Reviewer #1 (Public Review):

Summary:

The manuscript reports that expression of the E. coli operon topAI/yjhQ/yjhP is controlled by the translation status of a small open reading frame, that authors have discovered and named toiL, located in the leader region of the operon. The authors propose the following model for topAI activation: Under normal conditions, toiL is translated but topAI is not expressed because of Rho-dependent transcription termination within the topAI ORF and because its ribosome binding site and start codon are trapped in an mRNA hairpin. Ribosome stalling at various codons of the toiL ORF, caused by the presence of some ribosome-targeting antibiotics, triggers an mRNA conformational switch which allows translation of topAI and, in addition, activation of the operon's transcription because the presence of translating ribosomes at the topAI ORF blocks Rho from terminating transcription. Even though the model is appealing and several of the experimental data support some aspects of it, several inconsistencies remain to be solved. In addition, even though TopAI was shown to be an inhibitor of topoisomerase I (Yamaguchi & Inouye, 2015, NAR 43:10387), the authors suggest, without offering any experimental support, that, because ribosome-targeting antibiotics act as inducers, expression of the topAI/yjhQ/yjhP operon may confer resistance to these drugs.

Strengths:

- There is good experimental support of the transcriptional repression/activation switch aspect of the model, derived from well-designed transcriptional reporters and ChIP-qPCR approaches.

- There is a clever use of the topAI-lacZ reporter to find the 23S rRNA mutants where expression topAI was upregulated. This eventually led the authors to identify that translation events occurring at toiL are important to regulate the topAI/yjhQ/yjhP operon. This section can be strengthened if the authors suggest an explanation for how mutant ribosomes translating toiL increased topAI expression. Is there any published evidence that ribosomes with the identified mutations translate slowly (decreased fidelity does not necessarily mean slow translation, does it?)?

- Authors incorporate relevant links to the antibiotic-mediated expression regulation of bacterial resistance genes. Authors can also mention the tryptophan-mediated ribosome stalling at the tnaC leader ORF that activates the expression of tryptophan metabolism genes through blockage of Rho-mediated transcriptional attenuation.

Weaknesses:

The main weaknesses of the work are related to several experimental results that are not consistent with the model, or related to a lack of data that needs to be included to support the model.

The following are a few examples:

- It is surprising that authors do not mention that several published Ribo-seq data from E. coli cells show active translation of toiL (for example Li et al., 2014, Cell 157: 624). Therefore, it is hard to reconcile with the model that starts codon/Shine-Dalgarno mutations in the toiL-lux reporter have no effect on luciferase expression (Figure 2C, bar graphs of the no antibiotic control samples).

- The SHAPE reactivity data shown in Figure 5A are not consistent with the toiL ORF being translated. In addition, it is difficult to visualize the effect of tetracycline on mRNA conformation with the representation used in Figure 5B. It would be better to show SHAPE reactivity without/with Tet (as shown in panel A of the figure).

- The "increased coverage" of topAI/yjhP/yjhQ in the presence of tetracycline from the Ribo-seq data shown in Figure 6A can be due to activation of translation, transcription, or both. For readers to know which of these possibilities apply, authors need to provide RNA-seq data and show the profiles of the topAI/yjhQ/yjhP genes in control/Tet-treated cells.

- Similarly, to support the data of increased ribosomal footprints at the toiL start codon in the presence of Tet (Figure 6B), authors should show the profile of the toiL gene from control and Tet-treated cells.

- Representation of the mRNA structures in the model shown in Figure 5, does not help with visualizing 1) how ribosomes translate toiL since the ORF is trapped in double-stranded mRNA, and 2) how ribosome stalling on toiL would lead to the release of the initiation region of topAI to achieve expression activation.

- The authors speculate that, because ribosome-targeting antibiotics act as expression inducers [by the way, authors should mention and comment that, more than a decade ago, it had been reported that kanamycin (PMID: 12736533) and gentamycin (PMID: 19013277) are inducers of topAI and yjhQ], the genes of the topAI/yjhQ/yjhP operon may confer resistance to these antibiotics. Such a suggestion can be experimentally checked by simply testing whether strains lacking these genes have increased sensitivity to the antibiotic inducers.

Reviewer #1 (Public Review):

The question of whether eyespots mimic eyes has certainly been around for a very long time and led to a good deal of debate and contention. This isn't purely an issue of how eyespots work either, but more widely an example of the potential pitfalls of adopting 'just-so-stories' in biology before conducting the appropriate experiments. Recent years have seen a range of studies testing eye mimicry, often purporting to find evidence for or against it, and not always entirely objectively. Thus, the current study is very welcome, rigorously analysing the findings across a suite of papers based on evidence/effect sizes in a meta-analysis.

The work is very well conducted, robust, objective, and makes a range of valuable contributions and conclusions, with an extensive use of literature for the research. I have no issues with the analysis undertaken. The results and conclusions are compelling. It's probably fair to say that the topic needs more experiments to really reach firm conclusions but the authors do a good job of acknowledging this and highlighting where that future work would be best placed.

Reviewer #1 (Public Review):

Summary:

In this study, Bonnifet et al. profile the presence of L1 ORF1p in the mouse and human brain. They claim that ORF1p is expressed in the human and mouse brain at a steady state and that there is an age-dependent increase in expression. This is a timely report as two recent papers have extensively documented the presence of full-length L1 transcripts in the mouse and human brain (PMID: 38773348 & PMID: 37910626). Thus, the finding that L1 ORF1p is consistently expressed in the brain is not surprising, but important to document.

Strengths:

Several parts of this manuscript appear to be well done and include the necessary controls. In particular, the evidence for steady-state expression of ORF1p in the mouse brain appears robust.

Weaknesses:

Several parts of the manuscript appear to be more preliminary and need further experiments to validate their claims. In particular, the data suggesting expression of L1 ORF1p in the human brain and the data suggesting increased expression in the aged brain need further validation. Detailed comments:

(1) The expression of ORF1p in the human brain shown in Figure 1j is not convincing. Why are there two strong bands in the WB? How can the authors be sure that this signal represents ORF1p expression and not non-specific labelling? Additional validations and controls are needed to verify the specificity of this signal.

(2) The data shown in Figure 2g are not convincing. How can the authors be sure that this signal represents ORF1p expression and not non-specific labelling? Extensive additional validations and controls are needed to verify the specificity of this signal.

(3) The data showing a reduction in ORF1p expression in the aged mouse brain is confusing and maybe even misleading. Although there is an increase in the intensity of the ORF1p signal in ORF1p+ cells, the data clearly shows that fewer cells express ORF1p in the aged brain. If these changes indicate an overall loss or gain of ORF1p, expression in the aged brain is not resolved. Thus, conclusions should be more carefully phrased in this section. It is important to show the quantification of NeuN+ and NeuN- cells in young vs aged (not only the proportions as shown in Figure 3b) to determine if the difference in the number of ORF1p+ cells is due to loss of neurons or perhaps a sampling issue. More so, it would be essential to perform WB and/or proteomics experiments to complement the IHC data for the aged mouse samples.

(4) The transcriptomic data presented in Figure 4 and Figure 5 are not convincing. Quantification of transposon expression on short read sequencing has important limitations. Longer reads and complementary approaches are needed to study the expression of evolutionarily young L1s (see PMID: 38773348 & PMID: 37910626 for examples of the current state of the art). Given the read length and the unstranded sequencing approach, I would at least ask the authors to add genome browser tracks of the upregulated loci so that we can properly assess the clarity of the results. I would also suggest adding the mappability profile of the elements in question. In addition, since this manuscript focuses on ORF1p, it would be essential to document changes in protein levels (and not just transcripts) in the ageing human brain.

(5) More information is needed on RNAseq of microdissections of dopaminergic neurons from 'healthy' post-mortem samples of different ages. No further information on these samples is provided. I would suggest adding a table with the clinical information of these samples (especially age, sex, and cause of death). The authors should also discuss whether this experiment has sufficient power. The human ageing cohort seems very small to me.

(6) The findings in this manuscript apply to both human and mouse brains. However, the landscape of the evolutionarily young L1 subfamilies between these two species is very different and should be part of the discussion. For example, the regulatory sequences that drive L1 expression are quite different in human and mouse L1s. This should be discussed.

(7) On page 3 the authors write: "generally accepted that TE activation can be both, a cause and consequence of aging". This statement does not reflect the current state of the field. On the contrary, this is still an area of extensive investigation and many of the findings supporting this hypothesis need to be confirmed in independent studies. This statement should be revised to reflect this reality.

Reviewer #1 (Public review):

This study by Wu et al. provides valuable computational insights into PROTAC-related protein complexes, focusing on linker roles, protein-protein interaction stability, and lysine residue accessibility. The findings are significant for PROTAC development in cancer treatment, particularly breast and prostate cancers.

The authors' claims about the role of PROTAC linkers and protein-protein interaction stability are generally supported by their computational data. However, the conclusions regarding lysine accessibility could be strengthened with more in-depth analysis. The use of the term "protein functional dynamics" is not fully justified by the presented work, which focuses primarily on structural dynamics rather than functional aspects.

Strengths:

(1) Comprehensive computational analysis of PROTAC-related protein complexes.

(2) Focus on critical aspects: linker role, protein-protein interaction stability, and lysine accessibility.

Weaknesses:

(1) Limited examination of lysine accessibility despite its stated importance.

(2) Use of RMSD as the primary metric for conformational assessment, which may overlook important local structural changes.

Reviewer #1 (Public review):

Summary:

This work made a lot of efforts to explore the multifaceted roles of the inferior colliculus (IC) in auditory processing, extending beyond traditional sensory encoding. The authors recorded neuronal activitity from the IC at single unit level when monkeys were passively exposed or actively engaged in behavioral task. They concluded that 1）IC neurons showed sustained firing patterns related to sound duration, indicating their roles in temporal perception, 2) IC neuronal firing rates increased as sound sequences progress, reflecting modulation by behavioral context rather than reward anticipation, 3) IC neurons encode reward prediction error and their capability of adjusting responses based on reward predictability, 4) IC neural activity correlates with decision-making. In summary, this study tried to provide a new perspective on IC functions by exploring its roles in sensory prediction and reward processing, which are not traditionally associated with this structure.

Strengths:

The major strength of this work is that the authors performed electrophysiological recordings from the IC of behaving monkeys. Compared with the auditory cortex and thalamus, the IC in monkeys has not been adequately explored.

Weaknesses:

(1) The authors cited several papers focusing on dopaminergic inputs in the IC to suggest the involvement of this brain region in cognitive functions. However, all those cited work were done in rodents. Whether monkey's IC shares similar inputs is not clear.<br /> (2) The authors confused the two terms, novelty and deviation. According to their behavioral paradigm, deviation rather than novelty should be used in the paper because all the stimuli have been presented to the monkeys during training. Therefore, there is actually no novel stimuli but only deviant stimuli. This reflects that the author has misunderstood the basic concept.<br /> (3) Most of the conclusions were made based on correlational analysis or speculation without providing causal evidences.<br /> (4) Results are presented in a very "straightforward" manner with too many detailed descriptions of phenomena but lack of summary and information synthesis. For example, the first section of Results is very long but did not convey clear information.<br /> (5) The logic between different sections of Results is not clear.<br /> (6) In the Discussion, there is excessive repetition of results, and further comparison with and discussion of potentially related work are very insufficient. For example, Metzger, R.R., et al. (J Neurosc, 2006) have shown similar firing patterns of IC neurons and correlated their findings with reward.

Reviewer #1 (Public review):

Summary:

In the manuscript "Intergenerational transport of double-stranded RNA limits heritable epigenetic changes" Shugarts and colleagues investigate intergenerational dsRNA transport in the nematode C. elegans. They induce oxidative damage in worms, blocking dsRNA import into cells (and potentially affecting the worms in other ways). Oxidative stress inhibits dsRNA import and the associated heritable regulation of gene expression in the adult germline (Fig. 2). The authors identify a novel gene, sid-1-dependent gene-1 (sdg-1), which is induced upon inhibition of SID-1 (Fig. 3). Both transient inhibition and genetic depletion of SID-1 lead to the upregulation of sdg-1 and a second gene, sdg-2 (Fig. 5). The expression of SDG-1 is variable, potentially indicating buffering regulation. While the expression of Sdg-1 could be consistent with a role in intergenerational transport of dsRNA, neither its overexpression nor loss-of-function impacts dsRNA-mediated silencing (Fig. 7) in the germline. It would be interesting to test if sdg-2 functions redundantly.

In summary, the authors have identified a novel worm-specific protein (sdg-1) that is induced upon loss of dsRNA import via SID-1, but is not required to mediate SID-1 RNA regulatory effects.

Remaining Questions:

• The authors use an experimental system that induces oxidative damage specifically in neurons to release dsRNAs into the circulation. Would the same effect be observed if oxidative damage were induced in other cell types?

• Besides dsRNA, which other RNAs and cellular products (macromolecules and small signalling molecules) are released into the circulation that could affect the observed changes in germ cells?

• SID-1 modifies RNA regulation within the germline (Fig. 7) and upregulates sdg-1 and sdg-2 (Fig. 5). However, SID-1's effects do not appear to be mediated via sdg-1. Testing the role of sdg-2 would be intriguing.

• Are sdg-1 or sdg-2 conserved in other nematodes or potentially in other species? Sdg-1 appears to be encoded or captured by a retro-element in the C. elegans genome and exhibits stochastic expression in different isolates. Is this a recent adaptation in the C. elegans genome, or is it present in other nematodes? Does loss-of-function of sdg-1 or sdg-2 have any observable effect?

Clarification for Readability:

To enhance readability and avoid misunderstandings, it is crucial to specify the model organism and its specific dsRNA pathways that are not conserved in vertebrates:

• In the first sentence of the paragraph "Here, we dissect the intergenerational transport of extracellular dsRNA ...", the authors should specify "in the nematode C. elegans". Unlike vertebrates, which recognise dsRNA as a foreign threat, worms and other invertebrates pervasively use dsRNA for signalling. Additionally, worms, unlike vertebrates and insects, encode RNA-dependent RNA polymerases that generate dsRNA from ssRNA substrates, enabling amplification of small RNA production. Especially in dsRNA biology, specifying the model organism is essential to avoid confusion about potential effects in humans.

• Similarly, the authors should specify "in C. elegans" in the sentence "Therefore, we propose that the import of extracellular dsRNA into the germline tunes intracellular pathways that cause heritable RNA silencing." This is important because C. elegans small RNA pathways differ significantly from those in other organisms, particularly in the PIWI-interacting RNA (piRNA) pathways, which depend on dsRNA in C. elegans but uses ssRNA in vertebrates. Specification is crucial to prevent misinterpretation by the reader. It is well understood that mechanisms of transgenerational inheritance that operate in nematodes or plants are not conserved in mammals.

• The first sentence of the discussion, "Our analyses suggest a model for ...", would also benefit from specifying "in C. elegans". The same applies to the figure captions. Clarification of the model organism should be added to the first sentence, especially in Figure 1.

Reviewer #1 (Public review):

Summary:

Insulin is crucial for maintaining metabolic homeostasis, and its release is regulated by various pathways, including blood glucose levels and neuromodulatory systems. The authors investigated the role of neuromodulators in regulating the dynamics of the adult Drosophila IPC population. They showed that IPCs express various receptors for monoaminergic and peptidergic neuromodulators, as well as synaptic neurotransmitters with highly heterogeneous profiles across the IPC population. Activating specific modulatory inputs, e.g. dopaminergic, octopaminergic or peptidergic (Leucokinin) using an optogenetic approach coupled with in vivo electrophysiology unveiled heterogeneous responses of individual IPCs resulting in excitatory, inhibitory or no responses. Interestingly, calcium imaging of the entire IPC population with or without simultaneous electrophysiological recording of individual cells showed highly specific and stable responses of individual IPCs suggesting their intrinsic properties are determined by the expressed receptor repertoire. Using the adult fly connectome they further corroborate the synaptic input of excitatory and inhibitory neuronal subsets of IPCs. The authors conclude that the heterogeneous modulation of individual IPC activity is more likely to allow for flexible control of insulin release to adapt to changes in metabolic demand and environmental cues.

Strengths:

This study provides a comprehensive, multi-level analysis of IPC properties utilizing single-nucleus RNA sequencing, anatomical receptor expression mapping, connectomics, electrophysiological recordings, calcium-imaging and an optogenetics-based 'intrinsic pharmacology' approach. It highlights the heterogeneous receptor profiles of IPCs, demonstrating complex and differential modulation within the IPC population. The authors convincingly showed that different neuromodulatory inputs exhibit varied effects on IPC activity and simultaneous occurrence of heterogeneous responses in IPCs with some populations exciting a subset of IPCs while inhibiting others, showcasing the intricate nature of IPC modulation and diverse roles of IPC subgroups. The temporal dynamic of IPC modulation showed that polysynaptic and neuromodulatory connections play a major role in IPC response. The authors demonstrated that certain neuromodulatory inputs, e.g. dopamine, can shift the overall IPC population activity towards either an excited or inhibited state. The study thus provides a fundamental entry point to understanding the complex influence of neuromodulatory inputs on the insulinergic system of Drosophila.

Weakness:

GPCRs are typically expressed at low levels and while the transcriptomic and reporter expression analysis was comprehensive, both approaches have the caveat that they do not allow validating protein level expression. Thus, some receptors might have been missed while others might be false positives. The authors acknowledged the challenges in accurately accessing receptor expression in complex modulatory systems indicating there are limitations in full understanding of the receptor profiles of IPCs.

While this study provides valuable insights into the heterogeneity of IPC responses and receptor expression, it will require future studies to elucidate how these modulatory inputs affect insulin release and transcriptional long-term changes.<br /> The authors further analyzed male and female snRNAseq data and claimed that the differences in receptor expression were minimal. The experimental analyses used mated females only and while the study is very complete in this respect, it would have been extremely interesting to compare male flies in terms of their response profiles.<br /> Lastly as also pointed out by the authors, their approach of using optogenetically driven excitation of modulatory neuronal subsets limits the interpretation of the results due to the possibly confounding direct or indirect effect of fast synaptic transmission on IPC excitation/inhibition, and the broad expression of some neuromodulatory lines used in this analysis.

Overall, however, the conclusions of this study are well supported by the data provided by the authors. Moreover, their detailed and thorough analysis of IPC modulation will have a significant impact on the field of metabolic regulation to understand the complex regulatory mechanism of insulin release, which can now be studied further to provide insight about metabolic homeostasis and neural control of metabolic processes.

Reviewer #1 (Public Review):

Kreeger and colleagues have explored the balance of excitation and inhibition in the cochlear nucleus octopus cells of mice using morphological, electrophysiological, and computational methods. On the surface, the conclusion, that synaptic inhibition is present, does not seem like a leap. However, the octopus cells have been in the past portrayed as devoid of inhibition. This view was supported by the seeming lack of glycinergic fibers in the octopus cell area and the lack of apparent IPSPs. Here, Kreeger et al. used beautiful immunohistochemical and mouse genetic methods to quantify the inhibitory and excitatory boutons over the complete surface of individual octopus cells and further analysed the proportions of the different subtypes of spiral ganglion cell inputs. I think the analysis stands as one of the most complete descriptions of any neuron, leaving little doubt about the presence of glycinergic boutons.

Kreeger et al then examined inhibition physiologically, but here I felt that the study was incomplete. Specifically, no attempt was made to assess the actual, biological values of synaptic conductance for AMPAR and GlyR. Thus, we don't really know how potent the GlyR could be in mediating inhibition. Here are some numbered comments:

(1) "EPSPs" were evoked either optogenetically or with electrical stimulation. The resulting depolarizations are interpreted to be EPSPs. However previous studies from Oertel show that octopus cells have tiny spikes, and distinguishing them from EPSPs is tricky. No mention is made here about how or whether that was done. Thus, the analysis of EPSP amplitude is ambiguous.

(2) For this and later analysis, a voltage clamp of synaptic inputs would have been a simple alternative to avoid contaminating spikes or shunts by background or voltage-gated conductances. Yet only the current clamp was employed. I can understand that the authors might feel that the voltage clamp is 'flawed' because of the failure to clamp dendrites. But that may have been a good price to pay in this case. The authors should have at least justified their choice of method and detailed its caveats.

(3) The modeling raised several concerns. First, there is little presentation of assumptions, and of course, a model is entirely about its assumptions. For example, what excitatory conductance amplitudes were used? The same for inhibitory conductance? How were these values arrived at? The authors note that EPSGs and IPSGs had peaks at 0.3 and 3 ms. On what basis were these numbers obtained? The model's conclusions entirely depend on these values, and no measurements were made here that could have provided them. Parenthetical reference is made to Figure S5 where a range of values are tested, but with little explanation or justification.

(4) In experiments that combined E and I stimulation, what exactly were time timecourses of the conductance changes, and how 'synchronous' were they, given the different methods to evoke them? (had the authors done voltage clamp they would know the answers).

(5) Figure 4G is confusing to me. Its point, according to the text, is to show that changes in membrane properties induced by a block of Kv and HCN channels would not be expected to alter the amplitudes of EPSCs and IPSCs across the dendritic expanse. Now we are talking about currents (not shunting effects), and the presumption is that the blockers would alter the resting potential and thus the driving force for the currents. But what was the measured membrane potential change in the blockers? Surely that was documented. To me, the bigger concern (stated in the text) is whether the blockers altered exocytosis, and thus the increase in IPSP amplitude in blockers is due BOTH to loss of shunting and increase in presynaptic spike width. Added to this is that 4AP will reduce the spike threshold, thus allowing more ChR2-expressing axons to reach the threshold. Figure 4G does not address this point.

(6) Figure 5F is striking as the key piece of biological data that shows that inhibition does reduce the amplitude of "EPSPs" in octopus cells. Given the other uncertainties mentioned, I wondered if it makes sense as an example of shunting inhibition. Specifically, what are the relative synaptic conductances, and would you predict a 25% reduction given the actual (not modeled) values?

(7) Some of the supplemental figures, like 4 and 5, are hardly mentioned. Few will glean anything from them unless the authors direct attention to them and explain them better. In general, the readers would benefit from more complete explanations of what was done.

Reviewer #1 (Public Review):

Summary:

This paper conducted a GWAS meta-analysis for COVID-19 hospitalization among admixed American populations. The authors identified four genome-wide significant associations, including two novel loci (BAZ2B and DDIAS), and an additional risk locus near CREBBP using cross-ancestry meta-analysis. They utilized multiple strategies to prioritize risk variants and target genes. Finally, they constructed and assessed a polygenic risk score model with 49 variants associated with critical COVID-19 conditions.

Strengths:

Given that most of the previous studies were done in European ancestries, this study provides unique findings about the genetics of COVID-19 in admixed American populations. The GWAS data would be a valuable resource for the community. The authors conducted comprehensive analyses using multiple different strategies, including Bayesian fine mapping, colocalization, TWAS, etc., to prioritize risk variants and target genes. The polygenic risk score (PGS) result demonstrated the ability of cross-population PGS model for COVID-19 risk stratification.

Weaknesses:

(1) One of the major limitations of this study is that the GWAS sample size is relatively small, which limits its power.<br /> (2) Lack of replication cohort.<br /> (3) Colocalization and TWAS used eQTL data from GTEx data, which are mainly from European ancestries.

Comments on latest version:

The authors addressed most of my concerns.

Reviewer #1 (Public review):

Summary:

Rößling et al., report in this study that the perception of RALF1 by the FER receptor is mediated by the association of RALF1 with deesterified pectin, contributing to the regulation of the cell wall matrix and plasma membrane dynamics. In addition, they report that this mode of action is independent from the previously reported cell wall sensing mechanism mediated by the FER-LRX complex.

