Reviewer #3 (Public Review):

This manuscript provides a more or less quantitative analysis of protein synthesis in lymphocytes. I have no issue with the data as presented, as I'm sure all measurements have been expertly done. I see no need for additional experimental work, although it would be helpful if the authors could comment on the possibility of measuring the rate of synthesis of a defined protein, say a histone, in cells prior to and after activation. The conclusion the authors leave us with is the idea that the rates of protein synthesis recorded here are incompatible with observed rates of T cell division in vivo. Indeed, in the final paragraph of the discussion, the authors note the mismatch between what they consider a requirement for cell division, and the observed rates of protein synthesis. They then invoke unconventional mechanisms to make up for the shortfall, without -in this reviewer's opinion- discussing in adequate detail the technical limitations of the methodology used.

A key question is the broad interest, novelty, and extension of current knowledge, in comparison with Argüello's (reference 27) 'SunRise' method. It would be helpful for the authors to stake out a clear position as to the similarities and differences with reference 27: what have we learned that is new? The authors could cite reference 27 in the introduction of their manuscript, given the similarity in approach. That said, the findings reported here will generate further discussion.

The manuscript would increase in impact if the authors were to clearly define why a particular measurement is important and then show the actual experiment/result. As an example, it would be helpful to explain to the non-expert why the distinction between monosomes, polysomes, and stalled versions of the same is important, and then explain the rationale of the actual experiment: how can these distinctions be made with confidence, and what are confounding variables? The initial use of human cells, later abandoned in favor of the OT-1 in vitro and in vivo models, requires contextualization. If the goal is to address the relationship between rates of translation and cell division of antigen-activated T cells in vivo, then a lot of the work on the human model and the in vitro experiments becomes more of a distraction, unless properly contextualized. Is there any reason to assume that antigen-specific activation in vivo will impact translation differently than the use of the PMA/ionomycin/IL2 cocktail? The way the work is presented leaves me with the impression that everything that was done is included, regardless of whether it goes to the core of the question(s) of interest.

It would be helpful if the authors made explicit some of the assumptions that underlie their quantitative comparisons. Likewise, the authors should discuss the limitations of their methods and provide alternative interpretations where possible, even if they consider them less/not plausible, with justification. As they themselves note, improvements in the RPM protocols raised the increase in translating ribosomes upon activation from 10-fold to 15-fold. Who's to say that is the best achievable result? What about the reliability/optimization of the other measurements?

The composition of the set of proteins produced upon activation will differ from cell to cell (CD4, CD8, B, resting vs. dividing). Even if analyses are performed on fixed cells, the ability of the monoclonal anti-puromycin antibody to penetrate the matrix of the various fixed cell types may not be equal for all of them, depending on protein composition, susceptibility to fixation etc. Is it possible for puromycin to occupy the ribosome's A site and terminate translation without forming a covalent bond with the nascent chain? This could affect the staining with anti-puromycin antibodies and also underestimate the number of nascent chains.

I believe that the concept of FACS-based quantitation also requires an explanation for the non-expert. For the FACS plots shown, the differences between the highest and lowest RPM scores for cells that divided and that have a similar CFSE score is at least 10-fold. Does that mean that divided cells can differ by that margin in terms of the number of nascent chains present? If I make the assumption that cells stimulated with PMA/ionomycin/IL2 respond more or less synchronously, why would there be a 10-fold difference in absolute fluorescence intensity (anti=puromycin) for randomly chosen cells with similar CFSE values? While the use of MFI values is standard practice in cytofluorimetry, the authors should devote some comments to such variation at the population level.

It is assumed that for cells to complete division, they must have produced a full and complete copy of their proteome and only then divide. What if cells can proceed to divide even when expressing a subset of the proteome of departure (=the threshold set required for initiation of division), only to complete synthesis of the 'missing ' portion once cell division is complete? Would this obviate the requirement for an unusual mechanism of protein acquisition (trogocytosis; other)?

Translation is estimated to proceed at a rate of ~6 amino acids per second, but surely there is variability in this number attributable to inaccuracies of the methods used, in addition to biological variability. Were these so-called standard values determined for a range of different tissues? It stands to reason that there might be variation depending on the availability of initiation/elongation factors, NTPs, aminoacyl tRNAs etc. What is the margin of error in calculating chain elongation rates based on the results shown here?

Reviewer #3 (Public Review):

The authors introduce two new concepts for antimicrobial resistance borrowed from pharmacology, "variant vulnerability" (how susceptible a particular resistance gene variant is across a class of drugs) and "drug applicability" (how useful a particular drug is against multiple allelic variants). They group both terms under an umbrella term "drugability". They demonstrate these features for an important class of antibiotics, the beta-lactams, and allelic variants of TEM-1 beta-lactamase.

The strength of the result is in its conceptual advance and that the concepts seem to work for beta-lactam resistance. However, I do not necessarily see the advance of lumping both terms under "drugability", as this adds an extra layer of complication in my opinion.

I also think that the utility of the terms could be more comprehensively demonstrated by using examples across different antibiotic classes and/or resistance genes. For instance, another good model with published data might have been trimethoprim resistance, which arises through point mutations in the folA gene (although, clinical resistance tends to be instead conferred by a suite of horizontally acquired dihydrofolate reductase genes, which are not so closely related as the TEM variants explored here).

The impact of the work on the field depends on a more comprehensive demonstration of the applicability of these new concepts to other drugs.

Reviewer #3 (Public Review):

This study performs in vivo recordings of neurons in the mouse superior colliculus and their afferents from the retina, retinal ganglion cells (RGCs). Building on a preparation they previously published, this study adds the use of optogenetic identification of inhibitory neurons (aka optotagging) to compare RGC connectivity to excitatory and inhibitory neurons in SC. Using this approach, the authors characterize connection probability, strength, and response correlation between RGCs and their target neurons in SC, finding several differences from what is observed in the retina-thalamus-visual cortex pathway. As such, this may be a useful dataset for efforts to understand retinocollicular connectivity and computations.

Reviewer #3 (Public Review):

This manuscript describes the development of CRISPR knockouts for gh, fsh and tsh in the fast-aging Nothobranchius furzeri grz strain. CRISPR knockouts have been published before, and the strength of the paper is that here, the authors include a novel, easy and fast way of rescuing the loss of function in the entire body by electroporation in muscle. This offers flexibility in timing and dosage, and leads to intriguing results regarding the role of these hormones in growth and fertility. Finally they also add a conditional doxycycline-dependent overexpression model that would allow even more control over the modalities of the rescue. The phenotypes of the knockouts were not the key message of the paper and remained at times only superficially described. The doxycycline-dependent overexpression was only minimally validated, and here it is not yet clear how robust this system is in terms of overexpression levels, timing, and reversibility.

Overall this study brings a new set of tools in the killifish toolbox that can have much wider applications and will be appreciated also in other teleost models.

Reviewer #3 (Public Review):

The present study used novel data logging devices to record the foraging behavior of wandering albatrosses. Specifically, the authors showed how localized winds and wave heights influence their ability to take off from the sea surface, which is the most expensive behavior they engage in while foraging. There is no better platform for this initial work because these birds are so large, the equipment they can carry without creating significant impact is tremendous.

The results were impressive, presented well, and the paper was generally written in an accessible way to readers with less knowledge. The authors provide a convincing set of results that support the aims and conclusions. The theory and application could be used to inform our understanding of flight behavior in other seabirds.

Although the idea of taking off from the sea surface may sound trivial, it is essential to understand that albatrosses and other soaring seabirds have wings that are adapted for soaring (i.e. long and narrow). The trade off, however, is that powered flight through wing flapping is energetically expensive because the wings have a shallow amplitude and generate less power compared to a shorter, wider wing. Thus, wind is everything and this study shows how wind facilitates the ability of the birds to gain flight using wind and waves. Awesome!

Reviewer #3 (Public Review):

In this work, the authors tried to profile time-dependent changes in gene and protein expression during BMP-induced amnion differentiation from hPSCs. The authors depicted a GATA3 - TFAP2A - ISL1/HAND1 order of amniotic gene activation, which provides a more detailed temporary trajectory of amnion differentiation compared to previous works. As a primary goal of this study, the above temporal gene/protein activation order is amply supported by experimental data. However, the mechanistic insights on amniotic fate decision, as well as the transcriptomic analysis comparing amnion-like cells from this work and other works remain limited. While this work allows us to see more details of amnion differentiation and understand how different transcription factors were turned on in a sequence and might be useful for benchmarking the identity of amnion in ex utero cultured human embryos/embryoids, it provides limited insights on how amnion cells might diverge from primitive streak / mesoderm-like cells, despite some transcriptional similarity they shared, during early development.

Reviewer #3 (Public Review):

In this manuscript by Berrocal and coworkers, the authors do a deep dive into the transcriptional regulation of the eve gene in both an endogenous and ectopic background. The idea is that by looking at eve expression under non-native conditions, one might infer how enhancers control transcriptional bursting. The main conclusion is that eve enhancers have not evolved to have specific behaviors in the eve stripes, but rather the same rates in the telegraph model are utilized as control rates even under ectopic or 'de novo' conditions. For example, they achieve ectopic expression (outside of the canonical eve stripes) through a BAC construct where the binding sites for the TF Giant are disrupted along with one of the eve enhancers. Perhaps the most general conclusion is that burst duration is largely constant throughout at ~ 1 - 2 min. This conclusion is consistent with work in human cell lines that enhancers mostly control frequency and that burst duration is largely conserved across genes, pointing to an underlying mechanistic basis that has yet to be determined.

Reviewer #3 (Public Review):

Strengths:

On the positive side, I thought the use of ChatGPT to score the sentiment of text was novel and interesting, and I was largely convinced by the parts of the methods which illustrate that the AI provides broadly similar sentiment and politeness scores to humans who were asked to rank a sub-set of the reviews. The paper is mostly clear and well-written, and tackles a question of importance and broad interest (i.e. the potential for bias in the peer review process, and the objectivity of peer review).

Weaknesses:

The sample size and scope of the paper are a bit limited, and I have concerns covering diverse aspects including statistical/inferential issues, missing references, and suggestions for other material that could be included that would greatly increase the usefulness of the paper. A major limitation is that the paper focuses on published papers, and thus is a biased sample of all the reviews that were written, which prevents the paper properly answering the questions that it sets out to answer (e.g. is peer review repeatable, fair and objective).

Reviewer #3 (Public Review):

This paper reports a considerable technical achievement: the optogenetic activation of single retinal ganglion cells in vivo in monkeys. As clearly specified in the paper, this is an important step towards causal tests of the role of specific ganglion cell types in visual perception. Yet this methodological advance is not described currently in sufficient detail to replicate or evaluate. The paper could be improved substantially by including additional methodological details. Some specific suggestions follow.

The start of the results needs a paragraph or more to outline how you got to Figure 1. Figure 1 itself lacks scale bars, and it is unclear, for example, that the ganglion cells targeted are in the foveal slope.

The text mentions the potential difficulties targeting ganglion cells at larger eccentricities where the soma density increases. If this is something that you have tried it would be nice to include some of that data (whether or not selective activation was possible). Related to this point, it would be helpful to include a summary of the ganglion cell density in monkey retina.

Related to the point in the previous paragraph - do you have any experiments in which you systematically moved the stimulation spot away from the target ganglion cell to directly test the dependence of stimulation on distance? This would be a valuable addition to the paper.

The activity in Figure 1 recovers from activation very slowly - much more slowly than the light response of these cells, and much more slowly than the activity elicited in most optogenetic studies. Can you quantify this time course and comment on why it might be so slow?

Traces from non-targeted cells should be shown in Figure 1 along with those of targeted cells.

Reviewer #3 (Public Review):

a) Important findings<br /> - This study confirms that Gr28 subfamily members are expressed in distinct sets of taste neurons in Drosophila larvae, supporting previous findings (e.g., Kwon et al., 2011).<br /> - Neurons expressing different members of the Gr28 family exhibit distinct behavioral responses when chemically activated with capsaicin.<br /> - Silencing experiments reveal that neurons expressing Gr28bc are necessary for larval avoidance of four bitter compounds, whereas neurons expressing Gr28be are necessary for avoiding lobeline and caffeine.<br /> - Inserting either Gr28ba or Gr28bc into the GR28 mutant line restored larval avoidance of denatonium.<br /> - Calcium imaging experiments show that Gr28ba and Gr28bc are involved in sensing denatonium, while none of the GR28 family members are involved in detecting quinine.

b) Caveats<br /> - The authors did not acknowledge that neurons expressing members of the GR28 family also express other Gr family members, which could potentially contribute to the detection and behavioral responses to the tested bitter compounds.<br /> - Gal4 lines from various studies exhibit varying expression patterns, highlighting the necessity for improved reagents. These findings also suggest the importance of employing different Gal4 lines for each receptor to validate the results of the current study.<br /> - Activating or silencing neurons pertains to the function of the neurons rather than the receptors.<br /> - Inconsistency is observed in the use of different reagents across the experiments. Specifically, all six Gal4 lines were utilized in the Chemical Activation experiments, while only two lines were employed in the silencing experiments.<br /> - The Alphafold structure prediction is exciting but lacks conclusive evidence.

Reviewer #3 (Public Review):

Leeds et al. employ elegant in vitro experiments and sophisticated numerical modeling to investigate the ability of mechanical coupling to coordinate the growth of individual microtubules within microtubule bundles, specifically k-fibers. While individual microtubules naturally polymerize at varying rates, their growth must be tightly regulated to function as a cohesive unit during chromosome segregation. Although this coordination could potentially be achieved biochemically through selective binding of polymerases and depolymerases, the authors demonstrate, using a novel dual laser trap assay, that mechanical coupling alone can also coordinate the growth of in vitro microtubule pairs.

By reanalyzing recordings of single microtubules growing under constant force (data from their own previous work), the authors investigate the stochastic kinetics of pausing and show that pausing is suppressed by tension. Using a constant shared load, the authors then show that filament growth is tightly coordinated when pairs of microtubules are mechanically coupled by a material with sufficient stiffness. In addition, the authors develop a theoretical model to describe both the natural variability and force dependence of growth, using no freely adjustable parameters. Simulations based on this model, which accounts for stochastic force-dependent pausing and intrinsic variability in microtubule growth rate, fit the dual-trap data well.

Overall, this study illuminates the potential of mechanical coupling in coordinating microtubule growth and offers a framework for modeling k-fibers under shared loads. The research exhibits meticulous technical rigor and is presented with exceptional clarity. It provides compelling evidence that a minimal, reconstituted biological system can exhibit complex behavior. As it currently stands, the paper is highly informative and valuable to the field.

To provide further clarity regarding the implications of their study, the authors may wish to address the following points in more detail:

- Considering the authors' understanding of the quantitative relationship between forces, microtubule growth, and coordination, is the dual trap assay necessary to demonstrate this coordination? What advantages does the (semi)experimental system offer compared to a purely in silico treatment?

- What are the limitations of studying a system comprising only two individual microtubules? How might the presence of crosslinkers, which are typically present in vivo between microtubules, influence their behavior in this context?

- How dependent are the results on the chosen segmentation algorithm? Can the distributions of pause and run durations truly be fitted by "simple" Gaussians, as indicated in Figure S5-2? Given the inherent limitations in accurately measuring short durations and the application of threshold durations, it is likely that the first bins in the histograms underestimate events. Cumulative plots could potentially address this issue.

Reviewer #3 (Public Review):

The authors investigated the initial steps involved in angiogenesis. Using appropriate experimental tools they associated engineered vasculature models with a strong mathematical analysis. The study provides a dynamic view of the early steps involved in angiogenesis. It shows significant fluctuations in the onset of angiogenesis that suggest transitions between order and disorder in cell organization. The data obtained strongly support the hypothesis and support the conclusion of the study. This work brings new insights into the comprehension of the complex processes involved in the onset of angiogenesis and it provides a strong model to predict how VEGF will activate the delta-NOTCH signaling. Nevertheless, it would be important to describe in more detail how the current study can be used for a better understanding of the angiogenesis process in physiological and in pathological situations.

Reviewer #3 (Public Review):

Prior work from the Kaverina lab and others had determined that beta-cells build a microtubule network that differs from the canonical radial organization typical in most mammalian cell types and that this organization facilitates the regulated secretion of insulin-containing secretory granules (IGs). In this manuscript, the authors tested the hypothesis that kinesin-driven microtubule sliding is an underlying mechanism that establishes a sub-membranous microtubule array that regulates IG secretion. They employed knock-down and dominant-negative strategies to convincingly show microtubule sliding does, in fact, drive the assembly of the sub-membranous microtubule band. They also used live cell imaging assays to demonstrate that kinesin-mediated microtubule sliding in beta-cells is triggered by extracellular high glucose. Overall, this is an interesting and important study that relates microtubule dynamics to an important physiological process. The experiments were rigorous and well-controlled.

Reviewer #3 (Public Review):

Summary:<br /> Using a combination of approaches, including automated feature selection and hierarchical clustering, the author identified a set of genes persistently associated with extrachromosomal DNA (ecDNA) presence across cancer types. The authors further validated the gene set identified using gene ontology enrichment analysis and identified that upregulated genes in extrachromosomal DNA-containing tumors are enriched in biological processes like DNA damage and cell proliferation, whereas downregulated genes are enriched in immune response processes.

Major comments:<br /> 1. The authors presented a solid comparative analysis of ecDNA-containing and ecDNA-free tumors. An established automated feature selection approach, Boruta, was used to select differentially expressed genes (DEG) in ecDNA(+) and ecDNA(-) TCGA tumor samples, and the iterative selection process and two-tier multiple hypothesis testing ensured the selection of reliable DEGs. The author showed that the DEG selected using Boruta has stronger predictive power than genes with top log-fold changes.

2. The author performed a thorough interpretation of the findings with GO enrichment analysis of biological processes enriched in the identified DEG set, and presented interesting findings, including the enrichment in DNA damage process among the genes upregulated in ecDNA(+) tumors.

3. Overall, the authors achieved their aims with solid data mining and analysis approaches applied to public data tumor data sets.

4. While it may not be the scope of this study, it will be interesting to at least have some justification for choosing Boruta over other feature selection methods, such as Recursive Feature Elimination (RFE) and backward stepwise selection.

5. The authors showed that DESEQ-selected DEGs with top log-fold changes have less strong predictive power and speculated that this may be due to the fact that genes with top log-fold changes (LFC) are confined only to a small subset of samples. It will be interesting to select DEGs with top log-fold changes after first partitioning the tumor samples. For example, randomly partition the tumor samples, identify the DEGs with top LFC, combine the DEGs identified from each partition, then evaluate the predictive power of these DEGs against the Boruta-selected DEGs.

6. While the authors showed that the presence of mutations was not able to classify ecDNA(+) and (-) tumor samples, it will be interesting to see if variant allele frequencies of the genes containing these mutations have predictive power.

Reviewer #3 (Public Review):

Summary:<br /> Variants in the UBA5 gene are associated with rare developmental and epileptic encephalopathy, DEE44. This research developed a system to assess in vivo and in vitro genotype-phenotype relationships between UBA5 allele series by humanized UBA5 fly models and biochemical activity assays. This study provides a basis for evaluating current and future individuals afflicted with this rare disease.

Strengths:<br /> The authors developed a method to measure the enzymatic reaction activity of UBA5 mutants over time by applying the UbiReal method, which can monitor each reaction step of ubiquitination in real time using fluorescence polarization. They also classified fruit fly carrying humanized UBA5 variants into groups based on phenotype. They found a correlation between biochemical UBA5 activity and phenotype severity.

Weaknesses:<br /> In the case of human DEE44, compound heterozygotes with both loss-of-function and hypomorphic forms (e.g., p.Ala371Thr, p.Asp389Gly, p.Asp389Tyr) may cause disease states. The presented models have failed to evaluate such cases.

Reviewer #3 (Public Review):

The work presented in the manuscript tries to identify tRNA modifications present in Mycobacterium tuberculosis (Mtb) using reverse transcription-derived error signatures with tRNA-seq. The study identified enzyme homologs and correlates them with presence of respective tRNA modifications in Mtb. The study used several chemical treatments (IAA and alkali treatment) to further enhance the reverse transcription signals and confirms the presence of modifications in the bases. tRNA modifications by two enzymes TruB and MnmA were established by doing tRNA-seq of respective deletion mutants. Ultimately, authors show that MnmA-dependent tRNA modification is important for intracellular growth of Mtb. Overall, this report identifies multiple tRNA modifications and discuss their implication in Mtb infection.

Reviewer #3 (Public Review):

In this study, the authors sought to test the hypothesis that blocking triglyceride storage in adipose tissue by knockout of DGAT1 and DGAT2 in adipocytes would lead to ectopic lipid deposition, lipodystrophy, and impaired glucose homeostasis. Surprisingly, the authors found the opposite result, with DGAT1/2 DKO in adipocytes leading to increased energy expenditure, minimal ectopic lipid deposition, and improved glucose homeostasis with HFD feeding. These metabolic improvements were largely attributed to increased beiging of the white fat and increased brown adipose tissue activity. This study provides an interesting new paradigm whereby impairing fat storage, the major function of adipose tissue, does not lead to severe metabolic disease, but rather improves it. The authors provide a comprehensive assessment of the metabolism of these DKO mice under chow and HFD conditions, which support their claims. The study lacks in mechanistic insight, which would strengthen the study, but does not detract from the authors' major conclusions.

Reviewer #3 (Public Review):

In this study, Sun et al examine the role of the splicing factor SRSF1 in spermatogenesis in mice. Alternative splicing is important for spermatogenic development, but its regulation and major developmental roles during spermatogenesis are not well understood. The authors set out to better define both SRSF1 function in testes and the contribution of alternative splicing. They collect several large 'omics datasets to define SRSF1 targets in testis, including RNA interactions by CLIP-seq in whole testis, protein interactions by IP-mass spec in whole testis, and RNA sequencing to detect expression levels and splice variants. They also examine the phenotype of germline conditional knockouts (cKO) for Srsf1, using the early-acting Vasa-Cre, and find a severe depletion of germ cells starting at 7 days post partum (dpp) and culminating with a lack of germ cells (Sertoli Cell Only Syndrome) by adulthood. They detect differences in gene expression as well as differences in splicing between control and knockout, including 9 genes that are downregulated, experience alternative splicing, and whose transcripts are also bound by SRSF1, and identify the Tial1/Tiar transcript as one of these targets. They conclude that SRSF1 is required for homing and self-renewal of spermatogonial stem cells, at least in part through its regulation of Tial1/Tiar splicing.

Strengths of the paper include detailed phenotyping of the Srsf1 cKO, which convincingly supports the Sertoli Cell Only phenotype, establishes the timing of the first appearance of the spermatogonial defect, and provides new insight into the role of splicing factors and SRSF1 specifically in spermatogenesis. Another strength is the generation of CLIP-seq, IP-MS, and RNA-seq datasets which will be a useful resource for the field of germ cell development. Major weaknesses include a lack of robust support for two major claims: first, there is inadequate support for the claim of defects in either "homing" or "self-renewal" of spermatogonia in the cKO, and second, there is inadequate support for the claim that altered splicing of the Tial1 transcript mediates the effect of SRSF1 loss. A moderate weakness is the superficial discussion of the CLIP, RNA-seq, and IP-MS datasets, limiting their otherwise high utility for other researchers. Overall, the paper as it stands will have a moderate impact on the field of male reproductive biology. Specific points that should be addressed to improve support for the claims are below.

Major comments

1) In Fig 1D, it appears that SRSF1 is expressed most strongly in spermatogonia by immunofluorescence, but this is inconsistent with the sharp rise in expression detected by RT-qPCR at 20 days post partum (dpp) (Fig. 1B), which is when round spermatids are first added; this discrepancy should be explained or addressed.

2) It is important to provide a more comprehensive basic description of the CLIP-seq datasets beyond what is shown in the tracks shown in Fig. 2B. This would allow a better assessment of the data quality and would also provide information about the transcriptome-wide patterns of SRSF1 binding. No information or quality metrics are provided about the libraries, and it is not stated how replicates are handled to maximize the robustness of the analysis. The distribution of peaks across exons, introns, and other genomic elements should also be shown.

3) The claim that SRSF1 is required for "homing and self-renewal" of SSCs is made in multiple places in the manuscript. However, neither homing nor self-renewal is ever directly tested. A single image is shown in Fig. 5E of a spermatogonium at 5dpp that does not appropriately sit on the basal membrane, potentially indicating a homing defect, but this is not quantified or followed up. There is good evidence for depletion of spermatogonia starting at 7 dpp, but no further explanation of how homing and/or self-renewal fit into the phenotype.

4) In Fig. 6A (lines 258-260) very few genes downregulated in the cKO are bound by SRSF1 and undergo abnormal splicing. The small handful that falls into this overlap could simply be noise. A much larger fraction of differentially spliced genes are CLIP-seq targets (~33%), which is potentially interesting, but this set of genes is not explored.

5) The background gene set for Gene Ontology analyses is not specified. If these were done with the whole transcriptome as background, one would expect enrichment of spermatogenesis genes simply because they are expressed in testes. The more appropriate set of genes to use as background in these analyses is the total set of genes that are expressed in testis.

6) In general, the model is over-claimed: aside from interactions by IP-MS, little is demonstrated in this study about how SRSF1 affects alternative splicing in spermatogenesis, or how alternative splicing of TIAL1 specifically would result in the phenotype shown. It is not clear why Tial1/Tiar is selected as a candidate mediator of SRSF1 function from among the nine genes that are downregulated in the cKO, are bound by SRSF1, and undergo abnormal splicing. Although TIAL1 levels are reduced in cKO testes by Western blot (Fig. 7J), this could be due just be due to a depletion of germ cells from whole testis. The reported splicing difference for Tial1 seems very subtle and the ratio of isoforms does not look different in the Western blot image.

Reviewer #3 (Public Review):<br /> <br /> Tutor et al. present their work on Kelch13/K13 from Plasmodium falciparum, the causative agent of malaria. This protein is involved in resistance against artemisinin (ART), one of the most commonly used drugs to treat malaria. Despite having identified the mutation in K13 that leads to resistance to ART, the exact molecular mechanism, function of K13, and impact of the K13 mutations still need to be elucidated. This is where the authors step in to investigate the relationship between endocytosis and K13, as well as the impact of depleting the protein using knock-sideway (KS). Using light microscopy, the authors demonstrate how K13-YFP forms a pore associated with fluorescently labeled dextran, which is taken up into tubules that move toward the digestive vacuole. This tubule formation is not sensitive to jasplakinolide (JAS) treatment. Using electron microscopy, they show that K13 is localized at the dark contrast border of the cytostome, and knocking down K13 leads to the disruption of the cytostome structure. Upon removal of K13, the structure changes, and the opening enlarges. The impact of KS induction on the cytostome was quantified using TEM and tomography. The authors also provide reconstructions of the cytostome in both induced and non-induced parasites. Finally, they measure the impact of KS on haem degradation. These data provide clear information on the function of K13 in cytostome formation and the implication of this structure in endocytosis for Plasmodium falciparum.

The conclusions of this paper are well supported by the data, but some data analysis should be clarified and extended, and some complementary experiments would further strengthen the authors' claims.

Reviewer #3 (Public Review):

The authors report a study in which they use intracranial recordings to dissociate subjectively aware and subjectively unaware stimuli, focusing mainly on prefrontal cortex. Although this paper reports some interesting findings (the videos are very nice and informative!) the interpretation of the data is unfortunately problematic for several reasons. I will detail my main comments below. If the authors address these comments well, I believe the paper may provide an interesting contribution to further specifying the neural mechanisms important for conscious access (in line with Gaillard et al., Plos Biology 2009).

The main problem with the interpretation of the data is that the authors have NOT used a so-called "no-report paradigm". The idea of no report paradigms is that subjects passively view a certain stimulus without the instruction to "do something with it", e.g., detect the stimulus, immediately or later in time. Because of the confusion of this term, specifically being related to the "act of reporting", some have argued we should use the term no-cognition paradigm instead (Block, TiCS, 2019, see also Pitts et al., Phil Trans B 2018). The crucial aspect is that, in these types of paradigms, the critical stimulus should be task-irrelevant and thus not be associated with any task (immediately or later). Because in this experiment subjects were instructed to detect the gratings when cued 600 ms later in time, the stimuli are task relevant, they have to be reported about later and therefore trigger all kinds of (known and potentially unknown) cognitive processes at the moment the stimuli are detected in real-time (so stimulus-locked). You could argue that the setup of this delayed response task excludes some very specific report related processes (e.g., the preparation of an eye-movement), which is good, however this is usually not considered the main issue. For example when comparing masked versus unmasked stimuli (Gaillard et al., 2009 Plos Biology), these conditions usually also both contain responses but these response related processes are "averaged out" in the specific contrasts (unmasked > masked). In this paper, RT differences between conditions (that are present in this dataset) are taken care of by using this delayed response in this paper, which is a nice feature for that and is not the case for the above example set-up.

Given the task instructions, and this being merely a delayed-response task, it is to be expected that prefrontal cortex shows stronger activity for subjectively aware versus subjectively unaware stimuli. Unfortunately, given the nature of this task, the novelty of the findings is severely reduced. The authors cannot claim that prefrontal cortex is associated with "visual awareness", or what people have called phenomenal consciousness (this is the goal of using no-cognition paradigms). The only conclusion that can be drawn is that prefrontal cortex activity is associated with accessing sensory input: and hence conscious access. This less novel observation has been shown many times before and there is also little disagreement about this issue between different theories of consciousness (e.g., global workspace theory and local recurrency theories both agree on this).

The best solution at this point seems to rewrite the paper entirely in light of this. My advice would be to state in the introduction that the authors investigate conscious access using iEEG and then not refer too much to no-cognition paradigm or maybe highlight some different strategies about using task-irrelevant stimuli (see Canales-Johnson et al., Plos Biology 2023; Hesse et al., eLife 2020; Hatamimajoumerd et al Curr Bio 2022; Alilovic et al., Plos Biology 2023; Pitts et al., Frontiers 2014; Dwarakanth et al., Neuron 2023 and more). Obviously, the authors should then also not claim that their results solve debates about theories regarding visual awareness (in the "no-cognition" sense, or phenomenal consciousness), for example in relation to the debate about the "front or the back of the brain", because the data do not inform that discussion. Basically, the authors can just discuss their results in detail (related to timing, frequency, synchronization etc) and relate the different signatures that they have observed to conscious access.

