Reviewer #1 (Public review):

Summary:

In a heroic effort, Ozanna Burnicka-Turek et al. have made and investigated conduction system-specific Tbx3-Tbx5 deficient mice and investigated their cardiac phenotype. Perhaps according to expectations, given the body of literature on the function of the two T-box transcription factors in the heart/conduction system, the cardiomyocytes of the ventricular conduction system seemed to convert to "ordinary" ventricular working myocytes. As a consequence, loss of VCS-specific conduction system propagation was observed in the compound KO mice, associated with PR and QRS prolongation and elevated susceptibility to ventricular tachycardia.

Strengths:

Great genetic model. Phenotypic consequences at the organ and organismal levels are well investigated. The requirement of both Tbx3 and Tbx5 for maintaining VCS cell state has been demonstrated.

Weaknesses:

The actual cell state of the Tbx3/Tbx5 deficient conducting cells was not investigated in detail, and therefore, these cells could well only partially convert to working cardiomyocytes, and may, in reality, acquire a unique state.

Reviewer #1 (Public review):

Summary:

This paper developed a model of chromosome mosaicism by using a new aneuploidy-inducing drug (AZ3146), and compared this to their previous work where they used reversine, to demonstrate the fate of aneuploid cells during murine preimplantation embryo development. They found that AZ3146 acts similarly to reversine in inducing aneuploidy in embryos, but interestingly showed that the developmental potential of embryos is higher in AZ3146-treated vs. reversine-treated embryos. This difference was associated with changes in HIF1A, p53 gene regulation, DNA damage, and fate of euploid and aneuploid cells when embryos were cultured in a hypoxic environment.

Strengths:

In the current study, the authors investigate the fate of aneuploid cells in the preimplantation murine embryo using a specific aneuploidy-inducing compound to generate embryos that were chimeras of euploid and aneuploid cells. The strength of the work is that they investigate the developmental potential and changes in gene expression profiles under normoxic and hypoxic culture conditions. Further, they also assessed how levels of DNA damage and DNA repair are altered in these culture conditions. They also assessed the allocation of aneuploid cells to the divergent cell lineages of the blastocyst stage embryo.

Weaknesses:

Inconsistent/missing description for sample size, biological/technical replicates, label orientation, the appropriate number of * for each figure panel, and statistical tests used.

Reviewer #1 (Public review):

Summary:

Dopamine neurons contribute to motivated and motor behaviors in many ways, and ample recent evidence has suggested that distinct dopamine neuron subclasses support discrete behavioral and circuit functions. Prior studies have subdivided dopamine neurons by spatial localization, gene expression patterns, and physiological properties. However, many of these studies were bound by previous technical limitations that made comprehensive subclassification efforts difficult or impossible. The main goal of this manuscript was to characterize and further define dopamine neuron heterogeneity in the ventral midbrain. The study uses cutting-edge single nucleus RNA-seq (on the 10X Genomics platform) and spatial transcriptomics (on the MERFISH platform) to define dopamine neuron heterogeneity with unprecedented resolution. The result is a convincing and comprehensive subclassification of dopamine neurons into three main families, each with major branches and subtypes. In addition, the study reports comparisons between wild-type mice and mice that harbor a G2019S mutation in the Lrrk2 gene, which models a common cause of autosomally dominant Parkinson's Disease in humans. These results, while less robust due to the nature of the group comparisons, nevertheless identify vulnerability within specific dopamine neuron subpopulations. This vulnerability may contribute unique risk of dopamine neuron loss in the context of Parkinson's disease. Overall, the study is careful and rigorous and provides a critical resource for the rapidly evolving knowledge of dopamine neuron subtypes.

Strengths:

(1) The creation of a public-facing app where the snRNA-seq data can be investigated by anyone is a major strength.

(2) The manuscript includes careful comparisons to prior datasets that have sought to explore dopamine neuron heterogeneity. The result is a useful synthesis of new findings with previously published work, which is helpful for moving the field forward in this area.

(3) The integration of snRNA-seq with MERFISH results is particularly strong and enables insight not only into subclassification but also into how this relates to spatial localization. The careful neuroanatomy reveals important distinctions between Sox6, Calb1, and Gad2 positive dopamine neuron families, with some degree of spatial overlap.

Weaknesses:

(1) Important details about the nature of DEG comparisons between the wild type and the Lrrk2 G2019S model are missing.

(2) Some aspects of the integration between snRNA-seq and MERFISH data are not clear, and many MERFISH-identified cells do not appear to have a high-confidence cluster transfer into the snRNA-seq data space. Imputation is used to overcome some issues with the MERFISH dataset, but it is not clear that this is appropriate.

Reviewer #1 (Public review):

Mutations in CDHR1, the human gene encoding an atypical cadherin-related protein expressed in photoreceptors, are thought to cause cone-rod dystrophy (CRD). However, the pathogenesis leading to this disease is unknown. Previous work has led to the hypothesis that CDHR1 is part of a cadherin-based junction that facilitates the development of new membranous discs at the base of the photoreceptor outer segments, without which photoreceptors malfunction and ultimately degenerate. CDHR1 is hypothesized to bind to a transmembrane partner to accomplish this function, but the putative partner protein has yet to be identified.

The manuscript by Patel et al. makes an important contribution toward improving our understanding of the cellular and molecular basis of CDHR1-associated CRD. Using gene editing, they generate a loss of function mutation in the zebrafish cdhr1a gene, an ortholog of human CDHR1, and show that this novel mutant model has a retinal dystrophy phenotype, specifically related to defective growth and organization of photoreceptor outer segments (OS) and calyceal processes (CP). This phenotype seems to be progressive with age. Importantly, Patel et al, present intriguing evidence that pcdh15b, also known for causing retinal dystrophy in previous Xenopus and zebrafish loss of function studies, is the putative cdhr1a partner protein mediating the function of the junctional complex that regulates photoreceptor OS growth and stability.

This research is significant in that it:

(1) provides evidence for a progressive, dystrophic photoreceptor phenotype in the cdhr1a mutant and, therefore, effectively models human CRD; and

(2) identifies pcdh15b as the putative, and long sought after, binding partner for cdhr1a, further supporting the theory of a cadherin-based junction complex that facilitates OS disc biogenesis.

Nonetheless, the study has several shortcomings in methodology, analysis, and conceptual insight, which limits its overall impact.

Below I outline several issues that the authors should address to strengthen their findings.

Major comments:

(1) Co-localization of cdhr1a and pcdh15b proteins

The model proposed by the authors is that the interaction of cdhr1a and pcdh15b occurs in trans as a heterodimer. In cochlear hair cells, PCDH15 and CDHR23 are proposed to interact first as dimers in cis and then as heteromeric complexes in trans. This was not shown here for cdhr1a and pcdh15b, but it is a plausible configuration, as are single heteromeric dimers or homodimers. Regardless, this model depends on the differential compartmental expression of the cdhr1a and pcdh15b proteins. Data in Figure 1 show convincing evidence that these two proteins can, at least in some cases, be distributed along the length of photoreceptor membranes that are juxtaposed, as would be the case for OS and CP. If pcdh15b is predominantly expressed in CPs, whereas cdhr1a is predominantly expressed in OS, then this should be confirmed with actin double labeling with cdhr1a and pcdh15b since the apicobasal oriented (vertical) CPs would express actin in this same orientation but not in the OS. This would help to clarify whether cdhr1a and pcdh15b can be trafficked to both OS and CP compartments or whether they are mutually exclusive.

Photoreceptor heterogeneity goes beyond the cone versus rod subtypes discussed here and it is known that in zebrafish, CP morphology is distinct in different cone subtypes as well as cone versus rod. It would be important to know which specific photoreceptor subtypes are shown in zebrafish (Figures 1A-C) and the non-fish species depicted in Figures 1E-L. Also, a larger field of view of the staining patterns for Figures 1E-L would be a helpful comparison (could be added as a supplementary figure).

(2) Cdhr1a function in cell culture

The authors should explain the multiple bands in the anti-FLAG blots. Also, it would be interesting to confirm that the cdhr1a D173 mutant prevents the IP interaction with pcdh15b as well as the additive effects in aggregate assays of Figure 2.

Is it possible that the cultured cells undergo proliferation in the aggregation assays shown in Figure 2? Cells might differentially proliferate as clusters form in rotating cultures. A simple assay for cell proliferation under the different transfection conditions showing no differences would address this issue and lend further support to the proposed specific changes to cell adhesion as a readout of this assay.

Also, the authors report that the number of clusters was normalized to the field of view, but this was not defined. Were the n values different fields of view from one transfection experiment, or were they different fields of view from separate transfection experiments? More details and clarification are needed.

(3) Methodological issues in quantification and statistical analyses

Were all the OS and CP lengths counted in the observation region or just a sample within the region? If the latter, what were the sampling criteria? For CPs, it seems that the length was an average estimate based on all CPs observed surrounding one cone or one-rod cell. Is this correct? Again, if sampled, how was this implemented? In Fig 4M', the cdhr1a-/- ROS mostly looks curvilinear. Did the measurements account for this, or were they straight linear dimension measurements from base to tip of the OS as depicted in Fig 5A-E? A clearer explanation of the OS and CP length quantification methodology is required.

How were cone and rod photoreceptor cell counts performed? The legend in Figure 4 states that they again counted cells in the observation region, but no details were provided. For example, were cones and rods counted as an absolute number of cells in the observation region (e.g., number of cones per defined area) or relative to total (DAPI+) cell nuclei in the region? Changes in cell density in the mutant (smaller eye or thinner ONL) might affect this quantification so it would be important to know how cell quantification was normalized.

In Figure 6I, K, measuring the length of the signal seems problematic. The dimension of staining is not always in the apicobasal (vertical) orientation. It might be more accurate to measure the cdhr1a expression domain relative to the OS (since the length of the OS is already reduced in the mutants). Another possible approach could be to measure the intensity of cdhr1 staining relative to the intensity within a Prph2 expression domain in each group. The authors should provide complementary evidence to support their conclusion.

A better description of the statistical methodology is required. For example, the authors state that "each of the data points has an n of 5+ individuals." This is confusing and could indicate that in Figure 4F alone there were ~5000 individuals assayed (~100 data points per treatment group x n=5 individuals per data point x 10 treatment groups). I don't think that is what the authors intended. It would be clearer if the authors stated how many OS, CP, or cells were counted in their observation region averaged per individual, and then provided the n value of individuals used per treatment group (controls and mutants), on which the statistical analyses should be based.

There are hundreds of data points in the separate treatment groups shown in several of the graphs. It would not be correct to perform the ANOVA on the separate OS or CP length measurements alone as this will bias the estimates since they are not all independent samples. For example, in Figure 6H, 5dpf pcdh15b+/- have shorter CPs compared to WT but pcdh15b-/- have longer compared to WT. This could be an artifact of the analysis. Moreover, the authors should clarify in the Methods section which ANOVA post hoc tests were used to control for multiple pairwise comparisons.

(4) Cdhr1a function in photoreceptors

The cdhr1a IHC staining in 5dpf WT larvae in Figure 3E appears different from the cdhr1a IHC staining in 5dpf WT larvae in Figure 1A or Figure 6I. Perhaps this is just the choice of image. Can the authors comment or provide a more representative image?

The authors show that pcdh15b localization after 5dpf mirrored the disorganization of the CP observed with actin staining. They also show in Figure 5O that at 180dpf, very little pcdh15b signal remains. They suggest based on this data that total degradation of CPs has occurred in the cdhr1a-/- photoreceptors by this time. However, although reduced in length, COS and cone CPs are still present at 180dpf (Figure 5E, E'). Thus, contrary to the authors' general conclusion, it is possible that the localization, trafficking, and/or turnover of pcdh15b is maintained through a cdhr1a-dependent mechanism, irrespective of the degree to which CPs are maintained. The experiments presented here do not clearly distinguish between a requirement for maintenance of localization versus a secondary loss of localization due to defective CPs.

(5) Conceptual insights

The authors claim that cdhr1a and pcdh15b double mutants have synergistic OS and CP phenotypes. I think this interpretation should be revisited.

First, assuming the model of cdhr1a-pcdh15b interaction in trans is correct, the authors have not adequately explained the logic of why disrupting one side of this interaction in a single mutant would not give the same severity of phenotype as disrupting both sides of this interaction in a double mutant.

Second, and perhaps more critically, at 10dpf the OS and CP lengths in cdhr1a-/- mutants (Figure 7J, T) are significantly increased compared to WT. In contrast, there are no significant differences in these measurements in the pcdh15b-/- mutants. Yet in double homozygous mutants, there is a significant reduction of ~50% in these measurements compared to WT. A synergistic phenotype would imply that each mutant causes a change in the same direction and that the magnitude of this change is beyond additive in the double mutants (but still in the same direction). Instead, I would argue that the data presented in Figure 7 suggest that there might be a functionally antagonistic interaction between cdhr1a and pcdh15b with respect to OS and CP growth at 10dpf.

If these proteins physically interacted in vivo, it would appear that the interaction is complex and that this interaction underlies both OS growth-promoting and growth-restraining (stabilizing) mechanisms working in concert. Perhaps separate homodimers or heterodimers subserve distinct CP-OS functional interactions. This might explain the age-dependent differences in mutant CP and OS length phenotypes if these mechanisms are temporally dynamic or exhibit distinct OS growth versus maintenance phases. Regardless of my speculations, the model presented by the authors appears to be too simplistic to explain the data.

Reviewer #1 (Public review):

Gray and colleagues describe the identification of Integrator complex subunit 12 (INTS12) as a contributor to HIV latency in two different cell lines and in cells isolated from the blood of people living with HIV. The authors employed a high-throughput CRISPR screening strategy to knock down genes and assess their relevance in maintaining HIV latency. They had used a similar approach in two previous studies, finding genes required for latency reactivation or genes preventing it and whose knockdown could enhance the latency-reactivating effect of the NFκB activator AZD5582. This work builds on the latter approach by testing the ability of gene knockdowns to complement the latency-reactivating effects of AZD5582 in combination with the BET inhibitor I-BET151. This drug combination was selected because it has been previously shown to display synergistic effects on latency reactivation.

The finding that INTS12 may play a role in HIV latency is novel, and the effect of its knockdown in inducing HIV transcription in primary cells, albeit in only a subset of donors, is intriguing. However, there are some data and clarifications that would be important to include to complement the information provided in the current version of the manuscript.

Reviewer #1 (Public review):

Summary:

The authors were attempting to identify the molecular and cellular basis for why modulators of the HR pathway, specifically PARPi, are not effective in CDK12 deleted or mutant prostate cancers and they seek to identify new therapeutic agents to treat this subset of metastatic prostate cancer patients. Overall, this is an outstanding manuscript with a number of strengths and in my opinion represents a significant advance in the field of prostate cancer biology and experimental therapeutics.

Strengths:

The patient data cohort size and clinical annotation from Figure 1 are compelling and comprehensive in scope. The associations between tandem duplications and amplifications of oncogenes that have been well-credentialed to be drivers of cancer development and progression are fascinating and the authors identify that in those that have AR amplification for example, there is evidence for AR pathway activation. The association between CDK12 inactivation and various specific gene/pathway perturbations is fascinating and is consistent with previously published studies - it would be interesting to correlate these changes with cell line-based studies in which CDK12 is specifically deleted or inhibited with small molecules to see how many pathways/gene perturbations are shared between the clinical samples and cell and mouse models with CDK12 perturbation. The short-term inhibitor studies related to changes in HRD genes and protein expression with CDK12/13 inhibition are fascinating and suggest differential pathway effects between short inhibition of CDK12/13 and long-term loss of CDK12. The in vivo studies with the inhibitor of CDK12/13 are intriguing but not definitive

Weaknesses:

Given that there are different mutations identified at different CDK12 sites as illustrated in Figure 1B it would be nice to know which ones have been functionally classified as pathogenic and for which ones that the pathogenicity has not been determined. This would be especially interesting to perform in light of the differences in the LOH scores and WES data presented - specifically, are the pathogenic mutations vs the mutations for which true pathogenicity is unknown more likely to display LOH or TD? For the cell inhibition studies with the CDK12/13 inhibitor, more details characterizing the specificity of this molecule to these targets would be useful. Additionally, could the authors perform short-term depletion studies with a PROTAC to the target or short shRNA or non-selected pool CRISPR deletion studies of CDK12 in these same cell lines to complement their pharmacological studies with genetic depletion studies? Also perhaps performing these same inhibitor studies in CDK12/13 deleted cells to test the specificity of the molecule would be useful. Additionally, expanding these studies to additional prostate cancer cell lines or organdies models would strengthen the conclusions being made. More information should be provided about the dose and schedule chosen and the rationale for choosing those doses and schedules for the in vivo studies proposed should be presented and discussed. Was there evidence for maximal evidence of inhibition of the target CDK12/13 at the dose tested given the very modest tumor growth inhibition noted in these studies?

Reviewer #1 (Public review):

Summary:<br /> In this study by Fang et al., the authors show how STAMBPL1 promotes TNBC angiogenesis via a feed-forward GRHL3/HIF1a/VEGFA axis. They demonstrate that STAMBPL1 interacts with FOXO1, define the required domains in each protein, and illustrate that this interaction facilitates FOXO1 transcriptional factor activity, which then activating GRHL3/HIF1a/VEGFA signaling. Lastly, they show that the combination of VEGFR and FOXO1 inhibitors can synergistically suppress STAMBPL1-overexpressing TNBC.

Strengths:

The manuscript is clearly written, and the results are well explained. The observation that STAMBPL1 mediates GRHL3 transcription through its interaction with FOXO1 is novel. The findings also have important translational potential.

Weaknesses:<br /> The mechanism by which STAMBPL1 mediates GRHL3 transcription through its interaction with FOXO1 is not sufficiently discussed, especially in relation to how STAMBPL1 regulates FOXO1. Some reported effects are modest.

Reviewer #1 (Public review):

This is a well-done clinical study which provides new information on the effects of metabolic disturbances in the human skeleton. 63 postmenopausal women undergoing hip arthroplasty, consisting of T2D with obesity; obesity alone; and neither T2D nor obesity were studied. Most of the findings relate to T2D. Increased serum TNF-α was found in T2D, as well as increased bone gene expression of TNF- α, which was associated with reduced expression of Wnt pathway genes. mRNA levels of certain of the cytokines correlated with Wnt signaling components. In addition, the increased serum TNF- α in T2D was associated with reduced Young's modulus, a measure of bone strength. A strength of this paper is that it provides information in an area that is not well-understood. However, there are a number of concerns that warrant direct addressing.

(1) Can the authors speculate why the changes in cytokines and Wnt expression do not impact bone microarchitecture?

(2) The authors state that they are showing an association between inflammation and bone strength via the regulation of Wnt signaling. However they have only shown here that serum cytokines correlate with bone strength. It is true that the authors have previously shown that Wnt signaling correlated with bone strength. But here it would be useful to show if bone strength is also correlated with inflammatory genes.

(3) AGEs increase inflammation (by binding to RAGE which triggers an inflammatory cascade). AGEs might also increase SOST. From their previous work, it seems that the authors have bone AGE measures on these patients and they have shown their relationship with SOST. Do the increased AGEs relate to inflammation as measured by serum and bone expression?

(4) Were bone turnover markers done to show how the inflammation and Wnt findings relate to bone resorption and formation?

(5) RNA integrity values should be reported to confirm that the RNA has not degraded.

(6) The discussion of adiponectin could be clearer (studies are cited that show both positive and negative effects). Please clarify that adiponectin effects on bone are complex and what they are.

(7) Were patients excluded for prior as well as current antiresorptive medication use?

(8) Fig 4A. correlation between SOST mRNA and TNF-a mRNA seems to be driven by 1 outlier. Does the relationship persist if it is removed?

Reviewer #1 (Public review):

This article deals with the chemotactic behavior of E coli bacteria in thin channels (a situation close to 2D). It combines experiments and simulations.

The authors show experimentally that, in 2D, bacteria swim up a chemotactic gradient much more effectively when they are in the presence of lateral walls. Systematic experiments identify an optimum for chemotaxis for a channel width of ~8µm, close to the average radius of the circle trajectories of the unconfined bacteria in 2D. It is known that these circles are chiral and impose that the bacteria swim preferentially along the right-side wall when there is no chemotactic gradient. In the presence of a chemotactic gradient, this larger proportion of bacteria swimming on the right wall yields chemotaxis. This effect is backed by numerical simulations and a geometrical analysis.

If the conclusions drawn from the experiments presented in this article seem clear and interesting, I find that the key elements of the mechanism of this wall-directed chemotaxis are not sufficiently emphasized. Moreover, the paper would be clearer with more details on the hypotheses and the essential ingredients of the analyses.

Can this new probiotic reduce lactose intolerance? by [[Terence Eden]]

Reviewer #1 (Public review):

Summary:

The authors present a modelling study to test the hypothesis that horizontal gene transfer (HGT) can modulate the outcome of interspecies competition in microbiomes, and in particular promote bistability in systems across scales. The premise is a model developed by the same authors in a previous paper where bistability happens because of a balance between growth rates and competition for a mutual resource pool (common carrying capacity). They show that introducing a transferrable element that gives a "growth rate bonus" expands the region of parameter space where bistability happens. The authors then investigate how often (in terms of parameter space) this bistability occurs across different scales of complexity, and finally under selection for the mobile element (framed as ABR selection).

Strengths:

The authors tackle an important, yet complex, question: how do different evolutionary processes impact the ecology of microbial ecosystems? They do a nice job at increasing the scales of heterogeneity and asking how these impact their main observable: bistability.

Weaknesses:

The author's starting point is their interaction LV model and the manuscript then explores how this model behaves under different scenarios. Because the structure of the model and the underlying assumptions essentially dictate these outcomes, I would expect to see much more focus on how these two aspects relate to the specific scenarios that are discussed. For example:

A key assumption is that the mobile element conveys a multiplicative growth rate benefit (1+lambda). However, the competition between the species is modelled as a factor gamma that modulates the competition for overall resource and thus appears in the saturation term (1+ S1/Nm + gamma2*S2/Nm). This means that gamma changes the perceived abundance of the other species (if gamma > 1, then from the point of view of S1 it looks like there are more S2 than there really are). Most importantly, the relationship between these parameters dictates whether or not there will be bistability (as the authors state).

This decoupling between the transferred benefit and the competition can have different consequences. One of them is that - from the point of view of the mobile element - the mobile element competes at different strengths within the same population compared to between. To what degree introducing such a mobile element modifies the baseline bistability expectation thus strongly depends on how it modifies gamma and lambda.

Thus, this structural aspect needs to be much more carefully presented to help the reader follow how much of the results are just trivial given the model assumptions and which have more of an emergent flavour. From my point of view, this has an important impact on helping the reader understand how the model that the authors present can contribute to the understanding of the question "how microbes competing for a limited number of resources stably coexist". I do appreciate that this changes the focus of the manuscript from a presentation of simulation results to more of a discussion of mathematical modelling.

Reviewer #1 (Public review):

Weiler, Teichert, and Margrie systematically analyzed long-range cortical connectivity, using a retrograde viral tracing strategy to identify layer and region-specific cortical projections onto the primary visual, primary somatosensory, and primary motor cortices. Their analysis revealed several hundred thousand inputs into each region, with inputs originating from almost all cortical regions but dominated in number by connections within cortical sub-networks (e.g. anatomical modules). Generally, the relative areal distribution of contralateral inputs followed the distribution of corresponding ipsilateral inputs. The largest proportion of inputs originated from layer 6a cells, and this layer 6 dominance was more pronounced for contralateral than ipsilateral inputs, which suggests that these connections provide predominantly feedback inputs. The hierarchical organization of input regions was similar between ipsi- and contralateral regions, except for within-module connections, where ipsilateral connections were much more feed-forward than contralateral. These results contrast earlier studies which suggested that contralateral inputs only come from the same region (e.g. V1 to V1) and from L2/3 neurons. Thus, these results provide valuable data supporting a view of interhemispheric connectivity in which layer 6 neurons play an important role in providing modulatory feedback.

The conclusions of this paper are mostly well-supported by the data and analysis, but additional consideration of possible experimental biases is needed.

Further discussion or analysis is needed about possible biases in uptake efficiency for different cell types. Is it possible that the nuclear retro-AAV has a tropism for layer 6 axons? Quantitative comparisons with results obtained with alternative methods such as rabies virus (Yao et al., 2023) or anterograde tracing (Harris et al., 2019) may be helpful for this.

Quantitative analysis of the injection sites should be included to account for possible biases. For example, L6 neurons are known to be the main target of contralateral inputs into the visual cortex (Yao et al., 2023). Thus, if the injections are biased towards or against layer 6 neurons, this may change the layer distribution of retrogradely labeled input cells. Comparison across biological replicates may help reveal sensitivity to particular characteristics of the injections.

The possibility of labeling axons of passage within the white matter should be addressed. This could potentially lead to false positive connections, contributing to the broad connectivity from most cortical regions that were observed.

effacer cette phrase

Reviewer #1 (Public review):

D'Oliviera et al. have demonstrated cleavage of human TRMT1 by the SARS-CoV-2 main protease in vitro. Following, they solved the structure of Mpro (Nsp5)-C145A bound to TRMT1 substrate peptide, revealing binding conformation distinct from most viral substrates. Overall, this work enhances our understanding of substrate specificity for a key drug target of CoV2. The paper is well-written and the data is clearly presented. It complements the companion article by demonstrating interaction between Mpro and TRMT1, as well as TRMT1 cleavage under isolated conditions in vitro. They show that cleaved TRMT1 has reduced tRNA binding affinity, linking a functional consequence to TRMT1 cleavage by MPro. Importantly, the revelation for flexible substrate binding of Nsp5 is fundamental for understanding Nsp5 as a drug target. Trmt1 cleavage assays by Mpro revealed similar kinetics for TRMT1 cleavage as compared to nsp8/9 viral polyprotein cleavage site. They purify TRMT1-Q350K, in which there is a mutation in the predicted cleavage consensus sequence, and confirm that it is resistant to cleavage by recombinant Mpro. I am unable to comment critically on the structural analyses as it is outside of my expertise. Overall, I think that these findings are important for confirming TRMT1 as a substrate of Mpro, defining substrate binding and cleavage parameters for an important drug target of SARS-CoV-2, and may be of interest to researchers studying RNA modifications.

Reviewer #2 (Public review):

A high fraction of cells in early embryos carry aneuploid karyotypes, yet even chromosomally mosaic human blastocysts can implant and lead to healthy newborns with diploid karyotypes. Previous studies in other models have shown that genotoxic and proteotoxic stresses arising from aneuploidy lead to the activation of the p53 pathway and autophagy, which helps eliminate cells with aberrant karyotypes. These observations have been here evaluated and confirmed in human blastocysts. The study also demonstrates that the second lineage and formation of primitive endoderm are particularly impaired by aneuploidy.

Comments on revisions:

The authors have addressed the critical issues sufficiently. In particular, they improved the data analysis and added additional data from embryonal samples.

Reviewer #1 (Public review):

Summary:

In this manuscript, Yan and colleagues introduce a modification to the previously published PETRI-seq bacterial single cell protocol to include a ribosomal depletion step based on a DNA probe set that selectively hybridizes with ribosome-derived (rRNA) cDNA fragments. They show that their modification of the PETRI-seq protocol increases the fraction of informative non-rRNA reads from ~4-10% to 54-92%. The authors apply their protocol to investigating heterogeneity in a biofilm model of E. coli, and convincingly show how their technology can detect minority subpopulations within a complex community.

Strengths:

The method the authors propose is a straightforward and inexpensive modification of an established split-pool single cell RNA-seq protocol that greatly increases its utility, and should be of interest to a wide community working in the field of bacterial single cell RNA-seq.

Comments on revised version:

The reviewers have responded thoughtfully and comprehensively to all of my comments. I believe the details of the protocol are now much easier to understand, and the text and methods have been significantly clarified. I have no further comments.

Reviewer #1 (Public review):

Summary:

This work investigated the role of CXXC-finger protein 1 (CXXC1) in regulatory T cells. CXXC1-bound genomic regions largely overlap with Foxp3-bound regions and regions with H3K4me3 histone modifications in Treg cells. CXXC1 and Foxp3 interact with each other, as shown by co-immunoprecipitation. Mice with Treg-specific CXXC1 knockout (KO) succumb to lymphoproliferative diseases between 3 to 4 weeks of age, similar to Foxp3 KO mice. Although the immune suppression function of CXXC1 KO Treg is comparable to WT Treg in an in vitro assay, these KO Tregs failed to suppress autoimmune diseases such as EAE and colitis in Treg transfer models in vivo. This is partly due to the diminished survival of the KO Tregs after transfer. CXXC1 KO Tregs do not have an altered DNA methylation pattern; instead, they display weakened H3K4me3 modifications within the broad H3K4me3 domains, which contain a set of Treg signature genes. These results suggest that CXXC1 and Foxp3 collaborate to regulate Treg homeostasis and function by promoting Treg signature gene expression through maintaining H3K4me3 modification.

