Reviewer #4 (Public review):

The manuscript examines how patterns of selection on gene expression differ between a normal field environment and a field environment with elevated salinity based upon transcript abundances obtained from leaves of a diverse panel of rice germplasm. In addition, the manuscript also maps expression QTL (eQTL) that explains variation in each environment. One highlight from the mapping is that a small group of trans-mapping regulators explains some gene expression variation for large sets of transcripts in each environment.

The overall scope of the datasets is impressive, combining large field studies that capture information about fecundity, gene expression, and trait variation at multiple sites. The finding related to patterns indicating increased LD among eQTLs that have cis-trans compensatory or reinforcing effects in interesting in the context of other recent work finding patterns of epistatic selection. The authors have made some changes that address previous comments. However, some analyses in the manuscript remain less compelling or do not make the most from the value of collected data. Although the authors have made several improvements to the precision with which field-specific terminology is applied and to the language chosen when interpreting analytical findings, additional changes to improve these aspects of the manuscript remain necessary.

Selection of gene expression: One strength of the dataset is that gene expression and fecundity were measured for the same genotypes in multiple environments. However, the selection analyses are largely conducted within environments. Addition of phenotypic selection analyses that jointly analyze gene expression across environments and or selection on reaction norms would be worthwhile.

Gene expression trade-offs: The terminology and possibly methods involved in the section on gene expression trade-offs need amendment. I specifically recommend discontinuing reference to the analysis presented as an analysis of antagonistic pleiotropy (rather than more general as trade-offs) because pleiotropy is defined as a property of a genotype, not a phenotype. Gene expression levels are a molecular phenotype, influenced by both genotype and the environment. By conducting analyses of selection within environments as reported, the analysis does not account for the fact that the distribution of phenotypic values, the fitness surface, or both may differ across environments. Thus, this presents a very different situation than asking whether the genotypic effect of a QTL on fitness differs across environments, which is the context in which the contrasting terms antagonistic pleiotropy and conditional neutrality have been traditionally applied. The results reported do not persuasively support the assertion made in the response to reviewers that the terminology is reasonable due to strong coupling between genotype and phenotype. A more interesting analysis would be to examine whether the covariance of phenotype with fitness has truly changed between environments or whether the phenotypic distribution has just shifted to a different area of a static fitness surface.

Biological processes under selection / Decoherence: In the initial review, it was noted that PCA is likely not the most ideal way to cluster genes to generate consolidated metrics for a selection gradient analysis. Because individual genes will contribute to multiple PCs, the current fractional majority-rule method applied to determine whether a PC is under direct or indirect selection for increased or decreased expression comes across as arbitrary and with the potential for double-counting genes. A gene co-expression network analysis could be more appropriate, as genes only belong to one module and one can examine how selection is acting on the eigengene of a co-expression module. Building gene co-expression modules would also provide a complementary and more concrete framework for evaluating whether salinity stress induces "decoherence" and which functional groups of genes are most impacted. Although results of co-expression network analyses are now briefly discussed in the response to reviewers, the findings and their relationship to the PCA/"decoherence" analyses are not reported in the manuscript.

Selection of traits: Having paired organismal and molecular trait data is a strength of the manuscript, but the organismal trait data are underutilized. The manuscript as written only makes weak indirect inferences based on GO categories or assumed gene functions to connect selection at the organismal and molecular levels. After prompted by the initial reviews to test for correspondence between SNPs that explain organismal and gene expression trait variation or co-variance of co-expression module variation and trait variation, the response to reviewers indicates finding negative results. These findings should be included in the manuscript text and discussed.

Genetic architecture of gene expression variation: More descriptive statistics of the eQTL analysis have been included, although additional information about the variation in these measures within environments would be useful. The motivation for featuring patterns of cis-trans compensation specifically for the results obtained under high salinity conditions remains unclear to me. If the lines sampled have predominantly evolved under low salinity conditions, and the hypothesis being evaluated relates to historical experience of stabilizing selection, then evaluating the eQTL patterns under normal conditions provides the more relevant test of the hypothesis.

Lines 280-282: The revised sentence continues to read as an overstatement and merits additional revision with citations.

Lines 379-381: Following revision, it still remains unclear how the interpretation follows from the above analysis; the inference as written goes significantly beyond what may be specifically inferable from the result.

Reviewer #3 (Public review):

Summary:

This manuscript describes an in-depth analysis of the effect of the AAA+ ATPase PCH-2 on meiotic crossover formation in C. elegant. The authors reach several conclusions and attempt to synthesize a 'universal' framework for the role of this factor in eukaryotic meiosis.

Strengths:

The manuscript makes use of the advantages of the 'conveyor' belt system within the c.elegans reproductive tract, to enable a series of elegant genetic experiments

Weaknesses:

A weakness of this manuscript is that it heavily relies on certain genetic/cell biological assays that can report on distinct crossover outcomes, without clear and directed control over other aspects and variables that might also impact the final repair outcome. Such assays are currently out of reach in this model system.

Reviewer #3 (Public review):

Summary:

The authors submitted a revised manuscript that 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 authors have submitted a revised manuscript with much improvement and have answered many of this reviewer's questions. However, some of the previous questions have been dealt with inadequately. There are still several issues that need to be dealt with. In particular, there are questions regarding the specificity and/or purity of the recombinant human and mouse OVGP1 which could be detrimental to the reliability of the recombinant human and mouse OVGP1s used in the study and the validity of the results presented. This Discussion should cover more broadly what has already been published in literature.

Reviewer #3 (Public Review):

Summary:

Out of the 20 Neglected Tropical Diseases (NTD) highlighted by the WHO, three are caused by members of the trypanosomatids, namely Leishmanaisis, Trypanosomiasis, and Chagas disease. Trypanosomal glycolytic enzymes including pyruvate kinase (PyK) have long been recognised as potential targets. In this important study, single-chain camelid antibodies have been developed as novel and potent inhibitors of PyK from the T, congolense. To gain structural insight into the mode of action, binding was further characterised by biophysical and structural methods, including crystal structure determination of the enzyme-nanobody complex. The results revealed a novel allosteric mechanism/pathway with significant potential for the future development of novel drugs targeting allosteric and/or cryptic binding sites.

Strengths:

This paper covers an important area of science towards the development of novel therapies for three of the Neglected Tropical Diseases. The manuscript is very clearly written with excellent graphics making it accessible to a wide readership beyond experts. Particular strengths are the wide range of experimental and computational techniques applied to an important biological problem. The use of nanobodies in all areas from biophysical binding experiments and X-ray crystallography to in-vivo studies is particularly impressive. This is likely to inspire researchers from many areas to consider the use of nanobodies in their fields.

Weaknesses:

There is no particular weakness, but I think the computational analysis of allostery, which basically relies on a single server could have been more detailed.

DOI: 10.1016/j.xpro.2024.103587

Resource: RRID:ZFIN_ZDB-GENO-180906-3

Curator: @scibot

SciCrunch record: RRID:ZFIN_ZDB-GENO-180906-3

What is this?

Reviewer #3 (Public review):

Summary:

The authors established an experimental system that reproduced three-dimensional triphasic epithelia, i.e., the original epithelium, its EMT, and MET. Keratinocytes (KCs), skin epithelial cells, placed on a microporous membrane migrated through 3.0-um or larger micropores. The 3.0-um-pored membrane induced an epithelial structure with three states: stratified KCs above the membrane, KCs showing EMT within the micropores, and a new stratified epithelium under the membrane. The membrane with larger micropores failed to maintain this triphasic epithelium. Live imaging revealed that KCs moved in a reciprocating manner, with actin-rich filopodia-like KC structures extending into and out of the 3.0-um micropores, while the cells migrated unidirectionally into larger micropores. KO of Piezo1 and keratin 6 increased KC entry to and exit from the 3.0-um micropores. Their results demonstrate that benign keratinocytes migrate through confined spaces in a reciprocating manner, which might help form triphasic epithelia, recapitulating wound healing processes.

Strengths:

Careful observation of the behaviour of keratinocytes on the different-sized pores. CrispR-Cas9 gene editing to KO Piezo 1 and keratin 6 isoforms in HaCaT keratinocytes.

Weaknesses:

There is no analysis of the matrix produced by the keratinocytes on the different pore sizes as this may influence migration.

HaCaT cells are quite different from normal keratinocytes in terms of migration. Pilcher et al. PMID: 9182674

Reviewer #3 (Public review):

Strengths:

This work focuses on a problem of deep significance: quantifying the structure-tension relationship and underlying mechanism for the mechanosensitive Piezo 1 and 2 channels. This objective presents a few technical challenges for molecular dynamics simulations, due to the relatively large size of each membrane-protein system. Nonetheless, the technical approach chosen is based on the methodology that is, in principle, established and widely accessible. Therefore, another group of practitioners would likely be able to reproduce these findings with reasonable effort.

Weaknesses:

The two main results of this paper are (1) that both channels exhibit a flatter structure compared to cryo-EM measurements, and (2) their estimated force vs. displacement relationship. Although the former correlates at least quantitatively with prior experimental work, the latter relies exclusively on simulation results and model parameters.

Reviewer #3 (Public review):

Summary:

The manuscript by Wu D. et al. explores an innovative approach in 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.

Comments on revisions:

The author has revised the manuscript and addressed the most relevant comments raised by the reviewers. The paper is now significantly improved, though two minor issues remain.

(1) Studies were limited to male mice; this should be mentioned in the paper's Title.<br /> (2) Please include the sample size (n=) in all provided tables in the main manuscript and supplementary tables.

Reviewer #3 (Public review):

Summary:

In this study, Piersma et al. successfully generated a mouse model with all Ly49 genes knocked out, resulting in the complete absence of Ly49 receptor expression on the cell surface. The absence of Ly49 expression led to the loss of NK cell education/licensing and consequently, a failure in responsiveness against missing-self target cells. The authors demonstrate the restoration of NK cell licensing by knocking in a single Ly49 gene, Ly49A, in a mouse expressing the H-2Dd ligand for this receptor, which is a novel and important finding.

Strengths:

The authors established a novel mouse model enabling them to have a clean and thorough study on the function of Ly49 on NK cell licensing. Also, by knock in a single Ly49, they were able to investigate the function of a given Ly49 receptor excluding the "contamination" of co-expression any other Ly49 genes. The experiment designing and data interpretation were logically clear and the evidence was solid.

Weaknesses:

The mouse model was somehow genetically similar to a previous study. The experimental work and findings are partially overlapping with the previous work by Zhang et al. (2019), who also performed knockout of the entire Ly49 locus in mice and demonstrated that loss of NK responsiveness was due to the removal of inhibitory, and not activating Ly49 genes.

Potential achievements and discussions: The mouse model developed by the authors holds great potential for advancing NK cell functional studies, particularly regarding the regulation of NK cell functions through receptor-ligand interactions. Moreover, it provides a valuable tool for investigating NK cell education and the development of checkpoint inhibitors. These applications could significantly contribute to the broader research efforts in cancer therapy utilizing NK cells.

Comments on revisions: The authors have successfully addressed all the concerns raised in my previous feedback. They have significantly improved the logical structure, making it clearer and more coherent. Additionally, they have ensured consistency in the use of specific terminology throughout the manuscript. The substantial revisions and re-writing efforts are commendable and have greatly enhanced the overall quality of the manuscript.

Reviewer #3 (Public Review):

Summary:

The paper aims at providing a neurocomputational account on how social perception translates in prosocial behaviors. Participants first completed a novel social perception task during fMRI scanning, in which were asked to judge the merit or need of people depicted in different situations. Second , a separate altruistic choice task was used to examine how the perception of merit and need influences the weights people place on themselves, others and fairness when deciding to provide help. Finally, a link between perception and action was drawn in those participants who completed both tasks.

Strengths:

The paper is overall very well written and presented, leaving the reader at ease when describing complex methods and results. The approach used by the author is very compelling, as it combines computational modeling of behavior and neuroimaging data analyses. Despite not being able to comment on the computational model, I find the approach used (to disentangle sensitivity and biases, for merit and need) very well described and derived from previous theoretical work. Results are also clearly described and interpreted.

Weaknesses:

In the social perception task, merit and need are evaluated by means of very different cues that rely on different cognitive processes (more abstract thinking for merit than need). Despite this limitation of the task, the authors were able to argue convincingly in the revised version about the solidity of their findings. Sample size is quite small for study 2, nevertheless the results provide convincing evidence.

Reviewer #3 (Public review):

Summary:

Inoshita and Kawaguchi investigated the effects of GPR55 activation on synaptic transmission in vitro. To address this question, they performed direct patch-clamp recordings from axon terminals of cerebellar Purkinje cells and fluorescent imaging of vesicular exocytosis utilizing synapto-pHluorin. They found that exogenous activation of GPR55 suppresses GABA release at Purkinje cell to deep cerebellar nuclei (PC-DCN) synapses by reducing the readily releasable pool (RRP) of vesicles. This mechanism may also operate at other synapses.

Strengths:

The main strength of this study lies in combining patch-clamp recordings from axon terminals with imaging of presynaptic vesicular exocytosis to reveal a novel mechanism by which activation of GPR55 suppresses inhibitory synaptic strength. The results strongly suggest that GPR55 activation reduces the RRP size without altering presynaptic calcium influx.

Weaknesses:

The study relies on the exogenous application of GPR55 agonists. It remains unclear whether endogenous ligands released due to physiological or pathological activities would have similar effects. There is no information regarding the time course of the agonist-induced suppression. There is also little evidence that GPR55 is expressed in Purkinje cells. This study would benefit from using GPR55 knockout (KO) mice. The downstream mechanism by which GPR55 mediates the suppression of GABA release remains unknown.

Reviewer #3 (Public review):

Summary:

In this manuscript, Edwards et al. describe hamFISH, a customizable and cost-efficient method for performing targeted spatial transcriptomics. hamFISH utilizes highly amplified multiplexed branched DNA amplification, and the authors extensively describe hamFISH development and its advantages over prior variants of this approach.

The authors then used hamFISH to investigate an important circuit in the mouse brain for social behavior, the medial amygdala (MeA). To develop a hamFISH probe set capable of distinguishing MeA neurons, the authors mined published single-cell RNA-sequencing datasets of the MeA, ultimately creating a panel of 32 hamFISH probes that mostly cover the identified MeA cell types. They evaluated over 600,000 MeA cells and classified neurons into 16 inhibitory and 10 excitatory types, many of which are spatially clustered. The authors combined hamFISH with viral and other circuit tracer injections to determine whether the identified MeA cell populations sent and/or received unique inputs from connected brain regions, finding evidence that several cell types had unique patterns of input and output. Finally, the authors performed hamFISH on the brains of male mice that were placed in behavioral conditions that elicit aggressive, infanticidal, or mating behaviors, finding that some cell populations are selectively activated (as assessed by c-fos mRNA expression) in specific social contexts.

Strengths:

(1) The authors developed an optimized tissue preparation protocol for hamFISH and implemented oligopools instead of individually synthesized oligonucleotides to reduce costs. The branched DNA amplification scheme improved smFISH signal compared to previous methods, and multiple variants provide additional improvements in signal intensity and specificity. Compared to other spatial transcriptomics methods, the pipeline for imaging and analysis is streamlined and is compatible with other techniques like fluorescence-based circuit tracing. This approach is cost-effective and has several advantages that make it a valuable addition to the list of spatial transcriptomics toolkits.

(2) Using 31 probes, hamFISH was able to detect 16 inhibitory and 10 excitatory neuron types in the MeA subregions, including the vast majority of cell types identified by other transcriptomics approaches. The authors quantified the distributions of these cell types along the anterior-posterior, dorsal-ventral, and medial-lateral axes, finding spatial segregation among some, but not all, MeA excitatory and inhibitory cell types. The authors additionally identified a class of inhibitory neurons expressing Ndnf (and a subset of these that express Chrna7) that project multiple social chemosensory circuits.

(3) The authors combined hamFISH with MeA input and output mapping, finding cell-type biases in the projections to the MPOA, BNST, and VMHvl, and inputs from multiple regions.

(4) The authors identified excitatory and inhibitory cell types, and patterns of activity across cell types, that were selectively activated during various social behaviors, including aggression, mating, and infanticide, providing new insights and avenues for future research into MeA circuit function.

Weaknesses:

(1) Gene selection for hamFISH is likely to still be a limiting factor, even with the expanded (32-probe) capacity. This may have contributed to the lack of ability to identify sexually dimorphic cell types (Figure S2B). This is an expected tradeoff for a method that has major advantages in terms of cost and adaptability.

(2) Adaptation of hamFISH, for example, to adapt it to other brain regions or tissues, may require extensive optimization.

(3) Pairing this method with behavioral experiments is likely to require further optimization, as c-fos mRNA expression is an indirect and incomplete survey of neuronal activity (e.g. not all cell types upregulate c-fos when electrically active). As such, there is a risk of false negative results that limit its utility for understanding circuit function.

(4) The limited compatibility of hamFISH with thicker tissue samples and lack of optical sectioning introduce additional technical limitations. For example, it would be difficult to densely sample larger neural circuits using serial 20 micron sections. Also, because the imaging modality is not clear from the methods, it is difficult to know whether the analysis methods introduce the risk of misattributing gene expression to overlapping cells.

Reviewer #3 (Public review):

In this study, Bison et al. analyzed the role of the GATA6 transcription factor in patterning the early mesoderm and generating cardiomyocytes, using human embryonic stem cell differentiation assays and patient-derived hiPSCs with heart defects associated with mutations in the GATA6 gene. They identified a novel role for GATA6 in regulating genes involved in the WNT and BMP pathways. Modulation of the WNT and BMP pathways partially rescue early cardiac mesoderm defects in GATA6 mutant hESCs. These results provide significant insights into how GATA6 loss-of-function and heterozygous mutations contribute to heart defects.

Comments on revised version:

The authors have addressed all the concerns, using new data and modifications to the text to further strengthen the manuscript.

Reviewer #3 (Public review):

Summary:

Human cells deficient in delta-tubulin or epsilon-tubulin form unstable centrioles, which lack triplet microtubules and undergo a futile formation and disintegration cycle. In this study, the authors show that human cells lacking the associated proteins TEDC1 or TEDC2 have these identical phenotypes. They use genetics to knockout TEDC1 or TEDC2 in p53-negative RPE-1 cells and expansion microscopy to structurally characterize mutant centrioles. Biochemical methods and AlphaFold-multimer prediction software are used to investigate interactions between tubulins and TEDC1 and TEDC2.

The study shows that mutant centrioles are built only of A tubules, which elongate and extend their proximal region, fail to incorporate structural components, and finally disintegrate in mitosis. In addition, they demonstrate that delta-tubulin or epsilon-tubulin and TEDC1 and TEDC2 form one complex and that TEDC1 TEDC2 can interact independently of tubulins. Finally, they show that localization of four proteins is mutually dependent.

Strengths:

The results presented here are convincing, exciting, and important, and the manuscript is well-written. The study shows that delta-tubulin, epsilon-tubulin, TEDC1, and TEDC2 function together to build a stable and functional centriole, significantly contributing to the field and our understanding of the centriole assembly process.

Weaknesses:

The ultrastructural characterization of TEDC1 and TEDC2 in centrosomes remains challenging. Nevertheless, it is evident that these proteins occupy growing centrioles and the proximal parts of mother centrioles.

Comments on revisions:

The authors have done a great job extending the original experiments and measurements and answering outstanding questions.

Reviewer #3 (Public review):

The authors find that HERV expression patterns can be used as new criteria for differential diagnosis of FM and ME/CFS and patient subtyping. The data are based on transcriptome analysis by microarray for HERVs using patient blood samples, followed by differential expression of ERVs and bioinformatic analyses. This is a standard and solid data processing pipeline, and the results are well presented and support the authors' claim.

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):

Summary:

Redman and colleagues analyze grid cell data obtained from public databases. They show that there is significant variability in spacing and orientation within a module. They show that the difference in spacing and orientation for a pair of cells is larger than the one obtained for two independent maps of the same cell. They speculate that this variability could be useful to disambiguate the rat position if only information from a single module is used by a decoder.

Strengths:

The strengths of this work lie in its conciseness, clarity, and the potential significance of its findings for the grid cell community, which has largely overlooked this issue for the past two decades. Their hypothesis is well stated and the analyses are solid.

Weaknesses:

Major weaknesses identified in the original version have been addressed.

The authors have addressed all of our concerns, providing control analyses that strengthen their claim.

Reviewer #3 (Public review):

Summary:

The paper investigates the TMEM16 family of membrane proteins, which play roles in lipid scrambling and ion transport. A total of 27 experimental structures from five TMEM16 family members were analyzed, including mammalian and fungal homologs (e.g., TMEM16A, TMEM16F, TMEM16K, nhTMEM16, afTMEM16). The identified structures were in both Ca²⁺-bound (open) and Ca²⁺-free (closed) states to compare conformations and were preprocessed (e.g., modeling missing loops) and equilibrated. Coarse-grain simulations were performed in DOPC membranes for 10 microseconds to capture the scrambling events. These events were identified by tracking lipids transitioning between the two membrane leaflets and they analysed the correlation between scrambling rates, in addition, structural properties such as groove dilation and membrane thinning were calculated. They report 700 scrambling events across structures and Figure 2 elaborates on how open structures show higher activity, also as expected. The authors also address how structures may require open grooves, this and other mechanisms around scrambling are a bit controversial in the field.

Strengths:

The strength of this study emerges from a comparative analysis of multiple structural starting points and understanding global/local motions of the protein with respect to lipid movement. Although the protein is well-studied, both experimentally and computationally, the understanding of conformational events in different family members, especially membrane thickness less compared to fungal scramblases offers good insights.

Weaknesses:

The weakness of the work is to fully reconcile with experimental evidence of Ca²⁺-independent scrambling rates observed in prior studies, but this part is also challenging using coarse-grain molecular simulations. Previous reports have identified lipid crossing, packing defects, and other associated events, so it is difficult to place this paper in that context. However, the absence of validation leaves certain claims, like alternative scrambling pathways, speculative.

Reviewer #3 (Public review):

Summary:

Fahrenfort et al. investigate how liberal or conservative criterion placement in a detection task affects the construct validity of neural measures of unconscious cognition and conscious processing. Participants identified instances of "seen" or "unseen" in a detection task, a method known as post hoc sorting. Simulation data convincingly demonstrate that, counterintuitively, a conservative criterion inflates effect sizes of neural measures compared to a liberal criterion. While the impact of criterion shifts on effect size is suggested by signal detection theory, this study is the first to address this explicitly within the consciousness literature. Decoding analysis of data from two EEG experiments further shows that different criteria lead to differential effects on classifier performance in post hoc sorting. The findings underscore the pervasive influence of experimental design and participant reports on neural measures of consciousness, revealing that criterion placement poses a critical challenge for researchers.

Strengths and Weaknesses

One of the strengths of this study is the inclusion of the Perceptual Awareness Scale (PAS), which allows participants to provide more nuanced responses regarding their perceptual experiences. This approach ensures that responses at the lowest awareness level (selection 0) are made only when trials are genuinely unseen. This methodological choice is important as it helps prevent the overestimation of unconscious processing, enhancing the validity of the findings.<br /> The authors also do a commendable job in the discussion by addressing alternative paradigms, such as wagering paradigms, as a possible remedy to the criterion problem (Peters & Lau, 2015; Dienes & Seth, 2010). Their consideration of these alternatives provides a balanced view and strengthens the overall discussion.

Our initial review identified a lack of measures of variance as one potential weakness of this work. However we agree with the authors' response that plotting individual datapoints for each condition is indeed a good visualization of variance within a dataset.

Impact of the Work:

This study effectively demonstrates a phenomenon that, while understood within the context of signal detection theory, has been largely unexplored within the consciousness literature. Subjective measures may not reliably capture the construct they aim to measure due to criterion confounds. Future research on neural measures of consciousness should account for this issue, and no-report measures may be necessary until the criterion problem is resolved.

Reviewer #3 (Public review):

Summary:

Tubert et al. investigate the mechanisms underlying the pause response in striatal cholinergic interneurons (SCINs). The authors demonstrate that optogenetic activation of thalamic axons in the striatum induces burst activity in SCINs, followed by a brief pause in firing. They show that the duration of this pause correlates with the number of elicited action potentials, suggesting a burst-dependent pause mechanism. The authors demonstrated this burst-dependent pause relied on Kv1 channels. The pause is blocked by a SKF81297 and partially by sulpiride and mecamylamine, implicating D1/D5 receptor involvement. The study also shows that the ZD7288 does not reduce the duration of the pause, and that lesioning dopamine neurons abolishes this response, which can be restored by clozapine.

