces the behavior remain unclear. The identity of VMH cells that are activated by the cat saliva remains unclear. There is a lack of targeted functional manipulation to demonstrate the role of V2R-A4 or VMH cells in the behavioral response to cat saliva.

Reviewer #2 (Public Review):

Summary:

This study by Sun et al. identifies a novel role for IBTK in promoting cancer protein translation, through regulation of the translational helicase eIF4A1. Using a multifaceted approach, the authors demonstrate that IBTK interacts with and ubiquitinates eIF4A1 in a non-degradative manner, enhancing its activation downstream of mTORC1/S6K1 signaling. This represents a significant advance in elucidating the complex layers of dysregulated translational control in cancer.

Strengths:

A major strength of this work is the convincing biochemical evidence for a direct regulatory relationship between IBTK and eIF4A1. The authors utilize affinity purification and proximity labeling methods to comprehensively map the IBTK interactome, identifying eIF4A1 as a top hit. Importantly, they validate this interaction and the specificity for eIF4A1 over other eIF4 isoforms by co-immunoprecipitation in multiple cell lines. Building on this, they demonstrate that IBTK catalyzes non-degradative ubiquitination of eIF4A1 both in cells and in vitro through the E3 ligase activity of the CRL3-IBTK complex. Mapping IBTK phosphorylation sites and showing mTORC1/S6K1-dependent regulation provides mechanistic insight. The reduction in global translation and eIF4A1-dependent oncoproteins upon IBTK loss, along with clinical data linking IBTK to poor prognosis, support the functional importance.

Weaknesses:

While these data compellingly establish IBTK as a binding partner and modifier of eIF4A1, a remaining weakness is the lack of direct measurements showing IBTK regulates eIF4A1 helicase activity and translation of target mRNAs. While the effects of IBTK knockout/overexpression on bulk protein synthesis are shown, the expression of multiple eIF4A1 target oncogenes remains unchanged.

Summary:

Overall, this study significantly advances our understanding of how aberrant mTORC1/S6K1 signaling promotes cancer pathogenic translation via IBTK and eIF4A1. The proteomic, biochemical, and phosphorylation mapping approaches established here provide a blueprint for interrogating IBTK function. These data should galvanize future efforts to target the mTORC1/S6K1-IBTK-eIF4A1 axis as an avenue for cancer therapy, particularly in combination with eIF4A inhibitors.

Reviewer #2 (Public Review):

Summary:<br /> The authors seek to vary the integration site of a double-strand break repair reporter and assess how the chromatin state of different reporter integration sites impacts the contribution of various DSB repair pathways.

Strengths:<br /> It addresses repair in vivo. The reporter improves assay reliability (relative to previous fly DSB repair substrates) by inducing I-SceI within a more narrow and well-defined expression window. The authors' characterization of the spectrum of a-EJ products by sequencing is largely rigorous and thorough, and this often difficult to communicate data is presented in a clear and easily digested manner.

Weaknesses:<br /> The use of the single euchromatic site undercuts their ability to generalize the impact of chromatin state. This concern is minor when considering repair by HR, as repair efficiency appears to vary little when comparing repair across the 4 different heterochromatic sites. Still, it is possible the single euchromatic site they used is an outlier in its sparing use of HR. The assessment of repair by alt-EJ is more problematic, though, since the character of repair appears to vary as much across the different heterochromatic sites as it does comparing a given heterochromatic site vs. the euchromatic site. For example, focusing on their central argument (decreased deletion during SD-MMEJ at heterochromatic sites), the difference between Het2 and all other sites appears to be more dramatic than the difference between Het1 and the single euchromatic site (Figure 5A, Supp Fig 2).

Reviewer #2 (Public Review):

In this work, the authors investigated the pectoralis work loop and the function of the supracoracoideus muscle in the down stroke during slow flight in doves. The aim of this study was to determine how aerodynamic force is generated, using simultaneous high-speed measurements of the wings' kinematics, aerodynamics, and activation and strain of pectoralis muscles during slow flight. The measurements show a reduction in the angle of attack during mid-downstroke, which induces a peak power factor and facilitates the tensioning of the supracoracoideus tendon with pectoralis power, which then can be released in the up-stroke. By combining the data with a muscle mechanics model, the timely tuning of elastic storage in the supracoracoideus tendon was examined and showed an improvement of the pectoralis work loop shape factor. Finally, other bird species were integrated into the model for a comparative investigation.

The major strength of the methods is the simultaneous application of four high-speed techniques - to quantify kinematics, aerodynamics and muscle activation and strain - as well as the implementation of the time-resolved data into a muscle mechanics model. With a thorough analysis which supports the conclusions convincingly, the authors achieved their goal of reaching an improved understanding of the interplay of the pectoralis and supracoracoideus muscles during slow flight and the resulting energetic benefits.

Reviewer #2 (Public Review):

Summary:<br /> The manuscript by Kelbert et al. presents results on the involvement of the yeast transcription factor Sfp1 in the stabilisation of transcripts whose synthesis it stimulates. Sfp1 is known to affect the synthesis of a number of important cellular transcripts, such as many of those that code for ribosomal proteins. The hypothesis that a transcription factor can remain bound to the nascent transcript and affect its cytoplasmic half-life is attractive, but the methods used to demonstrate the half-life effects and the association of Sfp1 with cytoplasmic transcripts remain to be fully validated, as explained in my comments on the results below:

Comments on methodology and results:<br /> 1. A two-hybrid-based assay for protein-protein interactions identified Sfp1, a transcription factor known for its effects on ribosomal protein gene expression, as interacting with Rpb4, a subunit of RNA polymerase II. Classical two-hybrid experiments depend on the presence of the tested proteins in the nucleus of yeast cells, suggesting that the observed interaction occurs in the nucleus. Unfortunately, the two-hybrid method cannot determine whether the interaction is direct or mediated by nucleic acids.

2. Inactivation of nup49, a component of the nuclear pore complex, resulted in the redistribution of GFP-Sfp1 into the cytoplasm at the temperature non-permissive for the nup49-313 strain, suggesting that GFP-Sfp1 is a nucleo-cytoplasmic shuttling protein. This observation confirmed the dynamic nature of the nucleo-cytoplasmic distribution of Sfp1. For example, a similar redistribution to the cytoplasm was previously reported following rapamycin treatment and under starvation (Marion et al., PNAS 2004). In conjunction with the observation of an interaction with Rpb4, the authors observed slower nuclear import kinetics for GFP-Sfp1 in the absence of Rpb4 when cells were transferred to a glucose-containing medium after a period of starvation. Since the redistribution of GFP-Sfp1 was abolished in an rpb1-1/nup49-313 double mutant, the authors concluded that Sfp1 localisation to the cytoplasm depends on transcription. The double mutant yeast cells may show a variety of non-specific effects at the restrictive temperature, and whether transcription is required for Sfp1 cytoplasmic localisation remains incompletely demonstrated.

3. Under starvation conditions, which led to the presence of Sfp1 in the cytoplasm and have previously been correlated with a decrease in the transcription of Sfp1 target genes, the authors observed that a plasmid-based expressed GFP-Sfp1 accumulated in cytoplasmic foci. These foci were also labelled by P-body markers such as Dcp2 and Lsm1. The quality of the microscopic images provided does not allow to determine whether Rpb4-RFP colocalises with GFP-Sfp1.

4. To understand to which RNA Sfp1 might bind, the authors used an N-terminally tagged fusion protein in a cross-linking and purification experiment. This method identified 264 transcripts for which the CRAC signal was considered positive and which mostly correspond to abundant mRNAs, including 74 ribosomal protein mRNAs or metabolic enzyme-abundant mRNAs such as PGK1. The authors did not provide evidence for the specificity of the observed CRAC signal, in particular, what would be the background of a similar experiment performed without UV cross-linking. In a validation experiment, the presence of several mRNAs in a purified SFP1 fraction was measured at levels that reflect the relative levels of RNA in a total RNA extract. Negative controls showing that abundant mRNAs not found in the CRAC experiment were clearly depleted from the purified fraction with Sfp1 would be crucial to assessing the specificity of the observed protein-RNA interactions. The CRAC-selected mRNAs were enriched for genes whose expression was previously shown to be upregulated upon Sfp1 overexpression (Albert et al., 2019). The presence of unspliced RPL30 pre-mRNA in the Sfp1 purification was interpreted as a sign of co-transcriptional assembly of Sfp1 into mRNA, but in the absence of valid negative controls, this hypothesis would require further experimental validation.

5. To address the important question of whether co-transcriptional assembly of Spf1 with transcripts could alter their stability, the authors first used a reporter system in which the RPL30 transcription unit is transferred to vectors under different transcriptional contexts, as previously described by the Choder laboratory (Bregman et al. 2011). While RPL30 expressed under an ACT1 promoter was barely detectable, the highest levels of RNA were observed in the context of the native upstream RPL30 sequence when Rap1 binding sites were also present. Sfp1 showed better association with reporter mRNAs containing Rap1 binding sites in the promoter region. However, removal of the Rap1 binding sites from the reporter vector also led to a drastic decrease in reporter mRNA levels. Whether the fraction of co-purified RNA is nuclear and co-transcriptional or not cannot be inferred from these results.

6. To complement the biochemical data presented in the first part of the manuscript, the authors turned to the deletion or rapid depletion of SFP1 and used labelling experiments to assess changes in the rate of synthesis, abundance, and decay of mRNAs under these conditions. An important observation was that in the absence of Sfp1, mRNAs encoding ribosomal protein genes not only had a reduced synthesis rate but also an increased degradation rate. This important observation needs careful validation, as genomic run-on experiments were used to measure half-lives, and this particular method was found to give results that correlated poorly with other measures of half-life in yeast (e.g. Chappelboim et al., 2022 for a comparison). Similarly, the use of thiolutin to block transcription as a method of assessing mRNA half-life has been reported to be problematic, as thiolutin can specifically inhibit the degradation of ribosomal protein mRNA (Pelechano & Perez-Ortin, 2008). Specific repressible reporters, such as those used by Baudrimont et al. (2017), would need to be tested to validate the effect of Sfp1 on the half-life of specific mRNAs. Also, it would be very difficult to infer from the images presented whether the rate of deadenylation is altered by Sfp1.

7. The effects of SFP1 on transcription were investigated by chromatin purification with Rpb3, a subunit of RNA polymerase, and the results were compared with synthesis rates determined by genomic run-on experiments. The decrease in polII presence on transcripts in the absence of SFP1 was not accompanied by a marked decrease in transcript output, suggesting an effect of Sfp1 in ensuring robust transcription and avoiding RNA polymerase backtracking. To further investigate the phenotypes associated with the depletion or absence of Sfp1, the authors examined the presence of Rpb4 along transcription units compared to Rpb3. One effect of spf1 deficiency was that this ratio, which decreased from the start of transcription towards the end of transcripts, increased slightly. The results presented are largely correlative and could arise from the focus on very specific types of mRNAs, such as those of ribosomal protein genes, which are sensitive to stress and are targeted by very active RNA degradation mechanisms activated, for example, under heat stress (Bresson et al., 2020).

Strengths:<br /> - Diversity of experimental approaches used<br /> - Validation of large-scale results with appropriate reporters

Weaknesses:<br /> - Choice of evaluation method to test mRNA half-life<br /> - Lack of controls for the CRAC results

Reviewer #2 (Public Review):

Summary:<br /> The study by Li et al. aimed to demonstrate the role of the G𝛾13-mediated signal transduction pathway in tuft cell-driven inflammation resolution and repairing injured lung tissue. The authors showed a reduced number of tuft cells in the parenchyma of G𝛾13 null lungs following viral infection. Mice with a G𝛾13 null mutation showed increased lung damage and heightened macrophage infiltration when exposed to the H1N1 virus. Their further findings suggested that lung inflammation resolution, epithelial barrier, and fibrosis were worsened in G𝛾13 null mutants.

Strengths:<br /> The beautiful immunostaining findings do suggest that the number of tuft cells is decreased in Gr13 null mutants.

Weaknesses:<br /> The description of phenotypes, and the approaches used to measure the phenotypes are problematic. Rigorous investigation of the mouse lung phenotypes is needed to draw meaningful conclusions.

Reviewer #2 (Public Review):

Summary:<br /> In this work, Song et al. propose a locus-based framework for performing GWAS and related downstream analyses including finemapping and polygenic risk score (PRS) estimation. GWAS are not sufficiently powered to detect phenotype associations with low-frequency variants. To overcome this limitation, the manuscript proposes a method to aggregate variant impacts on chromatin and transcription across a 4096 base pair (bp) loci in the form of a haplotype function score (HFS). At each locus, an association is computed between the HFS and trait. Computing associations at the level of imputed functional genomic scores should enable the integration of information across variants spanning the allele frequency spectrum and bolster the power of GWAS.

The HFS for each locus is derived from a sequence-based predictive model. Sei. Sei predicts 21,907 chromatin and TF binding tracks, which can be projected onto 40 pre-defined sequence classes ( representing promoters, enhancers, etc.). For each 4096 bp haplotype in their UKB cohort, the proposed method uses the Sei sequence class scores to derive the haplotype function score (HFS). The authors apply their method to 14 polygenic traits, identifying ~16,500 HFS-trait associations. They finemap these trait-associated loci with SuSie, as well as perform target gene/pathway discovery and PRS estimation.

Strengths:<br /> Sequence-based deep learning predictors of chromatin status and TF binding have become increasingly accurate over the past few years. Imputing aggregated variant impact using Sei, and then performing an HFS-trait association is, therefore, an interesting approach to bolster power in GWAS discovery. The manuscript demonstrates that associations can be identified at the level of an aggregated functional score. The finemapping and pathway identification analyses suggest that HFS-based associations identify relevant causal pathways and genes from an association study. Identifying associations at the level of functional genomics increases the portability of PRSs across populations. Imputing functional genomic predictions using a sequence-based deep learning model does not suffer from the limitation of TWAS where gene expression is imputed from a limited-size reference panel such as GTEx.

However, there are several major limitations that need to be addressed.

Major concerns/weaknesses:<br /> 1. There is limited characterization of the locus-level associations to SNP-level associations. How does the set of HFS-based associations differ from SNP-level associations?

2. A clear advantage of performing HFS-trait associations is that the HFS score is imputed by considering variants across the allele frequency spectrum. However, no evidence is provided demonstrating that rare variants contribute to associations derived by the model. Similarly, do the authors find evidence that allelic heterogeneity is leveraged by the HFS-based association model? It would be useful to do simulations here to characterize the model behavior in the presence of trait-associated rare variants.

3. Sei predicts chromatin status / ChIP-seq peaks in the center of a 4kb region. It would therefore be more relevant to predict HFS using overlapping sequence windows that tile the genome as opposed to using non-overlapping windows for computing HFS scores. Specifically, in line 482, the authors state that "the HFS score represents overall activity of the entire sequence, not only the few bp at the center", but this would not hold given that Sei is predicting activity at the center for any sequence.

4. Is the HFS-based association going to miss coding variation and several regulatory variants such as splicing variants? There are also going to be cases where there's an association driven by a variant that is correlated with a Sei prediction in a neighboring window. These would represent false positives for the method, it would be useful to identify or characterize these cases.

Additional minor concerns:<br /> 1. It's not clear whether SuSie-based finemapping is appropriate at the locus level, when there is limited LD between neighboring HFS bins. How does the choice of the number of causal loci and the size of the segment being finemapped affect the results and is SuSie a good fit in this scenario?

2. It is not clear how a single score is chosen from the 117 values predicted by Sei for each locus. SuSie is run assuming a single causal signal per locus, an assumption which may not hold at ~4kb resolution (several classes could be associated with the trait of interest). It's not clear whether SuSie, run in this parameter setting, is a good choice for variable selection here.

3.. A single HFS score is being chosen from amongst multiple tracks at each locus independently. Does this require additional multiple-hypothesis correction?

4. The results show that a larger number of loci are identified with HFS-based finemapping & that causal loci are enriched for causal SNPs. However, it is not clear how the number of causal loci should relate to the number of SNPs. It would be really nice to see examples of cases where a previously unresolved association is resolved when using HFS-based GWAS + finemapping.

5. Sequence-based deep learning model predictions can be miscalibrated for insertions and deletions (INDELs) as compared to SNPs. Scaling INDEL predictions would likely improve the downstream modeling.

Reviewer #2 (Public Review):

This manuscript explores the seemingly paradoxical observation that enhanced synaptic plasticity impairs (rather than enhances) certain forms of learning and memory. The central hypothesis is that such impairments arise due to saturation of synaptic plasticity, such that the synaptic plasticity required for learning can no longer be induced. A prior study provided evidence for this hypothesis using transgenic mice that lack major histocompatibility class 1 molecules and show enhanced long-term depression (LTD) at synapses between granule cells and Purkinje cells of the cerebellum. The study found that a form of LTD-dependent motor learning-increasing the gain of the vestibulo-ocular reflex (VOR)-is impaired in these mice and can be rescued by manipulations designed to "unsaturate" LTD. The present study extends this line of investigation to another transgenic mouse line with enhanced LTD, namely, mice with the Fragile X gene knocked out. The main findings are that VOR gain increased learning is selectively impaired in these mice but can be rescued by specific manipulations of visuomotor experience known to reverse cerebellar LTD. Additionally, the authors show that a transient global enhancement of neuronal inhibition also selectively rescues gain increases learning. This latter finding has potential clinical relevance since the drug used to boost inhibition, diazepam, is FDA-approved and commonly used in the clinic. The evidence provided for the saturation is somewhat indirect because directly measuring synaptic strength in vivo is technically difficult. Nevertheless, the experimental results are solid. In particular, the specificity of the effects to forms of plasticity previously shown to require LTD is remarkable. The authors should consider including a brief discussion of some of the important untested assumptions of the saturation hypothesis, including the requirement that cerebellar LTD depends not only on pre- and postsynaptic activity (as is typically assumed) but also on the prior history of synaptic activation.

Reviewer #2 (Public Review):

Summary:

In this study, the authors sought to understand how the receptive fields of bipolar cells contribute to direction selectivity in starburst amacrine cell (SAC) dendrites, their post synaptic partners. In previous literature, this contribution is primarily conceptualized as the 'space-time wiring model', whereby bipolar cells with slow-release kinetics synapse onto proximal dendrites while bipolar cells with faster kinetics synapse more distally, leading to maximal summation of the slow proximal and fast distal depolarizations in response to motion away from the soma. The space-time wiring contribution to SAC direction selectivity has been extensively tested in previous literature using connectomic, functional, and modeling approaches. However, the authors argue that previous functional studies of bipolar cell kinetics have focused on static stimuli, which may not accurately represent the spatiotemporal properties of the bipolar cell receptive field in response to movement. Moreover, this group and others have recently shown that bipolar cell signal processing can change directionally when visual stimuli starts within the receptive field rather than passing through it, complicating the interpretation of moving stimuli that start within a bipolar cell of interest's receptive field (e.g. stimulating only one branch of a SAC or expanding/contracting rings). Thus, the authors choose to focus on modeling and functionally mapping bipolar cell kinetics in response to moving stimuli across the entire SAC dendritic field.