I think the authors have to discuss the Gaillard et al PLOS Biology 2009 paper in much more detail. Gaillard et al also report a study related to conscious access contrasting unmasked and masked stimuli using iEEG. In this paper they also report ERP, time frequency and phase synchronization results (and even Granger causality). Because of the similarities in approach, I think it would be important to directly compare the results presented in that paper with results presented here and highlight the commonalities and discrepancies in the Discussion.

In the Gaillard paper they report a figure plotting the percentage of significant frontal electrodes across time (figure 4A) in which it can be seen that significant electrodes emerge after approximately 250 ms in PFC as well. It would be great if the authors could make a similar figure to compare results. In the current paper there are much more frontal electrode contacts than in the Gaillard paper, so that is interesting in itself.

In my opinion, some of the most interesting results are not highlighted: the findings that subjectively unaware stimuli show increased activations in the prefrontal cortex as compared to stimulus absent trials (e.g., Figure 4D). Previous work has shown PFC activations to masked stimuli (e.g., van Gaal et al., J Neuroscience 2008, 2010; Lau and Passigngham J Neurosci 2007) as well as PFC activations to subjectively unaware stimuli (e.g., King, Pescetelli, and Dehaene, Neuron 2016) and this is a very nice illustration of that with methods having more detailed spatial precision. Although potentially interesting, I wonder about the objective detection performance of the stimuli in this task. So please report objective detection performance for the patients and the healthy subjects, using signal detection theoretic d'. This gives the reader an idea of how good subjects were in detecting the presence/absence of the gratings. Likely, this reveals far above chance detection performance and in that case I would interpret these findings as "PFC activation to stimuli indicated as subjectively unaware" and not unconscious stimuli. See Stein et al., Plos Biology 2021 for a direct comparison of subjectively and objectively unaware stimuli.

In Figure 7 of the paper the authors want to make the case that the contrast does not differ between subjectively aware stimuli and subjectively unaware stimuli. However so far they've done the majority of their analyses across subjects, and for this analysis the authors only performed within-subject tests, which is not a fair comparison imo. Because several P values are very close to significance I anticipate that a test across subjects will clearly show that the contrast level of the subjectively aware stimuli is higher than of the subjectively unaware stimuli, at the group level. A solution to this would be to subselect trials from one condition (NA) to match the contrast of the other condition (NU), and thereby create two conditions that are matched in contrast levels of the stimuli included. Then do all the analyses on the matched conditions.

Related, Figure 7B is confusing and the results are puzzling. Why is there such a strong below chance decoding on the diagonal? (also even before stimulus onset) Please clarify the goal and approach of this analysis and also discuss/explain better what they mean.

I was somewhat surprised by several statements in the paper and it felt that the authors may not be aware of several intricacies in the field of consciousness. For example a statement like the following "Consciousness, as a high-level cognitive function of the brain, should have some similar effects as other cognitive functions on behavior (for example, saccadic reaction time). With this question in mind, we carefully searched the literature about the relationship between consciousness and behavior; surprisingly, we failed to find any relevant literature." This is rather problematic for at least two reasons. First, not everyone would agree that consciousness is a high-level cognitive function and second there are many papers arguing for a certain relationship between consciousness and behavior (Dehaene and Naccache, 2001 Cognition; van Gaal et al., 2012, Frontiers in Neuroscience; Block 1995, BBS; Lamme, Frontiers in Psychology, 2020; Seth, 2008 and many more). Further, the explanation for the reaction time differences in this specific case is likely related to the fact that subjects' confidence in that decision is much higher in the aware trials than in the unaware trials, hence the speeded response for the first. This is a phenomenon that is often observed if one explores the "confidence literature". Although the authors have not measured confidence I would not make too much out of this RT difference.

I would be interested in a lateralized analysis, in which the authors compare the PFC responses and connectivity profiles using PLV as a factor of stimulus location (thus comparing electrodes contralateral to the presented stimulus and electrodes ipsilateral to the presented stimulus). If possible this may give interesting insights in the mechanism of global ignition (global broadcasting), supposing that for contralateral electrodes information does not have to cross from one hemisphere to another, whereas for ipsilateral electrodes that is the case (which may take time). Gaillard et al refer to this issue as well in their paper, and this issue is sometimes discussed regarding to Global workspace theory. This would add novelty to the findings of the paper in my opinion.

Reviewer #3 (Public Review):

The authors report on the nature of interventions that were applied to aid and improve engagement in cervical screening, brought about by the SARS CoV Pandemic in Sweden.

I appreciate that the impact of these interventions, given that they are recent, will take some time to quantify but the description (and reach) of the policy changes that occurred in a short amount of time is of significant interest to the screening community. The piece on HPV Even Faster is particularly novel; I am not aware of another example of where this has been enacted within a routine programme.

The authors make reference to (15) where the reader can find greater details relating to the population who received the offer of self sampling (and the nature of the device). However I was a little confused (in this stand alone piece) as to who the self sampling group constituted exactly. Did this group not include pregnant women, women invited for first screen or women on non routine recall?

The authors state that "the most likely explanation for the large increase in population coverage seen is that the sending of self-sampling kits resulted in improved attendance in particular among previously non-attending women" - why is this written as speculation at this stage (?) is it not possible to attribute directly the contribution made by self sampling, or is this in hand?

While self sampling is certainly an option that can support uptake and enfranchisement in cervical screening - its overall performance is fundamentally contingent on the number of women who then comply with follow up should the HPV test be positive; it is not simply about who returns the sample. It would have been of interest to see the proportion of women who did comply with follow up.

Reviewer #3 (Public Review):

'Collateral sensitivity' occurs when drug-resistance mutations render a drug target more sensitive to inhibition by another drug, which has been previously described in some detail for malaria parasite dihydroorotate dehydrogenase (DHODH - see refs 36, 46, and 47, for example). Although it has been suggested that combinations of such drugs could potentially suppress the emergence of resistance, cross-resistance-associated mutation (or copy-number variation, CNV) could render such combination strategies ineffective. In the current study, the authors assess a new pairing of DHODH-targeting drugs. Cross-resistant parasites with DHODH mutation or CNV arise following either sequential or combined drug selection, suggesting that the drug combination described would likely fail to effectively suppress the emergence of resistance.

The strength of the study is that it describes, for a particular drug combination, different mutations associated either with collateral sensitivity or with cross-resistance, and the authors conclude that "combination treatment with DSM265 and TCMDC-125334 failed to suppress resistance". They go on to say that this "brings into question the usefulness of pursuing further DHODH inhibitors." More specific interpretations and implications of the study are as follows:<br /> a. Other combinations may also fail but there may be combinations that can effectively suppress resistance. A more exhaustive analysis of mutational space will likely be required to determine which combinations if any, would be predicted to succeed in a clinical setting.<br /> b. It was previously reported that "a combination of [DHODH] wild-type and mutant-type selective inhibitors led to resistance far less often than either drug alone. ... Comparative growth assays demonstrated that two mutant parasites grew less robustly than their wild-type parent, and the purified protein of those mutants showed a decrease in catalytic efficiency, thereby suggesting a reason for the diminished growth rate" (Ref 46). Also, "selection with a combination of Genz-669178, a wild-type PfDHODH inhibitor, and IDI-6273, a mutant-selective PfDHODH inhibitor, did not yield resistant parasites" (Ref 36). It is possible that these previously tested combinations would also yield cross-resistant mutants if selected further.<br /> c. Although increased DHODH copy number "confers only moderately reduced susceptibility" to the drug used for selection and although these clones were not assessed here for cross-resistance, it seems likely that CNV may represent a general mechanism that could undermine other collateral resistance strategies.

Reviewer #3 (Public Review):

The authors described their extensive single-cell analysis of Candida undergoing (sub-inhibitory) antibiotic treatment versus no treatment. To do so, the authors used a microfluidics platform they had previously developed, and they optimized, characterized, and validated it for this particular application. Their findings included: (a) the transcription of untreated cells is driven mostly by cell cycle phase, (b) treated cells can be clustered into several major groups and a few outlier groups that the authors termed comets, (c) cells undergoing FCZ treatment can adopt one of two different states (possibly bistability). I found the results interesting and the approach to be sound, and much of the results confirmed my prior expectations. The authors provide a detailed depiction of what is going on in the transcriptome during sub-inhibitory treatment, although this did not always lead to a mechanistic explanation. The clinical relevance was unclear to me beyond a proof of concept application for single-cell transcriptomics. In my opinion, an interesting follow-up would be to follow the transcriptional trajectory of lineages undergoing antimicrobial switching (on and off). The main issues I identified were the author's use of the term tolerance versus resistance, interpretation of "comets", clustering approach, description of fitness, and comparison between time points.

Reviewer #3 (Public Review):

Increased LRRK2 kinase activity is known to confer Parkinson's disease risk. While much is known about disease-causing LRRK2 mutations that increase LRRK2 kinase activity, the normal cellular mechanisms of LRRK2 activation are less well understood. Rab GTPases are known to play a role in LRRK2 activation and to be substrates for the kinase activity of LRRK2. However, much of the data on Rabs in LRRK2 activation comes from over-expression studies and the contributions of endogenously expressed Rabs to LRRK2 activation are less clear. To address this problem, Bondar and colleagues tested the impact of systematically depleting candidate Rab GTPases on LRRK2 activity as measured by its ability to phosphorylate Rab10 in the human A549 type 2 pneumocyte cell line. This resulted in the identification of a major role for Rab12 in controlling LRRK2 activity towards Rab10 in this model system. Follow-up studies show that this role for Rab12 is of particular importance for the phosphorylation of Rab10 by LRRK2 at damaged lysosomes. Increases in LRRK2 activity in cells harboring disease-causing mutants of LRRK2 and VPS35 also depend (at least partially) on Rab12. Confidence in the role of Rab12 in supporting LRRK2 activity is strengthened by parallel experiments showing that either siRNA-mediated depletion of Rab12 or CRISPR-mediated Rab12 KO both have similar effects on LRRK2 activity. Collectively, these results demonstrate a novel role for Rab12 in supporting LRRK2 activation in A549 cells. It is likely that this effect is generalizable to other cell types. However, this remains to be established. It is also likely that lysosomes are the subcellular site where Rab12-dependent activation of LRRK2 occurs. Independent validation of these conclusions with additional experiments would strengthen this conclusion and help to address some concerns that much of the data supporting a lysosome localization for Rab12-dependent activation of LRRK2 comes from a single method (LysoIP). Furthermore, there is a discrepancy between panel 4A versus 4D in the effect of LLoMe-induced lysosome damage on LRRK2 recruitment to lysosomes that will need to be addressed to strengthen confidence in conclusions about lysosomes as sites of LRRK2 activation by Rab12.

Reviewer #3 (Public Review):

This manuscript by Bellegarda et al. examined the in vivo dynamic behavior of the Reissner fiber and its interactions with cilia and sensory neurons in the central canal of zebrafish larvae. The authors accomplished this by performing live imaging with a transgenic reporter zebrafish line in which the fiber is GFP-tagged and by finely tracking the movement of the fiber. Interestingly, they discovered that the fiber undergoes a dynamic vibratory-like movement along the dorsoventral axis. The authors then utilized a pulsed laser to precisely cut the fiber, which frequently resulted in a fast retraction behavior and a loss of calcium activity in sensory neurons in the central canal called CSF-CNs. Mechanical modeling of the elastic properties of the fiber indicated that the fiber is a soft elastic rod with graded tension along the rostrocaudal axis. Finally, by performing live imaging of motile cilia and the fiber in the central canal, they found that the two interact in close proximity and that cilia motility is affected when the fiber was cut. The authors concluded that the Reissner fiber is a dynamic structure under tension that interacts with sensory neurons and cilia in the central canal.

Strengths:<br /> 1. The study utilizes state-of-the-art microscopy techniques and beautiful transgenic zebrafish tools to characterize the in vivo behavior of the Reissner fiber and found that it exhibits surprising dynamic movements along the dorsal-ventral axis. This observation has important implications for the physiology and function of the Reissner fiber.

2. By performing a series of clever laser cutting experiments, the authors reveal that the Reissner fiber is under tension in the central canal of zebrafish. This finding provides direct experimental evidence to support the hypothesis that the Reissner fiber functions in a biomechanical manner during spinal cord development and body axis straightening.

3. By developing a mechanical model of the Reissner fiber and its retraction behavior, the authors estimate the elastic properties of the fiber and found that it is more akin to an elastic polymer rather than a stiff rod. This is a useful finding that illuminates the biophysical properties of the fiber.

4. Through calcium and cilia imaging studies, the authors demonstrate that the Reissner fiber likely interacts with motile cilia and regulates the activity of ciliated sensory neurons (CSF-CNs). The authors propose a model in which fiber-cilia interactions may occur via weak interactions or frictional forces. This model is plausible and opens several new doors for additional investigation.

Weaknesses:<br /> 1. All the live imaging experiments appear to be performed with animals paralyzed via the injection of a chemical agent (bungarotoxin). Does paralysis and/or bungarotoxin negatively impact the behavior of the Reissner fiber? Some data from non-paralyzed animals would ameliorate this concern.

2. Although the authors convincingly demonstrate that the Reissner fiber is under graded tension, it remains unclear what is the relevance and function of tension on this structure. The photoablation data presented do not delineate between the relevance of the fiber being intact or tension on the fiber as cutting the fiber impacts both. Is fiber tension required for body straightening? At the site of fiber photoablation, does a spinal curvature develop? If cultured, do the ablated animals exhibit a scoliotic phenotype?

3. One of the most potentially impactful conclusions of the paper is that the Reissner fiber interacts with cilia, but the evidence is insufficient to support this. Although some motile cilia are near the fiber (Figure 3A), many cilia are not near the fiber. The provided images and videos do not clearly demonstrate that cilia physically contact or influence the behavior of the Reissner fiber. Further, the data is lacking to conclude that the Reissner fiber directly impacts cilia motility as they did not observe an overall statistically significant difference before and after ablation (Supplemental Figure 1A). Higher magnification, higher resolution, higher acquisition rate and/or colocalization analyses of fiber-cilia interactions could alleviate this concern.

4. Similarly, how does the Reissner fiber interact with CSF-CN sensory neurons? The authors suggest that the fiber interacts with CSF-CN sensory neurons by modulating their spontaneous calcium activity via weak interactions or frictional forces from motile ciliated ependymal radial glial cells. While the calcium imaging data of the CSF-CNs is convincing and sound, the exact nature of the fiber-neuron interaction is unclear. Do cilia or apical extensions on CSF-CN sensory neurons sense the fiber or forces through a mechanosensing or chemosensing mechanism? There is some additional confusion as the authors appear to focus their cilia experiments on ependymal radial glial cells in section 4, rather than CSF-CNs. The addition of an illustrative cartoon would add clarity.

Overall, the conclusions of the study are well supported by the data presented. However, the strength of the conclusions could be enhanced by additional controls, alternative experimental approaches and clarifications.

This manuscript is an important contribution to the fields of spinal cord development and body axis development, which are fundamental questions in neurobiology, developmental biology, and musculoskeletal biology. In recent years, the Reissner fiber and motile cilia function have been linked to cerebrospinal fluid flow signaling and body straightening, but the precise form and function of the fiber remain unclear. This study provides new insight into the dynamic and biophysical properties of the Reissner fiber in vivo in zebrafish and proposes a model in which the fiber interacts with cilia and sensory neurons. This study provides novel insight into the cellular mechanisms that underlie the pathogenesis of disorders such as idiopathic scoliosis.

Reviewer #3 (Public Review):

CaMKII is a multimeric kinase of great biologic interest due to its crucial roles in long-term memory, cardiac pacemaking, and fertilization. CaMKII subunits organize into holoenzymes comprised of 12-14 subunits, adopting a donut-like, double-ringed structure. In this manuscript, Lucic et al challenge two models in the CaMKII field, which are somewhat related. The first is a longstanding topic in the field about whether the autophosphorylation of a crucial residue, Thr286, can be phosphorylated between intact holoenzymes (inter-holoenzyme phosphorylation). The second is a more recent biochemical finding, which tested the long-running theory that CaMKII exchanges subunits between holoenzymes to create mixed oligomers. These two models are connected by the idea that subunit exchange could facilitate phosphorylation between subunits of different holoenzymes by allowing subunits to integrate into a different holoenzyme and driving transphosphorylation within the CaMKII ring. Here, the authors attempt to show that one intact holoenzyme phosphorylates another intact holoenzyme at Thr286. The authors also provide evidence suggesting that subunit exchange is not occurring under their conditions, and therefore not driving this phosphorylation event. The authors propose a model where instead of exchanging subunits, two holoenzymes interact via their kinase domains to enable transphosphorylation at Thr286 without integrating into the holoenzyme structure. In order for the authors to successfully convince readers of all three facets of this new model, they need to provide evidence that 1) transphosphorylation at Thr286 happens when subunit exchange is blocked, 2) subunit exchange does not occur under their conditions, and 3) there are interactions between kinases of different holoenzymes that lead to productive autophosphorylation at Thr286.

Strengths:<br /> The authors have designed and performed a battery of cleverly designed and orthogonal experiments to test these models. Using mutagenesis, they mixed a kinase-dead mutant with an active kinase to ask whether transphosphorylation occurs. They observe phosphorylation of the kinase-dead variant in this experiment, which indicates that the active kinase must have phosphorylated it. A few key questions arise here: 1) whether this phosphorylation occurred within a single CaMKII holoenzyme ring (which is the canonical mechanism for Thr286 phosphorylation), 2) whether the phosphorylation occurred between two separate holoenzyme rings, and 3) why was this not observed in previous literature? To address questions 1 and 2, the authors implemented an innovative strategy introducing a genetically-encoded photocrosslinker in the oligomerization domain, which when crosslinked using UV light, should lock the holoenzyme in place. The rate of phosphorylation was the same when comparing uncrosslinked and crosslinked CaMKII variants, indicating that phosphorylation is occurring between holoenzymes, rather than through a subunit exchange mechanism that would require some type of disassembly and reassembly (presumably blocked by crosslinking). The 3rd question remains as to why this has not been previously observed, as it has not been for lack of effort. The authors mention low temperature and low concentration as culprits, however, Bradshaw et al, JBC v. 277, 2002 carry out a series of careful experiments that indicated that autophosphorylation at T286 is not concentration-dependent (meaning that the majority of phosphorylation occurs via intra-holoenzyme), and this is done over a concentration and temperature range. It is possible that due to the mutants used in the current manuscript, it allows for the different behavior of the kinase-dead domains, which will have an empty nucleotide-binding pocket. Further studies will need to elucidate these details, and importantly, understand what physiological conditions facilitate this mechanism.

The most convincing data that subunit exchange does not occur is from the crosslinking mass spectrometry experiment. The authors created mixtures of 'light' and 'heavy' CaMKII holoenzymes, either activated or not and then used a Lys-Lys crosslinker (DSS) to trap the enzyme in its final state. The results of this experiment indicate that subunit exchange is not occurring under their conditions. A caveat here is that there are not many lysines at hub-hub interfaces, which is the crux of this experiment. If there is no subunit exchange under their conditions, how does transphosphorylation occur between holoenzymes? The authors show very nice mass photometry data indicating that there are populations of 24-mers, which corresponds to a double-holoenzyme. Paired with the data from their crosslinking mass spectrometry which shows crosslinks between kinase domains of different holoenzymes, this indicates that perhaps kinases between holoenzymes do interact, and they do so in a competent manner to allow transphosphorylation to occur.

Weaknesses:<br /> The authors should be commended for performing three orthogonal experiments to test whether CaMKII holoenzymes exchange subunits to form heterooligomers. However, there are technical issues that dampen the strength of the results shown here. For simplicity, let's consider that CaMKII holoenzymes are comprised of two stacked hexameric rings. It has been proposed that the stable unit of CaMKII assembly and perhaps also disassembly and subunit exchange is a vertical dimer unit (comprised of one subunit from each hexameric ring). In the UV crosslinking data shown in this paper, the authors have a significant number of monomers, some crosslinked dimers (of which there are two populations), and fewer higher-order oligomers. To effectively block subunit exchange, robust crosslinking into hexamers is necessary, which the authors have not done. Incomplete crosslinking results in smaller species that can still exchange (and/or dissociate), confounding the results of this experiment. In addition, Figure 3 shows a trapping experiment, where if the exchange was occurring, there would be an oligomeric band in Lane 8, which is visible and highlighted with a blue arrow by the authors. This result is explained by nonspecific UV effects, however by eye it is not clear if there is an equivalent band in lane 10. The overall issue here is inefficient crosslinking.

The authors also employ a single-molecule TIRF experiment to further interrogate subunit exchange. Upon inspection of the TIRF images, it is not clear that the authors are achieving single molecule resolution (there are evident overlapping and distorted particles). The analysis employed here is Pearson's correlation coefficient, which is not sufficient for single molecule analysis and would not account for particle overlap, particles that are too bright, and/or particles that are too dim. For example, an alternative explanation for the authors' results is that activation results in aggregation (high correlation), and subsequent EGTA treatment leads to dissociation at these low concentrations (low correlation). However, further experimentation and analysis are necessary.

Taken together, the authors have provided important food for thought regarding inter-holoenzyme phosphorylation and subunit exchange. However, given the shortcomings discussed here, it remains unclear exactly what mechanisms are at play within and between CaMKII holoenzymes once activated.

Reviewer #3 (Public Review):

Joechner and their co-authors performed an extensive analysis of two existing datasets from sleeping children aged between 5 to 18 years. By identifying discrete events of slow oscillations (SOs) and (fast) sleep spindles they examined not only the developmental changes of these distinct sleep grapho-elements. They also took a closer look at their interplay, e.g., to what extend sleep spindles are co-occurring with slow oscillation up-states, as this coupling is thought to underlie sleep-dependent memory consolidation.

The authors found that both sleep spindles and slow oscillation undergo a change across the young age, e.g., while sleep spindles increased in frequency approaching the typical 12-16 Hz range found in adults, slow oscillation showed a shift in occurrence patterns from posterior to anterior sites. Likewise, the coupling of fast spindles within slow oscillation up-states manifested with age, which is almost non-existing in 5- to 6-year-old children. However, and most intriguingly, a coupling analysis based on the adult-like 12-16 Hz range revealed an already existing SO-spindle phase-relation across all age ranges. Altogether, this data nicely demonstrates the trajectory of sleep spindles and SOs in children and highlights the almost inherent coupling between SOs and "adult" sleep spindles. In my view, these results not only provide a good overview of a healthy development but also interesting food for thought regarding the function of SO-spindle coupling in healthy or clinical development.

Overall, this work is well-written, and the performed analyses are well conceptualized. Hence, there are one general and a few minor aspects that could be addressed to hopefully strengthen this manuscript a bit further.

The biggest aspect that was striking is the shear amount of data reported, e.g., a supplement with 28 tables is too extensive. The authors should consider reducing a few aspects.<br /> For example, the authors employ a linear mixed effects model and report coefficient etc. in the supplement. However, in the main text, the authors mainly report ANOVA-based results. Obviously, a LMM and an ANOVA are equivalent, however, focusing on one approach could streamline everything.<br /> Another example is the assessment of spindle frequency via the discrete events: First spindle peak frequency is derived via power spectra. Using the then individually identified peaks, discrete events are detected. Shouldn't it be obvious that these events show the same behavior with regard to their frequency?<br /> As a final example, the authors first report changes in fast spindle properties across age and, e.g., find an increase in frequency towards 12-16 Hz adult range. They then repeat the whole analysis in the 12-16 Hz range and examine the "distance" to the individualized results. It should again be obvious that this approach comes to the same conclusion, a smaller distance in older children. Even more obvious is the conclusion "Hence, it appears as if fast centro-parietal SPs become more dominant and adult-like in their frequency and amplitude characteristics in older children" because it describes a normal development of a healthy child. Altogether, the authors could streamline a few aspects by removing hidden redundancies and focus on the - in my view - central aspect of an inherent 12-16 Hz coupling across all ages.

Reviewer #3 (Public Review):

Mesenchymal stem cells have been shown to have potent immunomodulatory and regenerative properties and have been tested and tried in kidney transplantation. In a previous paper, the authors of this paper reviewed the beneficial actions of nitric oxide (NO) on the beneficial action of MSC. In this manuscript, they describe a method to generate NO in the therapeutic MSC. While NO donors like the short-acting nitrates have been used for angina pectoris patients few therapeutic approaches have been published aiming at the local delivery of NO to specific tissues or organs like the kidney. Gene therapy with adenoviral vectors, overexpressing the eNOS gene itself failed due to the fact that the eNOS enzyme, when overexpressed quickly runs out of sufficient co-factors like BH4. As a consequence, the enzyme uncouples and becomes cytotoxic due to the generation of peroxynitrate. Hence, the current strategy to generate NO in the MSC itself is novel and interesting.

The authors first describe the cryoprotective effects and antioxidant effects of NO generation in MSC in vitro and subsequently in vivo in a mouse model of ischemia-reperfusion injury that may reflect acute kidney injury (or ischemia associated with kidney transplantation) in patients. While the MSC are transplanted intracortical on a local position in the kidneys, the manuscript describes surprising effectivity on serum creatinine, ureum, casts, and protection of brush border. Also, upon immunohistochemical analyses, fibrosis, and kidney injury markers decrease. Most likely there is a strong paracrine effect. It is unfortunate that the control "PBS + MGP" is lacking to exclude some low-grade background conversion of the compound with subsequent release of NO. MGP only is tested however, studies in kidney sections with state-of-the-art EPR, give the authors the wanted control.

The paper provides an interesting proof of concept for a novel therapeutic approach. However, in the clinical arena, some questions remain involving the survival of the MSC after transplantation and the introduction of novel antigens associated with the engineered cells

Reviewer #3 (Public Review):

Pinatel and colleagues addressed a currently understudied topic in neurobiology, namely, the architecture and function of myelination in subsets of Parvalbumin (PV)- and Somatostatin (SST)-positive GABAergic hippocampal interneurons and its dependence on juxtaparanodal organizer proteins. In order to elucidate the structural and functional implications of interneuron myelination, the authors visualized inhibitory neurons by utilizing a Lhx2-tdTomato reporter line in combination with crucial cytoskeletal linker proteins such as Contactin2/TAG-1, Caspr2, and Protein 4.1B. They then applied a comprehensive set of histological, electrophysiological, and behavioral experiments to dissect the role these proteins play in proper myelination and function of PV- and SST-interneurons.

The bulk of the study's data is based on immunofluorescence, which is presented in a number of figures comprised of high-quality images. As much as this is a strength of the study, the underlying image analysis as described in the methods falls short. All structural data rely on the measurements of physical parameters such as length of internodes, the distance between (juxta)paranode and node, the distance between node and myelin sheath, length of the axon initial segment (AIS), etc. In light of this, and considering the small physical dimensions of the nodal region in general, the methods remain unclear about the depth of 3D reconstruction/deconvolution applied to the samples. Measurements presented in the results show significant differences in sub-micrometer dimension, which at least according to the stated methods, are unlikely to be precise given that the confocal imaging parameters do not seem to reach Nyquist conditions. For a study in which a third of all data is aimed at elucidating (sub)micrometer changes, this is crucial and the study would benefit from a more rigorous method description by the authors.

Another methodological weakness is the somewhat small n, and its incoherence across the experiments and therefore, the statistics performed in some of the experiments. Statistics are based on either n for animals, or n for individual data points from several animals. Why is not all data represented as mean/animal? Also, the sampling in general with n = 3 animals is borderline acceptable; in some cases, it seems that only 2 animals were used, and in others, no number is given at all (please refer to author comments for details). This needs to be addressed, either by explaining why so few animals were used, or by adding more data from individual animals. Assigning structures (AIS, nodes) as n results in overstating effects, since especially for AIS, there is significant heterogeneity in the length across neurons from the same type, and this is masked when 100 AIS are considered as individual n instead 100 AIS per animal, and the animal is (correctly) the n. Since the study seems to switch back and forth between these assignments, it would be helpful to level these data across all experiments unless there are specific reasons not to do so, which then need to be explained. As outlined in the methods, all values are given as means {plus minus} SEM; this needs to be corrected for those cases where the standard deviation is the appropriate choice (e.g. all graphs showing n = individual structure, and not the mean of an animal).

As far as the analysis of geometrical AIS changes is concerned, the method section should be extended to address how, if at all, AIS length and position were analyzed in 3D, also considering the somewhat "spotty" immunosignal outlined in Fig. 8D. The observed AIS length change is then discussed in the context of a study conducted in a pharmacological model of myelin loss, however, that particular study (Hamada & Kole, 2015) found not only a length change but a position change after cuprizone-induced AIS plasticity. The authors should therefore discuss this finding in a bit more detail than simply stating "Adaptation of the AIS has been reported in the cuprizone chemical model of demyelination" (p. 14, ll. 512).

Similarly to the points made about structural data above, the data from electrophysiological recordings should be presented in such a way that e.g. the number of cells and/or animals is readily accessible from the graph or legend. In its current form, this information - while available - needs to be pieced together from in-text information supplemented by figure legends. Sometimes, the authors do not include the number of animals behind individual cell data (for details please see author comments). Please carefully review all figures and edit accordingly.

The behavioral data presented in the study is interesting, but the conclusions drawn are not supported by the data presented, as many unknown factors remain in place that could contribute to the observed phenotype.

