Reviewer #3 (Public review):

Summary:

The authors are showing evidence that they claim establishes the controversial epigenetic mark, DNA 6mA, as promoting genome stability.

Strengths:

The identification of a poorly understood protein, METTL3, and its subsequent characterization in DDR is of high quality and interesting.

Weaknesses:

(1) The very presence of 6mA (DNA) in mammalian DNA is still highly controversial and numerous studies have been conclusively shown to have reported the presence of 6mA due to technical artifacts and bacterial contamination. Thus, to my knowledge there is no clear evidence for 6mA as an epigenetic mark in mammals, and consequently, no evidence of writers and readers of 6mA. None of this is mentioned in the introduction. Much of the introduction can be reduced, but a paragraph clearly stating the controversy and lack of evidence for 6mA in mammals needs to be added, otherwise, the reader is given an entirely distorted view of the field.

These concerns must also be clearly in the limitations section and even in the results section which fails to nuance the authors' findings.

(2) What is the motivation for using HT-29 cells? Moreover, the materials and methods do not state how the authors controlled for bacterial contamination, which has been the most common cause of erroneous 6mA signals to date. Did the authors routinely check for mycoplasma?

(3) The single cell imaging of 6mA in various cells is nice. The results are confirmed by mass spec as an orthogonal approach. Another orthogonal and quantitative approach to assessing 6mA levels would be PacBio. Similarly, it is unclear why the authors have not performed dot-blots of 6mA for genomic DNA from the given cell lines.

(4) The results of Figure 3 need further investigation and validation. If the results are correct the authors are suggesting that the majority of 6mA in their cell lines is present in the DNA, and not the RNA, which is completely contrary to every other study of 6mA in mammalian cells that I am aware of. This could suggest that the antibody is not, in fact, binding to 6mA, but to unmodified adenine, which would explain why the signal disappears after DNAse treatment. Indeed, binding of 6mA to unmethylated DNA is a commonly known problem with most 6mA antibodies and is well described elsewhere.

(5) Given the lack of orthologous validation of the observed DNA 6mA and the lack of evidence supporting the presence of 6mA in mammalian DNA and consequently any functional role for 6mA in mammalian biology, the manuscript's conclusions need to be toned down significantly, and the inherent difficulty in assessing 6mA accurately in mammals acknowledged throughout.

Reviewer #3 (Public review):

This manuscript reports a detailed model of the rat non-barrel somatosensory cortex, consisting of 4.2 million morphologically and biophysically detailed neuron models, arranged in space and connected according to highly sophisticated rules informed by diverse experimental data. Due to its breadth and sophistication the model will undoubtedly be of interest to the community, and the reporting of anatomical details of modeling in this paper is important for understanding all the assumptions and procedures involved in constructing the model. While a useful contribution to this field, the model and the manuscript could be improved by employing data more directly and comparing simple features of the model's connectivity - in particular, connection probabilities - with relevant experimental data.

The manuscript is overall well-written, but contains a substantial number of confusing or unclear statements, and some important information is not provided.

Comments on revisions:

The authors mostly addressed all my points and improved the paper substantially. I do not have further extensive comments except one general point below.

Regarding section 2.3 and metrics of connectivity like pairwise connection probabilities, it is great that the authors rewrote that section and added comparisons with experimental data in Figs. 4 and S9. Unfortunately, what one finds when direct comparisons are made is that the modeled pairwise connectivity is quite different from the data. Fig. S9 shows that the model's results do not agree with data in about half of the cases (purple and red arrows). Similarly large discrepancies can be seen for some other metrics, like in Fig. S10B and S10C1,C2. (And similar concerns apply to thalamocortical connections in section 2.5, where it looks like little to no data are available to verify the pairwise connectivity between the thalamic and cortical neurons via a direct comparison.)

This is concerning since this model forms the basis for multiple other studies of cortical dynamics and function by the same group and potentially others in the community, with multiple papers relying on it, whereas basic properties of connectivity are apparently not captured well.

On the other hand, this is also a "glass half full" situation, showing that the sophisticated algorithms for establishing connections, developed by the authors, are working well in at least half of the connection types explored. It is therefore imperative that the authors continue refining these algorithms to capture the remaining half in future iterations and producing improved models that the community can better rely on.

Please also note that Fig. S11 does not have a caption.

Reviewer #3 (Public review):

Summary:

The authors use high-depth, full-length scRNA-Seq analysis of fetal human retina to identify novel regulators of photoreceptor specification and retinoblastoma progression.

Strengths:

The use of high-depth, full-length scRNA-Seq to identify functionally important alternatively spliced variants of transcription factors controlling photoreceptor subtype specification, and identification of SYK as a potential mediator of RB1-dependent cell cycle reentry in immature cone photoreceptors.

Human developing fetal retinal tissue samples were collected between 13-19 gestational weeks and this provides a substantially higher depth of sequencing coverage, thereby identifying both rare transcripts and alternative splice forms, and thereby representing an important advance over previous droplet-based scRNA-Seq studies of human retinal development.

Weaknesses:

The weaknesses identified are relatively minor. This is a technically strong and thorough study, that is broadly useful to investigators studying retinal development and retinoblastoma.

Reviewer #3 (Public review):

Summary:

The submission from Cronshagen and colleagues describes the application of a previously described method (selection linked integration) to the systematic study of PfEMP1 trafficking in the human malaria parasite Plasmodium falciparum. PfEMP1 is the primary virulence factor and surface antigen of infected red blood cells and is therefore a major focus of research into malaria pathogenesis. Since the discovery of the var gene family that encodes PfEMP1 in the late 1990s, there have been multiple hypotheses for how the protein is trafficked to the infected cell surface, crossing multiple membranes along the way. One difficulty in studying this process is the large size of the var gene family and the propensity of the parasites to switch which var gene is expressed, thus preventing straightforward gene modification-based strategies for tagging the expressed PfEMP1. Here the authors solve this problem by forcing the expression of a targeted var gene by fusing the PfEMP1 coding region with a drug-selectable marker separated by a skip peptide. This enabled them to generate relatively homogenous populations of parasites all expressing tagged (or otherwise modified) forms of PfEMP1 suitable for study. They then applied this method to study various aspects of PfEMP1 trafficking.

Strengths:

The study is very thorough, and the data are well presented. The authors used SLI to target multiple var genes, thus demonstrating the robustness of their strategy. They then perform experiments to investigate possible trafficking through PTEX, they knock out proteins thought to be involved in PfEMP1 trafficking and observe defects in cytoadherence, and they perform proximity labeling to further identify proteins potentially involved in PfEMP1 export. These are independent and complimentary approaches that together tell a very compelling story.

Weaknesses:

(1) When the authors targeted IT4var19, they were successful in transcriptionally activating the gene, however, they did not initially obtain cytoadherent parasites. To observe binding to ICAM-1 and EPCR, they had to perform selection using panning. This is an interesting observation and potentially provides insights into PfEMP1 surface display, folding, etc. However, it also raises questions about other instances in which cytoadherence was not observed. Would panning of these other lines have been successfully selected for cytoadherent infected cells? Did the authors attempt panning of their 3D7 lines? Given that these parasites do export PfEMP1 to the infected cell surface (Figure 1D), it is possible that panning would similarly rescue binding. Likewise, the authors knocked out PTP1, TryThrA, and EMPIC3 and detected a loss of cytoadhesion, but they did not attempt panning to see if this could rescue binding. To ensure that the lack of cytoadhesion in these cases is not serendipitous (as it was when they activated IT4var19), they should demonstrate that panning cannot rescue binding.

(2) The authors perform a series of trafficking experiments to help discern whether PfEMP1 is trafficked through PTEX. While the results were not entirely definitive, they make a strong case for PTEX in PfEMP1 export. The authors then used BioID to obtain a proxiome for PfEMP1 and identified proteins they suggest are involved in PfEMP1 trafficking. However, it seemed that components of PTEX were missing from the list of interacting proteins. Is this surprising and does this observation shed any additional light on the possibility of PfEMP1 trafficking through PTEX? This warrants a comment or discussion.

Reviewer #3 (Public review):

The authors aim to understand how gene pleiotropy affects parallel evolutionary changes among independent replicates of adaptation to a new hot environment of a set of experimental lines of Drosophila simulans using experimental evolution. The flies were RNAsequenced after more than 100 generations of lab adaptation and the changes in average gene expression were obtained relative to ancestral expression levels from reconstructed ancestral lines. Parallelism of gene expression change among lines is evaluated as variance in differential gene expression among lines relative to error variance. Similarly, the authors ask how the standing variation in gene expression estimated from a handful of flies from a reconstructed outbred line affects parallelism. The main findings are that parallelism in gene expression responses is positively associated with pleiotropy and negatively associated with expression variation. Those results are in contradiction with theoretical predictions and empirical findings. To explain those seemingly contradictory results the authors invoke the role of synergistic pleiotropy and correlated selection, although they do not attempt to measure either.

Strengths:

(1) The study uses highly replicated outbred laboratory lines of Drosophila simulans evolved in the lab under a constant hot regime for over 100 generations. This allows for robust comparisons of evolutionary responses among lines.

(2) The manuscript is well written and the hypotheses are clearly delineated at the onset.

(3) The authors have run a causal analysis to understand the causal dependencies between pleiotropy and expression variation on parallelism.

(4) The use of whole-body RNA extraction to study gene expression variation is well justified.

Weaknesses:

(1) It is unclear how well phenotypic variation in gene expression of the evolved lines has been estimated by the sample of 20 males from a reconstructed outbred line not directly linked to the evolved lines under study. I see this as a general weakness of the experimental design.

(2) There are no estimates of standing genetic variation of expression levels of the genes under study, only phenotypic variation. I wished the authors had been clear about that limitation and had discussed the consequences of the analysis. This also constitutes a weakness of the study.

(3) Moreover, since the phenotype studied is gene expression, its genetic basis extends beyond expressed sequences. The phenotypic variation of a gene's expression may thus likely misrepresent the genetic variation available for its evolution. The genetic variation of gene expression phenotypes could be estimated from a cross or pedigree information but since individuals were pool-sequenced (by batches of 50 males), this type of analysis is not possible in this study.

(4) The authors have not attempted to estimate synergistic pleiotropy among genes, nor how selection acts on gene expression modules. It makes any conclusion regarding the role of synergistic pleiotropy highly speculative.

I don't understand the reason why the analysis would be restricted to significantly differentially expressed genes only. It is then unclear whether pleiotropy, parallelism, and expression variation do play a role in adaptation because the two groups of adaptive and non-adaptive genes have not been compared. I recommend performing those comparisons to help us better understand how "adaptive" genes differentially contribute to adaptation relative to "non-adaptive" genes relative to their difference in population and genetic properties.

There is a lack of theoretical groundings on the role of so-called synergistic pleiotropy for parallel genetic evolution. The Discussion does not address this particular prediction. It could be removed from the Introduction.

Reviewer #3 (Public review):

Summary:

Heterochromatin is characterized by low transcription activity and late replication timing, both dependent on the NAD-dependent protein deacetylase Sir2, the founding member of the sirtuins. This manuscript addresses the mechanism by which Sir2 delays replication timing at the rDNA in budding yeast. Previous work from the same laboratory (Foss et al. PLoS Genetics 15, e1008138) showed that Sir2 represses transcription-dependent displacement of the Mcm helicase in the rDNA. In this manuscript, the authors show convincingly that the repositioned Mcms fire earlier and that this early firing partly depends on the ATPase activity of the nucleosome remodeler Fun30. Using read-depth analysis of sorted G1/S cells, fun30 was the only chromatin remodeler mutant that somewhat delayed replication timing in sir2 mutants, while nhp10, chd1, isw1, htl1, swr1, isw2, and irc5 had no effect. The conclusion was corroborated with orthogonal assays including two-dimensional gel electrophoresis and analysis of EdU incorporation at early origins. Using an insightful analysis with an Mcm-MNase fusion (Mcm-ChEC), the authors show that the repositioned Mcms in sir2 mutants fire earlier than the Mcm at the normal position in wild type. This early firing at the repositioned Mcms is partially suppressed by Fun30. In addition, the authors show Fun30 affects nucleosome occupancy at the sites of the repositioned Mcm, providing a plausible mechanism for the effect of Fun30 on Mcm firing at that position. However, the results from the MNAse-seq and ChEC-seq assays are not fully congruent for the fun30 single mutant. Overall, the results support the conclusions providing a much better mechanistic understanding how Sir2 affects replication timing at rDNA,

Strengths:

(1) The data clearly show that the repositioned Mcm helicase fires earlier than the Mcm in the wild type position.

(2) The study identifies a specific role for Fun30 in replication timing and an effect on nucleosome occupancy around the newly positioned Mcm helicase in sir2 cells.

Comments on revisions:

In the previous revision the authors addressed my concerns and improved the manuscript and the presentation of the data. All my recommendations were implemented.

Reviewer #3 (Public review):

Significance:

About 5% of metastatic castration-resistant prostate cancers (mCRPC) display genomic alterations in the transcriptional kinase CDK12. The mechanisms by which CDK12 alterations drive tumorigenesis in this molecularly-defined subset of mCRPC have remained elusive. In particular, some studies have suggested that CDK12 loss confers a homologous recombination deficiency (HRd) phenotype, However, clinical studies have not borne out the benefit to PARP inhibitors in patients with CDK12 alterations, despite the fact that these agents are typically active against tumors with HRd.

In this study, Frank et al. reconcile these findings by showing that: (1) tumors with biallelic CDK12 alterations do not have genomic features of HRd; (2) in vitro, HR gene downregulation occurs with acute depletion of CDK12 but is far less pronounced with chronic CDK12 loss; (3) CDK12-altered cells are uniquely sensitive to genetic or pharmacologic inhibition of CDK13.

Strengths:

Overall, this is an important study that reconciles disparate experimental and clinical observations. The genomic analyses are comprehensive and conducted with a high degree of rigor and represent an important resource to the community regarding the features of this molecular subtype of mCRPC.

Weaknesses:

(1) It is generally assumed that CDK12 alterations are inactivating, but it is noteworthy that homozygous deletions are comparatively uncommon (Figure 1a). Instead many tumors show missense mutations on either one or both alleles, and many of these mutations are outside of the kinase domain (Figure 1b). It remains possible that the CDK12 alterations that occur in some tumors may retain residual CDK12 function, or may confer some other neomorphic function, and therefore may not be accurately modeled by CDK12 knockout or knockdown in vitro. This would also reconcile the observation that knockout of CDK12 is cell-essential while the human genetic data suggest that CDK12 functions as a tumor suppressor gene.

(2) It is not entirely clear whether CDK12 altered tumors may require a co-occurring mutation to prevent loss of fitness, either in vitro or in vivo (e.g. perhaps one or more of the alterations that occur as a result of the TDP may mitigate against the essentiality of CDK12 loss).

Reviewer #4 (Public review):

Summary:

Li and Chouhan et al. follow up on a previous publication describing the role of anterior-posterior (ap) and medial (m) ɑ′/β′ Kenyon cells in mediating sleep-dependent and sleep-independent memory consolidation, respectively, based on feeding state in Drosophila melanogaster. The authors sequenced bulk RNA of ap ɑ′/β′ Kenyon cells 1h after flies were either trained-fed, trained-starved or untrained-fed and find a small number of genes (59) differentially expressed (3 upregulated, 56 downregulated) between trained-fed and trained-starved conditions. Many of these genes encode proteins involved in the regulation of gene expression. The authors then screened these differentially expressed genes for sleep phenotypes by expressing RNAi hairpins constitutively in ap ɑ′/β′ Kenyon cells and measuring sleep patterns. Two hits were selected for further analysis: Polr1F, which promoted sleep, and Regnase-1, which reduced sleep. The pan-neuronal expression of Polr1F and Regnase-1 RNAi constructs was then temporally restricted to adult flies using the GeneSwitch system. Polr1F sleep phenotypes were still observed, while Regnase-1 sleep phenotypes were not, indicating developmental defects. Appetitive memory was then assessed in flies with constitutive knockdown of Polr1F and Regnase-1 in ap ɑ′/β′ Kenyon cells. Polr1F knockdown did not affect sleep-dependent or sleep-independent memory, while Regnase-1 knockdown disrupted sleep-dependent memory, sleep-independent memory, as well as learning. Polr1F knockdown increased pre-ribosomal RNA transcripts in the brain, as measured by qPCR, in line with its predicted role as part of the RNA polymerase I complex. A puromycin incorporation assay to fluorescently label newly synthesized proteins also indicated higher levels of bulk translation upon Polr1F knockdown. Regnase-1 knockdown did not lead to observable changes in measurements of bulk translation.

Strengths:

The proposed involvement of RNA processing genes in regulating sleep and memory processes is interesting, and relatively unexplored. The methods are satisfactory.

Weaknesses:

The main weakness of previous versions of the paper was the over-interpretation of results, particularly relating to the proposed link between sleep and memory consolidation. This has now been appropriately addressed, as reflected in the change of title and incorporation of alternative interpretations of the data in the text.

Reviewer #3 (Public review):

Yan et al. ("When do visual category representations emerge in infant brains?") present an EEG study of category-specific visual responses in infancy from 3 to 15 months of age. In their experiment, infants viewed visually controlled images of faces and several non-face categories in a steady state evoked potential paradigm. The authors find visual responses at all ages, but face responses only at 4-6 months and older, and other category-selective responses at later ages. They find that spatiotemporal patterns of response can discriminate faces from other categories at later ages.

Overall, I found the study well-executed and a useful contribution to the literature. The study advances prior work by using well-controlled stimuli, subgroups at different ages, and new analytic approaches. The data and analyses support their conclusions regarding developmental change in neural responses to high-level visual stimuli.

Reviewer #3 (Public review):

Summary:

Non-opioid analgesics derived from human amniotic membrane (AM) product represents a novel and unique approach to analgesia that may avoid the traditional harms associated with opioids. Here, the study investigators demonstrate that HC-HAPTX3 is the primary bioactive component of the AM product FLO responsible for anti-nociception in mouse-model and in-vitro dorsal root ganglion (DRG) cell culture experiments. The mechanism is demonstrated to be via CD44 with an acute cytoskeleton rearrangement that is induced that inhibits Na+ and Ca++ current through ion channels. Taken together, the studies reported in the manuscript provide supportive evidence clarifying the mechanisms and efficacy of HC-HAPTX3 antinociception and analgesia.

Strengths:

Extensive experiments including murine behavioral paw withdrawal latency and Catwalk test data demonstrating analgesic properties. Breadth and depth of experimental data are clearly supporting mechanisms and antinociceptive properties.

Weaknesses:

None. Only a few minor directed changes to the text of the manuscript.<br /> P4 last sentence - "Our findings highlight the potential of a naturally derived biologic from human birth tissues as an effective non-opioid treatment for post-surgical pain and unravel the underlying mechanisms." - another sentence clause is required before "unravel"<br /> P7 second paragraph - please edit the following sentence for clarity: "Since HC-HA/PTX3 mimics FLO in producing pain inhibition, and it has high-purity and is more water-soluble than FLO, making it suitable for probing cellular mechanisms."

Reviewer #3 (Public review):

Summary:

In the study presented by Burnicka-Turek et al., the authors generated for the first time a mouse model to cause the combined conditional deletion of Tbx3 and Tbx5 genes. This has been impossible to achieve to date due to the proximity of these genes in chromosome 5, preventing the generation of loss of function strategies to delete simultaneously both genes. It is known that both Tbx3 and Tbx5 are required for the development of the cardiac conduction system by transcription factor-specific but also overlapping roles as seen in the common and diverse cardiac defects found in patients with mutations for these genes. After validating the deletion efficiency and specificity of the line, the authors characterised the cardiac phenotype associated with the cardiac conduction system (CCS)-specific combined deletion of Tbx5 and Tbx3 in the adult by inducing the activation of the CCS-specific tamoxifen-inducible Cre recombination (MinK-creERT) at 6 weeks after birth. Their analysis of 8-9-week-old animals did not identify any major morphological cardiac defects. However, the authors found conduction defects including prolonged PR and QTR intervals and ventricular tachycardia causing the death of the double mutants, which do not survive more than 3 months after tamoxifen induction. Molecular and optical mapping analysis of the ventricular conduction system (VCS) of these mutants concluded that, in the absence of Tbx5 and Tbx3 function, the cells forming the ventricular conduction system (VCS) become working myocardium and lose the specific contractile features characterising VCS cells. Altogether, the study identified the critical combined role of Tbx3 and Tbx5 in the maintenance of the VCS in adulthood.

Strengths:

The study generated a new animal model to study the combined deletion of Tbx5 and Tbx3 in the cardiac conduction system. This unique model has provided the authors with the perfect tool to answer their biological questions. The study includes top-class methodologies to assess the functional defects present in the different mutants analysed, and gathered very robust functional data on the conduction defects present in these mutants. They also applied optical action potential (OAP) methods to demonstrate the loss of conduction action potential and the acquisition of working myocardium action potentials in the affected cells because of Tbx5/Tbx3 loss of function. The study used simpler molecular and morphological analysis to demonstrate that there are no major morphological defects in these mutants and that indeed, the conduction defects found are due to the acquisition of working myocardium features by the VCS cells. Altogether, this study identified the critical role of these transcription factors in the maintenance of the VCS in the adult heart.

Weaknesses:

In the opinion of this reviewer, the weakness in the study lies in the morphological and molecular characterization. The morphological analysis simply described the absence of general cardiac defects in the adult heart, however, whether the CCS tissues are present or not was not investigated. Lineage tracing analysis using the reporter lines included in the crosses described in the study will determine if there are changes in CCS tissue composition in the different mutants studied. Similarly, combining this reporter analysis with the molecular markers found to be dysregulated by qPCR and western blot, will demonstrate that indeed the cells that were specified as VCS in the adult heart, become working myocardium in the absence of Tbx3 and Tbx5 function.

Reviewer #3 (Public review):

Summary:

The manuscript by Patel et al investigates the hypothesis that CDHR1a on photoreceptor outer segments is the binding partner for PCDH15 on the calyceal processes, and the absence of either adhesion molecule results in separation between the two structures, eventually leading to degeneration. PCDH15 mutations cause Usher syndrome, a disease of combined hearing and vision loss. In the ear, PCDH15 binds CDH23 to form tip links between stereocilia. The vision loss is less understood. Previous work suggested PCDH15 is localized to the calyceal processes, but the expression of CDH23 is inconsistent between species. Patel et al suggest that CDHR1a (formerly PCDH21) fulfills the role of CDH23 in the retina.

The experiments are mainly performed using the zebrafish model system. Expression of Pcdh15b and Cdhr1a protein is shown in the photoreceptor layer through standard confocal and structured illumination microscopy. The two proteins co-IP and can induce aggregation in vitro. Loss of either Cdhr1a or Pcdh15, or both, results in degeneration of photoreceptor outer segments over time, with cones affected primarily.

The idea of the study is logical given the photoreceptor diseases caused by mutations in either gene, the comparisons to stereocilia tip links, and the protein localization near the outer segments. The work here demonstrates that the two proteins interact in vitro and are both required for ongoing outer segment maintenance. The major novelty of this paper would be the demonstration that Pcdh15 localized to calyceal processes interacts with Cdhr1a on the outer segment, thereby connecting the two structures. Unfortunately, the data presented are inadequate proof of this model.

Strengths:

The in vitro data to support the ability of Pcdh15b and Cdhr1a to bind is well done. The use of pcdh15b and cdhr1a single and double mutants is also a strength of the study, especially being that this would be the first characterization of a zebrafish cdhr1a mutant.

Weaknesses:

(1) The imaging data in Figure 1 is insufficient to show the specific localization of Pcdh15 to calyceal processes or Cdhr1a to the outer segment membrane. The addition of actin co-labelling with Pcdh15/Cdhr1a would be a good start, as would axial sections. The division into rod and cone-specific imaging panels is confusing because the two cell types are in close physical proximity at 5 dpf, but the cone Cdhr1a expression is somehow missing in the rod images. The SIM data appear to be disrupted by chromatic aberration but also have no context. In the zebrafish image, the lines of Pcdh15/Cdhr1a expression would be 40-50 um in length if the scale bar is correct, which is much longer than the outer segments at this stage and therefore hard to explain.

(2) Figure 3E staining of Cdhr1a looks very different from the staining in Figure 1. It is unclear what the authors are proposing as to the localization of Cdhr1a. In the lab's previous paper, they describe Cdhr1a as being associated with the connecting cilium and nascent OS discs, and fail to address how that reconciles with the new model of mediating CP-OS interaction. And whether Cdhr1a localizes to discrete domains on the disc edges, where it interacts with Pcdh15 on individual calyceal processes.

(3) The authors state "In PRCs, Pcdh15 has been unequivocally shown to be localized in the CPs". However, the immunostaining here does not match the pattern seen in the Miles et al 2021 paper, which used a different antibody. Both showed loss of staining in pcdh15b mutants so unclear how to reconcile the two patterns.

(4) The explanation for the CRISPR targets for cdhr1a and the diagram in Figure 3 does not fit with crRNA sequences or the mutation as shown. The mutation spans from the latter part of exon 5 to the initial portion of exon 6, removing intron 5-6. It should nevertheless be a frameshift mutation but requires proper documentation.

(5) There are complications with the quantification of data. First, the number of fish analyzed for each experiment is not provided, nor is the justification for performing statistics on individual cell measurements rather than using averages for individual fish. Second, all cone subtypes are lumped together for analysis despite their variable sizes. Third, t-tests are inappropriately used for post-hoc analysis of ANOVA calculations.

(6) Unclear how calyceal process length is being measured. The cone measurements are shown as starting at the external limiting membrane, which is not equivalent to the origin of calyceal processes, and it is uncertain what defines the apical limit given the multiple subtypes of cones. In Figure 5, the lines demonstrating the measurements seem inconsistently placed.

(7) The number of fish analyzed by TEM and the prevalence of the phenotype across cells are not provided. A lower magnification view would provide context. Also, the authors should explain whether or not overgrowth of basal discs was observed, as seen previously in cdhr1-null frogs (Carr et al., 2021).

(8) The statement describing the separation between calyceal processes and the outer segment in the mutants is not backed up by the data. TEM or co-labelling of the structures in SIM could be done to provide evidence.

(9) "Based on work in the murine model and our own observations of rod CPs, we hypothesize that zebrafish rod CPs only extend along the newly forming OS discs and do not provide structural support to the ROS." Unclear how murine work would support that conclusion given the lack of CPs in mice, or what data in the manuscript supports this conclusion.

(10) The authors state "from the fact that rod CPs are inherently much smaller than cone CPs" without providing a reference. In the manuscript, the measurements do show rod CPs to be shorter, but there are errors in the cone measurements, and it is possible that the RPE pigment is interfering with the rod measurements.

(11) The discussion should include a better comparison of the results with ocular phenotypes in previously generated pcdh15 and cdhr1 mutant animals.

(12) The images in panels B-F of the Supplemental Figure are uncannily similar, possibly even of the same fish at different focal planes.

Reviewer #3 (Public review):

Summary:

Transcriptionally silent HIV-1 genomes integrated into the host`s genome represent the main obstacle to an HIV-1 cure. Therefore, agents aimed at promoting HIV transcription, the so-called latency reactivating agents (LRAs) might represent useful tools to render these hidden proviruses visible to the immune system. The authors successfully identified, through multiple techniques, INTS12, a component of the Integrator complex involved in 3' processing of small nuclear RNAs U1 and U2, as a factor promoting HIV-1 latency and hindering elongation of the HIV RNA transcripts. This factor synergizes with a previously identified combination of LRAs, one of which, AZD5582, has been validated in the macaque model for HIV persistence during therapy (https://pubmed.ncbi.nlm.nih.gov/37783968/). The other compound, I-BET151, is known to synergize with AZD5582, and is a inhibitor of BET, factors counteracting the elongation of RNA transcripts.

Strengths:

The findings were confirmed through multiple screens and multiple techniques. The authors successfully mapped the identified HIV silencing factor at the HIV promoter.