General Comments:

There have been several studies that have addressed the contribution of space-time wiring to SAC process direction selectivity. This study offers a more complete assessment of potential impact space-time wiring can have on this dendrite computation. The experimental results based on glutamate imaging assess the kinetics of glutamate release under conditions of visual stimulation across a large region of retina largely confirm previous observations. By combining their model with this experiment data, they conclude that even the optimal space-time wiring is not sufficient to explain the SAC process DS. Though there is no conclusion which of the many other proposed cellular and circuit mechanisms could potentially contribute to this computation, the limited role for spacetime wiring is firmly established.

Reviewer #2 (Public Review):

Clarkson et al investigated the impact of in vivo ESR1 gene disruption selectively in preoptic area GABA neurons on the estrogen regulation of LH secretion. The hypothalamic pathways by which estradiol controls the secretion of gonadotrophins are incompletely understood and relevant to a better understanding of the mechanisms driving fertility and reproduction. Using CRISPR-Cas9 methodology, the authors were able to effectively reduce the expression of estrogen receptor (ER)-alpha in GABA neurons located in the preoptic area of adult female mice. The results obtained were rather variable except in the animals with concomitant suppression of kisspeptin in the rostral periventricular region of the third ventricle (RP3V), which displayed interruption of ovarian cyclicity and an altered estradiol-induced LH surge. The experimental approach used allowed for a cell-selective, temporally-controlled suppression of ER-alpha expression, providing further evidence of the critical role of RP3V kisspeptin neurons in the estrogen positive-feedback effect. The preovulatory LH surge is a variable phenomenon and is better evaluated using serial blood sampling. Although the assessment of the estradiol-induced LH surge was performed in one terminal blood collection, c-Fos expression in GnRH neurons was used as a reliable proxy of the LH surge occurrence. The present findings also suggest that GABA neurotransmission in the preoptic area itself is not involved in the positive-feedback effect of estradiol on LH secretion.

Reviewer #2 (Public Review):

Summary:<br /> The authors investigate the influence of serotonin on feeding behavior and electrophysiological responses in the antennal lobe of locusts. They find that serotonin injection changes behavior in an odor-specific way. In physiology experiments, they can show that antennal lobe neurons generally increase their baseline firing and odor responses upon serotonin injection. Using a modeling approach the authors propose a framework on how a general increase in antennal lobe output can lead to odor-specific changes in behavior. The authors finally suggest that serotonin injection can mimic a change in a hunger state.

Strengths:<br /> This study shows that serotonin affects feeding behavior and odor processing in the antennal lobe of locusts, as serotonin injection increases activity levels of antennal lobe neurons. This study provides another piece of evidence that serotonin is a general neuromodulator within the early olfactory processing system across insects and even phyla.

Weaknesses:<br /> I have several concerns regarding missing control experiments, unclear data analysis, and interpretation of results.

A detailed description of the behavioral experiments is lacking. Did the authors also provide a mineral oil control and did they analyze the baseline POR response? Is there an increase in baseline response after serotonin exposure already at the behavioral output level? It is generally unclear how naturalistic the chosen odor concentrations are. This is especially important as behavioral responses to different concentrations of odors are differently modulated after serotonin injection (Figure 2: Linalool and Ammonium).

Regarding recordings of potential PNs - the authors do not provide evidence that they did record from projection neurons and not other types of antennal lobe neurons. Thus, these claims should be phrased more carefully.

The presented model suggests labeled lines in the antennal lobe output of locusts. Could the presented model also explain a shift in behavior from aversion to attraction - such as seen in locusts when they switch from a solitarious to a gregarious state? The authors might want to discuss other possible scenarios, such as that odor evaluation and decision-making take place in higher brain regions, or that other neuromodulators might affect behavioral output. Serotonin injections could affect behavior via modulation of other cell types than antennal lobe neurons. This should also be discussed - the same is true for potential PNs - serotonin might not directly affect this cell type, but might rather shut down local inhibitory neurons.

Finally, the authors claim that serotonin injection can mimic the starved state behavioral response. However, this is only shown for one of the four odors that are tested for behavior (HEX), thus the data does not support this claim.

Reviewer #2 (Public Review):

Summary:<br /> This manuscript expands on previous work from the Haucke group which demonstrated the role of formins in synaptic vesicle endocytosis. The techniques used to address the research question are state-of-the-art. As stated above there is a significant advance in knowledge, with particular respect to Rho/Rac signalling.

Strengths:<br /> The major strength of the work was to reveal new information regarding the control of both presynaptic actin dynamics and synaptic vesicle endocytosis via Rho/Rac cascades. In addition, there was further mechanistic insight regarding the specific function of mDia1/3. The methods used were state-of-the-art.

Weaknesses:<br /> There are a number of instances where the conclusions drawn are not supported by the submitted data, or further work is required to confirm these conclusions.

Reviewer #2 (Public Review):

Summary:<br /> The manuscript examines an important question about how an inaccessible, natural forgotten memory can be retrieved through engram ensemble reactivation. It uses a variety of strategies including optogenetics, behavioral and pharmacological interventions to modulate engram accessibility. The data characterize the time course of natural forgetting using an object recognition task, in which animals can retrieve 1 day and 1 week after learning, but not 2 weeks later. Forgetting is correlated with lower levels of cell reactivation (c-fos expression during learning compared to retrieval) and reduction in spine density and volume in the engram cells. Artificial activation of the original engram was sufficient to induce recall of the forgotten object memory while artificial inhibition of the engram cells precluded memory retrieval. Mice housed in an enriched environment had a slower rate of forgetting, and a brief reminder before the retrieval session promoted retrieval of a forgotten memory. Repeated reintroduction to the training context in the absence of objects accelerated forgetting. Additionally, activation of Rac1-mediated plasticity mechanisms enhanced forgetting, while its inhibition prolonged memory retrieval. The authors also reproduce the behavioral findings using a computational model inspired by Rescorla-Wagner model. In essence, the model proposes that forgetting is a form of adaptive learning that can be updated based on prediction error rules in which engram relevancy is altered in response to environmental feedback.

Strengths:<br /> 1) The data presented in the current paper are consistent with the authors claim that seemingly forgotten engrams sometimes remain accessible. This suggests that retrieval deficits can lead to memory impairments rather than a loss of the original engram (at least in some cases).

2) The experimental procedures and statistics are appropriate, and the behavioral effects appear to be very robust. Several key effects are replicated multiple times in the manuscript.

Weaknesses:<br /> 1) My major issue with the paper is the forgetting model proposed in Figure 7. Prior work has shown that neutral stimuli become associated in a manner similar to conditioned and unconditioned stimuli. As a result, the Rescorla-Wagner model can be used to describe this learning (Todd & Homes, 2022). In the current experiments, the neutral context will become associated with the unpredicted objects during training (due to a positive prediction error). Consequently, the context will activate a memory for the objects during the test, which should facilitate performance. Conversely, any manipulation that degrades the association between the context and object should disrupt performance. An example of this can be found in Figure 5A. Exposing the mice to the context in the absence of the objects should violate their expectations and create a negative prediction error. According to the Rescorla-Wagner model, this error will create an inhibitory association between the context and the objects, which should make it harder for the former to activate a memory of the latter (Rescorla & Wagner, 1972). As a result, performance should be impaired, and this is what the authors find. However, if the cells encoding the context and objects were inhibited during the context-alone sessions (Figure 5D) then no prediction error should occur, and inhibitory associations would not be formed. As a result, performance should be intact, which is what the authors observe.

What about forgetting of the objects that occurs over time? Bouton and others have demonstrated that retrieval failure is often due to contextual changes that occur with the passage of time (Bouton, 1993; Rosas & Bouton, 1997, Bouton, Nelson & Rosas, 1999). That is, both internal (e.g. state of the animal) and external (e.g. testing room, chambers, experimenter) contextual cues change over time. This shift makes it difficult for the context to activate memories with which it was once associated (in the current paper, objects). To overcome this deficit, one can simply re-expose animals to the original context, which facilitates memory retrieval (Bouton, 1993). In Figure 2D, the authors do something similar. They activate the engram cells encoding the original context and objects, which enhances retrieval.

Therefore, the forgetting effects presented in the current paper can be explained by changes in the context and the associations it has formed with the objects (excitatory or inhibitory). The results are perfectly predicted by the Rescorla-Wagner model and the context-change findings of Bouton and others. As a result, the authors do not need to propose the existence of a new "forgetting" variable that is driven by negative prediction errors. This does not add anything novel to the paper as it is not necessary to explain the data (Figures 7 and 8).

2) I also have an issue with the conclusions drawn from the enriched environment experiment (Figure 3). The authors hypothesize that this manipulation alleviates forgetting because "Experiencing extra toys and objects during environmental enrichment that are reminiscent of the previously learned familiar object might help maintain or nudge mice to infer a higher engram relevancy that is more robust against forgetting.". This statement is completely speculative. A much simpler explanation (based on the existing literature) is that enrichment enhances synaptic plasticity, spine growth, etc., which in turn reduces forgetting. If the authors want to make their claim, then they need to test it experimentally. For example, the enriched environment could be filled with objects that are similar or dissimilar to those used in the memory experiments. If their hypothesis is correct, only the similar condition should prevent forgetting.

3) It is well-known that updating can both weaken or strengthen memory. The authors suggest that memory is updated when animals are exposed to the context in the absence of the objects. If the engram is artificially inhibited (opto) during context-only re-exposures, memory cannot be updated. To further support this updating idea, it would be good to run experiments that investigate whether multiple short re-exposures to the training context (in the presence of the objects or during optogenetic activation of the engram) could prevent forgetting. It would also be good to know the levels of neuronal reactivation during multiple re-exposures to the context in the absence versus context in the presence of the objects.

4) There are a number of studies that show boundary conditions for memory destabilization/reconsolidation. Is there any evidence that similar boundary conditions exist to make an inaccessible engram accessible?

5) More details about how the quantification of immunohistochemistry (c-fos, BrdU, DAPI) was performed should be provided (which software and parameters were used to consider a fos positive neurons, for example).

6) Duration of the enrichment environment was not detailed.

Reviewer #2 (Public Review):

This paper presents improved, chromosome level assemblies of the hadal snailfish and Tanaka's snailfish. This is an extension and update of previous work from the group on the hadal snailfish genome. The chromosomal assemblies allow comparisons of genome architecture between a shallow water snailfish and the hadal snailfish to aid inference on timing of colonization of trenches and genomic changes that may have been adaptive for that move.

The comparisons in genomic architecture are compelling: genes present in Tanaka's snailfish that are lost in hadal snailfish that involve whole regions of the genome that no longer map even though adjacent regions do map between the species and across a large evolutionary distance to stickleback. Or genes that are duplicated in hadal snailfish but only appear as single copy in other fishes. The paper focuses on genes in the eye, in hearing, in circadian rythms, and in ROS scavaging. These are all functions that could play a role in adapting to the hadal environment.

The genomic comparisons all seem sound. Stylistically I would prefer if the authors could introduce the gene product and protein function every time they introduce a gene locus. They introduce a gene and general function, but don't usually note what the protein encoded by the gene is and what it's specific function is.

I found the paper generally well written, and the data compelling and creatively displayed.

Upon revision, the authors have commendably addressed all reviewer comments and added a slew of additional analyses. I find the paper stronger, better argued and have no further questions or comments.

Reviewer #2 (Public Review):

Summary:<br /> In this manuscript, Mure et al investigated host-microbe interactions in wild-mimicked settings. They analyzed microbiome composition using bananas that had been fed on by wild larvae and found that the microbiota composition shifted from the early stage of feeding to the later stage of the fermentation process proceeded. They isolated several yeast and bacterial species from the food, and examined larval growth on banana-based food, mimicking natural setting where germ-free larvae cannot grow on it. The authors found that a yeast, Hanseniaspora uvarum, can support larval growth sufficiently, and insists that branched-chain amino acids (BCAAs) provided by the yeast may partly be accounted for the growth support. Interestingly, other isolated yeast species, some were non-supportive strains in terms of larval growth, can assist larval development when they were heat-killed. Besides, they showed that acetic acid bacteria, isolated from well-fermented banana (later-stage food), is sufficiently supportive but their presence depended on other microbes, lactic acid bacteria or yeast.

Strengths:<br /> So far, host-microbe studies using Drosophila melanogaster have relatively less focused on the roles of fungi and many studies used only "model" yeasts. In the experimental setting where natural conditions may be well mimicked, the authors successfully isolated wild yeast species and convincingly showed that wild yeast plays a critical role in promoting host growth. In addition, the authors provided intriguing observations that all of the heat-killed yeast promoted larval growth even though some of the yeast never support the development when they were alive, suggesting that wild yeasts produce the necessary nutrients for larval development, but the nutrients of non-supportive yeasts are not accessible to the host. This might be an interesting indication for further studies revealing host-fungi interactions.

Weaknesses:<br /> The experimental setting that, the authors think, reflects host-microbe interactions in nature is one of the key points. However, it is not explicitly mentioned whether isolated microbes are indeed colonized in wild larvae of Drosophila melanogaster who eat bananas. Another matter is that this work is rather descriptive. A molecular level explanation is missing in "interspecies interactions" between lactic acid bacteria (or yeast) and acetic acid bacteria that assure their inhabitation.

Reviewer #2 (Public Review):

Summary:

In the manuscript entitled "The Intricate Relationship of G-Quadruplexes and Pathogenicity Islands: A Window into Bacterial Pathogenicity" Bo Lyu explored the interactions between guanine-quadruplex (G4) structures and pathogenicity islands (PAIs) in 89 bacterial genomes through a rigorous computational approach. This paper handles an intriguing and complex topic in the field of pathogenomics. It has the potential to contribute significantly to the understanding of G4-PAI interactions and bacterial pathogenicity.

Strengths:

- The chosen research area.<br /> - The summarizing of the results through neat illustrations.

Weaknesses:

This reviewer did not find any significant weaknesses.

Reviewer #2 (Public Review):

This manuscript by Musselman and coworkers uses a commercial library of modified histone peptides and mononucleosomes to probe the substrate specificity of the PHD-bromodomain combination of the BPTF protein. They arrive at the conclusion that BPTF preferably binds H3K4me3 and H3K18ac in the H3 tail. By using NMR with lableled H4 protein in nucleosomes they show that the H4 tail interacts with DNA, which may limit its ability to interact with BPTF. Finally, experiments in cells demonstrate that BPTF, H3K4me3, and H3K18ac occupy overlapping regions of chromatin. The authors suggest that recruitment of BPTF to specific regions of chromatin is driven by the co-binding of H3K4me3 and H3K18ac by BPTF. This study is of interest to readers interested in understanding the functions of the BPTF protein in cells.

In this reviewer's opinion, the manuscript needs some revision and the inclusion of some missing information.

1) The authors seem to have overlooked the fact that mononucleosome substrates have been in use for determining the substrate specificity and mechanisms of quite a few enzymes that simply do not act on peptide substrates. For example, Dot1L doesn't do anything with peptides nor does COMPASS/Set1, both of which require intact nucleosomal substrates to measure their activity in response to ubiquitylated H2B. Thus, the authors' refinement of the "histone code hypothesis" is unnecessary and overdone. I would suggest that they instead cite examples where nucleosome substrates have provided answers that cannot be obtained from peptide substrates alone. For example, extensive work from the Muir and Allis labs.

2) Ruthenburg and Allis in Cell 2011 conducted similar experimentation and concluded that H3K4me3-H4K16ac is a modification state bound by BPTF in cells. They also showed co-localization in ChIP-seq experiments and demonstrated preferential pulldowns with BPTF and semisynthetic methylated and acetylated nucleosomes. The authors have entirely ignored these previous results in their own discussions. Readers would benefit from a side-by-side comparison of the two acetylation states to get a sense of which is a stronger interaction and why both seemingly correlate in CUTnRUN or ChIP-seq.

3) The idea that electrostatics may modulate tail accessibility was reported by Musselman and coworkers for the H3 tail in eLife 2018. Yet the PHD domain of BPTF clearly binds H3K4me3 in nucleosomes. In light of this prior observation, the NMR experiments now with H4 tail seem repetitive and not informative regarding BPTF's bromodomain binding. Also, missing is the effect of H4K16acetylation on H4 tail dynamics, which would be pertinent to addressing the hypothesis regarding the BPTF bromodomain binding H4K16ac

4) The NMR experiments are all undertaken with 150mM KCl with no NaCl present. While NMR experimental constraints are understandable, the authors should avoid sweeping statements from NMR experiments regarding the dynamism of histone tails in chromatin, unless specific experiments are cited/conducted to demonstrate the same in cells. Many factors may contribute to the exclusion of BPTF from modified histone tails in cells, including the binding of other reader proteins, and the precise genomic localization of these modifications vis-a-vis BPTF. The important role of anchoring proteins must also be taken into account when considering binding/non-binding of substrates by CAPs. Thus, the NMR experiments presented in the manuscript do not report on whether BPTF binds H4K16ac in cells or indeed in vitro. If the PHD domain is capable of ultimately binding the H3 tail despite the tail's fuzzy interaction with DNA, the question remains as to why the bromodomain may not do so for acetylated H4 tails?

This manuscript reports several interesting elements regarding BPTF regulation, but as presented it is missing some key comparisons with prior information that makes it hard for readers to assess the relevance of the results presented.

Reviewer #2 (Public Review):

This study aims to test whether and if so, how cholecystokinin (CCK) from the mice rhinal cortex influences neural activity in the motor cortex and motor learning behavior. While CCK has been previously shown to be involved in neural plasticity in other brain regions/behavioral contexts, this work is the first to demonstrate its relationship with motor cortical plasticity in the context of motor learning. The anatomical projection from the rhinal cortex to the motor cortex is also a novel and important finding and opens up new opportunities for studying the interactions between the limbic and motor systems. I think the results are convincing to support the claim that CCK and in particular CCK-expressing neurons in the rhinal cortex are critical for learning certain dexterous movements such as single pellet reaching. However, more work needs to be done, or at least the following concerns should be addressed, to support the hypothesis that it is specifically the projection from the rhinal cortex to the motor cortex that controls motor learning ability in mice.