Strengths:

Epigenetic regulation of Treg cells has been a constantly evolving area of research. The current study revealed CXXC1 as a previously unidentified epigenetic regulator of Tregs. The strong phenotype of the knockout mouse supports the critical role CXXC1 plays in Treg cells. Mechanistically, the link between CXXC1 and the maintenance of broad H3K4me3 domains is also a novel finding.

Weaknesses:

(1) It is not clear why the authors chose to compare H3K4me3 and H3K27me3 enriched genomic regions. There are other histone modifications associated with transcription activation or repression. Please provide justification.

(2) It is not clear what separates Clusters 1 and 3 in Figure 1C. It seems they share the same features.

(3) The claim, "These observations support the hypothesis that FOXP3 primarily functions as an activator by promoting H3K4me3 deposition in Treg cells." (line 344), seems to be a bit of an overstatement. Foxp3 certainly can promote transcription in ways other than promoting H3K3me3 deposition, and it also can repress gene transcription without affecting H3K27me3 deposition. Therefore, it is not justified to claim that promoting H3K4me3 deposition is Foxp3's primary function.

(4) For the in vitro suppression assay in Figure S4C, and the Treg transfer EAE and colitis experiments in Figure 4, the Tregs should be isolated from Cxxc1 fl/fl x Foxp3 cre/wt female heterozygous mice instead of Cxxc1 fl/fl x Foxp3 cre/cre (or cre/Y) mice. Tregs from the homozygous KO mice are already activated by the lymphoproliferative environment and could have vastly different gene expression patterns and homeostatic features compared to resting Tregs. Therefore, it's not a fair comparison between these activated KO Tregs and resting WT Tregs.

(5) The manuscript didn't provide a potential mechanism for how CXXC1 strengthens broad H3K4me3-modified genomic regions. The authors should perform Foxp3 ChIP-seq or Cut-n-Taq with WT and Cxxc1 cKO Tregs to determine whether CXXC1 deletion changes Foxp3's binding pattern in Treg cells.

Reviewer #1 (Public review):

Summary:

The manuscript by Rowell et al aims to identify differences in TCR recombination and selection between foetal and adult thymus in mice. Authors sequenced the unpaired bulk TCR repertoire in foetal and adult mice thymi and studied both TCRB and TCRa characteristics in the double negative (DN, CD4-CD8-) and single positive (SP4 CD4+CD8- and SP8 CD4-CD8+) populations. They identified age-related differences in TCRa and TCRB segment usage, including a preferential bias toward 3'TRAV and 5' TRAJ rearrangements in foetal cells compared to adults who had a larger perveance for 5'TRAV segments. By depleting the thymocyte population in adult thymi using hydrocortisone, the authors demonstrated that the repertoire became more foetal like, they, therefore, argue that the preferential 5'TRAV rearrangements in adults may be resulting from prolonged/progressive TCRa rearrangements in the adult thymocytes. In line with previous studies, Authors demonstrate that the foetal TCR repertoire was less diverse, less evenly distributed and had fewer non-template insertions while containing more clonal expansions. In addition, the authors claim that changes in V-J usage and CDR1 and CDR2 in the DN vs SP repertoires indicated that positive selection of foetal thymocytes are less dependent on interactions with the MHC.

Strengths:

Overall, the manuscript provides an extensive analysis of the foetal and adult TCR repertoire in the thymus, resulting in new insights in T cell development in foetal and adult thymi.

Weaknesses:

Three major concerns arise:<br /> (1) the authors have analysed TCR repertoires of only 4 foetal and 4 adult mice, considering the high spread the study may have been underpowered.

- The sample size was increased in the revised version

(2) Gating strategies are missing and

- These have now been provided in the revised version

(3) The manuscript is very technical and clearly aimed for a highly specialised audience with expertise in both thymocyte development and TCR analysis. Considering eLife is a scientific journal with a broader readership, Authors are recommended to provide schematics of the TCR rearrangements/their findings and include a summary of conclusions/implications of their findings at the end of each results section rather than waiting till the discussion. This will help the reader to interpret their findings while reading the results.

- These have now been included in the revised version

Reviewer #1 (Public Review):

The authors report compound heterozygous deleterious variants in the kinase domains of the non-receptor tyrosine kinases (NRTK) TNK2/ACK1 in familial SLE. They suggest that ACK1 and BRK deficiencies are associated with human SLE and impair efferocytosis.

The experiments in this revision showing that a weekly injection of ACK1 or BRK inhibitors induced various kinds of lupus-related autoantibodies in BALB/c supported the pivotal role of ACK1/BRK in systemic autoimmunity, although treated mice failed to demonstrate the full picture of lupus.

Reviewer #1 (Public Review):

This article is interesting because the phenotype of the virus with mutations that alter the affinity of HS has been associated with how the viral particle interacts with HS and, thus, with binding and entry. However, the data in this manuscript is compelling and strongly suggests that the mutation that increases the affinity of HS alters capsid stability. To my knowledge, this is the first evidence that such mutation causes capsid destabilization. Furthermore, the idea that this mutation increases infectivity in cell lines by also using a pH-independent route and that, in vivo, this mutation attenuates the virus is very novel. Last year Wa-Chu's lab proposed that encephalopathic Alphaviruses produce capsids with different sizes and that this helps to attenuate highly pathogenic viruses (which might not be the case for non encepahlopatic Alphavirsues). However, they did not demonstrate whether these alterations attenuate the virus and if the altered morphology affects capsid stability. Therefore, this manuscript is fundamental as it contributes to understanding how the assembly/disassembly mechanism can be used to attenuate a virus. Furthermore, it is possible this mechanism could not be restricted to viruses that belong to the Picornaviridae family and opens a new door to understanding viral attenuation in other icosahedral viruses.

Reviewer #1 (Public Review):

This manuscript was previously reviewed and this earlier evaluation resulted in two conflicting assessments. I fully endorse the favourable opinion of former Reviewer 1 and find most negative comments of former Reviewer 2 inappropriate.

This work is absolutely necessary. Even though the authors find it difficult to be fully assertive in the end, their ground work in trying to demonstrate the existence of bias in PPI data is undeniably valuable. Other authors have tried before to show the limitation of unequivocally assigning the degree distribution to a power law but these doubts have had a weak impact. This new study is a great opportunity to discuss further a concern for a simplistic view of PPI network topology. The recent contribution of Broido & Clauset was definitely one to bounce on. The approach of this new manuscript is compelling. Dividing the study in several parts, each reflecting an attempt to bring out commonly used shortcuts in PPI network analyses, makes sense.

Surprisingly, the authors do not refer to the endless controversy of labeling hubs as party or date, which is another manifestation of the interpretative bias of PPI data.

The only worthy point prompted by former Reviewer 2 is the effect of spoke expansion. In their response, the authors suggest that it would probably extend questioning and even if it is considered as future work, it could be mentioned in the main manuscript.

In the end, this submission is an invitation to constructively rethink the analysis of PPI networks and it feeds the discussion on modelling degree distributions that should not be considered as a solved issue.

Reviewer #1 (Public review):

This is a very relevant study, with the potential of having high impact on future research on the evolution of chemical defense mechanisms in animals. The authors present a substantial number of new and surprising experimental results, i.e., the presence in low quantities of alkaloids in amphibians previously deemed to lack these toxins. These data are then combined with literature data to weave the importance of passive accumulation mechanisms into a 4-phases scenario of the evolution of chemical defense in alkaloid-containing poison frogs.

In general, the new data presented in the manuscript are of high quality and high scientific interest, the suggested scenario compelling, and the discussion thorough. Also, the revised version of the manuscript has been carefully prepared with a high quality of illustrations. UI did not detect typos in the text

Understanding that the majority of dendrobatid frogs, including species considered undefended, can contain low quantities of alkaloids in their skin provides an entirely new perspective to our understanding of how the amazing specializations of poison frogs evolved. Although only few non-dendrobatids were included in the alkaloid screening, some of these also included minor quantities of alkaloids, and the capacity of passive alkaloid accumulation may therefore characterize numerous other frog clades, or even amphibians in general.

The overall quality of the work is exceptional. The authors also have done a fantastic job restructuring the manuscript in response to my initial comments, and it is now very clear which new hypotheses are presented and which testable predictions for future studies derive from these hypotheses. This study will be highly influential in informing and guiding future research on toxicity, alkaloid sequestration and resistance, and evolution of aposematism.

Reviewer #1 (Public review):

Summary:

Utilizing transgenic lineage tracing techniques and tissue clearing-based advanced imaging and three-dimensional slices reconstruction, the authors comprehensively mapped the distribution atlas of NFATc1+ and PDGFR-α+ cells in dental and periodontal mesenchyme and tracked their in vivo trajectories. This important work expands our understanding of both single and double positive NFATc1 and PDGFR-α cells in maintaining dental and periodontal mesenchyme homeostasis, and will provide impact on clinical application and investigation. The strength of this work is convincing, as it employed CRISPR/Cas9-mediated gene editing to generate two dual recombination systems, and mapped gNFATc1+ and PDGFR-α+ cells residing in dental and periodontal mesenchyme, their capacity for progeny cell generation, and their inclusive, exclusive and hierarchical relations in homeostasis, generating a spatiotemporal atlas of these skeletal stem cell population.

This work has theoretical or practical implications in the periodontal field. The methods, data and analyses support the claims.

Comments on revised version:

The authors have addressed my main concerns.

Reviewer #1 (Public review):

In this work, Veseli et al. present a computational framework to infer the functional diversity of microbiomes in relation to microbial diversity directly from metagenomic data. The framework reconstructs metabolic modules form metagenomes and calculates the per-population copy number of each module, resulting in the proportion of microbes in the sample carrying certain genes. They applied this framework to a dataset of gut microbiomes from 109 inflammatory bowel disease (IBD) patients, 78 patients with other gastrointestinal conditions, and 229 healthy controls. The found that the microbiomes of IBD patients were enriched in a high fraction of metabolic pathways, including biosynthesis pathways such as those for amino acids, vitamins, nucleotides, and lipids. Hence, they had higher metabolic independence compared with healthy controls. To an extent, the authors also found a pathway enrichment suggesting higher metabolic independence in patients with gastrointestinal conditions other than IBD indicating this could be a signal for a general loss in host health. Finally, a machine learning classifier using high metabolic independence in microbiomes could predict IBD with good accuracy. Overall, this is an interesting and well-written article and presents a novel workflow that enables a comprehensive characterization of microbiome cohorts.

Comments on revisions:

I believe that after the second round of revisions, the Reviewers sufficiently addressed the comments and improved the manuscript. Open questions have been answered. I have no further comments.

Joint Public Review:

The subject area will have general appeal to those interested in the study of Pavlovian conditioning. The paper is important, showcasing a rigorous experimental design, several different approaches to data analysis, careful consideration of prior literature, and a thorough introduction. The results indicate that the rate of Pavlovian learning is determined by the ratio of reward rate during cue to the overall reward rate, and that the asymptotic response rate is determined by the reward rate during cue. These findings provide context to many conflicting recent results on this topic and are supported by strong/convincing evidence.

It is additionally claimed that the parameter that governs the acquisition and asymptote of responding in rats is exactly the same as that which governs the acquisition and asymptote of responding in the Gibbon and Balsam (1981) study that used pigeons as experimental subjects; and that the rates of responding during the inter-trial interval and the cue are proportional to the corresponding reward rates with the same proportionality constant. In both of these respects, there are several points that stand in need of clarification - at present, the strength of the evidence in support of these claims is solid. More generally, there are some points that could clarify aspects of rate estimation theory and, thereby, increase the rating of the paper from important to fundamental. These points range from analytical to conceptual and are presented below.

ANALYTICAL

(1) A key claim made here is that the same relationship (including the same parameter) describes data from pigeons by Gibbon and Balsam (1981; Figure 1) and the rats in this study (Figure 3). The evidence for this claim, as presented here, is not as strong as it could be. This is because the measure used for identifying trials to criterion in Figure 1 appears to differ from any of the criteria used in Figure 3, and the exact measure used for identifying trials to criterion influences the interpretation of Figure 3***. To make the claim that the quantitative relationship is one and the same in the Gibbon-Balsam and present datasets, one would need to use the same measure of learning on both datasets and show that the resultant plots are statistically indistinguishable, rather than simply plotting the dots from both data sets and spotlighting their visual similarity. In terms of their visual characteristics, it is worth noting that the plots are in log-log axis and, as such, slight visual changes can mean a big difference in actual numbers. For instance, between Figure 3B and 3C, the highest information group moves up only "slightly" on the y-axis but the difference is a factor of 5 in the real numbers. Thus, in order to support the strong claim that the quantitative relationships obtained in the Gibbon-Balsam and present datasets are identical, a more rigorous approach is needed for the comparisons.

***The measure of acquisition in Figure 3A is based on a previously established metric, whereas the measure in Figure 3B employs the relatively novel nDKL measure that is argued to be a better and theoretically based metric. Surprisingly, when r and r2 values are converted to the same metric across analyses, it appears that this new metric (Figure 3B) does well but not as well as the approach in Figure 3A. This raises questions about why a theoretically derived measure might not be performing as well on this analysis, and whether the more effective measure is either more reliable or tapping into some aspect of the processes that underlie acquisition that is not accounted for by the nDKL metric.

(2) Another interesting claim here is that the rates of responding during ITI and the cue are proportional to the corresponding reward rates with the same proportionality constant. This too requires more quantification and conceptual explanation. For quantification, it would be more convincing to calculate the regression slope for the ITI data and the cue data separately and then show that the corresponding slopes are not statistically distinguishable from each other. Conceptually, it is not clear why the data used to test the ITI proportionality came from the last 5 conditioning sessions. What were the decision criteria used to decide on averaging the final 5 sessions as terminal responses for the analyses in Figure 5? Was this based on consistency with previous work, or based on the greatest number of sessions where stable data for all animals could be extracted?

If the model is that animals produce response rates during the ITI (a period with no possible rewards) based on the overall rate of rewards in the context, wouldn't it be better to test this before the cue learning has occurred? Before cue learning, the animals would presumably only have attributed rewards in the context to the context and thus, produce overall response rates in proportion to the contextual reward rate. After cue learning, the animals could technically know that the rate of rewards during ITI is zero. Why wouldn't it be better to test the plotted relationship for ITI before cue learning has occurred? Further, based on Figure 1, it seems that the overall ITI response rate reduces considerably with cue learning. What is the expected ITI response rate prior to learning based on the authors' conceptual model? Why does this rate differ from pre and post-cue learning? Finally, if the authors' conceptual framework predicts that ITI response rate after cue learning should be proportional to contextual reward rate, why should the cue response rate be proportional to the cue reward rate instead of the cue reward rate plus the contextual reward rate?

(3) There is a disconnect between the gradual nature of learning shown in Figures 7 and 8 and the information-theoretic model proposed by the authors. To the extent that we understand the model, the animals should simply learn the association once the evidence crosses a threshold (nDKL > threshold) and then produce behavior in proportion to the expected reward rate. If so, why should there be a gradual component of learning as shown in these figures? In terms of the proportional response rule to the rate of rewards, why is it changing as animals go from 10% to 90% of peak response? The manuscript would be greatly strengthened if these results were explained within the authors' conceptual framework. If these results are not anticipated by the authors' conceptual framework, this should be explicitly stated in the manuscript.

(4) Page 27, Procedure, final sentence: The magazine responding during the ITI is defined as the 20 s period immediately before CS onset. The range of ITI values (Table 1) always starts as low as 15 s in all 14 groups. Even in the case of an ITI on a trial that was exactly 20 s, this would also mean that the start of this period overlaps with the termination of the CS from the previous trial and delivery (and presumably consumption) of a pellet. It should be indicated whether the definition of the ITI period was modified on trials where the preceding ITI was < 20 s, and if any other criteria were used to define the ITI. Were the rats exposed to the reinforcers/pellets in their home cage prior to acquisition?

(5) For all the analyses, the exact models that were fit and the software used should be provided. For example, it is not necessarily clear to the reader (particularly in the absence of degrees of freedom) that the model discussed in Figure 3 fits on the individual subject data points or the group medians. Similarly, in Figure 6 there is no indication of whether a single regression model was fit to all the plotted data or whether tests of different slopes for each of the conditions were compared. With regards to the statistics in Figure 6, depending on how this was run, it is also a potential problem that the analyses do not correct for the potentially highly correlated multiple measurements from the same subjects, i.e. each rat provides 4 data points which are very unlikely to be independent observations.

CONCEPTUAL

(1) We take the point that where traditional theories (e.g., Rescorla-Wagner) and rate estimation theory (RET) both explain some phenomenon, the explanation in terms of RET may be preferred as it will be grounded in aspects of an animal's experience rather than a hypothetical construct. However, like traditional theories, RET does not explain a range of phenomena - notably, those that require some sort of expectancy/representation as part of their explanation. This being said, traditional theories have been incorporated within models that have the representational power to explain a broader array of phenomena, which makes me wonder: Can rate estimation be incorporated in models that have representational power; and, if so, what might this look like? Alternatively, do the authors intend to claim that expectancy and/or representation - which follow from probabilistic theories in the RW mould - are unnecessary for explanations of animal behaviour?***

***If the authors choose to reply to these points, they should consider taking advantage of an "Ideas and Speculation" subsection within the Discussion that is supported by eLife [ https://elifesciences.org/inside-elife/e3e52a93/elife-latest-including-ideas-and-speculation-in-elife-papers ].

(2) The discussion of Rescorla's (1967) and Kamin's (1968) findings needs some elaboration. These findings are already taken to mean that the target CS in each design is not informative about the occurrence of the US - hence, learning about this CS fails. In the case of blocking, we also know that changes in the rate of reinforcement across the shift from stage 1 to stage 2 of the protocol can produce unblocking. Perhaps more interesting from a rate estimation perspective, unblocking can also be achieved in a protocol that maintains the rate of reinforcement while varying the sensory properties of the US (Wagner). How does rate estimation theory account for these findings and/or the demonstrations of trans-reinforcer blocking (Pearce-Ganesan)? Are there other ways that the rate estimation account can be distinguished from traditional explanations of blocking and contingency effects? If so, these would be worth citing in the discussion. More generally, if one is going to highlight seminal findings (such as those by Rescorla and Kamin) that can be explained by rate estimation, it would be appropriate to acknowledge findings that challenge the theory - even if only to note that the theory, in its present form, is not all-encompassing. For example, it appears to me that the theory should not predict one-trial overshadowing or the overtraining reversal effect - both of which are amenable to discussion in terms of rates. I assume that the signature characteristics of latent inhibition and extinction would also pose a challenge to rate estimation theory, just as they pose a challenge to Rescorla-Wagner and other probability-based theories. Is this correct?

Reviewer #1 (Public Review):

Summary:

A key challenge at the second chemical step of splicing is the identification of the 3' splice site of an intron. This requires recruitment of factors dedicated to the second chemical step of splicing and exclusion of factors dedicated to the first chemical step of splicing. Through the highest resolution cyroEM structure of the spliceosome to-date, the authors show the binding site for Fyv6, a factor dedicated to the second chemical step of splicing, is mutually exclusive with the binding site for a distinct factor dedicated to the first chemical step of splicing, highlighting that splicing factors bind to the spliceosome at a specific stage not only by recognizing features specific to that stage but also by competing with factors that bind at other stages. The authors further reveal that Fyv6 functions at the second chemical step to promote selection of 3' splice sites distal to a branch point and thereby discriminate against proximal, suboptimal 3' splice site. Lastly, the authors show by cyroEM that Fyv6 physically interacts with the RNA helicase Prp22 and by genetics Fyv6 functionally interacts with this factor, implicating Fyv6 in 3'SS proofreading and mRNA release from the spliceosome. The evidence for this study is robust, with the inclusion of genomics, reporter assays, genetics, and cyroEM. Further, the data overall justify the conclusions, which will be of broad interest.

Strengths:

(1) The resolution of the cryoEM structure of Fyv6-bound spliceosomes at the second chemical step of splicing is exceptional (2.3 Angstroms at the catalytic core; 3.0-3.7 Angstroms at the periphery), providing the best view of this spliceosomal intermediate in particular and the core of the spliceosome in general.<br /> (2) The authors observe by cryoEM three distinct states of this spliceosome, each distinguished from the next by progressive loss of protein factors and/or RNA residues. The authors appropriately refrain from overinterpreting these states as reflecting distinct states in the splicing cycle, as too many cyroEM studies are prone to do, and instead interpret these observations to suggest interdependencies of binding. For example, when Fyv6, Slu7, and Prp18 are not observed, neither are the first and second residues of the intron, which otherwise interact, suggesting an interdependence between 3' splice site docking on the 5' splice site and binding of these second step factors to the spliceosome.<br /> (3) Conclusions are supported from multiple angles.<br /> (4) The interaction between Fyv6 and Syf1, revealed by the cyroEM structure, was shown to account for the temperature-sensitive phenotypes of a fyv6 deletion, through a truncation analysis.<br /> (5) Splicing changes were observed in vivo both by indirect copper reporter assays and directly by RT-PCR.<br /> (6) Changes observed by RNA-seq are validated by RT-PCR.<br /> (7) The authors go beyond simply observing a general shift to proximal 3'SS usage in the fyv6 deletion by RNA-seq by experimentally varying branch point to 3' splice site distance experimentally in a reporter and demonstrating in a controlled system that Fyv6 promotes distal 3' splice sites.<br /> (8) The importance of the Fyv6-Syf1 interaction for 3'SS recognition is demonstrated by truncations of both Fyv6 and of Syf1.<br /> (9) In general, the study was executed thoroughly and presented clearly.

Comments on revisions:

The authors have satisfactorily addressed the comments.

Reviewer #1 (Public review):

Summary:

This study reports single-cell RNA sequencing results of lung adenocarcinoma, comparing 4 treatment-naive and 5 post-neoadjuvant chemotherapy tumor samples.<br /> The authors claim that there are metabolic reprogramming in tumor cells as well as stromal and immune cells after chemotherapy.<br /> The most significant findings are in the macrophages that there are more pro-tumorigenic cells after chemotherapy, i.e. CD45+CD11b+ARG+ cells. In the treatment-naive samples, more anti-tumorigenic CD45+CD11b+CD86+ macrophages are found. They sorted each population and performed functional analyses.

Strengths:

Comparison of the treatment-naive and post-chemotherapy samples of lung adenocarcinoma.

Weaknesses:

After the revision, issues remain with lengthy descriptive clustering type analysis, insufficient statistical support, and inefficient figure presentation.

Reviewer #1 (Public review):

Summary:

This study examined the associations of healthy lifestyles with comprehensive and organ-specific biological ages. It emphasized the importance of lifestyle factors in determining biological ages, which were using common blood biomarkers and body measures.

Strengths:

The data were from a large cohort study and defined comprehensive and six-specified BA.

Weaknesses highlighted previously:

(1) Since only 8.5% of participants from the CMEC were included in the study, has any section bias happened?

(2) The author should specify the efficiency of FFQ. How FFQ can genuinely reflect the actual intake? Moreover, how was the aMED calculated in your study?

(3) HLI (range) and HLI (category) should be clearly defined.

(4) The rationale of comprehensive and specific BA construction should be clearly defined and discussed. For example, can cardiopulmonary BA be reflected only by using cardiopulmonary status? I do not think so.

(5) The lifestyle index is defined based on an equal-weight approach, but this does not reflect reality and can not fully answer the research questions it raises.

Comments on the revised version:

The author answered most of the questions raised. However, since wine is the most important component of aMED, removing wine or alcohol may result in biased estimates. In addition, The authors acknowledge the limitations of this approach, namely that some biomarkers may not fully capture the complete aging process of the system; this weakness is particularly remarkable in organ-specific BA. The authors emphasize that it is cost-effective and easy to implement. However, the results associated with organ-specific BA may not be credible because they do not fully reflect the state of a particular organ. It is recommended that these shortcomings and the applicability of the results should be discussed in the text.

Reviewer #1 (Public review):

The authors sought to determine the impact of early antiretroviral treatment on the size, composition, and decay of the HIV latent reservoir. This reservoir represents the source of viral rebound upon treatment interruption and therefore constitutes the greatest challenge to achieving an HIV cure. A particular strength of this study is that it reports on reservoir characteristics in African women, a significantly understudied population, of whom some have initiated treatment within days of acute HIV diagnosis. With the use of highly sensitive and current technologies, including digital droplet PCR and near full-length genome next-generation sequencing, the authors generated a valuable dataset for investigation of proviral dynamics in women initiating early treatment compared to those initiating treatment in chronic infection. The authors confirm previous reports that early antiretroviral treatment restricts reservoir size, but further show that this restriction extends to defective viral genomes, where late treatment initiation was associated with a greater frequency of defective genomes. Furthermore, an additional strength of this study is the longitudinal comparison of viral dynamics post-treatment, wherein early treatment was shown to be associated with a more rapid rate of decay in proviral genomes, regardless of intactness, over a period of one year post-treatment. While it is indicated that intact genomes were not detected after one year following early treatment initiation, sampling depth is noted as a limitation of the study by the authors, and caution should thus be taken with interpretation where sequence numbers are low. Defective genomes are more abundant than intact genomes and are therefore more likely to be sampled. Early treatment was also associated with reduced proviral diversity and fewer instances of polymorphisms associated with cytotoxic T-lymphocyte immune selection. This is expected given that rapid evolution and extensive immune selection are synonymous with HIV infection in the absence of treatment, yet points to an additional benefit of early treatment in the context of immune therapies to restrict the reservoir.

This is one of the first studies to report the mapping of longitudinal intactness of proviral genomes in the globally dominant subtype C. The data and findings from this study therefore represent a much-needed resource in furthering our understanding of HIV persistence and informing broadly impactful cure strategies. The analysis on clonal expansion of proviral genomes may be limited by higher sequence homogeneity in hyperacute infection i.e., cells with different proviral integration sites may have a higher likelihood of containing identical genomes compared to chronic infection.

Overall, these data demonstrate the distinct benefits of early treatment initiation at reducing the barrier to a functional cure for HIV, not only by restricting viral abundance and diversity but also potentially through the preservation of immune function and limiting immune escape. It therefore provides clues to curative strategies even in settings where early diagnosis and treatment may be unlikely.

Reviewer #1 (Public review):

Previous studies have highlighted some of these paracrine activities of Toxoplasma - and Rasogi et al (mBio, 2020) used a single cell sequencing approach of cells infected in vitro with the WT or MYR KO parasites - and one of their conclusions was that MYR-1 dependent paracrine activities counteract ROP-dependent processes. Similarly, Chen et al (JEM 2020) highlighted that a particular rhoptry protein (ROP16) could be injected into uninfected macrophages and move them to an anti-inflammatory state that might benefit the parasite.

Caveats around immunity and as yet no insight into how this works. In Fig 2 there is a marked defect in the ability of the parasites to expand at day 2 and day 5. Together, these data sets suggest that this paracrine effect mediated by MYR-1 works early - well before the development of adaptive responses.

Comments on revisions:

The authors have provided their perspective on the original review. There were some previous comments that revolved around whether some of the early changes were masked by pooling data sets where they have reiterated that it is not statistically different. Would have been nice to have seen out addressed by having experiments that were appropriately powered. But it's their call.

Reviewer #1 (Public review):

In their manuscript, authors Isotani et al used in vivo and ex vivo models to show that nicotine could promote stemness and tumorigenicity in murine model. The authors further provided data supporting that the effects of nicotine on stem cell proliferation and tumor initiation were mediated by the Hippo-YAP/TAZ and Notch signal pathway.

The major strength of this study is the using a set of tools, including Lgr5 reporter mice (Lgr5-EGFP-IRES-CreERT2 mice), stem cell-specific Apc knockout mice (Lgr5CreER Apcfl/fl mice), organoids derived from these mice and chemical compounds (agonists and antagonists) to demonstrate nicotine affects stem cells rather than Paneth cells, leading to increased intestinal stemness and tumorigenicity. Whereas, all models are restricted to mice, lacking analysis of human samples or human intestinal organoids to prove the human relevance of these findings.

Overall, the presented results support their conclusions. A previous study reported that nicotine acts through the α2β4 nAChR to enhance Wnt production by Paneth cells, which subsequently affects ISCs. In contrast, this manuscript demonstrated that nicotine directly promotes ISCs through α7-nAChR, independent of Paneth cells. Therefore, this manuscript offers novel insights into the mechanism of nicotine's effects on the mouse intestine.

Reviewer #2 (Public review):

In this manuscript, Tiedje and colleagues longitudinally track changes in parasite numbers across four time points as a way of assessing the effect of malaria control interventions in Ghana. Some of the study results have been reported previously, and in this publication, the authors focus on age-stratification of the results. Malaria prevalence was lower in all age groups after IRS. Follow-up with SMC, however, maintained lower parasite prevalence in the targeted age group but not the population as a whole. Additionally, they observe that diversity measures rebound more slowly than prevalence measures. This adds to a growing literature that demonstrates the relevance of asymptomatic reservoirs.

