Reviewer #2 (Public Review):

Summary:<br /> Pisanski and colleagues map regions of the brainstem that produce the rhythm for active expiratory breathing movements and influence their motor patterns. While the neural origins of inspiration are very well understood, the neural bases for expiration lag considerably. The problem is important and new knowledge pertaining to the neural origins of expiration is welcome.

The authors perturb the parafacial lateral (pFL) respiratory group of the brainstem with microinjection of bicuculline, to elucidate how disinhibition in specific locations of the pFL influences active expiration (and breathing in general) in anesthetized rats. They provide valuable, if not definitive, evidence that the borders of the pFL appear to extend more rostrally than previously appreciated. Prior research suggests that the expiratory pFL exists at the caudal pole of the facial cranial nucleus (VIIc). Here, the authors show that its borders probably extend as much as 1 mm rostral to VIIc. The evidence is convincing albeit with caveats.

Strengths:<br /> The authors achieve their aim in terms of showing that the borders of the expiratory pFL are not well understood at present and that it (the pFL) extends more rostrally. The results support that point. The data are strong enough to cause many respiratory neurobiologists to look at the sites rostral to the VIIc for expiratory rhythmogenic neurons and characterize their properties and mechanisms. At present my view is that most respiratory neurobiologists overlook the regions rostral to VIIc in their studies of expiratory rhythm and pattern.

Weaknesses:<br /> The injection of bicuculline has indiscriminate effects on excitatory and inhibitory neurons, and the parafacial region is populated by excitatory neurons that are expiratory rhythmogenic and GABA and glycinergic neurons whose roles in producing active expiration are contradictory (Flor et al. J Physiol, 2020, DOI: 10.1113/JP280243). It remains unclear how the microinjections of bicuculline differentially affect all three populations. A more selective approach would be able to disinhibit the populations separately. Nevertheless, for the main point at hand, the data do suggest that we should reconsider the borders of the expiratory pFL nucleus and begin to examine its physiology up to 1 mm rostral to VIIc.

The control experiment showed that bicuculline microinjections induced cFos expression in the pFL, which is good, but again we don't know which neurons were disinhibited: glutamatergic, GABAergic, or glycinergic.

The manuscript characterizes how bicuculline microinjections affect breathing parameters such as tidal volume, frequency, ventilation, inspiratory and expiratory time, as well as oxygen consumption. Those aspects of the manuscript are a bit tedious and sometimes overanalyzed. Plus, there was no predictive framework established at the outset for how one should expect disinhibition to affect breathing parameters. In other words, if the authors are seeking to map the pFL borders, then why analyze the breathing patterns so much? Does doing so provide more insight into the borders of pFL? I did not think it was compellingly argued.

Further, lines 382-386 make a point about decreasing inspiratory time even though the data do not meet the statistical threshold.

In lines 386-395, the reporting appears to reach significance (line 388) but not reach significance (line 389). I had trouble making sense of that disparity.

The other statistical hiccups include "tended towards significance" (line 454), "were found to only reach significance for a short portion of the response" (line 486-7), "did not reach the level of significance" (line 506), which gives one the sense of cherry picking or over-analysis. Frankly, this reviewer finds the paper much more compelling when just asking whether the microinjections evoke active expiration. If yes, then the site is probably part of the pFL.

I encourage the authors to consider the fickleness of p-values in general and urge them to consider not just p but also effect size.

Reviewer #2 (Public Review)

Summary:<br /> This paper by Maddox et al. presents the results of a study of Ca channel function in mouse cone photoreceptor synaptic terminals. It builds on earlier work by the same authors (Maddox et al. 2020 in eLife) which demonstrated that a non-conducting but voltage-sensing variant of Cav1.4 (G369i knock-in, or KI) could substitute for WT Cav1.4 to promote relatively normal rod synapse development despite an inability to support Ca2+-dependent glutamatergic transmission to postsynaptic bipolar cells. Cav1.4 knock-out (KO) rod synapses, however, were completely disorganized, indicating that the presence of Cav1.4 protein is critical for synaptic organization. Here, the authors extend their study of the G369i-KI retina to demonstrate that G369i-KI cones develop working (though disrupted and sometimes aberrant) synapses that support some visual function owing to compensatory expression of Cav3-containing Ca channels that can mediate some Ca2+-dependent transmission from cones to postsynaptic cells. This compensatory expression of a low voltage-activated Ca conductance was not noted previously (Maddox et al. 2020) in G369i-KI rods.

Strengths:<br /> In all, this is a scientifically sound study that shows obvious differences between synaptic terminal morphology and organization, macroscopic Ca currents, transmission to postsynaptic horizontal and bipolar cells (with whole-cell recording and ERG, respectively), and visually-guided behavior in experimental groups.

Weaknesses:<br /> The major criticism that I have of the study is that it infers Ca channel molecular composition based solely on pharmacological analysis, which, as the authors note, is confounded by the cross-reactivity of many of the "specific" channel-type antagonists. The authors note that Cav3 mRNAs have been found in cones, but here, they do not perform any analysis to examine Cav3 transcript expression after G369i-KI nor do they examine Ca channel transcript expression in monkey or squirrel cones, which serve as controls of sorts for the G369i-KI (i.e. like WT mouse cones, cones of these other species do not seem to exhibit LVA Ca currents).

Secondarily, in Maddox et al. 2020, the authors raise the possibility that G369i-KI, by virtue of having a functional voltage-sensing domain-might couple to intracellular Ca2+ stores, and it seems appropriate that this possibility be considered experimentally here.

As a minor point: the authors might wish to note - in comparison to another retinal ribbon synapse-that Zhang et al. 2022 (in J. Neuroscience) performed a study of mouse rod bipolar cells found a number of LVA and HVA Ca conductances in addition to the typical L-type conductance mediated by Cav1-containing channels.

Reviewer #2 (Public Review):

Summary:<br /> This manuscript proposes a modeling approach to capture nonlinear processes of photocurrents in mammalian (mouse, primate) rod and cone photoreceptors. The ultimate goal is to separate these nonlinearities at the level of photocurrent from subsequent nonlinear processing that occurs in retinal circuitry. The authors devised a strategy to generate stimuli that cancel the major nonlinearities in photocurrents. For example, modified stimuli would generate genuine sinusoidal modulation of the photocurrent, whereas a sinusoidal stimulus would not (i.e., because of asymmetries in the photocurrent to light vs. dark changes); and modified stimuli that could cancel the effects of light adaptation at the photocurrent level. Using these modified stimuli, one could record downstream neurons, knowing that any nonlinearities that emerge must happen post-photocurrent. This could be a useful method for separating nonlinear mechanisms across different stages of retinal processing, although there are some apparent limitations to the overall strategy.

Strengths:<br /> 1. This is a very quantitative and thoughtful approach and addresses a long-standing problem in the field: determining the location of nonlinearities within a complex circuit, including asymmetric responses to different polarities of contrast, adaptation, etc.<br /> 2. The study presents data for two primary models of mammalian retina, mouse, and primate, and shows that the basic strategy works in each case.<br /> 3. Ideally, the present results would generalize to the work in other labs and possibly other sensory systems. How easy would this be? Would one lab have to be able to record both receptor and post-receptor neurons? Would in vitro recordings be useful for interpreting in vivo studies? It would be useful to comment on how well the current strategy could be generalized.

Weaknesses:<br /> 1. The model is limited to describing photoreceptor responses at the level of photocurrents, as opposed to the output of the cell, which takes into account voltage-dependent mechanisms, horizontal cell feedback, etc., as the authors acknowledge. How would one distinguish nonlinearities that emerge at the level of post-photocurrent processing within the photoreceptor as opposed to downstream mechanisms? It would seem as if one is back to the earlier approach, recording at multiple levels of the circuit (e.g., Dunn et al., 2006, 2007).<br /> 2. It would have been nice to see additional confirmations of the approach beyond what is presented in Figure 9. This is limited by the sample (n = 1 horizontal cell) and the number of conditions (1). It would have been interesting to at least see the same test at a dimmer light level, where the major adaptation mechanisms are supposed to occur beyond the photoreceptors (Dunn et al., 2007).

Reviewer #2 (Public Review):

Summary:<br /> The present study addresses the role of enkephalins, which are specifically expressed by regulatory T cells (Treg), in sensory perception in mice. The authors used a combination of transcriptomic databases available online to characterize the molecular signature of Treg. The proenkephalin gene Penk is among the most enriched transcripts, suggesting that Treg plays an analgesic role through the release of endogenous opioids. In addition, in silico analysis suggests that Penk is regulated by the TNFR superfamily; this being experimentally confirmed. Using flow cytometry analysis, the authors then show that Penk is mostly expressed in Treg of the skin and colon, compared to other immune cells. Finally, genetic conditional excision of Penk, selectively in Treg, results in heat hypersensitivity, as assessed by behavior analysis.

Strengths:<br /> The manuscript is clear and reveals a previously unappreciated role of enkephalins, as released by immune cells, in sensory perception. The rationale in this manuscript is easy to follow, and conclusions are well supported by data.

Weaknesses:<br /> The sensory deficit of Penk cKO appears to be quite limited compared to control littermates.

Reviewer #2 (Public Review):

Understanding how the LC/noradrenaline system controls basic cognitive processes is important and timely. This study aims to understand the role Locus Coeurelus /noradrenaline system in extinction of conditioned responding. The authors used a discriminative appetitive procedure to show that photoexcitation of noradrenergic neurons of the Locus Coeruleus has no effect on the performance during extinction but impacts expression of extinguished responding through a decreased spontaneous recovery. This study is appropriately designed and the results are well analysed. Therefore, it provides an important and timely addition to the field

Reviewer #2 (Public Review):

Summary<br /> The manuscript by Galicia et al describes the structure of the bacterial GTPyS-bound CtRoco protein in the presence of nanobodies. The major relevance of this study is in the fact that the CtRoco protein is a homolog of the human LRRK2 protein with mutations that are associated with Parkinson's disease. The structure and activation mechanisms of these proteins are very complex and not well understood. Especially lacking is a structure of the protein in the GTP-bound state. Previously the authors have shown that two conformational nanobodies can be used to bring/stabilize the protein in a monomer-GTPyS-bound state. In this manuscript, the authors use these nanobodies to obtain the GTPyS-bound structure and importantly discuss their results in the context of the mammalian LRRK2 activation mechanism and mutations leading to Parkinson's disease. The work is well performed and clearly described. In general, the conclusions on the structure are reasonable and well-discussed in the context of the LRRK2 activation mechanism.

Strengths:<br /> The strong points are the innovative use of nanobodies to stabilize the otherwise flexible protein and the new GTPyS-bound structure that helps enormously in understanding the activation cycle of these proteins.

Weakness:<br /> The strong point of the use of nanobodies is also a potential weak point; these nanobodies may have induced some conformational changes in a part of the protein that will not be present in a GTPyS-bound protein in the absence of nanobodies.

Two major points need further attention.

1. Several parts of the protein are very flexible during the monomer-dimer activity cycle. This flexibility is crucial for protein function, but obviously hampers structure resolution. Forced experiments to reduce flexibility may allow better structure resolution, but at the same time may impede the activation cycle. Therefore, careful experiments and interpretation are very critical for this type of work. This especially relates to the influence of the nanobodies on the structure that may not occur during the "normal" monomer-dimer activation cycle in the absence of the nanobodies (see also point 2). So what is the evidence that the nanobody-bound GTPyS-bound state is biochemically a reliable representative of the "normal" GTP-bound state in the absence of nanobodies, and therefore the obtained structure can be confidentially used to interpret the activation mechanism as done in the manuscript.

2. The obtained structure with two nanobodies reveals that the nanobodies NbRoco1 and NbRoco2 bind to parts of the protein by which a dimer is impossible, respectively to a0-helix of the linker between Roc-COR and LRR, and to the cavity of the LRR that in the dimer binds to the dimerizing domain CORB. It is likely the open monomer GTP-bound structure is recognized by the nanobodies in the camelid, suggesting that overall the open monomer structure is a true GTP-bound state. However, it is also likely that the binding energy of the nanobody is used to stabilize the monomer structure. It is not automatically obvious that in the details the obtained nonobody-Roco-GTPyS structure will be identical to the "normal" Roco-GTPyS structure. What is the influence of nanobody-binding on the conformation of the domains where they bind; the binding energy may be used to stabilize a conformation that is not present in the absence of the nanobody. For instance, NbRoco1 binds to the a0 helix of the linker; what is here the "normal" active state of the Roco protein, and is e.g. the angle between RocCOR and LRR also rotated by 135 degrees? Furthermore, nanobody NbRoco2 in the LRR domain is expected to stabilize the LRR domain; it may allow a position of the LRR domain relative to the rest of the protein that is not present without nanobody in the LRR domain. I am convinced that the observed open structure is a correct representation of the active state, but many important details have to be supported by e,g, their CX-MS experiments, and in the end probably need confirmation by more structures of other active Roco proteins or confirmation by a more dynamic sampling of the active states by e.g. molecular dynamics or NMR.

Reviewer #2 (Public Review):

In their manuscript, Medina and colleagues investigate transcriptional differences between mild and severe SARS-CoV-2 infections. Their analyses are very comprehensive incorporating a multitude of bioinformatics tools ranging from PCA plots, GSEA and DEG analysis, protein-protein interaction network, and weighted correlation network analyses. They conclude that in mild COVID-19 infection NK cell functionality is compromised and this is connected to cytokine interactions and Th1/Th2 cell differentiation pathways cross-talk, bridging the innate and the adaptive arms of the immune system.

The authors successfully recruited participants with both mild and severe COVID-19 between November 2020 to May 2021. The analyzed cohort is gender and acceptably age-matched and the results reported are promising. Signatures associated with NK cell cytotoxicity in mild and neutrophil functions in the severe group during acute infection are the chief findings reported in this manuscript.

Reviewer #2 (Public Review):

Summary:<br /> This study by Vijay and colleagues addresses a clinically important, and often overlooked aspect of Tb treatment. Detecting for variations in the level of antibiotic tolerance amongst otherwise antibiotic-susceptible isolates is difficult to routinely screen for, and consequently not performed. The authors, present a convincing argument that indeed, there is significant variation in the susceptibility of isoniazid-resistant strains to killing by rifampicin, in some cases at the same tolerance levels as bona fide resistant strains. On the whole, the study is easy to follow and the results are justified. This work should be of interest to the wider TB community at both a clinical and basic level.

Weaknesses:<br /> The manuscript is long, repetitive in places, and the figures could use some amending to improve clarity (this could be a me-specific issue as they look ok on my screen, yet the colour is poor when printed).

It would have been great to have seen some correlation between increased rifampicin tolerance and treatment outcome, although I'm not sure if this data is available to the researchers. I agree with the researchers the use of a single media condition is a limitation. However, this is true of a lot of studies.

Reviewer #2 (Public Review):

Chen et al. investigated the regulatory mechanism of bacterial colonization in the intestinal mucus layer in mice and its implications for intestinal diseases. They demonstrated that Chi3l1 is a protein produced and secreted by intestinal epithelial cells into the mucus layer upon response to the gut microbiota, which has a turnover effect on facilitating the colonization of gram-positive bacteria in the mucosa. The data also indicate that Chi3l1 interacts with the peptidoglycan of the bacteria cell wall, supporting the colonization of beneficial bacteria strains such as Lactobacillus, and that deficiency in Chi3l1 predisposes mice to colitis. The inclusion of a small but pertinent piece of human data added to solidify their findings in mice.

Overall, the experiments performed were appropriate and well executed, but the data analysis is incomplete and needs to be extended. Also, additional experiments are necessary for clarification and stronger support for their conclusions.

1) Images are of great quality but lack proper quantification and statistical analysis. Statements such as "substantial increase of Chi3l1 expression in SPF mice" (Fig.1A), "reduced levels of Firmicutes in the colon lumen of IECChil1" (Fig.3F), "Chil1-/- had much lower colonization of E.faecalis" (Fig.4G), or "deletion of Chi3l1 significantly reduced mucus layer thickness" (Supplemental Figure 3A-B) are subjective. Since many conclusions were based on imaging data, the authors must provide reliable measures for comparison between conditions, as long as possible, such as fluorescence intensity, area, density, etc, as well as plots and statistical analysis.

2) In the fecal/Lactobacillus transplantation experiments, oral gavage of Lactobacillus to IECChil1 mice ameliorated the colitis phenotype, by preventing colon length reduction, weight loss, and colon inflammation. These findings seem to go against the notion that Chi3l1 is necessary for the colonization of Lactobacillus in the intestinal mucosa. The authors could speculate on how Lactobacillus administration is still beneficial in the absence of Chi3l1. Perhaps, additional data showing the localization of the orally administered bacteria in the gut of Chi3l1 deficient mice would clarify whether Lactobacillus are more successfully colonizing other regions of the gut, but not the mucus layer. Alternatively, later time points of 2% DSS challenge, after Lactobacillus transplantation, would suggest whether the gut colonization by Lactobacillus and therefore the milder colitis phenotype, is sustained for longer periods in the absence of Chi3l1.

Reviewer #2 (Public Review):

In this study, Zhenbang Ye and colleagues investigate the links between microenvironment signatures, gene expression profiles, and prognosis in diffuse large B-cell lymphoma (DLBCL). They show that increased tumor purity (ie, a higher proportion of tumor cells relative to surrounding stromal components) is associated with a worse prognosis. They then show that three genes associated with tumor purity (VCAN, CD3G, and C1QB) correlate with patterns of immune cell infiltration and can be used to create a risk-scoring system that predicts prognosis, which can be replicated by immunohistochemistry (IHC), and response to some therapies.

1. The two strengths of the study are its relatively large sample size (n = 190) and the strong prognostic significance of the risk-scoring system. It is worth noting that the validation of this scoring with IHC, a simple technique already routinely used for the diagnosis and classification of DLBCL, increases the potential for clinical translation. However, the correlative nature of the study limits the conclusions that can be drawn in regard to links between the risk scoring system, the tumor microenvironment, and the biology of DLBCL.

2. The tumor microenvironment has been extensively studied in DLBCL and a prognostic implication has already been established (for instance, Steen et al., Cancer Cell, 2021). In addition, associations have already been established in non-Hodgkin lymphoma between prognosis and expression of C1QB (Rapier-Sharman et al., Journal of Bioinformatics and Systems Biology, 2022), VCAN (S. Hu et al., Blood, 2013), and CD3G (Chen et al., Medical Oncology, 2022). Nevertheless, one of the strengths and novelty aspects of the study is the combination of these 3 genes into a risk score that is also valid by immunohistochemistry (IHC), which substantially facilitates a potential clinical translation.

3. Figures 1A-B: tumor purity is calculated using the ESTIMATE (Estimation of Stromal and Immune cells in Malignant Tumor tissues using Expression data) algorithm (Yoshihara et al., Nature Communications, 2013). The ESTIMATE algorithm is based on two gene signatures ("stromal" and "immune"). It is therefore expected that tumor purity measured by the ESTIMATE algorithm will correlate with the expression of multiple genes. Importantly, C1QB is included in the stromal signature of the ESTIMATE algorithm meaning that, by definition, it will be correlated with tumor purity in that setting.

4. Figure 2A: as established in Figure 1C, high tumor purity is associated with worse prognosis. Later in the manuscript, it is also shown that C1QB expression is associated with a worse prognosis. However, Figure 2A shows that C1QB is associated with decreased tumor purity. It therefore makes it less likely that the prognostic role of C1QB expression is related to its impact on tumor purity. The prognostic impact could be related to different patterns of immune cell infiltration, as shown later. However, the evidence presented in the study is correlative and natural and not sufficient to draw this conclusion.

5. Figure 3G: although there is a strong prognostic implication of the risk score on prognosis, the correlation between the risk score and tumor purity is significant but not very strong (R = 0.376). It is therefore likely that other important biological factors explain the correlation between the risk score and prognosis.

6. Figure 6: the drug sensitivity analysis includes a wide range of established and investigational drugs with varied mechanisms of action. Although the difference in sensitivity between tumors with low and high-risk scores shows statistical significance for certain drugs, the absolute difference appears small in most cases and is of unclear biological significance. In addition, even though the risk score is statistically related to drug sensitivity, there is no direct evidence that the differences in drug sensitivity are directly related to tumor purity.

Reviewer #2 (Public Review):

In the manuscript entitled "Linking the evolution of two prefrontal brain regions to social and foraging challenges in primates" the authors measure the volume of the frontal pole (FP, related to metacognition) and the dorsolateral prefrontal cortex (DLPFC, related to working memory) in 16 primate species to evaluate the influence of socio-ecological factors on the size of these cortical regions. The authors select 11 socio-ecological variables and use a phylogenetic generalized least squares (PGLS) approach to evaluate the joint influence of these socio-ecological variables on the neuro-anatomical variability of FP and DLPFC across the 16 selected primate species; in this way, the authors take into account the phylogenetic relations across primate species in their attempt to discover the the influence of socio-ecological variables on FP and DLPF evolution.

The authors run their studies on brains collected from 1920 to 1970 and preserved in formalin solution. Also, they obtained data from the Mussée National d´Histoire Naturelle in Paris and from the Allen Brain Institute in California. The main findings consist in showing that the volume of the FP, the DLPFC, and the Rest of the Brain (ROB) across the 16 selected primate species is related to three socio-ecological variables: body mass, daily traveled distance, and population density. The authors conclude that metacognition and working memory are critical for foraging in primates and that FP volume is more sensitive to social constraints than DLPFC volume.

The topic addressed in the present manuscript is relevant for understanding human brain evolution from the point of view of primate research, which, unfortunately, is a shrinking field in neuroscience. But the experimental design has two major weak points: the absence of lissencephalic primates among the selected species and the delimitation of FP and DLPFC. Also, a general theoretical and experimental frame linking evolution (phylogeny) and development (ontogeny) is lacking.

Reviewer #2 (Public Review):

Summary:<br /> In this manuscript, the authors aim to demonstrate that cardiac glycosides restore autophagy flux in an iPSC-derived mDA neuronal model of WDR45 deficiency. They established a patient-derived induced pluripotent stem cell (iPSC)-based midbrain dopaminergic (mDA) neuronal model and performed a medium-throughput drug screen using high-content imaging-based IF analysis. Several compounds were identified to ameliorate disease-specific phenotypes in vitro.

Strengths:<br /> This manuscript engaged in an important topic and yielded some interesting data.

Weaknesses:<br /> This manuscript failed to provide solid evidence to support the conclusion.

Reviewer #2 (Public Review):

Summary:<br /> This study examines the pattern of responses produced by the combination of left-eye and right-eye signals in V1. For this, they used calcium imaging of neurons in V1 of awake, fixating monkeys. They take advantage of calcium imaging, which yields large populations of neurons in each field of view. With their data set, they observe how response magnitude relates to ocular dominance across the entire population. They analyze carefully how the relationship changed as the visual stimulus switched from contra-eye only, ipsi-eye only, and binocular. As expected, the contra-eye-dominated neurons responded strongly with a contra-eye-only stimulus. The ipsi-eye-dominated neurons responded strongly with an ipsi-eye-only stimulus. The surprise was responses to a binocular stimulus. The responses were similarly weak across the entire population, regardless of each neuron's ocular dominance. They conclude that this pattern of responses could be explained by interocular divisive normalization, followed by binocular summation.

Strengths:<br /> A major strength of this work is that the model-fitting was done on a large population of simultaneously recorded neurons. This approach is an advancement over previous work, which did model-fitting on individual neurons. The fitted model in the manuscript represents the pattern observed across the large population in V1, and washes out any particular property of individual neurons. Given the large neuronal population from which the conclusion was drawn, the authors provide solid evidence supporting their conclusion. They also observed consistency across 5 fields of view.

The experiments were designed and executed appropriately to test their hypothesis. Their data support their conclusion.

Weaknesses:<br /> One weakness of their study is that calcium signals can exaggerate the nonlinear properties of neurons. Calcium imaging renders poor responses poorer and strong responses stronger, compared to single-unit recording. In particular, the dramatic change in the population response between monocular stimulation and binocular stimulation could actually be less pronounced when measured with single-unit recording methods. This means their choice of recording method could have accidentally exaggerated the evidence of their finding.

The implication of their finding is that strong ocular dominance is the result of release from interocular suppression by a monocular stimulus, rather than the lack of binocular combination as many traditional studies have assumed. This could significantly advance our understanding of the binocular combination circuitry of V1. The entire population of neurons could be part of a binocular combination circuitry present in V1.

Reviewer #2 (Public Review):

The authors set out to draw further links between neural patterns observed at "rest" during fMRI, with their related thought content and personality traits. More specifically, they approached this with a "tri-partite network" view in mind, whereby the ventral attention network (VAN), the dorsal attention network (DAN), and the default mode network (DMN) are proposed to play a special role in ongoing conscious thought. They used a gradients approach to determine the low dimensional organisation of these networks. In concert, using PCA they reduced thought patterns captured at four time points during the scan, as well as traits captured from a large battery of questionnaires.

The main findings were that specific thought and trait components were related to variations in the organisation of the tri-partite networks, with respect to cortical gradients.

Strengths of the methods/results: Having a long (1 hr) resting state MRI session, which could be broken down into four separate scanning/sampling components is a strength. Importantly, the authors could show (via intra-class correlation coefficients) the similarity of thoughts and connectivity gradients across the entire session. Not only did this approach increase the richness of the data available to them, it speaks in an interesting way to the stability of these measures. The inclusion of both thought patterns during scanning along with trait-level dispositional factors is most certainly a strength, as many studies will often include either/or of these, rather than trying to reconcile across. Of the two main findings, the finding that detailed self-generated thought was associated with a decoupling of regions of DAN from regions in DMN was particularly compelling, in light of mounting literature from several fields that support this.

Weaknesses of the methods/results: Considering the richness of the thought and personality data, I was a little surprised that only two main findings emerged (i.e., a relationship with trait introversion, and a relationship with the "specific internal" thought pattern). I wondered whether, at least in part and in relation to traits, this might stem from the large and varied set of questionnaires used to discern the traits. These questionnaires mostly comprised personality/mood, but some sampled things that do not fall into that category (e.g., musicality, internet addition, sleep), and some related directly to spontaneous thought properties (e.g., mind wandering, musical imagery). It would be interesting to see what relationships would emerge by being more selective in the traits measured, and in the tools to measure them.

Taken together, the main findings are interesting enough. However, the real significance of this work, and its impact, lie in the richness of the approach: combing across fMRI, spontaneous thought, and trait-level factors. Triangulating these data has important potential for furthering our understanding of brain-behaviour relationship across different levels of organisation.