Weaknesses:

(1) Initial bias:<br /> In the choice of the genes comprised in the library, the authors readdress their previous paper (Hsieh et al.) where it is stated: "To specifically investigate host epigenetic regulators involved in the maintenance of HIV-1 latency, we generated a custom human epigenome specific sgRNA CRISPR library (HuEpi). This library contains sgRNAs targeting epigenome factors such as histones, histone binders (e.g., histone readers and chaperones), histone modifiers (e.g., histone writers and erasers), and general chromatin associated factors (e.g., RNA and DNA modifiers) (Fig 1B and 1C)".

From these figure panels, it clearly appears that the genes chosen are all belonging to the indicated pathways. While I have nothing to object to on the pertinence to HIV latency of the pathways selected, the authors should spend some words on the criteria followed to select these pathways. Other pathways involving epigenetic modifications and containing genes not represented in the indicated pathways may have been left apart.

(2) Dereplication:<br /> From Figure 1 it appears that INTS12 alone reactivates HIV -1 from latency alone without any drug intervention as shown by the MACGeCk score of DMSO-alone controls. If INTS12 knockdown alone shows antilatency effects, why, then were they unable to identify it in their previous article (Hsieh et al., 2023)? The authors should include some words on the comparison of the results using DMSO alone with those of the previous screen that they conducted.

(3) Translational potential:<br /> In order to propose a protein as a drug target, it is necessary to adhere to the "primum non nocere" principle in medicine. It is therefore fundamental to show the effects of INTS12 knockdown on cell viability/proliferation (and, advisably, T-cell activation). These data are not reported in the manuscript in its current form, and the authors are strongly encouraged to provide them.

Finally, as many readers may not be very familiar with the general principles behind CRISPR Cas9 screening techniques, I suggest addressing them in this excellent review: https://pmc.ncbi.nlm.nih.gov/articles/PMC7479249/.

Reviewer #3 (Public review):

In this manuscript, Fang et al. describe a new oncogenic function of the STAMBPL1 protein in triple-negative breast cancer (TNBC). STAMBPL1 is a deubiquitinase that has been poorly studied in cancer. Previous reports identify it as a promoter of epithelial to mesenchymal transition or an inhibitor of cisplatin-induced cell death, but its participation to other cancer phenotypes has not been investigated. Fang et al. find that in cell line models of TNBC, STAMBPL1 promotes expression of the transcription factor HIF-1a and its downstream target VEGF, with the consequence of stimulating neo-angiogenesis in vitro and in vivo. Mechanistically, the authors find that this occurs via a non-enzymatic and indirect mechanism, that is by promoting the expression of GRHL3, a transcription factor that in turn binds to the HIF-1a promoter to stimulate its transcription. Interestingly, the way by which STAMPB1 promotes GRHL3 expression is by facilitating the transcriptional activity of FOXO1, a known regulator of GRHL3. Because the authors find that STAMBPL1 and FOXO1 interact, they suggest that STAMBPL1 may promote the formation of an active transcriptional complex containing FOXO1, perhaps by facilitating the recruitment of transcriptional coactivators.<br /> In conclusion, these data position for the first time the STAMBPL1 deubiquitinase in a FOXO-GRHL3 regulatory axis for the control of VEGF expression and tumor angiogenesis.<br /> The main weaknesses of this work are that the relevance of this molecular axis to the pathogenesis of TNBC is not clear, and it is not clearly established whether this is a regulatory pathway that occurs in hypoxic conditions or independently of oxygen levels.<br /> With respect to the first point, both FOXO1 and GRHL3 have been previously described as tumor suppressors, with reports of FOXO1 inhibiting tumor angiogenesis. Therefore, this works describes an apparently contradictory function of these proteins in TNBC. While it is not surprising that the same genes perform divergent functions in different tumor contexts, a stronger evidence in support of the oncogenic function of these two genes should be provided to make the data more convincing. As an example, the data in support of high STAMBPL1, FOXO and GRHL3 gene expression in TNBC TCGA specimens provided in Figure 8 is not very strong and it is not clear what the non-TNBC specimens are (whether other breast cancers or other tumors, perhaps those tumors whether these genes perform tumor suppressive functions). To strengthen the notion that STAMBPL1, FOXO and GRHL3 are overexpressed in TNCB, the authors could provide a comparison with normal tissue, as well as the analysis of other publicly available datasets (like the NCI Clinical Proteomic Tumor Analysis Consortium as an example). Finally, is it not clear what are the basal protein expression levels of STAMBPL1 in the cell lines used in this study, as based on the data presented in Figures 2D and F it appears that the protein is not expressed if not exogenously overexpressed. It would be helpful if the authors addressed this issue and provided further evidence of STAMBPL1 expression in TNBC cell lines.<br /> Linked to these considerations is the second major criticism, namely that it is not made clear if this new regulatory axis is proposed to act in normoxic or hypoxic conditions. The experiments presented in this paper are performed in both conditions but a clear explanation as to why cells are exposed to hypoxia is not given and would be necessary being that HIF-1a transcription and not protein stability is being analyzed. Also, different hypoxic conditions are sometimes used, resulting in different mRNA levels of HIF-1a and its downstream targets and quite significant fluctuations within the same cell line from one experimental setting to the next. The authors should provide an explanation as to why experimental conditions are changed and, more importantly, the experiments presented in Figure 2 should be performed also in normoxia.<br /> Another critical point is that necessary experimental controls are sometimes missing, and this is reducing the strength of some of the conclusions enunciated by the authors. As examples, experiments where overexpression of STAMBPL1 is coupled to silencing of FOXO1 to demonstrate dependency lack FOXO1silencing the absence of STAMBPL1 overexpression. Because diminishing FOXO1 expression affects HIF-1a/VEGF transcription even in the absence of STAMBPL1 (shown in Figure 7C, D), it is not clear if the data presented in Figure 7G are significant. The difference between HIF-1a expression upon FOXO1 silencing should be compared in the presence or absence of STAMBPL1 overexpression to understand if FOXO1 impacts HIF-1a transcription dependently or independently of STAMBPL1.

In addition, some minor comments to improve the quality of this manuscript are provided.<br /> (1) As a general statement, the manuscript is extremely synthetic. While this is not necessarily a negative feature, sometimes results are discussed in the figure legends and not in the main text (as an example, western blots showing HIF-1a expression) and this makes it hard to read thought the data in an easy and enjoyable manner.<br /> (2) The effect of STAMBPL1 overexpression on HIF-1a transcription is minor (Figure 2) The authors should explain why they think this is the case and whether hypoxia may provide a molecular environment that is more permissive to this type of regulation.<br /> (3) HIF-1a does not appear upregulated at the protein level protein by STAMBPL1 or GRLH3 overexpression, even though this is stated in the legends of Figures 2 and 6. The authors should show unsaturated western blots images and provide quantitative data of independent experiments to make this point.<br /> In summary, adding necessary controls and performing additional experiments to substantiate the oncogenic function of these genes in TNCB would strengthen the authors' conclusions.

Reviewer #3 (Public review):

In this manuscript, the authors examine circulating and bone parameters in patients with T2DM or obesity vs control subjects. Based on their findings they conclude that increased inflammation in bone of subjects with T2DM and obesity is negatively correlated with Wnt pathway signaling and bone strength.

Overall, this is a well done clinical study that provides further insights into the pathogenesis of bone loss associated with T2DM. However, there are a number of issues that the authors should address:

(1) The major conceptual problem is that the alterations in circulating and bone factors they observed would predominantly affect bone turnover and thus, bone mass. But bone mass is preserved in T2DM (as their own data show). They postulate that their findings lead to impaired bone quality, but it is not clear how this would occur. For example, the impairment in bone quality could be due to the accumulation of AGEs in bone in T2DM, and the correlations observed be true but unrelated. Along these lines, were serum or bone AGEs measured - and if not, is it possible for the authors to do so? At the least, this issue should be fully addressed in the Discussion if the authors are unable to provide additional data to address this.

(2) The T2DM patients were extremely well controlled. This may have limited some of the differences between groups. Was it not possible to select a group of less well-controlled patients - that is more the norm? This may also explain why the biomechanical indices in Table 3 were only marginally different in the T2DM vs the other groups. This point should also be addressed.

(3) The authors found some interesting differences in bone sclerostin levels. Were circulating sclerostin levels measured? This data would be of interest and should be provided.

(4) Fig 4A - the correlation between TNFa and SOST seems to be driven by one highly influential point. What happens if this point is removed? Is this point a formal statistical outlier? Please check this.

Reviewer #3 (Public review):

This paper addresses through experiment and simulation the combined effects of bacterial circular swimming near no-slip surfaces and chemotaxis in simple linear gradients. The authors have constructed a microfluidic device in which a gradient of L-aspartate is established to which bacteria respond while swimming while confined in channels of different widths. There is a clear effect that the chemotactic drift velocity reaches a maximum in channel widths of about 8 microns, similar in size to the circular orbits that would prevail in the absence of side walls. Numerical studies of simplified models confirm this connection.

The experimental aspects of this study are well executed. The design of the microfluidic system is clever in that it allows a kind of "multiplexing" in which all the different channel widths are available to a given sample of bacteria.

While the data analysis is reasonably convincing, I think that the authors could make much better use of what must be voluminous data on the trajectories of cells by formulating the mathematical problem in terms of a suitable Fokker-Planck equation for the probability distribution of swimming directions. In particular, I would like to see much more analysis of how incipient circular trajectories are interrupted by collisions with the walls and how this relates to enhanced chemotaxis. In essence, there needs to be a much clearer control analysis of trajectories without sidewalls to understand the mechanism in their presence.

The authors argue that these findings may have relevance to a number of physiological and ecological contexts. Yet, each of these would be characterized by significant heterogeneity in pore sizes and geometries, and thus it is very unclear whether or how the findings in this work would carry over to those situations.

Reviewer #3 (Public review):

Hong et al. used a model they previously developed to study the impact of horizontal gene transfer (HGT) on microbial multispecies communities. They investigated the effect of HGT on the existence of alternative stable states in a community. The model most closely resembles HGT through the conjugation of incompatible plasmids, where the transferred genes confer independent growth-related fitness effects. For this type of HGT, the authors find that increasing the rate of HGT leads to an increasing number of stable states. This effect of HGT persists when the model is extended to include multiple competitive niches (under a shared carrying capacity) or spatially distinct patches (that interact in a grid-like fashion). Instead, if the mobile gene is assumed to reduce between-species competition, increasing HGT leads to a smaller region of multistability and fewer stable states. Similarly, if the mobile gene is deleterious an increase in HGT reduces the parameter region that supports multistability.

This is an interesting and important topic, and I welcome the authors' efforts to explore these topics with mathematical modeling. The manuscript is well written and the analyses seem appropriate and well-carried out. However, I believe the model is not as general as the authors imply and more discussion of the assumptions would be helpful (both to readers + to promote future theoretical work on this topic). Also, given the model, it is not clear that the conclusions hold quite so generally as the authors claim and for biologically relevant parameters. To address this, I would recommend adding sensitivity analyses to the manuscript.

Specific points

(1) The model makes strong assumptions about the biology of HGT, that are not adequately spelled out in the main text or methods, and will not generally prove true in all biological systems. These include:<br /> a) The process of HGT can be described by mass action kinetics. This is a common assumption for plasmid conjugation, but for phage transduction and natural transformation, people use other models (e.g. with free phage that adsorp to all populations and transfer in bursts).<br /> b) A subpopulation will not acquire more than one mobile gene, subpopulations can not transfer multiple genes at a time, and populations do not lose their own mobilizable genes. [this may introduce bias, see below].<br /> c) The species internal inhibition is independent of the acquired MGE (i.e. for p1 the self-inhibition is by s1).<br /> These points are in addition to the assumptions explored in the supplementary materials, regarding epistasis, the independence of interspecies competition from the mobile genes, etc. I would appreciate it if the authors could be more explicit in the main text about the range of applicability of their model, and in the methods about the assumptions that are made.

(2) I am not surprised that a mechanism that creates diversity will lead to more alternative stable states. Specifically, the null model for the absence of HGT is to set gamma to zero, resulting in pij=0 for all subpopulations (line 454). This means that a model with N^2 classes is effectively reduced to N classes. It seems intuitive that an LV-model with many more species would also allow for more alternative stable states. For a fair comparison, one would really want to initialize these subpopulations in the model (with the same growth rates - e.g. mu1(1+lambda2)) but without gene mobility.

(3) I am worried that the absence of double gene acquisitions from the model may unintentionally promote bistability. This assumption is equivalent to an implicit assumption of incompatibility between the genes transferred from different species. A highly abundant species with high HGT rates could fill up the "MGE niche" in a species before any other species have reached appreciable size. This would lead to greater importance of initial conditions and could thus lead to increased multistability.

This concern also feels reminiscent of the "coexistence for free" literature (first described here http://dx.doi.org/10.1016/j.epidem.2008.07.001 ) which was recently discussed in the context of plasmid conjugation models in the supplementary material (section 3) of https://doi.org/10.1098/rstb.2020.0478 .

(4) The parameter values tested seem to focus on very large effects, which are unlikely to occur commonly in nature. If I understand the parameters in Figure 1b correctly for instance, lambda2 leads to a 60% increase in growth rate. Such huge effects of mobile genes (here also assumed independent from genetic background) seem unlikely except for rare cases. To make this figure easier to interpret and relate to real-world systems, it could be worthwhile to plot the axes in terms of the assumed cost/benefit of the mobile genes of each species.

Something similar holds for the HGT rate (eta): given that the population of E. coli or Klebsiella in the gut is probably closer to 10^9 than 10^12 (they make up only a fraction of all cells in the gut), the assumed rates for eta are definitely at the high end of measured plasmid transfer rates (e.g. F plasmid transfers at a rate of 10^-9 mL/CFU h-1, but it is derepressed and considered among the fastest - https://doi.org/10.1016/j.plasmid.2020.102489 ). To adequately assess the impact of the HGT rate on microbial community stability it would need to be scanned on a log (rather than a linear) scale. Considering the meta-analysis by Sheppard et al. it would make sense to scan it from 10^-7 to 1 for a community with a carrying capacity around 10^9.

(5) It is not clear how sensitive the results (e.g. Figure 2a on the effect of HGT) are to the assumption of the fitness effect distribution of the mobile genes. This is related to the previous point that these fitness effects seem quite large. I think some sensitivity analysis of the results to the other parameters of the simulation (also the assumed interspecies competition varies from figure to figure) would be helpful to put the results into perspective and relate them to real biological systems.

Reviewer #3 (Public review):

Summary:

In this manuscript, the authors have used a combination of enzymatic, crystallographic, and in silico approaches to provide compelling evidence for substrate selectivity of SARS-CoV-2 Mpro for human TRMT1.

Strengths:

In my opinion, the authors came close to achieving their intended aim of demonstrating the structural and biochemical basis of Mpro catalysis and cleavage of human TRMT1 protein. The revised version of the manuscript has addressed most of the questions I had posed in my earlier review.

Weaknesses:

Although several new hypotheses are generated from the Mpro structural data, the manuscript falls a bit short of testing them in functional assays, which would have solidified the conclusions the authors have drawn.

Reviewer #3 (Public review):

In the report entitled "CXXC-finger protein 1 associates with FOXP3 to stabilize homeostasis and suppressive functions of regulatory T cells", the authors demonstrated that Cxxc1-deletion in Treg cells leads to the development of severe inflammatory disease with impaired suppressive function. Mechanistically, CXXC1 interacts with Foxp3 and regulates the expression of key Treg signature genes by modulating H3K4me3 deposition. Their findings are interesting and significant. However, there are several concerns regarding their analysis and conclusions.

Major concerns:

(1) Despite cKO mice showing an increase in Treg cells in the lymph nodes and Cxxc1-deficient Treg cells having normal suppressive function, the majority of cKO mice died within a month. What causes cKO mice to die from severe inflammation?

Considering the results of Figures 4 and 5, a decrease in Treg cell population due to their reduced proliferative capacity may be one of the causes. It would be informative to analyze the population of tissue Treg cells.

(2) In Figure 5B, scRNA-seq analysis indicated that Mki67+ Treg subset are comparable between WT and Cxxc1-deficient Treg cells. On the other hand, FACS analysis demonstrated that Cxxc1-deficient Treg shows less Ki-67 expression compared to WT in Figure 5I. The authors should explain this discrepancy.

In addition, the authors concluded on line 441 that CXXC1 plays a crucial role in maintaining Treg cell stability. However, there appears to be no data on Treg stability. Which data represent the Treg stability?

(3) The authors found that Cxxc1-deficient Treg cells exhibit weaker H3K4me3 signals compared to WT in Figure 7. This result suggests that Cxxc1 regulates H3K4me3 modification via H3K4 methyltransferases in Treg cells. The authors should clarify which H3K4 methyltransferases contribute to the modulation of H3K4me3 deposition by Cxxc1 in Treg cells.

Furthermore, it would be important to investigate whether Cxxc1-deletion alters Foxp3 binding to target genes.

(4) In Figure 7, the authors concluded that CXXC1 promotes Treg cell homeostasis and function by preserving the H3K4me3 modification since Cxxc1-deficient Treg cells show lower H3K4me3 densities at the key Treg signature genes. Are these Cxxc1-deficient Treg cells derived from mosaic mice? If Cxxc1-deficient Treg cells are derived from cKO mice, the gene expression and H3K4me3 modification status are inconsistent because scRNA-seq analysis indicated that expression of these Treg signature genes was increased in Cxxc1-deficient Treg cells compared to WT (Figure 5F and G).

Reviewer #4 (Public Review):

In this work, Tee et al. study the implications of Heparan Sulfate (HS) binding mutations observed on the Enterovirus A71 (EV-A71) capsid. HS-binding mutations are observed for several virus infections and are often presumed to be a cell culture adaptation. However, in the case of EV-A71, the presence of HS-binding mutations in clinical samples and the contradictory findings in animal studies have made the clinical relevance of HS-binding a subject of debate. Therefore, to better understand the role of HS-binding in EV-A71, the authors use a mouse-adapted EV-A71 variant (MP4) and compare it to a cell-adapted strong HS-binder (MP4-97R/167G). Using these two variants, the authors show that the strong HS-binder does not require acidification for uncoating and genome release. Furthermore, it is demonstrated that the capsid stability of the HS-binding variant is compromised, resulting in pH-independent uncoating. Overall, this study provides new insights demonstrating that seemingly beneficial mutations increasing viral replication may be counterbalanced by other unintended consequences.

Strengths:

The thoroughness of the experiments performed to demonstrate that the HS-binding phenotype results in pH-independent entry and capsid destabilisation is worth highlighting. In this regard, the authors have explored viral entry using a range of approaches involving lysosomotropic drugs, viral binding assays, and neutral red-labelled viruses coupled with diverse techniques such as FISH, RNAscope, and transient expression of constitutively active molecules to inhibit parts of the viral cycle. In my opinion, this is necessary to rule out the other downstream effects of the lysomotropic drugs and to confirm the role of the HS-binding mutation in the entry phase. The use of in silico analysis coupled with negative staining electron microscopy and environmental challenge assays is notable. Finally, the demonstration of some of the work using a human-relevant strain is commendable.

Weaknesses:

A major weakness in this study is the focus on using a mouse-adapted EV-A71 strain (MP4). In the introduction, it is argued that HS-binding mutations are controversial due to their occurrence in cell culture. However, due to host limitations, mice are not the natural hosts for EV-A71 and thus, the same argument can be made for a mouse-adapted strain. It is not clear how different this strain is from circulating EV-A71 strains and the relevance of these findings to the human situation is questionable. This is particularly made evident in the discussion where it is highlighted that HS-binding variants (VP1-145G/Q mutants) have been associated with severe neurological cases while the same variants show attenuated phenotypes in mice and monkeys. This contrast between clinical data and animal studies should be highlighted in the introduction, rather than later in the discussion, as currently the in vivo animal studies are presented as the optimal situation and may lead to misconstrued conclusions from the results.

An important consideration is that the results are based primarily on image analysis. The inclusion of RT-qPCR and/or plaque assays as supplementary data will help strengthen the findings. Moreover, there are suggestions of an intermediate binder having a different phenotype. As this intermediate binder is the clinical phenotype, data on the entry of this intermediate binder will be valuable.

Another weakness in the study is the lack of contextualization of the results to current EV-A71 literature. For instance, SCARB2 is referred to as the internalization receptor but a recent study has shown that SCARB2 is not required for internalization (https://doi.org/10.1128%2Fjvi.02042-21). The findings from this study are consistent with the localization of SCARB2 in the lysosomal membranes. Furthermore, the same study has highlighted host sulfation as a key factor in EV-A71 entry. Post-translational sulfation introduces negatively charged residues on host proteins including HS and SCARB2. This increases the binding of HS-binding strains to these proteins. In this regard, the reduced infectivity upon soluble SCARB2 treatment may simply be due to enhanced binding rather than capsid opening as suggested in the results. Therefore, additional experiments (e.g. nSEM following soluble SCARB2 treatment) must be performed to support the conclusion of capsid opening, due to inherent instability, upon SCARB2 binding.

In addition to the above, other existing literature on EV-A71 pathogenesis using organoids contradicts some of the explanations of differential phenotype in clinical observations versus mice models. In the introduction, it is suggested that reduced neurovirulence of HS-binding strains is due to binding to the vascular endothelia. However, the correlation of clinical severity to viremia (https://doi.org/10.1186/1471-2334-14-417) and the association of HS-binding mutants to clinical disease counteract this suggestion. Similarly, viral infection in human organoids with EV-A71 results in as low as 0.4% of the cells being infected (https://doi.org/10.1038/s41564-023-01339-5). In this case, if viral binding to (ubiquitously expressed) HS results in viral trapping then the HS-binding mutants should show lowered infectivity in organoid models rather than the observed higher infectivity (https://doi.org/10.3389/fmicb.2023.1045587, https://doi.org/10.1038/s41426-018-0077-2). Finally, EV-A71 release has also been shown to occur in exosomes (https://doi.org/10.1093%2Finfdis%2Fjiaa174) which effectively provides a protective lipid membrane. These recent findings must be incorporated into the article and will help better contextualize their findings.

Overall, the authors present new findings with convincing methodology. The manuscript can be improved in the contextualization of the findings and highlighting the weakness in translating these findings to resolve the debate surrounding the relevance of HS-binding phenotype. The inclusion of additional experiments and data recommended to the authors will also help strengthen the manuscript.

Reviewer #3 (Public Review):

I would like to congratulate the authors to an impressive piece of work highlighting important real and potential biases, which may lead to power-law distributed node degrees in protein-protein interaction networks.<br /> This manuscript is easy to follow and very well written manuscript.<br /> I truly enjoyed the concise and convincing scientific presentation.<br /> Even if some of the concerns have already been discussed or raised in the past, the manuscript assesses potential biases in PPIs in a rigorous manner.

I deem the following observations highly relevant to be communicated to the community again:<br /> (1) PL-like distributions emerge by aggregation of data sets alone.<br /> (2) Research interest in itself is PL-distributed and drives PL-like properties in PPI networks<br /> (3) Bait usage is a major driver of PL-like behaviour.<br /> (4) Accounting for biases changes the biological interpretation of the networks<br /> (5) Simulation studies further corroborate these findings.

Reviewer #3 (Public review):

The major strength of this manuscript is the "anvi-estimate-metabolism' tool, which is already accessible online, extensively documented, and potentially broadly useful to microbial ecologists. Inclusion of extensive benchmarking and validation on simulated metagenomes has further increased confidence in this approach. Further, the conceptual insights raise interesting hypotheses that could be pursued in follow-on experimental work.

Comments on revisions:

Thank you for the very thorough response and congratulations!

Reviewer #3 (Public Review):

In this manuscript the authors expand their initial identification of Fyv6 as a protein involved in the second step of pre-mRNA splicing to investigate the transcriptome-wide impact of Fyv6 on splicing and gain a deeper understanding of the mechanism of Fyv6 action.

They first use deep sequencing of transcripts in cells depleted of Fyv6 together with Upf1 (to limit loss of mis-spliced transcripts) to identify broad changes in the transcriptome due to loss of Fyv6. This includes both changes in overall gene expression, that are not deeply discussed, as well as alterations in choice of 3' splice sites - which is the focus of the rest of the manuscript

They next provide the highest resolution structure of the post-catalytic spliceosome to date; providing unparalleled insight into details of the active site and peripheral components that haven't been well characterized previously.

Using this structure they identify functionally critical interactions of Fyv6 with Syf1 but not Prp22, Prp8 and Slu7. Finally, a suppressor screen additionally provides extensive new information regarding functional interactions between these second step factors.

Overall this manuscript reports new and essential information regarding molecular interactions within the spliceosome that determine the use of the 3' splice site. It would be helpful, especially to the non-expert, to summarize these in a table, figure or schematic in the discussion.

Comments on revisions:

I'm satisfied with the changes made in the revision.

Reviewer #3 (Public review):

Protein Phosphatase 1 (PP1), a vital member of the PPP superfamily, drives most cellular serine/threonine dephosphorylation. Despite PP1's low intrinsic sequence preference, its substrate specificity is finely tuned by over 200 PP1-interacting proteins (PIPs), which employ short linear motifs (SLIMs) to bind specific PP1 surface regions. By targeting PP1 to cellular sites, modifying substrate grooves, or altering surface electrostatics, PIPs influence substrate specificity. Although many PIP-PP1-substrate interactions remain uncharacterized, the Phactr family of PIPs uniquely imposes sequence specificity at dephosphorylation sites through a conserved "RVxF-ΦΦ-R-W" motif. In Phactr1-PP1, this motif forms a hydrophobic pocket that favors substrates with hydrophobic residues at +4/+5 in acidic contexts (the "LLD motif"), a specificity that endures even in PP1-Phactr1 fusions. Neurabin/Spinophilin remodel PP1's hydrophobic groove in distinct ways, creating unique holoenzyme surfaces, though the impact on substrate specificity remains underexplored. This study investigates Neurabin/Spinophilin specificity via PDZ domain-driven interactions, showing that Neurabin/PP1 specificity is governed more by PDZ domain interactions than by substrate sequence, unlike Phactr1/PP1.

A significant strength of this work is the use of PP1-PIP fusion proteins to effectively model intact PP1•PIP holoenzymes by replicating the interactions that remodel the PP1 interface and confer site-specific substrate specificity. When combined with proteomic analyses to assess phospho-site depletion in mammalian cells, these fusions offer critical insights into holoenzyme specificity, revealing new candidate substrates for Neurabin and Spinophilin. The studies present compelling evidence that the PDZ domain of PP1-Neurabin directs its specificity, with the remodelled PP1 hydrophobic groove interactions having minimal impact. This mechanism is supported by structural analysis of the PP1-4E-BP1 substrate fusion bound to a Neurabin construct, highlighting the 4E-BP1/PDZ interaction. This work delivers crucial insights into PP1-PIP holoenzyme function, combining biochemical, proteomic, and structural approaches. It validates the PP1-PIP fusion protein model as a powerful tool, suggesting it may extend to studying additional holoenzymes. While an extremely useful model, it must be considered unlikely the PP1-PIP fusions fully recapitulate the specificity and regulation of the holoenzyme.

Reviewer #3 (Public review):

Summary:

This manuscript, "Estimating bone marrow adiposity from head MRI and identifying its genetic 2 architecture", brings together the groups of Drs. Kaufmann and Hughes in a tour de force work to develop an artificial neural network that localizes calvaria bone marrow in T1-weighted MRI head scans, with the goal of studying its composition in several large MRI datasets, and to model sex-dimorphic age trajectories, including the effect of menopause.

Strengths:

Bone marrow adiposity is a very active tissue with far-reaching implications for tissue crosstalk and human health than we had initially recognized. Although MRI has been used to measure BM, studies such as the one by these two groups are still lacking whereas very large datasets are analyzed using advanced AI machine learning tools coupled with genetic studies and a specific pathology. The groups had to develop new methods and new AI machine-learning tools for the imaging analyses.

Weaknesses:

Some aspects of the work that authors could add additional clarification.

(1) Imaging Limitations: The authors provide an excellent overview and references supporting the use of MRI as a method for assessing marrow fat, particularly with some specific modifications. However, MRI images can be affected by various factors, including the presence of other tissues as well as specific MRI settings, which are much harder to precisely control when using different datasets.

