Reviewer #1 (Public Review):

In this manuscript, Liu et al. used scRNA-seq to characterize cell type-specific responses during allergic contact dermatitis (ACD) in a mouse model, specifically the hapten-induced DNFB model. Using the scRNA-seq data, they deconvolved the cell types responsible for the expression of major inflammatory cytokines such as IFNG (from CD4 and CD8 T cells), IL4/13 (from basophils), IL17A (from gd T cells), and IL1B from neutrophils and macrophages. They found the highest upregulation of a type 1 inflammatory response, centering around IFNG produced by CD4 and CD8 T cells. They further identified a subpopulation of dermal fibroblasts (pre-adipocytes found in the dermal white adipose tissue layer) that upregulate CXCL9/10 during ACD and provide functional genetic evidence in their mouse model that disrupting IFNG signaling in fibroblasts decreases CD8 T cell infiltration and overall inflammation. They identify an increase in IFNG-expressing CD8 T cells in human patient samples of ACD vs. healthy control skin and co-localization of CD8 T cells with PDGFRA+ fibroblasts, which suggests this mechanism is relevant to human ACD. This mechanism is reminiscent of recent work showing that IFNG signaling in dermal fibroblasts upregulates CXCL9/10 to recruit CD8 T cells in a mouse model of vitiligo. Overall, this is a well-presented, clear, and comprehensive manuscript. The conclusions of the study are well supported by the data, with thoughtful discussion on study limitations by the authors. One such limitation was the use of one ACD model (DNFB), which prevents an assessment of how broadly relevant this axis is. The human sample validation is limited by the multiplexing capacity of immunofluorescence markers but shows a predominance of CD8+/IFNG+ cells and PDGFRA+/CXCL10+ cells in ACD (which are virtually absent in healthy control), along with co-localization of CD8+ cells with PDGFRA+ cells. Thus, this mechanism is likely active in human ACD.

Strengths:<br /> Through deep characterization of the in vivo ACD model using scRNA-seq, the authors were able to determine which cell types were expressing the major cytokines involved in ACD inflammation, such as IFNG, IL4/13, IL17A, and IL1B. These analyses are well-presented and thoughtful, showing first that the response is IFNG-dominant, then focusing on deeper characterization of lymphocytes, myeloid cells, and fibroblasts, which are also validated and complemented by FACS experiments using canonical markers of these cell types as well as IF staining. Crosstalk analyses from the scRNA-seq data led the authors to focus on IFNG signaling fibroblasts, and in vitro experiments demonstrate that CXCL9 and CXCL10 are expressed by fibroblasts stimulated by IFNG. In vivo functional genetic evidence demonstrates an important role for IFNG signaling in fibroblasts, as KO of Ifngr1 using Pdgfra-Cre Ifngr1 fl/fl mice, showed a reduction in inflammation and CD8 T cell recruitment. Human ACD sample staining demonstrates the likely activity of the CD8 T cell IFNG-driven fibroblast response in human disease.

Weaknesses:<br /> The use of one model limits an understanding of how broad this fibroblast-T cell axis is during ACD. However, the authors chose the most commonly employed model and compared their data to work in a vitiligo model (another type 1 immune response) to demonstrate similar mechanisms at play. Human patient samples of ACD were co-stained with two markers at a time, demonstrating the presence of CD8+IFNG+ T cells, PDGFRA+CXCL10+ fibroblasts, and co-localization of PDGFRA+ fibroblasts and CD8+ T cells. However, no IF staining demonstrates co-expression of all 4 markers at once; thus, the human validation of co-localization of CD8+IFNG+ T cells and PDGFRA+CXCL10+ fibroblasts is ultimately indirect, although more likely than not to be true.

Reviewer #1 (Public Review):

Review after revision

Of note the main results of this article are very similar to the results present in the previous manuscript (same Figures 1 to 9, addition of Figure 10 with no quantification).<br /> Unfortunately, the main weaknesses of the article have not been addressed:

(1) The main findings have been obtained in clones of Jurkat cells. They have not been confirmed in primary T cells. The only experiment performed in primary cells is shown in Figure S7 (primary human T lymphoblasts) for which only the distribution of FMNL1 is shown without quantification. No results presenting the effect of FMNL1 KO and expression of mutants in primary T cells are shown.

(2) Analysis in- depth of the defect in actin remodeling (quantification of the images, analysis of some key actors of actin remodeling) is still lacking. Only F-actin is shown, no attempt to look more precisely at actors of actin remodeling has been done.

(3) The defect in the secretion of extracellular vesicles is still very preliminary. Examples of STED images given by the authors are nice, yet no quantification is performed.

(4) Results shown in Figure S12 on the colocalization of proteins phosphorylated on Ser/Thr are still not convincing. It seems indeed that "phospho-PKC" is labeling more preferentially the CMAC positive cells (Raji) than the Jurkat T cells. It is thus particularly difficult to conclude on the co-localization and even more on the recruitment of phosphorylated-FMNL1 at the IS. Thus, these experiments are not conclusive and cannot be the basis even for their cautious conclusion: "Although all these data did not allow us to infer that FMNL1b is phosphorylated at the IS due to the resolution limit of confocal and STED microscopes, the results are compatible with the idea that both endogenous FMNL1 and YFP-FMNL1bWT are specifically phosphorylated at the cIS".

The study would benefit from a more careful statistical analysis. The dot plots showing polarity are presented for one experiment. Yet, the distribution of the polarity is broad. Results of the 3 independent experiments should be shown and a statistical analysis performed on the independent experiments.

Reviewer #1 (Public Review):

Summary:

This paper presents valuable findings that gustation and feeding state influence the preferred environmental temperature preference in flies. Interestingly, the authors showed that by refeeding starved animals with non-nutritive sugar sucralose, they are able to tune their preference towards a higher temperature in addition to nutrient-dependent warm preference. The authors show that temperature sensing and sweet sensing gustatory neurons (SGNs) are involved in the former but not the latter. In addition, their data indicate that peptidergic signals involved in internal state and clock genes are required for taste-dependent warm preference behavior.

The authors made an analogy of their results to the cephalic phase response (CPR) in mammals where the thought, sight and taste of food prepares the animal for the consumption of food and nutrients. The authors showed that taste triggers CPR-induced temperature preference behaviors in flies. The authors also briefly covered that the combined modalities of smell and taste induced CPR responses, showing that starved orco mutant flies failed to recover temperature preference after refeeding with sucralose.

The findings of this work hold promising future research prospects, for example, whether the sight of food influences temperature preference behavior in hungry flies, or whether taste, smell and sight work together or independently in promoting CPR responses.

Futhermore, these valuable behavioral results can be further investigated in flies with the advantage of being able to dissect the neural circuitry underlying CPR and nutrient homeostasis.

Strengths:

(1) The authors convincingly showed that tasting is sufficient to drive warm temperature preference behavior in starved flies and show that it is independent of nutrient-driven warm preference.<br /> (2) By using the genetic manipulation of key internal sensors and genes controlling internal feeding and sleep state such as DH44 neurons and the per genes for eg the authors linked gustation and temperature preference behavior control to the internal state of the animal.

Weaknesses:

Most of the weaknesses of the paper have been addressed in the revision. The points mentioned below are meant to improve readability of the paper and to promote understanding of the significance of the work.<br /> (1) Supplementary fig 1 could replace Figure 1A. The purpose of Figure 1F is not clear to me as the comparison between the different food substances is not separately addressed anywhere in the text.<br /> (2) The data for the orco receptor mutant could be placed in the main figures to justify the discussion emphasising CPR-like responses.

Reviewer #1 (Public Review):

Summary:

This paper uses a model of binge alcohol consumption in mice to examine how the behaviour and its control by a pathway between the anterior insular cortex (AIC) to the dorsolateral striatum (DLS) may differ between males and females. Photometry is used to measure the activity of AIC terminals in the DLS when animals are drinking and this activity seems to correspond to drink bouts in males but not females. The effects appear to be lateralized with inputs to the left DLS being of particular interest.

Strengths:

Increasing alcohol intake in females is of concern and the consequences for substance use disorder and brain health are not fully understood, so this is an area that needs further study. The attempt to link fine-grained drinking behaviour with neural activity has the potential to enrich our understanding of the neural basis of behaviour, beyond what can be gleaned from coarser measures of volumes consumed etc.

Weaknesses:

The introduction to the drinking in the dark (DID) paradigm is rather narrow in scope (starting line 47). This would be improved if the authors framed this in the context of other common intermittent access paradigms and gave due credit to important studies and authors that were responsible for the innovation in this area (particularly studies by Wise, 1973 and returned to popular use by Simms et al 2010 and related papers; e.g., Wise RA (1973). Voluntary ethanol intake in rats following exposure to ethanol on various schedules. Psychopharmacologia 29: 203-210; Simms, J., Bito-Onon, J., Chatterjee, S. et al. Long-Evans Rats Acquire Operant Self-Administration of 20% Ethanol Without Sucrose Fading. Neuropsychopharmacol 35, 1453-1463 (2010).) The original drinking in the dark demonstrations should also be referenced (Rhodes et al., 2005). Line 154 Theile & Navarro 2014 is a review and not the original demonstration.

When sex differences in alcohol intake are described, more care should be taken to be clear about whether this is in terms of volume (e.g. ml) or blood alcohol levels (BAC, or at least g/kg as a proxy measure). This distinction was often lost when lick responses were being considered. If licking is similar (assuming a single lick from a male and female brings in a similar volume?), this might mean males and females consume similar volumes, but females due to their smaller size would become more intoxicated so the implications of these details need far closer consideration. What is described as identical in one measure, is not in another.

While the authors have some previous data on the AIC to DLS pathway, there are many brain regions and pathways impacted by alcohol and so the focus on this one in particular was not strongly justified. Since photometry is really an observational method, it's important to note that no causal link between activity in the pathway and drinking has been established here.

It would be helpful if the authors could further explain whether their modified lickometers actually measure individual licks. While in some systems contact with the tongue closes a circuit which is recorded, the interruption of a photobeam was used here. It's not clear to me whether the nose close to the spout would be sufficient to interrupt that beam, or whether a tongue protrusion is required. This detail is important for understanding how the photometry data is linked to behaviour. The temporal resolution of the GCaMP signal is likely not good enough to capture individual links but I think more caution or detail in the discussion of the correspondence of these events is required.

Even if the pattern of drinking differs between males and females, the use of the word "strategy" implies a cognitive process that was never described or measured.

Reviewer #1 (Public Review):

Summary:

This paper introduces an efficient approach to infer properties of receptive-field subunits from the ensemble of spike-triggered stimuli. This is an important general problem in sensory coding. The results introduced in the paper make a solid contribution to both how subunits can be identified and how subunits of different types are coordinated in space.

Strengths:

A primary strength of the paper is the development of approaches that substantially speed non-negative matrix factorization and by doing so create an opportunity for a more systematic exploration of how the procedure depends on various control parameters. The improved procedure is well documented and the direct comparisons with previous procedures are helpful. The improved efficiency enabled several improvements in the procedure - notably tests of good procedures for initializing NNMF and tests of the dependence of the results on the sparsity regularization parameter.

A second strength of the paper is the exploration of the spatial relationship between different subunits. This, to my knowledge, is new and is an interesting direction. There are some concerns about this analysis (see weaknesses below), but if this analysis can be strengthened it will provide new information that will be important both functionally and developmentally.

Weaknesses:

A primary concern is that choices made about parameters for several aspects of the analysis appear to be made subjectively. Much of this centers around how much of the structure in the extracted subunits is imposed by the procedure itself, and how much reflects the underlying neural circuitry. Some specific issues related to this concern are:

- Sparsity: the use of the autocorrelation function to differentiate real vs spurious subunits should be documented and validated. For example, can the authors split data in half and show that the real subunits are stable?

- Choice of regularization: the impact of the regularization parameter on subunit properties is nicely documented. However, the choice of an appropriate regularization parameter seems somewhat arbitrary. Line 253-256 is an example of this problem: this sentence sounds circular - as if the sparsity factor was turned up until the authors obtained what they expected to obtain. Could the choice of this parameter significantly impact the properties of the extracted subunits? How sensitive are the subunit properties to that parameter? Some additional control analyses are needed to validate the parameter choice (see the crossvalidation comment below).

- Crossvalidation was not used to identify the regularization constraint value because the weight matrix from NNMF does not generalize beyond the data it was fit to. Could the authors instead hold the components matrix fixed and recompute the weight matrix, and use that approach for cross-validation (especially since it is really the components matrix that needs validating)?

The paper would benefit from a more complete comparison with known anatomy. For example, can the authors estimate the number of cones within each subunit? This is well-constrained both anatomically (at least in macaque) and, especially for midget ganglion cell subunits, functionally. In macaque, most midget bipolar cells get input from single cones, so the number of extracted subunits should be close to the number of cones. This would be a useful point of comparison for the current work.

Is the analysis of the spatial relationship between different subunit mosaics robust to the incompleteness of those mosaics? The argument on lines 496-503 should be backed up by more analysis. For example, if subunits are removed from regions where the mosaic is pretty complete, do the authors change the spatial dependence? Alternatively, could they use synthetic mosaics with properties like those measured to check the sensitivity to missing cells?

NNMF relies on accounting for each spike-triggered stimulus with a linear combination of components. Would nonlinearities - e.g. those in the bipolar cell outputs - substantially change the results?

Does the approach work for cells that receive input from multiple bipolar types? Some ganglion cells, e.g. in mice, receive input from multiple bipolar types, each accounting for a sizable percentage of the total input. There is similar anatomical work indicating that parasol cells may receive input from multiple diffuse bipolar types. It is not clear whether the current approach works in cases where the subunits of a single ganglion cell overlap. Some discussion of this would be useful.

Gating of Kv10 channels is unique because it involves coupling between non-domain swapped voltage sensing domains, a domain-swapped cytoplasmic ring assembly formed by the N- and C-termini, and the pore domain. Recent structural data suggests that activation of the voltage sensing domain relieves a steric hindrance to pore opening, but the contribution of the cytoplasmic domain to gating is still not well understood. This aspect is of particular importance because proteins like calmodulin interact with the cytoplasmic domain to regulate channel activity. The effects of calmodulin (CaM) in WT and mutant channels with disrupted cytoplasmic gating ring assemblies are contradictory, resulting in inhibition or activation, respectively. The underlying mechanism for these discrepancies is not understood. In the present manuscript, Reham Abdelaziz and collaborators use electrophysiology, biochemistry and mathematical modeling to describe how mutations and deletions that disrupt inter-subunit interactions at the cytoplasmic gating ring assembly affect Kv10.1 channel gating and modulation by CaM. In the revised manuscript, additional information is provided to allow readers to identify within the Kv10.1 channel structure the location of E600R, one of the key channel mutants analyzed in this study. However, the mechanistic role of the cytoplasmic domains that this study focuses on, as well as the location of the ΔPASCap deletion and other perturbations investigated in the study remain difficult to visualize without additional graphical information.

The authors focused mainly on two structural perturbations that disrupt interactions within the cytoplasmic domain, the E600R mutant and the ΔPASCap deletion. By expressing mutants in oocytes and recording currents using Two Electrode Voltage-Clamp (TEV), it is found that both ΔPASCap and E600R mutants have biphasic conductance-voltage (G-V) relations and exhibit activation and deactivation kinetics with multiple voltage-dependent components. Importantly, the mutant-specific component in the G-V relations is observed at negative voltages where WT channels remain closed. The authors argue that the biphasic behavior in the G-V relations is unlikely to result from two different populations of channels in the oocytes, because they found that the relative amplitude between the two components in the G-V relations was highly reproducible across individual oocytes that otherwise tend to show high variability in expression levels. Instead, the G-V relations for all mutant channels could be well described by an equation that considers two open states O1 and O2, and a transition between them; O1 appeared to be unaffected by any of the structural manipulations tested (i.e. E600R, ΔPASCap, and other deletions) whereas the parameters for O2 and the transition between the two open states were different between constructs. The O1 state is not observed in WT channels and is hypothesized to be associated with voltage sensor activation. O2 represents the open state that is normally observed in WT channels and is speculated to be associated with conformational changes within the cytoplasmic gating ring that follow voltage sensor activation, which could explain why the mutations and deletions disrupting cytoplasmic interactions affect primarily O2.

Severing the covalent link between the voltage sensor and pore reduced O1 occupancy in one of the deletion constructs. Although this observation is consistent with the hypothesis that voltage-sensor activation drives entry into O1, this result is not conclusive. Structural as well as functional data has established that the coupling of the voltage sensor and pore does not entirely rely on the S4-S5 covalent linker between the sensor and the pore, and thus the severed construct could still retain coupling through other mechanisms, which is consistent with the prominent voltage dependence that is observed. If both states O1 and O2 require voltage sensor activation, it is unclear why the severed construct would affect state O1 primarily, as suggested in the manuscript, as opposed to decreasing occupancy of both open states. In line with this argument, the presence of Mg2+ in the extracellular solution affected both O1 and O2. This finding suggests that entry into both O1 and O2 requires voltage-sensor activation because Mg2+ ions are known to stabilize the voltage sensor in its most deactivated conformations.

Activation towards and closure from O1 is slow, whereas channels close rapidly from O2. A rapid alternating pulse protocol was used to take advantage of the difference in activation and deactivation kinetics between the two open components in the mutants and thus drive an increasing number of channels towards state O1. Currents activated by the alternating protocol reached larger amplitudes than those elicited by a long depolarization to the same voltage. This finding is interpreted as an indication that O1 has a larger macroscopic conductance than O2. In the revised manuscript, the authors performed single-channel recordings to determine why O1 and O2 have different macroscopic conductance. The results show that at voltages where the state O1 predominates, channels exhibited longer open times and overall higher open probability, whereas at more depolarized voltages where occupancy of O2 increases, channels exhibited more flickery gating behavior and decreased open probability. These results are informative but not conclusive since single-channel amplitudes could not be resolved at strong depolarizations, limiting the extent to which the data could be analyzed. In the last revision, the authors have included one representative example showing inhibition of single channel activity by the Kv10-specific inhibitor astemizole. Group data analysis would be needed to conclusively establish that the currents that were recorded indeed correspond to Kv10 channels.

It is shown that conditioning pulses to very negative voltages result in mutant channel currents that are larger and activate more slowly than those elicited at the same voltage but starting from less negative conditioning pulses. In voltage-activated curves, O1 occupancy is shown to be favored by increasingly negative conditioning voltages. This is interpreted as indicating that O1 is primarily accessed from deeply closed states in which voltage sensors are in their most deactivated position. Consistently, a mutation that destabilizes these deactivated states is shown to largely suppress the first component in voltage-activation curves for both ΔPASCap and E600R channels.

The authors then address the role of the hidden O1 state in channel regulation by calcium-calmodulin (CaM). Stimulating calcium entry into oocytes with ionomycin and thapsigargin, assumed to enhance CaM-dependent modulation, resulted in preferential potentiation of the first component in ΔPASCap and E600R channels. This potentiation was attenuated by including an additional mutation that disfavors deeply closed states. Together, these results are interpreted as an indication that calcium-CaM preferentially stabilizes deeply closed states from which O1 can be readily accessed in mutant channels, thus favoring current activation. In WT channels lacking a conducting O1 state, CaM stabilizes deeply closed states and is therefore inhibitory. It is found that the potentiation of ΔPASCap and E600R by CaM is more strongly attenuated by mutations in the channel that are assumed to disrupt interaction with the C-terminal lobe of CaM than mutations assumed to affect interaction with the N-terminal lobe. These results are intriguing but difficult to interpret in mechanistic terms. The strong effect that calcium-CaM had on the occupancy of the O1 state in the mutants raises the possibility that O1 can be only observed in channels that are constitutively associated with CaM. To address this, a biochemical pull-down assay was carried out to establish that only a small fraction of channels are associated with CaM under baseline conditions. These CaM experiments are potentially very interesting and could have wide physiological relevance. However, the approach utilized to activate CaM is indirect and could result in additional non-specific effects on the oocytes that could affect the results.

Finally, a mathematical model is proposed consisting of two layers involving two activation steps for the voltage sensor, and one conformational change in the cytoplasmic gating ring - completion of both sets of conformational changes is required to access state O2, but accessing state O1 only requires completion of the first voltage-sensor activation step in the four subunits. The model qualitatively reproduces most major findings on the mutants. Although the model used is highly symmetric and appears simple, the mathematical form used for the rate constants in the model adds a layer of complexity to the model that makes mechanistic interpretations difficult. In addition, many transitions that from a mechanistic standpoint should not depend on voltage were assigned a voltage dependence in the model. These limitations diminish the mechanistic insight that can be reliably extracted from the model.

Reviewer #1 (Public Review):

In this manuscript, Yang et al. conduct a comprehensive investigation to demonstrate the role of adipose tissue miR-802 in obesity-associated inflammation and metabolic dysfunction. Using multiple models and techniques, they propose a mechanism where elevated levels of miR-802 in adipose tissue (both in mouse models and humans) trigger fat accumulation and inflammation, leading to increased adiposity and insulin resistance. They suggest that increased miR-802 levels in adipocytes during obesity result in the downregulation of TRAF3, a negative regulator of canonical and non-canonical NF-κB pathways. This downregulation induces inflammation through the production of cytokines/chemokines that attract and polarize macrophages. Concurrently, the NF-κB pathway induces the lipogenic transcriptional factor SREBP1, which promotes fat accumulation and further recruits pro-inflammatory macrophages. While the proposed model is supported by multiple experiments and consistent data, there are areas where the manuscript could be improved. Some improvements can be addressed in the text, while others require additional controls, experiments, or analyses.

(1) The manuscript should provide measurements of lipid droplet/adipocyte size for all models, both in vitro and in vivo. In vivo studies should also include fat weight measurements. This is crucial to determine whether miR-802, TRAF3, and SREBP1 promote adiposity/fat accumulation across all models.<br /> (2) The rationale for co-culture experiments using WAT SVF is unclear, given that miR-802 is upregulated by obesity in adipocytes, not in the stromal-vascular fraction. These experiments would be more relevant if performed using isolated adipocytes or differentiated WAT SVF.<br /> (3) Figures 1G and 1H lack a control group (time 0 or NCD). Without this control, it is impossible to determine if inflammation precedes miR-802 upregulation.<br /> (4) The statement, "The knockout of miR-802 in adipose tissue did not alter food intake, body weight, glucose level, and adiposity (data not shown)," needs more detail regarding the age and sex of the animals. These data are important and should be reported, perhaps in a supplementary figure.<br /> (5) The terms "KO" (knockout) and "KI" (knock-in) are misleading for AAV models, as they do not modify the genome. "KD" (knockdown) and "OE" (overexpression) are more accurate.<br /> (6) The statement, "miR-802 expression was unaffected in other organs (Figure S3O)," should clarify that this is except for BAT.

By addressing these points, the manuscript would present a more robust and clear demonstration of the role of miR-802 in obesity-associated inflammation and metabolic dysfunction.

Reviewer #1 (Public Review):

In this paper, Tompary & Davachi present work looking at how memories become integrated over time in the brain, and relating those mechanisms to responses on a priming task as a behavioral measure of memory linkage. They find that remotely but not recently formed memories are behaviorally linked and that this is associated with a change in the neural representation in mPFC. They also find that the same behavioral outcomes are associated with the increased coupling of the posterior hippocampus with category-sensitive parts of the neocortex (LOC) during a post-learning rest period-again only for remotely learned information. There was also correspondence in rest connectivity (posterior hippocampus-LOC) and representational change (mPFC) such that for remote memories specifically, the initial post-learning connectivity enhancement during rest related to longer-term mPFC representational change.

This work has many strengths. The topic of this paper is very interesting, and the data provide a really nice package in terms of providing a mechanistic account of how memories become integrated over a delay. The paper is also exceptionally well-written and a pleasure to read. There are two studies, including one large behavioral study, and the findings replicate in the smaller fMRI sample. I do however have two fairly substantive concerns about the analytic approach, where more data will be required before we can know whether the interpretations are an appropriate reflection of the findings. These and other concerns are described below.

(1) One major concern relates to the lack of a pre-encoding baseline scan prior to recent learning.

a) First, I think it would be helpful if the authors could clarify why there was no pre-learning rest scan dedicated to the recent condition. Was this simply a feasibility consideration, or were there theoretical reasons why this would be less "clean"? Including this information in the paper would be helpful for context. Apologies if I missed this detail in the paper.

b) Second, I was hoping the authors could speak to what they think is reflected in the post-encoding "recent" scan. Is it possible that these data could also reflect the processing of the remote memories? I think, though am not positive, that the authors may be alluding to this in the penultimate paragraph of the discussion (p. 33) when noting the LOC-mPFC connectivity findings. Could there be the reinstatement of the old memories due to being back in the same experimental context and so forth? I wonder the extent to which the authors think the data from this scan can be reflected as strictly reflecting recent memories, particularly given it is relative to the pre-encoding baseline from before the remote memories, as well (and therefore in theory could reflect both the remote + recent). (I should also acknowledge that, if it is the case that the authors think there might be some remote memory processing during the recent learning session in general, a pre-learning rest scan might not have been "clean" either, in that it could have reflected some processing of the remote memories-i.e., perhaps a clean pre-learning scan for the recent learning session related to point 1a is simply not possible.)

c) Third, I am thinking about how both of the above issues might relate to the authors' findings, and would love to see more added to the paper to address this point. Specifically, I assume there are fluctuations in baseline connectivity profile across days within a person, such that the pre-learning connectivity on day 1 might be different from on day 2. Given that, and the lack of a pre-learning connectivity measure on day 2, it would logically follow that the measure of connectivity change from pre- to post-learning is going to be cleaner for the remote memories. In other words, could the lack of connectivity change observed for the recent scan simply be due to the lack of a within-day baseline? Given that otherwise, the post-learning rest should be the same in that it is an immediate reflection of how connectivity changes as a function of learning (depending on whether the authors think that the "recent" scan is actually reflecting "recent + remote"), it seems odd that they both don't show the same corresponding increase in connectivity-which makes me think it may be a baseline difference. I am not sure if this is what the authors are implying when they talk about how day 1 is most similar to prior investigation on p. 20, but if so it might be helpful to state that directly.

d) Fourth and very related to my point 1c, I wonder if the lack of correlations for the recent scan with behavior is interpretable, or if it might just be that this is a noisy measure due to imperfect baseline correction. Do the authors have any data or logic they might be able to provide that could speak to these points? One thing that comes to mind is seeing whether the raw post-learning connectivity values (separately for both recent and remote) show the same pattern as the different scores. However, the authors may come up with other clever ways to address this point. If not, it might be worth acknowledging this interpretive challenge in the Discussion.

(2) My second major concern is how the authors have operationalized integration and differentiation. The pattern similarity analysis uses an overall correspondence between the neural similarity and a predicted model as the main metric. In the predicted model, C items that are indirectly associated are more similar to one another than they are C items that are entirely unrelated. The authors are then looking at a change in correspondence (correlation) between the neural data and that prediction model from pre- to post-learning. However, a change in the degree of correspondence with the predicted matrix could be driven by either the unrelated items becoming less similar or the related ones becoming more similar (or both!). Since the interpretation in the paper focuses on change to indirectly related C items, it would be important to report those values directly. For instance, as evidence of differentiation, it would be important to show that there is a greater decrease in similarity for indirectly associated C items than it is for unrelated C items (or even a smaller increase) from pre to post, or that C items that are indirectly related are less similar than are unrelated C items post but not pre-learning. Performing this analysis would confirm that the pattern of results matches the authors' interpretation. This would also impact the interpretation of the subsequent analyses that involve the neural integration measures (e.g., correlation analyses like those on p. 16, which may or may not be driven by increased similarity among overlapping C pairs). I should add that given the specificity to the remote learning in mPFC versus recent in LOC and anterior hippocampus, it is clearly the case that something interesting is going on. However, I think we need more data to understand fully what that "something" is.