Weaknesses:

While this study presents an interesting mechanism for SCIN pausing after burst activity, there are several major concerns that should be addressed:

(1) Scope of the Mechanism: It is important to clarify that the proposed mechanism may apply specifically to the pause in SCINs following burst activity. The manuscript does not provide clear evidence that this mechanism contributes to the pause response observed in behavioral animals. While the thalamus is crucial for SCIN pauses in behavioral contexts, the exact mechanism remains unclear. Activating thalamic input triggers burst activity in SCINs, leading to a subsequent pause, but this mechanism may not be generalizable across different scenarios. For instance, approximately half of TANs do not exhibit initial excitation but still pause during behavior, suggesting that the burst-dependent pause mechanism is unlikely to explain this phenomenon. Furthermore, in behavioral animals, the duration of the pause seems consistent, whereas the proposed mechanism suggests it depends on the prior burst, which is not aligned with in vivo observations. Additionally, many in vivo recordings show that the pause response is a reduction in firing rate, not complete silence, which the mechanism described here does not explain. Please address these in the manuscript.

(2) Terminology: The use of "pause response" throughout the manuscript is misleading. The pause induced by thalamic input in brain slices is distinct from the pause observed in behavioral animals. Given the lack of a clear link between these two phenomena in the manuscript, it is essential to use more precise terminology throughout, including in the title, bullet points, and body of the manuscript.

(3) Kv1 Blocker Specificity: It is unclear how the authors ruled out the possibility that the Kv1 blocker did not act directly on SCINs. Could there be an indirect effect contributing to the burst-dependent pause? Clarification on this point would strengthen the interpretation of the results.

(4) Role of D1 Receptors: While it is well-established that activating thalamic input to SCINs triggers dopamine release, contributing to SCIN pausing (as shown in Figure 3), it would be helpful to assess the extent to which D1 receptors contribute to this burst-dependent pause. This could be achieved by applying the D1 agonist SKF81297 after blocking nAChRs and D2 receptors.

(5) Clozapine's Mechanism of Action: The restoration of the burst-dependent pause by clozapine following dopamine neuron lesioning is interesting, but clozapine acts on multiple receptors beyond D1 and D5. Although it may be challenging to find a specific D5 antagonist or inverse agonist, it would be more accurate to state that clozapine restores the burst-dependent pause without conclusively attributing this effect to D5 receptors.

Comments on revisions:

The authors have addressed many of my concerns. However, I remain unconvinced that adding an 'ex vivo' experiment fully resolves the fundamental differences between the burst-dependent pause observed in slices - defined by the duration of a single AHP - and the pause response in CHINs observed in vivo, which may involve contributions from more than one prolonged AHP. In vivo, neurons can still fire action potentials during the pause, albeit at a lower frequency. Moreover, in behaving animals, pause duration does not vary with or without initial excitation. The mechanism proposed demonstrates that the pause duration, defined by the length of a single AHP, is positively correlated with preceding burst activity.

To improve clarity, I recommend using the term 'SCIN pause' to describe the ex vivo findings, distinguishing them more explicitly from the 'pause response' observed in behaving animals. This distinction would help contextualize the ex vivo findings as potentially contributing to, but not fully representing, the pause response in vivo.

Again, it would be helpful to present raw data for pause durations rather than relying solely on ratios. This approach would provide the audience with a clearer understanding of the absolute duration of the burst-dependent pause and allow for better comparison to the ~200 ms pause observed in behaving animals.

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Reviewer #3 (Public review):

Summary:

Overall, this is a clearly written manuscript with nice hypothesis testing in a non-model organism that addresses the mechanism of Wolbachia-mediated male killing. The authors aim to determine how five previously identified male-killing genes (encoded in the prophage region of the wHm Wolbachia strain) impact the native host, Homona magnanima moths. This work builds on the authors' previous studies in which<br /> (1) they tested the impact of these same wHm genes via heterologous expression in Drosophila melanogaster<br /> (2) also examined the activity of other male-killing genes (e.g., from the wFur Wolbachia strain in its native host: Ostrinia furnacalis moths).

Advances here include identifying which wHm gene most strongly recapitulates the male-killing phenotype in the native host (rather than in Drosophila), and the finding that the Hm-Oscar protein has the potential for male-killing in a diverse set of lepidopterans, as inferred by the cell-culture assays.

Strengths:

Strengths of the manuscript include the reverse genetics approaches to dissect the impact of specific male-killing loci, and use of a "masculinization" assay in Lepidopteran cell lines to determine the impact of interactions between specific masc and oscar homologs.

Weaknesses:

It is clear from Figure 1 that the combinations of wmk homologs do not cause male killing on their own here. While I largely agree with the author's conclusions that oscar is the primary MK factor in this system, I don't think we can yet rule out that wmk(s) may work synergistically or interactively with oscar in vivo. This might be worth a small note in the discussion. (eg at line 294 'indicating that wmk likely targets factors other than masc." - this could be downstream of the impacts of oscar; perhaps dependent on oscar-mediated impacts on masc first).

Regarding the perceived male-bias in Figure 2a: I think readers might be interpreting "unhatched" as "total before hatching". You could eliminate ambiguity by perhaps splitting the bars into male and female, and then within a bar, coloring by hatched versus unhatched. But this is a minor point, and I think the updated text helps clarify this.

The new Figure 4b looks to be largely redundant with the oscar information in Figure 1a.

Updated statistical comparisons for the RNA-seq analysis are helpful. However these analyses are based on single libraries (albeit each a pool of many individuals), so this is still a weaker aspect of the manuscript.

The new information on masc similarity is useful (Fig 4d) - if the authors could please include a heatmap legend for the colors, that would be helpful. Also, please avoid green and red in the same figure when key for interpretation.

Figure 1A "helix-turn-helix" is misspelled. ("tern").

Reviewer #3 (Public review):

Summary

The manuscript investigates the role of norepinephrine (NE) release in the rodent hippocampus during event boundaries, such as transitions between spatial contexts and the introduction of novel objects. It also explores how NE release is altered by experience and how novelty drives the amplitude and decay times of extracellular NE. By utilizing the GRABNE sensor for sub-second resolution measurement of NE, the authors demonstrate that NE release is driven primarily by the time elapsed since an event boundary and is independent of behaviors like movement or reward. The study further explores how hippocampal neural representations are altered over time, showing that these representations stabilize shortly after event transitions, potentially linking NE release to episodic memory encoding.

Strengths

Overall, the work provides novel insights into the interplay between NE signaling and hippocampal activity and presents an intriguing hypothesis on how NE release may help push hippocampal activity into unique attractor states to encode novel experiences. The experiments are well-controlled, and the analysis is well-presented, with a detailed and engaging discussion that points towards several new and exciting research directions. The use of several behavioral paradigms to demonstrate the strongest predictor of NE release is a strength, as well as the regression analysis to disambiguate the contribution of other correlated variables. The suggestion that NE does not select ensembles for subsequent replay is also an interesting result.

Weaknesses

The authors have not convincingly established a link between hippocampal neural activity and NE release, showing qualitative rather than quantitative correlations. Therefore, at this stage, the role of NE on hippocampal function remains speculative.

Another general concern is that the smoothing/ kinetics of the sensor impacts the regression analyses. Most of the other variables, such as speed, acceleration, and even reward time points are highly dynamic and it is possible that the limitations of the sensor decorrelate the signal from (potentially) causal variables, therefore resulting in the time since the event start having the most explanatory power for most of the analyses.

More broadly, the figure legends should be expanded to better describe error bounds, mean vs median, sample sizes, and averaging choices for plots.

There are also some concerns regarding the nearest neighbor analysis and the reported differences in the rate of reactivations after familiar and novel environments, as outlined below.

(1) Lines 657-658. How far away in time can the top three nearest neighbor time points be? Must they lie in different trials, or can they also be within the same trial? Is there a systematic difference in the average time lags for the nearest neighbors over the course of the session?

The authors should only allow nearest neighbors to be in a different lap because systematic changes in behavior (running fast initially) might force earlier time bins in a certain location to match with a different trial, while the later time bins can be from within the same trial if the mice are moving slower and stay in the same spatial bin location longer. The authors should also provide information on how the averaging is performed because there are several axes of variability - spatial bin locations, sessions, different environments, and animals.

(2) Figure 8: These results are very interesting. However, I am confused by the differences between Figure 8B and D because the significant reactivations in A and C are very similar. The 1-minute and 10-minute windows seem somewhat arbitrary and prone to noise and variability. Perhaps the authors should fit a slope for the curves on A and C and compare whether the slope/ intercept are significantly different between the novel and familiar environments.

Reviewer #3 (Public review):

Summary:

This study examines neural activity recorded simultaneously in the hippocampus, dorsal striatum, and orbitofrontal cortex as rats performed an interval timing task. The analyses primarily focus on the activity of "time cells" which are neurons that fire at specific moments during the intervals. In this experiment, the intervals consist of periods when animals are running on a treadmill before selecting the arm associated with the interval duration. The results show that the theta oscillations induced by this running behavior were observed across the three regions and that this strong oscillation modulated the activity of neurons across regions. While these findings are correlative in nature, they provide an important characterization of activity patterns across regions during complex behavior. However, more research is needed to determine whether these activity patterns specifically contribute to temporal coding.

Strengths:

(1) Overall, the paper is very well written. Although I have specific concerns about the review of the relevant literature and the interpretation of the results (see below), I do want to commend the authors for their efforts toward presenting this complex work in an accessible manner.

(2) The study is well designed and the quality of the electrophysiological data collected from multiple brain regions in such a challenging behavioral experiment is impressive. This work is a technical tour de force.

(3) The analyses are very thorough, statistically rigorous, and clearly explained and visualized. The authors provide a thoughtful mixture of example data (at the level of individual cells or animals) and aggregated data (at the group or session level) to properly explain and quantify the activity patterns of interest.

Reviewer #3 (Public review):

Summary:

This is a solid study of stimulus-evoked neural activity dynamics in the feedforward pathway from mouse hand/forelimb mechanoreceptor afferents to S1 and M1 cortex. The conclusions are generally well supported, and match expectations from previous studies of hand/forelimb circuits by this same group (Yamawaki et al., 2021), from the well-studied whisker tactile pathway to whisker S1 and M1, and from the corresponding pathway in primates. The study uses the novel approach of optogenetic stimulation of PV afferents in the periphery, which provides an impulse-like volley of peripheral spikes, which is useful for studying feedforward circuit dynamics. These are primarily proprioceptors, so results could differ for specific mechanoreceptor populations, but this is a reasonable tool to probe basic circuit activation. Mice are awake but not engaged in a somatosensory task, which is sufficient for the study goals.

The main results are:<br /> (1) brief peripheral activation drives brief sensory-evoked responses at ~ 15 ms latency in S1 and ~25 ms latency in M1, which is consistent with classical fast propagation on the subcortical pathway to S1, followed by slow propagation on the polysynaptic, non-myelinated pathway from S1 to M1;<br /> (2) each peripheral impulse evokes a triphasic activation-suppression-rebound response in both S1 and M1;<br /> (3) PV interneurons carry the major component of spike modulation for each of these phases;<br /> (4) activation of PV neurons in each area (M1 or S1) drives suppression and rebound both in the local area and in the other downstream area;<br /> (5) peripheral-evoked neural activity in M1 is at least partially dependent on transmission through S1.

All conclusions are well-supported and reasonably interpreted. There are no major new findings that were not expected from standard models of somatosensory pathways or from prior work in the whisker system.

Strengths:

This is a well-conducted and analyzed study in which the findings are clearly presented. This will provide important baseline knowledge from which studies of more complex sensorimotor processing can build.

Weaknesses:

A few minor issues should be addressed to improve clarity of presentation and interpretation:

(1) It is critical for interpretation that the stimulus does not evoke a motor response, which could induce reafference-based activity that could drive, or mask, some of the triphasic response. Figure S1 shows that no motor response is evoked for one example session, but this would be stronger if results were analyzed over several mice.

(2) The recordings combine single and multi-units, which is fine for measures of response modulation, but not for absolute evoked firing rate, which is only interpretable for single units. For example, evoked firing rate in S1 could be higher than M1, if spike sorting were more difficult in S1, resulting in a higher fraction of multi-units relative to M1. Because of this, if reporting of absolute firing rates is an essential component of the paper, Figs 3D and 4E should be recalculated just for single units.

(3) In Figure 5B, the average light-evoked firing rate of PV neurons seems to come up before time 0, unlike the single-trial rasters above it. Presumably, this reflects binning for firing rate calculation. This should be corrected to avoid confusion.

(4) In Figure 6A bottom, please clarify what legends "W. suppression" and "W. rebound" mean.

Reviewer #3 (Public review):

The manuscript entitled "SMARCAD1 and TOPBP1 contribute to heterochromatin maintenance at the transition from the 2C-like to the pluripotent state" by Sebastian-Perez et al. adopted the iPOTD method to compare the chromatin-bound proteome in ESCs and 2CLCs induced by Dux overexpression. The authors identified 397 chromatin-bound proteins enriched specifically in non-2CLCs, among which they further investigated TOPBP1 due to its potential role in chromocenter reorganization. SMARCD1, a known interacting protein of TOPBP1, was also investigated in parallel. The authors report increased size and decreased number of H3K9me3-heterochromatin foci in Dux-induced 2CLCs. Remarkably, depletion of either TOPBP1 or SMARCD1 resulted in similar phenotypes. However, the absence of these proteins did not affect the entry into or exit from the 2C-like state. The authors further showed that both TOPBP1 and SMARCD1 are essential for early embryonic development.

This manuscript provides valuable insights into the features of 2CLCs regarding H3K9me3-heterochromatin reorganization. However, the findings are largely descriptive. Mechanistic studies are required in future studies, such as: 1) how SMARCD1 associates with H3K9me3 and contributes to heterochromatin maintenance, 2) how TOPBP1 regulates the expression of SMARCD1 and facilitates its localization in heterochromatin foci, 3) whether the remodelling of chromocenter directly influence the transitions between ESCs and 2CLCs.

Reviewer #3 (Public review):

Summary:

Papagiannakis et al. present a detailed study exploring the relationship between DNA/polysome phase separation and nucleoid segregation in Escherichia coli. Using a combination of experiments and modelling, the authors aim to link physical principles with biological processes to better understand nucleoid organisation and segregation during cell growth.

Strengths:

The authors have conducted a large number of experiments under different growth conditions and physiological perturbations (using antibiotics) to analyse the biophysical factors underlying the spatial organisation of nucleoids within growing E. coli cells. A simple model of ribosome-nucleoid segregation has been developed to explain the observations.

Weaknesses:

While the study addresses an important topic, several aspects of the modelling, assumptions, and claims warrant further consideration.

Major Concerns:

Oversimplification of Modelling Assumptions:

The model simplifies nucleoid organisation by focusing on the axial (long-axis) dimension of the cell while neglecting the radial dimension (cell width). While this approach simplifies the model, it fails to explain key experimental observations, such as:

(1) Inconsistencies with Experimental Evidence:

The simplified model presented in this study predicts that translation-inhibiting drugs like chloramphenicol would maintain separated nucleoids due to increased polysome fractions. However, experimental evidence shows the opposite-separated nucleoids condense into a single lobe post-treatment (Bakshi et al 2014), indicating limitations in the model's assumptions/predictions. For the nucleoids to coalesce into a single lobe, polysomes must cross the nucleoid zones via the radial shells around the nucleoid lobes.

(2) The peripheral localisation of nucleoids observed after A22 treatment in this study and others (e.g., Japaridze et al., 2020; Wu et al., 2019), which conflicts with the model's assumptions and predictions. The assumption of radial confinement would predict nucleoids to fill up the volume or ribosomes to go near the cell wall, not the nucleoid, as seen in the data.

(3) The radial compaction of the nucleoid upon rifampicin or chloramphenicol treatment, as reported by Bakshi et al. (2014) and Spahn et al. (2023), also contradicts the model's predictions. This is not expected if the nucleoid is already radially confined.

(4) Radial Distribution of Nucleoid and Ribosomal Shell:

The study does not account for well-documented features such as the membrane attachment of chromosomes and the ribosomal shell surrounding the nucleoid, observed in super-resolution studies (Bakshi et al., 2012; Sanamrad et al., 2014). These features are critical for understanding nucleoid dynamics, particularly under conditions of transcription-translation coupling or drug-induced detachment. Work by Yongren et al. (2014) has also shown that the radial organisation of the nucleoid is highly sensitive to growth and the multifork nature of DNA replication in bacteria.

The omission of organisation in the radial dimension and the entropic effects it entails, such as ribosome localisation near the membrane and nucleoid centralisation in expanded cells, undermines the model's explanatory power and predictive ability. Some observations have been previously explained by the membrane attachment of nucleoids (a hypothesis proposed by Rabinovitch et al., 2003, and supported by experiments from Bakshi et al., 2014, and recent super-resolution measurements by Spahn et al.).

Ignoring the radial dimension and membrane attachment of nucleoid (which might coordinate cell growth with nucleoid expansion and segregation) presents a simplistic but potentially misleading picture of the underlying factors.

This reviewer suggests that the authors consider an alternative mechanism, supported by strong experimental evidence, as a potential explanation for the observed phenomena:<br /> Nucleoids may transiently attach to the cell membrane, possibly through transertion, allowing for coordinated increases in nucleoid volume and length alongside cell growth and DNA replication. Polysomes likely occupy cellular spaces devoid of the nucleoid, contributing to nucleoid compaction due to mutual exclusion effects. After the nucleoids separate following ter separation, axial expansion of the cell membrane could lead to their spatial separation.

Incorporating this perspective into the discussion or future iterations of the model may provide a more comprehensive framework that aligns with the experimental observations in this study and previous work.

Simplification of Ribosome States:<br /> Combining monomeric and translating ribosomes into a single 'polysome' category may overlook spatial variations in these states, particularly during ribosome accumulation at the mid-cell. Without validating uniform mRNA distribution or conducting experimental controls such as FRAP or single-molecule measurements to estimate the proportions of ribosome states based on diffusion, this assumption remains speculative.

Reviewer #3 (Public review):

Summary:

This study profiled the single-cell transcriptome of human spermatogenesis and provided many potentials molecular markers for developing testicular puncture specific marker kits for NOA patients.

Strengths:

Perform single-cell RNA sequencing (scRNA-seq) and single-cell assay for transposase-accessible chromatin sequencing (scATAC-seq) on testicular tissues from two OA patients and three NOA patients

Weaknesses:

Most results are analytical and lack specific experiments to support these analytical results and hypotheses.

Comments on revisions:

In the revised version of the manuscript, the authors made some effort to revise their manuscript according to reviewers' comments and addressed the problems that I had raised before.

I have no other serious criticisms regarding the revised manuscript.

Reviewer #3 (Public review):

The authors offer an interesting computational study on the dynamics of PROTAC-driven protein degradation. They employed a combination of protein-protein docking, structural alignment, atomistic MD simulations, and post-analysis to model a series of CRBN-dBET-BRD4 ternary complexes, as well as the entire degradation machinery complex. These degraders, with different linker properties, were all capable of forming stable ternary complexes but had been shown experimentally to exhibit different degradation capabilities. While in the initial models of the degradation machinery complex, no surface Lys residue(s) of BRD4 were exposed sufficiently for the crucial ubiquitination step, MD simulations illustrated protein functional dynamics of the entire complex and local side-chain arrangements to bring Lys residue(s) to the catalytic pocket of E2/Ub for reactions. Using these simulations, the authors were able to present a hypothesis as to how linker property affects degradation potency. They were able to roughly correlate the distance of Lys residues to the catalytic pocket of E2/Ub with observed DC50/5h values. This is an interesting and timely study that presents interesting tools that could be used to guide future PROTAC design or optimization.

Reviewer #3 (Public review):

This manuscript examines the accuracy of DNA methylation-based epigenetic clocks across multiple cohorts of varying genetic ancestry. The authors find that clocks were generally less accurate at predicting age in cohorts with large proportions of non-European (especially African) ancestry, compared to cohorts with high European ancestry proportions. They suggest that some of this effect might be explained by meQTLs that occur near CpG sites included in clocks, because these variants may be at higher frequencies (or at least different frequencies) in cohorts with high proportions of non-European ancestry relative to the training set. They also provide discussions of potential paths forward to alleviate bias and improve portability for future clock algorithms.

The topic is timely due to the increasing popularity of DNA methylation-based clocks and the acknowledgment that many algorithms (e.g., polygenic risk scores) lack portability when applied to cohorts that substantially differ in ancestry or other characteristics from the training set. This has been discussed to some degree for DNA methylation-based clocks, but could of course use more discussion and empirical attention which the authors nicely provide using an impressive and diverse collection of data.

The manuscript is clear and well-written, however, some key background was missing (e.g., what we know already about the ancestry composition of clock training sets) and most importantly several analyses would benefit from being taken one step further. For example, the main argument of the paper is that ancestry impacts clock predictions, but this is determined by subsetting the data by recruitment cohort rather than analyzing ancestry as a continuous variable. Extending some of the analyses could really help the authors nail down their hypothesized sources of lack of portability, which is critical for making recommendations to the community and understanding the best paths forward.

Reviewer #3 (Public review):

This is a very interesting paper bringing truly fascinating insight into the genomic processes underlying the famous adaptive radiation seen in cichlid fishes from Lake Malawi. The authors use structural and sequence information from species belonging to distinct ecotypic categories, representing subclades of the radiation, to document structural variation across the evolutionary tree, infer introgression of inversions among branches of the clade, and even suggest that certain rearrangements constitute new sex-determining loci. The insight is intriguing and is likely to make a substantial contribution to the field and to seed new hypotheses about the ecological processes and adaptive traits involved in this radiation.

I think the paper could be clarified in its prose, and that the discussion could be more informative regarding the putative roles of the inversions in adaptation to each ecotypic niche. Identifying key, large inversions shared in various ways across the different taxa is really a great step forward. However, the population genomics analysis requires further work to describe and decipher in a more systematic way the evolutionary forces at play and their consequences on the various inversions identified.

The model of evolution involving multiple inversions putatively linking together co-adapted "cassettes" could be better spelled out since it is not entirely clear how the existing theory on the recruitment of inversions in local adaptation (e.g. Kirkpatrick and Barton) operates on multiple unlinked inversions. How such loci correspond to distinct suites of integrated traits, or not, is not very easy to envision in the current state of the manuscript.

The role of one inversion in sex determination is apparent and truly intriguing. However, the implication of such locus on ecological adaptation is somewhat puzzling. Also, whether sex determination loci can flow across species via introgression seems quite important as a route to chromosomal sex determination, so this could be discussed further.

Reviewer #3 (Public review):

Summary:

Zacharia et al report on the molecular function of the C-terminal domain of the intraflagellar transport IFT-B complex component IFT172 by structure determination and biochemical in vitro and cell culture-based assays. The authors identify an IFT-A binding site that mediates a mutually exclusive interaction to two different IFT-A subunits, IFT144 and IFT140, consistent with interactions suggested in anterograde and retrograde IFT trains by previous cryo-electron tomography studies. Additionally, the authors identify a U-box-like domain that binds ubiquitin and conveys ubiquitin conjugation activity in the presence of the UbcH5a E2 enzyme in vitro. RPE1 cell lines that lack the U-box domain show a reduction in ciliation rate with shorter cilia, and heterozygous cells manifest TGF-beta signaling defects, suggesting an involvement of the U-box domain in cilium-dependent signaling.

Strengths:

(1) The structural analyses of the C-terminal domain of IFT172 combine crystallography with structure prediction using state-of-the-art algorithms, which gives high confidence in the presented protein structures. The structure-based predictions of protein interactions are validated by further biochemical experiments to assess the specific binding of the IFT172 C-terminal domains with other proteins.

(2) The finding that the IFT172 C-terminus interactions with the IFT-A components IFT140 and IFT144 appear mutually exclusive confirm a suggested role in mediating the binding of IFT-B to IFT-A in anterograde and retrograde IFT trains, which is of very high scientific value.

(3) The suggested molecular mechanism of IFT train coordination explains previous findings in Chlamydomonas IFT172 mutants, in particular an IFT172 mutant that appeared defective in retrograde IFT, as well as mutations identified in ciliopathy patients.

(4) The identification of other IFT172 interactors by unbiased mass spectrometry-based proteomics is very exciting. Analysis of stoichiometries between IFT components suggests that these interactors could be part of IFT trains, either as cargos or additional components that may fulfill interesting functions in cilia and flagella.

(5) The authors unexpectedly identify a U-box-like fold in the IFT172 C-terminus and thoroughly dissect it by sequence and mutational analyses to reveal unexpected ubiquitin binding and potential intrinsic ubiquitination activity.