Reviewer #3 (Public Review):

This work contributes to the literature characterizing early and late waves of transcription and associated chromatin remodeling following neuronal depolarization, here in cultured embryonic striatum. While they find IEG transcription 1h after depolarization, they find chromatin remodeling is slower (opening at the 4h time point). This may be due to chromatin at IEG regulatory regions already being open (in embryonic striatum), although previous work has found remodeling occurring at the 1h time point (in adult dentate gyrus). The authors next show that the chromatin remodeling that occurs at the late (4h) stage is largely in putative regulatory regions of the genome (rather than gene bodies), and is dependent on translation, which validates and extends the prior literature. The authors then transition from genome-wide basic neuroscience to focus on a specific gene of interest, prodynorphin (Pdyn), and a putative enhancer they identify from their chromatin analysis. They target CRISPR-activating and -inhibiting complexes to the putative enhancer and demonstrate that accessibility of this locus is necessary and sufficient for Pdyn transcription. They then show that at least one PDYN enhancer is conserved from rodents to humans, and is only activity-regulated in human GABAergic but not glutamatergic neurons. Finally, the authors generate snATAC-seq and show Pdyn gene and enhancer activity are also cell-type-specific in the rat striatum. The Pdyn work in particular is thorough and novel.

Strengths:<br /> This work integrates multiple cutting-edge methods (multiple forms of genome-wide sequencing, combining new and published data across species, applying new forms of bioinformatic analysis, and targeted epigenome editing) to repeatedly and convincingly demonstrate these waves of chromatin remodeling and transcription. The figures and visual representations of data in particular set a new standard for the field. Although several findings within this paper are not novel, this paper ties previous findings all together in one place and goes on to show potential relevance for neuropsychiatric disorders beyond basic cellular neuroscience. The conclusions are mostly supported by the data.

Results and conclusions that would benefit from clarification/extension.<br /> 1. Throughout the paper, the authors emphasize a "temporal decoupling" of transcriptional and chromatin response to depolarization, based on a lack of significant chromatin changes at 1h, despite IEG transcription. However, previous publications show significant chromatin remodeling at 1h (e.g. Su et al., NN 2017 in adult dentate gyrus) or 2h (Kim et al., Nature 2010; Malik et al., NN 2014 in cultured embryonic cortical neurons). The discussion briefly mentions this contrast, but it remains difficult to conclude decisively whether there is temporal decoupling when such decoupling is not found consistently. If one is to make broad conclusions about basic neural chromatin response to depolarization, it would be ideal to know under which conditions there is temporal decoupling, or if this is a region-specific phenomenon.

2. The UMAP analysis is a novel way to probe transcription factor enrichment, but it's unclear what this is actually showing. The authors sought to ask whether "DARs could be separated based on transcription factor motifs in these regions." However, the motifs present in any genomic stretch are fixed based on genomic sequence, so it seems like this analysis might be asking whether certain motifs are more likely to be physically clustered together in the genome, in activity-regulated regions (rather than certain transcription factors acting in concert, as is implied in discussion). While still potentially interesting, this analysis does not seem to give much additional insight into activity-dependent chromatin remodeling beyond the motif enrichment analysis already performed. Nevertheless, to draw stronger conclusions, it would be necessary to compare clustering to a random set of genomic regions of the same length/size to interpret the clustering here. It would also be useful to know whether the ISL1 motif is also enriched in ubiquitously accessible genomic regions in the striatum (and not just DARs).

3. The authors identify late-response gene enhancers by 3 criteria. However, only Pdyn was highlighted thereafter. How many putative DARs met these three criteria in striatum? Only Pdyn?

Reviewer #3 (Public Review):

This work provides a novel framework for semi-automatic segmentation and parcellation of brain tissues from fetal magnetic resonance imaging (MRI) by fusing an advanced deep learning technique and manual correction by experts. Over the broad age spectrum spanning newborns to adults, several fully-automatic segmentation/parcellation techniques have been proposed, showing robust, reliable performance across MR images with varying imaging quality. Unlike other age groups, however, scanning of the fetal brain is conducted in the womb; thus, there are additional and unique challenges, such as ambiguous positioning of the fetal brain, the surrounding maternal tissue in the fetal MRI, and fetal and maternal motion. These challenges in fetal MRI have collectively served as important bottlenecks in developing robust, reliable automatic segmentation/parcellation frameworks to date. This paper proposes a methodological framework for the segmentation and parcellation of fetal MRI scans using a two-step deep learning model, each for segmentation and parcellation. It is also noteworthy that the validity of the proposed framework has been extensively tested over different datasets with different image quality and different recording parameters, so the robust generalizability of the framework over other fetal MRI datasets is clearly suggested.

Strengths:

In general, a novel design framework, with separation of segmentation and parcellation schemes under each deep learning model, provides ample room for improving the model performance, as suggested by the results of this study. In addition, thanks to the flexibility in the model design (e.g., the choice of deep learning model) and parameters (e.g., manual correction step during training), an identical or similar framework can be easily extended to other datasets for different age groups or diagnostic groups/brain disorders. Another strength is the minimal requirement of human interaction after the training stage as significant time and effort of manual correction is often required following the automatic segmentation of fetal MR images. Lastly, thorough investigation of the inter-dataset generalizability of the proposed segmentation/parcellation framework will be well-received by the fetal neuroscience community.

Weakness:

The main weakness of this paper is the vague definition of the scientific novelty. By design, this paper is a technical study. The technical advancement claimed by the authors is a novel design of deep learning and a two-step deep-learning framework; each for segmentation and parcellation. There have been, however, other deep learning studies, and some share nearly identical model architecture to the one published by Asis-Cruz et al. (Frontiers in Neuroscience, 2022). As such the conceptual improvement in terms of deep learning model architecture is overstated. Regarding the separate framework for segmentation and parcellation, the conventional preprocessing protocol (e.g., Draw-EM; Makropoulos et al. IEEE Transactions on Medical Imaging, 2014) already presented a similar concept. Overall, it is unclear what unique technical advances have been made in the current paper.

A second weakness of the work is the insufficient comparison to other conventional published methods. While the authors' claim that there is no "universally accepted" protocol for fetal brain segmentation/parcellation is at least partially true, Draw-EM, which was originally designed for neonatal brain segmentation, has been widely and successfully utilized in many fetal MRI studies, as discussed by the authors. Instead of a direct comparison to Draw-EM, the authors only performed a descriptive comparison using two exemplar MRI scans. It is unclear whether the superior performance of the proposed framework in these selected scans would be generalizable to others. Similarly, the authors claim that the proposed deep-learning-based segmentation/parcellation framework required minimal time for manual post-preprocessing refinement (1-3 mins), compared to 1-3 hours in another study using Draw-EM (Story et al. Neuroimage: Clinical, 2021). Again, this may not represent a fair comparison considering that the intensity/precision of manual refinement may differ depending on the different goals/objectives of other studies.

Reviewer #2 (Public Review):

In this study, the authors propose the possibility that some neurons in the enteric nervous system (ENS) originate postnatally from a non-ectodermal source. This possibility is investigated using a combination of transgenic lines, single cell RNA-sequencing (scRNA-seq), and immunofluorescence. Initially the authors identify a subset of neurons within myenteric enteric ganglia that are not lineage-labeled by canonical neural-crest derived cre-LoxP strategies. In their analysis, the group seeks to show that these neurons have an origin distinct from neural crest-derived progenitors that are known to initially colonize the developing gut. The team uses multiple cre lines (both Wnt1-cre and Pax3-cre) as well as several distinct reporter lines (ROSA-tdTomato, ROSA-EGFP, Hprt-tdTomato) to demonstrate that the lack of labeling by neural crest cre transgenes is consistent across several tools and not due to any transgene or reporter line artifact. Based on prior analysis that suggests some neurons in the ENS might be arising from a mesodermal lineage, the authors evaluate the possibility that mesoderm could contribute neurons to the ENS by evaluating expression of Tek-cre and Mesp1-cre tagged cell types in myenteric ganglia. The work with transgenic lines is convincing that some ENS neurons originate from an alternative source in the postnatal intestine and that this population increases in aging mice.

The authors apply single cell RNA-sequencing to identify additional markers of these non-neural crest enteric neurons. They rely on dissociation of laminar gut muscle preparations, stripped from the outside of the adult intestine, that contain many cell types including smooth muscle, vasculature, and enteric ganglia. In the analysis of this scRNA-seq data, the authors focus on a cluster of cells in the resulting UMAP plots as being the MENs cluster based on labeling of this cluster with three genes (Calcb (CGRP), Met, and Cdh3). Based on expression of these marker genes there are a very large number of MENs and very few neural crest-derived enteric neurons (NENs) seen in the UMAPs. It is not clear why this difference in cell numbers has occurred. The early lineage tracing data shown with cre transgenes (Figures 1 and 2) shows relatively equal numbers of NENs and MENs in confocal imaging studies, yet in the RNA-seq UMAPs thousands of MENs are displayed while very few NENs are present. There is the possibility that the authors have identified a cell cluster as MENs that does not coincide with the Mesp1-cre or Tek-cre lineage labeled neurons observed within enteric ganglia of the laminar gut muscle preparations. The authors state that they have "used the single cell transcriptomics to both confirm the presence of MENs and identify more MEN-specific markers", however there is not a direct relationship made in this study between the MENs imaged and the cells profiled by single cell RNA-sequencing.

In their analysis the authors note a difference in the percentage of enteric neurons labeled by the neural crest lineage tracer line, Wnt1-cre, relative to the total neurons labeled by the pan-neuronal marker HuC/D with age of the mice studied. They undertake a temporal analysis of the percentage of Wnt1-cre labeled neurons over total HuC/D neurons over the lifespan and note a decrease of Wnt1-cre labeled neurons with age. Further, the team assessed levels of growth factors that are known to promote proliferation and survival of NENs (GDNF-Ret signaling) versus factors known to promote growth of mesoderm (HGF) with age and document a decrease in GDNF-Ret signaling while HGF levels increase with age. The authors propose that the balance between these two signaling pathways is responsible for the shift in proportions of NENs versus MENs in aging animals.

Some of the conclusions of this paper are supported, but several additional analyses are needed to reach the outcomes that the authors infer:

1) Because the scRNA-seq data generated in this study derives from mixed cell populations present in laminar gut muscle preparations, there is a gap between the image data shown for the mesodermal cre lineage tracing and the MENs clusters the authors have selected in their single cell RNA-seq analysis. The absence of direct transcriptional profiling of cells labeled by Mesp1-cre or Tek1-cre expression prevents the authors from definitively connecting their in situ lineage labeling with specific clusters in the single cell RNA-seq analysis.

2) Differential gene expression is the standard approach for identifying markers of a particular cluster and yet this is lacking in this study, and the rationale for why some genes were prioritized as markers of MENs is missing from the manuscript. Reanalysis of the authors posted single cell RNA-seq data found that genes integral to calling MENs (marker genes) were detectable in the data. Met, Cdh3, Calcb, Elavl2, Hand2, Pde10a, Vsnl1, Tubb2b, Stmn2, Stx3, and Gpr88 were all expressed in very few cells and at low levels. Given this, how were these genes chosen to be marker genes for MENs, especially given the low sequencing depth utilized?

3) The authors rely on Phox2b as a marker for all ENS cells, including MENs. However, reprocessing of the authors posted single cell RNA-seq data finds that Phox2b is not detected in any of the cells in the MENs cluster and it's only expressed in very few cells of the neuroglia cluster. This discrepancy between the data the authors have generated and what is widely known about Phox2b expression in the ENS field must be explained as the absence of Phox2b message suggests there is an issue with reliance on low-depth scRNA-seq data for reaching the stated conclusions.

4) The authors have not considered potential similarities between their MENs and other developing ENS lineages, like enteric mesothelial fibroblasts reported by Zeisel et al. 2018, and further analysis is needed to show that MENs are indeed a distinct cell type. Top marker genes of the author's MENs clusters were expressed more often in the clusters that were left out of Morarach et al 2021's E15.5 and E18.5 datasets because those clusters were mostly Phox2b-negative on UMAPs. This lack of Phox2b expression matches the characteristic of the MENs clusters' Phox2b-negative status in the authors single cell dataset. It is important to note that the Morarach dataset consists of Wnt1-cre lineage labeled (originating from neural crest) flow sorted cells. This is of import as it implies that Phox2b-negative cells ARE present within the Wnt1-cre lineage labeled population, an aspect that is relevant to this study's data analysis.

5) Upon reprocessing of the authors MENs-genesis dataset with integration by sample as the authors describe, Met expression is evident within the cluster of NENs on the resulting UMAP plot and yet the authors rely on this gene as a marker of MENs. Whether Met expression is restricted to MENs should be resolved because the authors state it is exclusive to MENs and they subsequently investigate this gene across lifespan. Because it is not clear that Met is absent from neural crest derived enteric neurons this caveat complicates the interpretations of the present study.

6) The authors apply MHCst immunofluorescence to mark MENs, but do not show any RNA expression for the MHCst transcripts in their single cell data. How did the authors come to the conclusion that MHCst IHC would be an appropriate marker for MENs? This rationale is missing from the text.

Reviewer #3 (Public Review):

Human complex traits including common diseases are highly polygenic (influenced by thousands of loci). This observation is in need of an explanation. The authors of this manuscript propose a model that competition for a single global resource (such as RNA polymerase II) may lead to a highly polygenic architecture of traits. Following an analytical examination, the authors reject their hypothesis. This work is of clear interest to the field. It remains to be seen if the model covers the variety of possible competition models.

Reviewer #3 (Public Review):

Wang et al. explored the unique biology of the deep-sea mussel Gigantidas platifrons to understand the fundamental principles of animal-symbiont relationships. They used single-nucleus RNA sequencing and validation and visualization of many of the important cellular and molecular players that allow these organisms to survive in the deep sea. They demonstrate that a diversity of cell types that support the structure and function of the gill including bacteriocytes, specialized epithelial cells that host sulfur-oxidizing or methane-oxidizing symbionts as well as a suite of other cell types including supportive cells, ciliary, and smooth muscle cells. By performing experiments of transplanting mussels from one habitat which is rich in methane to methane-limited environments, the authors showed that starved mussels may consume endosymbionts versus in methane-rich environments upregulated genes involved in glutamate synthesis. These data add to the growing body of literature that organisms control their endosymbionts in response to environmental change.

The conclusions of the data are well supported. The authors adapted a technique that would have been technically impossible in their field environment by preserving the tissue and then performing nuclear isolation after the fact. The use of single-nucleus sequencing opens the possibility of new cellular and molecular biology that is not possible to study in the field. Additionally, the in-situ data (both WISH and FISH) are high-quality and easy to interpret. The use of cell-type-specific markers along with a symbiont-specific probe was effective. Finally, the SEM and TEM were used convincingly for specific purposes in the case of showing the cilia that may support water movement.

The one particular area for clarification and improvement surrounds the concept of a proliferative progenitor population within the gill. The authors imply that three types of proliferative cells within gills have long been known, but their study may be the first to recover molecular markers for these putative populations. The markers the authors present for gill posterior end budding zone cells (PEBZCs) and dorsal end proliferation cells (DEPCs) are not intuitively associated with cell proliferation and some additional exploration of the data could be performed to strengthen the argument that these are indeed proliferative cells. The authors do utilize a trajectory analysis tool called Slingshot which they claim may suggest that PEBZCs could be the origin of all gill epithelial cells, however, one of the assumptions of this analysis is that differentiated cells are developed from the same precursor PEBZC population.

However, these conclusions do not detract from the overall significance of the work of identifying the relationship between symbionts and bacteriocytes and how these host bacteriocytes modulate their gene expression in response to environmental change. It will be interesting to see how similar or different these data are across animal phyla. For instance, the work of symbiosis in cnidarians may converge on similar principles or there may be independent ways in which organisms have been able to solve these problems.

Reviewer #3 (Public Review):

In this manuscript, the authors describe the development of a machine-learning model to be used for gait assessment using insole data. They first developed a machine learning model using an existing, large data set of ground reaction forces collected during walking with force plates in a lab, from healthy adults and a group of people with knee injuries. Subsequently, they tested this model on ground reaction forces derived from insoles worn by a group of 19 healthy adults and a group of n=44 people with knee osteoarthritis (OA). The model was able to accurately identify individuals belonging to the knee OA group or the healthy group using the ground reaction forces during walking. Note: I do not have expertise on machine learning and will therefore refrain from reviewing the ML methods that were applied in this paper.

Strengths: The authors successfully externally validated the trained model for GRF on insole data. Insole data carries potentially rich information, including the path of the CoP during the stance phase. The additional value of insoles over force plates in itself is clear, as insoles can be used independently of laboratory facilities. Moreover, insoles provide information on the COP path, which can have added value over other mobile assessment methods such as inertial sensors.

Limitations: The second ML model, using only insole data to identify knee arthropathy from healthy subjects, was trained on a small sample of subjects. Although I have no background in ML, I can imagine that external validation in an independent and larger sample is needed to support the current findings.

Gait speed has a major influence on the majority of gait-related outcomes. Slow or more cautious gait, due to pain or other causes, is reflected in vertical GRF's with less pronounced peaks. A difference in gait speed between people with pain in their knee (due to injury) and healthy subjects can be expected. This raises the question of what the added value of a model to estimate vertical GRF is over a simpler output (e.g. gait speed itself). Moreover, the paper does not elucidate what the added value of machine learning is over a simpler statistical model.

In line with this issue, the current analyses are not strongly convincing me that the model described resulted in an identification of knee arthropathy-specific signature. Only knee arthropathy vs healthy (relatively young) subjects was compared, and we cannot rule out that this group only reflects general cautious, slow, or antalgic gait. As such, the data does not provide any evidence that the tool might be valuable to identify people with more or less severity of symptoms, or that the tool can be used to discriminate knee osteoarthritis from hip, or ankle osteoarthritis, or even to discriminate between people with musculoskeletal diseases and people with neurological gait disorders. This substantially limits the relevance for clinical (research) practice. In short, the output of the model seems to be restricted to "something is going on here", without further specification. Further development towards more specific aims using the insole data may substantially amplify clinical relevance.

Reviewer #3 (Public Review):

Hayashi et al., investigate the role of spinal neurons derived from the V2 progenitor domain. They identify a molecular marker, Hes2, specific to the V2 lineage in the spinal cord. The authors use this result to generate a new mouse line allowing specific access to the Hes2 lineage and show that this lineage is composed of excitatory V2a and inhibitory V2b spinal interneurons plus some populations of supraspinal neurons. Taking advantage of this new tool, they demonstrate that the developmental silencing of the Hes2 lineage leads to a disruption of mouse locomotor gait characterized by shorter strides and an increased cadence with no alteration of the alternation between flexion and extension. In addition, the authors show that the silencing of the Hes2 lineage also leads to an alteration of the interlimb coordination and a decreased capacity of the mice to achieve complex motor tasks. Using an intersectional genetic approach, the authors further demonstrate that the selective ablation of spinal V2 neurons in adult mice recapitulates the festination phenotype as well as the altered execution of complex motor tasks.

By identifying a novel marker of the V2 lineage in the spinal cord and using this finding to generate a new mouse line Hayashi and colleagues suggest an intriguing interplay between excitatory and inhibitory V2 spinal neurons modulating differentially, multiple facets of motor behavior.

The conclusions of this study are for the vast majority well supported by data. However, a few additional validations of the mouse model that is used and clarification about the methods of statistical analysis would improve the quality of this manuscript.

1) Additional validations of the Hes2iCre mouse line generated and used in this study would improve the quality of the manuscript as well as shed light on the potential value of the use of the Hes2iCre mouse line for future investigations.

- When reporting the cell population labeled by GFP in Hes2iCre; R26LSL-Sun1-GFP the authors need to report the number of animals on which these quantifications were performed to strengthen their conclusions (Figure 3C-E). Similarly, when showing the number of Hes2+, Chx10+ (V2a) and GATA3+ (V2b) neurons in Hes2iCre heterozygous vs homozygous the number of animals should be reported (Figure 3G; Figure S2E-F).

- The numbers of Hes2+, Chx10+ (V2a) and GATA3+ (V2b) neurons in Hes2iCre heterozygous vs homozygous is reported. However, it would improve the validation of the mouse line, if the authors could provide a quantification of the numbers of Chx10+ and GATA3+ cells in heterogygous Hes2WT/iCre animals versus littermates lacking the Cre.

- Although the study focus on spinal V2 neurons and the intersectional approach used in the last part of the paper is compelling, a better description of the supraspinal neurons that are part of the Hes2 lineage would give a better insight into the potential contribution of supraspinal Hes2 lineage to the motor phenotype described in Hes2-silenced mouse. In particular, an experiment showing if V2 (especially Chx10+ V2a) neurons from the medullary reticular nucleus are part of the Hes2 lineage would allow us to get a better grasp on the potential supraspinal effect of Hes2 neurons silencing.

2) Adding a part in the methods explaining the statistical analysis applied is needed. In this part, the choices of the statistical analysis performed should be clearly explained and the assumptions stated. Although the intersectional genetic approach is challenging and does not allow for obtaining numerous animals, the use of parametric Student's t-tests on groups with only 4 animals is discussable and at least needs to be justified in the methods (results presented in Figure 6 and Figure S5). When the number of statistical units allows it, the normality of the distributions and the homoscedasticity should be tested prior to the use a parametric test. In some instances, tests taking into account the hierarchical structure of the data could be used. Furthermore, running statistical analysis on what seems to be a group of n=2 statistical units (Figure S3L) is not appropriate.

3) Although this decision belongs to the authors, the use of the term "synergy" in the title and abstract might be misleading and might lead to confusion regarding the important outcome of this study. The authors show compelling evidence that the spinal ablation of the V2 lineage leads to a disruption of the ipsilateral coordination of body movements. However, as well explained by the authors, prior studies ablating individual V2a and V2b populations did not show any abnormal ipsilateral body coordination. This rather suggests a redundant or complementary function of inhibitory and excitatory V2 spinal neurons in spinal circuits, with the possibility for one individual population to compensate for the effect on the ipsilateral coordination following the ablation of the other population. Alternatively, "synergy" may suggest a simultaneous activity of V2a and V2b neurons that is not in the scope of this work.

Reviewer #3 (Public Review):

The authors previously showed that expressing formate dehydrogenase, rubisco, carbonic anhydrase, and phosphoribulokinase in Escherichia coli, followed by experimental evolution, led to the generation of strains that can metabolise CO2. Using two rounds of experimental evolution, the authors identify mutations in three genes - pgi, rpoB, and crp - that allow cells to metabolise CO2 in their engineered strain background. The authors make a strong case that mutations in pgi are loss-of-function mutations that prevent metabolic efflux from the reductive pentose phosphate autocatalytic cycle. The authors also argue that mutations in crp and rpoB lead to an increase in the NADH/NAD+ ratio, which would increase the concentration of the electron donor for carbon fixation. While this may explain the role of the crp and rpoB mutations, there is good reason to think that the two mutations have independent effects, and that the change in NADH/NAD+ ratio may not be the major reason for their importance in the CO2-metabolising strain.

Specific comments:

1. Deleting pgi rather than using a point mutation would allow the authors to more rigorously test whether loss-off-function mutants are being selected for in their experimental evolution pipeline. The same argument applies to crp.

2. Page 10, lines 10-11, the authors state "Since Crp and RpoB are known to physically interact in the cell (26-28), we address them as one unit, as it is hard to decouple the effect of one from the other". CRP and RpoB are connected, but the authors' description of them is misleading. CRP activates transcription by interacting with RNA polymerase holoenzyme, of which the Beta subunit (encoded by rpoB) is a part. The specific interaction of CRP is with a different RNA polymerase subunit. The functions of CRP and RpoB, while both related to transcription, are otherwise very different. The mutations in crp and rpoB are unlikely to be directly functionally connected. Hence, they should be considered separately.

3. A Beta-galactosidase assay would provide a very simple test of CRP H22N activity. There are also simple in vivo and in vitro assays for transcription activation (two different modes of activation) and DNA-binding. H22 is not near the DNA-binding domain, but may impact overall protein structure.

4. There are many high-resolution structures of both CRP and RpoB (in the context of RNA polymerase). The authors should compare the position of the sites of mutation of these proteins to known functional regions, assuming H22N is not a loss-of-function mutation in crp.

5. RNA-seq would provide a simple assay for the effects of the crp and rpoB mutations. While the precise effect of the rpoB mutation on RNA polymerase function may be hard to discern, the overall impact on gene expression would likely be informative.

Reviewer #3 (Public Review):

This work presents a novel approach for predicting fracture risk from high-resolution peripheral quantitative computed tomography (HR-pQCT): by training a deep learning model to predict five-year fracture risk where the sole input is the full 3D HR-pQCT image. Prior studies have developed models, of varying complexity, to predict fracture risk from HR-pQCT. However, this study is novel in that neither the typical manual efforts required for HR-pQCT image analysis nor additional biomarker collection are required, simplifying potential clinical implementation. The authors show that their model predicts fracture within five years with greater sensitivity than FRAX (with an assumed diagnostic threshold of FRAX > 20% or T-score < -2.5 SD), albeit with reduced specificity. The authors further investigate how their model output, the structural fragility score derived by artificial intelligence (SFS-AI), is correlated with two microarchitectural parameters that can be measured with HR-pQCT, demonstrating that their model captures many relevant characteristics of a patient's bone quality that cannot be captured by the standard clinical tools used to diagnose osteoporosis, and thus to identify patients at elevated risk of fracture.

Strengths

The authors use a very large dataset and a combination of state-of-the-art methods for training and validating their fracture prediction model: k-fold cross-validation is used for training and a held-out external test dataset is used to evaluate ensembled model predictions compared to the current clinical standard for fracture screening. The results with the test dataset show that the model can identify women at risk of fracture in the next five years with greater sensitivity than both FRAX with BMD and BMD alone.

Because the model takes only a full 3D HR-pQCT image as input, the feasibility of clinical implementation is maximized. Standard morphological analysis with HR-pQCT is semi-automated and the labour required for the manual portions of analysis poses a significant barrier to clinical implementation. There is mounting evidence for the clinical utility of HR-pQCT (see Gazzotti et al. Br. J. Radiol. 2023) and fully automated models such as the one presented in this work will be critical for making clinical applications of HR-pQCT feasible.

The authors quantify the contributions to the variance of the model output and examine activation maps overlaid on the HR-pQCT images. These sub-analyses indicate that the model is identifying relevant characteristics of hierarchical bone structure for fracture prediction that are not available from aBMD measurements from DXA and thus are not accounted for in the current standard clinical diagnostic tool.

Weaknesses

The authors make the claim that SFS-AI outperforms FRAX with BMD and BMD in terms of sensitivity and specificity of predicting fragility fractures within 5 years. This claim is supported by looking at the ROCs in figure 1, but the specific comparison made in the discussion is not completely fair as currently presented in the article. The thresholds of FRAX > 20% and T-score < -2.5SD were selected by the authors for binary comparison. FRAX and BMD achieve specificities of ~95% at these thresholds, while SFS-AI achieves a specificity of only 77% at the selected threshold, SFS-AI > 0.5. Conversely, SFS-AI achieves a sensitivity of 50% to 60% while FRAX and BMD achieve very poor sensitivities, between 4% and 16%. The authors have not justified their choice of binarization thresholds for FRAX or BMD by citing literature or clinical guidelines, nor have they motivated their choice of any of the thresholds with a discussion of how clinical considerations could influence the sensitivity-specificity trade-off. It is difficult to directly compare the prognosticative performance of SFS-AI to that of FRAX or BMD when the thresholds for FRAX and BMD are at such different locations on the respective ROCs when compared to where the threshold for SFS-AI places it on the ROC. The authors have also not compared their estimates of the sensitivity and specificity of FRAX and BMD to literature to provide important context for the comparison to SFS-AI. An additional unacknowledged limitation is that the FRAX tool is designed to predict 10-year fracture risk, while the outcome used to train the SFS-AI model and to compare to FRAX was 5-year fracture risk.

Direct comparison may be impossible due to differences in study design or reported performance metrics, but the authors have not at all discussed the quantitative performance of prior models for fracture prediction or discrimination that use HR-pQCT (see Lu et al. Bone 2023 or Whittier et al. JBMR 2023) to contextualize the performance of their novel model. While the model presented in this article has the advantage that it does not require the typical expertise and manual effort needed for HR-pQCT image analysis, it is still important to acknowledge the potential trade-off of ease of implementation vs performance. Models that incorporate additional clinical data or that use standard HR-pQCT analysis outputs rather than raw images may perform well enough to justify the increase in the difficulty of clinical implementation or to motivate further work on fully automating microarchitectural analysis with HR-pQCT images.

Finally, the article does not indicate that either the code used for model training or the trained model itself will be made publicly available. This limits the ability of future researchers to replicate and build on the results presented in the article.

Reviewer #3 (Public Review):

Royer et al. present a fully automated variant of the Barnes maze to reduce experimenter interference and ensure consistency across trials and subjects. They train mice in this maze over several days and analyze the progression of mouse search strategies during the course of the training. By fitting models involving stochastic processes, they demonstrate that a model combined of the random, spatial, and serial processes can best account for the observed changes in mice's search patterns. Their findings suggest that across training days the spatial strategy (using local landmarks) was progressively employed, mostly at the expense of the random strategy, while the serial strategy (consecutive nearby vestibule check) is reinforced from the early stages of training. Finally, they discuss potential mechanistic underpinnings within brain systems that could explain such behavioral adaptation and flexibility.

Strength:<br /> The development of an automated Barnes maze allows for more naturalistic and uninterrupted behavior, facilitating the study of spatial learning and memory, as well as the analysis of the brain's neural networks during behavior when combined with neurophysiological techniques. The system's design has been thoughtfully considered, encompassing numerous intricate details. These details include the incorporation of flexible options for selecting start, goal, and proximal landmark positions, the inclusion of a rotating platform to prevent the accumulation of olfactory cues, and careful attention given to atomization, taking into account specific considerations such as the rotation of the maze without causing wire shortage or breakage. When combined with neurophysiological manipulations or recordings, the system provides a powerful tool for studying spatial navigation system.<br /> The behavioral experiment protocols, along with the analysis of animal behavior, are conducted with care, and the development of behavioral modeling to capture the animal's search strategy is thoughtfully executed. It is intriguing to observe how the integration of these innovative stochastic models can elucidate the evolution of mice's search strategy within a variant of the Barnes maze.