1) Because CCK is expressed in multiple brain regions, as the authors recognized, results from the CCK knock-out mice could be due to a global loss of neural plasticity. In comparison, the antagonist experiment is in my opinion the most convincing result to support the specific effect of CCK in the motor cortex. However, it is unclear to me whether the CCK knock-out mice exhibited an impaired ability to learn in general, i.e., not confined to motor skills. For instance, it would be very valuable to show whether these mice also had severe memory deficits; this would help the field to understand different or similar behavioral effects of CCK in the case of global vs. local loss of function. If the CCK knock-out mice only exhibited motor learning deficits, that would be surprising but also very interesting given previous studies on its effect in other brain areas.

2) Related to my last point, I believe that normal neural plasticity should be essential to motor skill learning throughout development not just during the current task. Thus, it would be important to show whether these CCK knock-out mice present any motor deficits that could have resulted from a lack of CCK-mediated neural plasticity during development. If not, the authors should explain how this normal motor learning during development is consistent with their major hypothesis in this study (e.g., is CCK not critical for motor learning during early development).

3) Lines 198-200 and Fig. 2C: The authors found that the vehicle group showed significantly increased "no grasp" behavior, and reasoned that the implantation of a cannula may have caused injuries to the motor cortex. In order to support their reasoning and make the control results more convincing, I think it would be helpful to show histology from both the antagonist and control groups and demonstrate motor cortical injury in some mice of the vehicle group but not the antagonist group. Otherwise, I'm a bit concerned that the methods used here could be a significant confounding factor contributing to motor deficits.

4) The authors showed that chemogenetic inhibition of CCK neurons in the rhinal cortex impaired motor skill learning in the pellet-reaching task. However, we know that the rhinal cortex projects to multiple brain regions besides the motor cortex (e.g., other cortical areas and the hippocampus). Thus, the conclusion/claim that the observed behavioral deficits resulted from inhibited rhinal-motor cortical projections is not strongly supported without more targeted loss-of-function or rescue experiments.

It would also be very informative to the field to compare the specific behavioral deficits, if any, of inhibiting specific downstream targets of the rhinal CCK neurons. As a concrete example, the hippocampus may be involved in learning more sophisticated motor skills (as the authors pointed out in the Discussion) besides the motor cortex. It would be a critical result if the authors could either show or exclude the possibility that the motor learning deficits observed in CCK-/- mice were at least partially due to the inhibition of hippocampal plasticity. This echoes my earlier point (point 1) that it is unclear whether the effect of lacking CCK in knock-out mice is specific in the motor cortex or engages multiple brain regions.

Lastly, because Fig. 4 only showed histology in the rhinal and motor cortices, I am not sure whether the motor cortex solely receives CCK input from the rhinal cortex. A more comprehensive viral tracing result could be important to both supporting the circuit-specificity of the observed behavior in this study and providing a clearer picture of where the motor cortex receives CCK inputs.

5) I am glad to see the CCK4 rescue experiment to demonstrate the sufficiency of CCK in promoting motor learning. However, the rescue experiment lacked specificity: IP injection did not allow specific "gain of function" in the motor cortex but instead, the improved learning ability in CCK knock-out mice could be a result of a global effect of CCK4 across multiple brain regions. CCK4 injection specifically targeted at the motor cortex would be necessary to support the sufficiency of CCK-regulated neuroplasticity in the motor cortex to promote motor learning.

Reviewer #2 (Public Review):

The authors provide a nice resource of putative direct BMP target genes in Nematostella vectensis by performing ChIP-seq with an anti-pSmad1/5 antibody, while also performing bulk RNA-seq with BMP2/4 or GDF5 knockdown embryos. Genes that exhibit pSmad1/5 binding and have changes in transcription levels after BMP signaling loss were further annotated to identify those with conserved BMP response elements (BREs). Further characterization of one of the direct BMP target genes (zswim4-6) was performed by examining how expression changed following BMP receptor or ligand loss of function, as well as how loss or gain of function of zswim4-6 affected development and BMP signaling. The authors concluded that zswim4-6 modulates BMP signaling activity and likely acts as a pSMAD1/5 dependent co-repressor. However, the mechanism by which zswim4-6 affects the BMP gradient or interacts with pSMAD1/5 to repress target genes is not clear. The authors test the activity of a zswim4-6 homologue in zebrafish (zswim5) by over-expressing mRNA and find that pSMAD1/5/9 labeling is reduced and that embryos have a phenotype suggesting loss of BMP signaling, and conclude that zswim4-6 is a conserved regulator of BMP signaling. This conclusion needs further support to confirm BMP loss of function phenotypes in zswim5 over-expression embryos.

Major comments

1. The BMP direct target comparison was performed between Nematostella, Drosophila, and Xenopus, but not with existing data from zebrafish (Greenfeld 2021, Plos Biol). Given the functional analysis with zebrafish later in the paper it would be nice to see if there are conserved direct target genes in zebrafish, and in particular, is zswim5 (or other zswim genes) are direct targets. Since conservation of zswim4-6 as a direct BMP target between Nematostella and Xenopus seemed to be part of the rationale for further functional analysis, it would also be nice to know if this is a conserved target in zebrafish.

Related to this, in the discussion it is mentioned that zswim4/6 is also a direct BMP target in mouse hair follicle cells, but it wasn't obvious from looking at the supplemental data in that paper where this was drawn from.

2. The loss of zswim4-6 function via MO injection results in changes to pSmad1/5 staining, including a reduction in intensity in the endoderm and gain of intensity in the ectoderm, while over-expression results in a loss of intensity in the ectoderm and no apparent change in the endoderm. While this is interesting, it is not clear how zswim4-6 is functioning to modify BMP signaling, and how this might explain differential effects in ectoderm vs. endoderm. Is the assumption that the mechanism involves repression of chordin? And if so one could test the double knockdown of zswim4-6 and chordin and look for the rescue of pSad1/5 levels or morphological phenotype.

3. Several experiments are done to determine how zswim4-6 expression responds to the loss of function of different BMP ligands and receptors, with the conclusion being that swim4-6 is a BMP2/4 target but not a GDF5 target, with a lot of the discussion dedicated to this as well. However, the authors show a binary response to the loss of BMP2/4 function, where zswim4-6 is expressed normally until pSmad1/5 levels drop low enough, at which point expression is lost. Since the authors also show that GDF5 morphants do not have as strong a reduction in pSmad1/5 levels compared to BMP2/4 morphants, perhaps GDF5 plays a positive but redundant role in swim4-6 expression. To test this possibility the authors could inject suboptimal doses of BMP2/4 MO with GDF5 MO and look for synergy in the loss of zswim4-6 expression.

4. The zswim4-6 morphant embryos show increased expression of zswim4-6 mRNA, which is said to indicate that zswim4-6 negatively regulates its own expression. However in zebrafish translation blocking MOs can sometimes stabilize target transcripts, causing an artifact that can be mistakenly assumed to be increased transcription (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7162184/). Some additional controls here would be warranted for making this conclusion.

5. Zswim4-6 is proposed to be a co-repressor of pSmad1/5 targets based on the occupancy of zswim4-6 at the chordin BRE (which is normally repressed by BMP signaling) and lack of occupancy at the gremlin BRE (normally activated by BMP signaling). This is a promising preliminary result but is based only on the analysis of two genes. Since the authors identified BREs in other direct target genes, examining more genes would better support the model.

6. The rationale for further examination of zswim4-6 function in Nematostella was based in part on it being a conserved direct BMP target in Nematostella and Xenopus. The analysis of zebrafish zswim5 function however does not examine whether zswim5 is a BMP target gene (direct or indirect). BMP inhibition followed by an in situ hybridization for zswim5 would establish whether its expression is activated downstream of BMP.

7. Although there is a reduction in pSmad1/5/9 staining in zebrafish injected with zswim5 mRNA, it is difficult to tell whether the resulting morphological phenotypes closely resemble zebrafish with BMP pathway mutations (such as bmp2b). More analysis is warranted here to determine whether stereotypical BMP loss of function phenotypes are observed, such as dorsalization of the mesoderm and loss of ventral tail fin.

Reviewer #2 (Public Review):

The authors asked the question about whether and how changing feature values within the same feature dimensions are tracked. Using a series of behavioral studies combined with modeling approaches, the authors report interesting results regarding a robust, uneven distribution of attentional resources between two changing feature values (in a 2:1 ratio), alternating at 1 Hz. Although the results are clear, it is important to rule out the possible biases due to computational processes. The results advanced our understanding of how parallel tracking of multiple feature values within the same dimension is achieved.

Reviewer #2 (Public Review):

In this manuscript, the Chen group aimed to understand the role of FDX1 in vivo. While its role in the biogenesis of steroids and bile acids, Vitamin A/D metabolism, and lipoylation of TCA enzymes has been extensively studied biochemically, its role in physiology and lipid metabolism is still unknown. The authors established a conditional Fdx1 KO mice and performed a series of experiments to demonstrate the physiological role of Fdx1 in mice. The obtained evidence convincingly supports the major conclusion of the study. The manuscript is well and concisely written.

Strengths:<br /> • Solid data showing that Fdx1+/- mice are prone to steatohepatitis and Fdx1+/- cells accumulate lipids<br /> • Untargeted MS profiling the changes of lipids upon Fdx1 KO.<br /> • Clear evidence indicating that the ABCA1-SREBP1/2 pathway is involved in the function of Fdx1 in lipid metabolism.

Weaknesses:<br /> • use of Fdx1+/- MEFs, instead of using Fdx1-/- MEFs, could be well justified.

Reviewer #2 (Public Review):

The data generated for this paper provides an important resource for the neuroscience community. The locus coeruleus (LC) is the known seed of noradrenergic cells in the brain. Due to its location and size, it remains scarcely profiled in humans. Despite the physically minute structure containing these cells, its impact is wide-reaching due to the known neuromodulatory function of norepinephrine (NE) in processes like attention and mood. As such, profiling NE cells has important implications for most neurological and neuropsychiatric disorders. This paper generates transcriptomic profiles that are not only cell-specific but which also maintain their spatial context, providing the field with a map for the cells within the region.

Strengths:

Using spatial transcriptomics in a morphologically distinct region is a very attractive way to generate a map. Overlaying macroscopic information, i.e. a region with greater pigmentation, with its corresponding molecular profile in an unbiased manner is an extremely powerful way to understand the specific cellular and molecular composition of that brain structure.

The technologies were used with an astute awareness of their limitations, as such, multiple technologies were leveraged to paint a more complete and resolved picture of the cellular composition of the region. For example, the lack of resolution in the spatial transcriptomic platform was compensated by complementary snRNA-seq and single molecule FISH.

This work has been made publicly available and accessible through a user-friendly application such that any interested researcher can investigate the level of expression of their gene of interest within this region.

Two important implications from this work are 1) the potential that the gene regulatory profiles of these cells are only partially conserved across species, humans, and rodents, and 2) that there may be other neuromodulatory cell types within the region that were otherwise not previously localized to the LC

Weaknesses:

Given that the markers used to identify cells are not as specific as they need to be to definitively qualify the desired cell type, the results may be over-interpreted. Specifically, TH is the primary marker used to qualify cells as noradrenergic, however, TH catalyzes the synthesis of L-DOPA, a precursor to dopamine, which in turn is a precursor for epinephrine and norepinephrine suggesting some of the cells in the region may be dopaminergic and not NE cells. Indeed, there are publications to support the presence of dopaminergic cells in the LC (see Kempadoo et al. 2016, Takeuchi et al., 2016, Devoto et al. 2005). This discrepancy is further highlighted by the apparent lack of overlap per given Visium spots with TH, SCL6A2, or DBH. While the single-nucleus FISH confirms that some of the cells in the region are noradrenergic, others very possibly represent a different catecholamine. As such it is suggested that the nomenclature for the cells be reconsidered.

The authors are unable to successfully implement unsupervised clustering with the spatial data, this greatly reduces the impact of the spatial technology as it implies that the transcriptomic data generated in the study did not have enough resolution to identify individual cell types.

The sample contribution to the results is highly unbalanced, which consequently, may result in ungeneralizable findings in terms of regional cellular composition, limiting the usefulness of the publicly available data.

This study aimed to deeply profile the LC in humans and provide a resource to the community. The combination of data types (snRNA-seq, SRT, smFISH) does in fact represent this resource for the community. However, due to the limitations, of which, some were described in the manuscript, we should be cautious in the use of the data for secondary analysis. For example, some of the cellular annotations may lack precision, the cellular composition also may not reflect the general population, and the presence of unexpected cell types may represent the accidental inclusion of adjacent regions, in this case, serotonergic cells from the Raphe nucleus.

Nonetheless having a well-developed app to query and visualize these data will be an enormous asset to the community especially given the lack of information regarding the region in general.

Reviewer #2 (Public Review):

Summary:

The authors set out to discover a developmental pathway leading to functionally diverse mTEC subsets. They show that Ccl21 is expressed early during thymus ontogeny in the medullary area. Fate-mapping gives evidence for the Ccl21 positive history of Aire positive mTECs as well as of thymic tuft cells and postnatally of a certain percentage of cTECs. Therefore, the differentiation potential of Ccl21+ TECs is tested in reaggregate thymus experiments - using embryonic or postnatal Ccl21+ TECs. From these experiments, the authors conclude that at least embryonic mTECs in large part pass through a Ccl21 positive stage prior to differentiation towards an Aire expressing or tuft cell stage.

The authors are using Ccl21a as a marker for a bipotent progenitor that is detectable in the embryonic thymus and is still present at the adult stage mainly giving rise to mTECs. The choice of this marker gene is very interesting since Ccl21 expression can directly be linked to an important aspect in thymus biology: the expression of Ccl21 by cells in the thymic medulla allows trafficking of T cells into the medulla in order to undergo T cell selection.

Making use of the Ccl21 detection, the authors can nicely show that cells actively expressing Ccl21 are localized throughout the medulla at an embryonic stage but also in adult thymus tissue. This suggests, that this progenitor is not accumulating at a specific area inside the medulla. This is a new finding.

Moreover, the finding that a Ccl21+ progenitor population plays a functional role in thymocyte trafficking towards the medulla has not been described. Thus, Ccl21 expression may be used to localize a late bipotent progenitor in the thymic lobes.<br /> In addition, in Fig.8, the authors provide evidence that these progenitor cells have the potential to self-maintain as well as to differentiate in reaggregate experiments at E17 (not at 4 weeks of age). The first point is of great interest and importance since these cells in theory can be of therapeutic use.

Overall assessment:

The authors highlight a developmental pathway starting from a Ccl21-expressing TEC progenitor that contributes to a functionally diverse mTEC repertoire. This is a welcome addition to current knowledge of TEC differentiation.

Reviewer #2 (Public Review):

Summary:

This manuscript describes the study protocol, structure and logic of the PAVE strategy. The PAVE study is a multicentric study to evaluate a novel cervical screen-triage-treat strategy for resource-limited settings as part of a global strategy to reduce cervical cancer burden. The PAVE strategy involves: 1) screening with self-sampled HPV testing; 2) triage of HPV-positive participants with a combination of extended genotyping and visual evaluation of the cervix assisted by deep-learning-based automated visual evaluation (AVE); and 3) treatment with thermal ablation or excision (Large Loop Excision of the Transformation Zone). The PAVE study has two phases: efficacy (2023-2024) and effectiveness (planned to begin in 2024-2025). The efficacy phase aims to refine and validate the screen-triage portion of the protocol. The effectiveness phase will examine few implementation of the PAVE strategy into clinical practice. In following phases implementation will further explored.

Strengths and weaknesses

The Pave Study develops and evaluates a novel strategy that combines HPV self-collection -that has been proven effective to increase screening coverage in different settings-, with genotyping and Automated Visual Evaluation as triage. The proposed strategy combined three key innovations to improve an important step in the cervical cancer care continuum. If the strategy is effective it will contribute to enhance cervical cancer prevention in low resource settings.

As authors mentioned, despite the existence of effective preventive technologies (e.g., HPV vaccine and HPV test) translation of the HPV prevention methods has not yet occurred in many Low-Middle-Income Countries. So, in this context, new screen-triage-treat strategies are needed and if PAVE strategy were effective, it could be a landmark for cervical cancer prevention.

The PAVE Study is a solid and important study that is aimed to be carried out in nine countries and recruit tens thousands of women. It is a study with a large and diverse sample that can provide useful information for the development of this new screen-triage-treat strategy. Another strength is the fact that the PAVE project is integrated into the screening activities placed in the selected countries that will allow to evaluate efficacy and effectiveness in real-word context.

The manuscript does not present results because its aim is to describe the study protocol, structure and logic of the PAVE strategy.

Phase 1 aims to evaluate efficacy of the strategy. Methods are well described and are consistent with the study aims.

Phase 2 aims to evaluate the implementation of the PAVE strategy in clinical practice. The inclusion of implementation evaluation in this type of studies is an important milestone in the field of cervical cancer prevention. It has been shown that many strategies that have proven to be effective in controlled studies face barriers when they are implemented in real life. In that sense, results of phase 2 are key to ensure the future implementation of the strategy.

Reviewer #2 (Public Review):

Summary:<br /> This research involves conducting experiments to determine the role of Fmnl2 during oocyte meiosis I.

Strengths:<br /> Identifying the role of Fmnl2 during oocyte meiosis I is significant.

Weaknesses:<br /> The quantitative analysis and the used approach to perturb FMNL2 function are currently incomplete and would benefit from more confirmatory approaches and rigorous analysis.

1- Most of the results are expected. The new finding here is that FMNL2 regulates cytoplasmic F-actin in mouse oocytes, which is also expected given the role of FMNL2 in other cell types. Given that FMNL2 regulates cytoplasmic F-actin, it is very expected to see all the observed phenotypes. It is already established that F-actin is required for spindle migration to the oocyte cortex, extruding a small polar body and normal organelle distribution and functions.

2-The authors used Fmnl2 cRNA to rescue the effect of siRNA-mediated knockdown of Fmnl2. It is not clear how this works. It is expected that the siRNA will also target the exogenous cRNA construct (which should have the same sequence as endogenous Fmnl2) especially when both of them were injected at the same time. Is this construct mutated to be resistant to the siRNA?

3-The authors used only one approach to knockdown FMNL2 which is by siRNA. Using an additional approach to inhibit FMNL2 would be beneficial to confirm that the effect of siRNA-mediated knockdown of FMNL2 is specific.

Reviewer #2 (Public Review):

Summary:<br /> The authors solved the crystal structure of CDV H-protein head domain at 3,2 A resolution to better understand the detailed mechanism of membrane fusion triggering. The structure clearly showed that the orientation of the H monomers in the homodimer was similar to that of measles virus H and different from other paramyxoviruses. The authors used the available co-crystal strictures of the closely related measles virus H structures with the SLAM and Nectin4 receptors to map the receptor binding site on CDV H. The authors also confirmed which N-linked sites were glycosylated in the CDV H protein and showed that both wildtype and vaccine strains of CDV H have the same glycosylation pattern. The authors documented that the glycans cover a vast majority of the H surface while leaving the receptor binding site exposed, which may in part explain the long-term success of measles virus and CDV vaccines. Finally, the authors used HS-AFM to visualize the real-time dynamic characteristics of CDV-H under physiological conditions. This analysis indicated that homodimers may dissociate into monomers, which has implications for the model of fusion triggering.