(3) The priming task occurred before the post-learning exposure phase and could have impacted the representations. More consideration of this in the paper would be useful. Most critically, since the priming task involves seeing the related C items back-to-back, it would be important to consider whether this experience could have conceivably impacted the neural integration indices. I believe it never would have been the case that unrelated C items were presented sequentially during the priming task, i.e., that related C items always appeared together in this task. I think again the specificity of the remote condition is key and perhaps the authors can leverage this to support their interpretation. Can the authors consider this possibility in the Discussion?

(4) For the priming task, based on the Figure 2A caption it seems as though every sequence contributes to both the control and primed conditions, but (I believe) this means that the control transition always happens first (and they are always back-to-back). Is this a concern? If RTs are changing over time (getting faster), it would be helpful to know whether the priming effects hold after controlling for trial numbers. I do not think this is a big issue because if it were, you would not expect to see the specificity of the remotely learned information. However, it would be helpful to know given the order of these conditions has to be fixed in their design.

(5) The authors should be cautious about the general conclusion that memories with overlapping temporal regularities become neurally integrated - given their findings in MPFC are more consistent with overall differentiation (though as noted above, I think we need more data on this to know for sure what is going on).

(6) It would be worth stating a few more details and perhaps providing additional logic or justification in the main text about the pre and post-exposure phases were set up and why. How many times each object was presented pre and post, and how the sequencing was determined (were any constraints put in place e.g., such that C1 and C2 did not appear close in time?). What was the cover task (I think this is important to the interpretation & so belongs in the main paper)? Were there considerations involving the fact that this is a different sequence of the same objects the participants would later be learning - e.g., interference, etc.?

Reviewer #1 (Public Review):

In this study, Girardello et al. use proteomics to reveal the membrane tension sensitive caveolin-1 interactome in migrating cells. The authors use EM and surface rendering to demonstrate that caveolae formed at the rear of migrating cells are complex membrane-linked multilobed structures, and they devise a robust strategy to identify caveolin-1 associated proteins using APEX2-mediated proximity biotinylation. This important dataset is further validated using proximity ligation assays to confirm key interactions, and follows up with an interrogation of a surprising relationship between caveolae and RhoGTPase signalling, where caveolin-1 recruits ROCK1 under high membrane tension conditions, and ROCK1 activity is required to reform caveolae upon reversion to isotonic solution. However, caveolin-1 recruits the RhoA inactivator ARHGAP29 when membrane tension is low and ARHGAP29 overexpression leads to disassembly of caveolae and reduced cell motility. This study builds on previous findings linking caveolae to positive feedback regulation of RhoA signalling, and provides further evidence that caveolae serve to drive rear retraction in migration but also possess an intrinsic brake to limit RhoA activation, leading the authors to suggest that cycles of caveolae assembly and disassembly could thereby be central to establish a stable cell rear for persistent cell migration

A major strength of the manuscript is the robust proteomic dataset. The experimental set up is well defined and mostly well controlled, and there is good internal validation in that the high abundance of core caveolar proteins in low membrane tension (isotonic) conditions, and absence under high membrane tension (brief hypo-osmotic shock) conditions, correlating very well with previous finding. The data could however be better presented to show where statically robust changes occur, and supplementary information should include a table of showing abundance. It's very good to see a link to PRIDE, providing a useful resource for the community.

The authors detail several known interactions and their mechanosensitivty, but also report new interactors of caveolin-1. Several mechanosensitive interactions of caveolin-1 take place at the cell rear, but others are more diffuse across the cell looking at the PLA data (e.g FLN1, CTTN, HSPB1; Figure 4A-F and Figure 4 supplement 1). It is interesting to speculate that those at the cell rear are involved in caveolae, whilst others are linked specifically to caveolin-1 (e.g. dolines). PLA or localisation analysis with Cavin1/PTRF may be able to resolve this and further specify caveolae versus non-caveolae mechanosensitive interactions.

The Cav1/ARHGAP29 influence on YAP signalling is interesting, but appear to be quite isolated from the rest of the manuscript. Does overexpression of ARHGAP29 influence YAP signalling and/or caveolar protein expression/Cav1pY14?<br /> ARHGAP29 and RhoA/ROCK1 related observations are very interesting and potentially really important. However, the link between ARHGAP29 and caveolae is not well established (other than in proteomic data). PLA or FRET could help establish this.<br /> The relationship between ARHGAP29 and RhoA signalling is not well defined. Is GAP activity important in determining the effect on migration and caveolae formation? What is the effect on RhoA activity? Alternatively, the authors could investigate YAP dependent transcriptional regulation downstream of overexpression.

Reviewer #3 (Public Review):

Although the authors findings are interesting, they do little to demonstrate new scientific information or advancements in producing genetically modified livestock with improved production characteristics. While the MSTNDel273 sheep exhibited an increased number of muscle fibers, the data provided did not demonstrate a significant improvement in meat production, quality or quantity in the MSTNDel273 sheep vs WT.

The manuscript is very long, complicated and difficult to read, given the minimum amount of significant information that is provided. It reads more like a graduate student thesis than a scientific manuscript ready for publication. Given the significant findings are so minimal, the amount of text provided, figures and tables are excessive. A large number of different molecular techniques are employed to try and decipher the mechanism(s) that result in the observed phenotype = double muscling. The authors focus on the MEK-ERK-FOSL1 pathway and suggest this is the key pathway/mechanism resulting in the phenotype observed in MSTNDel273sheep. However, they provide very little "significant" evidence to support this. RNA-Seq data demonstrated that hundreds of different genes were either upregulated or down-regulated, but the authors chose to only focus on FOSL1 and associated genes. The findings do not support the idea that FOSL1 is not involved, but neither do they strongly support FOSL1 involvement. The observations made by the authors could be co-incidental and not causative in nature.

The authors indicate that sgRNA design changes in addition to changing the molar ratio of Cas9MRNA:sgRNA improved the ability to generate biallelic homozygous mutant sheep; however, the data provided to not demonstrate any significant difference. Given the small number of sheep that were actually produced and evaluated, it is extremely difficult to demonstrate anything that was analyzed to be significantly (statistically) different between MSTNDel273 sheep and WT, yet the authors seem to ignore this in much of their discussion. There is no explanation as to why the authors started with sheep that were FGF5 knockouts. The reviewer assumes that this was simply a line of sheep available from previous studies and the goal was to produce sheep with both improved hair/wool characteristics in addition to improved muscle development. However, the use of FGF5 knockout sheep complicates the ability to accurately decipher the unique aspects associated with targeting only myostatin for knock-out. At minimum, this is a variable that has to be considered in the statistical analysis. No information is provided on the methods used to produce the MSTNDel273 sheep, which seems fundamentally important. It is assumed they were produced by injecting one-cell zygotes then transferring these into surrogate females, but given the information provided, it is impossible to know. Certainly, the methods employed could have a profound effect on the outcome. There is no information provided on the sex of the animals produced and then analyzed.

Comments on revised version:

The manuscript by Chen et al. is improved and demonstrates successful gene editing in sheep embryos to obtain biallelic mutation of Mstn and FGF5. Despite the improvements in the revised manuscript, the cellular and molecular mechanism remain inadequate to conclude whether Fosl1 indeed acts downstream of myostatin. In addition, there is little that is new direction versus confirmatory for what is already well know regarding Mstn and FGF5

There are also a number of editorial mistakes e.g. the authors refer to tables S1-S4 in the materials and methods and results section, but there is no table S1-S4 provided.

Reviewer #1 (Public Review):

Summary:

The data clearly demonstrate that arpin is important for vessel barrier function, yet its genetic loss via a CRISPR strategy was not lethality, but led to viable animals in C57Blk strain at 12 weeks of age, albeit with leaky blood vessels. Pharmacological approaches were employed to demonstrate that loss of arpin led to ROCK1-dependent stress fiber formation that promoted increased permeability.

Strengths:

The results clearly demonstrate that arpin is expressed in the endothelium of blood vessels and its deficiency leads to leaky blood vessels in in vivo and in vitro models.

Weaknesses:

They conclude vessel leak was not related to enhanced Arp2/3 function through arpin deficiency, but no direct evidence of Arp2/3 activity is provided to support this conclusion. Instead, the authors concluded that ROCK1 activity was elevated in arpin knockdown cells and caused robust stress fiber formation. This idea could be strengthened by testing if ROCK1 inhibition by pharmacological block in arpin KO mice leads to less vascular leakage while pharmacological inhibition of Arp2/3 does not attenuate increased vessel permeability.

Reviewer #1 (Public Review):

Summary:

BMP signaling is, arguably, best known for its role in the dorsoventral patterning, but not in nematodes, where it regulates body size. In their paper, Vora et al. analyze ChIP-Seq and RNA-Seq data to identify direct transcriptional targets of SMA-3 (Smad) and SMA-9 (Schnurri) and understand the respective roles of SMA-3 and SMA-9 in the nematode model Caenorhabditis elegans. The authors use publicly available SMA-3 and SMA-9 ChIP-Seq data, own RNA-Seq data from SMA-3 and SMA-9 mutants, and bioinformatic analyses to identify the genes directly controlled by these two transcription factors (TFs) and find approximately 350 such targets for each. They show that all SMA-3-controlled targets are positively controlled by SMA-3 binding, while SMA-9-controlled targets can be either up or downregulated by SMA-9. 129 direct targets were shared by SMA-3 and SMA-9, and, curiously, the expression of 15 of them was activated by SMA-3 but repressed by SMA-9. Since genes responsible for cuticle collagen production were eminent among the SMA-3 targets, the authors focused on trying to understand the body size defect known to be elicited by the modulation of BMP signaling. Vora et al. provide compelling evidence that this defect is likely to be due to problems with the BMP signaling-dependent collagen secretion necessary for cuticle formation.

Strengths:

Vora et al. provide a valuable analysis of ChIP-Seq and RNA-Seq datasets, which will be very useful for the community. They also shed light on the mechanism of the BMP-dependent body size control by identifying SMA-3 target genes regulating cuticle collagen synthesis and by showing that downregulation of these genes affects body size in C. elegans.

Weaknesses:

(1) Although the analysis of the SMA-3 and SMA-9 ChIP-Seq and RNA-Seq data is extremely useful, the goal "to untangle the roles of Smad and Schnurri transcription factors in the developing C. elegans larva", has not been reached. While the role of SMA-3 as a transcriptional activator appears to be quite straightforward, the function of SMA-9 in the BMP signaling remains obscure. The authors write that in SMA-9 mutants, body size is affected, but they do not show any data on the mechanism of this effect.

(2) The authors clearly show that both TFs can bind independently of each other, however, by using distances between SMA-3 and SMA-9 ChIP peaks, they claim that when the peaks are close these two TFs act as complexes. In the absence of proof that SMA-3 and SMA-9 physically interact (e.g. that they co-immunoprecipitate - as they do in Drosophila), this is an unfounded claim, which should either be experimentally substantiated or toned down.

(3) The second part of the paper (the collagen story) is very loosely connected to the first part. dpy-11 encodes an enzyme important for cuticle development, and it is a differentially expressed direct target of SMA-3. dpy-11 can be bound by SMA-9, but it is not affected by this binding according to RNA-Seq. Thus, technically, this part of the paper does not require any information about SMA-9. However, this can likely be improved by addressing the function of the 15 genes, with the opposing mode of regulation by SMA-3 and SMA-9.

(4) The Discussion does not add much to the paper - it simply repeats the results in a more streamlined fashion.

Reviewer #1 (Public Review):

Summary:

This manuscript by Aybar-Torres et al investigated the effect of common human STING1 variants on STING-mediated T cell phenotypes in mice. The authors previously made knock-in mice expressing human STING1 alleles HAQ or AQ, and here they established a new knock-in line Q293. The authors stimulated cells isolated from these mice with STING agonists and found that all three human mutant alleles resist cell death, leading to the conclusion that R293 residue is essential for STING-mediated cell death (there are several caveats with this conclusion, more below). The authors also bred HAQ and AQ alleles to the mouse Sting1-N153S SAVI mouse and observed varying levels of rescue of disease phenotypes with the AQ allele showing more complete rescue than the HAQ allele. The Q293 allele was not tested in the SAVI model. They conclude that the human common variants such as HAQ and AQ have a dominant negative effect over the gain-of-function SAVI mutants.

Strengths:

The authors and Dr. Jin's group previously made important observations of common human STING1 variants, and these knock-in mouse models are essential for understanding the physiological function of these alleles.

Weaknesses:

However, although some of the observations reported here are interesting, the data collectively does not support a unified model. The authors seem to be drawing two sets of conclusions from in vitro and in vivo experiments, and neither mechanism is clear. Several experiments need better controls, and these knock-in mice need more comprehensive functional characterization.

Summary:

This paper described the dynamics of the nuclear substructure called PML Nucleolar Association (PNA) in response to DNA damage on ribosomal DNA (rDNA) repeats. The authors showed that the PNA with rDNA repeats is induced by the inhibition of topoisomerases and RNA polymerase I and that the PNA formation is modulated by RAD51, thus homologous recombination. Artificially induced DNA double-strand breaks (DSBs) in rDNA repeats stimulate the formation of PNA with DSB markers. This DSB-triggered PNA formation is regulated by DSB repair pathways.

Strengths:

This paper illustrates a unique DNA damage-induced sub-nuclear structure containing the PML body, which is specifically associated with the nucleolus. Moreover, the dynamics of this PML Nucleolar Association (PNA) require topoisomerases and RNA polymerase I and are modulated by RAD51-mediated homologous recombination and non-homologous end-joining. This study provides a unique regulation of DSB repair at rDNA repeats associated with the unique-membrane-less subnuclear structure.

Weaknesses:

Although the PNA formation on rDNA repeat is nicely shown by cytological analysis, the biological significance of PNA in DSB repair is not fully addressed.

Reviewer #1 (Public Review):

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

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

Major weaknesses:<br /> One weakness to me is the impact of identifying whether D1 and D2 had similar or different activity patterns. Does observing increasing/decreasing activity in D2 versus D1, or different activity patterns in D1 and D2, support one model of interval timing over another, or does it further support a more specific idea of how DMS contributes to interval timing?

I found the results presented in Figures 2 and 3 to be a little confusing or misleading. In Figure 2, the authors appear to claim that D1 neurons decrease their activity over the time interval while D2 neurons increase activity. The authors use this result to suggest that D1/D2 activity patterns are different. In Figure 3, a different analysis is done, and this time D2 neurons do not significantly increase their activity with time, conflicting with Figure 2. While in both figures, there is a significant difference between the mean slopes across the population, the secondary effect of positive/negative slope for D2/D1 neurons changes. I find this especially confusing as the authors refer back to the positive/negative slope for D2/D1 neurons result throughout the rest of the text.

It is a bit unclear to me how the authors chose the parameters for the model, and how well the model explains behavior is quantified. It seems that the authors didn't perform cross-validation across trials (i.e., they chose parameters that explained behavior across all trials combined, rather than choosing parameters from a subset of trials and determining whether those parameters are robust enough to explain behavior on held-out trials). I think this would increase the robustness of the result.

In addition, it remains a bit unclear to me how the authors changed the specific parameters they did to model the optogenetic manipulation. It seems these parameters were chosen because they fit the manipulation data. This makes me wonder if this model is flexible enough that there is almost always a set of parameters that would explain any experimental result; in other words, I'm not sure this model has high explanatory power.

Lastly, the results are based on a relatively small dataset (tens of cells).

Impact:<br /> The task and data presented by the authors are very intriguing, and there are many groups interested in how striatal activity contributes to the neural perception of time. The authors perform a wide variety of experiments and analysis to examine how DMS activity influences time perception during an interval-timing task, allowing for insight into this process. However, the significance of the key finding -- that D1 and D2 activity is distinct across time -- remains somewhat ambiguous to me.

Reviewer #1 (Public Review):

Summary:

This review evaluates the SCellBOW framework, which applies phenotype algebra to obtain vectors from cancer subclusters or user-defined subclusters.

Strengths:

SCellBOW employs an innovative application of NLP-inspired techniques to analyze scRNA-seq data, facilitating the identification and visualization of phenotypically divergent cell subpopulations.

The framework demonstrates robustness in accurately representing various cell types across multiple datasets, highlighting its versatility and utility in different biological contexts.

By simulating the impact of specific malignant subpopulations on disease prognosis, SCellBOW provides valuable insights into the relative risk and aggressiveness of cancer subpopulations, which is crucial for personalized therapeutic strategies.

The identification of a previously unknown and aggressive AR−/NElow subpopulation in metastatic prostate cancer underscores the potential of SCellBOW in uncovering clinically significant findings.

Weaknesses:

The reliance on bulk RNA-seq data as a reference raises concerns about potentially misleading results due to the presence of RNA expression from immune cells in the TME. It is unclear if SCellBOW adequately addresses this issue, which could affect the accuracy of the cancer subcluster vectors.

The method of extracting vectors in phenotype algebra appears to be a straightforward subtraction operation. This simplicity might limit its efficiency in excluding associations with phenotypes from specific subpopulations, potentially leading to inaccurate interpretations of the data.

The review would benefit from additional validation studies to assess the effectiveness of SCellBOW in distinguishing between cancerous and non-cancerous signals, particularly in heterogeneous tumor environments.

Further clarification on how SCellBOW handles mixed-cell populations within bulk RNA-seq data would strengthen the evaluation of its applicability and reliability in diverse research settings.

Reviewer #1 (Public Review):

This study unveils a novel role for ferritin in Drosophila larval brain development. Furthermore, it pinpoints that the observed defects in larval brain development resulting from ferritin knockdown are attributed to impaired Fe-S cluster activity and ATP production. Overall this is a well-conducted and novel study.

The author have adequately addressed the concerns.

In this study, the authors confirm that one of the genes classified as essential in a Tn-mutagenesis study in A. baumannii, Aeg1, is, in fact, an essential gene. The strength of the work is that it discovered that the depletion of Aeg1 leads to cell filamentation and that activation mutations in various cell division genes can suppress the requirement for Aeg1. These results suggest that Aeg1 plays an important role in cell division. The work's weakness is that it lacks convincing evidence to define Aeg1's place or role in the divisome assembly pathway. It is unclear whether proteins are at the division site under the wildtype condition and when Aeg1 is depleted, and whether Aeg1 is indeed required for a set of division proteins to the division site.

Reviewer comments:

The revised manuscript partially addressed two of the three major concerns from the previous assessment: (1) the functionality test of fluorescent fusion proteins using a spotting assay, and (2) membrane protein topology in the bacterial two-hybrid assays by constructing a C-terminal T25 fusion.

(1) In the spotting assay, all fluorescent fusion proteins rescued the growth of the corresponding deletion strain, which suggests these fusion proteins are functional. However, fluorescent images of these fusion proteins were diffusive, and only a few cells showed the expected midcell/membrane localization pattern for cell division proteins. This observation raised the concern that these fusion proteins may be cleaved in the middle, leading to the separation of the untagged fusion partner and diffusive fluorescent protein in the cytoplasm, which would explain the positive spotting rescue results. This phenomenon is commonly observed in other bacterial species. A western blot using an antibody targeting either the fluorescent protein or the fusion partner is widely used to examine whether the fusion protein is expressed at its full length.

(2) The authors constructed a C-terminal fusion of Aeg1 and showed that it still interacted with ZipA and FtsN. This result supports the authors' suggestion that the N-terminus of Aeg1 may not be the predicated membrane-targeting domain. Along the same line, the membrane topology of ZipA should also be considered. ZipA's N terminus is in the membrane facing the periplasm, and its C terminal domain is in the cytoplasm. Therefore, the PUT18C fusion will place the T18 domain of ZipA in the periplasm. All other division proteins' N termini are in the cytoplasm.

(3) Colocalization images did not show significant midcell localizations for each fluorescent protein; most cells showed diffusive cytoplasmic fluorescence. In all other species, midcell localization of cell division proteins is prominent in dividing cells, especially for early division proteins such as ZipA (at least 40-50% of cells show midcell bands). In A. baumannii, divisome localization timing may differ from other species, but this possibility needs to be established before the colocalization pattern is examined. Compounding this issue is that in Aeg1 depletion strains, some cells expressing ZipA, FtsB, FtsL, and FtsN fusions showed roughly regularly spaced puncta in long filamentous cells. It is hard to explain why this was observed if, under the WT condition, these fusions do not localize to the midcell. These results again raised concerns that these fusion proteins may not be functional and the observations are protein aggregates.

Besides these major issues, experimental observations did not support some claims in the main text. For example: (1) In the two-hybrid assay, only ZipA and FtsN showed significant interactions with Aeg1, as judged by the darkness of the blue spots. FtsL and FtsB showed pale spots. The quantified values accompanying this figure did not appear to agree with the image. (2) The spotting rescue assay showed that only FtsB-E56A and FtsA-E202K was able to bypass Aeg1 depletion (full dilution set comparable to that of Aeg1 complementation), but the main text claimed that FtsA-D124A and V144L, and FtsW-M254I and S274G also rescued the growth. These claims could be misleading.

Reviewer #1 (Public Review):

Summary:

Understanding the mechanisms of how organisms respond to environmental stresses is a key goal of biological research. Assessment of transcriptional responses to stress can provide some insights into those underlying mechanisms. The researchers quantified traits, fitness, and gene expression (transcriptional) response to salinity stress (control vs stress treatments) for 130 accessions of rice (three replicates for each accession), which were grown in the field in the Philippines. This experimental design allowed for many different types of downstream analyses to better understand the biology of the system. These analyses included estimating the strength of selection imposed on transcription in each environment, evaluating possible trade-offs in gene expression, testing whether salinity induces transcriptional decoherence, and conducting various eQTL-type analyses.

Strengths:

The study provides an extensive analysis of gene expression responses to stress in rice and offers some insights into underlying mechanisms of salinity responses in this important crop system. The fact that the study was conducted under field conditions is a major plus, as the gene expression responses to soil salinity are more realistic than if the study was conducted in a greenhouse or growth chamber. The preprint is generally well-written and the methods and results are mostly well-described.

Weaknesses:

While the study makes good use of analyzing the dataset, it is not clear how the current work advances our understanding of gene regulatory evolution or plant responses to soil salinity generally. Overall, the results are consistent with other prior studies of gene expression and studies of selection across environmental conditions. Some of the framing of the paper suggests that there is more novelty to this study than there is in reality. That said, the results will certainly be useful for those working in rice and should be interesting to scientists interested in how gene expression responses to stress occur under field conditions. I detail other concerns I had about the preprint below:

The abstract on lines 33-35 illustrates some of my concerns about the overstatement of the novelty of the current study. For example, is it really true that the role of gene expression in mediating stress response and adaptation is largely unexplored? There have been numerous studies that have evaluated gene expression responses to stresses in a wide range of organisms. Perhaps, I am missing something critically different about this study. If so, I would recommend that the authors reword this sentence to clarify what gap is being filled by this study. Further, is it really the case that none of them have evaluated how the correlational structure of gene expression changes in response to stresses in plants, as implied in lines 263-265? Don't the various modules and PC analyses of gene expression get at this question?

There were some places in the methods of the preprint that required more information to properly evaluate. For example, more information should be provided on lines 664-668 about how G, E, and GxE effects were established, especially since this is so central to this study. What programs/software (R? SAS? Other?) were used for these analyses? If R, how were the ANOVAs/models fit? What type of ANOVA was used? How exactly was significance determined for each term? Which effects were considered fixed and which were random? If the goal was to fit mixed models, why not use an approach like voom-limma (Law et al. 2014 Genome Biology)? More details should also be added to lines 688-709 about these analyses, including what software/programs were used for these analyses.

One thing that I found a bit confusing throughout was the intermixing of different terms and types of selection. In particular, there seemed to be some inconsistencies with the usage of quantitative genetics terms for selection (e.g. directional, stabilizing) vs molecular evolution terms for selection (e.g. positive, purifying). I would encourage the authors to think carefully about what they mean by each of these terms and make sure that those definitions are consistently applied here.

It would be useful to clarify the reasons for the inherent bias in the detection of conditional neutrality (CN) and antagonistic pleiotropy (AP; Lines 187-196). It is also not clear to me what the authors did to deal with the bias in terms of adjusting P-value thresholds for CN and AP the way it is currently written. Further, I found the discussion of antagonistic pleiotropy and conditional neutrality to be a bit confusing for a couple of reasons, especially around lines 489-491. First of all, does it really make sense to contrast gene expression versus local adaptation, when lots of local adaptation likely involves changes in gene expression? Second, the implication that antagonistic pleiotropy is more common for local adaptation than the results found in this study seems questionable. Conditional neutrality appears to be more common for local adaptation as well: see Table 2 of Wadgymar et al. 2017 Methods in Ecology and Evolution. That all said, it is always difficult to conclude that there are no trade-offs (antagonistic pleiotropy) for a particular locus, as the detecting trade-offs may only manifest in some years and not others and can require large sample sizes if they are subtle in effect.

Reviewer #1 (Public Review):

The study starts with the notion that in an AD-like disease model, ILC2s in the Rag1 knock-out were expanded and contained relatively more IL-5+ and IL-13+ ILC2s. This was confirmed in the Rag2 knock-out mouse model.

By using a chimeric mouse model in which wild-type knock-out splenocytes were injected into irradiated Rag1 knock-out mice, it was shown that even though the adaptive lymphocyte compartment was restored, there were increased AD-like symptoms and increased ILC2 expansion and activity. Moreover, in the reverse chimeric model, i.e. injecting a mix of wild-type and Rag1 knock-out splenocytes into irradiated wild-type animals, it was shown that the Rag1 knock-out ILC2s expanded more and were more active. Therefore, the authors could conclude that the RAG1 mediated effects were ILC2 cell-intrinsic.

Subsequent fate-mapping experiments using the Rag1Cre;reporter mouse model showed that there were indeed RAGnaïve and RAGexp ILC2 populations within naïve mice. Lastly, the authors performed multi-omic profiling, using single-cell RNA sequencing and ATAC-sequencing, in which a specific gene expression profile was associated with ILC2. These included well-known genes but the authors notably also found expression of Ccl1 and Ccr8 within the ILC2. The authors confirmed their earlier observations that in the RAGexp ILC2 population, the Th2 regulome was more suppressed, i.e. more closed, compared to the RAGnaïve population, indicative of the suppressive function of RAG on ILC2 activity. I do agree with the authors' notion that the main weakness was that this study lacks the mechanism by which RAG regulates these changes in ILC2s.

The manuscript is very well written and easy to follow, and the compelling conclusions are well supported by the data. The experiments are meticulously designed and presented. I wish to commend the authors for the study's quality.

Even though the study is compelling and well supported by the presented data, some additional context could increase the significance:

(1) The presence of the RAGnaïve and RAGexp ILC2 populations raises some questions on the (different?) origin of these populations. It is known that there are different waves of ILC2 origin (most notably shown in the Schneider et al Immunity 2019 publication, PMID 31128962). I believe it would be very interesting to further discuss or possibly show if there are different origins for these two ILC populations.