Weakness:<br /> 1. The development of the well-thought-out automated Barnes maze may attract the interest of researchers exploring spatial learning and memory. However, this aspect of the paper lacks significance due to insufficient coverage of the materials and methods required for readers to replicate the behavioral methodology for their own research inquiries.<br /> Moreover, as discussed by the authors, the methodology favors specialists who utilize wired recordings or manipulations (e.g. optogenetics) in awake, behaving rodents. However, it remains unclear how the current maze design, which involves trapping mice in start and goal positions and incorporating angled vestibules resulting in the addition of numerous corners, can be effectively adapted for animals with wired implants.

2. Novelty: In its current format, the main axis of the paper falls on the analysis of animal behavior and the development of behavioral modeling. In this respect, while it is interesting to see how thoughtfully designed models can explain the evolution of mice search strategy in a maze, the conclusions offer limited novel findings that align with the existing body of research and prior predictions.

3. Scalability and accessibility: While the approach may be intriguing to experts who have an interest in or are familiar with the Barnes maze, its presentation seems to primarily target this specific audience. Therefore, there is a lack of clarity and discussion regarding the scalability of behavioral modeling to experiments involving other search strategies (such as sequence or episodic learning), other animal models, or the potential for translational applications. The scalability of the method would greatly benefit a broader scientific community. In line with this view, the paper's conclusions heavily rely on the development of new models using custom-made codes. Therefore, it would be advantageous to make these codes readily available, and if possible, provide access to the processed data as well. This could enhance comprehension and enable a larger audience to benefit from the methodology.

4. Cross-validation of models: The authors have not implemented any measures to mitigate the risk of overfitting in their modeling. It would have been beneficial to include at least some form of cross-validation with stochastic models to address this concern. Additionally, the paper lacks the presence of analytics or measures that assess and compare the performance of the models.

5. Quantification of inter-animal variations in strategy development: It is important to investigate, and address the argument concerning the possibility that not all animals recruit and develop the three processes (random, spatial, and serial) in a similar manner over days of training. It would be valuable to quantify the transition in strategy across days for each individual mouse and analyze how the population average, reflecting data from individual mice, corresponds to these findings. Currently, there is a lack of such quantification and analysis in the paper.

Reviewer #3 (Public Review):

The authors identified the mefenamic (Mef) binding site and DIDS binding site on the KCNQ1 KCNE1 complex. The authors also identified the mechanism of interactions using electrophysiological recording, calculating V1/2 of different mutants, and looking at the instantaneous and tail currents. The contribution of each residue within the binding pocket was analysed using GBSA and PBSA and traditional molecular dynamics simulation.

The manuscript has been substantially revised from the previous version with a greater depth of computational analysis.

Reviewer #3 (Public Review):

The manuscript by Tejeda-Munoz examines signaling by Wnt and macropinocytosis in Xenopus embryos and colon cancer cells. A major problem with the study is the extensive use of pleiotropic inhibitors as "specific" inhibitors of macropinocytosis in embryos. It is true that BafA and EIPA block macropinocytosis, but they do many other things as well. A major target of EIPA is the NheI Na+/proton transporter, which also regulates invasive structures (podosomes, invadopodia) which could have major roles in development. Similarly, Baf1 will disrupt lysosomes and the endocytic system, which secondary effects on mTOR signaling and growth factor receptor trafficking. The authors cannot assume that processes inhibited by these drugs demonstrate a role of macropinocytosis. While correlations in tumor samples between increased expression of PAK1 and V0a3 and decreased expression of GSK3 are consistent with a link between macropinocytosis and Wnt-driven malignancy, the cell and embryo-based experiments do not convincingly make this connection. Finally, the data on FAK and TES are not well integrated with the rest of the manuscript.

1. The data in Fig. 1A do not convincingly demonstrate macropinocytosis - it is impossible to tell what is being labeled by the dextran.

2. The data in Fig. 2 do not make sense. LiCL2 bypasses the WNT activation pathway by inhibiting GSK3. If subsequent treatment with BafA blocks the effects of GSK3 inhibition, then BafrA is doing something unrelated to Wnt activation, whose target is the inhibition/sequestration of GSK3. While BafA might block GSK3 sequestration by inhibiting MVB function, it should have no effect on the inhibition of GSK3 by LiCl2.

3. The effect of EHT on MP in SW480 cells is not clearly related to what is happening in the embryos. The nearly total loss of staining for Rac and -catenin after overnight EIPA does not implicate MP in protein stability - critical controls for cell viability and overall protein turnover are absent. Inhibition of WNT signaling might be expected to enhance -catenin turnover, but the effect on Rac1 is surprising. A more quantitative analysis by western blotting is required.

4. The data on FAK inhibition and TES trafficking are poorly integrated with the rest of the paper.

Reviewer #3 (Public Review):

The work addresses challenges in linking anatomical information to transcriptomic data in single-cell sequencing. It proposes a method called Targeted Genetically-Encoded Multiplexing (TaG-EM), which uses genetic barcoding in Drosophila to label specific cell populations in vivo. By inserting a DNA barcode near the polyadenylation site in a UAS-GFP construct, cells of interest can be identified during single-cell sequencing. TaG-EM enables various applications, including cell type identification, multiplet droplet detection, and barcoding experimental parameters. The study demonstrates that TaG-EM barcodes can be decoded using next-generation sequencing for large-scale behavioral measurements. Overall, the results are solid in supporting the claims and will be useful for a broader fly community. I have only a few comments below:

Specific comments:

1. The authors mentioned that the results of structure pool tests in Fig. 2 showed a high level of quantitative accuracy in detecting the TaG-EM barcode abundance. Although the data were generally consistent with the input values in most cases, there were some obvious exceptions such as barcode 1 (under-represented) and barcodes 15, 20 (over-represented). It would be great if the authors could comment on these and provide a guideline for choosing the appropriate barcode lines when implementing this TaG-EM method.

2. In Supplemental Figure 6, the authors showed GFP antibody staining data with 20 different TaG-EM barcode lines. The variability in GFP antibody staining results among these different TaG-EM barcode lines concerns the use of these TaG-EM barcode lines for sequencing followed by FACS sorting of native GFP. I expected the native GFP expression would be weaker and much more variable than the GFP antibody staining results shown in Supplemental Figure 6. If this is the case, variation of tissue-specific expression of TaG-EM barcode lines will likely be a confounding factor.

3. As the authors mentioned in the manuscript, multiple barcodes for one experimental condition would be a better experimental design. Could the authors suggest a recommended number of barcodes for each experiential condition? 3? 4? Or more? Also, it would be great if the authors could provide a short discussion on the cost of such TaG-EM method. For example, for the phototaxis assay, if it is much more expensive to perform TaG-EM as compared to manually scoring the preference index by videotaping, what would be the practical considerations or benefits of doing TaG-EM over manual scoring?

Reviewer #3 (Public Review):

The study attempts to develop a Drosophila model for the human disease of LND. The issue here, and the main weakness of this study, is that Drosophila does not express the enzyme, HGPRT, which when mutated causes LND. The authors, instead, mutate the functionally-related Drosophila Aprt enzyme. However, it is unknown whether Aprt is also a structural homologue. Because of this, it will likely not be possible to identify pharmacological compounds that rescue HGPRT activity via a direct interaction (unless modelling predicts high conservation of substrate binding pocket between the two enzymes, etc). An additional weakness is that the study does not identify a molecule that may act as a lead compound for further development for treating LND. Rather, the various rescues reported are selective for only a subset of the disease-associated phenotypes. Thus, whilst informative, this first section of the study does not meet the study ambitions.

The second approach adopted is to express a 'humanised mutated' form of HGPRT in Drosophila, which holds more promise for the development of a pharmacological screen. In particular, the locomotor defect is recapitulated but the seizure-like activity, whilst reported as being recapitulated, is debatable. A recovery time of 2.3 seconds is very much less than timings for typical seizure mutants. Nevertheless, the SING behaviour could be sufficient to screen against. However, this is not explored.

In summary, this is a largely descriptive study reporting the behavioural effects of an Aprt loss-of-function mutation. RNAi KD and rescue expression studies suggest that a mix of neuronal (particularly dopaminergic and possibly adenosinergic signalling pathways) and glia are involved in the behavioural phenotypes affecting locomotion, sleep and seizure. There is insufficient evidence to have confidence that the Arpt fly model will prove valuable for understanding / treating LND.

Reviewer #3 (Public Review):

The authors thoroughly evaluate the performance and scalability of existing cell-type deconvolution methods. The paper builds on the existing knowledge by considering the suitability of deconvolution algorithms in the context of more challenging analyses where rare cell types are present or when dealing with unmatched references or noise introduced by a highly abundant cell type within the data. The paper also presents a new simulation framework for spatial transcriptomics data to support their benchmarking effort.

● Major strengths and weaknesses of the methods and results.

While most of the benchmarking studies rely on publicly available spatial transcriptomics datasets, one of the major strengths of the paper is the additional evidence support from their silver standard datasets. Leveraging computational processes synthspot, the authors generated abundant synthetic spatial transcriptomics data with replicates. In addition, the data generation process also accounts for 9 different biological patterns to stay close to real data quality. The authors also communicated with the original authors of each benchmarked method to ensure correct implementation and optimal performance. Figure 2 provides a clear and concise summary of the benchmark results, which will be of great assistance to users who are contemplating conducting deconvolution analysis.

The simulation setup has a significant weakness in the selection of reference single-cell RNAseq datasets used for generating synthetic spots. It is unclear why a mix of mouse and human scRNA-seq datasets were chosen, as this does not reflect a realistic biological scenario. This could call into question the findings of the "detecting rare cell types remains challenging even for top-performing methods" section of the paper, as the true "rare cell types" would not be as distinct as human skin cells in a mouse brain setting as simulated here. Furthermore, it is unclear why the authors developed Synthspot when other similar frameworks, such as SRTsim, exist. Have the authors explored other simulation frameworks? Finally, we would have appreciated the inclusion of tissue samples with more complex structures, such as those from tumors, where there may be more intricate mixing between cell types and spot types.

The authors have effectively accomplished their objectives in benchmarking deconvolution methods by thoughtfully designing the experiments and selecting appropriate evaluation metrics. This paper will be highly beneficial for the community.

This paper can provide guidance for selecting the most proper deconvolution methods under user-decided scenarios of the interests. Synthspot, allows for generating more realistic artificial tissue data with specific spatial patterns and is integrated as part of an easy-to-use and adaptable Nextflow pipeline. It might be worthwhile to clearly differentiate this work from previous work either in the benchmarking area or SRT data simulation area.

Reviewer #3 (Public Review):

Polygenic scores (PGS), constructed based on genetic effect sizes estimated in genome-wide association studies (GWAS) and used to predict phenotypes in humans have attracted considerable recent interest in human and evolutionary genetics, and in the social sciences. Recent work, however, has shown that PGSs have limited portability across ancestry groups, and that even within an ancestry group, their predictive accuracy varies markedly depending on characteristics such as the socio-economic status, age, and sex of the individuals in the samples used to construct them and to which they are applied. This study takes further steps in investigating and addressing the later problem, focusing on body mass index, a phenotype of substantial biomedical interest. Specifically, it quantifies the effects of a large number of co-variates and of interactions between these covariates and the PGS on prediction accuracy; it also examines the utility of including such covariates and interaction in the construction of predictors using both standard methods and artificial neural networks. This study would be of interest to investigators that develop and apply PGSs.

I should add that I have not worked on PGSs and am not a statistician, and apologize in advance if this has led to some misunderstandings.

Strengths:

- The paper presents a much more comprehensive assessment of the effects of covariates than previous studies. It finds many covariates to have a substantial effect, which further highlights the importance of this problem to the development and application of PGSs for BMI and more generally.<br /> - The findings re the relationships between the effects of covariates and interactions between covariates and PGSs are, to the best of my knowledge, novel and interesting.<br /> - The development of predictors that account for multiple covariates and their interaction with the PGS are, to the best of my knowledge, novel and may prove useful in future efforts to produce reliable PGSs.<br /> - The improvement offered by the predictors that account for PGS and covariates using neural networks highlights the importance of non-linear interactions that are not addressed by standard methods, which is both interesting and likely to be of future utility.

Weaknesses:

- The paper would benefit substantially from extensive editing. It also uses terminology that is specific to recent literature on PGSs, thus limiting accessibility to a broader readership.<br /> - The potential meaning of most of the results is not explored. Some examples are provided below:<br /> • the paper emphasizes that 18/62 covariates examined show significant effects, but this result clearly depends on the covariates included. It would be helpful to provide more detail on how these covariates were chosen. Moreover, many of these covariates are likely to be correlated, making this result more difficult to interpret. Could these questions at least be partially addressed using the predictors constructed using all covariates and their interactions jointly (i.e., with LASSO)? In that regard, it would be helpful to know how many of the covariates and interactions were used in this predictor (I apologize if I missed that).<br /> • While the relationship between covariate effects and covariate-PGS interaction effects is intriguing, it is difficult to interpret without articulating what one would expect, i.e., what would be an appropriate null.<br /> • The finding that using artificial neural networks substantially improves prediction over more standard methods is especially intriguing, and highlights the potential importance of non-linear relationships between PGSs and covariates. These relationships remain hidden in a black box, however. Even fairly straightforward analyses, based on using different combinations of the PGS and/or covariates may shed some light on these relationships. For example, analyzing which covariates have a substantial effect on the prediction or varying one covariate at a time for different values of the PGS, etc.<br /> - The relationship to previous work should be discussed in greater detail.

Reviewer #3 (Public Review):

Braithwaite et al. present data from a comprehensive large-scale study of 18-month-old's visual attention. The authors leverage a battery of well-known visual attention tasks to replicate canonical effects found in the literature and assess the latent structure of these tasks. They find that, while controlling for eye tracking precision and accuracy, two factors best fit the data - attention to social and non-social stimuli.

Strengths:<br /> The current study represents what amounts to years of hard work collecting data from a population that is challenging to work with - young children. The authors have diligently attended to data cleaning and sample size throughout the manuscript. Not only do they provide a large-scale replication of several well-known tasks, but they use advanced statistical modeling to discover the structure of visual attention in these 18-month-olds. Overall, this is a valuable contribution to the literature and provides a useful framework for studying visual attention development.

Weaknesses:<br /> While the study is clearly a valuable addition to the extant literature, I have several concerns that might be addressed to improve the manuscript. These primarily center around clarity and conciseness. First, the introduction seems to lack clarity at times. For example, the first paragraph seems to introduce several ideas (e.g., brain and cognitive development, direct and indirect measures of cognition, eyetracking, etc) that make it hard to understand where the paper is going. The authors might consider homing in on 2 main points to motivate eye tracking as a tool. Second, there are many different eye tracking measures may make it difficult for the reader to track which measures were used for each task and which were relevant for the larger model. This may be remedied by adding a section to the methods that briefly describes how each measure was calculated and perhaps a table that lists each task, the measure, and how it was calculated. Third, the results are exciting but hard to visualize in the supplementary figures. I commend them on using raincloud plots to visualize the individual data, but I would strongly encourage the authors to rethink how they display the data. For example, I find the supplementary images hard to see and as a result the effects reported are hard to discern in the image. Fourth, I believe the current data warrant a deeper discussion of what these findings mean. For example, given the developmental nature of the current study, it would be valuable for the authors to discuss how the structure visual attention might change or stay the same across development. For example, do the authors believe the current two factor model would replicate in older children, or would exogenous and endogenous attention emerge as separable components? How do these predictions relate to the extensive research in the adult literature?

Reviewer #3 (Public Review):

The manuscript "Mechanical activation of TWIK-related potassium channel by nanoscopic movement and second messenger signaling" presents a new mechanism for the activation of TREK-1 channel. The mechanism suggests that TREK1 is activated by phosphatidic acids that are produced via a mechanosensitive motion of PLD2 to PIP2-enriched domains. Overall, I found the topic interesting, but several typos and unclarities reduced the readability of the manuscript. Additionally, I have several major concerns on the interpretation of the results. Therefore, the proposed mechanism is not fully supported by the presented data. Lastly, the mechanism is based on several previous studies from the Hansen lab, however, the novelty of the current manuscript is not clearly stated. For example, in the 2nd result section, the authors stated, "fluid shear causes PLD2 to move from cholesterol dependent GM1 clusters to PIP2 clusters and this activated the enzyme". However, this is also presented as a new finding in section 3 "Mechanism of PLD2 activation by shear."

For PLD2 dependent TREK-1 activation. Overall, I found the results compelling. However, two key results are missing.<br /> 1. Does HEK cells have endogenous PLD2? If so, it's hard to claim that the authors can measure PLD2-independent TREK1 activation.<br /> 2. Does the plasma membrane trafficking of TREK1 remain the same under different conditions (PLD2 overexpression, truncation)? From Figure S2, the truncated TREK1 seem to have very poor trafficking. The change of trafficking could significantly contribute to the interpretation of the data in Figure 1.

For shear-induced movement of TREK1 between nanodomains. The section is convincing, however I'm not an expert on super-resolution imaging. Also, it would be helpful to clarify whether the shear stress was maintained during fixation. If not, what is the time gap between reduced shear and the fixed state. lastly, it's unclear why shear flow changes the level of TREK1 and PIP2.

For the mechanism of PLD2 activation by shear. I found this section not convincing. Therefore, the question of how does PLD2 sense mechanical force on the membrane is not fully addressed. Particularly, it's hard to imagine an acute 25% decrease cholesterol level by shear - where did the cholesterol go? Details on the measurements of free cholesterol level is unclear and additional/alternative experiments are needed to prove the reduction in cholesterol by shear.<br /> Importantly, there is no direct evidence for "shear thinning" of the membrane and the authors should avoid claiming shear thinning in the abstract and summary of the manuscript.

The authors should also be aware that hypotonic shock is a very dirty assay for stretching the cell membrane. Often, there is only a transient increase in membrane tension, accompanied by many biochemical changes in the cells (including acidification, changes of concentration etc). Therefore, I would not consider this as definitive proof that PLD2 can be activated by stretching membrane.

Reviewer #3 (Public Review):

A landmark work (Chouhan et al., 2022) from the Sehgal group previously investigated the relationship between sleep and long-term memory formation by dissecting the role of mushroom body intrinsic neurons, extrinsic neurons, and output neurons during sleep-dependent and sleep-independent memory consolidation. In this manuscript, Li et al., profiled transcriptome in the anterior-posterior (ap) α'/β' neurons and identified genes that are differentially expressed after training in fed condition, which supports sleep-dependent memory formation. By knocking down candidate genes systematically, the authors identified Polr1F and Regnase-1 as two important hits that play potential roles in sleep and memory formation. What is the function of sleep and how to create a memory are two long-standing questions in science. The present study used a creative approach to identify novel components that may link sleep and memory consolidation in a specific type of neuron. Importantly, these components implicated that RNA processing may play a role in these processes.

While I am enthusiastic about the innovative approach employed to identify RNA processing genes involved in sleep regulation and memory consolidation, I feel that the data presented in the manuscript is insufficient to support the claim that these two genes establish a definitive link between sleep and memory consolidation. First, the developmental role of Regnase-1 in reducing sleep remains unclear because knocking down Regnase-1 using the GeneSwitch system produced neither acute nor chronic sleep loss phenotype. To address potential confounding issues caused by the GeneSwtich system, I would suggest considering alternative methods, such as Gal80ts, to restrict the RNAi knockdown to adulthood. In addition, QPCR or other expression-measuring methods should be used to validate the specificity and efficiency of the knockdown. Further testing of additional RNAi fly lines and conducting overexpression experiments would also lend credibility to the phenotypes. Second, while constitutive Regnase-1 knockdown produced robust phenotypes for both sleep-dependent and sleep-independent memory, it also led to a severe short-term memory phenotype. This raises the possibility that flies with constitutive Regnase-1 knockdown are poor learners, thereby having little memory to consolidate. The defect in learning could be simply caused by chronic sleep loss before training. Thus, this set of results does not substantiate a strong link between sleep and long-term memory consolidation. Lastly, the discussion on the sequential function of training, sleep, and RNA processing on memory consolidation appears to be speculative based on the present data. While the novel approach did provide novel candidate genes with functions in sleep, memory, and potentially their link, the manuscript would greatly benefit from carefully adjusting the conclusions and incorporating rigorous validations for the RNAi knockdown experiments.

Reviewer #3 (Public Review):

In this manuscript, the authors investigated the effects of deletion of the ER-plasma membrane/Golgi tethering proteins tricalbins (Tcb1-3) on vacuolar morphology to demonstrate the role of membrane contact sites (MCSs) in regulating vacuolar morphology in Saccharomyces cerevisiae. Their data show that tricalbin deletion causes vacuolar fragmentation possibly in parallel with TORC1 pathway. In addition, their data reveal that levels of various lipids including ceramides, long-chain base (LCB)-1P and phytosphingosine (PHS) are increased in tricalbin-deleted cells. The authors find that exogenously added PHS can induce vacuole fragmentation and by performing analyses of genes involved in sphingolipid metabolism, they conclude that vacuolar fragmentation in tricalbin-deleted cells is due to the accumulated PHS in these cells. Importantly, exogenous PHS- or tricalbin deletion-induced vacuole fragmentation was suppressed by loss of the nucleus vacuole junction (NVJ), suggesting the possibility that PHS transported from the ER to vacuoles via the NVJ triggers vacuole fission.

This work provides valuable insights into the relationship between MCS-mediated sphingolipid metabolism and vacuole morphology. The conclusions of this paper are mostly supported by their results, but there is concern about physiological roles of tricalbins and PHS in regulating vacuole morphology under known vacuole fission-inducing conditions. That is, in this paper it is not addressed whether the functions of tricalbins and PHS levels are controlled in response to osmotic shock, nutrient status, or ER stress.

There is another weakness in their claim that the transmembrane domain of Tcb3 contributes to the formation of the tricalbin complex which is sufficient for tethering ER to the plasma membrane and the Golgi complex. Their claim is based only on the structural simulation, but not on biochemical experiments such as co-immunoprecipitation and pull-down.

Reviewer #3 (Public Review):

This manuscript deals with the sex-related gene, DMRT1, showing that it has a testis-promoting function in the rabbit. In loss-of-function studies in the mouse and human, DMRT1 has a role in testis maintenance after birth, although forced expression in the mouse can induce testis formation.

The authors used CRISPR/Cas9 genome editing to generate DMRT1-/- rabbit embryos. The gonads of these embryos developed as ovaries. Interestingly, in addition Y-linked SRY, DMRT1 is required for timely up-regulation of SOX9 during Sertoli cell differentiation in the male gonad. This is quite different to the situation in mice, where Dmrt1 is not required in the testis until after birth (and Sry induced up-regulation of Sox9 hence does not require Dmrt1).

The work adds to the field of sex determination by further broadening our understanding of the DMRT1 gene and the evolution of gonadal sex determination.

In the Discussion section, it is suggested that DMRT1 could act as a pioneering factor to allow SRY action upon Sox9 in the rabbit model. The data show that DMRT1 may be more central to testis formation in mammals than previously considered. The work supports the notion that our understanding that the genetics of gonadal development (and indeed development more generally) should not rest solely on findings in the mouse.

Reviewer #3 (Public Review):

This study on drug repurposing presents the identification of potent activators of the Hippo pathway. The authors successfully screen a drug library and identify two CLK kinase inhibitors as YAP activators, with SM04690 targeting specifically CLK2. They further investigate the molecular basis of SM04690-induced YAP activity and identify splicing events in AMOTL2 as strongly affected by CLK2 inhibition. Exon skipping within AMOTL2 decreases the interactions with membrane bound proteins and is sufficient to induce YAP target gene expression. Overall the study is well designed, the conclusions are supported by sufficient data and represent an exciting connection between alternative splicing and the HIPPO pathway. The specificity of the inhibitor towards CLK2 and the mode of action via AMOTL2 could be supported by further data:

1. The inconsistent inhibitor concentrations and varying results reported in the paper can be distracting. For instance, the response of endogenous targets to 100 nM concentration is described as a >5-fold increase in Figure 2B, whereas it is reported as a 1-1.5-fold response to 1000 nM in Figure 2D. This inconsistency should be addressed and clarified to provide a more accurate and reliable representation of the findings.<br /> 2. In the absence of a strong inhibitor induced YAP target gene expression (Figure 2D), it is difficult to conclude the dependency on YAP expression, as investigated by siRNA mediated knockdown. In a similar experiment, the dependency of the inhibitor on CLK2 expression could be confirmed<br /> 3. To further support the conclusion that CLK2 is the direct target of SM04690, it would be informative to investigate the effects of CLK1/4 inhibition on AMOTL2 exons (for example within RNA-seq data). If CLK1/4 inhibitors do not induce changes in AMOTL2 exons, it would strengthen the evidence for CLK2's role as the direct target. Including the results in the discussion would enhance the comprehensiveness of the study.<br /> 4. It would be important to determine the specific dose of SM04690 required to induce changes in AMOTL2 splicing. The authors observe that AMOTL2 protein levels appear unaffected at doses below 50 nM in Figure 3D, while YAP target genes are already affected at 20 nM in Figure 3G. Although Western blotting may not be the most sensitive method to detect minor changes in splicing, performing PCR experiments at lower doses could provide more insight into the splicing changes. Therefore, it is suggested that the authors include PCR experiments at lower doses to determine if changes in splicing are visible and to better establish the relationship between splicing and gene expression changes.

Reviewer #3 (Public Review):

The manuscript by Sun et al. reveals several crystal structures that help underpin the offensive-defensive relationship between the sea slug Aplysia kurodai and algae. These centre on TNA (a algal glycosyl hydrolase inhibitor), EHEP (a slug protein that protects against TNA and like compounds) and BGL (a glycosyl hydrolase that helps digest algae). The hypotheses generated from the crystal structures herein are supported by biochemical assays.

The crystal structures of apo and TNA-bound EHEP reveals the binding (and thus protection) mechanism. The authors then demonstrate that the precipitated EHEP-TNA complex can be resolubilised at an alkaline pH, potentially highlighting a mechanism for EHEP recycling in the A. kurodai midgut. The authors also present the crystal structures of akuBGL, a beta-glucosidase utilised by Aplysia kurodai to digest laminarin in algae into glucose. The structure revealed that akuBGL is composed of two GH1 domains, with only one GH1 domain having the necessary residue arrangement for catalytic activity, which was confirmed via hydrolytic activity assays. Docking was used to assess binding of the substrate laminaritetraose and the inhibitors TNA, eckol and phloroglucinol to akuBGL. The docking studies revealed that the inhibitors bound akuBGL at the glycone-binding suggesting a competitive inhibition mechanism. Overall, most of the claims made in this work are supported by the data presented.

Reviewer #3 (Public Review):

Light energy drives photosynthesis. However, excessive light can damage (i.e., photo-damage) and thus inactivate the photosynthetic process. A major target site of photo-damage is photosystem II (PSII). In particular, one component of PSII, the reaction center protein, D1, is very suspectable to photo-damage, however, this protein is maintained efficiently by an elaborate multi-step PSII-D1 turnover/repair cycle. Two proteases, FtsH and Deg, are known to contribute to this process, respectively, by efficient degradation of photo-damaged D1 protein processively and endoproteolytically. In this manuscript, Kato et al., propose an additional step (an early step) in the D1 degradation/repair pathway. They propose that "Tryptophan oxidation" at the N-terminus of D1 may be one of the key oxidations in the PSII repair, leading to processive degradation of D1 by FtsH. Both, their data and arguments are very compelling.

The D1 protein repair/degradation pathway in its simplest form can be defined essentially by five steps: (1) migration of damaged PSII core complex to the stroma thylakoid, (2) partial PSII disassembly of the PSII core monomer, (3) access of protease degrading damaged D1, (4) concomitant D1 synthesis, and (5) reassembly of PSII into grana thylakoid. An enormous amount of work has already been done to define and characterize these various steps. Kato et al., in this manuscript, are proposing a very early yet novel critical step in D1 protein turnover in which Tryptophan(Trp) oxidation in PSII core proteins influences D1 degradation mediated by FtsH.