This manuscript reproduces and aligns with the results from a recently published study (Liu et al., Cell) where they also report that RALF1 can interact with deesterified pectin, forming coacervates and promoting the recruitment of LLG-FER at the membrane.

Reviewer #1 (Public review):

Summary:

The authors investigate the mechanism behind the widely observed but poorly understood phenomenon of reversible vimentin disassembly upon hypotonic challenge. Using permeabilized COS-7 cells expressing vimentin-mEos3.2, the authors demonstrate that vimentin disassembly is not due to lower osmotic pressure but rather due to decreased intracellular ionic strength. They propose a model in which vimentin filament stability is predicted by the protein's net charge and support this idea through approaches that involve (i) manipulating buffer ionic strength, (ii) manipulating buffer pH, or (iii) introducing charged amino acids into the linker of the exogenously expressed vimentin-mEos3.2.

Strengths & Weaknesses:

While the discovery is intriguing and presents an interesting concept, significant shortcomings in experimental design and numerous inconsistencies prevent it from reaching the high standards expected. The lack of reproducibility, inadequate controls, and insufficient quantification make the findings feel very preliminary. Additionally, the authors need to address the apparent discrepancies between their current results and their previous work implicating calpains and altered calcium levels in vimentin disassembly upon hypotonic challenge (which has led to much confusion in the field). This discrepancy should be thoroughly addressed in the discussion with the authors citing their prior work and explaining why it was incorrect.

An additional concern is the relevance of the findings to vimentin biology inside cells. The most important insight in this work is the observation that an isotonic buffer balanced with non-electrolytes (glucose or sorbitol) is sufficient to drive vimentin disassembly. The authors show that vimentin disassembly is not due to changes in osmotic pressure but rather due to a change in the concentration of critical dissolved ions, specifically the number of charged states on vimentin. What is missing is when and how this is controlled within cells under physiological conditions - not just when cells are permeabilized with detergents (conditions that cells rarely survive). Without this deeper dive into vimentin states within cells and how it is controlled, the paper seems very narrow in its focus.

Reviewer #2 (Public review):

This study uses single-unit recordings in the monkey STN to examine the evidence for three theoretical models that propose distinct roles for the STN in perceptual decision-making. Importantly, the proposed functional roles are predictive of unique patterns of neural activity. Using k-means clustering with seeds informed by each model's predictions, the current study identified three neural clusters with activity dynamics that resembled those predicted by the described theoretical models. The authors are thorough and transparent in reporting the analyses used to validate the clustering procedure and the stability of the clustering results. To further establish a causal role for the STN in decision-making, the researchers applied microsimulation to the STN and found effects on response times, choice preferences, and latent decision parameters estimated with a drift-diffusion model. Overall, the study provides strong evidence for a functionally diverse population of STN neurons that could indeed support multiple roles involved in perceptual decision-making. The manuscript would benefit from stronger evidence linking each neural cluster to specific decision roles in order to strengthen the overall conclusions.

The interpretation of the results, and specifically, the degree to which the identified clusters support each model, is largely dependent on whether the artificial vectors used as model-based clustering seeds adequately capture the expected behavior under each theoretical model. The manuscript would benefit from providing further justification for the specific model predictions summarized in Figure 1B. Further, although each cluster's activity can be described in the context of the discussed models, these same neural dynamics could also reflect other processes not specific to the models. That is, while a model attributing the STN's role to assessing evidence accumulation may predict a ramping up of neural activity, activity ramping is not a selective correlate of evidence accumulation and could be indicative of a number of processes, e.g., uncertainty, the passage of time, etc.. This lack of specificity makes it challenging to infer the functional relevance of cluster activity and should be acknowledged in the discussion.

Additionally, although the effects of STN microstimulation on behavior provide important causal evidence linking the STN to decision processes, the stimulation results are highly variable and difficult to interpret. The authors provide a reasonable explanation for the variability, showing that neurons from unique clusters are anatomically intermingled such that stimulation likely affects neurons across several clusters. It is worth noting, however, that a substantial body of literature suggests that neural populations in the STN are topographically organized in a manner that is crucial for its role in action selection, providing "channels" that guide action execution. The authors should comment on how the current results, indicative of little anatomical clustering amongst the functional clusters, relates to other reports showing topographical organization.

Overall, the association between the identified clusters and the function ascribed to the STN by each of the models is largely descriptive and should be interpreted accordingly. For example, Figure 3 is referenced when describing which cluster activity is choice/coherence dependent, yet it is unclear what specific criteria and measures are being used to determine whether activity is choice/coherence "dependent." Visually, coherence activity seems to largely overlap in panel B (top row). Is there a statistically significant distinction between low and high coherence in this plot? The interpretation of these plots and the methods used to determine choice/coherence "dependence" needs further explanation.

In general, the association between cluster activity and each model could be more directly tested. At least two of the models assume coordination with other brain regions. Does the current dataset include recordings from any of these regions (e.g., mPFC or GPe) that could be used to bolster claims about the functional relevance of specific subpopulations? For example, one would expect coordinated activity between neural activity in mPFC and Cluster 2 according to the Ratcliff and Frank model. Additionally, the reported drift-diffusion model (DDM) results are difficult to interpret as microsimulation appears to have broad and varied effects across almost all the DDM model parameters. The DDM framework could, however, be used to more specifically test the relationships between each neural cluster and specific decision functions described in each model. Several studies have successfully shown that neural activity tracks specific latent decision parameters estimated by the DDM by including neural activity as a predictor in the model. Using this approach, the current study could examine whether each cluster's activity is predictive of specific decision parameters (e.g., evidence accumulation, decision thresholds, etc.). For example, according to the Ratcliff and Frank model, activity in cluster 2 might track decisions thresholds.

Review of revision

The authors have sufficiently addressed the concerns raised in the initial reviews and have revised their manuscript accordingly. We commend the authors for these efforts and feel that the revisions have strengthened the major claims of the manuscript.

Reviewer #1 (Public Review):

In this manuscript by Wu et al., the authors present the high resolution cryoEM structures of the WT Kv1.2 voltage-gated potassium channel. Along with this structure, the authors have solved several structures of mutants or experimental conditions relevant to the slow inactivation process that these channels undergo and which is not yet completely understood.

One of the main findings is the determination of the structure of a mutant (W366F) that is thought to correspond to the slow inactivated state. These experiments confirm results in similar mutants in different channels from Kv1.2 that indicate that inactivation is associated with an enlarged selectivity filter.

Another interesting structure is the complex of Kv1.2 with the pore blocking toxin Dendrotoxin 1. The results shown in the revised version indicate that the mechanism of block is similar to that of related blocking-toxins, in which a lysine residue penetrates in the pore. Surprisingly, in these new structures, the bound toxin results in a pore with empty external potassium binding sites.

The quality of the structural data presented in this revised manuscript is very high and allows for unambiguous assignment of side chains. The conclusions are supported by the data. This is an important contribution that should further our understanding of voltage-dependent potassium channel gating. In the revised version, the authors have addressed my previous specific comments.

Reviewer #1 (Public Review):

Summary:<br /> In this paper, authors investigated the role of RUNT-related transcription factor 2 (RUNX2) in oral squamous carcinoma (OSCC) growth and resistance to ferroptosis. They found that RUNX2 suppresses ferroptosis through transcriptional regulation of peroxiredoxin-2. They further explored the upstream positive regulator of RUNX2, HOXA10 and found that HOXA10/RUNX2/PRDX2 axis protects OSCC from ferroptosis.

Strengths:<br /> The study is well designed and provides a novel mechanism of HOXA10/RUNX2/PRDX2 control of ferroptosis in OSCC.

Weaknesses:

According to the data presented in (Figure 2F, Figure 3Fand G, Figure 5D and Figure 6E and F), apoptosis seems to be affected in the same amount as ferroptosis by HOXA10/RUNX2/PRDX2 axis, which raises questions on the authors' specific focus on ferroptosis in this study. Reasonably, authors should adapt the title and the abstract in a way that recapitulates the whole data, which is HOXA10/RUNX2/PRDX2 axis control of cell death, including ferroptosis and apoptosis in OSCC.

Comments:

- In the description of the result section related to Figure 3E, the author wrote "In addition, we found that isoform II-knockdown induced shrunken mitochondria with vanished cristae with transmission electron microscopy (Figure 3E). These results suggest that RUNX2 isoform II may suppress ferroptosis." The interpretation provided here is not clear to the reviewer. How shrunken mitochondria and vanished cristae can be linked to ferroptosis?<br /> - The electron microscopy images show more elongated mitochondria in the RUNX2 isoform II-KO cells than in RUNX2 isoform II positive cells, which might result from the fusion of mitochondria. These images should completed with a fluorescent mitochondria staining of these cells.<br /> - What is the oxygen consumption rate in RUNX2 KO cells?<br /> - The increase in cell proliferation after RUNX2 overexpression in Figure 2A is not convincing, is there any differences in their migration or invasion capacity?<br /> - The in vivo study shows 50% reduction in primary tumor growth after RUNX2 inhibition by shRNA in CAL 27 xenografts, but only one shRNA is shown. Is this one shRNA clone? At least 2 shRNA clones should be used.<br /> - Apoptosis and necroptosis seem to be affected in the same amount as ferroptosis by HOXA10/RUNX2/PRDX2 axis. This is evident from experiments in Figure 3E, F and from Figure 6E, F and Figure 3G. Either Fer-1, Z-VAD,or Nec-1 used alone, were not able to fully restore cell proliferation to control cell level, which implies an additive effect of ferroptosis, apoptosis and necrosis. The author should verify potential additive or synergistic effect of the combination of Fer-1 and Z-VAD in these assays after si-RUNX2 in Figure 3 F and G and after si-HOX assays.<br /> - What is the effect of PRDX2 or HOXA10 depletion on tumor growth?<br /> - What is the clinical relevance of HOXA10 in OSCC patients?

Reviewer #1 (Public review):

Summary:

This study develops and validates a neural subspace similarity analysis for testing whether neural representations of graph structures generalize across graph size and stimulus sets. The authors show the method works in rat grid and place cell data, finding that grid but not place cells generalize across different environments, as expected. The authors then perform additional analyses and simulations to show that this method should also work on fMRI data. Finally, the authors test their method on fMRI responses from the entorhinal cortex (EC) in a task that involves graphs that vary in size (and stimulus set) and statistical structure (hexagonal and community). They find neural representations of stimulus sets in lateral occipital complex (LOC) generalize across statistical structure and that EC activity generalizes across stimulus sets/graph size, but only for the hexagonal structures.

Strengths:

(1) The overall topic is very interesting and timely and the manuscript is well-written.

(2) The method is clever and powerful. It could be important for future research testing whether neural representations are aligned across problems with different state manifestations.

(3) The findings provide new insights into generalizable neural representations of abstract task states in the entorhinal cortex.

Weaknesses:

(1) The manuscript would benefit from improving the figures. Moreover, the clarity could be strengthened by including conceptual/schematic figures illustrating the logic and steps of the method early in the paper. This could be combined with an illustration of the remapping properties of grid and place cells and how the method captures these properties.

(2) Hexagonal and community structures appear to be confounded by training order. All subjects learned the hexagonal graph always before the community graph. As such, any differences between the two graphs could thus be explained (in theory) by order effects (although this is practically unlikely). However, given community and hexagonal structures shared the same stimuli, it is possible that subjects had to find ways to represent the community structures separately from the hexagonal structures. This could potentially explain why the authors did not find generalizations across graph sizes for community structures.

(3) The authors include the results from a searchlight analysis to show the specificity of the effects of EC. A better way to show specificity would be to test for a double dissociation between the visual and structural contrast in two independently defined regions (e.g., anatomical ROIs of LOC and EC).

(4) Subjects had more experience with the hexagonal and community structures before and during fMRI scanning. This is another confound, and possible reason why there was no generalization across stimulus sets for the community structure.

Reviewer #1 (Public review):

Summary:

Insects and their relatives are commonly infected with microbes that are transmitted from mothers to their offspring. A number of these microbes have independently evolved the ability to kill the sons of infected females very early in their development; this male killing strategy has evolved because males are transmission dead-ends for the microbe. A major question in the field has been to identify the genes that cause male killing and to understand how they work. This has been especially challenging because most male-killing microbes cannot be genetically manipulated. This study focuses on a male-killing bacterium called Wolbachia. Different Wolbachia strains kill male embryos in beetles, flies, moths, and other arthropods. This is remarkable because how sex is determined differs widely in these hosts. Two Wolbachia genes have been previously implicated in male-killing by Wolbachia: oscar (in moth male-killing) and wmk (in fly male-killing). The genomes of some male-killing Wolbachia contain both of these genes, so it is a challenge to disentangle the two.

This paper provides strong evidence that oscar is responsible for male-killing in moths. Here, the authors study a strain of Wolbachia that kills males in a pest of tea, Homona magnanima. Overexpressing oscar, but not wmk, kills male moth embryos. This is because oscar interferes with masculinizer, the master gene that controls sex determination in moths and butterflies. Interfering with the masculinizer gene in this way leads the (male) embryo down a path of female development, which causes problems in regulating the expression of genes that are found on the sex chromosomes.

Strengths:

The authors use a broad number of approaches to implicate oscar, and to dissect its mechanism of male lethality. These approaches include:<br /> (1) Overexpressing oscar (and wmk) by injecting RNA into moth eggs.<br /> (2) Determining the sex of embryos by staining female sex chromosomes.<br /> (3) Determining the consequences of oscar expression by assaying sex-specific splice variants of doublesex, a key sex determination gene, and by quantifying gene expression and dosage of sex chromosomes, using RNASeq.<br /> (4) Expressing oscar along with masculinizer from various moth and butterfly species, in a silkmoth cell line.

This extends recently published studies implicating oscar in male-killing by Wolbachia in Ostrinia corn borer moths, although the Homona and Ostrinia oscar proteins are quite divergent. Combined with other studies, there is now broad support for oscar as the male-killing gene in moths and butterflies (i.e. order Lepidoptera). So an outstanding question is to understand the role of wmk. Is it the master male-killing gene in insects other than Lepidoptera and if so, how does it operate?

Weaknesses:

I found the transfection assays of oscar and masculinizer in the silkworm cell line (Figure 4) to be difficult to follow. There are also places in the text where more explanation would be helpful for non-experts (see recommendations).

Reviewer #1 (Public Review):

Summary:

Machii et al. reported a possible molecular mechanism underlying the parallel evolution of lip hypertrophy in African cichlids. The multifaceted approach taken in this manuscript is highly valued, as it uses histology, proteomics, and transcriptomics to reveal how phylogenetically distinct thick-lips have evolved in parallel. Findings from histology and proteomics connected to wnt signaling through the transcriptome are very exciting.

Strengths:

There is consistency between the results and it is possible to make a strong argument from the results.

Weaknesses:

The authors do not discuss based on genomic information; the genomes of the cichlids from the three lakes have been decoded and are therefore available. However, indeed, the species in Lake Tanganyika and Lake Malawi/Victoria are genetically distant from each other, so a comparative genome analysis would not have yielded the results presented here. I recommend adding such a discussion to the Discussion.

Reviewer #1 (Public review):

The central finding of the current manuscript is that embryonic ablation of PRMT1 results in a craniofacial phenotype that is primarily linked to downstream intron splicing defects. This manuscript is one of several to underscore the relative importance of intron splicing to gene expression regulation during development, and moreover, to recapitulate splicing-related craniofacial defects. Specifically, authors introduce a regulatory axis consisting of PRMT1-SFPQ that directs mechanisms of long intron retention. This finding represents a significant contribution to our understanding of splicing regulation, in the sense that it highlights the regulatory impact that post-translational modification of splicing-related proteins can have on intron processing. Further, it emphasizes the importance of extending the study of splicing regulation beyond core components of the spliceosome, to include their upstream regulators as well.

The significance of neural crest cells in the development of craniofacial structures has long been considered a major contributor to developmental phenotypes. This specific symptomology is heavily associated with spliceosomopathies, wherein disruption of spliceosome components is the primary mechanism of disease pathogenesis. Thus, the PRMT1 associated phenotype is noteworthy. The role of PRMT1 in methylating downstream splicing factors introduces a new avenue of research focused on the mechanisms of spliceosome component activation and their effects on splicing. The strength of the current study lies in their establishing the molecular mechanism through which PRMT1 could alter craniofacial development through regulation of the transcriptome, but the data presented to support the claim that a PRMT1-SFPQ axis directly regulates intron retention of the relevant gene networks should be robust and with multiple forms of clear validation. For example, elevated intron retention findings are based on the intron retention index, and according to the manuscript, are assessed considering the relative expression of exons and introns from a given transcript. However, delineating between intron retention and other forms of alternative splicing (i.e., cryptic splice site recognition) requires a more comprehensive consideration of the intron splicing defects that could be represented in data. A certain threshold of intron read coverage (i.e., the percent of an intron that is covered by mapped reads) is needed to ascertain if those that are proximal to exons could represent alternative introns ends rather than full intron retention events. In other words, intron retention is a type of alternative splicing that can be difficult to analyze in isolation given the confounding influence of cryptic splicing and cryptic exon inclusion. If other forms of alternative splicing were assessed and not detected, more confident retention calls can be made.

While data presented to support the PRMT1-SFPQ activation axis is quite compelling, that this is directly responsible for the elevated intron retention remains enigmatic. First, in characterizing their PRMT1 knockout model, it is unclear whether the elevated intron retention events directly correspond to downregulated genes. Moreover, intron splicing is a well-documented node for gene regulation during embryogenesis and in other proliferation models, and craniofacial defects are known to be associated with 'spliceosomopathies'. However, reproduction of this phenotype does not suggest that the targets of interest are inherently splicing factors, and a more robust assessment is needed to determine the exact nature of alternative splicing in this system. Because there are several known splicing factors downstream of PRMT1 and presented in the supplemental data, the specific attribution of retention to SFPQ would be additionally served by separating its splicing footprint from that of other factors that are primed to cause alternative splicing.

Clarifying the relationship between SFPQ and splicing regulation is important given that the observed splicing defects are incongruous with published data presented by Takeuchi et al., (2018) regarding SFPQ control of neuronal apoptosis in mice. In this system, SFPQ was more specifically attributed to the regulation of transcription elongation over long introns and its knockout did not result in significant splicing changes. Thus, to establish the specificity for the SFPQ in regulating these retention events, authors would need to show that the same phenotype is not achieved by mis-regulation of other splicing factors. That the authors chose SFPQ based on its binding profile is understandable but potentially confounding given its mechanism of action in transcription of long introns (Takeuchi 2018). Because mechanisms and rates of transcription can influence splicing and exon definition interactions, the role of SFPQ as a transcription elongation factor versus a splicing factor is inadequately disentangled by authors.

Reviewer #2 (Public review):

Summary:

Hall et al describe the superiority of ONT sequencing and deep learning-based variant callers to deliver higher SNP and Indel accuracy compared to previous gold-standard Illumina short-read sequencing. Furthermore, they provide recommendations for read sequencing depth and computational requirements when performing variant calling.

Strengths:

The study describes compelling data showing ONT superiority when using deep learning-based variant callers, such as Clair3, compared to Illumina sequencing. This challenges the paradigm that Illumina sequencing is the gold standard for variant calling in bacterial genomes. The authors provide evidence that homopolymeric regions, a systematic and problematic issue with ONT data, are no longer a concern in ONT sequencing.

Weaknesses:

The study is limited in the number of samples included, even though it covers different species with divergent genome sequences, likely covering major evolutionary changes. The methods section could be more detailed. A structural variation analysis would be an interesting next step.

Reviewer #1 (Public Review):

Summary:

In this manuscript, Rohde et al. discuss how single cells isolated from the presomitic mesoderm of the zebrafish embryo follow a cell-autonomous differentiation "programme", which is dependent on the initial anteroposterior position in the embryo.

Strengths:

This work and, in particular, the comparison to cellular behaviour in vivo presents a detailed description of the oscillatory system that brings the developmental biology forward in their understanding of somitogenesis.<br /> The main novelty lies in the direct comparison of these isolated single cells to single cells tracked within the developing embryo. This allows them to show that isolated cells follow a similar path of differentiation without direct contact to neighbours or the presence of external morphogen gradients. Based on this, the authors propose an internal timer that starts ticking as cells traverse the presomitic mesoderm, while external signals modify this behaviour.

There are a few direct questions that follow up from this study, for instance, intercellular synchronization influences the variability of the timer. However, I agree with the authors that such experiments are out of the scope of this study.

Reviewer #1 (Public Review):

Summary:

The authors aimed to identify potential biomarkers for acute myocardial infarction (AMI) through blood metabolomics and fecal microbiome analysis. They found that long chain fatty acids (LCFAs) could serve as biomarkers for AMI and demonstrated a correlation between LCFAs and the gut microbiome. Additionally, in silico molecular docking and in vitro thrombogenic assays showed that these LCFAs can induce platelet aggregation.

Strengths:

The study utilized a comprehensive approach combining blood metabolomics and fecal microbiome analysis.

The findings suggest a novel use of LCFAs as biomarkers for AMI.

The correlation between LCFAs and the gut microbiome is a significant contribution to understanding the interplay between gut health and heart disease.

The use of in silico and in vitro assays provides mechanistic insights into how LCFAs may influence platelet aggregation.

Weaknesses:

The evidence is incomplete as it does not definitively prove that gut dysbiosis contributes to fatty acid dysmetabolism.

The study primarily shows an association between the gut microbiome and fatty acid metabolism without establishing causation.

Joint Public Review

The molecular mechanisms that mediate the regulated exocytosis of neuropeptides and neurotrophins from neurons via large dense-core vesicles (LDCVs) are still incompletely understood. Motivated by their earlier discovery that the Rab3-RIM1 pathway is essential for neuronal LDCV exocytosis, the authors now examined the role of the Rab3 effector Rabphilin-3A in neuronal LDCV secretion. Based on live, confocal, and super-resolution imaging approaches, the authors provide evidence for a synaptic enrichment of Rabphilin-3A and for independent trafficking of Rabphilin-3A and LDCVs. Using an elegant NPY-pHluorin imaging approach, they show that genetic deletion of Rabphilin-3A causes an increase in electrically triggered LDCV fusion events and increased neurite length. Finally, knock-out-replacement studies, involving Rabphilin-3A mutants deficient in either Rab3- or SNAP25-binding, indicate that the synaptic enrichment of Rabphilin-3A depends on its Rab3 binding ability, while its ability to bind to SNAP25 is required for its effects on LDCV secretion and neurite development. The authors conclude that Rabphilin-3A negatively regulates LDCV exocytosis and propose that this mechanism also affects neurite growth, e.g. by limiting neurotrophin secretion. These are important findings that advance our mechanistic understanding of neuronal large dense-core vesicle (LDCV) secretion.

The major strengths of the present paper:

(i) The use of a powerful Rabphilin-3A KO mouse model.<br /> (ii) Stringent lentiviral expression and rescue approaches as a strong genetic foundation of the study.<br /> (iii) An elegant FRAP imaging approach.<br /> (iv) A cutting-edge NPY-pHluorin-based imaging approach to detect LDCV fusion events.

Weaknesses of the present paper:

(i) It remains unclear why a process that affects a general synaptic SNARE fusion protein - SNAP25 - would specifically affect LDCV but not synaptic vesicle fusion.<br /> (iii) The mechanistic links between Rabphilin-3A function, LDCV density in neurites, neurite outgrowth, and the proposed underlying mechanisms involving trophic factor release remain unresolved.