Strengths:

Overall, I found these results clear, convincing, and well-presented. There is growing interest in developing an expanded toolkit for genomic epidemiology in malaria, and detecting changes in transmission intensity is one major application. As the authors summarize, there is no one-size-fits-all approach, and the Bayesian MOIvar estimate developed here has the potential to complement currently used methods, particularly in regions with high diversity/transmission. I find its extension to a calculation of absolute parasite numbers appealing as this could serve as both a conceptually straightforward and biologically meaningful metric.

Weaknesses:

While I understand the conceptual importance of distinguishing among parasite prevalence, mean MOI, and absolute parasite number, I am not fully convinced by this manuscript's implementation of "census population size". The authors reference the population genetic literature, but within the context of that field, "census population size" refers to the total population size (which, if not formally counted, can be extrapolated) as opposed to "effective population" size, which accounts for a multitude of demographic factors. There is often interesting biology to be gleaned from the magnitude of difference between N and Ne. In this manuscript, however, "census population size" is used to describe the number of distinct parasites detected within a sample, not a population. As a result, the counts do not have an immediate population genetic interpretation and cannot be directly compared to Ne. This doesn't negate their usefulness but does complicate the use of a standard population genetic term. In contrast, I think that sample parasite count will be most useful in an epidemiological context, where the total number of sampled parasites can be contrasted with other metrics to help us better understand how parasites are divided across hosts, space and time. However, for this use, I find it problematic that the metric does not appear to correct for variations in participant number. For instance, in this study, participant numbers especially varied across time for 1-5 year-olds (N=356, 216, 405, and 354 in 2012, 2014, 2015, and 2017 respectively). This sample size variability is accounted for with other metrics like mean MOI. In sum, while the manuscript opens up an interesting discussion, I'm left with an incomplete understanding of the robustness and interpretability of the new proposed metric.

Reviewer #1 (Public review):

Previous experimental studies demonstrated that membrane association drives avidity for several potent broadly HIV-neutralizing antibodies and its loss dramatically reduces neutralization. In this study, the authors present a tour de force analysis of molecular dynamics (MD) simulations that demonstrate how several HIV-neutralizing membrane-proximal external region (MPER)-targeting antibodies associate with a model lipid bilayer.

First, the authors compared how three MPER antibodies, 4E10, PGZL1, and 10E8, associated with model membranes, constructed with two lipid compositions similar to native viral membranes. They found that the related antibodies 4E10 and PGZL1 strongly associate with a phospholipid near heavy chain loop 1, consistent with prior crystallographic studies. They also discovered that a previously unappreciated framework region between loops 2-3 in the 4E10/PGZL1 heavy chain contributes to membrane association. Simulations of 10E8, an antibody from a different lineage, revealed several differences from published X-ray structures. Namely, a phosphatidylcholine binding site was offset and includes significant interaction with a nearby framework region. The revised manuscript demonstrates that these lipid interactions are robust to alterations in membrane composition and rigidity. However, it does not address the reverse-that phospholipids known experimentally not to associate with these antibodies (if any such lipids exist) also fail to interact in MD simulations.

Next, the authors simulate another MPER-targeting antibody, LN01, with a model HIV membrane either containing or missing an MPER antigen fragment within. Of note, LN01 inserts more deeply into the membrane when the MPER antigen is present, supporting an energy balance between the lowest energy conformations of LN01, MPER, and the complex. These simulations recapitulate lipid binding interactions solved in published crystallographic studies but also lead to the discovery of a novel lipid binding site the authors term the "Loading Site", which could guide future experiments with this antibody.

The authors next established course-grained (CG) MD simulations of the various antibodies with model membranes to study membrane embedding. These simulations facilitated greater sampling of different initial antibody geometries relative to membrane. These CG simulations , which cannot resolve atomistic interactions, are nonetheless compelling because negative controls (ab 13h11, BSA) that should not associate with membrane indeed sample significantly less membrane.

Distinct geometries derived from CG simulations were then used to initialize all-atom MD simulations to study insertion in finer detail (e.g., phospholipid association), which largely recapitulate their earlier results, albeit with more unbiased sampling. The multiscale model of an initial CG study with broad geometric sampling, followed by all-atom MD, provides a generalized framework for such simulations.

Finally, the authors construct velocity pulling simulations to estimate the energetics of antibody membrane embedding. Using the multiscale modelling workflow to achieve greater geometric sampling, they demonstrate that their model reliably predicts lower association energetics for known mutations in 4E10 that disrupt lipid binding. However, the model does have limitations: namely, its ability to predict more subtle changes along a lineage-intermediate mutations that reduce lipid binding are indistinguishable from mutations that completely ablate lipid association. Thus, while large/binary differences in lipid affinity might be predictable, the use of this method as a generative model are likely more limited.

The MD simulations conducted throughout are rigorous and the analysis are extensive, creative, and biologically inspired. Overall, these analyses provide an important mechanistic characterization of how broadly neutralizing antibodies associate with lipids proximal to membrane-associated epitopes to drive neutralization.

Reviewer #1 (Public review):

Summary:

In their manuscript, Gomez-Frittelli and colleagues characterize the expression of cadherin6 (and -8) in colonic IPANs of mice. Moreover, they found that these cdh6-expressing IPANs are capable of initiating colonic motor complexes in the distal colon, but not proximal and midcolon. They support their claim by morphological, electrophysiological, optogenetic, and pharmacological experiments.

Strengths:

The work is very impressive and involves several genetic models and state-of-the-art physiological setups including respective controls. It is a very well-written manuscript that truly contributes to our understanding of GI-motility and its anatomical and physiological basis. The authors were able to convincingly answer their research questions with a wide range of methods without overselling their results.

Weaknesses:

The authors put quite some emphasis on stating that cdh6 is a synaptic protein (in the title and throughout the text), which interacts in a homophilic fashion. They deduct that cdh6 might be involved in IPAN-IPAN synapses (line 247ff.). However, Cdh6 does not only interact in synapses and is expressed by non-neuronal cells as well (see e.g., expression in the proximal tubuli of the kidney). Moreover, cdh6 does not only build homodimers, but also heterodimers with Chd9 as well as Cdh7, -10, and -14 (see e.g., Shimoyama et al. 2000, DOI: 10.1042/0264-6021:3490159). It would therefore be interesting to assess the expression pattern of cdh6-proteins using immunostainings in combination with synaptic markers to substantiate the authors' claim or at least add the possibility of cell-cell-interactions other than synapses to the discussion. Additionally, an immunostaining of cdh6 would confirm if the expression of tdTomato in smooth muscle cells of the cdh6-creERT model is valid or a leaky expression (false positive).

Reviewer #1 (Public review):

Summary:

In this manuscript the Treisman and colleagues address the question of how protein phosphatase 1 (PP1) regulatory subunits (or PP1-interacting protein (PIPs)) confer specificity on the PP1 catalytic subunit which by itself possesses little substrate specificity. In prior work the authors showed that the PIP Phactrs confers specificity by remodelling a hydrophobic groove immediately adjacent to the PP1 catalytic site through residues within the RVxF- ø ø -R-W string of Phactrs. Specifically, the residues proximal and including the 'W' of the RVxF- ø ø -R-W string remodel the hydrophobic groove. Other residues of the RVxF- ø ø -R-W string (i.e. the RVxF- ø ø -R) are not involved in this remodelling.

The authors suggest that the RVxF- ø ø -R-W string is a conserved feature of many PIPs including PNUTS, Neurabin/spinophilin and R15A. However, from a sequence and structural perspective, only the RVxF- ø ø -R- is conserved. The W is not conserved in most and in the R15A structure (PDB:7NZM) the Trp side chain points away from the hydrophobic channel - this could be a questionable interpretation due to model-building into the low-resolution cryo-EM map (4 A).

In this paper, the authors convincingly show that Neurabin confers substrate specificity through interactions of its PDZ domain with the PDZ domain-binding motif (PBM) of 4E-BP. They show the PBM motif is required for Neurabin to increase PP1 activity towards 4E-BP and a synthetic peptide modelled on 4E-BP and also a synthetic peptide based on IRSp53 with a PBM added. The PBM of 4E-BP1 confers high affinity binding to the Neurabin PDZ domain. A crystal structure of a PP1-4E-BP1 fusion with Neurabin shows that the PBM of 4E-BP interacts with the PDZ domain of Neurabin. No interactions of 4E-BP and the catalytic site of PP1 are observed. Cell biology work showed that Neurabin-PP1 regulates the TOR signalling pathway by dephosphorylating 4E-BPs.

Strengths:

This work demonstrates convincingly using a variety of cell biology, proteomics, biophysics and structural biology that the PP1 interacting protein Neurabin confers specificity on PP1 through an interaction of its PDZ domain with a PDZ-binding motif of 4E-BP1 proteins. Remodelling of the hydrophobic groove of the PP1 catalytic subunit is not involved in Neurabin-dependent substrate specificity, in contrast to how Phactrs confers specificity on PP1. The active site of the Neurabin/PP1 complex does not recognise residues in the vicinity of the phospho-residue, thus allowing for multiple phospho-sites on 4E-BP to be dephosphorylated by Neurabin/PP1. This contrasts with substrate specificity conferred by the Phactrs PIP that confers specificity of Phactrs/PP1 towards its substrates in a sequence-specific context by remodelling the hydrophobic groove immediately adjacent to the catalytic. The structural and biochemical insights are used to explore the role of Neurabin/PP1 in dephosphorylation 4E-BPs in vivo, showing that Neurabin/PP1 regulates the TOR signalling pathway, specifically mTORC1-dependent translational control.

Weaknesses:

The only weakness is the suggestion that a conserved RVxF- ø ø -R-W string exists in PIPs. The 'W' is not conserved in sequence and 3 dimensions in most of the PIPs discussed in this manuscript. The lack of conservation of the W would be consistent with the finding based on multiple PP1-PIP structures that apart from Phactrs, no other PIP appears to remodel the PP1 hydrophobic channel.

Reviewer #1 (Public review):

The authors of this study developed a method to quantify calvarial bone marrow from MRI head scans, enabling the study of its composition in large datasets of adults, usually collected to study the brain. Bone marrow intensity can be semi-quantitatively measured in T1-weighted MRI scans due to the greater signal intensity of fat than watery red marrow. This is an ingenious use of the MRI-produced information for other important phenotypes, such as bone structure and marrow content. Different head types were tested for complying with the model, which is notable.

The model was also successfully validated using several publicly available MRI resources - real data - in (1) a dataset consisting of 30 individuals that were scanned 10 times each at 3-day intervals, and (2) the monozygotic (MZ) twin data from the Human Connectome Project cohort. Then the authors applied this validated method to head-MRI scans from the UK Biobank (n=33,042) to extract information on the spatial distribution of bone marrow adiposity (BMA) in the calvaria, allowing a GWAS to identify associated genes.

The authors revealed high heritability and identified 41 genetic loci significantly associated with the BMA trait, including six sex-specific loci. Of note, statistics estimate that 99% of BMA trait-influencing variants are shared with BMD (497 of 500 variants), which may mean these results demonstrate the biological relevance to bone health. Some of the BMA genes were found related to the Wnt pathway, including WNT16, WNT4, NXN; this is a "positive control", since the Wnt/β-catenin signaling pathway was suggested as an important determinant of BMA. Also, associations in genes (BMP4, DLX5, LGR4, LRP4, SFRP4) that are known to specifically influence adiposity, are encouraging. Integrating mapped genes with bone marrow single-cell RNA-seq data revealed patterns of adipogenic lineage differentiation and lipid loading.

The study also investigated the genetic overlap between BMA and twelve (or 13) "brain and body" traits and identified significant genetic correlations with BMI, cognitive ability, and Parkinson's disease.

In sum, since MRI head scans present a hitherto unexplored opportunity to address unresolved aspects of bone marrow biology, this study is both timely and innovative.

There are, however, some assumptions, findings, and their interpretation, which require more critical focus.

Sex-specificity is well described and studied here. Men have higher BMA than women, but post-menopausal women catch up in the BMA values. The authors believe that calvarial marrow has a number of features that make it particularly well-suited to the study of BMA process - which is clinically important in other bone sites. It has a simple "sandwiched" structure that they are able to model. This is true only to some extent: a condition called "Hyperostosis frontalis interna", of unknown etiology (described by Smith & Hemphill in 1956) - is characterized by irregular overgrowth of the inner table of the frontal bone (symmetric/bilateral). Although not of clinical significance, typically benign, studies report a prevalence of 12%; However, it's most common in postmenopausal women - where prevalences up to 49% in women over the age of 65 - have been reported. Thus, sexual dimorphism is obvious and the effect of estrogen is likely shared with whichever bone - and marrow - age-related pathology. So, for women not using HRT, this new layer of the bone might interfere with the calvarial BMA readings and in turn, affect the BMA-related analyses. The authors suspect that the effect of BMA on BMD may be biased in women; they should comment on those "with low BMD and high BMA" given that hyperostosis frontalis might be an issue. A strong effect of SNPs in the ESR1 chromosomal region might be akin to the above concern.

Then, there is a perfect overlap of the BMA SNPs that are shared with BMD (497 of 500 variants), which may prove a "face validity" of the MRI-derived BMA. However, the BMD in the study was heel-derived eBMD - which is a good proxy for osteoporosis and is mostly driven by trabecular bone. Thus, there might be a concern that the BMA metrics capture some trabecular BMD.

Next, integrating mapped genes with existing bone marrow single-cell RNA-sequencing data revealed patterns of adipogenic lineage differentiation and lipid loading. The problem here is that the scRNAseq studies of the Bone Marrow niche are overwhelmingly mouse. The authors might wish to justify why they are relevant to humans (in the absence of the human-specific scRNAseq).

For genetic correlation analysis, the authors selected 7 body and 6 brain traits. The latter traits reflect cognition (general cognitive ability and educational attainment) and brain-related disorders. This selection might seem arbitrary. The interpretation of genetic correlation with cognitive ability, education, and Parkinson's disease was attributed to the recently discovered vascular channels that link calvarial bone marrow to the meninges. This is a fascinating hypothesis, which requires functional proof. However, there might be simpler explanations. Thus, the diploe and the inner table of the calvarium are drained by the same veins as the dura. From the anatomy textbook, we know that diploic veins connect the pericranial and endocranial venous system through the skull.

Reviewer #1 (Public review):

Summary:

Ma, Yang et al. report a new investigation aimed at elucidating one of the key nutrients S. Typhimurium (STM) utilizes with the nutrient-poor intracellular niche within the macrophage, focusing on the amino acid beta-alanine. From these data, the authors report that beta-alanine plays an important role in mediating STM infection and virulence. The authors employ a multidisciplinary approach that includes some mouse studies and ultimately propose a mechanism by which panD, involved in B-Ala synthesis, mediates the regulation of zinc homeostasis in Salmonella. The impact of this work is questionable. There are already many studies reporting Salmonella-effector interactions, and while this adds to that knowledge it is not a significant advance over previous studies. While the authors are investigating an interesting question, the work has two important weaknesses; if addressed, the conclusions of this work and broader relevance to bacterial pathogenesis would be enhanced.

Strengths:

This reviewer appreciates the multidisciplinary nature of the work. The overall presentation of the figure graphics are clear and organized.

Weaknesses:

First, this study is very light on mechanistic investigations, even though a mechanism is proposed. Zinc homeostasis in cells, and roles in bacteria infections, are complex processes with many players. The authors have not thoroughly investigated the mechanisms underlying the roles of B-Ala and panD in impacting STM infection such that other factors cannot be ruled out. Defining the cellular content of Zn2+ STM in vivo would be one such route. With further mechanistic studies, the possibility cannot be ruled out that the authors have simply deleted two important genes and seen an infection defect - this may not relate directly to Zn2+ acquisition.

Second, the authors hint at their newly described mechanism/pathway being important for disease and possibly a target for therapeutics. This claim is not justified given that they have employed a single STM strain, which was isolated from chickens and is not even a clinical isolate. The authors could enhance the impact of their findings and relevance to human disease by demonstrating it occurs in human clinical isolates and possibly other serovars. Further, the use of mouse macrophage as a model, and mice, have limited translatability to human STM infections.

Reviewer #1 (Public review):

Summary:

The paper by Tolossa et al. presents classification studies that aim to predict the anatomical location of a neuron from the statistics of its in-vivo firing pattern. They study two types of statistics (ISI distribution, PSTH) and try to predict the location at different resolutions (region, subregion, cortical layer).

Strengths:

This paper provides a systematic quantification of the single-neuron firing vs location relationship.

The quality of the classification setup seems high.

The paper uncovers that, at the single neuron level, the firing pattern of a neuron carries some information on the neuron's anatomical location, although the predictive accuracy is not high enough to rely on this relationship in most cases.

Weaknesses:

As the authors mention in the Discussion, it is not clear whether the observed differences in firing are epiphenomenal. If the anatomical location information is useful to the neuron, to what extent can this be inferred from the vicinity of the synaptic site, based on the neurotransmitter and neuromodulator identities? Why would the neuron need to dynamically update its prediction of the anatomical location of its pre-synaptic partner based on activity when that location is static, and if that information is genetically encoded in synaptic proteins, etc (e.g., the type of the synaptic site)? Note that the neuron does not need to classify all possible locations to guess the location of its pre-synaptic partner because it may only receive input from a subset of locations. If an argument on activity-based estimation being more advantageous to the neuron than synaptic site-based estimation cannot be made, I believe limiting the scope of the paper (e.g., in the Introduction) to an epiphenomenal observation and its quantification will improve the scientific quality.Life Assessment

This article reports a useful set of findings on how electrophysiological response properties of neurons correlate with their position in the brain. The evidence currently remains incomplete, with reviewers making specific suggestions for how clustering needs to be redone. The manuscript would also benefit from a more focused presentation of results and the removal of incorrect claims about recording biases.

Reviewer #1 (Public review):

Summary:

Mitotic kinesins carry out crucial roles in intracellular motility and mitotic spindle organization. Although many mitotic kinesins have been extensively studied, a few conserved mitotic motors remain poorly explored, including chromosome-associated kinesins. Here, Furusaki et al reconstitute recombinant chromosome-associated kinesin or chromokinesin (Kid) and reveal processive plus-end motility along microtubules. The authors purify multiple versions of Kid, revealing dimeric organization and their processive microtubule plus-ended motility which depends on their conserved motor domains, neck linkers, and coiled-coil regions. The study reveals for the first time that KID can recruit and transport duplex DNA along microtubules using its conserved C-terminal DNA binding domain. The work provides crucial revised thinking about the mechanisms of Chromokinesins mitosis as physical processive motors that mobilize chromosomes towards the microtubule plus ends in early metaphase.

Strengths:

The authors reconstitute multiple chromosome-associated kinesin (KID) orthologs from Xenopus and humans with microtubules and determine their oligomerization. The study shows how coiled-coil and neck linker regions of KID are essential for its function as its deletion leads to non-processive motility. CHimeras placing the KID coiled-coil and neck linker on the KIF1A motor domain led to the production of a processive recombinant motor supporting the compatibility of their motility mechanisms. The KID c-terminal tail binds and transports only double-stranded DNA and its deletion or single-stranded DNA leads to defects in this activity.

Weaknesses:

A minor weakness in the studies is that they do not resolve the mechanisms of KID in binding large duplex DNA molecules or condensed chromatin. The authors suggest a model in which KID forms multimers along large chromosomes that lead to their transport, but this model was not directly tested.

Reviewer #1 (Public review):

Summary:

The study by McKim et al seeks to provide a comprehensive description of the connectivity of neurosecretory cells (NSCs) using a high-resolution electron microscopy dataset of the fly brain and several single-cell RNA seq transcriptomic datasets from the brain and peripheral tissues of the fly. They use connectomic analyses to identify discrete functional subgroups of NSCs and describe both the broad architecture of the synaptic inputs to these subgroups as well as some of the specific inputs including from chemosensory pathways. They then demonstrate that NSCs have very few traditional presynapses consistent with their known function as providing paracrine release of neuropeptides. Acknowledging that EM datasets can't account for paracrine release, the authors use several scRNAseq datasets to explore signaling between NSCs and characterize widespread patterns of neuropeptide receptor expression across the brain and several body tissues. The thoroughness of this study allows it to largely achieve it's goal and provides a useful resource for anyone studying neurohormonal signaling.

Strengths:

The strengths of this study are the thorough nature of the approach and the integration of several large-scale datasets to address short-comings of individual datasets. The study also acknowledges the limitations that are inherent to studying hormonal signaling and provides interpretations within the the context of these limitations.

Weaknesses:

Overall, the framing of this paper needs to be shifted from statements of what was done to what was found. Each subsection, and the narrative within each, is framed on topics such as "synaptic output pathways from NSC" when there are clear and impactful findings such as "NSCs have sparse synaptic output". Framing the manuscript in this way allows the reader to identify broad takeaways that are applicable to other model system. Otherwise, the manuscript risks being encyclopedic in nature. An overall synthesis of the results would help provide the larger context within which this study falls.

The cartoon schematic in Figure 5A (which is adapted from a 2020 review) has an error. This schematic depicts uniglomerular projection neurons of the antennal lobe projecting directly to the lateral horn (without synapsing in the mushroom bodies) and multiglomerular projection neurons projecting to the mushroom bodies and then lateral horn. This should be reversed (uniglomerular PNs synapse in the calyx and then further project to the LH and multiglomerular PNs project along the mlACT directly to the LH) and is nicely depicted in a Strutz et al 2014 publication in eLife.

Reviewer #1 (Public review):

Summary:

PROTACs are heterobifunctional molecules that utilize the Ubiquitin Proteasome System to selectively degrade target proteins within cells. Upon introduction to the cells, PROTACs capture the activity of the E3 ubiquitin ligases for ubiquitination of the targeted protein, leading to its subsequent degradation by the proteasome. The main benefit of PROTAC technology is that it expands the "druggable proteome" and provides numerous possibilities for therapeutic use. However, there are also some difficulties, including the one addressed in this manuscript: identifying suitable target-E3 ligase pairs for successful degradation. Currently, only a few out of about 600 E3 ligases are used to develop PROTAC compounds, which creates the need to identify other E3 ligases that could be used in PROTAC synthesis. Testing the efficacy of PROTAC compounds has been limited to empirical tests, leading to lengthy and often failure-prone processes. This manuscript addressed the need for faster and more reliable assays to identify the compatible pairs of E3 ligases-target proteins. The authors propose using the RiPA assay, which depends on rapamycin-induced dimerization of FKBP12 protein with FRB domain. The PROTAC technology is advancing rapidly, making this manuscript both timely and essential. The RiPA assay might be useful in identifying novel E3 ligases that could be utilized in PROTAC technology. Additionally, it could be used at the initial stages of PROTAC development, looking for the best E3 ligase for the specific target.

The authors described an elegant assay that is scalable, easy-to-use and applicable to a wide range of cellular models. This method allows for the quantitative validation of the degradation efficacy of a given pair of E3 ligase-target protein, using luciferase activity as a measure. Importantly, the assay also enables the measurement of kinetics in living cells, enhancing its practicality.

Strengths:

(1) The authors have addressed the crucial needs that arise during PROTAC development. In the introduction, they nicely describe the advantages and disadvantages of the PROTAC technology and explain why such an assay is needed.

(2) The study includes essential controls in experiments (important for generating new assay), such as using the FRB vector without E3 ligase as a negative control, testing different linkers (which may influence the efficacy of the degradation), and creating and testing K-less vectors to exclude the possibility of luciferase or FKBP12 ubiquitination instead of WDR5 (the target protein). Additionally, the position of the luc in the FKBP12 vector and the position of VHL in the FRB vector are tested. Different E3 ligases are tested using previously identified target proteins, confirming the assay's utility and accuracy.

(3) The study identified a "new" E3 ligase that is suitable for PROTAC technology (FBXL).

Weaknesses:

It is not clear how feasible it would be to adapt the assay for high-throughput screens.

Comments on revisions:

The authors have addressed my previous concerns and made changes to the manuscript, resulting in a well-written paper.

Reviewer #1 (Public review):

The study investigates light chains (LCs) using three distinct approaches, with a focus on identifying a conformational fingerprint to differentiate amyloidogenic light chains from multiple myeloma light chains. The study's major contribution is the identification of a low-populated "H state," which the authors propose as a unique marker for AL-LCs. While this finding is promising, the review highlights several strengths and weaknesses. Strengths include the valuable contribution of identifying the H state and the use of multiple approaches, which provide a comprehensive understanding of LC structural dynamics. However, the study suffers from weaknesses, particularly in the interpretation of SAXS data, lack of clarity in presentation, and methodological inconsistencies. Critical concerns include high error margins between SAXS profiles and MD fits, unclear validation of oligomeric species in SAXS measurements, and insufficient quantitative cross-validation between experimental (HDX) and computational data (MD). This reviewer calls for major revisions including clearer definitions, improved methodology, and additional validation, to strengthen the conclusions.

Reviewer #1 (Public review):

Summary:

This study investigated the heterogeneous responses to Mycobacterium tuberculosis (Mtb) in 19 wild-derived inbred mouse strains collected from various geographic locations. The goal of this study is to identify novel mechanisms that regulate host susceptibility to Mtb infection. Using the genetically resistant C57BL/6 mouse strain as the control, they successfully identified a few mouse strains that revealed higher bacterial burdens in the lung, implicating increased susceptibility in those mouse strains. Furthermore, using flow cytometry analysis, they discovered strong correlations between CFU and various immune cell types, including T cells and B cells. The higher neutrophil numbers correlated with significantly higher CFU in some of the newly identified susceptible mouse strains. Interestingly, MANB and MANC mice exhibited comparable numbers of neutrophils but showed drastically different bacterial burdens. The authors then focused on the neutrophil heterogeneity and utilized a single-cell RNA-seq approach, which led to identifying distinct neutrophil subsets in various mouse strains, including C57BL/6, MANA, MANB, and MANC. Pathway analysis on neutrophils in susceptible MANC strain revealed a highly activated and glycolytic phenotype, implicating a possible mechanism that may contribute to the susceptible phenotype. Lastly, the authors found that a small group of neutrophil-specific genes are expressed across many other cell types in the MANC strain.

Strengths:

This manuscript has many strengths.

(1) Utilizing and characterizing novel mouse strains that complement the current widely used mouse models in the field of TB. Many of those mouse strains will be novel tools for studying host responses to Mtb infection.

(2) The study revealed very unique biology of neutrophils during Mtb infection. It has been well-established that high numbers of neutrophils correlate with high bacterial burden in mice. However, this work uncovered that some mouse strains could be resistant to infection even with high numbers of neutrophils in the lung, indicating the diverse functions of neutrophils. This information is important.

Weaknesses:

The weaknesses of the manuscript are that the work is relatively descriptive. It is unclear whether the neutrophil subsets are indeed functionally different. While single-cell RNA seq did provide some clues at transcription levels, functional and mechanistic investigations are lacking. Similarly, it is unclear how highly activated and glycolytic neutrophils in MANC strain contribute to its susceptibility.

Reviewer #1 (Public review):

Summary:

In this manuscript, Guo and colleagues used a cell rounding assay to screen a library of compounds for inhibition of TcdB, an important toxin produced by Clostridioides difficile. Caffeic acid and derivatives were identified as promising leads, and caffeic acid phenethyl ester (CAPE) was further investigated.

Strengths:

Considering the high morbidity rate associated with C. difficile infections (CDI), this manuscript presents valuable research in the investigation of novel therapeutics to combat this pressing issue. Given the rising antibiotic resistance in CDI, the significance of this work is particularly noteworthy. The authors employed a robust set of methods and confirmatory tests, which strengthened the validity of the findings. The explanations provided are clear, and the scientific rationale behind the results is well-articulated. The manuscript is extremely well-written and organized. There is a clear flow in the description of the experiments performed. Also, the authors have investigated the effects of CAPE on TcdB in careful detail and reported compelling evidence that this is a meaningful and potentially useful metabolite for further studies.

Weaknesses:

This is really a manuscript about CAPE, not caffeic acid, and the title should reflect that. Also, a few details are missing from the description of the experiments. The authors should carefully revise the manuscript to ascertain that all details that could affect the interpretation of their results are presented clearly. Just as an example, the authors state in the results section that TcdB was incubated with compounds and then added to cells. Was there a wash step in between? Could compound carryover affect how the cells reacted independently from TcdB? This is just an example of how the authors should be careful with descriptions of their experimental procedures. Lastly, authors should be careful when drawing conclusions from the analysis of microbiota composition data. Ascribing causality to correlational relationships is a recurring issue in the microbiome field. Therefore, I suggest authors carefully revise the manuscript and tone down some statements about the impact of CAPE treatment on the gut microbiota.