Using a variety of approaches, such as mass-spectrometry (Table 1), site-directed mutagenesis (Figures 2-4), D1 degradation assays (Figures 3, and 4), and simulation modeling (Figure 5), Kato et al., provide both strong evidence and reasonable arguments that an N-terminal Trp oxidation may be likely to be a 'key' oxidative post-translational modification (OPTM) that is involved in triggering D1 degradation and thus activating the PSII repair pathway. Consequently, from their accumulated data, the authors propose a scenario in which the unraveling of the N-terminal of the D1 protein facilitated by Trp oxidation plays a critical 'recognition' role in alerting the plant that the D1 protein is photo-damaged and thus to kick start the processive degradation pathway initiated possibly by FtsH. Coincidently, Forsman and Eaton-Rye (Biochemistry 2021, 60, 1, 53-63), while working with the thermophilic cyanobacterium, Thermosynechococcus vulcanus, showed that when the N-terminal DE-loop of the D1 protein is photo-damaged a disruption of the interaction between the PsbT subunit and D1 occurs which may serve as a signal for PSII to undergo repair following photodamage. While the activation of the processive degradation pathways in Chlamydomonas versus Thermosynechococcus vulcanus have significant mechanistic differences, it's interesting to note and speculate that the stability of the N-terminal of their respective D1 proteins seems to play a critical role in 'signaling' the PSII repair system to be activated and initiate repair. But it's complicated. For instance, significant Trp oxidation also occurs on the lumen side of other PSII subunits which may also play a significant role in activating the repair processes as well. Indeed, Kato et al.,( Photosynthesis Research volume 126, pages 409-416 (2015)) proposed a two-step model whereby the primary event is disruption of a Mn-cluster in PSII on the lumen side. A secondary event is damage to D1 caused by energy that is absorbed by chlorophyll. But models adapt, change, and get updated. And the data provided by Kato et al., in this manuscript, gives us a unique glimpse/snapshot into the importance of the stability of the N-terminal during photo-damage and its role in D1-turnover. For instance, the author's use site-directed mutagenesis of Trp residues undergoing OPTM in the D1 protein coupled with their D1 degradation assays (Figure 3 and 4), provides evidence that Trp oxidation (in particular the oxidation of Trp14) in coordination with FtsH results in the degradation of D1 protein. Indeed, their D1 degradation assays coupled with the use of a ftsh mutant provide further significant support that Trp14 oxidation and FtsH activity are strongly linked. But for FstH to degrade D1 protein it needs to gain access to photo-damaged D1. FtsH access to D1 is achieved by having CP43 partially dissociate from the PSII complex. Hence, the authors also addressed the possibility that Trp oxidation may also play a role in CP43 disassembly from the PSII complex thereby giving FtsH access to D1. Using a site-directed mutagenesis approach, they showed that Trp oxidation in CP43 appeared to have little impact on the PSII repair (Supplemental Figure S6). This result shows that D1-Trp14 oxidation appears to be playing a role in D1 turnover that occurs after CP43 disassembly from the PSII complex. Alternatively, the authors cannot exclude the possibility that D1-Trp14 oxidation in some way facilitates CP43 dissociation. Further investigation is needed on this point. However, D1-Trp14 oxidation is causing an internal disruption of the D1 protein possibly at the N-terminus of the protein. Consequently, the role of Trp14 oxidation in disrupting the stability of the N-terminal domain of the D1 protein was analyzed computationally. Using a molecular dynamics approach (Figure 5), the authors attempted to create a mechanistic model to explain why when D1 protein Trp14 undergoes oxidation the N-terminal domain of D1protein becomes unraveled. Specifically, the authors propose that the interaction between D1 protein Trp14 with PsbI Ser25 becomes disrupted upon oxidation of Trp14. Consequently, the authors concluded from their molecular dynamics simulation analysis that " the increased fluctuation of the first α-helix of D1 would give a chance to recognize the photo-damaged D1 by FtsH protease". Hence, the author's experimental and computational approaches employed here develop a compelling early-stage repair model that integrates 1) Trp14 oxidation, 2) FtsH activation and 3) D1- turnover being initiated at its N-terminal domain. However, a word of caution should be emphasized here. This model is just a snapshot of the very early stages of the D1 protein turnover process. The data presented here gives us just a small glimpse into the unique relationship between Trp oxidation of the D1 protein which may trigger significant N-terminal structural changes of the D1 protein that both signals and provides an opportunity for FstH to begin protease digestion of the D1 protein. However, the authors go to great lengths in their discussion section to not overstate solely the role of Trp14 oxidation in the complicated process of D1 turnover. The authors certainly recognize that there are a lot of moving parts involved in D1 turnover. And while Trp14 oxidation is the major focus of this paper, the authors show in Supplemental Fig S4 the structural positions of various additional oxidized Trp residues in the Thermosynecoccocus vulcans PSII core proteins. Indeed, this figure shows that the majority of oxidized Trps are located on the luminal side of PSII complex clustered around the oxygen-evolving complex. So, while oxidized Trp14 may be involved in the early stages of D1 turnover certainly oxidized Trps on the lumen side are also more than likely playing a role in D1 turnover as well. To untangle this complex process will require additional research.

Nevertheless, identifying and characterizing the role of oxidative modification of tryptophan (Trp) residues, in particular, Trp14, in the PSII core provides another critical step in an already intricate multi-step process of D1 protein turnover during photo-damage.

Reviewer #3 (Public Review):

The data presented suggest that their algorithm can replace a human operator, which is a strong enough reason to publish and disseminate the technology. At the same time, aspects of the methods and results could benefit from a clearer explication. For example, the reported R^2 values for their model's performance are less than 0.5, (0.191, 0.2, 0.345, 0.467). I take this to mean the model's predictions are better than the mean value but that it will probably not generalize well for data it hasn't seen yet. Please comment.

Did the authors partition their data into a training set, a validation set, and a test set? From the manuscript, it wasn't obvious to me they withheld a test set (a set of data never seen by the model, which they used to evaluate the performance of the model selected based on the validation set). From Extended Data Figures 1 and 2, I inferred that the number of samples in the confusion matrix matches the validation size (n=2341). So, are they reporting validation results and not test results? Please explain.

Reviewer #3 (Public Review):

In this manuscript, Zhou et al. demonstrate that the pseudokinase ULK4 has an important role in Hedgehog signaling by scaffolding the active kinase Stk36 and the transcription factor Gli2, enabling Gli2 to be phosphorylated and activated.<br /> Through nice biochemistry experiments, they show convincingly that the N-terminal pseudokinase domain of ULK4 binds Stk36 and the C-terminal Heat repeats bind Gli2.

Lastly, they show that upon Sonic Hedgehog signaling, ULK4 localizes to the cilia and is needed to localize Stk36 and Gli2 for proper activation.

This manuscript is very solid and methodically shows the role of ULK4 and STK36 throughout the whole paper, with well controlled experiments. The phosphomimetic and incapable mutations are very convincing as well.<br /> I think this manuscript is strong and stands as is, and there is no need for additional experiments.

Overall, the strengths are the rigor of the methods, and the convincing case they bring for the formation of the ULK4-Gli2-Stk36 complex. There are no weaknesses noted. I think a little additional context for what is being observed in the immunofluorescence might benefit readers who are not familiar with these cell types and structures.

Reviewer #3 (Public Review):

The study by Thommen et al. sought to identify the native role of the Plasmodium falciparum FKBP35 protein, which has been identified as a potential drug target due to the antiplasmodial activity of the immunosuppressant FK506. This compound has multiple binding proteins in many organisms; however, only one FKBP exists in P. falciparum (FKBP35). Using genetically-modified parasites and mass spectrometry-based cellular thermal shift assays (CETSA), the authors suggest that this protein is in involved in ribosome homeostasis and that the antiplasmodial activity of FK506 is separate from its activity on the FKBP35 protein. The authors first created a conditional knockdown using the destruction domain/shield system, which demonstrated no change in asexual blood stage parasites. A conditional knockout was then generated using the DiCre system. FKBP35KO parasites survived the first generation but died in the second generation. The authors called this "a delayed death phenotype", although it was not secondary to drug treatment, so this may be a misnomer. This slow death was unrelated to apicoplast dysfunction, as demonstrated by lack of alterations in sensitivity to apicoplast inhibitors. Quantitative proteomics on the FKBP35KO vs FKBP35WT parasites demonstrated enrichment of proteins involved in pre-ribosome development and the nucleolus. Interestingly, the KO parasites were not more susceptible to cycloheximide, a translation inhibitor, in the first generation (G1), suggesting that mature ribosomes still exist at this point. The SunSET technique, which incorporates puromycin into nascent peptide chains, also showed that in G1 the FKBP35KO parasites were still able to synthesize proteins. But in the second generation (G2), there was a significant decrease in protein synthesis. Transcriptomics were also performed at multiple time points. The effects of knockout of FKBP35 were transcriptionally silent in G1, and the parasites then slowed their cell cycles as compared to the FKBP35WT parasites.

The authors next sought to evaluate whether killing by FK506 was dependent upon the inhibition of PfKBP35. Interestingly, both FKBP35KO and FKBP35WT parasites were equally susceptible to FK506. This suggested that the antiplasmodial activity of FK506 was related to activity targeting essential functions in the parasite separate from binding to FKBP35. To identify these potential targets, the authors used MS-CETSA on lysates to test for thermal stabilization of proteins after exposure to drug, which suggests drug-protein interactions. As expected, FK506 bound FKBP35 at low nM concentrations. However, given that the parasite IC50 of this compound is in the uM range, the authors searched for proteins stabilized at these concentrations as putative secondary targets. Using live cell MS-CETSA, FK506 bound FKBP35 at low nM concentrations; however, in these experiments over 50 ribosomal proteins were stabilized by the drug at higher concentrations. Of note, there was also an increase in soluble ribosomal factors in the absence of denaturing conditions. The authors suggested that the drug itself led to these smaller factors disengaging from a larger ribosomal complex, leading to an increase in soluble factors. Ultimately, the authors conclude that the native function of FKBP35 is involved in ribosome homeostasis and that the antiplasmodial activity of FK506 is not related to the binding of FKBP35, but instead results from inhibition of essential functions of secondary targets.

Strengths<br /> This study has many strengths. It addresses an important gap in parasite biology and drug development, by addressing the native role of the potential antiplasmodial drug target FKBP35 and whether the compound FK506 works through inhibition of that putative target. The knockout data provide compelling evidence that the KBP35 protein is essential for asexual parasite growth after one growth cycle. Analysis of the FKBP35KO line also provides evidence that the effects of FK506 are likely not solely due to inhibition of that protein, but instead must have secondary targets whose function is essential. These data are important in the field of drug development as they may guide development away from structure-based FK506 analogs that bind more specifically to the FKBP35 protein.

Weaknesses:<br /> There are also a few notable weaknesses in the evidence that call into question the conclusion in the article title that FKBP35 is definitely involved in ribosomal homeostasis. While the proteomics supports alterations in ribosome biogenesis factors, it is unclear whether this is a direct role of the loss of the FKBP35 protein or is more related to non-specific downstream effects of knocking down the protein. The CETSA data clearly demonstrate that FK506 binds PfKB35 at low nM concentrations, which is different than the IC50 noted in the parasite; however, the evidence that the proteins stabilized by uM concentrations of drug are actual targets is not completely convincing. Especially, given the high uM amounts of drug required to stabilize these proteins. This section of the manuscript would benefit from validation of a least one or two of the putative candidates noted in the text. In the live cell CETSA, it is noted that >50 ribosomal components are stabilized in drug treated but not lysate controls. Similarly, the authors suggest that the -soluble fraction of ribosomal components increases in drug-exposed parasites even at 37{degree sign}C and suggests that this is likely from smaller ribosomal proteins disengaging from larger ribosomal complexes. While the evidence is convincing that this protein may play a role in ribosome homeostasis in some capacity, it is not sure that the title of the paper "FKBP secures ribosome homeostasis" holds true given the lack of mechanistic data. A minor weakness, but one that should nonetheless be addressed, is the use of the term "delayed death phenotype" with regards to the knockout parasite killing. This term is most frequently used in a very specific setting of apicoplast drugs that inhibit apicoplast ribosomes, so the term is misleading. It is also possible that the parasites are able to go through a normal cycle because of the kinetics of the knockout and that the time needed for protein clearance in the parasite to a level that is lethal.

Overall, the authors set out to identify the native role of FKB35 in the P. falciparum parasites and to identify whether this is, in fact, the target of FK506. The data clearly demonstrate that FKBP35 is essential for parasite growth and provide evidence that alterations in its levels have proteomic but not transcriptional changes. However, the conclusion that FKBP35 actually stabilizes ribosomal complexes remains intermediate. The data are also very compelling that FK506 has secondary targets in the parasite aside from FKBP35; however, the high uM concentrations of the drug needed to attain results and the lack of biological validation of the CETSA hits makes it difficult to know whether any of these are actually the target of the compound or instead are nonspecific downstream consequences of treatment.

Reviewer #3 (Public Review):

GluK1 forms glutamate-gated ion channels with an important function in synaptic transmission and neuron excitability. Particularly, a GluK1 splice-variant (Gluk1-1) with significant expression in different regions of the brain has not been characterized before. The paper of Dhingra et al. aims to evaluate the role of the Exon 9 splice insert in GluK1 on channel function. This study relies mainly on electrophysiological approaches to determine the effect of the splice insert on GluK1 gating properties, including desensitization, agonist efficacy, recovery, and rectification. Overall, this work provides two major milestones: 1) the first functional characterization of the Gluk1-1a variant and 2) the first structure of this channel. The functional data supporting the role of the insert on channel properties are solid, although the current data does not provide significant insights about the mechanisms behind this. Also, the little information associated with the resolved structure precludes providing further insights about the structural basis that account for the impact of the insert on channel function. Overall, I consider this an interesting paper that represents an important advance in the study of glutamate receptors.

Reviewer #3 (Public Review):

Lee, Kyungtae and colleagues have discovered and mapped out alpha-arrestin interactomes in both human and Drosophila through the affinity purification/mass spectrometry and the SAINTexpress method. They found the high confident interactomes, consisting of 390 protein-protein interactions (PPIs) between six human alpha-arrestins and 307 preproteins, as well as 740 PPIs between twelve Drosophila alpha-arrestins and 467 prey proteins. To define and characterize these identified alpha-arrestin interactomes, the team employed a variety of widely recognized bioinformatics tools. These included protein domain enrichment analysis, PANTHER for protein class enrichment, DAVID for subcellular localization analysis, COMPLEAT for the identification of functional complexes, and DIOPT to identify evolutionary conserved interactomes. Through these analyses, they confirmed known alpha-arrestin interactors' role and associated functions such as ubiquitin ligase and protease. Furthermore, they found unexpected biological functions in the newly discovered interactomes, including RNA splicing and helicase, GTPase-activating proteins, ATP synthase. The authors carried out further study into the role of human TXNIP in transcription and epigenetic regulation, as well as the role of ARRDC5 in osteoclast differentiation. This study holds important value as the newly identified alpha-arrestin interactomes are likely aiding functional studies of this group of proteins. Despite the overall support from data for the paper's conclusions, certain elements related to data quantification, interpretation, and presentation demand more detailed explanation and clarification.

1) In Figure 1B, it is shown that human alpha-arrestins were N-GFP tagged (N-terminal) and Drosophila alpha-arrestins were C-GFP (C-terminal). However, the rationale of why the authors used different tags for human and fly proteins was not explained in the main text and methods.<br /> 2) In Figure 2A, there seems to be an error for labeling the GAL4p/GAL80p complex that includes NOTCH2, NOTCH1 and TSC2.<br /> 3) In Figure 5, given that knockdown of TXNIP did not affect the levels and nuclear localization of HDAC2, the authors suggest that TXNIP might modulate HDAC2 activity. However, the ChiP assay suggest a different model - TXNIP-HDAC2 interaction might inhibit the chromatin occupancy of HDAC2, reducing histone deacetylation and increasing global chromatin accessibly. The authors need to propose a model consistent with these sets of all data.<br /> 4) The authors showed that ectopic expression of ARRDC5 increased osteoclast differentiation and function. Does loss of ARDDC5 lead to defects in osteoclast function and fate determination?<br /> 5) From Figure 6D, the authors argued that ARRDC5 overexpression resulted in more V-ATPase signals: however, there is no quantification. Quantification of the confocal images will foster the conclusion. Also, western blots for V-ATPase proteins will provide an alternative way to determine the effects of ARRDC5.<br /> 6) The results from Figure 6D did not support the authors' argument that ARRDC5 might control the membrane localization of the V-ATPase, as bafilomycin is the V-ATPase inhibitor. ARRDC5 knockdown experiments will help to determine whether ARRDC5 can control the membrane localization of the V-ATPase in osteoclast.

• food supply chain vulnerability
• most US cities would run out of food in 3 days if there was a major food supply chain disruption

Reviewer #3 (Public Review):

The authors generated a novel sfGFP::Aβ C. elegans models of AD that expresses Abeta aggregates extracellularly; using this worm model, they identified that a disintegrin and metalloprotease ADM-2, an ortholog of human ADAM9, participated in removing these extracellular aggregates. This worm model may be very useful to the AD field after further characterization.

A novelty of this paper is the generation of a worm model of AD that produces extracellular Abeta aggregates, mimicking one of the two disease-defining pathological features of AD. The authors have also identified a protein which inhibits Abeta aggregation in the AD worm model; if these data are relevant to humans, they may reveal a new druggable target against AD.

Reviewer #3 (Public Review):

The study, performed in the animal model C. elegans, aims at characterizing functional differences in the meiosis-specific kleisins, REC-8 and COH-3/4.<br /> The authors conclude that in worms the identity of the kleisin subunit of the cohesin complex determines whether cohesin promotes cohesion, or controls higher-order chromosome structure. COH-3/4 is highly abundant and dynamic and responds to SCC-2 and WAPL-1. In contrast, REC-8 complexes associate stably and in low abundance and are resistant to SCC-2 and WAPL-1 perturbations.

Main points:

This study is a continuation and partially a repeat of a study Castellano-Pozo & Martinez-Perez published in Nat. Comm. 2020, in which they depleted COH-3/4 and REC-8 by injecting TEV and cleaved artificially engineered TEV sites in these kleisins.The results were slightly different though, as the authors concluded: "Disassembly of axial elements requires simultaneous removal of REC-8 and COH-3/4."

The current study uses a degron instead of TEV and SIM to revisit the same result. This time, degradation of COH-3/4 alone, but not of Rec8 alone completely eliminates axial elements. It seems that, if the conclusion is now correct, the previous headline must be incorrect, showing that more care has to be taken in the conclusions.

One new experiment in this study is the degradation of scc-2::AID::GFP. The authors treat the germline with auxin for 14 hours. How long scc-2::AID actually needs for degradation and thus, how long cells actually remain without SCC-2, is unknown. What is definitely needed is a serious analysis of the speed of degradation of Scc2 in the various stages.

It is currently not possible to estimate, as the authors do, how long cells have been without SCC-2. This estimation assumes an immediate depletion of SCC-2.<br /> If this were indeed the case, then depletion intervals should be much shorter, because the important primary phenotypes occur immediately after depletion, not 14 hours later.

Reviewer #3 (Public Review):

This paper was a significant and commendable effort, given all the challenges in TB genetics research. It was generally well written and analyses well done. Analytical methods were appropriate. The inclusion of polygenic heritability estimates is also nice to have within this large work. There is also a wealth of supplemental data provided, which will be useful to the field.

However, there are a number of important weaknesses that need to be addressed. These are listed here, and recommended revisions are addressed in the recommendations section:<br /> 1. As the authors point out, one of the challenges in this work is the varying phenotype definitions (diagnosis of TB cases, definition of controls) across all the included genetic studies. Table S1 is critical for this, however it is missing information, and some of the information is unclear. More importantly, the authors state multiple times that there is no evidence of heterogeneity due to these variable phenotype definitions, and that genetic ancestry contributes more to differences in effect sizes between GWAS than study design. However, these two things are confounded - different study designs / phenotype definitions were used in studies of different ancestry.<br /> 2. The polygenic heritability analysis table is not explained very well.<br /> 3. The supplemental data file is not very helpful without some sort of guide. It isn't clear whether the wealth of candidate genes that have been studied in TB were examined in these data. That would be a great benefit of this work.<br /> 4. There needs to be clarity on how unpublished works were sought. In non-genetic meta-analyses, there is usually some detail about a process of contacting authors, etc. There needs to be some assurance that every attempt was made to collect all the relevant data. It is also not clear why family-based analyses could not be included considering that summary statistics were the basis of analysis.<br /> 5. It is rather surprising that only one locus meets genome-wide significance. The authors do explain this well in terms of the ancestry-specific effects driving these results, but it is also surprising that no candidate genes (that had not been discovered in GWAS studies, but were rather studied separately) did not rise to some higher significance threshold.

Reviewer #3 (Public Review):

Liu and colleagues examined learning and brain plasticity in neurotypical children and children with autism. The main findings include autistic children relying more on rule-based versus memory-based learning strategies, altered associations between learning gains and brain plasticity in children with autism, and insistence on sameness as a moderator between brain plasticity and learning in autism. Although the sample size is limited in this study, the findings provide a significant contribution to the field.

The major strengths of this paper include an extensive pre and post training protocol, a detailed methods section, rationale behind the study, investigation of a potential moderator of learning gains and neural plasticity, and investigation of "neural plasticity" in association to learning in autism.

Weaknesses of the study include a small sample size, and some missing information/analyses from the study.

The authors laid out four clear aims of the study. They investigated these aims and the analytic approaches were appropriate.

The paper included significant findings toward better understanding the mechanisms underlying differences in learning strategies and behavior in children diagnosed with autism spectrum disorder. This holds significant value in educational and classroom settings. Further, the investigation of a potential moderator of learning gains and neural plasticity provides a potential mechanism to improve the relationship. Overall, this is a significant contribution to the field.

The autism literature is limited in understanding differences in learning styles and the underlying neural mechanisms of these differences.

Reviewer #3 (Public Review):

In this paper, the authors report cervical cancer screening practice during the covid pandemic in the US from the perspective of health professionals (HPs). Two methods were used: survey and regression analysis, and qualitative interviews. Analyses indicated that older, non-White, internal medicine, and family medicine clinicians and those practicing in community health centers had higher odds of reporting reduced screening. Interviews highlighted disruptions of services and a lack of tracking systems.<br /> The strengths of the paper are mainly i) using three different sources of HPs' recruitment and ii) being able to recruit a large number of participants in both survey and interviews and iii) the demographic characteristics of the interviewees were similar to those of the participants of the survey.

Reviewer #3 (Public Review):

Once inside a cellular vacuole, Salmonella senses the low pH and activates the transcriptional regulator SsrB to induce expression of the Salmonella pathogenicity island 2 genes that are essential for intracellular survival and replication inside the host. This study investigates the mechanisms by which SsrB senses the pH changes, and with a series of elegant experiments identify a conserved residue in the receiver domain, His12, as essential for pH sensing and Salmonella virulence.

Overall, this study identifies an important mechanism of pathogen virulence, which could be targeted to control intracellular replication of the pathogen. The experiments are well conducted, the manuscript is clearly written, and the data are convincing and well presented. The authors perform a logical and detailed analysis of several portions of SsrB to finally identify His12 as a key residue for pH sensing. This was not an easy task. Moreover, the fact that a single amino acid appears to be so important for SsrB pH sensing and SsrB phosphorylation is an important finding for potentially targeting SsrB and inhibiting Salmonella virulence.

Reviewer #3 (Public Review):

The work proposes a model of neural information processing based on a 'synergistic global workspace,' which processes information in three principal steps: a gatekeeping step (information gathering), an information integration step, and finally, a broadcasting step. The authors determined the synergistic global workspace based on previous work and extended the role of its elements using 100 fMRI recordings of the resting state of healthy participants of the HCP. The authors then applied network analysis and two different measures of information integration to examine changes in reduced states of consciousness (such as anesthesia and after-coma disorders of consciousness). They provided an interpretation of the results in terms of the proposed model of brain information processing, which could be helpful to be implemented in other states of consciousness and related to perturbative approaches. Overall, I found the manuscript to be well-organized, and the results are interesting and could be informative for a broad range of literature, suggesting interesting new ideas for the field to explore. However, there are some points that the authors could clarify to strengthen the paper. Key points include:

1. The work strongly relies on the identification of the regions belonging to the synergistic global workspace, which was primarily proposed and computed in a previous paper by the authors. It would be great if this computation could be included in a more explicit way in this manuscript to make it self-contained. Maybe include some table or figure being explicit in the Gradient of redundancy-to-synergy relative importance results and procedure.

2. It would be beneficial if the authors could provide further explanation regarding the differences in the procedure for selecting the workspace and its role within the proposed architecture. For instance, why does one case uses the strength of the nodes while the other case uses the participation coefficient? It would be interesting to explore what would happen if the workspace was defined directly using the participation coefficient instead of the strength. Additionally, what impact would it have on the procedure if a different selection of modules was used? For example, instead of using the RSN, other criteria, such as modularity algorithms, PCA, Hidden Markov Models, Variational Autoencoders, etc., could be considered. The main point of my question is that, probably, the RSN are quite redundant networks and other methods, as PCA generates independent networks. It would be helpful if the authors could offer some comments on their intuition regarding these points without necessarily requiring additional computations.

3. The authors acknowledged the potential relevance of perturbative approaches in terms of PCI and quantification of consciousness. It would be valuable if the authors could also discuss perturbative approaches in relation to inducing transitions between brain states. In other words, since the authors investigate disorders of consciousness where interventions could provide insights into treatment, as suggested by computational and experimental works, it would be interesting to explore the relationship between the synergistic workspace and its modifications from this perspective as well.

Reviewer #3 (Public Review):

The study by Ngodup and colleagues describes the contribution of sodium leak NALCN conductance on the effects of noradrenaline on cartwheel interneurons of the DCN. The manuscript is very well-written and the experiments are well-controlled. The scope of the study is of high biological relevance and recapitulates a primary finding of the Khaliq lab (Philippart et al., eLife, 2018) in ventral midbrain dopamine neurons, that Gi/o-coupled receptors inhibit NALCN current to reduce neuronal excitability. Together these studies provide unequivocable evidence for NALCN as a downstream target of these receptors. There are no major concerns. I have only minor suggestions:

Minor<br /> 1. As introduced in the introduction, NALCN is inhibited by extracellular calcium which has led to some discourse of the relevance of NALCN when recorded in 0.1 mM calcium. A strength of this study is the effect of NA on NALCN is recorded in physiological levels of calcium (1.2 mM). I suggest including the concentration of extracellular calcium in the aCSF in the Results section instead of relying on the reader to look to the Methods.

2. It would be interesting to include the basal membrane properties of the KO compared to wildtype, including membrane resistance and resting membrane potential. From the example recording in Figure 2, one might think that the KOs have lower membrane resistance, so it is interesting that the 2 mV hyperpolarization produced similar effects on rheobase. In addition, from the example in Figure 2G, it appears that NA has an effect on firing frequency with large current injection in the KO. Is this true in grouped data and if so, is there any speculation into how this occurs?

3. Please expand on the rationale for why GABAB and alpha2 must be physically close to NALCN. To my knowledge, the mechanism by which these receptors inhibit NALCN is not known. Must it be membrane-delimited?

Reviewer #3 (Public Review):

Functional and anatomical studies of spinal circuitry in vertebrates have formed the basis of our understanding of neuronal control of movements. Larval zebrafish provide a simplified system for deciphering spinal circuitry. In this manuscript, the authors performed scRNAseq on spinal cord neurons in larval zebrafish, identifying major classes of neuronal and glial types. Through transcriptome analysis, they validated several key interneuron types previously implicated in zebrafish locomotion circuitry. The authors went beyond identifying transcriptional markers and explored synaptic molecules associated with the strength of motor output. They discovered molecular distinctions causally related to the unique physiology of primary motoneuron (PMn) function, which involves providing strong synaptic outputs for escapes and fast swimming. They defined functional 'cassettes' comprising specific combinations of voltage-dependent ion channel types and synaptic proteins, likely responsible for generating maximal motor outputs.

Reviewer #3 (Public Review):

Syntactic parsing is a highly dynamic process: When an incoming word is inconsistent with the presumed syntactic structure, the brain has to reanalyze the sentence and construct an alternative syntactic structure. Since syntactic parsing is a hidden process, it is challenging to describe the syntactic structure a listener internally constructs at each time moment. Here, the authors overcome this problem by (1) asking listeners to complete a sentence at some break point to probe the syntactic structure mentally constructed at the break point, and (2) using a DNN model to extract the most likely structure a listener may extract at a time moment. After obtaining incremental syntactic features using the DNN model, the authors analyze how these syntactic features are represented in the brain using MEG.

Although the analyses are detailed, the current conclusion needs to be further specified. For example, in the abstract, it is concluded that "Our results reveal a detailed picture of the neurobiological processes involved in building structured interpretations through the integration across multifaceted constraints". The readers may remain puzzled after reading this conclusion.

Similarly, for the second part of the conclusion, i.e., "including an extensive set of bilateral brain regions beyond the classical fronto-temporal language system, which sheds light on the distributed nature of language processing in the brain."<br /> The more extensive cortical activation may be attributed to the spatial resolution of MEG, and it is quite well acknowledged that language processing is quite distributive in the brain.

The authors should also discuss:

(1) individual differences (whether the BERT representation is a good enough approximation of the mental representation of individual listeners).

(2) parallel parsing (I think the framework here should allow the brain to maintain parallel representations of different syntactic structures but the analysis does not consider parallel representations).

Reviewer #3 (Public Review):

Vitamin A is critical for the development of the brain and for neuronal function and plasticity, however the mechanisms responsible for the uptake of retinol across the blood brain barrier (BBB) are currently not known. The authors investigate vitamin A uptake across the blood brain barrier using an in vitro model based on endothelial cells differentiated from human derived induced pluripotent stem cells. Using recombinant cargo proteins and radioactive tracers the authors then propose a mechanism and a kinetic model for the uptake of retinol across the BBB that requires serum retinol binding protein 4 (RBP4 or RBP) and its receptor stimulated by retinoic acid 6 (STRA6). The results support a concentration dependent mechanism of transport combining a rapid fluid-phase retinol and a slower directed RBP-complexed retinol across the BBB. The data also hint at the potential regulatory roles of TTR on this process independent of its interaction with RBP.

Strengths:<br /> The studies are rigorous and careful and the authors consider free retinol uptake from the fluid-phase in addition to evaluating RBP-TTR and RBP-STRA6 interactions.<br /> The antibody to STRA6 is validated.<br /> The experiments performed are clearly described.

Weaknesses:<br /> The results presented do not offer significant new information regarding the uptake of retinol by tissues beyond what is known and published using genetic, structural and biochemical approaches.<br /> The use of the iPSC-derived BBB model is potentially interesting but this could have been complemented by a thorough genetic dissection of the cellular factors required for the uptake, transcellular transport, and secretion of retinol by the brain endothelial cells.<br /> The conclusions derived are not well supported by the data presented.<br /> It is difficult to infer a mechanism or to derive a meaningful conclusion regarding the in vivo relevance of the results presented.