Reviewer #1 (Public Review):

O'Leary and colleagues sought to understand the factors that underlie memory processes, including formation, retrieval, and forgetting. The present data identify time, environmental enrichment, Rac-1, context reexposure, and brief reminders of the familiar object as factors that alter discrimination between novel and familiar objects. This is complimented with an engram approach to quantify cells that are active during learning to examine how their activation is impacted with each of the above factors at test. There are many strengths in the manuscript, including systematic testing of several factors that contribute to poor discrimination between novel and familiar objects. These results are interesting and outline essential boundaries of incidental, nonaversive memory. With this behavioral data, authors apply a modeling approach to understand the factors that contribute to good and poor object memory recall.

Reviewer #1 (Public Review):

The authors present a model for multisensory correlation detection that is based on the neurobiologically plausible Hassenstein Reichardt detector (Parise & Ernst, 2016). They demonstrate that this model can account for human behaviour in synchrony or temporal order judgements and related temporal tasks in two new data sets (acquired in this study) and a range of previous data sets. While the current study is limited to the model assessment for relatively simple audiovisual signals, in future communications, the authors demonstrate that the model can also account for audiovisual integration of complex naturalistic signals such as speech and music.

The significance of this work lies in its ability to explain multisensory perception using fundamental neural mechanisms previously identified in insect motion processing.

Strengths:

(1) The model goes beyond descriptive models such as cumulative Gaussians for TOJ and differences in cumulative Gaussians for SJ tasks by providing a mechanism that builds on the neurobiologically plausible Hassenstein-Reichardt detector.<br /> (2) This model can account for results from two new experiments that focus on the detection of correlated transients and frequency doubling. The model also accounts for several behavioural results from experiments including stochastic sequences of A/V events and sine wave modulations (and naturalistic Av signals such as speech and music as shown in future communications).

Reviewer #1 (Public Review):

Summary:

"Neural noise", here operationalized as an imbalance between excitatory and inhibitory neural activity, has been posited as a core cause of developmental dyslexia, a prevalent learning disability that impacts reading accuracy and fluency. This study is the first to systematically evaluate the neural noise hypothesis of dyslexia. Neural noise was measured using neurophysiological (electroencephalography [EEG]) and neurochemical (magnetic resonance spectroscopy [MRS]) in adolescents and young adults with and without dyslexia. The authors did not find evidence of elevated neural noise in the dyslexia group from EEG or MRS measures, and Bayes factors generally informed against including the grouping factor in the models. Although the comparisons between groups with and without dyslexia did not support the neural noise hypothesis, a mediation model that quantified phonological processing and reading abilities continuously revealed that EEG beta power in the left superior temporal sulcus was positively associated with reading ability via phonological awareness. This finding lends support for analysis of associations between neural excitatory/inhibitory factors and reading ability along a continuum, rather than as with a case/control approach, and indicates the relevance of phonological awareness as an intermediate trait that may provide a more proximal link between neurobiology and reading ability. Further research is needed across developmental stages and over a broader set of brain regions to more comprehensively assess the neural noise hypothesis of dyslexia, and alternative neurobiological mechanisms of this disorder should be explored.

Strengths:

The inclusion of multiple methods of assessing neural noise (neurophysiological and neurochemical) is a major advantage of this paper. MRS at 7T confers an advantage of more accurately distinguishing and quantifying glutamate, which is a primary target of this study. In addition, the subject-specific functional localization of the MRS acquisition is an innovative approach. MRS acquisition and processing details are noted in the supplementary materials according to the experts' consensus-recommended checklist (https://doi.org/10.1002/nbm.4484). Commenting on the rigor, the EEG methods is beyond my expertise as a reviewer.

Participants recruited for this study included those with a clinical diagnosis of dyslexia, which strengthens confidence in the accuracy of the diagnosis. The assessment of reading and language abilities during the study further confirms the persistently poorer performance of the dyslexia group compared to the control group.

The correlational analysis and mediation analysis provide complementary information to the main case-control analyses, and the examination of associations between EEG and MRS measures of neural noise is novel and interesting.

The authors follow good practice for open science, including data and code sharing. They also apply statistical rigor, using Bayes Factors to support conclusions of null evidence rather than relying only on non-significant findings. In the discussion, they acknowledge the limitations and generalizability of the evidence and provide directions for future research on this topic.

Weaknesses:

Though the methods employed in the paper are generally strong, there are certain aspects that are not clearly described in the Materials & Methods section, such as a description of the statistical analyses used for hypothesis testing.

With regard to metabolite quantification, it is unclear why the authors chose to analyze and report metabolite values in terms of creatine ratios rather than quantification based on a water reference given that the MRS acquisition appears to support using a water reference. GABA is typically quantified using J-editing sequences as lower field strengths (~3T), and there is some evidence that the GABA signal can be reliably measured at 7T without editing, however, the authors should discuss potential limitations, such as reliability of Glu and GABA measurements with short-TE semi-laser at 7T. In addition, MRS measurements of GABA are known to be influenced by macromolecules, and GABA is often denoted as GABA+ to indicate that other compounds contribute to the measured signal, especially at a short TE and in the absence of symmetric spectral editing. A general discussion of the strengths and limitations of unedited Glu and GABA quantification at 7T is warranted given the interest of this work to researchers who may not be experts in MRS.

Further, the single MRS voxel location is a limitation of the study as neurochemistry can vary regionally within individuals, and the putative excitatory/inhibitory imbalance in dyslexia may appear in regions outside the left temporal cortex (e.g., network-wide or in frontal regions involved in top-down executive processes). While the functional localization of the MRS voxel is a novelty and a potential advantage, it is unclear whether voxel placement based on left-lateralized reading-related neural activity may bias the experiment to be more sensitive to small, activity-related fluctuations in neurotransmitters in the CON group vs. the DYS group who may have developed an altered, compensatory reading strategy.

As the authors note in the discussion, sex could serve as a moderator of associations between neural noise and reading abilities and should be considered in future studies.

Appraisal:

The authors present a thorough evaluation of the neural noise hypothesis of developmental dyslexia in a sample of adolescents and young adults using multiple methods of measuring excitatory/inhibitory imbalances as an indicator of neural noise. The authors concluded that there was no support for the neural noise hypothesis of dyslexia in their study based on null significance and Bayes factors. This conclusion is justified, and further research is called for to more broadly evaluate the neural noise hypothesis in developmental dyslexia.

Impact:

This study provides an exemplary foundation for the evaluation of the neural noise hypothesis of dyslexia. Other researchers may adopt the model applied in this paper to examine neural noise in various populations with/without dyslexia, or across a continuum of reading abilities, to more thoroughly examine the evidence (or lack thereof) for this hypothesis. Notably, the lack of evidence here does not rule out the possibility of a role for neural noise in dyslexia, and the authors point out that presentation with co-occurring conditions, such as ADHD, may contribute to neural noise in dyslexia. Dyslexia remains a multi-faceted and heterogenous neurodevelopmental condition, and many genetic, neurobiological, and environmental factors play a role. This study demonstrates one step toward evaluating neurobiological mechanisms that may contribute to reading difficulties.

Reviewer #1 (Public Review):

Summary:

This study analyzed biomarker data from 28 subjects with geographic atrophy (GA) in a Phase I/II clinical trial of PPY988, a subretinal AAV2 complement factor I (CFI) gene therapy, to evaluate pharmacokinetics and pharmacodynamics. Post-treatment, a 2-fold increase in the vitreous humor (VH) FI was observed, correlating with a reduction in FB breakdown product Ba but minimal changes in other complement factors. The aqueous humor (AH) was found to be an unreliable proxy for VH in assessing complement activation. In vitro assays showed that the increase in FI had a minor effect on the complement amplification loop compared to the more potent C3 inhibitor pegcetacoplan. These findings suggest that PPY988 may not provide enough FI protein to effectively modulate complement activation and slow GA progression, highlighting the need for a thorough biomarker review to determine optimal dosing in future studies.

Strengths:

This manuscript provides critical data on the efficacy of gene therapy for the eye, specifically introducing complement FI expression. It presents the results from a halted clinical trial, making sharing this data essential for understanding the outcomes of this gene therapy approach. The findings offer valuable insights and lessons for future gene therapy attempts in similar contexts.

Weaknesses:

No particular weaknesses. The study was carefully performed and limitations are discussed.

I have just some concerns about the methodology used. The authors use the MILLIPLEX assays, which allow for multiplexed detection of complement proteins and they mention extensive validation. How are the measurements with this assay correlating with gold standard methods? Is the specificity and the expected normal ranges preserved with this assay? This also stands for the Olink assay. Some of the proteins are measured by both assay and/or by standard ELISA. How do these measurements correlate?

Reviewer #1 (Public Review):

Summary:

Englert et al. proposed a functional connectome-based Hopfield artificial neural network (fcHNN) architecture to reveal attractor states and activity flows across various conditions, including resting state, task-evoked, and pathological conditions. The fcHNN can reconstruct characteristics of resting-state and task-evoked brain activities. Additionally, the fcHNN demonstrates differences in attractor states between individuals with autism and typically developing individuals.

Strengths:

(1) The study used seven datasets, which somewhat ensures robust replication and validation of generalization across various conditions.

(2) The proposed fcHNN improves upon existing activity flow models by mimicking artificial neural networks, thereby enhancing the representational ability of the model. This advancement enables the model to more accurately reconstruct the dynamic characteristics of brain activity.

(3) The fcHNN projection offers an interesting visualization, allowing researchers to observe attractor states and activity flow patterns directly.

Weaknesses:

(1) The fcHNN projection can offer low-dimensional dynamic visualizations, but its interpretability is limited, making it difficult to make strong claims based on these projections. The interpretability should be enhanced in the results and discussion.

(2) The presentation of results is not clear enough, including figures, wording, and statistical analysis, which contributes to the overall difficulty in understanding the manuscript. This lack of clarity in presenting key findings can obscure the insights that the study aims to convey, making it challenging for readers to fully grasp the implications and significance of the research.

Reviewer #1 (Public Review):

Summary:

The authors aimed to investigate the oscillatory activity of GnRH neurones in freely behaving mice. By utilising GCaMP fiber photometry, they sought to record real-time neuronal activity to understand the patterns and dynamics of GnRH neuron firing and their implications for reproductive physiology.

Strengths:

(1) The use of GCaMP fiber photometry allows for high temporal resolution recordings of neuronal activity, providing real-time data on the dynamics of GnRH neurones.

(2) Recording in freely behaving animals ensures that the findings are physiologically relevant and not artifacts of a controlled laboratory environment.

(3) The authors used statistical methods to characterise the oscillatory patterns, ensuring the reliability of their findings.

Weaknesses:

(1) While the study identifies distinct oscillatory patterns in GnRH neurones' calcium dynamics, it falls short in exploring the functional implications of these patterns for GnRH pulsatility and overall reproductive physiology.

(2) The study lacks a broader discussion to include comparisons with existing studies on GnRH neurone activity and pulsatility and highlight how the findings of this study align with or differ from previous research and what novel contributions are made.

(3) The authors aimed to characterise the oscillatory activity of GnRH neurons and successfully identified distinct oscillatory patterns. The results support the conclusion that GnRH neurons exhibit complex oscillatory behaviours, which are critical for understanding their role in reproductive physiology. However, it has not been made clear what exactly the authors mean by "multi-dimensional oscillatory patterns" and how has this been shown.

Reviewer #1 (Public Review):

Summary:

In this series of studies, Locantore et al. investigated the role of SST-expressing neurons in the entopeduncular nucleus (EPNSst+) in probabilistic switching tasks, a paradigm that requires continued learning to guide future actions. In prior work, this group had demonstrated EPNSst+ neurons co-release both glutamate and GABA and project to the lateral habenula (LHb), and LHb activity is also necessary for outcome evaluation necessary for performance in probabilistic decision-making tasks. Previous slice physiology works have shown that the balance of glutamate/GABA co-release is plastic, altering the net effect of EPN on downstream brain areas and neural circuit function. The authors used a combination of in vivo calcium monitoring with fiber photometry and computational modeling to demonstrate that EPNSst+ neural activity represents movement, choice direction, and reward outcomes in their behavioral task. However, viral-genetic manipulations to synaptically silence these neurons or selectively eliminate glutamate release had no effect on behavioral performance in well-trained animals. The authors conclude that despite their representation of task variables, EPN Sst+ neuron synaptic output is dispensable for task performance.

Strengths and Weaknesses:

Overall, the manuscript is exceptionally scholarly, with a clear articulation of the scientific question and a discussion of the findings and their limitations. The analyses and interpretations are careful and rigorous. This review appreciates the thorough explanation of the behavioral modeling and GLM for deconvolving the photometry signal around behavioral events, and the transparency and thoroughness of the analyses in the supplemental figures. This extra care has the result of increasing the accessibility for non-experts, and bolsters confidence in the results. To bolster a reader's understanding of results, we suggest it would be interesting to see the same mouse represented across panels (i.e. Figures 1 F-J, Supplementary Figures 1 F, K, etc i.e via the inclusion of faint hash lines connecting individual data points across variables. Additionally, Figure 3E demonstrates that eliminating the 'reward' and 'choice and reward' terms from the GLM significantly worsens model performance; to demonstrate the magnitude of this effect, it would be interesting to include a reconstruction of the photometry signal after holding out of both or one of these terms, alongside the 'original' and 'reconstructed' photometry traces in panel D. This would help give context for how the model performance degrades by exclusion of those key terms. Finally, the authors claimed calcium activity increased following ipsilateral movements. However, Figure 3C clearly shows that both SXcontra and SXipsi increase beta coefficients. Instead, the choice direction may be represented in these neurons, given that beta coefficients increase following CXipsi and before SEipsi, presumably when animals make executive decisions. Could the authors clarify their interpretation on this point? Also, it is not clear if there is a photometry response related to motor parameters (i.e. head direction or locomotion, licking), which could change the interpretation of the reward outcome if it is related to a motor response; could the authors show photometry signal from representative 'high licking' or 'low licking' reward trials, or from spontaneous periods of high vs. low locomotor speeds (if the sessions are recorded) to otherwise clarify this point?

There are a few limitations with the design and timing of the synaptic manipulations that would improve the manuscript if discussed or clarified. The authors take care to validate the intersectional genetic strategies: Tetanus Toxin virus (which eliminates synaptic vesicle fusion) or CRISPR editing of Slc17a6, which prevents glutamate loading into synaptic vesicles. The magnitude of effect in the slice physiology results is striking. However, this relies on the co-infection of a second AAV to express channelrhodopsin for the purposes of validation, and it is surely the case that there will not be 100% overlap between the proportion of cells infected. Alternative means of glutamate packaging (other VGluT isoforms, other transporters, etc) could also compensate for the partial absence of VGluT2, which should be discussed. The authors do not perform a complimentary experiment to delete GABA release (i.e. via VGAT editing), which is understandable, given the absence of an effect with the pan-synaptic manipulation. A more significant concern is the timing of these manipulations as the authors acknowledge. The manipulations are all done in well-trained animals, who continue to perform during the length of viral expression. Moreover, after carefully showing that mice use different strategies on the 70/30 version vs the 90/10 version of the task, only performance on the 90/10 version is assessed after the manipulation. Together, the observation that EPNsst activity does not alter performance on a well-learned, 90/10 switching task decreases the impact of the findings, as this population may play a larger role during task acquisition or under more dynamic task conditions. Additional experiments could be done to strengthen the current evidence, although the limitation is transparently discussed by the authors.

Finally, intersectional strategies target LHb-projecting neurons, although in the original characterization, it is not entirely clear that the LHb is the only projection target of EPNsst neurons. A projection map would help clarify this point.

Overall, the authors used a pertinent experimental paradigm and common cell-specific approaches to address a major gap in the field, which is the functional role of glutamate/GABA co-release from the major basal ganglia output nucleus in action selection and evaluation. The study is carefully conducted, their analyses are thorough, and the data are often convincing and thought-provoking. However, the limitations of their synaptic manipulations with respect to the behavioral assays reduce generalizability and to some extent the impact of their findings.

Warren Zevon at a JP-1 style typewriter in 1977 photo by Joel Bernstein

via https://www.1stdibs.com/art/photography/black-white-photography/joel-bernstein-warren-zevon-1977/id-a_5543612/

Reviewer #1 (Public review):

Using the UK Biobank, this study assessed the value of nuclear magnetic resonance measured metabolites as predictors of progression to diabetes. The authors identified a panel of 9 circulating metabolites that improved the ability in risk prediction of progression from prediabetes to diabetes. In general, this is a well-performed study, and the findings may provide a new approach to identifying those at high risk of developing diabetes.

Comments on the revised version:

Thanks so much for carefully addressing my comments.

Reviewer #1 (Public review):

Summary:

The study of human intelligence has been the focus of cognitive neuroscience research, and finding some objective behavioral or neural indicators of intelligence has been an ongoing problem for scientists for many years. Melnick et al, 2013 found for the first time that the phenomenon of spatial suppression in motion perception predicts an individual's IQ score. This is because IQ is likely associated with the ability to suppress irrelevant information. In this study, a high-resolution MRS approach was used to test this theory. In this paper, the phenomenon of spatial suppression in motion perception was found to be correlated with the visuo-spatial subtest of gF, while both variables were also correlated with the GABA concentration of MT+ in the human brain. In addition, there was no significant relationship with the excitatory transmitter Glu. At the same time, SI was also associated with MT+ and several frontal cortex FCs.

Strengths:

(1) 7T high-resolution MRS is used<br /> (2) This study combines the behavioral tests, MRS, and fMRI.

Major<br /> I have no further comments. The approach and experiment are sound. The only overall drawback is the relatively low sample size.

Weaknesses:<br /> (1) Line 138, "This finding supports the hypothesis that motion perception is associated with neural activity in MT+ area". This sentence is strange because it is a well-established finding in numerous human fMRI papers. I think the authors should be more specific about what this finding implies.

Response: We thank reviewer for pointing this out. We have revised it to:" This finding is in line with prior results, which indicates that motion perception is associated with neural activity in hMT+ area, but not in EVC (primarily in V1)" (lines 156-158)

Reply: This argument should be refined. Numerous studies have shown the key role of V1 in motion perception. V1 contains a vast proportion of direction selective neurons. I am asking how your results here are related to existing literature. This argument is incorrect and too rough. Can you please revise this?

(9) Line 213, as far as I know, the study (Melnick et al., 2013) is a psychophysical study and did not provide evidence that the spatial suppression effect is associated with MT+.

Response: We thank reviewer for pointing this out. It was a mistake to use this reference, and we have revised it accordingly. (line 242)

Reply: Thanks. New citation is good. But that paper is a modeling study. The direct empirical evidence on humans should be as follow:

Tadin, D., Silvanto, J., Pascual-Leone, A. & Battelli, L. (2011) Improved motion perception and impaired spatial suppression following disruption of cortical area MT/V5. Journal of Neuroscience, 31, 1279-1283.

Reviewer #1 (Public Review):

Summary:

In this work, Qiu and colleagues examined the effects of preovulatory (i.e., proestrous or late follicular phase) levels of circulating estradiol on multiple calcium and potassium channel conductances in arcuate nucleus kisspeptin neurons. Although these cells are strongly linked to a role as the "GnRH pulse generator," the goal here was to examine the physiological properties of these cells in a hormonal milieu mimicking late proestrus, the time of the preovulatory GnRH-LH surge. Computational modeling is used to manipulate multiple conductances simultaneously and support a role for certain calcium channels in facilitating a switch in firing mode from tonic to bursting. CRISPR knockdown of the TRPC5 channel reduced overall excitability, but this was only examined in cells from ovariectomized mice without estradiol treatment. The manuscript has been substantially improved from the initial version by the addition of new experiments and clarification of important figures. Importantly, the overlap of data with previous reports from the same group has been corrected.

Strengths:

(1) Examination of multiple types of calcium and potassium currents, both through electrophysiology and molecular biology.

(2) Focus on arcuate kisspeptin neurons during the surge is relatively conceptually novel as the anteroventral periventricular nucleus (AVPV) kisspeptin neurons have received much more attention as the "surge generator" population.

(3) The modeling studies allow for direct examination of manipulation of single and multiple conductances, whereas the electrophysiology studies necessarily require examination of each current in isolation. Construction of an arcuate kisspeptin neuron model promises to be of value to the reproductive neuroendocrinology field.

Weaknesses:

A remaining weakness in this revised version of the manuscript is that the relevance of the CRISPR experiments is still rather tenuous given that the goal is to understand what happens in the estrogen-treatment condition, and these experiments were performed only in OVX mice. Similar concerns reflect that the computational model examining the effect of E2 infers multiple conductances based on qPCR data and an assumption that the conductances are directionally proportional to the level of gene expression, and then tunes these to the current recordings obtained from OVX mice, without a direct confirmation in OVX+E2 conditions that the model parameters accurately reflect the properties of these currents in the presence of estrogen.

Reviewer #1 (Public Review):

Summary:

An online database called MRAD has been developed to identify the risk or protective factors for AD.

Strengths:

This study is a very intriguing study of great clinical and scientific significance that provided a thorough and comprehensive evaluation with regard to risk or protective factors for AD. It also provided physicians and scientists with a very convenient, free as well as user-friendly tool for further scientific investigation.

Comments on revised version:

The authors have resolved all of my previous comments. It's a decent paper worth to be published in this field.

Reviewer #1 (Public Review):

Summary:

This is a reviewed manuscript submission to better understand mechanisms for why HIV individuals have diastolic dysfunction. Due to a lack of robust animal models, the team developed iPS-CM models to study HFpEF. The revised manuscript has toned down claims regarding diastolic function given the lack of mechanical testing. The team has focused on the altered Ca2+ phenotype, which improves the precision of the claims of the team. There remain questions on the functional relevance of the altered calcium handling given the lack of physiological assays. There also remain some questions about whether SGLT2 protein is expressed in these models without testing it, and whether the effects of SGLT2i could be off-target.

Overall, the revised manuscript is improved. I have no major remaining concerns except that the lack of biomechanical assessments diminishes the significance of the study as altered calcium alone would not be considered sufficient evidence for diastolic dysfunction, which was major task set out to answer by the group.

Reviewer #1 (Public Review):

Summary:

This study, titled "Enhancing Bone Regeneration and Osseointegration using rhPTH(1-34) and Dimeric R25CPTH(1-34) in an Osteoporotic Beagle Model," provides valuable insights into the therapeutic effects of two parathyroid hormone (PTH) analogs on bone regeneration and osseointegration. The research is methodologically sound, employing a robust animal model and a comprehensive array of analytical techniques, including micro-CT, histological/histomorphometric analyses, and serum biochemical analysis.

Strengths:

The use of a large animal model, which closely mimics postmenopausal osteoporosis in humans, enhances the study's relevance to clinical applications. The study is well-structured, with clear objectives, detailed methods, and a logical flow from introduction to conclusion. The findings are significant, demonstrating the potential of rhPTH(1-34) and dimeric R25CPTH(1-34) in enhancing bone regeneration, particularly in the context of osteoporosis.

Weaknesses: There are no major weaknesses.

Reviewer #2 (Public Review):

Summary:

The authors performed a systematic review and meta-analysis to investigate whether the frequency of emergence of resistance is different if combination antibiotic therapy is used compared to fewer antibiotics. The review shows that there is currently insufficient evidence to reach a conclusion due to the limited sample size. High-quality studies evaluating appropriate antimicrobial resistance endpoints are needed.