(2) The specific density of cranial bones as it relates to the types of bone marrow: Cranial bones are extremely dense structures, which naturally interfere with MRI imaging. While it is thought that cranial bones have mostly "red bone marrow", this is only true for a short time in humans. How sensitive is their system in differentiating between red and yellow BM?

(3) Both items above are further complicated by aging, but aging is not a linear event as we have learned. There are specific bursts of aging in humans around the age of 45 and early 60s. How do the system and model predict or incorporate these peaks of aging? It seems from the data shown that aging is reflected more as a linear phenomenon. Is this because additional aging datasets are needed?

(4) The authors describe in richness of detail their AI learning programming and how it extracted the data from datasets. The authors also show some important correlations with specific genes, SNPs. What is not clear is how conditions such as anemia for example. An expected finding would be that patients with chronic anemia have lower bone marrow (BM) signal intensity on MRI scans than healthy people. This is because the signal intensity of BM depends on the fat-to-cell ratio in the tissue. Furthermore, patients with a host of musculoskeletal disorders ranging from osteopenia to osteoporosis, sarcopenia, and osteosarcopenia will also have altered MRI scans. When using such large datasets how did the authors control or exclude these pathological conditions, or were all these conditions likely present?

(5) Some of the genes and SNPs although significant showed very small correlations. What is their likely physiological significance?

(6) The authors could use this excellent manuscript to expand their discussion to include the need for studies like theirs to be also complemented by multi-OMICS studies that will include proteomics and lipidomics of BM, bones, and muscles.

Reviewer #3 (Public review):

Summary:

Salmonella is interesting due to its life within a compact compartment, which we call SCV or Salmonella containing vacuole in the field of Salmonella. SCV is a tight-fitting vacuole where the acquisition of nutrients is a key factor by Salmonella. The authors among many nutrients, focussed on beta-alanine. It is also known from many other studies that Salmonella requires beta-alanine. The authors have done in vitro RAW macrophage infection assays and In vivo mouse infection assays to see the life of Salmonella in the presence of beta-alanine. They concluded by comprehending that beta-alanine modulates the expression of many genes including zinc transporters which are required for pathogenesis.

Strengths:

This study made a couple of knockouts in Salmonella and did a transcriptomic investigation to understand the global gene expression pattern.

Weaknesses:

The following questions are unanswered:

(1) It is not clear how the exogenous beta-alanine is taken up by macrophages.

(2) It is not clear how the Beta-alanine from the cytosol of the macrophage enters the SCV.

(3) It is not clear how the beta-alanine from SCV enters the bacterial cytosol.

(4) There is no clarity on the utilization of exogenous beta-alanine of the host and the de novo synthesis of beta-alanine by panD of Salmonella.

Reviewer #3 (Public review):

Summary:

The manuscript presents an ambitious and comprehensive synaptic connectome of neurosecretory cells (NSC) in the Drosophila brain, which highlights the neural circuits underlying hormonal regulation of physiology and behaviour. The authors use EM-based connectomics, retrograde tracing, and previously characterised single-cell transcriptomic data. The goal was to map the inputs to and outputs from NSCs, revealing novel interactions between sensory, motor, and neurosecretory systems. The results are of great value for the field of neuroendocrinology, with implications for understanding how hormonal signals integrate with brain function to coordinate physiology.

The manuscript is well-written and provides novel insights into the neurosecretory connectome in the adult Drosophila brain. Some, additional behavioural experiments will significantly strengthen the conclusions.

Strengths:

(1) Rigorous anatomical analysis<br /> (2) Novel insights on the wiring logic of the neurosecretory cells.

Weaknesses:

(1) Functional validation of findings would greatly improve the manuscript.

Reviewer #3 (Public review):

Summary:

This study identifies confirmational fingerprints of amylodogenic light chains, that set them apart from the non-amylodogenic ones.

Strengths:

The research employs a comprehensive combination of structural and dynamic analysis techniques, providing evidence that conformational dynamics at VL-CL interface and structural expansion are distinguished features of amylodogenic LCs.

Weaknesses:

The sample size is limited, which may affect the generalizability of the findings. Additionally, the study could benefit from deeper analysis of specific mutations driving this unique conformation to further strengthen therapeutic relevance.

Reviewer #3 (Public review):

Summary:

The study is well written, and the results are solid and well demonstrated. It shows a field that can be explored for the treatment of CDI

Strengths:

The results are really good, and the CAPE shows a good and promising alternative for treating CDI. The methodology and results are well presented, with tables and figures that corroborate them. It is solid work and very promising.

Weaknesses:

Some references are too old or missing.

Reviewer #3 (Public review):

Summary:

In this manuscript, Wirz et al use neuroimaging (fMRI) to show that counterconditioning produces a longer lasting reduction in fear conditioning relative to extinction and appears to rely on the nucleus accumbens rather than the ventromedial prefrontal cortex. These important findings are supported by convincing evidence and will be of interest to researchers across multiple subfields, including neuroscientists, cognitive theory researchers, and clinicians.

In large part, the authors achieved their aims of giving a qualitative assessment of the behavioural mechanisms of counterconditioning versus extinction, as well as investigating the brain mechanisms. The results support their conclusions and give interesting insights into the psychological and neurobiological mechanisms of the processes that underlie the unlearning, or counteracting, of threat conditioning.

Strengths:

* Mostly clearly written with interesting psychological insights<br /> * Excellent behavioural design, well-controlled and tests for a number of different psychological phenomena (e.g. extinction, recovery, reinstatement, etc).<br /> * Very interesting results regarding the neural mechanisms of each process.<br /> * Good acknowledgement of the limitations of the study.

Weaknesses:

* I think the acquisition data belongs in the main figure, so the reader can discern whether or not there are directional differences prior to CC and extinction training that could account for the differences observed. This is particularly important for the valence data which appears to differ at baseline (supplemental figure 2C).<br /> * I was confused in several sections about the chronology of what was done and when. For instance, it appears that individuals went through re-extinction, but this is just called extinction in places.<br /> * I was also confused about the data in Figure 3. It appears that the CC group maintained differential pupil dilation during CC, whereas extinction participants didn't, and the authors suggest that this is indicative of the anticipation of reward. Do reward-associated cues typically cause pupil dilation? Is this a general arousal response? If so, does this mean that the CSs become equally arousing over time for the CC group whereas the opposite occurs for the extinction group (i.e. Figure 3, bottom graphs)? It is then further confusing as to why the CC group lose differential responding on the spontaneous recovery test. I'm not sure this was adequately addressed.<br /> * I am not sure that the memories tested were truly episodic<br /> * Twice as many female participants than males<br /> * No explanation as to why shocks were varied in intensity and how (psuedo-randomly?)

Reviewer #3 (Public review):

Summary:

The cognitive striatum, also known as the dorsomedial striatum, receives input from brain regions involved in high-level cognition and plays a crucial role in processing cognitive information. However, despite its importance, the extent to which different projection pathways of the striatum contribute to this information processing remains unclear. In this paper, Bruce et al. conducted a study using various causal and correlational techniques to investigate how these pathways collectively contribute to interval timing in mice. Their results were consistent with previous research, showing that the direct and indirect striatal pathways perform opposing roles in processing elapsed time. Based on their findings, the authors proposed a revised computational model in which two separate accumulators track evidence for elapsed time in opposing directions. These results have significant implications for understanding the neural mechanisms underlying cognitive impairment in neurological and psychiatric disorders, as disruptions in the balance between direct and indirect pathway activity are commonly observed in such conditions.

Strengths:

The authors employed a well-established approach to study interval timing and employed optogenetic tagging to observe the behavior of specific cell types in the striatum. Additionally, the authors utilized two complementary techniques to assess the impact of manipulating the activity of these pathways on behavior. Finally, the authors utilized their experimental findings to enhance the theoretical comprehension of interval timing using a computational model.

Weaknesses:

The behavioral task used in this study is best suited for investigating elapsed time perception rather than interval timing. Timing bisection tasks are often employed to study interval timing in humans and animals. Given the systemic delivery of pharmacological interventions, it is difficult to conclude that the effects are specific to the dorsomedial striatum. Future studies should use the local infusion of drugs into the dorsomedial striatum.

Reviewer #3 (Public review):

Summary:

In this study, Zhang et al. reported that CHMP5 restricts bone formation by controlling endolysosome-mitochondrion-mediated cell senescence. The effects of CHMP5 on osteoclastic bone resorption and bone turnover have been reported previously (PMID: 26195726), in which study the aberrant bone phenotype was observed in the CHMP5-ctsk-CKO mouse model, using the same mouse model, Zhang et al., report a novel role of CHMP5 on osteogenesis through affecting cell senescence. Overall, it is an interesting study and provides new insights in the field of cell senescence and bone.

Strengths:

Analyzed the bone phenotype OF CHMP5-periskeletal progenitor-CKO mouse model and found the novel role of senescent cells on osteogenesis and migration.

Weaknesses:

(1) There are a lot of papers that have reported that senescence impairs osteogenesis of skeletal stem cells. In this study, the author claimed that Chmp5 deficiency induces skeletal progennitor cell senescence and enhanced osteogenesis. Can the authors explain the controversial results?

(2) Co-culture of Chmp5-KO periskeletal progenitors with WT ones should be conducted to detect the migration and osteogenesis of WT cells in response to Chmp5-KO-induced senescent cells. In addition, the co-culture of WT periskeletal progenitors with senescent cells induced by H2O2, radiation, or from aged mice would provide more information.

(3) Many EVs were secreted from Chmp5-deleted periskeletal progenitors, compared to the rarely detected EVs around WT cells. Since EVs of BMSCs or osteoprogenitors show strong effects of promoting osteogenesis, did the EVs contribute to the enhanced osteogenesis induced by Chmp5-defeciency?

(4) EVs secreted from senescent cells propagate senescence and impair osteogenesis, why do EVs secreted from senescent cells induced by Chmp5-defeciency have opposite effects on osteogenesis?

(5) The Chmp5-ctsk mice show accelerated aging-related phenotypes, such as hair loss and joint stiffness. Did Ctsk also label cells in hair follicles or joint tissue?

(6) Fifteen proteins were found to increase and five proteins to decrease in the cell supernatant of Chmp5Ctsk periskeletal progenitors. How about SASP factors in the secretory profile?

(7) D+Q treatment mitigates musculoskeletal pathologies in Chmp5 conditional knockout mice. In the previously published paper (CHMP5 controls bone turnover rates by dampening NF-κB activity in osteoclasts), inhibition of osteoclastic bone resorption rescues the aberrant bone phenotype of the Chmp5 conditional knockout mice. Whether the effects of D+Q on bone overgrowth is because of the inhibition of bone resorption?

(8) The role of VPS4A in cell senescence should be measured to support the conclusion that CHMP5 regulates osteogenesis by affecting cell senescence.

(9) Cell senescence with markers, such as p21 and H2AX, co-stained with GFP should be performed in the mouse models to indicate the effects of Chmp5 on cell senescence in vivo.

(10) ADTC5 cell as osteochondromas cells line, is not a good cell model of periskeletal progenitors. Maybe primary periskeletal progenitor cell is a better choice.

Reviewer #3 (Public review):

Summary:

The authors performed snRNA-seq in the pre-optic area (POA), a heterogeneous brain region implicated in multiple innate behaviors, comparing two species of Peromyscus mice that possess strikingly different parenting behaviors. P. polionotus shows high levels of parental care from both sexes of parent, and P. maniculatus shows lower levels of care, predominantly displayed by dams rather than sires. The overall goal of understanding the genomic basis of behavioral variation is significant and of broad interest and comparative studies in POA in these two species is an excellent approach to tackle this question. The authors correctly point out that existing studies largely compare species that are highly divergent, such as mice and humans, which confounds the association of specific neuronal populations or gene expression patterns with distinct behaviors. They identify neuronal populations with differential abundance between species and sexes and additionally report sex and species differences in gene expression within each transcriptomic cell type. Their cell type classification is aided by mapping their Peromyscus cells onto a previously existing POA single-cell dataset generated in lab mice. However, a significant fraction of the cells cannot be assigned to Mus types, which confounds their analysis. The detection and validation of previously observed sex differences in the Gal/Moxd1 cell type and species differences in Avp expression provide additional support that their data are solid. This study provides an important resource for comparative single-cell studies in the brain.

Strengths:

This is a pioneering comparative snRNA-seq study that provides a roadmap for similar approaches in non-traditional model organisms.

The authors have identified populations that may underlie sex- and species- differences in parenting behavior in rodents.

A significant strength of the manuscript is the histological validation of their most robust marker genes.

Weaknesses:

My primary concern is that the dataset is limited: 52,121 neuronal nuclei across 24 samples, which does not provide many cells per cluster to analyze comparatively across sex and species, particularly given the heterogeneity of the region dissected. The Supplementary table reports lower UMIs/genes per cell than is typically seen as well. Perhaps additional information could be obtained from the data by not restricting the analyses to cells that can be assigned to Mus types. A direct comparison of the two Peromyscus species could be valuable as would a more complete Peromyscus POA atlas.

In Supplement 7, it appears that most neurons can be assigned as excitatory or inhibitory, but then so many of these cells remain in the unassigned "gray blob" seen in panel 1E. Clustering of excitatory and inhibitory neurons separately, as in in prior cited work in Mus POA (refs 31 and 57) may boost statistical power to detect sex and species differences in cell types. Perhaps the cells that cannot be assigned to Mus contain too few reads to be useful, in which case they should be filtered out in the QC. The technical challenges of a comparative single-cell approach are considerable, so it benefits the scientific community to provide transparency about them.

The Calb1 dimorphism as observed by immunostaining, appears much more extensive in P. maniculatus compared to P. polionotus (Figures 3 E and F). This finding is not reflected in the counts of the i20:Gal/Moxd1 cluster. The use of Calb1 staining as a proxy for the Gal/Moxd1 cluster would be strengthened if the number of POA Calb1+ neurons that are found in each cluster was apparent. There may be additional Calb+ neurons in the cells that are not annotated to a Mus cluster. This clarification would add support to the overall conclusion that there is reduced sexual dimorphism in P. polionotus.

The relationship between the sex steroid receptor expression and the sex bias in gene expression would be improved if the sex bias in sex steroid receptor expression was included in Supplementary Figure 10.

There is no explanation for the finding that there is a female bias in gene expression across all cell types in P. polionotus.

Reviewer #3 (Public review):

Summary:

This is an interesting manuscript which uses state of the art experimental and simulation approaches to quantify motor unit discharge patterns in the human TA and VL. The non-linear profiles of motor unit discharge were calculated and found to have an initial acceleration phase followed by an attenuation phase. Lower threshold motor units had a larger gain of the initial acceleration whereas the higher threshold motor unit had a higher gain in the attenuation phase. These data represent a technical feat and are important for understanding how humans generate and control voluntary force.

Strengths:

The authors used rigorous, state-of-the art analyses to decompose and validate their motor unit data during a wide range of voluntary efforts.

Analyses are clearly presented, applied, and visualized.

The supplemental data provides important transparency.

Weaknesses:

Number of participants and muscles tested are relatively small - particularly given the constraints on yield. It is unclear if this will translate to other motor pools. The justification for TA and VL should be provided.

While in impressive effort was made to identify and track motor units across a range of contractions, it appears that a substantial portion of muscle force was not identified. Though high intensity contractions are challenging to decompose - the authors are commended in their technical ability in recording population motor unit discharge times with recruitment thresholds up to 75% a participant's maximal voluntary contractions. However previous groups have seen substantial recruitment motor units above 80% and even 90% maximum activation in the soleus. Given the innervation ratios of higher threshold motor units, if recruitment continued to 100%, the top quartile would likely represent a substantial portion of the traditional fast-fatigable motor units. It would be highly interesting to understand the recruitment and rate coding of the highest threshold motor units, at a minimum I would suggest using terms other than "entire range" or "full spectrum of recruitment thresholds"

The quantification of hysteresis using torque appears to make self-evident the observation that lower threshold motor units demonstrate less hysteresis with respect to torque - If there was motor unit discharge there will be force. I believe this limitation goes beyond the floor effects discussed in the manuscript. Traditionally individuals have used the discharge of a lower threshold unit as the measure on which to apply hysteresis analyses to infer ion channel function in human spinal motoneurons.

The main findings are not entirely novel. See Monster and Chan 1977 and Kanosue et al 1979

Comments on revisions:

I thank the authors for their thoughtful revision.

Just to confirm, the ranges for motor unit yield are for a single contraction. So, for example, in a participant there were 71 unique and concurrently active VL motor units able to be decomposed.

Reviewer #3 (Public review):

This study explores sensory prediction errors in sensory cortex. It focuses on the question of how these signals are shaped by non-hierarchical interactions, specifically multimodal signals arising from same level cortical areas. The authors used 2-photon imaging of mouse auditory cortex in head-fixed mice that were presented with sounds and/or visual stimuli while moving on a ball. First, responses to pure tones, visual stimuli and movement onset were characterized. Then, the authors made the running speed of the mouse predictive of sound intensity and/or visual flow (closed loop). Mismatches were created through the interruption of sound and/or visual flow for 1 second, disrupting the expected sensory signal. As a control, sensory stimuli recorded during the close loop phase were presented again decoupled from the movement (open loop). The authors suggest that auditory responses to the unpredicted interruption of the sound, which affected neither running speed nor pupil size, reflect mismatch responses. That these mismatch responses were enhanced when the visual flow was congruently interrupted, indicates cross-modal influence of prediction error signals.

This study's strengths are the relevance of the question and the design of the experiment. The authors are experts in the techniques used. The analysis explores neither the full power of the experimental design nor the population activity recorded with 2-photon, leaving open the question of to what extend what the authors call mismatch responses are not sensory responses to sound interruption (offset responses). The auditory system is sensitive to transitions and indeed responses to the interruption of the sound are similar in quality, if not quantity, in the predictive and the control situation.

Comments on revisions:

The incorporation of the analysis of the animal's running speed and the pupil size upon sound interruption improves the interpretation of the data. The authors can now conclude that responses to the mismatch are not due to behavioral effects.<br /> The issue of the relationship between mismatch responses and offset responses remains uncommented. The auditory system is sensitive to transitions, also to silence. See the work of the Linden or the Barkat labs (including the work of the first author of this manuscript) on offset responses, and also that of the Mesgarani lab (Khalighinejad et al., 2019) on responses to transitions 'to clean' (Figure 1c) in human auditory cortex. Offset responses, as the first author knows well, are modulated by intensity and stimulus length (after adaptation?). That responses to the interruption of the sound are similar in quality, if not quantity, in the closed and open loop conditions suggest that offset response might modulate the mismatch response. A mismatch response that reflects a break in predictability would presumably be less modulated by the exact details of the sensory input than an offset response. Therefore, what is the relationship between the mismatch response and the mean sound amplitude prior to the sound interruption (for example during the preceding 1 second)? And between the mismatch response and the mean firing rate over the same period?<br /> Finally, how do visual stimuli modulate sound responses in the absence of a mismatch? Is the multimodal response potentiation specific to a mismatch?

Reviewer #3 (Public review):

Summary:

In this manuscript, Bosch and colleagues describe an unexpected function of Flamingo, a core component of the planar cell polarity pathway, in cell competition in Drosophila wing and eye disc. While Flamingo depletion has no impact on tumour growth (upon induction of Ras and depletion of Scribble throughout the eye disc), and no impact when depleted in WT cells, it specifically tunes down winner clone expansion in various genetic contexts, including the overexpression of Myc, the combination of Scribble depletion with activation of Ras in clones or the early clonal depletion of Scribble in eye disc. Flamingo depletion reduces proliferation rate and increases the rate of apoptosis in the winner clones, hence reducing their competitiveness up to forcing their full elimination (hence becoming now "loser"). This function of Flamingo in cell competition is specific of Flamingo as it cannot be recapitulated with other components of the PCP pathway, does not rely on interaction of Flamingo in trans, nor on the presence of its cadherin domain. Thus, this function is likely to rely on a non-canonical function of Flamingo which may rely on downstream GPCR signaling.

This unexpected function of Flamingo is by itself very interesting. In the framework of cell competition, these results are also important as they describe, to my knowledge, one of the only genetic conditions that specifically affect the winner cells without any impact when depleted in the loser cells. Moreover, Flamingo do not just suppress the competitive advantage of winner clones, but even turn them in putative losers. This specificity, while not clearly understood at this stage, opens a lot of exciting mechanistic questions, but also a very interesting long term avenue for therapeutic purpose as targeting Flamingo should then affect very specifically the putative winner/oncogenic clones without any impact in WT cells.

The data and the demonstration are very clean and compelling, with all the appropriate controls, proper quantifications and backed-up by observations in various tissues and genetic backgrounds. I don't see any weakness in the demonstration and all the points raised and claimed by the authors are all very well substantiated by the data. As such, I don't have any suggestions to reinforce the demonstration.

While not necessary for the demonstration, documenting the subcellular localisation and levels of Flamingo in these different competition scenarios may have been relevant and provide some hints on a putative mechanism (specifically by comparing its localisation in winner and loser cells).

Also, on a more interpretative note, the absence of impact of Flamingo depletion on JNK activation does not exclude some interesting genetic interactions. JNK output can be very contextual (for instance depending on Hippo pathway status), and it would be interesting in the future to check if Flamingo depletion could somehow alter the effect of JNK in the winner cells and promote downstream activation of apoptosis (which might normally be suppressed). It would be interesting to check if Flamingo depletion could have an impact in other contexts involving JNK activation or upon mild activation of JNK in clones.

Strengths:

- A clean and compelling demonstration of the function of Flamingo in winner cells during cell competition

- One of the rare genetic conditions that affects very specifically winner cells without any impact in losers, and then can completely switch the outcome of competition (which opens an interesting therapeutic perspective on the long term)

Reviewer #3 (Public review):

Summary:

The manuscript by Jaime Tobon and Moser uses patch-clamp electrophysiology in cochlear preparations to probe the pre- and post-synaptic specializations that give rise to diverse activity of spiral ganglion afferent neurons (SGN). The experiments are quite an achievement! They use paired recordings from pre-synaptic cochlear inner hair cells (IHC) that allow precise control of voltage and therefore calcium influx, with post-synaptic recordings from type I SGN boutons directly opposed to the IHC for both presynaptic control of membrane voltage and post-synaptic measurement of synaptic function with great temporal resolution.

Any of these techniques by themselves are challenging, but the authors do them in pairs, at physiological temperatures, and in hearing animals, all of which combined make these experiments a real tour de force. The data is carefully analyzed and presented, and the results are convincing. In particular, the authors demonstrate that post-synaptic features that contribute to the spontaneous rate (SR) of predominantly monophasic post-synaptic currents (PSCs), shorter EPSC latency, and higher PSC rates are directly paired with pre-synaptic features such as a lower IHC voltage activation and tighter calcium channel coupling for release to give a higher probability of release and subsequent increase in synaptic depression. Importantly, IHCs paired with Low and High SR afferent fibers had the same total calcium currents, indicating that the same IHC can connect to both low and high SR fibers. These fibers also followed expected organizational patterns, with high SR fibers primarily contacting the pillar IHC face and low SR fibers primarily contacting the modiolar face. The authors also use in vivo-like stimulation paradigms to show different RRP and release dynamics that are similar to results from SGN in vivo recordings. Overall, this work systematically examines many features giving rise to specializations and diversity of SGN neurons.

Reviewer #3 (Public review):

Summary:

This work aims to address a fundamental biological question: how do mammalian cells achieve/lose tolerance to cold exposure? The authors first tried to establish an experimental system for cell cold exposure and evaluation of cell death and then performed genome-scale CRISPR-Cas9 screening on immortalized cell lines from Syrian Hamster (BHK-21) and human (K562) for key genes that are associated with cell survival during prolonged cold exposure. From these screenings, they focused on glutathione peroxidase 4 (GPX4). Using genetic modifications or pharmacological interventions, and multiple cell models including primary cells from various mammalian species, they showed that GPX4 proteins are likely to retain their activities at 4 {degree sign}C, functioning to prevent cold-induced cell ferroptosis.

Strengths:

(1) This paper is neatly written and hence easy to follow.

(2) Experiments are well designed.

(3) The data showing the overall good cell survival after a prolonged cold exposure or repeated cold-warm cycles are helpful to show the advantages of the experimental instruments and methods the authors used, and hence the validity of their results.

(4) The CRISPR-Cas9 screening is a great attempt.

(5) Multiple cell types from hibernating mammals (cold tolerant) and cold-intolerant species are used to test their findings.

(6) Although some may argue that other labs have published works with different approaches that have pointed out the importance of GPX4 and ferroptosis in hamster cell survival from anoxia-reoxygenation or cold exposure models, hence hurting the novelty of this work, this reviewer thinks that it is highly valuable to have independent research groups and different methods/systems to validate an important concept.

Weaknesses:

(1) Only cell death was robustly surveyed; though cell proliferation was evaluated too in some experiments, other cellular functions, such as mitochondrial ATP production vs. glycolysis, and the extent of lipid peroxidation, could have been measured to reflect cellular physiology.

Validations on complex tissues or in vivo systems would have further strengthened the work and its impact.

CRISPR-Cas9 screening may have technical limitations as knock-out of some essential genes/pathways may lead to cell lethality during screening, and hence the relevance of these genes/pathways to cell cold tolerance may not be noted. From the data presented in this study, this reviewer thinks that the GPX4 pathway is likely a conserved mechanism for long-term cold survival, but not for cold sensitivity or acute cell death from cold exposure. In line with my such speculation, their CRISPR-Cas9 screening revealed genes in the GPX4 pathway from a relatively cold-sensitive human cell line, but the endogenous GPX4 pathway is seemingly operational in this cold-sensitive cell line. Also, these cells are viable after GPX4 knock-out. Dead cells from the acute cold exposure phase may detached, or their genomic DNAs have been severely damaged by the time of sample collection, hence not giving any meaningful sequencing reads. Crippling other factors/pathways such as FOXO1 (PMID: 38570500) or 5-aminolevulinic acid (ALA) metabolism (PMID: 35401816) have been shown to severely aggravate cold-induced cell death, including TUNEL-revealed DNA damage, within a much shorter time scale, whilst loss-function knockouts of FOXO1 or ALA Synthase 1 (ALAS1) are usually cell lethal. Thus, they and other possible essential genes may not be screenable from the current experimental protocol. These important points need to be taken into consideration by the authors.

Reviewer #3 (Public review):

Summary:

The manuscript by Chang et al. aims to investigate how the behavioral relevance of auditory and visual stimuli influences the way in which the primary auditory cortex encodes auditory, visual, and audiovisual information. The main result is that behavioral training induces an increase in the encoding of auditory and visual information and in multisensory enhancement that is mainly related to the choice located contralaterally with respect to the recorded hemisphere.

Strengths:

The manuscript reports the results of an elegant and well-planned experiment meant to investigate if the auditory cortex encodes visual information and how learning shapes visual responsiveness in the auditory cortex. Analyses are typically well done and properly address the questions raised

Weaknesses:

Major

(1) The authors apparently primarily focus their analyses of sensory-evoked responses in approximately the first 100 ms following stimulus onset. Even if I could not find an indication of which precise temporal range the authors used for analysis in the manuscript, this is the range where sensory-evoked responses are shown to occur in the manuscript figures. While this is a reasonable range for auditory evoked responses, the same cannot be said for visual responses, which commonly peak around 100-120 ms, in V1. In fact, the latency and overall shape of visual responses are quite different from typical visual responses, that are commonly shown to display a delay of up to 100 ms with respect to auditory responses. All traces that the authors show, instead, display visual responses strikingly overlapping with auditory ones, which is not in line with what one would expect based on our physiological understanding of cortical visually-evoked responses. Similarly, the fact that the onset of decoding accuracy (Figure 2j) anticipates during multisensory compared to auditory-only trials is hard to reconcile with the fact that visual responses have a later onset latency compared to auditory ones. The authors thus need to provide unequivocal evidence that the results they observe are truly visual in origin. This is especially important in view of the ever-growing literature showing that sensory cortices encode signals representing spontaneous motor actions, but also other forms of non-sensory information that can be taken prima facie to be of sensory origin. This is a problem that only now we realize has affected a lot of early literature, especially - but not only - in the field of multisensory processing. It is thus imperative that the authors provide evidence supporting the true visual nature of the activity reported during auditory and multisensory conditions, in both trained, free-choice, and anesthetised conditions. This could for example be achieved causally (e.g. via optogenetics) to provide the strongest evidence about the visual nature of the reported results, but it's up to the authors to identify a viable solution. This also applies to the enhancement of matched stimuli, that could potentially be explained in terms of spontaneous motor activity and/or pre-motor influences. In the absence of this evidence, I would discourage the author from drawing any conclusion about the visual nature of the observed activity in the auditory cortex.