(6) The overall data quality is very high. The use of IFT172 proteins from different organisms suggests a conserved function.

Weaknesses:

(1) Interaction studies were carried out by pulldown experiments, which identified more IFT172 interaction partners. Whether these interactions can be seen in living cells remains to be elucidated in subsequent studies.

(2) The cell culture-based experiments in the IFT172 mutants are exciting and show that the U-box domain is important for protein stability and point towards involvement of the U-box domain in cellular signaling processes. However, the characterization of the generated cell lines falls behind the very rigorous analysis of other aspects of this work.

Overall, the authors achieved to characterize an understudied protein domain of the ciliary intraflagellar transport machinery and gained important molecular insights into its role in primary cilia biology, beyond IFT. By identifying an unexpected functional protein domain and novel interaction partners the work makes an important contribution to further our understanding of how ciliary processes might be regulated by ubiquitination on a molecular level. Based on this work it will be important for future studies in the cilia community to consider direct ubiquitin binding by IFT complexes.

Conceptually, the study highlights that protein transport complexes can exhibit additional intrinsic structural features for potential auto-regulatory processes. Moreover, the study adds to the functional diversity of small U-box and ubiquitin-binding domains, which will be of interest to a broader cell biology and structural biology audience.

Additional comments:

The authors investigate the consequences of the U-box deletion on ciliary TGF-beta signaling. While a cilium-dependent effect of TGF-beta signaling on the phosphorylation of SMAD2 has been demonstrated, the precise function of cilia in AKT signaling has not been fully established in the field. Therefore, the relevance of this finding is somewhat unclear. It may help to discuss relevant literature on the topic, such as Shim et al., PNAS, 2020.

DOI: 10.1016/j.xpro.2024.103566

Resource: RRID:ZFIN_ZDB-GENO-180906-3

Curator: @scibot

SciCrunch record: RRID:ZFIN_ZDB-GENO-180906-3

What is this?

Reviewer #3 (Public review):

Summary:

This article provides a model for early diagnosis and prognostic prediction of Colorectal Cancer and demonstrates its accuracy and usability. However, there are still some minor issues that need to be revised and paid attention to.

Strengths:

A large amount of external datasets were used for verification, thus demonstrating robustness and accuracy. Meanwhile, various influencing factors of multiple samples were taken into account, providing usability.

Weaknesses:

There are notable language issues that hinder readability, as well as a lack of some key conclusions provided.

Reviewer #3 (Public review):

Summary:

In this experiment, the authors use a probe method along with time-frequency analyses to ascertain the attentional priority map prior to a visual search display in which one location is more likely to contain a salient distractor.  The main finding is that neural responses to the probe indicate that the high probability location is attended, rather than suppressed, prior to the search display onset.  The authors conclude that suppression of distractors at high probability locations is a result of reactive, rather than proactive, suppression.

Strengths:

This was a creative approach to a difficult and important question about attention.  The use of this "pinging" method to assess the attentional priority map has a lot of potential value for a number of questions related to attention and visual search. Here as well, the authors have used it to address a question about distractor suppression that has been the subject of competing theories for many years in the field. The authors have also conducted additional behavioral analyses to examine the relationship between memory and search. The paper is well-written, and the authors have done a good job placing their data in the larger context of recent findings in the field.

Weaknesses:

The authors addressed a number of weaknesses in a thorough revision during the review process. The present study raises important questions for future research - this is not a weakness, since one study cannot answer all questions, but points to the importance of the questions raised by this study and the value of additional future research in the area.

Reviewer #3 (Public review):

Summary:

In their paper the authors tackle three things at once in a theoretical model: how can spiking neural networks perform efficient coding, how can such networks limit the energy use at the same time, and how can this be done in a more biologically realistic way than previous work.

They start by working from a long-running theory on how networks operating in a precisely balanced state can perform efficient coding. First, they assume split networks of excitatory (E) and inhibitory (I) neurons. The E neurons have the task to represent some lower dimensional input signal, and the I neurons have the task to represent the signal represented by the E neurons. Additionally, the E and I populations should minimize an energy cost represented by the sum of all spikes. All this results in two loss functions for the E and I populations, and the networks are then derived by assuming E and I neurons should only spike if this improves their respective loss. This results in networks of spiking neurons that live in a balanced state, and can accurately represent the network inputs.

They then investigate in depth different aspects of the resulting networks, such as responses to perturbations, the effect of following Dale's law, spiking statistics, the excitation (E)/inhibition (I) balance, optimal E/I cell ratios, and others. Overall, they expand on previous work by taking a more biological angle on the theory and show the networks can operate in a biologically realistic regime.

Strengths:

* The authors take a much more biological angle on the efficient spiking networks theory than previous work, which is an essential contribution to the field<br /> * They make a very extensive investigation of many aspects of the network in this context, and do so thoroughly<br /> * They put sensible constraints on their networks, while still maintaining the good properties these networks should have

Weaknesses:

* One of the core goals of the paper is to make a more biophysically realistic network than previous work using similar optimization principles. One of the important things they consider is a split into E and I neurons. While this works fine, and they consider the coding consequences of this, it is not clear from an optimization perspective why the split into E and I neurons and following Dale's law would be beneficial. This would be out of scope for the current paper however.<br /> * The theoretical advances in the paper are not all novel by themselves, as most of them (in particular the split into E and I neurons and the use of biophysical constants) had been achieved in previous models. However, the authors discuss these links thoroughly and do more in-depth follow-up experiments with the resulting model.

Assessment and context:

Overall, although much of the underlying theory is not necessarily new, the work provides an important addition to the field. The authors succeeded well in their goal of making the networks more biologically realistic, and incorporate aspects of energy efficiency. For computational neuroscientists this paper is a good example of how to build models that link well to experimental knowledge and constraints, while still being computationally and mathematically tractable. For experimental readers the model provides a clearer link of efficient coding spiking networks to known experimental constraints and provides a few predictions.

Reviewer #3 (Public review):

Summary:

In this manuscript, Costa and colleagues investigate how asymmetry in dorsal root ganglion (DRG) neurons is established. The authors developed an in vitro system that mimics the pseudo-unipolar morphology and asymmetry of DRG neurons during the regeneration of the peripheral and central branch axons. They suggest that central-like DRG axons exhibit a higher density of growing microtubules. By reducing the polymerization of microtubules in these central-like axons, they were able to eliminate the asymmetry in DRG neurons.

Strengths:

The authors point out a distinct microtubule-associated protein signature that differentiates between DRG neurons' central and peripheral axonal branches. Experimental results demonstrate that genetic deletion of spastin eliminated the differences in microtubule dynamics and axon regeneration between the central and peripheral branches.

Weaknesses:

While some of the data are compelling, experimental evidence does not fully support the main claims.

In its current form, the study is primarily descriptive and lacks convincing mechanistic insights. It misses important controls and further validation using 3D in vitro models.

The significance of studying microtubule polymerization to DRG asymmetry in vitro is questionable, especially considering the model's validity. Classifying the central and peripheral-like branches in cultured DRG neurons will require further in-depth characterization. Additional validation using adult DRG neuron cultures not aged in vitro will be required in future studies.

The comparison of asymmetry associated with a regenerative response between in vitro and in vivo paradigms has significant limitations due to the nature of the in vitro culture system. When cultured in isolation, DRG neurons fail to form functional connections with appropriate postsynaptic target neurons (the central branch) or to differentiate the peripheral domains associated with the innervation of target organs. Rather than growing neurons on a flat, hard surface like glass, more physiologically relevant substrates and/or culturing conditions should be considered. This approach could help eliminate potential artifacts caused by plating adult DRG neurons on a flat surface. Additionally, the authors should consider replicating their findings in a 3D culture model or using dorsal root ganglia explants, where both centrally and peripherally projecting axons are present.

Panels 5H-J require additional processing with astrocyte markers to accurately define the lesion borders. Furthermore, including a lower magnification would facilitate a direct comparison of the lesion site. The use of cholera toxin subunit B (CTB) to trace dorsal column sensory axons is prone to misinterpretation, as the tracer accumulates at the axon's tip. This limitation makes it extremely challenging to distinguish between regenerating and degenerating axons.

Reviewer #3 (Public review):

Summary:

The manuscript by Troyer et al quantitatively measured the membrane localization and diffusion of RNase E, an essential ribonuclease for mRNA turnover as well as tRNA and rRNA processing in bacteria cells. Using single-molecule tracking in live E. coli cells, the authors investigated the impact of membrane targeting sequence (MTS) and the C-terminal domain (CTD) on the membrane localization and diffusion of RNase E under various perturbations. Finally, the authors tried to correlate the membrane localization of RNase E to its function on co- and post-transcriptional mRNA decay using lacZ mRNA as a model.

The major findings of the manuscripts include:

(1) WT RNase E is mostly membrane localized via MTS, confirming previous results. The diffusion of RNase E is increased upon removal of MTS or CTD, and more significantly increased upon removal of both regions.

(2) By tagging RNase E MTS and different lengths of LacY transmembrane domain (LacY2, LacY6, or LacY12) to mEos3.2, the results demonstrate that short LacY transmembrane sequence (LacY2 and LacY6) can increase the diffusion of mEos3.2 on the membrane compared to MTS, further supported by the molecular dynamics simulation. A similar trend was roughly observed in RNase E mutants with MTS switched to LacY transmembrane domains.

(3) The removal of RNase E MTS significantly increases the co-transcriptional degradation of lacZ mRNA, but has minimal effect on the post-transcriptional degradation of lacZ mRNA. Removal of CTD of RNase E overall decreases the mRNA decay rates, suggesting the synergistic effect of CTD on RNase E activity.

Strengths:

(1) The manuscript is clearly written with very detailed method descriptions and analysis parameters.

(2) The conclusions are mostly supported by the data and analysis.

(3) Some of the main conclusions are interesting and important for understanding the cellular behavior and function of RNase E.

Weaknesses:

(1) Some of the observations show inconsistent or context-dependent trends that make it hard to generalize certain conclusions. Those points are worth discussion at least. Examples include:

(a) The authors conclude that MTS segment exhibits reduced MB% when succinate is used as a carbon source compared to glycerol, whereas LacY2 segment maintains 100% membrane localization, suggesting that MTS can lose membrane affinity in the former growth condition (Ln 341-342). However, the opposite case was observed for the WT RNase E and RNase E-LacY2-CTD, in which RNase E-LacY2-CTD showed reduced MB% in the succinate-containing M9 media compared to the WT RNase E (Ln 264-267). This opposite trend was not discussed. In the absence of CTD, would the media-dependent membrane localization be similar to the membrane localization sequence or to the full-length RNase E?

(b) When using mEos3.2 reporter only, LacY2 and LacY6 both increase the diffusion of mEos3.2 compared to MTS. However, when inserting the LacY transmembrane sequence into RNase E or RNase E without CTD, only the LacY2 increases the diffusion of RNase E. This should also be discussed.

(2) The authors interpret that in some cases the increase in the diffusion coefficient is related to the increase in the cytoplasm localization portion, such as for the LacY2 inserted RNase E with CTD, which is rational. However, the authors can directly measure the diffusion coefficient of the membrane and cytoplasm portion of RNase E by classifying the trajectories based on their localizations first, rather than just the ensemble calculation.

(3) The error bars of the diffusion coefficient and MB% are all SEM from bootstrapping, which are very small. I am wondering how much of the difference is simply due to a batch effect. Were the data mixed from multiple biological replicates? The number of biological replicates should also be reported.

(4) Some figures lack p-values, such as Figures 4 and 5C-D. Also, adding p-values directly to the bar graphs will make it easier to read.

Disease for patient 1: Von Willebrand Disease Type1, transmitter VWD-type 3

Disease for patient 2: Von Willebrand Disease Type 3

Patient1: 90 YO female (Afro-Caribbean)

Patient2: 40 YO female (Afro-Caribbean)

Notes multiple variants in the VWF gene but have focused on variants in the D4 domain. However cannot discount the impact of some other variants.

Variant 1: VWF NM_000552.5: c.6647del p.(Cys2216Phefs*9), results in VWF protein missing D4 domain and C-terminal end of molecule

Phenotype patient 1: Reduced VWF levels in VWF:Ag, VWF:ristocetin cofactor, FVIII:C, FVIII(VWF:FVIIIB). Bleeding score 0, required Helixate treatment before and after receiving surgery.

Variant 2: VWF NM_000552.5: c.6432dup p.(Pro2145Thrfs*5)

Three sequence variations in family study showed other variants highlighted p.(Cys1149Arg) and p.(Pro2145Thrfs*5) are not on the same allele.

Does have other variants in VWF but they are stated by authors to not be detrimental. p.(Val510=) is noted to be potentially deleterious.

Phenotype patient 2: severely reduced VWF levels, absence of multimers, bleeding score 32, epistaxis, bruising, oral cavity bleeding, prolonged bleeding from minor wounds, menorrhagia, hemarthrosis, ankle arthropathy.

Suggests premature termination codons in these variants may lead to NMD but that this mechanism was found to be PTC position-dependent. Degradation was not 100% and need to perform cellular experiments.

Reviewer #3 (Public review):

Summary:

Alexander et al. reported the gene-regulatory networks underpinning sex determination of murine primordial germ cells (PGCs) through single-nucleus multiomics, offering a detailed chromatin accessibility and gene expression map across three embryonic stages in both male (XY) and female (XX) mice. It highlights how regulatory element accessibility may precede gene expression, pointing to chromatin accessibility as a primer for lineage commitment before differentiation. Sexual dimorphism in these elements and gene expression increases over time, and the study maps transcription factors regulating sexually dimorphic genes in PGCs, identifying sex-specific enrichment in various transcription factors.

Strengths:

The study includes step-wise multiomic analysis with some computational approach to identify candidate TFs regulating XX and XY PGC gene expression, providing a detailed timeline of chromatin accessibility and gene expression during PGC development, which identifies previously unknown PGC subpopulations and offers a multimodal reference atlas of differentiating PGC clusters. Furthermore, the study maps a complex network of transcription factors associated with sex determination in PGCs, adding depth to our understanding of these processes.

Weaknesses:

While the multiomics approach is powerful, it primarily offers correlational insights between chromatin accessibility, gene expression, and transcription factor activity, without direct functional validation of identified regulatory networks.

Comments on revised version:

The authors have answered my questions and concerns in the revised manuscript and correspondence.

Reviewer #3 (Public review):

Summary:

In their manuscript, "Disentangling acute motor deficits and adaptive responses evoked by the loss of cerebellar output," Sinha and colleagues aim to identify distinct causes of motor impairments seen when perturbing cerebellar circuits. This goal is an important one, given the diversity of movement-related phenotypes in patients with cerebellar lesions or injuries, which are especially difficult to dissect given the chronic nature of the circuit damage. To address this goal, the authors use high-frequency stimulation (HFS) of the superior cerebellar peduncle in monkeys performing reaching movements. HFS provides an attractive approach for transiently disrupting cerebellar function previously published by this group. First, they found a reduction in hand velocities during reaching, which was more pronounced for outward versus inward movements. By modeling inverse dynamics, they find evidence that shoulder muscle torques are especially affected. Next, the authors examine the temporal evolution of movement phenotypes over successive blocks of HFS trials. Using this analysis, they find that in addition to the acute, specific effects on muscle torques in early HFS trials, there was an additional progressive reduction in velocity during later trials, which they interpret as an adaptive response to the inability to effectively compensate for interaction torques during cerebellar block. Finally, the authors examine movement decomposition and trajectory, finding that even when low-velocity reaches are matched to controls, HFS produces abnormally decomposed movements and higher than expected variability in trajectory.

Strengths:

Overall, this work provides important insight into how perturbation of cerebellar circuits can elicit diverse effects on movement across multiple timescales.

The HFS approach provides temporal resolution and enables analysis that would be hard to perform in the context of chronic lesions or slow pharmacological interventions. Thus, this study describes an important advance over prior methods of circuit disruption, and their approach can be used as a framework for future studies that delve deeper into how additional aspects of sensorimotor control are disrupted (e.g., response to limb perturbations).

In addition, the authors use well-designed behavioral approaches and analysis methods to distinguish immediate from longer-term adaptive effects of HFS on behavior. Moreover, inverse dynamics modeling provides important insight into how movements with different kinematics and muscle dynamics might be differentially disrupted by cerebellar perturbation.

Weaknesses:

The argument that there are acute and adaptive effects to perturbing cerebellar circuits is compelling, but there seems to be a lost opportunity to leverage the fast and reversible nature of the perturbations to further test this idea and strengthen the interpretation. Specifically, the authors could have bolstered this argument by looking at the effects of terminating HFS - one might hypothesize that the acute impacts on muscle torques would quickly return to baseline in the absence of HFS, whereas the longer-term adaptive component would persist in the form of aftereffects during the 'washout' period. As is, the reversible nature of the perturbation seems underutilized in testing the authors' ideas.

The analysis showing that there is a gradual reduction in velocity during what the authors call an adaptive phase is convincing. That said, the argument is made that this is due to difficulty in compensating for interaction torques. Even if the inward targets (i.e., targets 6-8) do not show a deficit during the acute phase, these targets still have significant interaction torques (Figure 3c). Given the interpretation of the data as presented, it is not clear why disruption of movement during the adaptive phase would not be seen for these targets as well since they also have large interaction torques. Moreover, it is difficult to delve into this issue in more detail, as the analyses in Figures 4 and 5 omit the inward targets.

The text in the Introduction and in the prior work developing the HFS approach overstates the selectivity of the perturbations. First, there is an emphasis on signals transmitted to the neocortex. As the authors state several times in the Discussion, there are many subcortical targets of the cerebellar nuclei as well, and thus it is difficult to disentangle target-specific behavioral effects using this approach. Second, the superior cerebellar peduncle contains both cerebellar outputs and inputs (e.g., spinocerebellar). Therefore, the selectivity in perturbing cerebellar output feels overstated. Readers would benefit from a more agnostic claim that HFS affects cerebellar communication with the rest of the nervous system, which would not affect the major findings of the study.

The text implies that increased movement decomposition and variability must be due to noise. However, this assumption is not tested. It is possible that the impairments observed are caused by disrupted commands, independent of whether these command signals are noisy. In other words, commands could be low noise but still faulty.

Throughout the text, the use of the term 'feedforward control' seems unnecessary. To dig into the feedforward component of the deficit, the authors could quantify the trajectory errors only at the earliest time points (e.g., in Figure 5d), but even with this analysis, it is difficult to disentangle feedforward- and feedback-mediated effects when deficits are seen throughout the reach. While outside the scope of this study, it would be interesting to explore how feedback responses to limb perturbation are affected in control versus HFS conditions. However, as is, these questions are not explored, and the claim of impaired feedforward control feels overstated.

The terminology 'single-joint' movement is a bit confusing. At a minimum, it would be nice to show kinematics during different target reaches to demonstrate that certain targets are indeed single joint movements. More of an issue, however, is that it seems like these are not actually 'single-joint' movements. For example, Figure 2c shows that target 1 exhibits high elbow and shoulder torques, but in the text, T1 is described as a 'single-joint' reach (e.g. lines 155-156). The point that I think the authors are making is that these targets have low interaction torques. If that is the case, the terminology should be changed or clarified to avoid confusion.

The labels in Figure 3d are confusing and could use more explanation in the figure legend.

In Figure 3d, it is stated that data from all monkeys is pooled. However, if there is a systematic bias between animals, this could generate spurious correlations. Were correlations also calculated for each animal separately to confirm the same trend between velocity and coupling torques holds for each animal?

In Table S1, it would be nice to see target-specific success rates. The data would suggest that targets with the highest interaction torques will have the largest reduction in success rates, especially during later HFS trials. Is this the case?

Reviewer #3 (Public review):

Summary:

In this paper the authors conduct two experiments an fMRI experiment and intracranial recordings of neurons in two patients P1 and P2. In both experiments, they employ a SSVEP paradigm in which they show images at a fast rate (e.g. 6Hz) and then they show face images at a slower rate (e.g. 1.2Hz), where the rest of the images are a variety of object images. In the first patient, they record from neurons over a region in the mid fusiform gyrus that is face-selective and in the second patient, they record neurons from a region more medially that is not face selective (it responds more strongly to objects than faces). Results find similar selectivity between the electrophysiology data and the fMRI data in that the location which shows higher fMRI to faces also finds face-selective neurons and the location which finds preference to non faces also shows non face preferring neurons.

Strengths:

The data is important in that it shows that there is a relationship between category selectivity measured from electrophysiology data and category-selective from fMRI. The data is unique as it contains a lot of single and multiunit recordings (245 units) from the human fusiform gyrus - which the authors point out - is a humanoid specific gyrus.

Weaknesses:

My major concerns are two-fold:<br /> (i) There is a paucity of data; Thus, more information (results and methods) is warranted; and in particular there is no comparison between the fMRI data and the SEEG data.

(ii) One main claim of the paper is that there is evidence for suppressed responses to faces in the non-face selective region. That is, the reduction in activation to faces in the non-face selective region is interpreted as a suppression in the neural response and consequently the reduction in fMRI signal is interpreted as suppression. However, the SSVEP paradigm has no baseline (it alternates between faces and objects) and therefore it cannot distinguish between lower firing rate to faces vs suppression of response to faces.

(1) Additional data: the paper has 2 figures: figure 1 which shows the experimental design and figure 2 which presents data, the latter shows one example neuron raster plot from each patient and group average neural data from each patient. In this reader's opinion this is insufficient data to support the conclusions of the paper. The paper will be more impactful if the researchers would report the data more comprehensively.

(a) There is no direct comparison between the fMRI data and the SEEG data, except for a comparison of the location of the electrodes relative to the statistical parametric map generated from a contrast (Fig 2a,d). It will be helpful to build a model linking between the neural responses to the voxel response in the same location - i.e., estimate from the electrophysiology data the fMRI data (e.g. Logothetis & Wandell, 2004)

(b) More comprehensive analyses of the SSVEP neural data: It will be helpful to show the results of the frequency analyses of the SSVEP data for all neurons to show that there are significant visual responses and significant face responses. It will be also useful to compare and quantify the magnitude of the face responses compared to the visual responses.

(c) The neuron shown in E shows cyclical responses tied to the onset of the stimuli, is this the visual response? If so, why is there an increase in the firing rate of the neuron before the face stimulus is shown in time 0? The neuron's data seems different than the average response across neurons; This raises a concern about interpreting the average response across neurons in panel F which seems different than the single neuron responses

(d) Related to (c) it would be useful to show raster plots of all neurons and quantify if the neural responses within a region are homogeneous or heterogeneous. This would add data relating the single neuron response to the population responses measured from fMRI. See also Nir 2009.

(e) When reporting group average data (e.g., Fig 2C,F) it is necessary to show standard deviation of the response across neurons.

(f) Is it possible to estimate the latency of the neural responses to face and object images from the phase data? If so, this will add important information on the timing of neural responses in the human fusiform gyrus to face and object images.

(g) Related to (e) In total the authors recorded data from 245 units (some single units and some multiunits) and they found that both in the face and nonface selective most of the recoded neurons exhibited face -selectivity, which this reader found confusing: They write " Among all visually responsive neurons, we 87 found a very high proportion of face-selective neurons (p < 0.05) in both activated 88 and deactivated MidFG regions (P1: 98.1%; N = 51/52; P2: 86.6%; N = 110/127)'. Is the face selectivity in P1 an increase in response to faces and P2 a reduction in response to faces or in both it's an increase in response to faces

(1) Additional methods<br /> (a) it is unclear if the SSVEP analyses of neural responses were done on the spikes or the raw electrical signal. If the former, how is the SSVEP frequency analysis done on discrete data like action potentials?<br /> (b) it is unclear why the onset time was shifted by 33ms; one can measure the phase of the response relative to the cycle onset and use that to estimate the delay between the onset of a stimulus and the onset of the response. Adding phase information will be useful.

(2) Interpretation of suppression:

The SSVEP paradigm alternates between 2 conditions: faces and objects and has no baseline; In other words, responses to faces are measured relative to the baseline response to objects so that any region that contains neurons that have a lower firing rate to faces than objects is bound to show a lower response in the SSVEP signal. Therefore, because the experiment does not have a true baseline (e.g. blank screen, with no visual stimulation) this experimental design cannot distinguish between lower firing rate to faces vs suppression of response to faces.<br /> The strongest evidence put forward for suppression is the response of non-visual neurons that was also reduced when patients looked at faces, but since these are non-visual neurons, it is unclear how to interpret the responses to faces.