Reviewer #2 (Public Review):

Summary:<br /> Previous research shows that humans tend to adjust learning in environments where stimulus-outcome contingencies become more volatile. This learning rate adaptation is impaired in some psychiatric disorders, such as depression and anxiety. In this study, the authors reanalyze previously published data on a reversal-learning task with two volatility levels. Through a new model, they provide some evidence for an alternative explanation whereby the learning rate adaptation is driven by different decision-making strategies and not learning deficits. In particular, they propose that adjusting learning can be explained by deviations from the optimal decision-making strategy (based on maximizing expected utility) due to response stickiness or focus on reward magnitude. Furthermore, a factor related to the general psychopathology of individuals with anxiety and depression negatively correlated with the weight on the optimal strategy and response stickiness, while it correlated positively with the magnitude strategy (a strategy that ignores the probability of outcome).

Strengths:<br /> The main strength of the study is a novel and interesting explanation of an otherwise well-established finding in human reinforcement learning. This proposal is supported by rigorously conducted parameter retrieval and the comparison of the novel model to a wide range of previously published models.

Weaknesses:<br /> My main concern is that the winning model (MOS6) does not have an error term (inverse temperature parameter beta is fixed to 8.804).

1) It is not clear why the beta is not estimated and how were the values presented here chosen. It is reported as being an average value but it is not clear from which parameter estimation. Furthermore, with an average value for participants that would have lower values of inverse temperature (more stochastic behaviour) the model is likely overfitting.

2) In the absence of a noise parameter, the model will have to classify behaviour that is not explained by the optimal strategy (where participants simply did not pay attention or were not motivated) as being due to one of the other two strategies.

3) A model comparison among models with inverse temperature and variable subsets of the three strategies (EU + MO, EU + HA) would be interesting to see. Similarly, comparison of the MOS6 model to other models where the inverse temperature parameter is fixed to 8.804).

This is an important limitation because the same simulation as with the MOS model in Figure 3b can be achieved by a more parsimonious (but less interesting) manipulation of the inverse temperature parameter.

Furthermore, the claim that the EU represents an optimal strategy is a bit overstated. The EU strategy is the only one of the three that assumes participants learn about the stimulus-outcomes contingencies. Higher EU strategy utilisation will include participants that are more optimal (in maximum utility maximisation terms), but also those that just learned better and completely ignored the reward magnitude.

Other minor issues that I have are the following:<br /> The mixture strategies model is an interesting proposal, but seems to be a very convoluted way to ask: to what degree are decisions of subjects affected by reward, what they've learned, and response stickiness? It seems to me that the same set of questions could be addressed with a simpler model that would define choice decisions through a softmax with a linear combination of the difference in rewards, the difference in probabilities, and a stickiness parameter.

Learning rate adaptation was also shown with tasks where decision-making strategies play a less important role, such as the Predictive Inference task (see for instance Nassar et al, 2010). When discussing the merit of the findings of this study on learning rate adaptation across volatility blocks, this work would be essential to mention.

Reviewer #2 (Public Review):

In this study, Dietmar Funck and colleagues have made a significant breakthrough by identifying three isoforms of plant 2-oxoglutarate-dependent dioxygenases (2-ODD-C23) as homo/arginine-6-hydroxylases, catalyzing the degradation of 6-hydroxyhomoarginine into 2-aminoadipate-6-semialdehyde (AASA) and guanidine. This discovery marks the very first confirmation of plant or eukaryotic enzymes capable of guanidine production.

The authors selected three plant 2-ODD-C23 enzymes with the highest sequence similarity to bacterial guanidine-producing (EFE) enzymes. They proceeded to clone and express the recombinant enzymes in E coli, demonstrating capacity of all three Arabidopsis isoforms to produce guanidine. Additionally, by precise biochemical experiments, the authors established these three 2-ODD-C23 enzymes as homoarginine-6-hydroxylases (and arginine-hydroxylase for one of them). Furthermore, the authors utilized transgenic plants expressing GFP fusion proteins to show the cytoplasmic localization of all three 2-ODD-C23 enzymes. Most notably, using T-DNA mutant lines and CRISPR/Cas9-generated lines, along with combinations of them, they demonstrate the guanidine-producing capacity of each enzyme isoform in planta. These results provide robust evidence that these three 2-ODD-C23 Arabidopsis isoforms are indeed homoarginine-6-hydroxylases responsible for guanidine generation.<br /> The findings presented in this manuscript are a significant contribution for our understanding of plant biology, particularly given that this work is the first demonstration of enzymatic guanidine production in eukaryotic cells. However, there are a couple of concerns and potential ways for further investigation that the authors should (consider) incorporate.

Firstly, the observation of cytoplasmic and nuclear GFP signals in the transgenic plants may also indicate cleaved GFP from the fusion proteins. Thus, the authors should perform a Western blot analysis to confirm the correct size of the 2-ODD-C23 fusion proteins in the transgenic protoplasts.

Secondly, it may be worth measuring pipecolate (and proline?) levels under biotic stress conditions (particularly those that induce transcript changes of these enzymes, Fig S8). Given the results suggesting a potential regulation of the pathway by biotic stress conditions (eg. meJA), these experiments could provide valuable insights into the physiological role of guanidine-producing enzymes in plants. This additional analysis may give a significance of these enzymes in plant defense mechanisms.

Reviewer #2 (Public Review):

Summary:<br /> This study presents data from a broad range of methods (biochemical, EPR, SAXS, microscopy, etc.) on the large disordered protein FRQ relevant to circadian clocks and its interaction partners FRH and CK1, providing novel and fundamental insight into oligomerization state, local dynamics, and overall structure as a function of phosphorylation and association. Liquid-liquid phase separation is observed. These findings have bearings on the mechanistic understanding of circadian clocks, and on functional aspects of disordered proteins in general.

Strengths:<br /> This is a thorough work that is well presented. The data are of overall high quality given the difficulty of working with an intrinsically disordered protein, and the conclusions are sufficiently circumspect and qualitative to not overinterpret the mostly low-resolution data.

Weaknesses:<br /> None

Reviewer #2 (Public Review):

The paper is made of two parts. One deals with RNF146, the other with the development of compounds that may cause TEAD degradation. The two parts are rather unrelated to each other.

The main limit of this work is the lack of evidence that TEAD factors are in fact regulated by the proteasome and ubiquitylation under endogenous conditions. Also lacking is the demonstration that TEADs are labile proteins to the extent that such quantitative regulation at the level of stability can impact on YAP-TAZ biology. Without these two elements, the relevance and physiological significance of all these data is lacking.

As for the development of new inhibitors of TEAD, this is potentially very interesting but underdeveloped in this manuscript. Irrespectively, if TEAD is stable, these molecules are likely lead compounds of interest. If TEAD is unstable, as entertained in the first part of the paper, then these molecules are likely marginal.

Here are a few other specific observations:

1 The effect of MG is shown in a convoluted way, by MS. What about endogenous TEAD protein stability?

2 The relevance of siRNF on YAP target genes of Fig.2D is not statistically significant.

3 All assays are with protein overexpression and Ub-laddering

4 An inconsistency exists on the only biological validation (only by overexpression) on the fly eye size. RNF gain in Fig4C is doing the opposite of what is expected from what is portrayed here as a YAP/TEAD inhibitor: RNF gain is shown to INCREASE eye size, phenocopying a Hippo loss of function phenotype. According to the model proposed, RNF addition should reduce eye size. The authors stated that " This is in contrast to the anti-growth effect of RNF-146 in the Hpo loss-of-function background and indicates RNF146 may regulate other genes/pathways controlling eye sizes besides its role as a negative regulator of Sd/yki activity". This raises questions on what the authors are really studying: why, according to the authors, these caveats should occur on the controls, and not when they study Hpo mutants?

5 The role of TEAD inactivation on YAP function is already well known. Disappointingly no prior literature is cited. In any case, this is a mere control.

6 The second part of the paper on the Development and Screening of pan-TEAD lipid pocket degraders is interesting but unconnected to the above. The degradation pathway it involves has nothing to do with the enzyme described in the first figures.

7 The role of CIDE on YAP accessibility to Chromatin is superficially executed. Key controls are missing along with the connection with mechanisms and prior knowledge, of TEAD, YAP, chromatin, and other TEAD inhibitors, just to mention a few.

8 The physiological relevance and the mechanistic interpretation of what should be in the ATAC seq in ovcar cells is missing.

Reviewer #2 (Public Review):

Summary:<br /> In this manuscript, the authors conduct a detailed analysis of the molecular cues that control the guidance of bifurcated dorsal root ganglion axons in a key region of the spinal cord called the dorsal funiculus. This is a specific case of axon guidance that occurs in a precise way. The authors knew that Slit was important but many axons still target correctly in Slit knockouts, suggesting a role for other guidance factors. Netrin1 is also expressed in this region, so they looked at netrin mutants. The authors found axons outside the DREZ in the Ntn1 mutants, and they show by single-neuron genetic labeling that many of these come from DRG neurons. Quantified axonal tracing studies in Slit1/2, Ntn1, or triple mutant embryos support the idea that Slit and Ntr1 have distinct functions in guidance and that the effect of their loss is additive. Interestingly none of these knockouts affect bifurcation itself but rather the guidance of one or both of the bifurcated axon terminals. Knockout of the Slit receptors (Robo1/2) or the Netrin 1 receptor (DCC) in embryos causes similar guidance defects to loss of the ligands, providing additional confirmation of the requirement for both guidance pathways.

Strengths:<br /> This study expands understanding of the role of the axon guidance factors Ntr1/DCC and Slit/Robo in a specific axon guidance decision. The strength of the study is the careful axonal labeling and quantification, which allows the authors to establish precise consequences of the loss of each guidance factor or receptor.

Weaknesses:<br /> There are some places in the text where the discussion of these data is compared with other studies and models, but additional details would help clarify the arguments.

Reviewer #2 (Public Review):

Yu et al. investigated the structural landscape of 'secreted in xylem' (SIX) effector (virulence and avirulence) proteins from the plant-pathogenic fungus, Fusarium oxysporum f. sp. lycopersici (Fol), with the goal of better understanding effector function and recognition by host (tomato) immune receptors. In recent years, several experimental and computational studies have shown that many effector proteins of plant-associated fungi can be assigned to one of a few major structural families. In the study by Yu et al., X-ray crystallography was used to show that two avirulence effectors of Fol, Avr1 (SIX4) and Avr3 (SIX1), which are recognized by the tomato immune receptors I and I-3, respectively, form part of a new structural family, the Fol dual-domain (FOLD) family, found across three fungal divisions. Using AlphaFold2, an ab initio structural prediction tool, the authors then predicted the structures of all proteins within the Fol SIX effector repertoire (and other effector candidates) and provided evidence that two other effectors, SIX6 and SIX13, also belong to this family.

In addition to identifying members of the FOLD family, structural prediction revealed that proteins of the Fol effector repertoire can largely be classified into a reduced set of structural families. Examples included four members of the ToxA-like family (including Avr2 (SIX3) and SIX8), as well as four members of a new family, Family 4 (including SIX5 and PSL1). Given previous studies had demonstrated that Avr2 (ToxA-like) and SIX5 (Family 4) interact and function together, and that the genes encoding these proteins are divergently transcribed, and because homologues of SIX8 (ToxA-like) and PSL1 (Family 4) from another Fusarium pathogen are functionally dependent on each other and, in the case of Fol, are encoded by genes that are next to each other in the genome, the authors hypothesized that SIX8 and PSL1 may also physically interact. In line with this, co-incubation of the SIX8 and PSL1 proteins, followed by size exclusion chromatography (SEC), gave elution and gel migration profiles consistent with interaction in the form of a heterodimer. AlphaFold2-Multimer modelling then suggested that this interaction was mediated through an intermolecular disulfide bond. Such a prediction was subsequently confirmed through mutational analysis of the relevant cysteine residue in each protein in conjunction with SEC.

Finally, using a variant (homologue) of Avr1 from another Fusarium pathogen, as well as chimeric forms of this protein that integrated regions of Avr1 from Fol, Yu et al. determined through co-expression assays in Nicotiana benthamiana with the I immune receptor, as well as subsequent ion leakage assays, that the C-domain of Avr1 is recognized by the I immune receptor. Furthermore, through these assays, the authors were also able to show that surface-exposed residues in the C-domain enable Avr1 to evade recognition by a variant of the I receptor in Moneymaker tomato that does not provide resistance to Fol.

Overall, the manuscript presents a large body of work that is well supported by the data. A key strength of the manuscript is the validation (benchmarking) of protein structures predicted using AlphaFold2, which is a first for large-scale effector structure prediction papers published to date. Another key strength is the use of large-scale effector structure predictions to make hypotheses about functional relationships or interactions that are then tested (i.e. the SIX8-PSL1 protein interaction and recognition of Avr1 by the I immune receptor). This testing again goes above and beyond the large-scale effector structure prediction papers published to date. Taken together, this showcases how experimental and computational experiments can be effectively combined to provide biologically relevant data for the plant protection and molecular plant-microbe interactions fields.

In terms of weaknesses, the manuscript could have validated the SIX8-PSL1 protein interaction with in planta experiments, such as co-immunoprecipitation assays or co-localization experiments in conjunction with confocal microscopy, to provide support for the interaction in a plant setting. However, given what is already known about the Avr2-SIX5 interaction, these additional experiments are not crucial and could instead form part of a follow-up study.

Reviewer #2 (Public Review):

Summary:<br /> Zhao et al. aimed to explore an important question-how to overcome resistance of hepatocellular carcinoma cells to radiotherapy. Given that immune-suppressive microenvironment is a major mechanism underlying resistance to radiotherapy, they reasoned that a drug that blocks PD-1/PD-L1 pathway could improve efficacy of radiation therapy and chose to investigate the effect of Nifuroxazide, an inhibitor of stat3 activation, on radiotherapy efficacy in treating hepatocellular carcinoma cells. From in vitro experiments, they find combination treatment (Nifuroxazide+ radiotherapy) increases apoptosis and reduces proliferation and migration, in comparison to radiotherapy alone. From in vivo experiments, they demonstrate that combined treatment reduces size and weight of tumors in vivo and enhances mice survival. These data indicate a better efficacy of combination therapy compared to radiotherapy alone. Moreover, they also determined the effect of combination therapy on tumor microenvironment as well as peripheral immune response. Specifically, they find that combination therapy increases infiltration of CD4+, CD8+ t cells and NK cells, activates CD8+ t cells, enhances polarization of M1 macrophages and decreases Treg cells in the tumor microenvironment. These changes in tumor microenvironment is consistent with reduced tumor growth by combination therapy. The most intriguing part of the study is the determination of effect of Nifuroxazide on PD-L1 expression in the context of radiotherapy. Considering Nifuroxazide is a stat3 activation inhibitor and stat3 inhibition leads to reduced expression of PD-L1, one would expect Nifuroxazide decreases PD-L1 expression through stat3. However, they find the effect of Nifuroxazide on PD-L1 is dependent on GSK3 mediated Proteasome pathways and independent of stat3, in the given experimental context. To determine the relevance to human hepatocellular carcinoma, they also measured the PD-L1 expression in human tumor tissues of HCC patients pre- and post-radiotherapy. The increased PD-L1 expression level in HCC after radiotherapy is impressive.<br /> Overall, the data are convincing and supportive to the conclusions.

Strengths:<br /> 1) Novel finding: Identified novel mechanism underlying effect of Nifuroxazide on PD-L1 expression in hepatocellular carcinoma cells in the context of radiotherapy.<br /> 2) Comprehensive experimental approaches: using different approaches to prove same finding. For example, Fig4, both IHC and WB were used. Fig5. Both IF and WB were used.<br /> 3) Human disease relevance: Compared observations in mice with human tumor samples.

Reviewer #2 (Public Review):

This work provides a new tool (H3-Opt) for the prediction of antibody and nanobody structures, based on the combination of AlphaFold2 and a pre-trained protein language model, with a focus on predicting the challenging CDR-H3 loops with enhanced accuracy than previously developed approaches. This task is of high value for the development of new therapeutic antibodies. The paper provides an external validation consisting of 131 sequences, with further analysis of the results by segregating the test sets in three subsets of varying difficulty and comparison with other available methods. Furthermore, the approach was validated by comparing three experimentally solved 3D structures of anti-VEGF nanobodies with the H3-Opt predictions

Strengths:

The experimental design to train and validate the new approach has been clearly described, including the dataset compilation and its representative sampling into training, validation and test sets, and structure preparation. The results of the in silico validation are quite convincing and support the authors' conclusions.

The datasets used to train and validate the tool and the code are made available by the authors, which ensures transparency and reproducibiity, and allows future benchmarking exercises with incoming new tools.

Compared to AlphaFold2, the authors' optimization seems to produce better results for the most challenging subsets of the test set.

Weaknesses:

The comparison of affinity predictions derived from AlphaFold2 and H3-opt models, based on molecular dynamics simulations, should have been discussed in depth. In some cases, there are huge differences between the estimations from H3-opt models and those from experimental structures. It seems that the authors obtained average differences of the real delta, instead of average differences of the absolute value of the delta. This can be misleading, because high negative differences might be compensated by high positive differences when computing the mean value. Moreover, it would have been good for the authors to disclose the trajectories from the MD simulations.

Reviewer #2 (Public Review):

Summary:<br /> This manuscript explores mechanisms by which STAT3 may regulate KRAS mutant cancers.

In the first set of experiments, STAT3 GOF mutants diminished the transformation of p53-null mouse embryonic fibroblasts expressing endogenous mutant KRAS(G12D) (KP MEFs) and this was dependent on direct transcriptional activation induced by phosphorylated STAT3. It appears that this is mediated via a reduction in TGFb signaling such that knockout of either TGFBR2 or SMAD4 can phenocopy the effects of STAT3 GOF mutants in KP MEFs.

In the next part of the paper, the authors used murine pancreatic ductal adenocarcinoma (PDAC)-derived cell lines bearing endogenous KRAS(G12D) and TP53(R172H) mutations (KPC) to determine the extent to which STAT3 may regulate KRAS dependency. They determined that KRAS and STAT3 KO both induced mesenchymal-like phenotypes and that TGFBR2 and SMAD4 KO induced epithelial phenotypes. The loss of STAT3 appeared to correlate with a KRAS-independent signature, and SMAD4/TGFBR2 KO could not induce epithelial phenotypes when STAT 3 was also knocked out.

Strengths:<br /> Overall, this is an interesting paper that highlights the complicated interactions between KRAS, STAT3, and TGF beta signaling. The authors use multiple models and attempt to link data to patient cohorts.

Weaknesses:<br /> While correlations are strong, the study would benefit from additional cause-and-effect type experiments. It would also be beneficial to better tie together the first and second parts of the paper.

Reviewer #2 (Public Review):

Summary:<br /> In the current study, the authors investigated the role of loss of CTRP10 results in female obesity with preserved metabolic health. The overall conclusion is supported by the experimental data that CTRP10 negatively regulates body weight in females and that loss of CTRP10 results in benign obesity with largely preserved insulin sensitivity and metabolic health. The authors have shown the role of sex differences in the metabolically healthy obese (MHO) phenotype, which may increase the scope for research in this area.

Strengths:<br /> The study provides a detailed idea of how genes are regulated in a sex-dependent manner.

Weaknesses:<br /> Mechanistic details are missing.

Reviewer #2 (Public Review):

Summary

In this work, Bartolome and colleagues develop a new approach to identify proteasome interacting proteins and substrates. The approach is based on fusing proteasome subunits with a biotin ligase that will label proteins that come in close physical distance of the ligase. These biotin-labeled proteins (or their resulting tryptic peptides) can be affinity purified using streptavidin and identified by mass spectrometry.

This elegant solution was able to identify a large proportion of known proteasome interactors, as well as multiple potential new interactors. Combining this approach with a proteasome inhibitor allowed also for the enrichment of substrates, due to increased contact time between substrates and the proteasome. Again, the authors were able to identify novel substrates. Finally, the authors implemented this strategy in vivo, providing the hints for potential tissue-specific proteasome interactors.

This novel strategy provides an additional approach to identify new proteasome substrates, which can be particularly powerful for low abundant proteins, e.g., transcription factors. The possibility to implement it in vivo in specific cell types opens the possibility for identifying proteasome interactors in small cell subpopulations or in subpopulations involved in disease.

Strengths:

The authors carefully characterized their genetically engineered proteasome-biotin ligase fusions to ensure that proteasome structure and activity was not altered. This is key to ensure that the proteins identified to interact with the proteasome reflect interactions that occur under physiological conditions.

The authors implemented an algorithm that controls the false positive rate of the identified interactors of the proteasome. This is an important aspect to avoid spending time on the characterization of potential interactors that are just an artifact of the experimental setup.

The addition of a proteasome inhibitor allowed the authors to identify substrates of the proteasome. Although there are other strategies to do this (e.g., affinity purification of Gly-Gly modified peptides, which is a marker for ubiquitination), this additional approach can highlight currently unknown substrates. One example are low abundance proteins, such as transcription factors.

The overall strategy developed by the authors can be implemented in vivo, which opens for the possibility of determining cell type-specific proteasome interactors (and perhaps substrates).

Weaknesses:

There is a small proportion of the PSMA4-biotin ligase fusion that remains unassembled (i.e., not part of the functional proteasome) and that can contribute to a small proportion of false positive interactions.

Reviewer #2 (Public Review):

Zhang and Wei, et al. investigated the role of a centrosomal protein, CEP44, in regulating centrosomes and spindle integrity, with a focus on processes that may be dysregulated in breast cancer. The authors found that a breast cancer cell line, MDA-MB-436, lacks CEP44 protein and has amplified centrioles. CEP44 expression is reduced in samples from breast cancer patients. By super-resolution microscopy, the authors localize CEP44 to the proximal inner lumen of centrioles, as has also been previously shown by another group (Atorino et al 2020). Next, the authors investigate the role of CEP44 in centrosome regulation. They found that loss of CEP44 in HeLa cells results in extra puncta of CEP97 or Centrin-3, while ectopic overexpression of CEP44 in MDA-MB-436 cells reduces the number of CEP97 foci. Only one of the excess puncta in a CEP44-depleted HeLa cell recruits CEP164 or ODF2, indicating that extra foci were not the result of cytokinesis failure. In G1, most (~80%) of CEP44-depleted cells have 2 centrin foci, while in G2, a small population (~20%) have more than 4 centrin foci, and gamma-tubulin is recruited in foci in G2. The authors were able to observe centriole disengagement and amplification using live cell imaging. The authors propose that CEP44 acts in regulating centriole engagement by recruiting CEP57 and CEP57L1 to centrioles. The authors made CEP44 knockout cell lines using CRISPR and found that loss of CEP44 results in multipolar spindles, correlated with an increase in centriole amplification. Finally, the authors investigate the role of CEP44 at the mitotic spindle. The authors find that CEP44 localizes to spindles and is phosphorylated by Aurora A at G2/M on Ser324. Phosphorylation of CEP44 is required for its proper distribution between centrosomes and the spindle and microtubule stability within both spindles and interphase microtubules. Together, these studies shed light on the roles of CEP44 within centrosomes and spindles and will be of interest to cell biologists and cancer biologists studying cell division and centrosomes.

The conclusions of this paper are only partially supported. The analyses could be improved to address the concerns about the major conclusions.

Reviewer #2 (Public Review):

Summary:<br /> The manuscript analyzes the genetic requirement for DNA damage-induced cell cycle checkpoint induction and maintenance in budding yeast bearing one or two unrepairable DNA double-strand breaks using auxin-induced degradation (AID) of key DNA damage response (DDR) factors. The study paid particular attention to solving a puzzle regarding how yeast bearing two unrepaired DNA breaks fail to engage in "adaptation" whereas those with a single unrepairable break eventually resume cell cycling after a prolonged (up to 12 h) G2 arrest.

The most novel findings are: 1. The genetic requirement for the entry to DDC and the maintenance are separable. For instance, Dun1 is partially required for the entry but not DDC maintenance whereas Chk1 is only required for maintenance. 2. Cells with two irreparable breaks respond to DDR only up to a certain time (~12 h post damage) and beyond this point, depend on spindle assembly checkpoint (SAC) and mitotic exit network (MEN) to halt cell cycling. 3. The authors also propose an interesting model that the location of DNA breaks and their distance to centromeres can lead to the triggering of SAC/MEN and dictate the duration of cell cycle arrest and their adaptability following DNA damage. The results thus provide the most compelling evidence on the role of SAC/MEN in DNA damage response and cell cycle arrest albeit its impact might be limited to the current experimental set-up or under conditions when DNA repair is severely deficient.

Overall, the conclusion of the study is well supported by the elegant set of genetic experimental data and employed multiple readouts on DDC factor depletion on checkpoint integrity and cell cycle status. However, the study still relies heavily on Rad53 phosphorylation as the primary metric to assess checkpoint status. Since evidence exists the residual DDC still operates even when Rad53 phosphorylation is undetectable, additional readouts for DDC functions might be necessary to strengthen the study's conclusions. These and other concerns that need clarifications or further experimental validations are discussed below.

Reviewer #2 (Public Review):

Summary:<br /> This manuscript shows detailed evidence of the role of cohesin regulators in rice meiosis and mitosis.

Strengths:<br /> There is a very clear mechanism for its role during replication. The strength of the evidence and its novelty is very high. This paper makes a significant contribution to the body of knowledge on meiotic cohesion in a valuable plant model.

Weaknesses:<br /> The authors did not consider creating heterozygous mutants for the replication fork.<br /> Moderate English language editing may be required.

Reviewer #2 (Public Review):

Summary:<br /> The authors try to establish that there is an Abeta-dependent loss of nuclear pores early in Alzheimer's disease. To do so the authors compared different NUP proteins and assessed their function by analyzing nuclear leakage and resistance to induction of nuclear damage and the associated necroptosis. The authors use a mouse knockin for hAPP with familial Alzheimer's mutations to model amyloidosis related to Alzheimer's disease. Treatment with an inhibitor of beta-amyloid production partially rescued the loss of nuclear pore proteins in young KI neurons, implicating beta-amyloid in Nuclear Pore dysfunction, a mechanism already described in other neurodegenerative diseases but not in Alzheimer's disease.

The conclusions of this paper related to familial AD are well supported by data but are not related to an aging decline in NUP function, where it is required to extend data analysis and one additional experiment.

1. Adding statistics and comparisons between wild-type changes at different times/ages to determine if the nuclear pore changes with time in wild-type neurons. The images show differences in the Nuclear pore in neurons from the wild-type mice, with time in culture and age. However, a rigorous statistical analysis is lacking to address the impact of age/development on NUP function. Although the authors state that nuclear pore transport is reported to be altered in normal brain aging, the authors either did not design their experiments to account for the normal aging mechanisms or overlooked the analysis of their data in this light.