(2) The finding that AC neurons in trained mice preferentially respond - and enhance - auditory and visual responses pertaining to the contralateral choice is interesting, but the study does not show evidence for the functional relevance of this phenomenon. As has become more and more evident over the past few years (see e.g. the literature on mouse PPC), correlated neural activity is not an indication of functional role. Therefore, in the absence of causal evidence, the functional role of the reported AC correlates should not be overstated by the authors. My opinion is that, starting from the title, the authors need to much more carefully discuss the implications of their findings.

MINOR:

(1) The manuscript is lacking what pertains to the revised interpretation of most studies about audiovisual interactions in primary sensory cortices following the recent studies revealing that most of what was considered to be crossmodal actually reflects motor aspects. In particular, recent evidence suggests that sensory-induced spontaneous motor responses may have a surprisingly fast latency (within 40 ms; Clayton et al. 2024). Such responses might also underlie the contralaterally-tuned responses observed by the authors if one assumes that mice learn a stereotypical response that is primed by the upcoming goal-directed, learned response. Given that a full exploration of this issue would require high-speed tracking of orofacial and body motions, the authors should at least revise the discussion and the possible interpretation of their results not just on the basis of the literature, but after carefully revising the literature in view of the most recent findings, that challenge earlier interpretations of experimental results.

(2) The methods section is a bit lacking in details. For instance, information about the temporal window of analysis for sensory-evoked responses is lacking. Another example: for the spike sorting procedure, limited details are given about inclusion/exclusion criteria. This makes it hard to navigate the manuscript and fully understand the experimental paradigm. I would recommend critically revising and expanding the methods section.

Reviewer #3 (Public Review):

Summary:

This important paper provides the best-to-date characterization of chirping in weakly electric fish using a large number of variables. These include environment (free vs divided fish, with or without clutter), breeding state, gender, intruder vs resident, social status, locomotion state and social and environmental experience, without and with playback experiments. It applies state-of-the-art methods for reducing the dimensionality of the data and finding patterns of correlation between different kinds of variables (factor analysis, K-means). The strength of the evidence, collated from a large number of trials with many controls, leads to the conclusion that the traditionally assumed communication function of chirps may be secondary to its role in environmental assessment and exploration that takes social context into account. Based on their extensive analyses, the authors suggest that chirps are mainly used as probes that help detect beats caused by other fish as well as objects.

Strengths:

The work is based on completely novel recordings using interaction chambers. The amount of new data and associated analyses is simply staggering, and yet, well organized in presentation. The study further evaluates the electric field strength around a fish (via modelling with the boundary element method) and how its decay parallels the chirp rate, thereby relating the above variables to electric field geometry. The BEM modelling also convincingly predicts how the electric image of a receiver conspecific on a sending fish is enhanced by a chirp.

The main conclusions are that the lack of any significant behavioural correlates for chirping, and the lack of temporal patterning in chirp time series, cast doubt on a primary communication goal for most chirps. Rather, the key determinants of chirping are the difference in frequency between two interacting conspecifics as well as individual subjects' environmental and social experience. The paper concludes that there is a lack of evidence for stereotyped temporal patterning of chirp time series, as well as of sender-receiver chirp transitions beyond the known increase in chirp frequency during an interaction. The authors carefully submit that the new putative echolocation function of chirps is not mutually exclusive with a possible communication function.

These conclusions by themselves will be very useful to the field. They will also allow scientists working on other "communication" systems to perhaps reconsider and expand the goals of the probes used in those senses. A lot of data are summarized in this paper, with thorough referencing to past work.

The alternative hypotheses that arise from the work are that chirps are mainly used as environmental probes for better beat detection and processing and object localization, and in this sense are self-directed signals. This led to their prediction that environmental complexity ("clutter") should increase chirp rate, which is fact was revealed by their new experiments. The authors also argue that waveform EODs have less power across high spatial frequencies compared to pulse-type fish, with a resulting relatively impoverished power of resolution. Chirping in wave-type fish could temporarily compensate for the lower frequency resolution while still being able to resolve EOD perturbations with a good temporal definition (which pulse-type fish lack due to low pulse rates).

The authors also advance the interesting idea that the sinusoidal frequency modulations caused by chirps are the electric fish's solution to the minute (and undetectable by neural wetware) echo-delays available to it, due to the propagation of electric fields at the speed of light in water. The paper provides a number of experimental avenues to pursue in order to validate the non-communication role of chirps.

Reviewer #3 (Public review):

Summary:

This study investigated the expression of Osterix (Osx) not only in osteoblasts but also significantly in osteocytes. Through Osx knockout, the osteocytic dendritic network was damaged, leading to communication disruption. This study investigated the regulatory role of Osx on osteoblast dendrites through Cx43.

Strengths:

This paper provides a good explanation of the role of Osx in osteocyte synapse and cell communication, enriching the understanding of Osx's functional significance. The results of the experiment support the conclusions of the study. This is an interesting study with a clear logical structure.

Weaknesses:

Some experimental results need to be supplemented, and there are still some details and errors in the text that need to be revised.

Reviewer #3 (Public review):

Summary:

In this manuscript, the authors used structural biology approaches to determine the molecular mechanism underlying the inactivation of the PIEZO1 ion channel. To this end, the authors presented structures of human PIEZO1 and its slow-inactivating mutants. The authors also determined the structures of these PIEZO1 constructs in complexes with the auxiliary subunit MDFIC, which substantially slows down PIEZO1 inactivation. From these structures, the authors observed a unique feature of human PIEZO1 in which the lipid molecules plugged the channel pore in fast-inactivating constructs. The authors proposed that these lipid molecules prevent ion permeation and underlie the molecular mechanism of human PIEZO1 inactivation.

Strengths:

Notedly, this manuscript reported the first structures of a human PIEZO1 channel, its channelopathy mutants, and their complexes with MDFIC. The proposed role of pore lipids in modulating PIEZO1 ion permeation is interesting.

Weaknesses:

The authors' conclusion regarding the role of pore lipids in PIEZO inactivation is based on the assumption that all structures of human PIEZO1 resolved in this work represent comparable functional states relevant to channel inactivation. The authors should at least acknowledge that this is a critical assumption that is difficult to validate. The fitting of the lipid molecule to cryo-EM density could be improved.

Comments on revisions:

Upon revision, the authors substantially weakened the statement regarding the correlation between curvature and inactivation. The authors also toned down the statement regarding the role of pore lipids in channel inactivation. However, I have a few additional comments.

(1) As I have stated above, the assumption here is that all structures presented in this work represent comparable functional states relevant to channel inactivation. However, this assumption could be invalid. For example, the WT channel could be in the closed conformation, whereas the mutant could be stabilized in a different functional state. I understand that this is very difficult to test structurally and functionally. Therefore, I think the authors should at least acknowledge this limitation/assumption.<br /> (2) This time, I reviewed the coordinates and the map of the PIEZO1 structures. For example, in the WT channel, the fitting of the lipid to the cryo-EM density is questionable and I personally wouldn't model this lipid in this pose.

Reviewer #3 (Public review):

Summary:

Boffi and colleagues sought to quantify the single-trial, azimuthal information in the dorsal cortex of the inferior colliculus (DCIC), a relatively understudied subnucleus of the auditory midbrain. They accomplished this by using two complementary recording methods while mice passively listened to sounds at different locations: calcium imaging that recorded large neuronal populations but with poor temporal precision and multi-contact electrode arrays that recorded smaller neuronal populations with exact temporal precision. DCIC neurons respond variably, with inconsistent activity to sound onset and complex azimuthal tuning. Some of this variably was explained by ongoing head movements. The authors used a naïve Bayes decoder to probe the azimuthal information contained in the response of DCIC neurons on single trials. The decoder failed to classify sound location better than chance when using the raw population responses but performed significantly better than chance when using the top principal components of the population. Units with the most azimuthal tuning were distributed throughout the DCIC, possessed contralateral bias, and positively correlated responses. Interestingly, inter-trial shuffling decreased decoding performance, indicating that noise correlations contributed to decoder performance. Overall, Boffi and colleagues, quantified the azimuthal information available in the DCIC while mice passively listened to sounds, a first step in evaluating if and how the DCIC could contribute to sound localization.

Strengths:

The authors should be commended for collection of this dataset. When done in isolation (which is typical), calcium imaging and linear array recordings have intrinsic weaknesses. However, those weaknesses are alleviated when done in conjunction - especially when the data is consistent. This data set is extremely rich and will be of use for those interested in auditory midbrain responses to variable sound locations, correlations with head movements, and neural coding.

The DCIC neural responses are complex with variable responses to sound onset, complex azimuthal tuning and large inter-sound interval responses. Nonetheless, the authors do a decent job in wrangling these complex responses: finding non-canonical ways of determining dependence on azimuth and using interpretable decoders to extract information from the population.

Weaknesses:

The decoding results are a bit strange, likely because the population response is quite noisy on any given trial. Raw population responses failed to provide sufficient information concerning azimuth for significant decoding. Importantly, the decoder performed better than chance when certain principal components or top ranked units contributed but did not saturate with the addition of components or top ranked units. So, although there is azimuthal information in the recorded DCIC populations - azimuthal information appears somewhat difficult to extract.

Although necessary given the challenges associated with sampling many conditions with technically difficult recording methods, the limited number of stimulus repeats precludes interpretable characterization of the heterogeneity across the population. Nevertheless, the dataset is public so those interested can explore the diversity of the responses.

The observations from Boffi and colleagues raises the question: what drives neurons in the DCIC to respond? Sound azimuth appears to be a small aspect of the DCIC response. For example, the first 20 principal components which explain roughly 80% of the response variance are insufficient input for the decoder to predict sound azimuth above chance. Furthermore, snout and ear movements correlate with the population response in the DCIC (the ear movements are particularly peculiar given they seem to predict sound presentation). Other movements may be of particular interest to control for (e.g. eye movements are known to interact with IC responses in the primate). These observations, along with reported variance to sound onsets and inter-sound intervals, question the impact of azimuthal information emerging from DCIC responses. This is certainly out of scope for any one singular study to answer, but, hopefully, future work will elucidate the dominant signals in the DCIC population. It may be intuitive that engagement in a sound localization task may push azimuthal signals to the forefront of DCIC response, but azimuthal information could also easily be overtaken by other signals (e.g. movement, learning).

Boffi and colleagues set out to parse the azimuthal information available in the DCIC on a single trial. They largely accomplish this goal and are able to extract this information when allowing the units that contain more information about sound location to contribute to their decoding (e.g., through PCA or decoding on their activity specifically). Interestingly, they also found that positive noise correlations between units with similar azimuthal preferences facilitate this decoding - which is unusual given that this is typically thought to limit information. The dataset will be of value to those interested in the DCIC and to anyone interested in the role of noise correlations in population coding. Although this work is first step into parsing the information available in the DCIC, it remains difficult to interpret if/how this azimuthal information is used in localization behaviors of engaged mice.

Reviewer #3 (Public Review):

Summary:

The authors use docking and molecular dynamics (MD) simulations to investigate transient conformations that are otherwise difficult to resolve experimentally. The docking and simulations suggest an interesting series of events whereby agonists initially bind to the low affinity site and then flip 180 degrees as the site contracts to its high affinity conformation. This work will be of interest to the ion channel community and to biophysical studies of pentameric ligand-gated channels.

Strengths:

I find the premise for the simulations to be good, starting with an antagonist bound structure as an estimate of the low affinity binding site conformation, then docking agonists into the site and using MD to allow the site to relax to a higher affinity conformation that is similar to structures in complex with agonists. The predictions are interesting and provide a view into what a transient conformation that is difficult to observe experimentally might be like.

Weaknesses:

A weakness is that the relevance of the initial docked low affinity orientations depend solely on in silco results, for which simulated vs experimental binding energies deviate substantially for two of the four ligands tested. This raises some doubt as to the validity of the simulations. I acknowledge that the calculated binding energies for two of the ligands were closer to experiment, and simulated efficiencies were a good representation of experimental measures, which gives some support to the relevance of the in silico observations. Regardless, some of the reviewers comments regarding the simulation methodology were not seriously addressed.

Reviewer #3 (Public review):

Summary:

This manuscript represents a technology development- specifically an micrococcal nuclease chromatin capture approach, termed MChIP-C to identify promoter centered chromatin interactions at single nucleosome resolution via a specific protein, similar to HiChIP, ChIA-PET, etc.. In general the manuscript is technically well done.

Strengths:

Methods appear to hold promise to improve both the sensitivity and resolution of protein-centered chromatin capture approaches.

Weaknesses:

Downsampling analysis gives a better idea of the strengths of the approach, especially related to individual loci. While this method does outperform other approaches, it remains technically sophisticated and for some labs may not be worth the additional effort for the increase in information. Also, until tested and proven by other groups, it is difficult to know how impactful this approach will be.

Reviewer #3 (Public review):

Summary:

Krwawicz et al., present evidence that expression of DNMTs in E. coli results in (1) introduction of alkylation damage that is repaired by AlkB; (2) confers hypersensitivity to alkylating agents such as MMS (and exacerbated by loss of AlkB); (3) confers hypersensitivity to oxidative stress (H2O2 exposure); (4) results in a modest increase in ROS in the absence of exogenous H2O2 exposure; and (5) results in the production of oxidation products of 5mC, namely 5hmC and 5fC, leading to cellular toxicity. The findings reported here have interesting implications for the concept that such genotoxic and potentially mutagenic consequences of DNMT expression (resulting in 5mC) could be selectively disadvantageous for certain organisms. The other aspect of this work which is important for understanding the biological endpoints of genotoxic stress is the notion that DNA damage per se somehow induces elevated levels of ROS.

Strengths:

The manuscript is well-written, and the experiments have been carefully executed providing data that support the authors' proposed model presented in Fig. 7 (Discussion, sources of DNA damage due to DNMT expression).

Weaknesses:

(1) The authors have established an informative system relying on expression of DNMTs to gauge the effects of such expression and subsequent induction of 3mC and 5mC on cell survival and sensitivity to an alkylating agent (MMS) and exogenous oxidative stress (H2O2 exposure). The authors state (p4) that Fig. 2 shows that "Cells expressing either M.SssI or M.MpeI showed increased sensitivity to MMS treatment compared to WT C2523, supporting the conclusion that the expression of DNMTs increased the levels of alkylation damage." This is a confusing statement and requires revision as Fig. 2 does ALL cells shown in Fig. 2 are expressing DNMTs and have been treated with MMS. It is the absence of AlkB and the expression of DNMTs that that causes the MMS sensitivity.

(2) It would be important to know whether the increased sensitivity (toxicity) to DNMT expression and MMS is also accompanied by substantial increases in mutagenicity. The authors should explain in the text why mutation frequencies were not also measured in these experiments.

(3) Materials and Methods. ROS production monitoring. The "Total Reactive Oxygen Species (ROS) Assay Kit" has not been adequately described. Who is the Vendor? What is the nature of the ROS probes employed in this assay? Which specific ROS correspond to "total ROS"?

(4) The demonstration (Fig. 4) that DNMT expression results in elevated ROS and its further synergistic increase when cells are also exposed to H2O2 is the basis for the authors' discussion of DNA damage-induced increases in cellular ROS. S. cerevisiae does not possess DNMTs/5mC, yet exposure to MMS also results in substantial increases in intracellular ROS (Rowe et al, (2008) Free Rad. Biol. Med. 45:1167-1177. PMC2643028). The authors should be aware of previous studies that have linked DNA damage to intracellular increases in ROS in other organisms and should comment on this in the text.

Reviewer #3 (Public review):

Summary:

The authors report a novel, direct interaction of Spt6p tSH2 domain to Tom1p. This extends the function of Spt6p from communication with factors associated with RNAPII transcription to processes of ubiquitination. Tom1p is known to ubiquitinate a large variety of substrates, but it is unknown how substrate recognition is done in a specific manner. The team identified a conserved central acidic region of Tom1p which is essential for in vivo functions and binds to histones and nucleosomes, as well as Spt6p. They further describe the Tom1p occupancy pattern on chromatin, assigning it a stabilizing effect on nucleosomes near promotors and a destabilizing effect on nucleosomes within the gene bodies. The authors were able to resolve two different conformational states of Tom1p which are likely connected to its activity, and possibly substrate selectivity.<br /> Overall, the authors show that an intrinsically disordered region in Tom1p is important for substrate interaction and function of Tom1p. The protein is further involved in chromatin architecture and structural transitions control its activity.

Strengths:

By revealing the interaction of Spt6p and Tom1p, the authors discover a novel connection between transcriptional elongation and processes of ubiquitination.<br /> In recent years, disordered regions of MDa protein complexes have become a focus of research projects. The effects of disordered regions on protein localization and specificity of binding interactions have been discussed in great extent, including proteins that are involved in chromatin remodeling and transcription. Adding to these current efforts, the authors assign a function to a highly conserved disordered region of Tom1p in technically clean experiments. Furthermore, with their data, they pin down a specific functional region in Tom1p which is relevant for the previously observed temperature sensitivity caused by Tom1p deletion in yeast.<br /> The team performs a thorough and complete analysis of the cryo-EM structure and they nicely model the hinge motion and details of an open and closed conformation.

Weaknesses:

Despite the high number of interesting findings, there is little connection between the individual sections of the manuscript. For example, many experiments are not related to Spt6p binding although this protein is presented as a major actor in this manuscript during the introduction. Furthermore, the structural analysis is well done, but it is also not quite clear how structural rearrangements are connected to Spt6 binding or chromatin remodeling. Some experimental results lack novelty, as similar data has previously been presented for the human homolog.<br /> To confirm the novel, direct binding interaction of Spt6p and Tom1p, no orthogonal binding assays (SPR, MST, ITC) have been performed to confirm the interaction. To me, this is insufficient, especially since the team has purified both proteins to high quality levels, or could use peptides to test the function of the relevant regions.<br /> Additionally, interaction of Tom1p with Spt6p in the context of transcription elongation is proposed. Yet it is not clear on the mechanistic level how this is regulated if Tom1p and Rpb1p bind in a competitive manner. How is Tom1p tethered to the elongation complex if not through Spt6p? In addition to WT vs. knockout, the authors should further perform the genetic analyses with the intΔ11 mutant. This way they might be able pin down which interactions on chromatin are mediated by Spt6 vs. by other factors and could strengthen the overall model involving Spt6P.<br /> Although the authors try to describe a final model in the discussion, this section is not easy to follow and needs more explanation, ideally drawn as a Figure of the proposed mechanism.

Reviewer #3 (Public review):

Summary:

The authors performed a detailed single-cell analysis of the early embryonic cranial neural plate with unprecedented temporal resolution between embryonic days 7.5 and 8.75. They employed diffusion analysis to identify genes that correspond to different temporal and spatial locations within the embryo. Finally, they also examined the global response of cranial tissue to a Smoothened agonist.

Strengths:

Overall, this is an impressive resource, well-validated against sets of genes with known temporal and spatial patterns of expression. It will be of great value to investigators examining the early stages of neural plate patterning, neural progenitor diversity, and the roles of signaling molecules and gene regulatory networks controlling the regionalization and diversification of the neural plate.

Weaknesses:

The manuscript should be considered a resource. Experimental manipulation is limited to the analysis of neural plate cells that were cultured in vitro for 12 hours with SAG. Besides the identification of a significant set of previously unreported genes that are differentially expressed in the cranial neural plate, there is little new biological insight emerging from this study. Some additional analyses might help to highlight novel hypotheses arising from this remarkable resource.

Reviewer #3 (Public Review):

The work by Dar et al. examines RNA metabolism under cellular stress, focusing on stress-granule-dependent RNA decay. It employs direct RNA sequencing with a Nanopore-based method, revealing that cellular stress induces prevalent 5' end RNA decay that is coupled to translation and ribosome occupancy but is independent of the shortening of the poly(A) tail. This decay, however, is dependent on XRN1 and enriched in the stress granule transcriptome. Notably, inhibiting stress granule formation in G3BP1/2-null cells restores the RNA length to the same level as wild-type. It suppresses stress-induced decay, identifying RNA decay as a critical determinant of RNA metabolism during cellular stress and highlighting its dependence on stress-granule formation. This is an exciting and novel discovery utilizing innovative sequencing methods to studying mRNA decay.

Reviewer #3 (Public review):

The aim of the study was to map, a) whether different tissues exhibit different metabolic profiles (this is known already), what differences are found between female and male mice and how the profiles changes with age. In particular, the study recorded the activity of respirasomes, i.e. the concerted activity of mitochondrial respiratory complex chains consisting of CI+CIII2+CIV, CII+CIII2+CIV or CIV alone.

The strength is certainly the atlas of oxidative metabolism in the whole mouse body, the inclusion of the two different sexes and the comparison between young and old mice. The measurement was performed on frozen tissue, which is possible as already shown (Acin-Perez et al, EMBO J, 2020).

Weakness: The assay reveals the maximum capacity of enzyme activity, which is an artificial situation and may differ from in vivo respiration, as the authors themselves discuss. The material used was a very crude preparation of cells containing mitochondria and other cytosolic compounds and organelles. Thus, the conditions are not well defined and the respiratory chain activity was certainly uncoupled from ATP synthesis. Preparation of more pure mitochondria and testing for coupling would allow evaluation of additional parameters: P/O ratios, feedback mechanism, basal respiration, and ATP-coupled respiration, which reflect in vivo conditions much better. The discussion is rather descriptive and cautious and could lead to some speculations about what could cause the differences in respiration and also what consequences these could have, or what certain changes imply.<br /> Nevertheless, this study is an important step towards this kind of analysis.

Comments on the second revision:

I believe this is an important and interesting area of study, although I recognise that the assay which measures maximal enzyme activity under unphysiological conditions has its limitations. Nevertheless, it does seem possible to get a first glance of the respiratory situation in the respective tissue. There is a typo in the source data (Fig. xC) for skeletal muscle.

Reviewer #3 (Public review):

This paper seeks to understand the role of alveolar myofibroblasts in the abnormal lung development after saccular stage injury.

Strengths:

(1) Multiple models of neonatal injury are used, hyperoxia and transgenic models that target alveolar myofibroblasts.

(2) The authors integrate their data with prior published single-cell data from neonatal hyperoxia injury models and demonstrate concordant findings.

Weaknesses:

(1) As the authors acknowledge in the discussion, there are no spatial and temporal validation data of the single-cell findings. As the ductal myofibroblasts has many overlapping genes, localizing and quantifying the loss of these cells in injury as a plausible mechanistic driver would greatly strengthen the conclusion.

(2) As they note in their response, this proved to be technically difficult and current Pdgfra-lineage trace tools are not without their own limitations.

Summary:

Taken together, this manuscript provides a rich data set from a model of irreversible neonatal lung injury. The single-cell analysis methods are well-articulated and the limitations are acknowledged, allowing this paper to provide a foundation for future work to spatially and temporally validate these claims.

Reviewer #3 (Public review):

The paper addresses pivotal questions concerning the multifaceted functions of oyster hemocytes by integrating single-cell RNA sequencing (scRNA-seq) data with analyses of cell morphology, transcriptional profiles, and immune functions. In addition to investigating granulocyte cells, the study delves into the potential roles of blast and hyalinocyte cells. A key discovery highlighted in this research is the identification of cell types engaged in antimicrobial activities, encompassing processes such as phagocytosis, intracellular copper accumulation, oxidative bursts, and antimicrobial peptide synthesis.

A particularly intriguing aspect of the study lies in the exploration of hemocyte lineages, warranting further investigation, such as employing scRNA-seq on embryos at various developmental stages.

In the opinion of this reviewer, the discussion should compare and contrast the transcriptome characteristics of hemocytes, particularly granule cells, across the three species of bivalves, aligning with the published scRNA-seq studies in this field to elucidate the uniformities and variances in bivalve hemocytes.

Reviewer #3 (Public review):

Summary:

In multicellular organisms, autophagosomes are formed throughout the cytosol, while late endosomes/lysosomes are relatively confined in the perinuclear region. It is known that autophagosomes gain access to the lysosome-enriched region by microtubule-based trafficking. The mechanism by which autophagosomes move along microtubules remains incompletely understood. In this manuscript, Péter Lőrincz and colleagues investigated the mechanism driving the movement of nascent autophagosomes along the microtubule towards the non-centrosomal microtubule organizing center (ncMTOC) using the fly fat body as a model system. The authors took an approach whereby they examined autophagosome positioning in cells where autophagosome-lysosome fusion was inhibited by knocking down the HOPS subunit Vps16A. Despite being generated at random positions in the cytosol, autophagosomes accumulate around the nucleus when Vps16A is depleted. They then performed an RNA interference screen to identify the factors involved in autophagosome positioning. They found that the dynein-dynactin complex is required for the trafficking of autophagosomes toward ncMTOC. Dynein loss leads to the peripheral relocation of autophagosomes. They further revealed that a pair of small GTPases and their effectors, Rab7-Epg5 and Rab39-ema, are required for bidirectional autophagosome transport. Knockdown of these factors in Vps16a RNAi cells causes the scattering of autophagosomes throughout the cytosol.

Strengths:

The data presented in this study help us to understand the mechanism underlying the trafficking and positioning of autophagosomes.

Weaknesses:

Major concerns:

(1) The localization of EPG5 should be determined. The authors showed that EPG5 colocalizes with endogenous Rab7. Rab7 labels late endosomes and lysosomes. Previous studies in mammalian cells have shown that EPG5 is targeted to late endosomes/lysosomes by interacting with Rab7. EPG5 promotes the fusion of autophagosomes with late endosomes/lysosomes by directly recognizing LC3 on autophagosomes and also by facilitating the assembly of the SNARE complex for fusion. In Figure 5I, the EPG5/Rab7-colocalized vesicles are large and they are likely to be lysosomes/autolysosomes.

(2) The experiments were performed in Vps16A RNAi KD cells. Vps16A knockdown blocks fusion of vesicles derived from the endolysosomal compartments such as fusion between lysosomes. The pleiotropic effect of Vps16A RNAi may complicate the interpretation. The authors need to verify their findings in Stx17 KO cells, as it has a relatively specific effect on the fusion of autophagosomes with late endosomes/lysosomes.

(3) Quantification should be performed in many places such as in Figure S4D for the number of FYVE-GFP labeled endosomes and in Figures S4H and S4I for the number and size of lysosomes.

(4) In this study, the transport of autophagosomes is investigated in fly fat cells. In fat cells, a large number of large lipid droplets accumulate and the endomembrane systems are distinct from that in other cell types. The knowledge gained from this study may not apply to other cell types. This needs to be discussed.

Minor concerns:

(5) Data in some panels are of low quality. For example, the mCherry-Atg8a signal in Figure 5C is hard to see; the input bands of Dhc64c in Figure 5L are smeared.

(6) In this study, both 3xmCherry-Atg8a and mCherry-Atg8a were used. Different reporters make it difficult to compare the results presented in different figures.

(7) The small autophagosomes presented in Figures such as in Figure 1D and 1E are not clear. Enlarged images should be presented.

(8) The authors showed that Epg5-9xHA coprecipitates with the endogenous dynein motor Dhc64C. Is Rab7 required for the interaction?

(9) The perinuclear lysosome localization in Epg5 KD cells has no indication that Epg5 is an autophagosome-specific adaptor.