Several publications describe the presence and origin of ILC2s in/from the thymus (PMIDs 33432227 24155745). Could the authors discuss whether there might be a common origin for the RAGexp ILC2 and Th2 cells from a thymic lineage? If true that the two populations would be derived from different populations, e.g. being the embryonic (possibly RAGnaïve) vs. adult bone marrow/thymus (possibly RAGexp), this would show a unique functional difference between the embryonic derived ILC2 vs. adult ILC2.

(2) On line 104 & Figures 1C/G etc. the authors describe that in the RAG knock-out ILC2 are relatively more abundant in the lineage negative fraction. On line 108 they further briefly mentioned that this observation is an indication of enhanced ILC2 expansion. Since the study includes an extensive multi-omics analysis, could the authors discuss whether they have seen a correlation of RAG expression in ILC2 with regulation of genes associated with proliferation, which could explain this phenomenon?

Reviewer #1 (Public Review):

Summary:

In this manuscript, the authors experimentally demonstrated the heterogeneous behavior of sarcomeres in cardiomyocytes and that a stochastic component exists in their contractile activity, which cancels out at the level of myofibrils.

Strengths:

The experiments and data analysis are robust and valid. With very good statistics and unbiased methods, they show cellular activity at the individual level and highlight the heterogeneity between biological networks. The similarity of the results to the study cited in [24] demonstrates the validity of the in vitro setup for answering these questions and the feasibility of such in-vitro systems to extend our knowledge of physiology.

Weaknesses:

Compared to the current literature ([24]), the study does not show a high degree of innovation. It mainly confirms what has been established in the past. The authors complemented the published experiments by developing an in vitro setup with stem cells and by changing the stiffness of the substrate to simulate pathological conditions. However, the experiments they performed do not allow them to explain more than the study in [24], and the conclusions of their study are based on interpretation and speculation about the possible mechanism underlying the observations.

Reviewer #1 (Public Review):

Summary:

In this manuscript, Yang et al report a novel regulatory role of SIRT4 in the progression of kidney fibrosis. The authors showed that in the fibrotic kidney, SIRT4 exhibited an increased nuclear localization. Deletion of Sirt4 in renal tubule epithelium attenuated the extent of kidney fibrosis following injury, while overexpression of SIRT4 aggravates kidney fibrosis. Employing a battery of in vitro and in vivo experiments, the authors demonstrated that SIRT4 interacts with U2AF2 in the nucleus upon TGF-β1 stimulation or kidney injury and deacetylates U2AF2 at K413, resulting in elevated CCN2 expression through alternative splicing of Ccn2 gene to promote kidney fibrosis. The authors further showed that the translocation of SIRT4 is through the BAX/BAK pore complex and is dependent on the ERK1/2-mediated phosphorylation of SIRT4 at S36, and consequently the binding of SIRT4 to importin α1. This fundamental work substantially advances our understanding of the progression of kidney fibrosis and uncovers a novel SIRT4-U2AF2-CCN2 axis as a potential therapeutic target for kidney fibrosis.

Strengths:

Overall, this is an extensive, well-performed study. The results are convincing, and the conclusions are mostly well supported by the data. The message is interesting to a wider community working on kidney fibrosis, protein acetylation, and SIRT4 biology.

Weaknesses:

The manuscript could be further strengthened if the authors could address a few points listed below:

(1) In the results part 3.9, an in vitro deacetylation assay employing recombinant SIRT4 and U2AF2 should be included to support the conclusion that SIRT4 is a deacetylase of U2AF2. Similarly, an in vitro binding assay can be included to confirm whether SIRT4 and U2AF2 are directly interacted.

(2) In Figure 6D, the Western Blot data using U2AF2-K453Q is confusing and is quite disconnected from the rest of the data and not explained. This data can be removed or explained why U2AF2-K453Q is employed here.

(3) Although ERK inhibitor U0126 blocked the nuclear translocation of SIRT4 in vivo, have the authors checked whether treatment with U0126 could affect the expression of kidney fibrosis markers in UUO mice?

(4) The format of gene and protein abbreviations in the manuscript should be standardized.

(5) There are a few grammar issues throughout the manuscript. The English/grammar could be stronger, thus improving the overall accessibility of the science to readers.

Reviewer #1 (Public Review):

Summary:

Zhao et al. used the human forebrain organoid model, transgenic mice model, and embryonic neural progenitor cells to investigate the mutation previously identified in Williams Syndrome. They found abnormal proliferation and differentiation induced by this mutation, as well as altered expression profiles corresponding with aberrant cell clusters. This is regulated through the binding of GTF2IRD1 to transthyretin (TTR) promoter regions and tested on three models mentioned above on neurodevelopmental deficits.

Strengths:

Authors have applied both cell culture, organoid culture and in vivo model to test the previously reported mutation found in Williams Syndrome. They investigated cell behavior including proliferation and differentiation, while using the NGS technique to identify potential signaling pathways that are highly involved and can serve as a candidate to save the phenotype.

Reviewer #1 (Public Review):

Summary:

Young (2.5 mo [adolescent]) rats were tasked to either press one lever for immediate reward or another for delayed reward. The task had a complex structure in which (1) the number of pellets provided on the immediate reward lever changed as a function of the decisions made, (2) rats were prevented from pressing the same lever three times in a row. Importantly, this task is very different from most intertemporal choice tasks which adjust delay (to the delayed lever), whereas this task held the delay constant and adjusted the number of 20 mg sucrose pellets provided on the immediate value lever.

Analyses are based on separating sessions into groups, but group membership includes arbitrary requirements and many sessions have been dropped from the analyses. Computational modeling is based on an overly simple reinforcement learning model, as evidenced by fit parameters pegging to the extremes. The neural analysis is overly complex and does not contain the necessary statistics to assess the validity of their claims.

Strengthes:

The task is interesting.

Weaknesses:

Behavior:

The basic behavioral results from this task are not presented. For example, "each recording session consisted of 40 choice trials or 45 minutes". What was the distribution of choices over sessions? Did that change between rats? Did that change between delays? Were there any sequence effects? (I recommend looking at reaction times.) Were there any effects of pressing a lever twice vs after a forced trial? This task has a very complicated sequential structure that I think I would be hard pressed to follow if I were performing this task. Before diving into the complex analyses assuming reinforcement learning paradigms or cognitive control, I would have liked to have understood the basic behaviors the rats were taking. For example, what was the typical rate of lever pressing? If the rats are pressing 40 times in 45 minutes, does waiting 8s make a large difference?

For that matter, the reaction time from lever appearance to lever pressing would be very interesting (and important). Are they making a choice as soon as the levers appear? Are they leaning towards the delay side, but then give in and choose the immediate lever? What are the reaction time hazard distributions?

It is not clear that the animals on this task were actually using cognitive control strategies on this task. One cannot assume from the task that cognitive control is key. The authors only consider a very limited number of potential behaviors (an overly simple RL model). On this task, there are a lot of potential behavioral strategies: "win-stay/lose-shift", "perseveration", "alternation", even "random choices" should be considered.

The delay lever was assigned to the "non-preferred side". How did side bias affect the decisions made?

The analyses based on "group" are unjustified. The authors compare the proportion of delayed to immediate lever press choices on the non-forced trials and then did k-means clustering on this distribution. But the distribution itself was not shown, so it is unclear whether the "groups" were actually different. They used k=3, but do not describe how this arbitrary number was chosen. (Is 3 the optimal number of clusters to describe this distribution?) Moreover, they removed three group 1 sessions with an 8s delay and two group 2 sessions with a 4s delay, making all the group 1 sessions 4s delay sessions and all group 2 sessions 8s delay sessions. They then ignore group 3 completely. These analyses seem arbitrary and unnecessarily complex. I think they need to analyze the data by delay. (How do rats handle 4s delay sessions? How do rats handle 6s delay sessions? How do rats handle 8s delay sessions?). If they decide to analyze the data by strategy, then they should identify specific strategies, model those strategies, and do model comparison to identify the best explanatory strategy. Importantly, the groups were session-based, not rat based, suggesting that rats used different strategies based on the delay to the delayed lever.

The reinforcement learning model used was overly simple. In particular, the RL model assumes that the subjects understand the task structure, but we know that even humans have trouble following complex task structures. Moreover, we know that rodent decision-making depends on much more complex strategies (model-based decisions, multi-state decisions, rate-based decisions, etc). There are lots of other ways to encode these decision variables, such as softmax with an inverse temperature rather than epsilon-greedy. The RL model was stated as a given and not justified. As one critical example, the RL model fit to the data assumed a constant exponential discounting function, but it is well-established that all animals, including rodents, use hyperbolic discounting in intertemporal choice tasks. Presumably this changes dramatically the effect of 4s and 8s. As evidence that the RL model is incomplete, the parameters found for the two groups were extreme. (Alpha=1 implies no history and only reacting to the most recent event. Epsilon=0.4 in an epsilon-greedy algorithm is a 40% chance of responding randomly.)

The authors do add a "dbias" (which is a preference for the delayed lever) term to the RL model, but note that it has to be maximal in the 4s condition to reproduce group 2 behavior, which means they are not doing reinforcement learning anymore, just choosing the delayed lever.

Neurophysiology:

The neurophysiology figures are unclear and mostly uninterpretable; they do not show variability, statistics or conclusive results.

As with the behavior, I would have liked to have seen more traditional neurophysiological analyses first. What do the cells respond to? How do the manifolds change aligned to the lever presses? Are those different between lever presses? Are there changes in cellular information (both at the individual and ensemble level) over time in the session? How do cellular responses differ during that delay while both levers are out, but the rats are not choosing the immediate lever?

Figure 3, for example, claims that some of the principal components tracked the number of pellets on the immediate lever ("ival"), but they are just two curves. No statistics, controls, or justification for this is shown. BTW, on Figure 3, what is the event at 200s?

I'm confused. On Figure 4, the number of trials seems to go up to 50, but in the methods, they say that rats received 40 trials or 45 minutes of experience.

At the end of page 14, the authors state that the strength of the correlation did not differ by group and that this was "predicted" by the RL modeling, but this statement is nonsensical, given that the RL modeling did not fit the data well, depended on extreme values. Moreover, this claim is dependent on "not statistically detectable", which is, of course, not interpretable as "not different".

There is an interesting result on page 16 that the increases in theta power were observed before a delayed lever press but not an immediate lever press, and then that the theta power declined after an immediate lever press. These data are separated by session group (again group 1 is a subset of the 4s sessions, group 2 is a subset of the 8s sessions, and group 3 is ignored). I would much rather see these data analyzed by delay itself or by some sort of strategy fit across delays. That being said, I don't see how this description shows up in Figure 6. What does Figure 6 look like if you just separate the sessions by delay?

Discussion:

Finally, it is unclear to what extent this task actually gets at the questions originally laid out in the goals and returned to in the discussion. The idea of cognitive effort is interesting, but there is no data presented that this task is cognitive at all. The idea of a resourced cognitive effort and a resistance cognitive effort is interesting, but presumably the way one overcomes resistance is through resource-limited components, so it is unclear that these two cognitive effort strategies are different.

The authors state that "ival-tracking" (neurons and ensembles that presumably track the number of pellets being delivered on the immediate lever - a fancy name for "expectations") "taps into a resourced-based form of cognitive effort", but no evidence is actually provided that keeping track of the expectation of reward on the immediate lever depends on attention or mnemonic resources. They also state that a "dLP-biased strategy" (waiting out the delay) is a "resistance-based form of cognitive effort" but no evidence is made that going to the delayed side takes effort.

The authors talk about theta synchrony, but never actually measure theta synchrony, particularly across structures such as amygdala or ventral hippocampus. The authors try to connect this to "the unpleasantness of the delay", but provide no measures of pleasantness or unpleasantness. They have no evidence that waiting out an 8s delay is unpleasant.

The authors hypothesize that the "ival-tracking signal" (the expectation of number of pellets on the immediate lever) "could simply reflect the emotional or autonomic response". Aside from the fact that no evidence for this is provided, if this were to be true, then, in what sense would any of these signals be related to cognitive control?

Joint Public Review:

Summary:

This study retrospectively analyzed clinical data to develop a risk prediction model for pulmonary hypertension in high-altitude populations. This finding holds clinical significance as it can be used for intuitive and individualized prediction of pulmonary hypertension risk in these populations. The strength of evidence is high, utilizing a large cohort of 6,603 patients and employing statistical methods such as LASSO regression. The model demonstrates satisfactory performance metrics, including AUC values and calibration curves, enhancing its clinical applicability.

Strengths:

(1) Large Sample Size: The study utilizes a substantial cohort of 6,603 subjects, enhancing the reliability and generalizability of the findings.

(2) Robust Methodology: The use of advanced statistical techniques, including least absolute shrinkage and selection operator (LASSO) regression and multivariate logistic regression, ensures the selection of optimal predictive features.

(3) Clinical Utility: The developed nomograms are user-friendly and can be easily implemented in clinical settings, particularly in resource-limited high-altitude regions.

(4) Performance Metrics: The models demonstrate satisfactory performance, with strong AUC values and well-calibrated curves, indicating accurate predictions.

Weaknesses:

(1) Lack of External Validation: The models were validated internally, but external validation with cohorts from other high-altitude regions is necessary to confirm their generalizability.

(2) Simplistic Predictors: The reliance on ECG and basic demographic data may overlook other potential predictors that could improve the models' accuracy and predictive power.

(3) Regional Specificity: The study's cohort is limited to Tibet, and the findings may not be directly applicable to other high-altitude populations without further validation.

Reviewer #1 (Public Review):

The authors describe a comprehensive analysis of sex-biased expression across multiple tissues and species of mouse. Their results are broadly consistent with previous work, and their methods are robust, as the large volume of work in this area has converged toward a standardized approach.

I have a few quibbles with the findings, and the main novelty here is the rapid evolution of sex-biased expression over shorter evolutionary intervals than previously documented, although this is not statistically supported. The other main findings, detailed below, are somewhat overstated.

(1) In the introduction, the authors conflate gametic sex, which is indeed largely binary (with small sperm, large eggs, no intermediate gametic form, and no overlap in size) with somatic sexual dimorphism, which can be bimodal (though sometimes is even more complicated), with a large variance in either sex and generally with a great deal of overlap between males and females. A good appraisal of this distinction is at https://doi.org/10.1093/icb/icad113. This distinction in gene expression has been recognized for at least 20 years, with observations that sex-biased expression in the soma is far less than in the gonad.

For example, the authors frame their work with the following statement:<br /> "The different organs show a large individual variation in sex-biased gene expression, making it impossible to classify individuals in simple binary terms. Hence, the seemingly strong conservation of binary sex-states does not find an equivalent underpinning when one looks at the gene-expression makeup of the sexes"

The authors use this conflation to set up a straw man argument, perhaps in part due to recent political discussions on this topic. They seem to be implying one of two things. a) That previous studies of sex-biased expression of the soma claim a binary classification. I know of no such claim, and many have clearly shown quite the opposite, particularly studies of intra-sexual variation, which are common - see https://doi.org/10.1093/molbev/msx293, https://doi.org/10.1371/journal.pgen.1003697, https://doi.org/10.1111/mec.14408, https://doi.org/10.1111/mec.13919, https://doi.org/10.1111/j.1558-5646.2010.01106.x for just a few examples. Or b) They are the first to observe this non-binary pattern for the soma, but again, many have observed this. For example, many have noted that reproductive or gonad transcriptome data cluster first by sex, but somatic tissue clusters first by species or tissue, then by sex (https://doi.org/10.1073/pnas.1501339112, https://doi.org/10.7554/eLife.67485)<br /> Figure 4 illustrates the conceptual difference between bimodal and binary sexual conceptions. This figure makes it clear that males and females have different means, but in all cases the distributions are bimodal.

I would suggest that the authors heavily revise the paper with this more nuanced understanding of the literature and sex differences in their paper, and place their findings in the context of previous work.

(2) The authors also claim that "sexual conflict is one of the major drivers of evolutionary divergence already at the early species divergence level." However, making the connection between sex-biased genes and sexual conflict remains fraught. Although it is tempting to use sex-biased gene expression (or any form of phenotypic dimorphism) as an indicator of sexual conflict, resolved or not, as many have pointed out, one needs measures of sex-specific selection, ideally fitness, to make this case (https://doi.org/10.1086/595841, 10.1101/cshperspect.a017632). In many cases, sexual dimorphism can arise in one sex only without conflict (e.g. 10.1098/rspb.2010.2220). As such, sex-biased genes alone are not sufficient to discriminate between ongoing and resolved conflict.

(3) To make the case that sex-biased genes are under selection, the authors report alpha values in Figure 3B. Alpha value comparisons like this over large numbers of genes often have high variance. Are any of the values for male- female- and un-biased genes significantly different from one another? This is needed to make the claim of positive selection.

Reviewer #1 (Public Review):

Summary:

The title states "IL-2 enhances effector function but suppresses follicular localization of CD8+ T cells in chronic infection" which data from the paper show but does not seem to be the major goal of the authors. As stated in the short assessment above, the goal of this work seems to connect IL-2 signals, mostly given exogenously, to the differentiation of progenitor T cells (TPEX) that will help sustain effector T cell responses against chronic viral infection (TEX/TEFF). The authors mostly use chronic LCMV infection in mice as their model of choice, Flow cytometry, fluorescent microscopy, and some in vitro assays to explore how IL2 regulates TPEX and TEX/TEFF differentiation. Gain and loss of functions experiments are also conducted to explore the roles of L2 signaling and BLIMP-1 in regulating these processes. Lastly, a loose connection of their mouse findings on TPEX/TEX cells to a clinical study using low-dose IL-2 treatment in SLE patients is attempted.

Strengths:

(1) The impact of IL-2 treatment of TPEX/TEX differentiation is very clear.

(2) The flow cytometry data are convincing and state-of-the-art.

Weaknesses:

(1) The title appears disconnected from the major focus of the work.

(2) The number of TPEX cells is not changed. IL2 treatment increases the number of TEFF and the proportion of TPEX is lower suggesting it does not target TPEX formation. The conclusion about an inhibitory role of IL2 treatment on TPEX formation seems therefore largely overstated.

(3) Are the expanded TEX/TEFF cells really effectors? Only GrB and some cell surface markers are monitored (44, 62L). Other functions should be included, e.g., CD107a, IFNg, TNF, chemokines - Tbet?

(4) The rationale for IL2 treatment timing is unclear. Seems that this is given at the T cell contraction time and this is interesting compared to the early treatment that ablate TPEX generation. Maybe this should really be explored further?

(5) The TGFb/IL6/IL2 in vitro experiment does not bring much to the paper.

(6) The Figure 2 data try to provide an explanation for a prior lack of difference in viral titers after IL2 treatment. It is hard to be convinced by these tissue section data as presented. It also begs the question of how the host would benefit from the low dose IL-2 treatment if IL-2 TEFF are not contributing to viral control as a result of their inappropriate localization to viral reservoirs.

(7) It is unclear what the STA5CA and BLIMP-1 KO experiments in Figure 3 add to the story that is not already expected/known.

(8) The connection to the low-dose IL2 treatment in SLE patients is very loose and weak. This version is likely not the ligand that preferentially signals to CD122 either. SLE is different from a chronic viral infection and the question of timing seems critical from all the data shown in this manuscript. So it is very difficult to make any robust link to the mechanistic data.

(9) It is really unclear what the take-home message is. IL-2 is signaling via STAT5 and BLIMP1 is also a known target as published by many groups including this one, and these results are more than expected. The observation that TEFF may be differentially localized in the WP area is interesting but no mechanisms are really provided (guessing CXCR5 but again expected). Also, all these observations are highly dependent on the timing of IL2 administration which is fascinating but not explored at all. It also limits significance since underlying mechanisms are unknown and we do not know when such treatment would have to be given.

Reviewer #2 (Public Review):

Summary:

In this manuscript, Ghazi et reported that inhibition of KRASG12C signaling increases autophagy in KRASG12C expressing lung cancer cells. Moreover, the combination of DCC 3116, a selective ULK1/2 inhibitor, plus sotorasib displays cooperative/synergistic suppression of human KRASG12C driven lung cancer cell proliferation in vitro and tumor growth in vivo. Additionally, in genetically engineered mouse models of KRASG12C driven NSCLC, inhibition of either KRASG12C or ULK1/2 decreases tumor burden and increases mouse survival. Additionally, this study found that LKB1 deficiency diminishes the sensitivity of KRASG12C/LKB1Null-driven lung cancer to the combination treatment, perhaps through the emergence of mixed adeno/squamous cell carcinomas and mucinous adenocarcinomas.

Strengths:

Both human cancer cells and mouse models were employed in this study to illustrate that inhibiting ULK1/2 could enhance the responsiveness of KRASG12C lung cancer to sotorasib. This research holds translational importance.

Weaknesses:

The revised manuscript has addressed most of my previous concerns. However, I still have one issue: the sample size (n) for the GEMM study in Figures 4E and 4F is too small, despite the authors' explanation. The data do not support the conclusion due to the lack of significant difference in tumor burden. Additionally, the significance labels in Figure 4E are not clearly explained.

Reviewer #1 (Public Review):

Summary:

The authors profile gene expression, chromatin accessibility and chromosomal architecture (by Hi-C) in activated CD4 T cells and use this information to link non-coding variants associated with autoimmune diseases with putative target genes. They find over a 1000 genes physically linked with autoimmune disease loci in these cells, many of which are upregulated upon T cell activation. Focusing on IL2, they dissect the regulatory architecture of this locus, including the allelic effects of GWAS variants. They also intersect their variant-to-gene lists with data from CRISPR screens for genes involved in CD4 T cell activation and expression of inflammatory genes, finding enrichments for regulators. Finally, they showed that pharmacological inhibition of some of these genes impacts T cell activation.

This is a solid study that follows a well-established canvas for variant-to-gene prioritisation using 3D genomics, applying it to activated T cells. The authors go some way in validating the lists of candidate genes, as well as explore the regulatory architecture of a candidate GWAS locus. Jointly with data from previous studies performing variant-to-gene assignment in activated CD4 T cells (and other immune cells), this work provides a useful additional resource for interpreting autoimmune disease-associated genetic variation.

Autoimmune disease variants were already linked with genes in CD28-stimulated CD4 T cells using chromosome conformation capture, specifically Promoter CHi-C and the COGS pipeline (Javierre et al., Cell 2016; Burren et al., Genome Biol 2017; Yang et al., Nat Comms 2020). The authors cite these papers and present a comparative analysis of their variant-to-gene assignments (in addition to scRNA-seq eQTL-based assignments). Furthermore, they find that the Burren analysis yields a higher enrichment for gold standard genes.

I thank the authors for their revisions in response to my initial review. The revised version now includes a more comprehensive comparative analysis of different datasets and V2G approaches and discusses the potential sources of differences in the results. Most significantly, the authors have now included an interesting comparison of their methodology with the popular ABC technique and outlined the key limitations of ABC relative to their method and other (Capture) Hi-C-based V2G approaches.

Reviewer #1 (Public Review):

Summary:

The authors used structural and biophysical methods to provide insight into Parkin regulation. The breadth of data supporting their findings was impressive and generally well-orchestrated.

Strengths:

(1) They have done a better job explaining the rationale for their experiments thought-out.

(2) The use of molecular scissors in their construct represents a creative approach to examine inter-domain interactions. Appropriate controls were included.

(3) From my assessment, the experiments are well-conceived and executed.

(4) The authors do a better job of highlighting the question being addressed experimentally.

Reviewer #2 (Public Review):

Summary:

This is an exciting paper that explores the in vitro assembly of recombinant alpha-synuclein into amyloid filaments. The authors changed the pH and the composition of the assembly buffers, as well as the presence of different types of seeds, and analysed the resulting structures by cryo-EM.

Strengths:

By doing experiments at different pHs, the authors found that so-called type 2 and type-3 polymorphs form in a pH dependent manner. In addition, they find that type-1 filaments form in the presence of phosphate ions. One of their in vitro assembled type-1 polymorphs is similar to the alpha-synuclein filaments that were extracted from the brain of an individual with juvenile-onset synucleinopathy (JOS). They hypothesize that additional densities in a similar place as additional densities in the JOS fold correspond to phosphate ions.

Comments on the revised version:

This is OK now. I thank the authors for their constructive engagement with my comments.

Reviewer #1 (Public Review):

In this study, the authors introduced an essential role of AARS2 in maintaining cardiac function. They also investigated the underlying mechanism that through regulating alanine and PKM2 translation are regulated by AARS2. Accordingly, a therapeutic strategy for cardiomyopathy and MI was provided. Several points need to be addressed to make this article more comprehensive:

(1) Include apoptotic caspases in Figure 2B, and Figure 4 B and E as well.

(2) It would be better to show the change of apoptosis-related proteins upon the knocking down of AARS2 by small interfering RNA (siRNA).

(3) In Figure 5, the authors performed Mass Spectrometry to assess metabolites of homogenates. I was wondering if the change of other metabolites could be provided in the form of a heatmap.

(4) The amounts of lactate should be accessed using a lactate assay kit to validate the Mass Spectrometry results.

(5) How about the expression pattern of PKM2 before and after mouse MI. Furtherly, the correlation between AARS2 and PKM2?

(6) In Figure 5, how about the change of apoptosis-related proteins after administration of PKM2 activator TEPP-46?

Reviewer #1 (Public Review):

Tsai and Seymen et al. investigate associations between RTE expression and methylation and age and inflammation, using multiple public datasets. Compared to the previous round of review, the text of the manuscript has been polished and the phrasing of several findings has been made clearer and more precise. The authors also provided ample discussion to the prior reviewer comments in their rebuttal, including new analyses. All these changes are in the correct direction, however, I believe that part of the content of the rebuttal should be incorporated in the main text, for reasons that I will outline below.

Both reviewers found the reliance on microarray expression data to detract from the study. The authors argued that their choices are supported by existing publications which performed a similar quantification of TE expression using microarray data. It could still be argued that (as far as I can tell) Reichmann et al. used a substantially larger number of probes than this study, as a consequence of starting from different arrays, however, this is a minor point which the authors do not need to address. It is still undeniable that including the validation with RNA-seq data performed in the rebuttal would strengthen the manuscript. I especially believe that many readers would want to see this analysis be prominent in the manuscript, considering that both reviewers independently converged on the issue with microarray expression data. Personally, I would have included an RNA-seq dataset next to the microarray data in the main figures, however, I understand that this would require considerable restructuring and that placing RNA-seq data besides array data might be misleading. Instead, I would ask that the authors include their rebuttal figures R1 and R2 as supplementary figures.<br /> I would suggest introducing a new paragraph, between the section dedicated to expression data and the one dedicated to DNA methylation, mentioning the issues with microarray data (Some of which were mentioned by the reviewers and other which were mentioned by the authors in the discussion and introduction) to then introduce the validation with RNA-seq data.

Figure R3 is also a good addition and should be expanded to include the GTP and MESA study and possibly mentioned in the paragraph titled "RTE expression positively correlates with BAR gene signature scores except for SINEs."

"In this study, we did not compare MESA with GTP etc. We have analysed each dataset separately based on the available data for that dataset. Therefore, sacrificing one analysis because of the lack of information from the other does not make sense. We would do that if we were after comparing different datasets. Moreover, the datasets are not comparable because they were collected from different types of blood samples."