The structural data and analysis were thorough and well-presented. However, the HS-AFM data, while very exciting, was not presented in a manner that could be easily grasped by readers of this manuscript. I have some suggestions for improvement.

1) The authors claim their structure is very similar to the recently published croy-EM structure of CDV H. Can the authors provide us with a quantitative assessment of this statement?

2) The results for the HS-AFM are difficult to follow and it is not clear how the authors came to their conclusions. Can the authors better explain this data and justify their conclusions based on it?

3) The fusion triggering model in Figure 8 is ambiguous as to when H-F interactions are occurring and when they may be disrupted. The authors should clarify this point in their model.

Reviewer #2 (Public Review):

This study provides the proteomic and phosphoproteomics data for our understanding of the molecular alterations in adipose tissue and skeletal muscle from women with PCOS. This work is useful for understanding of the characteristics of PCOS, as it may provide potential targets and strategies for the future treatment of PCOS. While the manuscript presents interesting findings on omics and phenotypic research, the lack of in-depth mechanistic exploration limits its potential impact.

The study primarily presents findings from omics and phenotypic research, but fails to provide a thorough investigation into the underlying mechanisms driving the observed results. Without a thorough elucidation of the mechanistic underpinnings, the significance and novelty of the study are compromised.

Reviewer #2 (Public Review):

In the study by Hreich et al, the potency of P2RX7-specific positive modulator HEI3090, developed by the authors, for the treatment of Idiopathic pulmonary fibrosis (IPF) was investigated. Recently, the authors have shown that HEI3090 can protect against lung cancer by stimulating dendritic cell P2RX7, resulting in IL-18 production that stimulates IFN-γ production by T and NK cells (DOI: 10.1038/s41467-021-20912-2). Interestingly, HEI3090 increases IL-18 levels only in the presence of high eATP. Since the treatment options for IPF are limited, new therapeutic strategies and targets are needed. The authors first show that P2RX7/IL-18/IFNG axis is downregulated in patients with IPF. Next, they used a bleomycin-induced lung fibrosis mouse model to show that the use of a positive modulator of P2RX7 leads to the activation of the P2RX7/IL-18 axis in immune cells that limits lung fibrosis onset or progression. Mechanistically, treatment with HEI3090 enhanced IL-18-dependent IFN-γ production by lung T cells leading to a decreased production of IL-17 and TGFβ, major drivers of IPF. The major novelty is the use of the small molecule HEI3090 to stimulate the immune system to limit lung fibrosis progression by targeting the P2RX7, which could be potentially combined with current therapies available. Overall, the study was well performed and the manuscript is clear. However, there is need for more details on the description and interpretation of the adoptive transfer experiments, as well as the statistical analyses and number of replicate independent experiments.

Reviewer #2 (Public Review):

Summary:

The authors identified miR-199b-5p as a potential OA target gene using serum exosomal small RNA-seq from human healthy and OA patients. Their RNA-seq results were further compared with publicly available datasets to validate their finding of miR-199b-5p. In vitro chondrocyte culture with miR-199b-5p mimic/inhibitor and in vivo animal models were used to evaluate the function of miR-199b-5p in OA. The possible genes that were potentially regulated by miR-199b-5p were also predicted (i.e., Fzd6 and Gcnt2) and then validated by using Luciferase assays.

Strengths:

1. Strong in vivo animal models including pain tests.<br /> 2. Validates the binding of miR-199b-5p with Fzd6 and binding of miR-199b-5p with Gcnt2.

Weaknesses:

1. The authors may overinterpret their results. The current work shows the possible bindings between miR-199b-5p and Fzd6 as well as bindings between miR-199b-5p and Gcnt2. However, whether miR-199b-5p truly functions through Fzd6 and/or Gcnt2 requires genetic knockdown of Fzd6 and Gcnt2 in the presence of miR-199b-5p.<br /> 2. In vitro chondrocyte experiments were conducted in a 2D manner, which led to chondrocyte de-differentiation and thus may not represent the chondrocyte response to the treatments.<br /> 3. There is a lack of description for bioinformatic analysis.<br /> 4. There are several errors in figure labeling.

Reviewer #2 (Public Review):

Summary:

In this study, Christin Krause et al mapped the hepatic miRNA-transcriptome of type 2 diabetic obese subjects, and identified miR-182-5p and its target genes LRP6 as potential drivers of dysregulated glucose tolerance and fatty acid metabolism in obese T2-diabetics.

Strengths:

This study contains some interesting findings and is valuable for the understanding of the key regulatory role of miRNAs in the pathogenesis of T2D.

Weaknesses:

The authors didn't systemically investigate the function of miR-182 in T2DM or NAFLD.

Reviewer #2 (Public Review):

Summary:<br /> In this paper, Chamness and colleagues make a pioneering effort to map epistatic interactions among mutations in a membrane protein. They introduce thousands of mutations to the mouse GnRH Receptor (GnRHR), either under wild-type background or two mutant backgrounds, representing mutations that destabilize GnRHR by distinct mechanisms. The first mutant background is W107A, destabilizing the tertiary fold, and the second, V276T, perturbing the efficiency of cotranslational insertion of TM6 to the membrane, which is essential for proper folding. They then measure the surface expression of these three mutant libraries, using it as a proxy for protein stability, since misfolded proteins do not typically make it to the plasma membrane. The resulting dataset is then used to shed light on how diverse mutations interact epistatically with the two genetic background mutations. Their main conclusion is that epistatic interactions vary depending on the degree of destabilization and the mechanism through which they perturb the protein. The mutation V276T forms primarily negative (aggravating) epistatic interactions with many mutations, as is common to destabilizing mutations in soluble proteins. Surprisingly, W107A forms many positive (alleviating) epistatic interactions with other mutations. They further show that the locations of secondary mutations correlate with the types of epistatic interactions they form with the above two mutants.

Strengths:<br /> Such a high throughput study for epistasis in membrane proteins is pioneering, and the results are indeed illuminating. Examples of interesting findings are that: (1) No single mutation can dramatically rescue the destabilization introduced by W107A. (2) Epistasis with a secondary mutation is strongly influenced by the degree of destabilization introduced by the primary mutation. (3) Misfolding caused by mis-insertion tends to be aggravated by further mutations. The discussion of how protein folding energetics affects epistasis (Fig. 7) makes a lot of sense and lays out an interesting biophysical framework for the findings.

Weaknesses:<br /> The major weakness comes from the potential limitations in the measurements of surface expression of severely misfolded mutants. This point is discussed quite fairly in the paper, in statements like "the W107A variant already exhibits marginal surface immunostaining" and many others. It seems that only about 5% of the W107A makes it to the plasma membrane compared to wild-type (Figures 2 and 3). This might be a low starting point from which to accurately measure the effects of secondary mutations.

Still, the authors claim that measurements of W107A double mutants "still contain cellular subpopulations with surface immunostaining intensities that are well above or below that of the W107A single mutant, which suggests that this fluorescence signal is sensitive enough to detect subtle differences in the PME of these variants". I was not entirely convinced that this was true. Firstly, I think it would be important to test how much noise these measurements have and how much surface immunostaining the W107A mutant displays above the background of cells that do not express the protein at all. But more importantly, it is not clear if under this regimen surface expression still reports on stability/protein fitness. It is unknown if the W107A retains any function or folding at all. For example, it is possible that the low amount of surface protein represents misfolded receptors that escaped the ER quality control. The differential clustering of epistatic mutations (Fig. 6) provides some interesting insights as to the rules that dictate epistasis, but these too are dominated by the magnitude of destabilization caused by one of the mutations. In this case, the secondary mutations that had the most interesting epistasis were exceedingly destabilizing. With this in mind, it is hard to interpret the results that emerge regarding the epistatic interactions of W107A. Furthermore, the most significant positive epistasis is observed when W107A is combined with additional mutations that almost completely abolish surface expression. It is likely that either mutation destabilizes the protein beyond repair. Therefore, what we can learn from the fact that such mutations have positive epistasis is not clear to me. Based on this, I am not sure that another mutation that disrupts the tertiary folding more mildly would not yield different results.

With that said, I believe that the results regarding the epistasis of V276T with other mutations are strong and very interesting on their own.

Additionally, the study draws general conclusions from the characterization of only two mutations, W107A and V276T. At this point, it is hard to know if other mutations that perturb insertion or tertiary folding would behave similarly. This should be emphasized in the text.

Some statistical aspects of the study could be improved:

1. It would be nice to see the level of reproducibility of the biological replicates in a plot, such as scatter or similar, with correlation values that give a sense of the noise level of the measurements. This should be done before filtering out the inconsistent data.

2. The statements "Variants bearing mutations within the C- terminal region (ICL3-TMD6-ECL3-TMD7) fare consistently worse in the V276T background relative to WT (Fig. 4 B & E)." and "In contrast, mutations that are 210 better tolerated in the context of W107A mGnRHR are located 211 throughout the structure but are particularly abundant among residues 212 in the middle of the primary structure that form TMD4, ICL2, and ECL2 213 (Fig. 4 C & F)." are both hard to judge. Inspecting Figures 4B and C does not immediately show these trends, and importantly, a solid statistical test is missing here. In Figures 4E and F the locations of the different loops and TMs are not indicated on the structure, making these statements hard to judge.

3. The following statement lacks a statistical test: "Notably, these 98 variants are enriched with TMD variants (65% TMD) relative to the overall set of 251 variants (45% TMD)." Is this enrichment significant? Further in the same paragraph, the claim that "In contrast to the sparse epistasis that is generally observed between mutations within soluble proteins, these findings suggest a relatively large proportion of random mutations form epistatic interactions in the context of unstable mGnRHR variants". Needs to be backed by relevant data and statistics, or at least a reference.

Reviewer #2 (Public Review):

Members of the EphB family of tyrosine kinase receptors are involved in a multitude of diverse cellular functions, ranging from the control of axon growth to angiogenesis and synaptic plasticity. In order to provide these diverse functions, it is expected that these receptors interact in a cell-type specific manner with a diverse variety of downstream signalling molecules.

The authors have used proteomics approaches to characterise some of these molecules in further detail. This molecule, myc-binding protein 2 (MYCBP2) is also known as highwire, has been identified in the context of establishment of neural connectivity. Another molecule coming up on this screen was identified as FBXO45.

The authors use classical methods of co-IP to show a kinase-independent binding of MYCBP2 to EphB2. They further showed that FBXO45 within a ternary complex increased the stability of the EphB2/MYCBP2 complex.

To define the interacting domains, they used clearly designed swapping experiments to show that the extracellular and transmembrane domains are necessary and sufficient for the formation of the ternary complex.

Using a cellular contraction assay, the authors showed the necessity of MYCBP2 in mediating the cytoskeletal response of EphB2 forward signalling. Furthermore, they used the technically challenging stripe assay of alternating lanes of ephrinB-Fc and Fc to show that also in this migration-based essay MYCBP2 is required for EphB mediated differential migration pattern.

MYCBP2 in addition is necessary to stabilize EphB2, that is in the absence of MYCBP2, EphB2 is degraded in the lysosomal pathway.

Interestingly, the third protein in this complex, Fbxo45, was further characterized by overexpression of the domain of MYCBP2, known to interact with Fbxo45. Here the authors showed that this approach led to the disruption of the EphB2 / MYCBP2 complex, and also abolished the ephrinB mediated activation of EphB2 receptors and their differential outgrowth on ephrinB2-Fc / Fc stripes.

Finally, the authors demonstrated an in vivo function of this complex using another model system, C elegans where they were able to show a genetic interaction.

Data show in a nice set of experiments a novel level of EphB2 forward signalling where a ternary complex of this receptor with multifunctional MYCBP2 and Fbxo45 controls the activity of EphB2, allowing a further complex regulation of this important receptors. Additionally, the authors challenge pre-existing concepts of the function of MYCBP2 which might open up novel ways to think about this protein.<br /> Of interest is this work also in terms of development of the retinotectal projection in zebrafish where MYCBP2/highwire plays a crucial role, and thus might lead to a better understanding of patterning along the DV axis, for which it is known that EphB family members are crucial.

Overall, the experiments are classical experiments of co-immunoprecipitations, swapping experiments, collapse assays, and stripe assays which all are well carried out and are convincing.

Reviewer #2 (Public Review):

Summary:<br /> Transposable elements are known to have a strong potential to generate diversity and impact gene regulation, and they are thought to play an important role in plant adaptation to changing environments. Nevertheless, very few studies have performed genome-wide analyses to understand the global effect of selection on TEs in natural populations. Horvath et al. used available whole-genome re-sequencing data from a representative panel of B. distachyon accessions to detect TE insertion polymorphisms (TIPs) and estimate their time of origin. Using a thorough combination of population genomics approaches, the authors demonstrate that only a small amount of the TE polymorphisms are targeted by positive selection or potentially involved in adaptation. By comparing the age-adjusted population frequencies of TE polymorphisms and neutral SNPs, the authors found that retrotransposons are affected by purifying selection independently of their distance to genes. Finally, using forward simulations they were able to quantify the strength of selection acting on TE polymorphisms, finding that retrotransposons are mainly under moderate purifying selection, with only a minority of the insertions evolving neutrally.

Strengths:<br /> Horvath et al., use a convincing set of strategies, and their conclusions are well supported by the data. I think that incorporating polymorphism's age into the analysis of purifying selection is an interesting way to reduce the possible bias introduced by the fact that SNPs and TEs polymorphisms do not occur at the same pace. The fact that TE polymorphisms far from genes are also under purifying selection is an interesting result that reinforces the idea that the trans-regulatory effect of TE insertions might not be a rare phenomenon, a matter that may be demonstrated in future studies.

Weaknesses:<br /> TEs from different classes and orders strongly differ in multiple features such as size, the potential impact of close genes upon insertion, insertion/elimination ratio (ie, MITE/TIR excision, solo-LTR formation), or insertion preference. Given such diversity, it is expected that their survival rates on the genome and the strength of selection acting on them could be different. The authors differentiate DNA transposons and retrotransposons in some of the analyses, the specificities of the most abundant plant TE types (ie, LTR/Gypsy, LTR/Copia, MITE DNA transposons) are not considered.

The authors used a short-read-based approach to detect TIPs and TAPs. It is known that detecting TE polymorphisms is challenging and can lead to false negatives, depending on the method used and the sequencing coverage. The methodology used here (TEPID) has been previously applied to other species, but it is unclear if the sensitivity of the TIP/TAP caller is equivalent to that of the SNP caller and how these potential differences may affect the results.

Reviewer #2 (Public Review):

The Kinesin superfamily motors mediate the transport of a wide variety of cargos which are crucial for cells to develop into unique shapes and polarities. Kinesin-3 subfamily motors are among the most conserved and critical classes of kinesin motors which were shown to be self-inhibited in a monomeric state and dimerize to activate motility along microtubules. Recent studies have shown that different members of this family are uniquely activated by to undergo transition from monomers to dimers.

Niwa and colleagues study two well-described members of the kinesin-3 superfamily, unc104 and KLP6, to uncover the mechanism of monomer to dimer transition upon activation. Their studies reveal that although both Unc104 and KLP6 are both self-inhibited monomers, their propensities for forming dimers are quite different. The authors relate this difference to a region in the molecules called CC2 which has a higher propensity for forming homodimers. Unc104 readily forms homodimers if its self-inhibited state is disabled while KLP6 does not.

The work suggests that although mechanisms for self-inhibited monomeric states are similar, variations in the kinesin-3 dimerization may present a unique forms of kinesin-3 motor regulation with implications on the forms of motility functions carried out by these unique kinesin-3 motors.

Reviewer #2 (Public Review):

Hersperger et al. investigated the importance of Drosophila immune cells, called hemocytes, in the response to oxidative stress in adult flies. They found that hemocytes are essential in this response, and using state-of-the-art single-cell transcriptomics, they identified expression changes at the level of individual hemocytes. This allowed them to cluster hemocytes into subgroups with different responses, which certainly represents very valuable work. One of the clusters appears to respond directly to oxidative stress and shows a very specific expression response that could be related to the observed systemic metabolic changes and energy mobilization.

Using hemocyte-specific genetic manipulation, the authors convincingly show that the DNA damage response in hemocytes regulates JNK activity and subsequent expression of the JAK/STAT ligand Upd3. Silencing of the DNA damage response or excessive activation of JNK and Upd3 leads to increased susceptibility to oxidative stress. This nicely demonstrates the importance of tight control of JNK-Upd3 signaling in hemocytes during oxidative stress. The treatment the authors used is quite harsh, and in such a situation it is simply better not to use upd3 signaling, but it is still worth bearing in mind that upd3 signaling may have a protective role under milder stresses, but Upd3 could require very tight control - this could be an interesting objective for future studies.

The authors demonstrate that hemocytes play an important role in energy mobilization during oxidative stress, suggesting that control of energy mobilization by hemocytes is essential for the response. They further postulate that "hemocyte-derived upd3 is most likely released by the activated plasmatocyte cluster C6 during oxidative stress in vivo and is subsequently controlling energy mobilization and subsequent tissue wasting upon oxidative stress." It is important to note here that the association of upd3 with the observed changes in energy metabolism has not been tested, and the subsequent tissue wasting allegedly caused by excessive upd3 as a cause of death remains an open question.

Reviewer #2 (Public Review):

In this study, the authors tried to gauge the effect of human activity on three species, (1) the Hooded grow, an urban exploiter, (2) the Rose ring parakeet, an invasive, alien species that has adapted to exploit human resources, and (3) the Graceful prinia, an urban adapter, which is relatively shy of humans. A goal of the study was to increase awareness of the importance of urban parks.

Strengths:<br /> Strengths of the study include the fact that it was conducted at 17 different sites, including parks, roads and residential areas, and included three species with different habitat preferences. Each species produced relatively loud and repeatable vocalizations. To avoid the effect of seasonal changes, sounds were sampled within a 10 day period of the lockdown as well as post-lockdown. The analysis included a comparison of the number of sound files, binary values indicating emission of a common syllable, and also the total number of syllables emitted as a measurement of bird activity. Ambient temperatures and sound levels of human activity were also recorded. All of these factors speak to the comprehensive approach and analysis adopted in this study. The results are based on a rigorous statistical analysis, ruling out the effects of various extraneous parameters.