Reviewer #3 (Public review):

Summary:

Bennion et al. investigate how semantic relatedness proactively benefits the learning of new word pairs. The authors draw predictions from Osgood (1949), which posits that the degree of proactive interference (PI) and proactive facilitation (PF) of previously learned items on to-be-learned items depends on the semantic relationships between the old and new information. In the current study, participants subjects learn a set of word pairs ( "supplemental pairs"), followed by a second set of pairs ("base pairs"), in which the cue, target or both words are changed, or the pair was identical. Pairs were drawn from either a narrower or wider stimulus set and were tested after either a 5 minute or 48 hour delay. The results show that semantic relatedness overwhelmingly produces PF and greater memory interdependence between base and supplemental pairs, except in the case of unrelated pairs in a wider stimulus set after a short delay, which produced PI. In their final analyses, the authors compare their current results to previous work from their group studying the analogous retroactive effects of semantic relatedness on memory. These comparisons show generally similar, if slightly weaker, patterns of results. The authors interpret their results in the framework of recursive reminders (Hintzman, 2011), which posits that the semantic relationships between new and old word pairs promotes reminders of the old information during the learning of the new to-be-learned information. These reminders help to integrate the old and new information and result in additional retrieval practice opportunities that in turn improve later recall.

Strengths:

Overall, I thought that the analyses were thorough and well-thought-out and the results were incredibly well-situated in the literature, especially with the additional clarification and framing that the authors have made in response to reviewer comments. In particular, I found that the large sample size, inclusion of a wide range of semantic relatedness across the two stimulus sets, variable delays and the ability to directly compare the current results to their prior results on the retroactive effects of semantic relatedness were particular strengths of the authors' approach and make this an impressive contribution to the existing literature. I thought that their interpretations and conclusions were mostly reasonable and included appropriate caveats (where applicable).

Weaknesses:

The changes and additional analyses that the authors have made have addressed my concerns about their analyses. Including the additional Fig 1- Supp 1, panel C greatly helps with the interpretability across stimulus sets, and the additional analyses the authors have performed teasing apart whether cue and target similarity separately influence memorability and interdependence seem to support the rest of their conclusions.

Reviewer #3 (Public review):

Summary:

This important study combines in vitro and in vivo recording to determine how the firing of cortical and striatal neurons changes during a fever range temperature rise (37-40 oC). The authors found that certain neurons will start, stop, or maintain firing during these body temperature changes. The authors further suggested that the TRPV3 channel plays a role in maintaining cortical activity during fever.

Strengths:

The topic of how the firing pattern of neurons changes during fever is unique and interesting. The authors carefully used in vitro electrophysiology assays to study this interesting topic.

Weaknesses:

(1) In vivo recording is a strength of this study. However, data from in vivo recording is only shown in Figures 5A,B. This reviewer suggests the authors further expand on the analysis of the in vivo Neuropixels recording. For example, to show single spike waveforms and raster plots to provide more information on the recording. The authors can also separate the recording based on brain regions (cortex vs striatum) using the depth of the probe as a landmark to study the specific firing of cortical neurons and striatal neurons. It is also possible to use published parameters to separate the recording based on spike waveform to identify regular principal neurons vs fast-spiking interneurons. Since the authors studied E/I balance in brain slices, it would be very interesting to see whether the "E/I balance" based on the firing of excitatory neurons vs fast-spiking interneurons might be changed or not in the in vivo condition.

(2) The author should propose a potential mechanism for how TRPV3 helps to maintain cortical activity during fever. Would calcium influx-mediated change of membrane potential be the possible reason? Making a summary figure to put all the findings into perspective and propose a possible mechanism would also be appreciated.

(3) The author studied P7-8, P12-14, and P20-26 mice. How do these ages correspond to the human ages? it would be nice to provide a comparison to help the reader understand the context better.

Reviewer #3 (Public review):

Summary:

This study presents a useful computational tool, termed FLiSimBA. The MATLAB-based FLiSimBA simulations allow users to examine the effects of various noise factors (such as autofluorescence, afterpulse of the photomultiplier tube detector, and other background signals) and varying sensor expression levels. Under the conditions explored, the simulations unveiled how these factors affect the observed lifetime measurements, thereby providing useful guidelines for experimental designs. Further simulations with two distinct fluorophores uncovered conditions in which two different lifetime signals could be distinguished, indicating multiplexed dynamic imaging may be possible.

Strengths:

The simulations and their analyses were done systematically and rigorously. FliSimba can be useful for guiding and validating fluorescence lifetime imaging studies. The simulations could define useful parameters such as the minimum number of photons required to detect a specific lifetime, how sensor protein expression level may affect the lifetime data, the conditions under which the lifetime would be insensitive to the sensor expression levels, and whether certain multiplexing could be feasible.

Weaknesses:

The analyses have relied on a key premise that the fluorescence lifetime in the system can be described as two-component discrete exponential decay. This means that the experimenter should ensure that this is the right model for their fluorophores a priori and should keep in mind that the fluorescence lifetime of the fluorophores may not be perfectly described by a two-component discrete exponential (for which alternative algorithms have been implemented: e.g., Steinbach, P. J. Anal. Biochem. 427, 102-105, (2012)). In this regard, I also couldn't find how good the fits were for each simulation and experimental data to the given fitting equation (Equation 2, for example, for Figure 2C data).

Also, in Figure 2C, the 'sensor only' simulation without accounting for autofluorescence (as seen in Sensor + autoF) or afterpulse and background fluorescence (as seen in Final simulated data) seems to recapitulate the experimental data reasonably well. So, at least in this particular case where experimental data is limited by its broad spread with limited data points, being able to incorporate the additional noise factors into the simulation tool didn't seem to matter too much.

Reviewer #3 (Public review):

Summary:

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

Strengths:

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

Weaknesses:

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

Comments on revisions:

Thank you for addressing the comments and concerns. The author has responded to all points thoroughly and clarified them well. However, please include the key points from the responses to the comments (Introduction ((3), (5)) and Results ((5)) into the manuscript. While the explanations in the response letter are reasonable, the current descriptions in the manuscript may limit the reader's understanding. Expanding on these points in the Introduction, Results, or Discussion sections would enhance clarity and comprehensiveness.

Reviewer #3 (Public review):

Summary:

In their study, the authors combine developmental and comparative transcriptomics to identify candidate genes with plastic, canalized, or lineage-specific (i.e., divergent) expression patterns associated with an unusual overwintering phenomenon (Dehnel's phenomenon - seasonal size plasticity) in the Eurasian shrew. Their focus is on the shrinkage and regrowth of the hypothalamus, a brain region that undergoes significant seasonal size changes in shrews and plays a key role in regulating metabolic homeostasis. Through combined transcriptomic analysis, they identify genes showing derived (lineage-specific), plastic (seasonally regulated), and canalized (both lineage-specific and plastic) expression patterns. The authors hypothesize that genes involved in pathways such as the blood-brain barrier, metabolic state sensing, and ion-dependent signaling will be enriched among those with notable transcriptomic patterns. They complement their transcriptomic findings with a cell culture-based functional assessment of a candidate gene believed to reduce apoptosis.

Strengths:

The study's rationale and its integration of developmental and comparative transcriptomics are well-articulated and represent an advancement in the field. The transcriptome, known for its dynamic and plastic nature, is also influenced by evolutionary history. The authors effectively demonstrate how multiple signals-evolutionary, constitutive, and plastic-can be extracted, quantified, and interpreted. The chosen phenotype and study system are particularly compelling, as it not only exemplifies an extreme case of Dehnel's phenotype, but the metabolic requirements of the shrew suggest that genes regulating metabolic homeostasis are under strong selection.

Weaknesses:

(1) In a number of places (described in detail below), the motivation for the experimental, analytical, or visualization approach is unclear and may obscure or prevent discoveries.

(2) Temporal Expression - Figure 1 and Supplemental Figure 2 and associated text:<br /> - It is unclear whether quantitative criteria were used to distinguish "developmental shift" clusters from "season shift" clusters. A visual inspection of Supplemental Figure 2 suggests that some clusters (e.g., clusters 2, 8, and to a lesser extent 12) show seasonal variation, not just developmental differences between stages 1 and 2. While clustering helps to visualize expression patterns, it may not be the most appropriate filter in this case, particularly since all "season shift" clusters are later combined in KEGG pathway and GO analyses (Figure 1B).<br /> - The authors do not indicate whether they perform cluster-specific GO or KEGG pathway enrichment analyses. The current analysis picks up relevant pathways for hypothalamic control of homeostasis, which is a useful validation, but this approach might not fully address the study's key hypotheses.

(3) Differential expression between shrinkage (stage 2) and regrowth (stage 4) and cell culture targets<br /> - The rationale for selecting BCL2L1 for cell culture experiments should be clarified. While it is part of the apoptosis pathway, several other apoptosis-related genes were identified in the differential gene expression (DGE) analysis, some showing stronger differential expression or shrew-specific branch shifts. Why was BCL2L1 prioritized over these other candidates?<br /> - The authors mention maintaining (or at least attempting to maintain) a 1:1 sex ratio for the comparative analysis, but it is unclear if this was also done for the S. araneus analysis. If not, why? If so, was sex included as a covariate (e.g., a random effect) in the differential expression analysis? Sex-specific expression elevates with group variation and could impact the discovery of differentially expressed genes.

(4) Discussion: The term "adaptive" is used frequently and liberally throughout the discussion. The interpretation of seasonal changes in gene expression as indicators of adaptive evolution should be done cautiously as such changes do not necessarily imply causal or adaptive associations.

Reviewer #3 (Public review):

Summary:

Chen et al. identify endophilin A1 as a novel component of the inhibitory postsynaptic scaffold. Their data show impaired evoked inhibitory synaptic transmission in CA1 neurons of mice lacking endophilin A1, and an increased susceptibility to seizures. Endophilin can interact with the postsynaptic scaffold protein gephyrin and promote assembly of the inhibitory postsynaptic element. Endophilin A1 is known to play a role in presynaptic terminals and in dendritic spines, but a role for endophilin A1 at inhibitory postsynaptic densities has not yet been described.

Strengths:

The authors used a broad array of experimental approaches to investigate this, including tests of seizure susceptibility, electrophysiology, biochemistry, neuronal culture, and image analysis.

Weaknesses:

Many results are difficult to interpret, and the data quality is not always convincing, unfortunately. The basic premise of the study, that gephyrin and endophilin A1 interact, requires a more robust analysis to be convincing.

Reviewer #3 (Public review):

Summary:

The manuscript by Wu D. et al. explores an innovative approach to immunometabolism and obesity by investigating the potential of targeting macrophage Inositol-requiring enzyme 1α (IRE1α) in cases of overnutrition. Their findings suggest that pharmacological inhibition of IRE1α could influence key aspects such as adipose tissue inflammation, insulin resistance, and thermogenesis. Notable discoveries include the identification of High-Fat Diet (HFD)-induced CD9+ Trem2+ macrophages and the reversal of metabolically active macrophages' activity with IRE1α inhibition using STF. These insights could significantly impact future obesity treatments.

Strengths:

The study's key strengths lie in its identification of specific macrophage subsets and the demonstration that inhibiting IRE1α can reverse the activity of these macrophages. This provides a potential new avenue for developing obesity treatments and contributes valuable knowledge to the field.

Weaknesses:

The research lacks an in-depth exploration of the broader metabolic mechanisms involved in controlling diet-induced obesity (DIO). Addressing this gap would strengthen the understanding of how targeting IRE1α might fit into the larger metabolic landscape.

Impact and Utility:

The findings have the potential to advance the field of obesity treatment by offering a novel target for intervention. However, further research is needed to fully elucidate the metabolic pathways involved and to confirm the long-term efficacy and safety of this approach. The methods and data presented are useful, but additional context and exploration are required for broader application and understanding.

Reviewer #3 (Public review):

This study investigates how two cortical regions that are central to the study of rodent motor control (rostral forelimb area, RFA, and caudal forelimb area, CFA) interact during directional forelimb reaching in mice. The authors investigate this interaction using<br /> (1) optogenetic manipulations in one area while recording extracellularly from the other,<br /> (2) statistical analyses of simultaneous CFA/RFA extracellular recordings, and<br /> (3) network modeling.<br /> The authors provide solid evidence that asymmetry between RFA and CFA can be observed, although such asymmetry is only observed in certain experimental and analytical contexts.

The authors find asymmetry when applying optogenetic perturbations, reporting a greater impact of RFA inactivation on CFA activity than vice-versa. The authors then investigate asymmetry in endogenous activity during forelimb movements and find asymmetry with some analytical methods but not others. Asymmetry was observed in the onset timing of movement-related deviations of local latent components with RFA leading CFA (computed with PCA) and in a relatively higher proportion and importance of cross-area latent components with RFA leading than CFA leading (computed with DLAG). However, no asymmetry was observed using several other methods that compute cross-area latent dynamics, nor with methods computed on individual neuron pairs across regions. The authors follow up this experimental work by developing a two-area model with asymmetric dependence on cross-area input. This model is used to show that differences in local connectivity can drive asymmetry between two areas with equal amounts of across-region input.

Overall, this work provides a useful demonstration that different cross-area analysis methods result in different conclusions regarding asymmetric interactions between brain areas and suggests careful consideration of methods when analyzing such networks is critical. A deeper examination of why different analytical methods result in observed asymmetry or no asymmetry, analyses that specifically examine neural dynamics informative about details of the movement, or a biological investigation of the hypothesis provided by the model would provide greater clarity regarding the interaction between RFA and CFA.

Strengths:

The authors are rigorous in their experimental and analytical methods, carefully monitoring the impact of their perturbations with simultaneous recordings, and providing valid controls for their analytical methods. They cite relevant previous literature that largely agrees with the current work, highlighting the continued ambiguity regarding the extent to which there exists an asymmetry in endogenous activity between RFA and CFA.

A strength of the paper is the evidence for asymmetry provided by optogenetic manipulation. They show that RFA inactivation causes a greater absolute difference in muscle activity than CFA interaction (deviations begin 25-50 ms after laser onset, Figure 1) and that RFA inactivation causes a relatively larger decrease in CFA firing rate than CFA inactivation causes in RFA (deviations begin <25ms after laser onset, Figure 3). The timescales of these changes provide solid evidence for an asymmetry in the impact of inactivating RFA/CFA on the other region that could not be driven by differences in feedback from disrupted movement (which would appear with a ~50ms delay).

The authors also utilize a range of different analytical methods, showing an interesting difference between some population-based methods (PCA, DLAG) that observe asymmetry, and single neuron pair methods (granger causality, transfer entropy, and convergent cross mapping) that do not. Moreover, the modeling work presents an interesting potential cause of "hierarchy" or "asymmetry" between brain areas: local connectivity that impacts dependence on across-region input, rather than the amount of across-region input actually present.

Weaknesses:

There is no attempt to examine neural dynamics that are specifically relevant/informative about the details of the ongoing forelimb movement (e.g., kinematics, reach direction). Thus, it may be preemptive to claim that firing patterns alone do not reflect functional influence between RFA/CFA. For example, given evidence that the largest component of motor cortical activity doesn't reflect details of ongoing movement (reach direction or path; Kaufman, et al. PMID: 27761519) and that the analytical tools the authors use likely isolate this component (PCA, CCA), it may not be surprising that CFA and RFA do not show asymmetry if such asymmetry is related to the control of movement details. An asymmetry may still exist in the components of neural activity that encode information about movement details, and thus it may be necessary to isolate and examine the interaction of behaviorally-relevant dynamics (e.g., Sani, et al. PMID: 33169030).

The idea that local circuit dynamics play a central role in determining the asymmetry between RFA and CFA is not supported by experimental data in this paper. The plausibility of this hypothesis is supported by the model but is not explored in any analyses of the experimental data collected. Given the focus on this idea in the discussion, further experimental investigation is warranted.

Reviewer #3 (Public review):

Summary:

In this study, Harikrishnan Rajendran, Roi Weinberger, Ehud Fonio, and Ofer Feinerman measured the digging behaviours of queens and workers for the first 6 months of colony development, as well as groups of young or old ants. They also provide a quantitative model describing the digging behaviours and allowing predictions. They found that young ants dig more slanted tunnels, while older ants dig more vertically (straight down). This finding is important, as it describes a new form of age polyethism (a division of labour based on age). Age polyethism is described as a "yes or no" mechanism, where individuals perform or not a task according to their age (usually young individuals perform in-nest tasks, and older ones foraging). Here, the way of performing the task is modified, not only the propensity to carry it or not. This data therefore adds in an interesting way to the field of collective behaviours and division of labour.

The conclusions of the paper are well supported by the data. Measurements of the same individuals over time would have strengthened the claims.

Strengths:

I find that the measure of behaviour through development is of great value, as those studies are usually done at a specific time point with mature colonies. The description of a behaviour that is modified with age is a notable finding in the world of social insects. The sample sizes are adequate and all the information clearly provided either in the methods or supplementary.

Weaknesses:

I think the paper is failing to take into consideration or at least discuss the role of inter-individual variabilities. Tasks have been known to be undertaken by only a few hyper-active individuals for example. Comments on the choice to use averages and the potential roles of variations between individuals are in my opinion lacking. Throughout the paper wording should be modified to refer to the group and not the individuals, as it was the collective digging that was measured. Another issue I had was the use of "mature colony" for colonies with very few individuals and only 6 months of age. Comments on the low number of workers used compared to natural mature colonies would be welcome.

Reviewer #3 (Public review):

Summary:

In this study, the authors aimed to index individual variation in decision-making when decisions pit the interests of the self (gains in money, potential for electric shock) against the interests of an unknown stranger in another room (potential for unknown shock). In addition, the authors conducted an additional study in which male participants were either administered intranasal oxytocin or placebo before completing the task to identify the role of oxytocin in moderating task responses. Participants' choice data was analyzed using a harm aversion model in which choices were driven by the subjective value difference between the less and more painful options.

Strengths:

Overall I think this is a well-conducted, interesting, and novel set of research studies exploring decision-making that balances outcomes for the self versus a stranger, and the potential role of the hormone oxytocin (OT) in shaping these decisions. The pain component of the paradigm is well designed, as is the decision-making task, and overall the analyses were well suited to evaluating and interpreting the data. Advantages of the task design include the absence of deception, e.g., the use of a real study partner and real stakes, as a trial from the task was selected at random after the study and the choice the participant made was actually executed. 

Weaknesses:

The primary weakness of the paper concerns its framing. Although it purports to be measuring "hyper-altruism" it does not provide evidence to support why any of the behavior being measured is extreme enough to warrant the modifier "hyper" (and indeed throughout I believe the writing tends toward hyperbole, using, e.g., verbs like "obliterate" rather than "reduce"). More seriously, I do not believe that the task constitutes altruism, but rather the decision to engage, or not engage, in instrumental aggression.

I found it surprising that a paradigm that entails deciding to hurt or not hurt someone else for personal benefit (whether acquiring a financial gain or avoiding a loss) would be described as measuring "altruism." Deciding to hurt someone for personal benefit is the definition of instrumental aggression. I did not see that in any of the studies was there a possibility of acting to benefit the other participant in any condition. Altruism is not equivalent to refraining from engaging in instrumental aggression. True altruism would be to accept shocks to the self for the other's benefit (e.g., money).  The interpretation of this task as assessing instrumental aggression is supported by the fact that only the Instrumental Harm subscale of the OUS was associated with outcomes in the task, but not the Impartial Benevolence subscale. By contrast, the IB subscale is the one more consistently associated with altruism (e.g,. Kahane et al 2018; Amormino at al, 2022) I believe it is important for scientific accuracy for the paper, including the title, to be re-written to reflect what it is testing.

Relatedly: in the introduction I believe it would be important to discuss the non-symmetry of moral obligations related to help/harm--we have obligations not to harm strangers but no obligation to help strangers. This is another reason I do not think the term "hyper altruism" is a good description for this task--given it is typically viewed as morally obligatory not to harm strangers, choosing not to harm them is not "hyper" altruistic (and again, I do not view it as obviously altruism at all).

The framing of the role of OT also felt incomplete. In introducing the potential relevance of OT to behavior in this task, it is important to pull in evidence from non-human animals on origins of OT as a hormone selected for its role in maternal care and defense (including defensive aggression). The non-human animal literature regarding the effects of OT is on the whole much more robust and definitive than the human literature. The evidence is abundant that OT motivates the defensive care of offspring of all kinds. My read of the present OT findings is that they increase participants' willingness to refrain from shocking strangers even when incurring a loss (that is, in a context where the participant is weighing harm to themselves versus harm to the other). It will be important to explain why OT would be relevant to refraining from instrumental aggression, again, drawing on the non-human animal literature.

Another important limitation is the use of only male participants in Study 2. This was not an essential exclusion. It should be clear throughout sections of the manuscript that this study's effects can be generalized only to male participants.

Reviewer #3 (Public review):

Summary:

The study highlights how the initiation, reversal, and cessation of movements are linked to changes in beta synchronization within the basal ganglia-cortex loops. It was observed that different movement phases, such as starting, stopping briefly, and stopping completely, affect beta oscillations in the motor system.

It was found that unpredictable cues lead to stronger changes in STN-cortex beta coherence. Additionally, specific patterns of beta and gamma oscillations related to different movement actions and contexts were observed. Stopping movements was associated with a lack of the expected beta rebound during brief pauses within a movement sequence.

Overall, the results underline the complex and context-dependent nature of motor-control and emphasize the role of beta oscillations in managing movement according to changing external cues.

Strengths:

The paper is very well written, clear, and appears methodologically sound.

Although the use of continuous movement (turning) with reversals is more naturalistic than many previous button push paradigms.

Weaknesses:

The generalizability of the findings is somewhat curtailed by the fact that this was performed peri-operatively during the period of the microlesion effect. Given the availability of sensing-enabled DBS devices now and HD-EEG, does MEG offer a significant enough gain in spatial localizability to offset the fact that it has to be done shortly postoperatively with externalized leads, with an attendant stun effect? Specifically, for paradigms that are not asking very spatially localized questions as a primary hypothesis?

Further investigation of the gamma signal seems warranted, even though it has a slightly lower proportional change in amplitude in beta. Given that the changes in gamma here are relatively wide band, this could represent a marker of neural firing that could be interestingly contrasted against the rhythm account presented.

Reviewer #3 (Public review):

Summary:

The authors interrogated the putative role of microglia in determining AgRP fiber maturation in offspring exposed to a maternal high-fat diet. They found that changes in specific parts of the hypothalamus (but not in others) occur in microglia and that the effect of microglia on AgRP fibers appears to be beyond synaptic pruning, a classical function of these brain-resident macrophages.

Strengths:

The work is very strong in neuroanatomy. The images are clear and nicely convey the anatomical differences. The microglia depletion study adds functional relevance to the paper; however, the pitfalls of the technology regarding functional relevance should be discussed.

Weaknesses:

There was no attempt to interrogate microglia in different parts of the hypothalamus functionally. Morphology alone does not reflect a potential for significant signaling alterations that may occur within and between these and other cell types.

The authors should discuss the limitations of their approach and findings and propose future directions to address them.

Reviewer #3 (Public review):

Summary:

The authors investigate the role of ErbB4 in parvalbumin (PV) interneurons within the olfactory bulb (OB) and its regulation of odor discrimination behavior in mice. They demonstrate that odor discrimination increases ErbB4 kinase activity and that the loss of ErbB4 in the OB impairs the dishabituation of odor response and discrimination of complex odors. The study also characterizes the expression of ErbB4 in the OB, showing it is enriched in PV neurons. Furthermore, the authors utilize a mouse model in which ErbB4 is knocked out in PV neurons and perform a variety of behavioral, electrophysiological, and local field potential (LFP) recording experiments to characterize alterations in olfactory bulb activity. They then use a model in which ErbB4 is specifically knocked out in PV neurons in the OB and show that this manipulation disrupts odor-related behaviors in mice.

Strengths:

The study's strengths lie in its use of a diverse range of techniques, including RNAscope, IHC, and Western blotting, to assess the presence of ErbB4 in PV neurons within the OB. Additionally, the authors employ various behavioral tests to evaluate the effects of ErbB4 manipulation in different mouse models, alongside comprehensive electrophysiological experiments and LFP recordings to examine the impact of these manipulations on OB physiology.

Weaknesses:

While the data presented in this paper are interesting, several major concerns reduce my enthusiasm for this study, as outlined below:

(1) In reviewing Figure 1C/D, there are several concerns regarding the clarity and interpretation of the data:

a) While the Western blot for ErbB4 in other figures (Figure 1F, 2I) of the manuscript shows a clear single band, the blot presented in Figure 1C (for both p-ErbB4 and total ErbB4) shows multiple bands, which is unexpected. This discrepancy raises concerns about the consistency of the results.

b) The data presented in Figure 1D uses only 3 mice per group, and the reported p-value of 0.0492, while technically significant, is very close to the threshold. This raises concerns about the robustness of the finding, especially given the small sample size. Additionally, the p-ErbB4 band intensity in the Go/No-Go condition in Figure 1C does not appear to show a clear increase over the Go/Go condition, which is not congruent with the bar graph in Figure 1D showing a 50% increase in p-ErbB4/ErbB4 levels.

c) It is a standard practice in many journals to include full, uncropped Western blot images as supplementary material. This transparency helps ensure that no bands are selectively shown or omitted and increases confidence in the presented data.

(2) In Figure 2, the authors used the anti-ErbB4 antibody sc-283 from Santa Cruz to assess the expression of ErbB4 in PV neurons and the absence of its expression in PV-ErbB4 knock-out mice. However, this particular antibody has been shown to produce non-specific bands in Western blotting and also generate non-specific labeling in IHC. This non-specificity has been demonstrated in Vullhorst et al. (2009, J Neurosci), raising significant concerns about the reliability of the data generated using this antibody.

(3) In reviewing the statistical analysis for the series of odor discrimination tests, there could be a potential issue with the clarity of the significance testing. Although the figure legend reports the F and p values from the two-way ANOVA, it is unclear whether these values represent the main effects or the results of a post hoc test. Additionally, it is not clear whether the asterisk in the figures reflects significance from a post hoc test or from the overall ANOVA. The methods section does not explicitly state whether a post hoc test was performed to assess differences between the knockout and control groups. Given that the tests were conducted across multiple days or conditions, a post hoc test that can adjust for multiple comparisons would be necessary to accurately identify where specific differences between the groups exist.

(4) Throughout the manuscript, the authors use different mouse models, including ErbB4 knockout specifically in the OB (AAV-Cre-GFP), ErbB4 knockout in PV interneurons throughout the brain (PV-ErbB4-/-), and ErbB4 knockout in PV interneurons within the OB (AAV-PV-Cre-GFP). For Figures 4 and 5, the authors use the PV-ErbB4-/- model to examine odor-evoked activity and neural oscillations within the OB. Since the knockout affects PV interneurons across the entire brain, it is difficult to disentangle whether the observed changes in the OB are due to local effects or broader network alterations elsewhere in the brain.

(5) While the electrophysiological experiments shown in Figures 6-8 provide valuable insights into the reduced inhibition to MCs in PV-ErbB4 knockout mice, it appears that the authors did not record from PV interneurons themselves. Since PV interneurons are central to the proposed mechanism, directly recording them would provide critical information on how the ErbB4 knockout affects their intrinsic properties, synaptic inputs, and firing behavior. Without these direct recordings, the conclusions about the specific role of PV neurons in regulating MC activity remain somewhat indirect. Prior studies have established that knockout of ErbB4 in PV interneurons reduces mEPSC frequency in PV neurons (Del Pino et al., 2013).

(6) In Figure 9, the authors knock out ErbB4 in PV neurons in the OB with AAV-PV-Cre-GFP and show with western blotting that ErbB4 expression is reduced in the mouse injected with AAV-PV-Cre-GFP. However, it is not clear whether ErbB4 was selectively knocked out in PV neurons without the quantification from IHC assays.

Reviewer #3 (Public review):

Summary:

The authors aim to explore whether other subunits besides MED1 exert specific functions during the process of terminal erythropoiesis with global gene repression, and finally they demonstrated that MED26-enriched condensates drive erythropoiesis through modulating transcription pausing.

Strengths:

Through both in vitro and in vivo models, the authors showed that while MED1 and MED26 co-occupy a plethora of genes important for cell survival and proliferation at the HSPC stage, MED26 preferentially marks erythroid genes and recruits pausing-related factors for cell fate specification. Gradually, MED26 becomes the dominant factor in shaping the composition of transcription condensates and transforms the chromatin towards a repressive yet permissive state, achieving global transcription repression in erythropoiesis.

Weaknesses:

In the in vitro model, the author only used CD34+ cell-derived erythropoiesis as the validation, which is relatively simple, and more in vitro erythropoiesis models need to be used to strengthen the conclusion.