2. Add experiments to assess the contribution of wild-type beta-amyloid accumulation with aging. It was described in 2012 (Guix FX, Wahle T, Vennekens K, Snellinx A, Chávez-Gutiérrez L, Ill-Raga G, Ramos-Fernandez E, Guardia-Laguarta C, Lleó A, Arimon M, Berezovska O, Muñoz FJ, Dotti CG, De Strooper B. 2012. Modification of γ-secretase by nitrosative stress links neuronal ageing to sporadic Alzheimer's disease. EMBO Mol Med 4:660-673, doi:10.1002/emmm.201200243) and 2021 (Burrinha T, Martinsson I, Gomes R, Terrasso AP, Gouras GK, Almeida CG. 2021. Upregulation of APP endocytosis by neuronal aging drives amyloid-dependent synapse loss. J Cell Sci 134. doi:10.1242/jcs.255752), 28 DIV neurons are senescent and accumulate beta-amyloid42. In addition, beta-amyloid 42 accumulates normally in the human brain (Baker-Nigh A, Vahedi S, Davis EG, Weintraub S, Bigio EH, Klein WL, Geula C. 2015. Neuronal amyloid-β accumulation within cholinergic basal forebrain in ageing and Alzheimer's disease. Brain 138:1722-1737. doi:10.1093/brain/awv024), thus, it would be important to determine if it contributes to NUP dysfunction. Unfortunately, the authors tested the Abeta contribution at div14 when wild-type Abeta accumulation was undetected. It would enrich the paper and allow the authors to conclude about normal aging if additional experiments were performed, namely, treating 28Div neurons with DAPT and assessing if NUP is restored.

Reviewer #2 (Public Review):

Summary:<br /> This work investigates the enzymatic properties of lysostaphin (LSS) and LytM, two enzymes produced by Staphylococcus aureus and previously described as glycyl-glycyl endopeptidases. The authors use synthetic peptide substrates mimicking peptidoglycan fragments to determine the substrate specificity of both enzymes and identify the bonds they cleave.

Strengths:<br /> - This work is addressing a real gap in our knowledge since very little information is available about the substrate specificity of peptidoglycan hydrolases.<br /> - The experimental strategy and its implementation are robust and provide a thorough analysis of LSS and LytM enzymatic activities. The results are very convincing and demonstrate that the enzymatic properties of the model enzymes studied need to be revisited.

Weaknesses:<br /> - The manuscript is difficult to read in places and some figures are not always presented in a way that is easy to follow. This being said, the authors have made a good effort to present their experiments in an engaging manner. Some recommendations have been made to improve the current manuscript but these remain minor issues.

Reviewer #2 (Public Review):

The manuscript "Autoacetylation-mediated phase separation of TIP60 is critical for its functions" by Dubey S. et al reported that the acetyltransferase TIP60 undergoes phase separation in vitro and cell nuclei. The intrinsically disordered region (IDR) of TIP60, particularly K187 within the IDR, is critical for phase separation and nuclear import. The authors showed that K187 is autoacetylated, which is important for TIP60 nuclear localization and activity on histone H4. The authors did several experiments to examine the function of K187R mutants including chromatin binding, oligomerization, phase separation, and nuclear foci formation. However, the physiological relevance of these experiments is not clear since TIP60 K187R mutants do not get into nuclei. The authors also functionally tested the cancer-derived R188P mutant, which mimics K187R in nuclear localization, disruption of wound healing, and DNA damage repair. However, similar to K187R, the R188P mutant is also deficient in nuclear import, and therefore, its defects cannot be directly attributed to the disruption of the phase separation property of TIP60. The main deficiency of the manuscript is the lack of support for the conclusion that "autoacetylation-mediated phase separation of TIP60 is critical for its functions".

This study offers some intriguing observations. However, the evidence supporting the primary conclusion, specifically regarding the necessity of the intrinsically disordered region (IDR) and K187ac of TIP60 for its phase separation and function in cells, lacks sufficient support and warrants more scrutiny. Additionally, certain aspects of the experimental design are perplexing and lack controls to exclude alternative interpretations. The manuscript can benefit from additional editing and proofreading to improve clarity.

Reviewer #2 (Public Review):

EZH2 is upregulated in most advanced cancers and has been investigated as a therapeutic target for many years. However, how EZH2 activity is regulated remains to be fully elucidated. In this study, Guo et al. provided a new mechanism for the regulation of EZH2. The authors demonstrated that the protein stability of EZH2 is dynamically regulated by lysine methylation-dependent proteolysis. Specifically, K20 of EZH2 is monomethylated by SET7 methyltransferase and demethylated by LSD1 demethylase. The methylated K20 is recognized by specific methyl-lysine reader L3MBTL3 to promote EZH2 for ubiquitin-dependent proteolysis by the CRL4DCAF5 ubiquitin E3 ligase complex, resulting in the dysregulation of EZH2/PRC2 activity and reduction of H3K27me3. The authors further found a methylation-phosphorylation switch existed in some cancer cells and this switch controls EZH2 stability and hematopoiesis.

Overall, most conclusions of this paper are well-supported by the results presented, only some aspects of Figure 6 need to be extended. This work is of interest to biomedical researchers in the field of cancer epigenetics after minor revision.

Reviewer #2 (Public Review):

In a beautiful line of work, the authors have proposed the intriguing idea that activity patterns of neurons can fluctuate between representing one of multiple stimuli in its receptive field. This allows for time-multiplexing of information by neural populations. The idea was initially proposed by Caruso et al (2018) and tested for both auditory and visual stimuli and later extended in Jun et al (2022). The current study analyzes additional datasets to further extend the conclusions across multiple areas and different stimulus sets.

Together with the earlier work, the current study provides solid evidence for the hypothesis that fluctuating activity patterns in neurons representing multiple stimuli may be a general phenomenon. This exciting possibility may have implications for the studies of perception, attention, decision-making, and other cognitive functions.

In the current study, the claim that the fluctuating activity patterns may be a general phenomenon is supported by multiple data sets from area MT and face patches MF and AL in IT cortex, using multiple stimulus sets (moving dots and gratings for MT, and face-face and face-object pairs for IT cortex). The major strength of this study is the consistency of the results across these areas and stimulus sets.

The description of the results would benefit from a better explanation of how low spike counts may influence the outcome of the analysis. Due to a smoothing procedure used for visualization, the spike counts for the paired stimuli (AB, black lines) shown in Figure 3a-b and Figure 4a-d go below 0. However, the actual spike count on a trial can not go below 0. The symmetric smoothing procedure may hide an underlying skewed distribution of spike counts that can only be positive. The statistical analysis is not performed on the smoothed distribution but on the actual spike counts, and the validity of the result is therefore not in question. However, the paper would benefit from 1) visualization of the unsmoothed trial counts, and 2) an explanation of how assumptions of symmetric/skewed distributions may affect the outcome.

Overall, the authors have presented an interesting hypothesis that is supported by rigorous analysis, they clearly described the results, and they have given a fair discussion of what we can and cannot conclude from this dataset. This line of work deserves the attention of a broad audience within the field of neuroscience.

Reviewer #2 (Public Review):

The authors provide an analysis showing that the allele ages of putatively advantageous alleles tend to be older than those of neutral alleles. To do this, the authors first classify mutations as either neutral, advantageous or deleterious based on a metric called the 'evolutionary probability' which is correlated to the impact of selection acting on a mutation. Then, the authors quantify the age of the mutations using the GEVA method and they also quantify tc (the time of the ancestral node of the edge carrying the mutation). Interestingly, the authors find that advantageous mutations tend to have an older allele age and an older value of tc compared to neutral mutations. The authors posit some explanations for this result invoking the action of balancing selection.

This is an interesting paper and its results could merit an important change in our conception of how we believe that natural selection is acting on the human genome. I have concerns about some of the analysis presented on this paper that have to do with two main factors: 1) Showing that the estimates of allele ages and tc are robust on the dataset presented (more on this topic here below). 2) Presenting more simulations or analytical theory where the authors can show that the models presented by the authors to explain the results indeed fit the data well. As an example, the authors could perform some simulations (likely using SLiM) under the balancing selection models posited by the authors and then show that they can produce data where the allele ages for deleterious, neutral and advantageous alleles have similar patterns to what is observed on the genomic dataset analyzed.

Major concerns

- What is the impact of multiple mutations on the same site on the estimates of allele ages with GEVA?

- GEVA, which is one of the methods used by the authors, 'overestimates "intermediate" times and underestimates older times' according to Ragsdale and Thornton (2023) MBE. What is the impact of this effect for the analysis performed by the authors? Do RUNTC has any known biases on their estimate of tc?

- Additionally what is the impact of phasing errors on the estimates of allele age presented by the authors?

Reviewer #2 (Public Review):

This is an interesting study examining the question of whether CSD sensitizes meningeal afferent sensory neurons leading to spontaneous activity or whether CSD sensitizes these neurons to mechanical stimulation related to locomotion. Using two-photon in vivo calcium imaging based on viral expression of GCaMP6 in the TG, awake mice on a running wheel were imaged following CSD induction by cortical pinprick. The CSD wave evoked a rise in intracellular calcium in many sensory neurons during the propagation of the wave but several patterns of afferent activity developed after the CSD. The minority of recorded neurons (10%) showed spontaneous activity while slightly larger numbers (20%) showed depression of activity, the latter pattern developed earlier than the former. The vast majority of neurons (70%) were unaffected by the CSD. CSD decreased the time spent running and the numbers of bouts per minute but each bout was unaffected by CSD. There also was no influence of CSD on the parameters referred to as meningeal deformation including scale, shear, and Z-shift. Using GLM, the authors then determine that there there is an increase in locomotion/deformation-related afferent activity in 51% of neurons, a decrease in 12% of neurons, and no change in 37%. GLM coefficients were increased for deformation related activity but not locomotion related activity after CSD. There also were an increase in afferents responsive to locomotion/deformation following CSD that were previously silent. This study shows that unlike prior reports, CSD does not lead to spontaneous activity in the majority of sensory neurons but that it increases sensitivity to mechanical deformation of the meninges. This has important implications for headache disorders like migraine where CSD is thought to contribute to the pathology in unclear ways with this new study suggesting that it may lead to increased mechanical sensitivity characteristic of migraine attacks.

Reviewer #2 (Public Review):

Summary:

This study uses transcriptome sequence from a dioecious plant to compare evolutionary rates between genes with male- and female-biased expression and distinguish between relaxed selection and positive selection as causes for more rapid evolution. These questions have been explored in animals and algae, but few studies have investigated this in dioecious angiosperms, and none have so far identified faster rates of evolution in male-biased genes (though see Hough et al. 2014 https://doi.org/10.1073/pnas.1319227111).

Strengths:

The methods are appropriate to the questions asked. Both the sample size and the depth of sequencing are sufficient, and the methods used to estimate evolutionary rates and the strength of selection are appropriate. The data presented are consistent with faster evolution of genes with male-biased expression, due to both positive and relaxed selection.

This is a useful contribution to understanding the effect of sex-biased expression in genetic evolution in plants. It demonstrates the range of variation in evolutionary rates and selective mechanisms, and provides further context to connect these patterns to potential explanatory factors in plant diversity such as the age of sex chromosomes and the developmental trajectories of male and female flowers.

Weaknesses:

The presence of sex chromosomes is a potential confounding factor, since there are different evolutionary expectations for X-linked, Y-linked, and autosomal genes. Attempting to distinguish transcripts on the sex chromosomes from autosomal transcripts could provide additional insight into the relative contributions of positive and relaxed selection.

Reviewer #2 (Public Review):

In this study Hui Dong et al. identified and characterized two transporters of the monocarboxylate family, which they called Apcimplexan monocarboxylate 1 and 2 (AMC1/2) that the authors suggest are involved in the trafficking of metabolites in the non-photosynthetic plastid (apicoplast) of Toxoplasma gondii (the parasitic agent of human toxoplasmosis) to maintain parasite survival. To do so they first identified novel apicoplast transporters by conducting proximity-dependent protein labeling (TurboID), using the sole known apicoplast transporter (TgAPT) as a bait. They chose two out of the three MFS transporters identified by their screen based and protein sequence similarity and confirmed apicoplast localisation. They generated inducible knock down parasite strains for both AMC1 and AMC2, and confirmed that both transporters are essential for parasite intracellular survival, replication, and for the proper activity of key apicoplast pathways requiring pyruvate as carbon sources (FASII and MEP/DOXP). Then they show that deletion of each protein induces a loss of the apicoplast, more marked for AMC2 and affects its morphology both at its four surrounding membranes level and accumulation of material in the apicoplast stroma. The authors attempted to decipher the function of the transporters on metabolic functions of the apicoplast: (a) notably for IPP synthesis through the assessment of vesicle import allowed by IPP-based anchors, which was found to be affected in the mutants, as well as (b) apicoplast fatty acid synthesis by indirect assessment of vesicle import. However, none of them directly concluded on the actual function of the transporters. Furthermore heterologous complementation in bacterial system also failed to demonstrate the transporters' function.

However, this study is very timely, as the apicoplast holds several important metabolic functions (FASII, IPP, LPA, Heme, Fe-S clusters...), which have been revealed and studied in depth but no further respective transporter have been identified thus far. hence, new studies that could reveal how the apicoplast can acquire and deliver all the key metabolites it deals with, will have strong impact for the parasitology community as well as for the plastid evolution communities. The current study is well initiated with appropriate approaches to identify two new putatively important apicoplast transporters, and showing how essential those are for parasite intracellular development and survival. However, in its current state, this is all the study provides at this point (i.e. essential apicoplast transporters disrupting apicoplast integrity, and indirectly its major functions, FASII and IPP, as any essential apicoplast protein disruption does). The study fails to deliver further message or function regarding AMC1 and 2, and thus validate their study. Currently the manuscript just describes how AMC1/2 deletion impacts parasite survival without answering the key question about them: what do they transport. The authors yet have to perform key experiments that would reveal their metabolic function. Ideally the authors would work further and determine the function of AMC1 and 2.

Reviewer #3 (Public Review):

The work by Ghasemahmad et al. has the potential to significantly advance our understanding of how neuromodulators provide internal-state signals to the basolateral amygdala (BLA) while an animal listens to social vocalizations.

Ghasemahmad et al. made changes to the manuscript that have significantly improved the work. In particular, the transparency in showing the underlying levels of Ach, DA, and 5HIAA is excellent. My previous concerns have been adequately addressed.

Reviewer #2 (Public Review):

This paper considers methods for statistical analysis of autocorrelated neural recording time series: an important question for neuroscience, that is underappreciated in the community. The paper makes a valuable contribution to this topic by comparing methods based on cross-validation and cyclic shift on simulated grid-cell data. My main suggestions regard clarity, which would greatly benefit from a more didactic approach: explaining the methods compared to the main text and providing more explanatory figures. But there are also some additional analyses that would strengthen the paper.

There are two ways to build support for the validity of a statistical method: by mathematically proving that it is valid, or by empirically verifying it with simulated data where the correct answer is known. A mathematical proof removes all doubt to validity but empirical validation can still be useful even without proof, as it demonstrates that the method works in at least some circumstances. For empirical validation to be most convincing, it helps to also show some situations where the method doesn't work, ideally by varying a continuous parameter that reliably moves the simulation from a situation where it works to one where it doesn't. If the method works in all but extremely unrealistic cases, this builds confidence that it will work on real data.

The main conclusion of this paper's simulations is that the cyclic shift method most often detects valid correlations, while still not exceeding the false positive rate expected for a valid test. Readers may take this paper as indicating that the circular shift method is safe in all circumstances, but this is not correct. The authors acknowledge that circular shift can sometimes be invalid, and have made modifications to mitigate the problem. But there is neither a mathematical proof that these mitigations work, nor an analysis of the circumstances under which they succeed and fail. I doubt a formal proof is possible since there are likely situations in which even the new methods give false positive results. So the authors should include an empirical test of their modified circular shift method as compared to plain circular shift in various simulations. To gain confidence in the new method it is important to characterize the situations where both methods succeed; where the new method succeeds but traditional cyclic shift gives false positive errors; and situations in which both fail. If situations where the new method fails are so unrealistic that they would never occur in real data, we can have better confidence in the method.

The main contributions of the paper are the modifications to circular shifting and cross-validation that avoid problems of temporal contiguity, but these are only described in the Methods section. But this is a methods paper, so the description of the new methods should be in the main text, including explanatory figures currently in the Methods.

The introduction presents two problems that can occur in neural data: autocorrelation, and omitted variables. However, it is not clear that the current methods help with the problem of omitted variables. In fact, I don't see how any analysis method could solve the problem of omitted variables. If an experimenter observes a correlation between X and Y, there is no way to know this isn't because a third variable Z correlates with X and influences Y, without any effect of X on Y. It is generally impossible to prove causation without making randomized manipulations of one variable; although some methods claim to infer causality by observing all variables that could possibly have a causal effect, this is unlikely to occur in neuroscience. In any case, the problem of omitted variables seems irrelevant to the current study and could be removed.

The list of analysis methods mentioned in the first paragraph of the introduction (eg TDA, LVM) seems irrelevant: it is not clear how the methods evaluated here would be used to assess the significance of those methods. Better to stick to a description of how correlations are difficult to detect in autocorrelated signals, which is what the current methods address.

Reviewer #2 (Public Review):

Summary:<br /> This study discovered a neural mechanism that serves as a switch from rolling to fast crawling behaviors in Drosophila larvae. It addressed important open questions of how neural circuits determine the sequence of locomotor behaviors and how animals switch from one behavior to another. Overall, its results support the conclusions. The experimental approaches should be described more clearly.

The escape behavior of Drosophila larvae includes rolling followed by fast crawling, where the neural mechanism of this sequence is unclear. The authors identified SeIN128, a group of descending neurons that facilitates rolling termination and shortens crawling latency. By investigating the EM connectome of larval CNS, they found that SeIN128 receives inputs from Basin-2 and A00c neurons, which are reported to facilitate rolling. SeIN128 makes reciprocal inhibitory synapses onto Basin-2 and A00c. Gad staining indicates that SeIN128 neurons are GABAergic, and inhibition of SeIN128 caused increased rolling probability and prolonged rolling. RNAi knockdown of GABA receptors in Basins further validated that SeIN128 inhibits Basins via GABAergic inputs. Lastly, the authors found that SeIN128 inhibits rolling induced by two types of Basin neurons, Basin-2 and Basin-4. Overall, SeIN128 forms a feedback inhibition ensemble that terminates rolling and shifts the animal to crawling.

Strengths:<br /> - The question (i.e., the neural circuitry of action selection) addressed by this study is important.<br /> - Larval and adult Drosophila is a powerful model system in neuroscience study, with rich genetic tools, diverse behaviors, and well-studied nervous systems. This study makes good use of them.<br /> - The experiments, analyses, and results are mostly rigorous and support the major claims. This study combined multiple innovative approaches, such as automated, machine-learning-based behavioral assays, EM reconstruction of larval CNS neurons, and genetic manipulation of specific neurons.

Weaknesses:<br /> - The description of methods and quantification for certain analyses are not clear or detailed enough for a comprehensive judgment of rigorousness, or for other scientists to repeat the experiments. This especially applies to the algorithm.<br /> - "Corkscrew-like rolling" is not an accurate term for larval rolling. The neuromuscular basis of rolling was recently studied by Cooney et. al., showing that rolling is the circumferential propagation of muscle activity where all segments contract similarly and synchronously.<br /> - The readability of the manuscript (text and figures) needs improvement, especially in making it understandable for a general audience. The addition of visual representations, simplifying the complex names of neurons, avoiding overall long sentences, and providing sufficient background introduction may help.

Reviewer #2 (Public Review):

Summary:<br /> The authors present the Perceptual Error Adaptation (PEA) model, a computational approach offering a unified explanation for behavioral results that are inconsistent with standard state-space models. Beginning with the conventional state-space framework, the paper introduces two innovative concepts. Firstly, errors are calculated based on the perceived hand position, determined through Bayesian integration of visual, proprioceptive, and predictive cues. Secondly, the model accounts for the eccentricity of vision, proposing that the uncertainty of cursor position increases with distance from the fixation point. This elegantly simple model, with minimal free parameters, effectively explains the observed plateau in motor adaptation under the implicit motor adaptation paradigm using the error-clamp method. Furthermore, the authors experimentally manipulate visual cursor uncertainty, a method established in visuomotor studies, to provide causal evidence. Their results show that the adaptation rate correlates with perturbation sizes and visual noise, uniquely explained by the PEA model and not by previous models. Therefore, the study convincingly demonstrates that implicit motor adaptation is a process of Bayesian cue integration

Strengths:<br /> In the past decade, numerous perplexing results in visuomotor rotation tasks have questioned their underlying mechanisms. Prior models have individually addressed aspects like aiming strategies, motor adaptation plateaus, and sensory recalibration effects. However, a unified model encapsulating these phenomena with a simple computational principle was lacking. This paper addresses this gap with a robust Bayesian integration-based model. Its strength lies in two fundamental assumptions: motor adaptation's influence by visual eccentricity, a well-established vision science concept, and sensory estimation through Bayesian integration. By merging these well-founded principles, the authors elucidate previously incongruent and diverse results with an error-based update model. The incorporation of cursor feedback noise manipulation provides causal evidence for their model. The use of eye-tracking in their experimental design, and the analysis of adaptation studies based on estimated eccentricity, are particularly elegant. This paper makes a significant contribution to visuomotor learning research.

Weaknesses:<br /> The paper provides a comprehensive account of visuomotor rotation paradigms, addressing incongruent behavioral results with a solid Bayesian integration model. However, its focus is narrowly confined to visuomotor rotation, leaving its applicability to broader motor learning paradigms, such as force field adaptation, saccadic adaptation, and de novo learning paradigms, uncertain. The paper's impact on the broader fields of neuroscience and cognitive science may be limited due to this specificity. While the paper excellently demonstrates that specific behavioral results in visuomotor rotation can be explained by Bayesian integration, a general computational principle, its contributions to other motor learning paradigms remain to be explored. The paper would benefit from a discussion on the model's generality and its limitations, particularly in relation to the undercompensating effects in other motor learning paradigms.

Reviewer #3 (Public Review):

Summary:

The authors aim to provide a multidisciplinary resource on the structural and physiological organization of the hippocampal system and make the available experimental data available for further theoretical work, providing tools to do so in a very flexible and user-friendly way. Since this is a new version of an already existing data-resource, the authors certainly reach their aim and fulfil expectations that the reader might have. The content of the database is as good as the original data, collected from the published knowledge-database, sometimes with help of the original authors, and the overall quality depends further on how the data are curated by the team of authors and many others who helped them. That process is briefly described and more details are available in descriptions of previous versions and on the website. The data extraction, examples of how data can be used and the part on attempts to model the hippocampus are exiting and open doors to new and exciting research opportunities.

Strengths:

Excellent description with many outlined opportunities. Nicely illustrated and inviting to explore the online database. The database itself is easy to navigate and to access relevant information, allowing to do further research on the available data.

Weaknesses:

The figures are complex, containing a heavy information load. One needs some general knowlegde of the system in order to grasp the enormous potential of what is provided.

Reviewer #2 (Public Review):

Summary:

The main purpose of this investigation was to 1) compare the effects of a single knockout (sKO) of Numb or a double knockout (dKO) of Numb and NumbL on ex-vivo physiological properties of the extensor digitorium longus (EDL) muscle in C57BL/6NCrl mice; and 2) analyze protein complexes isolated from C2C12 myotubes via immunoprecipitation and LC/MS/MS for potential Numb binding partners. The main findings are 1) the muscles from sKO and dKO were significantly weaker with little difference between the sKO and dKO lines, indicating the reduced force is mainly due to the inactivation of the Numb gene; and 2) there were 11 potential Numb binding proteins that were identified and cytoskeletal specific proteins including Septin 7.

Strengths:

Straight-forward yet elegant design to help determine the important role the Numb has in skeletal muscle.

Weaknesses:

There were a limited number of samples (3-6) that were used for the physiological experiments; however, there was a very large effect size in terms of differences in muscle tension development between the induced KO models and the controls.

Reviewer #2 (Public Review):

Summary: To create a robust and specific fluorescent sensor for aspartate.

Strengths: Good quality characterisation in a range of environments and experimental conditions.

Weaknesses: Sensor basically identical to iGluSnFR3, but nevertheless useful and specific. The results support the conclusions, and the paper is very straightforward. I think the work will be useful to people working on the effects of free aspartate in biology and given it is basically iGluSnFR3, which is widely used, should be very reproducible and reliable.

Other context - it is a good quality study, although seems to be somewhat incremental.

Reviewer #2 (Public Review):

Summary:

Deng et al. investigate, for the first time to my knowledge, the role that hippocampal dentate gyrus mossy cells play in Fragile X Syndrome. They provide compelling evidence that, in slice preparations from Fmr1 knockout mice, mossy cells are hypoactive due to increased Kv7 function whereas granule cells are hyperactive compared to slices from wild-type mice. They provide strong evidence that weakness of mossy cell-interneuron connections contribute to granule cell hyperexcitability, despite converse adaptations to mossy cell inputs. The authors show that application of the Kv7 inhibitor XE991 is able to rescue granule cell hyperexcitability back to wild-type baseline, supporting the overall conclusion that inhibition of Kv7 in the dentate may be a potential therapeutic approach for Fragile X Syndrome.

Strengths:

Thorough electrophysiological characterization of mossy cells in Fmr1 knockout mice, a novel finding.

Their electrophysiological approach is quite rigorous: patched different neuron types (GC, MC, INs) one at a time within the dentate gyrus in FMR1 KO and WT, with and without 'circuit blockade' by pharmacologically inhibiting neurotransmission. This allows the most detailed characterization possible of passive membrane/intrinsic cell differences in dentate gyrus of Fmr1 knockout mice.

Provide several examples showing the use of Kv7 inhibitor XE991 is able to rescue excitability of granule cell circuit in Fmr1 knockout mice (AP firing in intact circuit, postsynaptic current recordings, theta-gamma coupling stimulation)

Weaknesses:

Previously identified weaknesses have been addressed.

Reviewer #2 (Public Review):

Summary:<br /> This manuscript provides microprobe serial oxygen isotope data from thin-sectioned modern and fossil orangutan teeth in an effort to reconstruct seasonality of rainfall in Borneo and Sumatra. The authors also explore the hypothesis that nursing could affect early tooth (first molar) isotope values. They find that all molars yield similar oxygen isotope values and therefore conclude that future research need not exclude use of first molars. With regard to seasonality, the modern orangutans yield similar results from both islands. The authors suggest differences between modern and fossil orangutan teeth.

Strengths:<br /> The study employs a sampling method that captures serial isotope values within thin sections of teeth using a microprobe that provides much higher resolution than traditional hand-held drilling.

Weaknesses:<br /> The study only examines six modern and six fossil orangutan individuals. Of those, only four modern individuals were samples across multiple molars.

Reviewer #2 (Public Review):

Summary:

The manuscript by Rydhmer et al. proposes a new technology to survey insects. They deployed optical sensors in agricultural landscapes and contrast their results to those in classical malaise and sweep nets survey methodologies. They found the results of optical sensors to be comparable with classical survey methodologies. The authors discuss the pros and cons of their near-infrared sensor.