Reviewer #1 (Public review):

Summary:

The present study aims to associate reproduction with age-related disease as support of the antagonistic pleiotorpy hypothesis of ageing, predominantly using Mendelian Randomization. The authors found evidence that early-life reproductive success is associated with advanced ageing.

Strengths:

Large sample size. Many analyses.

Weaknesses:

There are some errors in the methodology, that require revisions.

In particular, the main conclusions drawn by the authors refer to the Mendelian Randomization analyses. However, the authors made a few errors here that need to be reconsidered:

(1) Many of the outcomes investigated by the authors are continuous outcomes, while the authors report odds ratios. This is not correct and should be revised.

(2) Some of the odds ratios (for example the one for osteoporosis) are really small, while still reaching the level of statistical significance. After some checking, I found the GWAS data used to generate these MR estimates were processed by the program BOLT-LLM. This program is a linear mixed model program, which requires the transformation of the beta estimates to be useful for dichotomous outcomes. The authors should check the manual of BOLT-LLM and recalculate the beta estimates of the SNP-outcome associations prior to the Mendelian Randomization analyses. This should be checked for all outcomes as it doesn't apply to all.

(3) The authors should follow the MR-Strobe guidelines for presentation.

(4) The authors should report data in the text with a 95% confidence interval.

(5) The authors should consider correction for multiple testing.

Reviewer #1 (Public review):

Summary:

The characteristics of endometrium health are an increasing topic in women's health issues, especially in the context of endometriosis. In this respect, having access to information is hampered by the inaccessibility of the uterine tissue. The authors propose here using the menstrual fluid (easily accessible by non-invasive methods) as an access door towards getting relevant information.

Overall, the paper is divided into two parts:<br /> (1) The comparison between menstrual fluid samples and biopsies of the endometrium.<br /> 2) As a proof of concept, the authors then compared 11 controls and 7 endometriosis cases in this way, from different severity stages.

Strengths:

In Figure 1, general features of the 15 samples are presented (volume/number of cells/hematopoietic cells - cd45 labeling). The authors then used single-cell RNA-seq to characterize the different samples. Through having access to endometrium biopsies, they were able to compare the profiles obtained.

In the MF samples from the second part of the paper - aiming at comparing endometriosis and controls - one question is raised about the effect of culture. The authors compared freshly isolated and cultured tissues (ex vivo vs in vitro) by bulk RNA seq. Biases induced by the culture procedure were identified. Deconvolution was applied to strengthen this observation, with an important increase of seemingly stromal and unknown cells, especially in the unsorted cells and the CD45+ cells.

Interestingly, since the authors got successive samples from the same donor, they could evaluate the consistency of the samples and reveal indeed an overall stability of the molecular profile of the samples in a given patient.

The authors then attempted - quite originally - to characterize biomarkers in two major cell compartments that they studied - CD45- (stromal-like) and CD45+ (immune cells).

Weaknesses:

A potential problem is the justification of the a priori mix of cell types of three different phenotypes (CD45+, CD45- EPCAM+, and CD45- EPCAM-) from each patient before moving to the scRNAseq. It is not clear to me why this has been done, I guess that using directly the samples would supposedly bias the result. But in this case, why is it supposed that three categories are enough (immune cells, epithelial cells, and stromal cells)? I suppose that other markers could characterize other subtypes of the cells, and take into account the possibility of other cell types, for instance, connected to pain sensitivity, such as neuron precursor. Hence, the justification of the organized mixes should be much more detailed in my opinion.

It is a bit unclear to me when the biopsies were collected in the cycle of the donor patients.

The description of these markers that are deregulated is presented as a list, and connected with existing publications, which could rather be presented in discussion than in the results. The authors do tend to demonstrate that the Menstrual Fluid is a good proxy to analyse the endometrium health status of the women affected with endometriosis.

The identification of MTRNR2L1 seems to be a major discovery of the paper, as well as in a lesser measure HBG2, and it is a bit strange why these putative markers were not emphasized in the abstract. HBG2 was certainly identified previously in endometriosis endothelial cells but seems extremely variable from one sample to another - Geo profile (GDS3060, GDS3060 / 213515_x_at (inist.fr)).

Overall, the transcriptome analysis is a bit shallow, with no effort made to try to find potential transcription factors or miRNA that could activate/inhibit a series of modified genes; it could be relevant to identify such master genes or master regulators through bioinformatics analyses and wet-lab validations, to understand better the cascade of events.

Another issue that was overlooked is the presence of 'stem-cells' in the MF obtained. Since endometriosis is supposed to occur from the implantation of uterine stem cells, this category could be a major topic of scrutiny, in terms of quantity in the MF, as well as in terms of their specific molecular properties.

Reviewer #1 (Public review):

The authors attempted to replicate previous work showing that counterconditioning leads to more persistent reduction of threat responses, relative to extinction. They also aimed to examine the neural mechanisms underlying counterconditioning and extinction. They achieved both of these aims and were able to provide some additional information, such as how counterconditioning impacts memory consolidation. Having a better understanding of which neural networks are engaged during counterconditioning may provide novel pharmacological targets to aid in therapies for traumatic memories. It will be interesting to follow up by examining the impact of varying amounts of time between acquisition and counterconditioning phases, to enhance replicability to real-world therapeutic settings.

Major strengths

• This paper is very well written and attempts to comprehensively assess multiple aspects of counterconditioning and extinction processes. For instance, the addition of memory retrieval tests is not core to the primary hypotheses but provides additional mechanistic information on how episodic memory is impacted by counterconditioning. This methodical approach is commonly seen in animal literature, but less so in human studies.

• The Group x Cs-type x Phase repeated measure statistical tests with 'differentials' as outcome variables are quite complex, however, the authors have generally done a good job of teasing out significant F test findings with post hoc tests and presenting the data well visually. It is reassuring that there is a convergence between self-report data on arousal and valence and the pupil dilation response. Skin conductance is a notoriously challenging modality, so it is not too concerning that this was placed in the supplementary materials. Neural responses also occurred in logical regions with regard to reward learning.

• Strong methodology with regards to neuroimaging analysis, and physiological measures.

• The authors are very clear on documenting where there were discrepancies from their pre-registration and providing valid rationales for why.

Major Weaknesses

• The statistics showing that counterconditioning prevents differential spontaneous recovery are the weakest p values of the paper (and using one-tailed tests, although this is valid due to directions being pre-hypothesised). This may be due to a relatively small number of participants and some variability in responses. It is difficult to see how many people were included in the final PDR and neuroimaging analyses, with exclusions not clearly documented. Based on Figure 3, there are relatively small numbers in the PDR analyses (n=14 and n=12 in counterconditioning and extinction, respectively). Of these, each group had 4 people with differential PDR results in the opposing direction to the group mean. This perhaps warrants mention as the reported effects may not hold in a subgroup of individuals, which could have clinical implications.

Reviewer #1 (Public review):

Summary:

In this work, the authors examine the activity and function of D1 and D2 MSNs in dorsomedial striatum (DMS) during an interval timing task. In this task, animals must first nosepoke into a cued port on the left or right; if not rewarded after 6 seconds, they must switch to the other port. Thus, this task requires animals to estimate if at least 6 seconds have passed after the first nosepoke. After verifying that animals estimate the passage of 6 seconds, the authors examine striatal activity during this interval. They report that D1-MSNs tend to decrease activity, while D2-MSNs increase activity, throughout this interval. They suggest that this activity follows a drift-diffusion model, in which activity increases (or decreases) to a threshold after which a decision is made. The authors next report that optogenetically inhibiting D1 or D2 MSNs, or pharmacologically blocking D1 and D2 receptors, increased the average wait time. This suggests that both D1 and D2 neurons contribute to the estimate of time, with a decrease in their activity corresponding to a decrease in the rate of 'drift' in their drift-diffusion model. Lastly, the authors examine MSN activity while pharmacologically inhibiting D1 or D2 receptors. The authors observe most recorded MSNs neurons decrease their activity over the interval, with the rate decreasing with D1/D2 receptor inhibition.

Major strengths:

The study employs a wide range of techniques - including animal behavioral training, electrophysiology, optogenetic manipulation, pharmacological manipulations, and computational modeling. The question posed by the authors - how striatal activity contributes to interval timing - is of importance to the field and has been the focus of many studies and labs. This paper contributes to that line of work by investigating whether D1 and D2 neurons have similar activity patterns during the timed interval, as might be expected based on prior work based on striatal manipulations. However, the authors find that D1 and D2 neurons have distinct activity patterns. They then provide a decision-making model that is consistent with all results. The data within the paper is presented very clearly, and the authors have done a nice job presenting the data in a transparent manner (e.g., showing individual cells and animals). Overall, the manuscript is relatively easy to read and clear, with sufficient detail given in most places regarding the experimental paradigm or analyses used.

Major weaknesses:

The results are based on a relatively small dataset (tens of cells).

Impact:

The task and data presented by the authors are very intriguing, and there are many groups interested in how striatal activity contributes to the neural perception of time. The authors perform a wide variety of experiments and analysis to examine how DMS activity influences time perception during an interval-timing task, allowing for insight into this process.

Reviewer #1 (Public review):

Mitochondria are essential organelles consisting in mammalian cells of about 1500 different proteins. Most of those are synthesized in the cytosol as precursor proteins, imported into mitochondria, and sorted into one of the four sub-mitochondrial compartments. The TIM23 complex, which is embedded in the mitochondrial inner membrane, facilitates the import of proteins that harbor Mitochondrial Targeting Sequence (MTS) at their N-terminus. Such proteins are sorted mainly to the mitochondrial matrix while some sub-groups are destined also to the inner membrane or the intermembrane space. TIMM50 (Tim50 in yeast) is an essential component of the TIM23 complex and mutations in this protein were reported to cause several diseases.

Summary:

In the current study, the authors analyzed the impact of TIMM50 mutations on the mitochondrial proteome in both patients' cells and mouse neurons. They provide compelling evidence for several surprising and highly interesting observations: (i) TIMM50 mutations affect the steady-state levels of only a portion of the putative TIMM50 substrates, (ii) such mutations result in increased electrical activity in mice neurons and in reduced levels of some potassium ion channels in the plasma membrane. These findings shed new light on mitochondrial biogenesis in mammalian cells and hint at an unexpected link between mitochondria and ion channels at the plasma membrane.

Strengths:

The authors used both cells from patients and neurons from mice to investigate the impact of mutations in TIMM50 on mitochondrial proteome and function.

Comments on revisions:

The authors addressed all my concerns regarding the original submission.

Reviewer #2 (Public review):

Summary

The authors address three primary questions:<br /> (1) how FGF13 variants confer seizure susceptibility,<br /> (2) the specific cell types involved, and<br /> (3) the underlying mechanisms, particularly regarding Nav dysfunction.

They use different Cre drivers to generate cell type-specific knockouts (KOs). First, using Nestin-Cre to create a whole-brain Fgf13 KO, they observed spontaneous seizures and premature death. While KO of Fgf13 in excitatory neurons does not lead to spontaneous seizures, KO in inhibitory neurons recapitulates the seizures and premature death observed in the Nestin-Cre KO. They further narrow down the critical cell type to MGE-derived interneurons (INs), demonstrating that MGE-neuron-specific KO partially reproduces the observed phenotypes. "All interneuron" KOs exhibit deficits in synaptic transmission and interneuron excitability, not seen in excitatory neuron-specific KOs. Finally, they rescue the defects in the interneuron-specific KO by expressing specific Fgf13 isoforms. This is an elegant and important study adding to our knowledge of mechanisms that contribute to seizures.

Strengths<br /> • The study provides much-needed cell type-specific KO models.<br /> • The authors use appropriate Cre lines and characterize the phenotypes of the different KOs.<br /> • The metabolomic analysis complements the rest of the data effectively.<br /> • The study confirms and extends previous research using improved approaches (KO lines vs. in vitro KD or antibody infusion).<br /> • The methods and analyses are robust and well-executed.

Weaknesses

• One weakness lies in the use of the Nkx2.1 line (instead of Nkx2.1CreER) in the paper. As a result, some answers to key questions are incomplete. For instance, it remains unclear whether the observed effects are due to Chandelier cells or NGFCs, potentially both MGE and CGE derived, explaining why Nkx2.1 alone does not fully replicate the overall inhibitory KO. Using Nkx2.1CreER could have helped address the cell specificity. With the Nkx2.1 line used in the paper, the answer is partial.<br /> • While the mechanism behind the reduced inhibitory drive in the IN-specific KO is suggested to be presynaptic, the chosen method does not allow them to exactly identify the mechanisms (spontaneous vs mEPSC/mIPSC), and whether it is a loss of inhibitory synapses (potentially axo-axonic) or release probability.

General Assessment

The general conclusions of this paper are supported by data. As it is, the claim that "these results enhance our understanding of the molecular mechanisms that drive the pathogenesis of Fgf13-related seizures" is partially supported. A more cautious term may be more appropriate, as the study shows the mechanism is not Nav-mediated and suggests alternative mechanisms without unambiguously identifying them. The conclusion that the findings "expand our understanding of FGF13 functions in different neuron subsets" is supported, although somewhat overstated, as the work is not conclusive about the exact neuron subtypes. However, it does indeed show differential functions for specific neuronal classes, which is a significant result.

Impact and Utility

This paper is undoubtedly valuable. Understanding that excitatory neurons are not the primary contributors to the observed phenotypes is crucial. The finding that the effects are not MGE-unique is also important. This work provides a solid foundation for further research and will be a useful resource for future studies.

Reviewer #1 (Public review):

Summary:

This paper investigates the neural population activity patterns of the medial frontal cortex in rats performing a nose poking timing task using in vivo calcium imaging. The results showed neurons that were active at the beginning and end of the nose poking and neurons that formed sequential patterns of activation that covaried with the timed interval during nose poking on a trial-by-trial basis. The former were not stable across sessions, while the latter tended to remain stable over weeks. The analysis of incorrect trials suggests the shorter non-rewarded intervals were due to errors in the scaling of the sequential pattern of activity.

Strengths:

This study measured stable signals using in vivo calcium imaging during experimental sessions that were separated by many days in animals performing a nose poking timing task. The correlation analysis on the activation profile to separate the cells in the three groups was effective and the functional dissociation between beginning and end, and duration cells was revealing. The analysis on the stability of decoding of both the nose poking state and poking time was very informative. Hence, this study dissected a neural population that formed sequential patterns of activation that encoded timed intervals.

Weaknesses:

It is not clear whether animals had enough simultaneously recorded cells to perform the analyzes of Figures 2-4. In fact, rat 3 had 18 responsive neurons which probably is not enough to get robust neural sequences for the trial-by-trial analysis and the correct and incorrect trial analysis. In addition, the analysis of behavioral errors could be improved. The analysis in Figure 4A could be replaced by a detailed analysis on the speed, and the geometry of neural population trajectories for correct and incorrect trials. In the case of Figure 4G is not clear why the density of errors formed two clusters instead of having a linear relation with the produce duration. I would be recommendable to compute the scaling factor on neuronal population trajectories and single cell activity or the computation of the center of mass to test the type III errors.

Due to the slow time resolution of calcium imaging, it is difficult to perform robust analysis on ramping activity. Therefore, I recommend downplaying the conclusion that: "Together, our data suggest that sequential activity might be a more relevant coding regime than the ramping activity in representing time under physiological conditions."

Comments on revisions:

The authors responded properly to my initial comments. However, I have three additional recommendations for the reviewed manuscript.

First, the paper urgently needs proofreading by a professional English editor. Second, Figure 4 must be divided in 2, it has too many panels and the resolution of the figure is low. Finally, please consider that what is called scaling factor in Figure 4G should be called something like neural sequence position index. A scaling factor in the timing literature implies that the pattern of activation of a cell contracts or expands according to the timed interval.

Reviewer #2 (Public review):

Summary

Lines et al investigate the integration of sensory-evoked calcium signals in astrocytes of the primary somatosensory cortex in anesthetized mice. More precisely, their goal is to better characterize the mechanisms that govern the emergence of whole-cell events in astrocytes, here referred to as calcium surges. As a single astrocyte communicates with hundreds of thousands of synapses simultaneously, understanding the spatial and temporal integration of calcium signals in astrocytes and the mechanisms governing these phenomena is of tremendous importance to deepen our understanding of signal processing in the central nervous system. In line with previous reports in the field, the authors find that most signals originate in the arborization of astrocytes, occasionally leading to somatic and whole-cell events. On average, the latter occur following domain activity closer to the soma, suggesting a centripetal propagation of signals leading to somatic events. Moreover, they observe that the distance from the soma to active domains increases with time after somatic events, suggesting a potential centrifugal propagation of signals post-somatic activity. The results suggest that most calcium surges depend on the expression of IP3R2, the main calcium channel in astrocytes, located at the membrane of the endoplasmic reticulum. Finally, they report a correlation between the percentage of active domains in the astrocyte "arbor", the emergence of a somatic event, and the frequency of slow inward currents from neighboring neurons. The main claim of this manuscript is that there would be a spatial threshold inherent to astrocytes of ~23% of domain activation above which a calcium surge is observed. Although the study provides data and concepts that are important for the glia field, the conclusions seem a little too assertive and general with respect to what can be deduced from the data and methods used.

Strengths

The major strength of this study is the experimental approach that allowed the authors to obtain numerous and informative calcium recordings in vivo in the somatosensory cortex in mice in response to sensory stimuli as well as in situ. Notably, they developed an interesting approach to modulate the percentage of active domains in the astrocyte arborization by varying the intensity of peripheral stimulation (its amplitude, frequency, or duration). The question investigated is important as the mechanisms governing signal integration in astrocytes and its effect on neighboring cells are poorly understood.

Weaknesses

The major weakness of the manuscript is the method used to analyze and quantify calcium activity, which mostly relies on the analysis of averaged data and overlooks the variability of the signals measured. As a result, the main claims from the manuscript seem to be incompletely supported by the data.

Although the revised version includes more discussion on the experiments that could be done to extend the results from this study, more discussion would be needed to clarify the limitations on what can be deduced from the proposed experimental and analytical design. Notably, the analysis pipeline seems biased by the assumption of the existence of a spatial threshold dictating the emergence of global calcium events in astrocytes. Although there is a clear linear correlation between the percentage of active somas and the percentage of active domains in the arborization (Figure 2 panel F), concluding on the existence of an inherent threshold of domain activity is not completely supported by the data (see e.g. Figure 2 panel F or Figure 4 panel E). It would probably be more accurate to report that most somatic events occur when the percentage of arbor domains being active is above 21-24% (95% confidence interval of the reported threshold). Thus, some of the conclusions from the manuscript, such as p.14 l.34-35 " spatial threshold of domains that needs to be reached in order to lead to soma activation", seem a bit too assertive as some astrocytes did display soma activation with a much smaller percentage of active domains or on the contrary, no somatic event despite domain activity way above the threshold. Similarly, as Figure 6 demonstrates a strong effect of IP3R2 knock-out on somatic activation but reports a non-zero probability of soma activity in IP3R2 -/- mice (panel F), the conclusion that IP3R2 are necessary to trigger an astrocytic calcium surge seems a bit too strong. Finally, the results reported in Figure 7 demonstrate the existence of a strong correlation between SICs, the percentage of active astrocyte domains on, and somatic activation, so that the conclusion "These results indicate that spatial threshold of the astrocyte calcium surge has a functional impact on gliotransmission" (l.4&-48 page 13) also seems a bit too assertive.

Reviewer #1 (Public review):

Summary:

There is a long-standing idea that choices influence evaluation: options we choose are re-evaluated to be better than they were before the choice. There has been some debate about this finding, and the authors developed several novel methods for detecting these re-evaluations in task designs where options are repeatedly presented against several alternatives. Using these novel methods the authors clearly demonstrate this re-evaluation phenomenon in several existing datasets and show that estimations of dynamic valuation correlate with neural activity in prefrontal cortex.

Strengths:

The paper is well-written and figures are clear. The authors provided evidence for the behaviour effect using several techniques and generated surrogate data (where the ground truth is known) to demonstrate the robustness of their methods. The author avoid over-selling the work, with a lucid description of limitations, and potential for further exploration of the work, in the discussion.

Comments on revisions:

The authors did a good job responding to the comments.

Reviewer #1 (Public review):

Summary:

The authors investigated if/how distractor suppression derived from statistical learning may be implemented in early visual cortex. While in a scanner, participants conducted a standard additional singleton task in which one location more frequently contained a salient distractor. The results showed that activity in EVC was suppressed for the location of the salient distractor as well as for neighbouring neutral locations. This suppression was not stimulus specific - meaning it occurred equally for distractors, targets and neutral items - and it was even present in trials in which the search display was omitted. Generally, the paper was clear, the experiment was well-designed, and the data are interesting. Nevertheless, I do have several concerns mostly regarding the interpretation of the results.

(1) My biggest concern with the study is regarding the interpretation of some of the results. Specifically, regarding the dynamics of the suppression. I appreciate that there are some limitations with what you might be able to say here given the method but I do feel as if you have committed to a single interpretation where others might still be at play. Below I've listed a few alternatives to consider.

(a) Sustained Suppression. I was wondering if there is anything in your results that would speak for or against the suppression being task specific. That is, is it possible that people are just suppressing the HPDL throughout the entire experiment (i.e., also through ITI, breaks, etc., rather than just before and during the search). Since the suppression does not seem volitional, I wonder if participants might apply a blanket suppression to HPDL until they learn otherwise. Since your localiser comes after the task you might be able to see hints of sustained suppression in the HPDL during these trials.

(b) Enhancement followed by suppression. Another alternative that wasn't discussed would be an initial transient enhancement of the HPDL which might be brought on by the placeholders followed by more sustained suppression through the search task. Of course, on the whole this would look like suppression, but this still seems like it would hold different implications compared to simply "proactive suppression". This would be something like search and destroy however could be on the location level before the actual onset of the search display.

(2) I was also considering whether your effects might be at least partially attributable to priming type effects. This would be on the spatial (not feature) level as it is clear that the distractors are switching colours. Basically, is it possible that on trial n participants see the HPDL with the distractor in it and then on trial n+1 they suppress that location. This would be something distinct from the statistical learning framework and from the repetition suppression discussion you have already included. To test for this, you could look at the trials that follow omission or trials. If there is no suppression or less suppression on these trials it would seem fair to conclude that the suppression is at least in part due to the previous trial.

Joint Public Review:

In the microglia research community, it is accepted that microglia change their shape both gradually and acutely along a continuum that is influenced by external factors both in their microenvironments and in circulation. Ideally, a given morphological state reflects a functional state that provides insight into a microglia's role in physiological and pathological conditions. The current manuscript introduces MorphoCellSorter, an open-source tool designed for automated morphometric analysis of microglia. This method adds to the many programs and platforms available to assess the characteristics of microglial morphology; however, MorphoCellSorter is unique in that it uses Andrew's plotting to rank populations of cells together (in control and experimental groups) and presents "big picture" views of how entire populations of microglia alter under different conditions. Notably, MorphoCellSorter is versatile, as it can be used across a wide array of imaging techniques and equipment. For example, the authors use MorphoCellSorter on images of fixed and live tissues representing different biological contexts such as embryonic stages, Alzheimer's disease models, stroke, and primary cell cultures.

This manuscript outlines a strategy for efficiently ranking microglia beyond the classical homeostatic vs. active morphological states. The outcome offers only a minor improvement over the already available strategies that have the same challenge: how to interpret the ranking functionally.

Strengths and Weaknesses:

(1) The authors offer an alternative perspective on microglia morphology, exploring the option to rank microglia instead of categorizing them with means of clusterings like k-means, which should better reflect the concept of a microglia morphology continuum. They demonstrate that these ranked representations of morphology can be illustrated using histograms across the entire population, allowing the identification of potential shifts between experimental groups. Although the idea of using Andrews curves is innovative, the distance between ranked morphologies is challenging to measure, raising the question of whether the authors oversimplify the problem. Also, the discussion about the pipeline's uniqueness does not go into the details of alternative models. The introduction remains weak in outlining the limitations of current methods (L90). Acknowledging this limitation will be necessary.

(2) The manuscript suffers from several overstatements and simplifications, which need to be resolved. For example:

a) L40: The authors talk about "accurately ranked cells". Based on their results, the term "accuracy" is still unclear in this context.

b) L50: Microglial processes are not necessarily evenly distributed in the healthy brain. Depending on their embedded environment, they can have longer process extensions (e.g., frontal cortex versus cerebellum).

c) L69: The term "metabolic challenge" is very broad, ranging from glycolysis/FAO switches to ATP-mediated morphological adaptations, and it needs further clarification about the author's intended meaning.

d) L75: Is morphology truly "easy" to obtain?

e) L80: The sentence structure implies that clustering or artificial intelligence (AI) are parameters, which is incorrect. Furthermore, the authors should clarify the term "AI" in their intended context of morphological analysis.

f) L390f: An assumption is made that the contralateral hemisphere is a non-pathological condition. How confident are the authors about this statement? The brain is still exposed to a pathological condition, which does not stop at one brain hemisphere.

(3) Methodological questions:

a) L299: An inversion operation was applied to specific parameters. The description needs to clarify the necessity of this since the PCA does not require it.

b) Different biological samples have been collected across different species (rat, mouse) and disease conditions (stroke, Alzheimer's disease).<br /> Sex is a relevant component in microglia morphology. At first glance, information on sex is missing for several of the samples. The authors should always refer to Table 1 in their manuscript to avoid this confusion. Furthermore, how many biological animals have been analyzed? It would be beneficial for the study to compare different sexes and see how accurate Andrew's ranking would be in ranking differences between males and females. If they have a rationale for choosing one sex, this should be explained.<br /> In the methodology, the slice thickness has been given in a range. Is there a particular reason for this variability? Also, the slice thickness is inadequate to cover the entire microglia morphology. How do the authors include this limitation of their strategy? Did the authors define a cut-off for incomplete microglia?

c) The manuscript outlines that the authors have used different preprocessing pipelines, which is great for being transparent about this process. Yet, it would be relevant to provide a rationale for the different imaging processing and segmentation pipelines and platform usages (Supplementary Figure 7). For example, it is not clear why the Z maximum projection is performed at the end for the Alzheimer's Disease model, while it's done at the beginning of the others. The same holds through for cropping, filter values, etc. Would it be possible to analyze the images with the same pipelines and compare whether a specific pipeline should be preferable to others? On a note, Matlab is not open-access.<br /> This also includes combining the different animals to see which insights could be gained using the proposed pipelines.

d) L227: Performing manual thresholding isn't ideal because it implies the preprocessing could be improved. Additionally, it is important to consider that morphology may vary depending on the thresholding parameters. Comparing different acquisitions that have been binarized using different criteria could introduce biases.

e) Parameter choices:

L375: When using k-means clustering, it is good practice to determine the number of clusters (k) using silhouette or elbow scores. Simply selecting a value of k based on its previous usage in the literature is not rigorous, as the optimal number of clusters depends on the specific data structure. If they are seeking a more objective clustering approach, they could also consider employing other unsupervised techniques, (e.g. HDBSCAN) (L403f).

L373: A rationale for the choice of the 20 non-dimensional parameters as well as a detailed explanation of their computation such as the skeleton process ratio is missing. Also, how strongly correlated are those parameters, and how might this correlation bias the data outcomes? Differences between circularity and roundness factors are not coming across and require further clarification. One is applied to the soma and the other to the cell, but why is neither circularity nor loudness factor applied to both?

f) PCA analysis:

The authors spend a lot of text to describe the basic principles of PCA. PCA is mathematically well-described and does not require such depth in the description and would be sufficient with references. Furthermore, there are the following points that require attention:

L321: PC1 is the most important part of the data could be an incorrect statement because the highest dispersion could be noise, which would not be the most relevant part of the data. Therefore, the term "important" has to be clarified.

L323: As before, it's not given that the first two components hold all the information.

L327 and L331 contain mistakes in the nomenclature: Mix up of "wi" should be "wn" because "i" does not refer to anything. The same for "phi i = arctan(yn/wn)" should be "phi n".

L348: Spearman's correlation measures monotonic correlation, not linear correlation. Either the authors used Pearson Correlation for linearity or Spearman correlation for monotonic. This needs to be clarified to avoid misunderstandings.

g) If the authors find no morphological alteration, how can they ensure that the algorithm is sensitive enough to detect them? When morphologies are similar, it's harder to spot differences. In cases where morphological differences are more apparent, like stroke, classification is more straightforward.

h) Minor aspects:

{section sign} % notation requires to include (weight/volume) annotation.

{section sign} Citation/source of the different mouse lines should be included in the method sections (e.g. L117).

{section sign} L125: The length of the single housing should be specified to ensure no variability in this context.

{section sign} L673: Typo to the reference to the figure.

Reviewer #1 (Public review):

Summary:

The manuscript presents a significant and rigorous investigation into the role of CHMP5 in regulating bone formation and cellular senescence. The study provides compelling evidence that CHMP5 is essential for maintaining endolysosomal function and controlling mitochondrial ROS levels, thereby preventing the senescence of skeletal progenitor cells.