Indeed, the datasets are not compared directly, but the associations between age, BER and TE expression for each dataset are plotted and discussed right next to each other. It is therefore natural to wonder if the differences between datasets are due to differences in the type of blood sample or if they are a consequence of the different probe sets. Using a common set of probes would help answer that question.

Reviewer #1 (Public Review):

Summary:

This work focuses on the structure and regulation of the Anaphase-Promoting Complex/Cyclosome (APC/C), a large multi-subunit ubiquitin ligase that controls the onset of chromosome segregation in mitosis. Previous high-resolution structural studies have uncovered numerous structural features and regulatory mechanisms of the human APC/C, but it has remained unclear if these mechanisms are conserved in other model eukaryotes. To address this gap in our understanding, the authors employed cryo-electron microscopy to generate structural models of APC/C from the budding yeast S. cerevisiae, a key model organism in cell cycle analysis. In their comparison of the human and yeast complexes, the authors uncover many conserved structural features that are documented here in detail, revealing widespread similarities in the fundamental structural features of the enzyme. Interestingly, the authors also find evidence that two of the key mechanisms of human APC/C regulation are not conserved in the yeast enzyme. Specifically:

(1) The ubiquitin ligase activity of the APC/C depends on its association with a co-activator subunit such as CDH1 or CDC20, which serves both as a substrate-binding adaptor and as an activator of interactions with the E2 co-enzyme. Previous studies of the human APC/C revealed that co-activator binding induces a conformational change that enables E2 binding. In contrast, the current work shows that this E2-binding conformation already exists in the absence of a co-activator in the yeast enzyme, suggesting that the enhancement of E2 binding in yeast depends on other, as yet undiscovered, mechanisms.

(2) APC/C phosphorylation on multiple subunits is known to enhance APC/C activation by the CDC20 co-activator in mitosis. Previous studies showed that phosphorylation acts by promoting the displacement of an autoinhibitory loop that occupies part of the CDC20-binding site. In the yeast enzyme, however, there is no autoinhibitory loop in the CDC20-binding site, and there is no apparent effect of APC/C phosphorylation on co-activator binding sites. Thus, phosphorylation activates the yeast CDC20-APC/C by unknown mechanisms.

Strengths:

The strength of this paper is that it provides a comprehensive analysis of yeast APC/C structure and how it compares to previously determined human structures. The article systematically unwraps the key features of the structure in a subunit-by-subunit fashion, carefully revealing the key features that are the same or different in the two species. These descriptions are based on a thorough overview of past work in the field; indeed, this article serves as a concise review of the key features, conserved or otherwise, of APC/C structure and regulation.

Weaknesses:

No significant weaknesses were identified.

Reviewer #1 (Public Review):

Summary:

This study investigates how the human brain flexibly adjusts its representations of the world as the environment continually changes. The authors identified regions where the representation continuously drifted across multiple months. They also found that the representation in the parahippocampal cortex could be rapidly influenced by recent environmental inputs.

Strengths:

(1) This study touches upon a crucial but less-explored issue: the relationship between semantic knowledge updating and representation drift in the brain.

(2) This study addresses this issue with a unique dataset in which participants viewed objects embedded in thousands of natural scenes across many fMRI sessions over eight months.

(3) The method for investigating whether the recent inputs could change the neural representation is compelling (i.e., subtracting the backward correlation value from the forward correlation value).

Weaknesses:

(1) Statistical Inference.

(a) Statistical inference is across eight subjects. Low statistical power means high false positive rates.

(b) Multiple comparisons across brain regions were not corrected.

(2) Object Encoding

It is unclear whether the identified brain regions represent the objects (as declared in the manuscript) or the visual features shared by pictures of similar items. Such visual features could be those of the background (e.g., spatial layout or the color tone of the scene), not the objects.

(3) Semantic Content in the MTL

Items with higher levels of semantic association tend to cooccur in the same picture. The results could be driven by the number of pictures shared between each pair of items, not semantic similarity (as declared in the manuscript).

(4) Long-term Drift of Item Representations in the MTL

(a) The results show a long-term representational drift in the brain but provide no evidence suggesting that this long-term neural representational drift reflects the drift in semantic representation. Although the authors used the "semantic" mask defined in the previous step, it does not mean the representation drift in the semantic mask is semantic, and there is doubt whether the "semantic" mask defined in the previous step is really semantic (see the third point).

(b) The beta value of the drift can not be directly compared across regions. Different regions have different sizes and signal-to-noise ratios in the BOLD signal. Their within-item similarity can not be compared directly in the first place.

(5) Recent Structure Rapidly Influences Item Representations in PHC

(a) It is unclear why the authors implement additional modularity analysis instead of directly using the pairwise co-occurrence frequencies among the 80 items, which is more straightforward.

(b) It does not make sense to compare the recent structure to the long-term structure across all 30 sessions because the structure of the posterior sessions cannot influence the current structure updating.

(c) It is unclear how the authors calculate the structure-induced change in the PHC in Figure 7.

Reviewer #1 (Public Review):

In their paper, Kalidini et al. investigate why the motor system sometimes coarticulates movements within a sequence. They begin by examining this phenomenon in an optimal feedback controller (OFC) that performs reaching movements to two targets (T1 and T2). They show that coarticulation occurs only when the controller is not required to slow down at T1. When the controller must decelerate at T1, coarticulation does not occur. This observation holds true even though the controller has information about both targets in both scenarios. They test the same experiment on human participants and show that humans also coarticulate the reaches only when they are instructed to treat the first target as a via point. Both in human participants and OFC simulations, whenever the coarticulation is present, the long-latency response to perturbations during the first reach is also informed by the second target- suggesting that the information about the second target is already present in the circuitry that control the long-latency reflex.<br /> All experiments and analyses are standard and clearly explained. Their analysis of long-latency as a measure of coarticulation of sequence items is highly interesting and broadly useful for future experiment design. They successfully demonstrate that one reason the motor system sometimes coarticulates movements is due to high-level instructions on how to execute the sequence. These high-level instructions can, in turn, determine how and to what extent information about future sequence items is utilized by the low-level controller that governs muscle activity. However, the precise interaction between high-level task demands and low-level controllers at the neural tissue level remains an open question.

Reviewer #1 (Public Review):

Summary:

The authors sought to investigate the associations of age at breast cancer onset with the incidence of myocardial infarction (MI) and heart failure (HF). They employed a secondary data analysis of the UK Biobank. They used descriptive and inferential analysis including Cox proportional hazards models to investigate the associations. Propensity score matching was also used. They found that Among participants with breast cancer, younger onset age was significantly associated with elevated risks of MI (HR=1.36, 95%CI: 1.19 to 1.56, P<0.001) and HF (HR=1.31, 95% CI: 1.18 to 1.46, P<0.001). the reported similar findings after propensity matching.

Strengths:

The use of a large dataset is a strength of the study as the study is well-powered to detect differences. Reporting both the unmatched and the propensity-matched estimates was also important for statistical inference.

Weaknesses:

The authors have addressed all my previous comments. I have no further comments.

Reviewer #2 (Public Review):

Summary:

This work describes a new pharmacological targeting approach to inhibit selective functions of the ubiquitously expressed chemokine receptor CXCR4, a potential target of immunomodulatory or anti-cancer treatments. Overall, the results build a strong case for the potential of this new compound to target specific functions of CXCR4, particularly linked to tumorigenesis. However, a more thorough evaluation of the function of the compound as well as future studies in mammalian model systems are needed to better assess the promise of the compound.

Strengths:

The work elegantly utilizes in silico drug modelling to propose new small molecule compounds with specific features. This way, the authors designed compound AGR1.137, which abolishes ligand-induced CXCR4 receptor nanoclustering and the subsequent directed cell migration without affecting ligand-binding itself or some other ligand-induced signaling pathways. The authors have used a relatively broad set of experiments to validate and demonstrate the effects of the drug. Importantly, the authors also test AGR1.137 in vivo, using a zebra fish model of tumorigenesis and metastasis. A relatively strong inhibitory effect of the compound is reported.

Weaknesses:

The authors have been able to significantly strengthen their data from the first submission. The content of this manuscript is pretty solid, although studies in mammalian model systems are naturally needed in the future to better assess the promise of the compound.

Reviewer #1 (Public Review):

Ritvo and colleagues present an impressive suite of simulations that can account for three findings of differentiation in the literature. This is important because differentiation-in which items that have some features in common, or share a common associate are less similar to one another than are unrelated items-is difficult to explain with classic supervised learning models, as these predict the opposite (i.e., an increase in similarity). A few of their key findings are that differentiation requires a high learning rate and low inhibitory oscillations, and is virtually always asymmetric in nature.

This paper was very clear and thoughtful-an absolute joy to read. The model is simple and elegant, and powerful enough to re-create many aspects of existing differentiation findings. The interrogation of the model and presentation of the findings were both extremely thorough. The potential for this model to be used to drive future work is huge.

The authors have been very responsive to my previous reviews and I have no further concerns and identify no major weaknesses.

Reviewer #1 (Public Review):

Using a combination of cutting-edge high-resolution technologies (expansion microscopy, SIM, and CLEM) and biochemical approaches (in vitro translocation of actin filaments, cargo uptake assays, and drug treatment), the authors revisit and update previous results about TbMyo1 and TbACT in the bloodstream form (BSF) of Trypanosoma brucei. They show that a great part of the myosin motor is cytoplasmic but the fraction associated with organelles is in proximity to the endosomal system and in glycosomes. In addition, they show that TbMyo1 can move actin filaments in vitro and visualize for the first time this actomyosin system using specific antibodies, a "classical" antibody for TbMyo1, and a chromobody for actin. Finally, using latrunculin A, which sequesters G-actin and prevents F-actin assembly, the authors show the delocalization and eventually the loss of the filamentous actin signal and the concomitant loss of the endosomal system integrity.<br /> Overall this well-conducted and convincing study paves the way toward the elucidation of the role of an actomyosin system in the maintenance of the endosomal network in T. brucei.

Strengths:

The work is of high quality and uses advanced technologies to determine the involvement TbMyo1 and actin in the integrity of the endosomal system. The conclusions are not over-interpreted and are supported by the experimental results and their quantification.

Weaknesses:

Although disruption of the actomyosin system using either the actin-depolymerizing drug latrunculin A or the TbMyo1-RNAi cell line established an effect on the endosomal system integrity, it remains to understand how this occurs mechanistically and what are the intracellular components involved.

Reviewer #1 (Public Review):

Summary:

This research used cell-based signaling assay and Gaussian-accelerated molecular dynamics (GaMD) to study peptide-mediated signaling activation of Polycystin-1 (PC1), which is responsible for the majority of autosomal dominant polycystic kidney disease (ADPKD) cases. Synthetic peptides of various lengths derived from the N-terminal portion of the PC1 C-terminal fragment (CTF) were applied to HEK293T cells transfected with stalkless mouse CTF expression construct. It was shown that peptides including the first 7, 9, and 17 residues of the N-terminal portion could activate signaling to the NFAT reporter. To further understand the underlying mechanism, docking and peptide-GaMD simulations of peptides composed of the first 9, 17, and 21 residues from the N-terminal portion of the human PC1 CTF were performed. These simulations revealed the correlation between peptide-CTF binding and PC1 CTF activation characterized by the close contact (salt bridge interaction) between residues R3848 and E4078. Finally, a Potts statistical model was inferred from diverged PC1 homologs to identify strong/conserved interacting pairs within PC1 CTF, some of which are highly relevant to the findings from the peptide GaMD simulations. The peptide binding pockets identified in the GaMD simulations may serve as novel targets for design of therapeutic approaches for treating ADPKD.

Strengths:

(1) The experimental and computational parts of this study complement and mostly support each other, thus increasing the overall confidence in the claims made by the authors.

(2) The use of exogenous peptides and a stalkless CTF in the GaMD is a step forward compared to earlier simulations using the full CTF, CTF mutants, or the stalkless CTF alone. And it led to findings of novel binding pockets.

(3) Since the PC1 shares characteristics with the Adhesion class of GPCRs, the approaches used in this work may be extended to other similar systems.

Weaknesses:

(1) Only results for selective peptides (p9, p17 p21) binding with the protein were shown. It would be interesting to see the interaction between some (if not all) of the other peptides with the protein.

(2) The convergence of the simulations is not very good. The results should be interpreted more qualitatively rather than quantitively because large variations in the free energy profile were seen between different replicates. Although these simulations might have identified representative low-energy binding conformations of the peptides, whether they have explored all possible conformations is still a question.

Reviewer #1 (Public Review):

Summary:

In this study, Djebar et al. perform a comprehensive analysis of mutant phenotypes associated with the onset and progression of scoliosis in zebrafish ciliary transition zone mutants rpgrip1l and cep290. They determine that rpgrip1l is required in foxj1a-expressing cells for normal spine development, and that scoliosis is associated with brain ventricle dilations, loss of Reissner fiber polymerization, and the loss of 'tufts' of multi-cilia surrounding the subcommissural organ (the source of Reissner substance). Informed by transcriptomic and proteomic analyses, they identify a neuroinflammatory response in rpgrip1l and cep290 mutants that is associated with astrogliosis and CNS macrophage/microglia recruitment. Furthermore, anti-inflammatory drug treatment reduced scoliosis penetrance and severity in rpgrip1l mutants. Based on their data, the authors propose a feed-forward loop between astrogliosis, induced by perturbed ventricular homeostasis, and immune cells recruitment as a novel pathogenic mechanism of scoliosis in zebrafish ciliary transition zone mutants.

Strengths:

- Comprehensive characterization of the causes of scoliosis in ciliary transition zone mutants rpgrip1l and cep290<br /> - Comparison of rpgrip1l mutants pre- and post-scoliosis onset allowed authors to identify specific phenotypes as being correlated with spine curvature, including brain ventricle dilations, loss of Reissner fiber, and loss of cilia in proximity to the subcommissural organ<br /> - Elegant genetic demonstration that increased urotensin peptide levels do not account for spinal curvature in rpgrip1l mutants<br /> - The identification of astrogliosis and Annexin over-expression in glial cells surrounding diencephalic and rhombencephalic ventricles as being correlated with scoliosis onset and severe curve progression is a very interesting finding, which may ultimately inform pathogenic mechanisms driving spine curvature

Weaknesses:

- The fact that cilia loss/dysfunction and Reissner fiber defects cause scoliosis in zebrafish is already well established in the literature, as is the requirement for cilia in foxj1a-expressing cells<br /> - Neuroinflammation has already been identified as the underlying pathogenic mechanism in at least 2 previously published scoliosis models (zebrafish ptk7a and sspo mutants)<br /> - Anti-inflammatory drugs like aspirin, NAC and NACET have also previously been demonstrated to suppress scoliosis onset and severe curve progression in these models<br /> Therefore, although similar observations in rpgrip1l and cep290 mutants (as reported here) add to a growing body of literature that supports a common biological mechanism underlying spine curvature in zebrafish, novelty of reported findings is diminished.<br /> - Although authors demonstrate that astrogliosis and/or macrophage or microglia cell recruitment are correlated with scoliosis, they do not formally demonstrate that these events are sufficient to drive spine curvature. Thus, the functional consequences of astrogliosis and microglia infiltration remain uncertain.<br /> - Authors do not investigate the effect of anti-inflammatory treatments on other phenotypes they have correlated with spinal curve onset (like ventricle dilation, Reissner fiber loss, and multi-cilia loss around the subcommissural organ). This would help to identify causal events in scoliosis.

Reviewer #1 (Public Review):

This manuscript by Tyler and colleagues describes a thorough analysis of IR-induced changes in nascent RNA transcripts, and a genome-wide screening effort to identify the responsible proteins. The findings extend previous work describing DNA damage-induced transcriptional repression from DNA breaks in cis to bulk genomic DNA damage. A significant discovery is the inability of arrested cells to undergo DNA damage-induced gene silencing, which, at least at the rDNA locus, is attributed to an inability to mediate ATM-induced transcriptional repression. While the findings add to our knowledge of how DNA damage affects gene expression, there are several limitations to the current study that remain inadequately addressed. In addition, some of the proposed conclusions seem speculative and should be marked as such, omitted or experimentally supported.

Two major concerns were as follows and have been addressed as outlined in the authors' response to this review:

(1) The CIRSPR screen designed to detect regulators of damage-induced transcriptional repression is based on EU incorporation following a 7-day selection of stable knockout cells. As the authors point out, cell cycle arrest reduces rDNA transcription on its own. The screen, which assesses changes in sgRNA distribution in EU high cells, is thus likely to be dominated by factors that affect cell cycle progression. This is exemplified in the analyses of top hits related to neddylation. The screen's limitations in terms of identifying DDR effectors of damage-induced silencing needs to be clearly stated.

(2) The authors confirm previous findings of DNA damage-induced repression of rDNA and histone gene transcription. The authors propose that these highly transcribed genes are more susceptible to silencing than the bulk of protein coding genes and propose a global damage-induced signaling event that is independent of DNA breaks in cis. While this is possible, it is not demonstrated in this manuscript, and the authors should acknowledge alternative explanations. For example, the loci found to be repressed by bulk IR are highly repetitive gene arrays that tend to form nuclear sub-compartments (nucleoli, histone bodies). As such, their likelihood of being in the vicinity of DNA damage is high, at least for a fraction of gene copies. The findings, therefore, remain consistent with cis-induced silencing. Moreover, silencing may spread through the relevant nuclear sub-compartments, consistent with the formation of DNA damage compartments described recently (PMID: 37853125).

Other comments - also addressed in the authors' response:

(1) The statement that silencing is due to transcription initiation rather than elongation is not sufficiently supported by the data. Could equivalent nascent transcript reduction not be the result of the suppression of elongating RNA PolII? To draw the proposed conclusion, the authors would need to demonstrate that RNA PolII initiation is altered, using RNA PollII ChIP and/or analysis of relevant RNA PolII phosphorylation patterns.

(2) The lack of rDNA silencing in arrested cells is interesting, though the underlying mechanism remains unclear. To further corroborate the proposed defect in ATM-mediated signaling, the authors should look directly at ATM and Treacle phosphorylation upstream of TOPBP1.

(3) The "change in relative heights of the EU low (G1) and EU high (S/G2) peaks" in Figs 5D, 5E and 6B is central to the proposed model of transcriptional changes being affected by cell cycle arrest. These differences should be visualized more clearly and quantified across independent experiments. Ideally, cell cycle stage should be dissected as in Fig. 2B. How do the authors envision cell cycle arrest triggers the defect in transcriptional silencing?

Reviewer #1 (Public Review):

Summary:

This manuscript dissects the contribution of the CaBP 1 and 2 on the calcium current in the cochlear inner hair cells. The authors measured the calcium current inactivation from the double knock-out CaBP1 and 2 and show that both proteins contribute to the voltage-dependent and calcium-dependent inactivation. Synaptic release was reduced in the double KO. As a consequence, the authors observed a depressed activity within the auditory nerve. Taken together, this study identifies a new player that regulates the stimulation-secretion coupling in the auditory sensory cells.

Strengths:

In this study, the authors bring compelling evidence that CaBP 1 and 2 are both involved in the inactivation of the calcium current, from cellular up to system level and by taking care to probe different experimental conditions such as different holding potentials and by rescuing the phenotype with the re-expression of CaBP2. Indeed, while changing the holding potential worsen the secretion, it completely changes the kinetics of the inactivation recovery. It alerts the reader that probing different experimental conditions that may be closer to physiology are better suited to uncover any deleterious phenotype. This gave pretty solid results.

Weaknesses:

Although this study clearly points that CaBP1 is involved in the calcium current inactivation, it is not clear how CaBP1 and CaBP2 act together (but this is probably beyond the scope of the study). Another point is that the authors re-express CaBP2 to largely rescue the phenotype in the double KO but no data are available to know whether the re-expression of both CaBP1 and CaBP2 would achieve a full recovery and what would be the effect of the sole re-expression of CaBP1 in the double KO.

Reviewer #1 (Public Review):

Summary:

In this work, Wang and colleagues used Drosophila-Serratia as a host-microbe model to investigate the impact of the host on gut bacteria. The authors showed that Drosophila larvae reduce S. marcescens abundance in the food likely due to a combination of mechanical force and secretion of antimicrobial peptides. S. marcescens exposed to Drosophila larvae lost virulence to flies and could promote larval growth similar to typical Drosophila gut commensals. These phenotypic changes were reflected in the transcriptome and metabolome of bacteria, suggesting that the host could drive the switch from pathogenicity to commensalism in bacteria. Further, the authors used single-cell bacterial RNA-seq to demonstrate the heterogeneity in gut bacterial populations.

Strengths:

This is a valuable work that addresses an important question of the impact of the host on its gut microbes. The authors could convincingly demonstrate that gut bacteria are strongly affected by the host with important consequences for both interacting partners. Moreover, the authors used state-of-the-art bacterial single-cell RNA-seq to reveal heterogeneity in host-associated commensal populations.

Overall most parts of the study are solid and clear.

Reviewer #1 (Public Review):

Summary:

The manuscript by Bell et. al. describes an analysis of the effects of removing one of two mutually exclusive splice exons at two distinct sites in the Drosophila CaV2 calcium channel Cacophony (Cac). The authors perform imaging and electrophysiology, along with some behavioral analysis of larval locomotion, to determine whether these alternatively spliced variants have the potential to diversify Cac function in presynaptic output at larval neuromuscular junctions. The author provided valuable insights into how alternative splicing at two sites in the calcium channel alters its function.

Strengths:

The authors find that both of the second alternatively spliced exons (I-IIA and I-IIB) that are found in the intracellular loop between the 1st and 2nd set of transmembrane domains can support Cac function. However, loss of the I-IIB isoform (predicted to alter potential beta subunit interactions) results in 50% fewer channels at active zones and a decrease in neurotransmitter release and the ability to support presynaptic homeostatic potentiation. Overall, the study provides new insights into Cac diversity at two alternatively spliced sites within the protein, adding to our understanding of how regulation of presynaptic calcium channel function can be regulated by splicing.

Weaknesses:

The authors find that one splice isoform (IS4B) in the first S4 voltage sensor is essential for the protein's function in promoting neurotransmitter release, while the other isoform (IS4A) is dispensable. The authors conclude that IS4B is required to localize Cac channels to active zones. However, I find it more likely that IS4B is required for channel stability and leads to the protein being degraded, rather than any effect on active zone localization. More analysis would be required to establish that as the mechanism for the unique requirement for IS4B.

Reviewer #1 (Public Review):

This study addresses the temporal patterning of a specific Drosophila CNS neuroblast lineage, focusing on its larval development. They find that a temporal cascade, involving the Imp and Syb genes changes the fate of one daughter cell/branch, from glioblast (GB) to programmed cell death (PCD), as well as gates the decommissioning of the NB at the end of neurogenesis.

Reviewer #1 (Public Review):

This study introduces an innovative method for assessing the mean kurtosis, utilizing the mathematical foundation of the sub-diffusion framework. In particular, a new fitting technique that incorporates two different diffusion times is proposed to estimate the parameters of the sub-diffusion model. The evaluation of this technique, which generates kurtosis maps based on the sub-diffusion framework, is conducted through simulations and the examination of data obtained from human subjects.

The authors have revised the manuscript to address the initial critiques. However, there appears to be some confusion regarding the following responses.

"The comment "... using the new sub-diffusion model -an approximation of the DKI-based signal expression..." is a bit misleading. In fact we propose that the reverse interpretation is the more suitable way to view the relationship: the DKI model is a degree-2 approximation of the sub-diffusion model, as in eq. (7).<br /> We appreciate the suggestion. However, unfortunately, it is not appropriate to generate data with the DKI model, as the maximum b-value is limited to 2000~3000s/mm^2 and hence the DKI model cannot represent diffusion MRI signals from a full spectrum of b-values. A key strength of our proposed model is that it removes this limitation. "

The main motivation of this study is to investigate the feasibility of the sub-diffusion model, which was proposed in Yang et al., NeuroImage 2022, to provide fast and robust estimation of kurtosis model parameters. I understand that mathematically, the DKI model can be written as a degree two approximation of the sub-diffusion model. However, the hypothesis is that the proposed sub-diffusion model can be used to obtain practically useful mapping of mean kurtosis. Therefore, unless the authors use a different parameter or phenomenon as the "true" or "ground-truth kurtosis," this study examines whether the sub-diffusion model parameters can serve as an approximation to the conventional DKI parameters.

With the current simulation study design, 1) the data is generated by the proposed sub-diffusion model, 2) the "ground-truth" or "true" D* and K* are computed based on the proposed equality (Eq.7); 3) and then the data is fit with the conventional DKI model and also with the proposed sub-diffusion model. Since the data is generated by the proposed model, and the ground truth (or true) values calculated by the proposed equality, as expected, the fitted kurtosis values by the sub-diffusion model match better with the simulated ones compared to the conventional DKI model.

Furthermore, as the authors noted, the sub-diffusion model eliminates the restriction on b-value selection, allowing for DWI data acquisition with higher b-values. However, it is unclear how the new K* and D* values, calculated directly from the sub-diffusion model using a higher b-value DWI protocol, are superior to the K and D values from the conventional DKI model, which uses a DWI protocol limited to b-values of 2000-3000 s/mm². In clinical practice, b-values of 2000-3000 s/mm² are generally considered "high b-value."

Reviewer #1 (Public Review):

Summary:<br /> The manuscript entitled A Modified BPaL Regimen for Tuberculosis Treatment<br /> replaces Linezolid with Inhaled Spectinamides by Malik Zohaib Ali et al. is an extension of previous studies by this group looking at the new drug spectinamide 1599. The authors directly compare therapy with BPaL (bedaquiline, pretomanid, linezolid) to a therapy that substitutes spectinamide for linezolid (BPaS). The Spectinamide is given by aerosol exposure and the BPaS therapy is shown to be as effective as BPaL without adverse effects. The work is rigorously performed and analyses of the immune responses are consistent with curative therapy.

Strengths:<br /> 1) This group uses 2 different mouse models to show the effectiveness of the BPaS treatment.<br /> 2)Impressively the group demonstrates immunological correlates associated with Mtb cure with the BPaS therapy.<br /> 3)Linezolid is known to inhibit ribsomes and mitochondria whereas spectinaminde does not. The authors clearly demonstrate the lack of adverse effects of BPaS compared to BPaL.

Weaknesses:<br /> 1) Although this is not a weakness of this paper, a sentence describing how the spectinamide would be administered by aerosolization in humans would be welcomed.

Reviewer #3 (Public Review):

Summary:

ImmCellTyper is a new toolkit for Cytometry by time-of-flight data analysis. It includes BinaryClust, a semi-supervised clustering tool (which takes into account the prior biological knowledge), designed for automated classification and annotation of specific cell types and subpopulations. ImmCellTyper also integrates a variety of tools to perform data quality analysis, batch effect correction, dimension reduction, unsupervised clustering, and differential analysis.

Strengths:

The proposed algorithm takes into account the prior knowledge.<br /> The results on different benchmark indicates competitive or better performance (in terms of accuracy and speed) depending on the method.

Reviewer #1 (Public Review):

Summary:

Insects inhabit diverse environments and have neuroanatomical structures appropriate to each habitat. Although the molecular mechanism of insect neural development has been mainly studied in Drosophila, the beetle, Tribolium castaneum has been introduced as another model to understand the differences and similarities in the process of insect neural development. In this manuscript, the authors focused on the origin of the central complex. In Drosophila, type II neuroblasts have been known as the origin of the central complex. Then, the authors tried to identify those cells in the beetle brain. They established a Tribolium fez enhancer trap line to visualize putative type II neuroblasts and successfully identified 9 of those cells. In addition, they also examined expression patterns of several genes that are known to be expressed in the type II neuroblasts or their lineage in Drosophila. They concluded that the putative type II neuroblasts they identified were type II neuroblasts because those cells showed characteristics of type II neuroblasts in terms of genetic codes, cell diameter, and cell lineage.

