Reviewer #2 (Public review):

Summary:

In this manuscript, Shelton et al. explore the organization of the Claustrum. To do so, they focus on a specific claustrum population, the one projecting to the retrosplenial cortex (CLA-RSP neurons). Using elegant technical approach, they first described electrophysiological properties of claustrum neurons, including the CLA-RSP ones. Further, they showed that CLA-RSP neurons 1) directly excite other CLA neurons, in a 'projection-specific' pattern, i.e. CLA-RSP neurons mainly excite claustrum neurons not projecting to the RSP and 2) received excitatory inputs from multiple cortical territories (mainly frontal ones). In an effort to confirm the 'integrative' property of claustrum networks, they then imaged claustrum axons in the cortex during single- or multi-sensory stimulations. Finally, they investigated the effect of CLA-RSP lesion on performance in a sensory detection task.

Strengths:

Overall, this is a really good study, using state of the art technical approaches to probe the local/global organization of the Claustrum. The in-vitro part is impressive, and the results are compelling.

Weaknesses:

One noteworthy concern arises from the terminology used throughout the study. The authors claimed that the claustrum is an integrative structure. Yet, integration has a specific meaning, i.e. the production of a specific response by a single neuron (or network) in response to a specific combination of several input signals. In this study, the authors showed compelling results in favor of convergence rather than integration. On a lighter note, the in-vivo data are less convincing, and do not entirely support the claim of "integration" made by the authors.

Reviewer #2 (Public review):

This study explores the role of the mediodorsal thalamus (MD) and the T-type calcium channel Cav3.1 in ethanol-induced behavioral changes, focusing on transitions between sedation and shifts in brain-states. The authors utilize genetic knockdown, optogenetic manipulation, and electrophysiological recording techniques in mice to assess the contribution of MD Cav3.1 channels to ethanol's sedative effects. The central hypothesis is that Cav3.1-mediated burst firing in the MD is essential for regulating ethanol-induced sedation and arousal transitions.

The authors' detailed responses to reviewers' comments significantly improved the manuscript, particularly regarding experimental specificity and methodological transparency. They addressed concerns about the specificity of MD knockdowns versus neighboring thalamic nuclei by adding quantifications, enhancing figure clarity, and providing lesion localization data. The revised figures, with added quantification panels, strengthened the claim that the manipulations specifically targeted the MD. Improvements in lesion validation figures and electrode placement explanations further clarified the accuracy of their methods.

One major limitation, as highlighted by Reviewer 1, is the lack of direct evidence from inhibitory optogenetic studies to validate the role of Cav3.1 channels in modulating ethanol-induced transitions in the MD. While the authors acknowledged the challenges of such experiments, citing technical issues like the inability of Cav3.1 knockout to allow rebound burst firing, the absence of these controls limits definitive causal conclusions about the MD's role. Alternative experiments with varying ethanol doses and data on tonic versus burst firing were presented, but these do not fully compensate for the missing inhibitory optogenetics, leaving some uncertainty regarding the attribution of observed behavioral effects solely to Cav3.1-mediated burst activity in the MD.<br /> Another challenge is the complexity of distinguishing the specific contribution of the MD from that of other thalamic nuclei involved in regulating arousal and brain-states. Although additional quantification was provided to demonstrate MD specificity, control experiments targeting adjacent regions like the central lateral nucleus (CL) would have strengthened the manuscript. While the practical constraints are understandable, this limitation slightly weakens the argument regarding the MD's unique role in state transitions. The provided explanations about spatial targeting and electrophysiological methods were reasonable, but a broader set of thalamic controls would have offered a more comprehensive understanding.

Overall, the authors successfully achieved their aims, providing strong evidence that Cav3.1-mediated burst firing in the MD is crucial for ethanol-induced sedation. The knockdown experiments showed a clear reduction in ethanol sensitivity, and the behavioral assays supported the conclusion that MD Cav3.1 activity plays a key role in regulating arousal states. The combined use of Cav3.1 knockdown and optogenetic stimulation effectively linked MD activity to ethanol-induced behavioral changes. The evidence presented establishes a clear mechanistic connection between neuronal activity and behavioral responses.

The expanded discussion and clarifications in response to reviewer feedback enhanced the manuscript's coherence, and the revisions to the figures improved the transparency of the findings. Despite not implementing all the additional experiments suggested by Reviewer 1, the authors provided sufficient alternative evidence and a clear explanation of practical limitations, making their conclusions credible given the available data.

This study significantly advances our understanding of thalamic involvement in behavioral state transitions, particularly ethanol-induced sedation. By clarifying the role of Cav3.1-mediated burst firing in the MD, the research provides new insights into how specific neuronal activity patterns influence global brain states and behavioral arousal, which has implications for understanding mechanisms underlying anesthesia, sedation, and sleep regulation. Moreover, the transparency in data sharing and detailed methodological revisions make this work a valuable resource for replication or adaptation in similar studies.

Reviewer #2 (Public review):

Summary:

While selective attention is a crucial ability of human beings, previous studies on selective attention are primarily conducted in a strictly controlled context, leaving a notable gap in underlying the complexity and dynamic nature of selective attention in a naturalistic context. This issue is particularly important for classroom learning in individuals with ADHD, as selecting the target and ignoring the distractions are pretty difficult for them but are the prerequisites of effective learning. The authors of this study have addressed this challenge using a well-motivated study. I believe the findings of this study will be a nice addition to the fields of both cognitive neuroscience and educational neuroscience.

Strengths:

To achieve the purpose of setting up a naturalistic context, the authors have based their study on a novel Virtual Reality platform. This is clever as it is usually difficult to perform such a study in a real classroom. Moreover, various techniques such as brain imaging, eye-tracking, and physiological measurement are combined to collect multi-level data. They found that, different from the controls, individuals with ADHD had higher neural responses to the irrelevant rather than the target sounds, and reduced speech tracking of the teacher. Additionally, the power of alpha-oscillations and frequency of gaze shifts away from the teacher are found to be associated with ADHD symptoms. These results provide new insights into the mechanism of selective attention among ADHD populations.

Weaknesses:

It is worth noting that nowadays there have been some studies trying to do so in the real classroom, and thus the authors should acknowledge the difference between the virtual and real classroom context and foresee the potential future changes.

The approach of combining multi-level data has the advantage of obtaining reliable results, but also raises significant difficulty for the readers to understand the main results.

An appraisal of whether the authors achieved their aims, and whether the results support their conclusions.

As expected, individuals with ADHD showed anomalous patterns of neural responses, and eye-tracking patterns, compared to the controls. But there are also some similarities between groups such as the amount of time paying attention to teachers, etc. In general, their conclusions are supported.

A discussion of the likely impact of the work on the field, and the utility of the methods and data to the community, would highlight the contributions of the work.

The findings are an extension of previous efforts in understanding selective attention in the naturalistic context. The findings of this study are particularly helpful in inspiring teacher's practice and advancing the research of educational neuroscience. This study demonstrates, again, that it is important to understand the complexity of cognitive processes in the naturalistic context.

Reviewer #2 (Public review):

Summary:

This manuscript describes a workflow and software package, SMARTR, for mapping and analyzing neuronal ensembles tagged using activity-dependent methods. They showcase this pipeline by analyzing ensembles tagged during the learned helplessness paradigm. This is an impressive effort, and I commend the authors for developing open-source software to make whole-brain analyses more feasible for the community. Software development is essential for modern neuroscience and I hope more groups make the effort to develop open-source, easily usable packages. However, I do have concerns over the usability and maintainability of the SMARTR package. I hope that the authors will continue to develop this package, and encourage them to make the effort to publish it within either the Bioconductor or CRAN framework.

Strengths:

This is a novel software package aiming to make the analysis of brain-wide engrams more feasible, which is much needed. The documentation for the package and workflow is solid.

Weaknesses:

While I was able to install the SMARTR package, after trying for the better part of one hour, I could not install the "mjin1812/wholebrain" R package as instructed in OSF. I also could not find a function to load an example dataset to easily test SMARTR. So, unfortunately, I was unable to test out any of the packages for myself. Along with the currently broken "tractatus/wholebrain" package, this is a good example of why I would strongly encourage the authors to publish SMARTR on either Bioconductor or CRAN in the future. The high standards set by Bioc/CRAN will ensure that SMARTR is able to be easily installed and used across major operating systems for the long term.

The package is quite large (several thousand lines include comments and space). While impressive, this does inherently make the package more difficult to maintain - and the authors currently have not included any unit tests. The authors should add unit tests to cover a large percentage of the package to ensure code stability.

Why do the authors choose to perform image segmentation outside of the SMARTR package using ImageJ macros? Leading segmentation algorithms such as CellPose and StarMap have well-documented APIs that would be easy to wrap in R. They would likely be faster as well. As noted in the discussion, making SMARTR a one-stop shop for multi-ensemble analyses would be more appealing to a user.

Given the small number of observations for correlation analyses (n=6 per group), Pearson correlations would be highly susceptible to outliers. The authors chose to deal with potential outliers by dropping any subject per region that was> 2 SDs from the group mean. Another way to get at this would be using Spearman correlation. How do these analyses change if you use Spearman correlation instead of Pearson? It would be a valuable addition for the author to include Spearman correlations as an option in SMARTR.

I see the authors have incorporated the ability to adjust p-values in many of the analysis functions (and recommend the BH procedure) but did not use adjusted p-values for any of the analyses in the manuscript. Why is this? This is particularly relevant for the differential correlation analyses between groups (Figures 3P and 4P). Based on the un-adjusted p-values, I assume few if any data points will still be significant after adjusting. While it's logical to highlight the regional correlations that strongly change between groups, the authors should caution ¬ which correlations are "significant" without adjusting for multiple comparisons. As this package now makes this analysis easily usable for all researchers, the authors should also provide better explanations for when and why to use adjusted p-values in the online documentation for new users.

The package was developed in R3.6.3. This is several years and one major version behind the current R version (4.4.3). Have the authors tested if this package runs on modern R versions? If not, this could be a significant hurdle for potential users.

Reviewer #2 (Public review):

Summary:

This work brings important information regarding the composition of interneurons in the mammalian spinal cord, with a developmental perspective. Indeed, for the past decades, tools inspired from developmental biology have opened up promising avenues for challenging the functional heterogeneity in the spinal cord. They rely on the fact that neurons sharing similar mature properties also share a largely similar history of expression of specific transcription factor (TF) genes during embryogenic and postnatal development. For instance, neurons originating from p1 progenitors and expressing the TF Engrailed-1, form the V1 neuronal class. While such "cardinal" neuronal classes defined by one single RF indeed share numerous features - e.g., for the case of V1 neurons, a ventral positioning, an inhibitory nature and ipsilatetal projections - there is accumulating evidence for a finer-grained diversity and specialization in each class which is still largely obscure. The present work studies the heterogeneity of V1 interneurons and describes multiple classes based on their birthdate, final positioning, and expression of additional TF. It brings in particular a solid characterization of the Foxp2-expressing V1 interneurons for which authors also delve into the connectivity, and hence, possible functional implication. The work will be of interest to developmental biologists and those interested in the organization of the locomotor spinal network.

Strengths:

This study has deeply analyzed the diversity of V1 neurons by intersecting multiple criteria: TF expression, birthdate, location in the spinal cord, diversity along the rostro-caudal axis, and for some subsets, connectivity. This illustrates and exemplifies the absolute need to not consider cardinal classes, defined by one single TF, as homogeneous. Rather, it highlights the limits of single-TF classification and exemplifies the existence of further diversity within the cardinal class.

Experiments are generally well performed with a satisfactory number of animals and adequate statistical tests.

Authors have also paid strong attention to potential differences in cell-type classification when considering neurons currently expressing of a given TF (e.g., using antibodies), from those defined as having once expressed that TF (e.g., defined by a lineage-tracing strategy). This ambiguity is a frequent source of discrepancy of findings across studies.

Furthermore, there is a risk in developmental studies to overlook the fact that the spinal cord is functionally specialized rostro-caudally, and to generalize features that may only be applicable to a specific segment and hence to a specific motor pool. While motoneurons share the same dorso-ventral origin and appear homogenous on a ChAT staining, specific clusters are dedicated to specific muscle groups, e.g., axial, hypaxial or limb muscles. Here, the authors make the important distinction between different lumbar levels and detail the location and connectivity of their neurons of interest with respect to specific clusters of MN.

Finally, the authors are fully transparent on inter-animal variability in their representation and quantification. This is crucial to avoid the overgeneralization of findings but to rather provide a nuanced understanding of the complexities of spinal circuits.

Weaknesses:

The different V1 populations have been investigated in detail regarding their development and positioning, but their functional ambition is not directly investigated through gain or loss of function experiments in the present study. While the putative inputs onto motoneurons are interesting and suggestive of differences between V1 pools, they are only a little predictive of function.

Reviewer #2 (Public review):

Summary:

Napoli et al. provide a compelling study showing the importance of cytosolic S100A8/9 in maintaining calcium levels at LFA-1 nano clusters at the cell membrane, thus allowing the successful crawling and adherence of neutrophils under shear stress. The authors show that cytosolic S100A8/9 is responsible for retaining stable and high concentrations of calcium specifically at LFA-1 nanoclusters upon binding to ICAM-1, and imply that this process aids in facilitating actin polymerisation involved in cell shape and adherence. The authors show early on that S100A8/9 deficient neutrophils fail to extravasate successfully into the tissue, thus suggesting that targeting cytosolic S100A8/9 could be useful in settings of autoimmunity/acute inflammation where neutrophil-induced collateral damage is unwanted.

Strengths:

Using multiple complementary methods from imaging to western blotting and flow cytometry, including extracellular supplementation of S100A8/9 in vivo, the authors conclusively prove a defect in intracellular S100A8/9, rather than extracellular S100A8/9 was responsible for the loss in neutrophil adherence, and pinpointed that S100A8/9 aided in calcium stabilisation and retention at the plasma membrane.

Weaknesses:

(1) Extravasation is shown to be a major defect of Mrp14-/- neutrophils, but the Giemsa staining in Figure 1H seems to be quite unspecific to me, as neutrophils were determined by nuclear shape and granularity, which could be affected by the angle at which the nucleus is viewed. It would have perhaps been cleaner/clearer to use immunofluorescence staining for neutrophils instead as seen in Supplementary Figure 1A (staining for Ly6G or other markers instead of S100A9).

Addressed issues:

(1) The representative image for Mrp14-/- neutrophils used in Figure 4K to demonstrate the Ripley's K function seems to be very different from that shown above in Figure 4C and 4F. In their response to reviewers, the authors reassure that all data has been included in the analysis.

(2) In the initial submission the authors needed to provide a more direct linkage between cytosolic S100A8/9 and actin polymerisation, which subsequently results in the arrest and adherence of neutrophils. The authors did an additional experiment indicating the co-localization of S100A8/9 with LFA-1, indicating that the spatial localisation of S100A8/9 does shift towards the membrane with activation. Further, the authors confirm that the defect is only apparent only in conditions of shear stress, as transwell migration of Mrp14-/- neutrophils is not affected.

Reviewer #2 (Public review):

Summary:

This work reports the existence of spike timing-dependent long-term depression (t-LTD) of excitatory synaptic strength at two synapses of the dentate gyrus granule cell, which are differently connected to the entorhinal cortex via either the lateral or medial perforant pathways (LPP or MPP, respectively). Using patch-clamp electrophysiological recording of tLTD in combination with either pharmacology or a genetically modified mouse model, they provide information on the differences in the molecular mechanism underlying this t-LTD at the two synapses.

Strengths:

The two synapses analyzed in this study have been understudied. This new data thus provides interesting new information on a plasticity process at these synapses, and the authors demonstrate subtle differences in the underlying molecular mechanisms at play. Experiments are in general well controlled and provide robust data that are properly interpreted.<br /> The data provided to demonstrate that glutamate release from astrocytes is necessary for these plasticity mechanisms are strong. This is particularly interesting as another example of how astrocytes regulate synapse plasticity.

Weaknesses:

This work was performed at young synapses and the highlighted mechanisms are therefore pertinent to this age, as acknowledged by the authors. We currently don't know if these mechanisms are still at play at the adult synapse.

Significance:

While this is the first report of t-LTD at these synapses, this plasticity process has been mechanistically well investigated at other synapses in the hippocampus and in the cortex. Nevertheless, this new data suggests that mechanistic differences in the induction of t-LTD at these two DG synapses could contribute to the differences in the physiological influence of the LPP and MPP pathways.

Reviewer #2 (Public review):

Summary:

The authors examined several defensive responses elicited during Pavlovian conditioning using a serial compound stimulus (SCS) as the conditioned stimulus (CS) and a shock unconditioned stimulus (US) in male and female mice. The SCS consisted of a tone pips followed by white noise. Their design included conditions in which mice were exposed to the CS and US in a paired fashion, in an unpaired fashion, or only exposed to the shock US, as well as paired and unpaired conditions that reversed the order of the SCS. They compared freezing, jumping, darting, and tail rattling across all groups during conditioning and extinction. During conditioning, strong freezing responses to the tone pips followed by strong jumping and darting responses to the white noise were present in the paired group but less robust or not present in the unpaired or shock only groups. During extinction, tone-induced freezing diminished while the jumping was replaced by freezing and darting in the paired group. Together, these findings support the idea that associative pairings are necessary for conditioned defensive responses.

Strengths:

The study has strong control groups including a group that receives the same stimuli in an unpaired fashion and another control group that only receives the shock US and no CS to test the associative value of the SCS to the US. The authors examine a wide variety of defensive behaviors that emerge during conditioning and shift throughout extinction: in addition to the standard freezing response, jumping, darting, and tail rattling were also measured.

The revised version has greatly strengthened this study by including additional control groups (e.g., reversing the order of the compound stimuli in both paired and unpaired conditions).

Reviewer #2 (Public Review):

Summary:

In the manuscript, Zhao et al. have carried out a thorough examination of the effects of targeted ablation of resident astrocytes on behavior, cellular responses, and gene expression after spinal cord injury. Employing transgenic mice models alongside pharmacogenetic techniques, the authors have successfully achieved the selective removal of these resident astrocytes. This intervention led to a notable reduction in neuropathic pain and induced a shift in microglial cell reactivation states within the spinal cord, significantly altering transcriptome profiles predominantly associated with interferon (IFN) signaling pathways.

Strengths:

The findings presented add considerable value to the current understanding of the role of astrocyte elimination in neuropathic pain, offering convincing evidence that supports existing hypotheses and valuable insights into the interactions between astrocytes and microglial cells, likely through IFN-mediated mechanisms. This contribution is highly relevant and suggests that further exploration in this direction could yield meaningful results.

Weaknesses:

The authors have satisfactorily addressed the comments regarding further clarifications and statistical methods.

Reviewer #2 (Public review):

Summary:

The authors have established a femur graft model that allows the study of hematopoietic regeneration following transplantation. They have extensively characterized this model, demonstrating the loss of hematopoietic cells from the donor femur following transplantation, with recovery of hematopoiesis from recipient cells. They also show evidence that BM MSCs present in the graft following transplantation are graft-derived. They have utilized this model to show that following transplantation, periosteal cells respond by first expanding, then giving rise to more periosteal SSCs, and then migrating into the marrow to give rise to BM MSCs.

Strengths:

These studies are notable in several ways:

(1) Establishment of a novel femur graft model for the study of hematopoiesis;

(2) Use of lineage tracing and surgery models to demonstrate that periosteal cells can give rise to BM MSCs.

Weaknesses:

There are a few weaknesses. First, the authors do not definitively demonstrate the requirement of periosteal SSC movement into the BM cavity for hematopoietic recovery. Hematopoiesis recovers significantly before 5 months, even before significant P-SSC movement has been shown, and hematopoiesis recovers significantly even when periosteum has been stripped. Second, it is not clear how the periosteum is changing in the grafts. Which cells are expanding is unclear, and it is not clear if these cells have already adopted a more MSC-like phenotype prior to entering the marrow space. Indeed, given the presence of host-derived endothelial cells in the BM, these studies are reminiscent of prior studies from this group and others that re-endothelialization of the marrow may be much more important for determining hematopoietic regeneration, rather than the P-SSC migration. Third, the studies exploring the preferential depletion of BM MSCs vs P-SSCs are difficult to interpret. The single metabolic stress condition chosen was not well-justified, and the use of purified cell populations to study response to stress ex vivo may have introduced artifacts into the system.

Reviewer #2 (Public review):

Mortzfeld et al. describe their study of class IIb microcins. Furthering our awareness of the presence and action of microcins is an important line of research. However, several issues related to the premise, sequence analysis, and validation require attention to support the claims.

(1) Previous studies have been published on the broader distribution of microcins across bacteria. The software has been published for their identification. Comparison to this software and/or discussion of previous work should be included to place this work in the context of the field.

(2) It is not clear how immunity proteins were identified and there does not appear to be functional confirmation to show these predicted immunity proteins are real. Thus, it is premature to state that immunity genes have been found. This may also confound some of the validation studies below if proper immunity proteins have not been included.

(3) Please show the nt alignment used to generate the tree. Without seeing it, one would guess that the sequences are either quite similar (making the results from this study less novel) or there would be concerns that the phylogenetic relationship derived from the nt alignment is spurious.

(4) Figure 1 B-C: There are numerous branches that do not have phylogenetic support (values <50%). These are not statistically valid phylogenetic relationships and should be collapsed. The resulting tree should be used in the description of clades.

(5) The discovered microcins are not being directly tested since they are expressed heterologous and reliant on non-native modification systems. The results present the statement that novel microcins have been validated. This should be described accordingly.

(6) The key finding of this paper is the claim that 12 novel class IIb microcins have been validated. To substantiate this claim, original images showing evidence of antibacterial activity must be made available rather than a presence/absence chart. The negative controls for this table are unclear and should be included with the original images.

(7) Further data for the purified microcin is needed. The purification method described is standard practice and should allow for product quantification, which should be included. Standard practice includes an SDS page showing the purity of the microcin, or at least the TEV digest to show microcin has been produced, and importantly a control sample (scrambled sequence, empty vector purification, etc) to show that observed activity (Figure 2B) is not from a purification carry over. This data should be included to support that microcin has been purified and is active.

Reviewer #2 (Public review):

Summary

The study by Cao et al. highlights an interesting and important aspect of heat- and thermal biology: the effect of repetitive, long-term heat exposure and its impact on brain function.<br /> Even though peripheral, sensory temperature sensors and afferent neuronal pathways conveying acute temperature information to the CNS have been well established, it is largely unknown how persistent, long-term temperature stimuli interact with and shape CNS function, and how these thermally-induced CNS alterations modulate efferent pathways to change physiology and behavior. This study is therefore not only novel but, given global warming, also timely.

The authors provide compelling evidence that neurons of the paraventricular thalamus change plastically over three weeks of episodic heat stimulation and they convincingly show that these changes affect behavioral outputs such as social interactions, and anxiety-related behaviors.

Strengths

(1) It is impressive that the assessed behaviors can be (i) recruited by optogenetic fiber activation and (ii) inhibited by optogenetic fiber inhibition when mice are exposed to heat. Technically, when/how long is the fiber inhibition performed? It says in the text "3 min on and 3 min off". Is this only during the 20-minute heat stimulation or also at other times?

(2) It is interesting that the frequency of activity in pPVT neurons, as assessed by fiber photometry, stays increased after long-term heat exposure (day 22) when mice are back at normal room temperature. This appears similar to a previous study that found long-term heat exposure to transform POA neurons plastically to become tonically active (https://www.biorxiv.org/content/10.1101/2024.08.06.606929v1 ). Interestingly, the POA neurons that become tonically active by persistent heat exposure described in the above study are largely excitatory, and thus these could drive the activity of the pPVT neurons analyzed in this study.

(3) How can it be reconciled that the majority of the inputs from the POA are found to be largely inhibitory (Fig. 2H)? Is it possible that this result stems from the fact that non-selective POA-to-pPVT projections are labelled by the approach used in this study and not only those pathways activated by heat? These points would be nice to discuss.

(4) It is very interesting that no LTP can be induced after chronic heat exposure (Figures K-M); the authors suggest that "the pathway in these mice were already saturated" (line 375). Could this hypothesis be tested in slices by employing a protocol to extinguish pre-existing (chronic heat exposure-induced) LTP? This would provide further strength to the findings/suggestion that an important synaptic plasticity mechanism is at play that conveys behavioral changes upon chronic heat stimulation.

(5) It is interesting that long-term heat does not increase parameters associated with depression (Figure 1N-Q), how is it with acute heat stress, are those depression parameters increased acutely? It would be interesting to learn if "depression indicators" increase acutely but then adapt (as a consequence of heat acclimation) or if they are not changed at all and are also low during acute heat exposure.

Weaknesses/suggestions for improvements

(1) The introduction and general tenet of the study is, to us, a bit too one-sided/biased: generally, repetitive heat exposure --heat acclimation-- paradigms are known to not only be detrimental to animals and humans but also convey beneficial effects in allowing the animals and humans to gain heat tolerance (by strengthening the cardiovascular system, reducing energy metabolism and weight, etc.).

(2) The point is well taken that these authors here want to correlate their model (90 minutes of heat exposure per day) to heat waves. Nevertheless, and to more fully appreciate the entire biology of repetitive/chronic/persistent heat exposure (heat acclimation), it would be helpful to the general readership if the authors would also include these other aspects in their introduction (and/or discussion) and compare their 90-minute heat exposure paradigm to other heat acclimation paradigms. For example, many past studies (using mice or rats) have used more subtle temperatures but permanently (and not only for 90 minutes) stimulated them over several days and weeks (for example see PMID: 35413138). This can have several beneficial effects related to cardiovascular fitness, energy metabolism, and other aspects. In this regard: 38{degree sign}C used in this study is a very high temperature for mice, in particular when they are placed there without acclimating slowly to this temperature but are directly placed there from normal ambient temperatures (22{degree sign}C-24{degree sign}C) which is cold/coolish for mice. Since the accuracy of temperature measurement is given as +/- 2{degree sign}C, it could also be 40{degree sign}C -- this temperature, 40{degree sign}C, non-heat acclimated C57bl/6 mice will not survive for long.

The authors could consider discussing that this very strong, short episodic heat-stress model used here in this study may emphasize detrimental effects of heat, while more subtle long-term persistent exposure may be able to make animals adapt to heat, become more tolerant, and perhaps even prevent the detrimental cognitive effects observed in this study (which would be interesting to assess in a follow-up study).

(3) Line 140: It would help to be clear in the text that the behaviors are measured 1 day after the acute heat exposure - this is mentioned in the legend to the figure, but we believe it is important to stress this point also in the text. Similarly, this is also relevant for chronic heat stimulation: it needs to be made very clear that the behavior is measured 1 day after the last heat stimulus. If the behaviors had been measured during the heat stimulus, the results would likely be very different.

(4) Figure 2 D and Figure 2- Figure Supplement 1: since there is quite some baseline cFos activity in the pPVT region we believe it is important to include some control (room temperature) mice with anterograde labelling; in our view, it is difficult/not possible to conclude, based on Fig 2 supplement 2C, that nearly 100% of the cfos positive cells are contacted by POA fibre terminals (line 168). By eye there are several green cells that don't have any red label on (or next to) them; additionally, even if there is a little bit of red signal next to a green cell: this is not definitive proof that this is a synaptic contact. It is therefore advisable to revisit the quantification and also revisit the interpretation/wording about synaptic contacts.

In relation to the above: Figure 2h suggests that all neurons are connected (the majority receiving inhibitory inputs), is this really the case, is there not a single neuron out of the 63 recorded pPVT neurons that does not receive direct synaptic input from the POA?

(5) It would be nice to characterize the POA population that connects to the pPVT, it is possible/likely that not only warm-responsive POA neurons connect to that region but also others. The current POA-to-pPVT optogenetic fibre stimulations (Figure 4) are not selective for preoptic warm responsive neurons; since the POA subserves many different functions, this optogenetic strategy will likely activate other pathways. The referees acknowledge that molecular analysis of the POA population would be a major undertaking. Instead, this could be acknowledged in the discussion, for example in a section like "limitation of this study".

(6) Figure 3a the strategy to express Gcamp in a Cre-dependent manner: it seems that the Gcamp8f signal would be polluted by EGFP (coming from the Cre virus injected into the POA): The excitation peak for both is close to 490nm and emission spectra/peaks of GCaMP8f (510-520 nm) and EGFP (507-510 nm) are also highly overlapping. We presume that the high background (EGFP) fluorescence signal would preclude sensitive calcium detection via Gcamp8f, how did the authors tackle this problem?

(7) How did the authors perform the social interaction test (Figures 1F, G)? Was the intruder mouse male or female? If it was a male mouse would the interaction with the female mouse be a form of mating behavior? If so, the interpretation of the results (Figures 1F, G) could be "episodic heat exposure over the course of 3 weeks reduces mating behavior".

Reviewer #2 (Public review):

Summary:

This paper is a companion to Reminann et al. (2022), presenting a large-scale, data-driven, biophysically detailed model of the non-barrel primary somatosensory cortex (nbS1). To achieve this unprecedented scale of a bottom-up model, approximately 140 times larger than the previous model (Markram et al., 2015), they developed new methods to account for inputs from missing brain areas, among other improvements. Isbister et al. focus on detailing these methodological advancements and describing the model's ability to reproduce in vivo-like spontaneous, stimulus-evoked, and optogenetically modified activity.