Reviewer #3 (Public Review):

Here, the authors trained catElMo, a new context-aware embedding model for TCRβ CDR3 amino acid sequences for TCR-epitope specificity and clustering tasks. This method benchmarked existing work in protein and TCR language models and investigated the role that model architecture plays in the prediction performance. The major strength of this paper is comprehensively evaluating common model architectures used, which is useful for practitioners in the field. However, some key details were missing to assess whether the benchmarking study is a fair comparison between different architectures. Major comments are as follows:

- It is not clear why epitope sequences were also embedded using catELMo for the binding prediction task. Because catELMO is trained on TCRβ CDR3 sequences, it's not clear what benefit would come from this embedding. Were the other embedding models under comparison also applied to both the TCR and epitope sequences? It may be a fairer comparison if a single method is used to encode epitope sequence for all models under comparison, so that the performance reflects the quality of the TCR embedding only.<br /> - The tSNE visualization in Figure 3 is helpful. It makes sense that the last hidden layer features separate well by binding labels for the better performing models. However, it would be useful to know if positive and negative TCRs for each epitope group also separate well in the original TCR embedding space. In other words, how much separation between these groups is due to the neural network vs just the embedding?<br /> - To generate negative samples, the author randomly paired TCRs from healthy subjects to different epitopes. This could produce issues with false negatives if the epitopes used are common. Is there an estimate for how frequently there might be false negatives for those commonly occurring epitopes that most populations might also have been exposed to? Could there be a potential batch effect for the negative sampled TCR that confounds with the performance evaluation?<br /> - Most of the models being compared were trained on general proteins rather than TCR sequences. This makes their comparison to catELMO questionable since it's not clear if the improvement is due to the training data or architecture. The authors partially addressed this with BERT-based models in section 2.4. This concern would be more fully addressed if the authors also trained the Doc2vec model (Yang et al, Figure 2) on TCR sequences as baseline models instead of using the original models trained on general protein sequences. This would make clear the strength of context-aware embeddings if the performance is worse than catElmo and BERT.

Reviewer #3 (Public Review):

The study aims at creating novel episodic memories during slow wave sleep, that can be transferred in the awake state. To do so, participants were simultaneously presented during sleep both foreign words and their arbitrary translations in their language (one word in each ear), or as a control condition only the foreign word alone, binaurally. Stimuli were presented either at the trough or the peak of the slow oscillation using a closed-loop stimulation algorithm. To test for the creation of a flexible association during sleep, participant were then presented at wake with the foreign words alone and had (1) to decide whether they had the feeling of having heard that word before, (2) to attribute this word to one out of three possible conceptual categories (to which translations word actually belong), and (3) to rate their confidence about their decision.

The paper is well written, the protocol ingenious and the methods are robust. However, the results do not really add conceptually to a prior publication of this group showing the possibility to associate in slow wave sleep pairs of words denoting large or small object and non words, and then asking during ensuing wakefulness participant to categorise these non words to a "large" or "small" category. In both cases, the main finding is that this type of association can be formed during slow wave sleep if presented at the trough (versus the peak) of the slow oscillation. Crucially, whether these associations truly represent episodic memory formation during sleep, as claimed by the authors, is highly disputable as there is no control condition allowing to exclude the alternative, simpler hypothesis that mere perceptual associations between two elements (foreign word and translation) have been created and stored during sleep (which is already in itself an interesting finding). In this latter case, it would be only during the awake state when the foreign word is presented that its presentation would implicitly recall the associated translation, which in turn would "ignite" the associative/semantic association process eventually leading to the observed categorisation bias (i.e., foreign words tending to be put in the same conceptual category than their associated translation). In the absence of a dis-confirmation of this alternative and more economical hypothesis, and if we follow Ocam's razor assumption, the claim that there is episodic memory formation during sleep is speculative and unsupported, which is a serious limitation irrespective of the merits of the study. The title and interpretations should be toned down in this respect

Other remarks:

Lines 43-45 : the assumption that the sleeping brain decides whether external events can be disregarded, requires awakening or should be stored for further consideration in the waking state is dubious, and the supporting references date from a time (the 60') during which hypnopedia was investigated in badly controlled sleep conditions (leaving open the doubt about the possibility that it occurred during micro awakenings)

1st paragraph, lines 48-53 , the authors should be more specific about what kind of new associations and at which level they can be stored during sleep according to recent reports, as a wide variety of associations (mostly elementary levels) are shown in the cited references. Limitations in information processing during sleep should also be acknowledged.

The authors ran their main behavioural analyses on delayed retrieval at 36h rather than 12h with the argument that retrieval performance was numerically larger at 36 than 12h but the difference was non-significant (line 181-183), and that effects were essentially similar. Looking at Figure 2, is the trough effect really significant at 12h ? In any case, the fact that it is (numerically) higher at 36 than 12h might suggest that the association created at the first 12h retrieval (considering the alternative hypothesis proposed above) has been reinforced by subsequent sleep.

In the discussion section lines 419-427, the argument is somehow circular in claiming episodic memory mechanisms based on functional neuroanatomical elements that are not tested here, and the supporting studies conducted during sleep were in a different setting (e.g. TMR)

Supplementary Material: in the EEG data the differentiation between correct and incorrect ulterior classifications when presented at the peak of the slow oscillation is only significant in association with 36h delayed retrieval but not at 12h, how do the authors explain this lack of effect at 12 hour?

Reviewer #3 (Public Review):

SOCE is a ubiquitous cell signalling pathway that sustains long-lasting Ca2+ elevations required for the proliferation of T cells and the differentiation and contractility of skeletal muscle. Patients with loss of function mutations in either STIM1 or ORAI1 suffer from severe combined immunodeficiency while patients with gain-of-function mutations suffer from muscle weakness. The report that an intracellular calcium channel acts as a tether at membrane contact sites to regulate the activity of STIM/ORAI channels is thus relevant for health and disease, given the essential role of the SOCE pathway for immune and muscle cell function.

The IP3R is the major Ca2+ release pathway that initiates the STIM/ORAI activation cascade and the group of Colin Taylor (coauthor of the present study) showed that a pool of immobile receptors licensed to respond to physiological stimuli localizes near STIM-ORAI interaction sites at ER-PM junctions DOI: 10.1016/j.ceb.2018.10.001. This group further showed that IP3Rs are tethered to PM-bound actin by the KRas-induced actin-interacting protein (KRAP) DOI: 10.1038/s41467-021-24739-9 while the group of Indu Ambudkar showed that IP3R is juxtaposed to immobile STIM2 clusters within ER-PM junctions DOI: https://doi.org/10.1073/pnas.2114928118 The mechanism by which IP3R impinges on SOCE at ER-PM contact sites remains unclear, however.

The present study provides an important clue by showing that IP3Rs themselves can act as tethering proteins independently of their calcium release function. However, several important questions remain unanswered. Are the native and mutated receptors recruited differentially to ER-PM junctions? If so, what interacting partner(s) and mechanisms enable IP3-bound receptors to enhance the interactions between STIM1 and ORAI1? And why is this effect restricted to neuronal cells?

Previous studies indicate that IP3R can interact with actin via KRAP, with STIM proteins, with ORAI channels, and with phosphoinositides. The authors point to phosphoinositides as a potential target that could explain the need for IP3, but this possibility has not been experimentally addressed. They should establish whether phosphoinositides are involved in the recruitment of IP3R receptors and provide additional mechanistic insight by documenting whether IP3R depletion impacts the stability of contact sites or their ability to exchange lipids between membranes. Another unresolved question relates to the observation that the phenotype is restricted to neuronal cell types and absent in HEK-293 cells typically used for electrophysiological recordings of CRAC currents. The authors should attempt to clarify the molecular basis of this difference between cell types.

From a methodological standpoint, one limitation is that the functional assays used are quite indirect. One critical SOCE determinant is the filling state of intracellular calcium stores, which was estimated indirectly by measuring the amplitude of the Ca2+ elevation evoked by the addition of the SERCA inhibitor thapsigargin. Although this method is widely used it does not directly reflect the key parameter driving STIM1 activation which is the free calcium concentration within the ER lumen. Direct ER [Ca2+] recordings are required to clarify this critical point.

Reviewer #3 (Public Review):

Summary of Author's Results/Intended Achievements<br /> The authors were trying to ascertain the underlying learning mechanisms and network structure that could explain their primary experimental finding: passive exposure to a stimulus (independent of when the exposure occurs) can lead to improvements in active (supervised) learning. They modeled their task with 5 progressively more complex shallow neural networks classifying vectors drawn from multi-variate Gaussian distributions.

Account of Major Strengths:<br /> Overall, the experimental findings were interesting, albeit not necessarily novel. The modelling was also appropriate, with a solid attempt at matching the experimental condition to simplified network models.

Account of Major Weaknesses:<br /> I would say there are two major weaknesses of this work. The first is that even Model 5 differs from their data. For example, the A+P (passive interleaved condition) learning curve in Figure 7 seems to be non-monotonic, and has some sort of complex eigenvalue in its decay to the steady state performance as trials increase. This wasn't present in their experimental data (Figure 2D), and implies a subtle but important difference. There also appear to be differences in how quickly the initial learning (during early trials) occurs for the A+P and A:P conditions. While both A+P and A:P conditions learn faster than A only in M5, A+P and A:P seem to learn in different ways, which isn't supported in their data. The second major weakness is that the authors also don't generate any predictions with M5. Can they test this model of learning somehow in follow-up behavioural experiments in mice?

Discussion of Likely Impact:<br /> Without follow-up experiments to test their mechanism of why passive exposure helps in a schedule-independent way, the impact of this paper will be limited.

Additional Context:<br /> I believe the authors need to place this work in the context of a large amount of existing literature on passive (unsupervised) and active (supervised) learning interactions. This field is broad both experimentally and computationally. For example, there is an entire sub-field of machine learning, called semi-supervised learning that is not mentioned at all in this work.

Reviewer #3 (Public Review):

This study investigates the hypothesis that humans (but not non-human primates) spontaneously learn reversible temporal associations (i.e., learning a B-A association after only being exposed to A-B sequences), which the authors consider to be a foundational property of symbolic cognition. To do so, they expose humans and macaques to 2-item sequences (in a visual-auditory experiment, pairs of images and spoken nonwords, and in a visual-visual experiment, pairs of images and abstract geometric shapes) in a fixed temporal order, then measure the brain response during a test phase to congruent vs. incongruent pairs (relative to the trained associations) in canonical vs. reversed order (relative to the presentation order used in training). The advantage of neuroimaging for this question is that it removes the need for a behavioral test, which non-human primates can fail for reasons unrelated to the cognitive construct being investigated. In humans, the researchers find statistically indistinguishable incongruity effects in both directions (supporting a spontaneous reversible association), whereas in monkeys they only find incongruity effects in the canonical direction (supporting an association but a lack of spontaneous reversal). Although the precise pattern of activation varies by experiment type (visual-auditory vs. visual-visual) in both species, the authors point out that some of the regions involved are also those that are most anatomically different between humans and other primates. The authors interpret their finding to support the hypothesis that reversible associations, and by extension symbolic cognition, is uniquely human.

This study is a valuable complement to prior behavioral work on this question. However, I have some concerns about methods and framing.

Methods - Design issues:

1. The authors originally planned to use the same training/testing protocol for both species but the monkeys did not learn anything, so they dramatically increased the amount of training and evaluation. By my calculation from the methods section, humans were trained on 96 trials and tested on 176, whereas the monkeys got an additional 3,840 training trials and 1,408 testing trials. The authors are explicit that they continued training the monkeys until they got a congruity effect. On the one hand, it is commendable that they are honest about this in their write-up, given that this detail could easily be framed as deliberate after the fact. On the other hand, it is still a form of p-hacking, given that it's critical for their result that the monkeys learn the canonical association (otherwise, the critical comparison to the non-canonical association is meaningless).

2. Between-species comparisons are challenging. In addition to having differences in their DNA, human participants have spent many years living in a very different culture than that of NHPs, including years of formal education. As a result, attributing the observed differences to biology is challenging. One approach that has been adopted in some past studies is to examine either young children or adults from cultures that don't have formal educational structures. This is not the approach the authors take. This major confound needs to minimally be explicitly acknowledged up front.

3. Humans have big advantages in processing and discriminating spoken stimuli and associating them with visual stimuli (after all, this is what words are in spoken human languages). Experiment 2 ameliorates these concerns to some degree, but still, it is difficult to attribute the failure of NHPs to show reversible associations in Experiment 1 to cognitive differences rather than the relative importance of sound string to meaning associations in the human vs. NHP experiences.

4. More minor: The localizer task (math sentences vs. other sentences) makes sense for math but seems to make less sense for language: why would a language region respond more to sentences that don't describe math vs. ones that do?

Methods - Analysis issues:

5. The analyses appear to "double dip" by using the same data to define the clusters and to statistically test the average cluster activation (Kriegeskorte et al., 2009). The resulting effect sizes are therefore likely inflated, and the p-values are anticonservative.

Framing:

6. The framing ("Brain mechanisms of reversible symbolic reference: A potential singularity of the human brain") is bigger than the finding (monkeys don't spontaneously reverse a temporal association but humans do). The title and discussion are full of buzzy terms ("brain mechanisms", "symbolic", and "singularity") that are only connected to the experiments by a debatable chain of assumptions.

First, this study shows relatively little about brain "mechanisms" of reversible symbolic associations, which implies insights into how these associations are learned, recognized, and represented. But we're only given standard fMRI analyses that are quite inconsistent across similar experimental paradigms, with purely suggestive connections between these spatial patterns and prior work on comparative brain anatomy.

Second, it's not clear what the relationship is between symbolic cognition and a propensity to spontaneously reverse a temporal association. Certainly, if there are inter-species differences in learning preferences this is important to know about, but why is this construed as a difference in the presence or absence of symbols? Because the associations aren't used in any downstream computation, there is not even any way for participants to know which is the sign and which is the signified: these are merely labels imposed by the researchers on a sequential task.

Third, the word "singularity" is both problematically ambiguous and not well supported by the results. "Singularity" is a highly loaded word that the authors are simply using to mean "that which is uniquely human". Rather than picking a term with diverse technical meanings across fields and then trying to restrict the definition, it would be better to use a different term. Furthermore, even under the stated definition, this study performed a single pairwise comparison between humans and one other species (macaques), so it is a stretch to then conclude (or insinuate) that the "singularity" has been found (see also pt. 2 above).

7. Related to pt. 6, there is circularity in the framing whereby the authors say they are setting out to find out what is uniquely human, hypothesizing that the uniquely human thing is symbols, and then selecting a defining trait of symbols (spontaneous reversible association) *because* it seems to be uniquely human (see e.g., "Several studies previously found behavioral evidence for a uniquely human ability to spontaneously reverse a learned association (Imai et al., 2021; Kojima, 1984; Lipkens et al., 1988; Medam et al., 2016; Sidman et al., 1982), and such reversibility was therefore proposed as a defining feature of symbol representation reference (Deacon, 1998; Kabdebon and Dehaene-Lambertz, 2019; Nieder, 2009).", line 335). They can't have it both ways. Either "symbol" is an independently motivated construct whose presence can be independently tested in humans and other species, or it is by fiat synonymous with the "singularity". This circularity can be broken by a more modest framing that focuses on the core research question (e.g., "What is uniquely human? One possibility is spontaneous reversal of temporal associations.") and then connects (speculatively) to the bigger conceptual landscape in the discussion ("Spontaneous reversal of temporal associations may be a core ability underlying the acquisition of mental symbols").

Reviewer #3 (Public Review):

In this manuscript, Chang et al set out to find direct interactions with the Eph-B2 receptor, as our knowledge of its function/regulation is still incomplete. Using proteomic analysis of Hela cells expressing EPHB2, they identified MYCBP2 as a potential binder, which they then confirm using extensive biochemical analyses, an interaction that seems to be negatively affected by the binding of ephrin-B2 (but not B1). Furthermore, they find that FBXO45, a known MYCBP2 interaction, strongly facilitates its binding to EPHB2. Intriguingly, these interactions depend on the extracellular domains of EPHB2, something that is surprising given the fact that MYCBP2 is an intracellular protein. Finally, they find that, in contrast to what could be expected given the known function of MYCBP2 as a ubiquitin E3 ligase, it actually positively regulates EPHB2 protein stability, and function.

The strength of this manuscript is the extensive biochemical analysis of the EPHB2/MYCBP2/FBXO43 interactions. Most of the conclusions are warranted although I do not understand the physiological interpretation of how these proteins could interact in the extracellular space.

The attempt to extend the study to an in vivo animal using the worm is important. However, I find the results in the worm confusing and overly interpreted in their current form.

Reviewer #3 (Public Review):

Dux (or DUX4 in human) is a master transcription factor regulating early embryonic gene activation and has garnered much attention also for its involvement in reprogramming pluripotent embryonic stem cells to totipotent "2C-like" cells. The presented work starts with the recognition that DUX contains five conserved c. 100-amino acid carboxy-terminal repeats (called C1-C5) in the murine protein but not in that of other mammals (e.g. human DUX4). Using state-of-the-art techniques and cell models (BioID, Cut&Tag; rescue experiments and functional reporter assays in ESCs), the authors dissect the activity of each repeat, concluding that repeats C3 and C5 possess the strongest transactivation potential in synergy with a short C-terminal 14 AA acidic motif. In agreement with these findings, the authors find that full-length and active (C3) repeat containing Dux leads to increased chromatin accessibility and active histone mark (H3K9Ac) signals at genomic Dux binding sites. A further significant conclusion of this mutational analysis is the proposal that the weakly activating repeats C2 and C4 may function as attenuators of C3+C5-driven activity.

By next pulling down and identifying proteins bound to Dux (or its repeat-deleted derivatives) using BioID-LC/MS/MS, the authors find a significant number of interactors, notably chromatin remodellers (SMARCC1), a histone chaperone (CHAF1A/p150) and transcription factors previously (ZSCAN4D) implicated in embryonic gene activation.

The experiments are of high quality, with appropriate controls, and thus provide a rich compendium of Dux interactors for future study. Indeed, a number of these (SMARCC1, SMCHD1, ZSCAN4) make biological sense, both for embryonic genome activation and for FSHD (SMCHD1).

The central question raised by this study, however, concerns the function of the Dux repeats, apparently unique to mice. While it is possible, as the authors propose, that the weak activating C1, C2 C4 repeats may exert an attenuating function ("sub-functionalization") on activation mediated by C3 and/or C5, it could similarly be argued that the different repeats are indeed expected to display different activation potentials, chromatin opening, cofactor recruitment, due to, simply, the differences in their sequences. The argument for an active attenuating function would have been strengthened, for example, by the finding of repressor recruitment by C1/C2/C4 (and not just less of everything). The possible biological relevance of these repeats thus remains to be established.

Reviewer #3 (Public Review):

Peng et al. designed a computational framework for identifying pioneer factors using epigenomic data from five cell types. The identification of pioneer factors is important for our understanding of the epigenetic and transcriptional regulation of cells. A computational approach toward this goal can significantly reduce the burden of labor-intensive experimental validation. Nevertheless, there are several caveats in the current analysis which may require some modification of the computational methods and additional analysis to maximize the confidence of the pioneer factor prediction results.

A key consideration that arises during this review is that the current analysis anchors on H1 ESC and therefore may have biased the results toward the identification of pioneer factors that are relevant to the four other differentiated cell types. The low ranking of Yamanaka factors and known pioneer factors of NFYs and ESRRB may be due to the setup of the computational framework. Analysis should be repeated by using each of every cell type as an anchor for validating the reproducibility of the pioneer factors found so far and also to investigate whether TFs related to ESC identity (e.g. Yamanaka factors, NFYs and ESRRB) would show significant changes in their ranking. Given the potential cell type specificity of the pioneer factors, the extension to more cell types appears to be important for further demonstrating the utility of the computational framework.

Reviewer #3 (Public Review):

This paper combines experiments and simple modeling to try to identify the relationship between external muscle torque vs. a stimulus burst duration on several leg muscles of a stick insect. The authors created a setup to input PWM and voltage values and measured the output torque through load cells. They found an appropriate model for estimating muscle torque through different PWM burst durations and voltage values by comparing WAIC values for each modeling equation. They found that the linear hierarchical model relating burst duration and joint torque and a nonlinear hierarchical model relating burst duration and joint torque to a power function represent the muscle torque activation the best.

The problem that the study tries to address is of great importance to the field of cyborg, biomechanics, neuromechanics, mechano-sensing, and animal locomotion (see below). There have been very few studies that tried to quantify how muscle activation in invertebrates affects force/torque output, which is important for understanding the dynamics of their movement, and this is one of the first to investigate this. The approach is technically sound, and the experimental data and modeling analyses are solid and support the conclusions drawn.

Reviewer #3 (Public Review):

In this manuscript, Castano et al generate and test a small molecule inhibitor of CDKL5, an X-linked kinase whose loss-of-function is the cause of a severe neurodevelopmental disorder. Since the current knowledge of CDKL5 functions mainly rely on genetic models it is still unclear which effects are caused directly by CDKL5 loss and which can be ascribed to indirect effects. A specific inhibitor would therefore be an important tool for the field.

Castano and colleagues therefore tested a panel of twenty kinase inhibitors for their capacity to block phosphorylation of a EB2, a bona fide CDKL5 substrate, in rat neurons. Among the three that could inhibit EB2 phosphorylation at low concentrations, one was found to inhibit CDKL5 while not affecting GSK3 kinases, which share significant homology to CDKL5. Considering that genetic studies have previously linked CDKL5 to excitatory synaptic transmission, acute hippocampal slices were exploited to test the consequences of CDKL5 inhibition. While CDKL5 loss in the past was found to affect both AMPA- and NMDA-Rs, the small molecule-based inhibition affected only AMPA-R responses at the post-synaptic level. Since pharmacokinetic analyses showed that the inhibitor has a low capacity for brain penetration the molecule remains limited for testing the acute inhibition of CDKL5 in vitro and ex vivo. Such a tool represents an important aspect in the CDKL5 field and the findings suggesting a direct role of CDKL5 in regulating AMPA-R functions are interesting. However, the manuscript could be improved to render it more readable.

The description of the binding and orthogonal assays, which are the basis for the selection of the small molecule inhibitor, is not straightforward to understand for non-expert readers and could be improved.

While the in vitro and ex vivo assays are well presented, it is not clear why the myelin basic protein is used as a substrate for CDKL5 in the in vitro kinase assays. Does this protein contain a CDKL5 consensus site?

Reviewer #3 (Public Review):

The present manuscript describes a new method to identify the emitter of ultrasonic vocalisations during social interactions between 2 or 3 mice. The method combines two technologies (an "acoustic camera" and a set of four microphones) and succeeds in increasing the spatial precision and the attribution of USV emission to one of the mice. The manuscript describes the characteristics and advantages of each method and the advantages of using both to optimize the identification of USV emitter. The authors used the method to confirm that females are also vocalising during male-female interactions and that females emit USV mostly during nose-nose contact while this was not the case for males. Interestingly, the authors identified that the vocal behaviour of two competing males was strongly asymmetric when facing a female. This was not the case for two females facing one male.

The method is really promising since the identification of the emitter of USVs during mouse social interactions is a necessary step to speed up our understanding of this communication modality. The increase in spatial precision and in the proportion of attributed vocalisations is non-negligible and will be of great utility in the future.

Generally, the statistical analyses should be adjusted. Indeed, the statistical analyses do not consider the fact that the same individuals were recorded several times (if we understood well the methods). Each point was considered independent (in non-parametric Wilcoxon tests), while this is not the case given the repetitions with the same individuals (the number of repeated encounters per individual should be given in the methods section, by the way). We strongly recommend revising the statistical analyses of the results in Figures 4 and 5. In addition, it could be interesting to check whether the vocal behaviour is stable within each individual (i.e., a male that is vocalising frequently in one situation vocalises always frequently in other situations).

It is not easy to understand the rationale behind testing animals in pairs and in triads from the beginning of the manuscript. The authors should better introduce this aspect in the manuscript, especially given the fact that biological results deal with this aspect in Figure 5. The authors might strengthen the parts on the biological results extracted from their new method.

More specifically, the fact that one male takes over the vocal behaviour within a triad is of high interest. Nevertheless, some behavioural data would be needed to strengthen these findings.

A small proportion of USVs was not assigned. The authors did not discuss the potential reason for this failure (Were the USVs too soft? Did they include specific acoustic characteristics that render them difficult to localise?). These points could be of interest when testing other mouse strains or other species.

Reviewer #3 (Public Review):

In this manuscript, Castano et al generate and test a small molecule inhibitor of CDKL5, an X-linked kinase whose loss-of-function is the cause of a severe neurodevelopmental disorder. Since the current knowledge of CDKL5 functions mainly rely on genetic models it is still unclear which effects are caused directly by CDKL5 loss and which can be ascribed to indirect effects. A specific inhibitor would therefore be an important tool for the field.

Castano and colleagues therefore tested a panel of twenty kinase inhibitors for their capacity to block phosphorylation of a EB2, a bona fide CDKL5 substrate, in rat neurons. Among the three that could inhibit EB2 phosphorylation at low concentrations, one was found to inhibit CDKL5 while not affecting GSK3 kinases, which share significant homology to CDKL5. Considering that genetic studies have previously linked CDKL5 to excitatory synaptic transmission, acute hippocampal slices were exploited to test the consequences of CDKL5 inhibition. While CDKL5 loss in the past was found to affect both AMPA- and NMDA-Rs, the small molecule-based inhibition affected only AMPA-R responses at the post-synaptic level. Since pharmacokinetic analyses showed that the inhibitor has a low capacity for brain penetration the molecule remains limited for testing the acute inhibition of CDKL5 in vitro and ex vivo. Such a tool represents an important aspect in the CDKL5 field and the findings suggesting a direct role of CDKL5 in regulating AMPA-R functions are interesting. However, the manuscript could be improved to render it more readable.

The description of the binding and orthogonal assays, which are the basis for the selection of the small molecule inhibitor, is not straightforward to understand for non-expert readers and could be improved.

While the in vitro and ex vivo assays are well presented, it is not clear why the myelin basic protein is used as a substrate for CDKL5 in the in vitro kinase assays. Does this protein contain a CDKL5 consensus site?

:D!

Reviewer #3 (Public Review):

The paper by Li et al. describes the role of the TOR pathway in Aspergillus flavus. The authors tested the effect of rapamycin in WT and different deletion strains. This paper is based on a lot of experiments and work but remains rather descriptive and confirms the results obtained in other fungi. It shows that the TOR pathway is involved in conidiation, aflatoxin production, pathogenicity, and hyphal growth. This is inferred from rapamycin treatment and TOR1/2 deletions. Rapamycin treatment also causes lipid accumulation in hyphae. The phenotypes are not surprising as they have been shown already for several fungi. In addition, one caveat is in my opinion that the strains grow very slowly and this could cause many downstream effects. Several kinases and phosphatases are involved in the TOR pathway. They were known from S. cerevisiae or filamentous fungi. The authors characterized them as well with knock-out approaches.

As for many results, I miss the re-complementation of the created mutants throughout the manuscript. This is standard praxis.

Fig. 1: cultures were grown for 48 h before measuring the transcript level. The authors show that brlA, abaA, and some sexual regulators are less expressed. In my opinion, this does not allow the conclusion that there is a direct control through rapamycin. Since the colonies grow very slowly in the presence of rapamycin, the authors should add rapamycin and follow gene expression after 15, 30, 60, 90 min. The figure legend needs to be more detailed. Which type of cultures were used, liquid, solid medium? Etc.

Why in chapter one Fig. 9 is already cited? Those data should then be included in Fig. 1 for the general phenotype.

The authors wrote that radial growth and conidiation were gradually reduced with increasing rapamycin concentrations. This is not true. There is no gradient! However, it should be tested if there is a gradient if lower concentrations are used. The current data imply that there is a threshold concentration, so either there is 100 % growth or a reduction to 25 %. This looks strange.

Reviewer #3 (Public Review):

In this work, Kita et al., aim to understand the activation mechanisms of the kinesin-3 motors KLP-6 and UNC-104 from C. elegans. As with many other motor proteins involved in intracellular transport processes, KLP-6 and UNC-104 motors suppress their ATPase activities in the absence of cargo molecules. Relieving the autoinhibition is thus a crucial step that initiates the directional transport of intracellular cargo. To investigate the activation mechanisms, the authors make use of mass photometry to determine the oligomeric states of the full-length KLP-6 and the truncated UNC-104(1-653) motors at sub-micromolar concentrations. While full-length KLP-6 remains monomeric, the truncated UNC-104(1-653) displays a sub-population of dimeric motors that is much more pronounced at high concentrations, suggesting a monomer-to-dimer conversion. The authors push this equilibrium towards dimeric UNC-104(1-653) motors solely by introducing a point mutation into the coiled-coil domain and ultimately unleashing a robust processivity of the UNC-104 dimer. The authors find that the same mechanistic concept does not apply to the KLP-6 kinesin-3 motor, suggesting an alternative activation mechanism of the KLP-6 that remains to be resolved. The present study encourages further dissection of the kinesin-3 motors with the goal of uncovering the main factors needed to overcome the 'self-inflicted' deactivation.

Reviewer #3 (Public Review):

This is an interesting and carefully done study that will be of considerable value to the field of cortical interneurons. The main result is the development of a novel intersectional genetic strategy to identify and manipulate neurogliaform cells (NGFCs), an interneuron subtype that has been somewhat under-explored to date (but perhaps not quite as enigmatic as implied by the authors). The new strategy, using Id2-CreER transgenic mice crossed with a pan-interneuronal Flp line, appears to label all interneurons which do not express PV, Sst, or VIP, and thus defines a fourth subclass of interneurons. The main members of this subclass are NPY-expressing NGFCs. The strategy allows the targeting of NGFCs in all cortical layers, in contrast to previous strategies using the NDNF-Cre mice which target mostly Layer 1 NGFCs (and possibly also other Layer 1 subtypes). The same strategy also labels a relatively small population of non-NGF Id2 cells belonging to the CCK-expressing subtype(s).

In the first stage of the study, the authors characterize the labeled neurons by their expression of protein markers (most notably NPY and CCK), by their dendritic and axonal morphology, and by their electrophysiological properties. This characterization is detailed and rigorous and the observed characteristics are consistent with what is already known about the properties of NGFCs. The weaknesses here are that the morphological features are not analyzed quantitatively, the definition of electrophysiological subtypes remains somewhat subjective, and the authors do not attempt a multivariate analysis that could provide a data-driven parcellation into subtypes.

The authors then go two steps further. First, they use ex-vivo recordings to demonstrate that presumed CCK+ neurons (identified by their firing pattern as "non-late-spiking), but not NGFCs (identified by their "late-spiking" phenotype), are sensitive to endocannabinoids released from postsynaptic pyramidal cells upon depolarization of the latter. This DSI ("depolarization suppression of inhibition") is a well-studied property of hippocampal CCK+ basket cells, so its demonstration adds to the validation of the intersectional strategy in targeting this subtype in the neocortex. Somewhat surprisingly, the authors do not attempt to demonstrate in their ex-vivo experiments what may be the best-known property of NGFCs - their propensity to preferentially activate GABAB receptors.