Reviewer #3 (Public review):

Summary:

Targeted covalent inhibition of therapeutically relevant proteins is an attractive approach in drug development. This manuscript now reports a series of covalent inhibitors for human carbonic anhydrase (CA) isozymes (CAI, CAII, and CAIX, CAXIII) for irreversible binding to a critical histidine amino acid in the active site pocket. To support their findings, they included co-crystal structures of CAI, CAII, and CAIX in the presence of three such inhibitors. Mass spectrometry and enzymatic recovery assays validate these findings, and the results and cellular activity data are convincing.

Strengths:

The authors designed a series of covalent inhibitors and carefully selected non-covalent counterparts to make their findings about the selectivity of covalent inhibitors for CA isozymes quite convincing. The supportive X-ray crystallography and MS data are significant strengths. Their approach of targeted binding of the covalent inhibitors to histidine in CA isozyme may have broad utility for developing covalent inhibitors.

Weaknesses:

This reviewer did not find any significant weaknesses. The authors have incorporated most of my suggestions from the first round of review.

Reviewer #3 (Public review):

The paper presents a solid method for quantifying hematopoietic precursors using statistical variance as a proxy, providing valuable insights into hematopoietic dynamics across different physiological and pathological scenarios. The findings are pivotal for understanding hematopoietic dynamics. The strength of the evidence is convincing and acknowledges limitations such as the binomial assumption and the need of tools to measure clonality.

Liu et al. focus on a mathematical method to quantify active hematopoietic precursors in mice using Confetti reporter mice combined with Cre-lox technology. The paper explores the hematopoietic dynamics in various scenarios, including homeostasis, myeloablation with 5-fluorouracil, Fanconi anemia (FA), and post-transplant environments. The key findings and strengths of the paper include (1) precursor quantification: The study develops a method based on the binomial distribution of fluorescent protein expression to estimate precursor numbers. This method is validated across a wide dynamic range, proving more reliable than previous approaches that suffered from limited range and high variance outside this range; (2) dynamic response analysis: The paper examines how hematopoietic precursors respond to myeloablation and transplantation; (3) application in disease models: The method is applied to the FA mouse model, revealing that these mice maintain normal precursor numbers under steady-state conditions and post-transplantation, which challenges some assumptions about FA pathology. Despite the normal precursor count, a diminished repopulation capability suggests other factors at play, possibly related to cell proliferation or other cellular dysfunctions. In addition, the FA mouse model showed a reduction in active lymphoid precursors post-transplantation, contributing to decreased repopulation capacity as the mice aged. The authors are aware of the limitation of the assumption of uniform expansion. The paper assumes a uniform expansion from active precursor to progenies for quantifying precursor numbers. This assumption may not hold in all biological scenarios, especially in disease states where hematopoietic dynamics can be significantly altered. If non-uniformity is high, this could affect the accuracy of the quantification. Overall, the study underscores the importance of precise quantification of hematopoietic precursors in understanding both normal and pathological states in hematopoiesis, presenting a robust tool that could significantly enhance research in hematopoietic disorders and therapy development. This manuscript would be interesting to the readers of eLife.

Reviewer #3 (Public review):

This is a well-designed study examining an important, surprisingly understudied question: how does adaptation affect spatial frequency processing in the human visual cortex? Using a combination of psychophysics and neuroimaging, the authors test the hypothesis that spatial frequency tuning is shifted to higher or lower frequencies, depending on the preadapted state (low or high s.f. adaptation). They do so by first validating the phenomenon psychophysically, showing that adapting to 0.5 cpd stimuli causes an increase in perceived s.f., and 3.5 cpd causes a relative decrease in perceived s.f. Using the same stimuli, they then port these stimuli to a neuroimaging study, in which population receptive fields are measured under high and low spatial frequency adaptation states. They find that adaptation changes pRF size, depending on adaptation state: adapting to high s.f. led to broader overall pRF sizes across the early visual cortex, whereas adapting to low s.f. led to smaller overall pRF sizes. Finally, the authors carry out a control experiment to psychophysically rule out the possibility that the perceived contrast change w/ adaptation may have given rise to these imaging results (this doesn't appear to be the case). All in all, I found this to be a good manuscript: the writing is taut, and the study is well designed There are a few points of clarification that I think would help, though, including a little more detail about the pRF analyses carried out in this study. Moreover, one weakness is that the sample size is relatively small, given the variability in the effects.

(1) The pRF mapping stimuli and paradigm are slightly unconventional. This is, of course, fairly necessary to assess the question at hand. But, unless I missed it, there is a potentially critical piece of the analyses that I couldn't find in the results or methods: is the to-our adapter incorporated into the inputs for the pRF analyses, or was it simply estimating pRF size in response to the pRF mapping bar? Ignoring the large, full field-ish top-up seems like it might be dismissing an important nonlinearity in RF response to that aspect of the display (including that that had different s.f. content from the mapping stimulus) -especially because it occurred 50% of the time during the pRF mapping procedure. While the bar/top-up were events sub-TR, you could still model the prfprobe+topup response, then downsample to TR level afterwards. In any case, to fully understand this, some more detail is needed here regarding the prf fitting procedure.

(2) I appreciate the eccentricity-dependent breakdown in Figure 5b. However, it would be informative to have included the actual plots of the pRF size as a function of eccen, for the two conditions individually, in addition to the difference effects depicted in 5b.

(3) I know the N is small for this, but did the authors take a look at whether there was any relationship between the magnitude of the psychophysical effect and the change in pRF size, per individual? This is probably underpowered but could be worth a peek.

Reviewer #3 (Public review):

Summary:

One goal of this paper is to introduce a new approach for highly accurate decoding of finger movements from human magnetoencephalography data via dimension reduction of a "multi-scale, hybrid" feature space. Following this decoding approach, the authors aim to show that early skill learning involves "contextualization" of the neural coding of individual movements, relative to their position in a sequence of consecutive movements. Furthermore, they aim to show that this "contextualization" develops primarily during short rest periods interspersed with skill training, and correlates with a performance metric which the authors interpret as an indicator of offline learning.

Strengths:

A clear strength of the paper is the innovative decoding approach, which achieves impressive decoding accuracies via dimension reduction of a "multi-scale, hybrid space". This hybrid-space approach follows the neurobiologically plausible idea of the concurrent distribution of neural coding across local circuits as well as large-scale networks. A further strength of the study is the large number of tested dimension reduction techniques and classifiers (though the manuscript reveals little about the comparison of the latter).

A simple control analysis based on shuffled class labels could lend further support to this complex decoding approach. As a control analysis that completely rules out any source of overfitting, the authors could test the decoder after shuffling class labels. Following such shuffling, decoding accuracies should drop to chance level for all decoding approaches, including the optimized decoder. This would also provide an estimate of actual chance-level performance (which is informative over and beyond the theoretical chance level). Furthermore, currently, the manuscript does not explain the huge drop in decoding accuracies for the voxel-space decoding (Figure 3B). Finally, the authors' approach to cortical parcellation raises questions regarding the information carried by varying dipole orientations within a parcel (which currently seems to be ignored?) and the implementation of the mean-flipping method (given that there are two dimensions - space and time - what do the authors refer to when they talk about the sign of the "average source", line 477?).

Weaknesses:

A clear weakness of the paper lies in the authors' conclusions regarding "contextualization". Several potential confounds, described below, question the neurobiological implications proposed by the authors and provide a simpler explanation of the results. Furthermore, the paper follows the assumption that short breaks result in offline skill learning, while recent evidence, described below, casts doubt on this assumption.

The authors interpret the ordinal position information captured by their decoding approach as a reflection of neural coding dedicated to the local context of a movement (Figure 4). One way to dissociate ordinal position information from information about the moving effectors is to train a classifier on one sequence and test the classifier on other sequences that require the same movements, but in different positions (Kornysheva et al., Neuron 2019). In the present study, however, participants trained to repeat a single sequence (4-1-3-2-4). As a result, ordinal position information is potentially confounded by the fixed finger transitions around each of the two critical positions (first and fifth press). Across consecutive correct sequences, the first keypress in a given sequence was always preceded by a movement of the index finger (=last movement of the preceding sequence), and followed by a little finger movement. The last keypress, on the other hand, was always preceded by a ring finger movement, and followed by an index finger movement (=first movement of the next sequence). Figure 4 - Supplement 2 shows that finger identity can be decoded with high accuracy (>70%) across a large time window around the time of the key press, up to at least {plus minus}100 ms (and likely beyond, given that decoding accuracy is still high at the boundaries of the window depicted in that figure). This time window approaches the keypress transition times in this study. Given that distinct finger transitions characterized the first and fifth keypress, the classifier could thus rely on persistent (or "lingering") information from the preceding finger movement, and/or "preparatory" information about the subsequent finger movement, in order to dissociate the first and fifth keypress. Currently, the manuscript provides no evidence that the context information captured by the decoding approach is more than a by-product of temporally extended, and therefore overlapping, but independent neural representations of consecutive keypresses that are executed in close temporal proximity - rather than a neural representation dedicated to context.

Such temporal overlap of consecutive, independent finger representations may also account for the dynamics of "ordinal coding"/"contextualization", i.e., the increase in 2-class decoding accuracy, across Day 1 (Figure 4C). As learning progresses, both tapping speed and the consistency of keypress transition times increase (Figure 1), i.e., consecutive keypresses are closer in time, and more consistently so. As a result, information related to a given keypress is increasingly overlapping in time with information related to the preceding and subsequent keypresses. The authors seem to argue that their regression analysis in Figure 5 - Figure Supplement 3 speaks against any influence of tapping speed on "ordinal coding" (even though that argument is not made explicitly in the manuscript). However, Figure 5 - Figure Supplement 3 shows inter-individual differences in a between-subject analysis (across trials, as in panel A, or separately for each trial, as in panel B), and, therefore, says little about the within-subject dynamics of "ordinal coding" across the experiment. A regression of trial-by-trial "ordinal coding" on trial-by-trial tapping speed (either within-subject or at a group-level, after averaging across subjects) could address this issue. Given the highly similar dynamics of "ordinal coding" on the one hand (Figure 4C), and tapping speed on the other hand (Figure 1B), I would expect a strong relationship between the two in the suggested within-subject (or group-level) regression. Furthermore, learning should increase the number of (consecutively) correct sequences, and, thus, the consistency of finger transitions. Therefore, the increase in 2-class decoding accuracy may simply reflect an increasing overlap in time of increasingly consistent information from consecutive keypresses, which allows the classifier to dissociate the first and fifth keypress more reliably as learning progresses, simply based on the characteristic finger transitions associated with each. In other words, given that the physical context of a given keypress changes as learning progresses - keypresses move closer together in time and are more consistently correct - it seems problematic to conclude that the mental representation of that context changes. To draw that conclusion, the physical context should remain stable (or any changes to the physical context should be controlled for).

A similar difference in physical context may explain why neural representation distances ("differentiation") differ between rest and practice (Figure 5). The authors define "offline differentiation" by comparing the hybrid space features of the last index finger movement of a trial (ordinal position 5) and the first index finger movement of the next trial (ordinal position 1). However, the latter is not only the first movement in the sequence but also the very first movement in that trial (at least in trials that started with a correct sequence), i.e., not preceded by any recent movement. In contrast, the last index finger of the last correct sequence in the preceding trial includes the characteristic finger transition from the fourth to the fifth movement. Thus, there is more overlapping information arising from the consistent, neighbouring keypresses for the last index finger movement, compared to the first index finger movement of the next trial. A strong difference (larger neural representation distance) between these two movements is, therefore, not surprising, given the task design, and this difference is also expected to increase with learning, given the increase in tapping speed, and the consequent stronger overlap in representations for consecutive keypresses. Furthermore, initiating a new sequence involves pre-planning, while ongoing practice relies on online planning (Ariani et al., eNeuro 2021), i.e., two mental operations that are dissociable at the level of neural representation (Ariani et al., bioRxiv 2023).

Given these differences in the physical context and associated mental processes, it is not surprising that "offline differentiation", as defined here, is more pronounced than "online differentiation". For the latter, the authors compared movements that were better matched regarding the presence of consistent preceding and subsequent keypresses (online differentiation was defined as the mean difference between all first vs. last index finger movements during practice). It is unclear why the authors did not follow a similar definition for "online differentiation" as for "micro-online gains" (and, indeed, a definition that is more consistent with their definition of "offline differentiation"), i.e., the difference between the first index finger movement of the first correct sequence during practice, and the last index finger of the last correct sequence. While these two movements are, again, not matched for the presence of neighbouring keypresses (see the argument above), this mismatch would at least be the same across "offline differentiation" and "online differentiation", so they would be more comparable.

A further complication in interpreting the results regarding "contextualization" stems from the visual feedback that participants received during the task. Each keypress generated an asterisk shown above the string on the screen, irrespective of whether the keypress was correct or incorrect. As a result, incorrect (e.g., additional, or missing) keypresses could shift the phase of the visual feedback string (of asterisks) relative to the ordinal position of the current movement in the sequence (e.g., the fifth movement in the sequence could coincide with the presentation of any asterisk in the string, from the first to the fifth). Given that more incorrect keypresses are expected at the start of the experiment, compared to later stages, the consistency in visual feedback position, relative to the ordinal position of the movement in the sequence, increased across the experiment. A better differentiation between the first and the fifth movement with learning could, therefore, simply reflect better decoding of the more consistent visual feedback, based either on the feedback-induced brain response, or feedback-induced eye movements (the study did not include eye tracking). It is not clear why the authors introduced this complicated visual feedback in their task, besides consistency with their previous studies.

The authors report a significant correlation between "offline differentiation" and cumulative micro-offline gains. However, it would be more informative to correlate trial-by-trial changes in each of the two variables. This would address the question of whether there is a trial-by-trial relation between the degree of "contextualization" and the amount of micro-offline gains - are performance changes (micro-offline gains) less pronounced across rest periods for which the change in "contextualization" is relatively low? Furthermore, is the relationship between micro-offline gains and "offline differentiation" significantly stronger than the relationship between micro-offline gains and "online differentiation"?

The authors follow the assumption that micro-offline gains reflect offline learning. However, there is no direct evidence in the literature that micro-offline gains really result from offline learning, i.e., an improvement in skill level. On the contrary, recent evidence questions this interpretation (Gupta & Rickard, npj Sci Learn 2022; Gupta & Rickard, Sci Rep 2024; Das et al., bioRxiv 2024). Instead, there is evidence that micro-offline gains are transient performance benefits that emerge when participants train with breaks, compared to participants who train without breaks, however, these benefits vanish within seconds after training if both groups of participants perform under comparable conditions (Das et al., bioRxiv 2024).

Reviewer #3 (Public review):

Summary:

To make feeding decisions, animals need to process three types of information: positive cues like sweetness, negative cues like bitterness, and internal states such as hunger or satiety. This study aims to identify where the information is integrated into the fruit fly brain. The authors applied RNA sequencing on second-order gustatory neurons responsible for sweet and bitter processing, under fed and starved conditions. The sequencing data reveal significant changes in gene expression across sweet vs. bitter pathways and fed vs. starved states. The authors focus on the neuropeptide Leucokinin (Lk), whose expression is dependent on the starvation state. They identify a pair of neurons, named SELK neurons, which express Lk and receive direct input from both sweet and bitter gustatory neurons. These SELK neurons are ideal candidates to integrate gustatory and internal state information. Behavioral experiments show that blocking these neurons in starved flies alters their tolerance to bitter substances during feeding.

Strengths:

(1) The study employs a well-designed approach, targeting specific neuronal populations, which is more efficient and precise compared to traditional large-scale genetic screening methods.

(2) The RNAseq results provide valuable data that can be utilized in future studies to explore other molecules beyond Lk.

(3) The identification of SELK neurons offers a promising avenue for future research into how these neurons integrate conflicting gustatory signals and internal state information.

Weaknesses:

(1) Unfortunately, due to technical challenges, the authors were unable to directly image the functional activity of SELK neurons.

(2) In the behavioral experiments, tetanus toxin was used to block SELK neurons. Since these neurons may release multiple neurotransmitters or neuropeptides, the results do not specifically demonstrate that Leucokinin (Lk) is the critical factor, as suggested in Figure 8. To address this, I recommend using RNAi to inhibit Lk expression in SELK neurons and comparing the outcomes to wild-type controls via the PER assay.

DOI: 10.1038/s41598-023-51091-3

Resource: RRID:BDSC_33797

Curator: @maulamb

SciCrunch record: RRID:BDSC_33797

What is this?

Reviewer #3 (Public review):

Summary:

In this manuscript, Last and colleagues describe Ais, an open-source software package for the semi-automated segmentation of cryo-electron tomography (cryo-ET) maps. Specifically, Ais provides a graphical user interface (GUI) for the manual segmentation and annotation of specific features of interest. These manual annotations are then used as input ground-truth data for training a convolutional neural network (CNN) model, which can then be used for automatic segmentation. Ais provides the option of several CNNs so that users can compare their performance on their structures of interest in order to determine the CNN that best suits their needs. Additionally, pretrained models can be uploaded and shared to an online database.

Algorithms are also provided to characterize "model interactions" which allows users to define heuristic rules on how the different segmentations interact. For instance, a membrane adjacent protein can have rules where it must colocalize a certain distance away from a membrane segmentation. Such rules can help reduce false positives; as in the case above, false negatives predicted away from membranes are eliminated.

The authors then show how Ais can be used for particle picking and subsequent subtomogram averaging and for segmentation of cellular tomograms for visual analysis. For subtomogram averaging, they used a previously published dataset and compared the averages of their automated picking with the published manual picking. Analysis of cellular tomogram segmentations were primarily visual.

Strengths:

CNN-based segmentation of cryo-ET data is a rapidly developing area of research, as it promises substantially faster results than manual segmentation as well as the possibility for higher accuracy. However, this field is still very much in the development and the overall performance of these approaches, even across different algorithms, still leaves much to be desired. In this context, I think Ais is an interesting packages, as it aims to provide both new and experienced users streamlined approaches for manual annotation, access to a number of CNNs, and methods to refine the outputs of CNN models against each other. I think this can be quite useful for users, particularly as these methods develop.

Reviewer #3 (Public review):

Summary:

The manuscript by Wang and colleagues describes single molecule localization microscopy to quantify the distribution and organization of Nipah virus F expressed on cells and on virus-like particles. Notably the crystal structure of F indicated hexameric assemblies of F trimers. The authors propose that F clustering favors membrane fusion.

Strengths:

The manuscript provides solid data on imaging of F clustering with the main findings of:<br /> - F clusters are independent of expression levels<br /> - Proteolytic cleavage does not affect F clustering<br /> - Mutations that have been reported to affect the hexamer interface reduce clustering on cells and its distribution on VLPs<br /> - F nanoclusters are stabilized by AP

Comments on the revised version:

The authors addressed most of my previous concerns.

Reviewer #3 (Public review):

This valuable manuscript demonstrates the long-held prediction that the glycosyltransferase UGGT slows degradation of endoplasmic reticulum (ER)-associated degradation substrates through a mechanism involving re-glucosylation of asparagine-linked glycans following release from the calnexin/calreticulin lectins. The evidence supporting this conclusion is solid using genetically-deficient cell models and well established biochemical methods to monitor the degradation of trafficking-incompetent ER-associated degradation substrates, although this could be improved by better defining of the importance of UGGT in the secretion of trafficking competent substrates. This work will be of specific interest to those interested in mechanistic aspects of ER protein quality control and protein secretion.

The authors have largely addressed my comments from the previous round of review. The only remaining comment is about defining the impact of UGGT1 in the regulation of secretion-competent proteins, which the authors indicate they will continue to pursue in subsequent work, which is fine, but remains a minor limitation of the study.

As I mentioned in my previous review, I think that this work is interesting and addresses an important gap in experimental evidence supporting a previously asserted dogma in the field. I do think that the authors would be better suited for highlighting the limitations of the study, as discussed above. Ultimately, though, this is an important addition to the literature.

Reviewer #3 (Public review):

Jo and colleagues set out to investigate the origins and functions of localized FGF/ERK signaling for the differentiation and spatial patterning of primitive streak fates of human embryonic stem cells in a well-established micropattern system. They demonstrate that endogenous FGF signaling is required for ERK activation in a ring-domain in the micropatterns, and that this localized signaling is directly required for differentiation and spatial patterning of specific cell types. Through high-resolution microscopy and transwell assays, they show that cells receive FGF signals through basally localized receptors. Finally, the authors find that there is a requirement for exogenous FGF2 to initiate primitive streak-like differentiation, but endogenous FGFs, especially FGF4 and FGF17, fully take over at later stages.

Even though some of the authors' findings - such as the localized expression of FGF ligands during gastrulation and the importance of FGF/ERK signaling for cell differentiation in the primitive streak - have been reported in model organisms before, this is one of the first studies to investigate the role of FGF signaling during primitive streak-like differentiation of human cells. In doing so, the paper reports a number of interesting and valuable observations, namely the basal localization of FGF receptors which mirrors that of BMP and Nodal receptors, as well as the existence of a positive feedback loop centered on FGF signaling that drives primitive-streak differentiation. The authors also perform a comparison of the role of different FGFs across species and try to assign specific functions to individual FGFs. In the absence of clean genetic loss-of-function cell lines, this part of the work remains less strong.

Reviewer #3 (Public review):

Summary:

In this study, the authors show that DNA polymerase kappa POLK relocalizes in the cytoplasm as granules with age in mice. The reduction of nuclear POLK in old brains is congruent with an increase in DNA damage markers. The cytoplasmic granules colocalize with stress granules and endo-lysosome. The study proposes that protein localization of POLK could be used to determine the biological age of brain tissue sections.

Strengths:

Very few studies focus on the POLK protein in the peripheral nervous system (PNS). The microscopy approach used here is also very relevant: it allows the authors to highlight a radical change in POLK localization (nuclear versus cytoplasmic) depending on the age of the neurons.

The conclusions of the study are strong. Several types of neurones are compared, the colocalization with several proteins from the NHEJ and BER repair pathways is tested, and microscopy images are systematically quantified.

Weaknesses:

The authors do not discuss the physical nature of POLK granules. There is a large field of research dedicated to the nature and function of condensates: in particular numerous studies have shown that some condensates but not all exhibit liquid-like properties (https://www.nature.com/articles/nrm.2017.7, https://pubmed.ncbi.nlm.nih.gov/33510441/ https://www.mdpi.com/2073-4425/13/10/1846). The change of physical properties of condensates is particularly important in cells undergoing stress and during aging. The authors should discuss this literature.

Reviewer #3 (Public review):

This manuscript presents a macroevolutionary approach to the identification of novel high-level antibiotic resistance determinants that takes advantage of the natural genetic diversity within a genus (mycobacteria, in this case) by comparing antibiotic resistance profiles across related bacterial species and then using computational, molecular, and cellular approaches to identify and characterize the distinguishing mechanisms of resistance. The approach is contrasted with "microevolutionary" approaches based on comparing resistant and susceptible strains of the same species and approaches based on ecological sampling that may not include clinically relevant pathogens or related species. The potential for new discoveries with the macroevolution-inspired approach is evident in the diversity of drug susceptibility profiles revealed amongst the selected mycobacterial species and the identification and characterization of a new group of rifamycin-modifying ADP-ribosyltransferase (Arr) orthologs of previously described mycobacterial Arr enzymes. Additional findings that intra-bacterial antibiotic accumulation does not always predict potency within this genus, that M. marinum is a better proxy for M. tuberculosis drug susceptibility than the commonly used saprophyte M. smegmatis, and that susceptibility to semi-synthetic antibiotic classes is generally less variable than susceptibility to antibiotics more directly derived from natural products strengthen the claim that the macroevolutionary lens is valuable for elucidating general principles of susceptibility within a genus.

There are some limitations to the work. The argument for the novelty of the approach could be better articulated. While the opportunities for new discoveries presented by the identification of discrepant susceptibility results between related species are evident, it is less clear how the macroevolutionary approach is further leveraged for the discovery of truly novel resistance determinants. The example of the discovery of Arr-X enzymes presented here relied upon foundational knowledge of previously characterized Arr orthologs. There is little clarity on what the pipeline for identifying more novel resistance determinants would look like. In other words, what does the macroevolutionary perspective contribute to discovery from the point of finding interspecies differences in susceptibility? Does the framework still remain distinct from other discovery frameworks and approaches? If so, how?

While the experimentation and analyses performed appear well-designed and rigorous, there are a few instances in which broad claims are based on inferences from sample sets or data sets that are too limited to provide robust support. For example, the claim that rifampicin modification, and precisely ADP-ribosylation, is the dominant mechanism of resistance to rifampicin in mycobacteria may be a bit premature or an over-generalization, as other enzymatic modification mechanisms and other mechanisms such as helR-mediated dissociation of rifampicin-stalled RNA polymerases, efflux, etc were not examined nor were CRISPRi knockdown experiments conducted beyond an experiment to tease out the role of Arr-X and Arr-1 in one strain. The general claim that intra-bacterial antibiotic accumulation does not predict potency in mycobacteria may be another over-generalization based on the limited number of drugs and species studied, but perhaps the intended assertion was that antibiotic accumulation ALONE does not predict potency.

Reviewer #3 (Public review):

Summary:

In this manuscript, the authors were trying to establish whether competition between the RNA-binding proteins SF1 and QKI controlled splicing outcomes. These two proteins have similar binding sites and protein sequences, but SF1 lacks a dimerization motif and seems to bind a single version of the binding sequence. Importantly, these binding sequences correspond to branchpoint consensus sequences, with SF1 binding leading to productive splicing, but QKI binding leading instead to association with paraspeckle proteins. They show that in human cells SF1 generally activates exons and QKI represses, and a large group of the jointly regulated exons (43% of joint targets) are reciprocally controlled by SF1 and QKI. They focus on one of these exons RAI14 that shows this reciprocal pattern of regulation, and has 2 repeats of the binding site that make it a candidate for joint regulation, and confirm regulation within a minigene context. The authors used the assembly of proteins within nuclear extracts to explain the effect of QKI versus SF1 binding. Finally, the authors show that the expression of QKI is lethal in yeast, and causes splicing defects.

How this fits in the field. This study is interesting and provides a conceptual advance by providing a general rule on how SF1 and QKI interact in relation to binding sites, and the relative molecular fates followed, so is very useful. Most of the analysis seems to focus on one example, although the molecular analysis and global work significantly add to the picture from the previously published paper about NUMB joint regulation by QKI and SF (Zong et al, cited in text as reference 50, that looked at SF1 and QKI binding in relation to a duplicated binding site/branchpoint sequence in NUMB).

Strengths:

The data presented are strong and clear. The ideas discussed in this paper are of wide interest, and present a simple model where two binding sites generate a potentially repressive QKI response, whereas exons that have a single upstream sequence are just regulated by SF1. The assembly of splicing complexes on RNAs derived from RAI14 in nuclear extracts, followed by mass spec gave interesting mechanistic insight into what was occurring as a result of QKI versus SF1 binding.

Weaknesses:

I did not think the title best summarises the take-home message and could be perhaps a bit more modest. Although the authors investigated splicing patterns in yeast and human cells, yeast do not have QKI so there is no ancient competition in that case, and the study did not really investigate physiological or evolutionary outcomes in splicing, although it provides interesting speculation on them. Also as I understood it, the important issue was less conserved branchpoints in higher eukaryotes enabling alternative splicing, rather than competition for the conserved branchpoint sequence. So despite the the data being strong and properly analysed and discussed in the paper, could the authors think whether they fit best with the take-home message provided in the title? Just as a suggestion (I am sure the authors can do a better job), maybe "molecular competition between variant branchpoint sequences predict physiological and evolutionary outcomes in splicing"?

Although the authors do provide some global data, most of the detailed analysis is of RAI14. It would have been useful to examine members of the other quadrants in Figure 1C as well for potential binding sites to give a reason why these are not co-regulated in the same way as RAI14. How many of the RAI14 quadrants had single/double sites (the motif analysis seemed to pull out just one), and could one of the non-reciprocally regulated exons be moved into a different quadrant by addition or subtraction of a binding site or changing the branchpoint (using a minigene approach for example).