Reviewer #3 (Public review):

Summary:

In this paper, the authors made a sincere effort to show the effects of strip cropping, a technique of alternating crops in small strips of several meters wide, on ground beetle diversity. They state that strip cropping can be a useful tool for bending the curve of biodiversity loss in agricultural systems as strip cropping shows a relative increase in species diversity (i.e. abundance and species richness) of the ground beetle communities compared to monocultures. Moreover, strip cropping has the added advantage of not having to compromise on agricultural yields.

Strengths:

The article is well written; it has an easily readable tone of voice without too much jargon or overly complicated sentence structure. Moreover, as far as reviewing the models in depth without raw data and R scripts allows, the statistical work done by the authors looks good. They have well thought out how to handle heterogenous, yet spatially and temporarily correlated field data. The models applied and the model checks performed are appropriate for the data at hand. Combining RDA and PCA axes together is a nice touch.

Weaknesses:

The evidence for strip cropping bringing added value for biodiversity is mixed at best. Yes, there is an increase in relative abundance and species richness at the field level, but it is not convincingly shown this difference is robust or can be linked to clear structural and hypothesised advantages of the strip cropping system. The same results could have been used to conclude that there are only very limited signs of real added value of strip cropping compared to monocultures.

There are a number of reasons for this:

(1) Significant differences disappear at crop level, as the authors themselves clearly acknowledge, meaning that there are no differences between pairs of similar crops in the strip cropping fields and their respective monoculture. This would mean the strips effectively function as "mini-monocultures". The significant relative differences at the field level could be an artifact of aggregation instead of structural differences between strip cropping and monocultures; with enough data points things tend to get significant despite large variance. This should have been elaborated further upon by the authors with additional analyses, designed to find out where differences originate and what it tells about the functioning of the system. Or it should have provided ample reason for cautioning in drawing conclusions about the supposed effectiveness of strip cropping based on these findings.

(2) The authors report percentages calculated as relative change of species richness and abundance in strip cropping compared to monocultures after rarefaction. This is in itself correct, however, it can be rather tricky to interpret because the perspective on actual species richness and abundance in the fields and treatments is completely lost; the reported percentages are dimensionless. The authors could have provided the average cumulative number of species and abundance after rarefaction. Also, range and/or standard error would have been useful to provide information as to the scale of differences between treatments. This could provide a new perspective on the magnitude of differences between the two treatments which a dimensionless percentage cannot.

(3) The authors appear to not have modelled the abundance of any of the dominant ground beetle species themselves. Therefore it becomes impossible to assess which important species are responsible (if any) for the differences found in activity density between stripcropping and monocultures and the possible life history traits related reasons for the differences, or lack thereof, that are found. A big advantage of using ground beetles is that many life history traits are well studied and these should be used whenever there is reason, as there clearly is in this case. Moreover, it is unclear which species are responsible for the difference in species richness found at the field level. Are these dominant species or singletons? Do the strip cropping fields contain species that are absent in the monoculture fields and are not the cause of random variation or sampling? Unfortunately, the authors do not report on any of these details of the communities that were found, which makes the results much less robust.

(4) In the discussion they conclude that there is only a limited amount of interstrip movement by ground beetles. Otherwise, the results of the crop-level statistical tests would have shown significant deviation from corresponding monocultures. This is a clear indication that the strips function more like mini-monocultures instead of being more than the sum of its parts.

(5) The RDA results show a modelled variable of differences in community composition between strip cropping and monoculture. Percentages of explained variation of the first RDA axis are extremely low, and even then, the effect of location and/or year appear to peak through (Figure S3), even though these are not part of the modelling. Moreover, there is no indication of clustering of strip cropping on the RDA axis, or in fact on the first principal component axis in the larger RDA models. This means the explanatory power of different treatments is also extremely low. The crop level RDA's show some clustering, but hardly any consistent pattern in either communities of crops or species correlations, indicating that differences between strip cropping and monocultures are very small.

Furthermore, there are a number of additional weaknesses in the paper that should be addressed:

The introduction lacks focus on the issues at hand. Too much space is taken up by facts on insect decline and land sharing vs. land sparing and not enough attention is spent on the scientific discussion underlying the statements made about crop diversification as a restoration strategy. They are simply stated as facts or as hypotheses with many references that are not mentioned or linked to in the text. An explicit link to the results found in the large number of references should be provided.

The mechanistic understanding of strip cropping is what is at stake here. Does strip cropping behave similarly to intercropping, a technique that has been proven to be beneficial to biodiversity because of added effects due to increased resource efficiency and greater plant species richness? This should be the main testing point and agenda of strip cropping. Do the biodiversity benefits that have been shown for intercropping also work in strip cropping fields? The ground beetles are one way to test this. Hypotheses should originate from this and should be stated clearly and mechanistically.

One could question how useful indicator species analysis (ISA) is for a study in which predominantly highly eurytopic species are found. These are by definition uncritical of their habitat. Is there any mechanistic hypothesis underlying a suspected difference to be found in preferences for either strip cropping or monocultures of the species that were expected to be caught? In other words, did the authors have any a priori reasons to suspect differences, or has this been an exploratory exercise from which unexplained significant results should be used with great caution?

However, setting these objections aside there are in fact significant results with strong species associations both with monocultures and strip cropping. Unfortunately, the authors do not dig deeper into the patterns found a posteriori either. Why would some species associate so strongly with strip cropping? Do these species show a pattern of pitfall catches that deviate from other species, in that they are found in a wide range of strips with different crops in one strip cropping field and therefore may benefit from an increased abundance of food or shelter? Also, why would so many species associate with monocultures? Is this in any way logical? Could it be an artifact of the data instead of a meaningful pattern? Unfortunately, the authors do not progress along these lines in the methods and discussion at all.

A second question raised in the introduction is whether the arable fields that form part of this study contain rare species. Unfortunately, the authors do not elaborate further on this. Do they expect rare species to be more prevalent in the strip cropping fields? Why? Has it been shown elsewhere that intercropping provides room for additional rare species?

Considering the implications the results of this research can have on the wider discussion of bending the curve and the effects of agroecological measures, bold claims should be made with extreme restraint and be based on extensive proof and robust findings. I am not convinced by the evidence provided in this article that the claim made by the authors that strip cropping is a useful tool for bending the curve of biodiversity loss is warranted.

Reviewer #3 (Public review):

Summary:

Eapen and coworkers use a rational design approach to generate new peptide-inspired ligands at the D-box interface of cdc20. These new peptides serve as new starting points for blocking APC/C in the context of cancer, as well as manipulating APC/C for targeted protein degradation therapeutic approaches.

Strengths:

The characterization of new peptide-like ligands is generally solid and multifaceted, including binding assays, thermal stability enhancement in vitro and in cells, X-ray crystallography, and degradation assays.

Weaknesses:

One important finding of the study is that the strongest binders did not correlate with the fastest degradation in a cellular assay, but explanations for this behavior were not supported experimentally. Some minor issues regarding experimental replicates and details were also noted.

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. The authors then 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. Responses to the interruption of the sound are similar in quality, if not quantity, in the predictive and the control situation, yet the contribution of sound offset sensitivity to the observed mismatch responses is not discussed.

Reviewer #3 (Public review):

Summary:

Ai et al. studied texture, color and disparity selectivity in human visual cortex at mesoscale level using high-resolution fMRI. They reproduced earlier monkey and human studies showing interdigitated color-selective and disparity-selective sub-compartments within area V2, likely corresponding to thin and thick stripes, respectively. At least with the stimuli used, no clear evidence for texture-selective mesoscale activations were observed in area V2. The most interesting and novel part of this study focused on cortical-depth-dependent connectivity analyses across areas. The data suggest feedback and feedforward functional connectivity between V1 and V3A for disparity signals and feedback from V4 to the deep layers of V2 for textures.

Strengths:

High-resolution fMRI and highly interesting layer-specific informational connectivity analyses.

Weaknesses:

The authors tend to overclaim their results. Too few data to make conclusive inferences.

Reviewer #3 (Public review):

Summary:

In this manuscript, Outla Z et al described the analysis of Plectin in HCC pathogenesis. Specifically, it was found that elevated Plectin levels in liver tumors, correlated with poor prognosis for HCC patients. Mechanistically, it showed that Plectin-dependent disruption of cytoskeletal networks leads to the attenuation of oncogenic FAK, MAPK/Erk, and PI3K/AKT signals. Finally, the authors showed that Plectin inhibitor plecstatin-1 (PST) is well-tolerated and capable of overcoming therapy resistance in HCC.

Strengths:

The studies of Plectin are not entirely novel (Pubmed: 36613521). Nevertheless, the current manuscript provides a much more detailed mechanistic study and the results have translational implications. Additional strengths include convincing cell biology data, such as Plectin regulates cytoskeletal networks, and HCC migration/invasion.

Comments on latest version:

The authors have addressed my comments.

Reviewer #3 (Public review):

Summary:

The study explores a molecular mechanism by which C. elegans detects low-quality food through neuron-digestive crosstalk, offering new insights into food quality control systems. Liu and colleagues demonstrated that NSY-1, expressed in AWC neurons, is a key regulator for sensing Staphylococcus saprophyticus (SS), inducing avoidance behavior and shutting down the digestive system via intestinal BCF-1. They further revealed that INS-23, an insulin peptide, interacts with the DAF-2 receptor in the gut to modulate SS digestion. The study uncovers a food quality control system connecting neural and intestinal responses, enabling C. elegans to adapt to environmental challenges.

Strengths:

The study employs a genetic screening approach to identify nsy-1 as a critical regulator in detecting food quality and initiating adaptive responses in C. elegans. The use of RNA-seq analysis is particularly noteworthy, as it reveals distinct regulatory pathways involved in food sensing (Figure 4) and digestion of Staphylococcus saprophyticus (Figure 5). The strategic application of both positive and negative data mining enhances the depth of analysis. Importantly, the discovery that C. elegans halts digestion in response to harmful food and employs avoidance behavior highlights a physiological adaptation mechanism.

Weaknesses:

Major points:

(1) While NSY-1 positively regulates str-130 expression in AWC neurons and is critical for SS avoidance and survival, the authors should examine whether similar phenotypes are observed in str-130 mutants.

(2) NSY-1 promotes the AWC-OFF state through str-130, inhibiting SS digestion. The authors should investigate whether STR-130 in AWC neurons regulates bcf-1 expression levels in the intestine.

(3) The current results rely on str-2 expression levels to indicate the AWC state. Ablating AWC neurons and testing the effects on digestion would provide stronger evidence for their role in digestive regulation.

(4) The claim that NSY-1 inhibits INS-23 and that INS-23 interacts with DAF-2 to regulate bcf-1 expression (Line 339-340) requires further validation. Neuron-specific disruption of INS-23 and gut-specific rescue of DAF-2 should be tested.

(5) Figure Reference Errors: Lines 296-297 mention Figure 6E, which does not exist in the main text. This appears to refer to Figure 5E, which has not been described.

Reviewer #3 (Public review):

This is a very interesting study that aims to examine the effect of stress induction across about two hours on physiological, behavioral, and neural measures in several brain areas. This aim is of importance for the study of stress response and recovery and their neural bases. There are several strengths to the design, including a within-subject design, adequate sample size, and multiple levels of assessment (including lab-based and real-life), and the authors should really be commended for that. The results indicate an acute cortisol response following stress induction, although HR data show that the manipulation may have been effective only among those who did the stress scan first. Behaviorally, stress induction resulted in effects on one of the tasks. Neurally, temporal changes in response were observed in what is referred to as SN and DMN networks, and associations with real-life stress were evident for SN during early stress response. Together, evidence emerged for some temporal changes in stress response on neural function and its associations with behavior and real-life stress response as indicated by self-report EMA.

These findings, both positive and null, provide important insight to the field, and the authors should be praised for that. At the same time, it is important to emphasize that some aspects or findings complicate interpretation and limit the extent of inference, that many places in the manuscript could benefit from clarification, and that more discussion should be given to the null findings.

All in all, given the importance of the questions and the strengths of the design, this study could provide a major contribution to future research. But, to accurately and optimally guide research, it is important to accurately describe and interpret both what was tested and found, and what was not found. Some more specific points are noted below, where improvements could be made to facilitate extraction of insight by the reader, and thus increase the impact of the study on the field.

Reviewer #3 (Public review):

Summary:

This manuscript from Nichols, Lee, and Shen tackles an important question of how unc6/netrin promotes axon guidance: i.e. haptotaxis vs chemotaxis. This has recently been a large topic of investigation and discussion in the axon guidance field. Using live cell imaging of unc6/netrin and unc40/DCC in several neurons that extend axons ventrally during development, as well as TM localized mutants of Unc6, they suggest that unc6 promotes first haptotaxis of the emerging growth cone followed by chemotaxis of the growth cone. This is timely, as a recent preprint from the Lundquist group, using a similar strategy to make only a TM anchored unc6 similarly found that this could rescue only the haptotaxis like growth of the PDE neuron, but not the second phase of growth. However, their conclusions were quite different based on the overexpression of unc6 everywhere rescuing the second phase, and thus they conclude that a gradient is not present.

Strengths:

As this has been quite a controversy in both the invertebrate and vertebrate fields, one strength of this paper is that they use a unc6-neon green to demonstrate unc6 localization, and show localization. Further, they provide localisation of the transmembrane tether version of netrin, showing its restriction to nerve cords.

Reviewer #3 (Public review):

Summary:

The authors assessed the potential involvement of fmo-4 in a diverse set of longevity interventions, showing that this gene is required for DR and S6 kinase knockdown related lifespan extension. Using comprehensive epistasis experiments they find this gene to be a required downstream player in the longevity and stress resistance provided by fmo-2 overexpression. They further showed that fmo-4 ubiquitous overexpression is sufficient to provide longevity and paraquat (mitochondrial) stress resistance, and that overexpression specifically in the hypodermis is sufficient to recapitulate most of these effects.

Interestingly, they find that fmo-4 overexpression sensitizes worms to thapsigargin during development, an effect that they link with a potential dysregulation in calcium signalling. They go on to show that fmo-4 expression is sensitive to drugs that both increase or decrease calcium levels, and these drugs differentially affect lifespan of fmo-4 mutants compared to wild-type worms. Similarly, knockdown of genes involved in calcium binding and signalling also differentially affect lifespan and paraquat resistance of fmo-4 mutants.

Finally, they suggest that atf-6 limits the expression of fmo-4, and that fmo-4 is also acting downstream of benefits produced by atf-6 knockdown.

Strengths:

• comprehensive lifespans experiments: clear placement of fmo-4 within established longevity interventions.<br /> • clear distinction in functions and epistatic interactions between fmo-2 and fmo-4 which lays a strong foundation for a longevity pathway regulated by this enzyme family.

Weaknesses:

• no obvious transcriptomic evidence supporting a link between fmo-4 and calcium signalling: either for knockout worms or fmo-4 overexpressing strains.<br /> • no direct measures of alterations in calcium flux, signalling or binding that strongly support a connection with fmo-4.<br /> • no measures of mitochondrial morphology or activity that strongly support a connection with fmo-4.<br /> • lack of a complete model that places fmo-4 function downstream of DR and mTOR signalling (first Results section), fmo-2 (second Results section) and at the same time explains connection with calcium signalling.

Comments on revisions:

The authors have addressed and fixed all the private comments we had made. In terms of the public comments, I think nothing has changed in terms of strengths and weaknesses. They have multiple independent results (drugs, RNAi and transcriptomics) that suggest a connection between fmo-4 and calcium regulation, but there is no strong evidence for what this connection is. The work still lacks direct measures of calcium, ER or mitochondrial function in relation to fmo-4 (which they acknowledge in the discussion). The first four sections strongly place fmo-4 within established longevity interventions, but their model doesn't explain how calcium regulation would fit into these.

Reviewer #3 (Public review):

Summary:

Aguirre-Botero et al have studied the effect of a potent monoclonal antibody against the circumsporozoite protein, the major surface protein of the malaria sporozoite. This is an elegantly designed, performed, and analyzed study. They have efficiently delineated the mode of action of anti-CSP repeat mAb and confirmed previous in vitro work (not cited) that demonstrated the same intracellular effect.

Major comments from the previous round of review:

Line 51: The authors claim a correlation between high antibody levels and protection. However, they did not provide direct proof that these antibodies were responsible for protection, nor did they establish a cut-off level of anti-CSP antibodies that would distinguish between protected and unprotected individuals.

Line 326: The late intrahepatic effect of mAb against the CSP repeat has been previously reported (see Figure 2, Nudelman et al, J Immunol, 1989). The effect was shown to affect the transition from liver trophozoites to liver schizonts. This study should be cited and discussed.

Significance:

A well-done study that elucidates the mechanisms of a protective monoclonal antibody against malaria sporozoites. These data are important and will interest a large audience of researchers working in infectious diseases and immunology.

Comments on latest version:

With the addition of new experiments and proper addition of missing references and minor text correction, the manuscript has been improved.

Reviewer #3 (Public review):

Summary:

The manuscript by Kaya et al. explores the effects of feeding on sharp wave-ripples (SWRs) in the hippocampus, which could reveal a better understanding of how metabolism is regulated by neural processes. Expanding on prior work that showed that SWRs trigger a decrease in peripheral glucose levels, the authors further tested the relationship between SWRs and meal consumption by recording LFPs from the dorsal CA1 region of the hippocampus before and after meal consumption. They found an increase in SWR magnitude during sleep after food intake, in both food restricted and ad libitum fed conditions. Using fiber photometry to detect GABAergic neuron activity in the lateral hypothalamus, they found increased activity locked to the onset of SWRs. They conclude that the animal's satiety state modulates the amplitude and rate of SWRs, and that SWRs modulate downstream circuits involved in regulating feeding. These experiments provide an important step forward in understanding how metabolism is regulated in the brain. However, currently, the paper lacks sufficient analyses to control for factors related to sleep quality and duration; adding these analyses would further support the claim that food intake itself, as opposed to sleep quality, is primarily responsible for changes in SWR activity. Adding this, along with some minor clarifications and edits, would lead to a compelling case for SWRs being modulated by a satiety state. The study will likely be of great interest in the field of learning and memory while carrying broader implications for understanding brain-body physiology.

Strengths:

The paper makes an innovative foray into the emerging field of brain-body research, asking how sharp wave-ripples are affected by metabolism and hunger. The authors use a variety of advanced techniques including LFP recordings and fiber photometry to answer this question. Additionally, they perform comprehensive and logical follow-up experiments to the initial food-restricted paradigm to account for deeper sleep following meal times and the difference between consumption of calories versus the experience of eating. These experiments lay the groundwork for future studies in this field, as the authors pose several follow-up questions regarding the role of metabolic hormones and downstream brain regions.

Weaknesses:

Major comments:

(1) The authors conclude that food intake regulates SWR power during sleep beyond the effect of food intake on sleep quality. Specifically, they made an attempt to control for the confounding effect of delta power on SWRs through a mediation analysis. However, a similar analysis is not presented for SWR rate. Moreover, this does not seem to be a sufficient control. One alternative way to address this confound would be to subsample the sleep data from the ad lib and food restricted conditions (or high calorie and low calorie, etc), to match the delta power in each condition. When periods of similar mean delta power (i.e. similar sleep quality) are matched between datasets, the authors can then determine if a significant effect on SWR amplitude and rate remains in the subsampled data.

(2) Relatedly, are the animals spending the same amount of time sleeping in the ad lib vs. food restricted conditions? The amount of time spent sleeping could affect the probability of entering certain stages of sleep and thus affect SWR properties. A recent paper (Giri et al., Nature, 2024) demonstrated that sleep deprivation can alter the magnitude and frequency of SWRs. Could the authors quantify sleep quantity and control for the amount of time spent sleeping by subsampling the data, similar to the suggestion above?

(3) Plot 5I only reports significance but does not clearly show the underlying quantification of LH GABAergic activity. Upon reading the methods for how this analysis was conducted, it would be informative to see a plot of the pre-SWR and post-SWR integral values used for the paired t-test whose p-values are currently shown. For example, these values could be displayed as individual points overlaid on a pair of box-and-whisker plots of the pre- and post-distribution within the session (perhaps for one example session per mouse with the p-value reported, to supplement a plot of the distribution of p-values across sessions and mice). If these data are non-normal, the authors should also use a non-parametric statistical test.

Minor comments:

(4) A brief explanation (perhaps in the discussion) of what each change in SWR property (magnitude, rate, duration) could indicate in the context of the hypothesis may be helpful in bridging the fields of metabolism and memory. For example, by describing the hypothesized mechanistic consequence of each change, could the authors speculate on why ripple rate may not increase in all the instances where ripple power increases after feeding? Why do the authors speculate that ripple duration does not increase, given that prior work (Fernandez-Ruiz et al. 2019) has shown that prolonged ripples support enhanced memory?

(5) The authors suggest that "SWRs could modulate peripheral metabolism" as a future implication of their work. However, the lack of clear effects from GLP-1, leptin and insulin complicates this interpretation. It might be informative for readers if the authors expanded their discussion of what specific role they speculate that SWRs could play in regulating metabolism, given these negative results.

Reviewer #3 (Public review):

Summary:

In their manuscript, Armand and colleagues investigate the potential of continuing CDK4/6 inhibitors or combining them with CDK2 inhibitors in the treatment of breast cancer that has developed resistance to initial therapy. Utilizing cellular and animal models, the research examines whether maintaining CDK4/6 inhibition or adding CDK2 inhibitors can effectively control tumor growth after resistance has set in. The key findings from the study indicate that the sustained use of CDK4/6 inhibitors can slow down the proliferation of cancer cells that have become resistant, and the combination of CDK2 inhibitors with CDK4/6 inhibitors can further enhance the suppression of tumor growth. Additionally, the study identifies that high levels of Cyclin E play a significant role in resistance to the combined therapy. These results suggest that continuing CDK4/6 inhibitors along with the strategic use of CDK2 inhibitors could be an effective strategy to overcome treatment resistance in hormone receptor-positive breast cancer.

Strengths:

(1) Continuous CDK4/6 Inhibitor Treatment Significantly Suppresses the Growth of Drug-Resistant HR+ Breast Cancer: The study demonstrates that the continued use of CDK4/6 inhibitors, even after disease progression, can significantly inhibit the growth of drug-resistant breast cancer.

(2) Potential of Combined Use of CDK2 Inhibitors with CDK4/6 Inhibitors: The research highlights the potential of combining CDK2 inhibitors with CDK4/6 inhibitors to effectively suppress CDK2 activity and overcome drug resistance.

(3) Discovery of Cyclin E Overexpression as a Key Driver: The study identifies overexpression of cyclin E as a key driver of resistance to the combination of CDK4/6 and CDK2 inhibitors, providing insights for future cancer treatments.

(4) Consistency of In Vitro and In Vivo Experimental Results: The study obtained supportive results from both in vitro cell experiments and in vivo tumor models, enhancing the reliability of the research.

(5) Validation with Multiple Cell Lines: The research utilized multiple HR+/HER2- breast cancer cell lines (such as MCF-7, T47D, CAMA-1) and triple-negative breast cancer cell lines (such as MDA-MB-231), validating the broad applicability of the results.

Weaknesses:

(1) The manuscript presents intriguing findings on the sustained use of CDK4/6 inhibitors and the potential incorporation of CDK2 inhibitors in breast cancer treatment. However, I would appreciate a more detailed discussion of how these findings could be translated into clinical practice, particularly regarding the management of patients with drug-resistant breast cancer.

(2) While the emergence of resistance is acknowledged, the manuscript could benefit from a deeper exploration of the molecular mechanisms underlying resistance development. A more thorough understanding of how CDK2 inhibitors may overcome this resistance would be valuable.

(3) The manuscript supports the continued use of CDK4/6 inhibitors, but it lacks a discussion on the long-term efficacy and safety of this approach. Additional studies or data to support the safety profile of prolonged CDK4/6 inhibitor use would strengthen the manuscript.

Reviewer #3 (Public review):

Summary:

In this manuscript, the authors set out to test the "force from lipids" mechanism of mechanosensitive channel gating, which posits that mechanical properties of the membrane are directly responsible for converting membrane tension into useful energy for channel gating. They employ amphiphilic polymers called poloxamers to alter membrane mechanical properties and relate those to the threshold of mechanical activation of the MscL channel of E.coli.

The authors heterologously express the channel, perform electrical recordings, and assess the mechanical properties of vesicles derived from the same membranes. This allows them to directly compare derived mechanical parameters to channel gating in the same environment.

They further repeat experiments in an eukaryotic mechano-channel and show that the same principles apply to gating in this very different protein, providing support for the force from lipids hypothesis.

Strengths:

In this work, characterization of the mechanical properties of the plasma membrane and electrical recordings of channel activity are carried out in membranes derived from the same cells. This is a nice contribution to these experiments since usually these two properties are measured in separate membranes with differing compositions. The experiments are of high quality and the data analysis and interpretation are careful.