Strengths:<br /> Contrasting the results of optical sensors with those obtained with classical malaise and sweep nets was a clever idea.

Weaknesses:<br /> Maybe the first most important shortcoming is the lack of a larger question the new technology can help to answer. If the authors could frame their aims not only as a new tool to sample insects but maybe along the lines of a hypothesis to test in their (agricultural) field of research, this could be a more meaningful article.

The second more important shortcoming is the lack of more complex analyses. The authors seem to be so fixed on counts of abundance and species that they miss the opportunity to look for more complex patterns in their data. The addition of a simple analysis like an NMDS (to test composition changes) could improve the manuscript significantly.

The ecosystem process (granivory) assay is currently poorly contextualized and explained across the text; I was surprised to find this part in M&M without previous warning. It seems to me that adding this part could be a nice addition to the manuscript (see my comment above). But this needs to be explained better in all sections of the manuscript.

As I think that addressing my previous points will reshape the manuscript in important ways, I refrain from giving more specific details at this point. But there are some! Maybe only to mention that Figures 4 and 6 would benefit from individual regressions by crop and Figure 5 from adding results from optical sensors.

Reviewer #2 (Public Review):

Summary:<br /> This paper describes evolution experiments performed on yeast amino acid transporters aiming at the enlargement of the substrate range of these proteins. Yeast cells lacking 10 endogenous amino acid transporters and thus being strongly impaired to feed on amino acids were again complemented with amino acid transporters from yeast and grown on media with amino acids as the sole nitrogen source.

In the first set of experiments, complementation was done with seven different yeast amino acid transporters, followed by measuring growth rates. Despite most of them have been described before in other experimental contexts, the authors could show that many of them have a broader substrate range than initially thought.

Moving to the evolution experiments, the authors used the OrthoRep system to perform random mutagenesis of the transporter gene while it is actively expressed in yeast. The evolution experiments were conducted such that the medium would allow for poor/slow growth of cells expressing the wt transporters, but much better/faster growth if the amino acid transporter would mutate to efficiently take up a poorly transported (as in the case of citrulline and AGP1) or non-transported (as in case of Asp/Glu and PUT4) amino acid.

This way and using Sanger sequencing of plasmids isolated from faster-growing clones, the authors identified a number of mutations that were repeatedly present in biological replicates. When these mutations were re-introduced into the transporter using site-directed mutagenesis, faster growth on the said amino acids was confirmed. Growth phenotype data were attempted to be confirmed by uptake experiments using radioactive amino acids; however, the radioactive uptake data and growth-dependent analyses do not fully match, hinting at the existence of further parameters than only amino acid uptake alone to impact the growth rates.

When mapped to Alphafold prediction models on the transporters, the mutations mapped to the substrate permeation site, which suggests that the changes allow for more favourable molecular interactions with the newly transported amino acids.

Finally, the authors compared the growth rates of the evolved transporter variants with those of the wt transporter and found that some variants exhibit a somewhat diminished capacity to transport its original range of amino acids, while other variants were as fit as the wt transporter in terms of uptake of its original range of amino acids.

Based on these findings, the authors conclude that transporters can evolve novel substrates through generalist intermediates, either by increasing a weak activity or by establishing a new one.

Strengths:<br /> The study provides evidence in favour of an evolutionary model, wherein a transporter can "learn" to translocate novel substrates without "forgetting" what it used to transport before. This evolutionary concept has been proposed for enzymes before, and this study shows that it also can be applied to transporters. The concept behind the study is easy to understand, i.e. improving growth by uptake of more amino acids as nitrogen source. In addition, the study contains a large and extensive characterization of the transporter variants, including growth assays and radioactive uptake measurements.

Weaknesses:<br /> The authors took a genetic gain-of-function approach based on random mutagenesis of the transporter. While this has worked out for two transporters/substrate combinations, I wonder how comprehensive and general the insights are. In such approaches, it is difficult to know which mutation space is finally covered/tested. And information that can be gained from loss-of-function analyses is missed. The entire conclusions are grounded on a handful of variants analyzed. Accordingly, the outcome is somewhat anecdotal; in some cases, the fitness of the variants was changed and in others not. Highlighting the amino acid changes in the context of the structural models is interesting, but does not fully explain why the variants exhibit changed substrate ranges. Two important technical elements have not been studied in detail by the authors, but may well play a certain role in the interpretation of the results. Firstly, the authors did not quantify the amount of transporter being present on the cell surface; altered surface expression can impact uptake rates and thus growth rates. Secondly, the authors have not assessed whether overexpressing wt versus variant transporters has an impact on the growth rate per se. Overexpressing transporters from plasmids is quite a burden for the cells and often impacts growth rates. Variants may be more or less of a burden, an effect that may (or may also not) go hand in hand with increased/decreased surface production levels.

And finally, I was somewhat missing an evolutionary analysis of these transporters to gain insights into whether the identified substitutions also occurred during natural evolution under real-life conditions.

Reviewer #2 (Public Review):

Summary:<br /> This paper describes a new approach to detecting directed causal interactions between two genes without directly perturbing either gene. To check whether gene X influences gene Z, a reporter gene (Y) is engineered into the cell in such a way that (1) Y is under the same transcriptional control as X, and (2) Y does not influence Z. Then, under the null hypothesis that X does not affect Z, the authors derive an equation that describes the relationship between the covariance of X and Z and the covariance of Y and Z. Violation of this relationship can then be used to detect causality.

The authors benchmark their approach experimentally in several synthetic circuits. In four positive control circuits, X is a TetR-YFP fusion protein that represses Z, which is an RFP reporter. The proposed approach detected the repression interaction in two or three of the positive control circuits. The authors constructed sixteen negative control circuit designs in which X was again TetR-YFP, but where Z was either a constitutively expressed reporter or simply the cellular growth rate. The proposed method detected a causal effect in two of the sixteen negative controls, which the authors argue is not a false positive, but due to an unexpected causal effect. Overall, these pilot studies, albeit in simplified scenarios, provide encouraging results.

Strengths:<br /> The idea of a "no-causality control" in the context of detected directed gene interactions is a valuable conceptual advance that could potentially see play in a variety of settings where perturbation-based causality detection experiments are made difficult by practical considerations.

By proving their mathematical result in the context of a continuous-time Markov chain, the authors use a more realistic model of the cell than, for instance, a set of deterministic ordinary differential equations.

Caveats:<br /> The term "causally" is used in the main-text statement of the central theorem (Eq 2) without a definition of this term. This makes it difficult to fully understand the statement of the paper's central theorem without diving into the supplement.

The basic argument of theorem 1 appears to rely on establishing that x(t) and y(t) are independent of their initial conditions. Yet, there appear to be some scenarios where this property breaks down:

(1) Theorem 1 does not seem to hold in the edge case where R=beta=W=0, meaning that the components of interest do not vary with time, or perhaps vary in time only due to measurement noise. In this case x(t), y(t), and z(t) depend on x(0), y(0), and z(0). Since the distributions of x(0), y(0), and z(0) are unspecified, a counterexample to the theorem may be readily constructed by manipulating the covariance matrix of x(0), y(0), and z(0).

(2) A similar problem may occur when transition probabilities decay with time. For example, suppose that again R=0 and X are degraded by a protease (B), but this protease is subject to its own first-order degradation. The deterministic version of this situation can be written, for example, dx/dt=-bx and db/dt=-b. In this system, x(t) approaches x(0)exp(-b(0)) for large t. Thus, as above, x(t) depends on x(0). If similar dynamics apply to the Y and Z genes, we can make all genes depend on their initial conditions, thus producing a pathology analogous to the above example.

The reviewer does not know when such examples may occur in (bio)physical systems. Nevertheless, since one of the advantages of mathematics is the ability to correctly identify the domain of validity for a claim, the present work would be strengthened by "building a fence" around these edge cases, either by identifying the comprehensive set of such edge cases and explicitly prohibiting them in a stated assumption set, or by pointing out how the existing assumptions already exclude them.

Reviewer #2 (Public Review):

Summary:

The manuscript by Bomba-Warczak et al. applied multi-isotope imaging mass spectrometry (MIMS) analysis to identify the long-lived proteins in mouse ovaries during reproductive aging, and found some proteins related to cytoskeletal and mitochondrial dynamics persisting for 10 months.

Strengths:

The manuscript provides a useful dataset about protein turnover during ovarian aging in mice.

Weaknesses:

The study is pretty descriptive and short of further new findings based on the dataset. In addition, some results such as the numbers of follicles and ovulated oocytes in aged mice are not consistent with the published literature, and the method for follicle counting is not accurate. The conclusions are not fully supported by the presented evidence.

Reviewer #2 (Public Review):

Summary:<br /> Temporal binding, generally considered a timing illusion, results from actions triggering outcomes after a brief delay, distorting perceived timing. The present study investigates the relationship between attention and the perception of timing by employing a series of tasks involving auditory and visual stimuli. The results highlight the role of attention in event timing and the functional relevance of attention in outcome binding.

Strengths:<br /> - Experimental Design: The manuscript details a well-structured sequence of experiments investigating the attention effect in outcome binding. Thoughtful variations in manipulation conditions and stimuli contribute to a thorough and meaningful investigation of the phenomenon.<br /> - Statistical Analysis: The manuscript employs a diverse set of statistical tests, demonstrating careful selection and execution. This statistical approach enhances the reliability of the reported findings.<br /> - Narrative Clarity: Both in-text descriptions and figures provide clear insights into the experiments and their results, facilitating readers in following the logic of the study.

Weaknesses:<br /> - Conceptual Clarity: The manuscript aims to integrate key concepts in human cognitive functions, including attention, timing perception, and sensorimotor processes. However, before introducing experiments, there's a need for clearer definitions and explanations of these concepts and their known and unknown interrelationships. Given the complexity of attention, a more detailed discussion, including specific types and properties, would enhance reader comprehension.<br /> - Computational Modeling: The manuscript lacks clarity in explaining the model architecture and setup, and it's unclear if control comparisons were conducted. These details are critical for readers to properly interpret attention-related findings in the modeling section. Providing a clearer overview of these aspects will improve the overall understanding of the computational models used.

Reviewer #3 (Public Review):

Summary:

The manuscript authored by Lan Guan and colleagues reveals the structure of the cytosol-facing conformation of the MelB sodium/Li coupled permease using the nab-Fab approach and cryoEM for structure determination. The study reveals the conformational transitions in the melB transport cycle and allows understanding of the role of sugar and ion specificities within this transporter.

Strengths:

The study employs a very exciting strategy of transferring the CDRS of a conformation specific nano body to the nab-fab system to determine the inward-open structure of MelB. The resolution of the structure is reasonable enough to support the major conclusions of the study. This is a well-executed study.

Reviewer #2 (Public Review):

Summary:

In this manuscript, Hariharan and colleagues present an elegant study regarding the mechanistic basis of sugar transport by the prototypical Na+-coupled transporter MelB. The authors identified a nanobody (Nb 725) that reduces melibiose binding but not Na+ binding. In vitro (ITC) experiments suggest that the conformation targeted by this nanobody is different from the published outward-open structures. They go on to solve the structure of this other conformational by cryo-EM using the Nanobody grafted with a fiducial marker and enhancer and, as predicted, capture a new conformation of MelB, namely the inward-open conformation. Through MD simulations and ITC measurements, they demonstrate that such state has a reduced affinity for sugar but that Na+ binding is mostly unaffected. A detailed observation and comparison between previously published structures in the outward-open conformation and this new conformational intermediate allows to strengthen and develop the mobile barrier hypothesis underpinning sugar transport. The conformational transition to the inward-facing state leads to the formation of a barrier on the extracellular side that directly affects the amino acid arrangement of the sugar binding site, leading to a decreased affinity that drives the direction of transport. In contrast, the Na+ binding remains the same. This structural data is complemented with dynamic insights from HDX-MS experiments conducted in the presence and absence of the Nb. These measurements highlight the overall protective effect of nanobody binding, consistent with the stabilization of one conformational intermediate.

Strengths:

The experimental strategy to isolate this elusive conformational intermediate is smart and well-executed. The biochemical and biophysical data were obtained in a lipid system (nanodiscs), which allows dismissing questions about detergent induced artefacts. The new conformation observed is of great interest and allows to have a better mechanistic understanding of ion-coupled sugar transport. The comparison between the two structures and the mobile barrier mechanism hypothesis is convincingly depicted and tested.

Weaknesses:

This is excellent experimental work. My recommendations stem mostly from concerns regarding the interpretation of the observed results. In particular, I am somewhat puzzled by the important role the authors give to the regulatory protein EIIa with little structural or biophysical data to back up their claims. The hypothesis that the conformation captured by the Nb is physiologically and functionally equivalent to that caused by EIIa binding is definitely a worthy hypothesis, but it is not an experimental result.

Evidence in support could include a structure with EIIa bound. Since it does not bind at the same location as the Nb, it seems feasible. Or, the authors could have performed HDX-MS in the presence of EIIa to determine if the effect is similar to that of Nb_725 binding. In the absence of these experiments, discussion about EIIa should be limited. Along the same lines, I find it misleading to put in the abstract a sentence such as "It is the first structure of a major facilitator superfamily (MFS) transporter with experimentally determined cation binding, and also a structure mimicking the physiological regulatory state of MelB under the global regulator EIIAGlc of the glucose-specific phosphoenolpyruvate:phosphotransferase system." None of this is supported by the experimental work presented in this article: the Na+ is modelled (with great confidence, but still) and whether this structure mimics the physiological state of MelB bound to EIIa is not known. The results of the paper are strong and interesting enough per se, and there is no need to inflate them with hypothesis that belongs to the discussion section.

I also note that the HDX-MS experiments do not distinguish between two conformational states, but rather an ensemble of states vs one state.

Reviewer #3 (Public Review):

The authors collected BALF samples from lung cancer patients newly diagnosed with PCP, DI-ILD or ICI-ILD. CyTOF was performed on these samples, using two different panels (T-cell and B-cell/myeloid cell panels). Results were collected, cleaned-up, manually gated and pre-processed prior to visualisation with manifold learning approaches t-SNE (in the form of viSNE) or UMAP, and analysed by CITRUS (hierarchical clustering followed by feature selection and regression) for population identification - all using Cytobank implementation - in an attempt to identify possible biomarkers for these disease states. By comparing cell abundances from CITRUS results and qualitative inspection of a small number of marker expressions, the authors claimed to have identified an expansion of CD16+ T-cell population in PCP cases and an increase in CD57+ CD8+ T-cells, FCRL5+ B-cells and CCR2+ CCR5+ CD14+ monocytes in ICI-ILD cases.

By the authors' own admission, there is an absence of healthy donor samples and, perhaps as a result of retrospective experimental design and practical clinical reasons, also an absence of pre-treatment samples. The entire analysis effectively compares three yet-established disease states with no common baseline - what really constitutes a "biomarker" in such cases? These are very limited comparisons among three, and only these three, states.

By including a new scRNA-Seq analysis using publicly available dataset, the authors addressed this fundamental problem. Though more thorough and numerical analysis would be appreciated for a deeper and more impactful analysis, this is adequate for the intended objectives of the study.

Reviewer #2 (Public Review):

The manuscript by Wang et al., follows up on the group's previous publication on KLF1 (EKLF) K47R mice and reduced susceptibility to tumorigenesis and increased life span (Shyu et al., Adv Sci (Weinh). Sep 2022;9(25):e2201409. doi:10.1002/advs.202201409). In the current manuscript, the authors have described these phenotypes in the context of age, gender, genetic background, and hematopoietic transplantation of bone marrow mononuclear cells. Despite the revisions, significant conceptual concerns still remain in the study that make the inferences in the manuscript less convincing. Major concerns are listed below.

Major concerns:

1. The authors mention more than once in the manuscript that KLF1 is expressed in range of blood cells including hematopoietic stem cells, megakaryocytes, T cells and NK cells. In the case of megakaryocytes, studies from multiple labs have shown that while EKLF is expressed megakaryocyte-erythroid progenitors, EKLF is important for the bipotential lineage decision of these progenitors, and its high expression promotes erythropoiesis, while its expression is antagonized during megakaryopoiesis. In the case of HSCs, the authors reference to their previous publication for KLF1's expression in these cells- however, in this study nor in the current study, there is no western blot documented to convincingly show that KLF1 protein is expressed at detectable levels in these cells. For T cells, the authors have referenced a study which is based on ectopic expression of KLF1. For NK cells, the authors reference bioGPS: however, upon inspection, this is also questionable. As part of the revision, the authors have provided western blots in supplemental figure S4. However, these blots are difficult to interpret, since the EKLF bands for NK cells, and T cells are very faint and since the positive control EKLF band from MEL erythroid cell lysates is oversaturated, to interpret the data clearly. Therefore, although a quantification is shown, the representative blot included for EKLF protein levels is not convincing.

2. The current study rests on the premise that KLF1 is expressed in HSCs, NK cells and leukocytes, and the references cited are not sufficient to make this assumption, for the reasons mentioned in the first point. Therefore, the authors were asked to show both KLF1 mRNA and protein levels in these cells, and also compare them to the expression levels seen in KLF1 wild type erythroid cells along with knockout erythroid cells as controls, for context and specificity. The authors have now included western blots and mRNA levels and have compared it to MEL erythroid cells. This data raises additional questions. Overall, the mRNA levels in CD3+ T cells and B220+ B cells are approximately 3000 fold lower than MEL erythroid cells. Based on the information provided, although unclear, the assumption is that the MEL cell extracts are from undifferentiated cells. Therefore, this raises questions on the inference that the healthy aging phenotype is a result of cell intrinsic effects, since EKLF expression in these cells of interest is extremely low. This also allows for the consideration for potential systemic/indirect effects.

3. In the discussion, the authors make broad inferences that go beyond the data shown in the manuscript. For example, they mention that the tumorigenesis resistance and long lifespan is most likely due to changes in transcription regulatory properties and changes in global gene expression profile of the mutant protein relative to WT leukocytes. And based on reduced mRNA levels of Pd-1 Pd-l1 genes in the CD3+ T cells and B220+ B cells from mutant mice, they "assert" that EKLF is an upstream regulator of these genes and regulates the transcriptomes of a diverse range of hematopoietic cells. The authors were asked to perform a ChIP assay to show whether WT EKLF binds on these genes in these cells, and whether this binding is reduced or abolished in the mutant cells, to substantiate the above statements. The authors have now included a ChIP assay in Figure S5. The data on WT EKLF and K74R EKLF on Pd-1 promoter shows that both forms of EKLF bind at similar levels. Therefore, the mechanism remains unclear, and there is insufficient discussion on how their data support cell intrinsic differences in transcriptional regulation between WT and mutant EKLF.

Reviewer #2 (Public Review):

Summary:

The authors sampled the B cell receptor repertoires of Cancers, their draining lymph nodes, and blood. They characterized the clonal makeup of all B cells sampled and then analyzed these clones to identify clonal overlap between tissues and clonal activation as expressed by their mutation level and CDR3 amino acid characteristics and length. They conclude that B cell clones from the Tumor interact more with their draining lymph node than with the blood and that there is less mutation/expansion/activation of B cell clones in Tumors. These conclusions are interesting but hard to verify due to the under-sampling and short sequencing reads as well as confusion as to when analysis is across all individuals or of select individuals.

Strengths:

The main strength of their analysis is that they take into account multiple characteristics of clonal expansion and activation and their different modes of visualization, especially of clonal expansion and overlap. The triangle plots once one gets used to them are very nice.

Weaknesses:

The data used appears inadequate for the conclusions reached. The authors' sample size of B cells is small and they do not address how it could be sufficient. at such low sampling rates, compounded by the palsmablast bias they mention, it is unclear if the overlap trends they observe show real trends. Analyzing only top clones by size does not solve this issue. As it could be that the top 100 clones of one tissue are much bigger than those of another and that all overlap trends are simply because the clones are bigger in one tissue or the other. i.e there is equal overlap of clones with blood but blood is not sufficiently sampled given its greater diversity and smaller clones. Similarly, the read length (150bp X2) is too short missing FWR1 and CDR1 and often parts of FWR2 if CDR3 is long. As the authors themselves note (and as was shown in (Zhang 2015 - PMC4811607) this makes mutation analysis difficult. It also makes the identification of V genes and thus clonal identification ambiguous. This issue becomes especially egregious when clones are mutated. Finally, it is not completely clear when the analysis is of single individuals or across all individuals. If it is the former the authors did not explain how they chose the individuals analyzed and if the latter then it is not clear from the figures which measurements belong to which individual (i.e they are mixing measurements from different people). For all these reasons while the authors make many interesting suggestions about the potential relationships of B cell repertoires in cancer tissues and their draining lymph nodes and how to characterize and visualize them, it is hard to assess any of their conclusions and specific results.

Reviewer #2 (Public Review):

Summary:<br /> The study entitled "Different coexistence patterns between apex carnivores and mesocarnivores based on temporal, spatial, and dietary niche partitioning analysis in Qilian Mountain National Park, China" by Cong et al. addresses the compelling topic of carnivores' coexistence in a biodiversity hotspot in China. The study is interesting given it considers all three components affecting sympatric carnivores' distribution and co-occurrence, namely the temporal, the spatial, and the dietary partition within the carnivore guild. The authors have found that spatial co-occurrence is generally low, which represents the major strategy for coexistence, while there is temporal and dietary overlap. I also appreciated the huge sampling effort carried out for this study by the authors: they were able to deploy 280 camera trapping sites (which became 322 in the result section?) and collect a total of 480 scat samples. However, I have some concerns about the study on the non-consideration of the human dimension and potential anthropogenic disturbance that could affect the spatial and temporal distribution of carnivores, the choice of the statistical model to test co-occurrence, and the lack of clearly stated ecological hypotheses.

Strengths:<br /> The strengths of the study are the investigation of all three major strategies that can mitigate carnivores' coexistence, therefore, the use of multiple monitoring techniques (both camera trapping and DNA metabarcoding) and the big dataset produced that consists of a very large sampled area with a noteworthy number of camera tap stations and many scat samples for each species.

Weaknesses:<br /> I think that some parts of the manuscript should be written better and more clearly. A clear statement of the ecological hypotheses that could affect the partitioning among the carnivore guild is lacking. I think that the human component (thus anthropogenic disturbance) should have been considered more in the spatial analyses given it can influence the use of the environment by some carnivores. Additionally, a multi-species co-occurrence model would have been a more robust approach to test for spatial co-occurrence given it also considers imperfect detection.

Temporal and dietary results are solid and this latter in particular highlights a big predation pressure on some prey species such as the pika. This implies important conservation and management implications for this species, and therefore for the trophic chain, given that i) the pika population should be conserved and ii) a potential poisoning campaign against small mammals could be incredibly dangerous also for mesocarnivores feeding on them due to secondary poisoning.

Reviewer #2 (Public Review):

Summary:<br /> In this study, Zhang and colleagues characterise the behaviour of mouse hematopoietic stem cells when cultured in PVA conditions, a recently published method for HSC expansion (Wilkinson et al., Nature, 2019), using multiome analysis (scRNA-seq and scATACseq in the same single cell) and extensive transplantation experiments. The latter are performed in several settings including barcoding and avoiding recipient conditioning. Collectively the authors identify several interesting properties of these cultures namely: 1) only very few cells within these cultures have long-term repopulation capacity, many others however have progenitor properties which can rescue mice from lethal myeloablation; 2) single cell characterisation by combined scRNAseq and scATACseq is not sufficient to identify cells with repopulation capacity; 3) expanded HSCs can be engrafted in unconditioned host and return to quiescence.

The authors also confirm previous studies that EPCRhigh HSCs have better reconstitution capability than EPCRlow HSCs when transplanted.

Strengths:<br /> The major strength of this manuscript is that it describes how functional HSCs are expanded in PVA cultures to a deeper extent that what has been done in the original publication. The authors are also mindful of considering the complexities of interpreting transplantation data. As these PVA cultures become more widely used by the HSC community, this manuscript is valuable as it provides a better understanding of the model and its limitations.

Novelty aspects include:<br /> • The authors determined that small numbers of expanded HSCs enable transplantation into non-conditioned syngeneic recipients.<br /> • This is to my knowledge the first report characterising output of PVA cultures by multiome. This could be a very useful resource to the field.<br /> • They are also the first to my knowledge to use barcoding to quantify HSC repopulation capacity at the clonal level after PVA culture.<br /> • It is also useful to report that HSCs isolated from fetal livers do expand less than their adult counterparts in these PVA cultures.

Weaknesses:<br /> • The analysis of the multiome experiment is limited. The authors do not discuss what cell types, other than functional or phenotypic HSCs are present in these cultures (are they mostly progenitors or bona fide mature cells?) and no quantifications are provided. It seems nonetheless that most cells in these cultures do not acquire differentiation markers. In addition, the functional experiments demosntrate very few retain transplantation capacity. Future works will have to investigate the nature of the bulk of the other cells in these cultures.<br /> • Barcoding experiments are technically elegant but do not bring particularly novel insights.<br /> • Number of mice analysed in certain experiments is fairly low (Figure 1 and 5).<br /> • The manuscript remains largely descriptive. While the data can be used to make useful recommendations to future users working with PVA cultures and in general with HSCs, those recommendations could be more clearly spelled out in the discussion.<br /> • The authors could have provided discussion of the other publications/preprints which have used these methods to date. This would have been useful for researchers who have not used this technique.

Overall, the authors succeeded in providing a useful set of experiments to better interpret what type of HSCs are expanded in PVA cultures. More in depth mining of their bioinformatic data (by the authors or other groups) is likely to highlight other interesting/relevant aspects of HSC biology in relation to this expansion methodology.

Reviewer #2 (Public Review):

Summary:<br /> In this manuscript, the membrane component of the sialic acid-specific TRAP transporter, SiaQM (HiSiaQM), from H. influenzae, is structurally characterized. TRAP transporters are substrate binding protein (SBP)-dependent secondary-active transporters, and HiSiaQM is the most comprehensively studied member of this family. While all previous work on fused TRAP transporter membrane proteins suggests that they are monomeric (including the previous structural characterization of HiSiaQM by a different group), a surprising finding from this work is the observation that HiSiaQM can form higher oligomers, consistent with it being a dimer. These higher oligomeric states were initially observed after extraction of the protein with LMNG detergent, but were also observed in DDM detergent, amphipol and nanodiscs using analytical ultracentrifugation (AUC). Structural characterization of dimeric HiSiaQM revealed 2 arrangements, a parallel and antiparallel arrangements, the latter of which is unlikely to be physiologically relevant.

The higher resolution of this new structure of HiSiaQM (2.2-2.7 Å compared to 4.7 Å for the previous structure) facilitated the assignment of bound lipids at the dimer interface and a lipid molecule embedded in each of the protomers; allowed for a clearer refinement of the Na+ and putative substrate binding sites, which differ slightly from the previous structure; and produced better modelled side chains for the residues involved in the SBP:HiSiaQM interaction. The authors developed a useful AUC-based assay to determine the affinity for this interaction revealing an affinity of 65 µM. Finally, the authors make the very interesting observation that a sialic acid specific SBP from a different TRAP transporter can utilize HiSiaQM for transport, contrary to previous observations, revealing for the first time that TRAP membrane components can recognize multiple SBPs.