Strengths:

The strength of the manuscript is that the article addresses a relevant research question which is often debated. The article is well-written and the methodology used is valid. The review shows that there is currently insufficient evidence to reach a conclusion due to the limited sample size. High-quality studies evaluating appropriate antimicrobial resistance endpoints are needed. I have several comments and suggestions for the manuscript.

Weaknesses:

Weaknesses of the manuscript are the large clinical and statistical heterogeneity and the lack of clear definitions of acquisition of resistance. Both these weaknesses complicate the interpretation of the study results.

Comments on latest version:

The authors adressed all the comments that were shared in the previous peer review. I still believe that both clinical and statistical heterogeneity remains a problem with the interpretation of the meta-analysis. However, as the authors state, this is in line with the original research question as formulated on Prospero.

Reviewer #1 (Public Review):

Summary:

In this paper the authors provide a thorough demonstration of the role that one particular type of voltage-gated potassium channel, Kv1.8, plays in a low voltage activated conductance found in type I vestibular hair cells. Along the way, they find that this same channel protein appears to function in type II vestibular hair cells as well, contributing to other macroscopic conductances. Overall, Kv1.8 may provide especially low input resistance and short time constants to facilitate encoding of more rapid head movements in animals that have necks. Combination with other channel proteins, in different ratios, may contribute to the diversified excitability of vestibular hair cells.

Strengths:

The experiments are comprehensive and clearly described, both in text and in the figures. Statistical analyses are provided throughout.

Weaknesses:

None.

Reviewer #1 (Public Review):

The study investigates Cancer Driving Nucleotides (CDNs) using the TCGA database, finding that these recurring point mutations could greatly enhance our understanding of cancer genomics and improve personalized treatment strategies. Despite identifying 50-150 CDNs per cancer type, the research reveals that a significant number remain undiscovered, limiting current therapeutic applications, and underscoring the need for further larger-scale research.

Strengths:

The study provides a detailed examination of cancer-driving mutations at the nucleotide level, offering a more precise understanding than traditional gene-level analyses. The authors found a significant number of CDNs remain undiscovered, with only 0-2 identified per patient out of an expected 5-8, indicating that many important mutations are still missing. The study indicated that identifying more CDNs could potentially significantly impact the development of personalized cancer therapies, improving patient outcomes.

Weaknesses:

The study is constrained by relatively small sample sizes for each cancer type, which reduces the statistical power and robustness of the findings. ICGC and other large-scale WGS datasets are publicly available but were not included in this study.

To be able to identify rare driver mutations, more samples are needed to improve the statistical power, which is well-known in cancer research.

The challenges in direct functional testing of CDNs due to the complexity of tumor evolution and unknown mutation combinations limit the practical applicability of the findings.

The QC of the TCGA data was not very strict, i.e, "patients with more than 3000 coding region point mutations were filtered out as potential hypermutator phenotypes", it would be better to remove patients beyond +/- 3*S.D from the mean number of mutations for each cancer type. Given some point mutations with >3 hits in the TCGA dataset, they were just false positive mutation callings, particularly in the large repeat regions in the human genome.

The codes for the statistical calculation (i.e., calculation of Ai_e, et al) are not publicly available, which makes the findings hard to be replicated.

Reviewer #1 (Public Review):

Calcium channels are key regulators of synaptic strength and plasticity, yet how these channels are differentially utilized to enable synaptic diversity is not clear. In this manuscript, the authors use new endogenous tagging of the Drosophila CaV2 channel Cac and three auxiliary subunits to investigate distinct calcium channel functions at two motor neuron subtypes at the fly NMJ, Is and Ib. Although it is clear from previous studies that Pr is higher at Is over Ib, it is not clear why. The authors confirm these differences using postsynaptic calcium imaging combined with post-hoc Cac-TdTomato imaging. Then, through a series of confocal and super resolution imaging studies, the authors describe differences in calcium channel and active zone structure between Is and Ib motor neuron terminals, and the role of Brp and homeostatic plasticity in regulating channel abundance. Finally, the authors show that while the CaBeta subunit is present at similar levels at Is and Ib active zones, there is an interesting reduction in Stj at Is active zones. The authors conclude that these differences in active zone structure and architecture contribute to the generation of the observed heterogeneity in synaptic strength.

Overall the manuscript is well written, and the successful generation of the new endogenous Cac tags (Td-Tomato, Halo) and CaBeta, stj, and stolid genes with V5 tags will be powerful reagents for the field to enable new studies on calcium channels in synaptic structure, function, and plasticity. There are also some interesting, though not entirely unexpected, findings regarding how Brp and homeostatic plasticity modulate calcium channel abundance. The key factors generating diversity in synaptic strength beyond simple Ca2+ influx are well articulated in framing this study. Beyond the particularly useful new reagents for the field presented, the new data demonstrating a concerted and coupled increase in Cac, Stj, and CaB together after plasticity provides an interesting new dimension to the study and a foundation for new work moving forward.

Comments on revision:

This is a much improved revised manuscript, where the authors have done an excellent job of responding to my initial concerns. In particular, the key factors generating diversity in synaptic strength beyond simple Ca2+ influx are better articulated in framing this study. Beyond the particularly useful new reagents for the field presented, the new data demonstrating a concerted and coupled increase in Cac, Stj, and CaB together after plasticity provides an interesting new dimension to the study and a foundation for new work moving forward.

Upon reflection, I think my initial review came across as a bit harsh, and I am happy to now update my original evaluation to better reflect the importance and impact of this very nice study. I commend the authors on an outstanding study.

Reviewer #1 (Public Review):

Greter et al. provide an interesting and creative use of lactulose as a "microbial metabolism" inducer, combined with tracking of H2 and other fermentation end products. The topic is timely and will likely be of broad interest to researchers studying nutrition, circadian rhythm, and gut microbiota. However, a couple of moderate to major concerns were noted that may impact the interpretation of the current data:

(1) Much of the data relies on housing gnotobiotic mice in metabolic cages, but I couldn't find any details of methods to assess contamination during multiple days of housing outside of gnotobiotic isolators/cages. Given the complexity of the metabolic cage system used, sterility would likely be incredibly challenging to achieve. More details needed to be included about how potential contamination of the mice was assessed, ideally with 16S rRNA gene sequencing data of the endpoint samples and/or qPCR for total colonization levels relative to the more targeted data shown.

(2) The language could be softened to provide a more nuanced discussion of the results. While lactulose does seem to induce microbial metabolism it also could have direct effects on the host due to its osmotic activity or other off-target effects. Thus, it seems more precise to just refer to lactulose specifically in the figure titles and relevant text. Additionally, the degree to which lactulose "disrupts the diurnal rhythm" isn't clear from the data shown, especially given that the markers of circadian rhythm rapidly recover from the perturbation. It is probably more precise to instead state that lactulose transiently induces fermentation during the light phase or something to that effect. The discussion could also be expanded to address what methods are available or could be developed to build upon the concepts here; for example, the use of genetic inducers of metabolism which may avoid the more complex responses to lactulose.

Despite these concerns, this was still an intriguing and valuable addition to the growing literature on the interface of the microbiome and circadian fields.

Reviewer #1 (Public Review):

Summary:

Recordings were made from the dentate nucleus of two monkeys during a decision-making task. Correlates of stimulus position and stimulus information were found to varying degrees in the neuronal activities.

Strengths:

A difficult decision-making task was examined in two monkeys.

Weaknesses:

One of the monkeys did not fully learn the task. The manuscript lacked a coherent hypothesis to be tested, and no attempt was made to consider the possibility that this part of the brain may have little to do with the task that was being studied.

Reviewer #1 (Public Review):

Summary:<br /> In this manuscript, Singh, Wu and colleagues explore functional links between septins and the exocyst complex. The exocyst in a conserved octameric complex that mediates the tethering of secretory vesicles for exocytosis in eukaryotes. In fission yeast cells, the exocyst is necessary for cell division, where it localizes mostly at the rim of the division plane, but septins, which localize in a similar manner, are non-essential. The main findings of the work are that septins are required for the specific localization of the exocyst to the rim of the division plane, and the likely consequent localization of the glucanase Eng1 at this same location, where it is known to promote cell separation. In the absence of septins, the exocyst still localizes to the division plane but is not restricted to the rim. They also show some defects in the localization of secretory vesicles and glucan synthase cargo. They further propose that interactions between septins and exocysts are direct, as shown through Alphafold2 predictions (of unclear strength) and clean coIP experiments.

Strengths:<br /> The septin, exocyst and Eng1 localization data are well supported, showing that the septin rim recruits the exocyst and (likely consequently) the Eng1 glucanase at this location. One major finding of the manuscript is that of a physical interaction between septins and exocyst subunits. Indeed, many of the coIPs supporting this discovery are very clear.

Weaknesses:<br /> I am less convinced by the strength of the physical interaction of septins with the exocyst complex. Notably, one important open question is whether septins interact with the intact exocyst complex, as claimed in the text, or whether the interactions occur only with individual subunits. The two-hybrid and coIP data only show weak interactions with individual subunits, and some coIPs (for instance Sec3 and Exo70 with Spn1 and Spn4) are negative, suggesting that the exocyst complex does not remain intact in these experiments. Given the known structure of the full exocyst complex and septin filaments (at least in S. cerevisiae), the Alphafold2 predicted structure could be used to probe whether the proposed interaction sites are compatible with full complex formation.

The effect of spn1∆ on Eng1 localization is very clear, but the effect on secretory vesicles (Ypt3, Syb1) and glucan synthase Bgs1 is less convincing. The effect is small, and it is not clear how the cells are matched for the stage of cytokinesis.

Reviewer #1 (Public Review):

Summary:

This study was to examine the associations of a healthy lifestyle with comprehensive and organ-specific biological ages. It emphasized the importance of lifestyle factors in biological ages, which were defined using common blood biomarkers and body measures.

Strengths:

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

Weaknesses:

(1) Since only 8.5% of participants from the CMEC (China Multi-Ethnic Cohort Study) were included in the study, has any section bias happened?

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

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

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

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

Reviewer #1 (Public Review):

Summary:

The authors set out to understand the role played by a key global metabolic regulator called Crp/cAMP in the formation of persister Escherichia coli that survive antibiotic treatment without acquiring genetic mutations.

In order to achieve this aim, the authors employ an interdisciplinary approach exquisitely integrating standard microbiology assays with cutting-edge genomic, metabolomic, and proteomics screening.

The data presented by the authors convincingly demonstrate that the deletion of two key genes that are part of the Crp/cAMP complex (i.e. crp and cyaA) leads to a significant decrease in the number of persisters, thus pointing towards a key role played by the Crp/cAMP complex in the formation of persisters in E. coli.

The data presented also demonstrate that deletion of the crp gene leads to an overall decrease in energy metabolism and an overall increase in anabolic metabolism at the population level. It is not clear either what the contribution of the cyaA gene is in this respect, or why the deletion of cyaA has an opposite effect on cAMP concentration compared to crp deletion, although the authors present two reasonable untested hypotheses in the discussion. The authors might also want to explicitly acknowledge that these key data are obtained at the whole population level rather than at the level of the persister subpopulation.

Finally, the authors convincingly show that the persisters they investigated are non-growing and have a higher redox activity and that the deletion of key genes involved in energy metabolism leads to a decrease in the number of persisters.

These data will be key for future investigations on the biochemical mechanisms that allow bacteria to adapt to stressors such as nutrient depletion or exposure to antibiotics. As such this work will likely have an impact in a variety of fields such as bacterial biochemistry, antimicrobial resistance research, and environmental microbiology.

Strengths:

Interdisciplinary approach.<br /> Excellent use of replication and ensuring reproducibility.<br /> Excellent understanding and presentation of the biochemical mechanisms underpinning bacterial physiology via an integrated genomic, metabolomic, and proteomic screening.

Weaknesses:

Two genes from the Crp/cAMP complex (crp and cyaA) are hypothesised to be key for persistence but key metabolomics and proteomics data are obtained from only one deletion mutant in the crp gene.

The deletion of crp and cyaA have opposite effects on the concentration of cAMP, a comparison of metabolomics and proteomics data obtained using both mutants might aid in understanding this difference.

Metabolomics, proteomics, and metabolic activity data are obtained at the whole population level rather than at the level of the persister sub-population.

Joint Public Review:

Solitary Fibrous Tumors (SFTs) are a rare malignancy defined by NAB2-STAT6 fusions. Because the molecular understanding of the disease is largely lacking, there are currently no targeted treatment approaches. Using primary tumor and adjacent normal tissue samples and cells inducibly expressing NAB2-STAT6, Hill et al. perform a detailed characterization of the transcriptomic and epigenomic NAB2-STAT6 SFT signatures. They identify enrichment or EGR1/NAB2 (but not STAT6) sites bound by the fusion protein and increased expression of EGR1 targets. Their studies indicate that NAB2-STAT6 fusion may direct the nuclear translocation of NAB2 and EGR1 proteins and potentially NAB1. Transcriptionally, NAB2-STAT6 SFTs most closely resemble neuroendocrine tumors.

This pioneering study provides critical insight into the molecular pathogenesis of SFTs, pivotal for the future development of mechanistically informed treatment approaches. The study is rigorously executed and well-written. This new knowledge is an important addition to the field. Recommendations for minor improvements can be made.

Quotations and Literary Allusions spoken by Willy Wonka in the 1971 film, Willy Wonka and the Chocolate Factory<br /> by Thomas M. Brodhead<br /> https://bmt-systems.com/score/wonka.htm

Archived copy: https://web.archive.org/web/20200111135336/https://bmt-systems.com/score/wonka.htm

Reviewer #1 (Public Review):

Summary:

The overall goal of the manuscript is to delineate pathways that are conditionally essential with the Bam complex and associated chaperones. The Bam complex is made of several proteins, including BamA and BamD, which are essential. The protein complex works to insert proteins in the asymmetric outer membrane. Substrates are translated in the cytoplasm prior to transport across the cell envelope to the Bam complex. Transport includes non-essential periplasmic chaperones, SurA, Skp, and DegP. According to the authors, the pathways were assumed to be redundant. The Bam complex also includes non-essential components, BamBCE. These were thought to be accessory components that interact with BamA and BamD to coordinate optimal activity. While some roles have been assigned to BamE and BamB, a detailed understanding of the role of each accessory Bam protein is lacking. In this study, more specific roles for each non-essential Bam component are proposed.

Strengths:

The overall findings are intriguing and could advance our understanding as to how the Gram-negative cell envelope is assembled. These studies could provide new targets for antimicrobial treatment. In general, the manuscript was well-written.

Weaknesses:

While the overall findings are interesting, I had some concerns with the data analysis, presentation, and conclusions. Not all the conclusions are supported by data. The proposed revisions include experimental and editorial work. The manuscript is generally well-written and could provide impactful data to advance the field if the concerns are addressed.

Major concerns:

Overall Comments:

(1) The cutoffs the authors used to define "conditionally essential" mutants are not reported. The results also lack validation for lethality using a titratable system. It would be ideal to validate several genes in each dataset to determine cutoffs (i.e. 5-fold decrease in insertion mutants) for conditional lethality. It was not done (or described) here.

(2) Also, two mutations that both make the cells sick could provide an additive effect (i.e. dapF and BamB), which doesn't necessarily mean the pathways are linked. The authors should revise their wording. They have not shown genetic linkage in some cases.

(3) Mutations throughout the manuscript are not complemented. It would be ideal to add complementation data to show the gene-phenotype relationship is specific.

(4) Also, I would argue the term "conditionally essential genes" should be replaced with "synthetically lethal". Strains were compared in the same conditions but with different genetic backgrounds.

Reviewer #1 (Public Review):

Summary:

This study explores the roles of dact1 and dact2 in zebrafish embryonic axis formation and craniofacial morphogenesis. The researchers aim to uncover the mechanisms by which dact1/2 modulates Wnt signaling during embryonic development and patterning. They propose distinct spatiotemporal roles for Dact1 and Dact2 proteins in zebrafish embryonic development, particularly their involvement in modulating noncanonical Wnt signaling during convergent extension events. The findings demonstrate that dact1 and dact2 have unique spatiotemporal expression domains during development and that mutations in dact1/2 lead to convergent extension defects. Furthermore, the study attempts to link these defects to craniofacial abnormalities resulting from dact1/2 mutations. Compound mutants were used to investigate the connection between dact1 and dact2, as single mutants did not exhibit craniofacial phenotypes. The research also includes comprehensive transcriptomics and pathway analyses of differentially expressed genes in dact1/2 mutants, revealing the overexpression of calpain 8, a calcium-dependent cysteine protease. The study suggests that the upregulation of calpain 8 is linked to the observed craniofacial dysmorphology in dact1/2 mutants, implying a potential connection between calpain 8 expression and craniofacial abnormalities.

Strengths:

• The study effectively recapitulates previous findings on the role of dact1/2 in modulating convergent extension during zebrafish embryogenesis.<br /> • A combination of multiple approaches, including in vivo time-lapse imaging, is used to elucidate the etiology of the rod-like neurocranial phenotype in dact1/2 double mutants.<br /> • The study utilizes both traditional and newly created mutant lines, analyzing them through single-cell transcriptomics.

Weaknesses:

(1) The authors successfully addressed reviewers' suggestions with revised experiments and explanations. However, the overall narrative struggles to build a more coherent storyline.<br /> (2) The potential activity of truncated and upregulated dact mRNAs (Fig S2) and partially functional dact proteins needs further clarification.<br /> (3) Data-rich figures, specifically Figs 6, 7, and 8D, could be simplified for better clarity.

Reviewer #1 (Public Review):

In this manuscript, Laboy and colleagues investigated upstream regulators of MML-1/Mondo, a key transcription factor that regulates aging and metabolism, using the nematode C. elegans and cultured mammalian cells. By performing a targeted RNAi screen for genes encoding enzymes in glucose metabolism, the authors found that two hexokinases, HXK-1 and HXK-2, regulate nuclear localization of MML-1 in C. elegans. The authors showed that knockdown of hxk-1 and hxk-2 suppressed longevity caused by germline-deficient glp-1 mutations. The authors demonstrated that genetic or pharmacological inhibition of hexokinases decreased nuclear localization of MML-1, via promoting mitochondrial β-oxidation of fatty acids. They found that genetic inhibition of hxk-2 changed the localization of MML-1 from the nucleus to mitochondria and lipid droplets by activating pentose phosphate pathway (PPP). The authors further showed that the inhibition of PPP increased the nuclear localization of mammalian MondoA in cultured human cells under starvation conditions, suggesting the underlying mechanism is evolutionarily conserved. This paper provides compelling evidence for the mechanisms by which novel upstream metabolic pathways regulate MML-1/Mondo, a key transcription factor for longevity and glucose homeostasis, through altering organelle communications, using two different experimental systems, C. elegans and mammalian cells. This paper will be of interest to a broad range of biologists who work on aging, metabolism, and transcriptional regulation.

Reviewer #1 (Public Review):

Summary:

By combining an analysis of the evolutionary age of the genes expressed in male germ cells, a study of genes associated with spermatocyte protein-protein interaction networks and functional experiments in Drosophila, Brattig-Correia and colleagues provide evidence for an ancient origin of the genetic program underlying metazoan spermatogenesis. This leads to the identification of a relatively small core set of functional interactions between deeply conserved gene expression regulators, whose impairment is then shown to be associated with cases of human male infertility.

Strengths:

In my opinion, the work is important for three different reasons. First, it shows that, even though reproductive genes can evolve rapidly and male germ cells display a significant level of transcriptional noise, it is still possible to obtain convincing evidence that a conserved core of functionally interacting genes lies at the basis of the male germ transcriptome. Second, it reports an experimental strategy that could also be applied to gene networks involved in different biological problems. Third, the authors make a compelling case that, due to its effects on human spermatogenesis, disruption of the male germ cell orthoBackbone can be exploited to identify new genetic causes of infertility.

Weaknesses:

The main strength of the general approach followed by the authors is, inevitably, also a weakness. This is because a study rooted in comparative biology is unlikely to identify newly emerged genes that may adopt key roles in processes such as, for example, species-specific gamete recognition. Additionally, the use of a TPM >1 threshold for protein-coding transcripts - which, as the authors pointed out, was a necessary compromise due to the high transcriptional noise of the system under study - may exclude genes, such as those encoding proteins required for gamete fusion, which are thought to be expressed at a very low level. Although these considerations raise the possibility that the chosen approach may miss information that, depending on the species, could be potentially highly functionally important, this by no means reduces its value in identifying genes belonging to the conserved genetic program of spermatogenesis. Moreover, as mentioned in the Discussion, future variations of the pipeline described in the manuscript may allow us to extend the reach of the present analysis.

Reviewer #2 (Public Review):

Summary:

The authors used state-of-the-art microscopy to analyze the structural changes that occur in sperm tails after the acrosome reaction. They found that midpiece contraction and actin reorganization occurred, which is associated with the cessation of flagellar motility during sperm-egg fusion. The mechanism by which flagellar motility is arrested during sperm-oocyte fusion is unknown, and this study proposes its novel mechanism and provides important insights for cell and reproductive biologists.

In the revised manuscript, the authors addressed most of my concerns.

Strength:

Various microscopy techniques including super-resolution microscopy and scanning electron microscopy were used to analyze structural organization of the midpiece in detail.

Reviewer #1 (Public Review):

Summary

This study was designed to investigate changes in gene expression and associated chromatin accessibility patterns in spermatogonia in mice at different postnatal stages from pups to adults. The objective was to describe dynamic changes in these patterns that potentially correlate with functional changes in spermatogonia as a function of development and reproductive maturation. The potential utility of this information is to serve as a reference against which similar data from animals subjected to various disruptive environmental influences can be compared.

Major Strengths and Weaknesses of the Methods and Results

A strength of the study is that it reviews previously published datasets describing gene expression and chromatin accessibility patterns in mouse spermatogonia. A weakness of the study is that it is not clear what new information is provided by the data provided that was not already known from previously published studies (see below). Specific weaknesses include the following...

- Terminology - In the Abstract and first part of the Introduction the authors use the generic term "spermatogonial cells" in a manner that seems to be referring primarily to spermatogonial stem cells (SSCs) but initially ignores the well-known heterogeneity among spermatogonia - particularly the fact that only a small proportion of developing spermatogonia become SSCs - and ONLY those SSCs and NOT other developing spermatogonia - support steady-state spermatogenesis by retaining the capacity to either self-renew or contribute to the differentiating spermatogenic lineage throughout the male reproductive lifespan. The authors eventually mention other types of developing male germ cells, but their description of prospermatogonial stages that precede spermatogonial stages is deficient in that M-prospermatogonia - which occur after PGCs but before T1-prospermatogonia - are not mentioned. This description also seems to imply that all T2-prospermatogonia give rise to SSCs which is far from the case. It is the case that prospermatogonia give rise to spermatogonia, but only a very small proportion of undifferentiated spermatogonia form the foundational SSCs and ONLY SSCs possess the capacity to either self-renew or give rise to sequential waves of spermatogenesis.

- Introduction - Statements regarding distinguishing transcriptional signatures in spermatogonia at different postnatal stages appear to refer to ALL subtypes of spermatogonia present at each stage collectively, thereby ignoring the well-known fact that there are distinct spermatogonial subtypes present at each postnatal stage and that some of those occur at certain stages but not at others. This brings into question the usefulness of the authors' discussion of what types of genes are expressed and/or what types of changes in chromatin accessibility are detected in spermatogonia at each stage.