Weaknesses:

It is not clear to this reviewer what the relationship is between the mechanical properties the authors measure, the membrane area expansion modulus, and bending rigidity, to what they call "interfacial tension".

Reviewer #3 (Public review):

Summary:

Avila and colleagues investigate the role of glutamate signaling in the dorsomedial striatum in a treadmill-based task where rats learn to turn or stop their walking based on learning cue-associations that allow them to acquire rewards. Phenotypic variation in Pavlovian conditioned sign and goal-tracking behavior was examined, where behavioral differences in stopping and turning were observed. Glutamate signals in the DMS were recording during the treadmill task, and were related to features of cue-controlled movement, with a stronger relationship seen for goal trackers. Finally, chemogenic inhibition of prelimbic neurons projecting to the DMS (the predicted source of those glutamate signals), preferentially affected cued movement in goal trackers. The authors couch these experiments in the context of cognitive control-attentional mechanisms, movement disorders, and individual differences in cue reactivity.

Strengths:

Overall these studies are interesting and are of general relevance to a number of research questions in neurology and psychiatry. The assessment of intersection of individual differences in cue-related learning strategies with movement-related questions - in this case cued turning behavior - is interesting and understudied question. The link between this work and growing notions of corticostriatal control of action selection makes it timely.

Weaknesses:

The clarity of the manuscript could be improved in several places, including in the graphical visualization of data. It is difficult to interpret the glutamate results, as presented, in the context of specific behaviors. It is difficult to assess how many trials/subjects are represented in the data shown, and too much emphasis is placed on representative examples. Averages traces of the glutamate data and other standard analysis approaches would improve the paper and allow for easier interpretation of the data.

Reviewer #3 (Public review):

In this project, Garber and Fiser examined how the structure of incidentally learned regularities influences subsequent learning of regularities, that either have the same structure or a different one. Over a series of six online experiments, it was found that the structure (spatial arrangement) of the first set of regularities affected learning of the second set, indicating that it has indeed been abstracted away from the specific items that have been learned. The effect was found to depend on the explicitness of the original learning: Participants who noticed regularities in the stimuli were better at learning subsequent regularities of the same structure than of a different one. On the other hand, participants whose learning was only implicit had an opposite pattern: they were better in learning regularities of a novel structure than of the same one. However, when an overnight sleep separated the first and second learning phases, this opposite effect was reversed and came to match the pattern of the explicit group, suggesting that the abstraction and transfer in the implicit case were aided by memory consolidation.

In their revision the authors addressed my major comments successfully and I commend them for that.

Reviewer #3 (Public review):

The manuscript by Talbi R et al. generated transgenic mice to assess the reproduction function of MC4R in Kiss1 neurons in vivo and used electrophysiology to test how MC4R activation regulated Kiss1 neuronal firing in ARH and AVPV/PeN. This timely study is highly significant in neuroendocrinology research for the following reasons.

(1) The authors' findings are significant in the field of reproductive research. Despite the known presence of MC4R signaling in Kiss1 neurons, the exact mechanisms of how MC4R signaling regulates different Kiss1 neuronal populations in the context of sex hormone fluctuations are not entirely understood. The authors reported that knocking out Mc4r from Kiss1 neurons replicates the reproductive impairment of MC4RKO mice, and Mc4r expression in Kiss1 neurons in the MC4R null background partially restored the reproductive impairment. MC4R activation excites Kiss1 ARH neurons and inhibits Kiss1 AVPV/PeN neurons (except for elevated estradiol).

(2) Reproduction dysfunction is one of obesity comorbidities. MC4R loss-of-function mutations cause obesity phenotype and impaired reproduction. However, it is hard to determine the causality. The authors carefully measured the body weight of the different mouse models (Figure 1C, Figure 2A, Figure 3B). For example, the Kiss1-MC4RKO females showed no body weight difference at puberty onset. This clearly demonstrated the direct function of MC4R signaling in reproduction but was not a consequence of excessive adiposity.

(3) Gene expression findings in the "KNDy" system align with the reproduction phenotype.

(4) The electrophysiology results reported in this manuscript are innovative and provide more details of MC4R activation and Kiss1 neuronal activation.

Overall, the authors have presented sufficient background in a clear, logical, and organized structure, clearly stated the key question to be addressed, used the appropriate methodology, produced significant and innovative main findings, and made a justified conclusion.

Comments on revisions:

The authors have addressed my comments.

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):

This study was focused on the conserved mechanisms across the Transmembrane Channel/Scramblase superfamily, which includes members of the TMEM16, TMEM63/OSCA, and TMC families. In previous work, the authors have studied the role of the inner activation gate of these proteins. Here, the authors show that the introduction of mutations at the TM4-TM6 interface, which are close to the inactivation gate, can disrupt gating and confer scramblase activity to non-scramblases proteins.

Overall, the confocal imaging experiments, patch clamping experiments, and data analysis are performed well and in line with standard methods. The molecular dynamics simulation work is focused but adds supportive evidence to their findings. Although there could have been more extensive molecular analysis to bolster the authors' arguments on the role of the TM4-TM6 interface (e.g. evaluate effects of size/hydrophobicity, double mutants, cross-linking, more in-depth simulation data), there is adequate evidence to conclude that certain residues at this interface is critical to ion conduction and phospholipid scramblase activity. The data presented only adds incremental depth of knowledge for each individual channel, but together, they show this to be true for conserved TM4 residues across TMEM16F, TMEM16A, OSCA1.2, and TMEM63A proteins. This breadth of data is a major strength of this paper, and provides strong evidence for a coupled pathway for ion conduction and phospholipid transport, though the underlying biophysical mechanism is still speculative and remains to be elucidated.

Reviewer #3 (Public review):

Summary:

The previously described reporter SPOTlight is a fluorescence-based reporter of the integrated stress response, specifically, protein synthesis initiation dynamics. In the current study from the same lab, the authors describe the creation and characterization of a transgenic mouse that expresses SPOTlight.

Strengths:

The previously described reporter has now been made into a Cre-dependent transgene in mice. The authors replicate previous findings from their lab that were acquired using viral vector-mediated delivery of their reporter.

Weaknesses:

There is not a clear advantage to having the Cre-dependent SPOTlight reporter in a transgenic mouse over using a viral vector to deliver the same Cre-dependent SPOTlight based on the experiments presented. There are potential general advantages and disadvantages to virus vs transgenic mouse but no side-by-side comparisons are performed here.

It is not clear whether overexpressing the reporter alters basal ISR/UPR function and gene expression. The CAG is a strong promoter and overexpression of fluorescent proteins (or any protein) can potentially stress protein synthesis and processing mechanisms. The use of the animal as a reporter may be misleading if the presence of the reporter is already altering ISR/UPR.

Reviewer #3 (Public review):

The authors were interested in how Ankle2 regulates nuclear envelope reformation after cell division. They show that Ankle2 can bind in a PP2A complex without other known regulatory subunits of PP2A. The authors also identity a novel interaction with ER protein Vap33 that could be important for localization. This manuscript is a useful finding linking Ankle2 function during nuclear envelope reformation to the PP2A complex. The authors present solid data showing that Ankle2 can form a complex with PP2A-29B and Mts and generate a phosphoproteomic resource that is fundamentally important to understand Ankle2 biology. The caveat should be remembered that most experiments, including subcellular localization, are based on overexpression data. Keeping this in mind, the manuscript is a valuable resource.

Reviewer #3 (Public review):

Summary:

In this study, McAllester and Pool develop a new model to explain the maintenance of balanced inversion polymorphism, based on (sexually) antagonistic alleles and a trade-off between male reproduction and survival (in females or both sexes). Simulations of this model support the plausibility of this mechanism. In addition, the authors use experiments on four naturally occurring inversion polymorphisms in D. melanogaster and find tentative evidence for one aspect of their theoretical model, namely the existence of the above-mentioned trade-off in two out of the four inversions.

Strengths:

(1) The study develops and analyzes a new (Drosophila melanogaster-inspired) model for the maintenance of balanced inversion polymorphism, combining elements of (sexually) antagonistically (pleiotropic) alleles, negative frequency-dependent selection and synergistic epistasis. Simulations of the model suggest that the hypothesized mechanism might be plausible.

(2) The above-mentioned model assumes, as a specific example, a trade-off between male reproductive display and survival; in the second part of their study, the authors perform laboratory experiments on four common D. melanogaster inversions to study whether these polymorphisms may be subject to such a trade-off. The authors observe that two of the four inversions show suggestive evidence that is consistent with a trade-off between male reproduction and survival.

Open issues:

(1) A gap in the current modeling is that, while a diploid situation is being studied, the model does not investigate the effects of varying degrees of dominance. It would thus be important and interesting, as the authors mention, to fill this gap in future work,

(2) It will also be important to further explore and corroborate the potential importance and generality of trade-offs between different fitness components in maintaining inversion polymorphisms in future work.

Reviewer #3 (Public review):

Summary:

The migration of primordial germ cells (PGCs) to the developing gonad is a poorly understood, yet essential step in reproductive development. Here, the authors examine whether there are differences in leading and lagging migratory PGCs using single-cell RNA sequencing of mouse embryos. Cleverly, the authors dissected embryonic trunks along the anterior-to-posterior axis prior to scRNAseq in order to distinguish leading and lagging migratory PGCs. After batch corrections, their analyses revealed several known and novel differences in gene expression within and around leading and lagging PGCs, intercellular signaling networks, as well as number of genes upregulated upon gonad colonization. The authors then compared their datasets with publicly available human datasets to identify common biological themes. Altogether, this rigorous study reveals several differences between leading and lagging migratory PGCs, hints at signatures for different fates among the population of migratory PGCs, and provides new potential markers for post-migratory PGCs in both humans and mice. While many of the interesting hypotheses that arise from this work are not extensively tested, these data provide a rich platform for future investigations.

Strengths:

-The authors have successfully navigated significant technical challenges to obtain a substantial number of mouse migratory primordial germ cells for robust transcriptomic analysis. Here the authors were able to collect quality data on ~13,000 PGCs and ~7,800 surrounding somatic cells, which is ten times more PGCs than previous studies.

- The decision to physically separate leading and lagging primordial germ cells was clever and well-validated based on expected anterior-to-posterior transcriptional signatures.

- Within the PGCs and surrounding tissues, the authors found many gene expression dynamics they would expect to see both along the PGC migratory path as well as across developmental time, increasing confidence in the new differentially expressed genes they found.

- The comparison of their mouse-based migratory PGC datasets with existing human migratory PGC datasets is appreciated.

- The quality control, ambient RNA contamination elimination, batch correction, cell identification and analysis of scRNAseq data were thorough and well-done such that the new hypotheses and markers found through this study are dependable.

- The subsetting of cells in their trajectory analysis is appreciated, further strengthening their cell terminal state predictions.

Weaknesses:

- Although it is useful to compare their mouse-based dataset with human datasets, the authors used two different analysis pipelines for each dataset. While this may have been due to the small number of cells in the human dataset as mentioned, it does make it difficult to compare them.

- There were few validation experiments within this study. For one such experiment, whether there is a difference in pSMAD2/3 along the AP axis is unclear and not quantified as was nicely done for Lefty1/2.

Reviewer #3 (Public review):

Summary:

The paper describes the molecular pathway to regulate germ cell differentiation in zebrafish through ribosomal RNA biogenesis. Meioc sequesters Piwil1, a Piwi homolog, which suppresses the transcription of the 45S pre-rDNA by the formation of heterochromatin, to the perinuclear bodies. The key results are solid and useful to researchers in the field of germ cell/meiosis as well as RNA biosynthesis and chromatin.

Strengths:

The authors nicely provided the molecular evidence on the antagonism of Meioc to Piwil1 in the rRNA synthesis, which supported by the genetic evidence that the inability of the meioc mutant to enter meiosis is suppressed by the piwil1 heterozygosity.

Weaknesses:

(1) Although the paper provides very convincing evidence for the authors' claim, the scientific contents are poorly written and incorrectly described. As a result, it is hard to read the text. Checking by scientific experts would be highly recommended. For example, on line 38, "the global translation activity is generally [inhibited]", is incorrect and, rather, a sentence like "the activity is lowered relative to other cells" is more appropriate here. See minor points for more examples.<br /> (2) In some figures, it is hard for readers outside of zebrafish meiosis to evaluate the results without more explanation and drawing.<br /> (3) Figure 1E, F, cycloheximide experiments: Please mention the toxicity of the concentration of the drug in cell proliferation and viability.

Reviewer #3 (Public review):

Summary:

The authors provide an in-depth analysis of the function of Numb in adult Drosophila midgut. Based on RNAi combinations and double mutant clonal analyses, they propose that Numb has a function in inhibiting Notch pathway to maintain intestinal stem cells, and is a backup mechanism with BMP pathway in maintaining midgut stem cell mediated homeostasis.

Strengths:

Overall, this is a carefully constructed series of experiments, and the results and statistical analyses provides believable evidence that Numb has a role, albeit weak compared to other pathways, in sustaining ISC and in promoting regeneration especially after damage by bleomycin, which may damage enterocytes and therefore disrupt BMP pathway more. The results overall support their claim.

The data are highly coherent, and support a genetic function of Numb, in collaborating with BMP signaling, to maintain the number and proliferative function of ISCs in adult midguts. The authors used appropriate and sophisticated genetic tools of double RNAi, mutant clonal analysis and dual marker stem cell tracing approaches to ensure the results are reproducible and consistent. The statistical analyses provide confidence that the phenotypic changes are reliable albeit weaker than many other mutants previously studied.

Weaknesses:<br /> In the absence of Numb itself, the midgut has a weak reduction of ISC number (Fig. 3 and 5), as well as weak albeit not statistically significant reduction of ISC clone size/proliferation. I think the authors published similar experiments with BMP pathway mutants. The mad1-2 allele used here as stated below may not be very representative of other BMP pathway mutants. Therefore, it could be beneficial to compare the number of ISC number and clone sizes between other BMP experiments to provide the readers with a clearer picture of how these two pathways individually contribute (stronger/weaker effects) to the ISC number and gut homeostasis.

The main weakness of this manuscript is the analysis of the BMP pathway components, especially the mad1-2 allele. The mad RNAi and mad1-2 alleles (P insertion) are supposed to be weak alleles and that might be suitable for genetic enhancement assays here together with numb RNAi. However, the mad1-2 allele, and sometimes the mad RNAi, showed weakly increased ISC clone size. This is kind of counter-intuitive that they should have a similar ISC loss and ISC clone size reduction.

A much stronger phenotype was observed when numb mutants were subject to treatment of tissue damaging agents Bleomycin, which causes damage in different ways than DSS. Bleomycin as previously shown to be causing mainly enterocyte damage, and therefore disrupt BMP signaling from ECs more likely. Therefore, this treatment together with loss of numb led to a highly significant reduction of ISC in clones and reduction of clone size/proliferation. One improvement is that it is not clear whether the authors discussed the nature of the two numb mutant alleles used in this study and the comparison to the strength of the RNAi allele. Because the phenotypes are weak and more variable, the use of specific reagents is important.

Furthermore, the use of possible activating alleles of either or both pathways to test genetic enhancement or synergistic activation will provide strong support for the claims.

Reviewer #3 (Public review):

Summary:<br /> This study advances the field of β cell dysfunction by unveiling an epigenetic mechanism of β cell senescence. By connecting TET2-mediated DNA methylation to histone acetylation and cellular aging, it opens promising new avenues for therapeutic intervention. In particular, the authors aimed at identifying the mechanisms of pancreatic β cell senescence by epigenetic regulation. They conclude that increased TET2 expression in β cells is associated with ageing and metabolic dysfunction in type 2 diabetes by inducing β cell senescence. The authors further propose that TET2-mediated PTEN promoter methylation promotes β cell senescence by regulating H4K16ac. Last, the authors suggest that this could represent new molecular mechanism and therapeutic target against β cell senescence during type 2 diabetes.

Strengths:<br /> The major strengths of the study are the use of both biased and unbiased experimental tools to approach the topic. The authors also provide in vivo and in vitro mechanistic approaches to answer their questions. All of these approaches are valuable and provides robustness to their study. The authors provide solid evidence that TET2 is associated with ageing and that its absence improves glucose metabolism in ageing and β cell senescence. In addition, the mechanistic studies showing that TET2 regulates the PTEN/MOF/H4K16ac signaling pathway in β cell lines is convincing.

Weaknesses:<br /> Although the use of such a variety of tools is a strength, the outcome of each individual tool is somehow superficial. For instance, the authors focus on very specific targets emanating from their omics studies without a clear or logical justification. In addition, the metabolic studies are inaccurate and the authors do not follow an understandable and rational examination of the ageing versus their obesity cohorts. Last, the mechanistic studies using model cell lines are not validated in the available mouse models.

In my opinion, the evidence that TET2 regulates β cell senescence during obesity is not very strong. This is because the effect of deletion of TET2 in senescence markers is the same under 24weeks of age or 52 weeks of age (16 weeks HFD). Both ageing and HFD promoted the same extent of reduction of senescent markers and increase in β cell markers in the absence of TET2. There is no comparison between young glucose tolerant mice and old glucose intolerant mice. There is also no direct comparison of aged matched lean or obese mice. It may seem as if the mechanism by which TET2 regulates senescence in β cells is independent of the diabetic status but it is more related to ageing. Given that there is evidence that TET2 expression in β cells coordinates inflammatory responses in autoimmune diabetes, it would have been interested to check whether this is also the case for T2DM. Also, considering that expression of TET2 in Figure 3 does not seem to be in β cells in db/db mice but rather in the exocrine pancreas. In addition, senescent marker p16 in Figure 5 in the presence of TET2, seems to be localized in alpha cells or immune cells but not in β cells.<br /> Regarding the mechanistic studies, the authors convincingly show that TET2 regulates the PTEN/MOF/H4K16ac signaling pathway in β cell lines and that this is important for β cell senescence. However, there is no validation of whether this holds true in aged, or prediabetic, mice. Given the availability of mice and model samples, this should be possible and meaningful. Last, in the genome-wide bisulfite sequencing (Figure 7), it seems that the authors are cherry picking for PTEN and in the RNAseq, the same applies for MOF. Thus, although the mechanism seems valid, the lack of in vivo validation, and a proper rational for the selected targets in the omics studies, renders the mechanistic studies rather correlative.

In sum, I believe that the study in its current version, unfortunately, does not bear the conceptual advance or the robustness that is required to offer a strong impact on the field. The methods, on the other hand, mainly the omics analyses provided here, could be of potential benefit for the field of epigenetics in β cell biology. However, in the benefit of the current study, the relevance of this data could be more rigorously assessed experimentally. I believe that the study has the potential to provide the required impact, should the authors work on it further to provide more solid functional and mechanistic validation.

Reviewer #3 (Public review):

Summary:

In their paper the authors tackle three things at once in a theoretical model: how can spiking neural networks perform efficient coding, how can such networks limit the energy use at the same time, and how can this be done in a more biologically realistic way than previous work.

They start by working from a long-running theory on how networks operating in a precisely balanced state can perform efficient coding. First, they assume split networks of excitatory (E) and inhibitory (I) neurons. The E neurons have the task to represent some lower dimensional input signal, and the I neurons have the task to represent the signal represented by the E neurons. Additionally, the E and I populations should minimize an energy cost represented by the sum of all spikes. All this results in two loss functions for the E and I populations, and the networks are then derived by assuming E and I neurons should only spike if this improves their respective loss. This results in networks of spiking neurons that live in a balanced state, and can accurately represent the network inputs.

They then investigate in depth different aspects of the resulting networks, such as responses to perturbations, the effect of following Dale's law, spiking statistics, the excitation (E)/inhibition (I) balance, optimal E/I cell ratios, and others. Overall, they expand on previous work by taking a more biological angle on the theory and show the networks can operate in a biologically realistic regime.

Strengths:

* The authors take a much more biological angle on the efficient spiking networks theory than previous work, which is an essential contribution to the field<br /> * They make a very extensive investigation of many aspects of the network in this context, and do so thoroughly<br /> * They put sensible constraints on their networks, while still maintaining the good properties these networks should have

Weaknesses:

* One of the core goals of the paper is to make a more biophysically realistic network than previous work using similar optimization principles. One of the important things they consider is a split into E and I neurons. While this works fine, and they consider the coding consequences of this, it is not clear from an optimization perspective why the split into E and I neurons and following Dale's law would be beneficial. This would be out of scope for the current paper however.<br /> * The theoretical advances in the paper are not all novel by themselves, as most of them (in particular the split into E and I neurons and the use of biophysical constants) had been achieved in previous models. However, the authors discuss these links thoroughly and do more in-depth follow-up experiments with the resulting model.

Assessment and context:

Overall, although much of the underlying theory is not necessarily new, the work provides an important addition to the field. The authors succeeded well in their goal of making the networks more biologically realistic, and incorporate aspects of energy efficiency. For computational neuroscientists this paper is a good example of how to build models that link well to experimental knowledge and constraints, while still being computationally and mathematically tractable. For experimental readers the model provides a clearer link of efficient coding spiking networks to known experimental constraints and provides a few predictions.

Reviewer #3 (Public review):

Summary:

Rollenhagen at al. offer a detailed description of layer 1 of the human neocortex. They use electron microscopy to assess the morphological parameters of presynaptic terminals, active zones, vesicle density/distribution, mitochondrial morphology and astrocytic coverage. The data is collected from tissue from four patients undergoing epilepsy surgery. As the epileptic focus was localized in all patients to the hippocampus, the tissue examined in this manuscript is considered non-epileptic (access) tissue.

Strengths:

The quality of the electron microscopic images is very high, and the data is analyzed carefully. Data from human tissue is always precious and the authors here provide a detailed analysis using adequate approaches, and the data is clearly presented.

Weaknesses:

The text connects functional and morphological characteristics in a very direct way. For example, connecting plasticity to any measurement the authors present would be rather difficult without any additional functional experiments. References to various vesicle pools based on the location of the vesicles is also more complex than it is suggested in the manuscript. The text should better reflect the limitations of the conclusions that can be drawn from the authors' data.

Reviewer #3 (Public review):

Summary:

This paper uses a new chemogenetic tool to investigate the role of cerebellar Purkinje cells in postural control. Using a high-throughput behavioral assay, they show that activation or ablation of Purkinje cells affects various aspects of postural control in zebrafish larvae during spontaneous swimming, and that the effects are more pronounced at later developmental time points, where the Purkinje cell number is much greater. Using a sophisticated imaging assay, they record Purkinje cell activity in response to tilt of the fish, and show that some Purkinje cells are tuned to tilt direction, and that the direction can even be decoded from untuned neurons.

Strengths:

Overall the study is nice, using a variety of genetic tools and behavioral analysis to address a fundamental question about the role of the cerebellum in postural control in fish

Reviewer #3 (Public review):

This study is a part of the ongoing series of rigorous work from this group exploring neural coding deficits in the auditory nerve, and dissociating the effects of cochlear synaptopathy from other age-related deficits. They have previously shown no evidence of phase-locking deficits in the remaining auditory nerve fibers in quiet-aged gerbils. Here, they study the effects of aging on the perception and neural coding of temporal fine structure cues in the same Mongolian gerbil model.

They measure TFS coding in the auditory nerve using the TFS1 task which uses a combination of harmonic and tone-shifted inharmonic tones which differ primarily in their TFS cues (and not the envelope). They then follow this up with a behavioral paradigm using the TFS1 task in these gerbils. They test young normal hearing gerbils, aged gerbils, and young gerbils with cochlear synaptopathy induced using the neurotoxin ouabain to mimic synapse losses seen with age.

In the behavioral paradigm, they find that aging is associated with decreased performance compared to the young gerbils, whereas young gerbils with similar levels of synapse loss do not show these deficits. When looking at the auditory nerve responses, they find no differences in neural coding of TFS cues across any of the groups. However, aged gerbils show an increase in the representation of periodicity envelope cues (around f0) compared to young gerbils or those with induced synapse loss. The authors hence conclude that synapse loss by itself doesn't seem to be important for distinguishing TFS cues, and rather the behavioral deficits with age are likely having to do with the misrepresented envelope cues instead.

The manuscript is well written, and the data presented are robust. Some of the points below will need to be considered while interpreting the results of the study, in its current form. These considerations are addressable if deemed necessary, with some additional analysis in future versions of the manuscript.

Spontaneous rates - Figure S2 shows no differences in median spontaneous rates across groups. But taking the median glosses over some of the nuances there. Ouabain (in the Bourien study) famously affects low spont rates first, and at a higher degree than median or high spont rates. It seems to be the case (qualitatively) in Figure S2 as well, with almost no units in the low spont region in the ouabain group, compared to the other groups. Looking at distributions within each spont rate category and comparing differences across the groups might reveal some of the underlying causes for these changes. Given that overall, the study reports that low-SR fibers had a higher ENV/TFS log-z-ratio, the distribution of these fibers across groups may reveal specific effects of TFS coding by group.