Reviewer #3 (Public review):

Summary:

In this study, the authors set out to investigate whether and how Shigella avoids cell-autonomous immunity initiated through M1-linked ubiquitin and the immune sensor and E3 ligase RNF213. The key findings are that the Shigella flexneri T3SS effector, IpaH1.4 induces degradation of RNF213. Without IpaH1.4, the bacteria are marked with RNF213 and ubiquitin following stimulation with IFNg. Interestingly, this is not sufficient to initiate the destruction of the bacteria, leading the authors to conclude that Shigella deploys additional virulence factors to avoid this host immune response. The second key finding of this paper is the suggestion that M1 chains decorate the mxiE/ipaH Shigella mutant independent of LUBAC, which is, by and large, considered the only enzyme capable of generating M1-linked ubiquitin chains.

Strengths:

The data is for the most part well controlled and clearly presented with appropriate methodology. The authors convincingly demonstrate that IpaH1.4 is the effector responsible for the degradation of RNF213 via the proteasome, although the site of modification is not identified.

Weaknesses:

The work builds on prior work from the same laboratory that suggests that M1 ubiquitin chains can be formed independently of LUBAC (in the prior publication this related to Chlamydia inclusions). In this study, two pieces of evidence support this statement -fluorescence microscopy-based images and accompanying quantification in Hoip and Hoil knockout cells for association of M1-ub, using an antibody, to Shigella mutants and the use of an internally tagged Ub-K7R mutant, which is unable to be incorporated into ubiquitin chains via its lysine residues. Given that clones of the M1-specific antibody are not always specific for M1 chains, and because it remains formally possible that the Int-K7R Ub can be added to the end of the chain as a chain terminator or as mono-ub, the authors should strengthen these findings relating to the claim that another E3 ligase can generate M1 chains de novo.

The main weakness relating to the infection work is that no bacterial protein loading control is assayed in the western blots of infected cells, leaving the reader unable to determine if changes in RNF213 protein levels are the result of the absent bacterial protein (e.g. IpaH1.4) or altered infection levels.

The importance of IFNgamma priming for RNF213 association to the mxiE or ipaH1.4 strain could have been investigated further as it is unclear if RNF213 coating is enhanced due to increased protein expression of RNF213 or another factor. This is of interest as IFNgamma priming does not seem to be needed for RNF213 to detect and coat cytosolic Salmonella.

Overall, the findings are important for the host-pathogen field, cell-autonomous/innate immune signaling fields, and microbial pathogenesis fields. If further evidence for LUBAC independent M1 ubiquitylation is achieved this would represent a significant finding.

Reviewer #3 - Public Review

Summary:

Jin, Briggs et al. made use of light-sheet 3D imaging and data analysis to assess the collective network activity in isolated mouse islets. The major advantage of using whole islet imaging, despite compromising on the speed of acquisition, is that it provides a complete description of the network, while 2D networks are only an approximation of the islet network. In static-incubation conditions, excluding the effects of perfusion, they assessed two subpopulations of beta cells and their spatial consistency and metabolic dependence.

Strengths:

The authors confirmed that coordinated Ca2+ oscillations are important for glycemic control. In addition, they definitively disproved the role of individual privileged cells, which were suggested to lead or coordinate Ca²⁺ oscillations. They provided evidence for differential regional stability, confirming the previously described stochastic nature of the beta cells that act as strongly connected hubs as well as beta cells in initiating regions (doi.org/10.1103/PhysRevLett.127.168101).

The fact that islet cores contain beta cells that are more active and more coordinated has also been readily observed in high-frequency 2D recordings (e.g. DOI: 10.2337/db22-0952), suggesting that the high-speed capture of fast activity can partially compensate for incomplete topological information.

They also found an increased metabolic sensitivity of mantle regions of an islet with a subpopulation of beta cells with a high probability of leading the islet activity which can be entrained by fuel input. They discuss a potential role of alpha/delta cell interaction, however relative lack of beta cells in the islet border region could also be a factor contributing to less connectivity and higher excitability.

The Methods section contains a useful series of direct instructions on how to approach fast 3D imaging with currently available hardware and software.

The Discussion is clear and includes most of the issues regarding the interpretation of the presented results.

Some issues concerning inconsistencies between data presented and statements made as well as statistical analysis need to be addressed.

Taken together it is a strong technical paper to demonstrate the stochasticity regarding the functions subpopulations of beta cells in the islets may have and how less well-resolved approaches (both missing spatial resolution as well as missing temporal resolution) led us to jump to unjustified conclusions regarding the fixed roles of individual beta cells within an islet.

Reviewer #3 (Public review):

This study presents a detailed examination of the molecular and cellular organization of the mouse VNO, unveiling new cell types, receptor co-expression patterns, lineage specification regulation, and potential associations between transcription factors, guidance molecules, and receptor types crucial for vomeronasal circuitry wiring specificity. The study identifies a novel type of VSN molecularly different from classic VSNs, which may serve as accessory to other VSNs by secreting olfactory binding proteins and mucins in response to VNO activation. They also describe a previously undetected co-expression of multiple VRs in individual VSNs, providing an interesting view to the ongoing discussion on how receptor choice occurs in VSNs, either stochastic or deterministic. Finally, the study correlates the expression of axon guidance molecules associated with individual VRs, providing a putative molecular mechanism that specifies VSN axon projections and their connection with postsynaptic cells in the accessory olfactory bulb.

The conclusions of this paper are well supported by data, but some aspects of data analysis and acquisition need to be clarified and extended.

(1) The authors claim that they have identified two new classes of sensory neurons, one being a class of canonical olfactory sensory neurons (OSNs) within the VNO. This classification as canonical OSNs is based on expression data of neurons lacking the V1R or V2R markers but instead expressing ORs and signal transduction molecules, such as Gnal and Cnga2. Since OR-expressing neurons in the VNO have been previously described in many studies, it remains unclear to me why these OR-expressing cells are considered here a "new class of OSNs." Moreover, morphological features, including the presence of cilia, and functional data demonstrating the recognition of chemosignals by these neurons, are still lacking to classify these cells as OSNs akin to those present in the MOE. While these cells do express canonical markers of OSNs, they also appear to express other VSN-typical markers, such as Gnao1 and Gnai2 (Fig 2B), which are less commonly expressed by OSNs in the MOE. Therefore, it would be more precise to characterize this population as atypical VSNs that express ORs, rather than canonical OSNs.

(2) The second new class of sensory neurons identified corresponds to a group of VSNs expressing prototypical VSN markers (including V1Rs, V2Rs, and ORs), but exhibiting lower ribosomal gene expression. Clustering analysis reveals that this cell group is relatively isolated from V1R- and V2R-expressing clusters, particularly those comprising immature VSNs. The question then arises: where do these cells originate? Considering their fewer overall genes and lower total counts compared to mature VSNs, I wonder if these cells might represent regular VSNs in a later developmental stage, i.e., senescent VSNs. While the secretory cell hypothesis is compelling and supported by solid data, it could also align with a late developmental stage scenario. Further data supporting or excluding these hypotheses would aid in understanding the nature of this new cell cluster, with a comparison between juvenile and adult subjects appearing particularly relevant in this context.

(3) The authors' decision not to segregate the samples according to sex is understandable, especially considering previous bulk transcriptomic and functional studies supporting this approach. However, many of the highly expressed VR genes identified have been implicated in detecting sex-specific pheromones and triggering dimorphic behavior. It would be intriguing to investigate whether this lack of sex differences in VR expression persists at the single-cell level. Regardless of the outcome, understanding the presence or absence of major dimorphic changes would hold broad interest in the chemosensory field, offering insights into the regulation of dimorphic pheromone-induced behavior. Additionally, it could provide further support for proposed mechanisms of VR receptor choice in VSNs.

(4) The expression analysis of VRs and ORs seems to have been restricted to the cell clusters associated to the neuronal lineage. Are VRs/ORs expressed in other cell types, i.e. sustentacular, HBC or other cells?

Review update:

I believe the novel discovery of two classes of sensory neurons within the VNO-canonical olfactory sensory neurons (OSNs) and secretory vomeronasal sensory neurons (sVSNs)-should be interpreted with caution. Firstly, these cell types are relatively rare, constituting less than 2% of total cells and only 2-6% of the neuronal population (according to Fig. S3). While the OSNs exhibit gene expression profiles consistent with canonical olfactory signal transduction and cilia-related gene ontology, key aspects such as their cell morphology (including the presence of cilia) and functional evidence for chemosignal detection have yet to be demonstrated. The neuronal lineage of sVSNs remains unclear to me. It is uncertain what developmental trajectories these cells follow: do they arise as a specialized subtype of V1R or V2R lineages, or do they have an independent lineage determination, similar to OSNs? At what stage does the commitment to the sVSN lineage begin-during the INP stage or the immature sensory neuron stage? A pseudotime inference analysis of sVSNs could help clarify these questions.

Reviewer #3 (Public review):

Summary:

The cell wall of human fungal pathogens, such as Candida albicans, is crucial for structural support and modulating the host immune response. Although extensively studied in yeasts and molds, the structural composition has largely focused on the structural glucan b,1,3-glucan and the surface exposed mannans, while the fibrillar component β-1,6-glucan, a significant component of the well wall, has been largely overlooked. This comprehensive biochemical and immunological study by a highly experienced cell wall group provides a strong case for the importance of β-1,6-glucan contributing critically to cell wall integrity, filamentous growth, and cell wall stability resulting from defects in mannan elongation. Additionally, β-1,6-glucan responds to environmental stimuli and stresses, playing a key role in wall remodeling and immune response modulation, making it a potential critical factor for host-pathogen interactions.

Strengths:

Overall, this study is well designed and executed. It provides the first comprehensive assessment of β-1,6-glucan as a dynamic, albeit underappreciated, molecule. The role of β-1,6-glucan genetics and biochemistry has been explored in molds like Aspergillus fumigatus, but this work shines important light on its role in Candida albicans. This is important work that is of value to Medical Mycology, since β-1,6-glucan plays more than just a structural role in the wall. It may serve as a PAMP and a potential modulator of host-pathogen interactions.

Weaknesses:

In keeping with an important role in immune recognition, it was suggested that the manuscript rigor would benefit from a more physiological evaluation ex vivo and preferably in vivo, assessment on stimulating the immune system within in the cell wall and not just as a purified component. This is a critical outcome measure for this study and gets squarely at its importance for host-pathogen interactions, especially in response to environmental stimuli and drug exposure. The authors addressed this issue contextually and indicate that it will require a more detailed immunologic evaluation but is not in keeping with the intent of this foundational study.

Reviewer #3 (Public review):

Summary:

Understanding the molecular regulation of muscle stem cell quiescence. The authors evaluated the role of the MuSK-BMP pathway in regulating adult SC quiescence by the deletion of the BMP-binding MuSK Ig3 domain ('ΔIg3-MuSK').

Strengths:

A novel mouse model to interrogate muscle stem cell molecular regulators. The authors have developed a nice mouse model to interrogate the role of MuSK signaling in muscle stem cells and myofibers and have unique tools to do this.

Weaknesses:

Only minor technical questions remain and there is a need for additional data to support the conclusions.

(1) The authors claim that dIg3-MuSK satellite cells break quiescence and start fusing, based on the reduction of Pax7+ and increase of nuclei/fiber (Fig 2-3), and maybe the gene expression (Fig6). However, direct evidence is needed to support these findings such as quantifying quiescent (Pax7+Ki67-) or activated (Pax7+Ki67+) satellite cells (and maybe proliferating progenitors Pax7-Ki67+) in the dIg3-MuSK muscle.

(2) It is not clear if the MuSK-BMP pathway is required to maintain satellite cell quiescence, by the end of the regeneration (29dpi), how Pax7+ numbers are comparable to the WT (Fig4d). I would expect to have less Pax7+, as in uninjured muscle. Can the authors evaluate this in more detail?

(2) Figure 4 claims that regeneration is accelerated, but to claim this at a minimum they need to look at MYH3+ fibers, in addition to fiber size.

(3) The Pax7 specific dIg3-MuSK (Fig5) is very exciting. However, it will be important to quantify the Pax7+ number. Could the authors check the reduction of Pax7+ in this model since it would confirm the importance of MuSK in quiescence?

(3) Rescue of the BMP pathway in the model would be further supportive of the authors' findings.

(4) Is the stem cell pool maintained long term in the deleted dIg3-MuSK SCs? Or would they be lost with extended treatment since they are reduced at the 5-month experiments? This is an important point and should be considered/discussed relevant to thinking about these data therapeutically.

(5) Without the Pax7-specific targeting, when you target dIg3-MuSK in the entire muscle, what happens to the neuromuscular nuclei?

(6) Why were differences seen in males and not females? Is XIST downregulation occurring in both sexes? Could the authors explain these findings in more detail?

Reviewer #3 (Public review):

Summary:

In this manuscript by Mestre-Fos and colleagues, authors have analyzed the involvement of eIF3 binding to mRNA during differentiation of neural progenitor cells (NPC). The authors bring a lot of interesting observations leading to a novel function for eIF3 at the 3'UTR.

During the translational burst that occurs during NPC differentiation, analysis of eIF3-associated mRNA by Quick-irCLIP reveals the unexpected binding of this initiation factor at the 3'UTR of most mRNA. Further analysis of alternative polyadenylation by APAseq highlights the close proximity of the eIF3-crosslinking position and the poly(A) tail. Furthermore, this interaction is not detected in Poly(A)-less transcripts. Using Riboseq, the authors then attempted to correlate eIF3 binding with the translation efficacy of mRNA, which would suggest a common mechanism of translational control in these cells. These observations indicate that eIF3-binding at the 3'UTR of mRNA, near the poly(A) tail, may participate to the closed-loop model of mRNA translation, bridging 5' and 3', and allowing ribosomes recycling. However, authors failed to detect interactions of eIF3, with either PABP or Paip1 or 40S subunit proteins, which is quite unexpected.

Strength:

The well-written manuscript presents an attractive concept regarding the mechanism of eIF3 function at the 3'UTR. Most mRNA in NPC seems to have eIF3 binding at the 3'UTR and only a few at the 5'end where it's commonly thought to bind. In a previous study from the Cate lab, eIF3 was reported to bind to a small region of the 3'UTR of the TCRA and TCRB mRNA, which was responsible for their specific translational stimulation, during T cell activation. Surprisingly in this study, the eIF3 association with mRNA occurs near polyadenylation signals in NPC, independently of cell differentiation status. This compelling evidence suggests a general mechanism of translation control by eIF3 in NPC. This observation brings back the old concept of mRNA circularization with new arguments, independent of PABP and eIF4G interaction. Finally, the discussion adequately describes the potential technical limitations of the present study compared to previous ones by the same group, due to the use of Quick-irCLIP as opposed to the PAR-CLIP/thiouridine.

Weaknesses:

(1) These data were obtained from an unusual cell type, limiting the generalizability of the model.

(2) This study lacks a clear explanation for the increased translation associated with NPC differentiation, as eIF3 binding is observed in both differentiated and undifferentiated NPC. For example, I find a kind of inconsistency between changes in Riboseq density (Figure 3B) and changes in protein synthesis (Figure 1D). Thus, the title overstates a modest correlation between eIF3 binding and important changes in protein synthesis.

(3) This is illustrated by the candidate selection that supports this demonstration. Looking at Figure 3B, ID2, and SNAT2 mRNA are not part of the High TE transcripts (in red). In contrast, the increase in mRNA abundance could explain a proportionally increased association with eIF3 as well as with ribosomes. The example of increased protein abundance of these best candidates is overall weak and uncertain.

(4) Despite several attempts (chemical and UV cross-linking) to identify eIF3 partners in NPC such as PABP, PAIP1, or proteins from the 40S, the authors could not provide any evidence for such a mechanism consistent with the closed-loop model. Overall, this rather descriptive study lacks mechanistic insight (eIF3 binding partners).

(5) Finally, the authors suspect a potential impact of technical improvement provided by Quick-irCLIP, that could have been addressed rather than discussed.

Reviewer #3 (Public review):

Summary:

The manuscript by Eggan et al provides insights into conformational transitions in the cyclic nucleotide binding domain of a cyclic nucleotide-gated (CNG) channel. The authors use transition metal FRET (tmFRET) which has been pioneered by this lab and previously led to detailed insights into ion channel conformational changes. Here, the authors not only use steady-state measurements but also time-resolved, fluorescence lifetime measurements to gain detailed insights into conformational transitions within a protein construct that contains the cytosolic C-linker and cyclic nucleotide binding domain (CNBD) of a bacterial CNG channel. The use of time-resolved tmFRET is a clear advancement of this technique and a strength of this manuscript.

In summary, the present work introduces time-resolved tmFRET as a novel tool to study conformational distributions in proteins. This is a clear technological advance. The limitations of the truncated construct used in this study and how they relate to the energetics in full-length CNG channels are discussed. It will be interesting to see in the future how results compare to similar measurements on full-length channels, for example, reconstituted into nanodiscs.

Strengths:

The results capture known differences in promoting the open state between different ligands (cAMP and cGMP) and are consistent across three donor-acceptor FRET pairs. The calculated distance distributions are further in agreement with predicted values based on available structures. The finding that the C-helix is conformationally more mobile in the closed state as compared to the open state quantitatively increases our understanding of conformational changes in these channels.

Weaknesses:

The results describe movements of the C-helix in CNBDs, but detailed energetics as calculated in this study, need to be limited to the truncated protein construct. This is a weakness that cannot be overcome easily as it will require future experiments using the full-length channel.

The data only describe movements of the C-helix. Upon ligand binding, the C-helix moves upwards to coordinate the ligand. Thus, the results are ligand-induced conformational changes (as the title states). Allosteric regulation usually involves remote locations in the protein, which is applicable only in a limited fashion here.

Reviewer #3 (Public review):

Summary:

The manuscript by Rios-Jimenez developed a computational tool, BEHAV3D Tumor Profiler, to analyze intravital imaging data and extract distinctive tumor cell migratory phenotypes based on the quantified 3D image data.

Weaknesses:

(1) The most challenging task of analyzing 3D time-lapse imaging data is to accurately segment and track the individual cells in 3D over a long time duration. BEHAV3D Tumor Profiler did not provide any new advancement in this regard, and instead relies on commercial software, Imaris, for this critical step. Imaris is known to have a very high error rate when used for analyzing 3D time-lapse data. In the Methods section, the authors themselves stated that "Tumor cell tracks were manually corrected to ensure accurate tracking". Based on our own experience of using Imaris, such manual correction is tedious and often required for every time step of the movie. Therefore, Imaris is not a satisfactory tool for analyzing 3D time-lapse data. Moreover, Imaris is expensive and many research labs probably can't afford to buy it. The fact that BEHAV3D Tumor Profiler critically depends on the faulty ImarisTrack module makes it unclear whether the BEHAV3D tool or the results are reliable.

(2) The authors developed a "Heterogeneity module" to extract distinctive tumor migratory phenotypes from the cell tracks quantified by Imaris. The cell tracks of the individual tumor cells are all quite short, indicating relatively low motility of the tumor cells. It's unclear whether such short migratory tracks are sufficient to warrant the PCA analysis to identify the 7 distinctive migratory phenotypes shown in Figure 2d. It's also unclear whether these 7 migratory phenotypes correspond to unique functional phenotypes.

(3) Using only motility to classify tumor cell behaviours in the tumor microenvironment (TME) is probably not sufficient to capture the tumor cell difference. There are also other non-tumor cell types in the TME. If the authors aim to develop a computational tool that can elucidate tumor cell behaviors in the TME, they should consider other tumor cell features, e.g., morphology, proliferation state, and tumor cell interaction with other cell types, e.g., fibroblasts and distinct immune cells.

(4) The authors have already published two papers on BEHAV3D [Alieva M et al. Nat Protoc. 2024 Jul;19(7): 2052-2084; Dekkers JF, et al. Nat Biotechnol. 2023 Jan;41(1):60-69]. Although the previous two papers used BEHAV3D to analyze T cells, the basic pipeline and computational steps are similar, in particular regarding cell segmentation and tracking. The addition of a "Heterogeneity module" based on PCA analysis does not make a significant advancement in terms of image analysis and quantification.

Reviewer #3 (Public review):

Summary:

The manuscript by Zhao et al. explored the function of adhesion G protein-coupled receptor A3 (ADGRA3) in thermogenic fat biology.

Strengths:

Through both in vivo and in vitro studies, the authors found that the gain function of ADGRA3 leads to browning of white fat and ameliorates insulin resistance.

Comments on revised version:

The revised manuscript by Zhao et al. has limited improvement. The authors refused to perform revised experiments using primary cultures even though two reviewers pointed out the same weakness (3T3-L1 adipocytes are unsuitable). Using infrared thermography to measure body temperature is also problematic.

Reviewer #3 (Public review):

Summary:

REV7 facilitates the recruitment of Shieldin complex and thereby inhibits end resection and controls DSB repair choice in metazoan cells. Puzzlingly, Shieldin is absent in many organisms, and it is unknown if and how Rev7 regulates DSB repair in these cells. The authors surmised that yeast Rev7 physically interacts with Mre11/Rad50/Xrs2 (MRX), the short-range resection nuclease complex and tested this premise using yeast two hybrid (Y2H) and microscale thermophoresis (MST). The results convincingly showed that the individual subunits of MRX interacts robustly with Rev7. By AlphaFold Multimer modelling followed by Y2H confirmed that the carboxy terminal 42 amino acid is essential for interaction with MR and G4 DNA binding by REV7. The mutant rev7 lacking the binding interface (Rev7-C1) to MR shows moderate inhibition to the nuclease and the ATPase activity of Mre11/Rad50 in biochemical assays. Deletion of REV7 also causes a mild reduction in NHEJ using both plasmid and chromosome-based assays and increases mitotic recombination between chromosomal ura3-01 and the plasmid ura3 allele interrupted by G4. The revision also showed that rev7 deleted cells exhibit mild hyper-resection phenotype at 0.7 and 3 kb from the DSB using qPCR assays. The authors concluded that Rev7 facilitates NHEJ and antagonises HR even in budding yeast, but it achieves this by blocking Mre11 nuclease and Rad50 ATPase.

Weaknesses:

There are several strengths to the studies and the broad types of well-established assays were used to deduce the conclusion. Nevertheless, there are notable discrepancies on the mutant phenotypes that were to test the functionality of Rev7-MRX interaction on the repair outcomes, raising concerns on the validity of the proposed model. The manuscript also needs a few additional functional assays to reach the accurate conclusions as proposed. The revision responded to several comments raised by the reviewers, but they are inadequate to address the key concerns and did not offer sufficient and compelling experimental support to the main premise that Rev7-Mre11/Rad50/Xrs2 interactions regulate MRX activities in cells and thereby modulates DSB repair choice in budding yeast.

(1) AlphaFold model predicts that Mre11-Rev7 and Rad50-Rev7 binding interfaces overlap and Rev7 might bind only to Mre11 or Rad50 at a time. Interestingly, however, Rev7 appears dimerized (Fig.1). Since MR complex also forms with 2M and 2R in the complex, it should still be possible if REV7 can interact both M and R in the MR complex. The author should perform MST using MR complex instead of individual MR components. The authors should also analyze if Rev7-C1 is indeed deficient in interaction with MR individually and with complex using MST assay.

(2) The nuclease and the ATPase assays require additional controls. Does Rev7 inhibit the other nuclease or ATPase non-specifically? Are these outcomes due to the non-specific or promiscuous activity of Rev7? In fig.6, the effect of REV7 on the ATP binding of Rad50 could be hard to assess because the maximum Rad50 level (1 uM) was used in the experiments. The author should use the suboptimal level of Rad50 to check if REV7 still does not influence ATP binding by Rad50.

(3) The moderate deficiency in NHEJ using plasmid based assay in REV7 deleted cells can be attributed to aberrant cell cycle or mating type in rev7 deleted cells. The authors should demonstrate that rev7 deleted cells retain largely normal cell cycle pattern and the mating type phenotypes. The author should also analyze the breakpoints in plasmid based NHEJ assays in all mutants especially from rev7 and rev7-C1 cells.

(4) It is puzzling why the authors did not analyze end resection defects in rev7 deleted cells after a DSB. The author should employ the widely used resection assay after a HO break in rev3, rev7 and mre11 rev7 cells as described previously.

(5) Is it possible that Rev7 also contributes to NHEJ as the part of TLS polymerase complex? Although NHEJ largely depends on Pol4, the authors should not rule out the possibility if the observed NHEJ defect in rev7 cells are due at least partially to its well-known TLS defect and not all due to their role in MRX activity regulation as the authors proposed. In fact, rev3 or rev1 cells are partially defective in NHEJ (Fig. 7). Rev7-C1 is less deficient in NHEJ than REV7 deletion. These results predict that rev7-C1 rev3 could be more deficient than rev3 or rev7-C1, and such results might indicate that Rev7 contributes to NHEJ by two ways; one by interacting (and modulating) MRX and the other as part of Rev3-Rev7 complex. Additionally, the authors should examine if Rev7-C1 might be deficient in TLS. In this regard, does rev7-C1 reduce TLS and TLS dependent mutagenesis? Is it dominant? The authors should also check if Rev3/Rev1 complexes are stable in Rev7 deleted or rev7-C1 cells by immunoblot assays.

(6) Due to the G4 DNA and G4 binding activity of REV7, it is not clear which class of events the authors are measuring in plasmid-chromosome recombination assay in Fig.9. Do they measure G4 instability or the integrity of recombination or both in rev7 deleted cells. Instead, the effect of rev7 deletion or rev7-C1 on recombination should be measured directly by more standard mitotic recombination assays like mating type switch or his3 repeat recombination. The revision did not address these concerns, which still makes the interpretation of the provided recombination results difficult.

Reviewer #3 (Public review):

Papalamprou et al sought to fine tune existing tenogenic differentiation protocols to develop a robust multi-step differentiation protocol to induce tendon cells from human GMP-ready iPSCs. In so doing, they found that while existing protocols are capable of driving cells towards a syndetome-like fate, the resultant cultures contain highly heterogeneous cell populations with sub-optimal cell survival. Through single cell transcriptomic analysis they identify WNT signaling as a potential driver of an off-target neural population and show that inhibition of WNT signaling at the later 2 stages of differentiation can be used to promote higher efficiency of generation of syndetome-like cells.

This paper includes a useful paradigm for identifying transcriptional modulators of cell fate during differentiation and a clear example where transcriptional data can be used to guide the chemical modulation of a differentiation protocol to improve cell output. The paper's conclusions are mostly well supported by the data, but the image analysis and discussion need to be improved to strengthen the impact.

The data outlining the differences between the differentiation outcome of the two tested iPSCs is intriguing, but the authors fail to comment on potential differences between the two iPSC lines that could result in drastically different cell outputs from the same differentiation protocol. This is a critically important point, as the majority of the SCX+ cells generated from the 007i cells using their WNTi protocol were found in the FC subpopulation that failed to form from the 83i line under the same protocol. From the analysis of only these 2 cells lines in vitro, it is difficult to assess whether this WNTi protocol can be broadly used across multiple cell lines to generate tenogenic cells. The authors failed to update the text of the manuscript to reflect the potential differences in the two cell lines and the general applicability of their protocol, but rather just include the description of the proposed explanation in the response to reviewer comments. These critical differences in the response to their protocol and their implications for the applications of this proof-of-concept study should be included in the main text.

The authors make claims about changes in protein expression but fail to quantify either fluorescence intensity or percent cell expression from their immunofluorescence analyses to substantiate these claims. The authors state in their response to reviewers that immunofluorescence is qualitative but continue to make quantitative statements such as upregulated or downregulated in both the text and legend describing these images. The authors should either perform the quantification of the IFs, use Western blots for protein quantification of their cell cultures, use Flow Cytometry to count cell numbers, or remove these quantitative words from the description of the images. The image quality and staining specificity continue to be a limitation of this study. These claims are not fully supported by the data as presented as it is unclear whether there is increased expression of tendon markers at the protein level or more cells surviving the protocol.