Weaknesses:<br /> Most significant changes may occur near the ambient noise levels and this could lead to a different conclusion, but the authors authors acknowledge this possibility and clarify that they only analyzed vocalizations with high signal-to-noise signals to avoid ambiguity. In the revised version, they also replaced the previous ambient noise parameter with an estimate of ambient noise under 1kHz, assuming that it reflects most anthropogenic noise (not restricted to human speech). This seems reasonable and this new model gave very similar results to the previous one.

In interpreting the data, the authors mention the effect of human activity on bird vocalizations in the context of inter-species predator-prey interactions; however, the presence of humans could also modify intraspecies interactions by acting as triggers for communication of warning and alarm, and/or food calls (as may sometimes be the case) to conspecifics. The behavioral significance of the syllables used to monitor animal activity could be informative in this context; however, the authors acknowledge this possibility in the Discussion. Most importantly, the authors acknowledge the possibility of the above-noted bias, and the potential of a transient nature of the observed effects.

Conclusion:<br /> In general, the authors achieved their aim of illustrating the complexity of the affect of human activity on animal behavior notwithstanding the caveats noted above. Their study also makes it clear that estimating such affects is not simple given the dynamics of animal behavior. For example, seasonality, temperature changes, animal migration and movement, as well as interspecies interactions, such as those related to predator-prey behavior, and inter/intra-species competition in other respects can all play into site-specific changes in the vocal activity of a particular species.

Reviewer #2 (Public Review):

Summary:<br /> Caflisch and coworkers investigate the methyltransferase activity of the complex of methyltransferase-like proteins 3 and 14 (METTL3-14). To obtain a high-resolution description of the complete catalytic cycle they have carefully designed a combination of experiments and simulations. Starting from the identification of bisubstrate analogues (BAs) as binders to stabilise a putative transition state of the reaction, they have determined multiple crystal structures and validated relevant interactions by mutagenesis and enzymatic assays.

Using the resolved structure and classical MD simulations they obtained a kinetic picture of the binding and release of the substrates. Of note, they accumulated very good statistics on these processes using 16 simulation replicates over a time scale of 500 ns. To compare the time scale of the release of the products with that of the catalytic step they performed state-of-the-art QM/MM free energy calculations (testing multiple levels of theory) and obtained a free energy barrier that indicates how the release of the product is slower than the catalytic step.

Strengths:<br /> All the work proceeds through clear hypothesis testing based on a combination of literature and new results. Eventually, this allows them to present in Figure 10 a detailed step-by-step description of the catalytic cycle. The work is very well crafted and executed.

Weaknesses:<br /> To fulfill its potential of guiding similar studies for other systems as well as to allow researchers to dig into their vast work, the authors should share the results of their simulations (trajectories, key structures, input files, protocols, and analysis) using repositories like Zenodo, the plumed-nest, figshare or alike.

Reviewer #2 (Public Review):

Summary:<br /> In this manuscript, the authors reveal that GIF/MT-3 regulates zinc homeostasis depending on the cellular redox status. The manuscript technically sounds, and their data concretely suggest that the recombinant MTs, not only GIF/MT-3 but also canonical MTs such as MT-1 and MT-2, contain sulfane sulfur atoms for the Zn-binding. The scenario proposed by the authors seems to be reasonable to explain the Zn homeostasis by the cellular redox balance.

Strengths:<br /> The data presented in the manuscript solidly reveal that recombinant GIF/MT-3 contains sulfane sulfur.

Weaknesses:<br /> It is still unclear whether native MTs, in particular, induced MTs in vivo contain sulfane sulfur or not.

Reviewer #2 (Public Review):

Summary:<br /> Bates TA. et al. studied the biochemical characteristics of ESAT-6, a major virulence factor of Mycobacterium tuberculosis (Mtb), as part of the heterodimer with CFP10, a molecular chaperon of ESAT-6, as in homodimer and in homotetramer using recombinant ESAT-6 and CFP10 expressed in E. coli by applying several biochemical assays including Biolayer Interferometry (BLI) assay. The main findings show that ESAT-6 forms a tight interaction with CFP10 as a heterodimer at neutral pH, and ESAT-6 forms homodimer and even tetramer-based larger molecular aggregates at acidic pH. Although the discussion of the potential problems associated with the contamination of ESAT-6 preparations with ASB-14 during the LPS removal step is interesting, this research does not test the potential impact of residual ASB-14 contaminant on the biochemical behavior ESAT-6-CFP10 heterodimer and ESAT-6 homodimer or tetramer and their hemolytic activity in comparison with the ones without ASB-14. The main strength of this study is the generation of ESAT-6 specific nanobodies and the demonstration of its anti-tuberculosis efficiency in THP-1 cell lines infected with Mtb strains with reporter genes.

Strengths:<br /> Generation and demonstration of the anti-ESAT-6 nanobodies against tuberculosis infection in a cell line based Mtb infection model.

Weaknesses:<br /> Although the biochemistry studies provide quantitative data about the interactions of ESAT-6 with its molecular chaperon CFP10 and the interaction of ESAT-6 homodimer and tetramers, the novel information from these studies is minimal.

Reviewer #2 (Public Review):

Summary:<br /> The paper entitled "PAK3 downregulation induces cognitive 1 impairment following cranial irradiation" by Lee et al. aimed at investigating the functional impact of cranial irradiation in mouse and propose PAK3 as molecular element involved in radiation-induced cognitive decrement. The results provided in this paper are problematic as both the irradiation paradigm (5X2 Gy) as well as the timing of investigation (3 to 8 days post-IR) are completely irrelevant to investigate radiation induced neurocognitive impairment. This testifies to the team's lack of knowledge in radiobiology/radiotherapy and the methodology to explore radiation induced neurocognitive damages. It precludes any further relevance of the molecular results.

Weaknesses:

First and according to the BED equation a single dose of 10 Gy cannot not be approximated by 5 fractions of 2 Gy, as fractionation is known to decrease normal tissue toxicity. Note that in radiobiology/radio-oncology, the BED stands for "Biologically Effective Dose." This equation is used to compare the effects of different radiation treatments on biological tissues, taking into account the dose, fractionation, and the overall biological response of the tissue to radiation.<br /> The BED equation is commonly used to calculate the equivalent dose of a fractionated radiation treatment, which is the dose that would produce the same biological effect as a single, higher dose delivered in a single fraction.<br /> The general formula for BED is:BED = D * (1 + d / α/β)<br /> D is the total physical dose of radiation delivered in Grays (Gy)<br /> d is the dose per fraction in Gy<br /> α/β is the tissue-specific ratio of the linear (α) and quadratic (β) components of the radiation response. It is measured in Gy and describes how the tissue responds to different fractionation schedules (usually equal to 3 for the normal brain).<br /> Please refer to radiobiology/radiotherapy textbooks by Hall or Joiner.

Second, the brain is a late responding organ. GBM patients treated with 60 Gy exhibit progressive and debilitating impairments in memory, attention and executive function several month post-irradiation. In mice, neurocognitive decrements after a single dose of 10 Gy delivered to the whole brain does occur at late time point, usually > 2 months post-exposure. Multiple publications such as the one by Limoli C lab, Rossi S lab, Britten R lab or earlier Fike J lab and Robin M lab support this. Next, 5 fractions of 2 Gy will be more protective than a single dose of 10 Gy and neurocognitive decrements will require at least 5-6 months to occur if they ever occur. In Figure 1, the decrement reported is marginal, the number of animals included (4 to 5 at most?) The number of animals is not specified) is too low to draw any significant conclusions. In addition to the timing issue, the strategy described for NOR analysis shows methodological issues with the habituation period being too short and exploration level being very low.

Reviewer #2 (Public Review):

Summary: In this paper, Portillo-Ledesma et al. study chromatin organization in the length scale of a gene, simulating the polymer at nucleosome resolution. The authors have presented an extensive simulation study with an excellent model of chromatin. The model has linker DNA and nucleosomes with all relevant interactions (electrostatics, tails, etc). Authors simulate 10 to 26 kb chromatin with varying linker lengths, linker histones (LH), and acetylated tails. The authors then study the effect of a transcription factor (TF) Myc: Max binding. The critical physical feature of the TF in the model is that it binds to the linker region and bends the DNA to make loops/intra-chromatin contacts. Authors systematically investigate the interplay between different variables such as linker DNA length, LH density, and the TF concentration in determining chromatin compaction and 3D organization.

Strengths: The manuscript is well-written and is a relevant study with many useful results. The biggest strength of the work is the fact that the authors start with a relevant model that incorporates well-known biophysical properties of DNA, nucleosomes, linker histones, and the transcription factor Myc:Max. One of the novel results is the demonstration of how linker lengths play an important role in chromatin compaction (measured by computing packing ratio) in the presence of DNA-bending TFs. As the TF concentration increases, chromatin with short linker lengths does not compact much (only a small change in packing ratio). If the linker lengths are long, a higher percentage of TFs leads to an increase in packing ratio (higher compaction). Authors further show that TFs are able to compact Life-like chromatin fiber with linker length taken from a realistic distribution. The authors compute inter-nucleosomal contact maps from their simulated configurations and show that the map has features similar to what is observed in Hi-C/Micro-C experiments. Authors study the compaction of the Eed gene locus and show that TF binding leads to the formation of small domains known as micro-domains. Authors have predicted many relevant and testable quantities. Many of the results agree with known experiments like the formation of the micro-domains. Hence, the conclusions made in this study are justified - they follow from the simulation results.

Weaknesses: (1) While this has the advantage of a minimal model (model with minimal factors incorporated), it is a disadvantage for predicting in vivo organization; one might need to incorporate the action of many other proteins (for example, PRC, HP1, etc) and several other histone modifications to predict in vivo organization. (2) While this forward model produces features of relevant contact maps, one would need to tune some of the intra-chromatin interaction parameters to obtain an accurate contact map and radius of gyration.

Reviewer #2 (Public Review):

Strengths:<br /> The authors have conducted a large, well-designed experiment to test the response to eCO2. Overall, the experimental design is sound and appropriate for the questions about how a change in CO2 affects the ionome of Arabidopsis. Most of the conclusions in this area are well supported by the data that the authors present.

Weakness:<br /> While the authors have done good experiments, it is a big stretch from Arabidopsis grown in an arbitrary concentration of CO2 to relevance to human and animal nutrition in future climates. Arabidopsis is a great model plant, but its leaves are not generally eaten by humans or animals.

The authors don't justify their choice of a CO2 concentration. Given the importance of the parameter for the experiment, the rationale for selecting 900 ppm as elevated CO2 compared to any other concentration should be addressed. And CO2 is just one of the variables that plants will have to contend with in future climates, other variables will also affect elemental concentrations.

Given these concerns, I think the emphasis on biofortification for future climates is unwarranted for this study.

Additionally, I have trouble with these conclusions:

-Abstract "Finally, we demonstrate that manipulating the function of one of these genes can mitigate the negative effect of elevated CO2 on the plant mineral composition. "<br /> -Discussion "Consistent with these results, we show that manipulating TIP2;2 expressions with a knock-out mutant can modulate the Zn loss observed under high CO2."

The authors have not included the data to support this conclusion as stated. They have shown that this mutant increases the Zn content of the leaves when compared to WT but have not demonstrated that this response is different than in ambient CO2. This is an important distinction: one way to ameliorate the reduction of nutrients due to eCO2 is to try to identify genes that are involved in the mechanism of eCO2-induced reduction. Another way is to increase the concentration of nutrients so that the eCO2-induced reduction is not as important (i.e. a 10% reduction in Zn due to eCO2 is not as important if you have increased the baseline Zn concentration by 20%). The authors identified tip2 as a target from the GWAS on difference, but their validation experiment only looks at eCO2.

Reviewer #2 (Public Review):

In this study, the authors utilize a compendium of public genomic data to identify transcription factors (TF) that can identify their DNA binding motifs in the presence of nuclosome-wrapped chromatin and convert the chromatin to open chromatin. This class of TFs are termed Pioneer TFs (PTFs). A major strength of the study is the concept, whose premise is that motifs bound by PTFs (assessed by ChIP-seq for the respective TFs) should be present in both "closed" nucleosome wrapped DNA regions (measured by MNase-seq) as well as open regions (measured by DNAseI-seq) because the PTFs are able to open the chromatin. Use of multiple ENCODE cell lines, including the H1 stem cell line, enabled the authors to assess if binding at motifs changes from closed to open. Typical, non-PTF TFs are expected to only bind motifs in open chromatin regions (measured by DNaseI-seq) and not in regions closed in any cell type. This study contributes to the field a validation of PTFs that are already known to have pioneering activity and presents an interesting approach to quantify PTF activity.

For this reviewer, there were a few notable limitations. One was the uncertainty regarding whether expression of the respective TFs across cell types was taken into account. This would help inform if a TF would be able to open chromatin. Another limitation was the cell types used. While understandable that these cell types were used, because of their deep epigenetic phenotyping and public availability, they are mostly transformed and do not bear close similarity to lineages in a healthy organism. Next, the methods used to identify PTFs were not made available in an easy-to-use tool for other researchers who may seek to identify PTFs in their cell type(s) of interest. Lastly, some terms used were not define explicitly (e.g., meaning of dyads) and the language in the manuscript was often difficult to follow and contained improper English grammar.

Reviewer #2 (Public Review):

Summary:

In this manuscript, Yu and colleagues sought to identify new susceptibility genes for adolescent idiopathic scoliosis (AIS). Significance for this work is high, especially given the still large knowledge gap of the mechanistic underpinnings for AIS. In this multidisciplinary body of work, the authors first performed a genetic association study of AIS case-control cohorts (combined 9,161 cases and 80,731 controls) which leveraged common SNPs in 1027 previously defined matrisome genes. Two nonsynonymous variants were found to be significantly associated with AIS: MMP14 p.Asp273Asn and COL11A1 p.Pro1153Leu, the latter of which had the more robust association and remained significant when females were tested independent of males. Next, the authors followed a series of functional validation experiments to support biological involvement of COL11A1 p.Pro1153Leu in AIS through expression, biochemical, and histological studies in physiologically relevant cell and mouse models. Together, the authors propose a hitherto unreported model for AIS that involves the interplay of the COL11A1 susceptibility locus with estrogen signaling to alter a Pax1-Col11a1-Mmp3 signaling axis at the growth plate.

Strengths:

The manuscript is clearly written and follows a series of logical steps toward connecting multiple matrisome genes and putative AIS effectors in a new framework of pathomechanism. The multidisciplinary nature of the work makes it a strong body of work wherein multiple models offer multiple lines of supportive data.

Weaknesses:

This manuscript remains an important multidisciplinary study of the genetic and functional basis of adolescent idiopathic scoliosis (AIS). To the benefit of the overall manuscript quality, the reviewers have addressed most concerns to satisfaction. I have a few remaining suggestions:

1. Regarding the genetic association of the common COL11A1 variant rs3753841, p.Pro1335Leu, please soften this statement to indicate that the variant could be a "risk locus" rather than "causal" in the following sentence on page 7-8: "These observations suggested that rs3753841 itself could be causal, although our methods would not detect deep intronic variants that could contribute to the overall association signal."

2. Include the list of three rare missense variants mentioned in the response to reviewers as a supplementary table. Please also include methods for the SKATO rare variant burden analysis.

3. Thank you for addressing the question of whether p.Pro1335Leu is a loss of function, gain of function, or dominant negative variant. The rationale in the response to reviewers was helpful, so please include this line of reasoning, and that there remains uncertainty, in the Discussion of the main text of the manuscript.

Reviewer #2 (Public Review):

Summary:

In this article, the authors employed modified CRISPR screens ["guide-only (GO)-CRISPR"] in the attempt to identify the genes which may mediate cancer cell dormancy in the high grade serous ovarian cancer (HGSOC) spheroid culture models. Using this approach, they observed that abrogation of several of the components of the netrin (e.g., DCC, UNC5Hs) and MAPK pathways compromise the survival of non-proliferative ovarian cancer cells. This strategy was complemented by the RNAseq approach which revealed that a number of the components of the netrin pathway are upregulated in non-proliferative ovarian cancer cells and that their overexpression is lost upon disruption of DYRK1A kinase that has been previously demonstrated to play a major role in survival of these cells. Perampalam et al. then employed a battery of cell biology approaches to support the model whereby the Netrin signaling governs the MEK-ERK axis to support survival of non-proliferative ovarian cancer cells. Moreover, the authors show that overexpression of Netrins 1 and 3 bolsters dissemination of ovarian cancer cells in the xenograft mouse model, while also providing evidence that high levels of the aforementioned factors are associated with poor prognosis of HGSOC patients.

Strengths:

Overall it was thought that this study is of potentially broad interest inasmuch as it provides previously unappreciated insights into the potential molecular underpinnings of cancer cell dormancy, which has been associated with therapy resistance, disease dissemination, and relapse as well as poor prognosis. Notwithstanding the potential limitations of cellular models in mimicking cancer cell dormancy, it was thought that the authors provided sufficient support for their model that netrin signaling drives survival of non-proliferating ovarian cancer cells and their dissemination. Collectively, it was thought that these findings hold a promise to significantly contribute to the understanding of the molecular mechanisms of cancer cell dormancy and in the long term may provide a molecular basis to address this emerging major issue in the clinical practice.

Weaknesses:

Several issues were observed regarding methodology and data interpretation. The major concerns were related to the reliability of modelling cancer cell dormancy. To this end, it was relatively hard to appreciate how the employed spheroid model allows to distinguish between dormant and e.g., quiescent or even senescent cells. This was in contrast to solid evidence that netrin signaling stimulates abdominal dissemination of ovarian cancer cells in the mouse xenograft and their survival in organoid culture. Moreover, the role of ERK in mediating the effects of netrin signaling in the context of the survival of non-proliferative ovarian cancer cells was found to be somewhat underdeveloped.

Reviewer #2 (Public Review):

Summary:<br /> This study seeks to advance our knowledge of how vitamin D may be protective in allergic airway disease in both adult and neonatal mouse models. The rationale and starting point are important human clinical, genetic/bioinformatic data, with a proposed role for vitamin D regulation of 2 human chromosomal loci (Chr17q12-21.1 and Chr17q21.2) linked to the risk of immune-mediated/inflammatory disease. The authors have made significant contributions to this work specifically in airway disease/asthma. They link these data to propose a role for vitamin D in regulating IL-2 in Th2 cells implicating genes associated with these loci in this process.

Strengths:<br /> Here the authors draw together evidence form. multiple lines of investigation to propose that amongst murine CD4+ T cell populations, Th2 cells express high levels of VDR, and that vitamin D regulates many of the genes on the chromosomal loci identified to be of interest, in these cells. The bottom line is the proposal that vitamin D, via Ikfz3/Aiolos, suppresses IL-2 signalling and reduces IL-2 signalling in Th2 cells. This is a novel concept and whilst the availability of IL-2 and the control of IL-2 signalling is generally thought to play a role in the capacity of vitamin D to modulate both effector and especially regulatory T cell populations, this study provides new data.