Strengths:

The authors demonstrate that the deletion of Chmp5 results in endolysosomal dysfunction, elevated mitochondrial ROS, and ultimately enhanced bone formation through both autonomous and paracrine mechanisms. The innovative use of senolytic drugs to ameliorate musculoskeletal abnormalities in Chmp5-deficient mice is a novel and critical finding, suggesting potential therapeutic strategies for musculoskeletal disorders linked to endolysosomal dysfunction.

Weaknesses:

The manuscript requires a deeper discussion or exploration of CHMP5's roles and a more refined analysis of senolytic drug specificity and effects. This would greatly enhance the comprehensiveness and clarity of the manuscript.

Reviewer #1 (Public review):

Summary:

This manuscript explores the role of the Evening Complex (EC), specifically focusing on ELF3, a disordered protein component of the EC, and its temperature-dependent phase behavior. The study highlights the role of polyQ tracts in modulating temperature-sensitive condensate formation and provides a combination of computational approaches, including REST2 simulations and coarse-grained Martini simulations, to investigate how polyQ tract length and sequence context influence this behavior.

Strengths:

The study addresses a key question in plant biology - how temperature influences circadian clock-mediated growth regulation through protein phase behavior. The manuscript introduces the novel finding that polyQ tract length modulates the temperature-dependent formation of helices and condensates.

Weaknesses:

(1) Coarse-Grained Simulation Results Not Supported by Data:<br /> The results presented in Figure 6A of the manuscript do not seem to show a clear trend in the number of clusters formed as a function of polyQ tract length. This is particularly evident in the comparison between 0Q and 7Q polyQ lengths, which display statistically similar values in terms of the number of clusters. The lack of distinction between these values raises questions about the sensitivity of the coarse-grained simulations to polyQ tract length, which the authors claim as a key modulator of condensate formation. This discrepancy weakens the argument that polyQ length directly impacts the clustering behavior in the simulations.<br /> Suggested Analysis:<br /> - A more detailed statistical analysis should be performed to assess whether the observed differences between polyQ lengths are significant. This could involve hypothesis testing or the use of error bars in the graphs to better communicate the variability in the data.<br /> - Additionally, the authors should examine whether there are other features, such as cluster shape or internal structure, that might differentiate between different polyQ lengths, even if the total number of clusters is similar.

(2) Inconsistency in Cluster Size Across Temperatures (Figure 6B):<br /> The results in Figure 6B show a striking difference in the size of the largest cluster between temperatures of 290K and 300K. This abrupt shift in behavior lacks a clear mechanistic explanation. Typically, phase transitions driven by temperature are more gradual, unless there is some underlying structural or chemical shift that the authors have not accounted for. Without a clear explanation, this sudden change in behavior reduces confidence in the simulation results.<br /> Suggested Analysis:<br /> - The authors should explore possible explanations for the dramatic difference in cluster size between 290K and 300K. For example, they could investigate whether specific interactions (such as the breaking or formation of hydrogen bonds or hydrophobic contacts) might explain the behavior at higher temperatures.<br /> - It is important to check whether the coarse-grained simulation model has been adequately parameterized and scaled for accurate temperature dependence. Atomistic simulations of monomers and dimers with varying polyQ tract lengths could be used to fine-tune the coarse-grained model, ensuring it accurately reflects molecular behavior. The gross estimate of a 10% scaling factor might be insufficient and could lead to inaccurate representations of cluster formation.

(3) Scaling of Coarse-Grained Model with Atomistic Simulations:<br /> As mentioned, the coarse-grained model used in the study may not have been properly scaled against atomistic data. A simple scaling factor of 10% may not be appropriate for accurately capturing the behavior of polyQ tracts across different lengths, especially considering their sensitivity to subtle changes in temperature. Without rigorous validation against atomistic simulations, the coarse-grained model's predictions could be skewed.<br /> Suggested Analysis:

(4) To address this, the authors should compare the coarse-grained model with atomistic simulations of monomeric and dimeric forms of ELF3 with different polyQ tract lengths. By comparing key structural parameters (e.g., radius of gyration, contact maps, and clustering propensity), the authors could adjust the coarse-grained model to more accurately reflect the atomistic behavior. The authors have wealth of atomistic simulation data that could afford such benchmarking and identification of scaling factor<br /> o Additionally, the authors should investigate whether the assumed scaling factor of 10% is appropriate for each polyQ length or whether it needs to be refined based on specific properties, such as the number of hydrophobic interactions or secondary structure stability.

(5) Lack of Analysis for Liquid-Like Behavior in Phase Separation:<br /> The simulations presented in the manuscript do not analyze the liquid-like behavior of ELF3 condensates, which is a key characteristic of liquid-liquid phase separation (LLPS). In LLPS systems, condensates are often dynamic, with chains exchanging between clusters, indicating liquid-like rather than solid-like behavior. The authors fail to probe this crucial aspect, which is necessary to support the claim that ELF3 undergoes phase separation.<br /> Suggested Analysis:<br /> - The authors should conduct additional analyses to probe the liquid-like nature of the clusters formed by ELF3. One approach would be to analyze the dynamics of chain exchange between clusters, measuring how frequently chains leave one cluster and join another over time. This analysis would reveal whether the condensates behave as liquid-like, dynamic structures or more static, solid-like aggregates.<br /> - Additionally, the temperature dependence of these exchange dynamics should be investigated. In true liquid-liquid phase separation, the rate of chain exchange is often sensitive to temperature. Observing how this rate changes between 290K and 300K, for instance, could help explain the abrupt shift in cluster size seen in Figure 6B.<br /> - The authors should also analyze whether the internal structures of the condensates are consistent with a liquid-like phase. For example, radial distribution functions and contact lifetimes could be calculated to reveal whether the clusters exhibit liquid-like organization.

(6) Lack of justification of polydispersity of polyQ:<br /> The authors don't provide any rationale for choice of different copies of polyQ used in the manuscript for their chain-growth simulation studies. It will be more apt if it can be motivated via some precedent experimental observations.

(7) Lack of initiative to connect to Experiments:<br /> While the computational models and simulations provide robust theoretical insights, the absence of direct experimental validation weakens the overall impact of the manuscript. For example, experimental data on how specific mutations in the polyQ tract influence ELF3 behavior in vivo would significantly bolster the authors' claims. The manuscript would benefit from either citing existing experimental studies that corroborate these findings or from suggesting future experimental directions.

Reviewer #1 (Public review):

(1) Summary of the Paper:

This paper by Chen et al. examines the cellular composition and gene expression of the hypothalamic medial preoptic area (MPOA) in two closely related deer mouse species (P. maniculatus and P. polionotus) that exhibit distinct social behaviors. Through single-nucleus RNA sequencing (snRNA-seq), Chen et al., identify sex- and species-specific neuronal cell types that likely contribute to differences in mating and parental care. By comparing monogamous and promiscuous species, the study provides insights into how neuronal diversity and gene expression changes in the MPOA might underlie the evolution of social behaviors.

(2) Strengths of the Paper:

The paper excels in several areas. First, the data presentation is clear and well-organized, making the complex findings easy to follow. The writing is straightforward and highly accessible, which enhances the overall readability. The experimental design is innovative, particularly in how they combined samples from different species into the same dataset and then used post-hoc identification to distinguish cell types by species. This dramatically controls for potential batch effects in my opinion. Additionally, the authors contextualize their findings within the framework of previously published studies on Mus musculus, providing a strong comparative analysis that enhances the significance of their work.

3) Weaknesses of the Paper:

The major limitation of the study is the absence of causal experiments linking the observed changes in MPOA cell types to species-specific social behaviors. While the study provides valuable correlational data, it lacks functional experiments that would demonstrate a direct relationship between the neuronal differences and behavior. For instance, manipulating these cell types or gene expressions in vivo and observing their effects on behavior would have strengthened the conclusions, although I certainly appreciate the difficulty in this, especially in non-musculus mice. Without such experiments, the study remains speculative about how these neuronal differences contribute to the evolution of social behaviors.

Reviewer #1 (Public review):

Summary:

The researchers examined how individuals who were born blind or lost their vision early in life process information, specifically focusing on the decoding of Braille characters. They explored the transition of Braille character information from tactile sensory inputs, based on which hand was used for reading, to perceptual representations that are not dependent on the reading hand.

They identified tactile sensory representations in areas responsible for touch processing and perceptual representations in brain regions typically involved in visual reading, with the lateral occipital complex serving as a pivotal "hinge" region between them.

In terms of temporal information processing, they discovered that tactile sensory representations occur prior to cognitive perceptual representations. The researchers suggest that this pattern indicates that even in situations of significant brain adaptability, there is a consistent chronological progression from sensory to cognitive processing.

Strengths:

By combining fMRI and EEG, and focusing on the diagnostic case of Braille reading, the paper provides an integrated view of the transformation processing from sensation to perception in the visually deprived brain. Such a multimodal approach is still rare in the study of human brain plasticity and allows to discern the nature of information processing in blind people early visual cortex, as well as the timecourse of information processing in a situation of significant brain adaptability.

Weaknesses:

ROI and searchlight analyses are not completely overlapping, although this might be due to the specific limits and strengths of each approach. Moreover, the conclusions regarding the behavioral relevance of the sensory and perceptual representations in the putatively reorganized brain, although important, are limited due to the behavioral measurements adopted.

Reviewer #1 (Public review):

Summary:

Triple-negative breast cancer (TNBC) accounts for approximately 15-20% of all breast cancers. Compared to other types of breast cancer, TNBC exhibits highly aggressive clinical characteristics, a greater likelihood of metastasis, poorer clinical outcomes, and lower survival rates. Immunotherapy is an important treatment option for TNBC, but there is significant heterogeneity in treatment response. Therefore, it is crucial to accurately identify immunosuppressive patients before treatment and actively seek more effective therapeutic approaches for TNBC patients.

Strengths:

In this work, the authors collected and integrated data from single cells and large volumes of RNA sequencing and RNA-SEQ to analyze the TME landscape mediated by genes associated with iron death. On this basis, the prediction model of prognosis and treatment response of 131 patients was constructed using a machine learning algorithm, which is beneficial to provide individualized and precise treatment guidance for breast cancer patients.

Weaknesses:

However, there are still some issues that need to be clarified:

(1) The description of the research background is too brief and concise, and it is necessary to add some information about the limitations of existing methods and the differences and advantages of this study compared with other published relevant studies, so as to better highlight the necessity and research value of this study.

(2) This study is a retrospective analysis of a public data set and lacks experimental validation and prospective experiments to support the results of bioinformatics analysis. This should be added to the acknowledgment of limitations in the study.

Reviewer #3 (Public review):

Summary:

Juan Liu et al. investigated the interplay between habitat fragmentation and climate-driven thermophilization in birds in an island system in China. They used extensive bird monitoring data (9 surveys per year per island) across 36 islands of varying size and isolation from the mainland covering 10 years. The authors use extensive modeling frameworks to test a general increase of the occurrence and abundance of warm-dwelling species and vice versa for cold-dwelling species using the widely used Community Temperature Index (CTI), as well the relationship between island fragmentation in terms of island area and isolation from the mainland on extinction and colonization rates of cold- and warm-adapted species. They found that indeed there was thermophilization happening during the last 10 years, which was more pronounced for the CTI based on abundances and less clearly for the occurrence based metric. Generally, the authors show that this is driven by an increased colonization rate of warm-dwelling and an increased extinction rate of cold-dwelling species. Interestingly, they unravel some of the mechanisms behind this dynamic by showing that warm-adapted species increased while cold-dwelling decreased more strongly on smaller islands, which is - according to the authors - due to lowered thermal buffering on smaller islands (which was supported by air temperature monitoring done during the study period on small and large islands). They argue, that the increased extinction rate of cold-adapted species could also be due to lowered habitat heterogeneity on smaller islands. With regards to island isolation, they show that also both thermophilization processes (increase of warm and decrease of cold-adapted species) was stronger on islands closer to the mainland, due to closer sources to species populations of either group on the mainland as compared to limited dispersal (i.e. range shift potential) in more isolated islands.

The conclusions drawn in this study are sound, and mostly well supported by the results. Only few aspects leave open questions and could quite likely be further supported by the authors themselves thanks to their apparent extensive understanding of the study system.

Strengths:

The study questions and hypotheses are very well aligned with the methods used, ranging from field surveys to extensive modeling frameworks, as well as with the conclusions drawn from the results. The study addresses a complex question on the interplay between habitat fragmentation and climate-driven thermophilization which can naturally be affected by a multitude of additional factors than the ones included here. Nevertheless, the authors use a well balanced method of simplifying this to the most important factors in question (CTI change, extinction, colonization, together with habitat fragmentation metrics of isolation and island area). The interpretation of the results presents interesting mechanisms without being too bold on their findings and by providing important links to the existing literature as well as to additional data and analyses presented in the appendix.

Weaknesses:

The metric of island isolation based on distance to the mainland seems a bit too oversimplified as in real-life the study system rather represents an island network where the islands of different sizes are in varying distances to each other, such that smaller islands can potentially draw from the species pools from near-by larger islands too - rather than just from the mainland. Although the authors do explain the reason for this metric, backed up by earlier research, a network approach could be worthwhile exploring in future research done in this system. The fact, that the authors did find a signal of island isolation does support their method, but the variation in responses to this metric could hint on a more complex pattern going on in real-life than was assumed for this study.

Comments on revisions:

I'm happy with the revisions made by the authors.

Reviewer #1 (Public review):

Summary:

The Avrillon et al. explore the neural control of muscle by decomposing the firing activity of constituent motor units from the grid of surface electromyography (EMG) in the Tibialis (TA) Anterior and Vastus Lateralis (VL) during isometric contractions. The study involves extensive samples of motor units across the broadest range of voluntary contraction intensities up to 80% of MVC. The authors examine rate coding of the population of motor units, which describes the instantaneous firing rate of each motor unit as a function of muscle force. This relationship is characterized by a natural logarithm function that delineates two distinct phases: an initial phase with a steep acceleration in firing rate, particularly pronounced in low-threshold motor units, and a subsequent modest linear increase in firing rate, more significant in high-threshold motor units.

Strengths:

The study makes a significant contribution to the field of neuromuscular physiology by providing a detailed analysis of motor unit behavior during muscle contractions in a few ways.

(1) The significance lies in its comprehensive framework of motor unit activity during isometric contractions in the broad range of intensities, providing insights into the non-linear relationship between the firing rate and the muscle force. The extensive sample of motor units across the pool confirms the observation in animal studies in which the the spinal motoneuron exhibits a discharge consists of the distinct phases in response to synaptic currents, under the influence of persistent inward currents. As such, it is now reasonable to state the human motor units across the pool are also under control of gain modulation via some neuromodulatory effects in addition to synaptic inputs arising from ionotropic effects.<br /> (2) The firing scheme across in the entire motoneuron pool revealed in this study reconciles the discrepancy in firing organization under debate; i.e., whether it is 'onion skin' like or not (Heckman and Enoka 2012). The onion skin like model states that the low threshold motor units discharge higher than high threshold motor units and has been held for long time because the firing behaviors were examined in a partial range of contraction force range due to technical limitations. This reconciliation is crucial because it is fundamental to modelling the organization of motor unit recruitment and rate coding to achieve a desired force generation to advance our understanding of motor control.<br /> (3) The extensive data collection with a novel blind source separation algorithm on the expanded number of channel of surface EMG signal provides a robust dataset that enhances the reliability and validity of findings, setting a new standard for empirical studies in the field. \par<br /> Collectively, this study fills several knowledge gaps in the field and advances our understanding the mechanism underlying the isometric force generation.

Reviewer #2 (Public review):

Summary:

In this manuscript, Otero-Coronel and colleagues use a combination of acoustic stimuli and electrical stimulation of the tectum to study MSI in the M-cells of adult goldfish. They first perform a necessary piece of groundwork in calibrating tectal stimulation for maximal M-cell MSI, and then characterize this MSI with slightly varying tectal and acoustic inputs. Next, they quantify the magnitude and timing of FFI that each type of input has on the M-cell, finding that both the tectum and the auditory system drive FFI, but that FFI decays more slowly for auditory signals. These are novel results that would be of interest to a broader sensory neuroscience community. By then providing pairs of stimuli separated by 50ms, they assess the ability of the first stimulus to suppress responses to the second, finding that acoustic stimuli strongly suppress subsequent acoustic responses in the M-cell, that they weakly suppress subsequent tectal stimulation, and that tectal stimulation does not appreciably inhibit subsequent stimuli of either type. Finally, they show that M-cell physiology mirrors previously reported behavioural data in which stronger stimuli underwent less integration.

The manuscript is generally well written and clear. The discussion of results is appropriately broad and open-ended. It's a good document. Our major concerns regarding the study's validity are captured in the individual comments below. In terms of impact, the most compelling new observation is the quantification of the FFI from the two sources and the logical extension of these FFI dynamics to M-cell physiology during MSI. It is also nice, but unsurprising, to see that the relationship between stimulus strength that MSI is similar for M-cell physiology to what has previously been shown for behavior. While we find the results interesting, we think that they will be of greatest interest to those specifically interested in M-cell physiology and function.

Strengths:

The methods applied are challenging and appropriate and appear to be well executed. Open questions about the physiological underpinnings of M-cell function are addressed using sound experimental design and methodology, and convincing results are provided that advance our understanding of how two streams of sensory information can interact to control behavior.

Weaknesses:

Our concerns about the manuscript are captured in the following specific comments, which we hope will provide a useful perspective for readers and actionable suggestions for the authors.

Comments relevant to the revised manuscript:

Our general assessment (above) stands unchanged from the original version. All of our comments and concerns about the original manuscript have been addressed except for two, one very minor and one quite important:

Original Comment 1 (Minor):<br /> "Line 124. Direct stimulation of the tectum to drive M-cell-projecting tectal neurons not only bypasses the retina, it also bypasses intra-tectal processing and inputs to the tectum from other sources (notably the thalamus). This is not an issue with the interpretation of the results, but this description gives the (false) impression that bypassing the retina is sufficient to prevent adaptation. Adding a sentence or two to accurately reflect the complexity of the upstream circuitry (beyond the retina) would be welcome."

The authors have replied:<br /> "The reviewer is right in that direct tectal stimulation bypasses all neural processing upstream, not only that produced in the retina and that the tectum does not exclusively process visual information. The revised version now acknowledges (lines 245-252, revised manuscript) the complexity of the system."

We think that this is sufficient to address our concern. Some citations may be in order to underpin the new text.

Original Comment 5 (Major):<br /> Figure 4C and lines 398-410.<br /> "These are beautiful examples of M-cell firing, but the text suggests that they occurred rarely and nowhere close to significantly above events observed from single modalities. We do not see this a valid result to report because there is insufficient evidence that the phenomenon shown is consistent or representative of your data."

The authors have replied:<br /> "Our experimental conditions required anesthesia and paralysis, conditions designed to reduce neuronal firing and suppress motor output. We think it is valuable to report that we still see that simultaneous presentation subthreshold unisensory stimuli can add up to become suprathreshold, paralleling behavioral observations. We do not claim and acknowledge that those examples are representative of our recording conditions, but are likely to be more representative of the multisensory integration process taking place in freely moving fish. The revised manuscript adds context to these example traces to justify their inclusion (lines 420-426)."

We do not feel that this important concern has been addressed. The stats are definitively negative. There is no statistical evidence from these data that multisensory integration is occurring in this assay. The aesthesia, paralysis, and low n may provide explanations for this negative result, but it is still a negative result (p=0.5269). To show two examples of multisensory integration for subthreshold stimuli fits the narrative, but this result is not supported. Examples where individual stimuli caused APs (and combined stimuli did not) also occurred, presumably, and at a rate that is statistically indistinguishable to the examples shown in Figure 5. As such, if results from this assay are going to be in the manuscript, acoustic-only and tectum-only examples should be shown as well, although they would not fit the narrative. To be meaningful, this experiment would have to show that multisensory integration is happening in this circuit. Frustrating though it must be, the experiment has given a negative result to that question.

Reviewer #1 (Public review):

Summary

A novel statistical model of neural population activity called the Random Projection model has been recently proposed. Not only is this model accurate, efficient, and scalable, but also is naturally implemented as a shallow neural network. This work proposes a new class of RP model called the reshaped RP model. Inheriting the virtue of the original RP model, the proposed model is more accurate in terms of data fitting and efficient in terms of lower firing rate than the original, as well as compatible with various biological constraints. In particular, the authors have demonstrated that normalizing the total synaptic input in the reshaped model has a homeostatic effect on the firing rates of the neurons, resulting in even more efficient representations with equivalent accuracy. These results suggest that synaptic normalization contributes to synaptic homeostasis as well as efficiency in neural encoding.

Strength

This paper demonstrates that the accuracy and efficiency of the random projection models can be improved by extending the model with reshaped projections. Furthermore, it broadens the applicability of the model under biological constraints of synaptic regularization. It also suggests the advantage of the sparse connectivity structure over the fully connected model for modeling spiking statistics. In summary, this work successfully integrates two different elements, statistical modeling of the spikes and synaptic homeostasis in a single biologically plausible neural network model. The authors logically demonstrate their arguments with clear visual presentations and well-structured text, facilitating an unambiguous understanding for readers.

Discussions

The authors have clearly responded to most of our questions in the revised manuscript and we are happy to recommend publishing the final version of the article as it is. Below, we would like to present some alternative interpretations of the results. These comments are not exclusive with the claims made in the articles; it is rather intended to enhance the understanding of readers by providing additional perspectives.

As summarized above, the main contribution of the work consists of two parts; (1) the reshaped RP model achieved higher performance in explaining the statistics of the spiking activity of cortical neurons with more efficient representations (=lower firing rate), (2) synaptic homeostatic normalization in the reshaped RP model yields even more efficient representations without impairing the fitting performance.

For part (1),<br /> Suppl. Fig. 1B compares reshaped RP models with RP and RP with pruning and replacement (R&P). The better performance of RP with P&R might imply the advantage of pruning over gradient descent in this setting, reflecting the non-convexities of the problem. Alternatively, it might suggest the benefit of the increased number of parameters, since pruning allows the network to explore the broader parameter space during the learning process. This latter view might partially explain the superiority of the reshaped RP model over the original RP model.<br /> It is interesting that the backprop model has higher firing rate than the reshaped model (Fig. 1D). This trend is unchanged when optimization of the neural threshold is also allowed (Supp. Fig. 2A). Since backprop model overperforms reshaped model slightly but robustly, high firing rates in the backprop model might be a genuine feature of the spike statistics.

For part (2),<br /> We note that λ regulates the average firing rate, since maximizing the entropy <-ln p(x)> with a regularization term -λ <\sum _i f(x_i)> results in λ_i = λ for all i in the Boltzmann distribution of eq. 2. Suppl. Fig. 2B could be understood as demonstrating this "homeostatic" effect of λ.<br /> Suppl. Fig. 3 could be interpreted as demonstrating the interaction of two different homeostatic mechanisms: one at the firing-rate level (as regulated by λ) and the other at the synaptic level (as regulated by φ). It shows that the range of synaptic constraints where the fitting performance is not impaired differs by the value of λ. For example, if lambda is small (\lambda = 0.25), synaptic constraint can easily deteriorate the performance; on the other hand, if lambda is large (\lambda = 4), performance remains unchanged under strict synaptic constraint. Considering that practically we are most interested in the regime where the model performs best (λ = 2.0), an advantageous feature of the homeostatic model is that homeostatic constraint is harmless at λ=2.0 for the wide range of constraints.

Reviewer #1 (Public review):

Summary:

The manuscript presents a short report investigating mismatch responses in the auditory cortex, following previous studies focused on visual cortex. By correlating mouse locomotion speed with acoustic feedback levels, the authors demonstrate excitatory responses in a subset of neurons to halts in expected acoustic feedback. They show a lack of responses to mismatch in he visual modality. A subset of neurons show enhanced mismatch responses when both auditory and visual modalities are coupled to the animal's locomotion.

While the study is well-designed and addresses a timely question, several concerns exist regarding the quantification of animal behavior, potential alternative explanations for recorded signals, correlation between excitatory responses and animal velocity, discrepancies in reported values, and clarity regarding the identity of certain neurons.

Strengths:

(1) Well-designed study addressing a timely question in the field.<br /> (2) Successful transition from previous work focused on visual cortex to auditory cortex, demonstrating generic principles in mismatch responses.<br /> (3) Correlation between mouse locomotion speed and acoustic feedback levels provides evidence for prediction signal in the auditory cortex.<br /> (4) Coupling of visual and auditory feedback show putative multimodal integration in auditory cortex.

Weaknesses:

(1) Lack of quantification of animal behavior upon mismatches, potentially leading to alternative interpretations of recorded signals.<br /> (2) Unclear correlation between excitatory responses and animal velocity during halts, particularly in closed-loop versus playback conditions.<br /> (3) Discrepancies in reported values in a few figure panels raise questions about data consistency and interpretation.<br /> (4) Ambiguity regarding the identity of the [AM+VM] MM neurons.

Comments on revisions:

I am satisfied with all clarifications and additional analyses performed by the authors.<br /> The only concern I have is about changes in running after [AM+VM] mismatches.<br /> The authors reported that they "found no evidence of a change in running speed or pupil diameter following [AM + VM] mismatch (Figures S5A)" (line 197).<br /> Nevertheless, it seems that there is a clear increase in running speed for the [AM+VM] condition (S5A). Could this be more specifically quantified? I am concerned that part of the [AM+VM] could stem from this change in running behavior. Could one factor out the running contribution?

Reviewer #1 (Public review):

Summary:

This paper is focused on the role of Cadherin Flamingo (Fmi) in cell competition in developing Drosophila tissues. A primary genetic tool is monitoring tissue overgrowths caused by making clones in the eye disc that expression activated Ras (RasV12) and that are depleted for the polarity gene scribble (scrib). The main system that they use is ey-flp, which make continuous clones in the developing eye-antennal disc beginning at the earliest stages of disc development. It should be noted that RasV12, scrib-i (or lgl-i) clones only lead to tumors/overgrowths when generated by continuous clones, which presumably creates a privileged environment that insulates them from competition. Discrete (hs-flp) RasV12, lgl-i clones are in fact out-competed (PMID: 20679206), which is something to bear in mind. They assess the role of fmi in several kinds of winners, and their data support the conclusion that fmi is required for winner status. However, they make the claim that loss of fmi from Myc winners converts them to losers, and the data supporting this conclusion is not compelling.

Strengths:

Fmi has been studied for its role in planar cell polarity, and its potential role in competition is interesting.

Reviewer #1 (Public review):

Summary:

Tobón and Moser reveal a remarkable amount of presynaptic diversity in the fundamental Ca dependent exocytosis of synaptic vesicles at the afferent fiber bouton synapse onto the pilar or mediolar sides of single inner hair cells of mice. These are landmark findings with profound implications for understanding acoustic signal encoding and presynaptic mechanisms of synaptic diversity at inner hair cell ribbon synapses. The paper will have an immediate and long-lasting impact in the field of auditory neuroscience.

Main findings: 1) Synaptic delays and jitter of masker responses are significantly shorter (synaptic delay: 1.19 ms) at high SR fibers (pilar) than at low SR fibers (mediolar; 2.57 ms). 2) Masked evoked EPSC are significantly larger in high SR than in low SR. 3) Quantal content and RRP size are 14 vesicles in both high and low SR fibers. 4) Depression is faster in high SR synapses suggesting they have a higher release probability and tighter Ca nanodomain coupling to docked vesicles. 5) Recovery of master-EPSCs from depletion is similar for high and low SR synapses, although there is a slightly faster rate for low SR synapses that have bigger synaptic ribbons, which is very interesting. 6) High SR synapses had larger and more compact (monophasic) sEPSCs, well suited to trigger rapidly and faithfully spikes. 7) High SR synapses exhibit lower voltage (~sound pressure in vivo) dependent thresholds of exocytosis.

Great care was taken to use physiological external pH buffers and physiological external Ca concentrations. Paired recordings were also performed at higher temperatures with IHCs at physiological resting membrane potentials and in more mature animals than previously done for paired recordings. This is extremely challenging because it becomes increasingly difficult to visualize bouton terminals when myelination becomes more prominent in the cochlear afferents. In addition, perforated patch recordings were used in the IHC to preserve its intracellular milieu intact and thus extend the viability of the IHCs. The experiments are tour-de-force and reveal several novel aspects of IHC ribbon synapses. The data set is rich and extensive. The analysis is detailed and compelling.