- Methodology - The authors based recovery (enrichment) of spermatogonia from male pups on FACS sorting for THY1 and RMV-1. While sorting total testis cells for THY1+ cells does enrich for spermaogonia, this approach is now known to not be highly specific for spermatogonia (somatic cells are also recovered) and definitely not for SSCs. There are more effective means for isolating SSCs from total testis cells that have been validated by transplantation experiments (e.g. use of the Id4/eGFP transgene marker).

The authors then used "deconvolution" of bulk RNA-seq data in an attempt to discern spermatogonial subtype-specific transcriptomes. It is not clear why this is necessary or how it is beneficial given the availability of multiple single-cell RNA-seq datasets already published that accomplish this objective quite nicely - as the authors essentially acknowledge. Beyond this concern, a potential flaw with the deconvolution of bulk RNA-seq data is that this is a derivative approach that requires assumptions/computational manipulations of apparent mRNA abundance estimates that may confound interpretation of the relative abundance of different cellular subtypes within the hetergeneous cell population from which the bulk RNA-seq data is derived. Bottom line, it is not clear that this approach affords any experimental advantage over use of the publicly available scRNA-seq datasets and it is possible that attempts to employ this approach may be flawed yielding misleading data.

- Results & Discussion - In general, much of the information reported in this study is not novel. The authors' discussion of the makeup of various spermatogonial subtypes in the testis at various ages does not really add anything to what has been known for many years on the basis of classic morphological studies. Further, as noted above, the gene expression data provided by the authors on the basis of their deconvolution of bulk RNA-seq data does not add any novel information to what has been shown in recent years by multiple elegant scRNA-seq studies - and, in fact, as also noted above - represents an approach fraught with potential for misleading results. The potential value of the authors' report of "other cell types" not corresponding to major somatic cell types identified in earlier published studies seems quite limited given that they provide no follow-up data that might indicate the nature of these alternative cell types. Beyond this, much of the gene expression and chromatin accessibility data reported by the authors - by their own admission given the references they cite - is largely confirmatory of previously published results. Similarly, results of the authors' analyses of putative factor binding sites within regions of differentially accessible chromatin also appear to confirm previously reported results. Ultimately, it is not at all novel to note that changes in gene expression patterns are accompanied by changes in patterns of chromatin accessibility in either related promoters or enhancers. The discussion of these observations provided by the authors takes on more of a review nature than that of any sort of truly novel results. As a result, it is difficult to discern how the data reported in this manuscript advance the field in any sort of novel or useful way beyond providing a review of previously published studies on these topics.

Likely impact - The likely impact of this work is relatively low because, other than the value it provides as a review of previously published datasets, the new datasets provided are not novel and so do not advance the field in any significant manner.

Reviewer #1 (Public Review):

Summary:<br /> The manuscript provides a novel method for the automated detection of scent marks from urine and feces in rodents. Given the importance of scent communication in these animals and their role as model organisms, this is a welcome tool.

Strengths:<br /> The method uses a single video stream (thermal video) to allow for the distinction between urine and feces. It is automated.

Weaknesses:<br /> The accuracy level shown is lower than may be practically useful for many studies. The accuracy of urine is 80%. This is understandable given the variability of urine in its deposition, but makes it challenging to know if the data is accurate. If the same kinds of mistakes are maintained across many conditions it may be reasonable to use the software (i.e., if everyone is under/over counted to the same extent). Differences in deposition on the scale of 20% would be challenging to be confident in with the current method, though differences of the magnitude may be of biological interest. Understanding how well the data maintain the same relative ranking of individuals across various timing and spatial deposition metrics may help provide further evidence for the utility of the method.

Reviewer #1 (Public Review):

Summary:

De Waele et al. reported a dual-branch neural network model for predicting antibiotic resistance profiles using matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry data. Neural networks were trained on the recently available DRIAMS database of MALDI-TOF mass spectrometry data and their associated antibiotic susceptibility profiles. The authors used dual branch neural network to simultaneously represent information about mass spectra and antibiotics for a wide range of species and antibiotic combinations. The authors showed consistent performance of their strategy to predict antibiotic susceptibility for different spectrum and antibiotic representations (i.e., embedders). Remarkably, the authors showed how small datasets collected at one location can improve the performance of a model trained with limited data collected at a second location. The authors also showed that species-specific models (trained in multiple antibiotic resistance profiles) outperformed both the single recommender model and the individual species-antibiotic combination models. Despite the promising results, the authors should explain in more detail some of the analyses reported in the manuscript (see weaknesses).

Strengths:

• A single AMR recommender system could potentially facilitate the adoption of MALDI-TOF based antibiotic susceptibility profiling into clinical practices by reducing the number of models to be considered, and the efforts that may be required to periodically update them.<br /> • Authors tested multiple combinations of embedders for the mass spectra and antibiotics while using different metrics to evaluate the performance of the resulting models. Models trained using different spectrum embedder-antibiotic embedder combinations had remarkably good performance for all tested metrics. The average ROC AUC scores for global and species-specific evaluations were above 0.8.<br /> • Authors developed species-specific recommenders as an intermediate layer between the single recommender system and single species-antibiotic models. This intermediate approach achieved maximum performance (with one type of the species-specific recommender achieving a 0.9 ROC AUC), outlining the potential of this type of recommenders for frequent pathogens.<br /> • Authors showed that data collected in one location can be leveraged to improve the performance of models generated using a smaller number of samples collected at a different location. This result may encourage researchers to optimize data integration to reduce the burden of data generation for institutions interested in testing this method.

Weaknesses:

• Section 4.3 ("expert baseline model"): the authors need to explain how the probabilities defined as baselines were exactly used to predict individual patient susceptible profiles.<br /> • Authors do not offer information about the model features associated with resistance. Although I understand the difficulty of mapping mass spectra to specific pathways or metabolites, mechanistic insights are much more important in the context of AMR than in the context of bacterial identification. For example, this information may offer additional antimicrobial targets. Thus, authors should at least identify mass spectra peaks highly associated with resistance profiles. Are those peaks consistent across species? This would be a key step towards a proteomic survey of mechanisms of AMR. See previous work on this topic: PMIDs: 35586072 and 23297261.

Joint Public Review:

The study offers a compelling molecular model for the organization of rootlets, a critical organelle that links cilia to the basal body. Striations have been observed in rootlets, but their assembly, composition, and function remain unknown. While previous research has explored rootlet structure and organization, this study delivers an unprecedented level of resolution, valuable to the centrosome and cilia field. The authors isolated rootlets from mice's eyes. They apply EM to partially purified rootlets (first negative stain, then cryoET). From these micrographs, they observed striations along the membranes along the rootlet but no regular spacing was observed.

The thickness of the sample and membranes prevented good contrast in the tomograms. Thus they further purified the rootlets using detergent, which allowed them to obtain cryoET micrographs of the rootlets with greater details. The tomograms were segmented and further processed to improve the features of the rootlet structures. They proposed that a number of proteins, including rootletin, form parallel coiled coils that run along the rootlet longitudinally. They described how the cross-striations form 3 types of periodic structures -D1/D2/A bands- connected perpendicularly to filaments along the length of the rootlets and to membranes. Overall their data provide a detailed model for the molecular organization of the rootlet.

The major strength is that this high-quality study uses state-of-the-art cryo-electron tomography, sub-tomogram averaging, and image analysis to provide a model of the molecular organization of rootlets. The micrographs are exceptional, with excellent contrast and details, which also implies the sample preparation was well optimized to provide excellent samples for cryo-ET. The manuscript is also clear and accessible.

This research marks a significant step forward in our understanding of rootlets' molecular organization.

Reviewer #1 (Public review):

Summary:

Ctnnb1 encodes β-catenin, an essential component of the canonical Wnt signaling pathway. In this study, the authors identify an upstream enhancer of Ctnnb1 responsible for the specific expression level of β-catenin in the gastrointestinal track. Deletion of this promoter in mice and analyses of its association with human colorectal tumors support that it controls the dosage of Wnt signaling critical to the homeostasis in intestinal epithelia and colorectal cancers.

Strengths:

This study has provided convincing evidence to demonstrate the functions of a gastrointestinal enhancer of Ctnnb1 using combined approaches of bioinformatics, genomics, in vitro cell culture models, mouse genetics, and human genetics. The results support the idea that the dosage of Wnt/β-catenin signaling plays an important role in pathophysiological functions of intestinal epithelia. The experimental designs are solid and the data presented are of high quality. This study significantly contributes to the research fields of Wnt signaling, tissue-specific enhancers, and intestinal homeostasis.

Weaknesses:

Insufficient discussion on some findings was a major weakness in the previous submission, which has been addressed in the revised submission.

Reviewer #1 (Public Review):

The authors developed a rigorous methodology for identifying all Cancer Driving Nucleotides (CDNs) by leveraging the concept of massively repeated evolution in cancer. By focusing on mutations that recur frequently in pan-cancer, they aimed to differentiate between true driver mutations and neutral mutations, ultimately enhancing the understanding of the mutational landscape that drives tumorigenesis. Their goal was to call a comprehensive catalogue of CDNs to inform more effective targeted therapies and address issues such as drug resistance.

Strengths

(1) The authors introduced a concept of using massively repeated evolution to identify CDNs. This approach recognizes that advantageous mutations recur frequently (at least 3 times) across cancer patients, providing a lens to identify true cancer drivers.

(2) The theory showed the feasibility of identifying almost all CDNs if the number of sequenced patients increases to 100,000 for each cancer type.

Weaknesses

(1) The methodology remains theoretical and no novel true driver mutations were identified in this study.

(2) Different cancer types have unique mutational landscapes. The methodology, while robust, might face challenges in uniformly identifying CDNs across various cancers with distinct genetic and epigenetic contexts.

(3) L223, the statement "In other words, the sequences surrounding the high-recurrence sites appear rather random.". Since it was a pan-cancer analysis, the unique patterns of each cancer type could be strongly diluted in the pan-cancer data.

(4) To solidify the findings, the results need to be replicated in an independent dataset.

(5) The key scripts and the list of key results (i.e., CDN sites with i{greater than or equal to}3) need to be shared to enable replication, validation, and further research. So far, only CDN sites with i{greater than or equal to}20 have been shared.

(6) The versions of data used in this study are not clearly detailed, such as the specific version of gnomAD and the version and date of TCGA data downloaded from the GDC Data Portal.

Reviewer #1 (Public Review):

Summary:

Cai et al have investigated the role of msiCAT-tailed mitochondrial proteins that frequently exist in glioblastoma stem cells. Overexpression of msiCAT-tailed mitochondrial ATP synthase F1 subunit alpha (ATP5) protein increases the mitochondrial membrane potential and blocks mitochondrial permeability transition pore formation/opening. These changes in mitochondrial properties provide resistance to staurosporine (STS)-induced apoptosis in GBM cells. Therefore, msiCAT-tailing can promote cell survival and migration, while genetic and pharmacological inhibition of msiCAT-tailing can prevent the overgrowth of GBM cells.

Strengths:

The CAT-tailing concept has not been explored in cancer settings. Therefore, the present provides new insights for widening the therapeutic avenue.

Weaknesses:

Although the paper does have strengths in principle, the weaknesses of the paper are that these strengths are not directly demonstrated. The conclusions of this paper are mostly well-supported by data, but some aspects of image acquisition and data analysis need to be clarified and extended.

Reviewer #1 (Public Review):

Summary:

This work contributes several important and interesting observations regarding the heterotolerance of non-growing Escherichia coli and Pseudomonas aeruginosa to the antimicrobial peptide tachyplesin. The primary mechanism of action of tachyplesin is thought to be disruption of the bacterial cell envelope, leading to leakage of cellular contents after a threshold level of accumulation. Although the MIC for tachyplesin in exponentially growing E. coli is just 1 ug/ml, the authors observe that a substantial fraction of a stationary phase population of bacteria survive much higher concentrations, up to 64 ug/ml. By using a fluorescently-labelled analogue of tachyplesin, the authors show that the amount of per-cell intracellular accumulation of tachyplesin displays a bimodal distribution and that the fraction of "low accumulators" correlates with the fraction of survivors.

Using a microfluidic device, they show that low accumulators exclude propidium iodide, suggesting that their cell envelopes remain largely intact, while high accumulators of tachyplesin also stain with propidium iodide. They show that this phenomenon holds for several clinical isolates of E. coli with different genetic determinants of antibiotic resistance, and for a strain of Pseudomonas aeruginosa. However, the bimodal distribution does not occur in these organisms for several other antimicrobial peptides, or for tachyplesin in Klebsiella pneumoniae or Staphylococcus aureus, indicating some degree of specificity in the interaction between AMP and bacterial cell envelope. They next explore the dynamics of the fluorescent tachyplesin accumulation and show interestingly that a high degree of accumulation is initially seen in all cells, but that the "low accumulator" subpopulation manages to decrease the amount of intracellular fluorescence over time, while the "high accumulator" subpopulation continues to increase its intracellular fluorescence. Focusing on increased efflux as a hypothesised mechanism for the "low accumulator" phenotype, based on transcriptomic analysis of the two subpopulations, the authors screen putative efflux inhibitors to see if they can block the formation of the low accumulator subpopulation. They find that both the protonophore CCCP and the SSRI sertraline can block the formation of this subpopulation and that a combination of sertraline plus tachyplesin kills a greater fraction of the stationary phase cells than either agent alone, similar to the killing observed when growing cells are treated with tachyplesin.

Strengths:

This study provides new insight into the heterogeneous behaviours of non-growing bacteria when exposed to an antimicrobial peptide, and into the dynamics of their response. The single-cell analysis by FACS and microscopy is compelling. The results provide a much-needed single-cell perspective on the phenomenon of tolerance to AMPs and a good starting point for further exploration.

Weaknesses:

My main concerns surround the conclusions drawn about the physiological underpinnings of these behaviours, based in part on transcriptomic analysis and also on the observation of the dynamics. I think deeper consideration of the relative contributions of influx and efflux to the observed accumulation dynamics, and the slow/non-growing context of the observations would be helpful. In particular, these issues seem important:

(1) The initial high accumulation by all cells followed by the emergence of a sub-population that has reduced its intracellular levels of tachyplesin is a key observation and I agree with the authors' conclusion that this suggests an induced response to the AMP is important in facilitating the bimodal distribution. However, I think the conclusion that upregulated efflux is driving the reduction in signal in the "low accumulator" subpopulation is not fully supported. Steady-state amounts of intracellular fluorescent AMP are determined by the relative rates of influx and efflux and a decrease could be caused by decreasing influx (while efflux remained unchanged), increasing efflux (while influx remained unchanged), or both decreasing influx and increasing efflux. Given the transcriptomic data suggest possible changes in the expression of enzymes that could affect outer membrane permeability and outer membrane vesicle formation as well as efflux, it seems very possible that changes to both influx and efflux are important. The "efflux inhibitors" shown to block the formation of the low accumulator subpopulation have highly pleiotropic or incompletely characterised mechanisms of action so they also do not exclusively support a hypothesis of increased efflux.

(2) A conclusion of the transcriptomic analysis is that the lower accumulating subpopulation was exhibiting "a less translationally and metabolically active state" based on less upregulation of a cluster of genes including those involved in transcription and translation. This conclusion seems to borrow from well-described relationships referred to as bacterial growth laws in which the expression of genes involved in ribosome production and translation is directly related to the bacterial growth (and metabolic) rate. However, the assumptions that allow the formulation of the bacterial growth laws (balanced, steady state, exponential growth) do not hold in growth arrest. A non-growing cell could express no genes at all or could express ribosomal genes at a very low level, or efflux pumps at a high level. The distribution of transcripts among the functional classes of genes does not reveal anything about metabolic rates within the context of growth arrest - it only allows insight into metabolic rates when the constraint of exponential growth can be assumed. Efflux pumps can be highly metabolically costly; for example, Tn-Seq experiments have repeatedly shown that mutants for efflux pump gene transcriptional repressors have strong fitness disadvantages in energy-limited conditions. There are no data presented here to disprove a hypothesis that the low accumulators have high metabolic rates but allocate all of their metabolic resources to fortifying their outer membranes and upregulating efflux. This could be an important distinction for understanding the vulnerabilities of this subpopulation. Metabolic rates can be more directly estimated for single cells using respiratory dyes or pulsed metabolic labelling, for example, and these data could allow deeper insight into the metabolic rates of the two subpopulations.

The observation that adding nutrients to the stationary phase cultures pushes most of the cells to the "high accumulator" state is presented as support of the hypothesis that the high accumulator state is a higher metabolism/higher translational activity state. However, it is important to note that adding nutrients will cause most or all of the cells in the population to start to grow, thus re-entering the familiar regime in which bacterial growth laws apply. This is evident in the slightly larger cell sizes seen in the nutrient-amended condition. In contrast to stationary phase cells, growing cells largely do not exhibit the bimodal distribution, and they are much more sensitive to tachyplesin, as demonstrated clearly in the supplement. Growing cells are not necessarily the same as the high-accumulating subpopulation of non-growing cells.

It might also be worth adding some additional context around the potential to employ efflux inhibitors as therapeutics. It is very clear that obtaining sufficient antimicrobial drug accumulation within Gram-negative bacteria is a substantial barrier to effective treatments, and large concerted efforts to find and develop therapeutic efflux pump inhibitors have been undertaken repeatedly over the last 25 years. Sufficiently selective inhibitors of bacterial efflux pumps with appropriate drug-like properties have been challenging to find and none have entered clinical trials. Multiple psychoactive drugs have been shown to impact efflux in bacteria but usually using concentrations in the 10-100 uM range (as here). Meanwhile, the Ki values for their human targets are usually in the sub- to low-nanomolar range. The authors rightly note that the concentration of sertraline they have used is higher than that achieved in patients, but this is by many orders of magnitude, and it might be worth expanding a bit on the substantial challenge of finding efflux inhibitors that would be specific and non-toxic enough to be used therapeutically. Many advances in structural biology, molecular dynamics, and medicinal chemistry may make the quest for therapeutic efflux inhibitors more fruitful than it has been in the past but it is likely to remain a substantial challenge.

Reviewer #1 (Public Review):

Summary:

The study addresses the growing threat of multi-drug-resistant (MDR) pathogens, focusing on the efficacy of colistin (COL), a last-resort antibiotic, and its enhanced activity when combined with artesunate (AS) and ethylenediaminetetraacetic acid (EDTA) against colistin-resistant Salmonella strains. The researchers aim to explore whether these combinations can restore the effectiveness of colistin and understand the underlying mechanisms. The study used a combination of microbiological and molecular techniques to evaluate the antibacterial activity and mechanisms of action of COL, AS, and EDTA.

Key methods include:

(1) Antimicrobial Susceptibility Testing: Determining minimum inhibitory concentrations (MICs) of COL, AS, and EDTA, both alone and in combination, against various Salmonella strains;

(2) Time-Kill Assays: Measuring bacterial growth inhibition over time with different drug combinations;

(3) Fluorescent Probe-Permeability Assays: Assessing cell membrane integrity using fluorescent dyes;

(4) Proton Motive Force Assay: Evaluating the impact on the electrochemical proton gradient (PMF);

(5) Reactive Oxygen Species (ROS) Measurement: Quantifying intracellular ROS levels; (vi) Scanning Electron Microscopy (SEM): Observing morphological changes in bacterial cells; and

(6) Omics Analysis: Transcriptome and metabolome profiling to identify differentially expressed genes (DEGs) and significant differential metabolites (SDMs).

The combination of COL, AS, and EDTA (AEC) showed significant antibacterial activity against colistin-resistant Salmonella strains, reducing the MICs and enhancing bacterial killing compared to individual treatments. The AEC treatment caused extensive damage to both the outer and inner bacterial membranes, as evidenced by increased fluorescence of membrane-impermeant dyes and SEM images showing deformed cell membranes. AEC treatment selectively collapsed the Δψ component of PMF, indicating disruption of vital cellular processes. The combination therapy increased intracellular ROS levels, contributing to bacterial killing. Transcriptome data revealed changes in genes related to two-component systems, flagellar assembly, and ABC transporters. Metabolome analysis highlighted disruptions in pathways such as arachidonic acid metabolism. The findings suggest that AS and EDTA can potentiate the antibacterial effects of colistin by disrupting bacterial membranes, collapsing PMF, and increasing ROS levels. This combination therapy could serve as a promising approach to combat colistin-resistant Salmonella infections.

Strengths:

(1) The study employs a wide range of techniques to thoroughly investigate the antibacterial mechanisms and efficacy of the drug combinations.

(2) The results are consistent across multiple assays and supported by both in vitro and in vivo data.

(3) Combining AS and EDTA with COL represents a novel strategy to tackle antibiotic resistance.

Weaknesses:

(1) The study focuses on a limited number of Salmonella strains, and broader testing on various MDR pathogens would strengthen the findings.

(2) While the study elucidates several mechanisms, further molecular details could provide deeper insights into the interactions between these drugs and bacterial targets.

(3) The time-kill experiment was conducted over 12 hours instead of the recommended 24 hours. To demonstrate a synergistic effect among the drugs, a reduction of at least 2 log10 in colony count should be shown in a 24-hour experiment. Additionally, clarifying the criteria for selecting drug concentrations is important to improve the interpretation of the results.

(4) While the combination of EDTA, artesunate, and colistin shows promising in vitro results against Salmonella strains, the clinical application of this combination warrants careful consideration due to potential toxicity issues associated with these compounds.

Reviewer #1 (Public Review):

Summary:

In this study, the authors investigate the effect of mitochondrial transplantation on post-cardiac arrest myocardial dysfunction (PAMD), which is associated with mitochondrial dysfunction. The authors demonstrate that mitochondrial transplantation enhances cardiac function and increases survival rates after the return of spontaneous circulation (ROSC). Mechanistically, they found that myocardial tissues with transplanted mitochondria exhibit increased mitochondrial complex activity, higher ATP levels, reduced cardiomyocyte apoptosis, and lower myocardial oxidative stress post-ROSC.

Strengths:

Previous studies have reported that mitochondrial transplantation can improve myocardial recovery after regional ischemia, but its potential for treating myocardial injury following cardiac arrest has not been tested yet. Therefore, the findings are somewhat novel. Remarkably, the increased survival in mitochondria treated group post-ROSC is very promising and highlights its translational potential.

Weaknesses:

The organization of the paper, along with the analysis and interpretation of the results, requires significant revision.

Reviewer #1 (Public Review):

Drp1 supports mitochondrial fission (doi: 10.1038/s41586-019-1296-y). Viral sensing triggers mitochondrial fusion, leading to MAVS aggregation and improved type-1 IFN response. It was suggested that impairment of Drp1 upon phosphorylation by Tbk1 enhances mitochondrial fusion in virus-infected cells (doi.org/10.1016/j.molcel.2020.10.018). In this manuscript, Fang et al. describe an unexpected role of caspases activated upon Rift Valley fever virus (RVFV) infection in inactivating Drp1. They show that Drp1 is targeted by multiple caspases, including caspase-3, -6, -7 and -8. Indeed, cleavage of Drp1 leads to mitochondrial elongation, boosting the type-1 IFN response of infected cells. Finally, the authors establish the generalisability of the proposed mechanism in the context of cellular infections with H1N1, SeV, and HSV-1. Caspase-dependent and independent cell death processes provide important host defence mechanisms against obligatorily intracellular viral pathogens. This work suggests that caspases reinforce antiviral response involving also the mitochondria-type 1 IFN axis. As such, the manuscript is well written, and the proposal pertaining to caspase-mediated targeting of Drp1 may have implications beyond host-virus interaction studies. However, several loose ends remain, and these concerns need to be addressed to substantiate the mechanistic model.