Weaknesses:<br /> Overall, this is a highly complicated paper with numerous strands of investigation, methodologies etc. It is not "easy" reading to follow the logic between each series of experiments and also frequently fine detail of many of the experimental systems used (too numerous to list), which will likely frustrate immunologists interested in this. There is already extensive scientific literature on many aspects of the work presented, much of which is not acknowledged and largely ignored. For example, reports on the effects of vitamin D on Th2 cells are highly contradictory, especially in vitro, even though most studies agree that in vivo effects are largely protective. Similarly other reports on adult and neonatal models of vitamin D and modulation of allergic airway disease are not referenced. In summary, the data presentation is unwieldy, with numerous supplementary additions, that makes the data difficult to evaluate and the central message lost. Whilst there are novel data of interest to the vitamin D and wider community, this manuscript would benefit from editing to make it much more readily accessible to the reader.

Wider impact: Strategies to target the IL-2 pathway have long been considered and there is a wealth of knowledge here in autoimmune disease, transplantation, GvHD etc - with some great messages pertinent to the current study. This includes the use of IL-2, including low dose IL-2 to boost Treg but not effector T cell populations, to engineered molecules to target IL-2/IL-2R.

Reviewer #2 (Public Review):

Summary:

This manuscript from Liu et al. examines the role of Fat and Dachsous, two transmembrane proto-cadherins that function both in planar cell polarity and in tissue growth control mediated by the Hippo pathway. The authors developed a new method for measuring growth of the wing imaginal disc during late larval development and then used this approach to examine the effects of disruption of Fat/Dachsous function on disc growth. The authors show that during mid to late third instar the wing imaginal disc normally grows in a linear rather than exponential fashion and that this occurs due to slowing of the mitotic cell cycle as the disc grows during this period. Consistent with their known role in regulating Hippo pathway activity, this slowing of growth is disrupted by loss of Fat/Dachsous function. The authors also observed a previously unreported gradient of Fat protein across the wing blade. However, graded expression of Fat or Dachsous is not necessary for proper growth regulation in the late third instar because ectopic Dachsous expression, which affects gradients of both Dachsous and Fat, has no growth phenotype.

Strengths:

Although the role of the Hippo pathway in growth control has been extensively studied, our understanding of how the pathway controls growth during normal development remains relatively weak. This work addresses this question by examining normal growth of the wing imaginal disc during part of its development in the larva and characterizing the effects of Fat/Dachsous manipulation on that growth. The authors developed tools for measuring wing growth by measuring wing volume, an approach that could be useful in future studies of tissue growth.

Weaknesses:

1) Although the approach used to measure volume is new to this study, the basic finding that imaginal disc growth slows at the mid-third instar stage has been known for some time from studies that counted disc cell number during larval development (Fain and Stevens, 1982; Graves and Schubiger, 1982). Although these studies did not directly measure disc volume, because cell size in the disc is not known to change during larval development, cell number is an accurate measure of tissue volume. However, it is worth noting that the approach used here does potentially allow for differential growth of different regions of the disc.

2) Related to point 1, a main conclusion of this study, that cell cycle length scales with growth of the wing, is based on a developmentally limited analysis that is restricted to the mid-third instar larval stage and later (early third instar begins at 72 hr - the authors' analysis started at 84 hr). The previous studies cited above made measurements from the beginning of the 3rd instar and combined them with previous histological analyses of cell numbers starting at the beginning of the 2nd instar. Interestingly, both studies found that cell number increases exponentially from the start of the 2nd instar until mid-third instar, and only after that point does the cell cycle slow resulting in the linear growth reported here. The current study states that growth is linear due to scaling of cell cycle with disc size as though this is a general principle, but from the earlier studies, this is not the case earlier in disc development and instead applies only to the last day of larval life.

3) The analysis of the roles of Fat and Dachsous presented here has weaknesses that should be addressed. It is very curious that the authors found that depletion of Fat by RNAi in the wing blade had essentially no effect on growth while depletion of Dachsous did, given that the loss of function overgrowth phenotype of null mutations in fat is more severe than that of null mutations in dachsous (Matakatsu and Blair, 2006). An obvious possibility is that the Fat RNAi transgene employed in these experiments is not very efficient. The authors tried to address this by doubling the dose of the transgene, but it is not clear to me that this approach is known to be effective. The authors should test other RNAi transgenes and additionally include an analysis of growth of discs from animals homozygous for null alleles, which as they note survive to the late larval stages.

4) It is surprising that the authors detect a gradient of Fat expression that has not been seen previously given that this protein has been extensively studied. It is also surprising that they find that expression of Nubbin Gal4 is graded across the wing blade given that previous studies indicate that it is uniform (ie. Martín et al. 2004). These two surprising findings raise the possibility that the quantification of fluorescence could be inaccurate. The curvature of the wing blade makes it a challenging tissue to image, particularly for quantitative measurements.

5) Overall, in my view the impact of these findings is limited. The focus on growth solely at the end of larval development, when there are a number of potentially confounding variables (for example hormonal cues), makes the generality of the findings reported here difficult to judge. Additionally, the functional analysis of Fat/Dachsous function in this process is limited - for example does disruption of other Hippo pathway components have a similar effect?

Reviewer #2 (Public Review):

In the main text, the authors apply their metrics to a data set that was published by Mira et al. in 2015. The data consist of growth rate measurements for a combinatorially complete set of 16 genetic variants of the antibiotic resistance enzyme beta-lactamase across 10 drugs and drug combinations at 3 different drug concentrations, comprising a total of 30 different environmental conditions. In my previous report I had asked the authors to specify why they selected only 7 out of 30 environments for their analysis, with only one concentration for drug, but a clear explanation is still lacking. In the Data section of Material and Methods, the authors describe their criterion for data selection as follows: "we focus our analyses on drug treatments that had a significant negative effect on the growth of wildtype/TEM-1 strains". However, in Figure 2 it is seen that, even for the selected data sets, not all points are significant compared to wild type (grey points). So what criterion was actually applied?

In effect, for each chosen drug or drug combination, the authors choose the data set corresponding to the highest drug concentration. As a consequence, they cannot assess to what extent their metrics depend on drug concentration. This is a major concern, since Mira et al. concluded in their study that the differences between growth rate landscapes measured at different concentrations were comparable to the differences between drugs. I argued before that, if the new metrics display a significant dependence on drug concentration, this would considerably limit their usefulness. The authors challenge this, saying in their rebuttal that "no, that drug concentration would<br /> be a major actor in the value of the metrics does not limit the utility of the metric. It is simply another variable that one can consider when computing the metrics." While this is true in principle, I don't think any practicing scientist would disagree with the statement that the existence of additional confounding factors (in particular if they are unknown) reduces the usefulness<br /> of a quantitative metric.

As a consequence of the small number of variant-drug-combinations that are used, the conclusions that the authors draw from their analysis are mostly tentative. For example, on line 123 the authors write that the observation that<br /> the treatment of highest drug applicability is a combination of two drugs "fits intuition". In the Discussion this statement is partly retracted with reference to the piperacillin/tazobactam-combination which has low drug applicability. Being based on only a handful of data points, both observations are essentially anecdotal and it is unclear what the reader is supposed to learn.

To assess the environment-dependent epistasis among the genetic mutations comprising the variants under study, the authors decompose the data of Mira et al. into epistatic interactions of different orders. This part of the analysis is incomplete in two ways. First, in their study, Mira et al. pointed out that a fairly large fraction of the fitness differences between variants that they measured were not statistically significant. This information has been removed in the depiction of the Mira et al. fitness landscapes in Figure 1 of the present manuscript, and it does not seem to be reflected in the results of the interaction analysis in Figure 4. Second, the interpretation of the coefficients obtained from the epistatic decomposition depends strongly on the formalism that is being used. In a note added on page 15 of the revised manuscript, the authors write that they have used the LASSO regression for their analysis and refer the reader to a previous publication (Guerrero et al. 2019) which however (as far as I could see) also does not fully explain how the method works. To give an example of the difficulty of interpreting the data in Figure 4 without further information: The substitution C (G238S) is well known to have a strong positive effective in cefotaxime, but the corresponding coefficient is essentially zero. So whatever the LASSO regression does, it cannot simply measure the effect on growth.

Reviewer #2 (Public Review):

Summary:<br /> Gaikwad et al. investigated the role of eIF2A in translational response to stress in yeast. For this purpose, the authors conducted ribosome profiling under SM treatment in an eIF2A-depleted strain. Data analysis revealed that eIF2A did not influence translation from mRNAs bearing uORFs or cellular IRESes, in the stress condition, broadly. The authors found that only a small number of mRNAs were supported by eIF2A. The data should be helpful for researchers in the field.

Major points:<br /> 1. The weakness of this work is the lack of clarification on the function of eIF2A in general. The novelty of this study was limited.

2. Related to this, it would be worth investigating common features in mRNAs selectively regulated (surveyed in Figure 3A). Also, it would be worth analyzing the effect of eIF2A deletion on elongation (ribosome occupancy on each codon and/or global ribosome footprint distribution along CDS) and termination/recycling (footprint reads on stop codon and on 3′ UTR).

3. Regarding Figure 3D, the reporters were designed to include promoter and 5′ UTR of the target genes. Thus, it should be worth noting that reporter design was based on the assumption that eIF2A-dependency in translation regulation was not dependent on 3′ UTR or CDS region. The reason why the effects on ribosome profiling-supported mRNAs could not be recapitulated in reporter assay may originate from this design. This should be also discussed.

4. Related to the point above, the authors claimed that eIF2A affects "possibly only one" (HKR1) mRNA. However, this was due to the reporter assay which is technically variable and could not allow some of the constructs to pass the authors' threshold. Alternative wording for this point should be considered.

5. For Figure 3D, it would be worth considering testing the #-marked genes (in Figure 3C) in this set up.

6. In box plots, the authors should provide the statistical tests, at least where the authors explained in the main text.

Reviewer #2 (Public Review):

Summary:

The authors describe the discovery of a filovirus neutralizing antibody, AF03, by phage display, and its subsequent improvements to include NPC2 that resulted in a greater breadth of neutralization. Overall, the manuscript would benefit from considerable grammatical review, which would improve the communication of each point to the reader. The authors do not convincingly map the AF03 epitope, nor do they provide any strong support for their assumption that AF03 targets the NPC1 binding site. However, the authors do show that AF03 competes for MR78 binding to its epitope, and provides good support for the internalization of AF03-NL as the mechanism for improved breadth over the original AF03 antibody.

Strengths:

This study shows convincing binding to Marburgvirus GP and neutralization of Marburg viruses by AF03, as well as convincing neutralization of Ebolaviruses by AF03-NL. While there are no distinct populations of PE-stained cells shown by FACS in Figure 5A, the cell staining data in Figure 5C are compelling to a non-expert in endosomal staining like me. The control experiments in Figure 7 are compelling showing neutralization by AF03-NL but not AF03 or NPC2 alone or in combination. Altogether these data support the internalisation and stabilisation mechanism that is proposed for the gain in neutralization breadth observed for Ebolaviruses by AF03-NL over AF03 alone.

Weaknesses:

Overall, this reviewer is of the opinion that this paper is constructed haphazardly. For instance, the neutralization of mutant pseudoviruses is shown in Figure 2 before the concept of pseudovirus neutralization by AF03 is introduced in Figure 3. Similarly, the control experiments for AF03+NPC2 are described in Figure 7 after the data for breadth of neutralization are shown in Figure 6. GP quality controls are shown in Figure 2 after GP ELISAs / BLI experiments are done in Figure 1. This is disorienting for the reader.

Figure 1: The visualisation of AF03 modelling and docking endeavours is extremely difficult to interpret. Firstly, there is no effort to orient the non-specialist reader with respect to the Marburgvirus GP model. Secondly, from the figures presented it is impossible to tell if the Fv docks perfectly onto the GP surface, or if there are violent clashes between the deeply penetrating AF03 CDRs and GP. This information would be better presented on a white background, perhaps showing GP in surface view from multiple angles and slices. The authors attempt to label potential interactions, but these are impossible to read, and labels should be added separately to appropriately oriented zoomed-in views.

Figure 2: The neutralization of mutant pseudoviruses cannot be properly assessed using bar graphs. These data should be plotted as neutralization curves as they were done for the wild-type neutralization data in Figure 3. The authors conclude that Q128 & N129 are contact residues, but the neutralization data for this mutant appear odd as the lowest two concentrations of AF03 show higher neutralization than the second highest AF03 concentration. Neutralization of T204/Q205/T206 (green), Y218 (orange), K222 (blue), or C226 (purple) appears to be better than neutralization of the wild-type MARV. The authors do not discuss this oddity. What are the IC50's? The omission of antibody concentrations on the x-axis and missing IC50 values give a sense of obscuring the data, and the manuscript would benefit from greater transparency, and be much easier to interpret if these were included. I am intrigued that the Q128S/N129S mutant is reported as having little effect on the neutralization of MR78. The bar graph appears to show some effect (difficult to interpret without neutralization curves and IC50 data), and indeed PDB:5UQY seems to suggest that these amino acids form a central component of the MR78 epitope (Q128 forms potential hydrogen bonds with CDRH1 Y35 and CDRL3 Y91, while N129 packs against the MR78 CDRH3 and potentially makes additional polar contact with the backbone). Lastly, since neutralization was tested in both HEK293T cells and Huh7 cells in Figure 3, the authors should clarify which cells were used for neutralization in Figure 2.

Figure 3: The first two images in Figure 3C showing bioluminescent intensity from pseudovirus-injected mice pretreated with either 10mg/kg or 3mg/kg AF03 are identical images. This is apparent from the location, shape, and intensity of the bioluminescence, as well as the identical foot placement of each mouse in these two panels. Currently, this figure is incomplete and should be corrected to show the different mice treated with either 10mg/kg or 3mg/kg of AF03.

Figure 4 would benefit from a control experiment without antibodies comparing infection with GP-cleaved and GP-uncleaved pseudoviruses. The paragraph describing these data was also difficult to read and would benefit from additional grammatical review.

Figure 5: The authors should clarify in the methods section that the "mock" experiment included the PE anti-human IgG Fc antibody. Without this clarification, the lack of a distinct negative population in the FACS data could be interpreted as non-specific staining with PE. If the PE antibody was added at an equivalent concentration to all panels, what does the directionality of the arrowheads in Figure 5A (labelled PE) and 5B (labelled pHrodo Red) indicate?

Figure 6B: These data would benefit from the inclusion of IC50, transparency of antibody concentrations used, and consistency in the direction of antibody concentrations (increasing to the right or left of the x-axis) when compared to Figure 2.

Reviewer #2 (Public Review):

Summary:

Mandal et al. use WASP-deficient T cells to study the role of WASP in T cell signaling and activation and tying WASP to mechanosensing in T cells. Using both CD8 and CD4 T cells from WASP-deficient animals, the authors show defects in T cell signaling and function as well as defects in mechanosensing in activated CD8 T cells.

Strengths:

Confirming findings from many previous studies, Mandal et al. demonstrate that WASP-deficiency in T cells leads to defective T cell function (Figs 1, 2, 3, and 4). Fig 3 shows direct effects of mechanical stress on CD8 T cell signaling in the absence of WASP.

Weaknesses:

The title does not reflect the data presented as the only data demonstrating a role for WASP in mechanosensing in this manuscript doesn't directly connect WASP mechanosensing with tumors (Fig 3). The results shown in Fig 1 using an actin inhibitor doesn't directly connect WASP with mechanosensing. Fig 4 uses WASP-deficient animals in a tumor model, but doesn't demonstrate any role for mechanosensing in the WASP-deficient animals. The title should reflect the lack of data connecting WASP in mechanosensing to a tumor context.

One major oversight is the absence of discussion of a previous publication demonstrating a direct role of WASP in mechanosensing to the actin cytoskeleton in dendritic cells and naive CD4 and CD8 T cells (Gaertner et al. Dev Cell 2022). There should be a discussion of how the findings in Gaertner et al. shed light on the results from this manuscript.

The use of Myca to disrupt the actin cytoskeleton as a "modulator of stiffness" is problematic. While one of the potential effects of disrupting the actin cytoskeleton is changing stiffness, as shown in Figure 1, many other functions are simultaneously disturbed also. The use of B16 tumor cells is simply for antigen presentation, and not in a tumor context, so generalized statements about "stiffness" or "softness" and "tumor cells" in reference to Figure 1 should be changed to account for these alternative explanations.

Fig S2 shows Myca treatment of BMDCs leads to decreased functionality of OTII CD4s. Interpretation in the manuscript claims "This indicates that leaching of Myca from treated cells does not cause inhibition of bystander cells". This would not be my interpretation of the data. An alternative interpretation is that if Myca is remaining in the media, then effects on APCS (either BMDCs or B16s) could lead to decreased CD4 or CD8 T cell activation and thus be responsible for effects seen in Fig 1. This possibility should be considered.

Fig 4 claims that high rigidity leads to downstream effects of WASP-/- T cell function. But there is no demonstration of the role of mechanosensing in Figure 4. To make this claim, the authors would need to compare high and low rigidity conditions.

Fig 4 also shows that WASP-/- showed higher tumor growth in an implanted tumor model. For 4F, since WASP is deficient in all hematopoietic cells, the finding in 4G may not be due to T cells. In 4H-J, because implantation of tumors occurs within 1 day of lymphodepletion and assessing tumor growth prior to reconstitution of the hematopoietic compartment, there should be control experiments shown to demonstrate that other hematopoietic cell types that remain are not function and thus do not participate in the differences seen in tumor growth. Also, statistical tests need to be done to show the significance of the differences between groups in Fig 4I and 4J (also 4G).

Reviewer #2 (Public Review):

Summary:

The main purpose of this investigation was to 1) compare the effects of a single knockout (sKO) of Numb or a double knockout (dKO) of Numb and NumbL on ex-vivo physiological properties of the extensor digitorium longus (EDL) muscle in C57BL/6NCrl mice; and 2) analyze protein complexes isolated from C2C12 myotubes via immunoprecipitation and LC/MS/MS for potential Numb binding partners. The main findings are 1) the muscles from sKO and dKO were significantly weaker with little difference between the sKO and dKO lines, indicating the reduced force is mainly due to the inactivation of the Numb gene; and 2) there were 11 potential Numb binding proteins that were identified and cytoskeletal specific proteins including Septin 7.

Strengths:

Straight-forward yet elegant design to help determine the important role the Numb has in skeletal muscle.

Weaknesses:

There were a limited number of samples (3-6) that were used for the physiological experiments; however, there was a very large effect size in terms of differences in muscle tension development between the induced KO models and the controls.