Threshold shifts - It is unclear from the current version if the older gerbils have changes in hearing thresholds, and whether those changes may be affecting behavioral thresholds. The behavioral stimuli appear to have been presented at a fixed sound level for both young and aged gerbils, similar to the single unit recordings. Hence, age-related differences in behavior may have been due to changes in relative sensation level. Approaches such as using hearing thresholds as covariates in the analysis will help explore if older gerbils still show behavioral deficits.

Task learning in aged gerbils - It is unclear if the aged gerbils really learn the task well in two of the three TFS1 test conditions. The d' of 1 which is usually used as the criterion for learning was not reached in even the easiest condition for aged gerbils in all but one condition for the aged gerbils (Fig. 5H) and in that condition, there doesn't seem to be any age-related deficits in behavioral performance (Fig. 6B). Hence dissociating the inability to learn the task from the inability to perceive TFS 1 cues in those animals becomes challenging.

Increased representation of periodicity envelope in the AN - the mechanisms for increased representation of periodicity envelope cues is unclear. The authors point to some potential central mechanisms but given that these are recordings from the auditory nerve what central mechanisms these may be is unclear. If the authors are suggesting some form of efferent modulation only at the f0 frequency, no evidence for this is presented. It appears more likely that the enhancement may be due to outer hair cell dysfunction (widened tuning, distorted tonotopy). Given this increased envelope coding, the potential change in sensation level for the behavior (from the comment above), and no change in neural coding of TFS cues across any of the groups, a simpler interpretation may be -TFS coding is not affected in remaining auditory nerve fibers after age-related or ouabain induced synapse loss, but behavioral performance is affected by altered outer hair cell dysfunction with age.

Emerging evidence seems to suggest that cochlear synaptopathy and/or TFS encoding abilities might be reflected in listening effort rather than behavioral performance. Measuring some proxy of listening effort in these gerbils (like reaction time) to see if that has changed with synapse loss, especially in the young animals with induced synaptopathy, would make an interesting addition to explore perceptual deficits of TFS coding with synapse loss.

Reviewer #3 (Public review):

Summary:

The authors employ a series of well-conceived and well-executed experiments involving photometric imaging of the dentate gyrus and raphe nucleus, as well as cell-type specific genetic manipulations of serotonergic receptors that together serve to directly implicate serotonergic regulation of dentate gyrus (DG) granule (GC) and mossy cell (MC) activity in association with an infra slow oscillation (ISO) of neural activity has been previously linked to general cortical regulation during NREM sleep and microarousals.

Strengths:

There are a number of novel and important results, including the modulation of dentage granule cell activity by the infraslow oscillation during NREM sleep, the selective association of different subpopulations of granule cells to microarousals (MA), the anticorrelation of raphe activity with infraslow dentate activity.

The discussion includes a general survey of ISOs and recent work relating to their expression in other brain areas and other potential neuromodulatory system involvement, as well as possible connections with infraslow oscillations, micro arousals, and sensory sensitivity.

Weaknesses:

- The behavioral results showing contextual memory impairment resulting from 5-HT1a knockdown are fine, but are over-interpreted. The term memory consolidation is used several times, as well as references to sleep-dependence. This is not what was tested. The receptor was knocked down, and then 2 weeks later animals were found to have fear conditioning deficits. They can certainly describe this result as indicating a connection between 5-HT1a receptor function and memory performance, but the connection to sleep and consolidation would just be speculation. The fact that 5-HT1a knockdown also impacted DG ISOs does not establish dependency. Some examples of this are:<br /> o The final conclusion asserts "Together, our study highlights the role of neuromodulation in organizing neuronal activity during sleep and sleep-dependent brain functions, such as memory.", but the reported memory effects (impairment of fear conditioning) were not shown to be explicitly sleep-dependent.<br /> o Earlier in the discussion it mentions "Finally, we showed that local genetic ablation of 5-HT1a receptors in GCs impaired the ISO and memory consolidation". The effect shown was on general memory performance - consolidation was not specifically implicated.

- The assertion on page 9 that the results demonstrate "that the 5-HT is directly acting in the DG to gate the oscillations" is a bit strong given the magnitude of effect shown in Fig. 6D, and the absence of demonstration of negative effect on cortical areas that also show ISO activity and could impact DG activity (see requested cortical sigma power analysis).

- Recent work has shown that abnormal DG GC activity can result from the use of the specific Ca indicator being used (GCaMP6s). (Teng, S., Wang, W., Wen, J.J.J. et al. Expression of GCaMP6s in the dentate gyrus induces tonic-clonic seizures. Sci Rep 14, 8104 (2024). https://doi.org/10.1038/s41598-024-58819-9). The authors of that study found that the effect seemed to be specific to GCaMP6s and that GCaMP6f did not lead to abnormal excitability. Note this is of particular concern given similar infraslow variation of cortical excitability in epilepsy (cf Vanhatalo et al. PNAS 2004). While I don't think that the experiments need to be repeated with a different indicator to address this concern, you should be able to use the 2p GCaMP7 experiments that have already been done to provide additional validation by repeating the analyses done for the GCaMP6s photometry experiments. This should be done anyway to allow appropriate comparison of the 2p and photometry results.

- While the discussion mentions previous work that has linked ISOs during sleep with regulation of cortical oscillations in the sigma band, oddly no such analysis is performed in the current work even though it is presumably available and would be highly relevant to the interpretation of a number of primary results including the relationship between the ISOs and MAs observed in the DG and similar results reported in other areas, as well as the selective impact of DG 5-HT1a knockdown on DG ISOs. For example, in the initial results describing the cross correlation of calcium activity and EMG/EEG with MA episodes (paragraph 1, page 4), similar results relating brief arousals to the infraslow fluctuation in sleep spindles (sigma band) have been reported also at .02 Hz associated with variation in sensory arousability (cf. Cardis et al., "Cortico-autonomic local arousals and heightened somatosensory arousability during NREMS of mice in neuropathic pain", eLife 2021). It would be important to know whether the current results show similar cortical sigma band correlations. Also, in the results on ISO attenuation following 5-HT1 knockdown on page 7 (fig. 6), how is cortical EEG affected? is ISO still seen in EEG but attenuated in DG?

- The illustrations of the effect of 5-HT1a knockdown shown in Figure 6 are somewhat misleading. The examples in panels B and C show an effect that is much more dramatic than the overall effect shown in panel D. Panels B and C do not appear to be representative examples. Which of the sample points in panel D are illustrated in panels B, C? it is not appropriate to arbitrarily select two points from different animals for comparison, or worse, to take points from the extremes of the distributions. If the intent is to illustrate what the effect shown in D looks like in the raw data, then you need to select examples that reflect the means shown in panel D. It is also important to show the effect on cortical EEG, particularly in sigma band to see if the effects are restricted to the DG ISOs. It would also be helpful to show that MAs and their correlations as shown in Fig 1 or G as well as broader sleep architecture are not affected.

- On page 9 of the results it states that GCs and MCs are upregulated during NREM and their activity is abruptly terminated by MAs through a 5-HT mediated mechanism. I didn't see anything showing the 5-HT dependence of the MA activity correlation. The results indicate a reduction in ISO modulation of GC activity but not the MA correlated activity. I would like to see the equivalent of Fig 1,2 G panels with the 5-HT1a manipulation.

Reviewer #4 (Public review):

The work by Yingying Chen, Jeong Han Lee, and co-authors summarizes the morphological and functional outcomes of Cldn9 loss in the inner ear, particularly in the organ of Corti. While the study does not provide mechanistic insights into how the developmental loss of Cldn9 leads to ectopic hair cell formation, the phenomenon itself is curious. The work primarily focuses on a detailed characterization of the ectopic hair cells, which is well done. Despite the lack of mechanistic insights, the study will be of interest to the inner ear field if several major issues with the manuscript are addressed.

(1) The title, "Genetic and pharmacologic alterations of claudin9 levels suffice to induce functional and mature inner hair cells," is misleading. First, both manipulations (knockout and knockdown) are genetic, and no pharmacology is involved. Second, both manipulations are carried out during the embryonic and neonatal periods, and there is no evidence of mature hair cell regeneration in this study. The title should be revised to reflect this. A more accurate title could be: "Developmental loss of Cldn9 results in functional ectopic inner hair cells that persist through adulthood."<br /> (2) Contact-mediated lateral inhibition in hair cell fate determination is one of the most well-studied phenomena in the inner ear field, and numerous groups have shown that it is mediated by Notch signaling. This must be added to the introduction.<br /> (3) A large body of literature has demonstrated that Notch inhibition alone is not sufficient to regenerate hair cells in adult mice. Therefore, if the loss of claudins disrupts Notch signaling-the proposed mechanisms in the discussion - it is unlikely to be a viable therapeutic strategy for hair cell regeneration in the adult ear. Furthermore, no hair cell ablation experiments were conducted to demonstrate what could be considered true regeneration. These speculative statements should be removed or revised accordingly.<br /> (4) Cldn9 is a tight junction protein and should localize to the membrane. Yet, the data presented show what appears to be diffuse cytoplasmic staining, which is concerning.

Reviewer #3 (Public review):

In this paper, the authors use a three-phase economic game to examine the tendency to engage in prosocial versus competitive exchanges with three anonymous partners. In particular, they consider individual differences in the tendency to infer about others' tendencies based on one's preferences and to update one's preferences based on observations of others' behavior. The study includes a sample of individuals diagnosed with borderline personality disorder and a matched sample of psychiatrically healthy control participants.

On the whole, the experimental design is well-suited to the questions and the computational model analyses are thorough, including modern model-fitting procedures. I particularly appreciated the clear exposition regarding model parameterization and the descriptive Table 2 for qualitative model comparison. My broad question about the experiment (in terms of its clinical and cognitive process relevance): Does the task encourage competition or give participants a reason to take advantage of others? I don't think it does, so it would be useful to clarify the normative account for prosociality in the introduction (e.g., some of Robin Dunbar's work).

The finding that individuals with BPD do not engage in self-other generalization on this task of social intentions is novel and potentially clinically relevant. The authors find that BPD participants' tendency to be prosocial when splitting points with a partner does not transfer into their expectations of how a partner will treat them in a task where they are the passive recipient of points chosen by the partner. In the discussion, the authors reasonably focus on model differences between groups (Bayesian model comparison), yet I thought this finding -- BPD participants not assuming prosocial tendencies in phase 2 while CON participant did -- merited greater attention. Although the BPD group was close to 0 on the \beta prior in Phase 2, their difference from CON is still in the direction of being more mistrustful (or at least not assuming prosociality). This may line up with broader clinical literature on mistrustfulness and attributions of malevolence in the BPD literature (e.g., a 1992 paper by Nigg et al. in Journal of Abnormal Psychology). My broad point is to consider further the Phase 2 findings in terms of the clinical interpretation of the shift in \beta relative to controls.

On the conceptual level, I had two additional concerns. First, the authors note that they have "proposed a theory with testable predictions" (p. 4 but also elsewhere) but they do not state any clear predictions in the introduction, nor do they consider what sort of patterns will be observed in the BPD group in view of extant clinical and computational literature. Rather, the paper seems to be somewhat exploratory, largely looking at group differences (BPD vs. CON) on all of the shared computational parameters and additional indices such as belief updating and reaction times. Given this, I would suggest that the authors make stronger connections between extant research on intention representation in BPD and their framework (model and paradigm). In particular, the authors do not address related findings from Ereira (2020) and Story (2024) finding that in a false belief task that BPD participants *overgeneralize* from self to other. A critical comparison of this work to the present study, including an examination of the two tasks differ in the processes they measure, is important.

In addition, perhaps it is fairer to note more explicitly the exploratory nature of this work. Although the analyses are thorough, many of them are not argued for a priori (e.g., rate of belief updating in Figure 2C) and the reader amasses many individual findings that need to by synthesized.

Second, in the discussion, the authors are too quick to generalize to broad clinical phenomena in BPD that are not directly connected to the task at hand. For example, on p. 22: "Those with a diagnosis of BPD also show reduced permeability in generalising from other to self. While prior research has predominantly focused on how those with BPD use information to form impressions, it has not typically examined whether these impressions affect the self." Here, it's not self-representation per se (typically, identity or one's view of oneself), but instead cooperation and prosocial tendencies in an economic context. It is important to clarify what clinical phenomena may be closely related to the task and which are more distal and perhaps should not be approached here.

On a more technical level, I had two primary concerns. First, although the authors consider alternative models within a hierarchical Bayesian framework, some challenges arise when one analyzes parameter estimates fit separately to two groups, particularly when the best-fitting model is not shared. In particular, although the authors conduct a model confusion analysis, they do not as far I could tell (and apologies if I missed it) demonstrate that the dynamics of one model are nested within the other. Given that M4 has free parameters governing the expectations on the absolute and relative reward preferences in Phase 2, is it necessarily the case that the shared parameters between M1 and M4 can be interpreted on the same scale? Relatedly, group-specific model fitting has virtues when believes there to be two distinct populations, but there is also a risk of overfitting potentially irrelevant sample characteristics when parameters are fit group by group.

To resolve these issues, I saw one straightforward solution (though in modeling, my experience is that what seems straightforward on first glance may not be so upon further investigation). M1 assumes that participants' own preferences (posterior central tendency) in Phase 1 directly transfer to priors in Phase 2, but presumably the degree of transfer could vary somewhat without meriting an entirely new model (i.e., the authors currently place this question in terms of model selection, not within-model parameter variation). I would suggest that the authors consider a model parameterization fit to the full dataset (both groups) that contains free parameters capturing the *deviations* in the priors relative to the preceding phase's posterior. That is, the free parameters $\bar{\alpha}_{par}^m$ and $\bar{\beta}_{par}^m$ govern the central tendency of the Phase 2 prior parameter distributions directly, but could be reparametrized as deviations from Phase 1 $\theta^m_{ppt}$ parameters in an additive form. This allows for a single model to be fit all participants that encompasses the dynamics of interest such that between-group parameter comparisons are not biased by the strong assumptions imposed by M1 (that phase 1 preferences and phase 2 observations directly transfer to priors). In the case of controls, we would expect these deviation parameters to be centred on 0 insofar as the current M1 fit them best, whereas for BPD participants should have significant deviations from earlier-phase posteriors (e.g., the shift in \beta toward prior neutrality in phase 2 compared to one's own prosociality in phase 1). I think it's still valid for the authors to argue for stronger model constraints for Bayesian model comparison, as they do now, but inferences regarding parameter estimates should ideally be based on a model that can encompass the full dynamics of the entire sample, with simpler dynamics (like posterior -> prior transfer) being captured by near-zero parameter estimates.

My second concern pertains to the psychometric individual difference analyses. These were not clearly justified in the introduction, though I agree that they could offer potentially meaningful insight into which scales may be most related to model parameters of interest. So, perhaps these should be earmarked as exploratory and/or more clearly argued for. Crucially, however, these analyses appear to have been conducted on the full sample without considering the group structure. Indeed, many of the scales on which there are sizable group differences are also those that show correlations with psychometric scales. So, in essence, it is unclear whether most of these analyses are simply recapitulating the between-group tests reported earlier in the paper or offer additional insights. I think it's hard to have one's cake and eat it, too, in this regard and would suggest the authors review Preacher et al. 2005, Psychological Methods for additional detail. One solution might be to always include group as a binary covariate in the symptom dimension-parameter analyses, essentially partialing the correlations for group status. I remain skeptical regarding whether there is additional signal in these analyses, but such controls could convince the reader. Nevertheless, without such adjustments, I would caution against any transdiagnostic interpretations such as this one in the Highlights: "Higher reported childhood trauma, paranoia, and poorer trait mentalizing all diminish other-to-self information transfer irrespective of diagnosis." Since many of these analyses relate to scales on which the groups differ, the transdiagnostic relevance remains to be demonstrated.

Reviewer #3 (Public review):

The manuscript of Kowalewski et al. titled "Machine learning of honey bee olfactory behavior identifies repellent odorants in free flying bees in the field" did machine learning to predict potential candidates for honeybee repellents, which may keep foraging bees from pesticides. This is a pilot research with strong significance in the research of olfactory behavior and in pest control. However, some major issues need to be addressed to enhance the manuscript's clarity, strength, and overall coherence.

(1) Drosophila melanogaster is not considered as a true agricultural pest. The manuscript would be more compelling if using true pests, for example, Drosophila suzukii or others.<br /> (2) For repellency test, the result relies on dosage. An attractant may become a repellent at high concentration. Test a range of concentrations for each chemicals and compare responses between honeybees and pests.<br /> (3) Be more clear about bee behavior data and their scores (as in Page 4 Results "184 training chemicals and later for 203 chemicals" and Page 10 Methods). I suggest that authors add a supplemental table with each chemical and its behavioral score, feature and reference - which ones were used for training, and which ones for testing. Also add your own behavioral test data (second input) to this table.<br /> (4) The AUC in the first validation was 0.88 (Page 4), and in Page 5, "As expected, the computational validation results based on the AUC values, show an improvement." However, there were no other AUC values to show improvement.<br /> (5) Show plots of ROC AUC curves from Round 1 and Round 2.<br /> (6) In the Discussion, the authors mentioned olfactory receptors in honeybees. It would be useful to provide a general review of the current understanding of these receptors and their (potential) functions.<br /> (7) I suggest combining Fig. 1 and Fig. 3A as one pipeline for this work.<br /> (8) Figure 2C, some sample sizes are very small, such as 2-piperidone: 1 first-choice control vs 0 first-choice repellent? Increase sample size and do statistical analysis.<br /> (9) In general, to assist reviewers, include line numbers to the manuscript.

Reviewer #3 (Public review):

Summary:

The authors created and characterized genetic tools that allow for precise manipulation of individual or small subsets of central complex (CX) cell types in the Drosophila brain. They developed split-GAL4 driver lines and integrated this with a detailed survey of neurotransmitter and neuropeptide expression and receptor localization in the central brain. The manuscript also explores the functional relevance of CX cell types by evaluating their roles in sleep regulation and linking circadian clock signals to the CX. This work represents an ambitious and comprehensive effort to provide both molecular and functional insights into the CX, offering tools and data that will serve as a critical resource for researchers.

Strengths:

(1) The extensive collection of split-GAL4 lines targeting specific CX cell types fills a critical gap in the genetic toolkit for the Drosophila neuroscience community.<br /> (2) By combining anatomical, molecular, and functional analyses, the authors provide a holistic view of CX cell types that is both informative and immediately useful for researchers across diverse disciplines.<br /> (3) The identification of CX cell types involved in sleep regulation and their connection to circadian clock mechanisms highlights the functional importance of the CX and its integrative role in regulating behavior and physiological states.<br /> (4) The authors' decision to present this work as a single, comprehensive manuscript rather than fragmenting it into smaller publications each focusing on separate central complex components is commendable. This decision prioritizes accessibility and utility for the broader neuroscience community, which will enable researchers to approach CX-related questions with a ready-made toolkit.

Weaknesses:

While the manuscript is an outstanding resource, it leaves room for more detailed mechanistic exploration in some areas. Nonetheless, this does not diminish the immediate value of the tools and data provided.

Appraisal:

The authors have succeeded in achieving their aims of creating well-characterized genetic tools and providing a detailed survey of neurochemical and functional properties in the CX. The results strongly support their conclusions and open numerous avenues for future research. The work effectively bridges the gap between genetic manipulation, molecular characterization, and functional assessment, enabling a deeper understanding of the CX's diverse roles.

Impact and Utility

This manuscript will have a significant and lasting impact on the field, providing tools and data that facilitate new discoveries in the study of the CX, sleep regulation, circadian biology, and beyond. The genetic tools developed here are likely to become a standard resource for Drosophila researchers, and the comprehensive dataset on neurotransmitter and neuropeptide expression will inspire investigations into the interplay between neuromodulation and classical neurotransmission.

Additional Context

By delivering an integrated dataset that spans anatomy, molecular properties, and functional relevance, the authors have created a resource that will serve the neuroscience community for years to come.

Reviewer #3 (Public review):

The central goal of this paper as I understand it is to extract the "integration hierarchy" of stimulus in the dorsal and ventrolateral visual fields. The segregation of these responses is different from what is thought to occur in bees and flies and was established in the authors' prior work. Showing how the stimuli combine and are prioritized goes beyond the authors' prior conclusions that separated the response into two visual regions. The data presented do indeed support the hierarchy reported in Figure 5 and that is a nice summary of the authors' work. The moths respond to combinations of dorsal and lateral cues in a mixed way but also seem to strongly prioritize avoiding dorsal optic flow which the authors interpret as a closed and potentially dangerous ecological context for these animals. The authors use clever combinations of stimuli to put cues into conflict to reveal the response hierarchy.

My most significant concern is that this hierarchy of stimulus responses might be limited to the specific parameters chosen in this study. Presumably, there are parameters of these stimuli that modulate the response (spatial frequency, different amounts of optic flow, contrast, color, etc). While I agree that the hierarchy in Figure 5 is consistent for the particular stimuli given, this may not extend to other parameter combinations of the same cues. For example, as the contrast of the dorsal stimuli is reduced, the inequality may shift. This does not preclude the authors' conclusions but it does mean that they may not generalize, even within this species. For example, other cue conflict studies have quantified the responses to ranges of the parameters (e.g. frequency) and shown that one cue might be prioritized or up-weighted in one frequency band but not in others. I could imagine ecological signatures of dorsal clutter and translational positioning cues could depend on the dynamic range of the optic flow, or even having spatial-temporal frequency-dependent integration independent of net optic flow.

The second part of this concern is that there seems to be a missed opportunity to quantify the integration, especially when the optic flow magnitude is already calculated. The discussion even highlights that an advantage of the conflict paradigm is that the weights of the integration hierarchy can be compared. But these weights, which I would interpret as stimulus-responses gains, are not reported. What is the ratio of moth response to optic flow in the different regions? When the moth balances responses in the dorsal and ventrolateral region, is it a simple weighted average of the two? When it prioritizes one over the other is the response gain unchanged? This plays into the first concern because such gain responses could strongly depend on the specific stimulus parameters rather than being constant.

The authors do explain the choice of specific stimuli in the context of their very nice natural scene analysis in Fig. 1 and there is an excellent discussion of the ecological context for the behaviors. However, I struggled to directly map the results from the natural scenes to the conclusions of the paper. How do they directly inform the methods and conclusions for the laboratory experiments? Most important is the discussion in the middle paragraph of page 12, which suggests a relationship with Figure 1B, but seems provocative but lacking a quantification with respect to the laboratory stimuli.

The central conclusion of the first section of the results is that there are likely two different pathways mediating the dorsal and the ventrolateral response. This seems reasonable given the data, however, this was also the message that I got from the authors' prior paper (ref 11). There are certainly more comparisons being done here than in that paper and it is perfectly reasonable to reinforce the conclusion from that study but I think what is new about these results needs to be highlighted in this section and differentiated from prior results. Perhaps one way to help would be to be more explicit with the open hypotheses that remain from that prior paper.

Reviewer #3 (Public review):

Summary:

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

Strengths:

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

Reviewer #3 (Public review):

The manuscript contains a carefully designed fMRI study, using MVPA pattern analysis to investigate which high-level associate cortices contain target-related information to guide visual search. A special focus is hereby on so-called 'target-associated' information, that has previously been shown to help in guiding attention during visual search. For this purpose the author trained their participants and made them learn specific target-associations, in order to then test which brain regions may contain neural representations of those learnt associations. They found that at least some of the associations tested were encoded in prefrontal cortex during the cue and delay period.

The manuscript is very carefully prepared. As far as I can see, the statistical analyses are all sound and the results integrate well with previous findings.

I have no strong objections against the presented results and their interpretation.

Reviewer #3 (Public review):

Summary:

The authors optogenetically stimulate 5 neurons all preferring the same pure tone frequency (16 or 54 kHz) in the mouse auditory cortex using a holography-based single cell resolution optogenetics during sound presentation. They demonstrate that the response boosting of target neurons leads to a broad suppression of surrounding neurons, which is significantly more pronounced in neurons that have the same pure tone tuning as the target neurons. This effect is immediate and spans several hundred micrometers. This suggests that the auditory cortical network balances its activity in response to excess spikes, a phenomenon already seen in visual cortex.

Strengths:

The study is based on a technologically very solid approach based on single-cell resolution two-photon optogenetics. The authors demonstrate the potency and resolution of this approach. The inhibitory effects observed upon targeted stimulation are clear and the relative specificity to co-tuned neurons is statistically clear although the effect size is moderate.