Reviewer #1 (Public Review):

Summary:

The current manuscript uses electron spin resonance spectroscopy to understand how the dynamic behavior and conformational heterogeneity of the LPS transport system change during substrate transport and in response to the membrane, bound nucleotide (or transition state analog) and accessory subunits. The study builds on prior structural studies to expand our molecular understanding of this highly significant bacterial transport system.

Strengths

This series of well-designed and well-executed experiments provide new mechanistic insights into the dynamic behavior of the LPS transport system. Notable new insights provided by this study include its indication of the spatial organization of the LptC domain, which was poorly resolved in structures, and how the LptC domain modulates the dynamic behavior of the gate through which lipids access the binding site. In addition, a mass spectrometry approach designed to examine LPS binding at different stages in the nucleotide-dependent conformational cycle provides insight into the order of operations of LPS binding and transport.

Reviewer #1 (Public Review):

In this study, the Authors used a stopped-flow method to investigate the kinetics of substrate translocation through the channel in hexameric ClpB, an ATP-dependent bacterial protein disaggregase. They engineered a series of polypeptides with the N-terminal RepA ClpB-targeting sequence followed by a variable number of folded titin domains. The Authors detected translocation of the substrate polypeptides by observing the enhancement of fluorescence from a probe located at the substrate's C-terminus. The total time of the substrates' translocation correlated with their lengths, which allowed the Authors to determine the number of residues translocated by ClpB per unit time.

Strengths:

This study confirms a previously proposed model of processive translocation of polypeptides through the channel in ClpB. The novelty of this work is in a clever design of a series of kinetic experiments with an engineered substrate that includes stably folded domains. This approach produced a quantitative description of the reaction rates and kinetic step sizes. Another valuable aspect is that the method can be used for other translocases from the AAA+ family to characterize their mechanism of substrate processing.

Weaknesses:

The main limitation of the study is in using a single non-physiological substrate of ClpB, which does not replicate physical properties of the aggregated cellular proteins and includes a non-physiological ClpB-targeting sequence. Another limitation is in the use of ATPgammaS to stimulate the substrate processing. It is not clear how relevant the results are to the ClpB function in living cells with ATP as the source of energy, a multitude of various aggregated substrates without targeting sequences that need ClpB's assistance, and in the presence of the co-chaperones.

Evidence that ATPgammaS without ATP can provide sufficient energy for substrate translocation and unfolding is missing in the paper because the rate of phosphate release from ATPgammaS has not been determined. Thus, it is not clear if the observed translocation is linked to an actual chemical energy input or is a result of a diffusion-driven ratchet mediated by a substrate-trapping ClpB conformation obtained in the presence of ATPgammaS.

Reviewer #1 (Public Review):

Summary:

In this manuscript, the authors delineate the crucial role of the SIRT2-ACSS2 axis in ACSS2 degradation. They demonstrate that SIRT2 acts as an ACSS2 deacetylase specifically under nutrient stress conditions, notably during amino acid deficiency. The SIRT2-mediated deacetylation of ACSS2 at K271 consequently triggers its proteasomal degradation. Additionally, they illustrate that acetylation of ACSS2 at K271 enhances ACSS2 protein levels, thereby promoting De Novo lipogenesis.

Strengths:

The findings presented in this manuscript are clearly interesting.

Weaknesses:

Further support is required for the model put forward by the authors.

Reviewer #1 (Public Review):

Summary:

The authors want to determine the role of the sperm hook of the house mouse sperm in movement through the uterus. They use transgenic lines with fluorescent labels to sperm proteins, and they cross these males to C57BL/6 females in pathogen-free conditions. They use 2-photon microscopy on ex vivo uteri within 3 hours of mating and the appearance of a copulation plug. There are a total of 10 post-mating uteri that were imaged with 3 different males. They provide 10 supplementary movies that form the basis for some of the quantitative analysis in the main body figures. Their data suggest that the role of the sperm hook is to facilitate movement along the uterine wall.

Strengths:

Ex vivo live imaging of fluorescently labeled sperm with 2-photon microscopy is a powerful tool for studying the behavior of sperm.

Weaknesses:

The paper is descriptive and the data are correlations.

The authors cannot directly test their proposed function of the sperm hook in sliding and preventing backward slipping.

Reviewer #1 (Public Review):

Summary:

This study investigated the co-option of IGF2BP2, an RNA binding protein by ZIKV proteins. Designed experiments evaluated if IFG2BP2 co-localized to sites of viral RNA replication, interacted with ZIKV proteins and how ZIKV infection changed the IGF2BP2 interactome.

Strengths:

The authors have used multiple interdisciplinary techniques to address several questions regarding the interaction of ZIKV proteins and IGF2BP2.

The findings could be exciting if concerns are addressed, specifically regarding how ZIKV infection alters the interactome of IGF2BP2.

Comments on thee revised version:

Following response to reviews, the authors have addressed a majority of the concerns with the exception of the western blots:

As requested in the previous review, the authors did quantify the western blot data for half of the blot in 2A, but did not quantify blots in D and E. Please quantify ALL blots. Also, the first two lanes of 2A. The same goes for 4A only infected is quantified, please quantify Mock as well. In the quantification of 4C, all lanes should be quantified, not only the NS5 from C. Also, unclear which lanes were quantified (H/PF/2013 or MR766)? Also, quantification needs to be generally shown as a graph and not included on top of the western blot.

Combined Public Reviews:

Summary:

This study presents an immunotherapeutic strategy for treating mouse cutaneous squamous cell carcinoma (mCSCC) using a passive immunity-like strategy. The researcher induced tumors in healthy mice skin, then isolated the tumor cells and injected into other healthy mice to produce anti-tumor antibodies, and then administered these antibodies back into tumor-bearing mice. Results showed a reduction in tumor volume and altered expression of several cancer markers (p53, Bcl-xL, NF-κB, Bax). The analysis of results suggests a promising impact of antibody-rich serum in treating mouse cutaneous squamous cell carcinoma (mCSCC).

Strengths:

The approach does seem to have effect on preventing tumor progression, from both the tumor size and the cancer hallmarks expression level.

Weaknesses:

Despite the strength of the study, there are a few drawbacks in the study design and statistical analysis:

(1) Regarding the statistical analysis, the use of a paired t-test might be suboptimal for assessing the trend from weeks 15 to 17. It is recommended to consider alternative methods such as repeated measures ANOVA or linear regression to better capture and interpret the trend over this time period.

(2) To affirm the antibodies' role in the observed immune response, isolating antibodies rather than employing whole serum could provide more conclusive evidence. Comparative analyses with antibody-free serum or serum from healthy, non-immunized mice would clarify antibodies' specific contributions versus other serum components. The control group does not account for the potential immunostimulatory effects of serum injection itself. A better control would be tumor-bearing mice receiving serum from healthy non-mCSCC-exposed mice.

Response to author's rebuttal:

I acknowledge the value of evaluating serum therapy as a whole, considering the complex interactive networks and potential synergies involved. However, to scientifically understand and assess serum therapy, it remains essential to decompose the serum and identify the effective components. This decomposition would allow for a comparison of individual components with the overall effectiveness, thereby elucidating any synergistic effects.<br /> While I agree that identifying specific epitopes and paratopes is indeed challenging and may exceed the scope of academic research, the use of methods such as Protein A purification or other techniques to isolate antibodies and cytokines from the serum is both necessary and feasible. This approach would enable a more detailed analysis of the individual effects of these components. I understand that the authors might not have that much resource, and I acknowledge this limitation. Nonetheless, other than this aspect, I believe the authors have adequately addressed my other concerns.

Reviewer #1 (Public Review):

In this study, Le Moigne and coworkers shed light on the structural details of the Sedoheptulose-1,7-Bisphosphatase (SBPase) from the green algae Chlamydomonas reinhardtii. The SBPase is part of the Calvin cycle and catalyzes the dephosphorylation of sedoheptulose-1,7-bisphosphate (SBP), which is a crucial step in the regeneration of ribulose-1,5-bisphosphate (RuBP), the substrate for Rubisco. The authors determine the crystal structure of the CrSBPase in an untreated, oxidized state. Based on this structure, potential active site residues and sites of post-translational modifications are identified. Furthermore, the authors determine the CrSBPase structure in a reduced state revealing the disruption of a disulfide bond in close proximity to the dimer interface. The authors then use molecular dynamics (MD) to gain insights into the redox-controlled dynamics of the CrSBPase and investigate the oligomerization of the protein using small-angle X-ray scattering (SAXS) and size-exclusion chromatography. Despite the difference in oligomerization, disruption of this disulfide bond did not impact the activity of CrSBPase, suggesting additional thiol-dependent regulatory mechanisms modulating the activity of the CrSBPase.

The authors provide interesting new findings on a redox-mechanism that modulates the oligomeric behavior of the SBPase. Comparisons of the Chlamydomonas structure to the previously determined SBPase structure from the moss Physcomitrium patens confirm a high structural similarity between the two proteins suggesting that this mechanism might be evolutionary conserved. Future research will have to address this question experimentally, also considering potential cooperativity between the subunits to confirm the link between oligomerization and SBPase activity.

Reviewer #1 (Public Review):

Summary:

Mao and colleagues re-analysed published spatial, bulk and single-cell transcriptomic datasets from primary colorectal cancers and colorectal cancer derived liver metastases. The analyses of paired cancer and non-cancer tissue samples showed that T cells are enriched in tumour tissue, accompanied by a reduction in the fraction of NK cells in the cancer tissue transcriptional datasets. Furthermore, the authors show that tumour tissue has higher fraction of GZMK+ (resting) NK cells and suggested a correlation between the presence of these cells and poor prognosis for cancer patients. In contrast, the increased frequency of KIR2DL4+ (activated) NK cells correlates with improved survival of cancer patients.

Strengths:

Authors performed a comprehensive analysis of published datasets, integrating spatial and single-cell transcriptomic data, which allowed them to discover enrichment of GZMK+ NK cells in cancer tissues.

Weakness:

The authors provided insufficient experimental evidence to support their claim that GZMK+ NK cells contribute to worse prognosis for cancer patients or promote cancer progression. While one can visually observe an increased fraction of GZMK+ NK cells compared to KIR2DL4+ NK cells in cancer tissues, no quantification is shown. They did not present any preclinical (animal model) or clinical data suggesting a causal relationship between NK cells and tumour growth. Thus, while a correlation may exist between the presence of GZMK+ NK cells and poorer tumour prognosis, causation cannot be claimed based on the available evidence. Furthermore, the in vitro data provided is limited to a single NK cell line derived from a lymphoma patient, which does not fully represent the diversity and functionality of human NK cells.

Reviewer #1 (Public Review):

In the manuscript "Mechanistic target of rapamycin (mTOR) pathway in Sertoli cells regulates age-dependent changes in sperm DNA methylation", the authors proposed to test if the balance of mTOR complexes in Sertoli cells may play a significant role in age-dependent changes in the sperm epigenome. The paper could be of interest and has a good scientific aim but there are too many drawbacks that hamper the initial enthusiasm. All sections need extensive revision. The paper is mostly descriptive without a mechanistic-orientated explanation for the observed results.

Comments on revised version:

I am not sure that the authors have made an attempt to clearly answer the reviewers comments that aimed to improve the quality of the manuscript. It stands as mostly descriptive and with limited interest as it is.

Reviewer #1 (Public Review):

Summary:

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

Strengths:

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

Weaknesses:

(1) Despite the authors restraint in interpreting the three states of the spliceosome observed by cyroEM as sequential intermediates along the splicing pathway, it would be helpful to the general reader to explicitly acknowledge the alternative possibility that the difference states simply reflect decomposition from one intermediate during isolation of the complex (i.e., the loss of protein is an in vitro artifact, if an informative one).<br /> (2) The authors acknowledge that for prp8 suppressors of the fyv6 deletion, suppression may be indirect, as originally proposed by the Query and Konarska labs - that is, that defects in the second step conformation of the spliceosome can be indirectly suppressed by compensating, destabilizing mutations in the first step spliceosome. Whereas some of the other suppressors of the fyv6 deletion can be interpreted as impacting directly the second step spliceosome (e.g., because the gene product is only present in the second step conformation), it seems that many more suppressors beyond prp8 mutants, especially those corresponding to bulky substitutions, which would more likely destabilize than stabilize, could similarly act indirectly by destabilization of first step conformation. The authors should acknowledge this where appropriate (e.g., for factors like Prp8 that are present in both first and second step conformations).

Reviewer #1 (Public Review):

Summary:

This study sought to reveal the potential roles of m6A RNA methylation in gene dosage regulatory mechanisms, particularly in the context of aneuploid genomes in Drosophila. Specifically, this work looked at the relationships between the expression of m6A regulatory factors, RNA methylation status, classical and inverse dosage effects, and dosage compensation. Using RNA sequencing and m6A mapping experiments, an in-depth analysis was performed to reveal changes in m6A status and expression changes across multiple aneuploid Drosophila models. The authors propose that m6A methylation regulates MOF and, in turn, deposition of H4K16Ac, critical regulators of gene dosage in the context of genomic imbalance.

Strengths:

This study seeks to address an interesting question with respect to gene dosage regulation and the possible roles of m6A in that process. Previous work has linked m6A to X-inactivation in humans through the Xist lncRNA, and to the regulation of the Sxl in flies. This study seeks to broaden that understanding beyond these specific contexts to more broadly understand how m6A impacts imbalanced genomes in other contexts.

Weaknesses:

The methods being used particularly for analysis of m6A at both the bulk and transcript-specific level are not sufficiently specific or quantitative to be able to confidently draw the conclusions the authors seek to make. MeRIP m6A mapping experiments can be very valuable, but differential methylation is difficult to assess when changes are small (as they often are, in this study but also m6A studies more broadly). For instance, based on the data presented and the methods described, it is not clear that the statement that "expression levels at m6A sites in aneuploidies are significantly higher than that in wildtype" is supported. MeRIP experiments are not quantitative, and since there are far fewer peaks in aneuploidies, it stands to reason that more antibody binding sites may be available to enrich those fewer peaks to a larger extent. But based on the data as presented (figure 2D) this conclusion was drawn from RPKM in IP samples, which may not fully account for changing transcript abundances in absolute (expression level changes) and relative (proportion of transcripts in input RNA sample) terms.

The bulk-level m6A measurements as performed here also cannot effectively support these conclusions, as they are measured in total RNA. The focus of the work is mRNA m6A regulators, but m6A levels measured from total RNA samples will not reflect mRNA m6A levels as there are other abundance RNAs that contain m6A (including rRNA). As a result, conclusions about mRNA m6A levels from these measurements are not supported.

Reviewer #1 (Public Review):

Summary:<br /> In this manuscript, the authors use gene functional analysis, pharmacology and live imaging to develop a proposed model of diverse G protein family signalling that takes place in the papillae during the ascidian Ciona larval adhesion to regulate the timing of initiation of the morphological changes of metamorphosis. Their experiments provide solid evidence that antagonistic G protein signalling regulates cAMP levels in the papillae, which provides a threshold for triggering metamorphosis that is reflective of a larva keeping a strong and sustained level of contact with a substrate for a minimum period of approximately half an hour. The authors discuss their reasoning and address different specific aspects of their proposed timing mechanism to provide a logical flow to the manuscript. The results are nicely linked to<br /> the ecology of Ciona larval settlement and will be of interest to developmental biologists, neurobiologists, molecular biologists, marine biologists as well as provide information relevant to antifouling and aquaculture sectors.

First, they knock down the G proteins Gaq and Gas to show that these genes are important for Ciona larval metamorphosis. They then provide evidence that the Gaq protein acts through a Ca2+ pathway mediated by phospholipase C and inositol triphosphate by showing that inositol phosphate and phospholipase C gene knockdown also inhibits metamorphosis, while overexpression of Gaq or phospholipase C allows larvae to undergo metamorphosis even in the absence of their mechanosensory cue, which is deprived by removing the posterior half of the tail and culturing the larvae on agar-coated dishes. The authors used calcium imaging which is a genetically encoded fluorescent calcium sensor to show that Gq knockdown larvae lack a Ca2+ spike in their papillae after mechanostimulation, confirming that Gaq acts through a Ca2+ pathway. Similarly the authors show that overexpression of Gas also enables larvae to metamorphose in the absence of mechanostimulation, suggesting a role for both Gaq and Gas in this process.

To confirm that Gas acts through cAMP signalling, the authors use pharmacological treatment or overexpression of a photoactivating adenylate cyclase to increase cAMP, and show that this also enables larvae to metamorphose in the absence of mechanostimulation, but only<br /> when their adhesive papillae are still present. Transcriptome data indicate that both Gs and Gq pathway genes are expressed in the adhesive papillae of the Ciona larva. One missing detail seems to be the need for evidence that cAMP is elevated in the papillae directly as a result of Gs activation. The authors use a fluorescent cAMP indicator, Pink Flamindo, to show that cAMP increases in the papillae upon adhesion to a substrate. Complementary to this, larvae that fail to undergo metamorphosis lack a cAMP increase in papillae. However, it is unclear whether the measured larvae that failed to undergo metamorphosis were wildtype or Gas knockdown larvae. If they were Gas knockdown larvae, this could provide evidence that cAMP does act downstream of the Gas activation.

The authors then provide evidence that GABA signalling within the papillae is acting downstream of the G proteins to induce metamorphosis. Transcriptome data shows that the genes for the GABA-producing enzyme, and for GABAb receptors, are both expressed in papillae. Pharmacological experiments show that GABA induces metamorphosis in the absence of mechanosensory cues, but only in larvae that retain their papillae. To show that GABA signalling within the papillae, rather than from the brain of the larva is important, the authors also demonstrate that anterior segments of larvae lacking the brain can also be stimulated to metamorphose by GABA, and show changes in gene expression caused by GABA.

The authors then use a combination of pharmacology and knockdown experiments in the presence or absence of mechanosensory cues to show that Gq/Ca2+ signalling acts upstream of Gs/cAMP signalling. As the elevation of cAMP by pharmacology or photoactivating adenylate cyclase rescued GABA pathway mutant larvae, the Gq and Gs pathways were concluded to be downstream of GABA signaling. However, GABA treatment could still induce Gaq- and Gas-knockdown larvae to metamorphose, suggesting an alternative pathway to metamorphosis, which the authors deduce to be through a third G protein, Gai. They identify an unusual Gai protein that based on transcriptome data is strongly expressed in the papillae. Gai knockdown larvae fail to metamorphose but are rescued by GABA treatment, which can be explained by a potential additional Gai protein being still present (transcriptome evidence suggests this although it is not further confirmed experimentally, for example by hybridization, immunohistochemistry, fluorescent labelling, or knockdown). The authors then use overexpression and knockdown experiments to show that the Gai protein acts through Gβγi complex to activate phospholipase C. Their experiments also indicate a potential for a complementary or compensatory role for Gai and Gaq signalling through Gβγi. By inhibiting the potassium channel GIRK through knockdown, and the MAPK pathway gene MEK1/2 by pharmacology, the authors also establish a role for these in their proposed model of signalling, allowing GABA and cAMP to compensate or interact with each other.

Strengths:<br /> The strength of this paper is the meticulous and extensive experiments, which are carefully designed to be able to precisely target specific genes in the putative signalling pathway to build step by step a complex model that can demonstrate how metamorphosis of the ascidian larva is timed so as to only undergo metamorphosis when strongly attached to a<br /> suitable substrate. The unique possibility of inhibiting mechanosensory-induced metamorphosis by removing some of the tail and smoothing the attachment substrate allows the authors to investigate potential effects on both activation and inhibition of metamorphosis, and to confirm that specific signalling pathways are clearly downstream of the initial<br /> mechanosensory stimulation. The study is also clear about which aspects of the model still remain unknown, such as which ligands and receptors may be responsible for the binding and activation of Gaq and Gas. Experiments testing metamorphosis of just the anterior region of the larvae nicely demonstrates the need for signalling in the region of the papillae, as do experiments where the papillae are removed, which then block metamorphosis in treatments that would otherwise stimulate it. The final model is a nice end point and makes a clear summary of how the extensive experiments all fit together into a cohesive potential signalling network, which can be built upon in the future.

Weaknesses:<br /> The paper has few weaknesses, however the main difficulty it poses is that due to the sheer number of precise experiments carried out and the complexity of the interwoven signalling pathways, it quickly becomes very difficult to follow exactly what is going on when and why or to keep track of the story as it develops. To improve this, an initial section in the results could be included showing a summary of the known G proteins in Ciona, their types and potential downstream signalling or upstream receptors, where known, and their expression levels in papillae. This could be in the form of a table and/or include the phylogenetic tree from the supplementary data. This would help clarify why the study first focuses on Gaq and Gas, and only later looks at Gai. This could be supplemented by a schematic workflow giving an overview of the experimental process of the study. A second minor weakness (understandable as the focus of the study is metamorphosis induced by mechanosensory stimulation) is that the study does not take into account any potential role for other types of sensory modalities (light, chemicals) that may also feed into the regulation of Ciona larval metamorphosis. This aspect would be interesting to discuss in light of the recent paper suggesting that some sensory cells in the Ciona adhesive papillae are polymodal and detect both chemicals and mechanical stimuli (Hoyer et al. 2024 Current Biology 34(6): 1168 - 1182).

Reviewer #1 (Public Review):

Summary:

The fungal cell wall is a very important structure for the physiology of a fungus but also for the interaction of pathogenic fungi with the host. Although a lot of knowledge on the fungal cell wall has been gained, there is a lack of understanding of the meaning of ß-1,6-glucan in the cell wall. In the current manuscript, the authors studied in particular this carbohydrate in the important human-pathogenic fungus Candida albicans. The authors provide a comprehensive characterization of cell wall constituents under different environmental and physiological conditions, in particular of ß-1,6-glucan. Also, β-1,6-glucan biosynthesis was found to be likely a compensatory reaction when mannan elongation was defective. The absence of β-1,6-glucan resulted in a significantly sick growth phenotype and complete cell wall reorganization. The manuscript contains a detailed analysis of the genetic and biochemical basis of ß-1,6-glucan biosynthesis which is apparently in many aspects similar to yeast. Finally, the authors provide some initial studies on the immune modulatory effects of ß-1,6-glucan.

Strengths:

The findings are very well documented, and the data are clear and obtained by sophisticated biochemical methods. It is impressive that the authors successfully optimized methods for the analyses and quantification of ß-1-6-glucan under different environmental conditions and in different mutant strains.

Weaknesses:

However, although already very interesting, at this stage there are some loose ends that need to be combined to strengthen the manuscript. For example, the immunological studies are rather preliminary and need at least some substantiation. Also, at this stage, the manuscript in some places remains a bit too descriptive and needs the elucidation of potential causalities.

Reviewer #1 (Public Review):

Summary:<br /> In this study, Masroor Ahmad Paddar and his/her colleagues explore the noncanonical roles of ATG5 and membrane atg8ylation in regulating retromer assembly and function. They begin by examining the interactomes of ATG5 and expand the scope of these effects to include homeostatic responses to membrane stress and damage.

Strengths:<br /> This study provides novel insights into the noncanonical function of ATG8ylation in endosomal cargo sorting process.

Weaknesses:<br /> The direct mechanism by which ATG8ylation regulates the retromer remains unsolved.