Reviewer #1 (Public review):

Summary:

The study investigates protein-protein interactions (PPIs) within the nuage, a germline-specific organelle essential for piRNA biogenesis in Drosophila melanogaster, using AlphaFold2 to predict interactions among 20 nuage-localizing proteins. The authors identify five novel interaction candidates and experimentally validate three of them, including Spindle-E and Squash, through co-immunoprecipitation assays. They confirm the functional significance of these interactions by disrupting salt bridges at the Spn-E_Squ interface. The study further expands its scope to analyze approximately 430 oogenesis-related proteins, validating three additional interaction pairs. A comprehensive screen of around 12,000 Drosophila proteins for interactions with the key piRNA pathway player, Piwi, identifies 164 potential binding partners. Overall, the research demonstrates that in silico approaches using AlphaFold2 can link bioinformatics predictions with experimental validation, streamlining the identification of novel protein interactions and reducing the reliance on extensive experimental efforts. The manuscript is commendably clear and easy to follow; however, areas for improvement should be addressed to enhance its clarity and rigor.

Major Concerns:

(1) While AlphaFold2 was developed and trained primarily for predicting protein structures and their interactions, applying it to predict protein-protein interactions is an extrapolation of its intended use. This introduces several important considerations and risks. First, it assumes that AlphaFold's accuracy in structure prediction extends to interactions, despite not being explicitly trained for this task. Additionally, the assumption that high-scoring models with structural complementarity imply biologically relevant interactions is not always valid. Experimental validation is essential to address these uncertainties, as over-reliance on computational predictions without such validation can lead to false positives and inaccurate conclusions. The authors should expand on the assumptions, limitations, and risks associated with using AlphaFold2 for predicting protein-protein interactions.

(2) The authors experimentally validated three interactions, out of five predicted interactions, using co-immunoprecipitation (co-IP). They attributed the lack of validation for the other two predictions to the limitations of the co-IP method. However, further clarification on the potential limitations of the co-immunoprecipitation behind the negative results would strengthen the conclusions. While co-IP is a widely used technique, it may not detect weak or transient interactions, which could explain the failure to validate some predictions. Suggesting alternative validation methods such as FRET or mass spectrometry could further substantiate the results. On the other hand, AlphaFold2 predictions are not infallible and may generate false positives, particularly when dealing with structurally plausible but biologically irrelevant interactions. By acknowledging both the potential limitations of co-IP and the possibility of false positives from AlphaFold2, the authors can provide a more balanced interpretation of their findings.

(3) In line 143, the authors state that "This approach identified 13 pairs; seven of these were already known to form complexes, confirming the effectiveness of AlphaFold2 in predicting complex formations (Table 2). The highest pcScore pair was the Zuc homodimer, possibly because AlphaFold2 had learned from Zuc homodimer's crystal structure registered in the database." While the authors mentioned the presence of the Zuc homodimer's crystal structure, they do not provide a systematic bioinformatics analysis to evaluate pairwise sequence identity or check for the presence of existing structures for all the proteins or protein pairs (or their homologs) in databases such as the Protein Data Bank (PDB) or Swiss-Model. Conducting such an analysis is critical, as it significantly impacts the novelty and reliability of AlphaFold2 predictions. For instance, high sequence identity between the query proteins could lead to high-scoring models for biologically irrelevant interactions. Including this information would strengthen the conclusions regarding the accuracy and utility of the predictions.

(4) While the manuscript successfully identifies novel protein interactions, the broader biological significance of these interactions remains underexplored. The manuscript could benefit from elaborating on how these findings may contribute to understanding the piRNA pathway and its implications on germline development, transposon repression, and oogenesis.

Reviewer #1 (Public review):

Summary:

Through a series of CRISPR-Cas9 screens, the GPX4 antioxidant pathway was identified as a critical suppressor of cold-induced cell death in hibernator-derived cells. Hamster BHK-21 cells exposed to repeated cold and rewarming cycles revealed five genes (Gpx4, Eefsec, Pstk, Secisbp2, and Sepsecs) as critical components of the GPX4 pathway, which protects against cold-induced ferroptosis. A second screen with continuous cold exposure confirmed the essential role of GPX4 in prolonged cold tolerance. GPX4 knockout lines exhibited complete cell death within four days of cold exposure, and pharmacological inhibition of GPX4 further increased cell death, underscoring the necessity of GPX4's catalytic activity in cold conditions.

An additional CRISPR screen in human cold-sensitive K562 cells identified 176 genes for cold survival. The GPX4 pathway was found to confer significant resistance to cold in hibernators and human cells, with GPX4 loss significantly increasing cold-induced cell death.

Comparing hamster and human GPX4, overexpression of GPX4 in human K562 cells, whether hamster or human GPX4, dramatically improved cold tolerance, while catalytically dead mutants showed no such effect. These findings suggest that GPX4 abundance is a key limiting factor for cold tolerance in human cells, and primary cell types show strong sensitivity to GPX4 loss, highlighting that differences in cold tolerance across species may be due to varying GPX4-mediated protection.

Strengths:

(1) Innovative Approach: The study employs a series of unbiased genome-wide CRISPR-Cas9 screens in both hibernator- and non-hibernator-derived cells to investigate the mechanisms controlling cellular cold tolerance. Notably, this is the first genome-scale CRISPR-Cas9 screen conducted in cells derived from a hibernator, the Syrian hamster.

(2) Identification of the GPX4 Pathway: Identifying glutathione peroxidase 4 (GPX4) as a critical suppressor of cold-induced cell death significantly contributes to the field. Recently, GPX4 was also reported as a potent regulator of cold tolerance through overexpression screening (Sone et al.) in hamsters, which further supports this finding.

(3) Improved Cold Viability Assessment: The study identifies an important technical artifact in using trypan blue to assess cell viability following cold exposure. It reveals that cells stained immediately after cold exposure retain the dye, inaccurately indicating cell death. By introducing a brief rewarming period before viability assessment, the authors significantly improve the accuracy of detecting cold-induced cell death. This refinement in methodology ensures more reliable results and sets a new standard for future research on cold stress in cells.

Weaknesses:

(1) Mechanisms Regulating GPX4 Levels: While the study highlights GPX4 levels as a major determinant of cellular cold tolerance, it does not discuss how these levels are regulated or why they differ between hibernators and non-hibernators. This omission leaves an important aspect of GPX4's role in cold tolerance unexplored.

(2) Generalizability Across Species: Although the study demonstrates the role of GPX4 in several mammalian species, it does not investigate whether this mechanism extends to other vertebrates (e.g., fish and amphibians) that also face cold challenges. This limitation could restrict the broader evolutionary claims made by the study.

(3) Variability in Cold Sensitivity Across Human Cell Lines: The study observes significant variability in cold tolerance among different human cell lines but does not explain these differences clearly. This leaves a key aspect of human cell cold sensitivity insufficiently addressed.

Reviewer #1 (Public review):

Summary:

This is an important and very well-presented set of experiments following up on prior work from the lab investigating knock-down (KD) of EMC10 in the restoration of neuronal and cognitive deficits in 22q11.2 Del models, including now both human iPSCs and a mouse model in vivo now with ASOs.

The valuable progress in this current manuscript is the development of ASOs, and the proof of efficacy in vivo in mice of the ASO in knock-down of EMC10 and amelioration of in vivo behavioral phenotypes.

The experiments include iPSC studies demonstrating elevations of EMC10 in a solid collection of paired iPSC lines. These studies also provide evidence of manipulation of EMC10 by overexpression and inhibition of miRNAs that exist in the 22q11 interval. The iPSC studies also nicely demonstrate the rescue of impairments with KD of EMC10 in neuronal arborization as well as KCl-induced neuronal activity. The major in vivo contributions reflect an impressive demonstration of the efficacy of two ASOs in vivo on both KD of EMC10 in vivo and through improvement in behavioral abnormalities in the 22q11 mouse in a range of different behaviors, including social behavior and learning behaviors.

Overall, there are many strengths reflected in this study, including in particular the synergy between in vitro studies in human cell models and in vivo studies in the well-characterized mouse model. The experiments are generally rigorously performed, well-powered, and nicely presented. The claims with regard to the mechanisms of EMC10 elevations and the importance of restoration of EMC10 expression to neuronal morphology and behavior are well supported by the data. The work may be further supported in future studies, by investigation of rescue by ASOs of circuit dysfunction in vivo or ex vivo through electrophysiology in the mouse model. Also, in future studies, investigation of the mechanism by which EMC10, an ER protein involved in protein processing, may function in the observed neuronal abnormalities; however, these studies are clearly for future investigations.

The potential impact of the work is found in the potential value of the ASO approach to the treatment of 22q11, or the pre-clinical evidence that knock-down of this protein may lead to some amelioration of cognitive symptoms. Overall, a very convincing and complementary set of experiments to support EMC10 KD as a therapeutic strategy.

Reviewer #1 (Public review):

Summary:

Chang and colleagues used tetrode recordings in behaving rats to study how learning an audiovisual discrimination task shapes multisensory interactions in the auditory cortex. They found that a significant fraction of neurons in the auditory cortex responded to visual (crossmodal) and audiovisual stimuli. Both auditory-responsive and visually-responsive neurons preferentially responded to the cue signaling the contralateral choice in the two-alternative forced choice task. Importantly, multisensory interactions were similarly specific for the congruent audiovisual pairing for the contralateral side.

Strengths:

The experiments were conducted in a rigorous manner. Particularly thorough are the comparisons across cohorts of rats trained in a control task, in a unisensory auditory discrimination task, and the multisensory task, while also varying the recording hemisphere and behavioral state (engaged vs. anesthesia). The resulting contrasts strengthen the authors' findings and rule out important alternative explanations. Through the comparisons, they show that the enhancements of multisensory responses in the auditory cortex are specific to the paired audiovisual stimulus and specific to contralateral choices in correct trials and thus dependent on learned associations in a task-engaged state.

Weaknesses:

The main result is that multisensory interactions are specific for contralateral paired audiovisual stimuli, which is consistent across experiments and interpretable as a learned task-dependent effect. However, the alternative interpretation of behavioral signals is crucial to rule out, which would also be specific to contralateral, correct trials in trained animals. Although the authors focus on the first 150 ms after cue onset, some of the temporal profiles of activity suggest that choice-related activity could confound some of the results.

The auditory stimuli appear to be encoded by short transient activity (in line with much of what we know about the auditory system), likely with onset latencies (not reported) of 15-30 ms. Stimulus identity can be decoded (Figure 2j) apparently with an onset latency around 50-75 ms (only the difference between A and AV groups is reported) and can be decoded near perfectly for an extended time window, without a dip in decoding performance that is observed in the mean activity Figure 2e. The dynamics of the response of the example neurons presented in Figures 2c and d and the average in 2e therefore do not entirely match the population decoding profile in 2j. Population decoding uses the population activity distribution, rather than the mean, so this is not inherently problematic. It suggests however that the stimulus identity can be decoded from later (choice-related?) activity. The dynamics of the population decoding accuracy are in line with the dynamics one could expect based on choice-related activity. Also the results in Figures S2e,f suggest differences between the two learned stimuli can be in the late phase of the response, not in the early phase.

First, it would help to have the same time axis across panels 2,c,d,e,j,k. Second, a careful temporal dissociation of when the central result of multisensory enhancements occurs in time would discriminate better early sensory processing-related effects versus later decision-related modulations.

In the abstract, the authors mention "a unique integration model", "selective multisensory enhancement for specific auditory-visual pairings", and "using this distinct integrative mechanisms". I would strongly recommend that the authors try to phrase their results more concretely, which I believe would benefit many readers, i.e. selective how (which neurons) and specific for which pairings?

Reviewer #1 (Public Review):

The authors investigate the role of chirping in a species of weakly electric fish. They subject the fish to various scenarios and correlate the production of chirps with many different factors. They find major correlations between the background beat signals (continuously present during any social interactions) or some aspects of social and environmental conditions with the propensity to produce different types of chirps. By analyzing more specifically different aspects of these correlations they conclude that chirping patterns are related to navigation purposes and the need to localize the source of the beat signal (i.e. the location of the conspecific).

The study provides a wealth of interesting observations of behavior and much of this data constitutes a useful dataset to document the patterns of social interactions in these fish. Some data, in particular the high propensity to chirp in cluttered environments, raises interesting questions. Their main hypothesis is a useful addition to the debate on the function of these chirps and is worth being considered and explored further.

After the initial reviewers' comments, the authors performed a welcome revision of the way the results are presented. Overall the study has been improved by the revisions.

Reviewer #1 (Public review):

Summary:

The manuscript the authors have tried to dissect the functions of Proteasome activator 28γ (PA28γ) which is known to activate proteosomal function in an ATP independent manner. Although there are multiple works that have highlighted the role of this protein in tumour, this study specifically tried to develop a correlate with Complement C1q binding protein (C1QBp) that is associated with immune response and energy homeostasis.

Strengths:

The observations of the authors hint that beyond PA28y association with proteasome, it might also stabilize certain proteins such as C1QBP which influences the energy metabolism.

Weaknesses:

The strength of the work also becomes its main drawback. That is, how PA28y stabilizes C1QBP or how C1QBP elicits its pro-tumourigenic role under PA28y OE.

In most of the experiments the authors have been dependent on the parallel changes in the expression of both the proteins to justify their stabilizing interaction. However, this approach is indirect at best and does not confirm the direct stabilizing effect of this interaction. IP experiments do not indicate direct interaction and have some quality issues. The upregulation of C1QBP might be indirect at best. It is quite possible that PA28y might be degrading some secondary protein/complex which is responsible for C1QBP expression. Since the core idea of the work is PA28y direct interaction with C1QBP stabilizing it, the same should be demonstrated in more convincing manner.

In all of the assays C1QBP has been detected as doublet. However, the expression pattern of the two bands vary depending on the experiment. In some cases the upper band is intensely stained and in some the lower bands. Does C1QBP isoforms exist and whether they are differentially regulated depending on experiment conditions/tissue types?

Problems with the background of the work: Line 76. This statement is far-fetched. There are presently a number of literatures that have dealt with metabolic programming of OSCC including identification of specific metabolites. Moreover, beyond estimation of OCR, the authors have not conducted any experiments related to metabolism. In the Introduction, significance of this study and how it will extend our understanding of OSCC needs to be elaborated.

Review of Revised Version:

Although the authors have partly corrected the manuscript by removing the mislabeling in their Co-IP experiments, my primary concern on the actual functional connotations and direct interaction between PA28y and C1QBP still remains unaddressed. As already mentioned in my previous review, since the core idea of the work is PA28y's direct interaction with C1QBP, stabilizing it, the same should be demonstrated in a more convincing manner.

My other observation on the detection of C1QBP as a doublet has been addressed by usage of anti-C1QBP Monoclonal antibody against the polyclonal one used before. C1QBP doublets have not been observed in the present case.

The authors have also worked on the presentation of the background by suitably modifying the statements and incorporating appropriate citations.

However, the authors are requested to follow the recommendations provided to them by the reviewers to address the major concerns.

Reviewer #1 (Public Review):

Summary:

The manuscript by Poltavski and colleagues describes the discovery of previously unreported enteric neural crest-derived cells (ENCDC) which are marked by Pax2 and originating from the Placodes. By creating multiple conditional mouse mutants, the authors demonstrate these cells are a distinct population from the previously reported ENCDCs which originate from the Vagal neural crest cells and express Wnt1.

These Pax2-positive ENCDCs are affected due to the loss of both Ret and Ednrb highlighting that these cells are also ultimately part of the canonical processes governing ENCDC and enteric nervous system (ENS) development. The authors also make explant cultures from the mouse GI tract to detect how Ednrb signaling is important for Ret signaling pathways in these cells and rediscovers the interactions between these 2 pathways. One important observation the authors make is that CGRP-positive neurons in the adult distal colon seem to be primarily derived from these Pax2-positive ENCDCs, which are significantly reduced in the Ednrb mutants, thus highlighting the role of Ednrb in maintaining this neuronal type.

Comments on latest version:

Author response: We disagree that the datasets from previous studies provide additional insights that are relevant to the current study. It must be appreciated that Wnt1Cre and Pax2Cre are genetic lineage tracers and that migratory ENS progenitor cells labeled with these reagents do not maintain expression of Wnt1 and Pax2 mRNA or protein. The Wnt1 and Pax2 genes are only transiently expressed within their distinct regions of the ectoderm, and their expression turns off as cells delaminate and begin migration. Thus, Pax2Cre-labeled ENS progenitor cells are not Pax2-positive thereafter. The single cell RNA-Seq studies suggested by the reviewer were collected from older embryos and postnatal mice, and do not represent the E10.5-E11.5 period that accounts for genesis of Ret-mediated and Ednrb-mediated Hirschsprung disease pathology. Even with the most recent work by Zhou et al (Dev Cell, 2024) that included E10.5 cells, this analysis only evaluated neural crest-derived Sox10Cre lineage cells, which does not include the placode-derived Pax2Cre lineage (as we show explicitly in Fig. 2-figure supplement 2). Consequently, it would not be possible to find the "Pax2-positive cells" in these datasets. Performing a new transcriptomic analysis by isolating Pax2Cre-lineage and Wnt1Cre-lineage cells at the appropriate developmental time points could be the basis of future studies, but we think these are beyond the scope of the present paper.

Reviewer comment: Since these cells are a completely new discovery, additional validation would be beneficial. Whole early GI tract datasets are available, such as human 6-week fetal gut data (PMID: 29802404) and whole mouse embryo studies spanning development that include ENS (PMID: 38355799). If the authors believe that none of these existing datasets can detect these cells in their developmental state and that targeted cell studies with specific Cre drivers would be required, they should make this explicitly clear.

A key advantage of discovering a new cell type, particularly in the relatively understudied field of ENS, is the opportunity for the broader community to leverage this finding to inform their own research. If these cells are absent from current datasets, even those covering the whole GI tract, this should be clearly communicated.

I aim to support the authors here. New discoveries in science require robust validation to enhance their impact. The authors have generated an important reagent with great potential for broader use, and addressing these straightforward requests would strengthen the study and make it more valuable to the scientific community.

Author response: The observation that human mutations in RET and EDNRB both cause Hirschsprung disease is decades old, and of course numerous studies in human, mouse, and cells have addressed the relation between the two signaling pathways. We did not mean to imply that we were the first to discover that Ret and Ednrb signaling pathways interact. The reviewer cites a number of papers all from the Chakravarti lab that address this phenomenon; while these are a valuable contribution to the field, there is still more to be learned. The model elaborated in PMID: 31313802, in which Ret and Ednrb are both enmeshed in a common gene regulatory network, does not readily explain why each has a different phenotypic manifestation and doesn't take into account the importance of the placodal lineage. The main new contributions of our paper are the existence of a new cell lineage that contributes to the ENS, and that the placodal and neural crest lineages utilize Ret and Ednrb signaling differently. The clarification of how these elements are differentially used by the two lineages explains long-segment and short-segment Hirschsprung disease (Ret and Ednrb mutants, respectively) far better than in past studies. The reviewer unfortunately dismisses these insights and seems to feel that a biochemical exploration of one specific component of the signaling interaction (Y1015 phosphorylation) would be more relevant. This should be the basis of future studies and are beyond the scope of the new findings reported in the present paper

Reviewer comment: The authors completely miss the point. There is no association between phenotypic severity (L-HSCR, S-HSCR, or TCA) and mutations in a given gene in HSCR. EDNRB, for example, has a syndromic association with Waardenburg-Shah syndrome (WS4-A), which includes pigmentation anomalies due to EDNRB expression in neural crest cells that give rise to pigment cells.

The authors' discovery reinforces the current paradigm that nearly all HSCR is mediated by mutations in genes within the GRN, accounting for 72% of the population attributable risk. This is valuable; reinforcing established paradigms with new data is crucial, and the authors should appreciate the significance of this contribution.

The discovery of the signaling interaction is particularly important, as it offers a potential explanation for disease severity and provides a basis for classifying patients in future sequencing studies. It is surprising that the authors seem reluctant to highlight this novel finding, as it could greatly benefit future research, including the development of specific mouse mutants and advancing human genetics studies.

Author response: The reviewer overlooked that one of the review articles that we cited (Chen, Hsu, & Hung, 2020) has a dedicated paragraph for RET (section 3.14), which summarizes the work by Barheri-Yarmand et al (PMID: 25795775) which is the very paper noted by the reviewer in the comment above. The reviewer also somewhat misstated the results of the Barheri-Yarmand et al study. By immunostaining, this paper showed nuclear localization of endogenous Ret, albeit a version of Ret with a disease-associated mutation that makes it constitutively active by constitutive autophosphorylation. Nonetheless, this was endogenous Ret. The paper also used overexpression of GFP-tagged RET in HEK293 cells to show that wildtype RET can behave in a similar manner, at least under these circumstances. Our point is simply that Ret (and other receptor tyrosine kinases) can be found in the nucleus in certain biological contexts, and our observations are consistent with this precedent. The reviewer also suggests a biochemical follow-up analysis related to this observation, which we agree would be of interest. Such an investigation however is beyond the scope of the present study.

Reviewer comment: As the authors themselves now highlight from the cited paper that any evidence of RET entering the nucleus is of a mutant RET protein, How does this align with their discovery for wildtype protein?

This finding of nuclear localization of RET is both intriguing and unprecedented. Despite extensive biochemical studies on RET, given its role as an oncogene, this feature has not been identified before. If validated, this discovery could significantly advance the field and improve interpretation of future studies. I reiterate my previous point: a novel finding that challenges the current paradigm requires additional evidence.

Reviewer #1 (Public review):

The manuscript describes comprehensive structure-function studies combining structural studies, Alphafold2-based modelling, and extensive structural validation by mutagenesis and biochemical experiments. Consequently, a sophisticated activation mechanism of Mical1 as a representative of the MICAL family is elucidated at the molecular level. Since MICAL proteins are important regulators of membrane trafficking and cytoskeleton dynamics, the study is of high relevance for many groups. Structural data are of high quality, the modelling data appear to be sound, and the subsequent biochemical analyses are carried out in great detail, yielding a complete story. I have little to criticize on this beautiful work.

Reviewer #1 (Public review):

The manuscript "Osterix Facilitates Osteocytic Communication by Targeting Connexin43" investigates the role of Osterix (Osx) in osteocytes using a Col1α1-CreER;Osxfl/fl mouse model and cultured cells. The study reveals that Osx is expressed in osteocytes, and its deletion in vitro leads to a significant reduction in osteocyte dendrite formation, highlighting its critical role in maintaining cellular communication. Through ChIP-seq analysis, the authors identified Connexin43 (Cx43) as a direct downstream target of Osx. Moreover, treatment with all-trans retinoic acid (ATRA), a known agonist of Cx43, was able to rescue the dendritic network in osteocytes, restoring their communication capabilities in vitro.

This research provides valuable insights into the molecular mechanisms by which Osx influences osteocyte function, particularly through its regulation of Cx43. However, despite these findings, the study does not fully elucidate all the mechanisms involved in Osx-mediated osteocytic communication. Several conclusions, particularly those related to the broader signaling pathways, require additional experimental evidence and further investigation to be fully substantiated. This study provides a new aspect in understanding the complex role of Osx in bone biology but leaves open questions regarding the intricacies of its regulatory network.

Major Comments:

(1) In the Col1a1-CreER;tdTomato mice, the number of tdTomato+ cells in the cortical bone appears lower compared to Osx+ cells. The overlap between tdTomato+ and Osx+ cells in Figure 1 is limited. Could this affect the knockout efficiency? Can the authors provide data on Osx knockout efficiency in vivo? While immunostaining of Osx is shown in both control and mutant mice in Figure 2A, the Osx expression pattern differs from Figure 1A. Osx expression is relatively low in the bone marrow in Figure 1A, but much stronger in Figure 2A.

Additionally, Osx+ cells in Figure 1A seem confined to the bone surface, whereas Figure 2A shows a broader distribution. What developmental stage of mice was used in Figure 1? Could the authors also provide co-staining with other osteocyte markers alongside Osx?

(2) The authors mentioned using both siRNA and Lenti-Osx to modulate Osx expression. What was the specific purpose of these experiments? If the authors aim to demonstrate that Osx plays a critical role in osteocytes, they should provide data on downstream targets or markers relevant to osteocyte function. Additionally, did these treatments affect processes like differentiation or cell viability in osteocytes? The current results only demonstrate that siRNA and Lenti-Osx can successfully modulate Osx expression in vitro, but further evidence is needed to support broader functional conclusions.

(3) Osx knockout mice exhibited a decreased osteocyte dendritic network both in vivo and in vitro. To better understand how this affects overall bone health, could the authors provide additional parameters, such as bone thickness, bone strength, and other relevant metrics? Furthermore, to determine whether these phenotypes are primarily due to defects in the osteocyte dendritic network or a reduction in osteocyte numbers, the authors should also assess the number of osteocytes in the knockout mice Figure 2.

(4) Regarding the Lucifer Yellow Dye Transfer Assay in Figure 3, the authors should provide data on cell density and cell viability for both control and mutant groups. Additionally, although less dye is observed in the mutant group, the migration distance appears comparable to the control group. Could the authors explain this result? Furthermore, how was transmission speed between the groups evaluated in Figure 3D? More details on the method used to assess transmission speed would be helpful.

(5) For a more comprehensive and unbiased analysis of Osx function in osteocytes, the authors should present a full analysis of differentially expressed genes, rather than focusing solely on integrins. Additionally, it would be beneficial to include an analysis of the knockdown group alongside the other groups, considering the animal model used in this study involves knockout mice.

(6) In the immunofluorescence staining of integrin αvβ1 in the si-Osx and Lenti-Osx groups, the cellular localization of integrin αvβ1 appears altered. Unlike the control group, where it is mainly localized in the cytoplasm, positive signals are observed in the nucleus of the si-Osx and Lenti-Osx groups. Additionally, since integrin αvβ1 is a membrane protein, shouldn't it primarily be observed on the cell membrane rather than in the cytoplasm? Could the authors clarify this observation?

(7) The results regarding Cx43 expression after Lenti-Osx treatment are questionable. It appears that the images for the Lenti-GFP and Lenti-Osx groups have been misrepresented. The merged images for the Lenti-GFP control group seem to belong to the Lenti-Osx group, and vice versa. If the images were presented in their correct order, the conclusions would contradict the authors' claims. This issue needs to be addressed to ensure an accurate interpretation of the data.

(8) The authors demonstrated that ATRA treatment elevates Cx43 protein levels in the control group, where Osx function is normal. However, can ATRA also restore Cx43 protein levels in the si-Osx treated group, where Osx transcriptional function is impaired? Theoretically, Cx43 protein levels should not be restored in the si-Osx group. Could the observed rescue phenotype be due to effects downstream of Cx43? This possibility should be considered and clarified.

(9) Does the Cx43 mutation of knockout cause similar phenotypes in the animal model? Can restoration of Cx43 rescue the bone phenotype?

Reviewer #1 (Public review):

Summary:

In this manuscript, Yan and colleagues introduce a modification to the previously published PETRI-seq bacterial single cell protocol to include a ribosomal depletion step based on a DNA probe set that selectively hybridizes with ribosome-derived (rRNA) cDNA fragments. They show that their modification of the PETRI-seq protocol increases the fraction of informative non-rRNA reads from ~4-10% to 54-92%. The authors apply their protocol to investigating heterogeneity in a biofilm model of E. coli, and convincingly show how their technology can detect minority subpopulations within a complex community.

Strengths:

The method the authors propose is a straightforward and inexpensive modification of an established split-pool single cell RNA-seq protocol that greatly increases its utility, and should be of interest to a wide community working in the field of bacterial single cell RNA-seq.

Reviewer #1 (Public review):

The revision by Wang et al is a much more clear and readable manuscript than the original version, which I think was a bit too terse and hard to parse. In this version, I think I basically understand all the analyses that the authors undertake and how they argue that those analyses support their conclusions.

The fundamental claim of the manuscript is that rRNA genes experience substitutions much too quickly, given that they are a multi-copy gene system. As clarified by the authors in their response, and as I think is relatively clear in the manuscript, they are collapsing all copies of the rRNA array down. They first quantify polymorphism (in this expanded definition, where polymorphism means variable at a given site across any copy). The authors find elevated levels of heterozygosity in rRNA genes compared to single copy genes, which isn't surprising, given that there is a substantially higher target size; that being said, the increase in polymorphism is smaller than the increase in target size. They then look at substitutions between mouse species and also between human and chimp, and argue that the substitution rate is too fast compared to single copy genes in many cases.

I think that this is an interesting problem and one that obviously occupies some space in the literature. As the authors point out, one possibility for explaining the elevated fixation rate is that there is some kind of positive selection in these putatively non-functional regions. The authors, instead, argue that the elevated rate of evolution is due to neutral homogenizing processes. I'm sympathetic to this argument, I'm a neutralist myself :)

That being said, I find the whole analysis and the connection with the WFH model very strange. As I stated in my previous review, it feels very odd to chalk everything up to variance in reproductive success, rather than explicitly modeling the molecular processes that may lead to the homogenization. For example, the authors bring up gene conversion, and even do a small test of gene conversion. But a force like biased gene conversion is perhaps better modeled as a deterministic force, rather than a stochastic force. Indeed, I think that explicit modeling of mutation dynamics has been very helpful in understanding the role of replicative vs damage-related mutation in humans, as seen in Gao et al (2016) and Spisak et al (2024). I realize, as the authors say in their cover letter, that this is hard! But a major concern with this manuscript is that it's about whether drift can plausibly explain the pattern, but then it's basically impossible to know if it really can, because we have no way to compare the estimated parameters with biophysical or biochemical measurements of the rates of homogenizing forces, because the homogenizing forces are just wrapped up under "variance in reproductive success". I think a much more interesting manuscript would have a more explicit model of homogenizing forces.