Weaknesses:

The evaluation of the results is brief and some aspects of the observed homeostatic are not quantified. For example, it is unclear whether stimulation produces a net increase or decrease of population activity, or if the homeostatic phenomenon fully balances activity. A comparison of population activity for all imaged neurons with and without stimulation would be instructive. The selectivity for co-tuned neurons is significant but weak. Although it is difficult to evaluate this issue, this result may be trivial, as co-tuned neurons fire more strongly. Therefore, the net activity decrease is expected to be larger, in particular, for the number of non-co-tuned neurons which actually do not fire to the target sound. The net effect for the latter neurons will be zero just because they do not respond. The authors do not make a very strong case for a specific inhibition model in comparison to a broad and non-specific inhibitory effect. Complementary modeling work would be needed to fully establish this point.

Reviewer #3 (Public review):

In this work, the authors present an open-source system called behaviourMate for acquiring data related to animal behavior. The temporal alignment of recorded parameters across various devices is highlighted as crucial to avoid delays caused by electronics dependencies. This system not only addresses this issue but also offers an adaptable solution for VR setups. Given the significance of well-designed open-source platforms, this paper holds importance.

Advantages of behaviorMate:

The cost-effectiveness of the system provided.<br /> The reliability of PCBs compared to custom-made systems.<br /> Open-source nature for easy setup.<br /> Plug & Play feature requiring no coding experience for optimizing experiment performance (only text based Json files, 'context List' required for editing).

Reviewer #3 (Public review):

Summary:

The study uses structural MRI to identify how the number, degree of experience, and phonemic diversity of language(s) that a speaker knows can influence the thickness of different sub-segments of auditory cortex. In both a primary and replication sample of adult speakers, the authors find key differences in cortical thickness within specific subregions of cortex due to either the age at which languages are acquired (degree of experience) or the diversity of the phoneme inventories carried by that/those language(s) (breadth of experience).

Strengths:

The results are first and foremost quite fascinating and I do think they make a compelling case for the different ways in which linguistic experience shapes auditory cortex.

The study uses a number of different measures to quantify linguistic experience, related to how many languages a person knows (taking into account the age at which each was learned) as well as the diversity of the phoneme inventories contained within those languages. The primary sample is moderately large for a study that focuses on brain-behaviour relationships; a somewhat smaller replication sample is also deployed in order to test the generality of the effects.

Analytic approaches benefit from the careful use of brain segmentation techniques that nicely capture key landmarks and account for vagaries in the structure of STG that can vary across individuals (e.g., the number of transverse temporal gyri varies from 1-4 across individuals).

Weaknesses:

The specificity of these effects is interesting; some effects really do appear to be localized to left hemisphere and specific subregions of auditory cortex e.g., TTG. There is an ancillary analysis that examines regions outside auditory cortex to examine whether these are the only brain regions for which such effects occur. Expanding the search space to a whole-brain analysis, and a more lenient statistical threshold, does reveal only small patches of the brain outside auditory cortex show similar effects. Notably, these could be due to inflated type-1 error, but overall we would need a much larger sample to be certain.

Discussion of potential genetic differences underlying the findings is interesting. It does represent one alternative account that does not have to do with plasticity/experience, as the authors acknowledge.

The replication sample is useful and a great idea. It does however feature roughly half the number of participants. As the authors are careful to point out, that statistical power is weaker and given small effects in some cases we should not be surprised that the results only partially replicated in that sample.

Reviewer #3 (Public review):

Summary:

m6Am is an abundant mRNA modification present on the TSN. Unlike the structurally similar and abundant internal mRNA modification m6A, m6Am's function has been controversial. One way to resolve controversies surrounding mRNA modification functions has been to develop new ways to better profile said mRNA modification. Here, Liu et al. developed a new method (based on GLORI-seq for m6A-sequencing), for antibody-independent sequencing of m6Am (CROWN-seq). Using appropriate spike-in controls and knockout cell lines, Liu et al. clearly demonstrated CROWN-seq's precision and quantitative accuracy for profiling transcriptome-wide m6Am. Subsequently, the authors used CROWN-seq to greatly expand the number of known m6Am sites in various cell lines and also determine m6Am stoichiometry to generally be high for most genes. CROWN-seq identified gene promoter motifs that correlate best with high stoichiometry m6Am sites, thereby identifying new determinants of m6Am stoichiometry. CROWN-seq also helped reveal that m6Am does not regulate mRNA stability or translation (as opposed to past reported functions). Rather, m6Am stoichiometry correlates well with transcription levels. Finally, Liu et al. reaffirmed that FTO mainly demethylates m6Am, not of mRNA but of snRNAs and snoRNAs.

Strengths:

This is a well-written manuscript that describes and validates a new m6Am-sequencing method: CROWN-seq as the first m6Am-sequencing method that can both quantify m6Am stoichiometry and profile m6Am at single-base resolution. These advantages facilitated Liu et al. to uncover new potential findings related to m6Am regulation and function. I am confident that CROWN-seq will likely be the gold standard for m6Am-sequencing henceforth.

Weaknesses:

Though the authors have uncovered a potentially new function for m6Am, they need to be clear that without identifying a mechanism, their data might only be demonstrating a correlation between the presence of m6Am and transcriptional regulation rather than causality.

Reviewer #3 (Public review):

Summary:

In this paper, Chang and Meliala et al. demonstrate that PEBP1 is a modulator of the ISR, specifically through the induction of mitochondrial stress. The authors utilize thermal proteome profiling (TPP) by which they identify PEPB1 as a thermally stabilized protein upon oligomycin treatment, indicating its role in mitochondrial stress. Moreover, RNA-sequencing analysis indicated that PEBP1 may be specifically modulating the mitochondrial stress-induced ISR, as PEBP1 knock-out reduces phosphorylation of eIF2α. They also show that PEBP1 function is independent of ER stress specifically tunicamycin treatment and loss of PEBP1 does affect mitochondrial ISR but in an OMA1, DELE1 independent manner. Thus, the authors hypothesized that PEBP1 interacts directly with eIF2α, functioning as a scaffolding protein. However, direct co-immunoprecipitation failed to demonstrate PEBP1 and eIF2α potential interaction. The authors then used a NanoBiT luminescence complementation assay to show the PEBP1-eIF2a interaction and its disruption by S51 phosphorylation.

Strengths:

Taken together, this work is novel, and the data presented suggests PEBP1 has a role as a modulator of the mitochondrial ISR, enhancing the signal to elicit the necessary response.

Weaknesses:

The one major issue of this work is the lack of a mechanism showing precisely how PEBP1 amplifies the mitochondrial integrated stress response. The work, as it is described, presents data suggesting PEBP1's role in the ISR but fails to present a more conclusive mechanism.

Reviewer #3 (Public Review):

This work addresses an important question aimed at understanding how membrane docking to the distal appendages is regulated during ciliogenesis. In this study, Tomoharu and colleagues identified interactions between CEP89 (important for RAB34-positive membrane localization to the mother centriole) and NCS1 and C3ORF14. Both these CEP89 interacting proteins were characterized as distal appendage localized proteins between CEP89 and RAB34 based on super-resolution microscopy. Ciliogenesis investigations using knockout cells indicated that NCS1 and CEP89 have similar impaired ciliation due to disruption in vesicle recruitment/RAB34 to the mother centriole, while C3ORF14 had less effect on ciliogenesis. The authors refer to the ciliogenesis requirement for CEP89/NCS1 as ciliary vesicles, which has been previously referred to as preciliary vesicle or distal appendage vesicles. NCS1 distal appendage localization was dependent on CEP89 and TTBK2, but it is not clear how TTBK2 affects NCS1. The authors subsequently performed double knockouts with NCS1 and other distal appendage proteins and showed stronger effects on mother centriole RAB34 levels, suggesting efficient membrane docking during ciliogenesis requires several distal appendage proteins. This is consistent with NCS1 knockout mice which do not display typical ciliopathy phenotypes. These mice do display obesity, which is associated with cilia dysfunction, and show reduced ciliary protein levels. As noted by the authors, the in vivo results for NCS1 knockouts could be affected by the mouse background which was not evaluated. The authors demonstrate the NCS1 myristoylation motif is required for RAB34 localization to the mother centrioles, providing a mechanistic explanation for how distal appendage proteins could interact with membranes during ciliogenesis. Overall the authors' findings support an important role for NCS1 in regulating ciliogenesis via myristoylation-dependent interaction with RAB34-positive membranes docked at the mother centriole.

Reviewer #3 (Public review):

The superfamily I 3'-5' DNA helicase Srs2 is well known for its role as an anti-recombinase, stripping Rad51 from ssDNA, as well as an anti-crossover factor, dissociating extended D-loops and favoring non-crossover outcome during recombination. In addition, Srs2 plays a key role in in ribonucleotide excision repair. Besides DNA repair defects, srs2 mutants also show a reduced recovery after DNA damage that is related to its role in downregulating the DNA damage signaling or checkpoint response. Recent work from the Zhao laboratory (PMID: 33602817) identified a role of Srs2 in downregulating the DNA damage signaling response by removing RPA from ssDNA. This manuscript reports further mechanistic insights into the signaling downregulation function of Srs2.

Using the genetic interaction with mutations in RPA1, mainly rfa1-zm2, the authors test a panel of mutations in Srs2 that affect CDK sites (srs2-7AV), potential Mec1 sites (srs2-2SA), known sumoylation sites (srs2-3KR), Rad51 binding (delta 875-902), PCNA interaction (delta 1159-1163), and SUMO interaction (srs2-SIMmut). All mutants were generated by genomic replacement and the expression level of the mutant proteins was found to be unchanged. This alleviates some concern about the use of deletion mutants compared to point mutations. Double mutant analysis identified that PCNA interaction and SUMO sites were required for the Srs2 checkpoint dampening function, at least in the context of the rfa1-zm2 mutant. There was no effect of this mutants in a RFA1 wild type background. This latter result is likely explained by the activity of the parallel pathway of checkpoint dampening mediated by Slx4, and genetic data with an Slx4 point mutation affecting Rtt107 interaction and checkpoint downregulation support this notion. Further analysis of Srs2 sumoylation showed that Srs2 sumoylation depended on PCNA interaction, suggesting sequential events of Srs2 recruitment by PCNA and subsequent sumoylation. Kinetic analysis showed that sumoylation peaks after maximal Mec1 induction by DNA damage (using the Top1 poison camptothecin (CPT)) and depended on Mec1. This data are consistent with a model that Mec1 hyperactivation is ultimately leading to signaling downregulation by Srs2 through Srs2 sumoylation. Mec1-S1964 phosphorylation, a marker for Mec1 hyperactivation and a site found to be needed for checkpoint downregulation after DSB induction, did not appear to be involved in checkpoint downregulation after CPT damage. The data are in support of the model that Mec1 hyperactivation when targeted to RPA-covered ssDNA by its Ddc2 (human ATRIP) targeting factor, favors Srs2 sumoylation after Srs2 recruitment to PCNA to disrupt the RPA-Ddc2-Mec1 signaling complex. Presumably, this allows gap filling and disappearance of long-lived ssDNA as the initiator of checkpoint signaling, although the study does not extend to this step.

Strengths<br /> (1) The manuscript focuses on the novel function of Srs2 to downregulate the DNA damage signaling response and provide new mechanistic insights.<br /> (2) The conclusions that PCNA interaction and ensuing Srs2-sumoylation are involved in checkpoint downregulation are well supported by the data.

Weaknesses<br /> (1) Additional mutants of interest could have been tested, such as the recently reported Pin mutant, srs2-Y775A (PMID: 38065943), and the Rad51 interaction point mutant, srs2-F891A (PMID: 31142613).<br /> (2) The use of deletion mutants for PCNA and RAD51 interaction is inferior to using specific point mutants, as done for the SUMO interaction and the sites for post-translational modifications.<br /> (3) Figure 4D and Figure 5A report data with standard deviations, which is unusual for n=2. Maybe the individual data points could be plotted with a color for each independent experiment to allow the reader to evaluate the reproducibility of the results.

Comments on revisions:

In this revision, the authors adequately addressed my concerns. The only issue I see remaining is the site of Srs2 action. The authors argue in favor of gaps and against R-loops and ssDNA resulting from excessive supercoiling. The authors do not discuss ssDNA resulting from processing of one-sided DSBs, which are expected to result from replication run-off after CPT damage but are not expected to provide the 3'-junction for preferred PCNA loading. Can the authors exclude PCNA at the 5'-junction at a resected DSB?

Reviewer #3 (Public Review):

Summary:

This study characterizes classical and nonclassical osteoblasts as both types were analyzed independently (integrated ATAC-seq and RNAseq). It was found that gene expression in classical and nonclassical osteoblasts is not regulated in the same way. In classical osteoblasts, Dlx family factors seem to play an important role, while Hox family factors are involved in the regulation of spinal ossification by nonclassical osteoblasts. In the second part of the study, the authors focus on the promoter structure of entpd5a. Through the identification of enhancers, they reveal complex modes of regulation of the gene. The authors suggest candidate transcription factors that likely act on the identified enhancer elements. All the results taken together provide comprehensive new insights into the process of bone development, and point to spatio-temporally regulated promoter/enhancer interactions taking place at the entpd5a locus.

Strengths:

The authors have succeeded in justifying a sound and consistent buildup of their experiments, and meaningfully integrating the results into the design of each of their follow-up experiments. The data are solid, insightfully presented, and the conclusion valid. This makes this manuscript of great value and interest to those studying (fundamental) skeletal biology.

Weaknesses:

The study is solidly constructed, the manuscript is clearly written and the discussion is meaningful - I see no real weaknesses.

Reviewer #4 (Public review):

Summary:

The manuscript by Graça et al. explores the role of MftG in the ethanol metabolism of mycobacteria. The authors hypothesise that MftG functions as a mycofactocin dehydrogenase, regenerating mycofactocin by shuttling electrons to the respiratory chain of mycobacteria. Although the study primarily uses M. smegmatis as a model microorganism, the findings have more general implications for understanding mycobacterial metabolism. Identifying the specific partner to which MftG transfers its electrons within the respiratory chain of mycobacteria would be an important next step, as pointed out by the authors.

Strengths

The authors have used a wide range of tools to support their hypothesis, including co-occurrence analyses, gene knockout and complementation experiments, as well as biochemical assays and transcriptomics studies.<br /> An interesting observation that the mftG deletion mutant grown on ethanol as the sole carbon source exhibited a growth defect resembling a starvation phenotype.<br /> MftG was shown to catalyse the electron transfer from mycofactocinol to components of the respiratory chain, highlighting the flexibility and complexity of mycobacterial redox metabolism.

The authors have taken on the majority of recommendations by the reviewers and made changes in the manuscript accordingly. I don't have any further suggestions.

Reviewer #3 (Public review):

Summary:

This is a valuable study providing solid evidence that the putative non-canonical initiation factor eIF2A has little or no role in the translation of any expressed mRNAs in cultured human (primarily HeLa) cells. Previous studies have implicated eIF2A in GTP-independent recruitment of initiator tRNA to the small (40S) ribosomal subunit, a function analogous to canonical initiation factor eIF2, and in supporting initiation on mRNAs that do not require scanning to select the AUG codon or that contain near-cognate start codons, especially upstream ORFs with non-AUG start codons, and may use the cognate elongator tRNA for initiation. Moreover, the detected functions for eIF2A were limited to, or enhanced by, stress conditions where canonical eIF2 is phosphorylated and inactivated, suggesting that eIF2A provides a back-up function for eIF2 in such stress conditions. CRISPR gene editing was used to construct two different knock-out cell lines that were compared to the parental cell line in a large battery of assays for bulk or gene-specific translation in both unstressed conditions and when cells were treated with inhibitors that induce eIF2 phosphorylation. None of these assays identified any effects of eIF2A KO on translation in unstressed or stressed cells, indicating little or no role for eIF2A as a back-up to eIF2 and in translation initiation at near-cognate start codons, in these cultured cells.

The study is very thorough and generally well executed, examining bulk translation by puromycin labeling and polysome analysis and translational efficiencies of all expressed mRNAs by ribosome profiling, with extensive utilization of reporters equipped with the 5'UTRs of many different native transcripts to follow up on the limited number of genes whose transcripts showed significant differences in translational efficiencies (TEs) in the profiling experiments. They also looked for differences in translation of uORFs in the profiling data and examined reporters of uORF-containing mRNAs known to be translationally regulated by their uORFs in response to stress, going so far as to monitor peptide production from a uORF itself. The high precision and reproducibility of the replicate measurements instil strong confidence that the myriad of negative results they obtained reflects the lack of eIF2A function in these cells rather than data that would be too noisy to detect small effects on the eIF2A mutations. They also tested and found no evidence for a recent claim that eIF2A localizes to the cytoplasm in stress and exerts a global inhibition of translation. Given the numerous papers that have been published reporting functions of eIF2A in specific and general translational control, this study is important in providing abundant, high-quality data to the contrary, at least in these cultured cells.

Strengths:

The paper employed two CRISPR knock-out cell lines and subjected them to a combination of high-quality ribosome profiling experiments, interrogating both main coding sequences and uORFs throughout the translatome, which was complemented by extensive reporter analysis, and cell imaging in cells both unstressed and subjected to conditions of eIF2 phosphorylation, all in an effort to test previous conclusions about eIF2A functioning as an alternative to eIF2.

Weaknesses:

There is some question about whether their induction of eIF2 phosphorylation using tunicamycin was extensive enough to state forcefully that eIF2A has little or no role in the translatome when eIF2 function is strongly impaired. Also, similar conclusions regarding the minimal role of eIF2A were reached previously for a different human cell line from a study that also enlisted ribosome profiling under conditions of extensive eIF2 phosphorylation; although that study lacked the extensive use of reporters to confirm or refute the identification by ribosome profiling of a small group of mRNAs regulated by eIF2A during stress.

Reviewer #3 (Public review):

Summary:

Mitochondrial injury activates eiF2α kinases-PERK, GCN2, HRI and PKR-which collectively regulate the Integrated Stress Response (ISR) to preserve mitochondrial function and integrity. Previous work has demonstrated that stress-induced and pharmacologic stress-independent ISR activation promotes adaptive mitochondrial elongation via the PERK and GCN2 kinases, respectively. Here, the authors demonstrate that pharmacologic ISR inducers of HRI and GCN2 enhance mitochondrial elongation and suppress mitochondrial fragmentation in two disease models, illustrating the therapeutic potential of pharmacologic ISR activators. Specifically, the authors first used an innovative ISR translational reporter to screen for nucleoside mimetic compounds that induce ISR signaling, and identified two compounds, 0357 and 3610, that preferentially activate HRI. Using a mitochondrial-targeted GFP MEF cell line, the authors next determined that these compounds (as well as the GCN2 activator, halofuginone) enhance mitochondrial elongation in an ISR-dependent manner. Moreover, pretreatment of MEFs with these ISR kinase activators suppressed pathological mitochondrial fragmentation caused by a calcium ionophore. Finally, pharmacologic HRI and GCN2 activation was found to preserve mitochondrial morphology in human fibroblasts expressing a pathologic variant in MFN2, a defect that leads to mitochondrial fragmentation and is a cause of Charcot Marie Tooth Type 2A disease.

Strengths:

This well-written manuscript has several notable strengths, including the demonstration of the potential therapeutic benefit of ISR modulation. New chemical entities with which to further interrogate this stress response pathway are also reported. In addition, the authors used an elegant screen to isolate compounds that selectively activate the ISR and identify which of the four kinases was responsible for activation. Special attention was also paid to a thorough evaluation of the effect of their compounds on other stress response pathways (i.e. the UPR, and heat and oxidative stress responses), thereby minimizing the potential for off-target effects. The implementation of automated image analysis rather than manual scoring to quantify mitochondrial elongation is not only practical but also adds to the scientific rigor, as does the complementary use of both the calcium ionophore and MFN2 models to enhance confidence and the broad therapeutic potential for pharmacology ISR manipulation.

Weaknesses:

The only minor concerns are with regard to effects on cell health and the timing of pharmacological administration.

Comments on revisions:

In this revised manuscript the authors demonstrate that pharmacological activation of the eiF2α kinases, HRI and GCN2, induce adaptive mitochondrial elongation and suppress mitochondrial fragmentation in two disease models, illustrating the translational potential of pharmacological ISR modulation.

In revising their manuscript the authors adequately addressed the concerns. In response to comments about the potential toxicity of their compounds, 0357 and 3610, the authors furnish evidence that neither compound significantly reduced viability of HEK293 cells (Figure S1G). Understandably, the authors focused the present work on the acute effects of their compounds. Several other attributes are noteworthy: First, that injury attributable to chronic ISR activation in cell culture may ultimately be circumvented by altering the in vivo pharmacodynamic and pharmacodynamic properties of the compounds, thereby preserving the translation potential for these (and related) compounds. Second, the authors also reasonably explain that the rapidity of ionomycin-induced injury, necessitating that the inducers are administered prior to treatment. Their assessment of the effects of the compounds on mitochondrial fragmentation in MFN2 mutant fibroblasts-in combination with the preserved viability of HEK293 cells-is sufficient to demonstrate the practical pharmacological potential for these (or related) agents.

Reviewer #3 (Public review):

Summary:

This study characterizes classical and nonclassical osteoblasts as both types were analyzed independently (integrated ATAC-seq and RNAseq). It was found that gene expression in classical and nonclassical osteoblasts is not regulated in the same way. In classical osteoblasts Dlx family factors seem to play an important role, while Hox family factors are involved in the regulation of spinal ossification by nonclassical osteoblasts. In the second part of the study, the authors focus on the promoter structure of entpd5a. Through the identification of enhancers they reveal complex modes of regulation of the gene. The authors suggest candidate transcription factors that likely act on the identified enhancer elements. All the results taken together provide comprehensive new insights into the process of bone development, and point to spatio-temporally regulated promoter/enhancer interactions taking place at the entpd5a locus.

Strengths:

The authors have succeeded in justifying a sound and consistent buildup of their experiments, and meaningfully integrate the results into the design of each of their follow-up experiments. The data are solid, insightfully presented, and the conclusion valid. This makes this manuscript of great value and interest to those studying (fundamental) skeletal biology.

Weaknesses:

The study is solidly constructed, the manuscript is clearly written and the discussion is meaningful - I see no real weaknesses.

Reviewer #3 (Public review):

Summary:

The relationships of proteins and lipids: it's complicated. This paper illustrates how cardiolipins can stabilize membrane protein subunits - and not surprisingly, positively charged residues play an important role here. But more and stronger binding of such structural lipids does not necessarily translate to stabilization of oligomeric states, since many proteins have alternative binding sites for lipids which may be intra- rather than intermolecular. Mutations which abolish primary binding sites can cause redistribution to (weaker) secondary sites which nevertheless stabilize interactions between subunits. This may be at first sight counterintuitive but actually matches expectations from structural data and MD modelling. An analogous cardiolipin binding site between subunits is found in E.coli tetrameric GlpG, with cardiolipin (thermally) stabilizing the protein against aggregation.

Strengths:

The use of the artificial scaffold allows testing of hypothesis about the different roles of cardiolipin binding. It reveals effects which are at first sight counterintuitive and are explained by the existence of a weaker, secondary binding site which unlike the primary one allows easy lipid-mediated interaction between two subunits of the protein. Introducing different mutations either changes the balance between primary and secondary binding sites or introduced a kink in a helix - thus affecting subunit interactions which are experimentally verified by native mass spectrometry.

Weaknesses:

The artificial scaffold is not necessarily reflecting the conformational dynamics and local flexibility of real, functional membrane proteins. The example of GlpG, while also showing interesting cardiolipin dependency, illustrates the case of a binding site across helices further but does not add much to the main story. It should be evident that structural lipids can be stabilizing in more than one way depending on how they bind, leading to different and possibly opposite functional outcomes.

Reviewer #3 (Public review):

Summary:

The authors investigated the role of secretory leukocyte protease inhibitors (SLPI) in developing Lyme disease in mice infected with Borrelia burgdorferi. Using a combination of histological, gene expression, and flow cytometry analyses, they demonstrated significantly higher bacterial burden and elevated neutrophil and macrophage infiltration in SLPI-deficient mouse ankle joints. Furthermore, they also showed direct interaction of SLPI with B. burgdorferi, which likely depletes the local environment of SLPI and causes excessive protease activity. These results overall suggest ankle tissue inflammation in B. burgdorferi-infected mice is driven by unchecked protease activity.

Strengths:

Utilizing a comprehensive suite of techniques, this is the first study showing the importance of anti-protease-protease balance in the development of periarticular joint inflammation in Lyme disease.