The authors then perform in-vivo silicon probe recordings in which Id2 cells are "optotagged" with ChR2 and can thus be identified in extracellular recordings. These in-vivo recordings are probably the first ever from identified NGFCs below layer 1, although some uncertainty remains about the identification of optotagged cells as NGFCs vs CCK-expressing interneurons. They find several differences between firing patterns of NGFCs and other interneurons or pyramidal cells (identified by their extracellular spike waveforms), the most dramatic being a pronounced "rebound" of NGFC firing during slow-wave sleep immediately after a DOWN-to-UP state transition. While the functional significance of these findings is not clear, these experiments provide proof of concept that this fourth (and last?) interneuron subclass can be identified, recorded, and manipulated in freely behaving animals.

In summary, while adding only modestly to our knowledge of NGFCs and CCK-expressing interneurons per se, this work provides an important new tool that will no doubt be used in future studies to target cortical NGFCs and CCK interneurons for in-vivo and ex-vivo recordings, for optogenetic manipulations and for calcium or voltage imaging using genetically-encoded probes. In this sense, the current study is a breakthrough into what may truly be "the last frontier" of cortical interneurons.

Reviewer #3 (Public Review):

Overview: The authors propose a personalized ventricular computational model (Geno-DT) that incorporates the patient's structural remodeling (fibrosis and scar locations based on LGE-CMR scans) as well as genotyping (cell membrane kinetics based on genetic testing results) to predict VT locations and morphologies in ARVC setting.<br /> To test the model, the authors conducted a retrospective study using 16 ARVC patient data with two genotypes (PKP2, GE) and reported high degree of sensitivity, specificity, and accuracy. In addition, the authors determined that in GE patients, VT was driven by fibrotic remodeling, whereas, in PKP2 patients, VT was associated with a combination of structural and electrical remodeling (slowed conduction and altered restitution).<br /> Based on the findings, the authors recommend using Geno-DT approach to augment therapeutic accuracy in treatment of ARVC patients.

Critiques:

1. The small sample size is a limitation but has already been acknowledged and documented by the authors.

2. Another limitation is the consideration of only two of the possible genotypes in developing the cell membrane kinetics, but again has been acknowledged by the authors.

Final Thoughts: The authors have done a commendable job in targeting a disease phenotype that is relatively rare, which constrains the type of data that can be collected for research. Their personalized computational model approach makes a valuable contribution to furthering our understanding of ARVC mechanisms.

Reviewer #3 (Public Review):

Two studies published in 2020 independently identified the alPg, pC1d, and pC1e neurons to be involved in initiating and maintaining a state of aggression in female Drosophila. Both studies combined behavioural analyses, optogenitic manipulation of neurons, and connectomics. One of these studies proposed that the extensive interconnections seen between the alPg and pC1d+e neurons might represent a recurrent motif known to support persistent behvioural states in other systems. In this manuscript, the authors test this idea and report that their data do not support it. Specifically, they report that alPg or pC1d+e (but not pC1d alone) can initiate a persistent state of aggression. But they find that the persistent aggressive state is maintained even when the pC1d neurons are inactivated. Finally, they show that neither of these neurons themselves sustains neuronal activity upon stimulation, nor do either of them induce a persistent activity in the other. Together, their data suggest that the recurrent connection between alPg and pC1d is not what supports the persistent state. The data underlying these claims are convincing. A possibility to explore before ruling out recurrent motifs (at this circuit level) in maintaining aggression is that the connections between alPg and pC1e can compensate for the loss of pC1e. Overall, the study is important and will be of interest to those who study the circuit basis of persistent behavioural states, but also to neuroscientists in general.

Reviewer #3 (Public Review):

This study addresses the major question of 'whether and when grid cells contribute to behavior'. There is no doubt that this is a very important question. My major concern is that I'm not convinced that this study gives a significant contribution to this question, although this study is well-performed and potentially interesting. This is mainly due to the fact that the relation between grid cell properties and behavior is exclusively correlative and entirely based on single cell activity, although the introduction mentions quite often the grid cell network properties and dynamics. In general, this study gives the impression that grid cells exclusively support the cognitive processes involved in this task. This problem is in part related to the text. However, it would be interesting to look at the population level (even beyond grid cells) to test whether at the network level, the link between behavioral performance and neural activity is more straightforward compared to the single-cell level. This approach could reconcile the present results with those obtained in their previous study following MEC inactivation.

The authors used a statistical method based on the computation of the frequency spectrum of the spatial periodicity of the neural firing to classify grid cells as 'position-coding' (with fields anchored to the virtual track) and 'distance-coding' (with fields repeating at regular intervals across trials). This is an interesting approach that has nonetheless the default to be based exclusively on autocorelograms. It would be interesting to compare with a different method based on the similarities between raw maps. Beyond this minor point, cell categorization is performed using all trial types. Each trial type (i.e. beacon or non-beacon) is supposed to force mice to use different strategies and should induce different spatial representations within the entorhinal-hippocampal circuit (and not only in the grid cell system). In that context, since all trials are mixed, it is difficult to extrapolate general information. On page 5 the authors state that 'Since only position representations should reliably predict the reward location, ..., we reasoned that the presence of positional coding could be used to assess whether grid firing contributes to the ongoing behaviour'.

I do not agree with this statement. First of all, position coding should be more informative only in a cue-guided trial. Second, distance coding could be as informative as position coding since at the network level may provide information relevant to the task (such as distance from the reward). This possibility is not tested here. Third, position-coding is interpreted as more relevant because it predominates in correct trials. However, this does not imply that this coding scheme is indeed used to perform correct trials. It could be more informative to push forward the correlative analysis by looking at whether behavioral performance can be predicted by the coding scheme on a trial-by-trial basis. This analysis would not provide a causal relation between cell activity and behavior, but could strengthen the correlation between the two.

Reviewer #3 (Public Review):

In this work, the authors shed light onto the structures of Fusarium oxysporum f.sp. lycopersici proteins involved in the infection of tomato. They unravelled several new secreted effector protein structures and additionally used computational approaches to structurally classify the remaining effectors known from this pathogen. Through this they uncovered a new and unique structural class of proteins which they found to be present and widely distributed in fungal plant pathogens and plant symbiotic fungi. The authors further predicted structural models for the full SIX effector set revealing that genome-proximal effector pairs share similar structural classes. Building on their Avr1 structure, the authors also define the C-terminal domain and specific amino acid residues that are essential to Avr1 detection by its cognate immune receptor.

A major strength of this work is a portfolio of several (Avr1, Avr3, SIX6, SIX8) new structurally resolved proteins which led to the discovery that several of them fall into the same structural class. These findings are supported by strong results.

The experiments addressing the structure-function relationship of Avr1's avirulence activity are highly relevant to our understanding of disease resistance mechanisms against Fusarium, but will require additional controls to allow for solid conclusions to be drawn. In particular, it needs to be demonstrated that specific I gene alleles are at all required for FonSIX4's cell death activity in N.benthamiana leaves or whether FonSIX4 and those of some chimeric proteins is independent of the tomato I receptor. Complementary work in Fusarium mutants lacking Avr1 and expressing chimeric versions would document that the observations from transient expressions in Nicotiana benthamiana are relevant in the biological context of a Fusarium/tomato interaction.

The discovered solvent-exposed residues conditioning Avr1 recognition by the I receptor seem to be positioned in an area of the protein which had previously been highlighted as being highly variable in FOLD proteins of symbiotic fungi but it is not clear from the work whether this is indeed the case or whether Avr1 differs significantly in its structure from FOLD proteins found in other fungi.<br /> It also remains to be addressed whether the residues conditioning avirulence activity is also crucial for virulence activity in Fusarium?

This work uncovered a new structural class of proteins with critical roles in plant-pathogen interactions. Structure-based predictions and genome-wide comparisons have emerged as a new approach enabling the identification of similar proteins with divergent sequences. The work undertaken by the authors adds to a growing body of work in plant-microbe research, predominantly from pathogenic organisms, and more recently in symbiotic fungi.

Reviewer #3 (Public Review):

There has been a long-standing link between the biology of sulfur-containing molecules (e.g., hydrogen sulfide gas, the amino acid cysteine, and its close relative cystine, et cetera) and the biology of hypoxia, yet we have a poor understanding of how and why these two biological processes and are co-regulated. Here, the authors use C. elegans to explore the relationship between sulfur metabolism and hypoxia, examining the regulation of cysteine dioxygenase (CDO1 in humans, CDO-1 in C. elegans), which is critical to cysteine catabolism, by the hypoxia inducible factor (HIF1 alpha in humans, HIF-1 in C. elegans), which is the key terminal effector of the hypoxia response pathway that maintains oxygen homeostasis. The authors are trying to demonstrate that (1) the hypoxia response pathway is a key regulator of cysteine homeostasis, specifically through the regulation of cysteine dioxygenase, and (2) that the pathway responds to changes in cysteine homeostasis in a mechanistically distinct way from how it responds to hypoxic stress.

Briefly summarized here, the authors initiated this study by generating transgenic animals expressing a CDO-1::GFP protein chimera from the cdo-1 promoter so that they could identify regulators of CDO-1 expression through a forward genetic screen. This screen identified mutants with elevated CDO-1::GFP expression in two genes, egl-9 and rhy-1, whose wild-type products are negative regulators of HIF-1, raising the possibility that cdo-1 is a HIF-1 transcriptional target. Indeed, the authors provide data showing that cdo-1 regulation by EGL-9 and RHY-1 is dependent on HIF-1 and that regulation by RHY-1 is dependent on CYSL-1, as expected from other published findings of this pathway. The authors show that exogenous cysteine activates cdo-1 expression, reflective of what is known to occur in other systems. Moreover, they find that exogenous cysteine is toxic to worms lacking CYSL-1 or HIF-1 activity, but not CDO-1 activity, suggesting that HIF-1 mediates a survival response to toxic levels of cysteine and that this response requires more than just the regulation of CDO-1. The authors validate their expression studies using a GFP knockin at the cdo-1 locus, and they demonstrate that a key site of action for CDO-1 is the hypodermis. They present genetic epistasis analysis supporting a role for RHY-1, both as a regulator of HIF-1 and as a transcriptional target of HIF-1, in offsetting toxicity from aberrant sulfur metabolism. The authors use CRISPR/Cas9 editing to mutate a key amino acid in the prolyl hydroxylase domain of EGL-9, arguing that EGL-9 inhibits CDO-1 expression through a mechanism that is largely independent of the prolyl hydroxylase activity.

Overall, the data seem rigorous, and the conclusions drawn from the data seem appropriate. The experiments test the hypothesis using logical and clever molecular genetic tools and design. The sample size is a bit lower than is typical for C. elegans papers; however, the experiments are clearly not underpowered, so this is not an issue. The paper is likely to drive many in the field (including the authors themselves) into deeper experiments on (1) how the pathway senses hypoxia and sulfur/cysteine/H2S using these distinct mechanisms/modalities, (2) how oxygen and sulfur/cysteine/H2S homeostasis influence one another, and (3) how this single pathway evolved to sense and respond to both of these stress modalities.

Major strengths of the paper include (1) the use of the powerful whole animal C. elegans model to reveal results that have meaning in vivo, (2) the careful demonstration through mutant rescue experiments that key transgenes have functional activity, (3) the use of CRISPR/Cas9 editing to mutate a critical residue in the catalytic domain of the EGL-9 prolyl hydroxylase, (4) transgenic rescue experiments that show that CDO-1 operates in the hypodermis with regard to the larval arrest phenotype, and (5) the thorough epistatic analysis of different pathway mutants.

Major weaknesses of the paper include (1) the over-reliance on genetic approaches, (2) the lack of novelty regarding prolyl hydroxylase-independent activities of EGL-9, and (3) the lack of biochemical approaches to probe the underlying mechanism of the prolyl hydroxylase-independent activity of EGL-9.

Major Issues We Feel the Authors Should Address:

1. One particularly glaring concern is that the authors really do not know the extent to which the prolyl hydroxylase activity is (or is not) impacted by the H487A mutation in egl-9(rae276). If there is a fair amount of enzymatic activity left in this mutant, then it complicates interpretation. The paper would be strengthened if the authors could show that the egl-9(rae276) eliminates most if not all prolyl hydroxylase activity. In addition, the authors may want to consider doing RNAi for egl-9 in the egl-9(rae276) mutant as a control, as this would support the claim that whatever non-hydroxylase activity EGL-9 may have is indeed the causative agent for the elevation of CDO-1::GFP. Without such experiments, readers are left with the nagging concern that this allele is simply a hypomorph for the single biochemical activity of EGL-9 (i.e., the prolyl hydroxylase activity) rather than the more interesting, hypothesized scenario that EGL-9 has multiple biochemical activities, only one of which is the prolyl hydroxylase activity.

2. The authors observed that EGL-9 can inhibit HIF-1 and the expression of the HIF-1 target cdo-1 through a combination of activities that are (1) dependent on its prolyl hydroxylase activity (and subsequent VHL-1 activity that acts on the resulting hydroxylated prolines on HIF-1), and (2) independent of that activity. This is not a novel finding, as the authors themselves carefully note in their Discussion section, as this odd phenomenon has been observed for many HIF-1 target genes in multiple publications. While this manuscript adds to the description of this phenomenon, it does not really probe the underlying mechanism or shed light on how EGL-9 has these dual activities. This limits the overall impact and novelty of the paper.

3. Cysteine dioxygenases like CDO-1 operate in an oxygen-dependent manner to generate sulfites from cysteine. CDO-1 activity is dependent upon availability of molecular oxygen; this is an unexpected characteristic of a HIF-1 target, as its very activation is dependent on low molecular oxygen. Authors neither address this in the text nor experimentally, and it seems a glaring omission.

4. The authors determined that the hypodermis is the site of the most prominent CDO-1::GFP expression, relevant to Figure 4. This claim would be strengthened if a negative control tissue, in the animal with the knockin allele, were shown. The hypodermal specific expression is a highlight of this paper, so it would make this article even stronger if they could further substantiate this claim.

Minor issues to note:

Mutants for hif-1 and cysl-1 are sensitive to exogenous cysteine levels, yet loss of CDO-1 expression is not sufficient to explain this phenomenon, suggesting other targets of HIF-1 are involved. Given the findings the authors (and others) have had showing a role for RHY-1 in sulfur amino acid metabolism, shouldn't the authors consider testing rhy-1 mutants for sensitivity to exogenous cysteine?

The cysteine exposure assay was performed by incubating nematodes overnight in liquid M9 media containing OP50 culture. The liquid culture approach adds two complications: (1) the worms are arguably starving or at least undernourished compared to animals grown on NGM plates, and (2) the worms are probably mildly hypoxic in the liquid cultures, which complicates the interpretation.

An easily addressable concern is the wording of one of the main conclusions: that cdo-1 transcription is independent of the canonical prolyl hydroxylase function of EGL-9 and is instead dependent on one of EGL-9's non-canonical, non-characterized functions. There are several points in which the wording suggests that CDO-1 toxicity is independent of EGL-9. In their defense, the authors try to avoid this by saying, "EGL-9 PHD," to indicate that it is the prolyl hydroxylase function of EGL-9 that is not required for CDO-1 toxicity. However, this becomes confusing because much of the field uses PHD and EGL-9/EGLN as interchangeable protein names. The authors need to be clear about when they are describing the prolyl hydroxylase activity of EGL-9 rather than other (hypothesized) activities of EGL-9 that are independent of the prolyl hydroxylase activity.

The authors state in the text, "the egl-9; suox-1 double mutants are extremely sick and slow growing." We appreciate that their "health" assay, based on the exhaustion of food from the plate, is qualitative. We also appreciate that it is a functional measure of many factors that contribute to how fast a population of worms can grow, reproduce, and consume that lawn of food. However, unless they do a lifespan assay and/or measure developmental timing and specifically determine that the double mutant animals themselves are developing and/or growing more slowly, we do not think it is appropriate to use the words "slow growing" to describe the population. As they point out, the rate of consumption of food on the plate in their health assay is determined by a multitude and indeed a confluence of factors; the growth rate is one specific one that is commonly measured and has an established meaning.

Reviewer #3 (Public Review):

Sasani et al. develop and implement a new method for mutator allele discovery in the BXD mouse population. This new "IHD" method carries several notable strengths, including the ability to aggregate de novo mutations across individuals to reduce data sparsity and to combine mutation rate frequencies across multiple nucleotide contexts into a single estimate. These advantages may render the IHD method better suited to mutator discovery under certain scenarios, as compared to conventional QTL or association mapping. Overall, the theoretical premise of the IHD method is judged to be both strong and innovative, and careful simulation studies benchmark its power.

The authors then apply their method to the BXD mouse recombinant inbred mapping population. As proof-of-principle, they first successfully re-identify a known mutator locus in this population on chr4. Next, to assess possible genetic interactions involving this known mutator, Sasani et al. condition on the chr4 mutator genotype and reimplement the IHD scan. This strategy led them to identify a second locus on chr6 that interacts epistatically with the chr4 locus; mice with "D" alleles at both loci exhibit a significantly increased burden of C>A de novo mutations, even though mice with the D allele at the chr6 locus alone show no appreciable increase in the C>A mutation fraction. This exciting discovery not only adds to the catalog of known mutator alleles, but also reveals key aspects of mutator biology. Notably, this finding reinforces the hypothesis that segregating variants in genes associated with DNA repair influence germline mutation spectra. Further, Sasani et al.'s findings suggest that some mutators may lie dormant until recombined onto a permissive genetic background. This discovery could have intriguing implications for the evolution of mutators in natural populations.

Despite a high level of overall enthusiasm for this work, some weaknesses are identified in the IHD method, approach for nominating candidate genes within the newly identified chr6 locus, and the authors' conclusions.

Under simulated scenarios, the authors' new IHD method is not appreciably more powerful than conventional QTL mapping methods. While this does not diminish the rigor or novelty of the authors findings, it does temper enthusiasm for the IHD method's potential to uncover new mutators in other populations or datasets. Further, adaptation of this methodology to other datasets, including human trios or multigenerational families, will require some modification, which could present a barrier to broader community uptake. Notably, BXD mice are (mostly) inbred, justifying the authors consideration of just two genotype states at each locus, but this decision prevents out-of-the-box application to outbred populations and human genomic datasets. Lastly, some details of the IHD method are not clearly spelled out in the paper. In particular, it is unclear whether differences in BXD strain relatedness due to the breeding epoch structure are fully accounted for in permutations. The method's name - inter-haplotype distance - is also somewhat misleading, as it seems to imply that de novo mutations are aggregated at the scale of sub-chromosomal haplotype blocks, rather than across the whole genome.

Nominating candidates within the chr6 mutator locus requires an approach for defining a credible interval and excluding/including specific genes within that interval as candidates. Sasani et al. delimit their focal window to 5Mb on either side of the SNP with the most extreme P-value in their IHD scan. This strategy suffers from several weaknesses. First, no justification for using 10 Mb window, as opposed to, e.g., a 5 Mb window or a window size delimited by a specific threshold of P-value drop, is given, rendering the approach rather ad hoc. Second, within their focal 10Mb window, the authors prioritize genes with annotated functions in DNA repair that harbor protein coding variants between the B6 and D2 founder strains. While the logic for focusing on known DNA repair genes is sensible, this locus also houses an appreciable number of genes that are not functionally annotated, but could, conceivably, perform relevant biological roles. These genes should not be excluded outright, especially if they are expressed in the germline. Further, the vast majority of functional SNPs are non-coding, (including the likely causal variant at the chr4 mutator previously identified in the BXD population). Thus, the author's decision to focus most heavily on coding variants is not well-justified. Sasani et al. dedicate considerable speculation in the manuscript to the likely identity of the causal variant, ultimately favoring the conclusion that the causal variant is a predicted deleterious missense variant in Mbd4. However, using a 5Mb window centered on the peak IHD scan SNP, rather than a 10Mb window, Mbd4 would be excluded. Further, SNP functional prediction accuracy is modest [e.g., PMID 28511696], and exclusion of the missense variant in Ogg1 due its benign prediction is potentially premature, especially given the wealth of functional data implicating Ogg1 in C>A mutations in house mice. Finally, the DNA repair gene closest to the peak IHD SNP is Rad18, which the authors largely exclude as a candidate.

Additionally, some claims in the paper are not well-supported by the author's data. For example, in the Discussion, the authors assert that "multiple mutator alleles have spontaneously arisen during the evolutionary history of inbred laboratory mice" and that "... mutational pressure can cause mutation rates to rise in just a few generations of relaxed selection in captivity". However, these statements are undercut by data in this paper and the authors' prior publication demonstrating that a number of candidate variants are segregating in natural mouse populations. These variants almost certainly did not emerge de novo in laboratory colonies, but were inherited from their wild mouse ancestors. Further, the wild mouse population genomic dataset used by the authors falls far short of comprehensively sampling wild mouse diversity; variants in laboratory populations could derive from unsampled wild populations.

Finally, the implications of a discovering a mutator whose expression is potentially conditional on the genotype at a second locus are not raised in the Discussion. While not a weakness per se, this omission is perceived to be a missed opportunity to emphasize what, to this reviewer, is one of the most exciting impacts of this work. The potential background dependence of mutator expression could partially shelter it from the action of selection, allowing the allele persist in populations. This finding bears on theoretical models of mutation rate evolution and may have important implications for efforts to map additional mutator loci. It seems unfortunate to not elevate these points.

Reviewer #3 (Public Review):

The manuscript by Qin and Zhou presents an approach to predict dynamical properties of an intrinsically disordered protein (IDP) from sequence alone. In particular, the authors train a simple (but useful) machine learning model to predict (rescaled) NMR R2 values from sequence. Although these R2 rates only probe some aspects of IDR dynamics and the method does not provide insight into the molecular aspects of processes that lead to perturbed dynamics, the method can be useful to guide experiments.

A strength of the work is that the authors train their model on an observable that directly relates to protein dynamics. They also analyse a relatively broad set of proteins which means that one can see actual variation in accuracy across the proteins.

A weakness of the work is that it is not always clear what the measured R2 rates mean. In some cases, these may include both fast and slow motions (intrinsic R2 rates and exchange contributions). This in turn means that it is actually not clear what the authors are predicting. The work would also be strengthened by making the code available (in addition to the webservice), and by making it easier to compare the accuracy on the training and testing data.

• Title
  • Big Oil v the World Series 1 03 Delay
• Author
  • BBC

Reviewer #3 (Public Review):

Alternative polyadenylation is an important aspect of RNA processing that can alter the type or amount of proteins that are produced from a gene, with consequences for many aspects of biology. Herron et al. set out to identify how the mTORC1 pathway, which regulates cellular metabolism, influences alternative polyadenylation in the mouse brain. They identified a novel mTORC1-regulated gene with alternative polyadenylation - TRIM9 - and convincingly demonstrate that its alternative polyadenylation is controlled by the CFIm complex of the cleavage and polyadenylation machinery. A major strength of these results is that the authors use multiple orthogonal methods - including PAPERCLIP, qPCR and western blotting, to demonstrate that TRIM9 is regulated by mTORC1 and CFIm. They also demonstrate that this regulation is conserved between mice and humans by using multiple different model systems, and use synthetic reporter constructs to identify the cis-regulatory elements that are responsible for TRIM9 regulation by CFIm. These results highlight the importance of alternative polyadenylation in controlling gene expression and are important for researchers wishing to understand how the mTORC1 pathway functions.

The authors also identify that a "twin" UGUA motif in the poly(A) site of the short form of TRIM9 is responsible for its regulation by CFIm. They show that this motif is conserved across mammals and suggest that the adjacent UGUA motifs are necessary for regulation by CFIm. The evidence supporting this aspect of the manuscript is incomplete because the authors only ever mutate both UGUA motifs of TRIM9, and so it is not possible to determine whether the full motif or only one of the UGUA motifs is necessary for regulation, nor whether the effect of the two UGUA motifs is simply additive. The only evidence for the necessity of the full twin motif comes from a synthetic JUNB reporter construct, where a single UGUA motif was insufficient to induce proximal polyadenylation. However, given that there is previous evidence that individual UGUA motifs can act as enhancers of polyadenylation, this may be due to context-specific issues with the JUNB reporter, and evidence from different contexts would make the authors conclusions more convincing.

Reviewer #3 (Public Review):

The authors describe a mathematical and computational modeling study of RAF paradoxical activation (PA), a phenomenon in which RAF inhibitors exhibit a bell-shaped dose-response curve of Erk phosphorylation - activating signaling through wild-type RAF at low drug concentrations before inhibiting it at higher concentrations. They explore three distinct mechanisms that may contribute to PA - conformational autoinhibition, negative cooperativity, and drug-induced dimerization - and conclude that all three are required to best fit published data that show the PA phenomenon. They explore the effect of 14-3-3 binding to RAF both computationally and experimentally and reach the conclusion that 14-3-3 can potentiate the PA phenomenon via stabilization of the autoinhibited conformation.

Strengths:

One key finding will be quite valuable to the field - that paradoxical activation can arise in the absence of negative cooperativity and without any effect of the inhibitor on the propensity of RAF to dimerize, provided that there exists a "conformationally autoinhibited" state that cannot dimerize and cannot bind inhibitor. This finding is important because negative cooperativity and dimer-induction have been a major focus - arguably the main focus - of prior studies of the phenomenon and also a source of considerable confusion. Inhibitors with very different chemical structures and binding properties - type 1.5 inhibitors that are dimer-breakers (and may or may not exhibit negative cooperativity) and type I and II inhibitors that can promote dimers (and almost certainly do not exhibit negative cooperativity) can nevertheless both exhibit PA. Thus the authors' modeling provides a unifying explanation - it is not dimer-induction or negative cooperativity that is at the root of PA, rather it is that there exists an autoinhibited state that can neither bind inhibitor nor dimerize. The authors further show that negative cooperativity and dimer-induction can act in concert with "conformational autoinhibition" to modify the PA response in a drug-specific manner.

Weaknesses:

Unfortunately, the authors don't really explain in a straightforward manner what is going on with the conformational autoinhibition model (Figure 2A). One has to read carefully and all the way to section 3 of appendix 1 to piece it together. In short, what the math shows is that at least for certain ranges of parameter values, the presence of an inhibitor can increase the concentration of dimers, even when it does not change the equilibrium constant for dimer formation, and some of those dimers will have an active, drug-free protomer. This is because the inhibitor effectively traps open monomers, which can then capture drug-free open monomers to form active dimers (active in one subunit, inactive and drug-bound in the other). As inhibitor concentration increases, the pool of autoinhibited RAF is diminished, and eventually, it is shifted completely to fully inhibited dimers. But at low concentrations of inhibitor, there is a net increase in dimerized (active) but drug-free protomers (see figure on page 27 of the appendix). Voila, paradoxical activation, with no need to invoke negative cooperativity.

Considering the potential for confusion around what is meant by "drug-induced dimerization" as an effect distinct from the effect of the drug in promoting RAF dimerization in their conformational autoinhibition model, it would have been helpful for the authors to explicitly address the distinction (drug-induced dimerization alters the equilibrium constant for dimerization; this is not a feature of the conformational autoinhibition model).

Also, I am confused by Figure 3C. The figure shows, and the authors state in the text, that for type II inhibitors an f > ~1 indicates a propensity to break dimers. But type 1.5 inhibitors should break dimers, and Type I and II inhibitors should promote dimers (at least some Type I and II drugs have been shown to promote kinase dimers). Seems that the predictions of the model are inconsistent with experimental data, at least for some inhibitors.

A large part of the paper deals with the effect of 14-3-3 binding. In my view, this part of the manuscript is not particularly helpful. There is no evidence (that I am aware of) that 14-3-3 concentrations vary significantly, or that their variation affects RAF activity/signaling. Considering their abundance relative to RAF, and relatively high affinity for RAF, it is likely that both autoinhibited and active RAF are saturated with 14-3-3. (RAF that is not 14-3-3-bound is likely mostly bound to chaperones and not active). That said, the authors' conclusion (based on modeling) that 14-3-3 can increase the extent of paradoxical activation by stabilizing the autoinhibited state seems sensible, but hard to reconcile with their experimental result where they find increased basal signaling with 14-3-3 over-expression. It is also difficult to understand how increased 14-3-3 binding to RAF could lead to active RAF dimers that are not inhibited at 10-100 uM concentrations of potent RAF dimer inhibitors like LY3009120 (Fig. 5C). It seems more likely that 14-3-3 overexpression is promoting Erk phosphorylation in a manner that is (at least partially) Raf-independent. To their credit, the authors acknowledge this concern.

Finally, one comment regarding the presentation. The authors discuss conformational inhibition and 14-3-3 binding as if they are promoting and/or inducing paradoxical activation. This is pervasive in the paper, including in the title, and is distracting and potentially will mislead some readers. Obviously, it is RAF inhibitor that induces or promotes paradoxical activation. Conformational autoinhibition - mediated by 14-3-3 - is a feature of the system that makes paradoxical activation possible.

Reviewer #3 (Public Review):

The authors employed a set of cell-based and animal studies with tumor model systems that harbor a genetically deleted specific isoform of p73 to identify a novel function of this isoform in the regulation of lipid metabolism and obese disorder, which are associated with tumorigenesis. Interestingly, this new function was found to be through the increase in leptin expression. This is probably the first study showing the connection of the p73 family members with leptin, a molecule that has been shown to play a critical role in obesity and metabolism. Overall, their findings are novel, interesting, and important.

Reviewer #3 (Public Review):

Controlling the shape of biological tubes (blood vessels, lungs, etc) is essential for optimizing the traffick of liquid and gas in organisms. Tracheal tubulogenesis of Drosophila embryos is regulated separately in two dimensions, width, and length. Molecules controlling the tracheal tube length function at three levels of location, luminal ECM, plasma membrane mediating cell-apical ECM interaction, and the signaling at the membrane/cell junction. In this paper, Pinheiro et al. reported a novel function of a scavenger receptor family molecule, Emp, which mediates endocytosis of a subset of luminal proteins including chitin deacetylates Serp and Verm that are required for restricting the tube length. It was previously shown that endocytosis and recycling of Serp and Verm maintain the level of luminal chitin deacetylates for keeping the property of the apical ECM to restrict the tube length (10.1016/j.celrep.2014.03.066).