Strengths:

The authors established a useful enhancer trap line to visualize type II neuroblasts in Tribolium embryos. Using this tool, they have identified that there are 9 type II neuroblasts in the brain hemisphere during embryonic development. Since the enhancer trap line also visualized the lineage of those cells, the authors found that the lineage size of the type II neuroblasts in the beetle is larger than that in the fly. They also showed that several genetic markers are also expressed in the type II neuroblasts and their lineages as observed in Drosophila.

Weaknesses:

I recommend the authors reconstruct the manuscript because several parts of the present version are not logical. For example, the author should first examine the expression of dpn, a well-known marker of neuroblast. Without examining the expression of at least one neuroblast marker, no one can say confidently that it is a neuroblast. The purpose of this study is to understand what makes neuroanatomical differences between insects which is appropriate to their habitats. To obtain clues to the question, I think, functional analyses are necessary as well as descriptive analyses.

Reviewer #1 (Public Review):

Summary:

Hahn et al use bystander BRET, NanoBiT assays, and APEX2 proteomics to investigate endosomal signaling of CCR7 by two agonists, CCL19 and CCL21. The authors suggest that CCR7 signals from early endosomes following internalisation. They use spatial proteomics to try to identify novel interacting partners that may facilitate this signaling and use this data to specifically enhance a Rac1 signaling pathway. Many of the results in the first few figures showing simultaneous recruitment of Barr and G proteins by CCR7 have been shown previously (Laufer et al, 2019, Cell Reports), as has signaling from endomembranes, and Rac1 activation at intracellular sites. The new findings are the APEX2 proteomics studies, which could be useful to the scientific community. Unfortunately, the authors only follow up on a single finding, and the expansion of this section would improve the manuscript.

Strengths:

(1) The APEX2 resource will be valuable to the GPCR and immunology community. It offers many opportunities to follow up on findings and discover new biology. The resource could also be used to validate earlier findings in the current manuscript and in previous manuscripts. Was there enrichment of early endosomal markers, Barr and Gi as this would provide further evidence for their earlier claims regarding endosomal signaling? Previous studies have suggested signaling from the TGN, so it is possible that the different ligands also direct to different sites. This could easily be investigated using the APEX2 data.

(2) The results section is well written and can be followed very easily by the reader.

(3) Some findings verify previous studies (e.g. endomembrane signalling). This should be acknowledged as this shows the validity of the findings of both studies.

Weaknesses:

(1) The findings are interesting although the studies are almost all performed in HEK293 cells. I understand that these are commonly used in GPCR biology and are easy to transfect and don't express many GPCRs at high concentrations, but their use is still odd when there are many cell-lines available that express CCR7 and are more reflective of the endogenous state (e.g. they are polarised, they can perform chemotaxis/ migration). Some of the findings within the study should also be verified in more physiologically relevant cells. At the moment only the final figure looks at this, but findings need to be verified elsewhere.

(2) The authors acknowledge that the kinetic patterns of the signals at the early endosome are not consistent with the rates of internalisation. They mention that this could be due to trafficking elsewhere. This could be easily looked at in their APEX2 data. Is there evidence of proximity to markers of other membranes? Perhaps this could be added to the discussion. Similarly, previous studies have shown that CCR7 signaling may involve the TGN. Was there enrichment of these markers? If not, this could also be an interesting finding and should be discussed. It is also possible that the Rab5 reporter is just not as efficient as the trafficking one, especially as in later figures the very convincing differences in the two ligands are not as robust as the differences in trafficking.

(3) In the final sentence of paragraph 2 of the results the authors state that the internalisation is specific to CCR7 as there isn't recruitment to V2R. I'm not sure this is the best control. The authors can only really say it doesn't recruit to unrelated receptors. The authors could have used a different chemokine receptor which does not respond to these ligands to show this.

(4) The miniGi-Barr1 and imaging showing co-localisation could be more convincing if it was also repeated in a more physiological cell line as in the final figure. Imaging of CCR7, miniGi, and Barr1 would also provide further evidence that the receptor is also present within the complex.

(5) The findings regarding Rac1 are interesting, although an earlier paper found similar results (Laufer et al, 2019, Cell Reports), so perhaps following up on another APEX2-identified protein pathway would have been more interesting. The authors' statement that Rac1 is specifically activated, and RhoA and Cdc42 are not, is unconvincing from the current data. Only a single NanoBiT assay was used, and as raw values are not reported it is difficult for the reader to glean some essential information. The authors should show evidence that these reporters work well for other receptors (or cite previous studies) and also need evidence from an independent (i.e. non-NanoBiT or BRET) assay.

(6) At present, the studies in Figure 7 do not go beyond those in the previous Laufer et al study in which they showed blocking endocytosis affected Rac1 signalling. The authors could show that Rac1 signalling is from early endosomes to improve this, otherwise, it could be from the TGN as previously reported.

Reviewer #1 (Public Review):

Summary:

In this study, Nandy and colleagues examine neural, physiological and behavioral correlates of perceptual variability in monkeys performing a visual change detection task. They used a laminar probe to record from area V4 while two macaque monkeys detected a small change in stimulus orientation that occurred at a random time in one of two locations, focusing their analysis on stimulus conditions where the animal was equally likely to detect (hit) or not-detect (miss) a briefly presented orientation change (target). They discovered two behavioral and physiological measures that are significantly different between hit and miss trials - pupil size tends to be slightly larger on hits vs. misses, and monkeys are more likely to miss the target on trials in which they made a microsaccade shortly before target onset. They also examined multiple measures of neural activity across the cortical layers and found some measures that are significantly different between hits and misses.

Strengths:

Overall the study is well executed and the analyses are appropriate (though several issues still need to be addressed as discussed in Specific Comments).

Weaknesses:

My main concern with this study is that, with the exception of the pre-target microsaccades, the correlates of perceptual variability (differences between hits and misses) appear to be weak, potentially unreliable and disconnected. The GLM analysis of predictive power of trial outcome based on the behavioral and neural measures is only discussed at the end of the paper. This analysis shows that some of the measures have no significant predictive power, while others cannot be examined using the GLM analysis because these measures cannot be estimated in single trials. Given these weak and disconnected effects, my overall sense is that the current results provide limited advance to our understanding of the neural basis of perceptual variability.

Reviewer #1 (Public Review):

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

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

After the initial reviewers' comments, the authors performed a welcome revision of the way the results are presented. Overall the study has been improved by the revision. However, one piece of new data is perplexing to me. The new figure 7 presents the results of a model analysis of the strength of the EI caused by a second fish to localize when the focal fish is chirping. From my understanding of this type of model, EOD frequency is not a parameter in the model since it evaluates the strength of the field at a given point in time. Therefore the only thing that matters is the phase relationship and strength of the EOD. Assuming that the second fish's EOD is kept constant and the phase relationship is also the same, the only difference during a chirp that could affect the result of the calculation is the potential decrease in EOD amplitude during the chirp. It is indeed logical that if the focal fish decreased its EOD amplitude the target fish's EOD becomes relatively stronger. Where things are harder to understand is why the different types of chirps (e.g. type 1 vs type 2) lead to the same increase in signal even though they are typically associated with different levels of amplitude modulations. Also, it is hard to imagine that a type 2 chirp that is barely associated with any decrease in EOD amplitude (0-10% maybe), would cause a doubling of the EI strength. There might be something I don't understand but the authors should provide a lot more details on how this result is obtained and convince us that it makes sense.

Finally, the reviewer is concerned about this sentence in the rebuttal - "The methods section has been edited to clarify the approach (not yet)". This section is unfinished, which suggests that it is difficult to explain the modeling results from a logical point of view. Thus the reviewer's major concern from the previous review remains unresolved. To summarize, the model calculates field strengths at an instant in time and integrates over time with a 500 ms window. This window is 10 times longer than the small chirps, while the longer chirps cover a much larger proportion of the window. Yet, the small chirps have a bigger impact on discriminability than the longer chirps. The authors should attempt to explain this seemingly contradictory result. This remains a major issue because this analysis was the most direct evidence that chirping could impact localization accuracy.

Reviewer #1 (Public Review):

The present study provides a phylogenetic analysis of the size prefrontal areas in primates, aiming to investigate whether relative size of the rostral prefrontal cortex (frontal pole) and dorsolateral prefrontal cortex volume vary according to known ecological or social variables.

I am very much in favor of the general approach taken in this study. Neuroimaging now allows us to obtain more detailed anatomical data in a much larger range of species than ever before and this study shows the questions that can be asked using these types of data. In general, the study is conducted with care, focusing on anatomical precision in definition of the cortical areas and using appropriate statistical techniques, such as PGLS.

I have read the revised version of the manuscript with interest. I commend the authors for including the requested additional analyses. I believe these highlight some of the major debates in the field, such as the relationship between absolute and relative brain size of areas. Providing a full description of the data will help this field be more open about these issues. All too often, debates between different groups focus on narrow anatomical or statistical arguments, and having all the data here is important.

I do not agree with some of the statements of the other reviewers regarding development. Clearly, evolution works for a large part by tinkering (forgive the sense of agency) with development, but that does not mean that looking at the end result cannot provide insights. Ultimately, we will look at both phylogeny and ontogeny within the same framework, but the field is not quite there yet.

As I said before, I do believe this is a positive study. I am happy that we as a field are using imaging data to answer more wider phylogenetic questions. Combining detailed anatomy, big data, and phylogenetic statistical frameworks is an important approach.

Reviewer #1 (Public Review):

Summary:

This study further develops the potential of in vitro granulomas to study host-pathogen interactions in tuberculosis. It uses a human-based cellular model and a collection of M. tuberculosis isolates representative of the pathogen's diversity. It provides important methodologic information and some findings that help in defining protective responses in TB.

Strengths:

A strength of the study is the multitude of parameters addressed across different M. tuberculosis strains and donors. The inclusion of several strains of the same lineage shows that intra-lineage diversity is also relevant, illustrating how complex it is to model the immune response to M. tuberculosis.

Weaknesses:

A weakness of the study is that although several interesting findings are reported and a hypothesis proposed, the work is mainly descriptive and correlative. Some functional data based on the current observations would strengthen the findings.

Reviewer #1 (Public Review):

Summary:

The manuscript by Choi and co-authors presents "P3 editing", which leverages dual-component guide RNAs (gRNA) to induce protein-protein proximity. They explore three strategies for leveraging prime-editing gRNA (pegRNA) as a dimerization module to create a molecular proximity sensor that drives genome editing, splitting a pegRNA into two parts (sgRNA and petRNA), inserting self-splicing ribozymes within pegRNA, and dividing pegRNA at the crRNA junction. Among these, splitting at the crRNA junction proved the most promising, achieving significant editing efficiency. They further demonstrated the ability to control genome editing via protein-protein interactions and small molecule inducers by designing RNA-based systems that form active gRNA complexes. This approach was also adaptable to other genome editing methods like base editing and ADAR-based RNA editing.

Strengths:

The study demonstrates significant advancements in leveraging guide RNA (gRNA) as a dimerization module for genome editing, showcasing its high specificity and versatility. By investigating three distinct strategies-splitting pegRNA into sgRNA and petRNA, inserting self-splicing ribozymes within the pegRNA, and dividing the pegRNA at the repeat junction-the researchers present a comprehensive approach to achieving molecular proximity and reconstituting function. Among these methods, splitting the pegRNA at the repeat junction emerged as the most promising, achieving editing efficiencies up to 76% of the control, highlighting its potential for further development in CRISPR-Cas9 systems. Additionally, the study extends genome editing control by linking protein-protein interactions to RNA-mediated editing, using specific protein-RNA interaction pairs to regulate editing through engineered protein proximity. This innovative approach expands the toolkit for precision genome editing, demonstrating the feasibility of controlling genome editing with enhanced specificity and efficiency.

Weaknesses:

The initial experiments with splitting the pegRNA into sgRNA and petRNA showed low editing efficiency, less than 2%. Similarly, inserting self-splicing ribozymes within pegRNA was inefficient, achieving under 2% editing efficiency in all constructs tested, possibly hindered by the prime editing enzyme. The editing efficiency of the crRNA and petracrRNA split at the repeat junction varied, with the most promising configurations only reaching 76% of the control efficiency. The RNA-RNA duplex formation's inefficiency might be due to the lack of additional protein binding, leading to potential degradation outside the Cas9-gRNA complex. Extending the approach to control genome editing via protein-protein interactions introduced complexity, with a significant trade-off between efficiency and specificity, necessitating further optimization. The strategy combining RADARS and P3 editing to control genome editing with specific RNA expression events exhibited high background levels of non-specific editing, indicating the need for improved specificity and reduced leaky expression. Moreover, P3 editing efficiencies are exclusively quantified after transfecting DNA into HEK cells, a strategy that has resulted in past reproducibility concerns for other technologies. Overall, the various methods and combinations require further optimization to enhance efficiency and specificity, especially when integrating multiple synthetic modules.

Reviewer #1 (Public Review):

Summary:

The main conclusion of this manuscript is that the mediator kinases supporting the IFN response in Downs syndrome cell lines represent an important addition to understanding the pathology of this affliction.

Strengths:

Mediator kinase stimulates cytokine production. Both RNAseq and metabolomics clearly demonstrate a stimulatory role for CDK8/CDK19 in the IFN response. The nature of this role, direct vs. indirect, is inferred by previous studies demonstrating that inflammatory transcription factors are Cdk8/19 substrates. The cytokine and metabolic changes are clear-cut and provide a potential avenue to mitigate these associated pathologies.

Weaknesses:

This study revealed a previously undescribed role for the CKM in splicing. The previous identification of splicing factors as substrates of CDK8/CDK19 is also intriguing. However, additional studies seem to be necessary in order to attach this new function to the CKM. As the authors point out, the changes in splicing patterns are relatively modest compared to other regulators. In addition, some indication that the proteins encoded by these genes exhibit reduced levels or activities would support their RNAseq findings.

Seahorse analysis is normally calculated with specific units for oxygen consumption, ATP production, etc. It would be of interest to see the actual values of OCR between the D21 and T21 cell lines rather than standardizing the results. This will address the specific question about relative mitochondrial function between these cells. Reduced mitochondrial function has been associated with DS patients. Therefore, it would be important to know whether mitochondrial function is reduced in the T21 cells vs. the D21 control. Importantly for the authors' goal of investigating the use of CDK8/19 inhibitors in DS patients, does CA treatment reduce mitochondrial function to pathological levels?

DOI: 10.1038/s41593-024-01724-1

Resource: (IMSR Cat# JAX_026175,RRID:IMSR_JAX:026175)

Curator: @dhovakimyan1

SciCrunch record: RRID:IMSR_JAX:026175

What is this?

DOI: 10.1093/hmg/ddad011

Resource: ZFIN_ZDB-GENO-190225-1

Curator: @olekpark

SciCrunch record: RRID:ZFIN_ZDB-GENO-190225-1

What is this?

DOI: 10.1038/s41467-023-40595-1

Resource: RRID:BDSC_66632

Curator: @anisehay

SciCrunch record: RRID:BDSC_66632

What is this?

DOI: 10.1186/s12915-023-01800-1

Resource: RRID:BDSC_854

Curator: @anisehay

SciCrunch record: RRID:BDSC_854

What is this?

Reviewer #1 (Public Review):

Summary:

I have previously reviewed this manuscript as a submission to another journal in 2022. My recommendations here mirror those of my prior suggestions, now with further added details.

This manuscript describes the identification and isolation of several phage from deep sea isolates of Lentisphaerae strains WC36 and zth2. The authors observe induction of several putative chronic phages with the introduction of additional polysaccharides to the media. The authors suggest that two of the recovered phage genomes encode AMGs associated with polysaccharide use. The authors also suggest that adding the purified phage to cultures of Pseudomonas stutzeri 273 increased the growth of this bacteria due to augmented polysaccharide use genes from the phage.

Strengths:

Interesting isolate of deep sea Lentisphaerae strains which will undoubtedly further our understanding of deep sea microbial life.

The revisions have addressed the weaknesses raised in the previous review.

Reviewer #1 (Public Review):

In this work, the authors investigate an important question - under what circumstances should a recurrent neural network optimised to produce motor control signals receive preparatory input before the initiation of a movement, even though it is possible to use inputs to drive activity just-in-time for movement?

This question is important because many studies across animal models have shown that preparatory activity is widespread in neural populations close to motor output (e.g. motor cortex / M1), but it isn't clear under what circumstances this preparation is advantageous for performance, especially since preparation could cause unwanted motor output during a delay.

They show that networks optimised under reasonable constraints (speed, accuracy, lack of pre-movement) will use the input to seed the state of the network before movement and that these inputs reduce the need for ongoing input during the movement. By examining many different parameters in simplified models they identify a strong connection between the structure of the network and the amount of preparation that is optimal for control - namely, that preparation has the most value when nullspaces are highly observable relative to the readout dimension and when the controllability of readout dimensions is low. They conclude by showing that their model predictions are consistent with the observation in monkey motor cortex that even when a sequence of two movements is known in advance, preparatory activity only arises shortly before movement initiation.

Overall, this study provides valuable theoretical insight into the role of preparation in neural populations that generate motor output, and by treating input to motor cortex as a signal that is optimised directly this work is able to sidestep many of the problematic questions relating to estimating the potential inputs to motor cortex.

Reviewer #2 (Public Review):

Summary:

The authors investigated systemic inflammation induced by LPS in various tissues and also examined immune cells of the mice using tight junction protein-based PDZ peptide. They explored the mechanism of anti-systemic inflammatory action of PDZ peptides, which enhanced M1/M2 polarization and induced the proliferation of M2 macrophages. Additionally, they insisted the physiological mechanism that inhibited the production of ROS in mitochondria, thereby preventing systemic inflammation.

Strengths:

In the absence of specific treatments for septic shock or sepsis, the study demonstrating that tight junction-based PDZ peptides inhibit systemic inflammation caused by LPS is highly commendable. Whereas previous research focused on antibiotics, this study proves that modifying parts of intracellular proteins can significantly suppress symptoms caused by septic shock. The authors expanded the study of localized inflammation caused by LPS or PM2.5 in the respiratory tract to systemic inflammation, presenting promising results. They not only elucidated the physiological mechanism by identifying the transcriptome through RNA sequencing but also demonstrated that PDZ peptides inhibit the production of ROS in mitochondria and prevent mitochondrial fission. This research is highly regarded as an excellent study with potential as a treatment for septic shock or sepsis.

Weaknesses:

(1) They Focused intensively on acute inflammation for a short duration instead of chronic inflammation.

(2) LPS was used to induce septic shock but administrating actual microbes such as E.coli would yield more accurate results.

(3) The authors used pegylated peptides, but future research should utilize the optimized peptides to derive the optimal peptide, and further, PK/PD studies are also necessary.

Reviewer #1 (Public Review):

The manuscript introduces a bioinformatic pipeline designed to enhance the structure prediction of pyoverdines, revealing an extensive and previously overlooked diversity in siderophores and receptors. Utilizing a combination of feature sequence and phylogenetic approaches, the method aims to address the challenging task of predicting structures based on dispersed gene clusters, particularly relevant for pyoverdines.

Predicting structures based on gene clusters is still challenging, especially pyoverdines as the gene clusters are often spread to different locations in the genome. The revised manuscript has much improved in clarity and reproducibility. I believe that the method is not yet applicable to all NRPS in general and that there is a clear scalability issue when talking about Big Data. However, the method is highly useful for specific NRPS families such as the pyoverdines, so the manuscript presents a useful bioinformatic pipeline for pyoverdine structure prediction, showcasing a commendable exploration of siderophore diversity.

Reviewer #1 (Public Review):

This manuscript remains an intriguing investigation of the elephant brainstem, with particular attention drawn to possible sensory and motor representation of the renowned trunk of African and Asian elephants. As the authors note, this area has traditionally been identified as part of the superior olivary complex and associated with the fine motor control of the trunk; however, notable patterns within myelin stripes suggest that its parcellation may relate to specific regions/folds found along the long axis of the trunk, including elaborated regions for the trunk "finger" distal end.

In this iteration of the manuscript, the researchers have provided peripherin antibody staining within the regions they have identified as the trigeminal nucleus and the superior olive. These data, with abundant peripherin expression within climbing fibers of the presumed superior olive and relatively lower expression within the trigeminal nucleus, bolster their interpretation of having comprehensively identified the trigeminal nucleus and trunk representation via a battery of neuroanatomical methods.

All other conclusions remain the same, and these data have provoked intriguing and animated discussion on classification of neuroanatomical structure, particularly in species with relatively limited access to specimens. Most significantly, these discussions have underscored the fundamental nature of comparative methods (from protein to cellular to anatomical levels), including interpreting homologous structures among species of varying levels of relatedness.

Reviewer #2 (Public Review):

Summary:

Overall this is an interesting innovative study that examines chromatin accessibility in an inhibitory iPSC model of Dravet Syndrome. The authors detect a potential intriguing development defect in the patient-specific neurons, however the correlation with gene expression or protein abundance is not compelling and the variability of the data is still difficult to determine.

Strengths:

(1) This is a novel and interesting study that aims to investigate the epigenetic changes that occur in a sodium channel model of epilepsy, these are oft ignored, but also an interesting area for future therapeutics.

(2) The paper is well written with good graphics and flow.

(3) With caveats noted below, there is an intriguing developmental defect in GABAergic neuron differentiation in this model. It would be interesting to see how this correlated with the expression of SCN1A, and I was surprised this was not addressed in the manuscript via RNA/protein abundance, nor how the absence of a sodium channel can accelerate differentiation when a priori I might expect the opposite (as less 'neuronal' signal)

(4) There is exploratory analysis that VPA alters chromatin accessibility at an individual-specific level. Though it was not noted if any of the DS patients,

Weaknesses addressed:

(1) Representative images for cell-identity markers are now shown for D19 and D65.

(2) The methods now state that three differentiations were performed.

(3) The authors address a possible role for cell death in data obtained from their cultures by assessing viability with trypan blue staining.

(4) Some features of ATAC signal normalization and enrichment analysis have been better documented.

(5) Some of the variability in key results is better documented.

Weaknesses poorly or not addressed:

(1) Although the authors include prior RNAseq data and report on qPCR measurements for SCN1A (Supp Fig 1)these do not on the surface appear to agree, with the RNAseq showing little apparent difference between patients and controls, while the qPCR seems to show a two-fold difference at D65. This is likely a misleading artifact of normalizing PCR expression to that at D0 when the gene is not expressed but has mildly different low levels in patients and controls. No measurement of the protein product or its function is included. This is a major weakness that casts doubt on the core hypothesis that epigenetic changes play a key causal role in Dravet syndrome.

(2) Although some QC on ATAC is described, QC performed on iPSC lines, i.e. karyotype/CNV analysis and confirmation of genotypes is not described in the paper.

(3) The authors describe a method for trying to diminish variability but do not adequately explain this method or how much variability remains in many of their measures.

(4) Given that VPA would be administered in patients with fully mature inhibitory neurons, it is difficult to determine the biological relevance of these findings.

Reviewer #1 (Public Review):

In this manuscript, entitled " Merging Multi-OMICs with Proteome Integral Solubility Alteration Unveils Antibiotic Mode of Action", Dr. Maity and colleagues aim to elucidate the mechanisms of action of antibiotics through combined approaches of omics and the PISA tool to discover new targets of five drugs developed against Helicobacter pylori.

Strengths:<br /> Using transcriptomics, proteomic analysis, protein stability (PISA), and integrative analysis, Dr. Maity and colleagues have identified pathways targeted by five compounds initially discovered as inhibitors against H. pylori flavodoxin. This study underscores the necessity of a global approach to comprehensively understand the mechanisms of drug action. The experiments conducted in this paper are well designed and the obtained results support the authors' conclusions.

Reviewer #1 (Public Review):

Summary:

The article by Siachisumo, Luzzi and Aldalaquan et al. describes studies of RBMX and its role in maintaining proper splicing of ultra-long exons. They combine CLIP, RNA-seq, and individual example validations with manipulation of RBMX and its family members RBMY and RBMXL2 to show that the RBMX family plays a key role in maintaining proper splicing of these exons.

I think one of the main strengths of the manuscript is its ability to explore a unique but interesting question (splicing of ultra-long exons), and derive a relatively simple model from the resulting genomics data. The results shown are quite clean, suggesting that RBMX plays an important role in proper regulation of these exons. The ability of family members to rescue this phenotype (as well as only particular domains) is also quite intriguing and suggests that the mechanisms for keeping these exons properly spliced may be a quite important and highly conserved mechanism.

The revised manuscript addresses many of my earlier critiques and does an effective job of arguing that RBMX plays a large-scale role in regulating splicing of long exons. I think there are obvious open questions for future work (the mechanism of how RBMX/RBMXL2 achieve this splicing control is perhaps hinted at but not fully explored here), but I think the article provides an intriguing analysis of the role of RBMX that will activate interesting future studies.

Reviewer #1 (Public Review):

Summary:<br /> This work revealed an important finding that the blood-brain barrier (BBB) functionality changes with age and is more pronounced in males. The authors applied a non-invasive, contrast-agent-free approach of MRI called diffusion-prepared arterial spin labeling (DP-pCASL) to a large cohort of healthy human volunteers. DP-pCASL works by tracking the movement of magnetically labeled water (spins) in blood as it perfuses brain tissue. It probes the molecular diffusion of water, which is sensitive to microstructural barriers, and characterizes the signal coming from fast-moving spins as blood and slow-moving spins as tissue, using different diffusion gradients (b-values). This differentiation is then used to assess the water exchange rates (kw) across the BBB, which acts as a marker for BBB functionality. The main finding of the authors is that kw decreases with age, and in some brain regions, kw decreased faster in males. The neuroprotective role of the female sex hormone, estrogen, on BBB function is discussed as one of the explanations for this finding, supported by literature. The study also shows that BBB function remains stable until the early 60s and remarkably decreases thereafter.

Strengths:<br /> The two main strengths of the study are the MRI method used and the amount of data. The authors employed a contrast-agent-free MRI method called ASL, which offers the opportunity to repeat such experiments multiple times without any health risk-a significant advantage of ASL. Since ASL is an emerging field that requires further exploration and testing, a study evaluating blood-brain barrier functionality is of great importance. The authors utilized a large dataset of healthy humans, where volunteer data from various studies were combined to create a substantial pool. This strategy is effective for statistically evaluating differences in age and gender.

Weaknesses:<br /> The findings are of great interest as this assessment is the first of its kind to assess BBB function using ASL. Further studies are needed to compare DP-ASL findings with more established methods, such as PET and BBB molecular/ blood biomarkers.

Reviewer #1 (Public Review):

In this manuscript, by using simulation, in vitro and in vivo electrophysiology, and behavioral tests, Peng et al. nicely showed a new approach for the treatment of neuropathic pain in mice. They found that terahertz (THz) waves increased Kv conductance and decreased the frequency of action potentials in pyramidal neurons in the ACC region. Behaviorally, terahertz (THz) waves alleviated neuropathic pain in the mouse model. Overall, this is an interesting study. The experimental design is clear, the data is presented well, and the paper is well-written.