Strengths:

The model generated a series of predictions that are currently impossible in vivo, as summarized in Table S1. Additionally, the tools used in this study are made available online, fostering community-based exploration. Together with the companion paper, this study makes significant contributions by detailing the model's constraints, validations, and potential caveats, which are likely to serve as a basis for advancing further research in this area.

Weaknesses:

That said, I have several suggestions to improve clarity and strengthen the validation of the model's in vivo relevance.

Major:

(1) For the stimulus-response simulations, the authors should also reference, analyze, and compare data from O'Connor et al. (2010; https://pubmed.ncbi.nlm.nih.gov/20869600/) and Yu et al .(2016; https://pubmed.ncbi.nlm.nih.gov/27749825/) in addition to Yu et al. 2019, which is the only data source the authors consider for an awake response. The authors mentioned bias in spike rate measurements, but O'Connor et al. used cell-attached recordings, which do not suffer from activity-based selection bias (in addition, they also performed Ca2+ imaging of L2/3). This was done in the exact same task as Yu et al., 2019, and they recorded from over 100 neurons across layers. Combining this data with Yu et al., 2019 would provide a comprehensive view of activity across layers and inhibitory cell types. Additionally, Yu et al. (2016) recorded VPM neurons in the same task, alongside whole-cell recordings in L4, showing that L4 PV neurons filter movement-related signals encoded in thalamocortical inputs during active touch. This dataset is more suitable for extracting VPM activity, as it was collected under the same behavior and from the same species (Unlike Diamond et al., 1992, which used anesthetized rats). Furthermore, this filtering is an interesting computation performed by the network the authors modeled. The validation would be significantly strengthened and more biologically interesting if the authors could also reproduce the filtering properties, membrane potential dynamics, and variability in the encoding of touch across neurons, not just the latency (which is likely largely determined by the distance and number of synapses).

(2) The authors mention that in the model, the response of the main activated downstream area was confined to L6. Is this consistent with in vivo observations? Additionally, is there any in vivo characterization of the distance dependence of spiking correlation to validate Figure 8I?

(3) Across the figures, activity is averaged across neurons within layers and E or I cell types, with a limited description of single-cell type and single-cell responses. Were there any predictions regarding the responses of particular cell types that significantly differ from others in the same layer? Such predictions could be valuable for future investigations and could showcase the advantages of a data-driven, biophysically detailed model.

(4) 2.4: Are there caveats to assuming the OU process as a model for missing inputs? Inputs to the cortex are usually correlated and low-dimensional (i.e., communication subspace between cortical regions), but the OU process assumes independent conductance injection. Can (weakly) correlated inputs give rise to different activity regimes in the model? Can you add a discussion on this?

(5) 2.6: The network structure is well characterized in the companion paper, where the authors report that correlations in higher dimensions were driven by a small number of neurons with high participation ratios. It would be interesting to identify which cell types exhibit high node participation in high-dimensional simplices and examine the spiking activity of cells within these motifs. This could generate testable predictions and inform theoretical cell-type-specific point neuron models for excitatory/inhibitory balanced networks and cortical processing.

Minor:

(1) Since the previous model was published in 2015, the neuroscience field has seen significant advancements in single-cell and single-nucleus sequencing, leading to the clustering of transcriptomic cell types in the entire mouse brain. For instance, the Allen Institute has identified ~10 distinct glutamatergic cell types in layer 5, which exceeds the number incorporated into the current model. Could you discuss 1) the relationship between the modeled me-types and these transcriptomic cell types, and 2) how future models will evolve to integrate this new information? If there are gaps in knowledge in order to incorporate some transcriptome cell types into your model, it would be helpful to highlight them so that efforts can be directed toward addressing these areas.

(2) For the optogenetic manipulation, it would be interesting if the model could reproduce the paradoxical effects (for example, Mahrach et al. reported paradoxical effects caused by PV manipulation in S1; https://pubmed.ncbi.nlm.nih.gov/31951197/). This seems a more relevant and non-trivial network phenomenon than the V1 manipulation the authors attempted to replicate.

Reviewer #2 (Public review):

This study aims to elucidate the role of fibroblasts in regulating myocardium and vascular development through signaling to cardiomyocytes and endothelial cells. This focus is significant, given that fibroblasts, cardiomyocytes, and vascular endothelial cells are the three primary cell types in the heart. The authors employed a Pdgfra-CreER-controlled diphtheria toxin A (DTA) system to ablate fibroblasts at various embryonic and postnatal stages, characterizing the resulting cardiac defects, particularly in myocardium and vasculature development. scRNA-seq analysis of the ablated hearts identified collagen as a crucial signaling molecule from fibroblasts that influences the development of cardiomyocytes and vascular endothelial cells.

This is an interesting manuscript; however, there are several major issues, including an over-reliance on the scRNA-seq data, which shows inconsistencies between replicates.<br /> Some of the major issues are described below.

(1) The CD31 immunostaining data (Figures 3B-G) indicate a reduction in endothelial cell numbers following fibroblast deletion using PdgfraCreER+/-; RosaDTA+/- mice. However, the scRNA-seq data show no percentage change in the endothelial cell population (Figure 4D). Furthermore, while the percentage of Vas_ECs decreased in ablated samples at E16.5, the results at E18.5 were inconsistent, showing an increase in one replicate and a decrease in another, raising concerns about the reliability of the RNA-seq findings.

(2) Similarly, while the percentage of Ven_CMs increased at E18.5, it exhibited differing trends at E16.5 (Figure 4E), further highlighting the inconsistency of the scRNA-seq analysis with the other data.

(3) Furthermore, the authors noted that the ablated samples had slightly higher percentages of cardiomyocytes in the G1 phase compared to controls (Figures 4H, S11D), which aligns with the enrichment of pathways related to heart development, sarcomere organization, heart tube morphogenesis, and cell proliferation. However, it is unclear how this correlates with heart development, given that the hearts of ablated mice are significantly smaller than those of controls (Figure 3E). Additionally, the heart sections from ablated samples used for CD31/DAPI staining in Figure 3F appear much larger than those of the controls, raising further inconsistencies in the manuscript.

(4) The manuscript relies heavily on the scRNA-seq dataset, which shows inconsistencies between the two replicates. Furthermore, the morphological and histological analyses do not align with the scRNA-seq findings.

(5) There is a lack of mechanistic insight into how collagen, as a key signaling molecule from fibroblasts, affects the development of cardiomyocytes and vascular endothelial cells.

(6) In Figure 1B, Col1a1 expression is observed in the epicardial cells (Figure 1A, E11.5), but this is not represented in the accompanying cartoon.

(7) What is the genotype of the control animals used in the study?

(8) Do the PdgfraCreER+/-; RosaDTA+/- mice survive after birth when induced at E15.5, and do they exhibit any cardiac defects?

Reviewer #3 (Public review):

In this manuscript, Park and colleagues describe a series of experiments that investigate the role of R-loops in HIV-1 genome integration. The authors show that during HIV-1 infection, R-loops levels on the host genome accumulate. Using a synthetic R-loop prone gene construct, they show that HIV-1 integration sites target sites with high R-loop levels. They further show that integration sites on the endogenous host genome are correlated with sites prone to R-loops. Using biochemical approaches, as well as in vivo co-IP and proximity ligation experiments, the authors show that HIV-1 integrase physically interacts with R-loop structures.

The major strengths of this work is that the investigators use multiple independent experimental systems and multiple cell types to support their conclusions, including in vivo and biochemical experiments. Furthermore, their use of genome-wide analyses help to support their conclusion that HIV targets genomic regions enriched with R-loops versus those lacking such enrichment.

This work may have a significant impact on the field of HIV genomic integration by elucidating why transcription levels are not the sole determinant of HIV integration sites.

Reviewer #2 (Public review):

Summary:

This paper aims to understand the effects of plasticity in shaping the dynamics and structure of cortical circuits, as well as how that depends on aspects such as network structure and dendritic processing.

Strengths:

The level of biological detail included is impressive, and the numerical simulations appear to be well executed. Additionally, they have done a commendable job in open-sourcing the model.

Weaknesses:

The main result of this work is that activity in their network model remains stable without the need for a homeostatic mechanism. However, as the authors acknowledge, this has been demonstrated in previous studies (e.g., Higgins et al. 2014). In those studies, stability was attributed to calcium-based rules combined with calcium concentrations at in vivo levels and background neuronal activity. Since the authors use the same calcium-based rule, it is unclear what new result, if any, is being presented. If the authors are suggesting that the mechanism in their simulations differs, that should be stated clearly, and evidence supporting that claim should be provided.

The other findings discussed in the paper are related to a characterization of the dependency of plastic changes on network structure. While this analysis is potentially interesting, it has the following limitations.

First, I believe the authors should include an analysis of the generality and specificity of their results. All the findings seem to be derived from a single run of the simulation. How do the results vary with different network initializations, simulation times, or parameter choices?

Second, the presentation of the results is difficult to follow. The characterization comes across as a long list of experiments, making it hard to identify a central message or distinguish key findings from minor details. The authors provide little intuition about why certain outcomes arise, and the complexity of the simulation makes it challenging - if not impossible - to determine which model elements are essential for specific results and which mechanisms drive emergent properties. Additionally, the text often lacks crucial details. For instance, the description of k-edge participation should be expanded, and an explanation of what this method quantifies should be included. Overall, I believe the authors should focus on a smaller set of significant results and provide a more in-depth discussion.

The comparison of the model with the MICrONS dataset could be improved. In Figure 7B, the authors should show how the same quantification looks in a network model without plasticity. In Figure 8B, the data aligns with the model before plasticity, so it's unclear how this serves as a verification of the theoretical predictions.

“Modus tollens” 否定前件<br /> 是一个逻辑学术语，拉丁语原义为“否定方式”，它描述了一种常用的推理规则。

Reviewer #2 (Public review):

Summary:

In this strong study, the authors provide robust evidence for the role of proteostasis genes in the evolution of antimicrobial resistance, and moreover, for stabilizing the proteome in light of gene duplication events.

Strengths:

This strong study offers an important interaction between findings involving GDA, proteostasis, experimental evolution, protein evolution, and antimicrobial resistance. Overall, I found the study to be relatively well-grounded in each of these literatures, with experiments that spoke to potential concerns from each arena. For example, the literature on proteostasis and evolution is a growing one that includes organisms (even micro-organisms) of various sorts. One of my initial concerns involved whether the authors properly tested the mechanistic bases for the rule of Lon in promoting duplication events. The authors assuaged my concern with a set of assays (Figure 8).

More broadly, the study does a nice job of demonstrating the agility of molecular evolution, with responsible explanations for the findings: gene duplications are a quick-fix, but can be out-competed relative to their mutational counterparts. Without Lon protease to keep the proteome stable, the cell allows for less stable solutions to the problem of antibiotic resistance.

The study does what any bold and ambitious study should: it contains large claims and uses multiple sorts of evidence to test those claims.

Weaknesses:

While the general argument and conclusion are clear, this paper is written for a bacterial genetics audience that is familiar with the manner of bacterial experimental evolution. From the language to the visuals, the paper is written in a boutique fashion. The figures are even difficult for me - someone very familiar with proteostasis - to understand. I don't know if this is the fault of the authors or the modern culture of publishing (where figures are increasingly packed with information and hard to decipher), but I found the figures hard to follow with the captions. But let me also consider that the problem might be mine, and so I do not want to unfairly criticize the authors.

For a generalist journal, more could be done to make this study clear, and in particular, to connect to the greater community of proteostasis researchers. I think this study needs a schematic diagram that outlines exactly what was accomplished here, at the beginning. Diagrams like this are especially important for studies like this one that offer a clear and direct set of findings, but conduct many different sorts of tests to get there. I recommend developing a visual abstract that would orient the readers to the work that has been done.

Next, I will make some more specific suggestions. In general, this study is well done and rigorous, but doesn't adequately address a growing literature that examines how proteostasis machinery influences molecular evolution in bacteria.

While this paper might properly test the authors' claims about protein quality control and evolution, the paper does not engage a growing literature in this arena and is generally not very strong on the use of evolutionary theory. I recognize that this is not the aim of the paper, however, and I do not question the authors' authority on the topic. My thoughts here are less about the invocation of theory in evolution (which can be verbose and not relevant), and more about engagement with a growing literature in this very area.

The authors mention Rodrigues 2016, but there are many other studies that should be engaged when discussing the interaction between protein quality control and evolution.

A 2015 study demonstrated how proteostasis machinery can act as a barrier to the usage of novel genes: Bershtein, S., Serohijos, A. W., Bhattacharyya, S., Manhart, M., Choi, J. M., Mu, W., ... & Shakhnovich, E. I. (2015). Protein homeostasis imposes a barrier to functional integration of horizontally transferred genes in bacteria. PLoS genetics, 11(10), e1005612

A 2019 study examined how Lon deletion influenced resistance mutations in DHFR specifically: Guerrero RF, Scarpino SV, Rodrigues JV, Hartl DL, Ogbunugafor CB. The proteostasis environment shapes higher-order epistasis operating on antibiotic resistance. Genetics. 2019 Jun 1;212(2):565-75.

A 2020 study did something similar: Thompson, Samuel, et al. "Altered expression of a quality control protease in E. coli reshapes the in vivo mutational landscape of a model enzyme." Elife 9 (2020): e53476.

And there's a new review (preprint) on this very topic that speaks directly to the various ways proteostasis shapes molecular evolution:<br /> Arenas, Carolina Diaz, Maristella Alvarez, Robert H. Wilson, Eugene I. Shakhnovich, C. Brandon Ogbunugafor, and C. Brandon Ogbunugafor. "Proteostasis is a master modulator of molecular evolution in bacteria."

I am not simply attempting to list studies that should be cited, but rather, this study needs to be better situated in the contemporary discussion on how protein quality control is shaping evolution. This study adds to this list and is a unique and important contribution. However, the findings can be better summarized within the context of the current state of the field. This should be relatively easy to implement.

Reviewer #2 (Public review):

Summary:

In this manuscript, Frelih et al investigate the relationship between aperiodic neural activity, as measured by EEG, and working memory performance, and compare this to the more commonly analyzed periodic, and in particular theta, measures that are often associated with such tasks. To do so, they analyze a primary dataset of 57 participants engaging in an n-back task, as well as a replication dataset, and use spectral parameterization to measure periodic and aperiodic features of the data, across time. In doing so, they find both periodic and aperiodic features that relate to the task dynamics, but importantly the aperiodic component appears to explain away what otherwise looks like theta activity in a more traditional analysis. This study, therefore, helps to establish that aperiodic activity is a task-relevant dynamic feature in working memory tasks, and may be the underlying change in many other studies that reported 'theta' changes but did not use methods that could differentiate periodic and aperiodic features.

Strengths:

Key strengths of this paper include that it addresses an important question - that of properly adjudicating which features of EEG recordings relate to working memory tasks - and in doing so provides a compelling answer, with important implications for considering prior work and contributing to understanding the neural underpinnings of working memory. I do not find any significant faults or errors with the design, analysis, and main interpretations as presented by this paper, and as such, find the approach taken to be valid and well-enacted. The use of multiple variants of the working memory task, as well as a replication dataset significantly strengthens this manuscript, by demonstrating a degree of replicability and generalizability. This manuscript is also an important contribution to motivating best practices for analyzing neuro-electrophysiological data, including in relation to using baselining procedures.

Weaknesses:

Overall, I do not find any obvious weaknesses in this manuscript and its analyses that challenge the key results and conclusions. There are some minor reporting notes, on the methods and conclusions that I believe could be improved (details in the suggestions for authors). One aspect that could be improved is that while the figures demonstrate the main findings convincingly, the results as written could have more detailed quantifications of the analyzed effects (including, for example, more on the model results, effect sizes, and quantifications of the different features), in order to more fully report the dynamics of the analyzed features and to provide the reader with more information on the findings.

Reviewer #2 (Public review):

Summary:

The authors conduct a causal analysis of years of secondary education on brain structure in late life. They use a regression discontinuity analysis to measure the impact of a UK law change in 1972 that increased the years of mandatory education by 1 year. Using brain imaging data from the UK Biobank, they find essentially no evidence for 1 additional year of education altering brain structure in adulthood.

Strengths:

The authors pre-registered the study and the regression discontinuity was very carefully described and conducted. They completed a large number of diagnostic and alternate analyses to allow for different possible features in the data. (Unlike a positive finding, a negative finding is only bolstered by additional alternative analyses).

Weaknesses:

While the work is of high quality for the precise question asked, ultimately the exposure (1 additional year of education) is a very modest manipulation and the outcome is measured long after the intervention. Thus a null finding here is completely consistent educational attainment (EA) in fact having an impact on brain structure, where EA may reflect elements of training after a second education (e.g. university, post-graduate qualifications, etc) and not just stopping education at 16 yrs yes/no.

The work also does not address the impact of the UK Biobank's well-known healthy volunteer bias (Fry et al., 2017) which is yet further magnified in the imaging extension study (Littlejohns et al., 2020). Under-representation of people with low EA will dilute the effects of EA and impact the interpretation of these results.

References:

Fry, A., Littlejohns, T. J., Sudlow, C., Doherty, N., Adamska, L., Sprosen, T., Collins, R., & Allen, N. E. (2017). Comparison of Sociodemographic and Health-Related Characteristics of UK Biobank Participants With Those of the General Population. American Journal of Epidemiology, 186(9), 1026-1034. https://doi.org/10.1093/aje/kwx246

Littlejohns, T. J., Holliday, J., Gibson, L. M., Garratt, S., Oesingmann, N., Alfaro-Almagro, F., Bell, J. D., Boultwood, C., Collins, R., Conroy, M. C., Crabtree, N., Doherty, N., Frangi, A. F., Harvey, N. C., Leeson, P., Miller, K. L., Neubauer, S., Petersen, S. E., Sellors, J., ... Allen, N. E. (2020). The UK Biobank imaging enhancement of 100,000 participants: rationale, data collection, management and future directions. Nature Communications, 11(1), 2624. https://doi.org/10.1038/s41467-020-15948-9

Reviewer #2 (Public review):

Summary:

Here Vogt et al., provide new insights into the need for sleep and the molecular and physiological response to sleep loss. The authors expand on their previously published work (Bjorness et al., 2020) and draw from recent advances in the field to propose a neuron-centric molecular model for the accumulation and resolution of sleep need and basis of restorative sleep function. While speculative, the proposed model successfully links important observations in the field and provides a framework to stimulate further research and advances on the molecular basis of sleep function. In my review, I highlight the important advances of this current work, the clear merits of the proposed model, and indicate areas of the model that can serve to stimulate further investigation.

Strengths:

Reviewer comment on new data in Vogt et al., 2024<br /> Using classic slice electrophysiology, the authors conclude that wakefulness (sleep deprivation (SD)) drives a potentiation of excitatory glutamate synapses, mediated in large part by "un-silencing" of NMDAR-active synapses to AMPAR-active synapses. Using a modern single nuclear RNAseq approach the authors conclude that SD drives changes in gene expression primarily occurring in glutamatergic neurons. The two experiments combined highlight the accumulation and resolution of sleep need centered on the strength of excitatory synapses onto excitatory neurons. This view is entirely consistent with a large body of extant and emerging literature and provides important direction for future research.

Consistent with prior work, wakefulness/SD drives an LTP-type potentiation of excitatory synaptic strength on principle cortical neurons. It has been proposed that LTP associated with wake, leads to the accumulation of sleep need by increasing neuronal excitability, and by the "saturation" of LTP capacity. This saturation subsequently impairs the capacity for further ongoing learning. This new data provides a satisfying mechanism of this saturation phenomenon by introducing the concept of silent synapses. The new data show that in mice well rested, a substantial number of synapses are "silent", containing an NMDAR component but not AMPARs. Silent synapses provide a type of reservoir for learning in that activity can drive the un-silencing, increasing the number of functional synapses. SD depletes this reservoir of silent synapses to essentially zero, explaining how SD can exhaust learning capacity. Recovery sleep led to restoration of silent synapses, explaining how recovery sleep can renew learning capacity. In their prior work (Bjorness et al., 2020) this group showed that SD drives an increase in mEPSC frequency onto these same cortical neurons, but without a clear change in pre-synaptic release probability, implying a change in the number of functional synapses. This prediction is now born out in this new dataset.

The new snRNAseq dataset indicates the sleep need is primarily seen (at the transcriptional level) in excitatory neurons, consistent with a number of other studies. First, this conclusion is corroborated by an independent, contemporary snRNAseq analysis recently available as a pre-print (Ford et al., 2023 BioRxiv https://doi.org/10.1101/2023.11.28.569011). A recently published analysis on the effects of SD in drosophila imaged synapses in every brain region in a cell-type dependent manner (Weiss et al., PNAS 2024), concluding that SD drives brain wide increases in synaptic strength almost exclusively in excitatory neurons. Further, Kim et al., Nature 2022, heavily cited in this work, show that the newly described SIK3-HDAC4/5 pathway promotes sleep depth via excitatory neurons and not inhibitory neurons.

The new experiments provided in Fig1-3 are expertly conducted and presented. This reviewer has no comments of concern regarding the execution and conclusions of these experiments.

Reviewer comment on model in Vogt et al., 2024<br /> To the view of this reviewer the new model proposed by Vogt et al., is an important contribution. The model is not definitively supported by new data, and in this regard should be viewed as a perspective, providing mechanistic links between recent molecular advances, while still leaving areas that need to be addressed in future work. New snRNAseq analysis indicates SD drives expression of synaptic shaping components (SSCs) consistent with the excitatory synapse as a major target for the restorative basis of sleep function. SD induced gene expression is also enriched for autism spectrum disorder (ASD) risk genes. As pointed out by the authors, sleep problems are commonly reported in ASD, but the emphasis has been on sleep amount. This new analysis highlights the need to understand the impact on sleep's functional output (synapses) to fully understand the role of sleep problems in ASD.

Importantly, SD induced gene expression in excitatory neurons overlap with genes regulated by the transcription factor MEF2C and HDAC4/5 (Fig. 4). In their prior work, the authors show loss of MEF2C in excitatory neurons abolished the SD transcriptional response and the functional recovery of synapses from SD by recovery sleep. Recent advances identified HDAC4/5 as major regulators of sleep depth and duration (in excitatory neurons) downstream of the recently identified sleep promoting kinase SIK3. In Zhou et al., and Kim et al., Nature 2022, both groups propose a model whereby "sleep-need" signals from the synapse activate SIK3, which phosphorylates HDAC4/5, driving cytoplasmic targeting, allowing for the de-repression and transcriptional activation of "sleep genes". Prior work shows that HDAC4/5 are repressors of MEF2C. Therefore, the "sleep genes" derepressed by HDAC4/5 may be the same genes activated in response to SD by MEF2C. The new model thereby extends the signaling of sleep need at synapses (through SIK3-HDAC4/5) to the functional output of synaptic recovery by expression of synaptic/sleep genes by MEF2C. The model thereby links aspects of expression of sleep need with the resolution of sleep need by mediating sleep function: synapse renormalization.

Weaknesses:

Areas for further investigation.<br /> In the discussion section Vogt et al., explore the links between excitatory synapse strength, arguably the major target of "sleep function", and NREM slow-wave activity (SWA), the most established marker of sleep need. SIK3-HDAC4/5 have major effects on the "depth" of sleep by regulating NREM-SWA. The effects of MEF2C loss of function on NREM SWA activity are less obvious, but clearly impact the recovery of glutamatergic synapses from SD. The authors point out how adenosine signaling is well established as a mediator of SWA, but the links with adenosine and glutamatergic strength are far from clear. The mechanistic links between SIK3/HDAC4/5, adenosine signaling, and MEF2C, are far from understood. Therefore, the molecular/mechanistic links between a synaptic basis of sleep need and resolution with NREM-SWA activity require further investigation.

Additional work is also needed to understand the mechanistic links between SIK3-HDAC4/5 signaling and MEF2C activity. The authors point out that constitutively nuclear (cn) HDAC4/5 (acting as a repressor) will mimic MEF2C loss of function. This is reasonable, however, there are notable differences in the reported phenotypes of each. Notably, cnHDAC4/5 suppresses NREM amount and NREM SWA but had no effect on the NREM-SWA increase following SD (Zhou et al., Nature 2022). Loss of MEF2C in CaMKII neurons had no effect on NREM amount and suppressed the increase in NREM-SWA following SD (Bjorness et al., 2020). These instances indicate that cnHDAC4/5 and loss of MEF2C do not exactly match suggesting additional factors are relevant in these phenotypes. Likely HDAC4/5 have functionally important interactions with other transcription factors, and likewise for MEF2C, suggesting areas for future analysis.

One emerging theme may be that the SIK3-HDAC4/5 axis are major regulators of the sleep state, perhaps stabilizing the NREM state once the transition from wakefulness occurs. MEF2C is less involved in regulating sleep per se, and more involved in executing sleep function, by promoting restorative synaptic modifications to resolve sleep need.

Finally, advances in the roles of the respective SIK3-HDAC4/5 and MEF2C pathways point towards transcription of "sleep genes", as clearly indicated in the model of Fig.4. Clearly more work is needed to understand how the expression of such genes ultimately lead to resolution of sleep need by functional changes at synapses. What are these sleep genes and how do they mechanistically resolve sleep need? Thus, the current work provides a mechanistic framework to stimulate further advances in understanding the molecular basis for sleep need and the restorative basis of sleep function.

Reviewer #2 (Public review):

In the manuscript entitled "Oviductin sets the species-specificity of the mammalian zona pellucida." The study analyzes the species specificity of sperm-egg recognition by looking at sperm binding and penetration of zonae pellucidae from different mammalian species and find a role for the oviductal protein OVGP1 in determining species specificity.

Strengths:

By combining sperm, oocytes, zona pellucida (ZP), and oviductal fluid from different mammalian species, they elucidate the essential role of OVGP1 in conferring species-specific fertilization.

Weaknesses:

The authors postulate a role for oviductal fluid in species-specific fertilization, but in my opinion, they cannot rule out hormonal effects or differences in the method of oocyte maturation employed.

They also cannot unequivocally prove that OVGP1 is the oviductal protein involved in the effect. Additional experiments are necessary to rule out these alternative explanations.

When performing the EZPT assay on mouse oocytes obtained either from the ovary or from the oviduct, the oocytes obtained from the ovary came from mice primed with eCG, whereas the ones collected from the oviduct were obtained from superovulated mice (eCG plus hCG). This difference in the hormonal environment may make a difference in the properties of the ZP. Additionally, the ones obtained from the ovary were in vitro matured, which is also different from the freshly ovulated eggs and, again, may change the properties of the ZP. I suggest doing this experiment superovulating both groups of mice but collecting the fully matured MII eggs from the ovary before they get ovulated. In that way the hormonal environment will be the same in both groups and in both groups, oocytes will be matured in vivo. Hence, the only difference will be the exposure to oviductal fluids.

Mice with OVGP1 deletion are viable and fertile. It would be quite interesting to investigate the species-specificity of sperm-ZP binding in this model. That would indicate whether OVGP1 is the only glycoprotein involved in determining species-specificity. Alternatively, the authors could immunodeplete OVGP1 from oviductal fluid and then ascertain whether this depleted fluid retains the ability to impede cross-species fertilization.

What is the concentration of OVGP1 in the oviduct? How did the authors decide what concentration of protein to use in the experiments where they exposed ZPs to purified OVGP1? Why did they use this experimental design to check the structure of the ZP by SEM? Why not do it on oocytes exposed to oviductal fluid, which would be more physiological?

None of the figures show any statistical analysis. Please perform analysis for all the data presented, include p values, and indicate which statistical tests were performed. The Statistical analysis section in the Methods indicating that repeated measures ANOVA was used must refer to the tables. Was normality tested? I doubt all the data are normally distributed, in which case using ANOVA is not appropriate.

Why was OVGP1 selected as the probable culprit of the species specificity? In the Results section entitled "Homology of bovine, human and murine OVGP1 proteins..." the authors delve into the possible role of this protein without any rationale for investigating it. What about other oviductal proteins?

Reviewer #2 (Public Review):

Summary

In this study, Easwaran and Montell investigated the molecular, cellular, and genetic basis of adult reproductive diapause in Drosophila using the Drosophila Genetic Reference Panel (DGRP). Their GWAS revealed genes associated with variation in post-diapause fecundity across the DGRP and performed RNAi screens on these candidate genes. They also analyzed the functional implications of these genes, highlighting the role of genes involved in neural and germline development. In addition, in conjunction with other GWAS results, they noted the importance of the olfactory system within the nervous system, which was supported by genetic experiments. Overall, their solid research uncovered new aspects of adult diapause regulation and provided a useful reference for future studies in this field.

Strengths:

The authors used whole-genome sequenced DGRP to identify genes and regulatory mechanisms involved in adult diapause. The first Drosophila GWAS of diapause successfully uncovered many QTL underlying post-diapause fecundity variations across DGRP lines. Gene network analysis and comparative GWAS led them to reveal a key role for the olfactory system in diapause lifespan extension and post-diapause fecundity.