Reviewer #2 (Public Review):

Summary:

In this manuscript, the authors developed an open-top two-photon light sheet microscopy (OT-TP-LSM) that enables high-throughput and high-depth investigation of 3D cell structures. The data presented here shows that OT-T-LSM could be a complementary technique to traditional imaging workflows of human cancer cells.

Strengths:

High-speed and high-depth imaging of human cells in an open-top configuration is the main strength of the presented study. An extended depth of field of 180 µm in 0.9 µm thickness was achieved together with an acquisition of 0.24 mm2/s. This was confirmed by 3D visualization of human cancer cells in the skin, pancreas, and prostate.

Weaknesses:

The complementary aspect of the presented technique in human pathological samples is not convincingly presented. The traditional hematoxylin and eosin (H&E) staining is a well-established and widely used technique to detect human cancer cells. What would be the benefit of 3D cell visualization in an OT-TP-LSM microscope for cancer detection in addition to H&E staining?

Reviewer #2 (Public Review):

The authors provide convincing evidence that optogenetic stimulation of ChR2-expressing motor neurons implanted in muscles effectively restore innervation of severely affected skeletal muscles in the aggressive SOD1 mouse model of ALS, and concluded that this method can be applied to selectively control the function of implicated muscles, which was supported by convincing data presented in the paper.

Reviewer #2 (Public Review):

Summary:

The authors use single-cell "multi-comics" to study clonal heterogeneity in chronic myeloid leukemia (CML) and its impact on treatment response and resistance. Their main results suggest 1) Cell compartments and gene expression signatures both shared in CML cells (versus normal), yet 2) some heterogeneity of multiomic mapping correlated with ELN treatment response; 3) further definition of s unique combination of CD26 and CD35 surface markers associated with gene expression defined BCR::ABL1+ LSCs and BCR::ABL1- HSCs. The manuscript is well-written, and the method and figures are clear and informative. The results fit the expanding view of cancer and its therapy as a complex Darwinian exercise of clonal heterogeneity and the selective pressures of treatments.

Strengths:

Cutting-edge technology by one of the expert groups of single-cell 'comics.

Weaknesses:

Very small sample sizes, without a validation set.<br /> The obvious main problem with the study is that an enormous amount of results and conjecture arise from a very small data set: only nine cases for the treatment response section (three in each of the ELN categories), only two normal marrows, and only two patient cases for the division kinetic studies. Thus, it is very difficult to know the "noise" in the system - the stability of clusters and gene expression and the normal variation one might expect, versus patterns that may be reproducibly study artifact, effects of gene expression from freezing-thawing, time on the bench, antibody labeling, etc. This is not so much a criticism as a statement of reality: these elegant experiments are difficult, time-consuming, and very expensive. Thus in the Discussion, it would be helpful for the authors to just frankly lay out these limitations for the reader to consider. Also in the Discussion, it would be interesting for the authors to consider what's next: what type of validation would be needed to make these studies translatable to the clinic? Is there a clever way to use these data to design a faster/cheaper assay?

Reviewer #2 (Public Review):

Summary:

This manuscript provides important new findings regarding the connection between inflammation and metabolism. It also identifies a new type of post-translational modification and its connection to protein stability. This finding is expected to be generalizable to other protein targets. In vitro evidence is solid. In vivo evidence needs some additional controls.

Strengths:

A new connection between inflammation and metabolism.

A novel type of PTM was identified.

Findings would be of broad interest and the mechanisms are likely generalizable to related control systems.

In vitro data are well-supported.

The authors successfully demonstrated that treatment with 4-octyl Itaconate (4-OI), a prodrug form of itaconate, reduces neutral lipid accumulation in the AML12 cell line and primary hepatocytes. They show that 4-OI promotes fatty acid beta-oxidation through increased stability of CPT1a protein, the rate-limiting step in this process.

Weaknesses:

Some conclusions involving the Irg1 knockout mice require important controls and clarifications to be fully convincing and some controls are missing.

Reviewer #2 (Public Review):

Summary:

The goal of untargeted metabolomics is to identify differences between metabolomes of different biological samples. Untargeted metabolomics identifies features with specific mass-to-charge ratio (m/z) and retention time (RT). Matching those to specific metabolites based on the model compounds from databases is laborious and not always possible, which is why methods for comparing samples on the level of unmatched features are crucial.

The main purpose of the GromovMatcher method presented here is to merge and compare untargeted metabolomes from different experiments. These larger datasets could then be used to advance biological analyses, for example, for the identification of metabolic disease markers. The main problem that complicates merging different experiments is m/z and RT vary slightly for the same feature (metabolite).

The main idea behind the GromovMatcher is built on the assumption that if two features match between two datasets (that feature i from dataset 1 matches feature j from dataset 2, and feature k from dataset 1 matches feature l from dataset 2), then the correlations or distances between the two features within each of the datasets (i and k, and j and l) will be similar. The authors then use the Gromov-Wasserstein method to find the best matches matrix from these data.

The variation in m/z between the same features in different experiments is a user-defined value and it is initially set to 0.01 ppm. There is no clear limit for RT deviations, so the method estimates a non-linear deviation (drift) of RT between two studies. GromovMatcher estimates the drift between the two studies and then discards the matching pairs where the drift would deviate significantly from the estimate. It learns the drift from a weighted spline regression.

The authors validate the performance of their GromovMatcher method by a validation experiment using a dataset of cord blood. They use 20 different splits and compare the GromovMatcher (both its GM and GMT iterations, whereby the GMT version uses the deviation from estimated RT drift to filter the matching matrix) with two other matching methods: M2S and metabCombiner.

The second validation was done using a (scaled and centered) dataset of metabolics from cancer datasets from the EPIC cohort that was manually matched by an expert. This dataset was also used to show that using automatic methods can identify more features that are associated with a particular group of samples than what was found by manual matching. Specifically, the authors identify additional features connected to alcohol consumption.

Strengths:

I see the main strength of this work in its combination of all levels of information (m/z, RT, and higher-order information on correlations between features) and using each of the types of information in a way that is appropriate for the measure. The most innovative aspect is using the Gromov-Wasserstein method to match the features based on distance matrices.

The authors of the paper identify two main shortcomings with previously established methods that attempt to match features from different experiments: a) all other methods require fine-tuning of user-defined parameters, and, more importantly, b) do not consider correlations between features. The main strength of the GromovMatcher is that it incorporates the information on distances between the features (in addition to also using m/z and RT).

Weaknesses:

The first, minor, weakness I could identify is that there seem not to be plenty of manually curated datasets that could be used for validation. The second is also emphasized by the authors in the discussion. Namely, the method as it is set up now can be directly used only to compare two datasets.

Reviewer #2 (Public Review):

Summary:

The authors of this study have sought to better understand the timing and location of the attachment of the lpp lipoprotein to the peptidoglycan in E. coli, and to determine whether YafK is the hydrolase that cleaves lpp from the peptidoglycan.

Strengths:

The method is relatively straightforward. The authors are able to draw some clear conclusions from their results, that lpp molecules get cleaved from the peptidoglycan and then re-attached, and that YafK is important for that cleavage.

Weaknesses:

However, the authors make a few other conclusions from their data which are harder to understand the logic of, or to feel confident in based on the existing data. They claim that their 5-time point kinetic data indicates that new lpp is not substantially added to lipidII before it is added to the peptidoglycan, and that instead lpp is attached primarily to old peptidoglycan. I believe that this conclusion comes from the comparison of Fig.s 3A and 3C, where it appears that new lpp is added to old peptidoglycan a few minutes before new lpp is added to new peptidoglycan. However, the very small difference in the timing of this result, the minimal number of time points and the complete lack of any presentation of calculated error in any of the data make this conclusion very tenuous. In addition, the authors conclude that lpp is not significantly attached to septal peptidoglycan. The logic behind this conclusion appears to be based on the same data, but the authors do not provide a quantitative model to support this idea.

This work will have a moderate impact on the field of research in which the connections between the OM and peptidoglycan are being studied in E. coli. Since lpp is not widely conserved in gram negatives, the impact across species is not clear. The authors do not discuss the impact of their work in depth.

Reviewer #2 (Public Review):

Summary: CD8+ QFL T cells recognize a peptide, FYAEATPML (FL9), presented on Erap1-deficient cells. QFL T cells are present at a high frequency in the spleen of naïve mice. They express an antigen-experienced phenotype, and about 80% express an invariant TCRα chain Vα3.2Jα21.

Here, Guan and coll. report that QFL T cells are present not only in the spleen but also in the intestinal epithelium, where they display several phenotypic and functional peculiarities. The establishment of spleen and gut Vα3.2+ QFL T cells is TAP-dependent, and their phenotype is regulated by the presence/absence of Qa-1b and Erap1. Maintenance of gut Vα3.2+ QFL T cells depends on the gut microbiota and is associated with colonization by Pediococcus pentosaceus.

Strengths:

This article contains in-depth studies of a peculiar and interesting subset of unconventional CD8 T cells, based partly on generating two novel TCR-transgenic models.

The authors discovered a clear relation between the gut microbiome and the maintenance of gut QFL T cells. One notable observation is that monocolonization of the gut with Pediococcus pentosaceus is sufficient to sustain gut QFL T cells.

Weaknesses:

In the absence of immunopeptidomic analyses, the presence or absence of the FL9 peptide on various cell types is inferred based on indirect evidence. Hence, whether the FL9 peptide is presented by some cells that express Qa-1b but not Erap1 remains unknown.

Analyses of the homology between the FL9 and bacterial peptides were limited to two amino acid residues (P4 and P6). This limitation is mitigated in part by the justifications provided by the authors in the revised preprint.

The potential function of QFL T cells remains elusive. The present article should provide an incentive for further functional studies.

Reviewer #2 (Public Review):

Summary:

The paper examines the role L-cysteine metabolism plays in the biology of Mycobacterium tuberculosis. The authors have preliminary data showing that Mycobacterium tuberculosis has two unique pathways to synthesize cysteine. The data showing new compounds that act synergistically with INH is very interesting.

Strengths:

RNAseq data is interesting and important.

Weaknesses:

The paper would be strengthened if the authors were to add further detail to their genetic manipulations.

The authors provide evidence that they have successfully made a cysK2 mutant by recombineering. This data looks promising, but I do not see evidence for the cysM deletion. It is also important to state what sort of complementation was done (multicopy plasmid, integration proficient vector, or repair of the deletion). Since these mutants are the basis for most of the additional studies, these details are essential. It is important to include complementation in mouse studies as unexpected loss of PDIM could have occurred.

Reviewer #2 (Public Review):

Summary:<br /> In this paper, the authors have obtained an analytical expression that provides intuition about regimes of interfacial resistance that depend on droplet size. Additionally, through simulations, the authors provide microscopic insight into the arrangement of sticky and non-sticky functional groups at the interface. The authors introduce bouncing dynamics for rationalizing quantity recovery timescales.

I found several sections that felt incomplete or needed revision and additional data to support the central claim and make the paper self-contained and coherent.

First, the analytical theory operates with diffusion coefficients for dilute and dense phases. For the dilute phase, this is fine. For the dense phase, I have doubts that dynamics can be described as diffusive. Most likely, dynamics is highly subdiffusive due to crowded, entangled, and viscoelastic environments of densely packed interactive biomolecules. Some explanation and justification are in order here.

The second major issue is that I did not find a clean comparison of simulations with the derived analytical expression. Simulations test various microscopic properties on the value of k, which is important. But how do we know that it is the same quantity that appears in the expressions? Also, how can we be sure that analytical expressions can guide simulations and experiments as claimed? The authors should provide sound evidence of the predictive aspect of their derived expressions.

Are the plots in Figure 4 coming from experiment, theory, and simulation? I could not find any information either in the text or in the caption.

Reviewer #2 (Public Review):

Summary and Major Findings/Strengths:

Across diverse hosts, microbiota can influence viral infection and transmission. C. elegans is naturally infected by the Orsay virus, which infects intestinal cells and is transmitted via the fecal-oral route. Previous work has demonstrated that host immune defense pathways, such as antiviral RNAi and the intracellular pathogen response (IPR), can influence host susceptibility to virus infection. However, little is known about how bacteria modulate viral transmission and host susceptibility.

In this study, the authors investigate how diverse bacterial species influence Orsay virus transmission and host susceptibility in C. elegans. When C. elegans is grown in the presence of two Ochrobactrum species, the authors find that animals exhibit increased viral transmission, as measured by the increased proportion of newly infected worms (relative to growth on E. coli OP50). The presence of the two Ochrobactrum species also resulted in increased host susceptibility to the virus, which is reflected by the increased fraction of infected animals following exposure to the exogenous Orsay virus. In contrast, the presence of Pseudomonas lurida MYb11, as well as Pseudomonas PA01 or PA14, attenuates viral transmission and host susceptibility relative to E. coli OP50. For growth in the presence of P. aeruginosa PA01 and PA14, the attenuated transmission and susceptibility are suppressed by mutations in regulators of quorum sensing and the gacA two-component system. The authors also identify six virulence genes in P. aeruginosa PA14 that modulate host susceptibility to virus and viral transmission, albeit to a lesser extent. Based on the findings in P. aeruginosa, the authors further demonstrate that deletion of the gacA ortholog in P. lurida results in loss of the attenuation of viral transmission and host susceptibility.

Taken together, these findings provide important insights into the species-specific effects that bacteria can have on viral infection in C. elegans. The authors also describe a role for Pseudomonas quorum sensing and virulence genes in influencing viral transmission and host susceptibility.

Major weaknesses:

The manuscript has several issues that need to be addressed, such as insufficient rigor of the experiments performed and questions about the reproducibility of the data presented in some places. In addition, confounding variables complicate the interpretations that can be made from the authors' findings and weaken some of the conclusions that are stated in the manuscript.

1. The authors sometimes use pals-5p::GFP expression to indicate infection, however, this is not necessarily an accurate measure of the infection rate. Specifically, in Figures 4-6, the authors should include measurements of viral RNA, either by FISH staining or qRT-PCR, to support the claims related to differences in infection rate.

2. In several instances, the experimental setup and presentation of data lack sufficient rigor. For example, Fig 1D and Fig 2B only display data from one experimental replicate. The authors should include information from all 3 experimental replicates for more transparency. In Fig 3B, the authors should include a control that demonstrates how RNA1 levels change in the presence of E. coli OP50 for comparison with the results showing replication in the presence of PA14. In order to support the claim that "P. aeruginosa and P. lurida MYb11 do not eliminate Orsay virus infection", the authors should also measure RNA1 fold change in the presence of PA01 and P. lurida in the context of exogenous Orsay virus. Additionally, the authors should standardize the amount of bacteria added to the plate and specify how this was done in the Methods, as differing concentrations of bacteria could be the reason for species-specific effects on infection.

3. The authors should be more careful about conclusions that are made from experiments involving PA14, which is a P. aeruginosa strain (isolated from humans), that can rapidly kill C. elegans. To eliminate confounding factors that are introduced by the pathogenicity of PA14, the authors should address how PA14 affects the health of the worms in their assays. For example, the authors should perform bead-feeding assays to demonstrate that feeding rates are unaffected when worms are grown in the presence of PA14. Because Orsay virus infection occurs through feeding, a decrease in C. elegans feeding rates can influence the outcome of viral infection. The authors should also address whether or not the presence of PA14 affects the stability of viral particles because that could be another trivial reason for the attenuation of viral infection that occurs in the presence of PA14.

Ashby's law of requisite variety may also be at play for overloading our system 1 heuristic abilities with respect to misinformation (particularly in high velocity social media settings). Switching context from system 1 to system 2 on a constant basis to fact check everything in our (new digital) immediate environment can be very mentally and emotionally taxing. This can result in both mental exhaustion as well as anxiety.

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Reviewer #2 (Public Review):

Summary:<br /> This work analyses the historical spread and evolution, termed 'population dynamics', of a human bacterial pathogen, Neisseria gonorrhoeae, the cause of the sexually transmitted infection, gonorrhoea. N. gonorrhoeae is classified as a high priority pathogen by the World Health Organisation, due to infections numbering in the tens of millions annually, with high levels of antibiotic resistance and no vaccine available, meaning treating and preventing infections is becoming increasingly more difficult. To implement interventions effectively, important resistant lineages and their transmission routes must be identified on a national and international level.

In this work, Osnes et al. use genomic data, coupled with geographic, temporal and demographic metadata, to analyse the global population dynamics N. gonorrhoeae using 9,732 genomes. The study also includes a granular analysis of transmission between and within four regions of different sizes with high levels of data coverage: USA, Europe, Norway, and Victoria state in Australia.<br /> The authors built a phylogenetic tree including all genomes using a novel computationally efficient method for removing genome regions resulting from recombination, which would otherwise result in incorrect branch lengths and tree topology. Using the tree, the authors show that the effective population size of N. gonorrhoeae, describing population size and diversity, decreased in the period from 2010 to present day, and was not entirely an artefact of sampling bias. The authors then stratified the tree based on isolates that contained alleles that are associated with resistance to antibiotics commonly used to treat gonorrhoea. The authors found resistance was associated with particular lineages, of which most, but not all, underwent shrinking in effective population size in the last decade.<br /> Using the tree, the authors then inferred likely importation, exportation, and local transmission events, finding notable differences in the contribution of imports to local incidence between locations, as well as the likelihood of exportation. As inference of these events relies on sampling density, the authors used a novel method for identifying whether sampling was representative of the population diversity of a given location. Using this approach, they found that the densely sampled regions, Norway and Victoria, were likely representative of the local N. gonorrhoeae population diversity, whilst the larger, less densely sampled regions, Europe and USA, were not. Finally, they investigated the contribution of specific transmission networks to the spread gonorrhoea, finding that the frequency of males within a transmission network may play a role in the rate of N. gonorrhoeae transmission in Norway, but not Victoria.<br /> This work introduces several novel approaches to the analysis of pathogen population dynamics, and highlights notable differences in N. gonorrhoeae transmission between and within distinct geographic locations.

Strengths:<br /> • The authors have collated a large global collection of N. gonorrhoeae genomes with associated metadata, and in some cases generated assemblies themselves. A dataset of this size and detail is a valuable asset to the public health community, enabling analysis of both national and international population dynamics.<br /> • The stratification of the phylogenetic tree by antimicrobial resistance gene alleles enables the study of how antibiotic usage has shaped global and regional N. gonorrhoeae populations. Analysis of changes in the effective population size of clades harbouring resistance alleles is particularly impactful, as this can be used to show how changes in treatment patterns affect the growth or decline of drug-resistant pathogen populations. This analysis also enables the determination of the frequency of multiple resistance alleles being present in single isolates, important for determining the scale of multidrug resistance within the N. gonorrhoeae global population.<br /> • The use of ancestral trait reconstruction to quantify importation, exportation and local transmission is an important contribution to public health efforts tackling N. gonorrhoeae spread. Understanding the differences in transmission networks within and between different geographic locations provides public health researchers with crucial information to model and implement effective targeted interventions on regional and international scales.