I also have some concerns about the data analysis, echoing some concerns of the other reviewer. The biggest issue is that traditional read mapping and SNP calling pipelines for highly duplicated loci don't really make sense. I don't fully understand the variant calling pipeline. The authors state that "All mapping and analysis are performed among individual copies of rRNA genes." which makes it sound like the reads mapping to different copies were somehow deconvolved, which is what you'd need to do to use "normal" variant calling approaches that call look for homozygotes and heterozygotes. But I don't know enough about this literature to understand how they did that and if it makes any sense. If, instead, they called variants against collapsed rRNA copies, then using a standard variant calling approach does not make sense. If you have a variant in 2 out of 100 copies, a standard variant calling algorithm would very likely call that a homozygous ancestral site. Conditional on the variant calls being reasonable, however, I'm basically okay with their use of read counts to estimate "allele frequencies" within individuals.

I have some more minor comments:

(1) In the paragraph starting line 61, the authors say that WF models are unable to handle things like viral epidemics and transposons. I don't think that's really fair: the issue here isn't WF dynamics or not, it's that there is fundamentally evolution on two levels (which is also the case in the rRNA case considered in this manuscript). I certainly agree with the authors that you can't just naively apply standard pop gen theory in these systems, but I think the arrow at the WF model is misaimed, as the real issue is drift and selection on multiple levels.

(2) Line 268-269: The authors argue that the long term rate of evolution in rRNA genes is roughly similar to single copy genes, suggesting not a big influence of increased mutation rate. I'm not sure I understand where this number comes from, as opposed to the divergence numbers they look at in Table 3. These seem to be two different conclusions from roughly the same measurement? Surely I am misunderstanding something.

References:

Gao, Z., Wyman, M. J., Sella, G., & Przeworski, M. (2016). Interpreting the dependence of mutation rates on age and time. PLoS biology, 14(1), e1002355.

Spisak, N., de Manuel, M., Milligan, W., Sella, G., & Przeworski, M. (2024). The clock-like accumulation of germline and somatic mutations can arise from the interplay of DNA damage and repair. PLoS biology, 22(6), e3002678.

Reviewer #1 (Public review):

Summary:

The authors set out to measure the diffusion of small drug molecules inside live cells. To do this, they selected a range of fluorescent drugs, as well as some commonly used dyes, and used FRAP to quantify their diffusion. The authors find that drugs diffuse and localize within the cell in a way that is weakly correlated with their charge, with positively charged molecules displaying dramatically slower diffusion and a high degree of subcellular localization.

The study is important because it points to an important issue related to the way drugs behave inside cells beyond the simple "IC50" metric (a decidedly mesoscopic/systemic value). The authors conclude, and I agree, that their results point to nuanced effects that are governed by drug chemistry that could be optimized to make them more effective.

Strengths:

(1) The work examines an understudied aspect of drug delivery.

(2) The work uses well-established methodologies to measure diffusion in cells

(3) The work provides an extensive dataset, covering a range of chemistries that are common in small molecule drug design

(4) The authors consider several explanations as to the origin of changes in cellular diffusion

Comments on revised version:

In general, my comments were addressed, new discussions were added, and the paper has been improved significantly, which is great.

However, despite providing very clear instructions, a lot of my comments re statistical treatment were disregarded. Bar charts still do not show the repeats as individual points. Errors bars still represent SEM, which gives a wrong idea about the spread of the data. FRAP lines are still averages, and still do not show the spread of the data.

Significance assignments are done based on average and SEMs, as opposed to the full dataset. There is nothing technically wrong with this, but it generally creates an impression that things are more reproducible/rigorous/significant than they would be if the data was shown completely.

Reviewer #1 (Public review):

Summary:

This manuscript by Shan, Guo, Zhang, Chen et al., shows a raft of interesting data including the first cryo-EM structures of human PIEZO1. Clearly the molecular basis of PIEZO channel inactivation is of great interest and as such this manuscript provides some valuable extra information that may help to ultimately build a molecular picture of PIEZO channel inactivation. However, the current manuscript though does not provide any compelling evidence for a detailed mechanism of PIEZO inactivation.

Strengths:

This manuscript documents the first cryo-EM structures of human PIEZO1 and gain of function mutants associated with hereditary anaemia. It is also the first evidence showing that PIEZO1 gain of function mutants are also regulated by the auxiliary subunit MDFIC.

Weaknesses:

While the structures are interesting and clear differences can be seen in the presence of the auxiliary subunit MDFIC the major conclusions and central tenets of the paper, especially a role for pore lipids in inactivation, lack data to support them. The post translational modification of PIEZOs auxiliary subunit MDFIC is not modelled as a covalent interaction.

Comments on revisions:

The revisions do absolutely nothing to allay any of the major concerns documented in my initial review of this manuscript.

(1) Mouse vs Human inactivation<br /> Not only is a quantification not provided the literature on this point is still not at all referenced or discussed.<br /> (2) MDFIC -lipidation<br /> Even if they are not assigned in the PDB for illustration they can at least be modelled correctly as covalently bound acyl chains.<br /> (3) Pore lipids and inactivation<br /> None of the explanations are consistent with the data shown.<br /> (4) Cytosolic plug<br /> There is not even any extra discussion provided on this point.<br /> (5) Reduced sensitivity of PIEZO1 in the presence of MDFIC and its regulatory mechanism<br /> No quantification is provided.<br /> (6) Both referencing of the PIEZO1 literature and prose could be improved.<br /> There is little to no attempt to improve the referencing.

Reviewer #1 (Public review):

Summary:

Mehmet Mahsum Kaplan et al. demonstrate that Meis2 expression in neural crest-derived mesenchymal cells is crucial for whisker follicle (WF) development, as WF fails to develop in wnt1-Cre;Meis2 cKO mice. Advanced imaging techniques effectively support the idea that Meis2 is essential for proper WF development and that nerves, while affected in Meis2 cKO, are dispensable for WF development and not the primary cause of WF developmental failure. The study also reveals that although Meis2 significantly downregulates Foxd1 in the mesenchyme, this is not the main reason for WF development failure. The paper presents valuable data on the role of mesenchymal Meis2 in WF development. However, further quantification and analysis of the WF developmental phenotype would be beneficial in strengthening the claim that Meis2 controls early WF development rather than causing a delay or arrest in development. A deeper sequencing data analysis could also help link Meis2 to its downstream targets that directly impact the epithelial compartment.

Strengths:

(1) The authors describe a novel molecular mechanism involving Mesenchymal Meis2 expression, which plays a crucial role in early WF development.

(2) They employ multiple advanced imaging techniques to illustrate their findings beautifully.

(3) The study clearly shows that nerves are not essential for WF development.

Weaknesses:

(1) The authors claim that Meis2 acts very early during development, as evidenced by a significant reduction in EDAR expression, one of the earliest markers of placode development. While EDAR is indeed absent from the lower panel in Figure 3C of the Meis2 cKO, multiple placodes still express EDAR in the upper two panels of the Meis2 cKO. The authors also present subsequent analysis at E13.3, showing one escaped follicle positive for SHH and Sox9 in Figures 1 and 3. Does this suggest that follicles are specified but fail to develop? Alternatively, could there be a delay in follicle formation? The increase in Foxd1 expression between E12.5 and E13.5 might also indicate delayed follicle development, or as the authors suggest, follicles that have escaped the phenotype. The paper would significantly benefit from robust quantification to accompany their visual data, specifically quantifying EDAR, Sox9, and Foxd1 at different developmental stages. Additionally, analyzing later developmental stages could help distinguish between a delay or arrest in WF development and a complete failure to specify placodes.

(2) The authors show that single-cell sequencing reveals a reduction in the pre-DC population, reduced proliferation, and changes in cell adhesion and ECM. However, these changes appear to affect most mesenchymal cells, not just pre-DCs. Moreover, since E12.5 already contains WFs at different stages of development, as well as pre-DCs and DCs, it becomes challenging to connect these mesenchymal changes directly to WF development. Did the authors attempt to re-cluster only Cluster 2 to determine if a specific subpopulation is missing in Meis2 cKO? Alternatively, focusing on additional secreted molecules whose expression is disrupted across different clusters in Meis2 cKO could provide insights, especially since mesenchymal-epithelial communication is often mediated through secreted molecules. Did the authors include epithelial cells in the single-cell sequencing, can they look for changes in mesenchyme-epithelial cell interactions (Cell Chat) to indicate a possible mechanism?

(3) The authors aim to link Meis2 expression in the mesenchyme with epithelial Wnt signaling by analyzing Lef1, bat-gal, Axin1, and Wnt10b expression. However, the changes described in the figures are unclear, and the phenotype appears highly variable, making it difficult to establish a connection between Meis2 and Wnt signaling. For instance, some follicles and pre-condensates are Lef1 positive in Meis2 cKO. Including quantification or providing a clearer explanation could help clarify the relationship between mesenchymal Meis2 and Wnt signaling in both epidermal and mesenchymal cells. Did the authors include epithelial cells in the sequencing? Could they use single-cell analysis to demonstrate changes in Wnt signaling?

(4) Existing literature, including studies on Neurog KO and NGF KO, as well as the references cited by the authors, suggest that nerves are unlikely to mediate WF development. While the authors conduct a thorough analysis of WF development in Neurog KO, further supporting this notion, this point may not be central to the current work. Additionally, the claim that Meis2 influences trigeminal nerve patterning requires further analysis and quantification for validation.

(5) Meis2 expression seems reduced but has not entirely disappeared from the mesenchyme. Can the authors provide quantification?

Reviewer #1 (Public Review):

Summary:

In this manuscript, Yan and colleagues introduce a modification to the previously published PETRI-seq bacterial single-cell protocol to include a ribosomal depletion step based on a DNA probe set that selectively hybridizes with ribosome-derived (rRNA) cDNA fragments. They show that their modification of the PETRI-seq protocol increases the fraction of informative non-rRNA reads from ~4-10% to 54-92%. The authors apply their protocol to investigating heterogeneity in a biofilm model of E. coli, and convincingly show how their technology can detect minority subpopulations within a complex community.

Strengths:

The method the authors propose is a straightforward and inexpensive modification of an established split-pool single-cell RNA-seq protocol that greatly increases its utility, and should be of interest to a wide community working in the field of bacterial single-cell RNA-seq.

Weaknesses:

The manuscript is written in a very compressed style and many technical details of the evaluations conducted are unclear and processed data has not been made available for evaluation, limiting the ability of the reader to independently judge the merits of the method.

Reviewer #1 (Public review):

Summary:

In this study, the authors address whether the dorsal nucleus of the inferior colliculus (DCIC) in mice encodes sound source location within the front horizontal plane (i.e., azimuth). They do this using volumetric two-photon Ca2+ imaging and high-density silicon probes (Neuropixels) to collect single-unit data. Such recordings are beneficial because they allow large populations of simultaneous neural data to be collected. Their main results and the claims about those results are the following:

(1) DCIC single-unit responses have high trial-to-trial variability (i.e., neural noise);<br /> (2) approximately 32% to 40% of DCIC single units have responses that are sensitive to sound source azimuth;<br /> (3) single-trial population responses (i.e., the joint response across all sampled single units in an animal) encode sound source azimuth "effectively" (as stated in the title) in that localization decoding error matches average mouse discrimination thresholds;<br /> (4) DCIC can encode sound source azimuth in a similar format to that in the central nucleus of the inferior colliculus (as stated in the Abstract);<br /> (5) evidence of noise correlation between pairs of neurons exists;<br /> and 6) noise correlations between responses of neurons help reduce population decoding error.<br /> While simultaneous recordings are not necessary to demonstrate results #1, #2, and #4, they are necessary to demonstrate results #3, #5, and #6.

Strengths:

- Important research question to all researchers interested in sensory coding in the nervous system.<br /> - State-of-the-art data collection: volumetric two-photon Ca2+ imaging and extracellular recording using high-density probes. Large neuronal data sets.<br /> - Confirmation of imaging results (lower temporal resolution) with more traditional microelectrode results (higher temporal resolution).<br /> - Clear and appropriate explanation of surgical and electrophysiological methods. I cannot comment on the appropriateness of the imaging methods.

Strength of evidence for the claims of the study:

(1) DCIC single-unit responses have high trial-to-trial variability -<br /> The authors' data clearly shows this.

(2) Approximately 32% to 40% of DCIC single units have responses that are sensitive to sound source azimuth -<br /> The sensitivity of each neuron's response to sound source azimuth was tested with a Kruskal-Wallis test, which is appropriate since response distributions were not normal. Using this statistical test, only 8% of neurons (median for imaging data) were found to be sensitive to azimuth, and the authors noted this was not significantly different than the false positive rate. The Kruskal-Wallis test was not reported for electrophysiological data. The authors suggested that low numbers of azimuth-sensitive units resulting from the statistical analysis may be due to the combination of high neural noise and a relatively low number of trials, which would reduce the statistical power of the test. This is likely true and highlights a weakness in the experimental design (i.e., a relatively small number of trials). The authors went on to perform a second test of azimuth sensitivity-a chi-squared test-and found 32% (imaging) and 40% (e-phys) of single units to have statistically significant sensitivity. However, the use of a chi-squared test is questionable because it is meant to be used between two categorical variables, and neural response had to be binned before applying the test.

(3) Single-trial population responses encode sound source azimuth "effectively" in that localization decoding error matches average mouse discrimination thresholds -<br /> If only one neuron in a population had responses that were sensitive to azimuth, we would expect that decoding azimuth from observation of that one neuron's response would perform better than chance. By observing the responses of more than one neuron (if more than one were sensitive to azimuth), we would expect performance to increase. The authors found that decoding from the whole population response was no better than chance. They argue (reasonably) that this is because of overfitting of the decoder model-too few trials were used to fit too many parameters-and provide evidence from decoding combined with principal components analysis which suggests that overfitting is occurring. What is troubling is the performance of the decoder when using only a handful of "top-ranked" neurons (in terms of azimuth sensitivity) (Fig. 4F and G). Decoder performance seems to increase when going from one to two neurons, then decreases when going from two to three neurons, and doesn't get much better for more neurons than for one neuron alone. It seems likely there is more information about azimuth in the population response, but decoder performance is not able to capture it because spike count distributions in the decoder model are not being accurately estimated due to too few stimulus trials (14, on average). In other words, it seems likely that decoder performance is underestimating the ability of the DCIC population to encode sound source azimuth.

To get a sense of how effective a neural population is at coding a particular stimulus parameter, it is useful to compare population decoder performance to psychophysical performance. Unfortunately, mouse behavioral localization data do not exist. Instead, the authors compare decoder error to mouse left-right discrimination thresholds published previously by a different lab. However, this comparison is inappropriate because the decoder and the mice were performing different perceptual tasks. The decoder is classifying sound sources to 1 of 13 locations from left to right, whereas the mice were discriminating between left or right sources centered around zero degrees. The errors in these two tasks represent different things. The two data sets may potentially be more accurately compared by extracting information from the confusion matrices of population decoder performance. For example, when the stimulus was at -30 deg, how often did the decoder classify the stimulus to a lefthand azimuth? Likewise, when the stimulus was +30 deg, how often did the decoder classify the stimulus to a righthand azimuth?

(4) DCIC can encode sound source azimuth in a similar format to that in the central nucleus of the inferior colliculus -<br /> It is unclear what exactly the authors mean by this statement in the Abstract. There are major differences in the encoding of azimuth between the two neighboring brain areas: a large majority of neurons in the CNIC are sensitive to azimuth (and strongly so), whereas the present study shows a minority of azimuth-sensitive neurons in the DCIC. Furthermore, CNIC neurons fire reliably to sound stimuli (low neural noise), whereas the present study shows that DCIC neurons fire more erratically (high neural noise).

(5) Evidence of noise correlation between pairs of neurons exists -<br /> The authors' data and analyses seem appropriate and sufficient to justify this claim.

(6) Noise correlations between responses of neurons help reduce population decoding error -<br /> The authors show convincing analysis that performance of their decoder increased when simultaneously measured responses were tested (which include noise correlation) than when scrambled-trial responses were tested (eliminating noise correlation). This makes it seem likely that noise correlation in the responses improved decoder performance. The authors mention that the naïve Bayesian classifier was used as their decoder for computational efficiency, presumably because it assumes no noise correlation and, therefore, assumes responses of individual neurons are independent of each other across trials to the same stimulus. The use of a decoder that assumes independence seems key here in testing the hypothesis that noise correlation contains information about sound source azimuth. The logic of using this decoder could be more clearly spelled out to the reader. For example, if the null hypothesis is that noise correlations do not carry azimuth information, then a decoder that assumes independence should perform the same whether population responses are simultaneous or scrambled. The authors' analysis showing a difference in performance between these two cases provides evidence against this null hypothesis.

Minor weakness:<br /> - Most studies of neural encoding of sound source azimuth are done in a noise-free environment, but the experimental setup in the present study had substantial background noise. This complicates comparison of the azimuth tuning results in this study to those of other studies. One is left wondering if azimuth sensitivity would have been greater in the absence of background noise, particularly for the imaging data where the signal was only about 12 dB above the noise.

Reviewer #1 (Public review):

This study by Alejandro Rosell et al. reveals the immunoregulatory role of the RAS-p110α pathway in macrophages, specifically in regulating monocyte extravasation and lysosomal digestion during inflammation. Disrupting this pathway, through genetic tools or pharmacological intervention in mice, impairs the inflammatory response, leading to delayed resolution and more severe acute inflammation. The authors suggest that activating p110α with small molecules could be a potential therapeutic strategy for treating chronic inflammation. These findings provide important insights into the mechanisms by which p110α regulates macrophage function and the overall inflammatory response.

The updates made by the authors in the revised version have addressed the main points raised in the initial review, further improving the strength of their findings.

Reviewer #1 (Public review):

Summary:

Tian et al. describes how TIPE regulates melanoma progression, stemness, and glycolysis. The authors link high TIPE expression to increased melanoma cell proliferation and tumor growth. TIPE causes dimerization of PKM2, as well as translocation of PKM2 to the nucleus, thereby activating HIF-1alpha. TIPE promotes the phosphorylation of S37 on PKM2 in an ERK-dependent manner. TIPE is shown to increase stem-like phenotype markers. The expression of TIPE is positively correlated with the levels of PKM2 Ser37 phosphorylation in murine and clinical tissue samples. Taken together, the authors demonstrate how TIPE impacts melanoma progression, stemness, and glycolysis through dimeric PKM2 and HIF-1alpha crosstalk.

The authors manipulated TIPE expression using both shRNA and overexpression approaches throughout the manuscript. Using these models, they provide strong evidence of the involvement of TIPE in mediating PKM2 Ser37 phosphorylation and dimerization. The authors also used mutants of PKM2 at S37A to block its interaction with TIPE and HIF-1alpha. In addition, an ERK inhibitor (U0126) was used to block the phosphorylation of Ser37 on PKM2. The authors show how dimerization of PKM2 by TIPE causes nuclear import of PKM2 and activation of HIF-1alpha and target genes. Pyridoxine was used to induce PKM2 dimer formation, while TEPP-46 was used to suppress PKM2 dimer formation. TIPE maintains stem cell phenotypes by increasing expression of stem-like markers. Furthermore, the relationship between TIPE and Ser37 PKM2 was demonstrated in murine and clinical tissue samples.

The evaluation of how TIPE causes metabolic reprogramming can be further assessed using isotope tracing experiments.

Reviewer #1 (Public Review):

Summary:

The work by Joseph et al "Impact of the clinically approved BTK inhibitors on the conformation of full-length BTK and analysis of the development of BTK resistance mutations in chronic lymphocytic leukemia" seeks to comparatively analyze the effect of a range of covalent and noncovalent clinical BTK inhibitors upon BTK conformation. The novel aspect of this manuscript is that it seeks to evaluate the differential resistance mutations that arise distinctly from each of the inhibitors.

Strengths:

This is an exciting study that builds upon the fundamental notion of ensemble behavior in solutions for enzymes such as BTK. The HDX-MS and NMR experiments are adequately and comprehensively presented.

Comments on the revised version:

I am satisfied with the revisions and the clear explanations.

Reviewer #1 (Public Review):

Summary:

The authors want to understand fundamental steps in ligand binding to muscle nicotinic receptors using computational methods. Overall, although the work provides new information and support for existing models of ligand activation of this receptor type, some limitations in the methods and approach mean that the findings are not as conclusive as hoped.

Strengths:

The strengths include the number of ligands tried, and the comparison to the existing mature analysis of receptor function from the senior author's lab.

Weaknesses:

The weakness are the brevity of the simulations, the concomitant lack of scope of the simulations, the lack of depth in the analysis and the incomplete relation to other relevant work. The free energy methods used seem to lack accuracy - they are only correct for 2 out of 4 ligands.

Reviewer #1 (Public review):

Summary:

Zhang et al. describe a delicate relationship between Tet2 and FBP1 in the regulation of hepatic gluconeogenesis.

Strengths:

The studies are very mechanistic, indicating that this interaction occurs via demethylation of HNF4a. Phosphorylation of HNF4a at ser 313 induced by metformin also controls the interaction between Tet2 and FBP1.

Weaknesses:

The results are briefly described, and oftentimes, the necessary information is not provided to interpret the data. Similarly, the methods section is not well developed to inform the reader about how these experiments were performed. While the findings are interesting, the results section needs to be better developed to increase confidence in the interpretation of the results.

Reviewer #1 (Public review):

The authors presented a new MNase-based proximity ligation method called MChIP-C, allowing for the measurement of protein-mediated chromatin interactions at single-nucleosome resolution on a genome-wide scale. With improved resolution and sensitivity, they explored the spatial connectivity of active promoters and identified the potential candidates for establishing/maintaining E-P interactions. Finally, with published CRISPRi screens, they found that most functionally-verified enhancers do physically interact with their cognate promoters, supporting the enhancer-promoter looping model.

While the study's experimental approach and findings are interesting. However, several issues need to be addressed:

(1) The authors described that "the lack of interaction between experimentally-validated enhancers and their cognate promoters in some studies employing C-methods has raised doubts regarding the classical promoter-enhancer looping model", so it's intriguing to see whether the MChIP-C could indeed detect the E-P interactions which were not identified by C-methods as they mentioned (Benabdallah et al., 2019; Gupta et al., 2017). I agree that they identified more E-P interactions using MChIP-C, but specifically, they should show at least 2-3 cases. It's important since this is the main conclusion the authors want to draw.

(2) The authors compared their data to those of Chen et al. (Chen et al., 2022), who used PLAC-seq with anti-H3K4me3 antibodies in K562 cells and standard Micro-C data previously reported for K562, concluding that "MChIP-C achieves superior sensitivity and resolution compared to C-methods based on standard restriction enzymes.". This is not convincing since they only compared their data to one dataset. More datasets from other cell lines should be included.

(3) The reasons to choose Chen's data (Chen et al., 2022) and CRISPRi screens (Fulco et al., 2019; Gasperini et al., 2019) should be provided since there are so many out there.

(4) The authors identify EP300 histone acetyltransferase and the SWI/SNF remodeling complex as potential candidates for establishing and/or maintaining enhancer-promoter interactions, but not RNA polymerase II, mediator complex, YY1 and BRD4. More explanation is needed for this point since they're previously suggested to be associated with E-P interactions.

(5) The limitations of the method should be discussed.

Reviewer #1 (Public review):

Summary:

The manuscript proposes that 5mC modifications to DNA, despite being ancient and widespread throughout life, represent a vulnerability, making cells more susceptible to both chemical alkylation and, of more general importance, reactive oxygen species. Sarkies et al take the innovative approach of introducing enzymatic genome-wide cytosine methylation system (DNA methyltransferases, DNMTs) into E. coli, which normally lacks such a system. They provide compelling evidence that the introduction of DNMTs increases the sensitivity of E. coli to chemical alkylation damage. Surprisingly they also show DNMTs increase the sensitivity to reactive oxygen species and propose that the DNMT generated 5mC presents a target for the reactive oxygen species that is especially damaging to cells. Evidence is presented that DNMT activity directly or indirectly produces reactive oxygen species in vivo, which is an important discovery if correct, though the mechanism for this remains obscure.

Strengths:

This work is based on an interesting initial premise, it is well-motivated in the introduction and the manuscript is clearly written. The results themselves are compelling.

Weaknesses:

I am not currently convinced by the principal interpretations and think that other explanations based on known phenomena could account for key results. Specific points below.

(1) As noted in the manuscript, AlkB repairs alkylation damage by direct reversal (DNA strands are not cut). In the absence of AlkB, repair of alklylation damage/modification is likely through BER or other processes involving strand excision and resulting in single stranded DNA. It has previously been shown that 3mC modification from MMS exposure is highly specific to single stranded DNA (PMID:20663718) occurring at ~20,000 times the rate as double stranded DNA. Consequently, the introduction of DNMTs is expected to introduce many methylation adducts genome-wide that will generate single stranded DNA tracts when repaired in an AlkB deficient background (but not in an AlkB WT background), which are then hyper-susceptible to attack by MMS. Such ssDNA tracts are also vulnerable to generating double strand breaks, especially when they contain DNA polymerase stalling adducts such as 3mC. The generation of ssDNA during repair is similarly expected follow the H2O2 or TET based conversion of 5mC to 5hmC or 5fC neither of which can be directly repaired and depend on single strand excision for their removal. The potential importance of ssDNA generation in the experiments has not been considered.

(2) The authors emphasise the non-additivity of the MMS + DNMT + alkB experiment but the interpretation of the result is essentially an additive one: that both MMS and DNMT are introducing similar/same damage and AlkB acts to remove it. The non-additivity noted would seem to be more consistent with the ssDNA model proposed in #1. More generally non-additivity would also be seen if the survival to DNA methylation rate is non-linear over the range of the experiment, for example if there is a threshold effect where some repair process is overwhelmed. The linearity of MMS (and H2O2) exposure to survival could be directly tested with a dilution series of MMS (H2O2).

(3) The substantial transcriptional changes induced by DNMT expression (Supplemental Figure 4) are a cause for concern and highlight that the ectopic introduction of methylation into a complex system is potentially more confounded than it may at first seem. Though the expression analysis shows bulk transcription properties, my concern is that the disruptive influence of methylation in a system not evolved with it adds not just consistent transcriptional changes but transcriptional heterogeneity between cells which could influence net survival in a stressed environment. In practice I don't think this can be controlled for, possibly quantified by single-cell RNA-seq but that is beyond the reasonable scope of this paper.

(4) Figure 4 represents a striking result. From its current presentation it could be inferred that DNMTs are actively promoting ROS generation from H2O2 and also to a lesser extent in the absence of exogenous H2O2. That would be very surprising and a major finding with far-reaching implications. It would need to be further validated, for example by in vitro reconstitution of the reaction and monitoring ROS production. Rather, I think the authors are proposing that some currently undefined, indirect consequence of DNMT activity promotes ROS generation, especially when exogenous H2O2 is available. It would help if this were clarified.

Reviewer #1 (Public review):

In the current manuscript, the authors use theoretical and analytical tools to examine the possibility of neural projections to engage ensembles of synaptic clusters in active dendrites. The analysis is divided into multiple models that differ in the connectivity parameters, speed of interactions and identity of the signal (electric vs. second messenger). They first show that random connectivity almost ensures the representation of presynaptic ensembles. As expected, this convergence is much more likely for small group sizes and slow processes, such as calcium dynamics. Conversely, fast signals (spikes and postsynaptic potentials) and large groups are much less likely to recruit spatially clustered inputs. Dendritic nonlinearity in the postsynaptic cells was found to play a highly important role in distinguishing these clustered activation patterns, both when activated simultaneously and in sequence. The authors tackled the difficult issue of noise, showing a beneficiary effect when noise 'happen' to fill in gaps in a sequential pattern but degraded performance at higher background activity levels. Last, the authors simulated selectivity to chemical and electrical signals. While they find that longer sequences are less perturbed by noise, in more realistic activation conditions, the signals are not well resolved in the soma.

While I think the premise of the manuscript is worth exploring, I have a number of reservations regarding the results.