Comments on revised version:

While the authors have addressed many of the minor concerns raised by the reviewers, they have not fully resolved some of the key criticisms. Notably, two reviewers highlighted significant concerns regarding the phenotype and assay of post-diapause fecundity, which are critical to the study. The authors acknowledged that this assay could be confounded by the 'cold temperature endurance phenotype,' potentially altering the interpretation of their results. However, they responded by stating that it is not obvious how to separate these effects experimentally. This leaves the analysis in this research ambiguous, as also noted by Reviewer #3.

Additionally, I raised concerns about the validity of prioritizing genes with multiple associated variants. Although the authors agreed with this point, they did not revise the manuscript accordingly. The statement that 'Genes with multiple SNPs are good candidates for influencing diapause traits' is not a valid argument within the context of population and quantitative genetics.

In summary, the authors have not fully utilized the peer-review process to address the critical weaknesses identified, which ultimately leaves the quality of their work in question.

Reviewer #2 (Public review):

Summary:

Weinberg et al. show that spike LCB minibinders can be used as the extracellular domain for SynNotch, SNIPR, and CAR. They evaluated their designs against cells expressing the target proteins and live virus.

Strengths:

This is a good fundamental demonstration of alternative use of the minibinder. The results are unsurprising but robust and solid in most cases.

Weaknesses:

The manuscript can benefit from better descriptions of the study's novelty. Given that LCB previously worked in SynNotch, what unexpected finding was uncovered by this study? It is well known that the extracellular domain of CAR is amendable to different types of binding domains (e.g., scFv, nanobody, DARPin, natural ligands). So, it is not surprising that a minibinder also works with CAR. We don't know if the minibinders are more or less likely to be compatible with CAR or SNIPR.

The demonstrations are all done using just 1 minibinder. It is hard to conclude that minibinders, as a unique class of protein binders, are generalizable in different contexts. All it can conclude is that this specific Spike minibinder can be used in synNotch, SNIPR, and CAR. The LCB3 minibinder seems to be much weaker.

The sensing of live viruses is interesting, but the output is very weak. It is difficult to imagine a utility for such a weak response.

Reviewer #2 (Public review):

Summary:

The authors generated analogs consisting of modified neurotensin (NT) peptides capable of binding to low density lipoprotein (LDL) and NT receptors. Their lead analog was further evaluated for additional validation as a novel therapeutic. The putative mechanism of action for NT in its antiseizure activity is hypothermia, and as therapeutic hypothermia has been demonstrated in epilepsy, NT analogs may confer antiseizure activity and avoid the negative effects of induced hypothermia.

Strengths:

The authors demonstrate an innovative approach, i.e. using LDLR as a means of transport into the brain, that may extend to other compounds. They systematically validate their approach and its potential through binding, brain penetration, in vivo antiseizure efficacy, and neuroprotection studies.

Reviewer #2 (Public review):

Summary:

This revised manuscript describes the production of a mouse model for LAMA2-Related Muscular Dystrophy. The authors investigate changes in transcripts within the brain and blood barrier. The authors also investigate changes in the transcriptome associated with the muscle cytoskeleton.

Strengths:

(1) The authors produced a mouse model of LAMA2-CMD using CRISPR-Cas9

(2) The authors identify cellular changes that disrupted the blood-brain barrier.

Weaknesses:

(1) The authors throughout the manuscript overstate "discoveries" which have been previously described, published and not appropriately cited.

(2) Alternations in the blood brain barrier and in the muscle cell cytoskeleton in LAMA2-CMD have been extensively studied and published in the literature and are not cited appropriately.

(3) The authors have increased animal number to N=6, but this is still insufficient based on Power analysis results in statistical errors and conclusions that may be incorrect.

(4) The use of "novel mouse model" in the manuscript overstates the impact of the study.

(5) All studies presented are descriptive and do not more to the field except for producing yet another mouse model of LAMA2-CMD and is the same as all the others produced.

(6) Grip strength measurements are considered error prone and do not give an accurate measurement of muscle strength, which is better achieved using ex vivo or in vivo muscle contractility studies.

(7) A lack of blinded studies as pointed out of the authors is a concern for the scientific rigor of the study.

Reviewer #2 (Public review):

The manuscript from Wappner and Melani labs claims a novel for the exocyst subunits in multiple aspects of secretory granule exocytosis. This an intriguing paper for it suggests multiple roles of the exocyst in granule maturation and fusion with roles at the ER/Golgi interface, TGN, granule homotypic fusion.

A key strength is the breadth of the assays and study of all 8 exocyst subunits in a powerful model system (fly larvae). But why do KD of different exocysts have different effects on presumed granule formation? Also it can be hard to disentangle direct vs. secondary effects, as much of the TGN seems to be altered in the KDs. The authors ascribe many of the results to the holocomplex, but there are major differences between the proteins -- this may be all related to the different levels of expression (as the authors propose), but only limited mRNA was examined.

Unresolved Comments:

(A) Explanation variability of exocyst KD on the appearance of MSG. What is remarkable is a highly variable effect of different subunit KD on the percentage of cells with MLS (Fig. 4C). Controls = 100 %, Exo70=~75% (at 19 deg), Sec3 = ~30%, Sec10 = 0%, Exo84 = 100% ... This is interesting for the functional exocyst is an octameric holocomples, thus why the huge subunit variability in the phenotypes? One explanation is that the levels of KD varied between the subunits. Another is that not all subunits have equivalent roles (as seen for instance in exocyst's roles in autophagy).

This should be addressed by quantification of the KD of the 8 different exocyst proteins (and or mRNA as only 2 subunits were studied). If their data holds up then the underlying mechanism here needs to be considered. (Note: there is some precedent from the autophagy field of differential exocyst effects).

(B) Golgi: It is unclear from their model (Fig. 5) why after exocyst KD of Sec15 the cis-Golgi is more preserved than the TGN, which appears as large vacuoles.

(C) Granule homotypic fusion. Over-expression of just one subunit, Sec15-GFP, made giant secretory granules (SG) that were over 8 microns big. Does it act like a seed to promote exocyst assembly as the authors propose? If so is there evidence that there is biochemically more holocomplex with expression of Sec15, but not other subunits?

(D) The authors should better frame their interpretations of other studies of the exocyst that includes role in autophagy, Palade body trafficking and differential roles of the subunits.

In summary, there clearly are striking new effects on secretory granule biogenesis by dysfunction of the exocyst which are important and should inspire other studies for new roles of the exocyst; e.g. in non cannonical roles. Secondly, the power of the system to partially deplete proteins (if further validated) suggests that one may need to consider protein expression as an important variable that can be used to unmask multiple phenotypes in granule maturation. Last this paper implies new roles of the exocyst in homotypic fusion, which could be investigated in future work.

Reviewer #2 (Public review):

Summary:

Fallah et al carefully dissect projections from SNr and GPe - two key basal ganglia nuclei - to the PPN, an important brainstem nucleus for motor control. They consider inputs from these two areas onto 3 types of downstream PPN neurons: GABAergic, glutamatergic, and cholinergic neurons. They also carefully map connectivity along the rostrocaudal axis of the PPN.

Strengths:

The slice electrophysiology work is technically well done and provides useful information for further studies of PPN. The optogenetics and behavioral studies are thought-provoking, showing that SNr and GPe projections to PPN play distinct roles in behavior.

Weaknesses:

Although the optogenetics and behavioral studies are intriguing, they are somewhat difficult to fit together into a specific model of circuit function. Perhaps the authors can work to solidify the connection between these two arms of the work. Otherwise, there are a few questions whose answers could add context to the interpretation of these results:

(1) Male and female mice are used, but the authors do not discuss any analysis of sex differences. If there are no sex differences, it is still useful to report data disaggregated by sex in addition to pooled data.

(2) There is some lack of clarity in the current manuscript on the ages used - 2-5 months vs "at least 7 weeks." Is 7 weeks the time of virus injection surgery, then recordings 3 weeks later (at least 10 weeks)? Please clarify if these ages apply equally to electrophysiological and behavioral studies. If the age range used for the test is large, it may be useful to analyze and report if there are age-related effects.

(3) Were any exclusion criteria applied, e.g. to account for missed injections?

(4) 28-34degC is a fairly wide range of temperatures for electrophysiological recording, which could affect kinetics.

(5) It would be good to report the number of mice used for each condition in addition to n=cells. Statistically, it would be preferable not to assume that each cell from the same mouse is an independent measurement and to use a nested ANOVA.

Reviewer #3 (Public review):

Summary:

In this manuscript the authors explore the roles of dact1 and dact2 during zebrafish gastrulation and craniofacial development. Previous studies used morpholino (MO) knockdowns to show that these scaffolding proteins, which interact with dissheveled (Dsh), are expressed during zebrafish gastrulation and suggested that dact1 promotes canonical Wnt/B-catenin signaling, while dact2 promotes non-canonical Wnt/PCP-dependent convergent-extension (Waxman et al 2004). This study goes beyond this work by creating loss-of-function mutant alleles for each gene and unlike the MO studies finds little (dact2) to no (dact1) phenotypic defects in the homozygous mutants. Interestingly, dact1/2 double mutants have a more severe phenotype, which resembles those reported with MOs as well as homozygous wnt11/silberblick (wnt11/slb) mutants that disrupt non-canonical Wnt signaling (Heisenberg et al., 1997; 2000). Further analyses in this paper try to connect gastrulation and craniofacial defects in dact1/2 mutants with wnt11/slb and other wnt-pathway mutants. scRNAseq conducted in mutants identifies calpain 8 as a potential new target of dact1/2 and Wnt signaling.

Previous comments:<br /> Strengths:

When considered separately the new mutants are an improvement over the MOs and the paper contains a lot of new data.

Weaknesses:

However, the hypotheses are very poorly defined and misinterpret key previous findings surrounding the roles of wnt11 and gpc4, which results in a very confusing manuscript. Many of the results are not novel and focus on secondary defects. The most novel result overexpressing calpain8 in dact1/2 mutants is preliminary and not convincing.

The authors addressed some of our comments, but not our main criticisms, which we reiterate here:

(1) The authors argue that morpholino studies are unreliable and here they made new mutants to solve this uncertainty for dap 1/2. However, creating stable mutant lines to largely confirm previous results obtained by using morpholino knock-down phenotypes does not justify publication in eLife.

(2) The authors argue that since it has not been shown conclusively that craniofacial defects in wnt11 and dap1/2 mutants are secondary to gastrulation defects there is no solid evidence preventing them from investigating these craniofacial defects. However, since it is extremely likely that the rod-like ethmoid plates of wnt11f2- and dact1/2 mutants focused on here are secondary to gastrulation defects previously described by others (Heisenberg and NussleinVolhard 1997; Waxman et al., 2004), the burden of proof is on the authors to provide much stronger evidence against this interpretation.

(3) The data for calpain overexpression remains too preliminary.

Reviewer #2 (Public review):

Summary:

This paper has some intriguing data regarding the different potential roles of Pch-2 in ensuring crossing over. In particular, the alterations in crossover distribution and Msh-5 foci are compelling. My main issue is that some of the models are confusingly presented and would benefit from some reframing. The role of Pch-2 across organisms has been difficult to determine, the ability to separate pairing and synapsis roles in worms provides a great advantage for this paper.

Strengths:

Beautiful genetic data, clearly made figures. Great system for studying the role of Pch-2 in crossing over.

Weaknesses:

(1) For a general audience, definitions of crossover assurance, crossover eligible intermediates, and crossover designation would be helpful. This applies to both the proposed molecular model and the cytological manifestation that is being scored specifically in C. Elegans.

(2) Line 62: Is there evidence that DSBs are introduced gradually throughout the early prophase? Please provide references.

(3) Do double crossovers show strong interference in worms? Given that the PC is at the ends of chromosomes don't you expect double crossovers to be near the chromosome ends and thus the PC?

(4) Line 155 - if the previous data in Deshong et al is helpful it would be useful to briefly describe it and how the experimental caveats led to misinterpretation (or state that further investigation suggests a different model etc.). Many readers are unlikely to look up the paper to find out what this means.

(5) Line 248: I am confused by the meaning of crossover assurance here - you see no difference in the average number of COSA-1 foci in Pch-2 vs. wt at any time point. Is it the increase in cells with >6 COSA-1 foci that shows a loss of crossover assurance? That is the only thing that shows a significant difference (at the one time point) in COSA-1 foci. The number of dapi bodies shows the loss of Pch-2 increases crossover assurance (fewer cells with unattached homologs). So this part is confusing to me. How does reliably detecting foci vs. DAPI bodies explain this?

(6) Line 384: I am confused. I understand that in the dsb-2/pch2 mutant there are fewer COSA-1 foci. So fewer crossovers are designated when DSBs are reduced in the absence of PCH-2. How then does this suggest that PCH-2's presence on the SC prevents crossover designation? Its absence is preventing crossover designation at least in the dsb-2 mutant.

(7) Discussion Line 535: How do you know that the crossovers that form near the PCs are Class II and not the other way around? Perhaps early forming Class I crossovers give time for a second Class II crossover to form. In budding yeast, it is thought that synapsis initiation sites are likely sites of crossover designation and class I crossing over. Also, the precursors that form class I and II crossovers may be the same or highly similar to each other, such that Pch-2's actions could equally affect both pathways.

Reviewer #2 (Public review):

Summary:

The authors set out to determine how the microbiome and host genotype impact host protein-based nutrition.

Strengths:

The quantification of protein uptake dynamics is a major strength of this work and the sensitivity of this assay shows that the microbiome and even mono-associated bacterial strains dampen protein uptake in the host by causing down-regulation of genes involved in this process rather than a change in cell type.

The use of fluorescent proteins in combination with transcript clustering in the single cell seq analysis deepens our understanding of the cells that participate in protein uptake along the intestine. In addition to the lysozome-rich enterocytes (LRE), subsets of enteroendocrine cells, acinar, and goblet cells also take up protein. Intriguingly, these non-LRE cells did not show lysosomal-based protein degradation; but importantly analysis of the transcripts upregulated in these cells include dab2 and cubn, genes shown previously as being essential to protein uptake.

The derivation of zebrafish mono-associated with single strains of microbes paired with HCR to localize and quantify the expression of host protein absorption genes shows that different bacterial strains suppress these genes to variable extents.

The analysis of microbiome composition, when host protein absorption is compromised in cubn-/- larvae or by reducing protein in the food, demonstrates that changes to host uptake can alter the abundance of specific microbial taxa like Aeramonas.

Weaknesses:

The finding that neurons are positive for protein uptake in the single-cell data set is not adequately discussed. It is curious because the cldn:GFP line used for sorting does not mark neurons and if the neurons are taking up mCherry via trans-synaptic uptake from EECs, those neurons should be mCherry+/GFP-; yet methods indicate GFP+ and GFP+/mCherry+ cells were the ones collected and analyzed.

Reviewer #2 (Public review):

Summary:

The manuscript investigates to what degree neonates show evidence for statistical learning from regularities in streams of syllables, either with respect to phonemes or with respect to speaker identity. Using EEG, the authors found evidence for both, stronger entrainment to regularities as well as ERP differences in response to violations of previously introduced regularities. In addition, violations of phoneme regularities elicited an ERP pattern which the authors argue might index a precursor of the N400 response in older children and adults.

Strengths:

All in all, this is a very convincing paper, which uses a clever manipulation of syllable streams to target the processing of different features. The combination of neural entrainment and ERP analysis allows for the assessment of different processing stages, and implementing this paradigm in a comparably large sample of neonates is impressive. I only have some smaller comments.

Weaknesses:

I am skeptical regarding the interpretation of the phoneme-specific ERP effect as a precursor of the N400 and would suggest toning it down. While the authors are correct in that infant ERP components are typically slower and more posterior compared to adult components, and the observed pattern is hence consistent with an adult N400, at the same time, it could also be a lot of other things. On a functional level, I can't follow the author's argument as to why a violation in phoneme regularity should elicit an N400, since there is no evidence for any semantic processing involved. In sum, I think there is just not enough evidence from the present paradigm to confidently call it an N400.

Why did the authors choose to include male and female voices? While using both female and male stimuli of course leads to a higher generalizability, it also introduces a second dimension for one feature that is not present for this other (i.e., phoneme for Experiment 1 and voice identity plus gender for Experiment 2). Hence, couldn't it also be that the infants extracted the regularity with which one gender voice followed the other? For instance, in List B, in the words, one gender is always followed by the other (M-F or F-M), while in 2/3 of the part-words, the gender is repeated (F-F and M-M). Wouldn't you expect the same pattern of results if infants learned regularities based on gender rather than identity?

Do you have any idea why the duplet entrainment effect occurs over the electrodes it does, in particular over the occipital electrodes (which seems a bit unintuitive given that this is a purely auditory experiment with sleeping neonates).

Reviewer #2 (Public review):

In this manuscript from Wang et al., the authors seek to examine the role of capsular polysaccharides (CPS) in invasive S. suis pathogenesis. They show that CPS thickness variations associate with isolation from different compartments within the infected mouse and that CPS promotes resistance to blood borne immune mechanisms. The authors conclude that thick CPS inhibits colonization/invasion of the NALT and rather antisera against non-CPS. These results are interesting and thought provoking and provide the continued basis for future experiments that delve further into immune mechanisms. However, there are serious concerns about data collection and interpretation that require further data to provide an accurate conclusion. Some of these concerns are highlighted below:

In figure 2, the authors conclude that high levels of CPS confer resistance to phagocytic killing in blood exposed S. suis. However, it seems equally likely that this is resistance against complement mediated killing. It would be important to compare S. suis killing in animals depleted of complement components (C3 and C5-9).

Intranasal administration non-CPS antisera provides a nice contrast to intravenous administration, especially in light of the recently identified "blood-olfactory barrier". Can the authors provide any insight into how long and where this antibody would be located after intranasal administration? Would this be antibody mediated cellular resistance, or something akin to simple antibody "neutralization"

The micrographs in Figure 7 depict anatomy from the respiratory mucosa. While there is no histochemical identification of neurons, the tissues labeled OE are almost certainly not olfactory and in fact respiratory. However, more troubling is that in figures 7A,a,b,e, and f, the lateral nasal organ has been labeled as the olfactory bulb. This undermines the conclusion of CNS invasion, and also draws into question other experiments in which the brain and CSF are measured.

Micrographs of brain tissue in 7B are taken from distal parts of the brain, whereas if olfactory neuroinvasion were occurring, the bacteria would be expected to arrive in the olfactory bulb. It's also difficult to understand how an inflammatory process would be developed to this point in the brain -even if we were looking at the appropriate region of the brain -within an hour of inoculation (is there a control for acetic acid induced brain inflammation?). Some explanations about the speed of the immune responses recorded are warranted.

The detected presence of S. suis in the CSF 0.5hr following intranasal inoculation is difficult to understand from an anatomical perspective. This is especially true when the amount of S. suis is nearly the same as that found within the NALT. Even motile pathogens would need far longer than 0.5hr to get into the brain, so it's exceedingly difficult to understand how this could occur so extensively in under an hour. The authors are quantifying CSF as anything that comes out of the brain after mincing. Firstly, this should more accurately be referred to as "brain", not CSF. Secondly, is it possible that the lateral nasal organ -which is mistakenly identified as olfactory bulb in figure 7- is being included in the CNS processing? This would explain the equivalent amounts of S. suis in NALT and "CSF".

To support their conclusions about neuroinvasion along the olfactory route and /CSF titer the authors should provide more compelling images to support this conclusion: sections stained for neurons and S. suis, images of the actual olfactory bulb (neurons, glomerular structure etc).

Reviewer #2 (Public review):

Summary:

The authors are trying to come up with a list of genes (GEAR genes) that are consistently associated with cancer patient survival based on TCGA database. A method named "Multi-gradient Permutation Survival Analysis" was created based on bootstrapping and gradually increasing the sample size of the analysis. Only the genes with consistent performance in this analysis process are chosen as potential candidates for further analyses.

Strengths:

The authors describe in detail their proposed method and the list of the chosen genes from the analysis. The scientific meaning and potential values of their findings are discussed in the context of published results in this field.

Weaknesses:

Some steps of the proposed method (especially the definition of survival analysis similarity (SAS) need further clarification or details since it would be difficult if anyone tries to reproduce the results. In addition, the multiplicity (a large number of p-values are generated) needs to be discussed and/or the potential inflation of false findings needs to be part of the manuscript.

If the authors can improve the clarity of the proposed method and there is no major mistake there, the proposed approach can be applied to other diseases (assuming TCGA type of data is available for them) to identify potential gene lists, based on which drug screening can be performed to identify potential target for development.

Reviewer #2 (Public review):

Summary:

In this study, the authors aimed to elucidate the formation and differentiation of syncytiotrophoblast (STB) cells by analyzing placental tissue and trophoblast organoids (TOs) using single-nucleus (SN) and single-cell (SC) RNA sequencing. They identified three distinct nuclear subtypes within the STB and explored the relationship between STB gene expression changes, developmental stages, and environmental contexts. The study emphasizes the utility of TOs as models for understanding STB differentiation and highlights novel gene markers, such as RYBP, involved in STB development.

Strengths:

(1) The use of SN and SC RNA sequencing provides a detailed analysis of STB formation and differentiation.

(2) The identification of distinct STB subtypes and novel gene markers such as RYBP offers new insights into STB development.

Weaknesses:

(1) Inconsistencies in data presentation.

(2) Questionable interpretation of lncRNA signals: The use of long non-coding RNA (lncRNA) signals as cell type-specific markers may represent sequencing noise rather than true markers.

To improve the study's validity and significance, it is crucial to address the inconsistencies and to provide additional evidence for the claims. Supplementing with immunofluorescence staining for validating the distribution of STB_in, STB_out, and EVT_enrich in the organoid models is recommended to strengthen the results and conclusions.

Reviewer #2 (Public review):

Summary

The authors characterize the cell-cycle arrest induced by HIV-1 Vif in infected cells. They show this arrest is not at G2/M as previously thought but during metaphase. They show that the metaphase plate forms normally but progression to anaphase is massively delayed, and chromosome segregation is dysregulated in a manner consistent with impaired assembly of microtubules at the kinetochore. This correlates with the lack of recruitment of B56-subunits of PP2 phosphatase which are known degradation targets of Vif, suggesting that this weakens and unbalances the microtubule-mediated forces on the separating chromosomes.

Strengths

The authors present a very well-performed set of quantitative live cell imaging experiments that convincingly show a difference between Vif and Vpr-mediated cell cycle arrests. Through an in-depth characterization of the Vif-mediated block in metaphase, they make a strong case for this phenotype being tied to the degradation of PP2-B56 by Vif. Furthermore, it is important that they have performed most of these experiments with virally infected cells, meaning that their observations are observable at relevant viral expression levels of Vif.

Weaknesses

Experimentally there is very little to criticize with respect to the cellular systems used. Data from 10.1016/j.bbrc.2020.04.123 has identified selective mutants that fail to degrade B56 while maintaining A3G degradation by Cul5, and it would be nice to confirm that such a mutant behaves like the delta-Vif virus when examining metaphase, but selective ablation of B56 during mitosis to mimic Vif is would expect to be very challenging and beyond the scope.

Where I would raise some criticism is in the relevance of these observations to the replication and pathogenesis of the virus itself, which the authors do not address or discuss. Firstly, despite clear data that both Vpr and Vif can lead to a cell cycle arrest in cycling cells, it has never been particularly clear why the virus does this. While I would agree with the authors that Vif results in the metaphase arrest through targeting B56-PP2A, this may not be the reason WHY the virus targets one of the cell's major phosphatases, but rather a knock-on effect of doing so. I appreciate that this is beyond the scope of the study, but it is something I feel should be discussed rather than the narrow mechanistic points made in the discussion. Secondly, the authors suggest that this activity of Vif is a major cause of apoptosis in infected cells and perhaps CD4+ T cell depletion in vivo. It would be good to quantify how much apoptosis is Vif-dependent in infected primary human CD4+ T cells rather than transformed tumor cells, and whether this correlates with the Vif-mediated induction of a pseudometaphase.

Reviewer #2 (Public review):

Shen and Dayan build a Bayes adaptive Markov decision process model with three key components: an adaptive hazard function capturing potential predation, an intrinsic reward function providing the urge to explore, and a conditional value at risk (CvaR, closely related to probability distortion explanations of risk traits). The model itself is very interesting and has many strengths including considering different sources of risk preference in generating behavior under uncertainty. I think this model will be useful to consider for those studying approach/avoid behaviors in dynamic contexts.

The authors argue that the model explains behavior in a very simple and unconstrained behavioral task in which animals are shown novel objects and retreat from them in various manners (different body postures and patterns of motor chunks/syllables). The model itself does capture lots of the key mouse behavioral variability (at least on average on a mouse-by-mouse basis) which is interesting and potentially useful. However, the variables in the model - and the internal states it implies the mice have during the behavior - are relatively unconstrained given the wide range of explanations one can offer for the mouse behavior in the original study (Akiti et al). This reviewer commends the authors on an original and innovative expansion of existing models of animal behaviour, but recommends that the authors revise their study to reflect the obvious challenges. I would also recommend a reduction in claiming that this exercise gives a normative-like or at least quantitative account of mental disorders.

My main comment is that this paper is a very nice model creation that can characterize the heterogeneity rodent behavior in a very simple approach/avoid context (Akiti et al; when a novel object is placed in an arena) that itself can be interpreted in a multitude of ways. The use of terms like "exploration", "brave", etc in this context is tricky because the task does not allow the original authors (Akiti et al) to quantify these "internal states" or "traits" with the appropriate level of quantitative detail to say whether this model is correct or not in capturing the internal states that result in the rodent behavior. That said, the original behavioral setup is so simple that one could imagine capturing the behavioral variability in multiple ways (potentially without evoking complex computations that the original authors never showed the mouse brain performs). I would recommend reframing the paper as a new model that proposes a set of internal states that could give rise to the behavioral heterogeneity observed in Akiti et al, but nonetheless is at this time only a hypothesis. Furthermore, an explanation of what would be really required to test this would be appreciated to make the point clearer.

Reviewer #2 (Public review):

Summary:

This work attempted to investigate how the gene rnc, which showed higher expression in clinical strains of Salmonella Enteritidis compared to those isolated from food, affects the virulence of this bacteria through modulating dsRNA levels and the immune response of host cells.

Strengths:

The authors clearly demonstrated that the deletion of rnc Salmonella Enteritidis leads to an accumulation of dsRNA inside the cells, which further activates the immune response of host cells. It is also well demonstrated that the rnc gene deletion results in an increased ROS level through regulating the SodA protein.

Weaknesses:

(1) It is unclear whether the higher rnc expression in clinical strains of Salmonella Enteritidis is universal or just specific to several strains, because of the inadequate data provided and different strains used for different tests in this study.

(2) A lot of specific information is missing in the Figure legends and Method section, which makes it hard to understand some of the key results in the manuscript.

Reviewer #2 (Public review):

This manuscript by Tao et al. reports on an effort to better specify the underlying interactions driving the effects of biodiversity on productivity in biodiversity experiments. The authors are especially concerned with the potential for competitive interactions to drive positive biodiversity-ecosystem functioning relationships by driving down the biomass of subdominant species. The authors suggest a new partitioning schema that utilizes a suite of partial density treatments to capture so-called competitive ability. While I agree with the authors that understanding the underlying drivers of biodiversity-ecosystem functioning relationships is valuable - I am unsure of the added value of this specific approach for several reasons.

Comments on revised version:

The authors changed only one minor detail in response to the last round of reviews.

Reviewer #2 (Public review):

Peterson et al., perform a series of behavioral experiments to study the repertoire and variance of Mongolian gerbil vocalizations across social groups (families). A key strength of the study is the use of a behavioral paradigm which allows for long term audio recordings under naturalistic conditions. This new experimental set-up results in the identification of additional vocalization types, not previously described the literature. In combination with state-of-the-art methods for vocalization analysis, the authors demonstrate that the distribution of sound types and the transitions between these sound types across three gerbil families is different. This is a highly compelling finding which suggests that individual families may develop distinct vocal repertories. One potential limitation of the study lies in the cluster analysis used for identifying distinct vocalization types. The authors use a Gaussian Mixed Model (GMM) trained on variational auto Encoder derived latent representation of vocalizations to classify recorded sounds into clusters. Through the analysis the authors identify 70 distinct clusters and demonstrate a differential usage of these sound clusters across families. While the authors acknowledge the inherent challenges in cluster analysis and provide additional analyses (i.e. maximum mean discrepancy, MMD), additional analysis would increase the strength of the conclusions. In particular, analysis with different cluster sizes would be valuable. An additional limitation of the study is that due to the methodology that is used, the authors can not provide any information about the bioacoustic features that contribute to differences in sound types across families which limits interpretations about how the animals may perceive and react to these sounds in an ethologically relevant manner.

The conclusions of this paper are well supported by data.

• Can the authors comment on the potential biological significance of the 70 sound clusters? Does each cluster represent a single sound type? How many vocal clusters can be attributed to a single individual? Similarly, can the authors comment on the intra-individual and inter-individual variability of the sound types within and across families?<br /> • As a main conclusion of the paper rests on the different distribution of sound clusters across families, it is important to validate the robustness of these differences across different cluster parameters. Specifically, the authors state that "we selected 70 clusters as the most parsimonious fit". Could the authors provide more details about how this was fit? Specifically, could the authors expand upon what is meant by "prior domain knowledge about the number of vocal types...". If the authors chose a range of cluster values (i.e. 10, 30, 50, 90) does the significance of the results still hold?<br /> • While VAEs are powerful tools for analyzing complex datasets in this case they are restricted to analysis of spectrogram images. Have the authors identified any acoustic differences (i.e. in pitch, frequency, other sound components) across families?