I have a few suggestions.<br /> (1) The authors provide strong theoretical and experimental evidence for the impact of voltage-gated potassium channels by terahertz wave frequency. However, the modulation of action potential also relies on non-voltage-dependent ion channels. For example, I noticed that the RMP was affected by THz application (Fig. 3F) as well. As the RMP is largely regulated by the leak potassium channels (Tandem-pore potassium channels), I would suggest testing whether terahertz wave photons have also any impact on the Kleak channels as well.

(2) The activation curves of the Kv currents in Fig. 2h seem to be not well-fitted. I would suggest testing a higher voltage (>100 mV) to collect more data to achieve a better fitting.

(3) In the part of behavior tests, the pain threshold increased after THz application and lasted within 60 mins. I suggest conducting prolonged tests to determine the end of the analgesic effect of terahertz waves.

(4) Regarding in vivo electrophysiological recordings, the post-HFTS recordings were acquired from a time window of up to 20 min. It seems that the HFTS effect lasted for minutes, but this was not tested in vitro where they looked at potassium currents. This long-lasting effect of HFTS is interesting. Can the authors discuss it and its possible mechanisms, or test it in slice electrophysiological experiments?

(5) How did the authors arrange the fiber for HFTS delivery and the electrode for in vivo multi-channel recordings? Providing a schematic illustration in Fig. 4 would be useful.

(6) Language is largely OK, but some grammar errors should be corrected.

The authors have completely addressed my concerns. I have no further comments.

Reviewer #1 (Public Review):

In this manuscript, Yoo et al describe the role of a specialized cell type found in muscle, Fibro-adipogenic progenitors (FAPs), in promoting regeneration following sciatic nerve injury. Using single-cell transcriptomics, they characterize the expression profiles of FAPs at various times after nerve crush or denervation. Their results reveal that a population of these muscle-resident mesenchymal progenitors up regulate the receptors for GDNF, which is secreted by Schwann cells following crush injury, suggesting that FAPs respond to this growth factor. They also find that FAPs increase expression of BDNF, which promotes nerve regeneration. The authors demonstrate FAP production of BDNF in vivo is up regulated in response to injection of GDNF and that conditional deletion of BDNF in FAPs results in delayed nerve regeneration after crush injury, primarily due to lagging remyelination. Finally, they also find reduced BDNF expression following crush injury in aged mice, suggesting a potential mechanism to explain the decrease in peripheral nerve regenerative capability in aged animals. These results are very interesting and novel and provide important insights into the mechanisms regulating peripheral nerve regeneration, which has important clinical implications for understanding and treating nerve injuries.

However, the authors should provide more compelling evidence that BDNF is produced by FAPs in response to GDNF signaling. The suggestion that Schwann cell-derived GDNF is responsible for up regulation of BDNF in the FAPs is primarily indirect, based on the data showing that injection of GDNF into the muscle is sufficient to up regulate BDNF (Fig. 4H). The authors more directly test their hypothesis by administering GDNF blocking antibody and find a trend toward reduced BDNF (Fig. 4S2), but it is not statistically significant at this point. Additional replicates should be performed to determine if BDNF levels are indeed reduced when GDNF is blocked.

Reviewer #1 (Public Review):

Summary:

Using a mouse model of head and neck cancer, Barr et al show that tumor-infiltrating nerves connect to brain regions via the ipsilateral trigeminal ganglion, and they demonstrate the effect this has on behavior. The authors show that there are neurites surrounding the tumors using a WGA assay and show that the brain regions that are involved in this tumor-containing circuit have elevated Fos and FosB expression and increased calcium response. Behaviorally, tumor-bearing mice have decreased nest building and wheel running and increased anhedonia. The behavior, Fos expression, and heightened calcium activity were all decreased in tumor-bearing mice following nociceptor neuron elimination.

Strengths:

This paper establishes that sensory neurons innervate head and neck cancers and that these tumors impact select brain areas. This paper also establishes that behavior is altered following these tumors and that drugs to treat pain restore some but not all of the behavior. The results from the experiments (predominantly gene and protein expression assays, cFos expression, and calcium imaging) support their behavioral findings both with and without drug treatment.

Comments on previously identified weaknesses:

The authors have addressed the majority of my concerns.

Reviewer #1 (Public Review):

The manuscript involves 11 research vignettes that interrogate key aspects of GnRH pulse generator in two established mouse models of PCOS (peripubertal and prenatal androgenisation; PPA and PNA) (9 of the vignettes focus on the latter model).

A key message of this paper is that the oft-quoted idea of rapid GnRH/LH pulses associated with PCOS is in fact not readily demonstrable in PNA and PPA mice. This is an important message to make known, but when established dogmas are being challenged, the experiments behind them need to be robust. In this case, underpowered experiments and one or two other issues greatly limit the overall robustness of the study.

General critiques

(1) My main concern is that many/most of the experiments were limited to 4-5 mice per group (PPA experiments 1 and 2, PNA experiments 3, 5, 6, 8, and 9). This seems very underpowered for trying to disprove established dogmas (sometimes falling back on "non-significant trends" - lines 105 and 239).

(2) Page 133-142: it is concerning that the PNA mice didn't have elevated testosterone levels, and this clearly isn't the fault of the assay as this was re-tested in the laboratory of Prof Handelsman, an expert in the field, using LCMS. The point (clearly made in lines 315-336 of the Discussion) that elevated testosterone in PNA mice has been shown in some but not other publications is an important concern to describe for the field. However, the fact remains that it IS elevated in numerous studies, and in the current study it is not so, yet the authors go on to present GnRH pulse generator data as characteristic of the PNA model. Perhaps a demonstration of elevated testosterone levels (by LCMS?) should become a standard model validation prerequisite for publishing any PNA model data.

(3) Line 191-196: the lack of a significant increase in LH pulse frequency in PNA mice is based on measurements using reasonable group sizes (7-8), although the sampling frequency is low for this type of analysis (10-minute intervals; 6-minute intervals would seem safer for not missing some pulses). The significance of the LH pulse frequency results is not stated (looks like about p=0.01). The authors note that LH concentration IS elevated (approximately doubled), and this clearly is not caused by an increase in amplitude (Figure 4 G, H, I). These things are worth commenting on in the discussion.

(4) An interesting observation is that PNA mice appear to continue to have cyclical patterns of GnRH pulse generator activity despite reproductive acyclicity as determined by vaginal cytology (lines 209-241). This finding was used to analyse the frequency of GnRH pulse generator SEs in the machine-learning-identified diestrous-like stage of PNA mice and compare it to diestrous control mice (as identified by vaginal cytology?) (lines 245-254). The idea of a cycle stage-specific comparison is good, but surely the only valid comparison would be to use machine-learning to identify the diestrous-like stage in both groups of mice. Why use machine learning for one and vaginal cytology for the other?

Specific points

(5) With regard to point 2 above, it would be helpful to note the age at which the testosterone samples were taken.

(6) Lines 198-205 and 258-266: I think these are repeated measures of ANOVA data? If so, report the main relevant effect before the post hoc test result.

(7) Line 415: I don't think the word "although" works in this sentence.

(8) Lines 514-518: what are the limits of hormone detection in the LCMS assay?

Reviewer #1 (Public Review):

Summary:

This paper investigates the mechanism of axon growth directed by the conserved guidance cue UNC-6/Netrin. Experiments were designed to distinguish between alternative models in which UNC-6/Netrin functions as either a short-range (haptotactic) cue or a diffusible (chemotactic) signal that steers axons to their final destinations. In each case, axonal growth cones execute ventrally directed outgrowth toward a proximal source of UNC-6/Netrin. This work concludes that UNC-6/Netrin functions as both a haptotactic and chemotactic cue to polarize the UNC-40/DCC receptor on the growth cone membrane facing the direction of growth. Ventrally directed axons initially contact a minor longitudinal nerve tract (vSLNC) at which UNC-6/Netrin appears to be concentrated before proceeding in the direction of the ventral nerve cord (VNC) from which UNC-6/Netrin is secreted. Time-lapse imaging revealed that growth cones appear to pause at the vSLNC before actively extending ventrally directed filopodia that eventually contact the VNC. Growth cone contacts with the vSLNC were unstable in unc-6 mutants but were restored by the expression of a membrane-tethered UNC-6 in vSLNC neurons. In addition, the expression of membrane-tethered UNC-6/Netrin in the VNC was not sufficient to rescue initial ventral outgrowth in an unc-6 mutant. Finally, dual expression of membrane-tethered UNC-6/Netrin in both vSLNC and VNC partially rescued the unc-6 mutant axon guidance defect, thus suggesting that diffusible UNC-6 is also required. This work is important because it potentially resolves the controversial question of how UNC-6/Netrin directs axon guidance by proposing a model in which both of the competing mechanisms, e.g., haptotaxis vs chemotaxis, are successively employed. The impact of this work is bolstered by its use of powerful imaging and genetic methods to test models of UNC-6/Netrin function in vivo thereby obviating potential artifacts arising from in vitro analysis.

Strengths:

A strength of this approach is the adoption of the model organism C. elegans to exploit its ready accessibility to live cell imaging and powerful methods for genetic analysis.

Weaknesses:

A membrane-tethered version of UNC-6/Netrin was constructed to test its haptotactic role, but its neuron-specific expression and membrane localization are not directly determined although this should be technically feasible. Time-lapse imaging is a key strength of multiple experiments but only one movie is provided for readers to review.

Reviewer #1 (Public Review):

Summary:

In this study, Setogawa et al. employ an auditory discrimination task in freely moving rats, coupled with small animal imaging, electrophysiological recordings, and pharmacological inhibition/lesioning experiments to better understand the role of two striatal subregions: the anterior Dorsal Lateral Striatum (aDLS) and the posterior Ventrolateral Striatum (pVLS), during auditory discrimination learning. Attempting to better understand the contribution of different striatal subregions to sensory discrimination learning strikes me as a highly relevant and timely question, and the data presented in this study are certainly of major interest to the field. The authors have set up a robust behavioral task and systematically tackled the question about a striatal role in learning with multiple observational and manipulative techniques. Additionally, the structured approach the authors take by using neuroimaging to inform their pharmacological manipulation experiments and electrophysiological recordings is a strength.

However, the results as they are currently presented are not easy to follow and could use some restructuring, especially the electrophysiology. Also, the main conclusion that the authors draw from the data, that aDLS and pVLS contribute to different phases of discrimination learning and influence the animal's response strategy in different ways, is not strongly supported by the data and deserves some additional caveats and limitations of the study in the discussion.

Strengths:

See above. In addition, the electrophysiology data is a major strength.

Weaknesses:

(1) The authors have rigorously used PET neuroimaging, which is an interesting non-invasive method to track brain activity during behavioral states. However, in the case of a freely moving behavior where the scans are performed ~30 minutes after the behavioral task, it is unclear what conclusions can be drawn about task-specific brain activity. The study hinges on the neuroimaging findings that both areas of the lateral striatum (aDLS and pVLS) show increased activity during acquisition, but the DMS shows a reduction in activity during the late stages of behavior, and some of these findings are later validated with complementary experiments. However, the limitations of this technique can be further elaborated on in the discussion and the conclusions.

a) In commenting on the unilateral shifts in brain striatal activity during behavior, the authors use the single lever task as a control, where many variables affecting neuronal activity might be different than in the discriminatory task. The study might be better served using Day 2 measurements as a control against which to compare activity of all other sessions since the task structures are similar.<br /> b) From the plots in J, K, and L, it seems that shifts in activity in the different substructures are not unilateral but consistently bilateral, in contrast to what is mentioned in the text. Possibly the text reflects comparisons to the single lever task, and here again, I would emphasize comparing within the same task.

(2) In Figure 2, the authors present compelling data that chronic excitotoxic lesions with ibotenic acid in the aDLS, pVLS, and DMS produce differential effects on discrimination learning. However, the significant reduction in success rate of performance happens as early as Day 6 in both IBO groups in both aDLS and pVLS mice. This would seem to agree with conclusions drawn about the role of aDLS in the middle stages of learning in Figure 2, but not the pVLS, which only shows an increased activity during the late stages of the behavior.

(3) In Figure 4, the authors show interesting data with transient inactivation of subregions of the striatum with muscimol, validating their findings that the aDLS mediates the middle and the pVLS the late stages of learning, and the function of each area serves different strategies. However, the inference that aDLS inactivation suppresses the WSW strategy "moderately" is not reflected in the formal statistical value p=0.06. While there still may be a subtle effect, the authors would need to revise their conclusions appropriately to reflect the data. In addition, the authors could try a direct comparison between the success rate during muscimol inhibition in the mid-learning session between the aDLS and pVLS-treated groups in Figure 4C (middle) and 4D (middle). If this comparison is not significant, the authors should be careful to claim that inhibition of these two areas differentially affects behavior.

(4) The authors have used in-vivo electrophysiological techniques to systematically investigate the roles of the aDLS and the pVLS in discriminatory learning, and have done a thorough analysis of responses with each phase of behavior over the course of learning. This is a commendable and extremely informative dataset and is a strength of the study. However, the result could be better organized following the sequence of events of the behavioral task to give the reader an easier structure to follow. Ideally, this would involve an individual figure to compare the responses in both areas to Cue, Lever Press, Reward Sound, and First Lick (in this order).

(5) An important conceptual point presented in the study is that the aDLS neurons, with learning, show a reduction in firing rates and responsiveness to the first lick as well as the behavioral outcome, and don't play a role in other task-related events such as cue onset. However, the neuroimaging data in Figure 2 seems to suggest a transient enhancement of aDLS activity in the mid-stage of discriminatory learning, that is not reflected in the electrophysiology data. Is there an explanation for this difference?

(6) A significant finding of the study is that CO-HR and CO-LL responses are strikingly obvious in the pVLS, but not in the aDLS, in line with the literature that the posterior (sensory) striatum processes sound. This study also shows that responses to the high-frequency tone indicating a correct right-lever choice increase with learning in contrast to the low-frequency tone responses. To further address whether this difference arises from the task contingency, and not from the frequency representation of the pVLS, an important control would be to switch the cue-response association in a separate group of mice, such that high-frequency tones require a left lever press and vice versa. This would also help tease apart task-evoked responses in the aDLS, as I am given to understand all the recording sites were in the left striatum.

Reviewer #1 (Public Review):

In this study, Li et al. aim to determine the effect of navigational experience on visual representations of scenes. Participants first learn to navigate within simple virtual environments where navigation is either unrestricted or restricted by an invisible wall. Environments are matched in terms of their spatial layout and instead differ primarily in terms of their background visual features. In a later same/different task, participants are slower to distinguish between pairs of scenes taken from the same navigation condition (i.e. both restricted or both unrestricted) than different navigation conditions. Neural response patterns in the PPA also discriminate between scenes from different navigation conditions. These results suggest that navigational experience influences perceptual representations of scenes. This is an interesting study, and the results and conclusions are clearly explained and easy to follow. There are a few points that I think would benefit from further consideration or elaboration from the authors, which I detail below.

First, I am a little sceptical of the extent to which the tasks are able to measure navigational or perceptual experience with the scenes. The training procedure seems like it wouldn't require obtaining substantial navigational experience as the environments are all relatively simple and only require participants to follow basic paths, rather than encouraging more active exploration of a more complex environment. Furthermore, in the same/different task, all images show the same view of the environment (meaning they show the exact same image in the "same environment" condition). The task is therefore really a simple image-matching task and doesn't require participants to meaningfully extract the perceptual or spatial features of the scenes. An alternative would have been to present different views of the scenes, which would have prevented the use of image-matching and encouraged further engagement with the scenes themselves. Ultimately, the authors do still find a response time difference between the navigation conditions, but the effect does appear quite small. I wonder if the design choices could be obscuring larger effects, which might have been better evident if the navigational and perceptual tasks had encouraged greater encoding of the spatial and perceptual features of the environment. I think it would be helpful for the authors to explain their reasons for not employing such designs, or to at least give some consideration to alternative designs.

Figure 1B illustrates that the non-navigable condition includes a more complicated environment than the navigable condition, and requires following a longer path with more turns in it. I guess this is a necessary consequence of the experiment design, as the non-navigable condition requires participants to turn around and find an alternative route. Still, this does introduce spatial and perceptual differences between the two navigation conditions, which could be a confounding factor. What do the response times for the "matched" condition in the same/different task look like if they are broken down by the navigable and non-navigable environments? If there is a substantial difference between them, it could be that this is driving the difference between the matched and mismatched conditions, rather than the matching/mismatching experience itself.

In both experiments, the authors determined their sample sizes via a priori power analyses. This is good, but a bit more detail on these analyses would be helpful. How were the effect sizes estimated? The authors say it was based on other studies with similar methodologies - does this mean the effect sizes were obtained from a literature search? If so, it would be good to give some details of the studies included in this search, and how the effect size was obtained from these (e.g., it is generally recommended to take a lower bound over studies). Or is the effect size based on standard guidelines (e.g., Cohen's d ≈ 0.5 is a medium effect size)? If so, why are the effect sizes different for the two studies?

Reviewer #1 (Public Review):

The authors conducted cross-species comparisons between the human brain and the macaque brain to disentangle the specific characteristics of structural development of the human brain. Although previous studies had revealed similarities and differences in brain anatomy between the two species by spatially aligning the brains, the authors made the comparison along the chronological axis by establishing models for predicting the chronological ages with the inputting brain structural features. The rationale is actually clear given that brain development occurs over time in both. More interestingly, the model trained on macaque data was better able to predict the age of humans than the human-trained model was at predicting macaque age. This revealed a brain cross-species age gap (BCAP) that quantified the discrepancy in brain development between the two species, and the authors even found this BCAP measure was associated with performance on behavioral tests in humans. Overall, this study provides important and novel insights into the unique characteristics of human brain development. The authors have employed a rigorous scientific approach, reflecting diligent efforts to scrutinize the patterns of brain age models across species. The clarity of the rationale, the interpretability of the methods, and the quality of the presentation all contribute to the strength of this work.

Reviewer #1 (Public Review):

Using structural analysis, Bonchuk and colleagues demonstrate that the TTK-like BTB/POZs of insects form stable hexameric assemblies composed of trimers of POZ dimers, a configuration observed consistently across both homomultimers and heteromultimers, which are known to be formed by TTK-like BTB/POZ domains. The structural data is comprehensive, unambiguous, and further supported by theoretical fold prediction analyses. In particular the judicious complementation of experiments and fold prediction is commendable. This study now adds an important cog that might help generalize the general principles of the evolution of multimerization in members of this fold family.

I strongly feel that enhancing the inclusivity of the discussion would strengthen the paper. Below, I suggest some additional points for consideration for the same.

Major points.<br /> (1) It would be valuable to discuss alternative multimer assembly interfaces, considering the diverse ways POZs can multimerize. For instance, the Potassium channel POZ domains form tetramers. A comparison of their inter-subunit interface with that of TTK and non-TTK POZs could provide insightful contrasts.

(2) The so-called TTK motif, despite its unique sequence signature, essentially corresponds to the N-terminal extension observed in other "non-TTK" proteins such as Miz-1. Given Miz-1's structure, it becomes evident that the utilization of the N-terminal extension for dimerization is shared with the TTK family, suggesting a common evolutionary origin in metazoan transcription factors. Early phylogenetic trees (e.g. in PMID: 9917379) support the grouping of the TTK-like POZs with other animal Transcription factors containing POZ domains such as those with Kelch repeats further suggesting that the extension might be ancestral. Structural investigations by modeling prominent examples or comparing known structures of similar POZ domains, could support this inference. Control comparisons with POZ domains from fungi, plants and amoebozoans like Dictyostelium could offer additional insights.

(3) Exploring the ancestral presence of the aforementioned extension in metazoan transcription factors could serve as a foundation for understanding the evolutionary pathway of hexamerization. This analysis could shed light on exposed structural regions that had the potential to interact post-dimerization with the N-terminal extension and also might provide insights into the evolution of multimer interfaces, as observed in the Potassium channel.

(4) Considering the role of conserved residues in the multimer interface is crucial. Reference to conserved residues involved in multimer formation, such as discussed in PMID: 9917379, would enrich the discussion.

Reviewer #1 (Public Review):

This report describes work aiming to delineate multi-modal MRI correlates of psychopathology from a large cohort of children of 9-11 years from the ABCD cohort. While uni-modal characterisations have been made, the authors rightly argue that multi-modal approaches in imaging are vital to comprehensively and robustly capture modes of large-scale brain variation that may be associated with pathology. The primary analysis integrates structural and resting-state functional data, while post-hoc analyses on subsamples incorporate task and diffusion data. Five latent components (LCs) are identified, with the first three, corresponding to p-factor, internal/externalising, and neurodevelopmental Michelini Factors, described in detail. In addition, associations of these components with primary and secondary RSFC functional gradients were identified, and LCs were validated in a replication sample via assessment of correlations of loadings.

This work is clearly novel and a comprehensive study of associations within this dataset. Multi-modal analyses are challenging to perform, but this work is methodologically rigorous, with careful implementation of discovery and replication assessments, and primary and exploratory analyses. The ABCD dataset is large, and behavioural and MRI protocols seem appropriate and extensive enough for this study. The study lays out comprehensive associations between MRI brain measures and behaviour that appear to recapitulate the established hierarchical structure of psychopathology.

The work does have weaknesses, some of them acknowledged. There is limited focus on the strength of observed associations. While the latent component loadings seem reliably reproducible in the behavourial domain, this is considerably less the case in the imaging modalities. A considerable proportion of statistical results focuses on spatial associations in loadings between modalities - it seems likely that these reflect intrinsic correlations between modalities, rather than associations specific to any latent component. Assessment of associations with functional gradients is similarly a little hard to interpret. Thus, it is hard to judge the implications for our understanding of the neurophysiological basis of psychopathology and the ability of MRI to provide clinical tools for, say, stratification. The observation of a recapitulation of psychopathology hierarchy may be somewhat undermined by the relatively modest strength of the components in the imaging domain. The task fMRI was assessed with a fairly basic functional connectivity approach, not using task timings to more specifically extract network responses.

Overall, the authors achieve their aim to provide a detailed multimodal characterisation of MRI correlations of psychopathology. Code and data are available and well organised and should provide a valuable resource for researchers wanting to understand MRI-based neural correlates of psycho-pathology-related behavioural traits in this important age group. It is largely a descriptive study, with comparisons to previous uni-modal work, but without particularly strong testing of neuroscience hypotheses.

Reviewer #1 (Public Review):

In this manuscript, the authors present Tronko, a novel tool for performing phylogenetic assignment of DNA sequences using an approximate likelihood approach. Through a benchmark experiment utilizing several real datasets from mock communities with pre-known composition as well as simulated datasets, the authors show that Tronko is able to achieve higher accuracy than several existing best-practice methods with runtime comparable to the fastest existing method, albeit with significantly higher peak memory usage than existing methods. The benchmark experiment was thorough, and the results clearly support the authors' conclusions. However, the paper could be improved by exploring how certain design choices (e.g. tool selection and parameter choices) may impact Tronko's performance/accuracy, and some relevant existing phylogenetic placement tools are missing and should be included.

Reviewer #1 (Public Review):

In this manuscript, Perez-Lopez et al. examine the function of the chemokine CCL28, which is expressed highly in mucosal tissues during infection, but its role during infection is poorly understood. They find that CCL28 promotes neutrophil accumulation in the intestines of mice infected with Salmonella and in the lungs of mice infected with Acinetobacter. They find that Ccl28-/- mice are highly susceptible to Salmonella infection, and highly resistant and protected from lethality following Acinetobacter infection. They find that neutrophils express the CCL28 receptors CCR3 and CCR10. CCR3 was pre-formed and intracellular and translocated to the cell surface following phagocytosis or inflammatory stimuli. They also find that CCL28 stimulation of CCR3 promoted neutrophil antimicrobial activity, ROS production, and NET formation, using a combination of primary mouse and human neutrophils for their studies. Overall, the authors' findings provide new and fundamental insight into the role of the CCL28:CCR3 chemokine:chemokine receptor pair in regulating neutrophil recruitment and effector function during infection with the intestinal pathogen Salmonella Typhimurium and the lung pathogen Acinetobacter baumanii.

Reviewer #1 (Public Review):

Summary:

In the manuscript entitled "Magnesium modulates phospholipid metabolism to promote bacterial phenotypic resistance to antibiotics", Li et al demonstrated the role of magnesium in promoting phenotypic resistance in V. alginolyticus. Using standard microbiological and metabolomic techniques, the authors have shown the significance of fatty acid biosynthesis pathway behind the resistance mechanism. This study is significant as it sheds light on the role of an exogenous factor in altering membrane composition, polarization, and fluidity which ultimately leads to antimicrobial resistance.

Strengths:

(1) The experiments were carried out methodically and logically.

(2) An adequate number of replicates were used for the experiments.

Weaknesses:

(1) The introduction section needs to be more informative and to the point.

(2) The weakest point of this paper is in the logistics through the results section. The way authors represented the figures and interpreted them in the results section (or the figure legends) does not match. The figures are difficult to interpret and are not at all self-explanatory.

(3) There are too many mislabeling of the figure panels in the main text which makes it difficult to find out which figures the authors are explaining. There should be more explanation on why and how they did the experiments and how the results were interpreted.

Reviewer #1 (Public Review):

I feel that the changes to the manuscript have significantly improved it. It's unfortunate that the single biotin/anti-biotin antibodies were not more illuminating but I think the attempts were worthwhile. My only comment is that the rebuttal to the second part of point 3 still does not fully deal with the issue. By marking proximal proteins other than the fusion with biotin, TurboID significantly increases the detectable signal, but it is formally no longer possible to be certain what the biotin is attached to. None of the controls that the authors suggest will actually give you certainty about what you are detecting while imaging. Mass spectrometry will give you an ensemble measurement of all the biotinylated proteins in the cell without being able to relate that back to what you are observing in a specific cellular region when you are imaging. Colocalization with a tagged protein/specific antibody could suggest that a portion of the signal could be attributable to the TurboID-biotin signal, but it could also be a tight binding partner or part of a larger protein complex. PLA assays would have similar issues- some of the protein could be labeled but it will be impossible to show what portion of the signal is attributable to the protein of interest and how much is attributable to other proximal proteins. I think the key thing here is that in this implementation, TurboID allows you to enhance the labeling of protein structures in cells, such as NUPS, but at the expense of certainty about the specific proteins you are labeling. I personally cannot think of a reasonable control that will allow you to avoid this issue. I feel that this point needs to be clearly made if people are going to use this method for signal enhancement, otherwise people may be misled about what they are actually looking at. The method should be useful, but the limitations need to be clear.

Reviewer #1 (Public Review):

Through a combination of in vitro and in vivo analyses, the authors demonstrate that CD56/CD29 positive progenitor cells from human muscle can be driven towards muscle or tendon fate in vitro and are able to contribute to muscle and tendon fates following transplantation in injured mice. This is in contrast to Pax7-lineage cells from mice which do not contribute to tendon repair in vivo. While the data strongly support that a subset of cells captured by this sorting strategy has tenogenic potential, their claims of progenitor bi-potency are not fully supported by the data as currently presented.

As discussed below, some aspects of the data analysis and sample preparation are incomplete and should be clarified to fully support the claims of the paper.