This work is novel in two ways. First, Emp was shown to mediate the endocytosis of Serp and Verm by most likely interacting with the LDLr domains of cargo molecules and acting in parallel with the clathrin-mediated endocytosis to clear luminal materials. Second and surprisingly, the Emp-mediate endocytosis is coupled with the widespread alteration of the apical plasma membrane, including reduction of junctional E-cadherin and Crumbs, apical membrane protein DAAM1, and the cortical membrane skeleton component beta heavy spectrin (Kst). The elevation of junctional Crumbs protein in Emp mutants is noteworthy because the authors showed Crumbs was selectively upregulated in the longitudinal cell junctions. This change in Crumbs polarity may be related to the axial over-elongation of the trachea in Emp mutants. Furthermore, the authors showed that Src42A, which was previously shown to promote tube elongation, is also regulated negatively by Emp.

Overall, the information provided in this work supports a model of endocytic coupling of luminal materials and the axial polarity of the tracheal tube. This leads to a new idea distinct (but none-exclusive) from the previously proposed mechanical coupling model (10.1016/j.celrep.2014.03.066) and would advance a fundamental understanding of biological tube shape regulation. One critical point of linking endocytosis to the axial polarity is the selective enrichment of Crumbs to the longitudinal cell boundaries (10.1371/journal.pgen.1007824), which is shown to be enhanced in Emp mutants (Fig. 5D-F). Discussing how the junction-enriched Crmbs contribute to selective axial cell elongation will be desirable to expand the scope of this work. This point is essential, given that the expression of the dominant-active form of Crumbs lacking the extracellular domain (Crumbs-intra) is mislocalized in the cytoplasmic puncta promotes axial cell elongation (Laprise et al., 2010).

Reviewer #3 (Public Review):

Because of the position of pigeon embryos in eggs, light exposure will only stimulate the right eye, leading to lateralisation of brain responses and behaviour. Lorenzi and colleagues injected manganese chloride into pigeon eggs, to assess neuronal activation in the embryonic brain. While the eggs were placed in the light or dark, manganese ions accumulated in neurons that were activated (in cell bodies and axons), which was then visualized with MRI of the embryos before hatching. The authors report lateralisation of neuronal activity in three brain regions, which could potentially be important for our understanding of experience-dependent development of lateralised neural activation.

The tectofugal pathway in pigeons projects from the retina to the optical tectum, then to the nucleus rotundus in the thalamus, and then to the entopallium. The thalamofugal pathway projects from the retina to the GLd in the thalamus, and then to the wulst in the hyperpallium. The two pathways involve different thalamic nuclei (e.g., Deng 2006). In the methods and throughout the manuscript it should be specified which thalamic region is used as ROI.

This manuscript only describes neural activity, but the MEMRI technique should also be used to assess the effect of experimental manipulations on axonal connectivity. It is important to learn about the asymmetry of contralateral projections in the light vs dark groups for answering the research question.

There is an overinterpretation of post-hoc statistics that are reported without correction for multiple testing. The wulst light group lateralization is probably not actually different from zero (uncorrected p=0.04).

The first line in the discussion states that there is thalamofugal lateralization, but no lateralization in the tectofugal pathway. To my understanding, previous literature reported it the other way around: in altricial pigeons, light exposure in the egg mainly affected the tectofugal pathway (Deng & Rogers 2002), while the thalamofugal pathway in pigeons was not lateralized (Strockens et al., 2013). The manuscript should compare the current findings with the literature and discuss differences.

Moreover, the tectum is the only region shown here from the tectofugal pathway. However, lateralization of contralateral connections is expected from tectum to the nucleus rotundus in the thalamus, and thus lateralization of activation may only arise in downstream brain regions from the optical tectum. Therefore, the conclusion that there is no lateralization in the tectofugal pathway is not supported by the data.

In conclusion, I think it is interesting and worthwhile that the authors assessed neural activity in response to visual stimulation in the embryo prior to hatching, but multiple methodological weaknesses and unclarities should be addressed.

Reviewer #3 (Public Review):

In this latest installment of a growing body of work from Henry Colecraft's lab in which native enzymes, ion channels, and other machinery are hijacked for therapeutic potential, cells can be made to respond to beta-adrenergic signals even when lacking the critical adaptor protein AKAP9. Normally, the cardiac repolarizing current IKs is enhanced in the face of beta-adrenergic signaling when increased cAMP activates PKA anchored to the channel protein by AKAP9. PKA phosphorylates the channel, increasing function or density in the membrane, especially during exercise or fright. Under these circumstances, when AKAP9 is missing in patients, the action potential fails to repolarize in a timely manner and arrhythmias can result. In this study, targeting the PKA catalytic or regulatory subunit to the E1 auxiliary channel subunit via a targeting nanobody restores at least some of the normal modulation in the presence of cAMP. This primary finding demonstrates a potential therapeutic approach when mutations disrupt its interaction with the channel complex.

A secondary finding of the study is that, contrary to expectation, targeting the enzyme to the Q1 alpha subunit C-terminus does not restore modulation but rather inhibits current by tying up the protein in the ER. Retention apparently depends on phosphorylation because a kinase-dead PKA catalytic subunit exhibits normal current. These findings demonstrate that the efficacy of correction is critically dependent on the site of recruitment. The results represent a starting point whereby kinase-based signaling can be synthetically harnessed to restore normal function in a disease setting.

The strengths of the study are the therapeutic potential of its principal finding and the clever approach to redirecting cellular components. Controls for the constructs are carefully designed and executed. Most of the conclusions are supported by the data presented. The weaknesses are minor and include providing more than an exemplar to support findings of enhanced phosphorylation and an accounting of how the findings from immunofluorescent images were quantitatively established. The study represents a major contribution to an emerging field of study in which modulation is induced by the proximity of enzymes to otherwise undruggable targets.

Reviewer #3 (Public Review):

This manuscript proposes to tackle a very interesting and methodologically challenging topic: the mechanistic underpinnings of neural specialization in the infant brain. The authors presented 4- to 7-month-old infants with social and non-social stimuli while their neural, hemodynamic, and metabolic activity was monitored, and they report a complex pattern of relationships between neural and metabolic or hemodynamic responses during social processing on the one hand, and during non-social processing on the other hand.

The approach described in this manuscript is very interesting and the combined use of EEG and bNIRS data appears very promising. However, there is some confusion between the initial aims of the study, and the analyses performed, which jeopardizes the clarity and the impact of this manuscript. Besides, the predictions of the authors are often underspecified which complexifies the interpretation of the results.

Based on its abstract, the goal of this work is to "combine simultaneous measures of coordinated neural activity metabolic rate and oxygenated blood supply to measure emerging specialization in the infant brain". The introduction nicely elaborates on the "interactive specialization theory" and the potential role of the interplay between brain energy consumption and neural activity in the emergence of functionally specialized brain regions during development. The authors present a novel multimodal approach, with potentially important implications for the study of brain specialization as a function of experience or maturation. Yet the experimental procedure presented in this manuscript only assesses specialized brain activity in response to social processing in 4- to 7-month-old infants, using multimodal neuroimaging.<br /> Indeed, the authors presented 4- to 7-month-old infants with social and non-social stimuli while their neural, hemodynamic, and metabolic activity was monitored. The authors report significant differences between the two conditions in terms of neural activity in the delta, alpha, beta, and gamma bands; as well as in the pattern of hemodynamic to metabolic coupling. Using a GLM approach, the authors report on fNIRS channels and EEG sensors showing significant relationships between the evoked neural activity in the beta and gamma frequency bands, and each of the bNIRS signals (HbO, HbR & CCO), in the social and in the non-social conditions. The authors identify a particular fNIRS channel overlaying posterior STS, showing a positive relationship between Pz EEG beta activity and HbO, as well as CCO, together with a negative relationship between that same neural activity and HbR, in the social condition. This pattern of activity was not observed in the non-social condition.<br /> Overall, these results indicate differential neural responses to social and non-social stimuli, coupled metabolic and hemodynamic activity in response to social as well as nonsocial stimuli. These results additionally indicate coordinated metabolic, hemodynamic, and neural responses in brain regions selective for social processing, but it does not allow us to conclude that this coordinated activity is actually related to the functional specialization process (e.g. last sentence of the abstract).

Another weakness of this manuscript relates to the unclear or underspecified motivations behind some of the performed analyses. For example, the authors contrast brain responses to social vs. baseline, non-social vs. baseline, and social vs. non-social. For clarity in the manuscript, the authors should specify the motivation behind each of these contrasts and their predictions.

Another example is in the analysis of the hemodynamic and metabolic coupling analysis, here the authors analyze only the social vs. baseline and non-social vs. baseline contrast, and they do not analyze the social vs non-social contrast. It would be useful for the reader to understand why only these two contrasts are performed and not the social vs. non-social, and what are the predictions of the authors.

Finally, the core result of this work derives from the final GLM analysis which relates EEG activity to hemodynamic or metabolic responses. This analysis implies the inspection of interactions between 3 neuroimaging modalities, with 4 EEG measures, 2 hemodynamic measures, and 1 metabolic measure, which represents a very rich and relatively complex analytic approach. Unfortunately, the predictions are not clearly specified, which makes results interpretation difficult.

Based on the results (L160-162) and discussion (L233-235) sections, it appears that the authors aim at identifying brain regions showing a precise pattern of activity, with a positive relationship between EEG activity and HbO/CCO responses together with a concurrent negative relationship between EEG and HbR responses in response to social events, but not in response to non-social events. Importantly, the social vs. non-social contrast seems crucial to assess the selectivity of the response. Yet, the authors analyze the 3 chromophores separately, and they do not contrast the two conditions (figure 3). As a result, the authors are limited to reporting a descriptive pattern of relationships between EEG and HbO/HbR/CCO activations for the social condition. And another one for the non-social condition. Overall, the authors conclude that channel 14, overlaying the right TPJ, shows the expected pattern of activity, specifically in response to social stimuli. Yet, this statement is only supported by visual inspection/comparison of the results between the social vs baseline and non-social vs baseline conditions. The authors do not assess analytically the differential patterns of activations between the two conditions. Instead, a GLM including all 3 chromophores and contrasting the two experimental conditions would allow us to directly test the predicted pattern of activity, and the selectivity of the activity for social stimuli.

Reviewer #3 (Public Review):

The authors used passive acoustic monitoring over a vast range of the North Atlantic to study the call rates of fin whales. They found a 'take over' of a new rythm (inter call intervals) during their study period. This was interpreted as a change in song production.

I am not completely convinced the authors are correct in describing this change in rate as a change in the song. Even though fin whale calls are evidently a male mating ground display, little is known about its function. Compared to humpback whales with their impressive repertoire of vocalizations, repeating themselves on the breeding grounds after some tens of minutes and therefore qualifying as a very slow 'song' similar to bird song, fin whale only emit a single type of call, which is remaining the same throughout the study period. It can be contested, I would assume, that a ,erely change the repetition rate of calls, even though seemingly done here in an 'overtake' fasion, can qualify as a change and learning of song,

Reviewer #3 (Public Review):

The authors have made significant improvements in addressing my major concerns raised during the previous review. However, I still have some lingering concerns regarding the quantification and statistical analysis presented in the manuscript. Specifically, there is a lack of robust quantification and statistical analysis to support the conclusions drawn, particularly in relation to the numbers of DG, CA1, and CA3 neurons.

To strengthen the validity and reliability of the findings, I would strongly recommend the authors to incorporate a more rigorous quantitative approach in their research. This could involve implementing stereological methods or other appropriate techniques to accurately estimate the numbers of neurons in the DG, CA1, and CA3 regions. By doing so, the authors would enhance the credibility of their conclusions and provide more solid evidence for their claims.

Reviewer #3 (Public Review):

As naturalistic neuroscience becomes increasingly popular, the importance of new computational tools that facilitate the study of animals behaving in minimally constrained environments grows. Yi et al convincingly demonstrate the usefulness of their new method on data from neuroethological studies involving multiple animals, including those with social interactions. Briefly, their method improves upon prior semi-supervised machine learning methods in that extracted latent variables can be more cleanly separated into those representing the behavior of individual subjects and those representing social interactions between subjects. Such an improvement is broadly useful for downstream analysis tasks in multi-subject or social neuroethological studies.

Strengths:<br /> The authors tackle an important problem encountered in behavior analyses in an emerging subfield of neuroscience, naturalistic social neuroscience. They make a case for doing so using semi-unsupervised methods, a toolbox which balances competing scientific needs for building models using large neural-behavioral datasets and for model explainability. The paper is well written, with well-designed figures and relevant analyses that make for an enjoyable reading experience.

The authors provide a remarkable variety of examples that make a convincing case for the utility of their method when used by itself or in conjunction with other data analysis techniques commonly used in modern neuroscience (behavioral motif extraction, neural decoding, etc.). The examples show not just that the extracted latents are more disentangled, but also that the improvement in disentangling has positive effects in downstream analysis tasks.

Weaknesses:<br /> While the paper does a great job of applying the method to real world data, the components of the method itself are not as thoroughly investigated. For example, the contribution of the novel Cauchy-Schwarz regularization technique has not been systematically investigated. This could be done either by sharing additional data where hyperparameters control the contribution of the regularizer, or cite relevant papers where such an analysis have been carried out. It would also be valuable to understand what other regularization techniques might potentially have been applicable here.

The authors conclude from their empirical investigations that the specific prior distribution does not matter to the regularization process. This seems reasonable given that the neural network can learn a complex and arbitrary transformation of the data during training. It would be helpful if the authors could cite prior work where this type of prior distribution does matter and how their approach is different from such prior work. If there is a visualization/explainability related motivation for choosing one prior distribution over another, this could be clarified.

Reviewer #3 (Public Review):

This paper reveals interesting physical connections between Elg1 and CST proteins that suggest a model where Elg1-mediated PCNA unloading is linked to regulation of telomere length extension via Stn1, Cdc13, and presumably Ten1 proteins. Some of these interactions appear to be modulated by sumolyation and connected with Elg1's PCNA unloading activity. The strength of the paper is in the observations of new interactions between CST, Elg1, and PCNA. These interactions should be of interest to a broad audience interested in telomeres and DNA replication.

What is not well demonstrated from the paper is the functional significance of the interactions described. The model presented by the authors is one interpretation of the data shown, and proposes that the role of sumolyation is temporally regulate the Elg1, PCNA and CST interactions at telomeres. This model makes some assumptions that are not demonstrated by this work (such as Stn1 sumolyation, as noted) and are left for future testing. Alternative models that envision sumolyation as a key in promoting spatial localization could also be proposed based on the data here (as mentioned in the discussion), in addition to or instead of a role for sumolyation in enforcing a series of switches governing a tightly sequenced series of interactions and events at telomeres. Critically, the telomere length data from the paper indicates that the proposed model depicts interactions that are not necessary for telomerase activation or inhibition, as telomeres in pol30-RR strains are normal length and telomeres in elg1∆ strains are not nearly as elongated as in stn1 strains. One possibility mentioned in the paper is the PCNAS and Elg1 interactions are contributing to the negative regulation of telomerase under certain conditions that are not defined in this work. Could it also be possible that the role of these interactions is not primarily directed toward modulating telomerase activity? It will be of interest to learn more about how these interactions and regulation by Sumo function intersect with regulation of telomere extension.

Reviewer #3 (Public Review):

The introduction/background is excellent. It reviews evidence showing that the extinction of conditioned responding is regulated by noradrenaline and suggests that the locus coeruleus (LC) may be a critical locus of this regulation. This naturally leads to the aim of the study: to determine whether the locus coeruleus is involved in the extinction of an appetitive conditioned response. Overall, the study is well-designed, nicely conducted and the results advance our understanding of the role of the LC in the extinction of conditioned behaviour. As such, I believe that these results will be of interest to readers. I do, however, feel that the paper would benefit from the inclusion of additional data to clarify the impact of the LC manipulations (stimulation and inhibition) on performance in the task; and some comment regarding the likely source of differences between the groups at test.

Reviewer #3 (Public Review):

Complex behavior requires complex neural control involving multiple brain regions. The currently available tools to measure neural activity in multiple brain regions in small animals are limited and often involve obligatory head-fixation. The latter, obviously, impacts the behaviors under study. Hur and colleagues present a novel recording device, the E-Scope, that combines optical imaging of fluorescent calcium imaging in one brain region with high-density electrodes in another. Importantly, the E-Scope can be implanted and is, therefore, compatible with usage in freely moving mice. The authors used their new E-Scope to study neural activity during social interactions in mice. They demonstrate the presence of neural correlates of social interaction that happen simultaneously in the cerebellum and the anterior cingulate cortex.

The major accomplishment of this study is the development and introduction of the E-Scope. The evaluation of this part can be short: it works, so the authors succeeded.

The authors managed to reduce the weight of the implant to 4.5 g, which is - given all functionality - quite an accomplishment in my view. However, a mouse weighs between 20 and 40 g, so that an implant of 4.5 g is still quite considerable. It can be expected that this has an impact on the behavior and, possibly, the well-being of the animals. Whether this is the case or not, is not really addressed in this study. The authors suffice with the statement that "Recorded animals made more contact with the other mouse than with the object (Figure 2A), suggesting a normal preference for social contact with the E-Scope attached."

Overall, the description of animal behavior is rather sparse. The methods state only that stranger age-matched mice were used, but do not state their gender. The nature of the social interactions was not described? Was their aggressive behavior, sexual approach and/or intercourse? Did the stranger mice attack/damage the E-Scope? Were the interactions comparable (using which parameters?) with and without E-Scope attached? It is not even described what the authors define as an "interaction bout" (Figure 2A). The number of interaction bouts is counted per 7 minutes, I presume? This is not specified explicitly.

In Figure 1 D-G, the authors present raw data from the neurophysiological recordings. In panel D, we see events with vastly different amplitudes. It would be very insightful if the authors would describe which events they considered to be action potentials, and which not. Similarly, the raw traces of Figure 1E are declared to be single-unit recordings of Purkinje cells. Partially due to the small size of the traces (invisible in print and pixelated in the digital version), I have a hard time recognizing complex spikes and simple spikes in these traces. This is a bit worrisome, as the authors declare the typical duration of the pause in simple spike firing after a complex spike to be 20-100 ms. In my experience, such long pauses are rare in this region, and definitely not typical. In the right panel of Figure 1A, an example of a complex spike-induced pause is shown. This pause is around 15 ms, so not typical according to the text, and starts only around 4 ms after the complex spike, which should not be the case and suggests either a misalignment of the figure or the detection of complex spike spikelets as simple spikes, while the abnormally long pause suggests that the authors fail to detect a lot of simple spikes. The authors could provide more confidence in their data by including more raw data, making explicit how they analyzed the signals, and by reporting basic statistics of firing properties (like rate, cv or cv2, pause duration). In this respect, Figure 2 - figure supplement 3 shows quite a large percentage of cells to have either a very low or a very high firing rate.

The number of Purkinje cells recorded during social interactions is quite low: only 11 cells showed a modulation in their spiking activity (unclear whether in complex spikes, simple spikes or both. During object interaction, only 4 cells showed a significant modulation. Unclear is whether the latter 4 are a subset of the former 11, or whether "social cells" and "object cells" are different categories. Having so few cells, and with these having different types of modulation, the group of cells for each type of modulation is really small, going down to 2 cells/group. It is doubtful whether meaningful interpretation is possible here.

This brings us to the next point: neural correlates of social interaction are notoriously difficult to interpret. Social behavior is complex, and involves the processing of sensory cues (olfaction, touch (whiskers), visual and auditory), the production of ultrasonic vocalizations (in specific contexts), movements, and emotional behavior (fear, pleasure, sexual interest). In other words, neural activity patterns observed during social interaction do not necessarily relate specifically to social interaction, but can also occur in a non-social context. The authors control this by comparing social interactions with object interactions, but I miss a direct comparison between the two conditions, both in terms of behavior (now only the number of interactions is counted, not their duration or intensity), and in terms of neural activity. There is some analysis done on the interaction between movement and cerebellar activity (Figure 2 - figure supplement 4), but it is unclear to what extent social interactions and movements are separated here. It would already help to indicate in the plots with trajectories (e.g., Fig. 2H) indicate the social interactions (e.g., social interaction-related movements in red, the rest of the trajectories in black).

The neuron count in the anterior cingulate cortex is much higher than for the cerebellum, but also here it is not so clear what is "social" and what is "non-social". In Figure 3G-H, the authors indicate a near-perfect separation between cells active during social encounters and those active during object encounters. This could indicate that there is here indeed a social aspect, but as we do not know to what extent the sensory and motor aspects differ between social and non-social interactions, this is still hard to interpret.

Finally, the authors show that there are correlations between the modulation in neurons of the anterior cingulate cortex and cerebellar neurons related to bouts of social activity. Here, it could be interesting to see whether there are differences in latency between the two brain areas.

In conclusion, the authors present a novel method to record neural activity with single cell-resolution in two brain regions in freely moving mice. Given the challenges associated with understanding of complex behaviors, this approach can be useful for many neuroscientists. The authors demonstrate the potential of their approach by studying social interactions in mice. Clearly, there are correlations in the activity of neurons in the anterior cingulate cortex and the cerebellum related to social interactions. To bring our understanding of these patterns to a higher level, more detailed analyses (and probably also larger group sizes of cerebellar neurons) are required, though.

Reviewer #3 (Public Review):

This study investigated what kind of reference (allocentric or egocentric) frame we used for perception in darkness. This question is essential and was not addressed much before. The authors compared the perception in the walking condition with that in the stationary condition, which successfully separated the contribution of self-movement to the spatial representation. In addition, the authors also carefully manipulated the contribution of the waiting period, attentional load, vestibular input, testing task, and walking direction (forward or backward) to examine the nature of the reference frame in darkness systematically.

I am a bit confused by Figure 2b. Allocentric coordinate refers to the representation of the distance and direction of an object relative to other objects but not relative to the observer. In Figure 2, however, the authors assumed that the perceived target was located on the interception between the intrinsic bias curve and the viewing line from the NEW eye position to the target. This suggests that the perceived object depends on the observer's new location, which seems odd with the allocentric coordinate hypothesis.

According to Fig 2b, the perceived size should be left-shifted and lifted up in the walking condition compared to that in the stationary condition. However, in Figure 3C and Fig 4, the perceived size was the same height as that in the baseline condition.

Is the left-shifted perceived distance possibly reflecting a kind of compensation mechanism? Participants could not see the target's location but knew they had moved forward. Therefore, their brain automatically compensates for this self-movement when judging the location of a target. This would perfectly predict the left-shifted but not upward-shifted data in Fig 3C. A similar compensation mechanism exists for size constancy in which we tend to compensate for distance in computing object size.

According to Fig 2a, the target, perceived target, and eye should be aligned in one straight line. This means that connecting the physical targets and the corresponding perceived target results in straight lines that converge at the eye position. This seems, however, unlikely in Figure 3c.

Reviewer #3 (Public Review):

Prior studies have shown that locomotion (e.g., running) modulates mouse V1 activity to a similar extent as visual stimuli. However, it's unclear if these findings hold in species with more specialized and advanced visual systems such as nonhuman primates. In this work, Liska et al. leverage population and single neuron analyses to investigate potential differences and similarities in how running modulates V1 activity in marmosets and mice. Specifically, they discovered that although a shared gain model could describe well the trial-to-trial variations of population-level neural activity for both species, locomotion more strongly modulated V1 population activity in mice. Furthermore, they found that at the level of individual units, marmoset V1 neurons, unlike mice V1 neurons, experience suppression of their activity during running.

A major strength of this work is the introduction and completion of primate electrophysiology recordings during locomotion. Data of this kind was previously limited, and this work moves the field forward in terms of data collection in a domain previously inaccessible in primates. Another core strength of this work is that it adds to a limited collection of cross-species data collection and analysis of neural activity at the single-unit and population level, attempting to standardize analysis and data collection to be able to make inferences across species.

However, the authors did not take full advantage of the quantity and diversity of the marmoset visual cortex recordings in their analyses. They mention recording and analyzing the activity of peripheral V1 neurons but mainly present results involving foveal V1 neurons. Foveal neurons, with their small receptive fields strongly affected by precise eye position, would seem to be less likely to be comparable to rodent data. If the authors have a reason for not doing so, they should provide an explanation. Given that the marmosets are motivated to run with liquid rewards, the authors should provide more context as to how this may or may not affect marmoset V1 activity. Additionally, the lack of consideration of eye movements or position presents a major absence for the marmoset results, and fails to take advantage of one of the key differences between primate and rodent visual systems - the marmosets have a fovea, and make eye movements that fixate in various locations on the screen during the task. Finally, the model provides a strong basis for comparison at the level of neuronal populations, but some methodological choices are insufficiently described and may have an impact on interpreting the claims.

Overall, the methods and data are supportive of the main claims of the work. The use of single neuron and population level approaches demonstrate that the activity of V1 in mice and marmoset is categorically different. Since primate V1 is so diverse, this limits the interpretation of the cross-species comparison. Still, the work is a great step forward in the field, especially with the novel methodology of collecting neural activity from running primates.

Reviewer #3 (Public Review):

Yin-wei Lin et al set out to visualize the inactive conformation of full-length Bruton's Tyrosine Kinase (BTK), a molecule that has evaded high-resolution structural studies in its full-length form to this date. An open question in the field is how the Pleckstrin Homology-Tec Homology (PHTH) domain inhibits BTK activity, with multiple competing models in the field. The authors used a complimentary set of biophysical techniques combined with well-thought-out stabilizing mutations to obtain structural insights into BTK regulation in its full-length form. They were able to crystallize the full-length construct of BTK but unfortunately, the PHTH was not resolved yielding a structure similar to that previously obtained in the field. The investigation of the same construct by SAXS yielded an elongated structural model, consistent with previous SAXS studies. Using cryo-EM the authors obtained a low-resolution model for the FL BTK with a loosely connected density assigned to the dynamic PHTH around the compact SH2-SH3-Kinase Domain (KD) core. To gain further molecular insights into PHTH-KD interactions the authors followed a previously reported strategy and generated a fusion of PHTH-KD with a longer linker, yielding a crystal structure with a novel PHTH-KD interface which they tested in biochemical assays. Lastly, Yin-wei Lin et al crystallized the BTK KD in a novel partially active state in a "face-to-face" dimer with kinases exchanging the activation loops, although partially disordered, being theoretically perfectly positioned for transphosphorylation. Overall this presents a valiant effort to gain molecular insights into what clearly is a dynamic regulatory motif on BTK and is a valuable addition to the field.

However, this work can be improved by considering these points:

1) The cryo-EM reconstructions are potentially over-interpreted. The reported resolution for all of the analyzed reconstructions is better than 8Å, at which point helices should be recognized as well-resolved structural elements. In the current view/depiction of the cryo-EM maps/models it is hard to see such structural features and it would be great if the authors could include a panel showing maps at higher thresholds to show correspondence between the helices in the kinase C lobe and the cryo-EM maps. Otherwise, the overall positioning of the models within the cryo-EM maps is hard to evaluate and may very well be wrong. (Fig 4, S2).

2) With the above in mind, if the maps are not at the point where helices are well resolved, it may be beneficial to low-pass filter the maps to a more conservative resolution for fitting, analysis, and representation. (Fig 4, S2).

3) It would be valuable to get a quantitative metric on the model/map fitting for the cryo-EM work. One good package for this is Situs which provides cross-correlation values for the top orthogonal fits, without user input for initial fitting. This would again increase the confidence in the correctness of model positioning on the map. (Fig 4, S2).

4) It would be great to see 2D class averages from the particles contributing to each of the 3D classes. Theoretically, a clear bright "blob" (hypothesized to be the PHTH domain) should be observable in the 2D class averages. In the current 2D class averages that region is unconvincingly weak. (Fig 4, S2).

5) It seems like there was quite a large circular mask applied during 2D classification. Are authors confident that the weak density attributed to the PHTH domain is not neighboring particles making their way into the extraction box? It would be great if the authors would trim their particle stack with a very stringent inter-particle distance cutoff (or report the cutoff in the manuscript if already done so) to minimize this possibility.

6) The cryo-EM processing may benefit from more stringent particle picking. The authors picked over 2M particles from 750 micrographs which likely represents very heavy overpicking. I would encourage the authors to re-pick the micrographs with 2D class averages and use more stringent metrics to reduce the overpicking. This may result in higher-resolution reconstructions. (Fig 4, S2).

7) The Dmax from SAXS for the Full Length BTK is at 190Å. It would be great if the authors could make a cartoon of what domain arrangement may satisfy this distance, as it is quite extended for such a small particle. Can the authors rule out dimerization at SAXS concentrations? (Fig 1).

8) In Figure S1 (C) it seems that the curves are just scattering curves with Guinier plots in the inserts, but are labeled as Guinier plots in the legend. The Guinier plots for some samples (FL 4P1F) show signs of aggregation, which may complicate the analysis, it could be beneficial to redo.

9) Have the authors verified that the activation loop mutations that they introduce do not disrupt the PHTH binding as they previously reported an activation loop on BTK to interact with PHTH, an interaction they do not see here? If so, a citation would be helpful in the text. If not, testing this would strengthen the paper.

10) Can the authors comment on the surfaces which are accessible and inaccessible to the PHTH in the crystal (Fig 3E)? The fact that PHTH doesn't adopt a stable conformation in the solvent channel to some degree indicates that the accessible interaction surfaces are not suitable for PHTH interactions, as the "effective concentration" of the PHTH would be quite high. Are these surfaces consistent with the cryo-EM analysis?

11) For the novel active state dimer of the Kinase Domain it would be great to see some functional validation of the dimerization interface. It is structurally certainly quite suggestive, but without such experiments the functional significance is unclear. If appropriate mutations have been published previously a citation would be helpful.