Following a revision of the manuscript the authors have taken many of these points under consideration and as a result have significantly improved the manuscript. Critically, they have now provided additional quantification that differences across family repertories are robust against cluster selection size.

Reviewer #2 (Public review):

The axon initial segment (AIS) is the axonal domain where most neurons integrate inputs and generate action potentials. Though structural and electrophysiological studies have allowed to better understand the mechanisms of assembly and maintenance of this domain, as well as its functions, there is still a need for efficient tools to study its structural organization and plasticity in vivo.

In this article, the authors describe the generation of a knock-in mouse reporter line allowing the conditional expression of a GFP-tagged version of AnkyrinG (Ank-G), which is a major protein of the axon initial segment and the nodes of Ranvier in neurons. This reporter line can in particular be used to study axon initial segment assembly and plasticity, by combining it with mouse lines or viruses expressing the Cre recombinase under the control of a neuronal promoter. Furthermore, the design of the line should allow to preserve the expression of the main Ank-G isoforms observed in neurons and could thus allow to study Ank-G related mechanisms in various neuronal subcompartments.

Some mouse lines allowing the neuronal expression of AIS/node of Ranvier markers coupled to a fluorescent protein exist, however they correspond to transgenic lines leading to potential overexpression of the tagged protein. Depending on the promoter used, their expression can vary and be absent in some neuronal populations (in particular, the Thy-1 promoter can lead to variable expression depending on the transgene insertion locus). Furthermore, these lines do not allow conditional expression of the protein regarding neuronal subtypes nor controlled temporal expression. Finally, a thorough description of the in vivo expression of the tagged protein at the AIS, and its impact on the structural and electrophysiological properties of the AIS are missing for these lines.

The present reporter line is thus definitely of interest, as the authors convincingly show that it can be used in various contexts (from in vitro to in vivo). It could in particular be used to study the assembly and plasticity of the domains where Ank-G is expressed. The strength of this work is that it thoroughly characterizes the reporter line expression and shows that it does not alter the structural nor the electrophysiological properties of the labeled neurons. The additional data presented by the authors in the revised version adequately complete the previously shown data and address the questions raised by the reviewers.

Reviewer #2 (Public review):

Since neurocysticercosis is associated with epilepsy, the authors wish to establish how cestode larvae affect neurons. The underlying hypothesis is that the larvae may directly excite neurons and thus favor seizure genesis.

To test this hypothesis, the authors collected biological materials from larvae (from either homogenates or excretory/secretory products), and applied them to hippocampal neurons (rats and mice) and human cortical neurons.

This constitutes a major strength of the paper, providing a direct reading of larvae's biological effects. Another strength is the combination of methods, including patch clamp, Ca, and glutamate imaging.

Comments on revised version:

The concerns have been addressed.

Reviewer #2 (Public review):

Summary

Liu and MacGann et al. introduce the method DNA O-MAP that uses oligo-based ISH probes to recruit horseradish peroxidase for targeted proximity biotinylation at specific DNA loci. The method's specificity was tested by profiling the proteomic composition at repetitive DNA loci such as telomeres and pericentromeric alpha satellite repeats. In addition, the authors provide proof-of-principle for the capture and mapping of contact frequencies between individual DNA loop anchors.

Strengths

Identifying locus-specific proteomes still represents a major technical challenge and remains an outstanding issue (1). Theoretically, this method could benefit from the specificity of ISH probes and be applied to identify proteomes at non-repetitive DNA loci. This method also requires significantly fewer cells than other ISH- or dCas9-based locus-enrichment methods. Another potential advantage to be tested is the lack of cell line engineering that allows its application to primary cell lines or tissue.

Weaknesses

The authors indicate that DNA O-MAP is superior to other methods for identifying locus-specific proteomes. Still, no proof exists that this method could uncover proteomes at non-repetitive DNA loci. Also, there is very little validation of novel factors to confirm the superiority of the technique regarding specificity.<br /> The authors first tested their method's specificity at repetitive telomeric regions, and like other approaches, expected low-abundant telomere-specific proteins were absent (for example, all subunits of the telomerase holoenzyme complex). Detecting known proteins while identifying noncanonical and unexpected protein factors with high confidence could indicate that DNA O-MAP does not fully capture biologically crucial proteins due to insufficient enrichment of locus-specific factors. The newly identified proteins in Figure 1E might still be relevant, but independent validation is missing entirely. In my opinion, the current data cannot be interpreted as successfully describing local protein composition.

Finally, the authors could have discussed the limitations of DNA O-MAP and made a fair comparison to other existing methods (2-5). Unlike targeted proximity biotinylation methods, DNA O-MAP requires paraformaldehyde crosslinking, which has several disadvantages. For instance, transient protein-protein interactions may not be efficiently retained on crosslinked chromatin. Similarly, some proteins may not be crosslinked by formaldehyde and thus will be lost during preparation (6).

(1) Gauchier M, van Mierlo G, Vermeulen M, Dejardin J. Purification and enrichment of specific chromatin loci. Nat Methods. 2020;17(4):380-9.<br /> (2) Dejardin J, Kingston RE. Purification of proteins associated with specific genomic Loci. Cell. 2009;136(1):175-86.<br /> (3) Liu X, Zhang Y, Chen Y, Li M, Zhou F, Li K, et al. In Situ Capture of Chromatin Interactions by Biotinylated dCas9. Cell. 2017;170(5):1028-43 e19.<br /> (4) Villasenor R, Pfaendler R, Ambrosi C, Butz S, Giuliani S, Bryan E, et al. ChromID identifies the protein interactome at chromatin marks. Nat Biotechnol. 2020;38(6):728-36.<br /> (5) Santos-Barriopedro I, van Mierlo G, Vermeulen M. Off-the-shelf proximity biotinylation for interaction proteomics. Nat Commun. 2021;12(1):5015.<br /> (6) Schmiedeberg L, Skene P, Deaton A, Bird A. A temporal threshold for formaldehyde crosslinking and fixation. PLoS One. 2009;4(2):e4636.

Reviewer #2 (Public review):

Summary

The manuscript presents valuable findings, particularly in the crystal structure of the Sld3CBD-Cdc45 interaction and the identification of additional sequences involved in their binding. The modeling of the Sld7-Sld3CBD-CDC45 subcomplex is novel, and the results provide insights into potential conformational changes that occur upon interaction. However, the work remains incomplete as several main claims are only partially supported by experimental data, particularly the proposed model for Sld3 interaction with GINS on the CMG. Additionally, the single-stranded DNA binding data from different species do not convincingly advance the manuscript's central arguments.

Strengths

(1) The Sld3CBD-Cdc45 structure is a novel contribution, revealing critical residues involved in the interaction.

(2) The model structures generated from the crystal data are well presented and provide valuable insights into the interaction sequences between Sld3 and Cdc45.

(3) The experiments testing the requirements for interaction sequences are thorough and conducted well, with clear figures supporting the conclusions.

(4) The conformational changes observed in Sld3 and Cdc45 upon binding are interesting and enhance our understanding of the interaction.

(5) The modeling of the Sld7-Sld3CBD-CDC45 subcomplex is a new and valuable addition to the field.

Weaknesses

(1) The proposed model for Sld3 interacting with GINS on the CMG needs more experimental validation and conflicts with published findings. These discrepancies need more detailed discussion and exploration.

(2) The section on the binding of Sld3 complexes to origin single-stranded DNA needs significant improvement. The comparisons between Sld3-CBD, Sld3CBD-Cdc45, and Sld7-Sld3CBD-Cdc45 involve complexes from different species, limiting the comparisons' value.

(3) The authors' model proposing the release of Sld3 from CMG based on its binding to single-stranded DNA is unclear and needs more elaboration.

Reviewer #2 (Public review):

Summary:

The authors use the TRAP2 mouse line to label dentate gyrus cells active during an enriched environment paradigm and cut brain slices from these animals one week later to determine whether granule cells (GC) and semilunar granule cells (SGC) labelled during the exposure share common features. They particularly focus on the role of SGCs and potential circuit mechanisms by which they could be selectively embedded in the labelled assembly. The authors claim that SGCs are disproportionately recruited into IEG-expressing assemblies due to intrinsic firing characteristics but cannot identify any contributing circuit connectivity motives in the slice preparation, although they claim that an increased correlation between spontaneous synaptic currents in the slice could signify common synaptic inputs as the source of assembly formation.

Strengths:

The authors chose a timely and relevant question, namely how memory-bearing neuronal assemblies, or 'engrams', are established and maintained in the dentate gyrus. After the initial discovery of such memory-specific ensembles of immediate-early gene expressing engrams in 2012 (Ramirez et al.) this issue has been explored by several high-profile studies that have considerably expanded our understanding of the underlying molecular and cellular mechanisms, but still leave a lot of unanswered questions.

Weaknesses:

Unfortunately, there are several major methodological issues that put into question most if not all central claims made by the authors:

(1) The authors conclude that SGCs are disproportionately recruited into cfos assemblies during the enriched environment and Barnes maze task given that their classifier identifies about 30% of labelled cells as SGCs in both cases and that another study using a different method (Save et al., 2019) identified less than 5% of an unbiased sample of granule cells as SGCs. To make matters worse, the classifier deployed here was itself established on a biased sample of GCs patched in the molecular layer and granule cell layer, respectively, at even numbers (Gupta et al., 2020). The first thing the authors would need to show to make the claim that SGCs are disproportionately recruited into memory ensembles is that the fraction of GCs identified as SGCs with their own classifier is significantly lower than 30% using their own method on a random sample of GCs (e.g. through sparse viral labelling). As the authors correctly state in their discussion, morphological samples from patch-clamp studies are problematic for this purpose because of inherent technical issues (i.e. easier access to scattered GCs in the molecular layer).

(2) The authors claim that recurrent excitation from SGCs onto GCs or other SGCs is irrelevant because they did not find any connections in 32 simultaneous recordings (plus 63 in the next experiment). Without a demonstration that other connections from SGCs (e.g. onto mossy cells or interneurons) are preserved in their preparation and if so at what rates, it is unclear whether this experiment is indicative of the underlying biology or the quality of the preparation. The argument that spontaneous EPSCs are observed is not very convincing as these could equally well arise from severed axons (in fact we would expect that the vast majority of inputs are not from local excitatory cells). The argument on line 418 that SGCs have compact axons isn't particularly convincing either given that the morphologies from which they were derived were also obtained in slice preparations and would be subject to the same likelihood of severing the axon. Finally, even in paired slice recordings from CA3 pyramidal cells the experimentally detected connectivity rates are only around 1% (Guzman et al., 2016). The authors would need to record from a lot more than 32 pairs (and show convincing positive controls regarding other connections) to make the claim that connectivity is too low to be relevant.

(3) Another troubling sign is the fact that optogenetic GC stimulation rarely ever evokes feedback inhibition onto other cells which contrasts with both other in vitro (e.g. Braganza et al., 2020) and in vivo studies (Stefanelli et al., 2016) studies. Without a convincing demonstration that monosynaptic connections between SGCs/GCs and interneurons in both directions is preserved at least at the rates previously described in other slice studies (e.g. Geiger et al., 1997, Neuron, Hainmueller et al., 2014, PNAS, Savanthrapadian et al., 2014, J. Neurosci), the notion that this setting could be closer to naturalistic memory processing than the in vivo experiments in Stefanelli et al. (e.g. lines 443-444) strikes me as odd. In any case, the discussion should clearly state that compromised connectivity in the slice preparation is likely a significant confound when comparing these results.

(4) Probably the most convincing finding in this study is the higher zero-time lag correlation of spontaneous EPSCs in labelled vs. unlabeled pairs. Unfortunately, the fact that the authors use spontaneous EPSCs to begin with, which likely represent a mixture of spontaneous release from severed axons, minis, and coordinated discharge from intact axon segments or entire neurons, makes it very hard to determine the meaning and relevance of this finding. At the bare minimum, the authors need to show if and how strongly differences in baseline spontaneous EPSC rates between different cells and slices are contributing to this phenomenon. I would encourage the authors to use low-intensity extracellular stimulation at multiple foci to determine whether labelled pairs really share higher numbers of input from common presynaptic axons or cells compared to unlabeled pairs as they claim. I would also suggest the authors use conventional Cross correlograms (CCG; see e.g. English et al., 2017, Neuron; Senzai and Buzsaki, 2017, Neuron) instead of their somewhat convoluted interval-selective correlation analysis to illustrate co-dependencies between the event time series. The references above also illustrate a more robust approach to determining whether peaks in the CCGs exceed chance levels.

(5) Finally, one of the biggest caveats of the study is that the ensemble is labelled a full week before the slice experiment and thereby represents a latent state of a memory rather than encoding consolidation, or recall processes. The authors acknowledge that in the discussion but they should also be mindful of this when discussing other (especially in vivo) studies and comparing their results to these. For instance, Pignatelli et al 2018 show drastic changes in GC engram activity and features driven by behavioral memory recall, so the results of the current study may be very different if slices were cut immediately after memory acquisition (if that was possible with a different labelling strategy), or if animals were re-exposed to the enriched environment right before sacrificing the animal.

Reviewer #2 (Public review):

The manuscript by Mahadevaraju and colleagues addresses the very interesting question of how sex-specific gene expression is regulated downstream of the sex-determination decision during sexually dimorphic development. Most previous work has been done with adult "endpoint" analysis long after sex-specific gene expression and sex-specific development has been initiated, but this study appropriately focuses on earlier developmental stages. The authors use bulk RNA-seq of ovaries and testes where key sex determination factors have been altered, allowing for a comparison of XX "testes" and XY "ovaries" to their normal XX ovary and XY testis counterparts. This is interesting work that appears to be conducted in a rigorous manner, and will be beneficial for the community. However, I also feel that the authors miss some key opportunities in their analysis. In particular, they focus on the sexual state of the germline, which is a very interesting question, but they may actually be more poised to make interesting conclusions about the somatic cells of the gonad.

One issue with the work is that there are no simple conclusions. This is not the fault of the authors or the work but of mother nature, which has made it particularly difficult to parse out the different contributions that regulate germline sex determination-those regulated by the germline's own sex chromosome constitution and those regulated by the sex of the surrounding soma. While this makes a paper more difficult to write and interpret, it is simply the truth, and the authors deal with this complexity very well. One aspect of this work that is more clear than others is that germ cells do not enter, or at least go very far, down the spermatogenesis pathway unless they are XY germ cells in a male soma. This conclusion could be made more clear in the manuscript. The experiment generating genotypes where a Y chromosome is present regardless of X chromosome number or tra state, and then examining kl-3 expression is particularly nice, and makes the point clearly. The authors could be stronger overall about this conclusion.

I also feel that there is a missed opportunity here. The experimental design utilizes sex transformation of the soma, but the manuscript focuses almost entirely on the germline. On one hand, this is problematic since the samples are mixed cell types with very different contributions of the germline to the overall tissue. While they can identify genes that are expressed primarily in the germline in normal males and females and use these for their analysis, there's no way to really tell whether this is also the case in transformed gonads or the total germline contribution to the bulk RNA-seq. I certainly don't discount their germline analysis, but these issues should be made clear in the manuscript. Second, and more important, is the fact that there would seem to be a wealth of changes in somatic gene expression, more directly regulated by the somatic sex determination machinery, that seems ripe for analysis. In addition, nice experiments like the comparison of tra- XX males with dsxD/- XX males, which can beautifully identify genes that are regulated by tra independently of dsx, are only glossed over in the analysis, results, and discussion.

I feel that a better analysis of somatic sexual development would be highly beneficial.

Reviewer #2 (Public review):

Summary:

The study by Sun et al. introduces a useful system utilizing the proteasomal accessory factor A (PafA) and HaloTag for investigating drug-protein interactions in both in vitro (cell culture) and in vivo (zebrafish) settings. The authors presented the development and optimization of the system, as well as examples of its application and the identification of potential novel drug targets. However, the manuscript requires considerable improvements, particularly in writing and justification of experimental design. There are several inaccuracies in data description and a lack of statistics in some figures, undermining the conclusions drawn in the manuscript. Additionally, the authors introduced variants of the ligands and their cognate substrates, yet their use in different experiments appears random and lacks justification. It is challenging for readers to remember and track the specific properties of each variant, further complicating the interpretation of the results.

The conclusions of this paper are mostly backed by data, but certain aspects of data analysis and description require further clarification and expansion.

Reviewer #2 (Public review):

Summary:

Immunostaining of chromatin-associated proteins and visualization of these factors through fluorescence microscopy is a powerful technique to study molecular processes such as DNA damage and repair, their timing, and their genetic dependencies. Nonetheless, it is well-established that this methodology (sometimes called "foci-ology") is subject to biases introduced during sample preparation, immunostaining, foci visualization, and scoring. This manuscript addresses several of the shortcomings associated with immunostaining by using image correlation spectroscopy (ICS) to quantify the recruitment of several DNA damage response-associated proteins following various types of DNA damage.

The study compares automated foci counting and fluorescence intensity to image correlation spectroscopy degree of aggregation study the recruitment of DNA repair proteins to chromatin following DNA damage. After validating image correlation spectroscopy as a reliable method to visualize the recruitment of γH2AX to chromatin following DNA damage in two separate cell lines, the study demonstrates that this new method can also be used to quantify RPA1 and Rad51 recruitment to chromatin following DNA damage. The study further shows that RPA1 signal as measured by this method correlates with cell sensitivity to Olaparib, a widely-used PARP inhibitor.

Strengths:

Multiple proof-of-concept experiments demonstrate that using image correlation spectroscopy degree of aggregation is typically more sensitive than foci counting or foci intensity as a measure of recruitment of a protein of interest to a site of DNA damage. The sensitivity of the SKOV3 and OVCA429 cell lines to MMS and the PARP inhibitors Olaparib and Veliparib as measured by cell viability in response to increasing amounts of each compound is a valuable correlate to the image correlation spectroscopy degree of aggregation measurements.

Weaknesses:

The subjectivity of foci counting has been well-recognized in the DNA repair field, and thus foci counts are usually interpreted relative to a set of technical and biological controls and across a meaningful time period. As such:

(1) A more detailed description of the numerous prior studies examining the immunostaining of proteins such as γH2AX, RAD51, and RPA is needed to give context to the findings presented herein.

(2) The benefits of adopting image correlation spectroscopy should be discussed in comparison to other methods, such as super-resolution microscopy, which may also offer enhanced sensitivity over traditional microscopy.

(3) Additional controls demonstrating the specificity of their antibodies to detection of the proteins of interest should be added, or the appropriate citations validating these antibodies included.

Reviewer #2 (Public review):

Summary:

This manuscript provides a comprehensive overview of potential resistance mutations within MET Receptor Tyrosine Kinase and defines how specific mutations affect different inhibitors and modes of target engagement. The goal is to identify inhibitor combinations with the lowest overlap in their sensitivity to resistant mutations and determine if certain resistance mutations/mechanisms are more prevalent for specific modes of ATP-binding site engagement. To achieve this, the authors measured the ability of ~6000 single mutants of MET's kinase domain (in the context of a cytosolic TPR fusion) to drive IL-3-independent proliferation (used as a proxy for activity) of Ba/F3 cells (deep mutational profiling) in the presence of 11 different inhibitors. The authors then used co-crystal and docked structures of inhibitor-bound MET complexes to define the mechanistic basis of resistance and applied a protein language model to develop a predictive model of inhibitor sensitivity/resistance.

Strengths:

The major strengths of this manuscript are the comprehensive nature of the study and the rigorous methods used to measure the sensitivity of ~6000 MET mutants in a pooled format. The dataset generated will be a valuable resource for researchers interested in understanding kinase inhibitor sensitivity and, more broadly, small molecule ligand/protein interactions. The structural analyses are systematic and comprehensive, providing interesting insights into resistance mechanisms. Furthermore, the use of machine learning to define inhibitor-specific fitness landscapes is a valuable addition to the narrative. Although the ESM1b protein language model is only moderately successful in identifying the underlying mechanistic basis of resistance, the authors' attempt to integrate systematic sequence/function datasets with machine learning serves as a foundation for future efforts.

Weaknesses:

The main limitation of this study is that the authors' efforts to define general mechanisms between inhibitor classes were only moderately successful due to the challenge of uncoupling inhibitor-specific interaction effects from more general mechanisms related to the mode of ATP-binding site engagement. However, this is a minor limitation that only minimally detracts from the impressive overall scope of the study.

Reviewer #2 (Public review):

Summary:

Dasari et al present an interesting study investigating the use of 'microbiota age' as an alternative to other measures of 'biological age'. The study provides several curious insights into biological aging. Although 'microbiota age' holds potential as a proxy of biological age, it comes with limitations considering the gut microbial community can be influenced by various non-age related factors, and various age-related stressors may not manifest in changes in the gut microbiota. The work would benefit from a more comprehensive discussion, that includes the limitations of the study and what these mean to the interpretation of the results.

Strengths:

The dataset this study is based on is impressive, and can reveal various insights into biological ageing and beyond. The analysis implemented is extensive and high-level.

Weaknesses:

The key weakness is the use of microbiota age instead of e.g., DNA-methylation-based epigenetic age as a proxy of biological ageing, for reasons stated in the summary. DNA methylation levels can be measured from faecal samples, and as such epigenetic clocks too can be non-invasive. I will provide authors a list of minor edits to improve the read, to provide more details on Methods, and to make sure study limitations are discussed comprehensively.

Reviewer #2 (Public review):

Summary:

In this study, Bossen et al. looked at the immune status of the tracheal terminal cells (TTCs) in Drosophila larvae. The authors propose that these cells do show PGFP-LCx expression and, hence, lack immune function. Artificial overexpression of the PGRP-LCx in the TTCs causes these cells to undergo apoptosis.

Strengths:

Only a few groups have tried to look at the immune status of the trachea, though we know that AMPs are expressed there after infection. This exciting study attempts to understand the differences in the tracheal cells that do not produce AMPs upon infection.

Weaknesses:

The reason why the TTCs have some immune privilege still needs to be completely clear. Whether the phenotype is cell autonomous or contributes to the cellular immune system is not evaluated. As we know, crystal cells also maintain oxygen levels in larvae; whether in the absence of terminal trachea, the crystal cells have any role is not explored.

Reviewer #2 (Public review):

Summary:

This study investigates the potential role of CD131, a cytokine receptor subunit shared by GM-CSF and IL-3, in intestinal inflammation. Using heterozygous mice with an inactivating mutation on this gene, the study demonstrates ameliorated inflammation, associated with less infiltration of macrophages. Moreover, the depletion of macrophages prevented many of the inflammatory effects of DSS and made both WT and mutant mice equivalent in terms of inflammation severity. Correlative data showing increased CD131+ cells in tissues of patients with ulcerative colitis is also demonstrating, evidence for plausibility for these pathways in human disease.

Strengths:

The phenotype of mutant mice seems quite robust and the pathways proposed, GM-CSF signaling in macrophages with CCL4 as a downstream pathway, are all plausible and concordant with existing models. Many of the experiments included meaningful endpoints and were overall well performed.

Weaknesses:

(1) Experimental rigor was lacking in this manuscript, which provided limited or no details on the number of independent iterations that each experiment was done, the number of animals per group, the number of technical or biological replicates in each graph, etc.

(2) Details of animal model validation showing that this particular mutant allele results in a lack of CD131 protein expression were not shown. Moreover, since the paper uses heterozygous mice, it is critical to show that at the protein level, there is indeed reduced expression of CD131 in het mice compared to controls (many heterozygous states do not lead to appreciable protein depletion).

(3) Another major weakness is that the paper asserts a causal relationship between CD131 signaling and CCL4 production: the data shown indicates that the phenotypes of CCL4 deficiency (through Ab blockade) and CD131 partial deficiency (in het mice) are similar. However, this does not establish that CD131 signaling acts through CCL4.

(4) Lastly, while the paper claims that CD131 acts through macrophage recruitment, the evidence is circumstantial and not direct. DSS-induced acute colitis is largely mediated by macrophages, so any manipulation associated with less severe inflammation is accompanied by lesser macrophage infiltration in this model: this does not directly establish that CD131 acts directly on macrophages, which would require cell-specific knockout or complex cell reconstitution experiments.

Reviewer #2 (Public review):

Summary:

The authors have completed MRI-based descriptions of the sulcal anatomy of 18 carnivoran species that vary greatly in behaviour and ecology. In this descriptive study, different sulcal patterns are identified in relation to phylogeny and, to some extent, behaviour. The authors argue that the reported differences across families reflect behaviour and electrophysiology, but these correlations are not supported by any analyses.

Strengths:

A major strength of this paper is using very similar imaging methods across all specimens. Often papers like this rely on highly variable methods so that consistency reduces some of the variability that can arise due to methodology.

The descriptive anatomy was accurate and precise. I could readily follow exactly where on the cortical surface the authors referring. This is not always the case for descriptive anatomy papers, so I appreciated the efforts the authors took to make the results understandable for a broader audience.

I also greatly appreciate the authors making the images open access through their website.

Weaknesses:

Although I enjoyed many aspects of this manuscript, it is lacking in any quantitative analyses that would provide more insights into what these variations in sulcal anatomy might mean. The authors do discuss inter-clade differences in relation to behaviour and older electrophysiology papers by Welker, Campos, Johnson, and others, but it would be more biologically relevant to try to calculate surface areas or volumes of cortical fields defined by some of these sulci. For example, something like the endocast surface area measurements used by Sakai and colleagues would allow the authors to test for differences among clades, in relation to brain/body size, or behaviour. Quantitative measurements would also aid significantly in supporting some of the potential correlations hinted at in the Discussion.

Although quantitative measurements would be helpful, there are also some significant concerns in relation to the specimens themselves. First, almost all of these are captive individuals. We know that environmental differences can alter neocortical development and humans and nonhuman animals and domestication affects neocortical volume and morphology. Whether captive breeding affects neocortical anatomy might not be known, but it can affect other brain regions and overall brain size and could affect sulcal patterns. Second, despite using similar imaging methods across specimens, fixation varied markedly across specimens. Fixation is unlikely to affect the ability to recognize deep sulci, but variations in shrinkage could nevertheless affect overall brain size and morphology, including the ability to recognize shallow sulci. Third, the sample size = 1 for every species examined. In humans and nonhuman animals, sulcal patterns can vary significantly among individuals. In domestic dogs, it can even vary greatly across breeds. It therefore remains unclear to what extent the pattern observed in one individual can be generalized for a species let alone an entire genus or family. The lack of accounting for inter-individual variability makes it difficult to make any firm conclusions regarding the functional relevance of sulcal patterns.

Reviewer #2 (Public review):

Summary:

The manuscript from Prado-Mantilla and co-workers addresses mechanisms of embryonic epidermis development, focusing on the intermediate layer cells, a transient population of suprabasal cells that contributes to the expansion of the epidermis through proliferation. Using bulk-RNA they show that these cells are transcriptionally distinct from the suprabasal spinous cells and identify specific marker genes for these populations. They then use transgenesis to demonstrate that one of these selected spinous layer-specific markers, the transcription factor MafB is capable of suppressing proliferation in the intermediate layers, providing a potential explanation for the shift of suprabasal cells into a non-proliferative state during development. Further, lineage tracing experiments show that the intermediate cells become granular cells without a spinous layer intermediate. Finally, the authors show that the intermediate layer cells express higher levels of contractility-related genes than spinous layers and overexpression of cytoskeletal regulators accelerates the differentiation of spinous layer cells into granular cells.

Overall the manuscript presents a number of interesting observations on the developmental stage-specific identities of suprabasal cells and their differentiation trajectories and points to a potential role of contractility in promoting differentiation of suprabasal cells into granular cells. The precise mechanisms by which MafB suppresses proliferation, how the intermediate cells bypass the spinous layer stage to differentiate into granular cells, and how contractility feeds into these mechanisms remain open. Interestingly, while the mechanosensitive transcription factor YAP appears deferentially active in the two states, it is shown to be downstream rather than upstream of the observed differences in mechanics.

Strengths:

The authors use a nice combination of RNA sequencing, imaging, lineage tracing, and transgenesis to address the suprabasal to granular layer transition. The imaging is convincing and the biological effects appear robust. The manuscript is clearly written and logical to follow.

Weaknesses:

While the data overall supports the authors' claims, there are a few minor weaknesses that pertain to the aspect of the role of contractility, The choice of spastin overexpression to modulate contractility is not ideal as spastin has multiple roles in regulating microtubule dynamics and membrane transport which could also be potential mechanisms explaining some of the phenotypes. Use of Arghap11 overexpression mitigates this effect to some extent but overall it would have been more convincing to manipulate myosin activity directly. It would also be important to show that these manipulations increase the levels of F-actin and myosin II as shown for the intermediate layer. It would also be logical to address if further increasing contractility in the intermediate layer would enhance the differentiation of these cells.