Weaknesses:<br /> • The method used to generate the phylogenetic tree and mask regions of recombination is likely flawed. The authors repeatedly down-sampled the whole population to 500 genomes, using Gubbins to identify regions that have recombined and therefore would not follow the clonal history of the N. gonorrhoeae population. This small sample size will result in the same ancient internal nodes being sampled repeatedly, whilst more recent internal nodes will not. Therefore, more recent recombination events would not be identified by this method and were therefore likely included in the whole genome alignment used to build the tree. Furthermore, Gubbins was designed to identify recombination between closely related genomes, not across a whole species, where the background mutation rate will be too high to differentiate between recombined regions and the clonal frame. Both of these factors will mean that the amount of the genome predicted to have recombined will likely be underestimated, resulting in inflated branch lengths and incorrect tree topology. This effect is potentially the cause of the observed drop in N. gonorrhoeae effective population size between 2010-present day in Figure 2, which does not align with gonorrhoea incidence, and the elevated estimated mutation rate of 7.41x10-6 substitutions per site per year, which is higher than previous estimates based on N. gonorrhoeae global populations. The result of underestimation of recombined regions will be two-fold. Inclusion of recombined regions in the alignment will result in inflated branch lengths, which will impact all estimates of effective population size in the study. Furthermore, tree topology may be incorrect, which will impact ancestral trait reconstruction and result in incorrect inference of import, export and local transmission events in Figures 3, 4 and 5. Additionally, the clade-specific resistance gene analyses will be affected in Figure 2, as certain isolates may be incorrectly included or excluded within stratified clades. Therefore, the conclusions made about the changes in effective population size for the global population, and individual clades, as well as the differences in transmission dynamics between locations, are likely to be incorrect.<br /> • The method used to identify sampling bias, shown in Figure 4, is a novel and interesting take on the problem. However, it is not clear whether the effect being measured is the presence of sampling bias or an artefact of differences in N. gonorrhoeae diversity between locations. The results in Figure 4 do align with what is known about the population datasets; the data from Norway and Victoria is more comprehensive than that of the USA and Europe due to the difference in size of the respective human populations, meaning the likelihood of sampling bias will be lower in the smaller population. However, with increased human population size, we would also expect a greater amount of pathogen diversity, due to increased within-region transmission and greater numbers of importation events. Supporting this, we see in Figure 3 that the transmission lineages in the USA and Europe are estimated to have emerged earlier than Norway or Victoria, indicative of a greater amount of standing population diversity. Therefore, the reason why convergence is observed when up-sampling from smaller populations may be because a vast majority of isolates will sit within a small part of the tree, whilst from a larger, more diverse population, isolates will be placed all across the tree and so convergence will never be observed. In effect, it is unknown whether increasing the sample size of the USA and Europe to be truly representative of their respective N. gonorrhoeae populations would ever result in convergence between the two methods of up-sampling. Testing this method using simulations could be used to determine whether it is sensitive to sampling bias, or population diversity.<br /> • In Figure 5, a significant difference in transmission lineage size was only found between male-dominated and mixed lineages in Norway and not Victoria. Therefore, the conclusion that sex distribution within transmission networks affects the size of transmission lineages is not supported by the data, and could also be due to geographical and other demographic differences between the datasets which were not accounted for.

Reviewer #2 (Public Review):

Li et al present a method to extract "behaviorally relevant" signals from neural activity. The method is meant to solve a problem which likely has high utility for neuroscience researchers. There are numerous existing methods to achieve this goal some of which the authors compare their method to, though there are notable omissions. However, I do believe that d-VAE is a promising approach that has its own advantages.

That being said, there are issues with the paper as-is. This could have been a straightforward "methods" paper describing their approach and validating it on different ground truth and experimental datasets. Instead, the authors focus on the neuroscientific results and their implications for brain mechanisms. Unfortunately, while the underlying method seems sound and performs well relative to the assessed competition, the scientific results and presentation they put forward were not sufficiently strong to support these claims, especially given the small amount of data (recordings of one monkey per task, with considerable variability between them).

Specific comments<br /> - Is the apparently increased complexity of encoding vs decoding so unexpected given the entropy, sparseness, and high dimensionality of neural signals (the "encoding") compared to the smoothness and low dimensionality of typical behavioural signals (the "decoding") recorded in neuroscience experiments? This is the title of the paper so it seems to be the main result on which the authors expect readers to focus.

- I take issue with the premise that signals in the brain are "irrelevant" simply because they do not correlate with a fixed temporal lag with a particular behavioural feature hand-chosen by the experimenter. As an example, the presence of a reward signal in motor cortex [1] after the movement is likely to be of little use from the perspective of predicting kinematics from time-bin to time-bin using a fixed model across trials (the apparent definition of "relevant" for behaviour here), but an entire sub-field of neuroscience is dedicated to understanding the impact of these reward-related signals on future behaviour. Is there method sophisticated enough to see the behavioural "relevance" of this brief, transient, post-movement signal? This may just be an issue of semantics, and perhaps I read too much into the choice of words here. Perhaps the authors truly treat "irrelevant" and "without a fixed temporal correlation" as synonymous phrases and the issue is easily resolved with a clarifying parenthetical the first time the word "irrelevant" is used. But I remain troubled by some claims in the paper which lead me to believe that they read more deeply into the "irrelevancy" of these components.

- The authors claim the "irrelevant" responses underpin an unprecedented neuronal redundancy and reveal that movement behaviors are distributed in a higher-dimensional neural space than previously thought." Perhaps I just missed the logic, but I fail to see the evidence for this. The neural space is a fixed dimensionality based on the number of neurons. A more sparse and nonlinear distribution across this set of neurons may mean that linear methods such as PCA are not effective ways to approximate the dimensionality. But ultimately the behaviourally relevant signals seem quite low-dimensional in this paper even if they show some nonlinearity may help.

- Relatedly, I would like to note that the exercise of arbitrarily dividing a continuous distribution of a statistic (the "R2") based on an arbitrary threshold is a conceptually flawed exercise. The authors read too much into the fact that neurons which have a low R2 w.r.t. PDs have behavioural information w.r.t. other methods. To this reviewer, it speaks more about the irrelevance, so to speak, of the preferred direction metric than anything fundamental about the brain.

- there is an apparent logical fallacy that begins in the abstract and persists in the paper: "Surprisingly, when incorporating often-ignored neural dimensions, behavioral information can be decoded linearly as accurately as nonlinear decoding, suggesting linear readout is performed in motor cortex." Don't get me wrong: the equivalency of linear and nonlinear decoding approaches on this dataset is interesting, and useful for neuroscientists in a practical sense. However, the paper expends much effort trying to make fundamental scientific claims that do not feel very strongly supported. This reviewer fails to see what we can learn about a set of neurons in the brain which are presumed to "read out" from motor cortex. These neurons will not have access to the data analyzed here. That a linear model can be conceived by an experimenter does not imply that the brain must use a linear model. The claim may be true, and it may well be that a linear readout is implemented in the brain. Other work [2,3] has shown that linear readouts of nonlinear neural activity patterns can explain some behavioural features. The claim in this paper, however, is not given enough

- I am afraid I may be missing something, as I did not understand the fano factor analysis of Figure 3. In a sense the behaviourally relevant signals must have lower FF given they are in effect tied to the temporally smooth (and consistent on average across trials) behavioural covariates. The point of the original Churchland paper was to show that producing a behaviour squelches the variance; naturally these must appear in the behaviourally relevant components. A control distribution or reference of some type would possibly help here.

- The authors compare the method to LFADS. While this is a reasonable benchmark as a prominent method in the field, LFADS does not attempt to solve the same problem as d-VAE. A better and much more fair comparison would be TNDM [4], an extension of LFADS which is designed to identify behaviourally relevant dimensions.

[1] https://doi.org/10.1371/journal.pone.0160851<br /> [2] https://doi.org/10.1101/2022.03.31.486635<br /> [3] https://doi.org/10.1038/s41593-017-0028-6<br /> [4] Hurwitz et al, Targeted Neural Dynamical Modeling, NeurIPS 2021.

Reviewer #2 (Public Review):

In this manuscript, the authors propose a computational method based on deep convolutional neural networks (CNNs) to automatically detect cell divisions in two-dimensional fluorescence microscopy timelapse images. Three deep learning models are proposed to detect the timing of division, predict the division axis, and enhance cell boundary images to segment cells before and after division. Using this computational pipeline, the authors analyze the dynamics of cell divisions in the epithelium of the Drosophila pupal wing and find that a wound first induces a reduction in the frequency of division followed by a synchronised burst of cell divisions about 100 minutes after its induction.

In general, novelty over previous work does not seem particularly important. From a methodological point of view, the models are based on generic architectures of convolutional neural networks, with minimal changes, and on ideas already explored in general. The authors seem to have missed much (most?) of the literature on the specific topic of detecting mitotic events in 2D timelapse images, which has been published in more specialized journals or Proceedings. (TPMAI, CCVPR etc., see references below). Even though the image modality or biological structure may be different (non-fluorescent images sometimes), I don't believe it makes a big difference. How the authors' approach compares to this previously published work is not discussed, which prevents me from objectively assessing the true contribution of this article from a methodological perspective.

On the contrary, some competing works have proposed methods based on newer - and generally more efficient - architectures specifically designed to model temporal sequences (Phan 2018, Kitrungrotsakul 2019, 2021, Mao 2019, Shi 2020). These natural candidates (recurrent networks, long-short-term memory (LSTM), gated recurrent units (GRU), or even more recently transformers), coupled to CNNs are not even mentioned in the manuscript, although they have proved their generic superiority for inference tasks involving time series (Major point 2). Even though the original idea/trick of exploiting the different channels of RGB images to address the temporal aspect might seem smart in the first place - as it reduces the task of changing/testing a new architecture to a minimum - I guess that CNNs trained this way may not generalize very well to videos where the temporal resolution is changed slightly (Major point 1). This could be quite problematic as each new dataset acquired with a different temporal resolution or temperature may require manual relabeling and retraining of the network. In this perspective, recent alternatives (Phan 2018, Gilad 2019) have proposed unsupervised approaches, which could largely reduce the need for manual labeling of datasets.

Regarding the other convolutional neural networks described in the manuscript:

1) the one proposed to predict the orientation of mitosis performs a regression task, predicting a probability for the division angle. The architecture, which must be different from a simple Unet, is not detailed anywhere, so the way it was designed is difficult to assess. It is unclear if it also performs mitosis detection, or if it is instead used to infer orientation once the timing and location of the division have been inferred by the previous network.

2) the one proposed to improve the quality of cell boundary images before segmentation is nothing new, it has now become a classic step in segmentation, see for example Wolny et al. eLife 2020.

As a side note, I found it a bit frustrating to realise that all the analysis was done in 2D while the original images are 3D z-stacks, so a lot of the 3D information had to be compressed and has not been used. A novelty, in my opinion, could have resided in the generalisation to 3D of the deep-learning approaches previously proposed in that context, which are exclusively 2D, in particular, to predict the orientation of the division.

Concerning the biological application of the proposed methods, I found the results interesting, showing the potential of such a method to automatise mitosis quantification for a particular biological question of interest, here wound healing. However, the deep learning methods/applications that are put forward as the central point of the manuscript are not particularly original.

Major point 1: generalisation potential of the proposed method.

The neural network model proposed for mitosis detection relies on a 2D convolutional neural network (CNN), more specifically on the Unet architecture, which has become widespread for the analysis of biology and medical images. The strategy proposed here exploits the fact that the input of such an architecture is natively composed of several channels (originally 3 to handle the 3 RGB channels, which is actually a holdover from computer vision, since most medical/biological images are gray images with a single channel), to directly feed the network with 3 successive images of a timelapse at a time. This idea is, in itself, interesting because no modification of the original architecture had to be carried out. The latest 10-channel model (U-NetCellDivision10), which includes more channels for better performance, required minimal modification to the original U-Net architecture but also simultaneous imaging of cadherin in addition to histone markers, which may not be a generic solution.

Since CNN-based methods accept only fixed-size vectors (fixed image size and fixed channel number) as input (and output), the length or time resolution of the extracted sequences should not vary from one experience to another. As such, the method proposed here may lack generalization capabilities, as it would have to be retrained for each experiment with a slightly different temporal resolution. The paper should have compared results with slightly different temporal resolutions to assess its inference robustness toward fluctuations in division speed.

Another approach (not discussed) consists in directly convolving several temporal frames using a 3D CNN (2D+time) instead of a 2D, in order to detect a temporal event. Such an idea shares some similarities with the proposed approach, although in this previous work (Ji et al. TPAMI 2012 and for split detection Nie et al. CCVPR 2016) convolution is performed spatio-temporally, which may present advantages. How does the authors' method compare to such an (also very simple) approach?

Major point 2: innovatory nature of the proposed method.

The authors' idea of exploiting existing channels in the input vector to feed successive frames is interesting, but the natural choice in deep learning for manipulating time series is to use recurrent networks or their newer and more stable variants (LSTM, GRU, attention networks, or transformers). Several papers exploiting such approaches have been proposed for the mitotic division detection task, but they are not mentioned or discussed in this manuscript: Phan et al. 2018, Mao et al. 2019, Kitrungrotaskul et al. 2019, She et al 2020.

An obvious advantage of an LSTM architecture combined with CNN is that it is able to address variable length inputs, therefore time sequences of different lengths, whereas a CNN alone can only be fed with an input of fixed size.

Another advantage of some of these approaches is that they rely on unsupervised learning, which can avoid the tedious relabeling of data (Phan et al. 2018, Gilad et al. 2019).

References :<br /> Ji, S., Xu, W., Yang, M., & Yu, K. (2012). 3D convolutional neural networks for human action recognition. IEEE transactions on pattern analysis and machine intelligence, 35(1), 221-231. >6000 citations

Nie, W. Z., Li, W. H., Liu, A. A., Hao, T., & Su, Y. T. (2016). 3D convolutional networks-based mitotic event detection in time-lapse phase contrast microscopy image sequences of stem cell populations. In Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition Workshops (pp. 55-62).

Phan, H. T. H., Kumar, A., Feng, D., Fulham, M., & Kim, J. (2018). Unsupervised two-path neural network for cell event detection and classification using spatiotemporal patterns. IEEE Transactions on Medical Imaging, 38(6), 1477-1487.

Gilad, T., Reyes, J., Chen, J. Y., Lahav, G., & Riklin Raviv, T. (2019). Fully unsupervised symmetry-based mitosis detection in time-lapse cell microscopy. Bioinformatics, 35(15), 2644-2653.

Mao, Y., Han, L., & Yin, Z. (2019). Cell mitosis event analysis in phase contrast microscopy images using deep learning. Medical image analysis, 57, 32-43.

Kitrungrotsakul, T., Han, X. H., Iwamoto, Y., Takemoto, S., Yokota, H., Ipponjima, S., ... & Chen, Y. W. (2019). A cascade of 2.5 D CNN and bidirectional CLSTM network for mitotic cell detection in 4D microscopy image. IEEE/ACM transactions on computational biology and bioinformatics, 18(2), 396-404.

Shi, J., Xin, Y., Xu, B., Lu, M., & Cong, J. (2020, November). A Deep Framework for Cell Mitosis Detection in Microscopy Images. In 2020 16th International Conference on Computational Intelligence and Security (CIS) (pp. 100-103). IEEE.

Wolny, A., Cerrone, L., Vijayan, A., Tofanelli, R., Barro, A. V., Louveaux, M., ... & Kreshuk, A. (2020). Accurate and versatile 3D segmentation of plant tissues at cellular resolution. Elife, 9, e57613.

Reviewer #2 (Public Review):

This manuscript by Port and colleagues describes rigorous experiments that provide a wealth of virologic, respiratory physiology, and particle aerodynamic data pertaining to aerosol transmission of SARS-CoV-2 between infected Syrian hamsters. The data is particularly significant because infection is compared between alpha and delta variants, and because viral load is assessed via numerous assays (gRNA, sgRNA, TCID) and in tissues as well as the ambient environment of the cage. The paper will be of interest to a broad range of scientists including infectious diseases physicians, virologists, immunologists and potentially epidemiologists. The strength of evidence is relatively high but limited by unclear presentation in certain parts of the paper.

Important conclusions are that infectious virus is only detectable in air samples during a narrow window of time relative to tissue samples, that airway constriction increases dynamically over time during infection limiting production of fine aerosol droplets, that variants do not appear to exclude one another during simultaneous exposures and that exposures to virus via the aerosol route lead to lower viral loads relative to direct inoculation suggesting an exposure dose response relationship.

While the paper is valuable, I found certain elements of the data presentation to be unclear and overly complex.

Reviewer #2 (Public Review):

Tian et al. performed a meta-analysis of 113 genome-wide origin profile datasets in humans to assess the reproducibility of experimental techniques and shared genomics features of origins. Techniques to map DNA replication sites have quickly evolved over the last decade, yet little is known about how these methods fare against each other (pros and cons), nor how consistent their maps are. The authors show that high-confidence origins recapitulate several known features of origins (e.g., correspondence with open chromatin, overlap with transcriptional promoters, CTCF binding sites). However, surprisingly, they find little overlap between ORC/MCM binding sites and origin locations.

Overall, this meta-analysis provides the field with a good assessment of the current state of experimental techniques and their reproducibility, but I am worried about: (a) whether we've learned any new biology from this analysis; (b) how binding sites and origin locations can be so mismatched, in light of numerous studies that suggest otherwise; and (c) some methodological details described below.

-- I understand better the inclusion/exclusion logic for the samples. But I'm still not sure about the fragments. As the authors wrote, there is both noise and stochasticity; the former is not important but the latter is essential to include. How can these two be differentiated, and what may be the expected overlap as a function of different stochasticity rates?

-- Many of the major genomic features analyzed have already been found to be associated with origin sites. For example, the correspondence with TSS has been reported before:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6320713/<br /> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6547456/

-- Line 250: The most surprising finding is that there is little overlap between ORC/MCM binding sites and origin locations. The authors speculate that the overlap between ORC1 and ORC2 could be low because they come from different cell types. Equally concerning is the lack of overlap with MCM. If true, these are potentially major discoveries that butts heads with numerous other studies that have suggested otherwise.

The key missing dataset is ORC1 and ORC2 CHiP-seq from the same cell type. This shouldn't be too expensive to perform, and I hope someone performs this test soon. Without this, I remain on the fence about how much existing datasets are "junk" vs how much the prevailing hypothesis about replication needs to be revisited. Nonetheless, the authors do perform a nice analysis showing that existing techniques should be carefully used and interpreted.