Weaknesses:

Due to the limited sample availability, the authors investigated the serum level of SLPI in both in Lyme arthritis patients and patients with earlier disease manifestations.

Reviewer #3 (Public review):

Summary:

In this report, De Franceschi et al. purify components of the Cdv machinery in archaeon M. sedula and probe their interactions with membrane and with one-another in vitro using two main assays - liposome flotation and fluorescent imaging of encapsulated proteins. This has the potential to add to the field by showing how the order of protein recruitment seen in cells is related to the differential capacity of individual proteins to bind membranes when alone or when combined.

Strengths:

Using the floatation assay, they demonstrate that CdvA and CdvB bind liposomes when combined. While CdvB1 also binds liposomes under these conditions, in the floatation assay, CdvB2 lacking its C-terminus is not efficiently recruited to membranes unless CdvAB or CdvB1 are present. The authors then employ a clever liposome assay that generates chained spherical liposomes connected by thin membrane necks, which allows them to accurately control the buffer composition inside and outside of the liposome. With this, they show that all four proteins accumulate in necks of dumbbell-shaped liposomes that mimic the shape of constricting necks in cell division. Taken altogether, these data lead them to propose that Cdv proteins are sequentially recruited to the membrane as has also been suggested by in vivo studies of ESCRT-III dependent cell division in crenarchaea.

Weaknesses:

These experiments provide a good starting point for the in vitro study the interaction of Cdv system components with the membrane and their consecutive recruitment. However, several experimental controls are missing that complicate their ability to draw strong conclusions. Moreover, some results are inconsistent across the two main assays which make the findings difficult to interpret.

(1) Missing controls.

Various protein mixtures are assessed for their membrane-binding properties in different ways. However, it is difficult to interpret the effect of any specific protein combination, when the same experiment is not presented in a way that includes separate tests for all individual components. In this sense, the paper lacks important controls.

For example, Fig 1C is missing the CdvB-only control. The authors remark that CdvB did not polymerise (data not shown) but do not comment on whether it binds membrane in their assays. In the introduction, Samson et al., 2011 is cited as a reference to show that CdvB does not bind membrane. However, here the authors are working with protein from a different organism in a different buffer, using a different membrane composition and a different assay. Given that so many variables are changing, it would be good to present how M. sedula CdvB behaves under these conditions.

Similarly, there is no data showing how CdvB alone or CdvA alone behave in the dumbbell liposome assay. Without these controls, it's impossible to say whether CdvA recruits CdvB or the other way around.

The manuscript would be much stronger if such data could be added.

(2) Some of the discrepancies in the data generated using different assays are not discussed.

The authors show that CdvB2∆C binds membrane and localizes to membrane necks in the dumbbell liposome assay, but no membrane binding is detected in the flotation assay. The discrepancy between these results further highlights the need for CdvB-only and CdvA-only controls.

(3) Validation of the liposome assay.

The experimental setup to create dumbbell-shaped liposomes seems great and is a clever novel approach pioneered by the team. Not only can the authors manipulate liposome shape, they also state that this allows them to accurately control the species present on the inside and outside of the liposome. Interpreting the results of the liposome assay, however, depends on the geometry being correct. To make this clearer, it would seem important to include controls to prove that all the protein imaged at membrane necks lie on the inside of liposomes. In the images in SFig3 there appears to be protein outside of the liposome. It would also be helpful to present data to show test whether the necks are open, as suggested in the paper, by using FRAP or some other related technique.

(4) Quantification of results from the liposome assay.

The paper would be strengthened by the inclusion of more quantitative data relating to the liposome assay. Firstly, only a single field of view is shown for each condition. Because of this, the reader cannot know whether this is a representative image, or an outlier? Can the authors do some quantification of the data to demonstrate this? The line scan profiles in the supplemental figures would be an example of this, but again in these Figures only a single image is analyzed.

We would recommend that the authors present quantitative data to show the extent of co-localization at the necks in each case. They also need a metric to report instances in which protein is not seen at the neck, e.g. CdvB2 but not CdvB1 in Fig2I, which rules out a simple curvature preference for CdvB2 as stated in line 182.

Secondly, the authors state that they see CdvB2∆C recruited to the membrane by CdvB1 (lines 184-187, Fig 2I). However, this simple conclusion is not borne out in the data. Inspecting the CdvB2∆C panels of Fig 2I, Fig3C, and Fig3D, CdvB2∆C signal can be seen at positions which don't colocalize with other proteins. The authors also observe CdvB2∆C localizing to membrane necks by itself (Fig 2E). Therefore, while CdvB1 and CdvB2∆C colocalize in the flotation assay, there is no strong evidence for CdvB2∆C recruitment by CdvB1 in dumbbells. This is further underscored by the observation that in the presented data, all Cdv proteins always appear to localize at dumbbell necks, irrespective of what other components are present inside the liposome. Although one nice control is presented (ZipA), this suggests that more work is required to be sure that the proteins are behaving properly in this assay. For example, if membrane binding surfaces of Cdv proteins are mutated, does this lead to the accumulation of proteins in the bulk of the liposome as expected?

(5) Rings.

The authors should comment on why they never observe large Cdv rings in their experiments. In crenarchaeal cell division, CdvA and CdvB have been observed to form large rings in the middle of the 1 micron cell, before constriction. Only in the later stages of division are the ESCRTs localized to the constricting neck, at a time when CdvA is no longer present in the ring. Therefore, if the in vitro assay used by the authors really recapitulated the biology, one would expect to see large CdvAB rings in Figs 1EF. This is ignored in the model. In the proposed model of ring assembly (line 252), CdvAB ring formation is mentioned, but authors do not discuss the fact that they do not observe CdvAB rings - only foci at membrane necks. The discussion section would benefit from the authors commenting on this.

(6) Stoichiometry

It is not clear why 100% of the visible CdvA and 100% of the the visible CdvB are shifted to the lipid fraction in 1C. Perhaps this is a matter of quantification. Can the authors comment on the stoichiometry here?

(7) Significance of quantification of MBP-tagged filaments.

Authors use tagging and removal of MBP as a convenient, controllable system to trigger polymerisation of various Cdv proteins. However, it is unclear what is the value and significance of reporting the width and length of the short linear filaments that are formed by the MBP-tagged proteins. Presumably they are artefactual assemblies generated by the presence of the tag? Similar Figure 2C doesn't seem a useful addition to the paper.

DOI: 10.1038/s41419-025-07335-3

Resource: (IMSR Cat# JAX_007850,RRID:IMSR_JAX:007850)

Curator: @dhovakimyan1

SciCrunch record: RRID:IMSR_JAX:007850

What is this?

Reviewer #3 (Public review):

Summary:<br /> In this paper, Xu, Dantu and coworkers report a protocol for analyzing coevolutionary and dynamical information to identify a subset of communities that capture functionally relevant sites in beta-lactamases.

Strengths:<br /> The combination of coevolutionary information and metrics from MD simulations is interesting for capturing functionally relevant sites, which can have implications in the fields of drug discovery but also in protein design.

Weaknesses:<br /> The combination of coevolutionary information and metrics from MD simulations is not new as other protocols have been proposed along the years (the current version of the paper neglects some of them, see below), and there are a few parameters of the protocol that, in my opinion, should be better analyzed and discussed.

(1) As mentioned, the introduction of the paper lacks some important publications in the field of using graph theory to represent important interaction networks extracted from MD simulations (DOI: 10.1002/pro.4911), and also combining MD data with MSA to identify functionally relevant sites for enzyme design (doi: 10.1021/acscatal.4c04587, 10.1093/protein/gzae005).<br /> (2) The matrix used to apply graph theory (J_ij) is built from summing the scaled coevolution and degree of correlation values. The alpha and beta weights are defined, and the authors mention that alpha is set to 0.5, thus beta as well to fulfil with the alpha + beta = 1. Why a value of 0.5 has been selected? How this affects the overall results and conclusions extracted? The finding that many catalytically relevant residues are identified in the communities is not surprising given that such sites usually present a high conservation score.<br /> (3) Another important point that needs further explanation is the selection of the relevant descriptor of protein dynamics. In this study two different strategies have been used (one more global the other more local), but more details should be provided regarding their choice. What is the best strategy according to the authors? Why not using the same strategy for both related systems? The obtained results using one methodology or the other will have a large impact on the dynamical score. Another related point is: what is the impact of the MD simulation length, how the MSA is generated and number of sequences used for MSA construction?

Reviewer #3 (Public review):

Summary:

Fibroblast growth factor receptor 2 (FGFR2) is a receptor tyrosine kinase that can be amplified in gastric cancer and serves as a potential therapeutic target for this patient population. However, targeting FGFR2 has shown limited efficacy. Thus, this study seeks to identify additional molecules that can be effectively targeted in FGFR2 amplified gastric cancer, with a focus on Src homology region 2-containing protein tyrosine phosphatase 2 (SHP2). The authors first demonstrate that 6% of gastric cancer patients in a cohort of human patient samples exhibit FGFR2 amplification. Furthermore, they demonstrate that FGFR2 mRNA expression is positively correlated with PTPN11 gene expression (which is the gene that encodes the SHP2 protein). Using human gastric cancer cell lines with amplified FGFR2, the authors then test the effects of combining the FGFR inhibitor AZD4547 with the SHP2 inhibitor SHP099 on tumor cell death and signaling molecules. They demonstrate that combining the two inhibitors is more effective at tumor cell killing and reducing activation of downstream signaling pathways than either inhibitor alone. In further studies, the authors obtained gastric cancer cells with FGFR2 amplification from a patient that was treated with FGFR2 inhibitor. While this patient initially showed a partial response, the patient ultimately progressed, demonstrating resistance to FGFR2 inhibition. Following isolation of tumor cells from the patient's ascites, the authors demonstrate that these cells are sensitive to the combination treatment of AZD4547 and SHP099. Further studies were performed using a xenograft model using athymic nude mice in which the combination of SHP099 and AZD4547 were found to reduce tumor growth more significantly than either treatment alone. Finally, the authors demonstrate using an in vitro culture model that this combination treatment enhances T cell mediated cytotoxicity. The authors conclude that targeting FGFR2 and SHP2 represents a potential combination strategy in gastric patients with FGFR2 amplification.

Strengths:

The authors demonstrate that FGFR2 amplification positively correlates with PTPN11 in human gastric cancer samples, providing rationale for combination therapies. Furthermore, convincing data are provided demonstrating that targeting both FGFR and SHP2 is more effective than targeting either pathway alone using in vitro and in vivo models. The use of cells derived from a gastric cancer patient that progressed following treatment with an FGFR inhibitor is also a strength. The findings from this study support the conclusion that SHP2 inhibitors enhance the efficacy of FGFR-targeted therapies in cancer patients. This study also suggests that targeting SHP2 may also be an effective strategy for targeting cancers that are resistant to FGFR-targeted therapies.

Weaknesses:

The main caveat with these studies is the lack of an immune competent model with which to test the finding that this combination therapy enhances T cell cytotoxicity in vivo. Discussing this limitation within the context of these findings and future directions for this work, particularly since the combination therapy appears to work quite well without the presence of T cells in the environment, would be beneficial.

Reviewer #3 (Public review):

Xiaoyu Wu and colleagues examined the potential role in sleep of a Drosophila ribosomal RNA methyltransferase, mettl5. Based on sleep defects reported in CRISPR generated mutants, the authors performed both RNA-seq and Ribo-seq analyses of head tissue from mutants and compared to control animals collected at the same time point. While these data were subjected to a thorough analysis, it was difficult to understand the relative direction of differential expression between the two genotypes. In any case, a major conclusion was that the mutant showed altered expression of circadian clock genes, and that the altered expression of the period gene in particular accounted for the sleep defect reported in the mettl5 mutant. As noted above, a strength of this work is its relevance to a human developmental disorder as well as the transcriptomic and ribosomal profiling of the mutant. However, there are numerous weaknesses in the manuscript, most of which stem from misinterpretation of the findings, some methodological approaches, and also a lack of method detail provided. The authors seemed to have missed a major phenotype associated with the mettl5 mutant, which is that it caused a significant increase in period length, which was apparent even in a light: dark cycle. Thus the effect of the mutant on clock gene expression more likely contributed to this phenotype than any associated with changes in sleep behavior.

Reviewer #3 (Public review):

Summary:

The authors describe important new biochemical elements in the synthesis of a class of critical developmental signaling molecules, BMP4. They also present a highly detailed description of developmental anomalies in mice bearing known human mutations at these specific elements.

Strengths:

Exceptionally detailed descriptions of pathologies occurring in mutant mice. Novel findings regarding the interaction of propeptide phosphorylation and convertase cleavage, both of which will move the field forward. Provocative hypothesis regarding furin access to cleavage sites, supported by Alphafold predictions.

Weaknesses:

Figure 6A presents two testable models for pre-release access of furin to cleavage sites since physical separation of enzyme from substrate only occurs in one model; could immunocytochemistry resolve?

Reviewer #3 (Public review):

Summary:

In this report, the authors tested how manipulating the contiguous set of stimuli on the screen that should be used to guide behavior - that is, the scope of visual spatial attention - impacts the magnitude and profile of well-established attentional enhancements in visual retinotopic cortex. During fMRI scanning, participants attended to a cued section of the screen for blocks of trials and performed a letter vs digit discrimination task at each attended location (and judged whether the majority of characters were letters/digits). Importantly, the visual stimulus was identical across attention conditions, so any observed response modulations are due to top-down task demands rather than visual input. The authors employ population receptive field (pRF) models, which are used to sort voxel activation with respect to the location and scope of spatial attention and fit a Gaussian-like function to the profile of attentional enhancement from each region and condition. The authors find that attending to a broader region of space expands the profile of attentional enhancement across the cortex (with a larger effect in higher visual areas), but does not strongly impact the magnitude of this enhancement, such that each attended stimulus is enhanced to a similar degree. Interestingly, these modulations, overall, mimic changes in response properties caused by changes to the stimulus itself (increase in contrast matching the attended location in the primary experiment). The finding that attentional enhancement primarily broadens, but does not substantially weaken in most regions, is an important addition to our understanding of the impact of distributed attention on neural responses, and will provide meaningful constraints to neural models of attentional enhancement.

Strengths:

- Well-designed manipulations (changing location and scope of spatial attention), and careful retinotopic/pRF mapping, allow for a robust assay of the spatial profile of attentional enhancement, which has not been carefully measured in previous studies<br /> - Results are overall clear, especially concerning width of the spatial region of attentional enhancement, and lack of clear and consistent evidence for reduction in the amplitude of enhancement profile<br /> - Model-fitting to characterize spatial scope of enhancement improves interpretability of findings

Weaknesses:

- Task difficulty seems to vary as a function of spatial scope of attention, with varying ratios of letters/digits across spatial scope conditions, which may complicate interpretations of neural modulation results<br /> - Some aspects of analysis/data sorting are unclear (e.g., how are voxels selected for analyses?)<br /> - While the focus of this report is on modulations of visual cortex responses due to attention, the lack of inclusion of results from other retinotopic areas (e.g. V3AB, hV4, IPS regions like IPS0/1) is a weakness<br /> - Additional analyses comparing model fits across amounts of data analyzed suggest the model fitting procedure is biased, with some parameters (e.g., FWHM, error, gain) scaling with noise.

Reviewer #3 (Public review):

Summary:

This manuscript describes the characterization of mycobacterial cytoskeleton protein Wag31, examining its role in orchestrating protein-lipid and protein-protein interactions essential for mycobacterial survival. The most significant finding is that Wag31, which directs polar elongation and maintains the intracellular membrane domain, was revealed to have membrane tethering capabilities.

Strengths:

The authors provided a detailed analysis of Wag31 domain architecture, revealing distinct functional roles: the N-terminal domain facilitates lipid binding and membrane tethering, while the C-terminal domain mediates protein-protein interactions. Overall, this study offers a robust and new understanding of Wag31 function.

Weaknesses:

The following major concerns should be addressed.

• Authors use 10-N-Nonyl-acridine orange (NAO) as a marker for cardiolipin localization. However, given that NAO is known to bind to various anionic phospholipids, how do the authors know that what they are seeing is specifically visualizing cardiolipin and not a different anionic phospholipid? For example, phosphatidylinositol is another abundant anionic phospholipid in mycobacterial plasma membrane.

• Authors' data show that the N-terminal region of Wag31 is important for membrane tethering. The authors' data also show that the N-terminal region is important for sustaining mycobacterial morphology. However, the authors' statement in Line 256 "These results highlight the importance of tethering for sustaining mycobacterial morphology and survival" requires additional proof. It remains possible that the N-terminal region has another unknown activity, and this yet-unknown activity rather than the membrane tethering activity drives the morphological maintenance. Similarly, the N-terminal region is important for lipid homeostasis, but the statement in Line 270, "the maintenance of lipid homeostasis by Wag31 is a consequence of its tethering activity" requires additional proof. The authors should tone down these overstatements, or provide additional data to support their claims.

• Authors suggest that Wag31 acts as a scaffold for the IMD (Fig. 8). However, Meniche et. al. has shown that MurG as well as GlfT2, two well-characterized IMD proteins, do not colocalize with Wag31 (DivIVA) (https://doi.org/10.1073/pnas.1402158111). IMD proteins are always slightly subpolar while Wag31 is located to the tip of the cell. Therefore, the authors' biochemical data cannot be easily reconciled with microscopic observations in the literature. This raises a question regarding the validity of protein-protein interaction shown in Figure 7. Since this pull-down assay was conducted by mixing E. coli lysate expressing Wag31 and Msm lysate expression Wag31 interactors like MurG, it is possible that the interactions are not direct. Authors should interpret their data more cautiously. If authors cannot provide additional data and sufficient justifications, they should avoid proposing a confusing model like Figure 8 that contradicts published observations.

Reviewer #3 (Public review):

Summary:

In their manuscript titled "Multiplexed Assays of Human Disease‐relevant Mutations Reveal UTR Dinucleotide Composition as a Major Determinant of RNA Stability" the authors aim to investigate the effect of sequence variations in 3'UTR and 5'UTRs on the stability of mRNAs in two different human cell lines.

To do so, the authors use a massively parallel reporter assay (MPRA). They transfect cells with a set of mRNA reporters that contain sequence variants in their 3' or 5' UTRs, which were previously reported in human diseases. They follow their clearance from cells over time relative to the matching non-variant sequence. To analyze their results, they define a set of factors (RBP and miRNA binding sites, sequence features, secondary structure etc.) and test their association with differences in mRNA stability. For features with a significant association, they use clustering to select a subset of factors for LASSO regression and identify factors that affect mRNA stability.<br /> They conclude that the TA dinucleotide content of UTRs is the strongest destabilizing sequence feature. Within that context, elevated GC content and protein binding can protect susceptible mRNAs from degradation. They also show that TA dinucleotide content of UTRs affects native mRNA stability and that it is associated with specific functional groups. Finally, they link disease associated sequence variants with differences in mRNA stability of reporters.

Strengths:

(1) This work introduces a different MPRA approach to analyze the effect of genetic variants. While previous works in tissue culture use DNA transfections that require normalization for transcription efficiency, here the mRNA is directly introduced into cells at fixed amounts, allowing a more direct view of the mRNA regulation.

(2) The authors also introduce a unique analysis approach, which takes into account multiple factors that might affect mRNA stability. This approach allows them to identify general sequence features that affect mRNA stability beyond specific genetic variants, and reach important insights on mRNA stability regulation. Indeed, while the conclusions to genetic variants identified in this work are interesting, the main strength of the work involves general effect of sequence features rather than specific variants.

(3) The authors provide adequate support for their claims and validate their analysis using both their reporter data and native genes. For the main feature identified, TA di-nucleotides, they perform follow-up experiments with modified reporters that further strengthen their claims, and also validate the effect on native cellular transcripts (beyond reporters), demonstrating its validity also within native scenarios.

(4) The work provides a broad analysis of mRNA stability, across two mRNA regulatory segments (3'UTR and 5'UTR) and is performed in two separate cell-types. Comparison between two different cell-types is adequate, and the results demonstrate, as expected, the dependence of mRNA stability on the cellular context. Analysis of 3'UTR and 5'UTR regulatory effects also shows interesting differences and similarities between these two regulatory regions.

Weaknesses:

In their revised manuscripts, the authors successfully address many of the weaknesses raised in the original review, including the effect of possible confounding effects, and additional methodology details. Notably, two of the issues raised in the original report, have only been partially addressed in the revision.

(1) The analysis and regression models built in this work are not thoroughly investigated relative to native genes within cells.<br /> While using MPRAs indeed allows to isolate regulatory effects that are less influential in-vivo, the resulting effects still provide some regulatory function in-vivo. The goal of such an analysis would not be to demonstrate the predictive power of the models, or to make any claims regarding using these models to fully explain or predict the stability of native transcripts. Clearly, additional more prominent factors could function in controlling endogenous RNA stability.<br /> Instead, the goal of such an investigation is to simply assess the fraction of in-vivo regulation that the factors identified in this work contribute in native contexts, and what is the relative contribution of the phenomena captured by the well-controlled MPRA study.<br /> This reviewer believes that even if the effects identified by the current MPRA study only contribute a small fraction of in-vivo variation, an analysis that aim to estimate what this fraction is, will be very relevant to this study for several reasons. First, in order to appreciate the results of this study within their in-vivo context. Second, in light of the questions raised as motivation for this study, and particularly the need to identify the effect of disease-associated 3'UTR variants, which clearly have an in-vivo effect.

(2) Methodology validation can be performed with simulated data (generated in-silico by the authors) to provide an independent support for the ability of the current methodology to correctly extract regulatory effects from the data.

Reviewer #3 (Public review):

Summary:

Li et al. describe an audiovisual temporal recalibration experiment in which participants perform baseline sessions of ternary order judgments about audiovisual stimulus pairs with various stimulus-onset asynchronies (SOAs). These are followed by adaptation at several adapting SOAs (each on a different day), followed by post-adaptation sessions to assess changes in psychometric functions. The key novelty is the formal specification and application/fit of a causal-inference model for the perception of relative timing, providing simulated predictions for the complete set of psychometric functions both pre and post adaptation.

Strengths:

(1) Formal models are preferable to vague theoretical statements about a process, and prior to this work, certain accounts of temporal recalibration (specifically those that do not rely on a population code) had only qualitative theoretical statements to explain how/why the magnitude of recalibration changes non-linearly with the stimulus-onset asynchrony of the adaptor.<br /> (2) The experiment is appropriate, the methods are well described, and the average model prediction is a good match to the average data (Figure 4). Conclusions are supported by the data and modelling.<br /> (3) The work should be impactful. There seems a good chance that this will become the go-to modelling framework for those exploring non population-code accounts of temporal recalibration (or comparing them with population-code accounts).<br /> (4) Key issues for the generality of the model, such as recalibration asymmetries reported by other authors that are inconsistent with those reported here, are thoughtfully discussed.

Weaknesses:

(1) Models are not compared using a gold-standard measure such as leave-one-out cross validation. However, this is legitimate given lengthy model fitting times, and a sensible approximation is presented.<br /> (2) The model misses in a systematic way for the psychometric functions of some participants/conditions. In addition to misses relating to occasional failures to estimate the magnitude of recalibration, some of the misses are because all functions are only permitted to shift in central tendency (whereas some participants show changes better characterized at one or both decision criteria). Given the fact that the modelling in general embraces individual differences, it might have been worth allowing different kinds of change for different participants. However, this is not really critical for the central concern (changes in the magnitude of recalibration for different adaptors) and there is a limit to how much can be done along these lines without making the model too flexible to test.<br /> (3) As a minor point, the model relies on simulation, which may limit its take-up/application by others in the field (although open access code will be provided).

Reviewer #3 (Public review):

Summary:

In this manuscript, Bimbard and colleagues describe a new implant apparatus called "Apollo Implant", which should facilitate recording in freely moving rodents (both mice and rats) using Neuropixels probes. The authors collected data from both mice and rats, they used 3 different versions of Neuropixels, multiple labs have already adopted this method, which is impressive. They openly share their CAD designs and surgery protocol to further facilitate the adaptation of their method.

Strengths:

Overall, the "Apollo Implant" is easy to use and adapt, as it has been used in other laboratories successfully and custom modifications are already available. The device is reproducible using common 3D printing services and can be easily modified thanks to its CAD design (the video explaining this is extremely helpful). The weight and price are amazing compared to other systems for rigid silicon probes allowing a wide range of use of the "Apollo Implant".

Weaknesses:

The "Apollo Implant" can only handle Neuropixels probes. It cannot hold other widely used and commercially available silicon probes. Certain angles and distances may be better served by 2 implants.