The gene expression analyses are relatively superficial and rely heavily on GO term analyses which are of course informative but do not give the reader a good sense of what kind of genes and transcriptional programs are regulated. It would be useful to show volcano plots or heatmaps of actual gene expression changes as well as to perform additional analyses of for example gene set enrichment and/or transcription factor enrichment analyses to better describe the transcriptional programs

Claims of changes in cell division/proliferation changes are made exclusively by quantifying EdU incorporation. It would be useful to more directly look at mitosis. At minimum Y-axis labels should be changed from "% Dividing cells" to % EdU+ cells to more accurately represent findings

Despite these minor weaknesses the manuscript is overall of high quality, sheds new light on the fundamental mechanisms of epidermal stratification during embryogenesis, and will likely be of interest to the skin research community.

Reviewer #2 (Public review):

The authors make the interesting observation that the developmental refinement of apical M/T cell dendrites into individual glomeruli proceeds normally even when the majority of neighboring M/T cells are ablated. At later stages, the remaining neurons develop additional dendrites that invade multiple glomeruli ectopically and, similarly, OSN inputs to glomeruli lose projection specificity as well. The authors conclude that the normal density of M/T neurons is not required for developmental refinement, but rather for maintaining specific connectivity in adults.

Comments on revised submission:

The authors have adjusted the interpretation of their findings and as a consequence, the conclusions are now better supported by the data. However, the evidence for the absence of a role of firing in regulating ectopic dendrites is still insufficient.

Reviewer #2 (Public review):

Summary:

The manuscript by Isotani et al characterizes the hyperproliferation of intestinal stem cells (ISCs) induced by nicotine treatment in vivo. Employing a range of small molecule inhibitors, the authors systematically investigated potential receptors and downstream pathways associated with nicotine-induced phenotypes through in vitro organoid experiments. Notably, the study specifically highlights a signaling cascade involving α7-nAChR/PKC/YAP/TAZ/Notch as a key driver of nicotine-induced stem cell hyperproliferation. Utilizing a Lgr5CreER Apcfl/fl mouse model, the authors extend their findings to propose a potential role of nicotine in stem cell tumorgenesis. The study posits that Notch signaling is essential during this process.

Strengths and Weaknesses:

One noteworthy research highlight in this study is the indication, as shown in Figure 2 and S2, that the trophic effect of nicotine on ISC expansion is independent of Paneth cells. In the Discussion section, the authors propose that this independence may be attributed to distinct expression patterns of nAChRs in different cell types. To further substantiate these findings, the authors provided qPCR analysis of nAchRs in ISCs and Paneth cells from isolated whole small intestine, indicating that α7-nAChR uniquely responds to nicotine treatment among various nAChRs. And the authors further strengthen the clinical relevance of the study by exploring human scRNA-seq dataset, in which α7-nAChR is indeed also expressed in human ISCs and Paneth cells.

As shown in the same result section, the effect of nicotine on ISC organoid formation appears to be independent of CHIR99021, a Wnt activator. In the Lgr5CreER Apcfl/fl mouse model, it is known that APC loss results in a constitutive stabilization of β-catenin, thus the hyperproliferation of ISCs by nicotine treatment in this mouse model is likely beyond Wnt activation. The authors have included such discussion.

In Figure 4, the authors investigate ISC organoid formation with a pan-PKC inhibitor, revealing that PKC inhibition blocks nicotine-induced ISC expansion. It's noteworthy that PKC inhibitors have historically been used successfully to isolate and maintain stem cells by promoting self-renewal. Therefore, it is surprising to observe no or reversal effect on ISCs in this context. The authors have now included an additional PKC inhibitor Sotrastaurin to confirm the role of PKC in nicotine-induced ISC expansion.

Overall, the manuscript has provided sufficient experimental evidence to address my concerns and also significantly enhanced its quality.

Reviewer #2 (Public review):

This manuscript by Petty and Bruno delves into the still poorly understood role of higher-order thalamic nuclei in the encoding of sensory information by examining the activity in the Pom and LP cells in mice performing an associative learning task. They developed an elegant paradigm in which they conditioned head-fixed mice to attend to a stimulus of one sensory modality (visual or tactile) and ignore a second stimulus of the other modality. They recorded simultaneously from POm and LP, using 64-channels electrode arrays, to reveal the context-dependency of the firing activity of cells in higher-order thalamic nuclei. They concluded that behavioral training reshapes activity in these secondary thalamic nuclei. The authors brought new analyses and figures which greatly improve their manuscript and support their conclusion. The manuscript benefits now from a better communication about both the methodology and the results. I have no more major concerns, but I feel that the readability of the manuscript could be improved with the following revisions.

Strengths

The authors developed an original and elegant paradigm in which they conditioned head-fixed mice to attend to a stimulus of one sensory modality, either visual or tactile and ignore a second stimulus of the other modality. As a tactile stimulus, they applied gentle air puffs on the distal part of the vibrissae, ensuring that the stimulus was innocuous and therefore none aversive which is crucial in their study.

It is commonly viewed that first-order thalamus performs filtering and re-encoding of the sensory flow; in contrast the computations taking place in high-order nuclei are poorly understood. They may contribute to cognitive functions. By integrating top-down control, high-order nuclei may participate in generating update models of the environment based on sensory activity; how this can take place is a key question that Petty and Bruno addressed in the present study.

Weaknesses

(1) It's difficult when reading the text to understand which results were quantified and which were not, in part because mean data as well as (s.e.m. or S.D.) do not appear either in the main text nor in the legends of the figures. Only vague and unquantified data are given in the main text. I understand that the authors may want to make the main text less heavy, but having these data fully written somewhere (i.e., main text, summary table, figure legends) rather than having to estimate through looking at a graph (especially when the data are constraint in the first 20% of the graph (Figure 4c)), would greatly improve the text's clarity and precision.

For instance, Line #173, "At the population level, POm cells in both conditioning groups had a peak of activity 40ms after air puff onset (Figure 4a)." Is this 40 ms a result of quantified data, then a s.e.m. would be informative, or a reading measurement on the Figure 4a graphs? As it stands, it is too vague a value.

(2) The authors give clearer definition of what they analyzed, which greatly improved the readability of the manuscript. The clarity of the manuscript could still be improved by solving remaining ambiguities about sensory- versus non-sensory-responses to the applied stimuli throughout the manuscript, in order to better convey the authors' conclusion that behavioral training reshapes activity in these secondary thalamic nuclei which then may participate in generating update models of the context in which the animal is performing the task.

Line #24 in the abstract "In mice trained to respond to tactile stimuli and ignore visual stimuli, POm was robustly activated by touch and largely unresponsive to visual stimuli". The abstract would better reflect the manuscript conclusions indicating that POm was robustly activated during tactile stimuli.

(3) The new analysis of the "early" responses in Pom cells pointed out, Line #173, that "At the population level, POm cells in both conditioning groups had a peak of activity 40ms after air puff onset (Figure 4a)." Previous works cited by the authors, Diamond et al. (1992), described tactile responses in Pom cells at 15-20ms latency which were suppressed by the barrel cortex inactivation.

The 40ms-latency responses described in this manuscript therefore do not fit with "purely sensory" and barely with S1-feedbacks, as proposed on line #168 "Such responses could be "purely sensory" (i.e. driven by ascending brainstem inputs)" or line #334 "It is likely that the observed activity in lateral dorsal POm is driven by true whisker responses in SpVi and S1."

In the same way, Line #315 "we observed POm cells that responded to the onset of the air puff in both conditioning groups". This conclusion should be dampened, to better fit the results, by "we observed POm cells that responded 40 ms after the onset of the air puff in both conditioning groups."

Reviewer #2 (Public review):

Summary:

This is a very interesting paper that leveraged several publicly available datasets: invasive cortical recording in epilepsy patients, functional and structural connectomic data, and PET data related to dopaminergic and gaba-ergic synapses. These were combined to create a unified hypothesis of beta band oscillatory activity in the human brain. They show that beta frequency activity is ubiquitous, and does not just occur in sensorimotor areas. Cortical regions where beta oscillations predominated had high connectivity to regions that are high in dopamine re-update.

Strengths:

The authors leverage and integrate three publicly available human brain datasets in a creative way. These public datasets are powerful tools for human neuroscience, and it is innovative to combine these three types of data into a common brain space to generate novel findings and hypotheses. Findings are nicely controlled by separately examining cortical regions where alpha predominates (which have a different connectivity pattern). GABA uptake from PET studies is used as a control for the specificity of the relationship between beta activity and dopamine uptake. There is much interest in synchronized oscillatory activity as a mechanism of brain function and dysfunction, but the field is short on unifying hypotheses of why particular rhythms predominate in particular regions. This paper contributes nicely to that gap. It is ambitious in generating hypotheses, particularly that modulation of beta activity may be used as a "proxy" for modulating phasic dopamine release.

Weaknesses:

As the authors point out, the use of normative data is excellent for exploring hypotheses but does not address or explore individual variations which could lead to other insights. It is also biased to resting state activity; maps of task related activity (if they were available) might show different findings.

Challenges:

In the Discussion, the authors do a fairly deep dive into the implications of their findings, particularly with respect to the hypothesis that beta band activity "preserves the status quo", and with respect to the use of beta band activity in controlling brain-machine interfaces. Mechanistically and theoretically oriented readers might gain rewarding new insights by a careful read of the discussion, but full appreciation of their deep dive may require real time interaction with the authors.

Reviewer #2 (Public review):

Summary:

The authors aimed to understand whether polarised moonlight could be used as a directional cue for nocturnal animals homing at night, particularly at times of night when polarised light is not available from the sun. To do this, the authors used nocturnal ants, and previously established methods, to show that the walking paths of ants can be altered predictably when the angle of polarised moonlight illuminating them from above is turned by a known angle (here +/- 45 degrees).

Strengths:

The behavioural data are very clear and unambiguous. The results clearly show that when the angle of downwelling polarised moonlight is turned, ants turn in the same direction. The data also clearly show that this result is maintained even for different phases (and intensities) of the moon, although during the waning cycle of the moon the ants' turn is considerably less than may be expected.

Impact:

The authors have discovered that nocturnal bull ants, while homing back to their nest holes at night, are able to use the dim polarised light pattern formed around the moon for path integration. Even though similar methods have previously shown the ability of dung beetles to orient along straight trajectories for short distances using polarised moonlight, this the first evidence of an animal that uses polarised moonlight in homing. This is quite significant, and their findings are well supported by their data.

Comments on revised version:

The authors have made a good effort to accommodate my suggestions for improvement (and from what I can tell, those of the other reviewers). I have no further comments.

Reviewer #2 (Public review):

Summary:

This work describes a statistical framework that combines functional linear mixed modeling with joint 95% confidence intervals, which improves statistical power and provides less conservative and more robust statistical inferences than in previous studies. Pointwise linear regression analysis has been used extensively to analyze time series signals from a wide range of neuroscience recording techniques, with recent studies applying them to photometry data. The novelty of this study lies in 1) the introduction of joint 95% confidence intervals for statistical testing of functional mixed models with nested random-effects, and 2) providing an open-source R package implementing this framework. This study also highlights how summary statistics as opposed to trial-by-trial analysis can obscure or even change the direction of statistical results by reanalyzing two other studies.

Strengths:

The open-source package in R using a similar syntax as lme4 package for the implementation of this framework, the high fitting speed and the low memory footprint, even in complex models, enhance the accessibility and usage by other researchers.

The reanalysis of two studies using summary statistics on photometry data (Jeong et al., 2022; Coddington et al., 2023) highlights how trial-by-trial analysis at each time-point on the trial can reveal information obscured by averaging across trials. Furthermore, this work also exemplifies how session and subject variability can lead to different conclusions when not considered.

This study also showcases the statistical robustness of FLMM by comparing this method to fitting pointwise linear mixed models and performing t-test and Benjamini-Hochberg correction as performed by Lee et al. (2019).

Reviewer #2 (Public review):

Summary:

The study proposes that many cancer driver mutations are not yet identified but could be identified if they harbor recurrent SNVs. The paper leverages the analysis from Paper #1 that used quantitative analysis to demonstrate that SNVs or CDNs seen 3 or more times are more likely due to selection (ie a driver mutation) than by chance or random mutation.

Strengths:

Empirically, mutation frequency is an excellent marker of a driver gene because canonical driver mutations typically have recurrent SNVs. Using the TCGA database, the paper illustrates that CDNs can identify canonical driver mutations (Fig 3) and that most CDN are likely to disrupt protein function (Fig 2). In addition, CDNs can be shared between cancer types (Fig 4).

Weaknesses:

Driver alteration validation is difficult, with disagreements on what defines a driver mutation, and how many driver mutations are present in a cancer. The value proposed by the authors is that the identification of all driver genes can facilitate the design of patient specific targeting therapies, but most targeted therapies are already directed towards known driver genes. There is an incomplete discussion of oncogenes (where activating mutations tend to target a single amino acid or repeat) and tumor suppressor genes (where inactivating mutations may be more spread across the gene). Other alterations (epigenetic, indels, translocations, CNVs) would be missed by this type of analysis.

The method could be more valuable when applied to the noncoding genome, where driver mutations in promoters or enhancers are relatively rare, or as yet to be discovered. Increasingly more cancers have had whole genome sequencing. Compared to WES, criteria for driver mutations in noncoding regions are less clear, and this method could potentially provide new noncoding driver CDNs. Observing the same mutation in more than one cancer specimen is empirically unusual, and the authors provide a solid quantitative analysis that indicates many recurrent mutations are likely to be cancer-driver mutations.

Reviewer #2 (Public review):

Summary:

The authors propose that cancer driver mutations can be identified by Cancer Driving Nucleotides (CDNs). CDNs are defined as SNVs that occur frequently in genes. There are many ways to define cancer driver mutations, and strengths and weaknesses are the reliance of statistics to define them.

Strengths:

There are many well-known approaches and studies that have already identified many canonical driver mutations. A potential strength is that mutation frequencies may be able to identify, as yet, unrecognized driver mutations. They use of a previously developed method to estimate mutation hotspots across the genome (Dig, Sherman et al 2022). This publication has already used cancer sequence data to infer driver mutations based on higher than expected mutation frequencies. The advance here is to further illustrate that recurrent mutations (estimated at 3 or more mutations (CDNs) at the same base) are more likely to be the result of selection for a driver mutation (Fig 3). Further analysis indicates that mutation sequence context (Fig 4) or mutation mechanisms (Fig 5) are unlikely to be major causes for recurrent point mutations. Finally, they calculate (Fig 6) that most driver mutations identifiable by the CDN approach could be identified with about 100,000 to one million tumor coding genomes.

Weaknesses:

The manuscript does provide specific examples where recurrent mutations identify known driver mutations, but does not identify "new" candidate driver mutations. Driver mutation validation is difficult and at least clinically, frequency (ie observed in multiple other cancer samples) is indeed commonly used to judge if a SNV has driver potential. The method would miss alternative ways to trigger driver alterations (translocations, indels, epigenetic, CNVs). Nevertheless, the value of the manuscript is its quantitative analysis of why mutation frequencies can identify cancer driver mutations.

Reviewer #2 (Public review):

Summary:

The authors improve the work of Jallais et al. (2022) by including a novel module capable of automatically learning feature selection from different acquisition protocols inside a supervised learning framework. Combining the module above with an estimation framework for estimating the posterior distribution of model parameters, they obtain rich probabilistic information (uncertainty and degeneracy) on the parameters in a reasonable computation time.

The main contributions of the work are:

(1) The whole framework allows the user to avoid manually defining summary statistics, which may be slow and tedious and affect the quality of the results.

(2) The authors tested the proposal by tackling three different biophysical models for brain tissue and using data with characteristics commonly used by the diffusion-MR-microstructure research community.

(3) The authors validated their method well with the state-of-the-art.

(4) The methodology allows the quantification of the inherent model's degeneration and how it increases with strong noise.

The authors showed the utility of their proposal by computing complex parameter descriptors automatically in an achievable time for three different and relevant biophysical models.

Importantly, this proposal promotes tackling, analyzing, and considering the degenerated nature of the most used models in brain microstructure estimation.

Reviewer #2 (Public review):

Summary:

This manuscript by Tubert et al presents the role of the D5 receptor in modulating the striatal cholinergic interneuron (CIN) pause response through D5R-cAMP-Kv1 inhibitory signaling. Their model elucidates the on / off switch of CIN pause, likely due to the different DA affinity between D2R and D5R. This machinery may be crucial in modulating synaptic plasticity in cortical-striatal circuits during motor learning and execution. Furthermore, the study bridges their previous finding of CIN hyperexcitability (Paz et al., Movement Disorder 2022) with the loss of pause response in LID mice.

Strengths:

The study had solid findings, and the writing was logically structured and easy to follow. The experiments are well-designed, and they properly combined electrophysiology recording, optogenetics, and pharmacological treatment to dissect/rule out most, if not all, possible mechanisms in their model.

Weaknesses:

The manuscript is overall satisfying with only some minor concerns that need to be addressed. Manipulation of intracellular cAMP (e.g. using pharmacological analogs or inhibitors) can add additional evidence to strengthen the conclusion.

Reviewer #2 (Public review):

Summary:

In this paper, the authors analyze the organization of phases across different spatial scales. The authors analyze intracranial, stereo-electroencephalogram (sEEG) recordings from human clinical patients. The authors estimate the phase at each sEEG electrode at discrete temporal frequencies. They then use higher-order SVD (HOSVD) to estimate the spatial frequency spectrum of the organization of phase in a data-driven manner. Based on this analysis, the authors conclude that most of the variance explained is due to spatially extended organizations of phase, suggesting that the best description of brain activity in space and time is in fact a globally organized process. The authors' analysis is also able to rule out several important potential confounds for the analysis of spatiotemporal dynamics in EEG.

Strengths:

There are many strengths in the manuscript, including the authors' use of SVD to address the limitation of irregular sampling and their analyses ruling out potential confounds for these signals in the EEG.

Weaknesses:

Some important weaknesses are not properly acknowledged, and some conclusions are over-interpreted given the evidence presented.

The central weakness is that the analyses estimate phase from all signal time points using wavelets with a narrow frequency band (see Methods - "Numerical methods"). This step makes the assumption that phase at a particular frequency band is meaningful at all times; however, this is not necessarily the case. Take, for example, the analysis in Figure 3, which focuses on a temporal frequency of 9.2 Hz. If we compare the corresponding wavelet to the raw sEEG signal across multiple points in time, this will look like an amplitude-modulated 9.2 Hz sinusoid to which the raw sEEG signal will not correspond at all. While the authors may argue that analyzing the spatial organization of phase across many temporal frequencies will provide insight into the system, there is no guarantee that the spatial organization of phase at many individual temporal frequencies converges to the correct description of the full sEEG signal. This is a critical point for the analysis because while this analysis of the spatial organization of phase could provide some interesting results, this analysis also requires a very strong assumption about oscillations, specifically that the phase at a particular frequency (e.g. 9.2 Hz in Figure 3, or 8.0 Hz in Figure 5) is meaningful at all points in time. If this is not true, then the foundation of the analysis may not be precisely clear. This has an impact on the results presented here, specifically where the authors assert that "phase measured at a single contact in the grey matter is more strongly a function of global phase organization than local". Finally, the phase examples given in Supplementary Figure 5 are not strongly convincing to support this point.

Another weakness is in the discussion on spatial scale. In the analyses, the authors separate contributions at (approximately) > 15 cm as macroscopic and < 15 cm as mesoscopic. The problem with the "macroscopic" here is that 15 cm is essentially on the scale of the whole brain, without accounting for the fact that organization in sub-systems may occur. For example, if a specific set of cortical regions, spanning over a 10 cm range, were to exhibit a consistent organization of phase at a particular temporal frequency (required by the analysis technique, as noted above), it is not clear why that would not be considered a "macroscopic" organization of phase, since it comprises multiple areas of the brain acting in coordination. Further, while this point could be considered as mostly semantic in nature, there is also an important technical consideration here: would spatial phase organizations occurring in varying subsets of electrodes and with somewhat variable temporal frequency reliably be detected? If this is not the case, then could it be possible that the lowest spatial frequencies are detected more often simply because it would be difficult to detect variable organizations in subsets of electrodes?

Another weakness is disregarding the potential spike waveform artifact in the sEEG signal in the context of these analyses. Specifically, Zanos et al. (J Neurophysiol, 2011) showed that spike waveform artifacts can contaminate electrode recordings down to approximately 60 Hz. This point is important to consider in the context of the manuscript's results on spatial organization at temporal frequencies up to 100 Hz. Because the spike waveform artifact might affect signal phase at frequencies above 60 Hz, caution may be important in interpreting this point as evidence that there is significant phase organization across the cortex at these temporal frequencies.

A last point is that, even though the present results provide some insight into the organization of phase across the human brain, the analyses do not directly link this to spiking activity. The predictive power that these spatial organizations of phase could provide for spiking activity - even if the analyses were not affected by the distortion due to the narrow-frequency assumption - remains unknown. This is important because relating back to spiking activity is the key factor in assessing whether these specific analyses of phase can provide insight into neural circuit dynamics. This type of analysis may be possible to do with the sEEG recordings, as well, by analyzing high-gamma power (Ray and Maunsell, PLoS Biology, 2011), which can provide an index of multi-unit spiking activity around the electrodes.

Reviewer #2 (Public review):

Summary:

Min et al. attempt to demonstrate that magnetic resonance imaging (MRI) can detect changes in neuronal membrane potentials. They approach this goal by studying how MRI contrast and cellular potentials together respond to treatment of cultured cells with ionic solutions. The authors specifically study two MRI-based measurements: (A) the transverse (T2) relaxation rate, which reflects microscopic magnetic fields caused by solutes and biological structures; and (B) the fraction or "pool size ratio" (PSR) of water molecules estimated to be bound to macromolecules, using an MRI technique called magnetization transfer (MT) imaging. They see that depolarizing K+ and Ba2+ concentrations lead to T2 increases and PSR decreases that vary approximately linearly with voltage in a neuroblastoma cell line and that change similarly in a second cell type. They also show that depolarizing potassium concentrations evoke reversible T2 increases in rat brains and that these changes are reversed when potassium is renormalized. Min et al. argue that this implies that membrane potential changes cause the MRI effects, providing a potential basis for detecting cellular voltages by noninvasive imaging. If this were true, it would help validate a recent paper published by some of the authors (Toi et al., Science 378:160-8, 2022), in which they claimed to be able to detect millisecond-scale neuronal responses by MRI.

Strengths:

The discovery of a mechanism for relating cellular membrane potential to MRI contrast could yield an important means for studying functions of the nervous system. Achieving this has been a longstanding goal in the MRI community, but previous strategies have proven too weak or insufficiently reproducible for neuroscientific or clinical applications. The current paper suggests remarkably that one of the simplest and most widely used MRI contrast mechanisms-T2 weighted imaging-may indicate membrane potentials if measured in the absence of the hemodynamic signals that most functional MRI (fMRI) experiments rely on. The authors make their case using a diverse set of quantitative tests that include controls for ion and cell type-specificity of their in vitro results and reversibility of MRI changes observed in vivo.

Weaknesses:

The major weakness of the paper is that it uses correlational data to conclude that there is a causational relationship between membrane potential and MRI contrast. Alternative explanations that could explain the authors' findings are not adequately considered. Most notably, depolarizing ionic solutions can also induce changes in cellular volume and tissue structure that in turn alter MRI contrast properties similarly to the results shown here. For example, a study by Stroman et al. (Magn Reson Med 59:700-6, 2008) reported reversible potassium-dependent T2 increases in neural tissue that correlate closely with light scattering-based indications of cell swelling. Phi Van et al. (Sci Adv 10:eadl2034, 2024) showed that potassium addition to one of the cell lines used here likewise leads to cell size increases and T2 increases. Such effects could in principle account for Min et al.'s results, and indeed it is difficult to see how they would not contribute, but they occur on a time scale far too slow to yield useful indications of membrane potential. The authors' observation that PSR correlates negatively with T2 in their experiments is also consistent with this explanation, given the inverse relationship usually observed (and mechanistically expected) between these two parameters. If the authors could show a tight correspondence between millisecond-scale membrane potential changes and MRI contrast, their argument for a causal connection or a useful correlational relationship between membrane potential and image contrast would be much stronger. As it is, however, the article does not succeed in demonstrating that membrane potential changes can be detected by MRI.

Reviewer #2 (Public review):

Summary:

The authors sought to evaluate whether observations made in separate individual laboratories are reproducible when they use standardized procedures and quality control measures. This is a key question for the field. If ten systems neuroscience labs try very hard to do the exact same experiment and analyses, do they get the same core results? If the answer is no, this is very bad news for everyone else! Fortunately, they were able to reproduce most of their experimental findings across all labs. Despite attempting to target the same brain areas in each recording, variability in electrode targeting was a source of some differences between datasets.

Major Comments:

The paper had two principal goals:<br /> (1) to assess reproducibility between labs on a carefully coordinated experiment<br /> (2) distill the knowledge learned into a set of standards that can be applied across the field.<br /> The manuscript made progress towards both of these goals but leaves room for improvement.

(1) The first goal of the study was to perform exactly the same experiment and analyses across 10 different labs and see if you got the same results. The rationale for doing this was to test how reproducible large-scale rodent systems neuroscience experiments really are. In this, the study did a great job showing that when a consortium of labs went to great lengths to do everything the same, even decoding algorithms could not discern laboratory identity was not clearly from looking at the raw data. However, the amount of coordination between the labs was so great that these findings are hard to generalize to the situation where similar (or conflicting!) results are generated by two labs working independently.

Importantly, the study found that electrode placement (and thus likely also errors inherent to the electrode placement reconstruction pipeline) was a key source of variability between datasets. To remedy this, they implemented a very sophisticated electrode reconstruction pipeline (involving two-photon tomography and multiple blinded data validators) in just one lab-and all brains were sliced and reconstructed in this one location. This is a fantastic approach for ensuring similar results within the IBL collaboration, but makes it unclear how much variance would have been observed if each lab had attempted to reconstruct their probe trajectories themselves using a mix of histology techniques from conventional brain slicing, to light sheet microscopy, to MRI imaging.

This approach also raises a few questions. The use of standard procedures, pipelines, etc. is a great goal, but most labs are trying to do something unique with their setup. Bigger picture, shouldn't highly "significant" biological findings akin to the discovery of place cells or grid cells, be so clear and robust that they can be identified with different recording modalities and analysis pipelines?

Related to this, how many labs outside of the IBL collaboration have implemented the IBL pipeline for their own purposes? In what aspects do these other labs find it challenging to reproduce the approaches presented in the paper? If labs were supposed to perform this same experiment, but without coordinating directly, how much more variance between labs would have been seen? Obviously investigating these topics is beyond the scope of this paper. The current manuscript is well-written and clear as is, and I think it is a valuable contribution to the field. However, some additional discussion of these issues would be helpful.

(2) The second goal of the study was to present a set of data curation standards (RIGOR) that could be applied widely across the field. This is a great idea, but its implementation needs to be improved if adoption outside of the IBL is to be expected. Here are three issues:

(a) The GitHub repo for this project (https://github.com/int-brain-lab/paper-reproducible-ephys/) is nicely documented if the reader's goal is to reproduce the figures in the manuscript. Consequently, the code for producing the RIGOR statistics seems mostly designed for re-computing statistics on the existing IBL-formatted datasets. There doesn't appear to be any clear documentation about how to run it on arbitrary outputs from a spike sorter (i.e. the inputs to Phy).

(b) Other sets of spike sorting metrics that are more easily computed for labs that are not using the IBL pipeline already exist (e.g. "quality_metrics" from the Allen Institute ecephys pipeline [https://github.com/AllenInstitute/ecephys_spike_sorting/blob/main/ecephys_spike_sorting/modules/quality_metrics/README.md] and the similar module in the Spike Interface package [https://spikeinterface.readthedocs.io/en/latest/modules/qualitymetrics.html]). The manuscript does not compare these approaches to those proposed here, but some of the same statistics already exist (amplitude cutoff, median spike amplitude, refractory period violation).

(c) Some of the RIGOR criteria are qualitative and must be visually assessed manually. Conceptually, these features make sense to include as metrics to examine, but would ideally be applied in a standardized way across the field. The manuscript doesn't appear to contain a detailed protocol for how to assess these features. A procedure for how to apply these criteria for curating non-IBL data (or for implementing an automated classifier) would be helpful.

Other Comments:

(1) How did the authors select the metrics they would use to evaluate reproducibility? Was this selection made before doing the study?

(2) Was reproducibility within-lab dependent on experimenter identity?

(3) They note that UCLA and UW datasets tended to miss deeper brain region targets (lines 185-188) - they do not speculate why these labs show systematic differences. Were they not following standardized procedures?

(4) The authors suggest that geometrical variance (difference between planned and final identified probe position acquired from reconstructed histology) in probe placement at the brain surface is driven by inaccuracies in defining the stereotaxic coordinate system, including discrepancies between skull landmarks and the underlying brain structures. In this case, the use of skull landmarks (e.g. bregma) to determine locations of brain structures might be unreliable and provide an error of ~360 microns. While it is known that there is indeed variance in the position between skull landmarks and brain areas in different animals, the quantification of this error is a useful value for the field.

(5) Why are the thalamic recording results particularly hard to reproduce? Does the anatomy of the thalamus simply make it more sensitive to small errors in probe positioning relative to the other recorded areas?