Overall, this is a well written and presented manuscript detailing some interesting new observations about this interesting protein family. One of the main findings, that the protein can form a dimer, is supported by data, but the physiological relevance of this is questionable, and the possibility that this is artefactual has not been ruled out. Conclusions regarding the mechanistic importance of the lipid bindings sites is not currently supported by the data.

Strengths:<br /> The main strength of this work is the increased resolution of HiSiaQM, which allows for much more precise assignment of side chains and their orientation. This will be of importance for subsequent mechanistic studies on the contributions of these residues to Na+ and sialic acid binding and conformational changes.<br /> The observation of the lipids, especially the lipid embedded near the fusion helix, is an intriguing observation, which lays the groundwork for future work to understand the lipid-dependence of these transporters.<br /> The development of the AUC-based approach to measure SBP affinity for the membrane component will likely prove be useful to future studies.

Weaknesses:<br /> One of the main results from this work is the observation that HiSiaQM can form a dimer. Two arrangements were observed, parallel and antiparallel, the latter of which is almost certainly physiologically irrelevant as it would preclude essential interactions with the extracytoplasmic substrate binding protein. As acknowledged by the author, this non-physiological arrangement is likely a consequence of protein preparation (overexpression, extraction, purification, etc.). However, if one dismisses the antiparallel arrangement as non-relevant and an artefact of protein preparation, it is difficult for the parallel arrangement to maintain its credibility, as it was also processed in the same way. This is especially true when one considers that there is only 100 Å2 buried surface area in the parallel arrangement that does not involve any sidechains; it is difficult to envisage this as a specific interaction, e.g. compared to related proteins that have ~2000 Å2 buried surface area. Unless this dimerization is observed in a bacterial membrane at physiological protein concentrations, it is difficult to rule out the possibility that the observed dimerization is merely an artefact caused by the expression, purification and concentration of the protein.

The manuscript contains some excellent structural analysis of this protein, whose higher resolution reveals some new and interesting insight. However, a weakness of the current work is a lack of validation of these observations using other approaches. For example, lipid interactions are observed in the structure that the authors claim is mechanistically important. However, without disrupting these interactions to look at the effect on transport, this conclusion is not supported. Similarly, the authors use their structure to predict residues that are important for the SBP:membrane protein interaction, and they develop an AUC-based binding assay to study this interaction, but they do not test their predictions using this approach.

Reviewer #2 (Public Review):

Summary:

In this manuscript, the authors reported a study to uncover that β-catenin inhibition disrupting the homeostasis of osteogenic/adipogenic differentiation contributes to the development of Glucocorticoid-induced osteonecrosis of the femoral head (GONFH). In this study, they first observed abnormal osteogenesis and adipogenesis associated with decreased β-catenin in the necrotic femoral head of GONFH patients, but the exact pathological mechanisms of GONFH remain unknown. They then performed in vivo and in vitro studies to further revealed that glucocorticoid exposure disrupted osteogenic/adipogenic differentiation bone marrow stromal cells (BMSCs) by inhibiting β-catenin signaling in glucocorticoid-induced GONFH rats, and specific deletion of β-catenin in Col2+ cells shifted BMSCs commitment from osteoblasts to adipocytes, leading to a full spectrum of disease phenotype of GONFH in adult mice.

Strengths:

This innovative study provides strong evidence supporting that β-catenin inhibition disrupts the homeostasis of osteogenic/adipogenic differentiation that contributes to the development of GONFH. This study also identifies an ideal genetic modified mouse model of GONFH. Overall, the experiment is logically designed, the figures are clear, and the data generated from humans and animals is abundant supporting their conclusions.

Weaknesses:

Lack of the discussion to explain how the Wnt agonist 1 works. There are several types of Wnt ligands. It is not clear if this agonist only targets Wnt1 or other Wnts as well? Also, why Wnt agonist 1 couldn't rescue the GONFH-like phenotype in β-cateninCol2ER mice needs to be discussed.

Reviewer #2 (Public Review):

Strengths<br /> - the study combines different methods (pupillometry, RNNs, fMRI).<br /> - the study combines different viewpoints and fields of the scientific literature, including neuroscience, psychology, physics, dynamical systems.<br /> - This combination of methods and viewpoints is rarely done, it is thus very useful.<br /> - Overall well-written.

Weaknesses<br /> - The study relies on a report paradigm: participants report when they identify a switch in the item category. The sequence corresponds to the drawing of an object being gradually morphed into another object. Perceptual switches are therefore behaviorally relevant, and it is not clear whether the effect reported correspond to the perceptual switch per se, or the detection of an event that should change behavior (participant press a button indicating the perceived category, and thus switch buttons when they identify a perceptual change). The text mentions that motor actions are controlled for, but this fact only indicates that a motor action is performed on each trial (not only on the switch trial); there is still a motor change confounded with the switch. As a result, it is not clear whether the effect reported in pupil size, brain dynamics, and brain states is related to a perceptual change, or a decision process (to report this change).

- The study presents events that co-occur (perceptual switch, change in pupil size, energy landscape of brain dynamics) but we cannot identify the causes and consequences. Yet, the paper makes several claims about causality (e.g. in the abstract "neuromodulatory tone ... causally mediates perceptual switches", in the results "the system flattening the energy landscape ... facilitated an updating of the content of perception").

- Some effects may reflect the expectation of a perceptual switch, rather than the perceptual switch per se. Given the structure of the task, participants know that there will be a perceptual switch occurring once during a sequence of morphed drawings. This change is expected to occur roughly in the middle of the sequence, making early switches more surprising, and later switches less surprising. Differences in pupil response to early, medium, and late switches could reflect this expectation. The authors interpret this effect very differently ("the speed of a perceptual switch should be dependent on LC activity").

- The RNN is far more complex than needed for the task. It has two input units that indicate the level of evidence for the two categories being morphed, and it is trained to output the dominant category. A (non-recurrent) network with only these two units and an output unit whose activity is a sigmoid transform of the difference in the inputs can solve the task perfectly. The RNN activity is almost 1-dimensional probably for this reason. In addition, the difficult part of the computation done by the human brain in this task is already solved in the input that is provided to the network (the brain is not provided with the evidence level for each category, and in fact, it does not know in advance what the second category will be).

- Basic fMRI results are missing and would be useful, before using elaborate analyses. For instance, what are the regions that are more active when a switch is detected?

- The use of methods from physics may obscure some simple facts and simpler explanations. For instance, does the flatter energy landscape in the higher gain condition reflect a smaller number of states visited in the state space of the RNN because the activity of each unit gets in the saturation range? If correct, then it may be a more straightforward way of explaining the results.

- Some results are not as expected as the authors claim, at least in the current form of the paper. For instance, they show that, when trained to identify which of two inputs u1 and u2 is the largest (with u2=1-u1, starting with u1=1 and gradually decreasing u1), a higher gain results in the RNN reporting a switch in dominance before the true switch (e.g. when u1=0.6 and u2=0.4), and vice et versa with a lower gain. In other words, it seems to correspond to a change in criterion or bias in the RNN's decision. The authors should discuss more specifically how this result is related to previous studies and models on gain modulation. An alternative finding could have been that the network output is a more (or less) deterministic function of its inputs, but this aspect is not reported.

Reviewer #2 (Public Review):

This work presents a remarkably extensive set of experiments, assaying the interaction between methylation and expression across most CpG positions in the genome in two cell types. To this end, the authors use mSTARR-seq, a high-throughput method, which they have previously developed, where sequences are tested for their regulatory activity in two conditions (methylated and unmethylated) using a reporter gene. The authors use these data to study two aspects of DNA methylation: 1. Its effect on expression, and 2. Its interaction with the environment. Overall, they identify a small number of 600 bp windows that show regulatory potential, and a relatively large fraction of these show an effect of methylation on expression. In addition, the authors find regions exhibiting methylation-dependent response to two environmental stimuli (interferon alpha and glucocorticoid dexamethasone).

The questions the authors address represent some of the most central in functional genomics, and the method utilized is currently the best method to do so. The scope of this study is very impressive and I am certain that these data will become an important resource for the community. The authors are also able to report several important findings, including that pre-existing DNA methylation patterns can influence the response to subsequent environmental exposures.

Reviewer #2 (Public Review):

Summary: In this manuscript, the authors examined the role of the bile acid receptor TGR5 in the bone marrow under steady-state and stress hematopoiesis. They initially showed the expression of TGR5 in hematopoietic compartments and that loss of TGR5 doesn't impair steady-state hematopoiesis. They further demonstrated that TGR5 knockout significantly decreases BMAT, increases the APC population, and accelerates the recovery upon bone marrow transplantation.

Strengths: The manuscript is well-structured and well-written.

Weaknesses: The mechanism is not clear, and additional studies need to be performed to support the authors' conclusion.

Reviewer #3 (Public Review):

Male infertility is an important health problem. Among pathologies with multiple morphological abnormalities of the flagellum (MMAF), only 50% of the patients have no identified genetic causes. It is thus primordial to find novel genes that cause the MMAF syndrome. In the current work, the authors follow up the identification of two patients with MMAF carrying a mutation in the CCDC146 gene. To understand how mutations in CCDC146 lead to male infertility, the authors generated two mouse models: a CCDC146-knockout mouse, and a knockin mouse in which the CCDC146 locus is tagged with an HA tag. Male CCDC146-knockout mice are infertile, which proves the causative role of this gene in the observed MMAF cases. Strikingly, animals develop no other obvious pathologies, thus underpinning the specific role of CCDC146 in male fertility. The authors have carefully characterised the subcellular roles of CCDC146 by using a combination of expansion and electron microscopy. They demonstrate that all microtubule-based organelles, such as the sperm manchette, the centrioles, as well as the sperm axonemes are defective when CCDC146 is absent. Their data show that CCDC146 is a microtubule-associated protein, and indicate, but do not prove beyond any doubt, that it could be a microtubule-inner protein (MIP).

This is a solid work that defines CCDC146 as a novel cause of male infertility. The authors have performed comprehensive phenotypic analysis to define the defects in CCDC146 knockout mice. The manuscript text is well written and easy to follow also for non-specialists. The introduction and discussion chapters contain important background information that allow to put the current work into the greater context of fertility research. Overall, this manuscript provides convincing evidence for CCDC146 being essential for male fertility and illustrates this with a large panel of phenotypic observations. Together, the work provides important first insights into the role of a so-far unexplored proteins, CCDC146, in spermatogenesis, thereby broadening the spectrum of genes involved in male infertility.

Reviewer #2 (Public Review):

Summary:<br /> In this study, the authors hypothesized that individuals with diabetes have elevated blood CTSL levels, which facilitates SARS-CoV-2 infection. The authors conducted in vitro experiments, revealing that elevated glucose levels promote SARS-CoV-2 infection in wild-type cells. In contrast, CTSL knockout cells show reduced susceptibility to high glucose-promoted effects. Additionally, the authors utilized lung tissue samples obtained from both diabetic and non-diabetic patients, along with db/db diabetic and control mice. Their findings indicate that diabetic conditions lead to an elevation in CTSL activity in both humans and mice.

Strengths:<br /> The authors have effectively met their research objectives, and their conclusions are supported by the data presented. Their findings suggest that high glucose levels promote CTSL maturation and translocation from the endoplasmic reticulum to the lysosome, potentially contributing to diabetic comorbidities and complications.

Weaknesses:<br /> 1. In Figure 1e, the authors measured plasma levels of COVID-19 related proteins, including ACE2, CTSL, and CTSB, in both diabetic and non-diabetic COVID-19 patients. Notably, only CTSL levels exhibited a significant increase in diabetic patients compared to non-diabetic patients, and these levels varied throughout the course of COVID-19. Given that the diabetes groups encompass both male and female patients, it is essential to ascertain whether the authors considered the potential impact of gender on CTSL levels. The diabetes groups comprised a higher percentage of male patients (61.3%) compared to the non-diabetes group, where males constituted only 38.7%.

2. Lines 145-149: "The results showed that WT Huh7 cell cultured in high glucose medium exhibited a much higher infective rate than those in low glucose medium. However, CTSL KO Huh7 cells maintained a low infective rate of SARS-CoV-2 regardless of glucose or insulin levels (Fig. 3f-h). Therefore, hyperglycemia enhanced SARS-CoV-2 infection dependent on CTSL." However, this evidence may be insufficient to support the claim that hyperglycemia enhances SARS-CoV-2 infection dependent on CTSL. The human hepatoma cell line Huh7 might not be an ideal model to validate the authors' hypothesis regarding high blood glucose promoting SARS-CoV-2 infection through CTSL.

3. The Abstract and Introduction sections lack effective organization.

Reviewer #2 (Public Review):

The present work analyzed the mitochondrial function and bioenergetics in the context of cancer cachexia induced by pancreatic cancer (PDAC). The authors used the KIC transgenic mice that spontaneously develop PDAC within 9-11 weeks of age. They deeply characterize bioenergetics in living mice by magnetic resonance (MR) and mitochondrial function/morphology mainly by oxygraphy and imaging on ex vivo muscles. By MR they found that phosphocreatine resynthesis and maximal oxidative capacity were reduced in the gastrocnemius muscle of tumor-bearing mice during the recovery phase after 6 minutes of 1 Hz electrical stimulation while pH was reduced in muscle during the stimulation time. By oxygraphy, the authors showed a decrease in basal respiration, proton leak, and maximal respiration in tumor-bearing mice that was associated with the decrease of complex I, II, and IV activity, a reduction of OXPHOS proteins, mitochondrial mass, mtDNA, and to several morphological alterations of mitochondrial shape. The authors performed transcriptomic and proteomic analyses to get insights into mitochondrial defects in the muscles of PDAC mice. By IPA analyses on transcriptomics, they found an increase in the signature of protein degradation, atrophy, and glycolysis and a downregulation of muscle function. Focusing on mitochondria they showed a downregulation mainly in OXPHOS, TCA cycle, and mitochondrial dynamics genes and upregulation of glycolysis, ROS defense, mitophagy, and amino acid metabolism. IPA analysis on proteomics revealed major changes in muscle contraction and metabolic pathways related to lipids, protein, nucleotide, and DNA metabolism. Focusing on mitochondria, the protein changes mainly were related to OXPHOS, TCA cycle, translation, and amino acid metabolism.

The major strength of the paper is the bioenergetics and mitochondrial characterization associated with the transcriptomic and proteomic analyses in PDAC mice that confirmed some published data of mitochondrial dysfunction but underlined some novel metabolic insights such as nucleotide metabolism.

There are minor weaknesses related to some analyses on mitochondrial proteins and to the fact that proteomic and transcriptomic comparison may be problematic in catabolic conditions because some gene expression is required to maintain or re-establish enzymes/proteins that are destroyed by the proteolytic systems (including the autophagy proteins and ubiquitin ligases). The authors should consider the following points.

Point1. The authors used the name sarcopenia as synonymous with muscle atrophy. However, sarcopenia clearly defines the disease state (disease code: ICD-10-CM (M62.84)) of excessive muscle loss and force drop during ageing (Ref: Anker SD et al. J Cachexia Sarcopenia Muscle 2016 Dec;7(5):512-514.). Therefore, the word sarcopenia must be used only when pathological age-related muscle loss is the subject of study. Sarcopenia can be present in cancer patients who also experience cachexia, however since the age of tumor-bearing mice in this study is 7-9 weeks old, the authors should refrain from using sarcopenia and instead replace it with the words muscle atrophy/ muscle wasting/muscle loss.

Point2. Most of the analyses of mitochondrial function are appropriate. However, the methodological approach to determining mitochondrial fusion and fission machinery shown in Fig. 5F is wrong. The correct way is to normalize the OPA1, MFn1/2 on mitochondrial proteins such as VDAC/porin. In fact, by loading the same amount of total protein (see actin in panel 5F) the difference between a normal and a muscle with enhanced protein breakdown is lost. In fact, we should expect a decrease in actin level in tumor-bearing mice with muscle atrophy while the blots clearly show the same level due to the normalization of protein content. Moreover, by loading the same amount of proteins in the gel, the atrophying muscle lysates become enriched in the proteins/organelles that are less affected by the proteolysis resulting in an artefactual increase. The correct way should be to lyse the whole muscle of control and tumor-bearing mice in an identical volume and to load in western blot the same volume between control cachectic muscles. Alternatively, the relative abundance of mitochondrial shaping proteins related to mitochondrial transmembrane or matrix proteins (mito mass) should compensate for the loading normalization. Because the authors showed elongated mitochondria despite mitophagy genes being up, fragmentation may be altered. Moreover, DNM1l gene is suppressed and therefore DRP1 protein must be analyzed. Finally, OPA 1 protein has different isoforms due to the action of proteases like OMA1, and YME1L that elicit different functions being the long one pro-fusion while the short ones do not. The authors must quantify the long and short isoforms of OPA1.

Point3. The comparison of proteomic and transcriptomic profiles to identify concordance or not is problematic when atrophy programs are induced. In fact, most of the transcriptional-dependent upregulation is to preserve/maintain/reestablish enzymes that are consumed during enhanced protein breakdown. For instance, the ubiquitin ligases when activated undergo autoubiquitination and proteasome degradation. The same happens for several autophagy-related genes belonging to the conjugation system (LC3, Gabarap), the cargo recognition pathways (e.g. Ubiquitin, p62/SQSTM1) and the selective autophagy system (e.g. BNIP3, PINK/PARKIN) and metabolic enzymes (e.g. GAPDH, lipin). Finally, in case identical amounts of proteins have been loaded in mass spec the issues rise in point 2 of selective enrichment should be considered. Therefore, when comparing proteomic and transcriptomic these issues should be considered in discussion.

Reviewer #2 (Public Review):

Summary:<br /> This work focuses on the biochemical features of the SARS-CoV-2 Nucleocapsid (N) protein, which condenses the large viral RNA genome inside the virus and also plays other roles in the infected cell. The N protein of SARS-CoV-2 and other coronaviruses is known to contain two globular RNA-binding domains, the NTD and CTD, flanked by disordered regions. The central disordered linker is particularly well understood: it contains a long SR-rich region that is extensively phosphorylated in infected cells, followed by a leucine-rich helical segment that was shown previously by these authors to promote N protein oligomerization.

In the current work, the authors analyze 5 million viral sequence variants to assess the conservation of specific amino acids and general sequence features in the major regions of the N protein. This analysis shows that disordered regions are particularly variable but that the general hydrophobic and charge character of these regions are conserved, particularly in the SR and leucine-rich regions of the central linker. The authors then construct a series of N proteins bearing the most prevalent mutations seen in the Delta and Omicron variants, and they subject these mutant proteins to a comprehensive array of biophysical analyses (temperature sensitivity, circular dichroism, oligomerization, RNA binding, and phase separation).

Strengths:<br /> The results include a number of novel findings that are worthy of further exploration. Most notable are the analyses of the previously unstudied P31L mutation of the Omicron variant. The authors use ColabFold and sedimentation analysis to suggest that this mutation promotes the self-association of the disordered N-terminal region and stimulates the formation of N protein condensates. Although the affinity of this interaction is low, it seems likely that this mutation enhances viral fitness by promoting N-terminal interactions. The work also addresses the impact of another unstudied mutation, D63G, that is located on the surface of the globular NTD and has no significant effect on the properties analyzed here, raising interesting questions about how this mutation enhances viral fitness. Finally, the paper ends with studies showing that another common mutant, R203K/G204R, disrupts phase separation and might thereby alter N protein function in a way that enhances viral fitness.

Weaknesses:<br /> In general, the results in the paper confirm previous ideas about the role of N protein regions. The key novelty of the paper lies in the identification of point mutations, notably P13L, that suggest previously unsuspected functions of the N-terminal disordered region in protein oligomerization. The paper would benefit from further exploration of these possibilities.

Reviewer #2 (Public Review):

This manuscript by Geng et al. aims to demonstrate that MDA5 compensates for the loss of RIG-I in certain species, such as teleofish miiuy croacker. The authors use siniperca cheats rhabdovirus (SCRV) and poly(I:C) to demonstrate that these RNA ligands induce an IFN response in an MDA5-dependent manner in m.miiuy derived cells. Furthermore, they show that MDA5 requires its RD domain to directly bind to SCRV RNA and to induce an IFN response. They use in vitro synthesized RNA with a 5'triphosphate (or lacking a 5'triphosphate as a control) to demonstrate that MDA5 can directly bind to 5'-triphosphorylated RNA. The second part of the paper is devoted to m6A modification of MDA5 transcripts by SCRV as an immune evasion strategy. The authors demonstrate that the modification of MDA5 with m6A is increased upon infection and that this causes increased decay of MDA5 and consequently a decreased IFN response.

The key message of this paper, i.e. MDA5 can sense 5'-triphosphorylated RNA and thereby compensate for the loss of RIG-I, is novel and interesting, yet there is insufficient evidence provided to prove this hypothesis. Most importantly, it is crucial to test the capacity of in vitro synthesized 5'-triphosphorylated RNA to induce an IFN response in MDA5-sufficient and -deficient cells. In addition, a number of important controls are missing, as detailed below. The authors describe an interaction between MDA5 and STING which, if true, is very interesting. However, the functional implications of this interaction are not further investigated in the manuscript. Is STING required to relay signalling downstream of MDA5? The second part of the paper is quite distinct from the first part. The fact that MDA5 is an interferon-stimulated gene is not mentioned and complicates the analyses (i.e. is there truly more m6A modification of MDA5 on a per molecule basis, or is there simply more total MDA5 and therefore more total m6A modification of MDA5).

Finally, it should be pointed out that several figures require additional labels, markings, or information in the figure itself or in the accompanying legend to increase the overall clarity of the manuscript. There are frequently details missing from figures that make them difficult to interpret and not self-explanatory. These details are sometimes not even found in the legend, only in the materials and methods section. The manuscript also requires extensive language editing by the editorial team or the authors.

Reviewer #2 (Public Review):

In this article, Tian et al present a convincing analysis of the molecular mechanisms underpinning TIPE-mediated regulation of glycolysis and tumor growth in melanoma. The authors begin by confirming TIPE expression in melanoma cell lines and identify "high" and "low" expressing models for functional analysis. They show that TIPE depletion slows tumour growth in vivo, and using both knockdown and over-expression approaches, show that this is associated with changes in glycolysis in vitro. Compelling data using multiple independent approaches is presented to support an interaction between TIPE and the glycolysis regulator PKM2, and the over-expression of TIPE-promoted nuclear translocation of PKM2 dimers. Mechanistically, the authors also demonstrate that PKM2 is required for TIPE-mediated activation of HIF1a transcriptional activity, as assessed using an HRE-promoter reporter assay, and that TIPE-mediated PKM2 dimerization is p-ERK dependent. Finally, the dependence of TIPE activity on PKM2 dimerization was demonstrated on tumor growth in vivo and in the regulation of glycolysis in vitro, and ectopic expression of HIF1a could rescue the inhibition of PKM2 dimerization in TIPE overexpressing cells and reduced induction of general cancer stem cell markers, showing a clear role for HIF1a in this pathway. The main conclusions of this paper are well supported by data, but some aspects of the experiments need clarification and some data panels are difficult to read and interpret as currently presented.

The detailed mechanistic analysis of TIPE-mediated regulation of PKM2 to control aerobic glycolysis and tumor growth is a major strength of the study and provides new insights into the molecular mechanisms that underpin the Warburg effect in cancer cells. However, despite these strengths, some weaknesses were noted, which if addressed will further strengthen the study.

1. The analysis of patient samples should be expanded to more directly measure the relationship between TIPE levels and melanoma patient outcome and progression (primary vs metastasis), to build on the association between TIPE levels and proliferation (Ki67) and hypoxia gene sets that are currently shown.

2. The duration of the in vivo experiments was not clearly defined in the figures, however, it was clear from the tumor volume measurements that they ended well before standard ethical endpoints in some of the experiments. A rationale for this should be provided because longer-duration experiments might significantly change the interpretation of the data. For example, does TIPE depletion transiently reduce or lead to sustained reductions in tumor growth?

3. The analysis of general cancer stem cell markers is solid and interesting, however inclusion of neural crest stem cell markers that are more relevant to melanoma biology would greatly strengthen this aspect of the study.

4. The authors should take care that all data panels are clearly readable in the figures to facilitate appropriate interpretation by the reader.

Reviewer #2 (Public Review):

Xu et al. introduce a cellular automaton model to investigate the spatiotemporal spreading of viral infection. In this study, the author first analyzes the single-cell RNA sequencing data from experiments and identifies four clusters of cells at 48 hours post-viral infection, including susceptible cells (O), infected cells (V), IFN-secreting cells (N), and antiviral cells (A). Next, a cellular automaton model (NOVAa model) is introduced by assuming the existence of a transient pre-antiviral state (a). The model consists of an LxL lattice; each site represents one cell. The cells change their state following the rules depending on the interaction of neighboring cells. The model introduces a key parameter, p_a, representing the fraction of pre-antiviral state cells. Cell apoptosis is omitted in the model. Model simulations show a threshold-like behavior of the final attack rate of the virus when p_a changes continuously. There is a critical value p_c, so that when p_a < p_c, infections typically spread to the entire system, while at a higher p_a > p_c, the propagation of the infected state is inhibited. Moreover, the radius R that quantifies the diffusion range of N cells may affect the critical value p_c; a larger R yields a smaller value of the critical value p_c. The structure of clusters is different for different values of R; greater R leads to a different microscopic structure with fewer A and N cells in the final state. Compared with the single-cell RNA seq data, which implies a low fraction of IFN-positive cells - around 1.7% - the model simulation suggests R=5. The authors also explored a simplified version of the model, the OVA model, with only three states. The OVA model also has an outbreak size. The OVA model shows dynamics similar to the NOVAa model. However, the change in microstructure as a function of the IFN range R observed in the NOVAa model is not observed in the OVA model.

Data and model simulation mainly support the conclusions of this paper, but some weaknesses should be considered or clarified.

1) In the automaton model, the authors introduce a parameter p_a, representing the fraction of pre-antiviral state cells. The authors wrote: ``The parameter p_a can also be understood as the probability that an O cell will switch to the N or A state when exposed to the virus of IFNs, respectively.' Nevertheless, biologically, the fraction of pre-antiviral state cells does not mean the same value as the probability that an O cell switches to the N or A state. Moreover, in the numerical scheme, the cell state changes according to the deterministic role N(O)=a and N(a)=A. Hence, the probability p_a did not apply to the model simulation. It may need to clarify the exact meaning of the parameter p_a.