For the colony analysis, it is unclear from the methods and main text whether the initial individual sorted colonies were split and subject to different conditions to support the claim of bi-potency. The finding that 40% of colonies displayed tenogenic differentiation, may instead suggest heterogeneity of the sorted progenitor population. The methods as currently described, suggest that two different plates were subject to different induction conditions. It is therefore difficult to assess the strength of the claim of bi-potency.

This group uses the well-established CD56+/CD29+ sorting strategy to isolate muscle progenitor cells, however recent work has identified transcriptional heterogeneity within these human satellite cells (ie Barruet et al, eLife 2020). Given that they identify a tenocyte population in their human muscle biopsy in Figure 1a, it is critical to understand the heterogeneity contained within the population of human progenitors captured by the authors' FACS strategy and whether tenocytes contained within the muscle biopsy are also CD56+/CD29+.

The bulk RNA sequencing data presented in Figure 3 to contrast the expression of progenitor cells under different differentiation conditions are not sufficiently convincing. In particular, it is unclear whether more than one sample was used for the RNAseq analyses shown in Figure 3. The volcano plots have many genes aligned on distinct curves suggesting that there are few replicates or low expression. There is also a concern that the sorted cells may contain tenocytes as tendon genes SCX, MKX, and THBS4 were among the genes upregulated in the myogenic differentiation conditions (shown in Figure 3b).

Reviewer #1 (Public Review):

Summary:

The authors examined the salt-dependent phase separation of the low-complexity domain of hnRN-PA1 (A1-LCD). Using all-atom molecular dynamics simulations, they identified four distinct classes of salt dependence in the phase separation of intrinsically disordered proteins (IDPs), which can be predicted based on their amino acid composition. However, the simulations and analysis, in their current form, are inadequate and incomplete.

Strengths:

The authors attempt to unravel the mechanistic insights into the interplay between salt and protein phase separation, which is important given the complex behavior of salt effects on this process. Their effort to correlate the influence of salt on the low-complexity domain of hnRNPA1 (A1-LCD) with a range of other proteins known to undergo salt-dependent phase separation is an interesting and valuable topic.

Weaknesses:

(1) The simulations performed are not sufficiently long (Figure 2A) to accurately comment on phase separation behavior. The simulations do not appear to have converged well, indicating that the system has not reached a steady state, rendering the analysis of the trajectories unreliable.

(2) The majority of the data presented shows no significant alteration with changes in salt concentration. However, the authors have based conclusions and made significant comments regarding salt activities. The absence of error bars in the data representation raises questions about its reliability. Additionally, the manuscript lacks sufficient scientific details of the calculations.

(3) In Figures 2B and 2C, the changes in the radius of gyration and the number of contacts do not display significant variations with changes in salt concentration. The change in the radius of gyration with salt concentration is less than 1 Å, and the number of contacts does not change by at least 1. The authors' conclusions based on these minor changes seem unfounded.

Reviewer #1 (Public Review):

Summary:

This study demonstrates a key role of oxLDL in enhancing Ang II-induced Gq signaling by promoting the AT1/LOX1 receptor complex formation. Importantly, Gq-mediated calcium influx was only observed in LOX1 and AT1 both expressing cells, and AT1-LOX1 interaction aggravated renal damage and dysfunction under the condition of a high-fat diet with Ang II infusion, so this study indicated a new therapeutic potential of AT1-LOX1 receptor complex in CKD patients with dyslipidemia and hypertension.

Strengths:

This study is very exciting and the work is also very detailed, especially regarding the mechanism of LOX1-AT1 receptor interaction and its impact on oxidative stress, fibrosis, and inflammation.

Weaknesses:

The direct evidence for the interaction between AT1 and LOX1 receptors in cell membrane localization is relatively weak. Here I raise some questions that may further improve the study.

Major points:

(1) The authors hypothesized that in the interaction of AT1/LOX1 receptor complex in response to ox-LDL and AngII, there should be strong evidence of fluorescence detection of colocalization for these two membrane receptors, both in vivo and in vitro. Although the video evidence for AT1 internalization upon complex activation is shown in Figure S1, the more important evidence should be membrane interaction and enhanced signal of intracellular calcium influx.

(2) Co-IP experiment should be provided to prove the AT1/LOX1 receptor interaction in response to ox-LDL and AngII in AT1 and LOX1 both expressing cells but not in AT1 only expressing cells.

(3) The authors mentioned that the Gq signaling-mediated calcium influx may change gene expression and cellular characteristics, including EMT and cell proliferation. They also provided evidence that oxidative stress, fibrosis, and inflammation were all enhanced after activating both receptors and inhibiting Gq was effective in reversing these changes. However, single stimulation with ox-LDL or AngII also has strong effects on ROS production, inflammation, and cell EMT, which has been extensively proved by previous studies. So, how to distinguish the biased effect of LOX1 or AT1r alone or the enhanced effect of receptor conformational changes mediated by their receptor interaction? Is there any better evidence to elucidate this point?

(4) How does the interaction between AT1 and LOX1 affect the RAS system and blood pressure? What about the serum levels of rennin, angiotensin, and aldosterone in ND-fed or HFD-fed mice?

Reviewer #1 (Public Review):

With socioeconomic development, more and more people are obese which is an important reason for sub-fertility and infertility. Maternal obesity reduces oocyte quality which may be a reason for the high risk of metabolic diseases for offspring in adulthood. Yet the underlying mechanisms are not well elucidated. Here the authors examined the effects of maternal obesity on oocyte methylation. Hyper-methylation in oocytes was reported by the authors, and the altered methylation in oocytes may be partially transmitted to F2. The authors further explored the association between the metabolome of serum and the altered methylation in oocytes. The authors identified decreased melatonin. Melatonin is involved in regulating the hyper-methylation of high-fat diet (HFD) oocytes, via increasing the expression of DNMTs which is mediated by the cAMP/PKA/CREB pathway.

Strengths:

This study is interesting and should have significant implications for the understanding of the transgenerational inheritance of GDM in humans.

Weaknesses:

The link between altered DNA methylation and offspring metabolic disorders is not well elucidated; how the altered DNA methylation in oocytes escapes reprogramming in transgenerational inheritance is also unclear.

Reviewer #1 (Public Review):

Summary:

This article identifies ADGR3 as a candidate GPCR for mediating beige fat development. The authors use human expression data from the Human protein atlas and Gtex databases and combine this with experiments performed in mice and a murine cell line. They refer to a GPCR bioactivity screening tool PRESTO-Salsa, with which it was found that Hesperetin activates ADGR3. From their experiments, authors conclude that Hesperetin activates ADGR3, inducing a Gs-PKA-CREB axis resulting in adipose thermogenesis.

Strengths:

The authors analyze human data from public databases and perform functional studies in mouse models. They identify a new GPCR with a role in the thermogenic activation of adipocytes.

Weaknesses:

(1) Selection of ADGRA3 as a candidate GPCR relevant for mediating beiging in humans:

The authors identify genes upregulated in iBAT compared to iWAT in response to cold, and among these differentially expressed genes, they identify highly expressed GPCRs in human white adipocytes (visceral or subcutaneous). Finally, among these genes, they select a GPCR not previously studied in the literature.

If the authors are interested in beiging, why do they not focus on genes upregulated in iWAT (the depot where beiging is described to occur in mice), comparing thermoneutral to cold-induced genes? I would expect that genes induced in iWAT in response to cold would be extremely relevant targets for beiging. With their strategy, the authors exclude receptors that are induced in the tissue where beiging is actually described to occur.

Furthermore, the authors are comparing genes upregulated in cold in BAT (but not WAT) to highly expressed genes in human white adipocytes during thermoneutrality. Overall, the authors fail to discuss the logic behind their strategy and the obvious limitations of it.

(2) Relevance of ADGRA3 and comparison to established literature:

There has been a lot of literature and discussion about which receptor should be targeted in humans to recruit thermogenic fat. The current article unfortunately does not discuss this literature nor explain how it relates to their findings. For example, O'Mara et al (PMID: 31961826) demonstrated that chronic stimulation with the B3 adrenergic agonist, Mirabegron, resulted in the recruitment of thermogenic fat and improvement in insulin sensitivity and cholesterol. Later, Blondin et al (PMID: 32755608), highlighted the B2 adrenergic receptor as the main activation path of thermogenic fat in humans. There is also a recent report on an agonist activating B2 and B3 simultaneously (PMID: 38796310). Thus, to bring the literature forward, it would be beneficial if the current manuscript compared their identified activation path with the activation of these already established receptors and discussed their findings in relation to previous studies.

In Figures 1d and e, the authors show the expression of ADGRA3 in comparison to the expression of ADRB3. In human brown adipocytes, ADRB2 has been shown to be the main receptor through which adrenergic activation occurs (PMID: 32755608), thus authors should show the relative expression of this gene as well.

(3) Strategy to investigate the role of ADGRA3 in WAT beiging:

Having identified ADGRA3 as their candidate receptor, the authors proceed with investigations of this receptor in mouse models and the murine inguinal adipocyte cell line 3T3.

First of all, in Figure 1D, the authors show a substantially lower expression of ADGRA3 compared to ADRB3. It could thus be argued that a mouse would not be the best model system for studying this receptor. It would be interesting to see data from experiments in human adipocytes. Moreover, if the authors are interested in inducing beiging, why do they show expression in iBAT and not iWAT?

The authors perform in vivo experiments using intraperitoneal injections of shRNA or overexpression CMV-driven vectors and report effects on body temperature and glucose metabolism. It is here important to note that ADGRA3 is not uniquely expressed in adipocytes. A major advantage of databases like the Human Protein Atlas and Gtex, is that they give an overview of the gene expression across tissues and cell types. When looking up ADGRA3 in these databases, it is expressed in subcutaneous and visceral adipocytes. However, other cell types and tissues demonstrate an even higher expression. In the Human protein atlas, the enhanced cell types are astrocytes and hepatocytes. In the Gtex database tissues with the highest expression are Brain, Liver, and Thyroid.

With this information in mind, IP injections for modification of ADGRA3 receptor expression could be expected to affect any of these tissues and cells.

The manuscript report changes body temperature. However, temperature is regulated by the brain and also affected by thyroid activity. Did the authors measure the levels of circulating thyroid hormones? Gene expression changes in the brain? The authors report that Adgra3 overexpression decreased the TG level in serum and liver. The liver could be the primary targeted organ here, and the adipose effects might be secondary. The data would be easier to interpret if authors reported the effects on the liver, thyroid, and brain, and the gene expression across tissues should be discussed in the article.

Finally, the identification of Hesperetin using the PRESTO-Salsa tool, and how specific the effect of Hesperetin is on ADGRA3, is currently unclear. This should be better discussed, and authors should consider measuring the established effects of Hesperetin in their model systems, including apoptosis.

Reviewer #1 (Public Review):

Summary:

The authors report a study aimed at understanding the brain's representations of viewed actions, with a particular aim to distinguish regions that encode observed body movements, from those that encode the effects of actions on objects. They adopt a cross-decoding multivariate fMRI approach, scanning adult observers who viewed full-cue actions, pantomimes of those actions, minimal skeletal depictions of those actions, and abstract animations that captured analogous effects to those actions. Decoding across different pairs of these actions allowed the authors to pull out the contributions of different action features in a given region's representation. The main hypothesis, which was largely confirmed, was that the superior parietal lobe (SPL) more strongly encodes movements of the body, whereas the anterior inferior parietal lobe (aIPL) codes for action effects of outcomes. Specifically, region of interest analyses showed dissociations in the successful cross-decoding of action category across full-cue and skeletal or abstract depictions. Their analyses also highlight the importance of the lateral occipito-temporal cortex (LOTC) in coding action effects. They also find some preliminary evidence about the organisation of action kinds in the regions examined.

Strengths:

The paper is well-written, and it addresses a topic of emerging interest where social vision and intuitive physics intersect. The use of cross-decoding to examine actions and their effects across four different stimulus formats is a strength of the study. Likewise, the a priori identification of regions of interest (supplemented by additional full-brain analyses) is a strength.

Weaknesses:

I found that the main limitation of the article was in the underpinning theoretical reasoning. The authors appeal to the idea of "action effect structures (AES)", as an abstract representation of the consequences of an action that does not specify (as I understand it) the exact means by which that effect is caused, nor the specific objects involved. This concept has some face validity, but it is not developed very fully in the paper, rather simply asserted. The authors make the claim that "The identification of action effect structure representations in aIPL has implications for theories of action understanding" but it would have been nice to hear more about what those theoretical implications are. More generally, I was not very clear on the direction of the claim here. Is there independent evidence for AES (if so, what is it?) and this study tests the following prediction, that AES should be associated with a specific brain region that does not also code other action properties such as body movements? Or, is the idea that this finding -- that there is a brain region that is sensitive to outcomes more than movements -- is the key new evidence for AES?

On a more specific but still important point, I was not always clear that the significant, but numerically rather small, decoding effects are sufficient to support strong claims about what is encoded or represented in a region. This concern of course applies to many multivariate decoding neuroimaging studies. In this instance, I wondered specifically whether the decoding effects necessarily reflected fully five-way distinction amongst the action kinds, or instead (for example) a significantly different pattern evoked by one action compared to all of the other four (which in turn might be similar). This concern is partly increased by the confusion matrices that are presented in the supplementary materials, which don't necessarily convey a strong classification amongst action kinds. The cluster analyses are interesting and appear to be somewhat regular over the different regions, which helps. However: it is hard to assess these findings statistically, and it may be that similar clusters would be found in early visual areas too.

Reviewer #1 (Public Review):

Summary:

The authors used a motivated saccade task with distractors to measure response vigor and reaction time (RT) in healthy human males under placebo or muscarinic antagonism. They also simultaneously recorded neural activity using EEG with event-related potential (ERP) focused analyses. This study provides evidence that the muscarinic antagonist Trihexyphenidyl (THP) modulates the motivational effects of reward on both saccade velocity and RT, and also increases the distractibility of participants. The study also examined the correlational relationships between reaction time and vigor and manipulations (THP, incentives) with components of the EEG-derived ERPs. While an interesting correlation structure emerged from the analyses relating the ERP biomarkers to behavior, it is unclear how these potentially epiphenomenal biomarkers relate to relevant underlying neurophysiology.

Strengths:

This study is a logical translational extension from preclinical findings of cholinergic modulation of motivation and vigor and the CNV biomarker to a normative human population, utilizing a placebo-controlled, double-blind approach.

While framed in the context of Parkinson's disease where cholinergic medications can be used, the authors do a good job in the discussion describing the limitations in generalizing their findings obtained in a normative and non-age-matched cohort to an aged PD patient population.

The exploratory analyses suggest alternative brain targets and/or ERP components that relate to the behavior and manipulations tested. These will need to be further validated in an adequately powered study. Once validated, the most relevant biomarkers could be assessed in a more clinically relevant population.

Weaknesses:

The relatively weak correlations between the main experimental outcomes provide unclear insight into the neural mechanisms by which the manipulations lead to behavioral manifestations outside the context of the ERP. It would have been interesting to evaluate how other quantifications of the EEG signal through time-frequency analyses relate to the behavioral outcomes and manipulations.

The ERP correlations to relevant behavioral outcomes were not consistent across manipulations demonstrating they are not reliable biomarkers to behavior but do suggest that multiple underlying mechanisms can give rise to the same changes in the ERP-based biomarkers and lead to different behavioral outcomes.

Reviewer #1 (Public Review):

Summary:

Qi and colleagues investigated the role of the Kallistatin pathway in increasing hippocampal amyloid-β plaque accumulation and tau hyperphosphorylation in Alzheimer's disease, linking the increased Kallistatin level in diabetic patients with a higher risk of Alzheimer's disease development. A Kallistatin-overexpressing animal model was utilized, and memory impairment was assessed using Morris water maze and Y-maze. Kallistatin-related pathway protein levels were measured in the hippocampus, and phenotypes were rescued using fenofibrate and rosiglitazone. The current study provides evidence of a novel molecular mechanism linking diabetes and Alzheimer's disease and suggests the potential use of fenofibrate to alleviate memory impairment. However, several issues need to be addressed before further consideration.

Strengths:

The findings of this study are novel. The findings will have great impacts on diabetes and AD research. The studies were well conducted, and the results were convincing.

Weaknesses:

(1) The mechanism by which fenofibrate rescues memory loss in Kallistatin-transgenic mice is unclear. As a PPARalpha agonist, does fenofibrate target the Kallistatin pathway directly or indirectly? Please provide a discussion based on literature supporting either possibility.

(2) The current study exclusively investigated the hippocampus. What about other cognitive memory-related regions, such as the prefrontal cortex? Including data from these regions or discussing the possibility of their involvement could provide a more comprehensive understanding of the role of Kallistatin in memory impairment.

(3) Fenofibrate rescued phenotypes in Kallistatin-transgenic mice while rosiglitazone, a PPARgamma agonist, did not. This result contradicts the manuscript's emphasis on a PPARgamma-associated mechanism. Please address this inconsistency.

(4) Most of the immunohistochemistry images are unclear. Inserts have similar magnification to the original representative images, making judgments difficult. Please provide larger inserts with higher resolution.

(5) The immunohistochemistry images in different figures were taken from different hippocampal subregions with different magnifications. Please maintain consistency, or explain why CA1, CA3, or DG was analyzed in each experiment.

(6) Figure 5B is missing a title. Please add a title to maintain consistency with other graphs.

(7) Please list statistical methods used in the figure legends, such as t-test or One-way ANOVA with post-hoc tests.

Reviewer #1 (Public Review):

Summary:

The authors report a study on how stimulation of receptive-field surround of V1 and LGN neurons affects their firing rates. Specifically, they examine stimuli in which a grey patch covers the classical RF of the cell and a stimulus appears in the surround. Using a number of different stimulus paradigms they find a long latency response in V1 (but not the LGN) which does not depend strongly on the characteristics of the surround grating (drifting vs static, continuous vs discontinuous, predictable grating vs unpredictable pink noise). They find that population responses to simple achromatic stimuli have a different structure that does not distinguish so clearly between the grey patch and other conditions and the latency of the response was similar regardless of whether the center or surround was stimulated by the achromatic surface. Taken together they propose that the surround-response is related to the representation of the grey surface itself. They relate their findings to previous studies that have put forward the concept of an 'inverse RF' based on strong responses to small grey patches on a full-screen grating. They also discuss their results in the context of studies that suggest that surround responses are related to predictions of the RF content or figure-ground segregation.

Strengths:

I find the study to be an interesting extension of the work on surround stimulation and the addition of the LGN data is useful showing that the surround-induced responses are not present in the feed-forward path. The conclusions appear solid, being based on large numbers of neurons obtained through Neuropixels recordings. The use of many different stimulus combinations provides a rich view of the nature of the surround-induced responses.

Weaknesses:

The statistics are pooled across animals, which is less appropriate for hierarchical data. There is no histological confirmation of placement of the electrode in the LGN and there is no analysis of eye or face movements which may have contributed to the surround-induced responses. There are also some missing statistics and methods details which make interpretation more difficult.

Reviewer #1 (Public Review):

Summary:

The study aimed to better understand the role of the H3 protein of the Monkeypox virus (MPXV) in host cell adhesion, identifying a crucial α-helical domain for interaction with heparan sulfate (HS). Using a combination of advanced computational simulations and experimental validations, the authors discovered that this domain is essential for viral adhesion and potentially a new target for developing antiviral therapies.

Strengths:

The study's main strengths include the use of cutting-edge computational tools such as AlphaFold2 and molecular dynamics simulations, combined with robust experimental techniques like single-molecule force spectroscopy and flow cytometry. These methods provided a detailed and reliable view of the interactions between the H3 protein and HS. The study also highlighted the importance of the α-helical domain's electric charge and the influence of the Mg(II) ion in stabilizing this interaction. The work's impact on the field is significant, offering new perspectives for developing antiviral treatments for MPXV and potentially other viruses with similar adhesion mechanisms. The provided methods and data are highly useful for researchers working with viral proteins and protein-polysaccharide interactions, offering a solid foundation for future investigations and therapeutic innovations.

Weaknesses:

However, some limitations are notable. Despite the robust use of computational methodologies, the limitations of this approach are not discussed, such as potential sources of error, standard deviation rates, and known controls for the H3 protein to justify the claims. Additionally, validations with methodologies like X-ray crystallography would further benefit the visualization of the H3 and HS interaction.

Reviewer #2 (Public Review):

In this manuscript, the authors analyze the shapes of cerebral cortices from several primate species, including subgroups of young and old humans, to characterize commonalities in patterns of gyrification, cortical thickness, and cortical surface area. The authors state that the observed scaling law shares properties with fractals, where shape properties are similar across several spatial scales. One way the authors assess this is to perform a "cortical melting" operation that they have devised on surface models obtained from several primate species. The authors also explore differences in shape properties between brains of young (~20 year old) and old (~80) humans. A challenge the authors acknowledge struggling with in reviewing the manuscript is merging "complex mathematical concepts and a perplexing biological phenomenon." This reviewer remains a bit skeptical about whether the complexity of the mathematical concepts being drawn from are justified by the advances made in our ability to infer new things about the shape of the cerebral cortex.

(1) The series of operations to coarse-grain the cortex illustrated in Figure 1 produces image segmentations that do not resemble real brains. The process to assign voxels in downsampled images to cortex and white matter is biased towards the former, as only 4 corners of a given voxel are needed to intersect the original pial surface, but all 8 corners are needed to be assigned a white matter voxel. The reason for introducing this bias (and to the extent that it is present in the authors' implementation) is not provided. The authors provide an intuitive explanation of why thickness relates to folding characteristics, but ultimately an issue for this reviewer is, e.g., for the right-most panel in Figure 2b, the cortex consists of several 4.9-sided voxels and thus a >2 cm thick cortex. A structure with these morphological properties is not consistent with the anatomical organization of typical mammalian neocortex.

(2) For the comparison between 20-year-old and 80-year-old brains, a well-documented difference is that the older age group possesses more cerebral spinal fluid due to tissue atrophy, and the distances between the walls of gyri becomes greater. This difference is born out in the left column of Figure 4b. It seems this additional spacing between gyri in 80 year olds requires more extensive down-sampling (larger scale values in Figure 4a) to achieve a similar shape parameter K as for the 20 year olds. The authors assert that K provides a more sensitive measure (associated with a large effect size) than currently used ones for distinguishing brains of young vs. old people. A more explicit, or elaborate, interpretation of the numbers produced in this manuscript, in terms of brain shape, might make this analysis more appealing to researchers in the aging field.

(3) In the Discussion, it is stated that self-similarity, operating on all length scales, should be used as a test for existing and future models of gyrification mechanisms. Given the lack of association between the abstract mathematical parameters described in this study and explicit properties of brain tissue and its constituents, it is difficult to envision how the coarse-graining operation can be used to guide development of "models of cortical gyrification."

(4) There are several who advocate for analyzing cortical mid-thickness surfaces, as the pial surface over-represents gyral tips compared to the bottoms of sulci in the surface area. The authors indicate that analyses of mid-thickness representations will be taken on in future work, but this seems to be a relevant control for accepting the conclusions of this manuscript.

Reviewer #2 (Public Review):

Summary:

The manuscript focuses on comparison of two PLP-dependent enzyme classes that perform amino acyl decarboxylations. The goal of the work is to understand the substrate specificity and factors that influence catalytic rate in an enzyme linked to theanine production in tea plants.

Strengths:

The work includes x-ray crystal structures of modest resolution of the enzymes of interest. These structures provide the basis for design of mutagenesis experiments to test hypotheses about substrate specificity and the factors that control catalytic rate. These ideas are tested via mutagenesis and activity assays, in some cases both in vitro and in plants.

Weaknesses:

Although improved in a revision, the manuscript could be more clear in explaining the contents of the x-ray structures and how the complexes studied relate to the reactant and product complexes. Some of the figures lack sufficient clarity and description. Some of the claims about the health benefits of tea are not well supported by literature citations.

Reviewer #2 (Public Review):

Significance:

Rubio et al. study the behavior of the transcription factor Hsf1 under ethanol stress, examining its distribution within the nucleus and the coalescence of heat shock response genes in budding yeast. In comparison to the heat shock response, the response to ethanol stress shows similar gene coalescence and Hsf1 binding. However, there is a notable delay in the transcriptional response to ethanol, and a disconnect between it and the appearance of irreversible Hsf1 condensates/puncta, highlighting important differences in how Hsf1 responds to these two related but distinct environmental stresses.

Overview and general concerns (from the original review):

The authors studied how yeast responds to ethanol stress (8.5%) and compared it to the heat shock response (from 25{degree sign}C to 39{degree sign}C). They observed a more gradual increase in the expression of heat shock response (HSR) genes during ethanol stress compared to heat shock. Additionally, the recruitment of Hsf1 and Pol II to HSR genes, and the inter- and intrachromosomal interactions among these genes, showed slower kinetics under ethanol stress. They attribute the delay in transcriptional response to chromatin compaction induced by ethanol. Despite this delay, these interactions persisted longer. Hsf1 clusters, previously documented during the heat shock response, were also observed during ethanol stress and persisted for an extended period. The conditional degradation of Hsf1 and Rpb1 eliminated most inter- and intrachromosomal interactions for heat shock responsive genes in both ethanol stress and heat shock conditions, indicating the importance of these factors for long distance interactions between HSR genes. Overall, this manuscript provides novel insights into the differential behavior of HSR genes under different stress conditions. This contributes to the broader understanding of how different stressors might elicit unique responses at the genomic and topographical level under the regulation of transcription factor Hsf1.

The central finding of the study highlights the different dynamics of Hsf1, Pol II, and gene organization in response to heat shock versus ethanol stress. However, one important limitation to consider is that the two chosen conditions may not be directly comparable. For a balanced assessment, the authors should ideally expose yeast to various ethanol concentrations and different heat shock temperatures, ensuring the observed differences stem from the nature of the stressor rather than suboptimal stress intensity. At the very least, an additional single ethanol concentration point on each side of 8.5% should be investigated to ensure that 8.5% is near the optimum. In fact, comparing the number of Hsp104 foci in the two conditions in Fig. 1E and F suggests that the yeast is likely experiencing different intensities of stress for the chosen heat shock condition and ethanol concentration used in this study.

A second significant concern is the use of the term "Hsf1 condensate". Chowdhary et al.'s 2022 Molecular Cell study highlighted an inhomogeneous distribution and rapid dynamics of Hsf1 clustering upon heat shock, with sensitivity to 1,6-hexandiol, which is interpreted as evidence for condensation by LLPS. But this interpretation has been criticized severely by McSwiggen at al. Genes Dev 2019 and Mussacchio EMBO J 2022. It is important to mention that 1,6-hexandiol is known to affect chromatin organization (Itoh et al. Life Science Alliance 2021). Describing such clusters as 'condensates' without further experimental evidence is premature. I encourage authors to settle on their neutral term 'puncta' which they use interchangeably with 'condensate' so as not to confuse the reader. The dynamic binding and unbinding of the low-abundance Hsf1 at coalescent chromatin target sites might explain the liquid-like properties of these clusters without the need for invoking the phase-separation hypothesis. While Hsf1 clusters exhibit features consistent with phase-separated condensates, other equally plausible alternative mechanisms, such as dynamic site-specific interactions (Musacchio, EMBO J, 2022), should also be considered. This is best left for the discussion where the underlying mechanism for puncta formation can be addressed.