Reviewer #1 (Public Review):

Summary:<br /> In this study, the authors developed a novel radiotherapy sensitivity score (NPC-RSS) for nasopharyngeal carcinoma patients using machine learning algorithms. They identified 18 key genes associated with radiosensitivity and demonstrated that NPC-RSS could effectively predict radiotherapy response in both public and in-house datasets. Furthermore, they found that the key genes of NPC-RSS were closely related to immune characteristics, the expression of radiosensitivity-related genes, and signaling pathways involved in disease progression. The authors validated the consistency of expression of two key genes, SMARCA2 and CD9, with NPC-RSS in their own cell lines. They also showed that the radiosensitive group, classified by NPC-RSS, exhibited a more enriched and activated state of immune infiltration compared to the radioresistant group.

Strengths:<br /> (1) The study employed a comprehensive approach by integrating multiple machine learning algorithms to develop a robust predictive model for radiotherapy sensitivity in nasopharyngeal carcinoma patients.<br /> (2) The predictive performance of NPC-RSS was validated using both public and in-house datasets, demonstrating its potential clinical applicability.<br /> (3) The authors conducted extensive analyses to investigate the biological mechanisms underlying the association between NPC-RSS and radiotherapy response, including immune characteristics, radiosensitivity-related gene expression, and relevant signaling pathways.<br /> (4) The consistency of key gene expression with NPC-RSS was validated in the authors' own cell lines, providing additional experimental evidence.

Weaknesses:<br /> (1) The sample size of the in-house dataset used for training the model was relatively small (34 patients), which might limit the generalizability of the findings.<br /> (2) The authors did not perform functional experiments to directly validate the roles of the identified key genes in radiotherapy sensitivity, relying instead on associations with immune features and signaling pathways.<br /> (3) The study did not discuss the potential limitations of using machine learning algorithms, such as the risk of overfitting and the need for larger, diverse datasets for more robust model development and validation.

Reviewer #1 (Public Review):

In this study, the authors conducted a single-cell RNA sequencing analysis of the cellular and transcriptional landscape of the gastric cancer tumor microenvironment, stratifying patients according to their H. pylori status into currently infected, previously infected, and non-infected patients. The authors comprehensively dissect various cellular compartments, including epithelial, stromal, and immune cells, and describe specific cell types and signatures to be associated with H. pylori infection, including i) inflammatory and EMT signatures in malignant epithelial cells, ii) inflammatory CAFs in stromal cells, iii) Angio-TAMs, TREM2+ TAMs, exhausted and suppressive T cells in immune cells. Looking at ligand-receptor interactions as well as correlations between cell type abundances, they suggest that iCAFs interact with immunosuppressive T cells via a NECTIN2-TIGIT axis, as well as Angio-TAMs through a VEGFA/B-VEGFR1 axis and thereby promote immune escape, tumor angiogenesis and resistance to immunotherapy.

The authors conduct a comprehensive and thorough analysis of the complex tumor microenvironment of gastric cancer, both single-cell RNA sequencing data as well as the analysis seem of high quality and according to best practices. The authors validate their findings using external datasets, and include some prognostic value of the identified signatures and cell types. However, most of their conclusions throughout the manuscript are based on the comparison between HPGC and healthy controls, which is not a valid comparison to determine which of the phenotypes are specifically driven by HP infection, e.g. Tregs are high in all GC types, independent of HP status. The same holds true for TREM+ TAMs and iCAFs, which are higher in GC in general. This makes it very difficult to assess the actual HP-driven signatures and cell types. Also, when looking at the correlation/transcriptional differences across different cell types and cellular interactions, the authors do not explicitly define if they are looking at the whole dataset (including healthy controls?) or only at certain patients (HPGC?), which again makes it difficult to interpret the results.

The authors aim to confirm some of their findings via immunofluorescence, which in principle is a great approach to validate their results. However, to be able to conclude that e.g. suppressive TIGIT+ T cells are located close to NECTIN2+ malignant epithelium and that this might facilitate immune escape in HPGC (Figure 4K), the authors should include stains that show that this is not the case in the other groups (nonHPGC, exHPGC and HC). The same holds true for Figure 5G.

In summary, this study provides a valuable resource on the cellular and transcriptional heterogeneity of the tumor microenvironment in gastric cancers, distinguishing between positive, negative, and previously positive HP-infected gastric cancer patients. Given that HP is the main risk factor for gastric cancer development, the study provides valuable insights into HP-driven transcriptional signatures and how these might contribute to this increased risk, however, the study would highly benefit from a clearer and more stringent comparison between HPGC and nonHPGC.

Reviewer #1 (Public Review):

The paper titled "STAG3 promotes exit from pluripotency through post-transcriptional mRNA regulation in the cytoplasm" suggests a new and unexpected role for STAG3, a protein traditionally associated with the cohesin complex during meiosis, in regulating the exit from pluripotency in mouse embryonic stem cells (mESCs). While STAG3 is traditionally studied for its role in meiosis, this paper reveals that STAG3 is expressed in mouse embryonic stem cells (mESCs) and primordial germ cell-like cells (PGCLCs) and may be necessary for PGCLC-like specification and exit from pluripotency. In ESCs, the study reports that STAG3 is found in the cytoplasm, where it interacts with various RNA-binding proteins (RBPs) and localizes to centrosomes. Knockdown of STAG3 disrupts centrosome stability and RNA-induced silencing complex (RISC) components, leading to the misregulation of mRNAs such as DPPA3, Nanog, and TNRC6C. In summary, this study expands the known functions of STAG3 beyond cohesin, highlighting a potential role in cytoplasmic post-transcriptional regulation.

The authors perform a comprehensive characterization of RNA and protein changes in ESCs and differentiated cells upon loss of STAG3, providing preliminary and intriguing insights. However, there are several aspects that require further exploration:

(1) A rescue experiment for the STAG3 RNAi is missing, making it unclear whether the observed effects are indeed due to the knockdown of STAG3.

(2) While the paper identifies several interactions and effects of STAG3, it lacks detailed mechanistic insights into how STAG3 regulates specific mRNAs and proteins. Specifically, it is unclear which proteins directly interact with STAG3 or recruit STAG3 to RNP complexes. AlphaFold may help in this analysis.

(3) It is unclear whether this is an alternative STAG3 isoform or if STAG3 is modified. What dictates its interaction with cohesin versus RNPs?

(5) Are there unique features or sequence barcodes present on the misregulated RNAs?

(6) Does STAG3 associate with a single type of RNP or is it present in all types?

Reviewer #1 (Public Review):

Summary:<br /> The authors used multiple approaches to study salt effects in liquid-liquid phase separation (LLPS). Results on both wild-type Caprin1 and mutants and on different types of salts contribute to a comprehensive understanding.

Strengths:<br /> The main strength of this work is the thoroughness of investigation. This aspect is highlighted by the multiple approaches used in the study, and reinforced by the multiple protein variants and different salts studied.

Weaknesses:<br /> (1) The multiple computational approaches are a strength, but they're cruder than explicit-solvent all-atom molecular dynamics (MD) simulations and may miss subtle effects of salts. In particular, all-atom MD simulations demonstrate that high salt strengthens pi-types of interactions (ref. 42 and MacAinsh et al, https://www.biorxiv.org/content/10.1101/2024.05.26.596000v3).

(2) The paper can be improved by distilling the various results into a simple set of conclusions. By example, based on salt effects revealed by all-atom MD simulations, MacAinsh et al. presented a sequence-based predictor for classes of salt dependence. Wild-type Caprin1 fits right into the "high net charge" class, with a high net charge and a high aromatic content, showing no LLPS at 0 NaCl and an increasing tendency of LLPS with increasing NaCl. In contrast, pY-Caprin1 belongs to the "screening" class, with a high level of charged residues and showing a decreasing tendency of LLPS.

(3) Mechanistic interpretations can be further simplified or clarified. (i) Reentrant salt effects (e.g., Fig. 4a) are reported but no simple explanation seems to have been provided. Fig. 4a,b look very similar to what has been reported as strong-attraction promotor and weak-attraction suppressor, respectively (ref. 50; see also PMC5928213 Fig. 2d,b). According to the latter two studies, the "reentrant" behavior of a strong-attraction promotor, CL- in the present case, is due to Cl-mediated attraction at low to medium [NaCl] and repulsion between Cl- ions at high salt. Do the authors agree with this explanation? If not, could they provide another simple physical explanation? (ii) The authors attributed the promotional effect of Cl- to counterion-bridged interchain contacts, based on a single instance. There is another simple explanation, i.e., neutralization of the net charge on Caprin1. The authors should analyze their simulation results to distinguish net charge neutralization and interchain bridging; see MacAinsh et al.

(4) The authors presented ATP-Mg both as a single ion and as two separate ions; there is no explanation of which of the two versions reflects reality. When presenting ATP-Mg as a single ion, it's as though it forms a salt with Na+. I assume NaCl, ATP, and MgCl2 were used in the experiment. Why is Cl- not considered? Related to this point, it looks like ATP is just another salt ion studied and much of the Results section is on NaCl, so the emphasis of ATP ("Diverse Roles of ATP" in the title is somewhat misleading.

Reviewer #1 (Public Review):

Summary:

During vertebrate gastrulation, mesendoderm cells are initially specified by morphogens (e.g. Nodal) and segregate into endoderm and mesoderm in part based on Nodal concentrations. Using zebrafish genetics, live imaging, and single-cell multi-omics, the manuscript by Cheng et al presents evidence to support a claim that anterior endoderm progenitors derive primarily from prechordal plate progenitors, with transcriptional regulators goosecoid (Gsc) and ripply1 playing key roles in this cell fate determination. Such a finding would represent a significant advance in our understanding of how anterior endoderm is specified in vertebrate embryos.

Strengths:

Live imaging-based tracking of PP and endo reporters (Figure 2) is well executed and convincing, though a larger number of individual cell tracks will be needed. Currently, only a single cell track (n=1) is provided.

Weaknesses:

(1) The central claim of the paper - that the anterior endoderm progenitors arise directly from prechordal plate progenitors - is not adequately supported by the evidence presented. This is a claim about cell lineage, which the authors are attempting to support with data from single-cell profiling and genetic manipulations in embryos and explants. The construction of gene expression (pseudo-time) trajectories, while a modern and powerful approach for hypothesis generation, should not be used as a substitute for bona fide lineage tracing methods. If the authors' central hypothesis is correct, a CRE-based lineage tracing experiment (e.g. driving CRE using a PP marker such as Gsc) should be able to label PP progenitor cells that ultimately contribute to anterior endoderm-derived tissues. Such an experiment would also allow the authors to quantify the relative contribution of PP (vs non-PP) cells to the anterior endoderm, which is not possible to estimate from the indirect data currently provided. Note: while the present version of the manuscript does describe a sox17:CRE lineage tracing experiment, this actually goes in the opposite direction that would be informative (sox:17:CRE-marked descendants will be a mixture of PP-derived and non-PP derived cells, and the Gsc-based reporter does not allow for long-term tracking the fates of these cells).

(2) The authors' descriptions of gene expression patterns in the single-cell trajectory analyses do not always match the data. For example, it is stated that goosecoid expression marks progenitor cells that exist prior to a PP vs endo fate bifurcation (e.g. lines 124-130). Yet, in Figure 1C it appears that in fact goosecoid expression largely does not precede (but actually follows) the split and is predominantly expressed in cells that have already been specified into the PP branch. Likewise, most of the cells in the endo branch (or prior) appear to never express Gsc. While these trends do indeed appear to be more muddled in the explant data (Figure 1H), it still seems quite far-fetched to claim that Gsc expression is a hallmark of endoderm-PP progenitors.

(3) The study seems to refer to "endoderm" and "anterior endoderm" somewhat interchangeably, and this is potentially problematic. Most single-cell-based analyses appearing in the study rely on global endoderm markers (sox17, sox32) which are expressed in endodermal precursors along the entire ventrolateral margin. Some of these cells are adjacent to the prechordal plate on the dorsal side of the gastrula, but many (most in fact) are quite some distance away. The microscopy-based evidence presented in Figure 2 and elsewhere, however, focuses on a small number of sox17-expressing cells that are directly adjacent to, or intermingled with, the prechordal plate. It, therefore, seems problematic for the authors to generalize potential overlaps with the PP lineage to the entire endoderm, which includes cells in ventral locations. It would be helpful if the authors could search for additional markers that might stratify and/or mark the anterior endoderm and perform their trajectory analysis specifically on these cells.

(4) It is not clear that the use of the nodal explant system is allowing for rigorous assessment of endoderm specification. Why are the numbers of endoderm cells so vanishingly few in the nodal explant experiments (Figure 1H, 3H), especially when compared to the embryo itself (e.g. Figures 1C-D)? It seems difficult to perform a rigorous analysis of endoderm specification using this particular model which seems inherently more biased towards PP vs. endoderm than the embryo itself. Why not simply perform nodal pathway manipulations in embryos?

(5) The authors should not claim that proximity in UMAP space is an indication of transcriptional similarity (lines 207-208), especially for well-separated clusters. This is a serious misrepresentation of the proper usage of the UMAP algorithm. The authors make a similar claim later on (lines 272-274).

Reviewer #1 (Public Review):

Summary:

The authors wanted to identify genes that are critical for regulating the asymmetric fates of limbal stem cells and their transit amplified progeny in the central cornea. To this end, they utilized an in vivo cell cycle reporter to isolate proliferating basal cells from the anterior ocular surface epithelium and performed single-cell RNA-seq. This strategy revealed distinct basal cell identities with unique expression profiles of structural genes and transcription factors. The authors then focused on the Sox9 transcription factor implicated in stem cell regulation. It was differentially expressed between limbal stem cells and their progeny in the central cornea. Lineage tracing analysis confirmed that Sox9 marks long-lived limbal stem cells. Conditional deletion of Sox9 led to abnormal differentiation and squamous metaplasia in the central cornea. The authors suggest that Sox9 is required for the switch to asymmetric fate and commitment toward differentiation, as transit cells exit the limbal niche. By inhibiting the terminal differentiation of corneal progenitors and forcing them into continuous symmetric divisions, the Sox9 loss-of-function phenotype was replicated.

Strengths:

Thus, the paper shows the important role of Sox9 in the spatial regulation of asymmetric fate in the corneal epithelium and its proliferation and cell differentiation. The work is elegantly done using several models that converge on the main conclusions. It is very novel and delineates a new player in determining corneal epithelial cell fate. The experiments are well done, and the data are credible.

Weaknesses:

This reviewer has some minor concerns mostly related to data interpretation and the use of the LSC term.

Reviewer #1 (Public Review):

Summary:

In this manuscript, Fuchsberger et al. demonstrate a set of experiments that ultimately identifies the de novo synthesis of GluA1-, but not GluA2-containing Ca2+ permeable AMPA receptors as a key driver of dopamine-dependent LTP (DA-LTP) during conventional post-before-pre spike-timing dependent (t-LTD) induction. The authors further identify adenylate cyclase 1/8, cAMP, and PKA as the crucial mitigators of these actions. While some comments have been identified below, the experiments presented are thorough and address the aims of the manuscript, figures are presented clearly (with minor comments), and experimental sample sizes and statistical analyses are suitable. Suitable controls have been utilized to confirm the role of Ca2+ permeable AMPAR. This work provides a valuable step forward built on convincing data toward understanding the underlying mechanisms of spike-timing-dependent plasticity and dopamine.

Strengths:

Appropriate controls were used.

The flow of data presented is logical and easy to follow.

The quality of the data, except for a few minor issues, is solid.

Weaknesses:

The drug treatment duration of anisomycin is longer than the standard 30-45 minute duration (as is the 500uM vs 40uM concentration) typically used in the field. Given the toxicity of these kinds of drugs long term it's unclear why the authors used such a long and intense drug treatment.

With some of the normalizations (such as those in S1) there are dramatic differences in the baseline "untreated" puromycin intensities - raising some questions about the overall health of slices used in the experiments.

Reviewer #1 (Public Review):

The authors are attempting to use the internal workings of a language hierarchy model, comprising phonemes, syllables, words, phrases, and sentences, as regressors to predict EEG recorded during listening to speech. They also use standard acoustic features as regressors, such as the overall envelope and the envelopes in log-spaced frequency bands. This is valuable and timely research, including the attempt to show differences between normal-hearing and hearing-impaired people in these regards.

I will start with a couple of broader questions/points, and then focus my comments on three aspects of this study: The HM-LSTM language model and its usage, the time windows of relevant EEG analysis, and the usage of ridge regression.

Firstly, as far as I can tell, the OSF repository of code, data, and stimuli is not accessible without requesting access. This needs to be changed so that reviewers and anybody who wants or needs to can access these materials.

What is the quantification of model fit? Does it mean that you generate predicted EEG time series from deconvolved TRFs, and then give the R2 coefficient of determination between the actual EEG and predicted EEG constructed from the convolution of TRFs and regressors? Whether or not this is exactly right, it should be made more explicit.

About the HM-LSTM:

• In the Methods paragraph about the HM-LSTM, a lot more detail is necessary to understand how you are using this model. Firstly, what do you mean that you "extended" it, and what was that procedure? And generally, this is the model that produces most of the "features", or regressors, whichever word we like, for the TRF deconvolution and EEG prediction, correct? A lot more detail is necessary then, about what form these regressors take, and some example plots of the regressors alongside the sentences.<br /> • Generally, it is necessary to know what these regressors look like compared to other similar language-related TRF and EEG/MEG prediction studies. Usually, in the case of e.g. Lalor lab papers or Simon lab papers, these regressors take the form of single-sample event markers, surrounded by zeros elsewhere. For example, a phoneme regressor might have a sample up at the onset of each phoneme, and a word onset regressor might have a sample up at the onset of each word, with zeros elsewhere in the regressor. A phoneme surprisal regressor might have a sample up at each phoneme onset, with the value of that sample corresponding to the rarity of that phoneme in common speech. Etc. Are these regressors like that? Or do they code for these 5 linguistic levels in some other way? Either way, much more description and plotting is necessary in order to compare the results here to others in the literature.<br /> • You say that the 5 regressors that are taken from the trained model's hidden layers do not have much correlation with each other. However, the highest correlations are between syllable and sentence (0.22), and syllable and word (0.17). It is necessary to give some reason and interpretation of these numbers. One would think the highest correlation might be between syllable and phoneme, but this one is almost zero. Why would the syllable and sentence regressors have such a relatively high correlation with each other, and what form do those regressors take such that this is the case?<br /> • If these regressors are something like the time series of zeros along with single sample event markers as described above, with the event marker samples indicating the onset of the relevant thing, then one would think e.g. the syllable regressor would be a subset of the phoneme regressor because the onset of every syllable is a phoneme. And the onset of every word is a syllable, etc.

For the time windows of analysis:

• I am very confused, because sometimes the times are relative to "sentence onset", which would mean the beginning of sentences, and sometimes they are relative to "sentence offset", which would mean the end of sentences. It seems to vary which is mentioned. Did you use sentence onsets, offsets, or both, and what is the motivation?<br /> • If you used onsets, then the results at negative times would not seem to mean anything, because that would be during silence unless the stimulus sentences were all back to back with no gaps, which would also make that difficult to interpret.<br /> • If you used offsets, then the results at positive times would not seem to mean anything, because that would be during silence after the sentence is done. Unless you want to interpret those as important brain activity after the stimuli are done, in which case a detailed discussion of this is warranted.<br /> • For the plots in the figures where the time windows and their regression outcomes are shown, it needs to be explicitly stated every time whether those time windows are relative to sentence onset, offset, or something else.<br /> • Whether the running correlations are relative to sentence onset or offset, the fact that you can have numbers outside of the time of the sentence (negative times for onset, or positive times for offset) is highly confusing. Why would the regressors have values outside of the sentence, meaning before or after the sentence/utterance? In order to get the running correlations, you presumably had the regressor convolved with the TRF/impulse response to get the predicted EEG first. In order to get running correlation values outside the sentence to correlate with the EEG, you would have to have regressor values at those time points, correct? How does this work?<br /> • In general, it seems arbitrary to choose sentence onset or offset, especially if the comparison is the correlation between predicted and actual EEG over the course of a sentence, with each regressor. What is going on with these correlations during the middle of the sentences, for example? In ridge regression TRF techniques for EEG/MEG, the relevant measure is often the overall correlation between the predicted and actual, calculated over a longer period of time, maybe the entire experiment. Here, you have calculated a running comparison between predicted and actual, and thus the time windows you choose to actually analyze can seem highly cherry-picked, because this means that most of the data is not actually analyzed.<br /> • In figures 5 and 6, some of the time window portions that are highlighted as significant between the two lines have the lines intersecting. This looks like, even though you have found that the two lines are significantly different during that period of time, the difference between those lines is not of a constant sign, even during that short period. For instance, in figure 5, for the syllable feature, the period of 0 - 200 ms is significantly different between the two populations, correct? But between 0 and 50, normal-hearing are higher, between 50 and 150, hearing-impaired are higher, and between 150 and 200, normal-hearing are higher again, correct? But somehow they still end up significantly different overall between 0 and 200 ms. More explanation of occurrences like these is needed.

Using ridge regression:

• What software package(s) and procedure(s) were specifically done to accomplish this? If this is ridge regression and not just ordinary least squares, then there was at least one non-zero regularization parameter in the process. What was it, how did it figure in the modeling and analysis, etc.?<br /> • It sounds like the regressors are the hidden layer activations, which you reduced from 2,048 to 150 non-acoustic, or linguistic, regressors, per linguistic level, correct? So you have 150 regressors, for each of 5 linguistic levels. These regressors collectively contribute to the deconvolution and EEG prediction from the resulting TRFs, correct? This sounds like a lot of overfitting. How much correlation is there from one of these 150 regressors to the next? Elsewhere, it sounds like you end up with only one regressor for each of the 5 linguistic levels. So these aspects need to be clarified.<br /> • For these regressors, you are comparing the "regression outcomes" for different conditions; "regression outcomes" are the R2 between predicted and actual EEG, which is the coefficient of determination, correct? If this is R2, how is it that you have some negative numbers in some of the plots? R2 should be only positive, between 0 and 1.

Reviewer #2 (Public Review):

Summary:

Cells cultured in high glucose tend to repress mitochondrial biogenesis and activity, a prevailing phenotype type called Crabtree effect that observed in different cell types and cancer. Many signaling pathways have been put forward to explain this effect. Vengayil et al proposed a new mechanism involved in Ubp3/Ubp10 and phosphate that controls the glucose repression of mitochondria. The central hypothesis is that ∆ubp3 shift the glycolysis to trehalose synthesis, therefore lead to the increase of Pi availability in the cytosol, then mitochondrial received more Pi and therefore the glucose repression is reduced.

Strengths:

The strength is that the authors used an array of different assays to test their hypothesis. Most assays were well-designed and controlled.

Weaknesses:

The author addressed my major concerns.

Reviewer #2 (Public Review):

Summary.

The objective of this study was to further our understanding of the brain mechanisms associated with facial expressions of pain. To achieve this, participants' facial expressions and brain activity were recorded while they received noxious heat stimulation. The authors then used a decoding approach to predict facial expressions from functional magnetic resonance imaging (fMRI) data. They found a distinctive brain signature for pain facial expressions (FEPS). This signature had minimal overlap with brain signatures reflecting other components of pain phenomenology, such as signatures reflecting subjective pain intensity or negative effects.

Strength.

The authors used a rigorous approach involving multivariate brain decoding to predict the occurrence and intensity of pain facial expressions during noxious heat stimulation. The analyses are solid and well-conducted. This is an important study of fundamental and clinical relevance.

Weakness.

Despite those major strengths, the main weakness of the study is that the design and analyses do not allow us to know if the FEPS is really specific to pain expressions. Based on the analysis, it is possible to conclude that this brain signature is present when a participant is in a state of pain and displays a facial expression. However, it is possible that it would also be present when a participant experiences (another) negative state and displays (another) facial expression. It will be important, in future work, to investigate the specificity of this brain signature.