2) The current model is deterministic. However, biologically, considering the probabilistic model may be more realistic. Are the results valid when the probability update strategy is considered? By the probability model, the cells change their state randomly to the state of the neighbor cells. The probability of cell state changes may be relevant for the threshold of p_a. It is interesting to know how the random response of cells may affect the main results and the critical value of p_a.

3) Figure 2 shows a critical value p_c = 27.8% following a simulation on a lattice with dimension L = 1000. However, it is unclear if dimension changes may affect the critical value.

Reviewer #2 (Public Review):

In their study, Zaman et al. demonstrate that deletion of either the receptor tyrosine kinase Kit from cerebellar interneurons or the kit ligand (KL) from Purkinje cells reduces the inhibition of Purkinje cells. They delete Kit or KL at different developmental time points, illustrating that Kit-KL interactions are not only required for developmental synapse formation but also for synapse maintenance in adult animals. The study is interesting as it highlights a molecular mechanism for the formation of inhibitory synapses onto Purkinje cells.

The tools generated, such as the floxed Kit mouse line and the virus for Kit overexpression, may have broader applications in neuroscience and beyond.

One general weakness is that Kit expression is not limited to molecular layer interneurons but also extends to the Purkinje layer and Golgi interneurons. But this expression does not conflict with the principal conclusions, as Purkinje layer interneurons form few or no synapses onto Purkinje cells.

In summary, the data support the hypothesis that the interaction between Kit and KL between cerebellar Molecular Layer Interneurons and Purkinje Cells plays a crucial role in promoting the formation and maintenance of inhibitory synapses onto PCs. This study provides valuable insights that could inform future investigations on how this mechanism contributes to the dynamic regulation of Purkinje cell inhibition across development and its impact on mouse behavior.

Reviewer #2 (Public Review):

Summary:

The manuscript by Kaneda et al "FBXO24 ensures male fertility by preventing abnormal accumulation 2 of membraneless granules in sperm flagella" is a significant paper on the role of FBXO24 in murine male germ cell development and sperm ultrastructure and function. The body of experimental evidence that the authors present is extraordinarily strong in both breadth and depth. The authors investigate the protein's functions in male germ cells and sperm using a wide variety of approaches but focusing predominantly on their novel mouse model featuring deletion of the Fbxo24 gene and its product. Using this mouse, and a cross of it with another model that expresses reporters in the head and midpiece, they logically build from one experiment to the next. Together, their data show that this protein is involved in the regulation of membraneless electron-dense structures; loss of FBXO24 led to an accumulation of these materials and defects in the sperm flagellum and fertilizing ability. Interestingly, the authors found that several of the best-known components of electron-dense ribonucleoprotein granules that are found in the intermitochondrial cement and chromatoid body were not disrupted in the Fbxo24 knockout, suggesting that the electron-dense material and these structures are not all the same, and the biology is more complicated than some might have thought. They found evidence for the most changes in IPO5 and KPNB1, and biochemical evidence that FBXO24 and IPO5 could interact.

Strengths:

The authors are to be commended for the thoroughness of their experimental approaches and the extent to which they investigated impacts on sperm function and potential biochemical mechanisms. Very briefly, they start by showing that the Fbxo24 message is present in spermatids and that the protein can interact with SKP1, in a way that is dependent on its F-box domain. This points toward a potential function in protein degradation. To test this, they next made the knockout mouse, validated it, and found the males to be sterile, although capable of plugging a female. Looking at the sperm, they identified a number of ultrastructural and morphological abnormalities, which they looked at in high resolution using TEM. They also cross their model with RBGS mice so that they have reporters in both the acrosome and mitochondria. The authors test a variety of sperm functions, including motility parameters, ability to fertilize by IVF, cumulus-free IVF, zona-free-IVF, and ICSI. They found that ICSI could rescue the knockout but not other assisted reproductive technologies. Defects in male fertility likely resulted from motility disruption and failure to get through the utero-tubal junction but defects in acrosome exocytosis also were noted. The authors performed thorough investigations including both targeted and unbiased approaches such as mass spectrometry. These enabled them to show that although the loss of the FBXO24 protein led to more RNA and elevated levels of some proteins, it did not change others that were previously identified in the electron-dense RNP material.

The manuscript will be highly significant in the field because the exact functions of the electron-dense RNP materials have remained somewhat elusive for decades. Much progress has been made in the past 15 years but this work shows that the situation is more complex than previously recognized. The results show critical impacts of protein degradation in the differentiation process that enables sperm to change from non-descript round cells into highly polarized and compartmentalized mature sperm, with an equally highly compartmentalized flagellum. This manuscript also sets a high bar for the field in terms of how thorough it is, which reveals wide-ranging impacts on processes such as mitochondrial compaction and arrangement in the midpiece, the correct building of the major cytoskeletal elements in the flagellum, etc.

Weaknesses:

There are no real weaknesses in the manuscript that result from anything in the control of the authors. They attempted to rescue the knockout by expressing a FLAG-tagged Fbxo24 transgene, but that did not rescue the phenotype, either because of inappropriate levels/timing/location of expression, or because of interference by the tag. They also could not make anti-FBXO24 that worked for co-immunoprecipitation experiments, so relied on the FLAG epitope, an approach that successfully showed co-IP with IPO5 and SKP1.

Reviewer #2 (Public Review):

Summary:<br /> In this study, researchers aimed to understand how a transmitted/founder (T/F) HIV virus escapes host immune pressure during early infection. They focused on the V1V2 domain of the HIV-1 envelope protein, a key determinant of virus escape. The study involved four participants from the RV217 Early Capture HIV Cohort (ECHO) project, which allowed tracking HIV infection from just days after infection.

The study identified a significant H173Y escape mutation in the V2 domain of a T/F virus from one participant. This mutation, located in the relatively conserved "C" β-strand, was linked to viral escape against host immune pressure. The study further investigated the epitope specificity of antibodies in the participant's plasma, revealing that the H173Y mutation played a crucial role in epitope switching during virus escape. Monoclonal antibodies from the RV144 vaccine trial, CH58, and CH59, showed reduced binding to the V1V2-Y173 escape variant. Additionally, the study examined antibody-dependent cellular cytotoxicity (ADCC) responses and found resistance to killing in the Y173 mutants. The H173Y mutation was identified as the key variant selected against the host's immune pressure directed at the V2 domain.

The researchers hypothesized that the H173Y mutation caused a structural/conformational change in the C β-strand epitope, leading to viral escape. This was supported by molecular dynamics simulations and structural modeling analyses. They then designed combinatorial V2 immunogen libraries based on natural HIV-1 sequence diversity, aiming to broaden antibody responses. Mouse immunizations with these libraries demonstrated enhanced recognition of diverse Env antigens, suggesting a potential strategy for developing a more effective HIV vaccine.

In summary, the study provides insights into the early evolution of HIV-1 during infection, highlighting the importance of the V1V2 domain and identifying key escape mutations. The findings suggest a novel approach for designing HIV vaccine candidates that consider the diversity of escape mutations to induce broader and more effective immune responses.

Strengths:<br /> The article presents several strengths:

1. The experimental design is well-structured, involving multiple stages from phylogenetic analyses to mouse model testing, providing a comprehensive approach to studying virus escape mutations.

2. The study utilizes a unique dataset from the RV217 Early Capture HIV Cohort (ECHO) project, allowing for the tracking of HIV infection from the very early stages in the absence of antiretroviral therapy. This provides valuable insights into the evolution of the virus.

3. The use of advanced techniques such as phylogenetic analyses, nanoscaffold technology, controlled mutagenesis, and monoclonal antibody evaluations demonstrates the application of cutting-edge methodologies in the study.

4. The research goes beyond genetic analysis and provides an in-depth characterization of the escape mutation's impact, including structural analyses through Molecular Dynamics simulations, antibody responses, and functional implications for virus survival.

5. The study provides insights into the immune responses triggered by the escape mutation, including the specificity of antibodies and their ability to recognize diverse HIV-1 Env antigens.

7. The exploration of combinatorial immunogen libraries is a strength, as it offers a novel approach to broaden antibody responses, providing a potential avenue for future vaccine design.

8. The research is highly relevant to vaccine development, as it sheds light on the dynamics of HIV escape mutations and their interaction with the host immune system. This information is crucial for designing effective vaccines that can preemptively interfere with viral acquisition.

9. The study integrates findings from virology, immunology, structural biology, and bioinformatics, showcasing an interdisciplinary approach that enhances the depth and breadth of the research.

10. The article is well-written, with a clear presentation of methods, results, and implications, making it accessible to both specialists and a broader scientific audience.

Weaknesses:<br /> While the article presents several strengths, it's important to consider potential weaknesses as well:

1. While the exploration of combinatorial immunogen libraries is innovative, the complexity of this approach may pose challenges in terms of practical implementation, scalability, and cost-effectiveness in large-scale vaccine development.

2. The article will benefit from a more explicit discussion of the limitations and potential drawbacks of the methodologies employed. For example, structural analyses, such as Molecular Dynamics simulations, involve complex computational models. The accuracy and reliability of these simulations may vary, and uncertainties in the interpretation of structural data should be acknowledged.

Reviewer #2 (Public Review):

Mignerot et al. study variations in egg retention in a large set of wild C. elegans strains use detailed analysis of a subset of these strains to those that these variations in egg retention appear to arise from variations in egg-laying behavior. The authors then take advantage of the advanced genetic technology available in C. elegans, and the fact that the cellular and molecular mechanisms that drive egg-laying behavior in the N2 laboratory strain of C. elegans have been studied intensely for decades. Thus, they demonstrate that variations multiple genetic loci appear to drive variations in egg laying across species, although they are unable to identify the specific genes that vary other than a potassium channel already identified in a previous study from some of these same authors (Vigne et al., 2021). Mignerot et al. also present evidence that variations in response of the egg-laying system to the neuromodulator serotonin appear to underlie variations in egg-laying behavior across species. Finally, the authors present a series of studies examining how the retention of eggs in utero affects the fertility and survival of mothers versus the survival of their progeny in a variety of adverse conditions, including limiting food, and the presence of acute environmental insults such as alcohol or acid. The results suggest that variations in egg-laying behavior evolved as a response to adverse environmental conditions that impose a trade-off between survival of the mothers versus their progeny.

Strengths:

The analysis of variations in egg laying by a large set of wild species significantly extends the previous work of Vigne et al. (2021), who focused on just one wild variant strain. Mignerot find that variations in egg laying are widespread across C. elegans strains and result from changes in multiple genetic loci.

To determine why various strains vary in their egg-laying behavior, the authors take advantage the genetic tractability of C. elegans and the huge body of previous studies on the cellular and molecular basis of egg-laying behavior in the laboratory N2 strain. Since serotonin is one signal that induces egg laying, the authors subject various strains to serotonin and to drugs thought to alter serotonin signaling, and they also use CRISPR induced gene editing to mutate a serotonin reuptake transporter in some strains. The results are largely consistent with the idea that variations across strains alter how the egg-laying system responds to serotonin.

The final figures in the paper presents a far more detailed analysis than did Vigne et al. (2021) of how variations in egg retention across species can affect fitness under various environmental stresses. Thus, Mignerot et al. look at competition under conditions of limiting food, and response to acute environmental insults, and compare the ability of adults, in utero eggs, and ex vivo eggs to survive. The results lead to an interesting discussion of how variations in behavior result in a trade-off in survival of mothers versus their progeny. The authors in their Discussion do a good job describing the challenges in interpreting the relevance of these laboratory results to the poorly-understood environmental conditions that C. elegans may experience in the wild. The Discussion also had an excellent section about how the ability of a single species to strongly regulate egg-laying behavior in response to its environment, and how this ability could be adaptive. Overall, these were the strongest and most interesting aspects of Mignerot et al.

Weaknesses<br /> The specific potassium channel variation studied by Vigne et al. (2021) has by far the strongest effect on egg laying seen in the Mignerot et al. study and remains the only genetic variation that has been molecularly identified. So, Mignerot et al. were not able to identify any additional specific genes that vary across species to cause changes in egg laying, and this limited their ability to generate new insights into the specific cellular and molecular mechanisms that have changed across species to result in changes in egg laying behavior.

The authors' use of drug treatments and CRISPR to alter serotonin signaling yielded some insights into mechanistic variations in how the egg-laying system functions across strains, but these experiments only allow very indirect inferences into what is going on. The analysis in Figures 4 and 5 generates a complex set of results that are not easy to interpret. The clearest result seems to be that strains carrying the KCNL-1 point mutation lay eggs poorly and exogenous serotonin inhibits rather than stimulates egg laying in these strains. This basic result was to a large extent reported previously in Vigne et al. 2021.

The analysis of how differences between strains mechanistically result in changes in egg-laying behavior and egg retention, while excellent in concept, is only modestly successful. The analysis of the temporal pattern egg-laying behavior in Figure 3B-3F is relatively weak. Whereas the state of the art in analyzing this behavior is to take videos of animals and track exactly when they lay eggs, analyzing 40 or more hours of behavior per strain, the authors used a lower-tech method of just examining how many eggs were laid within 5-minute intervals over a period of just three hours per strain. While this analysis was sufficient to demonstrate some statistically significant differences in the pattern of egg laying in some strains, it is unclear to what extent these differences could be sufficient to explain the differences in accumulation of unlaid eggs between these strains. In contrast, the variations in age of the onset of egg-laying behavior in Fig 3G and 3H between strains were very strong and may be more likely to reflect mechanistic differences in how egg laying is controlled that could result in the differences in retention of unlaid eggs seen among the strains tested. In the Discussion, the authors extensively write about the work of the Collins lab showing that retained eggs stretch the uterus to produce a signal that activates egg-laying muscles. Could it be that really this mechanism is the main one that varies between strains, leading to the observed variations in time to laying the first egg as well as variations in the number of retained eggs throughout adulthood?

Reviewer #2 (Public Review):

This manuscript describes experiments that further investigate the actions of the transcription factor Bcl11b in regulating mossy fiber (MF) synapses in the hippocampus. Prior work from the same group had demonstrated that loss of Bcl11b results in loss of MF synapses as well as a decrease in LTP. Here the authors focus on a target of Bcl11b a secreted synaptic organizer C1ql2 which is almost completed lost in Bcl11b KO. Viral reintroduction of C1ql2 rescues the synaptic phenotypes, whereas direct KD of C1ql2 recapitulates the Bcl1 phenotype. C1ql2 itself interacts directly with Nrxn3 and replacement with a binding deficient mutant C1q was not able to rescue the Bcl11b KO phenotype. Overall there are some interesting observations in the study, however there are also some concerns about the measures and interpretation of data.

The authors state they used a differential transcriptomic analysis to screen for candidate targets of Bcl11b, yet they do not present any details of this screen. This should be included and at the very least a table of all DE genes included. It is likely that many other genes are also regulated by Bcl11b so it would be important to the reader to see the rationale for focusing attention on C1ql2 in this study.

All viral mediated expression uses AAVs which are known to ablate neurogenesis in the DG (Johnston DOI: 10.7554/eLife.59291) through the ITR regions and leads to hyperexcitability of the dentate. While it is not clear how this would impact the measurements the authors make in MF-CA3 synapses, this should be acknowledged as a potential caveat in this study.

The authors claim that the viral re-introduction "restored C1ql2 protein expression to control levels. This is misleading given that the mean of the data is 2.5x the control (Figure 1d and also see Figure 6c). The low n and large variance are a problem for these data. Moreover, they are marked ns but the authors should report p values for these. At the least this likely large overexpression and variability should be acknowledged. In addition, the use of clipped bands on Western blots should be avoided. Please show the complete protein gel in primary figures of supplemental information.

Measurement of EM micrographs: As prior work suggested that MF synapse structure is disrupted the authors should report active zone length as this may itself affect "synapse score" defined by the number of vesicles docked. More concerning is that the example KO micrographs seem to have lost all the densely clustered synaptic vesicles that are away from the AZ in normal MF synapses e.g. compare control and KO terminals in Fig 2a or 6f or 7f. These terminals look aberrant and suggest that the important measure is not what is docked but what is present in the terminal cytoplasm that normally makes up the reserve pool. This needs to be addressed with further analysis and modifications to the manuscript.

The study also presents correlated changes in MF LTP in Bcl11b KO which are rescued by C1ql2 expression. It is not clear whether the structural and functional deficits are causally linked and this should be made clearer in the manuscript. It is also not apparent why this functional measure was chosen as it is unlikely that C1ql2 plays a direct role in presynaptic plasticity mechanisms that are through a cAMP/ PKA pathway and likely disrupted LTP is due to dysfunctional synapses rather than a specific LTP effect. The authors should consider measures that might support the role of Bcl11b targets in SV recruitment during depletion of synapses or measurements of the readily releasable pool size that would complement their finding in structural studies.

Bcl11b KO reduces the number of synapses, yet the I-O curve reported in Supp Fig 2 is not changed. How is that possible? This should be explained.

Matsuda et al DOI: 10.1016/j.neuron.2016.04.001 previously reported that C1ql2 organizes MF synapses by aligning postsynaptic kainate receptors with presynaptic elements. As this may have consequences for the functional properties of MF synapses including their plasticity, the authors should report whether they see deficient postsynaptic glutamate receptor signaling in the Bcl11b KO and rescue in the C1ql2 re-expression.

These are all addressed in the revised version.

Reviewer #2 (Public Review):

Summary: In this manuscript, Shen and collaborators described the generation of conditional double knockout (cDKO) mice lacking LRRK1 and LRRK2 selectively in DAT positive dopaminergic neurons. The Authors asked whether selective deletion of both LRRK isoforms could lead to a Parkinsonian phenotype, as previously reported by the same group in germline double LRRK1 and LRRK2 knockout mice (PMID: 29056298). Indeed, cDKO mice developed a late reduction of TH+ neurons in SNpc that partially correlated with the reduction of NeuN+ cells. This was associated with increased apoptotic cell and microglial cell numbers in SNpc. Unlike the constitutive DKO mice described earlier, however, cDKO mice did not replicate the dramatic increase in the number of autophagic vacuoles. The study supports the authors' hypothesis that loss of function rather than gain of function of LRRK2 leads to Parkinson's Disease.

Strengths: The study described for the first time a model where both the Parkinson's disease-associated gene LRRK2 and its homolog LRRK1 are deleted selectively in dopaminergic neurons, offering a new tool to understand the physiopathological role of LRRK2 and the compensating role of LRRK1 in modulating dopaminergic cell function.

Weaknesses: The model has no construct validity since loss of function mutations of LRRK2 are well tolerated in humans and do not lead to Parkinson's disease. The evidence of a Parkinsonian phenotype in these conditional knockout mice is limited and should be considered preliminary.

Reviewer #2 (Public Review):

Summary:<br /> The authors present a comprehensive technical overview of the challenging acquisition of large-scale cortical activity, including surgical procedures and custom 3D-printed headbar designs to obtain neural activity from large parts of the dorsal or lateral neocortex. They then describe technical adjustments for stable head fixation, light shielding, and noise insulation in a 2-photon mesoscope and provide a workflow for multisensory mapping and alignment of the obtained large-scale neural data sets in the Allen CCF framework. Lastly, they show different analytical approaches to relate single-cell activity from various cortical areas to spontaneous activity by using visualization and clustering tools, such as Rastermap, PCA-based cell sorting, and B-SOID behavioral motif detection.

The study contains a lot of useful technical information that should be of interest to the field. It tackles a timely problem that an increasing number of labs will be facing as recent technical advances allow the activity measurement of an increasing number of neurons across multiple areas in awake mice. Since the acquisition of cortical data with a large field of view in awake animals poses unique experimental challenges, the provided information could be very helpful to promote standard workflows for data acquisition and analysis and push the field forward.

Strengths:<br /> The proposed methodology is technically sound and the authors provide convincing data to suggest that they successfully solved various problems, such as motion artifacts or high-frequency noise emissions, during 2-photon imaging. Overall, the authors achieved their goal of demonstrating a comprehensive approach for the imaging of neural data across many cortical areas and providing several examples that demonstrate the validity of their methods and recapitulate and further extend some recent findings in the field.

Weaknesses:<br /> Most of the descriptions are quite focused on a specific acquisition system, the Thorlabs Mesoscope, and the manuscript is in part highly technical making it harder to understand the motivation and reasoning behind some of the proposed implementations. A revised version would benefit from a more general description of common problems and the thought process behind the proposed solutions to broaden the impact of the work and make it more accessible for labs that do not have access to a Thorlabs mesoscope. A better introduction of some of the specific issues would also promote the development of other solutions in labs that are just starting to use similar tools.

Reviewer #2 (Public Review):

Summary:<br /> In this work, the authors aim to better understand how C. elegans detects and responds to heat-killed (HK) E. coli, a low-quality food. They find that HK food activates two canonical stress pathways, ER-UPR, and innate immunity, in the nervous system to promote food aversion. Through the creative use of E. coli genetics and metabolomics, the authors provide evidence that the altered carbohydrate content of HK food is the trigger for the activation of these stress responses and that supplementation of HK food with sugars (or their biosynthetic product, vitamin C), reduces stress pathway induction and food avoidance. This work makes a valuable addition to the literature on metabolite detection as a mechanism for the evaluation of nutritional value; it also provides some new insight into the physiologically relevant roles of well-known stress pathways in modulating behavior.

Strengths:<br /> -The work addresses an important question by focusing on understanding how the nervous system evaluates food quality and couples this with behavioral change.<br /> -The work takes full advantage of the tools available in this powerful system and builds on extensive previous studies on feeding behavior and stress responses in C. elegans.<br /> -Creative use of E. coli genetics and metabolite profiling enabled the identification of carbohydrate metabolism as a candidate source of food-quality signals.<br /> -For the most part, the studies are rigorous and logically designed, providing good support for the authors' model.

Weaknesses:<br /> -It is not clear how the mechanism identified here is connected to previously described, related processes. In particular, it is not clear whether this mechanism has a role in the detection of other low-quality foods. Further, the specificity of the ability of sugar/vitamin C to suppress stress pathway induction is unclear (i.e., does sugar/vitamin C have any effect on the activation of these pathways through other means?). Additionally, the relationship of this pathway to the vitamin B2-sensing mechanism previously described by the senior author is unclear. These issues do not weaken confidence in the authors' conclusions, but they do reduce the potential significance of the work.

-The authors claim that the induction of the innate immune pathway reporter irg-5::GFP is "abolished" in pmk-1(RNAi) animals, but Figure S2K seems to show a clear GFP signal when these animals are fed HK-OP50. Similarly, the claim that feeding WT animals HK-OP50 enriches phospho-PMK-1 levels (Fig 2E) is unconvincing - only one western blot is shown, with no quantification, and there is a smear in the critical first lane.

-The rationales for some of the paper's hypotheses could be improved. For example, the rationale for screening the E. coli mutant library is that some mutants, when heat-killed, may be missing a metabolite that induces the ER-UPR. A more straightforward hypothesis might be that some mutant E. coli strains aberrantly induce the ER-UPR when *not* heat-killed, because they are missing a metabolite that prevents stress pathway induction. This is not in itself a major concern, but it would be useful for the authors to provide a rationale for their hypothesis.

-The authors do not provide any explanation for some unexpected results from the E. coli screen. Earlier in the paper, the authors found that innate immune signaling is downstream of ER-UPR activation. However, of the 20 E. coli mutants that, when heat-killed, "did not induce... the UPR-ER reporter," 9 of them still activate the innate immune response. This seems at odds with the authors' simple model since it suggests that low-quality food can induce innate immune signaling independently of the ER-UPR. Further, only one of the 9 has an effect on behavior, even though failure to activate the innate immune pathway might be expected to lead to a behavioral defect in all of these.

-In a number of places, the writing style can make the authors' arguments difficult to follow.

-Some of the effect sizes observed by the authors are exceedingly small (e.g, the suppression of hsp-4::gfp induction by sugar supplementation in Figs 3C-E), raising some concern about the biological significance of the effect.

-In some cases, there is a discrepancy between the fluorescence images and their quantitation (e.g., Figure 3E, where the effect of glucose on GFP fluorescence seems much stronger in the image than in the graph).

Reviewer #2 (Public Review):

Summary:

This study proposed a new mechanism by which the TGF-beta signaling pathway promotes contacts between oocytes and the surrounding somatic cells in mice, by regulating the numbers of transzonal projections (TZPs).

Strengths:

The conditional Smad4 knockout and three-dimensional observation of transzonal projections are solid and sufficiently support the major conclusions.

Weaknesses:

The physiological significance of SMAD4-dependent formation of transzonal projection networks is not assessed in this study.

Reviewer #2 (Public Review):

The authors describe the structure of the S. pneumoniae Nox protein (SpNOX). This is a first. The relevance of it to the structure and function of eukaryotic Noxes is discussed in depth.

Strengths and Weaknesses<br /> One of the strengths of this work is the effort put into preparing a pure and functionally active SpNOX preparation. The protein was expressed in E. coli and the purification and optimization of its thermostability and activity are described in detail, involving salt concentration, glycerol concentration, and pH.

This reviewer was surprised by the fact that the purification protocol in THIS paper differs from those in the mBio and Biophys. J. papers by the absence of the detergent lauryl maltose neopentyl glycol (LMNG). LMNG is only present in the activity assay at a low concentration (0.003%; molar data should be given; by my calculation, this corresponds to 30 μM).

In light of the presence of lipids in cryo-EM-solved structures of DUOX and NOX2, it is surprising that the authors did not use reconstitution of the purified SpNOX in phospholipid (nanodisk?). The issue is made more complicated by the statement on p. 18 of "structures solved in detergent like ours" when no use of detergent in the solubilization and purification of SpNOX is mentioned in the Methods section (p. 21-22).

Can the authors provide information on whether E. coli BL21 is sufficiently equipped for the heme synthesis required for the expression of the TM domain of SpN NOX. Was supplementation with δ-aminolevulinic acid used?

The 3 papers on SpNOX present more than convincing evidence that SpNOX is a legitimate Nox that can serve as a legitimate model for eukaryotic Noxes (cyanide resistance, inhibition by DPI, absolute FAD dependence, and NADPH/NADH as the donor or electrons to FAD). It is also understood that the physiological role of SpNOX in S. pneumoniae is unknown and that the fact that it can reduce molecular oxygen may be an experimental situation that does not occur in vivo.

I am, however, linguistically confused by the statement that "SpNOX requires "supplemental" FAD". Noxes have FAD bound non-covalently and this is the reason that, starting from the key finding of Babior on NOX2 back in 1977 to the present, FAD has to be added to in vitro systems to compensate for the loss of FAD in the course of the purification of the enzyme from natural sources or expression in a bacterial host. I wonder whether this makes FAD more of a co-substrate than a prosthetic group unless what the authors intend to state is that SpNOX is not a genuine flavoprotein.

I am also puzzled by the statement that SpNOX "does not require the addition of Cyt c to sustain superoxide production". Researchers with a Cartesian background should differentiate between cause and effect. Cyt c serves merely as an electron acceptor from superoxide made by SpNOX but superoxide production and NADPH oxidation occur independently of the presence of added Cyt c.