Reviewer #2 (Public review):

Summary:

This study aims to investigate how social observation influences risky decision-making. Using a gambling task, the study explored how participants adjusted their risk-taking behavior when they believed their decisions were being observed by either a risk-averse or risk-seeking partner. The authors hypothesized that individuals would simulate the choices of their observers based on learned preferences and integrate these simulated choices into their own decision-making. In addition to behavioral experiments, the study employed computational modeling to formalize decision processes and fMRI to identify the neural underpinnings of risky decision-making under social observation.

Strengths:

The study provides a fresh perspective on social influence in decision-making, moving beyond the simple notion that social observation leads to uniformly riskier behavior. Instead, it shows that individuals adjust their choices depending on their beliefs about the observer's risk preferences, offering a more nuanced understanding of how social contexts shape decision-making. The authors provide evidence using comprehensive approaches, including behavioral data based on a well-designed task, computational modeling, and neuroimaging. The three models are well selected to compare at which level (e.g., computing utility, risk preference shift, and choice probability) the social influence alters one's risky decision-making. This approach allows for a more precise understanding of the cognitive processes underlying decision-making under social observation.

Weaknesses:

While the neuroimaging results are generally consistent with the behavioral and computational findings, the strength of the neural evidence could be improved. The authors' claims about the involvement of the TPJ and mPFC in integrating social information are plausible, but further analysis, such as model comparisons at the neuroimaging level, is needed to decisively rule out alternative interpretations that other computational models suggest.

Reviewer #2 (Public review):

Summary:

In this article Wen et. al., describe the development of a 'proof-of-concept' bi-functional vector based out of HSV-deltaICP-34.5's ability to purge latent HIV-1 and SIV genomes from cells. They show that co-infection of latent J-lat T-cell lines with a HSV-deltaICP-34.5 vector can reactivate HIV-1 from a latent state. Over- or stable expression of ICP 34.5 ORF in these cells can arrest latent HIV-1 genomes from transcription, even in the presence of latency reversal agents. ICP34.5 can co-IP with- and de-phosphorylate IKKa/b to block its interaction with NF-k/B transcription factor. Additionally, ICP34.5 can interact with HSF1 which was identified by mass-spec. Thus, the authors propose that the latency reversal effect of HSV-deltaICP-34.5 in co-infected JLat cells is due to modulatory effects on the IKKa/b-NF-kB and PP1-HSF-1 pathway.

Next the authors cleverly construct a bifunctional HSV based vector with deleted ICP34.5 and 47 ORFs to purge latency and avoid immunological refluxes, and additionally expand the application of this construct as a vaccine by introducing SIV genes. They use this 'vaccine' in mouse models and show the expected SIV-immune responses. Experiments in rhesus macaques (RM), further elicit potential for their approach to reactivate SIV genomes and at the same time block their replication by antibodies. What was interesting in the SIV experiments is that the dual-functional vector vaccine containing sPD1- and SIV Gag/Env ORFs effectively delayed SIV rebound in RMs and in some cases almost neutralized viral DNA copy detection in serum. Very promising indeed, however there are some questions I wish the authors explored to answer, detailed below.

Overall, this is an elegant and timely work demonstrating the feasibility of reducing virus rebound in animals, and potentially expand to clinical studies. The work was well written, and sections were clearly discussed.

Strengths:

The work is well designed, rationale explained and written very clearly for lay readers.<br /> Claims are adequately supported by evidence and well designed experiments including controls.

Weaknesses:

(1) It looks like ICP0 is also involved in latency reversal effects. More follow-up work will be required to test if this is in fact true.

(2) It is difficult to estimate the depletion of the latent viral reservoir. The authors have tried to address this issue. A more convincing argument to this reviewer will be data to demonstrate that after the bi-functional vaccine, the animals show overall reduction in the number of circulating latent cells. The feasibility to obtain such a result is not clearly demonstrated.

(3) The authors state that the reduced virus rebound detected following bi-functional vaccine delivery is due to latent genomes becoming activated and steady-state neutralization of these viruses by antibody response. This needs to be demonstrated. Perhaps cell-culture experiments from specimen taken from animals might help address this issue. In lab cultures one could create environments without antibody responses, under these conditions one would expect higher level of viral loads being released in response to the vaccine in question.

Reviewer #2 (Public review):

Summary

In this study, the authors evaluate the impact of selective pressure from chemotherapeutic drugs on the development of drug resistance in Mycobacteria, specifically through the acquisition of genetic mutations or phenotypic tolerance. Their findings indicate that treatment with sublethal concentrations of first-line antibiotics does not lead to enhanced mutation rates.

Strengths

The use of the mutation accumulation assay demonstrating low spontaneous mutation rates combined with the display of an increased MIC supports drug resistance as a consequence of phenotypic tolerance. Additionally, the use of the ciprofloxacin tolerance assay in combination with whole genome sequencing demonstrating a lack of mutations provides further support of this. The results now support the authors claims.

Weaknesses

Besides an increase in DNA stress response other underlying tolerance mechanisms were not established - increased efflux pump, thickening of the cell wall, decrease in metabolic processes, rerouting of metabolic processes etc.

Reviewer #2 (Public review):

Summary:

DAVID syndrome is a rare autosomal dominant disorder characterized by variable immune dysfunction and variable ACTH deficiency. Nine different families have been reported, and all have heterozygous mutations in NFKB2. The mechanism of NFKB2 action in the immune systems has been well-studied, but nothing is known about its role in pituitary gland.

The DAVID mutations cluster in the C-terminus of the NFKB2 and interfere with cleavage and nuclear translocation. The mutations are likely dominant negative, by affecting dimer function. ACTH deficiency can be life-threatening in neonates and adults, thus, understanding the mechanism of NFKB2 action in pituitary development and/or function is important.

The authors use CRISPR/Cas gene editing of human iPSC derived pituitary-hypothalamic organoids to assess the function of NFKB2 and TBX19 in pituitary development. Mutations in TBX19 are the most common, known cause of pituitary ACTH deficiency, and the mechanism of action has been studied in mice, which phenocopy the human condition. Thus, the TBX19 organoids can serve as a positive control. The Nfkb2 mouse model has a p.Y868* mutation that impairs cleavage of NFKB2 p100, and the immune phenotype mimics the patients with DAVID mutations, but no pituitary phenotype was evident. Thus, a human organoid model might be the only approach suitable to discover the etiology of the pituitary phenotype.

Overall, the authors have selected an important problem, and the results suggest that the pituitary insufficiency in DAVID syndrome is caused by a developmental defect rather than an autoimmune hypophysitis condition. The use of gene editing in human iPSC derived hypothalamic-pituitary organoids is significant, as there is only one example of this previously, namely studies on OTX2. Only a few laboratories have demonstrated the ability to differentiate iPSC or ES cells to these organoids, and the authors have improved the efficiency of differentiation, which is also significant.

The strength of the evidence is excellent. The authors have thoroughly analyzed the genetically engineered organoids compared to isogenic controls. They have validated their findings with analysis of RNA and proteins. They have studied the time course of differentiation in the organoids and have a robust experimental design involving many replicates. Analysis of additional clones could strengthen the evidence.

Strengths:

The authors make mutations in TBX19 and NFKB2 that exist in affected patients. The TBX19 p.K146R mutation is recessive and causes isolated ACTH deficiency. Mutations in this gene account for 2/3 of isolated ACTH deficiency cases. The NFKB2 p.D865G mutation is heterozygous in a patient with recurrent infections and isolated ACTH deficiency. NFKB2 mutations are a rare cause of ACTH deficiency, and they can be associated with loss of other pituitary hormones in some cases. However, all reported cases are heterozygous.<br /> The developmental studies of organoid differentiation are rigorous in that 200 organoids were generated for each hiPSC line, and 3-10 organoids were analyzed for each time point and genotype. Differentiation analysis relied on both RNA transcript measurements and immunohistochemistry of cleared organoids using light sheet microscopy. Multiple time points were examined, including seven times for gene expression at the RNA level and two times in the later stages of differentiation for IHC.<br /> TBX19 deficient organoids exhibit reduced levels of PITX1, LHX3, and POMC (ACTH precursor) expression at the RNA and IHC level, and there are fewer corticotropes in the organoids, as ascertained by POMC IHC.<br /> The NFKB2 deficient organoids have normal expression of the early pituitary transcription factor HESX1, but reduced expression of PITX2, LHX3 and POMC. Because there is no immune component in the organoid, this shows that NFKB2 mutations can affect corticotrope differentiation to produce POMC. RNA sequencing analysis of the organoids reveals potential downstream targets of NFKB2 action, including a potential effect on epithelial to mesenchymal like transition and selected pituitary and hypothalamic transcription factors and signaling pathways.

It is important to note that all NFKB2 patients are heterozygous for what appear to be dominant negative mutations that affect protein cleavage and nuclear localization of processed protein as homo or heterodimers. The organoids are homozygous for this mutation.

Weakness:

There could be variation between individual iPSC lines that is unrelated to the genetically engineered change. The work would be strengthened by analysis of independently engineered clones or by correcting the engineered clone to wild type and demonstrating that the phenotypic effects are reversed. The authors do check for off target effects of the guide RNA at predicted sites using WGS.

Reviewer #2 (Public review):

Summary:

The primary goal of this study was to identify the transport pathway that is responsible for the release of dietary citrate from enterocytes into blood across the basolateral membrane.

Strengths:

The transport pathway responsible for the entry of dietary citrate into enterocytes was already known, but the transporter responsible for the second step remained unidentified. The studies presented in this manuscript identify SLC35G1 as the most likely transporter that mediates the release of absorbed citrate from intestinal cells into the serosal side. This fills an important gap in our current knowledge on the transcellular absorption of dietary citrate. The exclusive localization of the transporter in the basolateral membrane of human intestinal cells and the human intestinal cell line Caco-2 and the inhibition of the transporter function by chloride support this conclusion.

Weaknesses:

(i) The substrate specificity experiments have been done with relatively low concentrations of potential competing substrates, considering the relatively low affinity of the transporter for citrate. Given that NaDC1 brings in not only citrate as a divalent anion and also other divalent anions such as succinate, it is possible that SLC35G1 is responsible for the release of not only citrate but also other dicarboxylates. However the substrate specificity studies show that the dicarboxylates tested did not compete with citrate, meaning that SLC35G1 is selective for the citrate (2-), but this conclusion might be flawed because of the low concentration of the competing substrates used in the experiment. Furthermore, the apical NaDC1 is not selective for citrate; in fact, it transports citrate with a much lower affinity than it transports dicarboxylates such as succinate. If what the authors suggest that SLC35G1 is selective for citrate is correct, there must be another transporter for the efflux of dicarboxylates. The authors should have performed a dose-response experiment for the dicarboxylates tested as potential substrates before making the conclusion that SLC35G1 is selective for citrate.

(ii) The authors have used MDCK cells for assessment of the transcellular transfer of citrate via SLC35G1, but it is not clear whether this cell line expresses NaDC1 in the apical membrane as the enterocytes do. Even though the authors expressed SLC35G1 ectopically in MDCK cells and showed that the transporter localizes to the basolateral membrane, the question as to how citrate actually enters the apical membrane for SLC35G1 in the other membrane to work remains unanswered.

(iii) The role of chloride in the efflux of citrate remains not evaluated in detail. Similarly, the potential role of membrane potential in the transport function of SLC35G1 remains unknown. Since the SLC35G1-mediated uptake appears to be similar in the presence and absence of potassium, the authors argue that membrane potential has no role in the transport process. Since it is proposed that the divalent citrate is the substrate for the transporter, it is difficult to reconcile with the conclusion that the membrane potential has no impact on the transport process, especially given the fact that no other exchangeable anion has been shown or suggested. Even if chloride is the potential exchangeable anion, it still begs the question as to the stoichiometry of citrate:chloride if membrane potential plays no role. Obviously, additional work is needed to figure out the actual transport mechanism for SLC35G1.

Reviewer #2 (Public Review):

Summary:

Galanti et al investigate genetic variation in plant pest resistance using non-target reads from whole-genome sequencing of 207 field lines spontaneously colonized by aphids and mildew. They calculate significant differences in pest DNA load between populations and lines, with heritability and correlation with climate and glucosinolate content. By genome-wide association analyses they identify known defence genes and novel regions potentially associated with pest load variation. Additionally, they suggest that differential methylation at transposons and some genes are involved in responses to pathogen pressure. The authors present in this study the potential of leveraging non-target sequencing reads to estimate plant biotic interactions, in general for GWAS, and provide insights into the defence mechanisms of Thlaspi arvense.

Strengths:

The authors ask an interesting and important question. Overall, I found the manuscript very well-written, with a very concrete and clear question, a well-structured experimental design, and clear differences from previous work. Their important results could potentially have implications and utility for many systems in phenotype-genotype prediction. In particular, I think the use of unmapped reads for GWAS is intriguing.

Comments on revised version:

The revisions to the manuscript have significantly enhanced its clarity and scientific rigor. Methodological clarifications, especially regarding the normalization of read counts, now provide a stronger foundation for the presented results. Statistical enhancements, including more robust methods for controlling population structure and refined GWAS approaches, have solidified the reliability of the findings, effectively linking genetic variants and epigenetic modifications to pest loads. The discussion section has been improved to offer a more cautious interpretation of the correlations between transposable element (TE) methylation and pathogen load, emphasizing the associative nature of these findings. Additionally, increased transparency in data handling, particularly the treatment of ambiguous reads, has significantly reduced potential biases. These improvements have made the manuscript better suited to the readership, providing clearer insights into the genomic and epigenetic underpinnings of plant pest resistance.

Reviewer #3 (Public review):

Summary:

After the previous identification that the Streptococcus agalactiae MprF enzyme can synthesize also lysyl-glucosyl-diacylglycerol (Lys-Glc-DAG), besides the already known lysyl-phosphatidylglycerol (Lys-PG), the authors aim for the current manuscript was to investigate the molecular determinants of MprF lipid substrate specificity, for which MprF from a variety of bacterial species were used. This then led to the coincidental discovery of a novel lipid species.

The manuscript is well constructed and easy to follow, especially taking into account the multidisciplinary aspect of it (computational machine learning combined with lipid biology). The Restricted Boltzmann machines (RBM) approach enables the successful, although not perfect, classification and categorization of MprF activity. The computational approach is validated by lab experiments in which LC-MS analysis reveals the specific activity of the lipid synthesizing enzymes. In a few cases lipid synthesis activity is completely absent. Due to the lack of protein expression data, it is unclear if this is caused by enzyme inactivity or the overall absence of enzyme.

Overall, the authors largely achieved their goals, as the applied RBM approach led to specific sequence determinants in MprF enzymes that could categorize the specificity of these enzymes. The experimental data could largely confirm this categorization, although a stronger connection between synthesized lipids and enzyme activity would have further strengthened the observations.

The work now focuses only on MprF enzymes, but could in theory be expanded to other categories of lipid synthesizing enzymes. In other words, the RBM approach could have an impact on the lipid synthesis field, if it would be a tool that is easy applicable. Moreover, the lipids synthesized by MprF (Lys-PG, but also other cationic lipids) play an important role in the bacterial resistance against certain antibiotics.

Reviewer #2 (Public review):

Summary:

We have known for some time that neural progenitors in the cerebral cortex switch their output from cortical neurons to glia at late embryonic stages, however little is known about how this switch is regulated at the molecular level. Bose et al present a convincing set of findings, demonstrating that the transcription factor Foxg1 plays a key role in this process, mediated through FGF signalling. Foxg1 cell-autonomously inhibits gliogenesis in progenitor cells (thereby promoting neuronal identity), and lower Foxg1 expression in postnatal neurons leads to increased expression of FGF ligand, promoting glial development from nearby progenitors.

Strengths:

The study is very well designed, having a systematic, thorough, and logical approach. The data is convincing. The authors make full use of a range of existing transgenic strains, published 'omics data, and elegant genetic approaches such as MADM. This combination of approaches is particularly rigorous, lending significant weight to the study. The manuscript is well-written, clear, and easy to follow.

Weaknesses:

It wasn't clear to me why the authors chose postnatal day 14 to examine the effects of Foxg1 deletion at E15 - this is a long time window, giving time for indirect consequences of Foxg1 deletion to influence development and thereby potentially complicating the interpretation of findings. For example, the authors show that there is no increased proliferation of astrocytes or death of neurons lacking Foxg1 shortly after cre-mediated deletion, but it remains formally possible (if perhaps unlikely) that these processes could be affected later during the time window. The rationale underlying the choice of this time point should be explained.

I don't agree with the statement in the very last sentence of the results section that "neurogenesis is not possible in the absence of [Foxg1]" as there are multiple reports in the literature demonstrating the presence of neurons in Foxg1-/- mice (eg: Xuan et al., 1995; Hanashima et al., 2002, Martynoga et al., 2005, Muzio and Mallamaci 2005). Perhaps the statement refers specifically to late-born cortical neurons. This point also arises in the discussion section.

Impact

This manuscript identifies a previously unknown role for Foxg1 in forebrain development and a mechanism underlying the neurogenic-to-gliogenic switch that occurs at late embryonic stages of cortex development. These findings will stimulate further research to uncover more details of how this important switch is controlled and may provide useful insight into some of the symptoms experienced by children with FOXG1 Syndrome.

Reviewer #2 (Public review):

Summary:

Cell cycle duration and cell fate choice are critical to understanding the cellular plasticity of neoblasts in planarians. In this study, Tamar et al. integrated experimental and computational approaches to simulate a model for neoblast behaviors during colony expansion.

Strengths:

The finding that "arresting differentiation into specific lineages disrupts neoblast proliferative capacities without inducing compensatory expression of other lineages" is particularly intriguing. This concept could inspire further studies on pluripotent stem cells and their application for regenerative biology.

Weaknesses:

However, the absence of a cell-cell feedback mechanism during colony growth and the likelihood of the difference needs to be clarified. Is there any difference in interpreting the results if this mechanism is considered? More explanation and discussion should be included to distinguish the stages controlled by the one-step model from those discussed in this study. Although hnf-4 and foxF have been silenced together to validate the model, a deeper understanding of the tgs-1+ cell type and the non-significant reduction of tgs-1+ neoblasts in zfp-1 RNAi colonies is necessary, considering a high neural lineage frequency.

Reviewer #2 (Public review):

This paper examines how structural plasticity in neural circuits, particularly in dopaminergic systems, is regulated by Drosophila neurotrophin-2 (DNT-2) and its receptors, Toll-6 and Kek-6. The authors show that these molecules are critical for modulating circuit structure and dopaminergic neuron survival, synaptogenesis, and connectivity. They show that loss of DNT-2 or Toll-6 function leads to loss of dopaminergic neurons, dendritic arborization, and synaptic impairment, whereas overexpression of DNT-2 increases dendritic complexity and synaptogenesis. In addition, DNT-2 and Toll-6 modulate dopamine-dependent behaviors, including locomotion and long-term memory, suggesting a link between DNT-2 signaling, structural plasticity, and behavior.

A major strength of this study is the impressive cellular resolution achieved. By focusing on specific dopaminergic neurons, such as the PAM and PPL1 clusters, and using a range of molecular markers, the authors were able to clearly visualize intricate details of synapse formation, dendritic complexity, and axonal targeting within defined circuits. Given the critical role of dopaminergic pathways in learning and memory, this approach provides a good opportunity to explore the role of DNT-2, Toll-6, and Kek-6 in experience-dependent structural plasticity. However, despite the promise in the abstract and introduction of the paper, the study falls short of establishing a direct causal link between neurotrophin signaling and experience-induced plasticity.

Simply put, this study does not provide strong evidence that experience-induced structural plasticity requires DNT-2 signaling. To support this idea, it would be necessary to observe experience-induced structural changes and demonstrate that downregulation of DNT-2 signaling prevents these changes. The closest attempt to address this in this study was the artificial activation of DNT-2 neurons using TrpA1, which resulted in overgrowth of axonal arbors and an increase in synaptic sites in both DNT-2 and PAM neurons. However, this activation method is quite artificial, and the authors did not test whether the observed structural changes were dependent on DNT-2 signaling. Although they also showed that overexpression of DNT-2FL in DNT-2 neurons promotes synaptogenesis, this phenotype was not fully consistent with the TrpA1 activation results (Figures 5C and D).

In conclusion, this study demonstrates that DNT-2 and its receptors play a role in regulating the structure of dopaminergic circuits in the adult fly brain. However, it does not provide convincing evidence for a causal link between DNT-2 signaling and experience-dependent structural plasticity within these circuits.

Reviewer #2 (Public review):

Summary:

In their manuscript, "Mitochondrial calcium modulates odor-mediated behavioural plasticity in C. elegans", Lee et al. aim to link a mitochondrial calcium transporter to higher-order neuronal functions that mediate memory and aversive learning behaviours. The authors characterise the role of the mitochondrial calcium uniporter, and a specific subunit of this complex, MCU-1, within a single chemosensory neuron (AWCOFF) during aversive odor learning in the nematode. By genetically manipulating mcu-1 as well as using pharmacological activators and blockers of MCU activity, the study presents compelling evidence that the activity of this individual mitochondrial ion transporter in AWCOFF is sufficient to drive animal behaviour through aversive memory formation. The authors show that perturbations to mcu-1 and MCU activity prevent aversive learning to several chemical odors associated with food absence. The authors propose a model, experimentally validated at several steps, whereby an increase in MCU activity during odor conditioning stimulates mitochondrial calcium influx and an increase in mitochondrial reactive oxygen species (mtROS) production, triggering the release of the neuropeptide NLP-1 from AWC, all of which are required to mediate future avoidance behaviour of the chemical odor.

Strengths:

Overall, the authors provided robust evidence that mitochondrial function, mediated through MCU activity, contributes to behavioural plasticity. They also demonstrated that ectopic MCU activation or mtROS during odor exposure could accelerate learning. This is quite profound, as it highlights the importance of mitochondrial function in complex neuronal processes beyond their general roles in the development and maintenance of neurons through energy homeostasis and biosynthesis, amongst their other cell-non-specific roles.

Weaknesses:

While the manuscript is generally robust, there are some concerns that should be addressed to improve the strength of the proposed model:

(1) Throughout the manuscript, it is implied that MCU activation caused by odor conditioning changes mitochondrial calcium levels. However, there is no direct experimental evidence of this. For example, the authors write on p.10 "This shows that H2O2 production occurs downstream of MCU activation and calcium influx into the mitochondria", and on p. 11, the statement that prolonged exposure to odors causes calcium influx. Because this is a key element of the proposed model, experimental evidence would be required to support it.

(2) Some controls missing, e.g. a heat-shock-only control in WT and mcu-1 (non-transgenic) background in Figure 1h is required to ensure the heat-shock stress does not interfere with odor learning.

(3) Lee et al propose that mcu-1 is required at the adult stage to accomplish odor learning because inducing mcu-1 expression at larval stages did not rescue the phenotype of mcu-1 mutants during adulthood. However, the requirement of MCU for odor learning was narrowed down to a 15' window at the end of odor conditioning (Figure 5c). Is it possible that MCU-1 protein levels decline after larval induction so that MCU-1 is no longer present during adulthood when odor conditioning is performed?

(4) There is a limited learning effect observable after 30 minutes, and a very pronounced effect in all animals after 90 minutes. The authors very carefully dissect the learning mechanism at 60 minutes of exposure and distinguish processes that are relevant at 60 minutes from those important at 30 minutes. Some explanation or speculation as to why the processes crucial at the 60-minute mark are redundant at 90 minutes of exposure would be important.

(5) Given the presumably ubiquitous function of mcu-1/MCU in mitochondrial calcium homeostasis, it is remarkable that its perturbation impacts only a very specific neuronal process in AWC at a very specific time. The authors should elaborate on this surprising aspect of their discovery in the discussion.

(6) Associated with the above comment, it remains possible that mcu-1 is required in coelomocytes for their ability to absorb NLP-1::Venus (Figure 3B), and the AWC-specific role of mcu-1 for this phenotype should be determined.

Reviewer #2 (Public review):

In this study, the authors aim to investigate habituation, the phenomenon of increasing reduction in activity following repeated stimuli, in the context of its information-theoretic advantage. To this end, they consider a highly simplified three-species reaction network where habituation is encoded by a slow memory variable that suppresses the receptor and therefore the readout activity. Using analytical and numerical methods, they show that in their model the information gain, the difference between the mutual information between the signal and readout after and before habituation, is maximal for intermediate habituation strength. Furthermore, they demonstrate that the Pareto front corresponds to an optimization strategy that maximizes the mutual information between signal and readout in the steady state, minimizes some form of dissipation, and also exhibits similar intermediate habituation strength. Finally, they briefly compare predictions of their model to whole-brain recordings of zebrafish larvae under visual stimulation.

The author's simplified model might serve as a solid starting point for understanding habituation in different biological contexts as the model is simple enough to allow for some analytic understanding but at the same time exhibits all basic properties of habituation in sensory systems. Furthermore, the author's finding of maximal information gain for intermediate habituation strength via an optimization principle is, in general, interesting. However, the following points remain unclear or are weakly explained:

(1) Is it unclear what the meaning of the finding of maximal information gain for intermediate habituation strength is for biological systems? Why is information gain as defined in the paper a relevant quantity for an organism/cell? For instance, why is a system with low mutual information after the first stimulus and intermediate mutual information after habituation better than one with consistently intermediate mutual information? Or, in other words, couldn't the system try to maximize the mutual information acquired over the whole time series, e.g., the time series mutual information between the stimulus and readout?

(2) The model is very similar to (or a simplification of previous models) for adaptation in living systems, e.g., for adaptation in chemotaxis via activity-dependent methylation and demethylation. This should be made clearer.

(3) It remains unclear why this optimization principle is the most relevant one. While it makes sense to maximize the mutual information between stimulus and readout, there are various choices for what kind of dissipation is minimized. Why was \delta Q_R chosen and not, for instance, \dot{\Sigma}_int or the sum of both? How would the results change in that case? And how different are the results if the mutual information is not calculated for the strong stimulation input statistics but for the background one?

(4) The comparison to the experimental data is not too strong of an argument in favor of the model. Is the agreement between the model and the experimental data surprising? What other behavior in the PCA space could one have expected in the data? Shouldn't the 1st PC mostly reflect the "features", by construction, and other variability should be due to progressively reduced activity levels?

Reviewer #2 (Public review):

Summary:

By measuring intracellular changes in membrane voltage from a single neuron of the medulla the authors describe a method for determining the balance of excitatory and inhibitory synaptic drive onto a single neuron within this important brain region.

Strengths:

This approach could be valuable in describing the microcircuits that generate rhythms within this respiratory control centre. This method could more generally be used to enable microcircuits to be studied without the need for time-consuming anatomical tracing or other more involved electrophysiological techniques.

Weaknesses:

This approach involves assuming the reversal potential that is associated with the different permeant ions that underlie the excitation and inhibition as well as the application of Ohms law to estimate the contribution of excitation and inhibitory conductance. My first concern is that this approach relies on a linear I-V relationship between the measured voltage and the estimated reversal potential. However, open rectification is a feature of any I-V relationship generated by asymmetric distributions of ions (see the GHK current equation) and will therefore be a particular issue for the inhibition resulting from asymmetrical Cl- ion gradients across GABA-A receptors. The mixed cation conductance that underlies most synaptic excitation will also generate a non-linear I-V relationship due to the inward rectification associated with the polyamine block of AMPA receptors. Could the authors please speculate what impact these non-linearities could have on results obtained using their approach?

This approach has similarities to earlier studies undertaken in the visual cortex that estimated the excitatory and inhibitory synaptic conductance changes that contributed to membrane voltage changes during receptive field stimulation. However, these approaches also involved the recording of transmembrane current changes during visual stimulation that were undertaken in voltage-clamp at various command voltages to estimate the underlying conductance changes. Molkov et al have attempted to essentially deconvolve the underlying conductance changes without this information and I am concerned that this simply may not be possible. The current balance equation (1) cited in this study is based on the parallel conductance model developed by Hodgkin & Huxley. However, one key element of the HH equations is the inclusion of an estimate of the capacitive current generated due to the change in voltage across the membrane capacitance. I would always consider this to be the most important motivation for the development of the voltage-clamp technique in the 1930's. Indeed, without subtraction of the membrane capacitance, it is not possible to isolate the transmembrane current in the way that previous studies have done. In the current study, I feel it is important that the voltage change due to capacitive currents is taken into consideration in some way before the contribution of the underlying conductance changes are inferred.

Studies using acute slicing preparations to examine circuit effects have often been limited to the study of small microcircuits - especially feedforward and feedback interneuron circuits. It is widely accepted that any information gained from this approach will always be compromised by the absence of patterned afferent input from outside the brain region being studied. In this study, descending control from the Pons and the neocortex will not be contributing much to the synaptic drive and ascending information from respiratory muscles will also be absent completely. This may not have been such a major concern if this study was limited to demonstrating the feasibility of a methodological approach. However, this limitation does need to be considered when using an approach of this type to speculate on the prevalence of specific circuit motifs within the medulla (Figure 4). Therefore, I would argue that some discussion of this limitation should be included in this manuscript.