Reviewer #1 (Public Review):

Summary:

This manuscript investigates the regulation of chlorophyll biosynthesis in rice embryos, focusing on the role of OsNF-YB7. The rigorous experimental approach, combining genetic, biochemical, and molecular analyses, provides a robust foundation for these findings. The research achieves its objectives, offering new insights into chlorophyll biosynthesis regulation, with the results convincingly supporting the authors' conclusions.

Strengths:

The major strengths include the detailed experimental design and the findings regarding OsNF-YB7's inhibitory role.

Weaknesses:

However, the manuscript's discussion on the practical implications for agriculture and the evolutionary analysis of regulatory mechanisms could be expanded.

Reviewer #3 (Public Review):

Summary:

Kundu et al. investigated the effects of pre-exposure to a non-pathogenic Leptospira strain in prevention of severe disease following subsequent infection by a pathogenic strain. They utilized a single or double exposure method to the non-pathogen prior to challenge with a pathogenic strain. They found that prior exposure to a non-pathogen prevented many of the disease manifestations of the pathogen. Bacteria, however, were able to disseminate, colonize the kidneys, and be shed in the urine. This is important foundational work to describe a novel method of vaccination against leptospirosis. Numerous studies have attempted to use recombinant proteins to vaccinate against leptospirosis, with limited success. The authors provide a new approach that takes advantage of the homology between a non-pathogen and a pathogen to provide heterologous protection. This will provide a new direction in which we can approach creating vaccines against this re-emerging disease.

Strengths:

The major strength of this paper is that it is one of the first studies utilizing a live non-pathogenic strain of Leptospira to immunize against severe disease associated with leptospirosis. They utilize two independent experiments (a single and double vaccination) to define this strategy. This represents a very interesting and novel approach to vaccine development. This is of clear importance to the field.

The authors use a variety of experiments to show the protection imparted by pre-exposure to the non-pathogen. They look at disease manifestations such as death and weight loss. They define the ability of Leptospira to disseminate and colonize the kidney. They show the effects infection has on kidney architecture and a marker of fibrosis. And they begin to define the immune response in both of these exposure methods. This provides evidence of the numerous advantages this vaccination strategy may have. Thus, this study provides an important foundation for future studies utilizing this method to protect against leptospirosis.

Weaknesses:

A direct comparison between single and double exposure to the non-pathogen is not possible with the data presented. The ages of mice infected were different between the single (8 weeks) and double (10 weeks) exposure methods, thus the phenotypes associated with LIC infection are different at these two ages. The authors state that this is expected, but do not provide a reasoning for this drastic difference in phenotypes. It cannot be determined if double-vaccination would provide an additional benefit, which is of importance to future work developing any vaccine treatment. An experiment directly comparing the two exposure methods while infecting mice at the same age would be of great relevance to and strengthen this work.

Reviewer #1 (Public Review):

Summary:

The "optorepressilator", an optically controllable genetic oscillator based on the famous E. coli 3-repressor (LacI, TetR, CI) oscillator "repressilator", was developed. An individual repressilator shows a stable oscillation of the protein levels with a relatively long period that extends a few doubling times of E. coli, but when many cells oscillate, their phases tend to desynchronize. The authors introduced an additional optically controllable promoter through a conformal change of CcaS protein and let it control how much additional CI is produced. By tightly controlling the leak from the added promoter, the authors successfully kept the original repressilator oscillation when the added promoter was not activated. In contrast, the oscillation was stopped by expressing the additional CI. Using this system, the authors showed that it is possible to synchronise the phase of the oscillation, especially when the activation happens as a short pulse at the right phase of the repressilator oscillation. The authors further show that, by changing the frequency of the short pulses, the repressilator was entrained to various ratios to the pulse period, and the author could reconstruct the so-called "Arnold tongues", the signature of entrainment of the nonlinear oscillator to externally added periodic perturbation. The behaviour is consistent with the simplified mathematical model that simulates the protein concentration using ordinary differential equations.

Strengths:

Optical control of the oscillation of the protein clock is a powerful and clean tool for studying the synthetic oscillator's response to perturbation in a well-controlled and tunable manner. The article utilizes the plate reader setup for population average measurements and the mother machine setup for single-cell measurements, and they complement nicely to acquire necessary information.

Reviewer #1 (Public Review):

Summary:

The authors use a combination of biochemistry and cryo-EM studies to explore a complex between the cap binding complex and an RNA binding protein, ALYREF, that coordinates mRNA processing and export.

Strengths:

The biochemistry and structural biology are supported by mutagenesis that tests the model in vitro. The structure provides new insight into how key events in RNA processing and export are likely to be coordinated.

Weaknesses:

The authors provide biochemical studies to confirm the interactions that they identify; however, they do not perform any studies to test these models in cells or explore the consequences for mRNA export from the nucleus. In fact, several of the amino acids that they identified in ALYREF that are critical for the interaction, as determined by their own biochemical studies are conserved in budding yeast Yra1 (residues E124/E128 are E/Q in budding yeast and residues Y135/V138/P139 are F/S/P), where the impact on poly(A) RNA export from the nucleus could be readily evaluated. The authors mention the potential for future studies in the manuscript, but they do not perform any analysis in this study that would explore the contributions of these new interactions.

Reviewer #1 (Public Review):

Summary:

This study provides the detailed molecular mechanism of how OGT, an O-GlcNac transferase, promotes cancer progression. Using loss-of-function OGT models, the authors demonstrated that OGT cleaves HCF-1, an important guardian of genomic stability. The resulting genomic instability in OGT-knockout tumors leads to cytosolic DNA accumulation, the activation of cGAS-mediated type I IFN responses, and increased CD8+ T cell infiltration into the tumors. Moreover, treatment with OGT inhibitor synergized with anti-PDL1 immune-checkpoint blockade.

Strengths:

Novel findings of how OGT promotes tumor progression.

Reviewer #1 (Public Review):

The authors of this study developed a software application, which aims to identify images as either "friendly" or "unfriendly" for readers with deuteranopia, the most common color-vision deficiency. Using previously published algorithms that recolor images to approximate how they would appear to a deuteranope (someone with deuteranopia), authors first manually assessed a set of images from biology-oriented research articles published in eLife between 2012 and 2022, as well as an additional hold-out set of 2000 articles selected randomly from the PubMed Central Open Access Subset. The researchers identified 636 out of 4964 images as difficult to interpret ("unfriendly") for deuteranopes in the eLife dataset. In the PubMed Central dataset 104 out of 1191 non-grayscale images were identified as unfriendly. The results for the eLife dataset show a decrease in "unfriendly" images over time and a higher probability for articles from cell-oriented research fields to contain "unfriendly" images.

The researchers used the manually classified images from eLife to develop, train, and validate an automated screening tool. They also created a user-friendly web application of the tool, where users can upload images and be informed about the status of each image as "friendly" or "unfriendly" for deuteranopes.

Strengths:

The authors have identified an important accessibility issue in the scientific literature: the use of color combinations that make figures difficult to interpret for people with color-vision deficiency. The metrics proposed and evaluated in the study are a valuable theoretical contribution. The automated screening tool they provide is well-documented, open source, and relatively easy to install and use. It has the potential to provide a useful service to the scientists who want to make their figures more accessible. The data are open and freely accessible, well documented, and a valuable resource for further research. The manuscript is well-written, logically structured, and easy to follow.

Weaknesses:

(1) The authors themselves acknowledge the limitations that arise from the way they defined what constitutes an "unfriendly" image. There is a missed chance here to have engaged deuteranopes as stakeholders earlier in the experimental design. This would have allowed to determine to what extent spatial separation and labelling of problematic color combinations responds to their needs and whether setting the bar at a simulated severity of 80% is inclusive enough. A slightly lowered barrier is still a barrier to accessibility.

(2) The use of training images from a single journal limits the generalizability of the empirical findings as well as of the automated screening tool itself. This is evidenced by a decrease in performance of the tool on the holdout dataset from PubMed Central. Machine-learning algorithms are highly configurable but also notorious for their lack of transparency and for being easily biased by the training data set. A quick and unsystematic test of the web application shows that the classifier works well for electron microscopy images but fails at recognizing the classical diagnostic images for color-vision deficiency (Ishihara test images) as "unfriendly". A future iteration of the tool should be trained on a wider variety of images, ideally enriched with diagnostic images found in scientific publications.

Reviewer #1 (Public Review):

Summary:

The authors fabricated a novel cancer vaccine using endogenous virus-like particles with tumor neoantigen. The vaccine ePAC was proven to elicit strong immune stimulation with an increased killing effect against tumor cells in 2 mouse models.

Strengths:

The author achieved high protein loading and transfection efficiency using PEG10 self-assembly while packaging tumor neoantigens inside for cancer immunotherapy. The author also enhanced the targeting effect towards dendritic cells by surface modification using CpG-ODN.

Weaknesses:

There were some minor issues but they have been resolved in the revision process. It would be great if the authors could compare this with commercially available treatments and other vaccines.

Discussion:

Since the ePAC vaccine particle functions as a delivery platform, it can be tailored to different tumors when packed with their specific tumor neoantigens. Thus, the ePAC platform can be potentially employed in a broad range of cancer vaccine therapies. It would be exciting to see this platform being developed for other major cancer types.

Reviewer #1 (Public Review):

Summary:

The manuscript aimed at elucidating the substrate specificity of two M23 endopeptidase Lysostaphin (LSS) and LytM in S. aureus. Endopeptidases are known to cleave the glycine-bridges of staphylococcal cell wall peptidoglycan (PG). To address this question, various glycine-bridge peptides were synthesized as substrates, the catalytic domain of LSS and LytM were recombinantly expressed and purified, and the reactions were analyzed using solution-state NMR. The major finding is that LytM is not only a Gly-Gly endopeptidase, but also cleaves D-Ala-Gly. Technically, the advantage of using real-time NMR was emphasized in the manuscript. The study explores an interesting aspect of cell wall hydrolases in terms of substrate-level regulation. It potentially identified new enzymatic activity of LytM. However, the biological significance and relevance of the conclusions remain clear, as the results are mostly from synthetic substrates.

Strengths:

The study explores an interesting aspect of cell wall hydrolases in terms of substrate-level regulation. It potentially identified new enzymatic activity of LytM.

Comments on the revised version:

The authors have addressed most of my concerns. I agree that the physiological functions of LytM are not in the scope of the current study.

Reviewer #1 (Public Review):

Summary:

This manuscript aimed to investigate the emergence of emotional sensitivity and its relationship with gestational age. Using an oddball paradigm and event-related potentials, the authors conducted an experiment in 120 healthy neonates with a gestational age range of 35 to 40 weeks. A significant developmental milestone was identified at 37 weeks gestational age, marking a crucial juncture in neonatal emotional responsiveness.

Strengths:

This study has several strengths, by providing profound insights into the early development of social-emotional functioning and unveiling the role of gestational age in shaping neonatal perceptual abilities. The methodology of this study demonstrates rigor and well-controlled experimental design, particularly involving matched control sounds, which enhances the reliability of the research. Their findings not only contribute to the field of neurodevelopment, but also showcase potential clinical applications, especially in the context of autism screening and early intervention for neurodevelopmental disorders.

Reviewer #1 (Public Review):

Summary:

A nice study trying to identify the relationship between E. coli O157 from cattle and humans in Alberta, Canada.

Strengths:

(1) The combined human and animal sampling is a great foundation for this kind of study.

(2) Phylogenetic analyses seem to have been carried out in a high-quality fashion.

Weaknesses:

I think there may be a problem with the selection of the isolates for the primary analysis. This is what I'm thinking:

(1) Transmission analyses are strongly influenced by the sampling frame.

(2) While the authors have randomly selected from their isolate collections, which is fine, the collections themselves are not random.

(3) The animal isolates are likely to represent a broad swathe of diversity, because of the structured sampling of animal reservoirs undertaken (as I understand it).

(4) The human isolates are all from clinical cases. Clinical cases of the disease are likely to be closely related to other clinical cases, because of outbreaks (either detected, or undetected), and the high ascertainment rate for serious infections.

(5) Therefore, taking an equivalent number of animal and clinical isolates, will underestimate the total diversity in the clinical isolates because the sampling of the clinical isolates is less "independent" (in the statistical sense) than sampling from the animal isolates.

(6) This could lead to over-estimating of transmission from cattle to humans.

(7) "We hypothesize that the large proportion of disease associated with local transmission systems is a principal cause of Alberta's high E. coli O157:H7 incidence" - this seems a bit tautological. There is a lot of O157 because there's a lot of transmission. What part of the fact it is local means that it is a principal cause of high incidence? It seems that they've observed a high rate of local transmission, but the reasons for this are not apparent, and hence the cause of Alberta's incidence is not apparent. Would a better conclusion not be that "X% of STEC in Alberta is the result of transmission of local variants"? And then, this poses a question for future epi studies of what the transmission pathway is.

Reviewer #1 (Public Review):

Summary:<br /> In this study, Zhao and colleagues investigate inflammasome activation by E. tarda infections. They show that E. tarda induces the activation of the NLRC4 inflammasome as well as the non-canonical pathway in human THP1 macrophages. Further dissecting NLRC4 activation, they find that T3SS translocon components eseB, eseC and eseD are necessary for NLRC4 activation and that delivery of purified eseB is sufficient to trigger NAIP-dependent NLRC4 activation. Sequence analysis reveals that eseB shares homology within the C-terminus with T3SS needle and rod proteins, leading the authors to test if this region is necessary for inflammasome activation. They show that the eseB CT is required and that it mediates interaction with NAIP. Finally, they that homologs of eseB in other bacteria also share the same sequence and that they can activate NLRC4 in a HEK293T cell overexpression system.

Strengths:<br /> This is a very nice study that convincingly shows that eseB and its homologs can be recognized by the human NAIP/NLRC4 inflammasome. The experiments are well designed, controlled and described, and the papers is convincing as a whole.

Weaknesses:<br /> The authors need to discuss their study in the context of previous papers that have shown an important role for E. tarda flagellin in inflammasome activation and test whether flagellin and/or E. tarda T3SSs needle or rod can activate NLRC4.

The authors show that eseB and its homologs can activate NLRC4, but there are also other translocon proteins that are very different such as YopB or PopB. and share little homology with eseB. It would be nice to include a section comparing the different type 3 secretion systems. are there 2 different families of T3SSs, those that feature translocon components that are recognized by NAIP-NLRC4 and those that cannot be recognized?

Reviewer #1 (Public Review):

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

Summary:

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

Strengths:

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

Weaknesses:

(1) It will be interesting to monitor the levels of another MIM insertase namely, OXA1. This will help to understand whether some of the observed changes in levels of OXPHOS subunits are related to alterations in the amounts of this insertase.

(2) The authors did not provide explanations for several key findings like:<br /> A. Figure 3: How do the authors explain that although TIMM17 and TIMM23 were found to be significantly reduced by Western analysis they were not detected as such by the Mass Spec. method?<br /> B. How do the authors explain the higher levels of some proteins in the TIMM50 mutated cells?<br /> C. Can the authors elaborate on why mutated cells are impaired in their ability to switch their energetic emphasis to glycolysis when needed?

Reviewer #1 (Public Review):

Time periods in which experience regulates early plasticity in sensory circuits are well established, but the mechanisms that control these critical periods are poorly understood. In this manuscript, Leier and Foden and colleagues examine early-life critical periods that regulate the Drosophila antennal lobe, a model sensory circuit for understanding synaptic organization. Using early-life (0-2 days old) exposure to distinct odorants, they show that constant odor exposure markedly reduces the volume, synapse number, and function of the VM7 glomerulus. The authors offer evidence that these changes are mediated by invasion of ensheathing glia into the glomerulus where they phagocytose connections via a mechanism involving the engulfment receptor Draper.

This manuscript is a striking example of a study where the questions are interesting, the authors spent a considerable amount of time to clearly think out the best experiments to ask their questions in the most straightforward way, and expressed the results in a careful, cogent, and well-written fashion. It was a genuine delight to read this paper. I have two experimental suggestions that would really round out existing work to better support the existing conclusions and some instances where additional data or tempered language in describing results would better support their conclusions. Overall, though, this is an incredibly important finding, a careful analysis, and an excellent mechanistic advance in understanding sensory critical period biology.

Reviewer #1 (Public Review):

Summary:

This article presents a meta-analysis that challenges established abundance-occupancy relationships (AORs) by utilizing the largest known bird observation database. The analysis yields contentious outcomes, raising the question of whether these findings could potentially refute AORs.

Strengths:

The study employed an extensive aggregation of datasets to date to scrutinize the abundance-occupancy relationships (AORs).

Weaknesses:

While the dataset employed in this research holds promise, a rigorous justification of the core assumptions underpinning the analytical framework is inadequate. The authors should thoroughly address the correlation between checklist data and global range data, ensuring that the foundational assumptions and potential confounding factors are explicitly examined and articulated within the study's context.

Reviewer #1 (Public Review):

Summary:<br /> The authors present experimental and numerical results on the motility Magnetospirillum gryphiswaldense MSR-1, a magnetotactic bacterium living in sedimentary environments. The authors manufactured microfluidic chips containing three-dimensional obstacles of irregular shape, that match the statistical features of the grains observed in the sediment via micro-computer tomography. The bacteria are furthermore subject to an external magnetic field, whose intensity can be varied. The key quantity measured in the experiments is the throughput ratio, defined as the ratio between the number of bacteria that reach the end of the microfluidic channel and the number of bacteria entering it. The main result is that the throughput ratio is non-monotonic and exhibits a maximum at magnetic field strength comparable with Earth's magnetic field. The authors rationalize the throughput suppression at large magnetic fields by quantifying the number of bacteria trapped in corners between grains.

Strengths:<br /> While magnetotactic bacteria's general motility in bulk has been characterized, we know much less about their dynamics in a realistic setting, such as a disordered porous material. The micro-computer tomography of sediments and their artificial reconstruction in a microfluidic channel is a powerful method that establishes the rigorous methodology of this work. This technique can give access to further characterization of microbial motility. The coupling of experiments and computer simulations lends considerable strength to the claims of the authors, because the model parameters (with one exception) are directly measured in the experiments.

Weaknesses:<br /> The main weakness of the manuscript pertains to the discussion of the statistical significance of the experimental throughput ratio. Especially when comparing results at zero and 50 micro Tesla. The simulations seem to predict a stronger effect than seen in the experiments. The authors do not address this discrepancy.

Reviewer #1 (Public Review):

Summary:<br /> The paper investigates the interplay between fluid flow and biofilm development using Pseudomonas aeruginosa PAO1 in microfluidic channels. By combining experimental observations with mathematical modeling, the study identifies the significant impact of nutrient limitation and hydrodynamic forces on biofilm growth and detachment. The authors demonstrate that nutrient limitation drives the longitudinal distribution of biomass, while flow-induced detachment influences the maximum clogging and temporal dynamics. The study highlights that pressure buildup plays a critical role in biofilm detachment, leading to cyclic episodes of sloughing and regrowth. A stochastic model is used to describe the detachment process, capturing the apparent randomness of sloughing events. The findings offer insights into biofilm behavior during clogging and fouling, potentially relevant to infections, environmental processes, and engineering applications.

Strengths:<br /> This paper demonstrates a strong integration of experimental work and mathematical modeling, providing a comprehensive understanding of biofilm dynamics in straight microfluidic channel. The simplicity of the microchannel geometry allows for accurate modeling, and the findings have the potential to be applied to more complex geometries. The detailed analysis of nutrient limitation and its impact on biofilm growth offers valuable insights into the conditions that drive biofilm formation. The model effectively describes biofilm development across different stages, capturing both initial growth and cyclic detachment processes. While cyclic pressure buildup has been studied previously, the incorporation of a stochastic model to describe detachment events is a novel and significant contribution, capturing the complexity and randomness of biofilm behavior. Finally, the investigation of pressure buildup and its role in cyclic detachment and regrowth enhances our understanding of the mechanical forces at play, making the findings applicable to a wide range of technological and clinical contexts.

Weaknesses:<br /> The study achieves its primary goal of integrating experiments and modeling to understand the coupling between flow and biofilm growth and detachment in a microfluidic channel, but it should have highlighted the weaknesses of the methods. I list the ones that, in my opinion, are the main ones:

• The study does not consider biofilm porosity, which could significantly affect the flow and forces exerted on the biofilm. Porosity could impact the boundary conditions, such as the no-slip condition, which should be validated experimentally.<br /> • The research suggests EPS development as a stage in biofilm growth but does not probe it using lectin staining. This makes it impossible to accurately assess the role of EPS in biofilm development and detachment processes.<br /> • While the force and flow are three-dimensional, the images are taken in two dimensions. The paper does not clearly explain how the 2D images are extrapolated to make 3D assessments, which could lead to inaccuracies.<br /> • Although the findings are tested using polysaccharide-deficient mutants, the results could have been analyzed in greater detail. A more thorough analysis would help to better understand the role of matrix composition on the stochastic model of detachment.

DOI: 10.1016/j.cub.2023.07.021

Resource: (ZFIN Cat# ZDB-GENO-060207-1,RRID:ZFIN_ZDB-GENO-060207-1)

Curator: @vtello

SciCrunch record: RRID:ZFIN_ZDB-GENO-060207-1

What is this?

Reviewer #1 (Public Review):

This manuscript builds upon the authors' previous work on the cross-talk between transcription initiation and post-transcriptional events in yeast gene expression. These prior studies identified an mRNA 'imprinting' phenomenon linked to genes activated by the Rap1 transcription factor (TF), a surprising role for the Sfp1 TF in promoting RNA polymerase II (RNAPII) backtracking, and a role for the non-essential RNAPII subunits Rpb4/7 in the regulation of mRNA decay and translation. Here the authors aimed to extend these observations to provide a more coherent picture of the role of Sfp1 in transcription initiation and subsequent steps in gene expression. They provide evidence for (1) a physical interaction between Sfp1 and Rpb4, (2) Sfp1 binding and stabilization of mRNAs derived from genes whose promoters are bound by both Rap1 and Sfp1 and (3) an effect of Sfp1 on Rpb4 binding or conformation during transcription elongation.

Reviewer #1 (Public Review):

Summary:

In this manuscript, Wu et al. introduce a novel approach to reactivate the Muller glia cell cycle in the mouse retina by simultaneously reducing p27Kip1 and increasing cyclin D1 using a single AAV vector. The approach effectively promotes Muller glia proliferation and reprograming without disrupting retinal structure or function. Interestingly, reactivation of the Muller glia cell cycle downregulates IFN pathway, which may contribute to the induced retinal regeneration. The results presented in this manuscript may offer a promising approach for developing Müller glia cell-mediated regenerative therapies for retinal diseases.

Strengths:

The data are convincing and supported by appropriate, validated methodology. These results are both technically and scientifically exciting and are likely to appeal to retinal specialists and neuroscientists in general.

Weaknesses:

There are some data gaps that need to be addressed.

(1) Please label the time points of AAV injection, EdU labeling, and harvest in Figure 1B.

(2) What fraction of Müller cells were transduced by AAV under the experimental conditions?

(3) It seems unusually rapid for MG proliferation to begin as early as the third day after CCA injection. Can the authors provide evidence for cyclin D1 overexpression and p27 Kip1 knockdown three days after CCA injection?

(4) The authors reported that MG proliferation largely ceased two weeks after CCA treatment. While this is an interesting finding, the explanation that it might be due to the dilution of AAV episomal genome copies in the dividing cells seems far-fetched.