The ability of the DH domain of SpNOX (SpNOXDH) to produce superoxide is surprising to this reviewer. The result is based on the inhibition of Cyt c reduction by added superoxide dismutase (SOD) by 40%. In all eukaryotic Noxes superoxide is produced by the one-electron reduction of molecular oxygen by electrons originating from the distal heme, having passed from reduced FAD via two hemes. The proposal that superoxide is generated by direct transfer of electrons from FAD to oxygen deserves a more in-depth discussion and relies too heavily on the inhibitory effect of SOD. A control experiment with inactivated SOD should have been done (SOD is notoriously heat resistant and inactivation might require autoclaving).

An unasked and unanswered question is that, since under aerobic conditions, both direct Cyt c reduction (60%) and superoxide production (40%) occur, what are the electron paths responsible for the two phenomena occurring simultaneously?

This reviewer had difficulty in following the argument that the fact that the kcat of SpNOX and SpNOXDH are similar supports the thesis that the rate of enzyme activation is dependent on hydride transfer from nicotinamide to FAD.

The section dealing with mutating F397 is a key part of the paper. There is a proper reference to the work of the Karplus group on plant FNRs (Deng et al). However, later work, addressing comparison with NOX2, should be cited (Kean et al., FEBS J., 284, 3302-3319, 2017). Also, work from the Dinauer group on the minimal effect of mutating or deleting the C-terminal F570 in NOX2 on superoxide production should be cited (Zhen et al., J. Biol. Chem. 273, 6575-6581, 1998).

It is not clear why mutating F397 to W (both residues having aromatic side chains) would stabilize FAD binding. Also, what is meant by "locking the two subdomains of the DH domain"? What subdomains are meant?

Methodological details on crystallization (p. 11) should be delegated to the Methodology section. How many readers are aware that SAD means "Single Wavelength Anomalous Diffraction" or know what is the role of sodium bromide?

The data on the structure of SpNOX are supportive of a model of Nox activation that is "dissident" relative to the models offered for DUOX and NOX2 activation. These latter models suggested that the movement of the DH domain versus the TM domain was related to conversion from the resting to the activated state. The findings reported in this paper show that, unexpectedly, the domain orientation in SpNOX (constitutively active!) is much closer to that of resting NOX2. One of the criteria associated with the activated state in Noxes was the reduction of the distance between FAD and the proximal heme. The authors report that, paradoxically, this distance is larger in the constitutively active SpNOX (9.2 Å)<br /> than that in resting state NOX2 (7.6 Å) and the distance in Ca2+-activated DUOX is even larger (10.2 Å).

A point made by the authors is the questioning of the paradigm that activation of Noxes requires DH domain motion. Instead, the authors introduce the term "tensing", within the DH domain, from a "relaxed" to a more rigid conformation. I believe that this proposal requires a somewhat clearer elaboration.

The statement on p. 18, in connection to the phospholipid environment of Noxes, that the structure of SpNOX was "solved in detergent" is puzzling since the method of SpNOX preparation and purification does not mention the use of a detergent. As mentioned before, this absence of detergent in the present report was surprising because LMNG was used in the methods described in the mBio and Biophys. J. papers. The only mention of LMNG in the present paper was as an addition at a concentration of 0.003% in the activity assay buffers.

The Conclusions section contains a proposal for the mechanism of conversion of NOX2 from the resting to the activated state. The inclusion of this discussion is welcome but the structural information on the constitutively active SpNOX can, unfortunately, contribute little to solving this important problem. The work of the Lambeth group, back in 1999 (cited as Nisimoto et al.), on the role of p67-phox in regulating hydride transfer from NADPH to FAD in NOX2 may indeed turn out to have been prophetic. However, only solving the structure of the assembled NOX2 complex will provide the much-awaited answer. The heterodimerization of NOX2 with p22-phox, the regulation of NOX2 by four cytosolic components, and the still present uncertainty about whether p67-phox is indeed the final distal component that converts NOX2 to the activated state make this a formidable task.<br /> The work of the Fieschi group on SpNOX is important and relevant but the absence of external regulation, the absence of p22-phox, and the uncertainty about the target molecule make it a rather questionable model for eukaryotic Noxes. The information on the role of the C-terminal Phe is of special value although its extension to the mechanism of eukaryotic Nox activation proved, so far, to be elusive.

Reviewer #2 (Public Review):

The authors investigated the role of the Jak1-Stat1 signaling pathway in myogenic differentiation by screening the transcriptional targets of Jak1-Stat1 and identified Styxl2, a pseudophosphatase, as one of them. Styxl2 expression was induced in differentiating muscles. The authors used a zebrafish knockdown model and conditional knockout mouse models to show that Styxl2 is required for de novo sarcomere assembly but is dispensable for the maintenance of existing sarcomeres. Styxl2 interacts with the non-muscle myosin IIs, Myh9 and Myh10, and promotes the replacement of these non-muscle myosin IIs by muscle myosin IIs through inducing autophagic degradation of Myh9 and Myh10. This function is independent of its phosphatase domain.

A previous study using zebrafish found that Styxl2 (previously known as DUSP27) is expressed during embryonic muscle development and is crucial for sarcomere assembly, but its mechanism remains unknown. This paper provides important information on how Styxl2 mediates the replacement of non-muscle myosin with muscle myosin during differentiation. This study may also explain why autophagy deficiency in muscles and the heart causes sarcomere assembly defects in previous mouse models.

Reviewer #2 (Public Review):

This study focuses on the differential binding of the RNA-binding protein HuR to CCL2 transcript (genetic variants rs13900 T or C). The study explores how this interaction influences the stability and translation of CCL2 mRNA. Employing a combination of bioinformatics, reporter assays, binding assays, and modulation of HuR expression, the study proposes that the rs13900T allele confers increased binding to HuR, leading to greater mRNA stability and higher translational efficiency. These findings indicate that rs13900T allele might contribute to heightened disease susceptibility due to enhanced CCL2 expression mediated by HuR. The study is interesting but needs appropriate experimental design and further strengthening. In its current form, the study suffers from several critical issues, including inadequate experimental design and the absence of control groups in key experiments.

Reviewer #2 (Public Review):

This paper takes a novel look at the protein economy of primary human and mouse T-cells - in both resting and activated state. Their findings in primary human T-cells are that:

1. A large fraction of ribosomes are stalled in resting cultured primary human lymphocytes. and these stalled ribosomes are likely to be monosomes.<br /> 2. Elongation occurs at similar rates for HeLa cells and lymphocytes, with the active ribosomes in resting lymphocytes translating at a similar rate as fully activated lymphocytes.

They then turn their attention to mouse OT-1 lymphocytes, looking at translation rates both in vitro and in vivo. Day1 resting T-cells also show stalling - which curiously wasn't seen on freshly purified cells - I didn't understand these differences.

In vivo they show that it is possible to monitor accurate translation and to measure rates in vivo. Perhaps most interestingly they note a paradoxically high ratio of cellular protein to ribosomes insufficient to support their rapid in vivo division, suggesting that the activated lymphocyte proteome in vivo may be generated in an unusual manner.

This was an interesting and provocative paper. Lots of interesting techniques and throwing down challenges to the community - it manages to address a number of important issues without necessarily providing answers.

Reviewer #2 (Public Review):

Summary:<br /> This study seeks to advance our knowledge of how vitamin D may be protective in allergic airway disease using both adult and neonatal mouse models. The rationale and starting point are important human clinical, genetic/bioinformatic data, with a proposed role for vitamin D regulation of 2 human chromosomal loci (Chr17q12-21.1 and Chr17q21.2) linked to risk of immune-mediated/inflammatory disease. The authors have historically made significant contributions to this work specifically in airway disease/asthma. They now link these data to propose a role for vitamin D in regulating IL-2 in Th2 cells implicating genes associated with these loci in this process.

Strengths:<br /> Here the authors draw together evidence from multiple interdisciplinary lines of investigation to propose that amongst murine CD4+ T cell populations, Th2 cells express high levels of VDR, and that vitamin D regulates many of the genes on the chromosomal loci identified to be of interest, in these cells. The bottom line is the proposal that vitamin D, via Ikfz3/Aiolos, suppresses IL-2 signalling in Th2 cells. This is a novel concept and whilst the availability of IL-2 and the control of IL-2 signalling is generally thought to play a role in the capacity of vitamin D to modulate both effector and especially regulatory T cell populations, this study provides new insights.

Weaknesses:<br /> Ultimately the data are associative, nevertheless this study makes an important and innovative contribution to our understanding of the mechanism whereby vitamin D may beneficially control immune/inflammatory disease, specifically Th2 driven allergic airway inflammation. Future work advancing these studies, including in humans, are awaited with interest.

Wider impact: Maternal 17q21 genotype has an important influence on the protective effects of high dose vitamin D3 supplementation in pregnancy against the development of asthma/recurrent wheeze in her offspring. The current study provides exciting mechanistic data that may underpin this important observation.

Reviewer #2 (Public Review):

This manuscript explores the mechanism underlying the accumulation of phytosphingosine (PHS) and its role in initiating vacuole fission. The study posits the involvement of membrane contact sites (MCSs) in two key stages of this process. Firstly, MCSs tethered by tricalbin between the endoplasmic reticulum (ER) and the plasma membrane (PM) or Golgi regulate the intracellular levels of PHS. Secondly, the amassed PHS triggers vacuole fission, most likely through the nuclear-vacuolar junction (NVJ). The authors propose that MCSs play a regulatory role in vacuole morphology via sphingolipid metabolism.

While some results in the manuscript are intriguing, certain broad conclusions occasionally surpass the available data. Despite the authors' efforts to enhance the manuscript, certain aspects remain unclear. It is still uncertain whether subtle changes in PHS levels could induce such effects on vacuolar fission. Additionally, it is regrettable that the lipid measurements are not comparable with previous studies by the authors. Future advancements in methods for determining intracellular lipid transport and levels are anticipated to shed light on the remaining uncertainties in this study.

Reviewer #2 (Public Review):

Summary:<br /> The aster, consisting of microtubules, plays important roles in spindle positioning and the determination of the cleavage site in animals. The mechanics of aster movement and positioning have been extensively studied in several cell types. However, there is no unified biophysical model, as different mechanisms appear to predominate in different model systems. In the present manuscript, the authors studied aster positioning mechanics in the Drosophila syncytial embryo, in which short-ranged aster repulsion generates a separation force. Taking advantage of the ex vivo system developed by the group and the fly gnu mutant, in which the nuclear number can be minimized, the authors performed time-lapse observations of single asters and multiple asters in the explant. The observed aster dynamics were interpreted by building a mathematical model dealing with forces. They found that aster dissociation from the boundary depends on the microtubule pushing force. Additionally, laser ablation targeting two separating asters showed that aster-aster separation is also mediated by the microtubule pushing force. Furthermore, they built a simulation model based on the experimental results, which reproduced aster movement in the explant under various conditions. Notably, the actual aster dynamics were best reproduced in the model by including a short-ranged inhibitory term when asters are close to the boundary or each other.

Strengths:<br /> This study reveals a unique aster positioning mechanics in the syncytial embryo explant, which leads to an understanding of the mechanism underlying the positioning of multiple asters associated with nuclei in the embryo. The use of explants enabled accurate measurement of aster motility and, therefore, the construction of a quantitative model. This is a notable achievement.

Weaknesses:<br /> The main conclusion that aster repulsion predominates in this system has already been drawn by the same authors in their recent study (de-Carvalho et al., Development, 2022). Therefore, the conceptual advance in the current study is marginal. The molecular mechanisms underlying aster repulsion remain unexplored since the authors were unable to identify specific factor(s) responsible for aster repulsion in the explant.

Specific suggestions on the original manuscript:<br /> Microtubules should be visualized more clearly (either in live or fixed samples). This is particularly important in Figure 4E and Video 4 (laser ablation experiment to create asymmetric asters).

Comments on the revised manuscript:<br /> Despite my suggestion, the authors did not provide evidence confirming the actual ablation of microtubules in the specified target region. The authors argue, "Given our controls and previous experience, we are confident we are ablating the microtubules." Then, at the very least, the authors should describe (in Materials and Methods) the "controls" they employed and provide a citation to the previous study where proper ablation was validated using the same laser settings. Otherwise, readers might not be convinced of the authors' claim.

Reviewer #2 (Public Review):

This manuscript describes an adaptive laboratory evolution (ALE) study with a previously constructed genome-reduced E. coli. The growth performance of the end-point lineages evolved in M63 medium was comparable to the full-length wild-type level at lower cell densities. Subsequent mutation profiling and RNA-Seq analysis revealed many changes in the genome and transcriptomes of the evolved lineages. The authors did a great deal of analyzing the patterns of evolutionary changes between independent lineages, such as the chromosomal periodicity of transcriptomes, pathway enrichment analysis, weight gene co-expression analysis, and so on. They observed a striking diversity in the molecular characteristics amongst the evolved lineages, which, as they suggest, reflect divergent evolutionary strategies adopted by the genome-reduced organism.

As for the overall quality of the manuscript, I am rather torn. The manuscript leans towards elaborating observed findings, rather than explaining their biological significance. For this reason, readers are left with more questions than answers. For example, fitness assay on reconstituted (single and combinatorial) mutants was not performed, nor was any supporting evidence on the proposed contributions of each mutant provided. This leaves the nature of mutations - be they beneficial, neutral, or deleterious, the presence of epistatic interactions, and the magnitude of fitness contribution, largely elusive. Also, it is difficult to tell whether the RNA-Seq analysis in this study managed to draw biologically meaningful conclusions or instill insight into the nature of genome-reduced bacteria. The analysis primarily highlighted the differences in transcriptome profiles among each lineage based on metrics such as 'DEG counts' and the 'GO enrichment'. However, I could not see any specific implications regarding the biology of the evolved minimal genome drawn. In their concluding remark, 'Multiple evolutionary paths for the reduced genome to improve growth fitness were likely all roads leading to Rome,' the authors observed the first half of the sentence, but the distinctive characteristics of 'all roads' or 'evolutionary paths', which I think should have been the key aspect in this investigation, remains elusive.

Reviewer #2 (Public Review):

Summary:

Sang-Hyeon et al. laid out a compelling rationale to explore the role of the SMN protein in mesenchymal cells, to determine whether SMN deficiency there could be a pathologic mechanism of SMA. They crossed Smnf7/f7 mice with Prrx1Cre mice to produce SmnΔMPC mice where exon 7 was specifically deleted and thus SMN protein was eliminated in limb mesenchymal progenitor cells (MPCs). To demonstrate gene dosage-dependence of phenotypes, SmnΔMPC mice were crossed with transgenic mice expressing human SMN2 to produce SmnΔMPC mice with different copies of SMN2 (0, 1, or 2). The paper provides genetic evidence that SMN in mesenchymal cells regulates the development of bones and neuromuscular junctions. Genetic data were convincing and revealed novel functions of SMN.

Strengths:

Overall, the paper provided genetic evidence that SMN deficiency in mesenchymal cells caused abnormalities in bones and NMJs, revealing novel functions of SMN and leading to future experiments. As far as genetics is concerned, the data were convincing (except for the rescue experiment, see below); the conclusions are important.

Weaknesses:

The paper seemed to be descriptive in nature and could be improved with more experiments to investigate underlying mechanisms. In addition, some data appeared to be contradicting or difficult to explain. The rescue data were not convincing.

Reviewer #2 (Public Review):

Summary<br /> This study examines the construct of "cognitive spaces" as they relate to neural coding schemes present in response conflict tasks. The authors use a novel experimental design in which different types of response conflict (spatial Stroop, Simon) are parametrically manipulated. These conflict types are hypothesized to be encoded jointly, within an abstract "cognitive space", in which distances between task conditions depend only on the similarity of conflict types (i.e., where conditions with similar relative proportions of spatial-Stroop versus Simon conflicts are represented with similar activity patterns). Authors contrast such a representational scheme for conflict with several other conceptually distinct schemes, including a domain-general, domain-specific, and two task-specific schemes. The authors conduct a behavioral and fMRI study to test whether prefrontal cortex activity is correlated to one of these coding schemes. Replicating the authors' prior work, this study demonstrates that sequential behavioral adjustments (the congruency sequence effect) are modulated as a function of the similarity between conflict types. In fMRI data, univariate analyses identified activation in left prefrontal and dorsomedial frontal cortex that was modulated by the amount of Stroop or Simon conflict present, and representational similarity analyses that identified coding of conflict similarity, as predicted under the cognitive space model, in right lateral prefrontal cortex.

Strengths

This study addresses an important question regarding how conflict or difficulty might be encoded in the brain within a computationally efficient representational format. Relative to the other models reported in the paper, the evidence in support of the cognitive space model is solid. The ideas postulated by the authors are interesting and valuable ones, worthy of follow-up work that provides additional necessary scrutiny of the cognitive-space account.

Weaknesses

Future, within-subject experiments will be necessary to disentangle the cognitive space model from confounded task variables. A between-subjects manipulation of stimulus orientation/location renders the results difficult to interpret, as the source and spatial scale of the conflict encoding on cortex may differ from more rigorous (and more typical) within-subject manipulations.

Results are also difficult to interpret because Stroop and Simon conflict are confounded with each other. For interpretability, these two sources of conflict need to be manipulated orthogonally, so that each source of conflict (as well as their interaction) could be separately estimated and compared in terms of neural encoding. For example, it is therefore not clear whether the RSA results are due to encoding of only one type of conflict (Stroop or Simon), to a combination of both, and/or to interactive effects.

Finally, the motivation for the use of the term "cognitive space" to describe results is unclear. Evidence for the mere presence of a graded/parametric neural encoding (i.e., the reported conflict RSA effects) would not seem to be sufficient. Indeed, it is discussed in the manuscript that cognitive spaces/maps allow for flexibility through inference and generalization. Future work should therefore focus on linking neural conflict encoding to inference and generalization more directly.

Reviewer #2 (Public Review):

Summary:

In this manuscript, "KinCytE- a Kinase to Cytokine Explorer to Identify Molecular Regulators and Potential Therapeutic", the authors present a web resource, KinCytE, that lets researchers search for kinase inhibitors that have been shown to affect cytokine and chemokine release and signaling networks. I think it's a valuable resource that has a lot of potential and could be very useful in deciding on statistical analysis that might precede lab experiments.

Opportunities:

With the release of the manuscript and the code base in place, I hope the authors continue to build upon the platform, perhaps by increasing the number of cell types that are probed (beyond macrophages). Additionally, when new drug-response data becomes available, perhaps it can be used to further validate the findings. Overall, I see this as a great project that can evolve.

Strengths:

The site contains valuable content, and the structure is such that growing that content should be possible.

Weaknesses:

Only based on macrophage experiments, would be nice to have other cell types investigated, but I'm sure that will be remedied with some time.

Reviewer #2 (Public Review):

Summary:<br /> This manuscript describes the analysis of blood transcriptomic data from patients with TB meningitis, with and without HIV infection, with some comparison to those of patients with pulmonary tuberculosis and healthy volunteers. The objectives were to describe the comparative biological differences represented by the blood transcriptome in TBM associated with HIV co-infection or survival/mortality outcomes and to identify a blood transcriptional signature to predict these outcomes. The authors report an association between mortality and increased levels of acute inflammation and neutrophil activation, but decreased levels of adaptive immunity and T/B cell activation. They propose a 4-gene prognostic signature to predict mortality.

Strengths:<br /> -Biological evaluations of blood transcriptomes in TB meningitis and their relationship to outcomes have not been extensively reported previously.<br /> -The size of the data set is a major strength and is likely to be used extensively for secondary analyses in this field of research.

Weaknesses:<br /> The bioinformatic analysis is limited to a descriptive narrative of gene-level functional annotations curated in GO and KEGG databases. This analysis can not be used to make causal inferences. In addition, the functional annotations are limited to 'high-level' terms that fail to define biology very precisely. At best, they require independent validation for a given context. As a result, the conclusions are not adequately substantiated. The identification of a prognostic blood transcriptomic signature uses an unusual discovery approach that leverages weighted gene network analysis that underpins the bioinformatic analyses. However, the main problem is that authors seem to use all the data for discovery and do not undertake any true external validation of their gene signature. As a result, the proposed gene signature is likely to be overfitted to these data and not generalisable. Even this does not achieve significantly better prognostic discrimination than the existing clinical scoring.

Reviewer #2 (Public Review):

Summary:<br /> 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:<br /> The strengths of the manuscript are that the article addresses a relevant research question that 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:<br /> 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.

Major comments:<br /> My main concern about the manuscript is the extent of both clinical and statistical heterogeneity, which complicates the interpretation of the results. I don't understand some of the antibiotic comparisons that are included in the systematic review. For instance the study by Paul et al (50), where vancomycin (as monotherapy) is compared to co-trimoxazole (as combination therapy). Emergence (or selection) of co-trimoxazole in S. aureus is in itself much more common than vancomycin resistance. It is logical and expected to have more resistance in the co-trimoxazole group compared to the vancomycin group, however, this difference is due to the drug itself and not due to co-trimoxazole being a combination therapy. It is therefore unfair to attribute the difference in resistance to combination therapy. Another example is the study by Walsh (71) where rifampin + novobiocin is compared to rifampin + co-trimoxazole. There is more emergence of resistance in the rifampin + co-trimoxazole group but this could be attributed to novobiocin being a different type of antibiotic than co-trimoxazole instead of the difference being attributed to combination therapy. To improve interpretation and reduce heterogeneity my suggestion would be to limit the primary analyses to regimens where the antibiotics compared are the same but in one group one or more antibiotic(s) are added (i.e. A versus A+B). The other analyses are problematic in their interpretation and should be clearly labeled as secondary and their interpretation discussed.

Another concern is about the definition of acquisition of resistance, which is unclear to me. If for example meropenem is administered and the follow-up cultures show Enterococcus species (which is intrinsically resistant to meropenem), does this constitute acquisition of resistance? If so, it would be misleading to determine this as an acquisition of resistance, as many people are colonized with Enterococci and selection of Enterococci under therapy is very common. If this is not considered as the acquisition of resistance please include how the acquisition of resistance is defined per included study. Table S1 is not sufficiently clear because it often only contains how susceptibility testing was done but not which antibiotics were tested and how a strain was classified as resistant or susceptible.

Line 85: "Even though within-patient antibiotic resistance development is rare, it may contribute to the emergence and spread of resistance."<br /> Depending on the bug-drug combination, there is great variation in the propensity to develop within-patient antibiotic resistance. For example: within-patient development of ciprofloxacin resistance in Pseudomonas is fairly common while within-patient development of methicillin resistance in S. aureus is rare. Based on these differences, large clinical heterogeneity is expected and it is questionable where these studies should be pooled.

Line 114: "The overall pooled OR for acquisition of resistance comparing a lower number of antibiotics versus a higher one was 1.23 (95% CI 0.68 - 2.25), with substantial heterogeneity between studies (I2=77.4%)"<br /> What consequential measures did the authors take after determining this high heterogeneity? Did they explore the source of this large heterogeneity? Considering this large heterogeneity, do the authors consider it appropriate to pool these studies?

Reviewer #2 (Public Review):

Summary:

This manuscript highlights very important findings in the field, especially in designing clinical trials for the evaluation of antivirals.

Strengths:

The study shows significant differences between the kinetics of viral loads between serotypes, which is very interesting and should be taken into account when designing trials for antivirals.

Weaknesses:

The kinetics of the viral loads based on disease severity throughout the illness are not described, and it would be important if this could be analyzed.

Reviewer #2 (Public Review):

The manuscript by Ma et al. tries to develop a protocol for cell-based meat production using chicken fibroblasts as three-dimensional (3D) muscle tissues with fat accumulation. The authors used genetically modified fibroblasts which can be forced to differentiate into muscle cells and formulated 3D tissues with these cells and a biphasic material (hydrogel). The degrees of muscle differentiation and lipid deposition in culture were determined by immunohistochemical, biochemical, and molecular biological evaluations. Notably, the protocol successfully achieved the process of myogenic and lipogenic stimulation in the 3D tissues.

Overall, the study is reasonably designed and performed including adequate analysis. The manuscript is clearly written with well-supported figures. While it presents valuable results in the field of cultivated meat science and skeletal muscle biology, some critical concerns were identified. First, it is unclear whether some technical approaches were really the best choice for cell-based meat production. Next, more careful evaluations and justifications would be required to properly explain biological events in the results. These points include additional evaluations and considerations with regard to myocyte alignment and lipid accumulation in the differentiated 3D tissues. The present data are very suggestive in general, but further clarifications and arguments would properly support the findings and conclusions.

Reviewer #2 (Public Review):

Manassaro et al. present an extensive three-session study in which they aimed to change defensive responses (skin conductance; SCR) to an aversively conditioned stimulus by targeting medial prefrontal cortex (their words) using repetitive TMS prior to retrieval. They report that stimulating mPFC using TMS abolishes SCR responses to the conditioned stimulus, and that this effect is specific for the stimulated region and the specific CS-US association, given that SCR responses to a different modality US are not changed.

I like how the authors have clearly attempted to control for several potential confounds by including multiple stimulation sites, measured SCR responses to several unconditioned stimuli, and applied the experiment in multiple contexts. However, several conceptual and practical issues remain that I think limit the value of potential conclusions drawn from this work.

The first issue that I have with this study concerns the relationship between the TMS manipulation and the theoretical background the authors present in their rationale. In the introduction the authors sketch that what they call 'mPFC' is involved in regulation of threat responses. They make a convincing case, however, almost all of the evidence they present concerns the ventromedial part of the prefrontal cortex (refs 18-25). The authors then mention that no one has ever studied the effects of 'mPFC'-TMS on threat memories. That is not surprising given that stimulating vmPFC with TMS is very difficult, if not impossible. Simulation of the electrical field that develops as a consequence from the authors manipulation (using the same TMS coil and positioning the authors use) shows that vmPFC (or mPFC for that matter) is not stimulated. The authors then continue in the methods section stating that the region they aimed for was BA10. This region they presumably do stimulate, however, that does not follow logically from their argument. BA10 is anatomically, cytoarchitectonically and functionally a wholly different area than vmPFC and I wonder if their rationale would hold given that they stimulate BA10.

The second concern I have is that although I think the authors should be praised for including both sham and active control regions, the controls might not be optimally chosen to control for the potential confounds of their condition of interest (mPFC-TMS). Namely, TMS on the forehead can be unpleasant, if not painful, whereas sham-TMS or TMS applied to the back of the head or even over dlPFC is not (or less so at the very least). Given that the SCR results after mPFC TMS show exactly the same temporal pattern as the sham-TMS but with a lower starting point, one could wonder whether a painful stimulation prior to the retrieval might have already caused habituation to painful stimulation observed in SCR in consequent CS presentations. A control region that would have been more obvious to take is the lateral part of BA10, by moving the TMS coil several centimeters to the left or right, circumventing all things potentially called medial but giving similar unpleasant sensations (pain etc).