Comments on revised version:

The authors have addressed the majority of my comments effectively. The new Sis1 experiment provides a clear illustration of a distinctive response to ethanol and heat. This work offers a comprehensive perspective on Hsf1 in stress response from multiple angles. I have two additional comments to improve the paper without re-review:

(Original point #3) Could the authors clarify the differences between DPY1561 and the original strain used? There appears to be missing statistical analysis for Figure 1E at the bottom.

(Original point #4) In the new Figure 7F, '% transcription' and '% coalescence' are presented. My understanding is that Figures 7D and 7E aim to demonstrate the correlation between HSP104 transcription (a continuous variable) and HSP104-HSP12 coalescence (a binary variable) at the single-cell level. However, averaging the data across cells masks individual variations and potential anti-correlations. The authors could explore statistical methods that handle correlations between a continuous variable and a binary variable. Alternatively, consider converting 'HSP104 transcription' to a binary variable and then performing a chi-square test to assess the association.

Reviewer #1 (Public Review):

(1) Significance of the findings:

Cell-to-cell communication is essential for higher functions in bacterial biofilms. Electrical signals have proven effective in transmitting signals across biofilms. These signals are then used to coordinate cellular metabolisms or to increase antibiotic tolerance. Here, the authors have reported for the first time coordinated oscillation of membrane potential in E. coli biofilms that may have a functional role in photoprotection.

(2) Strengths of the manuscript:

- The authors report original data.<br /> - For the first time, they showed that coordinated oscillations in membrane potential occur in E. Coli biofilms.<br /> - The authors revealed a complex two-phase dynamic involving distinct molecular response mechanisms.<br /> - The authors developed two rigorous models inspired by 1) Hodgkin-Huxley model for the temporal dynamics of membrane potential and 2) Fire-Diffuse-Fire model for the propagation of the electric signal.<br /> - Since its discovery by comparative genomics, the Kch ion channel has not been associated with any specific phenotype in E. coli. Here, the authors proposed a functional role for the putative gated-voltage-gated K+ ion channel (Kch channel) : enhancing survival under photo-toxic conditions.

(3) Weakness:

- Contrarily to what is stated in the abstract, the group of B. Maier has already reported collective electrical oscillations in the Gram-negative bacterium Neisseria gonorrhoeae (Hennes et al., PLoS Biol, 2023).<br /> - The data presented in the manuscript are not sufficient to conclude on the photo-protective role of the Kch channel. The authors should perform the appropriate control experiments related to Fig4D,E, i.e. reproduce these experiments without ThT to rule out possible photo-conversion effects on ThT that would modify its toxicity. In addition, it looks like the data reported on Fig 4E are extracted from Fig 4D. If this is indeed the case, it would be more conclusive to report the percentage of PI-positive cells in the population for each condition. This percentage should be calculated independently for each replicate. The authors should then report the average value and standard deviation of the percentage of dead cells for each condition.<br /> - Although Fig 4A clearly shows that light stimulation has an influence on the dynamics of ThT signal in the biofilm, it is important to rule out possible contributions of other environmental variations that occur when the flow is stopped at the onset of light stimulation. I understand that for technical reasons, the flow of fresh medium must be stopped for the sake of imaging. Therefore, I suggest to perform control experiments consisting in stopping the flow at different time intervals before image acquisition (30min or 1h before). If there is no significant contribution from environmental variations due to medium perfusion arrest, the dynamics of ThT signal must be unchanged regardless of the delay between flow stop and the start of light stimulation.<br /> - To precise the role of K+ in the habituation response, I suggest using the ionophore valinomycin at sub-inhibitory concentrations (5 or 10µM). It should abolish the habituation response. In addition, the Kch complementation experiment exhibits a sharp drop after the first peak but on a single point. It would be more convincing to increase the temporal resolution (1min->10s) to show that there are indeed a first and a second peak. Finally, the high concentration (100µM) of CCCP used in this study completely inhibits cell activity. Therefore, it is not surprising that no ThT dynamics was observed upon light stimulation at such concentration of CCCP.<br /> - Since TMRM signal exhibits a linear increase after the first response peak (Supp Fig1D), I recommend to mitigate the statement at line 78.<br /> - Electrical signal propagation is an important aspect of the manuscript. However, a detailed quantitative analysis of the spatial dynamics within the biofilm is lacking. At minima, I recommend to plot the spatio-temporal diagram of ThT intensity profile averaged along the azimuthal direction in the biofilm. In addition, it is unclear if the electrical signal propagates within the biofilm during the second peak regime, which is mediated by the Kch channel: I have plotted the spatio-temporal diagram for Video S3 and no electrical propagation is evident at the second peak. In addition, the authors should provide technical details of how R^2(t) is measured in the first regime (Fig 7E).<br /> - In the series of images presented in supplementary Figure 4A, no wavefront is apparent. Although the microscopy technics used in this figure differs from other images (like in Fig2), the wavefront should be still present. In addition, there is no second peak in confocal images as well (Supp Fig4B) .<br /> - Many important technical details are missing (e.g. biofilm size, R^2, curvature and 445nm irradiance measurements). The description of how these quantitates are measured should be detailed in the Material & Methods section.<br /> - Fig 5C: The curve in Fig 5D seems to correspond to the biofilm case. Since the model is made for single cells, the curve obtained by the model should be compared with the average curve presented in Fig 1B (i.e. single cell experiments).<br /> - For clarity, I suggest to indicate on the panels if the experiments concern single cell or biofilm experiments. Finally, please provide bright-field images associated to ThT images to locate bacteria.<br /> - In Fig 7B, the plateau is higher in the simulations than in the biofilm experiments. The authors should add a comment in the paper to explain this discrepancy.

Reviewer #1 (Public Review):

Summary:

In this study of metabolism using Xenopus, explanted porcine hearts and limbs, and human organs-on-chips, Sperry et al studied the ability of WB3 to slow metabolism and mobility. The group developed WB3, an analog of SNC80, void of SNC80's delta-opioid receptor binding capacity and studied its metabolic impact. The authors concluded that SNC80 and its analog WB3 can induce "biostasis" and produce a hypometabolic state which holds promise for prolonging organ viability in transplant surgery as well as other potential clinical benefits.

Strengths:

This study also opens new avenues for therapeutic possibilities in areas such as trauma, acute infection, and brain injuries. The overall methodology is acceptable, but certain concerns should be addressed.

Weaknesses:

Major comments:

(1) In cardiac and renal transplantation, cold preservation in ice remains a common practice for transporting explanted hearts to donors which remains a cheap and easily accessible way of preserving organs. While ex-vivo mechanical circulatory platforms have been developed and are increasingly being utilized to prolong organ viability, cold preservation remains widely used. The authors perfused explanted hearts with oxygenated perfusion preservation devices at subnormothermic temperatures (20-23C) which is even much lower than routinely used in clinical cardiopulmonary bypass scenarios (28-32C) (in the discussion, the authors allude to SNC80's possible "protective effect" in cardiac bypass). It is unclear how much of the hypometabolic state is related to WB3 administration versus hypothermia. The study will benefit from a comparison of WB3 administration and hypothermia in Xenopus, explanted porcine organs versus cold preservation alone to show distinction in biostasis parameters.

(2) The authors selected SNC80 based on a literature survey where it was identified based on its ability to induce hypothermia and protect against the effects of spinal cord ischemia in rodents. While this makes sense, were other drugs (eg. Puerarin) considered? The induction of hypothermia and spinal cord protective effect of SNC80 may be multifactorial and not necessarily related to its biostatic effects as the authors describe. Please provide some more context into the background of SNC80.

(3) In most of the models, the primary metric that the authors utilize to characterize metabolic activity is oxygen consumption, which is a somewhat limited indicator. For instance, this does not provide any information, however, on anaerobic metabolic activity. In addition, the ATP/ADP ratio was found to decrease in the organ chips where SNC80 was utilized, but similar findings were not presented for the other models.

(4) The authors should provide a more detailed explanation of SNC80's mechanisms of interaction with proteins related to transmembrane transport, mitochondrial activity, and metabolic processes. What is the impact of SNC80 on mitochondrial function, particularly ATP production and mitochondrial respiration? Are there changes in mitochondrial membrane potential, electron transport chain activity, or oxidative phosphorylation? In this context, authors discuss the potential role of NCX1 as a binding target for SNC80 and its various mechanisms in slowing metabolism. However, no experiments have been done to confirm this binding in the present study. Co-immunoprecipitation studies using appropriate antibodies against SNC80 and NCX1 should be considered to demonstrate their direct binding. Additionally, surface plasmon resonance (SPR) or isothermal titration calorimetry (ITC) experiments could be employed to quantify the binding affinity between SNC80 and NCX1, providing further evidence of their interaction. These experiments would elucidate the binding mechanism between SNC80 and NCX1 and reveal more information on the mechanism of action for SNC80.

(5) The manuscript notes that histological analysis was conducted, but it seems that only example images are provided, such as Fig 4f. Quantified histological data would provide a more thorough understanding of tissue integrity.

(6) Some of the points mentioned in the discussion and conclusion are rather strong and based on possible associations such as SNC80's potential vasodilatory capacity conferring a cardioprotective effect, ability to reversibly suppress metabolism across different temperatures and species. Please tone this down and stay limited to the organs studied. Further, the reversibility of the findings may be more objectively assessed by biomarkers with decreased immunofluorescence in response to ischemia such as troponin I for heart and albumin for liver. Additionally, an investigation of proteins involved in inflammation, hypoxia, and key cell death pathways using immunohistochemistry analysis can better describe the impact of treatment on apoptosis/necroptosis.

(7) What could be the underlying cause of the observed increase in intercellular spacing after SNC80 administration in porcine limbs which also seems to be evident in the heart histology samples? This seems to be more prominent in the SNC80 compared to the vehicle group.

(8) In the Discussion section, it would be valuable to provide a concise interpretation of the lipidomic data, particularly explaining how changes in acylcarnitine and cholesterol ester levels may relate to tadpole metabolism, hibernation, or other biological processes.

(9) What are the limitations or disadvantages of the study? Does SNC80 possess any immunomodulatory properties that might affect the outcomes of organ transplantation? Are there specific organs for which SNC80 may not be a suitable preservation agent, and if so, what are the reasons behind this?

Comments on revised version:

The authors have satisfactorily addressed our comments in the rebuttal letter. The limitations described by the authors in point #9, however, need to be incorporated in the revised manuscript in detail as they are important in guiding interpretation of the present data. Congratulations again on the important study.

Reviewer #3 (Public Review):

Summary:

Plasmacytoid dendritic cells (pDCs) represent a specialized subset of dendritic cells (DCs) known for their role in producing type I interferons (IFN-I) in response to viral infections. It was believed that pDCs originated from common DC progenitors (CDP). However, recent studies by Rodrigues et al. (Nature Immunology, 2018) and Dress et al. (Nature Immunology, 2019) have challenged this perspective, proposing that pDCs predominantly develop from lymphoid progenitors expressing IL-7R and Ly6D. A minor subset of pDCs arising from CDP has also been identified as functionally distinct, exhibiting reduced IFN-I production but a strong capability to activate T cell responses. On the other hand, clonal lineage tracing experiments, as recently reported by Feng et al. (Immunity, 2022), have demonstrated a shared origin between pDCs and conventional DCs (cDCs), suggesting a contribution of common DC precursors to the pDC lineage.

In this context, Araujo et al. investigated the heterogeneity of pDCs in terms of both development and function. Their findings revealed that approximately 20% of pDCs originate from lymphoid progenitors common to B cells. Using Mb1-Cre x Bcl11a floxed mice, the authors demonstrated that the development of this subset of pDCs, referred to as "B-pDCs," relied on the transcription factor BCL11a. Functionally, B-pDCs exhibited a diminished capacity to produce IFN-I in response to TLR9 agonists but secreted more IL-12 compared to conventional pDCs. Moreover, B-pDCs, either spontaneously or upon activation, exhibited increased expression of activation markers (CD80/CD86/MHC-II) and a heightened ability to activate T cell responses in vitro compared to conventional pDCs. Finally, Araujo et al. characterized these B-pDCs at the transcriptomic level using bulk and single-cell RNA sequencing, revealing them as a unique subset of pDCs expressing certain B cell markers such as Mb1, as well as specific markers (Axl) associated with cells recently described as transitional DCs.<br /> Thus, in contrast to previous findings, this study posits that a small proportion of pDCs derive from B cell-committed lymphoid progenitors, and this subset of B-pDCs exhibits distinct functional characteristics, being less specialized in IFN-I production but rather in T cell activation.

Strengths:

Previously, the same research group delineated the significance of BCL11a as a critical transcription factor in pDC development (Ippolito et al., PNAS, 2014). This study elucidates the precise stage during hematopoiesis at which BCL11a expression becomes essential for the emergence of a distinct subset of pDCs, substantiated by robust genetic evidence in vivo. Furthermore, it underscores the shared developmental origin between pDCs and B cells, reinforcing prior research in the field that suggests a lymphoid origin of pDCs. Finally, this works attributes specific functional properties to pDCs originating from these lymphoid progenitors shared with B cells, emphasizing the early imprinting of functional heterogeneity during their development.

Weaknesses:

Using their Mb1-reporter mice, the authors demonstrate that YFP pDCs originating from lymphoid progenitors are functionally distinct from conventional pDCs, mostly in vitro, but their in vivo relevance remains unknown. As underlined by both reviewers I believe that it is crucial to investigate how Bcl11a conditional deficiency in Mb1 expressing cells affects the anti-viral immune response, for example, using the M-CoV infection model as described by Sulczewski et al. in Nature Immunology, 2023. The current in vivo data using TLR9 agonist and in vitro data using B-pDCs co-cultures with T cells insufficiently address what B-pDCs might be doing in infectious contexts.

Revisions:

I thank the authors for their responses to my questions and for addressing most of my comments clearly and thoroughly. However, one major question remains unanswered: What is the functional relevance of the subset of B-pDCs that they have characterized? This key question, also highlighted by the other reviewer, requires further investigation. The current in vivo data using TLR9 agonist and in vitro data using B-pDCs co-cultures with T cells insufficiently address what B-pDCs might be doing in infectious contexts.

Reviewer #1 (Public Review):

Summary:<br /> In this study the authors advance their previous findings on the role of the SLAM-SAP signaling pathway in the development and function of multiple innate-like gamma-delta T cell subsets. Using high throughput single cell proteogenomics approach, the authors uncover SAP-dependent developmental checkpoints, and the role of SAP signaling in regulating the diversion of γδ T cells into the αβ T cell developmental pathway. Finally, the authors define TRGV4/TRAV13-4(DV7)-expressing T cells as a novel, SAP-dependent Vγ4 γδT1 subset.

Strengths:<br /> This study furthers our understanding of the importance and complexity of the SLAM-SAP signaling pathway not only in the development of innate-like γδ T cells but also the how it potentially balances the γδ/αβ T cell lineage commitment. Additionally, this study reveals the role of SAP-dependent events in generation of γδ TCR repertoire.

Comments on revised version:

The conclusions of the study are supported by well thought-out experiments and compelling data.

Weaknesses:<br /> There are no major weakness in the study.

A few minor points:<br /> (1) In the subsets of the γδ T cells that exhibit reduced BLK expression in B6. SAP KO mice, have the authors examined the expression of Lck and/or Fyn?<br /> (2) Does BLK directly associate with SLAM F1 and or SLAM F6 receptors?<br /> (3) Given the emerging role of γδ T cells in host immunity, it will be useful if the authors add a discussion of how their findings are relevant in disease conditions such as in cancer.

The author has adequately addressed all the reviewers' comments.

Reviewer #1 (Public Review):

Summary:

The manuscript by van Heerden et al. reports growth rate variations in the cell cycle of E. coli and links this variation to uneven ribosome concentrations in the cell at birth that arise from an uneven division of cell volumes between the daughter cells. The authors propose a model to explain the experimental data, whose main premises are the exclusion of ribosomes from the nucleoid volume and a linear dependence of the growth rate on ribosome concentration in the cell.

Strengths:

(1) The manuscript highlights an interesting aspect of growth rate variability in bacteria and proposes a mechanism for how this variation is homeostatically corrected.

(2) A sophisticated modeling to explain the experimental data.

Weaknesses:

(1) The experiments lack controls. A partially functional label (L9-mCherry) can make ribosomes much more limiting for growth than are not labeled ribosomes.

(2) The large variation of interdivision times 72-89 min in repeat experiments in Glc is problematic. Some parameters in the measurements related to cell growth appear not properly controlled. It is problematic for a work that aims to establish a new universal behavior related to cell growth.

(3) The authors have not provided convincing evidence that cells in their experiment grow in a steady state.

4) The findings are over-generalized. The existing data show the effects only at some growth rates, but the findings are presented as a new universal principle.

5) The model relies on many assumptions that are not clearly brought out and the choice of model parameters is questionable (in some cases, the parameters seem to contradict well-established experimental data, including the one from the experiments from the very same work). Small changes in parameters and various approximations can have large effects on the model's outcomes; without understanding these responses, the model has a rather limited value.

6) There appears to be a qualitative discrepancy between the model and the experimental data in Glc (the main condition studied). The model predicts that the cells born large have a specific elongation rate that is smaller than the average growth rate of cells, but it grows in time at the beginning of the cell cycle, while the experiments show a decreasing growth rate (Figure 1C, SI Figure S2).

Reviewer #1 (Public Review):

This article by Navratna et al. reports the first structure of human HGSNAT in an acetyl-CoA-bound state. Through careful structural analysis, the authors propose potential reasons why certain human mutations lead to lysosomal storage disorders and outline a catalytic mechanism. The structural data are of good quality, and the manuscript is clearly written. This study represents an important step toward understanding the mechanism of HGSNAT and is valuable to the field. I have the following suggestions:

(1) The authors should characterize whether the purified protein is active. Otherwise, how does one know if the detergent used maintains the protein in a biologically relevant state? The authors should at least attempt to do so. If these prove to be challenging, at the very least, the authors should try a cell-based assay to demonstrate that the GFP tag does not interfere with the function.

(2) In Figure 5, the authors present a detailed schematic of the catalytic cycle, which I find to be too speculative. There is no evidence to suggest that this enzyme undergoes isomerization, similar to a transporter, between open-to-lumen and open-to-cytosol states. Could it not simply involve some movements of side chains to complete the acetyl transfer?

Reviewer #1 (Public Review):

Summary:

This manuscript reports the effects of a heterozygous mutation in the KCNT1 potassium channels on the properties of ion currents and firing behavior of excitatory and inhibitory neurons in the cortex of mice expressing KCNT1-Y777H. In humans, this mutation as well as multiple other heterozygotic mutations produce very severe early-onset seizures and produce a major disruption of all intellectual function. In contrast, in mice, this heterozygous mutation appears to have no behavioral phenotype or any increased propensity to seizures. A relevant phenotype is, however, evident in mice with the homozygous mutation, and the authors have previously published the results of similar experiments with the homozygotes. As perhaps expected, the neuronal effects of the heterozygous mutation presented in this manuscript are generally similar but markedly smaller than the previously published findings on homozygotes. There are, however, some interesting differences, particularly on PV+ interneurons, which appear to be more excitable than wild type in the heterozygotes but more excitable in the heterozygotes. This raises the interesting question, which has been explicitly discussed by the authors in the revised manuscript, as to whether the reported changes represent homeostatic events that suppress the seizure phenotype in the mouse heterozygotes or simply changes in excitability that do not reach the threshold for behavioral outcomes.

Strengths and Weaknesses:

(1) The authors find that the heterozygous mutation in PV+ interneurons increases their excitability, a result that is opposite from their previous observation in neurons with the corresponding homozygous mutation. They propose that this results from the selective upregulation of a persistent sodium current INaP in the PV+ interneurons. These observations are very interesting ones, and they raised some issues in the original submission:

A) The protocol for measuring the INaP current could potentially lead to results that could be (mis)interpreted in different ways in different cells. First, neither K currents nor Ca currents are blocked in these experiments. Instead, TTX is applied to the cells relatively rapidly (within 1 second) and the ramp protocol is applied immediately thereafter. It is stated that, at this time, Na currents and INaP are fully blocked but that any effects on Na-activated K currents are minimal. In theory this would allow the pre- to post- difference current to represent a relatively uncontaminated INaP. This would, however, only work if activation of KNa currents following Na entry is very slow, taking many seconds. A good deal of literature has suggested that the kinetics of activation of KNa currents by Na influx vary substantially between cell types, such that single action potentials and single excitatory synaptic events rapidly evoke KNa currents in some cell types. This is, of course, much faster than the time of TTX application. Most importantly, the kinetics of KNa activation may be different in different neuronal types, which would lead to errors that could produce different estimates of INaP in PV+ interneurons vs other cell types.

In their revised manuscript, the authors have provided good data demonstrating that, at least for the PV and SST neurons, loss of KNa currents after TTX application is slow relative to the time course of loss of INaP, justifying the use of this protocol for these neuronal types.

B) As the authors recognize, INaP current provides a major source of cytoplasmic sodium ions for the activation. An expected outcome of increased INaP is, therefore, further activation of KNa currents, rather than a compensatory increase in an inward current that counteracts the increase in KNa currents, as is suggested in the discussion.

The authors comment in the rebuttal that, despite the fact that sodium entry through INaP is known to activate KNa channels, an increase in INaP does not necessarily imply increased KNa current. This issue should be addressed directly somewhere in the text, perhaps most appropriately in the discussion.

C) The numerical simulations, in general, provide a very useful way to evaluate the significance of experimental findings. Nevertheless, while the in-silico modeling suggests that increases in INaP can increase firing rate in models of PV+ neurons, there is as yet insufficient information on the relative locations of the INaP channels and the kinetics of sodium transfer to KNa channels to evaluate the validity of this specific model.

The authors have now put in all of the appropriate caveats on this very nicely in the revised manuscript.

(2) The effects of the KCNT1 channel blocker VU170 on potassium currents are somewhat larger and different from those of TTX, suggesting that additional sources of sodium may contribute to activating KCNT1, as suggested by the authors. Because VU170 is, however, a novel pharmacological agent, it may be appropriate to make more careful statements on this. While the original published description of this compound reported no effect on a variety of other channels, there are many that were not tested, including Na and cation channels that are known to activate KCNT1, raising the possibility of off-target effects.

In the revised version, the authors have added more to the manuscript on this issue and have added a very clear discussion of this to the text (in the discussion section).

This is a very clear and thorough piece of work, and the authors are to be congratulated on this. My one remaining suggestion would be to make an explicit statement about whether increased sodium influx through INaP channels, which is thought to activate KNa channels, would be likely to increase KNa current in these neurons (see comment 1B).

Reviewer #1 (Public Review):

Summary:

Using chromaffin cells as a powerful model system for studying secretion, the authors study the regulatory role of complexin in secretion. Complexin is still enigmatic in its regulatory role, as it both provides inhibitory and facilitatory functions in release. The authors perform an extensive structure-function analysis of both the C- and N-terminal regions of complexin. There are several interesting findings that significantly advances our understanding of cpx/SNARe interactions in regulating release. C-terminal amphipathic helix interferes with SNARE complex assembly and thus clamps fusion. There are acidic residues in the C-term that may be seen as putative interaction partners for Synaptotagmin. The N-terminus of Complexin promoting role may be associated with an interaction with Syt1. In particular the putative interaction with Syt1 is of high interest and supported by quite strong functional and biochemical evidence. The experimental approaches are state of the art, and the results are of the highest quality and convincing throughout. They are adequate and intelligently discussed in the rich context of the standing literature. Whilst there are some concerns about whether the facilitatory actions of complexion have to be tightly linked to Syt1 interactions, the proposed model will significantly advance the field by providing new directions in future research.

Reviewer #1 (Public Review):

Summary:

In this research, Soni and Frank investigate the network mechanisms underlying capacity limitations in working memory from a new perspective, with a focus on visual working memory (VWM). The authors have advanced beyond the classical neural network model, which incorporates the prefrontal cortex and basal ganglia (PBWM), by introducing an adaptive chunking variant. This model is trained using a biologically plausible, dopaminergic reinforcement learning framework. The adaptive chunking mechanism is particularly well-suited to the VWM tasks involving continuous stimuli and elegantly integrates the 'slot' and 'resource' theories of working memory constraints. The chunk-augmented PBWM operates as a slot-like system with resource-like limitations.

Through numerical simulations under various conditions, Soni and Frank demonstrate the performance of the chunk-augmented PBWM model surpasses the no-chunk control model. The improvements are evident in enhanced effective capacity, optimized resource management, and reduced error rates. The retention of these benefits, even with increased capacity allocation, suggests that working memory limitations are due to a combination of factors, including the efficient credit assignments that are learned flexibly through reinforcement learning. In essence, this work addresses fundamental questions related to a computational working memory limitation using a biologically-inspired neural network, and thus has implications for clinical conditions in which working memory is affected, such as Parkinson's disease, ADHD, and schizophrenia.

Strengths:

The integration of mechanistic flexibility, reconciling two theories for WM capacity into a single unified model, results in a neural network that is both more adaptive and human-like. Building on the PBWM framework ensures the robustness of the findings. The addition of the chunking mechanism tailors the original model for continuous visual stimuli. Chunk-stripe mechanisms contribute to the 'resource' aspect, while input-stripes contribute to the 'slot' aspect. This combined network architecture enables flexible and diverse computational functions, enhancing performance beyond that of the classical model.

Moreover, unlike previous studies that design networks for specific task demands, the proposed network model can dynamically adapt to varying task demands by optimizing the chunking gating policy through RL.

The implementation of a dopaminergic reinforcement learning protocol, as opposed to a hard-wired design, leads to the emergence of strategic gating mechanisms that enhance the network's computational flexibility and adaptability. These gating strategies are vital for VWM tasks and are developed in a manner consistent with ecological and evolutionary learning held by humans. Further examination of how reward prediction error signals, both positive and negative, collaborate to refine gating strategies reveals the crucial role of reward feedback in fine-tuning the working memory computations and the model's behavior, aligning with the current neuroscientific understanding that reward matters.

Furthermore, assessing the impact of a healthy balance of dopaminergic reward prediction error signals on information manipulation holds implications for patients with altered striatal dopaminergic signaling.

Weaknesses:

While I appreciate the novelty of the idea presented in this paper, which aligns with common interests in cognitive neuroscience, I believe there are several areas that require further clarification.

First, the method section appears somewhat challenging to follow. To enhance clarity, it might be beneficial to include a figure illustrating the overall model architecture. This visual aid could provide readers with a clearer understanding of the overall network model.

Additionally, the structure depicted in Figure 2 could be potentially confusing. Notably, the absence of an arrow pointing from the thalamus to the PFC and the apparent presence of two separate pathways, one from sensory input to the PFC and another from sensory input to the BG and then to the thalamus, may lead to confusion. While I recognize that Figure 2 aims to explain network gating, there is room for improvement in presenting the content accurately.

Still, for the method part, it would enhance clarity to explicitly differentiate between predesigned (fixed) components and trainable components. Specifically, does the supplementary material state that synaptic connection weights in striatal units (Go&NoGo) are trained using XCAL, while other components, such as those in the PFC and lateral inhibition, are not trained (I found some sentences in 'Limitations and Future Directions')?

I'm not sure about the training process shown in Figure 8. It appears that the training may not have been completed, given that the blue line representing the chunk stripe is still ascending at the endpoint. The weights depicted in panel d) seem to correspond with those shown in panels b) and c), no? Then, how is the optimization process determined to be finished? Alternatively, could it be stated that these weight differences approach a certain value asymptotically? It would be better to clarify the convergence criteria of the optimization process.