(1) In the analysis, the authors made a simplifying assumption that the chemical and electrical processes are independent. However, this is not the case; excitatory inputs to spines often trigger depolarization combined with pronounced calcium influx; this mixed signaling could have dramatic implications on the analysis, particularly if the dendrites are nonlinear (see below)<br /> (2) Sequence detection in active dendrites is often simplified to investigating activation in a part of or the entirety of individual branches. However, the authors did not do that for most of their analysis. Instead, they treat the entire dendritic tree as one long branch and count how many inputs form clusters. I fail to see why the simplification is required and suspect it can lead to wrong results. For example, two inputs that are mapped to different dendrites in the 'original' morphology but then happen to fall next to each other when the branches are staggered to form the long dendrites would be counted as neighbors.<br /> (3) The simulations were poorly executed. Figures 5 and 6 show examples but no summary statistics. The authors emphasize the importance of nonlinear dendritic interactions, but they do not include them in their analysis of the ectopic signals! I find it to be wholly expected that the effects of dendritic ensembles are not pronounced when the dendrites are linear.

To provide a comprehensive analysis of dendritic integration, the authors could simulate more realistic synaptic conductances and voltage-gated channels. They would find much more complicated interactions between inputs on a single site, a sliding temporal and spatial window of nonlinear integration that depends on dendritic morphology, active and passive parameters and synaptic properties. At different activation levels, the rules of synaptic integration shift to cooperativity between different dendrites and cellular compartments, further complicated by nonlinear interactions between somatic spikes and dendritic events.

While it is tempting to extend back-of-the-napkin calculations of how many inputs can recruit nonlinear integration in active dendrites, the biological implementation is very different from this hypothetical. It is important to consider these questions, but I am not convinced that this manuscript adequately addressed the questions it set out to probe, nor does it provide information that was unknown beforehand.

Update after the first revision:

In this revision, the authors significantly improved the manuscript. They now address some of my concerns. Specifically, they show the contribution of end-effects on spreading the inputs between dendrites. This analysis reveals greater applicability of their findings to cortical cells, with long, unbranching dendrites than other neuronal types, such as Purkinje cells in the cerebellum.

They now explain better the interactions between calcium and voltage signals, which I believe improve the take-away message of their manuscript. They modified and added new figures that helped to provide more information about their simulations.<br /> However, some of my points remain valid. Figure 6 shows depolarization of ~5mV from -75. This weak depolarization would not effectively recruit nonlinear activation of NMDARs. In their paper, Branco and Hausser (2010) showed depolarizations of ~10-15mV. More importantly, the signature of NMDAR activation is the prolonged plateau potential and activation at more depolarized resting membrane potentials (their Figure 4). Thus, despite including NMDARs in the simulation, the authors do not model functional recruitment of these channels. Their simulation is thus equivalent to AMPA only drive, which can indeed summate somewhat nonlinearly.

Reviewer #1 (Public review):

Summary:

The authors introduced neutron crystallography coupled with room temperature X-ray crystallography to exam the redox properties of the BtFt [4Fe-4S] cluster expressed in E. coli. Neutron structure allowed the authors to exam the influence of Asp64 on the redox properties of the [4Fe-4S] cluster. The neutron structure also allowed for the identification of the hydrogen network around the [4Fe-4S] structure. This work was followed by density functional theory calculation to examine different redox states which also pointed to the role of Asp64 in affecting or dictating redox function of the [4Fe-4S] cluster. Based on the DFT work the authors examine the redox properties under oxic and anoxic conditions in wild type enzymes and in a D64N mutant again showing the role of Asp64 on the redox kinetics and redox potential of the [4Fe-4S] cluster. Lastly, the authors examined similar [4Fe-4S] ferredoxins from several organisms and with a Asp64 or Glu64 observed a similar role of Asp64 on the low potential state of the [4Fe-4S] cluster. The major conclusion of the study was to identify the role of specific amino acids, in this case Asp64, in controlling the redox state and kinetics of [4Fe-4S] clusters. The authors also demonstrate the strength of neutron crystallography when combined with classical X-ray crystallography and classical spectral/redox studies.

Strengths:

In general, the experimental design is logical and the results are convincing demonstrating the role of Asp64 on the redox properties of [4Fe-4S] clusters in ferredoxins.

Weaknesses:

The role(s) of coordinating amino acids on the redox properties of a functional group is not surprising, this reviewer believes this is a novel result in ferredoxins and does make a nice contribution to the field.

Reviewer #1 (Public review):

Summary:

A description of small phosphatised fossils from the Kuanchuanpu, formations that are claimed to represent unequivocal early segmented bilaterians with limbs, ie annelids or panarthropods. All material from the Kuanchuanpu is of interest, and the mode of preservation is certainly striking.

However, few details apart from bilateral symmetry and paired protrusions are present. In addition, fragments of potential progenitors such as anabaritiids cannot be entirely ruled out. In addition, the broader claims about the nature of the Cambrian explosion, the gap between the fossil record and molecular clocks, and what various authors have said about them are either inadequate or incorrect. For example, Budd and Jackson did not at all make the claim that the earliest bilaterians were soft-bodied and tiny. Glaessner (1958) is a very out-of-date reference to use. We know that bilaterians certainly existed by the time of Kuanchuanpo.

Even so, it is possible that these fragments do represent internal moulds of taxa such as lobopod-like organisms, even if the evidence is not totally persuasive.

Reviewer #1 (Public review):

Summary:

In this manuscript, Corso-Diaz et al, focus on the NRL transcription factor (TF), which is critical for retinal rod photoreceptor development and function. The authors profile NRL's protein interactome, revealing several RNA-binding proteins (RBPs) among its components. Notably, many of these RBPs are associated with R-loop biology, including DHX9 helicase, which is the primary focus of this study. R-loops are three-stranded nucleic acid structures that frequently form during transcription. The authors demonstrate that R-loop levels increase during photoreceptor maturation and establish an interaction between NRL TF and DHX9 helicase. The association between NRL and RBPs like DHX9 suggests a cooperative regulation of gene expression in a cell-type-specific manner, an intriguing discovery relevant to photoreceptor health. Since DHX9 is a key regulator of R-loop homeostasis, the study proposes a potential mechanism where a cell-type-specific TF controls the expression of certain genes by modulating R-loop homeostasis. This study also presents the first data on R-loop mapping in mammalian retinas and shows the enrichment of R-loops over intergenic regions as well as genes encoding neuronal function factors. While the research topic is very important, there is some concern regarding the data presented: there are substantial data supporting the interaction between NRL and DHX9, including pull-down experiments and proximity labeling assay (PLA), however, the data showing an interaction between NRL and DDX5, another R-loop-associated helicase, are inadequate. Importantly, the data supporting the claim that NRL interacts with R-loops are absolutely insufficient and at best, correlative. The next concerns are regarding the R-loop mapping data analysis and visualization.

Strengths:

There is compelling evidence that the NRL transcription factor interacts with several RNA binding proteins, and specifically, sufficient data supporting the interaction of NRL with DHX9 helicase.<br /> A major strength is the use of the single-stranded R-loop mapping method in the mouse retina.

Weaknesses:

(1) Figure S1A: There is a strong band in GST-IP (control IP) for either HNRNPUI1 or HNRNPU, although the authors state in their results that there is a strong interaction of these two RBPs with NRL. Both DHX9 and DDX5 samples have a faint band in the GST-IP. There is an extremely faint band for HNRNPA2B1 in the GST-NRL IP lane. Given this is a pull-down with added benzonase treatment to remove all nucleic acids, these data suggest, that previously observed NRL interactions with these particular RBPs are mediated via nucleic acids. Similarly, there is a loss of band signal for HNRNM in this assay, although it was identified as an NRL-interacting protein in three assays, which again suggests that nucleic acids mediate the interaction.

(2) The data supporting NRL-DDX5 interaction in rod photoreceptor nuclei is very weak. In Figure 2D, the PLA signal for DDX5-NRL is very weak in the adult mouse retina and is absent in the human retina, as shown in Figure 2H. Given that there is no NRL-KO available for the human PLA assay, the control experiments using single-protein antibodies should be included in the assay. Similarly, the single-protein antibody control PLA experiments should be included in the experimental data presented in Figure 2J.

(3) The EMSA experiment using a probe containing NRL binding motif within the DHX9 promoter should include incubation with retina nuclear extracts depleted for NRL as a control.

(4) There is a reduced amount of DHX9 pulled down in NRL-IP in HEK293 cells, but there is no statistically significant difference in the reciprocal IP (DHX9-IP and blotting for NRL) (Figure 4C).

(5) The only data supporting the claim that NRL interacts with R-loops are presented in Figure 5A. This is a co-IP of R-loops and then blotting for NRL, DHX9, and DDX5. Here, there is no signal for DDX5, quantification of DHX9 signal shows no statistically significant difference between RNase H treated and untreated samples, while NRL shows a signal in RNase H treated sample. These data are not sufficient to make the statement regarding the interaction of NRL with R-loops.

(6) Regarding R-loop mapping, the data analysis is quite confusing. The authors perform two different types of analyses: either overall narrow and broad peak analysis or strand-specific analysis. Given that the authors used ssDRIP-seq, which is a method designed to map R-loops strand specifically, it is confusing to perform different types of analyses. Next, the peak analysis is usually performed based on the RNase H treated R-loop mapping; what does it mean then to have a pool of "Not R-loops", see Figure 6B? In that regard, what does the term "unstranded" R-loops mean? Based on the authors' definition, these are R-loops that do not fall within the group of strand-specific R-loops. The authors should explain the reasons behind these types of analyses and explain, what the biological relevance of these different types of R-loops is.

(7) It would be more useful to show the percent distribution of R-loops over the different genomic regions, instead of showing p-value enrichment, see Figure 6C.

(8) Based on the model presented, NRL regulates R-loop biology via interaction with RBPs, such as DHX9, a known R-loop resolution helicase. Given that the gene targets of NRL TF are known, it would be useful to then analyze the R-loop mapping data across this gene set.

Reviewer #1 (Public review):

Summary:

In this preprint, Madrigal et al present "Tom1p ubiquitin ligase structure, interaction with Spt6p, and function in maintaining normal transcript levels and the stability of chromatin in promoters" which describes the identification of Tom1p, a conserved ubiquitin ligase, as a potential binding partner for the transcription elongation/histone chaperone Spt6p, and reveal the Tom1p structure as determined by CryoEM. Tom1p is a homolog of human HUWE1, which has been implicated in decay for a variety of basic protein substrates such as ribosomal proteins and histones. Structure-function analyses identify regions required for Spt6p interaction, suggesting that the interaction with Spt6p is phosphorylation dependent, and for interactions with histones, the latter of which confers phenotypes in vivo when mutated, suggesting that the Tom1p acidic region is important for its function. What is less clear is the function or interaction with Spt6p. The manuscript speculates that Spt6p-Tom1p interactions may tune Tom1p localization, and it is shown that Tom1p is recruited to transcribed genes by chromatin IP. In addition, the Tom1p structure will be valuable to those trying to understand the mechanisms of this very large ubiquitin ligase. Here, structures of homologs from other organisms have already been described elsewhere, however, the authors here indicate some details potentially not previously visualized in other structures.

Strengths:

It has not previously been known that the Spt6p tSH2 had any additional targets. Interaction with a ubiquitin ligase already implicated in histone turnover given Spt6p's role as histone chaperone is interesting. A structure of Tom1p also provides insight into this very large, conserved protein and structure-function analysis in a model system is a good start towards mechanistic dissection.

Weaknesses:

Some aspects of the manuscript seem less cohesive in that there are two halves of the manuscript and both don't quite solidify insights into the Spt6p relationship to Tom1p or deepen our understanding of Tom1p mechanism extensively, though results are a great start on both sides of the paper. There are several points that are less clear in that it is not known if Spt6p interacts with Tom1p and in what context. The interaction surface of Spt6p able to interact with Tom1p is the identical tSH2 that would be predicted to be occupied by phosphorylated RNAPII when Spt6p is incorporated into the RNAPII elongation complex. This means how and when Spt6p might be available to interact with Tom1p is not clear. Previous work from the Hill and Formosa groups on the tSH2 domain and its RNAPII linker target have suggested that phenotypes of mutants in the two are similar, suggesting that their main function is to interact with each other. A simple test of examining Tom1p interaction with genes in the tSH2 mutant was not done. Additionally, the Spt6p interacting surface on Tom1p is not narrowed to a specific putatively phosphorylated residue that it might target. It remains possible that mutations in other regions of Tom1p affect potential phosphorylation of this target, and therefore it is possible that some mutations that alter Spt6p interaction could do so indirectly. Finally, the authors might consider additional models for their discussion where Spt6p potentially could function to deliver histones to Tom1p.

Reviewer #1 (Public review):

Summary:

This impressive study presents a comprehensive scRNAseq atlas of the cranial region during neural induction, patterning, and morphogenesis. The authors collected a robust scRNAseq dataset covering six distinct developmental stages. The analysis focused on the neural tissue, resulting in a highly detailed temporal map of neural plate development. The findings demonstrate how different cell fates are organized in specific spatial patterns along the anterior-posterior and medial-lateral axes within the developing neural tissue. Additionally, the research utilized high-density single-cell RNA sequencing (scRNAseq) to reveal intricate spatial and temporal patterns independent of traditional spatial techniques.

The investigation utilized diffusion component analysis to spatially order cells based on their positioning along the anterior-posterior axis, corresponding to the forebrain, midbrain, hindbrain, and medial-lateral axis. By cross-referencing with MGI expression data, the identification of cell types was validated, affirming the expression patterns of numerous known genes and implicating others as differentially expressed along these axes. These findings significantly advance our understanding of the spatially regulated genes in neural tissues during early developmental stages. The emphasis on transcription factors, cell surface, and secreted proteins provides valuable insights into the intricate gene regulatory networks underpinning neural tissue patterning. Analysis of a second scRNAseq dataset where Shh signaling was inhibited by culturing embryos in SAG identified known and previously unknown transcripts regulated by Shh, including the Wnt pathway.

The data includes the neural plate and captures all major cell types in the head, including the mesoderm, endoderm, non-neural ectoderm, neural crest, notochord, and blood. With further analyses, this high-quality data promises to significantly advance our understanding of how these tissues develop in conjunction with the neural tissue, paving the way for future breakthroughs in developmental biology and genomics.

Strengths:

The data is well presented in the figures and thoroughly described in the text. The quality of the scRNAseq data and bioinformatic analysis is exceptional.

Weaknesses:

No weaknesses were identified by this reviewer.

Reviewer #1 (Public review):

Summary:

In this manuscript, Javid and colleagues worked to understand the molecular mechanisms involved in mistranslation in mycobacteria. They had previously discovered that mistranslation is an important mechanism underlying antibiotic tolerance in mycobacteria. Using a clever genetic screen they identify that deletion of gidB, a 16S ribosomal RNA methyltransferase, leads to lowered mistranslation (i.e. higher translational fidelity), but only in genetic backgrounds or environmental conditions that increase mistranslation rates.

Strengths:

The strengths of this manuscript are the clever genetic screen, the powerful mistranslation assays, and the clear writing and figures explaining a complex biological problem. Their identification of gidB as a factor important for mistranslation deepens our knowledge about this interesting phenomenon.

Weaknesses:

The structural work at the end feels like both an afterthought in terms of the science and the writing. I would suggest re-writing that section to be clearer about what the figure says and does not say. For example, the caption of Figure 6 appears to be more informative than the text and refers to concepts not present in the main text. In general, I found this section to be the most difficult to understand.

Reviewer #1 (Public review):

This paper focuses on secondary structure and homodimers in the HIV genome. The authors introduce a new method called HiCapR which reveals secondary structure, homodimer, and long-range interactions in the HIV genome. The experimental design and data analysis are well-documented and statistically sound. However, the manuscript could be further improved in the following aspects.

Major comments:

(1) Please give the full name of an abbreviation the first time it appears in the paper, for example, in L37, "5' UTR" "RRE".

(2) The introduction could be strengthened by discussing the limitations of existing methods for studying HIV RNA structures and interactions and highlighting the specific advantages of the HiCapR method.

(3) Please reorganize Results Part 1.

(4) Is there any reason that the authors mention "genome structure of SARS-CoV-2" in L95?

(5) L102: Please clarify the purpose of comparing "NL4-3" and "GX2005002." Additionally, could you explain what NL4-3 and GX2005002 are? The connection between NL4-3, GX2005002, and HIV appears to be missing.

(6) Figure 1A is not able to clearly present the innovation point of HiCapR.

(7) Please compare the contact metrics detected by HiCapR and current techniques like SHAPE on the local interactions to assess the accuracy of HiCapR in capturing local RNA interactions relative to established methods.

(8) The paper needs further language editing.

Reviewer #1 (Public review):

Summary:

This study seeks to identify a molecular mechanism whereby the small molecule RY785 selectively inhibits Kv2.1 channels. Specifically, it sought to explain some of the functional differences that RY785 exhibits in experimental electrophysiology experiments as compared to other Kv inhibitors, namely the charged and non-specific inhibitor tetraethylammonium (TEA). This study used a recently published cryo-EM Kv2.1 channel structure in the open activated state and performed a series of multi-microsecond-long all-atom molecular dynamics simulations to study Kv2.1 channel conduction under the applied membrane voltage with and without RY785 or TEA present. While TEA directly blocks K+ permeation by occluding ion permeation pathway, RY785 binds to multiple non-polar residues near the hydrophobic gate of the channel driving it to a semi-closed non-conductive state. This mechanism was confirmed using an additional set of simulations and used to explain experimental electrophysiology data,

Strengths:

The total length of simulation time is impressive, totaling many tens of microseconds. The study develops forcefield parameters for the RY785 molecule based on extensive QM-based parameterization. The computed permeation rate of K+ ions through the channel observed under applied voltage conditions is in reasonable agreement with experimental estimates of the single-channel conductance. The study performed extensive simulations with the apo channel as well as both TEA and RY785. The simulations with TEA reasonably demonstrate that TEA directly blocks K+ permeation by binding in the center of the Kv2.1 channel cavity, preventing K+ ions from reaching the SCav site. The conclusion is that RY785 likely stabilizes a partially closed conformation of the Kv2.1 channel and thereby inhibits the K+ current. This conclusion is plausible given that RY785 makes stable contact with multiple hydrophobic residues in the S6 helix. This further provides a possible mechanism for the experimental observations that RY785 speeds up the deactivation kinetics of Kv2 channels from a previous experimental electrophysiology study.

Weaknesses:

The study, however, did not produce this semi-closed channel conformation and acknowledges that more direct simulation evidence would require extensive enhanced-sampling simulations. The study has not estimated the effect of RY785 binding on the protein-based hydrophobic pore constriction, which may further substantiate their proposed mechanism. And while the study quantified K+ permeation, it does not make any estimates of the ligand binding affinities or rates, which could have been potentially compared to the experiment and used to validate the models.

Reviewer #1 (Public review):

Summary:

In this paper, the authors have leveraged Single-cell RNA sequencing of the various stages of the evolution of lung adenocarcinoma to identify the population of macrophages that contribute to tumor progression. They show that S100a4+ alveolar macrophages, active in fatty acid metabolic activity, such as palmitic acid metabolism, seem to drive the atypical adenomatous hyperplasia (AAH) stage. These macrophages also seem to induce angiogenesis promoting tumor growth. Similar types of macrophage infiltration were demonstrated in the progression of the human lung adenocarcinomas.

Strengths:

Identification of the metabolic pathways that promote angiogenesis-dependent progression of lung adenocarcinomas from early atypical changes to aggressive invasive phenotype could lead to the development of strategies to abort tumor progression.

Weaknesses:

(1) Can the authors demonstrate what are the functional specialization of the S100a4+ alveolar macrophages that promote the progression of the AAH to the more aggressive phenotype? What are the factors produced by these unique macrophages that induce tumor progression and invasiveness?

(2) Angiogenic factors are not only produced by the S100a4+ cells but also by pericytes and potentially by the tumor cells themselves. Then, how do these factors aberrantly trigger tumor angiogenesis that drives tumor growth?

(3) It is not clear how abnormal fatty acid uptake by the macrophages drives the progression of tumors.

(4) Does infusion or introduction of S100a4+ polarized macrophages promote the progression of AAH to a more aggressive phenotype?

(5) How does Anxa and Ramp1 induction in inflammatory cells induce angiogenesis and tumor progression?

(6) For the in vitro studies the authors might consider using primary tumor cells and not cell lines.

Reviewer #2 (Public review):

Summary:

In this manuscript, the authors consider the effects of eugenol (EUG), a plant-produced substance known to reduce oxidative stress in various cellular contexts via Nrf2, in alleviating the effects of streptozotocin (STZ), a known rodent beta cell toxin. They claim that EUG treatment would be useful for T1D therapy.

Strengths:

The experiments shown are sufficiently clear and rather convincing in documenting that eugenol can revert the effects of streptozotocin on animal physiology as well as beta cell oxidative stress and cell death via activation of Nrf2.

In the revised manuscript the authors corrected/explained most of the specific inconsistencies/mistakes pointed out.

However, they did not address the opening paragraph that points out major concerns. I summarize them below, together with some that were dealt with in their response but still remain unaddressed or not commented upon.

- STZ treatment cannot be used as a T1D model for the reasons I outlined in my previous letter. I would have been happy to see a response on that but they did not provide any. The manuscript is misleading in this important respect.

- Mechanistically, the manuscript remains at a rather superficial level. I highlighted some possibilities to enrich the manuscript but none was addressed even in the discussion.<br /> (a) How is eugenol penetrating the cell, is there a receptor that could be potentially targeted?<br /> (b) Are there intermediary proteins that convey the effect to the Nrf2/Keap1 complex or is eugenol directly disrupting their interaction?<br /> (c) What are direct downstream Nrf2 effectors?<br /> (d) Besides, streptozotocin is also a powerful DNA alkylating agent, are such effects relieved by eugenol?

- It is puzzling that all molecular analyses show a gradual reversion effect with increasing doses of eugenol but this gradual effect is apparently missing in many of the physiological parameters assessed in Figure 1, including the all-important OGTT assays. Can the authors interpret this? In the high eugenol group in the OGTT assays there is a group of mice that are clearly outliers. Most likely the STZ treatment for these mice was not efficient and their inclusion skews the results. Besides, it is important to assess differences among eugenol groups (one way ANOVA). The statistical tests provided are incomplete and sometimes not done correctly.

- Given that medical research is still heavily biased in favor of analyses in males and given that the authors have analyzed in Figure 1 a very large number of animals what are the results stratified by sex?

Reviewer #1 (Public review):

Summary:

It is evident that studying leukocyte extravasation in vitro is a challenge. One needs to include physiological flow, culture cells and isolate primary immune cells. Timing is of utmost importance and a reproducible setup essential. Extra challenges are met when extravasation kinetics in different vascular beds is required, e.g., across the blood-brain barrier. In this study, the authors describe a reliable and reproducible method to analyze leukocyte TEM under physiological flow conditions, including this analysis. That the software can also detect reverse TEM is a plus.

Strengths:

It is quite a challenge to get this assay reproducible and stable, in particular as there is flow included. Also for the analysis, there is currently no clear software analysis program, and many labs have their own methods. This paper gives the opportunity to unify the data and results obtained with this assay under label-free conditions. This should eventually lead to more solid and reproducible results.

Also, the comparison between manual and software analysis is appreciated.

Weaknesses:

The authors stress that it can be done in BBB models, but I would argue that it is much more broadly applicable. This is not necessarily a weakness of the study but more an opportunity to strengthen the method. So I would encourage the authors to rewrite some parts and make it more broadly applicable.

Reviewer #1 (Public Review):

In this manuscript, the authors employed direct RNA sequencing with nanopores, enhanced by 5' end adaptor ligation, to comprehensively interrogate the human transcriptome at single-molecule and nucleotide resolution. They conclude that cellular stress induces prevalent 5' end RNA decay that is coupled to translation and ribosome occupancy. Contrary to the literature, they found that, unlike typical RNA decay models in normal conditions, stress-induced RNA decay is dependent on XRN1 but does not depend on the removal of the poly(A) tail. The findings presented are interesting and the authors fully established these paradigm-shifting findings using cutting-edge technologies.

Reviewer #1 (Public review):

Summary:

The authors report an fMRI investigation of the neural mechanisms by which selective attention allows capacity-limited perceptual systems to preferentially represent task-relevant visual stimuli. Specifically, they examine competitive interactions between two simultaneously-presented items from different categories, to reveal how task-directed attention to one of them modulates the activity of brain regions that respond to both. The specific hypothesis is that attention will bias responses to be more like those elicited by the relevant object presented on its own, and further that this modulation will be stronger for more dissimilar stimulus pairs. This pattern was confirmed in univariate analyses that measured the mass response of a priori regions of interest, as well as multivariate analyses that considered the patterns of evoked activity within the same regions. The authors follow these neuroimaging results with a simulation study that favours a "tuning" mechanism of attention (enhanced responses to highly effective stimuli, and suppression for ineffective stimuli) to explain this pattern.

Strengths:

The manuscript clearly articulates a core issue in the cognitive neuroscience of attention, namely the need to understand how limited perceptual systems cope with complex environments in the service of the observer's goals. The use of a priori regions of interest (and a control region), and the inclusion of both univariate and multivariate analyses as well as a simple model, are further strengths. The authors carefully derive clear indices of attentional effects (for both univariate and multivariate analyses) which makes explication of their findings easy to follow.

Weaknesses:

Direct estimation of baseline responses may have improved the validity of the modelling. The presentation of transparently overlapping items has some methodological advantages, but somewhat limits the ecological validity of connections to real-world visual "clutter".

Reviewer #1 (Public review):

Summary:

This article investigated the relationship between different intensities of exercise training and intestinal barrier dysfunction, and further explores the possible mechanisms, including the contribution of stress response, inflammatory response, gut microbiota alterations, and derived metabolites.

Strengths:

This article mainly focused on different aspects of the phenotypes and the morphology of intestinal barrier dysfunction induced by exercise training.

Weaknesses:

This article lacks the verification of the association of causality among various phenotypes and lacks a comprehensive understanding of the underlying mechanisms of how exercise contributes to intestinal barrier dysfunction.

(1) For example, the author claimed that heat shock and ischemia are the causes of intestinal epithelial damage caused by exercise, and it is not only evidenced by detecting the expression of a few regulators, such as HSF and HSP70 after exercise; and by Immunohistochemical analysis of intestinal morphology and inflammation.

(2) Many kinds of intestinal bacteria could produce short-chain fatty acids, such as Faecalibacterium Prausnitzii, did the authors check their abundance in the intestine after exercise training?

(3) How to define exercise intensity? Was VO2 Max testing used in this study?

(4) As the strict control, it is recommended to set 4 groups of exercise training groups: daily vigorous exercise training, daily moderate exercise training, daily vigorous exercise training with intermittent rest days, and daily moderate exercise training with intermittent rest days.

(5) Are there any differences in diet and metabolism between different groups of mice, which may affect the phenotypes, especially the composition and the the diverstiy of gut microbiota?

Reviewer #1 (Public review):

In this study, Sarver and colleagues carried out an exhaustive analysis of the functioning of various components (Complex I/II/IV) of the mitochondrial electron transport chain (ETC) using a real-time cell metabolic analysis technique (commonly referred as Seahorse oxygen consumption rate (OCR) assay). The authors aimed to generate an atlas of ETC function in about 3 dozen tissue types isolated from all major mammalian organ systems. They used a recently published improvised method by which ETC function can be quantified in freshly frozen tissues. This method enabled them to collect data from almost all organ systems from the same mouse and use many biological replicates (10 mice/experiment) required for an unbiased and statistically robust analysis. Moreover, they studied the influence of sex (male and female) and aging (young adult and old age) on ETC function in these organ systems. The main findings of this study are (1) cells in the heart and kidneys have very active ETC complexes compared to other organ systems, (2) the sex of the mice has little influence on the ETC function, and (3) aging undermined the mitochondrial function in most tissue, but surprisingly in some tissue aging promoted the activity of ETC complexes (e.g., Quadriceps, plantaris muscle, and Diaphragm).

Comments on the second revision:

My previous concern remains unaddressed in the new revision. As I mentioned earlier, it is crucial for the authors to include a detailed discussion on the limitations of their method, specifically how maximal respiration does not accurately reflect the actual ATP production rate. Additionally, the authors should highlight the fact that data provided in the manuscript should be interpreted with caution.

Reviewer #1 (Public review):

Summary:

In this study, the authors used both the commonly used neonatal hyperoxia model as well as cell-type-specific genetic inactivation of Tgfbr2 models to study the basis of BPD. The bulk of the analyses focus on the mesenchymal cells. Results indicate impaired myofibroblast proliferation, resulting in decreased cell number. Inactivation of Etc2 in Pdgfra-lineaged cells, preventing cytokinesis of myofibroblasts, led to alveolar simplification. Together, the findings demonstrate that disrupted myofibroblast proliferation is a key contributor to BPD pathogenesis.

Strengths:

Overall, this comprehensive study of BPD models advances our understanding of the disease. The data are of high quality.

Comments on latest version:

In the revision, the authors addressed all critiques.