My final concern is that the main analyses are performed on single trials of SCR responses, which is a relatively noise measure to use on single trials. This is also done in relatively small groups (n=21). I would have liked to see both the raw or at least averaged timeseries SCR data plotted, and a rationale explaining how the authors decided on the current sample sizes, if that was based on a power analyses one must have expected quite strong effects.

Reviewer #2 (Public Review):

This study applies a new neuromodulation algorithm, adaptive delayed feedback control (aDFC) to in vitro and in silico neuron populations to demonstrate its effectiveness at desynchronizing synchronous neural population activity. The study compares aDFC to other neuromodulation approaches such as non-adaptive DFC and random stimulation and demonstrates that in a subset of controllable networks, aDFC succeeds in reducing overall synchrony in the neural population. Further, when characterizing population firing bouts as asynchronous versus synchronous, aDFC increased the fraction of time that the neural population was in the asynchronous versus synchronous state (albeit in one network). Overall, this study is an impressive combination of computational and experimental work that details a promising new adaptive neuromodulation algorithm that may be relevant for neurological disorders where excessive synchronous brain activity is currently treated with conventional open-loop DBS.

Strengths: The authors build on existing work that has suggested DFC may be a viable algorithm for desynchronizing hyper-synchronous neural populations. They demonstrate by performing in vivo experiments that, contrary to the suggestions of previous work, DFC exacerbates oscillatory intensity. As a result, they develop a new adaptive DFC (aDFC) that updates the estimate of the population's periodicity, enabling superior desynchronization of the population. Further, aDFC enables more population spiking activity that is not just a response to the stimulation (Fig. S3), potentially making the approach conducive to reducing excessive synchronization while also being permissive to neural encoding.

Another innovation of this study is developing a framework for detecting which neural populations are controllable vs. uncontrollable, i.e. consistently responsive to stimulation vs. not consistently responsive. The authors find that populations with intermediate levels of synchrony and firing rate are controllable, whereas populations outside this regime are uncontrollable. These findings are substantiated with a neural network model, where a controllable regime is also detected. The controllable subspace in the in vivo networks and in silico networks also appear to roughly correspond (intermediate synchrony and firing rates) though a direct comparison is not made.

Finally, not only do the authors find that aDFC reduces synchrony, they further identify extended periods of time when the network is in an asynchronous state and find that aDFC can extend the amount of time that the network spends in this state. While these results are compelling, there is only a single network that is able to demonstrate this effect so it is unclear how general a property this is.

Overall, the study presents a novel closed loop neuromodulation algorithm and presents compelling data demonstrating that the algorithm reduces synchrony in in vitro and in silico neural populations.

Weaknesses: The authors point out Parkinson's disease, essential tremor, epilepsy, and dystonia as the neurological disorders that suffer from excessive neural synchronization. In two of these disorders the frequency of the neural synchronization is ~15-30 Hz (Parkinson's disease) and ~5-7 Hz (essential tremor). These frequencies are well above the ~1 Hz synchronization frequency observed in the in vitro population. While this study exhibits a nice proof of principle, how readily it would extend to populations that exhibit higher synchronization frequencies is unclear.

In addition, the study relies on computing population spiking activity of neurons. Current closed-loop neuromodulation devices are outfitted with large electrodes that can sense local field potentials. The impact of this study would have been higher and more readily translatable if the authors could have detected neural population synchronization using local field potential features.

Finally, since the authors were seeking to develop a closed-loop neuromodulation solution that exhibited an improvement over existing open-loop solutions, it would have strengthened the findings and relevance of this study to have done comparisons between aDFC and high frequency open-loop stimulation (~100-120 Hz). Without this comparison it is difficult to know how aDFC may differ from existing therapeutics.

Reviewer #2 (Public Review):

The manuscript addresses the role of TEAD1 in developmental myelination and nerve regeneration after nerve injury and establishes TEAD1 as a key component for YAP/TAZ-related Schwann cell biology. The authors use genetic and biochemical techniques, as well as immunostainings of tissues to address TEAD1's function in myelin biology. While the constitutive knockout of TEAD1 is convincing, the tamoxifen-induced variation requires some validation. Experimental procedures to study the effect of TEAD1 on myelin development and regeneration were properly performed. TEAD1 is believed to be the major driver of the TEAD family in regulating myelination in Schwann cells. However, the delineation of TEAD1 in myelin biology from the other TEAD family members TEAD2, 3, and 4 needs further verification. In particular, the biochemical techniques assessing the potentially competitive binding of TEAD1 versus TEAD2, 3, and 4 to YAP1 and TAZ (WWTR1) require a thorough functional validation. Overall, the identification of TEAD1 as the major driver of myelin in development and regeneration is a very important finding for Schwann cell biology.

Reviewer #3 (Public Review):

Reactive oxygen species (ROS) have been previously shown to regulate glutamate receptor phosphorylation, long-distance transport, and delivery of glutamate receptors to synapses, however, the source of ROS is unclear. In this study, the authors test if mitochondria act as a signaling hub and produce ROS in response to neuronal activity in order to regulate glutamate receptor trafficking. The authors use a variety of optogenetic tools including the calcium reporter mitoGCaMP and the ROS reporter mito-roGFP to monitor changes in calcium and ROS, respectively, in mitochondria after activating neurons with ChRimson in the genetic model organism C. elegans. Repeated stimulation of interneurons called AVA with ChRimson leads to increased calcium uptake into mitochondria in dendrites and increased mitochondrial ROS production. The mitochondrial calcium uniporter mcu-1 is required for these effects because mcu-1 genetic loss of function or treatment with Ru360, a drug that inhibits mcu-1, inhibits the uptake of calcium into mitochondria and ROS production after neuronal activation. Mcu-1 genetic loss of function is correlated with an increase in exocytosis of glutamate receptors but a decrease in glutamate receptor transport and delivery to dendrites. This study suggests that mitochondria monitor neuronal activity by taking up calcium and downregulating glutamate receptor trafficking via ROS, as a means to negatively regulate excitatory synapse function.

Strengths<br /> -The use of multiple optogenetic tools and approaches to monitor mitochondrial calcium, reactive oxygen species, and glutamate receptor trafficking in live organisms.<br /> -Identifying a novel signaling role for dendritic mitochondria which is to monitor neuronal activity (via calcium uptake into mitochondria) and generate a signal (reactive oxygen species) that regulates glutamate receptors at synapses.

Weaknesses<br /> -Although the use of KillerRed to generate ROS downstream of mcu-1 is a clever approach, the fact that activation of KillerRed results in reduced GLR-1 exocytosis, delivery, and transport raises the concern that KillerRed is generating a high level or ROS that might be toxic to cellular processes. Experiments showing that other cellular processes are not affected by KillerRed activation and testing if reduced ROS production mimics the effects of blocking mcu-1 would strengthen the conclusions in this study.

Reviewer #2 (Public Review):

Payne et al. use a computational approach to predict the sites and directions of plasticity within the vestibular cerebellum that explain an unresolved controversy regarding the basis of VOR learning. Specifically, the conclusion by Miles and Lisberger (1981) that vestibular inputs onto Purkinje cells (PCs) must potentiate, rather than depress (as in the Marr/Albus/Ito model), following gain-increase learning because when the VOR is cancelled, PC firing increases rather than decreases. Payne et al. provide a novel model solution that recapitulates the results of Miles and Lisberger but, paradoxically, uses plasticity in the cerebellar cortex that weakens PC output rather than strengthens it. However, the model only succeeds when efference copy feedback to the cerebellar cortex is relatively weak thereby allowing a second feedback pathway to drive PC activity during VOR cancellation to counteract the learned change in gain. Because the model is biologically constrained, the findings are well supported. This work will likely benefit the field by providing a number of potentially experimentally testable conclusions. The findings will be of interest to a wider audience if the results can be extrapolated to other cerebellar-dependent learning behaviors rather then just VOR gain-increase learning. Overall, the manuscript is very well written with clearly delineated results and conclusions.

Reviewer #2 (Public Review):

Summary: The proper expression and organization of CaV channels at the presynaptic release sites are subject to coordinative and redundant control of many active zone specific molecules including RIM-BPs. Previous studies have demonstrated that ablation of RIM-BPs in various mammalian synapses causes significant impairment of synaptic transmission, either by reducing CaV expression or decoupling CaV from synaptic vesicles. The mechanisms remain unknown.

In the manuscript, Sakaba and colleagues aimed to examine the specific role of RIM-BP2 at the hippocampal mossy fiber-CA3 pyramidal cell synapse, which is well-characterized by low initial release probability and strong facilitation during repetitive stimulation. By directly recording Ca2+ currents and capacitance jumps from the MF boutons, which is very challenging but feasible, they showed that depolarization-evoked Ca2+ influx was reduced significantly (~39%) by KO of RIM-BP2, but no impacts on Ca-induced exocytosis and RRP (measured by capacitance change). They used STED microscopy to image the spatial distribution of CaV2.1 cluster but found no change in the cluster number with slight decrease in cluster intensity (~20%). They concluded that RIM-BP2 function in tonic synapses by reducing CaV expression and thus differentially from phasic synpases by decoupling CaV-SV.

In general, they provide solid data showing that RIM-BP2 KO reduces Ca influx at MF-CA3 synapse, but the phenotype is not new as Moser and colleagues have also used presynaptic recording and capacitance measurement and shown that RIM-BP2 KO reduces Ca2+ influx at hair cell active zone (Krinner et al., 2017), although at different synapse model expressing CaV1.3 instead of CaV2.1. Further, the concept that RIM-BP2 plays diverse functions in transmitter release at different central synapses has also been proposed with solid evidence (Brockmann et al., 2019).

Reviewer #3 (Public Review):

Summary:

The receptor tyrosine kinase Anaplastic Lymphoma Kinase (ALK) in humans is nervous system expressed and plays an important role as an oncogene. A number of groups have been studying ALK signalling in flies to gain mechanistic insight into its various roles. In flies, ALK plays a critical role in development, particularly embryonic development and axon targeting. In addition, ALK also was also shown to regulate adult functions including sleep and memory. In this manuscript, Sukumar et al., used a suite of molecular techniques to identify downstream targets of ALK signalling. They first used targeted DamID, a technique that involves a DNA methylase to RNA polymerase II, so that GATC sites in close proximity to PolII binding sites are marked. They performed these experiments in wild type and ALK loss of function mutants (using an Alk dominant negative ALkDN), to identify Alk responsive loci. Comparing these loci with a larval single cell RNAseq dataset identified neuroendocrine cells as an important site of Alk action. They further combined these TaDa hits with data from RNA seq in Alk Loss and Gain of Function manipulations to identify a single novel target of Alk signalling - a neuropeptide precursor they named Sparkly (Spar) for its expression pattern. They generated a mutant allele of Spar, raised an antibody against Spar, and characterised its expression pattern and mutant behavioural phenotypes including defects in sleep and circadian function.

Strengths:

The molecular biology experiments using TaDa and RNAseq were elegant and very convincing. The authors identified a novel gene they named Spar. They also generated a mutant allele of Spar (using CrisprCas technology) and raised an antibody against Spar. These experiments are lovely, and the reagents will be useful to the community. The paper is also well written, and the figures are very nicely laid out making the manuscript a pleasure to read.

Weaknesses:

The manuscript has improved substantially in the revision. Yet, some concerns remain around the genetics and behavioural analysis which is incomplete and confusing. The authors generated a novel allele of Spar - Spar ΔExon1 and examined sleep and circadian phenotypes of this allele and of RNAi knockdown of Spar. The RNAi knockdown is a welcome addition. However, the authors only show one parental control the GAL4 / +, but leave out the other parental control i.e. the UAS RNAi / + e.g. in Fig. 9. It is important to show both parental controls.

Further, the sleep and circadian characterisation could be substantially improved. It is unclear how sleep was calculated - what program was used or what the criteria to define a sleep bout was. In the legend for Fig 8c, it says sleep was shown as "percentage of time flies spend sleeping measured every 5min across a 24h time span". Sleep in flies is (usually) defined as at least 5 min of inactivity. With this definition, I'm not sure how one can calculate the % time asleep in a 5 min bin! Typically people use 30min or 60min bins. The sleep numbers for controls also seem off to me e.g. in Fig. 8H and H' average sleep / day is ~100. Is this minutes of sleep? 100 min / day is far too low, is it a typo? The same applies to Figure 8, figure supplement 2. Other places e.g. Fig 8 figure supplement 1, avg sleep is around 1000 min / day. The numbers for sleep bouts are also too low to me e.g. in Fig 9 number of sleep bouts avg around 4, and in Fig. 8 figure supplement 2 they average 1 sleep bout. There are several free software packages to analyse sleep data (e.g. Sleep Mat, PMID 35998317, or SCAMP). I would recommend that the authors reanalyse their data using one of these standard packages that are used routinely in the field. That should help resolve many issues.

The circadian anticipatory activity analyses could also be improved. The standard in the field is to perform eduction analyses and quantify anticipatory activity e.g. using the method of Harrisingh et al. (PMID: 18003827). This typically computed as the ratio of activity in the 3hrs preceding light transition to activity in the 6hrs preceding light transition. The programs referenced above should help with this.

Finally, in many cases I'm not sure that the appropriate statistical tests have been used e.g. in Fig 8c, 8e, 8h t-tests have been used when are three groups in the figure. The appropriate test here would an ANOVA, followed by post-hoc comparisons.

Reviewer #2 (Public Review):

The authors presented a well-written manuscript describing the comparison of active-learning methods with state-of-art methods for several datasets of pharmaceutical interest. This is a very important topic since active learning is similar to a cyclic drug design campaign such as testing compounds followed by designing new ones which could be used to further tests and a new design cycle and so on. The experimental design is comprehensive and adequate for proposed comparisons.

1) Text in figures still very small and difficult to read. Please redraw the figures increasing the font size: 10-12pt is ideal in comparison with the main text. In my opinion, it seems like the authors drew the Figure properly but there is an automatic resizing by inserting it in the document. Please consider ensuring that the font size will remain legible in the final document.

2) I think this work will benefit from a comparison of obtained models to other models reported in the literature and the interpretability of models (e.g. contribution of molecule groups to the modeled activity) as it is required by OECD guide for QSAR purposes.

Reviewer #3 (Public Review):

Zhang and Lauder characterized both aerobic and anaerobic metabolic energy contributions in schools and solitary fishes in the Giant danio (Devario aequipinnatus) over a wide range of water velocities. By using a highly sophisticated respirometer system, the authors measure the aerobic metabolisms by oxygen uptake rate and the non-aerobic oxygen cost as excess post-exercise oxygen consumption (EPOC). With these data, the authors model the bioenergetic cost of schools and solitary fishes. The authors found that fish schools have a J-shaped metabolism-speed curve, with reduced total energy expenditure per tail beat compared to solitary fish. Fish in schools also recovered from exercise faster than solitary fish. Finally, the authors conclude that these energetic savings may underlie the prevalence of coordinated group locomotion in fish.

The conclusions of this paper are mostly well supported by data.

Reviewer #2 (Public Review):

Summary:<br /> In this study, human induced pluripotent stem cell (hiPSC)-derived liver progenitor cell organoids were transplanted into four different transplantation sites in a mouse model of liver disease, using five organoid delivery methods. Organoids were transplanted into the vascularised chamber device established in the groin, or into the liver, spleen, and subcutaneous fat. Results show that the vascularised chamber had the highest organoid survival, 5.1x higher than the site with the second highest survival (p=0.0002), being the intra-hepatic scaffold approach. Animals with the vascularised chamber also had the highest human albumin levels (0.33 {plus minus} 0.09 ng/mL). No organoid survival was observed when delivered into the liver without a scaffold, or when injected into the spleen. Meager survival occurred in transplantations into subcutaneous fat.

Strengths:<br /> A systematic study with a clear line of experiments and well-presented results. The manuscript is well-written and easy to follow. The results and conclusions drawn are convincing.

Weaknesses:<br /> Although the number of organoids and albumin secretion is visibly higher in the vascularised chamber device, the organoids possess relatively higher Sox9+ cells compared to HNFa4a+ cells suggesting higher biliary differentiation than hepatic differentiation. On the other hand, although the intrahepatic scaffold approach, with a relatively smaller number of organoids and less albumin secretion, showed higher hepatic differentiation (although non-significant) suggesting that better scaffolds could be researched further to assess the clinical application of intrahepatic scaffold-based organoid transplantation.

Reviewer #2 (Public Review):

Summary:<br /> This paper described the role of BRCT repeat 5 in TOPBP1, a DNA damage response protein, in the maintenance of meiotic sex chromosome inactivation (MSCI). By analyzing a Topbp1 mutant mouse with amino acid substitutions in BRCT repeat 5, the authors found reduced phosphorylation of a DNA/RNA helicase, Sentaxin, and decreased localization of the protein to the X-Y sex body in pachynema. Moreover, the authors also found decreased repression of several genes on the sex chromosomes in the male mice.

Strengths:<br /> The works including phospho-proteomics and single-cell RNA sequencing with lots of data have been done with great care and most of the results are convincing.

Weaknesses:<br /> No weakness.

Reviewer #2 (Public Review):

In this manuscript, Libert et al. develop a model to predict an individual's age using physiological traits from multiple organ systems. The difference between the predicted biological age and the chronological age -- ∆Age, has an effect equivalent to that of a chronological year on Gompertz mortality risk. By conducting GWAS on ∆Age, the authors identify genetic factors that affect aging and distinguish those associated with age-related diseases. The study also uncovers environmental factors and employs dropout analysis to identify potential biomarkers and drivers for ∆Age. This research not only reveals new factors potentially affecting aging but also shows promise for evaluating therapeutics aimed at prolonging a healthy lifespan. This work represents a significant advancement in data-driven understanding of aging and provides new insights into human aging. Addressing the points raised would enhance its scientific validity and broaden its implications.

Major points:

1. Enhance the description and clarity of model evaluation.

The manuscript requires additional details regarding the model's evaluation. The authors have stated "To develop a model that predicts age, we experimented with several algorithms, including simple linear regression, Gradient Boosting Machine (GBM) and Partial Least Squares regression (PLS). The outcomes of these approaches were almost identical". It is currently unclear whether the 'almost identical outcomes' mentioned refer to the similarity in top contribution phenotypes, the accuracy of age prediction, or both. To resolve this ambiguity, it would be beneficial to include specific results and comparisons from each of these models.

Furthermore, the authors mention "to test for overfitting, a PLS model had been generated on randomly selected 90% of individuals and tested on the remaining 10% with similar results". To comprehensively assess the model's performance, it is crucial to provide detailed results for both the test and validation datasets. This should at least include metrics such as correlation coefficients and mean squared error for both training and test datasets.

2. External validation and generalization of results

To enhance the robustness and generalizability of the study's findings, it is crucial to perform external validation using an independent population. Specifically, conducting validation with the participants of the 'All of Us' research program offers a unique opportunity. This diverse and extensive cohort, distinct from the initial study group, will serve as an independent validation set, providing insights into the applicability of the study's conclusions across varied demographics.

Reviewer #2 (Public Review):

Kádková, Murach, Pedersen, and colleagues studied how three disease-causing missense mutations in SNAP25 affect synaptic vesicle exocytosis. These mutations have previously been studied by Alten et al., 2021. The authors observed similar impairments in spontaneous and evoked release as Alten et al., 2021, but the measurement of readily releasable pool (RRP) size differed between the two studies. The authors found that the V48F and D166Y mutations affect the interaction with the Ca2+ sensor synaptotagmin-1 (Syt1), but do not entirely phenocopy Syt1 loss-of-function because they also exhibit a gain-of-function. Thus, these mutations affect multiple aspects of the energy landscape for vesicle priming and fusion. The I67N mutation specifically increases the fusion energy barrier without affecting upstream vesicle priming.

The strength of the study includes careful and technically excellent dissection of the synaptic release process and a combination of electrophysiology, biophysics, and modeling approaches. This study gained a deeper mechanistic understanding of these mutations in vesicle exocytosis than the previous study but did not result in a paradigm shift in our understanding of SNAP25-associated encephalopathy because the same spontaneous and evoked release phenotypes were previously identified.

Comments on revised version:

The authors fully addressed the two previous technical concerns and improved the introduction of the paper.

Reviewer #2 (Public Review):

Summary:<br /> In the paper "Inter-regional Delays Fluctuate in the Human Cerebral Cortex," the authors aim to investigate how global changes in the power of brain oscillations affect the latency and strength of cortico-cortical couplings. They measured changes in brain oscillations and inter-regional couplings using human intracranial recordings. Additionally, the authors employed oscillator models to elucidate their empirical findings.

Strengths:<br /> The authors tested their hypotheses using human intracranial data, which provides a direct measurement of brain activity with high spatial and temporal resolution. This offers a unique insight into the interplay between oscillatory power and inter-regional coupling in the human brain.

Weaknesses:<br /> The authors had access to only a subset of brain regions. Although this limitation is common in many intracranial studies, their discussion of global changes in brain oscillations is impacted by the lack of whole-brain coverage, and thus the global nature of these oscillations should be interpreted with caution.

The description of the analysis procedure is not always clear.

Summary of main concerns:<br /> My primary concerns relate to possible circularity in the analysis and the incomplete reporting of statistical results. For instance, correlation values are often provided without associated p-values, making it difficult to assess their significance. Furthermore, in some sections of the text, it is unclear whether specific results are supported by any statistical tests.

Crucial information is buried in the supplemental materials (e.g., the figure showing results for broad-band high-frequency power). Some details about the specific paradigm are missing in the methods section, making it challenging to determine if additional controls are necessary in the analyses. I encourage the authors to clarify certain aspects of the analysis and results to ensure their conclusions are substantiated by the data. Should the results be robust, I believe the study will be significant for researchers interested in brain oscillations and beyond.

Reviewer #2 (Public Review):

Summary:<br /> Both human and non-human animals modulate the frequency of their vocalizations to communicate important information about context and internal state. While regulation of the size of the laryngeal opening is a well-established mechanism to regulate vocal pitch, the contribution of expiratory airflow to vocal pitch is less clear. To consider this question, this study first characterizes the relationship between the dominant frequency contours of adult mouse ultrasonic vocalizations (USVs) and expiratory airflow using whole-body plethysmography. Next, the authors build off of their previous work characterizing intermediate reticular oscillator (iRO) neurons in mouse pups to establish the existence of a genetically similar population of neurons in adults and show that artificial activation of iRO neurons elicits USV production in adults. Third, the authors examine the acoustic features of USV elicited by optogenetic activation of iRO and find that a majority of natural USV types (as defined by pitch contour) are elicited by iRO activation.

Strengths:<br /> Strengths of the study include the novel consideration of expiratory airflow as a mechanism to regulate vocal pitch and the use of intersectional methods to identify and activate the iRO in adult mice. The establishment of iRO neurons as a brainstem population that regulates vocal production across development is an important finding.

Weaknesses:<br /> The study does not include statistical analyses to compare the observed relationships between expiratory airflow and USV pitch to a null model in which expiratory airflow and USV pitch are unrelated. The findings of the study also do not provide clear evidence to support the authors' model in which distinct brainstem populations (iRO and RAm) independently regulate expiratory airflow and laryngeal adduction. Although this study establishes iRO as an important population that regulates USV production in adult mice, the question of whether and how different brainstem populations contribute differentially to vocal production remains an important open question. Lastly, the addition of statistical analyses would help to strengthen the study's conclusion that iRO activation positively biases the relationship between expiratory airflow and USV pitch across multiple USV types.

Reviewer #2 (Public Review):

Summary:<br /> Feng et al. investigated dynamic changes in functional and structural connectivity relationships across a broad age range from childhood to early adulthood (6-22 years) using the large open-source HCP-Development database of multimodal magnetic resonance imaging (MRI). Employing a multilinear model, the study integrates three white-matter structural descriptors derived from diffusion tractography with 'microstructure profile covariance' (MPC) descriptors of relationships between cortical regions in terms of regional T1w/T2w ratio, and evaluates the coupling between these structural connectome (SC) descriptors and functional connectivity (FC) as adjusted coefficients of determination, i.e. how well the structural descriptors correspond to the functional connectivity derived from resting-state functional MRI.

The findings reveal a global increase in SC-FC coupling over development. At a regional level, coupling exhibited distinct profiles of age-related increases and decreases within and between functional networks. Individual variability captured by the presented measures of SC-FC coupling was implicated as a potential marker for the prediction of general intelligence scores. Additionally, the investigation extended to associating changes in SC-FC coupling with age to regional gene expression profiles (derived from Allen Human Brain Atlas that analysed six neurotypical adult brains), suggesting positive associations with oligodendrocyte-related pathways and negative associations with astrocyte-related genes.

Strengths:<br /> Overall, the paper offers an interesting and valuable contribution to our understanding of structure-function relationships in the context of brain development. The commendable efforts to assess robustness across various methodologies, including brain parcellation and tractography, and reproducibility analyses on different data subsets enhance the paper's credibility. Combining cortical MPC with more usual white-matter descriptors of structural connectivity is interesting and provides (potentially) complementary information for the study of structure-function relationships with age. Analysing the changes in SC-FC coupling in relation to profiles of evolutionary expansion and functional principal gradients shows a good effort to position the present observations on SC-FC coupling within the previously described work.

Weaknesses:<br /> Although the paper has many strengths, some aspects of the analysis need to be clarified to further support the proposed conclusions. In particular:

* The authors propose that combining cortical and white-matter connectivity measures yields a more comprehensive descriptor of SC-FC coupling. While this is likely true, the claim is not directly tested by assessing different descriptors separately and then in combination to compare the benefits of incorporating additional information for the description of SC-FC coupling.

* The authors report changes in SC-FC coupling with myelin content (reporting a positive association of coupling with regional myelin) and report positive associations between SC-FC correlation with age and expression of oligodendrocyte-related genes. Given that the computation of SC-FC coupling involves the T1w/T2w ratios within cortical regions (recognised as a myelin marker), it's plausible that these findings may be influenced by potential bias introduced by myelin-related measures in the coupling computation process.

* The authors investigate the predictive power of SC-FC coupling, suggesting non-random (but weak) prediction of individual variability in general intelligence (after age correction). However, again the benefit of using SC-FC coupling measures over using each modality alone is not evaluated. Such comparison might indicate whether the coupling is an informative measure in itself or whether it might be informative only to the extent to which it is a proxy measure of SC and FC (in case the predictive power of each separate modality is much higher).

* Generally, more information on quality assessment of tractography and parcellations (including potential age effects on processing given the wide age range of the participants), additional details on the distribution of cognitive scores used in the predictive section, and further clarifications regarding the design choices and validation strategy would provide the reader with a more detailed understanding of the cohort and proposed analytical pipeline (these minor comments are included in the private recommendations to authors).