Reviewer #4 (Public review):

Summary:

In this elegant study XX and colleagues use a combination of fixed tissue analyses and live imaging to characterise the role of Laminin in olfactory placode development and neuronal pathfinding in the zebrafish embryo. They describe Laminin dynamics in the developing olfactory placode and adjacent brain structures and identify potential roles for Laminin in facilitating neuronal pathfinding from the olfactory placode to the brain. To test whether Laminin is required for olfactory placode neuronal pathfinding they analyse olfactory system development in a well-established laminin-gamma-1 mutant, in which the laminin-rich basement membrane is disrupted. They show that while the OP still coalesces in the absence of Laminin, Laminin is required to contain OP cells during forebrain flexure during development and maintain separation of the OP and adjacent brain region. They further demonstrate that Laminin is required for growth of OP neurons from the OP-brain interface towards the olfactory bulb. The authors also present data describing that while the Laminin mutant has partial defects in neural crest cell migration towards the developing OP, these NCC defects are unlikely to be the cause of the neuronal pathfinding defects upon loss of Laminin. Altogether the study is extremely well carried out, with careful analysis of high-quality data. Their findings are likely to be of interest to those working on olfactory system development, or with an interest in extracellular matrix in organ morphogenesis, cell migration, and axonal pathfinding.

Strengths:

The authors describe for the first time Laminin dynamics during the early development of the olfactory placode and olfactory axon extension. They use an appropriate model to perturb the system (lamc1 zebrafish mutant), and demonstrate novel requirements for Laminin in pathfinding of OP neurons towards the olfactory bulb.<br /> The study utilises careful and impressive live imaging to draw most of its conclusions, really drawing upon the strengths of the zebrafish model to investigate the role of laminin in OP pathfinding. This imaging is combined with deep learning methodology to characterise and describe phenotypes in their Laminin-perturbed models, along with detailed quantifications of cell behaviours, together providing a relatively complete picture of the impact of loss of Laminin on OP development.

Weaknesses:

Some of the statistical tests are performed on experiments where n=2 for each condition (for example the measurements in Figure S2) - in places the data is non-significant, but clear trends are observed, and one wonders whether some experiments are under-powered.

Reviewer #3 (Public review):

Summary:

Varani et al present important findings regarding the role of distinct cerebellothalamic connections in motor learning and performance. Their key findings are that:<br /> (1) cerebellothalamic connections are important for learning motor skills<br /> (2) cerebellar efferents specifically to the central lateral (CL) thalamus are important for short-term learning<br /> (3) cerebellar efferents specifically to the ventral anterior lateral (VAL) complex are important for offline consolidation of learned skills, and<br /> (4) that once a skill is acquired, cerebellothalamic connections become important for online task performance.

The authors went to great lengths to separate effects on motor performance from learning, for the most part successfully. While one could argue about some of the specifics, there is little doubt that the CN-CL and CN-VAL pathways play distinct roles in motor learning and performance. An important next step will be to dissect the downstream mechanisms by which these cerebellothalamic pathways mediate motor learning and adaptation.

Strengths:

(1) The dissociation between online learning through CN-CL and offline consolidation through CN-VAL is convincing.

(2) The ability to tease learning apart from performance using their titrated chemogenetic approach is impressive. In particular, their use of multiple motor assays to demonstrate preserved motor function and balance is an important control.

(3) The evidence supporting the main claims is convincing, with multiple replications of the findings and appropriate controls.

Weaknesses:

(1) Despite the care the authors took to demonstrate that their chemogenetic approach does not impair online performance, there is a trend towards impaired rotarod performance at higher speeds in Supplementary Figure 4f, suggesting that there could be subtle changes in motor performance below the level of detection of their assays.

(2) There is likely some overlap between CN neurons projecting to VAL and CL, somewhat limiting the specificity of their conclusions.

Reviewer #3 (Public review):

Summary:

In their manuscript entitled "Parallel mechanisms signal a hierarchy of sequence structure violations in the auditory cortex", Jamali et al. provide evidence for cellular-level mechanisms in the auditory cortex of mice for the encoding of predictive information on different temporal and contextual scales. The study design separates more clearly than previous studies between the effects of local and global deviants and separates their respective effects on the neuronal responses clearly through the use of various contextual conditions and short and long time scales. Further, it identifies a contribution from a small set of VIP interneurons to the detection of omitted sounds, and shows the influence of isofluorane anesthesia on the neural responses.

Strengths:

(1) The study provides a rather encompassing set of experimental techniques to study the cellular level responses, using two complementary recording techniques in the same animal and similar cortical location.

(2) Comparison between awake and anesthetized states are conducted in the same animals, which allows for rather a direct comparison of populations under different conditions, thus reducing sampling variability.

(3) The set of paradigms is well developed and specifically chosen to provide appropriate and meaningful controls/comparisons, which were missing from previous studies.

(4) The addition of cell-type specific recordings is valuable and in particular in combination with the contrast of awake and anesthetized animals provides novel insights into the cellular level representation of deviant signals, such as surprise, prediction error, and general adaptation.

(5) The analysis and presentation of the data are clear and quite complete, yet remain succinct and perform insightful contrasts.

(6) The study will have an impact on multiple levels, as it introduces important variations in the paradigm and analytical contrasts that both human and animal researchers can pick up and improve their studies. The cell-type-specific results are particularly intriguing, although these would likely require replication before being completely reliable. Further, the study provides a substantial and diverse dataset that others can explore.

Weaknesses:

(1) The responses from cells recorded via Neuropixel and 2p differ qualitatively, as noted by the authors, with NP-recorded cells showing much more inhibited/reduced responses between acoustic stimulations. The authors briefly qualify these differences as potentially indicating a sampling issue, however, this matter deserves more detailed consideration in my opinion. Specifically, the authors could try to compare the different depths at which these neurons were sampled or relate the locations in the cortex to each other (as the Neuropixel recordings were collected in the same animals, a subset of the 2p recordings could be compared to the Neuropixel recordings.).

(2) The current study did not monitor the attentional state of the mouse in relation to the stimulus by either including a behavioral component or pupil monitoring, which could influence the neural responses to deviant stimuli and omissions. .

(3) Given the complexity and variety of the paradigms, conditions, and analyzed cell-types, the manuscript could profit from a more visual summary figure that provides an easy-to-access overview of what was found.

Reviewer #3 (Public Review):

Summary:

Previous research on the Drosophila mushroom body (MB) has made this structure the best-understood example of an associative memory center in the animal kingdom. This is in no small part due to the generation of cell-type specific driver lines that have allowed consistent and reproducible genetic access to many of the MB's component neurons. The manuscript by Shuai et al. now vastly extends the number of driver lines available to researchers interested in studying learning and memory circuits in the fly. It is an 800-plus collection of new cell-type specific drivers target neurons that either provide input (direct or indirect) to MB neurons or that receive output from them. Many of the new drivers target neurons in sensory pathways that convey conditioned and unconditioned stimuli to the MB. Most drivers are exquisitely selective, and researchers will benefit from the fact that whenever possible, the authors have identified the targeted cell types within the Drosophila connectome. Driver expression patterns are beautifully documented and are publicly available through the Janelia Research Campus's Flylight database where full imaging results can be accessed. Overall, the manuscript significantly augments the number of cell type-specific driver lines available to the Drosophila research community for investigating the cellular mechanisms underlying learning and memory in the fly. Many of the lines will also be useful in dissecting the function of the neural circuits that mediate sensorimotor circuits.

Strengths:

The manuscript represents a huge amount of careful work and leverages numerous important developments from the last several years. These include the thousands of recently generated split-Gal4 lines at Janelia and the computational tools for pairing them to make exquisitely specific targeting reagents. In addition, the manuscript takes full advantage of the recently released Drosophila connectomes. Driver expression patterns are beautifully illustrated side-by-side with corresponding skeletonized neurons reconstructed by EM. A comprehensive table of the new lines, their split-Gal4 components, their neuronal targets, and other valuable information will make this collection eminently useful to end-users. In addition to the anatomical characterization, the manuscript also illustrates the functional utility of the new lines in optogenetic experiments. In one example, the authors identify a specific subset of sugar reward neurons that robustly promotes associative learning.

Comments on revised version:

Overall, I thought the authors addressed my comments well with the possible exception of what is actually new here. This was the most important thing that I thought should be included in the revision. Although the authors rewrote the paragraph describing the lines presented in the paper, I still can't tell exactly which ones haven't been previously published. Their revised paragraph says that 40 lines have been "previously used," but Supplemental Table 1 shows references for over 200 of the lines, which sounds more reasonable based on papers that have come out.

Also, in the revised paragraph they state that "All transgenic lines newly generated in this study are listed in Supplementary File 2" but that table lists only the 36 LexA hemidriver lines! Confusingly, this comment cites the same 8 references as are cited for the 40 line that they say were previously published. I am thus only more confused about how many previously uncharacterized lines are presented in this paper.

Further clarification would be helpful. On the one hand, I think this paper is a very nice summary of a ton of work and brings it all under one umbrella in a way that will be useful for many in the field. In that sense, the manuscript is worth publishing simply as a useful resource even if all the lines were previously published. On the other hand, it would be useful for readers to know which lines were previously characterized in other publications and which ones were not. This information may or may not be in Supplementary Tables 1 and 2 (but I can't tell).

Reviewer #3 (Public review):

Public review:

The claustrum is one of the most enigmatic regions of the cerebral cortex, with a potential role in consciousness and integrating multisensory information. Despite extensive connections with almost all cortical areas, its functions and mechanisms are not well understood. In an attempt to unravel these complexities, Shelton et al. employed advanced circuit mapping technologies to examine specific neurons within the claustrum. They focused on how these neurons integrate incoming information and manage the output. Their findings suggest that claustrum neurons selectively communicate based on cortical projection targets and that their responsiveness to cortical inputs varies by cell type.

Imaging studies demonstrated that claustrum axons respond to both single and multiple sensory stimuli. Extended inhibition of the claustrum significantly reduced animals' responsiveness to multisensory stimuli, highlighting its critical role as an integrative hub in the cortex.

However, the study's conclusions at times rely on assumptions that may undermine their validity. For instance, the comparison between RSC projecting and non-RSC projecting neurons is problematic due to potential false negatives in the cell labeling process, which might not capture the entire neuron population projecting to a brain area. This issue casts doubt on the findings related to neuron interconnectivity and projections, suggesting that the results should be interpreted with caution. The study's approach to defining neuron types based on projection could benefit from a more critical evaluation or a broader methodological perspective.

Nevertheless, the study sets the stage for many promising future research directions. Future work could particularly focus on exploring the functional and molecular differences between E1 and E2 neurons and further assess the implications of the distinct responses of excitatory and inhibitory claustrum neurons for internal computations. Additionally, adopting a different behavioral paradigm that more directly tests the integration of sensory information for purposeful behavior could also prove valuable.

Reviewer #3 (Public review):

Summary:

The authors conducted a well-designed experiment, incorporating VR classroom scenes and background sound events, with both control and ADHD participants. They employed multiple neurophysiological measures, such as EEG, eye movements, and skin conductance, to investigate the mechanistic underpinnings of paying attention in class and the disruptive effects of background noise.

The results revealed that individuals with ADHD exhibited heightened sensory responses to irrelevant sounds and reduced tracking of the teacher's speech. Overall, this manuscript presented an ecologically valid paradigm for assessing neurophysiological responses in both control and ADHD groups. The analyses were comprehensive and clear, making the study potentially valuable for the application of detecting attentional deficits.

Strengths:

• The VR learning paradigm is well-designed and ecologically valid.

• The neurophysiological metrics and analyses are comprehensive, and two physiological markers are identified capable of diagnosing ADHD.

• This research provides a valuable dataset that could serve as a benchmark for future studies on attention deficits.

Weaknesses:

• Several results are null results, i.e., no significant differences were found between ADHD and control populations.

• Although the paradigm is well-designed and ecologically valid, the specific contributions or insights from the results remain unclear.

• Lack of information regarding code and data availability.

Reviewer #3 (Public review):

Coatl et al. investigated the mechanisms of synaptic plasticity of two important hippocampal synapses, the excitatory afferents from lateral and medial perforant pathways (LPP and MPP, respectively) of the entorhinal cortex (EC) connecting to granule cells of the hippocampal dentate gyrus (DG). They find that these two different EC-DG synaptic connections in mice show a presynaptically expressed form of long-term depression (LTD) requiring postsynaptic calcium, eCB synthesis, CB1R activation, astrocyte activity, and metabotropic glutamate receptor activation. Interestingly, LTD at MPP-GC synapses requires ionotropic NMDAR activation whereas LTD at LPP-GC synapse is NMDAR independent. Thus, they discovered two novel forms of t-LTD that require astrocytes at EC-GC synapses. Although plasticity of EC-DG granule cell (GC) synapses has been studied using classical protocols, These are the first analyses of the synaptic plasticity induced by spike timing dependent protocols at these synapses. Interestingly, the data also indicate that t-LTD at each type of synapse require different group I mGluRs, with LPP-GC synapses dependent on mGluR5 and MPP-GC t-LTD requiring mGluR1.

The authors performed a detailed analysis of the coefficient of variation of the EPSP slopes, miniature responses and different approaches (failure rate, PPRs, CV, and mEPSP frequency and amplitude analysis) they demonstrate a decrease in the probability of neurotransmitter release and a presynaptic locus for these two forms of LTD at both types of synapses. By using elegant electrophysiological experiments and taking the advantage of the conditional dominant-negative (dn) SNARE mice in which doxycycline administration blocks exocytosis and impairs vesicle release by astrocytes, they demonstrate that both LTD forms require the release of gliotransmitters from astrocytes. These data add in an interesting way to the ongoing discussion on whether LTD induced by STDP participates in refining synapses potentially weakening excitatory synapses under the control of different astrocytic networks. The conclusions of this paper are well supported by data.

Reviewer #3 (Public review):

Summary:

Marchand, Akinnola, et al. describe the use of the novel model to study BM regeneration. Here, they harvest intact femurs and subcutaneously graft them into recipient mice. Similar to standard BM regeneration models, there is a rapid decrease in cellularity followed by a gradual recovery over 5 months within the grafts. At 5 months, these grafts have robust HSC activity, similar to HSCs isolated from the host femur. They find that periosteum skeletal stem cells (p-SSCs) are the primary source of BM-MSCs within the grafted femur and that these cells are more resistant to the acute stress of grafting the femur.

Strengths:

This is an interesting manuscript that describes a novel model to study BM regeneration. The model has tremendous promise.

Weaknesses:

The authors claim that grafting intact femurs subcutaneously is a model of BM regeneration and can be used as a replacement for gold standard BM regeneration assays such as sublethal chemo/irradiation. However, there isn't enough explanation as to how this model is equivalent or superior to the traditional models. For instance, the authors claim that this model allows for the study of "BM regeneration in vivo in response to acute injury using genetic tools." This can and has been done numerous times with established, physiologically relevant BM regeneration models. The onus is on the authors to discuss or perform the necessary experiments to justify the use of this model. For example, standard BM regeneration models involve systemic damage that is akin to therapies that require BM regeneration. How is studying the current model that provides only an acute injury more relevant and useful than other models? As it stands, it seems as if the authors could have done all the experiments demonstrating the importance of these p-SSCs in the traditional myelosuppressive BM regeneration models to be more physiologically relevant. Along these lines, the use of a standard BM regeneration model (e.g., sublethal chemo/irradiation) as a critical control is missing and should be included. Even if the control doesn't demonstrate that p-SSCs can contribute to the BM-MSC during regeneration, it will still be important because it could be the justification for using the described model to specifically study p-SSCs' regulation of BM regeneration.

The authors perform some analysis that suggests that grafting a whole femur mimics BM regeneration, but there are many experiments missing from the manuscript that will be necessary to support the use of this model. To demonstrate that this new model mimics current BM regeneration models, the authors need to perform a careful examination of the early kinetics of hematopoietic recovery post-transplant. Complete blood counts should be performed on the grafts, focusing on white blood cells (particularly neutrophils), red blood cells, platelets, all critical indicators of BM regeneration. This analysis should be done at early time points that include weekly analysis for a minimum of 28 days following the graft. Additionally, understanding how and when the vasculature recovers is critical. This is particularly important because it is well-established that if there is a delay in vascular recovery, there is a delay in hematopoietic recovery. As mentioned above, a standard BM regeneration model should be used as a control.

The contribution of donor and host cells to the BM regeneration of the graft is interesting. Particularly, the chimerism of the vasculature. One can assume that for the graft to undergo BM regeneration, there needs to be the delivery of nutrients into the graft via the vasculature. The chimerism of the vascular network suggests that host endothelial cells anastomose with the graft. Host mice should have their vascular system labeled with a dye such as dextran to determine if anastomosis has occurred. If not, the authors need to explain how this graft survives up to 5 months. If anastomosis does occur, then it is very surprising that the hematopoietic system of the graft is not a chimera because this would essentially be a parabiosis model. This needs to be explained.

Most of the data presented for the resistance of p-SSCs to stress suggests DNA damage response. Do p-SSCs demonstrate a higher ability to resolve DNA damage? Do they accumulate less DNA damage? Staining for DNA damage foci or performing comet assays could be done to further define the mechanism of stress resistance properties of p-SSCs.

Given the importance of BM-MSCs in hematopoiesis and that the majority of the emerging BM-MSCs appear to be derived from p-SSCs, the authors should perform experiments to determine if p-SSC-derived BM-MSCs are critical regulators of BM regeneration. For example, the authors could test this by crossing the Postn-creER mice with iDTR mice to ablate these cells and see if recovery is inhibited or delayed. This should be done with the described periosteum-wrapped femur graft model as well as a control BM regeneration model. Demonstrating that the deletion of these cells affects BM regeneration in both models would further justify the physiological relevance and utility of the femur graft model.

Reviewer #3 (Public review):

Summary:

In this study, several novel class IIb microcin biosynthetic gene clusters have been discovered by specific homology searches and manual curation. Using a specific E. coli expression system, the microcins were expressed and conjugated to monoglycosylated enterobactin as siderophore moiety. While this synthetic biology approach cannot account for other siderophores being coupled to the microcin core peptide in the original producing strains, it nonetheless allows for a general screening for the activity of the heterologously produced compounds. Through this approach, the activity of several predicted microcins has been confirmed and three novel class IIb microcin clades were identified.

Strengths:

The experimental design is sound, the results are corroborated by suitable controls, and the findings have a high level of novelty and significance. Furthermore, the comments of the initial round of peer review have been answered satisfactorily by the authors.

Reviewer #3 (Public review):

In this study, Cao et al. explore the neural mechanisms by which chronic heat exposure induces negative valence and hyperarousal in mice, focusing on the role of the posterior paraventricular nucleus (pPVT) neurons that receive projections from the preoptic area (POA). The authors show that chronic heat exposure leads to heightened activity of the POA projection-receiving pPVT neurons, potentially contributing to behavioral changes such as increased anxiety level and reduced sociability, along with heightened startle responses. In addition, using electrophysiological methods, the authors suggest that increased membrane excitability of pPVT neurons may underlie these behavioral changes. The use of a variety of behavioral assays enhances the robustness of their claim. Moreover, while previous research on thermoregulation has predominantly focused on physiological responses to thermal stress, this study adds a unique and valuable perspective by exploring how thermal stress impacts affective states and behaviors, thereby broadening the field of thermoregulation. However, a few points warrant further consideration to enhance the clarity and impact of the findings.

(1) The authors claim that behavior changes induced by chronic heat exposure are mediated by the POA-pPVT circuit. However, it remains unclear whether these changes are unique to heat exposure or if this circuit represents a more general response to chronic stress. It would be valuable to include control experiments with other forms of chronic stress, such as chronic pain, social defeat, or restraint stress, to determine if the observed changes in the POA-pPVT circuit are indeed specific to thermal stress or indicative of a more universal stress response mechanism.

(2) The authors use the term "negative emotion and hyperarousal" to interpret behavioral changes induced by chronic heat (consistently throughout the manuscript, including the title and lines 33-34). However, the term "emotion" is broad and inherently difficult to quantify, as it encompasses various factors, including both valence and arousal (Tye, 2018; Barrett, L. F. 1999; Schachter, S. 1962). Therefore, the reviewer suggests the authors use a more precise term to describe these behaviors, such as valence. Additionally, in lines 117 and 137-139, replacing "emotion" with "stress responses," a term that aligns more closely with the physiological observations, would provide greater specificity and clarity in interpreting the findings.

(3) Related to the role of POA input to pPVT,<br /> a) The authors showed increased activity in pPVT neurons that receive projections from the POA (Figure 3), and these neurons are necessary for heat-induced behavioral changes (Figures 4N-W). However, is the POA input to the pPVT circuit truly critical? Since recipient pPVT neurons can receive inputs from various brain regions, the reviewer suggests that experiments directly inhibiting the POA-to-pPVT projection itself are needed to confirm the role of POA input. Alternatively, the authors could show that the increased activity of pPVT neurons due to chronic heat exposure is not observed when the POA is blocked. If these experiments are not feasible, the reviewer suggests that the authors consider toning down the emphasis on the role of the POA throughout the manuscript and discuss this as a limitation.<br /> b) In the electrophysiology experiments shown in Figures 6A-I, the authors conducted in vitro slice recordings on pPVT neurons. However, the interpretation of these results (e.g., "The increase in presynaptic excitability of the POA to pPVT excitatory pathway suggested plastic changes induced by the chronic heat treatment.", lines 349-350) appears to be an overclaim. It is difficult to conclude that the increased excitability of pPVT neurons due to heat exposure is specifically caused by inputs from the POA. To clarify this, the reviewer suggests the authors conduct experiments targeting recipient neurons in the pPVT, with anterograde labeling from the POA to validate the source of excitatory inputs.

(4) The authors focus on the excitatory connection between the POA and pPVT (e.g., "Together, our results indicate that most of the pPVT-projecting POA neurons responded to heat treatment, which would then recruit their downstream neurons in the pPVT by exerting a net excitatory influence.", lines 169-171). However, are the POA neurons projecting to the pPVT indeed excitatory? This is surprising, considering i) the electrophysiological data shown in Figures 2E-K that inhibitory current was recorded in 52.4% of pPVT neurons by stimulation of POA terminal, and ii) POA projection neurons involved in modulating thermoregulatory responses to other brain regions are primarily GABAergic (Tan et al., 2016; Morrison and Nakamura, 2019). The reviewer suggests showing whether the heat-responsive POA neurons projecting to the pPVT are indeed excitatory (This could be achieved by retrogradely labeling POA neurons that project to the pPVT and conducting fluorescence in situ hybridization (FISH) assays against Slc32a1, Slc17a6, and Fos to label neurons activated by warmth). Alternatively, demonstrate, at least, that pPVT-projecting POA neurons are a distinct population from the GABAergic POA neurons that project to thermoregulatory regions such as DMH or rRPa. This would clarify how the POA-pPVT circuit integrates with the previously established thermoregulatory pathways.

Reviewer #3 (Public review):

The authors investigated fibroblasts' communication with key cell types in developing and neonatal hearts, with a focus on the critical roles of fibroblast-cardiomyocyte and fibroblast-endothelial cell networks in cardiac morphogenesis. They tried to map the spatial distribution of these cell types and reported the major pathways and signaling molecules driving the communication. They also used Cre-DTA system to ablate Pdgfra labeled cells and observed myocardial and endothelial cell defects at development. They screened the pathways and genes using sequencing data of ablated hearts. Lastly, they reported compensatory collagen expression in long-term ablated neonate hearts. Overall, this study provides us with important insight into fibroblasts' roles in cardiac development and will be a powerful resource for collagens and ECM-focused research.

Strengths:

The authors utilized good analyzing tools to investigate multiple databases of single-cell sequencing and Multi-seq. They identified significant pathways and cellular and molecular interactions of fibroblasts. Additionally, they compared some of their analytic findings with a human database, and identified several groups of ECM genes with varying roles in mice.

Weaknesses:

This study is majorly based on sequencing data analysis. At the bench, they used a very strident technique to study fibroblast functions by ablating one of the major cell populations of the heart. Considering the importance of the fibroblast population, intriguing in vivo findings were expected. Also, they analyzed the downstream genes in ablated hearts, but did not execute any experimental validation for any of the targets.

Reviewer #3 (Public review):

Summary:

Ecker et al. utilized a biologically realistic, large-scale cortical model of the rat's non-barrel somatosensory cortex, incorporating a calcium-dependent plasticity rule to examine how various factors influence synaptic plasticity under in vivo-like conditions. Their analysis characterized the resulting plastic changes and revealed that key factors, including the co-firing of stimulus-evoked neuronal ensembles, the spatial organization of synaptic clusters, and the overall network topology, play an important role in affecting the extent of synaptic plasticity.

Strengths:

The detailed, large-scale model employed in this study enables the evaluation of diverse factors across various levels that influence the extent of plastic changes. Specifically, it facilitates the assessment of synaptic organization at the subcellular level, network topology at the macroscopic level, and the co-activation of neuronal ensembles at the activity level. Moreover, modeling plasticity under in vivo-like conditions enhances the model's relevance to experiments.

Weaknesses:

(1) The authors claimed that, under in vivo-like conditions and in the presence of plasticity, firing rates and weight distributions remain stable without additional homeostatic mechanisms during a 10-minute stimulation period. However, the weights do not reach the steady state immediately after the 10-minute stimulation. Therefore, extended simulations are necessary to substantiate the claim.

(2) Another major limitation of the paper lies in its lack of mechanistic insights into the observed phenomena (particularly on aspects that are typically impossible to assess in traditional simplified models, like layer-specific and layer-to-layer pathways-specific plasticity changes), as well as the absence of discussions on the potential computational implications of the corresponding observed plastic changes.

这是一整句话而不是逗号后面另起一句的意思，因为“that” 引导了一个宾语从句，这个从句需要包含完整的主谓结构来表达意思，to look good不是一个句子而是一个目的性不定式短语，说明为了“看起来好”，所以需要后面的a proof has to have lots of symbols and almost no English text.去补充

Reviewer #3 (Public review):

Summary:

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

Strengths:

The major strength of this paper is identifying an example of antibiotic resistance evolution that illustrates the interplay between the proteolytic stability and copy number of an antibiotic target in the setting of antibiotic selection. If the weaknesses are addressed, then this paper will be of interest to microbiologists who study the evolution of antibiotic resistance.

Weaknesses:

Although the proposed mechanism is highly plausible and consistent with the data presented, the analysis of the experiments supporting the claim is incomplete and requires more rigor and reproducibility. The impact of this finding is somewhat limited given that it is a single example that occurred in a lon strain and compensatory mutations for evolved antibiotic resistance mechanisms are described. In this case, it is not clear that there is a functional difference between the evolution of copy number versus any other mechanism that meets a requirement for increased "expression demand" (e.g. promoter mutations that increase expression and protein stabilizing mutations).

Reviewer #3 (Public review):

Summary:

Using a specparam (1/f) analysis of task-evoked activity, the authors propose that "substantial changes traditionally attributed to theta oscillations in working memory tasks are, in fact, due to shifts in the spectral slope of aperiodic activity." This is a very bold and ambitious statement, and the field of event-related EEG would benefit from more critical assessments of the role of aperiodic changes during task events. Unfortunately, the data shown here does not support the main conclusion advanced by the authors.

Strengths:

The field of event-related EEG would benefit from more critical assessments of the role of aperiodic changes during task events. The authors perform a number of additional control analyses, including different types of baseline correction, ERP subtraction, as well as replication of the experiment with two additional datasets.

Weaknesses:

The authors did not first show that their first task successfully evoked theta power, nor that specparam is capable of quantifying the background around a short theta burst, nor that theta effects are different between baseline corrected vs. spectral parameterized quantifications.

Reviewer #3 (Public review):

Summary:

The present study reports findings from a series of experiments suggesting that bovine oviductal fluid and species-specific oviductal glycoprotein (OVGP1 or oviductin) from bovine, murine, or human sources modulate the species specificity of bovine and murine oocytes.

Strengths:

The study reported in the manuscript deals with an important topic of interest in reproductive biology.

Weaknesses:

The manuscript began with a well-written introduction, but problems started to surface in the Results section, in the Discussion, as well as in the Materials and Methods. Major concerns include inconsistencies, misinterpretation of results, lacking up-to-date literature search, numerous errors found in the figure legends, misleading and incorrect information given in the Materials and Methods, missing information regarding statistical analysis, and inadequate discussion. These concerns raise questions regarding the authenticity of the study, reliability of the findings, and interpretation of the results. The manuscript does not provide solid and convincing findings to support the conclusion.