Reviewer #2 (Public review):

Summary:

This study uses in vivo multimodal high-resolution imaging to track how microglia and neutrophils respond to light-induced retinal injury from soon after injury to 2 months post-injury. The in vivo imaging finding was subsequently verified by an ex vivo study. The results suggest that despite the highly active microglia at the injury site, neutrophils were not recruited in response to acute light-induced retinal injury.

Strengths:

An extremely thorough examination of the cellular-level immune activity at the injury site. In vivo imaging observations being verified using ex vivo techniques is a strong plus.

Weaknesses:

This paper is extremely long, and in the perspective of this reviewer, needs to be better organized.

Study weakness: though the finding prompts more questions and future studies, the findings discussed in this paper are potentially important for us to understand how the immune cells respond differently to different severity levels of injury.

Reviewer #2 (Public review):

In the manuscript by Kim et al titled, "Characterizing the Spatial Distribution of Dendritic RNA at Single Molecule Resolution," the authors perform multiplex single-molecule FISH in cultured neurons, along with analysis and modeling, to show the spatial features, including differing mRNA densities between soma and dendrites, dendritic length-related distributions and clustering, of multiple mRNAs in dendrites. Although the clustering analyses and modeling are intriguing and offer previously underappreciated spatial association within and across mRNA molecules, the data is difficult to interpret and the conclusions lack novelty in their current form. There is a need for a stronger rationale as to why the methodology employed in the manuscript is better suited to characterize the clustering of mRNA in dendrites compared to previously published works and how such clustering or declustering can affect dendritic/neuronal function.

(1) Validation of mRNA labeling, detection, and quantification is necessary. Single-molecule fluorescence in situ hybridization (smFISH) is the gold standard to detect RNA inside cells. The method utilizes multiple fluorescent probes (~48) designed to hybridize along a single RNA, resulting in a population of diffraction-limited fluorescent puncta with varying intensities. A histogram of cytoplasmic smFISH puncta intensities should reveal a normally distributed population with a single major peak, where the upper and lower tails indicate the maximum probe binding and the lower detection limit, respectively. Once single molecule detection (and limits) have been established, smFISH should be performed for each gene individually to obtain ground truth of detection under identical experimentally-defined conditions using the same fluorophore. Total RNA counts from different probe combinations (Figure S1A) or total mRNA density (Figure 2A) is not sufficient to inform individual gene labeling efficiency or detection. It is difficult to interpret whether observed variabilities across different probe combinations are of significance. For example, the mRNA densities of Adap2 and Dtx3L in soma seem to vary even after normalization with the pixel area (Figure 2A).

Absolute counts and normalized counts for each gene detected should be included in the results or in supplementary data/table to provide the reader with a reference point for evaluation.

As a control, it is recommended to perform smFISH against beta-actin or aCaMKII, which are the two most abundant mRNA in dendrites, and serve as internal validation that the technique, detection, and quantification are consistent with previously published works.

(2) The rationale for single dendrite selection is unclear. To suggest that dendrite length, as a feature of dendritic morphology, may affect mRNA localization in dendrites, the authors manually selected segments of dendrites that have no branching or overlap, 'biased for shorter dendrites,' resulting in a subset of dendritic segments that changes mRNA distribution in raw distances (Figure S3A) into the normalized distance (Figure 4A). As a result, the distribution appears to convert from a monotonic- or exponential-decay to a more even distribution of mRNA (plateau). The rationale for this normalization is unclear, as manual curation of dendritic segments can incorporate experimenter bias. Moreover, the inclusion of short dendritic segments can stretch out their mRNA distributions following distance normalization which can give the appearance of an even distribution of mRNAs when aggregated.

Next, the authors use pairwise Jensen-Shannon distance cluster analysis to identify 4 different patterns of clustering among mRNAs. Although the patterns are quite intriguing, the distributions of mRNA clusters were i) difficult to interpret and ii) compared to Fonkeu et al (2019) protein distribution is not a sufficient explanation for the observed clustering. For example, the clustering patterns (C1-4) are quite striking and even if the authors' analyses were an improvement in identifying mRNA clustering in dendrites, the authors need to provide better justification or modeling on what role such clustering can play on dendritic function or cellular physiology. This is important and necessary as the authors are suggesting that their analysis is different from mRNA distributions previously observed or modeled by Buxbaum et al (2014) and Fonkeu et al (2019), respectively.<br /> Of note, the identity-independent and dendritic length-dependent aspect of spatial distributions of mRNAs is striking (Figure S3E-F, Figure 4), and this length-related feature is one of the major take-home points in the first part of the manuscript. However, it is evident that some mRNAs (e.g. Adap2 and Dtx3L) or probe combinations (e.g. Colec12-Adap2-Nsmf) disproportionally make up the mRNA distribution clusters (Figure 4D and Figure S3F). It seems plausible that the copy numbers of mRNAs can differentially affect clusters' distribution patterns. Appropriate statistical tests among the cluster groups, therefore, will help to strengthen the interpretation of the results provided in the supplementary figures (Figures S3E and S3F).

(3) It is not clear how Figure 5 GradCAM analysis helps the point that the authors put forth in previous sections or forthcoming sections. Unless this section and figure are more effectively linked to the general theme of the paper - the morphological features as a determinant of mRNA distribution or clustering of mRNA molecules, it may be included in the supplementary figure section.

(4) Clustering of mRNA remains an exception rather than the rule. From their high-resolution triple smFISH data, the authors make some interesting findings regarding colocalization in dendrites. Among the six genes tested, the authors found higher incidents of colocalization between pair-wise genes (up to 23%) than previously reported (5-10%). Also, they report higher levels of colocalization within the same gene (17-23%) than previously reported (5-10%). First, to better evaluate this increased colocalization efficiency overall, the histograms of smFISH puncta intensity are necessary (as stated in 1) to determine whether a second peak is present in the population. Second, even though 23% is higher than previously reported, it remains that 77% do not colocalize and does not suggest that colocalization is the rule but remains the exception. Given the results in Table 1, it is likely that the increased colocalization could be a gene-specific effect and not transcriptome-wide as the majority of values between genes are below 10%, consistent with previous findings. Third, labeling of a control gene (i.e. b-actin or aCaMKII) would provide higher confidence that the detection and colocalization comparisons are consistent with previous findings.

It is recommended to refrain from concluding that mRNA is 'co-transported' from smFISH results. Typically co-transport is best identified through observations in live cells where two fluorescent particles of different colors are moving together. Although stationary particles positioned in close proximity to one another could potentially be co-transported, there has been very little evidence to support this.

The use of Ripley's K-function is an interesting way to look at clustering neighborhoods within a single or pairwise sets of genes. Previous studies from the Singer group have looked at mRNA clustering and have observed that mRNA in living cells tends to cluster within a 6-micron range for b-actin and for both b-actin and Arc after local stimulation. What was intriguing in the results in Figure 7 was that there was an exclusion zone 2-4 microns away from the area of colocalization that may suggest that mRNA are able to avoid over-clustering and maintain an even distribution throughout the dendrite--perhaps with a goal of not devoting too many resources (mRNA) to a single dendritic area. Modeling how mRNAs avoid over-clustering to a specific 2-micron segment of dendrites could provide an explanation on how dendrites can respond to multiple or simultaneous synaptic activity at different sites along the same dendrite.

Reviewer #2 (Public review):

Summary:

The authors present an intriguing study utilizing datasets from spinal cord injury (SCI) research to identify potential microglial genes involved in SCI-induced neuronal damage. They identify that inhibiting TREM2 and enhancing the TGF-b signal pathway can inhibit reactive microglia-mediated neuroinflammation. Microglia transplantation using iPSC-derived microglia could also be beneficial for SCI recovery.

Strengths:

This research aims to identify potential genes and signaling pathways involved in microglia-mediated inflammation in spinal cord injury (SCI) models. Meanwhile, analyzing transplanted microglia gene expression provides an extra layer of potential in SCI therapy. The approach represents a good data mining strategy for identifying potential targets to combat neurological diseases.

Weaknesses:

Microglial gene expression patterns may vary significantly between these models. Without proper normalization or justification, combining these datasets to draw conclusions is problematic. Moreover, other factors also need to be considered, like the gender of the microglia source. Are there any gender differences? How were the iPSC-derived microglia generated? Different protocols may affect microglia gene expression.

While the concept is interesting, the data presented in this study appears preliminary. Without further experiments to support their findings, the conclusions are not convincing.

Reviewer #2 (Public review):

Summary:

In this study, Barzo and colleagues aim to establish an appraisal for the development of basal electrophysiology of human layer 2/3 pyramidal cells across life and compare their morphological features at the same ages.

Strengths:

The authors have generated recordings from an impressive array of patient samples, allowing them to directly compare the same electrophysiological features as a function of age and other biological features. These data are extremely robust and well organised.

Weaknesses:

The use of spine density and shape characteristics is performed from an extremely limited sample (2 individuals). How reflective these data are of the population is not possible to interpret. Furthermore, these data assume that spines fall into discrete types - which is an increasingly controversial assumption.

Many data are shown according to somewhat arbitrary age ranges. It would have been more informative to plot by absolute age, and then perform more rigourous statistics to test age-dependent effects.

Overall, the authors achieve their aims by assessing the physiological and morphological properties of human L2/3 pyramidal neurons across life. Their findings have extremely important ramifications for our understanding of human life and implications for how different neuronal properties may influence neurological conditions.

Reviewer #2 (Public review):

Summary:

This is a clear and systematic study of trial history influences on the performance of monkeys in a target selection paradigm. The primary contribution of the paper is to add a twist in which the target information is revealed after, rather than before, the cue to make a foveating eye movement. This twist results in a kind of countermanding of an earlier "uninformed" saccade plan by a new one occurring right after the visual information is provided. As with countermanding tasks in general, time now plays a key factor in the success of this task, and it is time that allows the authors to quantitatively assess the parametric influences of things like previous target location, previous target identity, and previous correctness rate on choice performance. The results are logical and consistent with the prior literature, but the authors also highlight novelties in the interpretation of prior-trial effects that they argue are enabled by the use of their paradigm.

Strengths:

Careful analysis of a multitude of variables influencing behavior

Weaknesses:

Results appear largely confirmatory.

Reviewer #2 (Public review):

Summary:

The work presented in the manuscript by Tran et al deals with bacterial evolution in the presence of bacteriophage. Here, the authors have taken three methicillin-resistant S. aureus strains that are also resistant to beta-lactams. Eventually, upon being exposed to phage, these strains develop beta-lactam sensitivity. Besides this, the strains also show other changes in their phenotype such as reduced binding to fibrinogen and hemolysis.

Strengths:

The experiments carried out are convincing to suggest such in vitro development of sensitivity to the antibiotics. Authors were also able to "evolve" phage in a similar fashion thus showing enhanced virulence against the bacterium. In the end, authors carry out DNA sequencing of both evolved bacteria and phage and show mutations occurring in various genes. Overall, the experiments that have been carried out are convincing.

Weaknesses:

Although more experiments are not needed, additional experiments could add more information. For example, the phage gene showing the HTH motif could be reintroduced in the bacterial genome and such a strain can then be assayed with wildtype phage infection to see enhanced virulence as suggested. At least one such experiment proves the discoveries regarding the identification of mutations and their outcome. Secondly, I also feel that authors looked for beta-lactam sensitivity and they found it. I am sure that if they look for rifampicin resistance in these strains, they will find that too. In this case, I cannot say that the evolution was directed to beta-lactam sensitivity; this is perhaps just one trait that was observed. This is the only weakness I find in the work. Nevertheless, I find the experiments convincing enough; more experiments only add value to the work.

Reviewer #2 (Public review):

The authors tested a dietary intervention focused on improving meal regularity. Participants first utilized a smartphone application to track participants' meal frequencies, participants were then asked to restrict their meal intake to times when they most often eat to enhance meal regularity for six weeks, resulting in significant weight loss despite supposedly no changes in caloric intake.

While the concept is appealing, and the use of a smartphone app in participants' typical everyday environment to regularize food intake is interesting, significant weaknesses severely limit the value of the study due to a lack of rigor, such as the reliance on self-reported food intake which has been discredited in the field. The study's major conclusions are insufficiently supported, particularly that weight loss occurred even though food intake supposedly is not altered. This intervention may merely represent another restrictive diet among countless others that all seem to work for a few weeks to months resulting in a few pounds of weight loss

(1) Unreliable method of caloric intake

The trial's reliance on self-reported caloric intake is problematic, as participants tend to underreport intake. For example, as cited in the revised manuscript, the NEJM paper (DOI: 10.1056/NEJM199212313272701) reported that some participants underreported caloric intake by approximately 50%, rendering such data unreliable and hence misleading. More rigorous methods for assessing food intake should have been utilized. Further, the control group was not asked to restrict their diet in any way, and hence, to do that in the treatment group may be sufficient to reduce caloric intake and weight loss. Merely acknowledging the unreliability of self-reported caloric intake is insufficient, as it still leaves the reader with the impression that there is no change in food intake when, in reality, we actually have no idea if food intake was altered. A more robust approach to assessing food intake is imperative. Even if a decrease in caloric intake is observed through rigorous measurement, as I am convinced that a more rigorous study would unveil testing this paradigm, this intervention may merely represent another restrictive diet among countless others that show that one may lose weight by going on a diet. Seemingly, any restrictive diet works for a few months.

(2) Lack of objective data regarding circadian rhythm

The assessment of circadian rhythm using the MCTQ, a self-reported measure of chronotype, is unreliable, and it is unclear why more objective methods like actigraphy was not used.

In the revised version, the authors emphasize these limitations in the manuscript. The study's major conclusions are insufficiently supported, in particular, that weight loss occurred even though food intake supposedly is not altered and that circadian rhythm was improved.

Reviewer #2 (Public review):

Chambers et al. (2024) present a systematic and unbiased approach to explore the evolutionary potential of the kinase domain of the human antiviral protein kinase R (PKR) to evade inhibition by a poxviral antagonist while maintaining one of its essential functions.

The authors generated a library of 426 single-nucleotide polymorphism (SNP)-accessible non-synonymous variants of PKR kinase domain and used a yeast-based heterologous virus-host system to assess PKR variants' ability to escape antagonism by the vaccinia virus pseudo-substrate inhibitor K3. The study identified determinant sites in the PKR kinase domain that harbor K3-resistant variants, as well as sites where variation leads to PKR loss of function. The authors found that multiple K3-resistant variants are readily available throughout the domain interface and are enriched at sites under positive selection. They further found some evidence of PKR resilience to viral antagonist diversification. These findings highlight the remarkable adaptability of PKR in response to viral antagonism by mimicry.

Significance of the findings: The findings are important with implications to various fields, including evolutionary biology, virus-host interfaces, genetic conflicts, antiviral immunity.

Strength of the evidence: Convincing methodology using state-of-the-art mutational scanning approach in an elegant and simple setup to address important challenges in virus-host molecular conflicts and protein adaptations.

Strengths

Systematic and Unbiased Approach: The study's comprehensive approach to generating and characterizing a large library of PKR variants provides valuable insights into the evolutionary landscape of PKR kinase domain. By focusing on SNP-accessible variants, the authors ensure the relevance of their findings to naturally occurring mutations.<br /> Identification of Key Sites: The identification of specific sites in the PKR kinase domain that confer resistance or susceptibility to a poxvirus pseudosubstrate inhibition is a significant contribution.<br /> Evolutionary Implications: The authors performed meticulous comparative analyses throughout the study between the functional variants from their mutagenesis screen ("prospective") and the evolutionarily-relevant past adaptations ("retrospective").<br /> Experimental Design: The use of a yeast-based assay to simultaneously assess PKR capacity to induce cell growth arrest and susceptibility/resistance to various VACV K3 alleles is an efficient approach. The combination of this assay with high-throughput sequencing allows for the rapid characterization of a large number of PKR variants.

Areas of improvement

Validation of the screen: In the revised version, the authors now provide the results of two independent experiments in a complete yeast growth assay on a handful of candidates to control the screen's results. This strengthens the direct findings from the screen. It would strengthen the study to complement this validation by another method to assess PKR functions; for example, in human PKR-KO cells, because results between yeast and human cells can differ. These limitations are now acknowledged in the revised version.<br /> Evolutionary Data: Beyond residues under positive selection, the screen allows the authors to also perform a comparative analysis with PKR residues under purifying selection. Because they are assessing one of the most conserved ancestral functions of PKR (i.e. cell translation arrest), it may also be of interest to discuss these highly conserved sites. The authors now discuss the implications for the conserved residues.<br /> Mechanistic insights and viral diversity: While the study identifies key sites and residues involved in vaccinia K3 resistance, it could benefit from further investigation into the underlying molecular mechanisms and the diversity of viral antagonists. The authors have now acknowledged these limitations in the Discussion and updated the manuscript to be more specific. These exciting research avenues will be the objectives of a next study.

Overall Assessment

The systematic approach, identification of key sites, and evolutionary implications are all notable strengths. While there is room for a stronger validation of the functions and further investigation into the mechanistic details and broader viral diversity, the findings are robust and already provide important advancements. The manuscript is well-written and clear, and the revised figures are informative and improved.

Reviewer #2 (Public review):

This work investigates the use of extracellular vesicles (EVs) in blood as a noninvasive 'liquid biopsy' to aid in differentiation of patients with pancreatic cancer (PDAC) from those with benign pancreatic disease and healthy controls, an important clinical question where biopsies are frequently non-diagnostic. The use of extracellular vesicles as biomarkers of disease has been gaining interest in recent history, with a variety of published methods and techniques, looking at a variety of different compositions ('the molecular cargo') of EVs particularly in cancer diagnosis (Shah R, et al, N Engl J Med 2018; 379:958-966).

This study adds to the growing body of evidence in using EVs for earlier detection of pancreatic cancer, identifying both new and known proteins of interest. Limitations in studying EVs in general include dealing with low concentrations in circulation and identifying the most relevant molecular cargo. This study provides validation of assaying EVs using the novel EVtrap method (Extracellular Vesicles Total Recovery And Purification), which the authors show to be more efficient than current standard techniques and potentially more scalable for larger clinical studies.

The strength of this study is in its numbers - the authors worked with a cohort of 124 cases, 93 of them which were PDAC samples, which considered large for an EV study (Jia, E et al. BMC Cancer 22, 573 (2022)). The benign disease group (n=20, between chronic pancreatitis and IPMNs) and healthy control groups (n=11) were relatively small, but the authors were not only able to identify candidate biomarkers for diagnosis that clearly stood out in the PDAC cohort, but also validate it in an independent cohort of 36 new subjects. Proteins they've identified as associated with pancreatic cancer over benign disease included PDCD6IP, SERPINA12 and RUVBL2. They were even able to identify a set of EV proteins associated with metastasis and poorer prognosis , which include the proteins PSMB4, RUVBL2 and ANKAR and CRP, RALB and CD55. Their 7-EV protein signature yielded an 89% prediction accuracy for the diagnosis of PDAC against a background of benign pancreatic diseases that is compelling and comparable to other studies in the literature (Jia, E. et al. BMC Cancer 22, 573 (2022)).

The limitations of this study are its containment within a single institution - further studies are warranted to apply the authors' 7-EV protein PRAC panel to multiple other cases at other institutions in a larger cohort.

Reviewer #2 (Public review):

In this work, the authors uncovered the effects of DNA dilution on E. coli, including a decrease in growth rate and a significant change in proteome composition. The authors demonstrated that the decline in growth rate is due to the reduction of active ribosomes and active RNA polymerases because of the limited DNA copy numbers. They further showed that the change in the DNA-to-volume ratio leads to concentration changes in almost 60% of proteins, and these changes mainly stem from the change in the mRNA levels.

Comments on revised version:

The authors have satisfyingly answered all of our questions.

Reviewer #2 (Public review):

The authors have conducted a valuable comparative analysis of perturbation responses in three nonlinear kinetic models of E. coli central carbon metabolism found in the literature. They aimed to uncover commonalities and emergent properties in the perturbation responses of bacterial metabolism. They discovered that perturbations in the initial concentrations of specific metabolites, such as adenylate cofactors and pyruvate, significantly affect the maximal deviation of the responses from steady-state values. Furthermore, they explored whether the network connectivity (sparse versus dense connections) influences these perturbation responses. The manuscript is reasonably well written.

Comments on revised version:

The authors have addressed my concerns to a large extent. However, a few minor issues remain, as listed below:

(1) The authors identified key metabolites affecting responses to perturbations in two ways: (i) by fixing a metabolite's value and (ii) by performing a sensitivity analysis. It would be helpful for the modeling community to understand better the differences and similarities in the obtained results. Do both methods identify substrate-level regulators? Is freezing a metabolite's dynamics dramatically changing the metabolic response (and if yes, which ones are so different in the two cases)? Does the scope of the network affect these differences and similarities?

(2) Regarding the issues the authors encountered when performing the sensitivity analysis, they can be approached in two ways. First, the authors can check the methods for computing conserved moieties nicely explained by Sauro's group (doi:10.1093/bioinformatics/bti800) and compute them for large-scale networks (but beware of metabolites that belong to several conserved pools). Otherwise, the conserved pools of metabolites can be considered as variables in the sensitivity analysis-grouping multiple parameters is a common approach in sensitivity analysis.

Reviewer #2 (Public review):

Summary:

The authors described cell type mapping was conducted for both WT and fracture types. Through this, unique cell populations specific to fracture conditions were identified. To determine these, the most undifferentiated cells were initially targeted using stemness-related markers and CytoTrace scoring. This led to the identification of SSPC differentiating into fibroblasts. It was observed that the fibroblast cell type significantly increased under fracture conditions, followed by subsequent increases in chondrocytes and osteoblasts.

Strengths:

This study presented the injury-induced fibrogenic cell (IIFC) as a characteristic cell type appearing in the bone regeneration process and proposed that the IIFC is a progenitor undergoing osteochondrogenic differentiation.

Comments on revised version:

The authors have thoroughly addressed the reviewer's comments and have conducted additional experiments.

Reviewer #3 (Public review):

Summary:

Landau et al. have submitted a manuscript describing for the first time that mammalian adenylyl cyclases can serve as membrane receptors. They have also identified the respective endogenouse ligands which act via AC membrane linkers to modify and control Gs-stimulated AC activity either towards enhancement or inhibition of ACs which is family and ligand-specific. Overall, they have used classical assays such as adenylyl cyclase and cAMP accumulation assays combined with molecular cloning and mutagenesis to provide exceptionally strong biochemical evidence for the mechanism of the involved pathway regulation.

Strengths:

The authors have gone the whole long classical way from having a hypothesis that ACs could be receptors to a series of MS studies aimed at ligand indentification, to functional studies of how these candidate substances affect the activity of various AC families in intact cells. They have used a large array of techniques with a paper having clear conceptual story and several strong lines of evidence.

Comments on revised version:

In general, the authors have addressed my comments satisfactorily apart from the suggestion to use a lower ISO concentration in their assay or at least to discuss this issue, cite relevant literature etc. Pending this small amendment I would to fine to proceed.

Reviewer #2 (Public review):

Summary:

This manuscript explores the role of Nrn1 in T cell tolerance. A previous study has demonstrated that Nrn1 is up-regulated in the Tfr fraction of Foxp3+ T regulatory cells. These authors now confirm expression of Nrn1 in iTregs as well as report here that Nrn1 is also greatly over-expressed in anergic CD4 T cells, and this is the stepping off point for this investigation.

Most remarkably, experiments show that anergy induction is defective when T cells cannot express Nrn1. Furthermore, differentiation to a Foxp3+ iTreg phenotype is inhibited in the absence of Nrn1, and the iTregs that do develop appear functionally defective. On the other hand, the differentiation and expansion of Teff cells appears to be enhanced following deletion of Nrn1. With such defects in anergy induction as well as dysregulated Treg and Teff cell survival and function, auto reactive effector T cell activation becomes unrestrained and Nrn1-/- mice are more susceptible to severe EAE development.

Strengths:

The characterizations of T cell Nrn1 expression both in vitro and in vivo are comprehensive and convincing. The author's use of both Nrn1-/- T cells as well as anti-Nrn1 neutralizing Ab to achieve similar results is a strength. The in vivo functional studies of anergy development, Treg suppression, and EAE development are also well performed and strengthen the notion that Nrn1 is an important regulator of CD4 responsiveness.

Weaknesses:

The major weakness of this study stems from a lack of a clear molecular mechanism involving Nrn1. Previous studies of Nrn1 have suggested its role as a soluble molecule involved in intracellular communication, perhaps influencing cellular ion channel function and/or triggering downstream NFAT and mTOR activation. However, a unique receptor for Nrn1 has not been discovered and it remains unclear whether it acts in a cell-intrinsic or cell-extrinsic fashion for any particular cell type.

Data shown here provide evidence for alterations in the electrical and metabolic state of iTreg and Teff cells when the Nrn1 gene is deleted. Nrn1-/- Tregs and Teff cells each express a unique pattern of genes associated with Neurotransmitter receptor, Metal ion transmembrane transport, Amino acid transport, and mTORC1 signaling activities, different than that seen in wild-type mice. It remains unclear how Nrn1 reinforces the membrane potential and facilitates aerobic glycolysis during and after iTreg differentiation, and yet suppresses the membrane potential and restrains aerobic glycolysis during Teff cell differentiation. Importantly, naive cells lacking Nrn1 expression show normal electrical and metabolic behaviors.

Reviewer #2 (Public review):

Summary:

In this study, the authors combine the study of clinical samples of antibiotic resistant bacteria with experimental evolution and evolutionary genomics to address important questions about the propensity for reversion in two different schema: de novo resistance arising within a patient, and transmitted resistance. The authors' use of a combination of methods help to answer the question outlined in their hypothesis, that de novo resistance mechanisms appear to revert to sensitive phenotypes more readily in a drug-free environment.

Strengths:

This study is exceptionally well-written and organized. The authors state their hypothesis clearly, and follow it up with an impressive effort that is truly translational-they make direct use of clinical samples of bacteria, and combine that with approaches in experimental evolution and evolutionary genomics. The conclusions follow naturally from the results, and there are no irresponsible leaps made.

Weaknesses:

I will divide my criticism into two areas, conceptual (most of my critique), with a very small methodological question.

(1) In the end, the authors offer findings that appear to be correct, and (again) are reported very clearly. However, this study is very surface-level in its theoretical underpinnings and construction, which is puzzling, because the field of antibiotic resistance and adaptation more broadly, is full of relevant studies and explanatory tools. Below I'll identify several areas where this manifests.

For one, the authors do not engage with a large recent literature on reversion, reversal, and compensation. It provides much more conceptual grounding for what the authors observe, much of it compatible with the findings from this study:

To offer two quick examples:<br /> - Avrani S, Katz S, Hershberg R. Adaptations accumulated under prolonged resource exhaustion are highly transient. MSphere. 2020 Aug 26;5(4):10-128.<br /> - Pennings, P.S., Ogbunugafor, C.B. and Hershberg, R., 2022. Reversion is most likely under high mutation supply when compensatory mutations do not fully restore fitness costs. G3, 12(9), p.jkac190.

Examinations of the studies on adaptation and reversion offer a richer mechanistic take on what was observed. But this literature alone is less of a problem than the general offering of different takes for the results. One can turn to a different literature - from ecology - to find a different explanation that is compatible with the findings.

De novo evolution involves the strong selection and rapid fixation of populations that are evolving largely to a relatively simple ecological milieu: their only primary function is to promote replication and survival of populations experiencing the negative fitness effects of drug pressure. Alternatively, transmitted resistant populations must deal with a multitude of selective pressures, working dynamically across time and space. In such a scenario, one would expect populations to locate places on the fitness landscape that are commensurate with survival in both drug-poor and drug-rich environments, as this is the ecological reality of the transmitted resistant bacteria. I could envision selection for "generalism" in this setting, corresponding to populations that have fixed mutations that promote resistance, but also those that ensure replication in drug-free environments. This regime might even reflect selection for "generalism" or "increased niche breadth." That is, transmitted resistance may have adopted a "jack of all trades, master of none" phenotype. The de novo resistance strains, alternatively, are selected for "generalism."

See the following for examples (there are many):

- Kassen R. The experimental evolution of specialists, generalists, and the maintenance of diversity. Journal of evolutionary biology. 2002 Mar 1;15(2):173-90.<br /> - Bell TH, Bell T. Many roads to bacterial generalism. FEMS microbiology ecology. 2021 Jan;97(1):fiaa240.

Note that this classically ecological explanation is only one of several other literatures that offer models for the findings in this study.

To the authors' credit, their study was about the very real-world problem of antibiotic resistance, using a system that is far less tractable than the model systems research that has generated a lot of data and theory. And sure: the study is valuable because it communicates an interesting finding using a combination of methods (impressively). But in some ways, the study almost reads as a descriptive exercise: it offers a good question (does de novo or transmitted resistance revert more readily), and tells you what they found (de novo does). However the explanatory mechanisms do not advance our understanding much. Reporting the presence of unstable and disruptive mutations in the de novo populations is hardly an explanation. That is, alternatively, data in support of a proper explanation. There is nothing magical about de novo evolution that should be selected for disruptive mutations.

The reasons for the different sorts of mutation could have to do with the population genetic particulars of the de novo regime: large populations, strong selective pressure, relatively static fitness landscape. In such a setting, selection marches a population greedily up a peak. Alternatively, a transmitted population arises from a lineage that has observed a multitude of ecologies, across different fitness landscapes and has fixed mutations that confer survival across all of them.

There's a literature that speaks to this:<br /> - Miller CM, Draghi JA. Range expansion can promote the evolution of plastic generalism in coarse-grained landscapes. Evolution Letters. 2024 Apr 1;8(2):322-30.<br /> - Bono LM, Draghi JA, Turner PE. Evolvability costs of niche expansion. Trends in genetics. 2020 Jan 1;36(1):14-23.

The findings are simple enough (a testament to the strong study design and execution) that supporting population genetic simulations, or analytical descriptions (maybe not relevant) could offer insight as to what really happened here.

(2) I recognize the challenge of working with clinical samples. It is very difficult to understand everything about them. But even having considered that, I might be missing something.

My main question here involves the origin of the putatively transmitted strains. The authors state that " Isolates were also obtained from six patients with a putatively transmitted resistant bacteria (hereafter PT), where a daptomycin-resistant, E. faecium bacteremia was identified on their first culture."

This seems like an awfully dubious way to identify transmitted resistance. I suppose I understand the logic (de novo evolution requires the observer to have seen the evolution happen in real-time). But this definition leaves the study wide open for an "apples to oranges" comparison that might render the other aspects questionable.

The de novo strains are being compared to transmitted strains that may have been part of lineages that had passed between many, many patients. If this were true, then we should expect the genomic architecture of the transmitted strains to be far different. The transmitted strains might have undergone more selection in different regimes and genetic drift. Drift might have fixed mutations in transmission bottlenecks, altering the genetic architecture. In such a scenario, one might expect these populations to have a more difficult time unwinding their resistance phenotype.

In the end, I applaud the authors on a well-done and well-written study.

Reviewer #2 (Public review):

Summary:

Juvenile hormone (JH) is a pleiotropic terpenoid hormone in insects that mainly regulates their development and reproduction. In particular, its developmental functions are described as the "status quo" action, as its presence in the hemolymph (the insect blood) prevents metamorphosis-initiating effects of ecdysone, another important hormone in insect development, and maintains the juvenile status of insects.

While such canonical functions of JH are known to be mediated by its intracellular receptor complex composed of Met and Tai, there have been multiple reports suggesting the presence of cell membrane receptor(s) for JH, which mediate non-genomic effects of this terpenoid hormone. In particular, the presence of receptor tyrosine kinase(s) that phosphorylate Met/Tai in response to JH and thus indirectly affect the canonical JH signaling pathway has been strongly suggested. Given the importance of JH in insect physiology and the fact that the JH signaling pathway is a major target of insect growth regulators, elucidating the identify and functions of putative JH membrane receptors is of great significance from both basic and applied perspectives.

In the present study, the authors identified candidate receptors for such cell membrane JH receptors, CAD96CA and FGFR1, in the cotton bollworm Helicoverpa armigera.

Strengths:

Their in vitro analyses are conducted thoroughly using multiple methods, which overall supports their claim that these receptors can bind to JH and mediate their non-genomic effects.

Weaknesses:

Results of their in vivo experiments, particularly those of their loss-of-function analyses using CRISPR mutants are still preliminary, and the results rather indicate that these membrane receptors do not have any physiologically significant roles in vivo. More specifically, previous studies in lepidopteran species have clearly and repeatedly shown that precocious metamorphosis is the hallmark phenotype for all JH signaling-deficient larvae. In contrast, the present study showed that Cad96ca and Fgfr1 G0 mutants only showed slight acceleration in their pupation timing, which is not a typical phenotype one would expect from JH signaling deficiency. This is inconsistent with their working model provided in Figure 6, which indicates that these cell membrane JH receptors promote the canonical JH signaling by phosphorylating Met/Tai.

If the authors argue that this slight acceleration of pupation is indeed a major JH signaling-deficient phenotype in Helicoverpa, they need to provide more data to support their claim by analyzing CRISPR mutants of other genes involved in JH signaling, such as Jhamt and Met. An alternative explanation is that there is functional redundancy between CAD96CA and FGFR1 in mediating phosphorylation of Met/Tai. This possibility can be tested by analyzing double knockouts of these two receptors.

Currently, the validity of their calcium imaging analysis in Figure 5 is also questionable. When performing calcium imaging in cultured cells, it is critically important to treat all the cells at the end of each experiment with a hormone or other chemical reagents that universally induce calcium increase in each particular cell line. Without such positive control, the validity of calcium imaging data remains unknown, and readers cannot properly evaluate their results.

Reviewer #2 (Public review):

Id proteins are thought to function by binding and antagonizing basic helix-loop-helix (bHLH) transcription factors but new findings demonstrate roles for emc including in tissues where no proneural (Drosophila bHLH) genes are known to function. The authors propose a new mechanism for developmental regulation that entails restraining new/novel non-apoptotic functions of apoptotic caspases.

Specifically, the data suggest that loss of emc leads to reduced expression of diap1 and increased apoptotic caspase activity, which does not induce apoptosis but elevates Delta expression to increase N activity and cause developmental defects. Indeed, many of the phenotypes of emc mutant clones can be rescued by a chromosomal deficiency that reduces caspase activation or by mutations in the initiator caspase Dronc. A related manuscript that shows that loss of emc results in increased da, linked previously to diap1 expression, provides supporting data. There is increasing appreciation that apoptotic caspases have non-apoptotic roles. This study adds to the emerging field and should be of interest to the readers.

The revised manuscript addresses my concerns from the first round of review.

Reviewer #2 (Public review):

Summary:

This study focuses on changes in brain organization associated with congenital deafness. The authors investigate differences in functional connectivity (FC) and differences in the variability of FC. By comparing congenitally deaf individuals to individuals with normal hearing, and by further separating congenitally deaf individuals into groups of early and late signers, the authors can distinguish between changes in FC due to auditory deprivation and changes in FC due to late language acquisition. They find larger FC variability in deaf than normal-hearing individuals in temporal, frontal, parietal, and midline brain structures, and that FC variability is largely driven by auditory deprivation. They suggest that the regions that show a greater FC difference between groups also show greater FC variability.

Strengths:

The manuscript is well-written, and the methods are clearly described and appropriate. Including the three different groups enables the critical contrasts distinguishing between different causes of FC variability changes. The results are interesting and novel.

Weaknesses:

Analyses were conducted for task-based data rather than resting-state data. The authors report behavioral differences between groups and include behavioral performance as a nuisance regressor in their analysis. This is a good approach to account for behavioral task differences, given the data. Nevertheless, additional work using resting-state functional connectivity could remove the potential confound fully.

The authors have addressed my concerns well.

Reviewer #2 (Public review):

Summary:

In the present manuscript So et al describe an optimized method for nuclei isolation and single nucleus RNA sequencing (snRNA-Seq), which they use to characterize cell populations in lean and obese murine adipose tissues.

Strengths:

The detailed description of the protocol for single-nuclei isolation incorporating VRC may be useful to researchers studying adipose tissues, which contain high levels of RNAses.

While the majority of the findings largely confirm previous published adipose data sets, the authors present a detailed description of a mature adipocyte sub-cluster that appears to represent stressed or dying adipocytes present in obesity, and which is better characterized using the described protocol.

Weaknesses:

The use of VRC to enhance snRNA-seq has been previously published in other tissues, somewhat diminishing the novelty of this protocol.

The snRNA-seq data sets presented in this manuscript, when compared with numerous previously published single-cell analysis of adipose tissue, represent an incremental contribution. The nuclei-isolation protocol may represent an improvement in transcriptional analysis for mature adipocytes, however other stromal populations may be better sequenced using single intact-cell cytoplasmic RNA-Seq.

Reviewer #2 (Public review):

Sadanandan et al describe their studies in mice of HDAC and Polycomb function in the context of vascular endothelial cell (EC) gene expression relevant to the blood-brain barrier, (BBB). This topic is of interest because the BBB gene expression program represents an interesting and important vascular diversification mechanism. From an applied point of view, modifying this program could have therapeutic benefits in situations where BBB function is compromised.

The study involves comparing the transcriptomes of cultured CNS ECs at E13 and adult stages and then perturbing EC gene expression pharmacologically in cell culture (with HDAC and Polycomb inhibitors) and genetically in vivo by EC-specific conditional KO of HDAC2 and Polycomb component EZH2.

This reviewer has several critiques of the study.

First, based on published data, the effect of culturing CNS ECs is likely to have profound effects on their differentiation, especially as related to their CNS-specific phenotypes. Related to this, the authors do not state how long the cells were cultured.

Second, the use of qPCR assays for quantifying ChIP and transcript levels is inferior to ChIPseq and RNAseq. Whole genome methods, such as ChIPseq, permit a level of quality assessment that is not possible with qPCR methods. The authors should use whole genome NextGen sequencing approaches, show the alignment of reads to the genome from replicate experiments, and quantitatively analyze the technical quality of the data.

Third, the observation that pharmacologic inhibitor experiments and conditional KO experiments targeting HDAC2 and the Polycomb complex perturb EC gene expression or BBB integrity, respectively, is not particularly surprising as these proteins have broad roles in epigenetic regulation is a wide variety of cell types.

Reviewer #2 (Public review):

Summary:<br /> In this manuscript, Bosch et al. reveal Flamingo (Fmi), a planar cell polarity (PCP) protein, is essential for maintaining 'winner' cells in cell competition, using Drosophila imaginal epithelia as a model. They argue that tumor growth induced by scrib-RNAi and RasV12 competition is slowed by Fmi depletion. This effect is unique to Fmi, not seen with other PCP proteins. Additional cell competition models are applied to further confirm Fmi's role in 'winner' cells. The authors also show that Fmi's role in cell competition is separate from its function in PCP formation.

Strengths:

(1) The identification of Fmi as a potential regulator of cell competition under various conditions is interesting.<br /> (2) The authors demonstrate that the involvement of Fmi in cell competition is distinct from its role in planar cell polarity (PCP) development.

Weaknesses:

(1) The authors provide a superficial description of the related phenotypes, lacking a mechanistic understanding of how Fmi regulates cell competition. While induction of apoptosis and JNK activation are commonly observed outcomes in various cell competition conditions, it is crucial to determine the specific mechanisms through which they are induced in fmi-depleted clones. Furthermore, it is recommended that the authors utilize the power of fly genetics to conduct a series of genetic epistasis analyses.

Reviewer #3 (Public review):

Summary:

Grogan et al examine a role for muscarinic receptor activation in action vigor in a saccadic system. This work is motivated by a strong literature linking dopamine to vigor, and some animal studies suggesting that ACH might modulate these effects, and is important because patient populations with symptoms related to reduced vigor are prescribed muscarinic antagonists. The authors use a motivated saccade task with distractors to measure the speed and vigor of actions in humans under placebo or muscarinic antagonism. They show that muscarinic antagonism blunts the motivational effects of reward on both saccade velocity and RT, and also modulates the distractibility of participants, in particular by increasing the repulsion of saccades away from distractors. They show that preparatory EEG signals reflect both motivation and drug condition, and make a case that these EEG signals mediate the effects of the drug on behavior.

Strengths:

This manuscript addresses an interesting and timely question and does so using an impressive within subject pharmacological design and a task well designed to measure constructs of interest. The authors show clear causal evidence that ACH affects different metrics of saccade generation related to effort expenditure and their modulation by incentive manipulations. The authors link these behavioral effects to motor preparatory signatures, indexed with EEG, that relate to behavioral measures of interest and in at least one case statistically mediate the behavioral effects of ACH antagonism.

Weaknesses:

A primary weakness of this paper is the sample size - since only 20 participants completed the study. The authors address the sample size in several places and I completely understand the reason for the reduced sample size (study halt due to covid). Nonetheless, it is worth stating explicitly that this sample size is relatively small for the effect sizes typically observed in such studies highlighting the need for future confirmatory studies.

Reviewer #2 (Public review):

In the present study, Boffi et al. investigate the manner in which the dorsal cortex of the of the inferior colliculus (DCIC), an auditory midbrain area, encodes sound location azimuth in awake, passively listening mice. By employing volumetric calcium imaging (scanned temporal focusing or s-TeFo), complemented with high-density electrode electrophysiological recordings (neuropixels probes), they show that sound-evoked responses are exquisitely noisy, with only a small portion of neurons (units) exhibiting spatial sensitivity. Nevertheless, a naïve Bayesian classifier was able to predict the presented azimuth based on the responses from small populations of these spatially sensitive units. A portion of the spatial information was provided by correlated trial-to-trial response variability between individual units (noise correlations). The study presents a novel characterization of spatial auditory coding in a non-canonical structure, representing a noteworthy contribution specifically to the auditory field and generally to systems neuroscience, due to its implementation of state-of-the-art techniques in an experimentally challenging brain region. However, nuances in the calcium imaging dataset and the naïve Bayesian classifier warrant caution when interpreting some of the results.

Strengths:

The primary strength of the study lies in its methodological achievements, which allowed the authors to collect a comprehensive and novel dataset. While the DCIC is a dorsal structure, it extends up to a millimetre in depth, making it optically challenging to access in its entirety. It is also more highly myelinated and vascularised compared to e.g., the cerebral cortex, compounding the problem. The authors successfully overcame these challenges and present an impressive volumetric calcium imaging dataset. Furthermore, they corroborated this dataset with electrophysiological recordings, which produced overlapping results. This methodological combination ameliorates the natural concerns that arise from inferring neuronal activity from calcium signals alone, which are in essence an indirect measurement thereof.

Another strength of the study is its interdisciplinary relevance. For the auditory field, it represents a significant contribution to the question of how auditory space is represented in the mammalian brain. "Space" per se is not mapped onto the basilar membrane of the cochlea and must be computed entirely within the brain. For azimuth, this requires the comparison between miniscule differences between the timing and intensity of sounds arriving at each ear. It is now generally thought that azimuth is initially encoded in two, opposing hemispheric channels, but the extent to which this initial arrangement is maintained throughout the auditory system remains an open question. The authors observe only a slight contralateral bias in their data, suggesting that sound source azimuth in the DCIC is encoded in a more nuanced manner compared to earlier processing stages of the auditory hindbrain. This is interesting because it is also known to be an auditory structure to receive more descending inputs from the cortex.

Systems neuroscience continues to strive for the perfection of imaging novel, less accessible brain regions. Volumetric calcium imaging is a promising emerging technique, allowing the simultaneous measurement of large populations of neurons in three dimensions. But this necessitates corroboration with other methods, such as electrophysiological recordings, which the authors achieve. The dataset moreover highlights the distinctive characteristics of neuronal auditory representations in the brain. Its signals can be exceptionally sparse and noisy, which provide an additional layer of complexity in the processing and analysis of such datasets. This will undoubtedly be useful for future studies of other less accessible structures with sparse responsiveness.

Weaknesses:

Although the primary finding that small populations of neurons carry enough spatial information for a naïve Bayesian classifier to reasonably decode the presented stimulus is not called into question, certain idiosyncrasies, in particular the calcium imaging dataset and model, complicate specific interpretations of the model output, and the readership is urged to interpret these aspects of the study's conclusions with caution.

I remain in favour of volumetric calcium imaging as a suitable technique for the study, but the presently constrained spatial resolution is insufficient to unequivocally identify regions of interest as cell bodies (and are instead referred to as "units" akin to those of electrophysiological recordings). It remains possible that the imaging set is inadvertently influenced by non-somatic structures (including neuropil), which could report neuronal activity differently than cell bodies. Due to the lack of a comprehensive ground-truth comparison in this regard (which to my knowledge is impossible to achieve with current technology), it is difficult to imagine how many informative such units might have been missed because their signals were influenced by spurious, non-somatic signals, which could have subsequently misled the models. The authors reference the original Nature Methods article (Prevedel et al., 2016) throughout the manuscript, presumably in order to avoid having to repeat previously published experimental metrics. But the DCIC is neither the cortex nor hippocampus (for which the method was originally developed) and may not have the same light scattering properties (not to mention neuronal noise levels). Although the corroborative electrophysiology data largely eleviates these concerns for this particular study, the readership should be cognisant of such caveats, in particular those who are interested in implementing the technique for their own research.

A related technical limitation of the calcium imaging dataset is the relatively low number of trials (14) given the inherently high level of noise (both neuronal and imaging). Volumetric calcium imaging, while offering a uniquely expansive field of view, requires relatively high average excitation laser power (in this case nearly 200 mW), a level of exposure the authors may have wanted to minimise by maintaining a low number of repetitions, but I yield to them to explain. Calcium imaging is also inherently slow, requiring relatively long inter-stimulus intervals (in this case 5 s). This unfortunately renders any model designed to predict a stimulus (in this case sound azimuth) from particularly noisy population neuronal data like these as highly prone to overfitting, to which the authors correctly admit after a model trained on the entire raw dataset failed to perform significantly above chance level. This prompted them to feed the model only with data from neurons with the highest spatial sensitivity. This ultimately produced reasonable performance (and was implemented throughout the rest of the study), but it remains possible that if the model was fed with more repetitions of imaging data, its performance would have been more stable across the number of units used to train it. (All models trained with imaging data eventually failed to converge.) However, I also see these limitations as an opportunity to improve the technology further, which I reiterate will be generally important for volume imaging of other sparse or noisy calcium signals in the brain.

Indeed, in separate comments to these remarks, the authors confirmed that the low number of trials was technically limited, to which I emphasise is to no fault of their own. However, they also do not report this as a typical imaging constraint, such as photobleaching, but rather because the animals exhibited signs of stress and discomfort at longer imaging periods. From an animal welfare perspective, I would encourage the authors to state this in the methods for transparency. It would demonstrate their adherence to animal welfare policies, which I find to be an incredibly strong argument for limiting the number of trials in their study.

Transitioning to the naïve Bayesian classifier itself, I first openly ask the authors to justify their choice of this specific model. There are countless types of classifiers for these data, each with their own pros and cons. Did they actually try other models (such as support vector machines), which ultimately failed? If so, these negative results (even if mentioned en passant) would be extremely valuable to the community, in my view. I ask this specifically because different methods assume correspondingly different statistical properties of the input data, and to my knowledge naïve Bayesian classifiers assume that predictors (neuronal responses) are assumed to be independent within a class (azimuth). As the authors show that noise correlations are informative in predicting azimuth, I wonder why they chose a model that doesn't take advantage of these statistical regularities. It could be because of technical considerations (they mention computing efficiency), but I am left generally uncertain about the specific logic that was used to guide the authors through their analytical journey.

In a revised version of the manuscript, the authors indeed justify their choice of the naïve Bayesian classifier as a conservative approach (not taking into account noise correlations), which could only improve with other models (that do). They even tested various other commonly used models, such as support vector machines and k-nearest neighbours, to name a few, but do not report these efforts in the main manuscript. Interestingly, these models, which I supposed would perform better in fact did not overall - a finding that I have no way of interpreting but nevertheless find interesting. I would thus encourage the authors to include these results in a figure supplement and mention it en passant while justifying their selection of model (but please include detailed model parameters in the methods section).

That aside, there remain other peculiarities in model performance that warrant further investigation. For example, what spurious features (or lack of informative features) in these additional units prevented the models of imaging data from converging? In an orthogonal question, did the most spatially sensitive units share any detectable tuning features? A different model trained with electrophysiology data in contrast did not collapse in the range of top-ranked units plotted. Did this model collapse at some point after adding enough units, and how well did that correlate with the model for the imaging data? How well did the form (and diversity) of the spatial tuning functions as recorded with electrophysiology resemble their calcium imaging counterparts? These fundamental questions could be addressed with more basic, but transparent analyses of the data (e.g., the diversity of spatial tuning functions of their recorded units across the population). Even if the model extracts features that are not obvious to the human eye in traditional visualisations, I would still find this interesting.

Although these questions were not specifically addressed in the revised version of the manuscript, I also admit that I did not indent do assert that these should necessarily fall within the scope of the present study. I rather posed them as hypothetical directions one could pursue in future studies. Finally, further concerns I had with statements regarding the physiological meaning of the findings have been ameliorated by nicely modified statements, thus bringing transparency to the readership, which I appreciate.

In summary, the present study represents a significant body of work that contributes substantially to the field of spatial auditory coding and systems neuroscience. However, limitations of the imaging dataset and model as applied in the study muddles concrete conclusions about how the DCIC precisely encodes sound source azimuth and even more so to sound localisation in a behaving animal. Nevertheless, it presents a novel and unique dataset, which, regardless of secondary interpretation, corroborates the general notion that auditory space is encoded in an extraordinarily complex manner in the mammalian brain.

Reviewer #2 (Public review):

In this article, Kong and authors sought to determine the encoding properties of central amygdala (CeA) neurons in response to oppositely valenced stimuli and cues predicting those stimuli. The amygdala and its subregional components have historically been understood to be regions that encode associative information, including valence stimuli. The authors performed calcium imaging of GABA-ergic CeA neurons in freely-moving mice conditioned in Pavlovian appetitive and fear paradigms, and showed that CeA neurons are responsive to both appetitive and aversive unconditioned and conditioned stimuli. They used a variant of a previously published 'circular shifting' technique (Harris, 2021), which allowed them to delineate between excited/non-responsive/inhibited neurons. While there is considerable overlap of CeA neurons responding to both unconditioned stimuli (in this case, food and shock, deemed "salience-encoding" neurons), there are considerably fewer CeA neurons that respond to both conditioned stimuli that predict the food and shock. The authors finally demonstrated that there are no differences in the order of Pavlovian paradigms (fear - shock vs. shock - fear), which is an interesting result, and convincingly presented given their counterbalanced experimental design.

In total, I find the presented study useful in understanding the dynamics of CeA neurons during a Pavlovian learning paradigm. There are many strengths of this study, including the important question and clear presentation, the circular shifting analysis was convincing to me, and the manuscript was well written. We hope the authors will find our comments constructive if they choose to revise their manuscript.

While the experiments and data are of value, I do not agree with the authors interpretation of their data, and take issue with the way they used the terms "salience" and "valence" (and would encourage them to check out Namburi et al., NPP, 2016) regarding the operational definitions of salience and valence which differ from my reading of the literature. To be fair, a recent study from another group that reports experiments/findings which are very similar to the ones in the present study (Yang et al., 2023, describing valence coding in the CeA using a similar approach) also uses the terms valence and salience in a rather liberal way that I would also have issues with (see below). Either new experiments or revised claims would be needed here, and more balanced discussion on this topic would be nice to see, and I felt that there were some aspects of novelty in this study that could be better highlighted (see below).

One noteworthy point of alarm is that it seems as if two data panels including heatmaps are duplicated (perhaps that panel G of Figure 5-figure supplement 2 is a cut and paste error? It is duplicated from panel E and does not match the associated histogram).

Major concerns:

(1) The authors wish to make claims about salience and valence. This is my biggest gripe, so I will start here.<br /> (1a) Valence scales for positive and negative stimuli and as stated in Namburi et al., NPP, 2016 where we operationalize "valence" as having different responses for positive and negative values and no response for stimuli that are not motivational significant (neutral cues that do not predict an outcome). The threshold for claiming salience, which we define as scaling with the absolute value of the stimulus, and not responding to a neutral stimulus (Namburi et al., NPP, 2016; Tye, Neuron, 2018; Li et al., Nature, 2022) would require the lack of response to a neutral cue.<br /> (1b) The other major issue is that the authors choose to make claims about the neural responses to the USs rather than the CSs. However, being shocked and receiving sucrose also would have very different sensorimotor representations, and any differences in responses could be attributed to those confounds rather than valence or salience. They could make claims regarding salience or valence with respect to the differences in the CSs but they should restrict analysis to the period prior to the US delivery.<br /> (1c) The third obstacle to using the terms "salience" or "valence" is the lack of scaling, which is perhaps a bigger ask. At minimum either the scaling or the neutral cue would be needed to make claims about valence or salience encoding. Perhaps the authors disagree - that is fine. But they should at least acknowledge that there is literature that would say otherwise.<br /> (1d) In order to make claims about valence, the authors must take into account the sensory confound of the modality of the US (also mentioned in Namburi et al., 2016). The claim that these CeA neurons are indeed valence-encoding (based on their responses to the unconditioned stimuli) is confounded by the fact that the appetitive US (food) is a gustatory stimulus while the aversive US (shock) is a tactile stimulus.

(2) Much of the central findings in this manuscript have been previously described in the literature. Yang et al., 2023 for instance shows that the CeA encodes salience (as demonstrated by the scaled responses to the increased value of unconditioned stimuli, Figure 1 j-m), and that learning amplifies responsiveness to unconditioned stimuli (Figure 2). It is nice to see a reproduction of the finding that learning amplifies CeA responses, though one study is in SST::Cre and this one in VGAT::cre - perhaps highlighting this difference could maximize the collective utility for the scientific community?

(3) There is at least one instance of copy-paste error in the figures that raised alarm. In the supplementary information (Figure 5- figure supplement 2 E;G), the heat maps for food-responsive neurons and shock-responsive neurons are identical. While this almost certainly is a clerical error, the authors would benefit from carefully reviewing each figure to ensure that no data is incorrectly duplicated.

(4) The authors describe experiments to compare shock and reward learning; however, there are temporal differences in what they compare in Figure 5. The authors compare the 10th day of reward learning with the 1st day of fear conditioning, which effectively represent different points of learning and retrieval. At the end of reward conditioning, animals are utilizing a learned association to the cue, which demonstrates retrieval. On the day of fear conditioning, animals are still learning the cue at the beginning of the session, but they are not necessarily retrieving an association to a learned cue. The authors would benefit from recording at a later timepoint (to be consistent with reward learning- 10 days after fear conditioning), to more accurately compare these two timepoints. Or perhaps, it might be easier to just make the comparison between Day 1 of reward learning and Day 1 of fear learning, since they must already have these data.

(5) The authors make a claim of valence encoding in their title and throughout the paper, which is not possible to make given their experimental design. However, they would greatly benefit from actually using a decoder to demonstrate their encoding claim (decoding performance for shock-food versus shuffled labels) and simply make claims about decoding food-predictive cues and shock-predictive cues. Interestingly, it seems like relatively few CeA neurons actually show differential responses to the food and shock CSs, and that is interesting in itself.

Reviewer #2 (Public review):

Garbelli et. al. set out to elucidate the function of two glutamate transporters, EAAT5b and EAAT7, in the functional and behavioral responses to different wavelengths of light. The question is an interesting one, because these transporters are well positioned to affect responses to light, and their distribution in the retina suggests that they could play differential roles in visual behaviors. However, the low resolution of both the functional and behavioral data presented here means that the conclusions are necessarily a bit vague.

In Figure 1, the authors show that the double KO has a decreased ERG response to UV/blue and red wavelengths. However, the individual mutations only affect the response to red light, suggesting that they might affect behaviors such as OMR which typically rely on this part of the visual spectrum. However, there was no significant change in the response to UV/blue light of any intensity, making it unclear whether the mutations could individually play roles in the detection of UV prey. Based on the later behavioral data, it seems likely that at least the EAAT7 KO should affect retinal responses to UV light, but it may be that the ERG does not have the spatial or temporal resolution to detect the difference, or that the presence of blue light overwhelmed any effect of the individual knockouts on the response to UV light.

In Figures 5 and 6, the authors compare the two knockouts to wild-type fish in terms of their sensitivity to UV prey in a hunting assay. The EAAT5b KO showed no significant impairment in UV sensitivity, while the EAAT7 KO fish actually had an increased hunting response to UV prey. However, there is no comparison of the KO and WT responses to different UV intensities, only in bulk, so we cannot conclude that the EAAT7 KO is allowing the fish to detect weaker prey-like stimuli.

In Figure 7, the EAAT5b KO seems to cause a decrease in OMR behavior to red grating stimuli, but only one stimulus is tested, so it is unclear whether this is due to a change in visual sensitivity or resolution.

The conclusions made in the manuscript are appropriately conservative; the abstract states that these transporters somehow influence prey detection and motion sensing, and this is probably true. However, it is unclear to what extent and how they might be acting on these processes, so the conclusions are a bit unsatisfying.

In terms of impact on the field, this work highlights the potential importance of these two transporters to visual processing, but further studies will be required to say how important they are and what they are doing. The methods presented here are not novel, as UV prey and red OMR stimuli and behaviors have previously been described.

Reviewer #2 (Public review):

Summary:

This is an elegant study investigating possible mechanisms underlying the hysteresis effect in the perception of perceptually ambiguous Shepard tones. The authors make a fairly convincing case that the adaptation of pitch direction sensitive cells in auditory cortex is likely responsible for this phenomenon.

Strengths:

The manuscript is overall well written. My only slight criticism is that, in places, particularly for non-expert readers, it might be helpful to work a little bit more methods detail into the results section, so readers don't have to work quite so hard jumping from results to methods and back.

The methods seem sound and the conclusions warranted and carefully stated. Overall I would rate the quality of this study as very high, and I do not have any major issues to raise.

Weaknesses:

I think this study is about as good as it can be with the current state of the art. Generally speaking, one has to bear in mind that this is an observational, rather than an interventional study, and therefore only able to identify plausible candidate mechanisms rather than making definitive identifications. However, the study nevertheless represents a significant advance over the current state of knowledge, and about as good as it can be with the techniques that are currently widely available.

Reviewer #2 (Public review):

Summary: