Reviewer #3 (Public Review):

The manuscript by Li et al. presents an elegant application of sterile insect technology (pgSIT) utilizing a CRISPR-Cas9 system to suppress mosquito vector populations. The pgSIT technique outlined in this paper employs a binary system where Cas9 and gRNA are conjoined in experimental crosses to yield sterile male mosquitoes. Employing a multiplexed strategy, the authors combine multiple gRNA to concurrently target various genes within a single locus. This approach successfully showcases the disruption of three distinct genes at different genomic positions, resulting in the creation of highly effective sterile mosquitoes for population control. The pioneering work of the Akbari lab has been instrumental in developing this technology, previously demonstrating its efficacy in Drosophila and Aedes aegypti.

By targeting the female-specific splice isoform (exon-5) of doublesex in conjunction with intersex and β-tubulin, the researchers induce female lethality, leading to a predominance of sterile male mosquitoes. This innovation is particularly noteworthy as the deployment of sterile mosquitoes on a large scale typically requires substantial investment in sex sorting. However, this study circumvents this challenge through genetic manipulation.

Reviewer #3 (Public Review):

The authors use a set of reporter assays to probe the impact of TnpB on IS605 transposition. This is an innovative approach to studying transposition that will be of interest to other groups. The authors conclude that TnpB likely has two activities: (ii) promoting "homing", where the transposon is restored following excision, and (ii) promoting the transposition activity of the transposase TnpA. The paper provides an independent validation of the recently reported homing activity of TnpB, where the transposon is restored following excision, and suggests an additional function for TnpB in enhancing the transposase activity of the TnpA transposase.

Strengths<br /> - The innovative use of reporter assays is an excellent way to infer the details of transposition, making a convincing case that TnpB plays two distinct roles.

Weaknesses<br /> - The authors need to discuss their conclusions in light of a very relevant recent paper from the Sternberg group demonstrating a role for TnpB in homing.<br /> - There doesn't appear to be an assessment of how well the model fits the experimental data, or any attempt to test how accurately the model can predict the effects of perturbing the system.<br /> - The figures could be presented more clearly.

Reviewer #3 (Public Review):

George et al. present a convincing new Python toolbox that allows researchers to generate synthetic behavior and neural data specifically focusing on hippocampal functional cell types (place cells, grid cells, boundary vector cells, head direction cells). This is highly useful for theory-driven research where synthetic benchmarks should be used. Beyond just navigation, it can be highly useful for novel tool development that requires jointly modeling behavior and neural data. The code is well organized and written and it was easy for us to test.

We have a few constructive points that they might want to consider.

- Right now the code only supports X,Y movements, but Z is also critical and opens new questions in 3D coding of space (such as grid cells in bats, etc). Many animals effectively navigate in 2D, as a whole, but they certainly make a large number of 3D head movements, and modeling this will become increasingly important and the authors should consider how to support this.

- What about other environments that are not "Boxes" as in the name - can the environment only be a Box, what about a circular environment? Or Bat flight? This also has implications for the velocity of the agent, etc. What are the parameters for the motion model to simulate a bat, which likely has a higher velocity than a rat?

- Semi-related, the name suggests limitations: why Rat? Why Not Agent? (But its a personal choice)

- A future extension (or now) could be the ability to interface with common trajectory estimation tools; for example, taking in the (X, Y, (Z), time) outputs of animal pose estimation tools (like DeepLabCut or such) would also allow experimentalists to generate neural synthetic data from other sources of real-behavior.

- What if a place cell is not encoding place but is influenced by reward or encodes a more abstract concept? Should a PlaceCell class inherit from an AbstractPlaceCell class, which could be used for encoding more conceptual spaces? How could their tool support this?

- This a bit odd in the Discussion: "If there is a small contribution you would like to make, please open a pull request. If there is a larger contribution you are considering, please contact the corresponding author3" This should be left to the repo contribution guide, which ideally shows people how to contribute and your expectations (code formatting guide, how to use git, etc). Also this can be very off-putting to new contributors: what is small? What is big? we suggest use more inclusive language.

- Could you expand on the run time for BoundaryVectorCells, namely, for how long of an exploration period? We found it was on the order of 1 min to simulate 30 min of exploration (which is of course fast, but mentioning relative times would be useful).

- Regarding the Geometry and Boundary conditions, would supporting hyperbolic distance might be useful, given the interest in alternative geometry of representations (ie, https://www.nature.com/articles/s41593-022-01212-4)?

- In general, the set of default parameters might want to be included in the main text (vs in the supplement).

- It still says you can only simulate 4 velocity or head directions, which might be limiting.

- The code license should be mentioned in the Methods.

Reviewer #3 (Public Review):

Summary:<br /> The authors aim to demonstrate the effectiveness of their developed methodology, which utilizes super-resolution microscopy and single-molecule tracking in live cells on a high-throughput scale. Their study focuses on measuring the diffusion state of a molecule target, the estrogen receptor, in both ligand-bound and unbound forms in live cells. By showcasing the ability to screen 5067 compounds and measure the diffusive state of the estrogen receptor for each compound in live cells, they illustrate the capability and power of their methodology.

Strengths:<br /> Readers are well introduced to the principles in the initial stages of the manuscript with highly convincing video examples. The methods and metrics used (fbound) are robust. The authors demonstrate high reproducibility of their screening method (R2=0.92). They also showcase the great sensitivity of their method in predicting the proliferation/viability state of cells (R2=0.84). The outcome of the screen is sound, with multiple compounds clustering identified in line with known estrogen receptor biology.

Weaknesses:<br /> - Potential overstatement on the relationship of low diffusion state of ER bound to compound and chromatin state without any work on chromatin level.<br /> - Could the authors clarify if the identified lead compound effects are novel at any level?<br /> - More video example cases on the final lead compounds identified would be a good addition to the current data package.

Reviewer #3 (Public Review):

Summary of Author's Results/Intended Achievements<br /> The authors were trying to ascertain the underlying learning mechanisms and network structure that could explain their primary experimental finding: passive exposure to a stimulus (independent of when the exposure occurs) can lead to improvements in active (supervised) learning. They modeled their task with 5 progressively more complex shallow neural networks classifying vectors drawn from multi-variate Gaussian distributions.

Account of Major Strengths:<br /> Overall, the experimental findings were interesting. The modelling was also appropriate, with a solid attempt at matching the experimental condition to simplified network models.

Reviewer #3 (Public Review):

Complex behavior requires complex neural control involving multiple brain regions. The currently available tools to measure neural activity in multiple brain regions in small animals are limited and often involve obligatory head-fixation. The latter, obviously, impacts the behaviors under study. Hur and colleagues present a novel recording device, the E-Scope, that combines optical imaging of fluorescent calcium imaging in one brain region with high-density electrodes in another. Importantly, the E-Scope can be implanted and is, therefore, compatible with usage in freely moving mice. The authors used their new E-Scope to study neural activity during social interactions in mice. They demonstrate the presence of neural correlates of social interaction that happen simultaneously in the cerebellum and the anterior cingulate cortex.

The major accomplishment of this study is the development and introduction of the E-Scope. The evaluation of this part can be short: it works, so the authors succeeded.

The authors managed to reduce the weight of the implant to 4.5 g, which is - given all functionality - quite an accomplishment in my view. However, a mouse weighs between 20 and 40 g, so that an implant of 4.5 g is still quite considerable. It can be expected that this has an impact on the behavior and, possibly, the well-being of the animals. Whether this is the case or not, is not really addressed in this study. The authors suffice with the statement that "Recorded animals made more contact with the other mouse than with the object (Figure 2A), suggesting a normal preference for social contact with the E-Scope attached." A direct comparison between mice before and after implant, or between mice with and without an implant would provide more insight into the putative impact of the E-Scope on (social) behavior.

In Figure 1 D-G, the authors present raw data from the neurophysiological recordings. In panel D, we see events with vastly different amplitudes. It would be very insightful if the authors would describe which events they considered to be action potentials, and which not. Similarly, indicating the detected complex spikes in the raw traces of Figure 1E would provide more insight into the interpretation of the data. Although the authors mention to consider the occurrence of complex spikes and simple spikes, a clear definition of what is considered a single unit recording is lacking. As there is quite a wide range in reported firing rates in Figure 2 - figure supplement 3, more clarity on this aspect would be insightful. Furthermore, in their text, the authors state that the pause in simple spike firing following a complex spike normally lasts until around 40 ms, and for this statement they refer to Figure 1G that shows a pause of less than 10 ms.

The number of Purkinje cells recorded during social interactions is quite low: only 11 cells showed a modulation in their spiking activity (unclear whether in complex spikes, simple spikes or both. During object interaction, only 4 cells showed a significant modulation. Unclear is whether the latter 4 are a subset of the former 11, or whether "social cells" and "object cells" are different categories. Having so few cells, and with these having different types of modulation, the group of cells for each type of modulation is really small, going down to 2 cells/group. The small group sizes complicate the interpretation of the data - in particular also on the analysis of movement-related activity that is now very noisy (Figure 2 - figure supplement 4).

In conclusion, the authors present a novel method to record neural activity with single cell-resolution in two brain regions in freely moving mice. Given the challenges associated with understanding of complex behaviors, this approach can be useful for many neuroscientists. The authors demonstrate the potential of their approach by studying social interactions in mice. Clearly, there are correlations in activity of neurons in the anterior cingulate cortex and the cerebellum related to social interactions. To bring our understanding of these patterns to a higher level, more detailed analyses (and probably also larger group sizes of cerebellar neurons) are required, though.

Reviewer #3 (Public Review):

The authors report a study in which they use intracranial recordings to dissociate subjectively aware and subjectively unaware stimuli, focusing mainly on prefrontal cortex.

The authors have dealt successfully with some of my previous concerns, especially the more direct link to the Gaillard et al., (2009) paper, and the associated analyses, has improved the manuscript. Some of my other concerns regarding the theoretical embedding of the findings have only been partially mitigated and some interesting results derived from suggestions for additional analyses will be used for future papers.

Reviewer #3 (Public Review):

This study examines context-dependent stimulus selection by recording neural activity from several sensory and motor cortical areas along a sensorimotor pathway, including S1, S2, MM, and ALM. Mice are trained to either withhold licking or perform directional licking in response to visual or tactile stimulus. Depending on the task rule, the mice have to respond to one stimulus modality while ignoring the other. Neural activity to the same tactile stimulus is modulated by task in all the areas recorded, with significant activity changes in a subset of neurons and population activity occupying distinct activity subspaces. Recordings further reveal a contextual signal in the pre-stimulus baseline activity that differentiates task context. This signal is correlated with subsequent task modulation of stimulus activity. Comparison across brain areas shows that this contextual signal is stronger in frontal cortical regions than in sensory regions. Analyses link this signal to behavior by showing that it tracks the behavioral performance switch during task rule transitions. Silencing activity in frontal cortical regions during the baseline period impairs behavioral performance.

Overall, this is a superb study with solid results and thorough controls. The results are relevant for context-specific neural computation and provide a neural substrate that will surely inspire follow-up mechanistic investigations. We only have a couple of suggestions to help the authors further improve the paper.

1. We have a comment regarding the calculation of the choice CD in Fig S3. The text on page 7 concludes that "Choice coding dimensions change with task rule". However, the motor choice response is different across blocks, i.e. lick right vs. no lick for one task and lick left vs. no lick for the other task. Therefore, the differences in the choice CD may be simply due to the motor response being different across the tasks and not due to the task rule per se. The authors may consider adding this caveat in their interpretation. This should not affect their main conclusion.

2. We have a couple of questions about the effect size on single neurons vs. population dynamics. From Fig 1, about 20% of neurons in frontal cortical regions show task rule modulation in their stimulus activity. This seems like a small effect in terms of population dynamics. There is somewhat of a disconnect from Figs 4 and S3 (for stimulus CD), which show remarkably low subspace overlap in population activity across tasks. Can the authors help bridge this disconnect? Is this because the neurons showing a difference in Fig 1 are disproportionally stimulus selective neurons?

Reviewer #3 (Public Review):

Summary:<br /> This article aims to investigate the impact of neuroprosthesis (intracortical microstimulation) implanted unilaterally on the lesion side in the context of locomotor recovery following unilateral thoracic spinal cord injury.

Strength:<br /> The study reveals that stimulating the left motor cortex, on the same side as the lesion, not only activates the expected right (contralateral) muscle activity but also influences unexpected muscle activity on the left (ipsilateral) side. These muscle activities resulted in a substantial enhancement in lift during the swing phase of the contralateral limb and improved trunk-limb support for the ipsilateral limb. They used different experimental and stimulation conditions to show the ipsilateral limb control evoked by the stimulation. This outcome holds significance, shedding light on the engagement of the "contralateral projecting" corticospinal tract in activating not only the contralateral but also the ipsilateral spinal network.

The experimental design and findings align with the investigation of the stimulation effect of contralateral projecting corticospinal tracts. They carefully examined the recovery of ipsilateral limb control with motor maps. They also tested the effective sites of cortical stimulation. The study successfully demonstrates the impact of electrical stimulation on the contralateral projecting neurons on ipsilateral limb control during locomotion, as well as identifying important stimulation spots for such an effect. These results contribute to our understanding of how these neurons influence bilateral spinal circuitry. The study's findings contribute valuable insights to the broader neuroscience and rehabilitation communities.

Weakness:<br /> The term "ipsilateral" lacks a clear definition in the title, abstract, introduction, and discussion, potentially causing confusion for the reader.

The unexpected ipsilateral (left) muscle activity is most likely due to the left corticospinal neurons recruiting not only the right spinal network but also the left spinal network. This is probably due to the joint efforts of the neuroprosthesis and activation of spinal motor networks which work bilaterally at the spinal level.

However, in my opinion, readers can easily link the ipsilateral cortical network to the ipsilateral-projecting corticospinal tract, which is less likely to play a role in ipsilateral limb control in this study since this tract is disrupted by the thoracic spinal injury.

Reviewer #3 (Public Review):

Summary:<br /> The manuscript explores the behavioral responses of C. elegans to hydrogen sulfide, which is known to exert remarkable effects on animal physiology in a range of contexts. The possibility of genetic and precise neuronal dissection of responses to H2S motivates the study of responses in C. elegans. The manuscript is well-written in communicating the complex physiology around C. elegans behavioral responses to H2S and in appropriately citing prior and related relevant work.

There are three parts to the manuscript.

In the first, an immediate behavioral response-increased locomotory rate-upon exposure to H2S is characterized. The experimental conditions are critical, and data are obtained from exposure of animals to 150ppm H2S at 7% O2. The authors provide evidence that this is a chemosensory response to H2S, showing a requirement for genes encoding components of the cilia apparatus and implicating a role for tax-4 and daf-11. Neuron-specific rescue in the ASJ neurons suggests the ASJ neurons contribute to the response to H2S. One caveat is that previous work has shown that the dauer-constitutive phenotype of daf-11 mutants can be suppressed by ASJ ablation, suggesting that there may be pervasive changes in animal nervous system signaling that are ASJ-dependent in daf-11 mutants, which may indirectly alter chemosensory responses to H2S. More direct methods to assess whether ASJ senses H2S, e.g. using calcium imaging, would better assess a direct role for the ASJ neurons in a behavioral response to H2S. The authors also point out interesting parallels between the response to H2S and CO2 though provide some genetic data separating the two responses. Importantly, the authors note that when aerotaxis (O2-sensing and movement) in the presence of bacterial food is intact, as in npr-1 215F animals, the response to H2S is abrogated. Mutation in gcy-35 in the npr-1 215F background restores the H2S chemosensory response.

There is a second part of the paper that conducts transcriptional profiling of the response to H2S that corroborates and extends prior work in this area.

The final part of the paper is the most intriguing, but for me, also the most problematic. The authors examine how H2S-evoked locomotory behavioral responses are affected in mutants defective in the stress and detoxification response to H2S, most notably hif-1. Prior genetic studies have established the pathways leading to HIF-1 activation/stabilization, as well as potential downstream mechanisms. The authors conduct logical genetic analysis to complement studies of the hif-1 mutant and in part motivated by their transcriptional profiling studies, examine the role of iron sequestration/free iron in the locomotory response to H2S, and further speculate on how the behavior of mutants defective in mitochondrial function might be affected by exposure to H2S.

In some regard, this part of the manuscript is interesting because the analysis begins to connect how the behavior of an animal to a toxic compound is affected by mutations that affect sensitivity to the toxic compound. However, what is unclear is what is being studied at this point. In the context, of noting that H2S at 150ppm is known to be lethal, its addition to mutants clearly sensitized to its effects would be anticipated to have pervasive effects on animal physiology and nervous system function. The authors note that the continued increased locomotion of wild-type animals upon H2S exposure might be due to the byproducts of detoxification or the detrimental effects of H2S. The latter explanation seems much more likely, in which case what one may be observing is the effects of general animal sickness, or even a bit more specifically, neuronal dysfunction in the presence of a toxic compound, on locomotion. As such, what is unclear is what conclusions can be taken away from this part of the work.

Strengths:<br /> 1. Characterization of a motor behavior response to H2S<br /> 2. Transcriptional profiling of the response to H2S corroborating prior work.

Weaknesses:<br /> Unclear significance and experimental challenges regarding the study of locomotory responses to animals sensitized to the toxic effects of H2S under exposure to H2S.

Reviewer #3 (Public Review):

Summary:<br /> There is a growing body of literature on the clustering of co-active synapses in adult mice, which has important implications for understanding dendritic integration and sensory processing more broadly. However, it has been unclear when this spatial organization of co-active synapses arises during development. In this manuscript, Leighton et al. investigate the emergence of spatially organized, co-active synapses on pyramidal dendrites in the mouse visual cortex before eye-opening. They find that some dendrite segments contain highly active synapses that are co-active with their neighbors as early as postnatal day (P) 8-10, and that these domains of co-active synapses increase their coverage of the dendritic arbor by P12-13. Interestingly, Leighton et al. demonstrate that synapses co-active with their neighbors are more likely to increase their activity across a single recording session, compared to synapses that are not co-active with their neighbors, suggesting local plasticity driven by coincident activity before eye-opening.

The current manuscript includes some replication of earlier results from the same research group (Winnubst et al., 2015), including the presence of clustered, co-active synapses in the visual cortex of mouse pups, and the finding that synapses co-active with their neighbors show an increase in transmission frequency during a recording session. The main novelty in the current study compared to Winnubst et al. (2015) is the inclusion of younger animals (P8-13 in the current study compared to P10-15 in Winnubst et al., 2015). The current manuscript is the first demonstration that active synapses are clustered on specific dendrite segments as early as P8-10 in the mouse visual cortex, and the first to show the progression in active synapse distribution along the dendrite during the 2nd postnatal week. These results from the visual cortex may help inform our understanding of sensory development more broadly.

Strengths:<br /> The authors ask a novel question about the emergence of synaptic spatial organization, and they use well-chosen techniques that directly address their questions despite the challenging nature of these techniques. To capture both structural and functional information from dendrites simultaneously, the authors performed a whole-cell voltage clamp to record synaptic currents arriving at the soma while imaging calcium influx at individual synaptic sites on dendrites. The simultaneous voltage clamp and calcium imaging allowed the authors to isolate individual synaptic inputs without their occlusion by widespread calcium influx from back-propagating action potentials. Achieving in vivo dendrite imaging in live mice that are as young as P8 is challenging, and the resulting data provides a unique view of synaptic activity along individual dendrites in the visual cortex at an early stage in development that is otherwise difficult to assess.

The authors provide convincing evidence that synapses are more likely to be co-active with their neighbors compared to synapses located farther away (Fig. 6F-H), and that synapses co-active with their neighbors increase their transmission frequency during a recording session (Figure 7C). These findings are particularly interesting given that the recordings occur before eye-opening, suggesting a relationship between co-activity and local synaptic plasticity even before the onset of detailed visual input. These results replicate previously published findings from P10-15 pups (Winnubst et al., 2015), increasing confidence in the reproducibility of the data.

The authors also provide novel data documenting for the first time spatially organized, co-active synapses in pups as young as P8. Comparing the younger (P8-10) and older (P12-13) pups, provides insight into how clusters of co-active synapses might emerge during development.

Weaknesses:<br /> This manuscript provides insufficient detail for assessing the rigor and reproducibility of the methods, particularly for age comparisons. The P8-10 vs P12-13 age comparisons are the primary novel finding in this manuscript, and it is, therefore, critical to avoid systematic age differences in the methods and analysis whenever possible. Specific concerns related to the age comparisons are listed below:

• Given that the same research group previously published P12-13 data (Winnubst et al., 2015), it is unclear whether both age groups in the current study were imaged/analyzed in parallel by the same researcher(s), or whether previous data was used for the P12-13 group.

• The authors mention that they used 2 different microscopes, and used a fairly wide range of imaging frame rates (5-15 Hz). It is unclear from the current manuscript whether the same imaging parameters were used across the two age groups. If data for the two experimental groups was collected separately, perhaps at different times, by a different person, or on a different microscope, there is a concern that some differences between the groups may not necessarily be due to age.

• It is unclear whether the image analysis was performed blind to age. Blinding to age during analysis is particularly important for this study, in which it was not possible to blind to age during imaging due to visible differences in size and developmental stage between younger and older pups.

• The relatively low N (where N is the number of dendrites or the number of mice) in this study is acceptable due to the challenging nature of the techniques used, but unintentional sampling bias is a concern. For example, if higher-order dendrites from the apical tuft were imaged at P12-13, while more segments of the apical trunk were imaged at P8-10, this could inadvertently create apparent age differences that were in fact due to dendrite location on the arbor or dendrite depth.

Additional general methodological concerns, which are not specifically related to the age comparisons, are listed below:

• The authors assert that clustered, co-active synapses emerge in the visual cortex before eye-opening, which is an important finding in that it suggests this phenomenon is driven by spontaneous activity rather than visual input. However, this finding hinges on the imaged cells being reliably located in the visual cortex, which is difficult to identify with certainty in animals that have not yet opened their eyes and therefore cannot undergo intrinsic signal imaging to demarcate the boundaries of the visual cortex. If the imaged cells were in, for example, nearby somatosensory cortex, then the observed spatial organization could be due to sensory input rather than spontaneous activity.

• It is unclear how the authors defined a synaptic transmission event in the GCaMP signal (e.g. whether there was a quantitative deltaF/F threshold).

• The authors' division of synapses into spine vs shaft is unconvincing due to the difficulty of identifying Z-projecting spines in images from 2-photon microscopy, where the Z resolution is insufficient to definitively identify Z-projecting spines, and the fact that spines in young animals may be thin and dim. The authors' examples of spine synapses (e.g. in Fig. 2A) are convincing, but some of the putative shaft synapses may in fact be on spines.

Reviewer #3 (Public Review):

Summary:

"Bridging the gap between presynaptic hair cell function and neural sound encoding" by Jaime Tobon and Moser uses patch-clamp electrophysiology in cochlear preparations to probe the pre- and post-synaptic specializations that give rise to the diverse activity of spiral ganglion afferent neurons (SGN). The experiments are quite an achievement! They use paired recordings from pre-synaptic cochlear inner hair cells (IHC) that allow precise control of voltage and therefore calcium influx, with post-synaptic recordings from type I SGN boutons directly opposed to the IHC for both presynaptic control of membrane voltage and post-synaptic measurement of synaptic function with great temporal resolution.

Strengths<br /> Any of these techniques by themselves are challenging, but the authors do them in pairs, at physiological temperatures, and in hearing animals, all of which combined make these experiments a real tour de force. The data is carefully analyzed and presented, and the results are convincing. In particular, the authors demonstrate that post-synaptic features that contribute to the spontaneous rate (SR) of predominantly monophasic post-synaptic currents (PSCs), shorter EPSC latency, and higher PSC rates are directly paired with pre-synaptic features such as a lower IHC voltage activation and tighter calcium channel coupling for release to give a higher probability of release and subsequent increase in synaptic depression. Importantly, IHCs paired with Low and High SR afferent fibers had the same total calcium currents, indicating that the same IHC can connect to both low and high SR fibers. These fibers also followed expected organizational patterns, with high SR fibers primarily contacting the pillar IHC face and low SR fibers primarily contacting the modiolar face. The authors also use in vivo-like stimulation paradigms to show different RRP and release dynamics that are similar to results from SGN in vivo recordings. Overall, this work systematically examines many features giving rise to specializations and diversity of SGN neurons.

Weaknesses / Comments / edits:<br /> 1) The careful analysis of calcium coupling and EPSC metrics is especially nice. Can the authors speculate as to why different synapses (likely in the same IHC) would have different calcium cooperativity?

2) On the bottom of page 6 it would be helpful to mention earlier how many pillar vs modiolar fibers were recorded from, otherwise the skewness of SRs (figure 2H could be thought to be due to predominantly recordings from modiolar fibers. As is, it reads a bit like a cliff-hanger.

3) The contrasts for some of the data could be used to point out that while significant differences occur between low and high SR fibers, some of these differences are no longer apparent when comparing modiolar vs pillar fibers (eg by contrasting Figure 2C and 2K). This can indicate that indeed there are differences between the fiber activity, but that the activity likely exists in a gradient across the hair cell faces. Pointing this out at the top of page 10 (end of the first paragraph) would be helpful, it would make the seemingly contradictory voltage-dependence data easier to understand on first read (voltage-dependence of release is significantly different between different SR fibers (figure 3) but is not significantly different between fibers on different HC faces (figure S3).

4) It should be acknowledged that although the use of post-hearing animals here (P14-23) ensures that SGN have begun to develop more mature activity patterns (Grant et al 2010), the features of the synapses and SGN activity may not be completely mature (Wu et al 2016 PMID: 27733610). Could this explain some of the 'challenges' (authors' section title) detailed on page 28, first full paragraph?

5) In the discussion on page 24, the authors compare their recorded SR of EPSCs to measure values in vivo which are higher. Could this indicate that in vivo, the resting membrane potential of IHCs is more depolarized than is currently used for in vitro cochlear experiments?

6) The results showing lower calcium cooperativity of high SR fibers are powerful, but do the authors have an explanation for why the calcium cooperativity of < 2 is different from that (m = 3-4) observed in other manuscripts?

Reviewer #3 (Public Review):

Summary:<br /> Sang et al. successfully demonstrate that a set of single sensory neurons in the pharynx of _Drosophila_ promotes avoidance of food with high salt concentrations, complementing previous findings on Ir7c neurons with an additional internal sensing mechanism. The experiments are well-conducted and presented, convincingly supporting their important findings and extending the understanding of internal sensing mechanisms. However, a few suggestions could enhance the clarity of the work.

Strengths:<br /> The authors convincingly demonstrate the avoidance phenotype using different behavioral assays, thus comprehensively analyzing different aspects of the behavior. The experiments are straightforward and well-contextualized within existing literature.

Weaknesses:<br /> Discussion<br /> While the authors effectively relate their findings to existing literature, expanding the discussion on the surprising role of Ir60b neurons in both sucrose and salt rejection would add depth. Additionally, considering Yang et al. 2021's (https://doi.org/10.1016/j.celrep.2021.109983) result that Ir60b neurons activate feeding-promoting IN1 neurons, the authors should discuss how this aligns with their own findings.

Lines 187ff: The discussion primarily focuses on taste sensillae outside the labellum, neglecting peg-type sensillae on the inner surface. Clarification on whether these pegs contribute to the described behaviors and if the Poxn mutants described also affect the pegs would strengthen the discussion.

In line 261 the authors state: "We attempted to induce salt activation in the I-type sensilla by ectopically expressing Ir60b, similar to what was observed with Ir56b 8; however, this did not generate a salt receptor (Figures S6A)"<br /> An obvious explanation would be that these neurons are missing the identified necessary co-receptors Ir76b and Ir25a. The authors should discuss here if the Gr33a neurons they target also express these co-receptors, if yes this would strengthen their conclusion that an additional receptor might be missing.

Methods<br /> The description of the Droso-X assay seems to be missing some details. Currently, it is not obvious how the two-choice is established. Only one capillary is mentioned, I assume there were two used? Also, the meaning of the variables used in the equation (DrosoX and DrosoXD) are not explained.

The description of the ex-vivo calcium imaging prep. is unclear in several points:<br /> 1. It is lacking information on how the stimulus was applied (was it manually washed in? If so how was it removed?).<br /> 2. The authors write: "A mild swallow deep well was prepared for sample fixation." I assume they might have wanted to describe a "shallow well"?<br /> 3. "...followed by excising a small portion of the labellum in the extended proboscis region to facilitate tastant access to pharyngeal organs." It is not clear to me how one would excise a small portion of the labellum, the labellum depicts the most distal part of the proboscis that carries the sensillae and pegs. Did the authors mean to say that they cut a part of the proboscis?

Reviewer #3 (Public Review):

In the current manuscript, Matsuo-Takasaki et al. have demonstrated that the addition of PKCβ and WNT signaling pathway inhibitors to the suspension cultures of iPSCs suppresses spontaneous differentiation. These conditions are suitable for large-scale expansion of iPSCs. The authors have shown that they can perform single-cell cloning, direct cryopreservation, and iPSC derivation from PBMCs in these conditions. Moreover, the authors have performed a thorough characterization of iPSCs cultured in these conditions, including an assessment of undifferentiated stem cell markers and genetic stability. The authors have elegantly shown that iPSCs cultured in these conditions can be differentiated into derivatives of three germ layers. By differentiating iPSCs into dopaminergic neural progenitors, cardiomyocytes, and hepatocytes they have shown that differentiation is comparable to adherent cultures. This new method of expanding iPSCs will benefit the clinical applications of iPSCs.

Recently, multiple protocols have been optimized for culturing human pluripotent stem cells in suspension conditions and their expansion. Additionally, a variety of commercially available media for suspension cultures are also accessible. However, the authors have not adequately justified why their conditions are superior to previously published protocols (indicated in Table 1) and commercially available media. They have not conducted direct comparisons. Additionally, the authors have not adequately addressed the observed variability among iPSC lines. While they claim in the Materials and Methods section to have tested multiple pluripotent stem cell lines, they do not clarify in the Results section which line they used for specific experiments and the rationale behind their choices. There is a lack of comparison among the different cell lines. It would also be beneficial to include testing with human embryonic stem cell lines. Additionally, there is a lack of information regarding the specific role of the two small molecules in these conditions. The authors have not attempted to elucidate the underlying mechanism other than RNA expression analysis.

For these reasons some aspects of the manuscript need to be extended:

1. It is crucial for authors to specify the culture media used for suspension cultures. In the Materials and Methods section, the authors mentioned that cells in suspension were cultured in either StemFit AK02N medium, 415 StemFit AK03N (Cat# AK03N, Ajinomoto, Co., Ltd., Tokyo, Japan), or StemScale PSC416 suspension medium (A4965001, Thermo Fisher Scientific, MA, USA). The authors should clarify in the text which medium was used for suspension cultures and whether they observed any differences among these media.

2. In the Materials and Methods section, the authors mentioned that they used multiple cell lines for this study. However, it is not clear in the text which cell lines were used for various experiments. Since there is considerable variation among iPSC lines, I suggest that the authors simultaneously compare 2 to 3 pluripotent stem cell lines for expansion, differentiation, etc.

3. Single-cell sorting can be confusing. Can iPSCs grown in suspensions be single-cell sorted? Additionally, what was the cloning efficiency? The cloning efficiency should be compared with adherent cultures.

4. The authors have not addressed the naïve pluripotent state in their suspension cultures, even though PKC inhibition has been shown to drive cells toward this state. I suggest the authors measure the expression of a few naïve pluripotent state markers and compare them with adherent cultures

Reviewer #3 (Public Review):

Summary: Irisin has previously been demonstrated to be a muscle-secreted factor that affects skeletal homeostasis. Through the use of different experimental approaches, such as genetic knockout models, recombinant Irisin treatment, or different cell lines, the role of Irisin on skeletal homeostasis has been revealed to be more complex than previously thought and this warrants further examination of its role. Therefore, the current study sought to rigorously examine the effects of global Irisin knockout (KO) in male and female mouse bone. Authors demonstrated that in calcium-demanding settings, such as lactation or low-calcium diet, female Irisin KO mice lose less bone compared to wild-type (WT) female mice. Interestingly male Irisin KO mice exhibited worse skeletal deterioration compared to WT male mice when fed a low-calcium diet. When examined for transcriptomic profiles of osteocyte-enriched cortical bone, authors found that Irisin KO altered the expression of osteocytic osteolysis genes as well as steroid and fatty acid metabolism genes in males but not in females. These data support the authors' conclusion that Irisin regulates skeletal homeostasis in sex-dependent manner.

Strengths: The major strength of the study is the rigorous examination of the effects of Irisin deletion in the settings of skeletal maturity and increased calcium demands in female and male mice. Since many of the common musculoskeletal disorders are dependent on sex, examining both sexes in the preclinical setting is crucial. Had the investigators only examined females or males in this study, the conclusions from each sex would have contradicted each other regarding the role of Irisin on bone. Also, the approaches are thorough and comprehensive that assess the functional (mechanical testing), morphological (microCT, BSEM, and histology), and cellular (RNA-seq) properties of bone.

Weaknesses: One of the weaknesses of this study is a lack of detailed mechanistic analysis of why Irisin has a sex-dependent role on skeletal homeostasis. This absence is particularly notable in the osteocyte transcriptomic results where such data could have been used to further probe potential candidate pathways between LC females vs. LC males.

Another weakness is authors did not present data that convincingly demonstrate that Irisin secretion is altered in the skeletal muscle between female vs. male WT mice in response to calcium restriction. The supplement skeletal muscle data only present functional and electrophysiolgical outcomes. Since Itgav or Itgb5 were not different in any of the experimental groups, it is assumed that the changes in the level of Irisin is responsible for the phenotypes observed in WT mice. Assessing Irisin expression will further strengthen the conclusion based on observing skeletal changes that occur in Irisin KO male and female mice.

Reviewer #3 (Public Review):

The work extends earlier studies on the Drosophila Id protein EMC to uncover a potential pathway that explains several tissue-scale developmental abnormalities in emc mutants. It also describes a non-apoptotic role for caspases in cell biology.

Strengths:<br /> The work adds to an emerging new set of functions for caspases beyond their canonical roles as cell death mediators. This novelty is a major strength as well as its reliance on genetic-based in vivo study. The study will be of interest to those who are curious about caspases in general.

Weaknesses:<br /> The manuscript relies on imaging experiments using genetic mosaic imaginal discs. It is for the most part a qualitative analysis, showing representative samples with a small number of mutant clones in each. Although the senior author has a long track record of using experiments like this to rigorously discover regulatory mechanisms in this system, it is straightforward in 2023 to use Fiji and other image analysis tools to measure fluorescence. Such measurements could be done for all replicate clones of a given genotype as well as genetic control sampling. These could be presented in plots that would not only provide quantitative and statistical measurements, but will be more reader-friendly to those who are not fly people.

Likewise, more details are needed to describe how clone areas were measured in Figure 1. Did they measure each clone and its twin spot, and then calculate the area ratio for each clone and its paired twin spot? This would be the correct way to analyze the data, yielding many independent measurements of the ratio. And doing so would obviate the need to log transform the data which is inexplicable unless they were averaging clones and twins within a disc and making replicates. More explanation is needed and if they indeed averaged, then they need to calculate the ratios pairwise for each clone and twin.

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Reviewer #3 (Public Review):

Summary:

Allosteric regulations are complicated in multi-domain proteins and many large-scale mutational data cannot be explained by current theoretical models,, especially for those that are neither in the functional/allosteric sites nor on the allosteric pathways. This work provides a statistical thermodynamic model for a two-domain protein, in which one domain contains an effector binding site and the other domain contains a functional site. The authors build the model to explain the mutational experimental data of TetR, a transcriptional repress protein that contains a ligand and a DNA-binding domain. They incorporate three basic parameters, the energy change of the ligand and DNA binding domains before and after binding, and the coupling between the two domains to explain the free energy landscape of TetR's conformational and binding states. They go further to quantitatively explain the in vivo expression level of the TetR-regulated gene by fitting into the induction curves of TetR mutants. The effects of most of the mutants studied could be well explained by the model. This approach can be extended to understand the allosteric regulation of other two-domain proteins, especially to explain the effects of widespread mutants not on the allosteric pathways.

Strengths:

The effects of mutations that are neither in the functional or allosteric sites nor in the allosteric pathways are difficult to explain and quantify. This work develops a statistical thermodynamic model to explain these complicated effects. For simple two-domain proteins, the model is quite clean and theoretically solid. For the real TetR protein that forms a dimeric structure containing two chains with each of them composed of two domains, the model can explain many of the experimental observations. The model separates intra and inter-domain influences that provide a novel angle to analyse allosteric effects in multi-domain proteins.

Weaknesses:

As mentioned above, the TetR protein is not a simple two-main protein, but forms a dimeric structure in which the DNA binding domain in each chain forms contacts with the ligand-binding domain in the other chain. In addition, the two ligand-binding domains have strong interactions. Without considering these interactions, especially those mutants that are on these interfaces, the model may be oversimplified for TetR.

Reviewer #3 (Public Review):

Summary: This manuscript explores the development of a rodent voluntary oral THC consumption model. The authors use the model to demonstrate that similar effect levels of THC can be observed to what has previously been described for i.p. THC administration.

Strengths: Overall this is an interesting study with compelling data presented. There is a growing need within the field of cannabinoid research to explore more 'realistic' routes of cannabinoid administration, such as oral consumption or inhalation. The evidence presented here shows the utility of this oral administration model.

Weaknesses: The main weaknesses of the manuscript revolve around clarification of the Methods section. All of these weaknesses are described in the "Recommendations to authors" section. Revising the manuscript would account for many of these weaknesses.

Reviewer #3 (Public Review):

Summary:<br /> The paper investigates the effects of long-term linguistic experience on early auditory processing, a subject that has been relatively less studied compared to short-term influences. Using MEG, the study examines brain responses to auditory stimuli in speakers of Spanish and Basque, whose syntactic rules provide different degrees of exposure to durational patterns (long-short vs short-long). The findings suggest that both long-term language experience, as well as short-term transitional probabilities, can shape auditory predictive coding for non-linguistic sound sequences, evidenced by differences in mismatch negativity amplitudes localised to the left auditory cortex.

Strengths:<br /> The study integrates linguistics and auditory neuroscience in an interesting interdisciplinary way that may interest linguists as well as neuroscientists. The fact that long-term language experience affects early auditory predictive coding is important for understanding group and individual differences in domain-general auditory perception. It has importance for neurocognitive models of auditory perception (e.g. inclusion of long-term priors), and will be of interest to researchers in linguistics, auditory neuroscience, and the relationship between language and perception. The inclusion of a control condition based on pitch is also a strength.

Weaknesses:<br /> The main weaknesses are the strength of the effects and generalisability. The sample size is also relatively small by today's standards, with N=20 in each group. Furthermore, the crucial effects are all mostly in the .01>P<.05 range, such as the crucial interaction P=.03. It would be nice to see it replicated in the future, with more participants and other languages. It would also have been nice to see behavioural data that could be correlated with neural data to better understand the real-world consequences of the effect.

Reviewer #3 (Public Review):

Summary:<br /> Hauser et al. provide an exceptional study describing the role of resident mast cells in amphibian epidermis that produce anti-inflammatory cytokines that prevent Batrachochytrium dendrobatidis (Bd) infection from causing harmful inflammation, and also protect frogs from changes in skin microbiomes and loss of mucin in glands and loss of mucus integrity that otherwise cause changes to their skin microbiomes. Neutrophils, in contrast, were not protective against Bd infection. Beyond the beautiful cytology and transcriptional profiling, the authors utilized elegant cell enrichment experiments to enrich mast cells by recombinant stem cell factor, or to enrich neutrophils by recombinant colony-stimulating factor-3, and examined respective infection outcomes in Xenopus.

Strengths:<br /> Through the use of recombinant IL4, the authors were able to test and eliminate the hypothesis that mast cell production of IL4 was the mechanism of host protection from Bd infection. Instead, impacts on the mucus glands and interaction with the skin microbiome are implicated as the protective mechanism. These results will press disease ecologists to examine the relative importance of this immune defense among species, the influence of mast cells on the skin microbiome and mucosal function, and open the potential for modulating mucosal defense.

Weaknesses:<br /> A reduction of bacterial diversity upon infection, as described at the end of the results section, may not always be an "adverse effect," particularly given that anti-Bd function of the microbiome increased. Some authors (see Letourneau et al. 2022 ISME, or Woodhams et al. 2023 DCI) consider these short-term alterations as encoding ecological memory, such that continued exposure to a pathogen would encounter an enriched microbial defense. Regardless, mast cell-initiated protection of the mucus layer may negate the need for this microbial memory defense.

While the description of the mast cell location in the epidermal skin layer in amphibians is novel, it is not known how representative these results are across species ranging in chytridiomycosis susceptibility. No management applications are provided such as methods to increase this defense without the use of recombinant stem cell factor, and more discussion is needed on how the mast cell component (abundance, distribution in the skin) of the epidermis develops or is regulated.

Reviewer #3 (Public Review):

Summary:<br /> The authors have examined the 5-HT3 receptor using voltage clamp fluorometry, which enables them to detect structural changes at the same time as the state of receptor activation. These are ensemble measurements, but they enable a picture of the action of different agonists and antagonists to be built up.

Strengths:<br /> The combination of rigorously tested fluorescence reporters with oocyte electrophysiology is a solid development for this receptor class.

Weaknesses:<br /> The interpretation of the data is solid but relevant foundational work is ignored. Although the data represent a new way of examining the 5-HT3 receptor, nothing that is found is original in the context of the superfamily. Quantitative information is discussed but not presented.

Reviewer #3 (Public Review):

Summary:<br /> In this report, Ravala et al demonstrate that IP4, the soluble head-group of phosphatiylinositol 3,4,5 - trisphosphate (PIP3), is an inhibitor of pREX-1, a guanine nucleotide exchange factor (GEF) for Rac1 and related small G proteins that regulate cell migration. This finding is perhaps unexpected since pREX-1 activity is PIP3-dependent. By way of Cryo-EM (revealing the structure of the p-REX-1/IP4 complex at 4.2Å resolution), hydrogen-deuterium mass spectrometry, and small angle X-ray scattering, they deduce a mechanism for IP4 activation, and conduct mutagenic and cell-based signaling assays that support it. The major finding is that IP4 stabilizes two interdomain interfaces that block access to the DH domain, which conveys GEF activity towards small G protein substrates. One of these is the interface between the PH domain that binds to IP4 and a 4-helix bundle extension of the IP4 Phosphatase domain and the DEP1 domain. The two interfaces are connected by a long helix that extends from PH to DEP1. Although the structure of fully activated pREX-1 has not been determined, the authors propose a "jackknife" mechanism, similar to that described earlier by Chang et al (2022) (referenced in the author's manuscript) in which binding of IP3 relieves a kink in a helix that links the PH/DH modules and allows the DH-PH-DEP triad to assume an extended conformation in which the DH domain is accessible. While the structure of the activated pREX-1 has not been determined, cysteine mutagenesis that enforces the proposed kink is consistent with this hypothesis. SAXS and HDX-MS experiments suggest that IP4 acts by stiffening the inhibitory interfaces, rather than by reorganizing them. Indeed, the cryo-EM structure of ligand-free pREX-1 shows that interdomain contacts are largely retained in the absence of IP4.

Strengths:<br /> The manuscript thus describes a novel regulatory role for IP4 and is thus of considerable significance to our understanding of regulatory mechanisms that control cell migration, particularly in immune cell populations. Specifically, they show how the inositol polyphosphate IP4 controls the activity of pREX-1, a guanine nucleotide exchange factor that controls the activity of small G proteins Rac and CDC42 . In their clearly written discussion, the authors explain how PIP3, the cell membrane, and the Gbeta-gamma subunits of heterotrimeric membranes together localize pREX-1 at the membrane and induce activation. The quality of experimental data is high and both in vitro and cell-based assays of site-directed mutants designed to test the author's hypotheses are confirmatory. The results strongly support the conclusions. The combination of cryo-EM data, that describe the static (if heterogeneous) structures with experiments (small angle x-ray scattering and hydrogen-deuterium exchange-mass spectrometry) that report on dynamics are well employed by the authors

Weaknesses:<br /> There are a few weaknesses. While the resolution of the cryo-EM structure is modest, it is sufficient to identify the domain-domain interactions that are mechanistically important, since higher-resolution structures of various pREX-1 modules are available.

Reviewer #3 (Public Review):

Summary:<br /> The manuscript by Yao et al. investigates the intracellular trafficking of Botulinum neurotoxin A (BoNT/A), a potent toxin used in clinical and cosmetic applications. Contrary to the prevailing understanding of BoNT/A translocation into the cytosol, the study suggests a retrograde migration from the synapse to the soma-localized Golgi in neurons. Using a genome-wide siRNA screen in genetically engineered neurons, the researchers identified over three hundred genes involved in this process. The study employs organelle-specific split-mNG complementation, revealing that BoNT/A traffics through the Golgi in a retromer-dependent manner before moving to the endoplasmic reticulum (ER). The Sec61 complex is implicated in the retro-translocation of BoNT/A from the ER to the cytosol. Overall, the research challenges the conventional model of BoNT/A translocation, uncovering a complex route from synapse to cytosol for efficient intoxication. The findings are based on a comprehensive approach, including the introduction of a fluorescent reporter for BoNT/A catalytic activity and genetic manipulations in neuronal cell lines. The conclusions highlight the importance of retrograde trafficking and the involvement of specific genes and cellular processes in BoNT/A intoxication.

Strengths:<br /> The major part of the experiments are convincing. They are well-controlled and the interpretation of their results is balanced and sensitive.

Weaknesses:<br /> To my opinion, the main weakness of the paper is in the interpretation of the data equating loss of tGFP signal (when using the Red SNAPR assay) with proteolytic cleavage by the toxin. Indeed, the first step for loss of tGFP signal by degradation of the cleaved part is the actual cleavage. However, this needs to be degraded (by the proteasome, I presume), a process that could in principle be affected (in speed or extent) by the toxin.

Reviewer #3 (Public Review):

In this manuscript, Gustison et al., describe the development of an automated whole-brain mapping pipeline, including the first 3D histological atlas of the prairie vole, and then use that pipeline to quantify Fos immunohistochemistry as a measure of neural activity during mating and pair bonding in male and female prairie voles. Prairie voles have become a useful animal model for examining the neural bases of social bonding due to their socially monogamous mating strategy. Prior studies have focused on identifying the role of a few neuromodulators (oxytocin, vasopressin, dopamine) acting in limited number of brain regions. The authors use this unbiased approach to determine which areas become activated during mating, cohabitation, and pair bonding in both sexes to identify 68 brain regions clustered in seven brain-wide neuronal circuits that are activated over the course of pair bonding. This is an important study because i) it generates a valuable tool and analysis pipeline for other investigators in the prairie vole research community and ii) it highlights potential involvement of many brain regions in regulating sexual behavior, social engagement and pair bonding that have not been previously investigated.

Strengths of the study include the unbiased assessment of neural activity using the automated whole brain activity mapped onto the 3D histological atlas. The design of the behavioral aspect of study is also a strength. Brains were collected at baseline and 2.5, 6 and 22 hrs after cohabitation with either a sibling or opposite sex partner. These times were strategically chosen to correspond to milestones in pair bond development. Behavior was also quantified during epochs over the 22 hr period providing useful information on the progression of behaviors (e.g. mating) during pair bonding and relating Fos activation to specific behaviors (e.g. sex vs bonding). The sibling co-housed group provided an important control, enabling identification of areas specifically activated by sex and bond formation. The analyses of the data were rigorous, resulting in convincing conclusions. While there was nothing particularly surprising in terms of the structures that were identified to be active during the mating and cohabitation, the statistical analysis revealed interesting relationships in terms of interactions of the various clusters, and also some level of synchrony in brain activation between partners. Furthermore, ejaculation was found to be the strongest predictor of Fos activation in both males and females. The sex differences identified in the study was subtle and less than the authors expected, which is interesting.

While the study provides a potentially useful tool and approach that may be general use to the prairie vole community and identifies in an anatomically precise manner areas that may be important for mating or pair bond formation, there are some weaknesses as well. The study is largely descriptive. It is impossible to determine whether the activated areas are simply involved in sex or in the pair bond process itself. In other words, the authors did not use the Fos data to inform functional testing of circuits in pair bonding or mating behaviors. However, that is likely beyond the scope of this paper in which the goal was more to describe the automated, unbiased approach. This weakness is offset by the value of the comprehensive and detailed analysis of the Fos activation data providing temporal and precise anatomical relationships between brain clusters and in relation to behavior. The manuscript concludes with some speculative interpretations of the data, but these speculations may be valuable for guiding future investigations.

Reviewer #3 (Public Review):

Summary:

In this manuscript, the authors present a new automated image analysis pipeline named WormPsyQi which allows researchers to quantify various parameters of synapses in C. elegans. Using a collection of newly generated transgenic strains in which synaptic proteins are tagged with fluorescent proteins, the authors showed that WormPsyQi can reliably detect puncta of synaptic proteins, and measure several parameters, including puncta number, location, and size.

Strengths:

The image analysis of fluorescently labeled synaptic (or other types of) puncta pattern requires extensive experience such that one can tell which puncta likely represent bona fide synapse or background noise. The authors showed that WormPsyQi nicely reproduced the quantifications done manually for most of the marker strains they tested. Many researchers conducting such types of quantifications would receive significant benefits in saving their time by utilizing the pipeline developed by the authors. The collection of new markers would also help researchers examine synapse patterning in different neuron types which may have unique mechanisms in synapse assembly and specificity. The authors describe the limitations of the use of toolkits and potential solutions users can take.

Reviewer #3 (Public Review):

Summary:

This hybrid experimental/computational study by Hernandez-Hernandez sheds new light on sex-specific differences between male and female arterial myocytes from resistance arteries. The authors conduct careful experiments in isolated myocytes from male and female mice to obtain the data needed to parameterized sex-specific models of two important ionic currents (i.e., those mediated by CaV1.2 and KV2.1). Available experimental data suggest that KV1.5 channel currents from male and female myocytes are similar, but simulations conducted in the novel Hernandez-Hernandez sex-specific models provide a more nuanced view. This gives rise to the first of the authors' three key scientific claims: (1) In males, KV1.5 is the dominant current regulating membrane potential; whereas, in females, KV2.1 plays a primary role in voltage regulation. They further show that this (2) the latter distinction drives drive sex-specific differences in intracellular Ca2+ and cellular excitability. Finally, working with one-dimensional models comprising several copies of the male/female myocyte models linked by resistive junctions, they use simulations to (3) predict that sensitivity of arterial smooth muscle to Ca2+ channel-blocking drugs commonly used to treat hypertension is heightened in female compared to male cells.

In my opinion, the following strengths of the work are particularly notable:

• The Methodology is described in exquisite detail in straightforward language that will be easy to understand for most if not all peer groups working in computational physiology. The authors have deployed standard protocols (e.g., parameter fitting as described by Kernik et al., sensitivity analysis as described by Sobie et al.) and appropriate brief explanations of these techniques are provided. The manoeuvre used to represent stochastic effects on voltage dynamics is particularly clever and something I have not personally encountered before. Collectively, these strengthen the credibility of the model and greatly enrich the manuscript.<br /> • The Results section describes findings that robustly support the three key scientific claims outlined in my Summary. It is evident these experiments were carefully designed and carried out with care and intentionality. Several figures show experimental data side-by-side with outputs from the corresponding models. These are an excellent illustration of the power of the authors' novel sex-specific computational simulation platform.

Reviewer #3 (Public Review):

Summary:<br /> A mechanical model is used with input force patterns to generate output curvature patterns, corresponding to a number of different locomotion behaviors in C. elegans

Strengths:<br /> The use of a mechanical model to study a variety of locomotor sequences and the grounding in empirical data are strengths. The matching of speeds (though qualitative and shown only on agar) is a strength.

Weaknesses:<br /> What is the relation between input and output data? How does the input-output relation depend on the parameters of the model? What biological questions are addressed and can significant model predictions be made?

Reviewer #3 (Public Review):

The manuscript "Mechanical activation of TWIK-related potassium channel by nanoscopic movement and second messenger signaling" presents a new mechanism for the activation of TREK-1 channel. The mechanism suggests that TREK1 is activated by phosphatidic acids that are produced via a mechanosensitive motion of PLD2 to PIP2-enriched domains. Overall, I found the topic interesting but several typos and unclarities reduced the readability of the manuscript. Additionally, I have several major concerns on the interpretation of the results. Therefore, the proposed mechanism is not fully supported by the presented data. Lastly, the mechanism is based on several previous studies from the Hansen lab, however, the novelty of the current manuscript is not clearly stated. For example, in the 2nd result section, the authors stated, "fluid shear causes PLD2 to move from cholesterol dependent GM1 clusters to PIP2 clusters and this activated the enzyme". However, this is also presented as a new finding in section 3 "Mechanism of PLD2 activation by shear."<br /> In the revised manuscript, the authors addressed most of my concerns. I still have the following suggestions/confusions.<br /> 1. the reviewer would highly appreciate verification of the cholesterol assay, either by additional experiment or by citations of independent work.

2. The claim on "shear thinning" is still very confusing. First, asymmetric insertion of molecules to one monolayer of the membrane is a main mechanism for membrane bending and curvature formation. Second, why is "shear thinning" equivalent to entropy/order?

Reviewer #3 (Public Review):

Summary:<br /> The paper explores chemosensory behaviour in surface and cave morphs and F2 hybrids in the Mexican cavefish Astyanax mexicanus. The authors develop a new behavioural assay for the long-term imaging of individual fish in a parallel high-throughput setup. The authors first demonstrate that the different morphs show different basal exploratory swimming patterns and that these patterns are stable for individual fish. Next, the authors test the attraction of fish to various concentrations of alanine and other amino acids. They find that the cave morph is a lot more sensitive to chemicals and shows directional chemotaxis along a diffusion gradient of amino acids. For surface fish, although they can detect the chemicals, they do not show marked chemotaxis behaviour and have an overall lower sensitivity. These differences have been reported previously but the authors report longer-term observations on many individual fish of both morphs and their F2 hybrids. The data also indicate that the observed behavior is a quantitative genetic trait. The approach presented will allow the mapping of genes' contribution to these traits. The work will be of general interest to behavioural neuroscientists and those interested in olfactory behaviours and the individual variability in behavioural patterns.

Strengths:<br /> A particular strength of this paper is the development of a new and improved setup for the behavioural imaging of individual fish for extended periods and under chemosensory stimulation. The authors show that cavefish need up to 24 h of habituation to display a behavioural pattern that is consistent and unlikely to be due to the stressed state of the animals. The setup also uses relatively large tanks that allow the build-up of chemical gradients that are apparently present for at least 30 min.

The paper is well written, and the presentation of the data and the analyses are clear and to a high standard.

Weaknesses:<br /> One point that would benefit from some clarification or additional experiments is the diffusion of chemicals within the behavioural chamber. The behavioural data suggest that the chemical gradient is stable for up to 30 min, which is quite surprising. It would be great if the authors could quantify e.g. by the use of a dye the diffusion and stability of chemical gradients.

The paper starts with a statement that reflects a simplified input-output (sensory-motor) view of the organisation of nervous systems. "Their brains perceive the external world via their sensory systems, compute information and generate appropriate behavioral outputs." The authors' data also clearly show that this is a biased perspective. There is a lot of spontaneous organised activity even in fish that are not exposed to sensory stimulation. This sentence should be reworded, e.g. "The nervous system generates autonomous activity that is modified by sensory systems to adapt the behavioural pattern to the external world." or something along these lines.

Reviewer #3 (Public Review):

Summary:<br /> In human patients with Huntington's disease (HD), caused by a CAG repeat expansion mutation, the number of uninterrupted CAG repeats at the genomic level influences age-at-onset of clinical signs independent of the number of polyglutamine repeats at the protein level. In most patients, the CAG repeat terminates with a CAA-CAG doublet. However, CAG repeat variants exist that either do not have that doublet or have two doublets. These variants consequently differ in their number of uninterrupted CAG repeats, while the number of glutamine repeats is the same as both CAA and CAG codes for glutamine. The authors first confirm that a shorter uninterrupted CAG repeat number in human HD patients is associated with developing the first clinical signs of HD later. They predict that introducing a further CAA-CAG doublet will result in years of delay of clinical onset. Based on this observation, the authors tested the hypothesis that turning CAG to CAA within a CAG repeat sequence using base editing techniques will benefit HD biology. They show that, indeed, in HD cell models (HEK293 cells expressing 16/17 CAG repeats; a single human stem cell line carrying a CAG repeat expansion in the fully penetrant range with 42 CAG repeats), their base editing strategies do induce the desired CAG-CAA conversion. The efficiency of conversion differed depending on the strategy used. In stem cells, delivery posed a problem, so to test allele specificity, the authors then used a HEK 293 cell line with 51 CAG repeats on the expanded allele. Conversion occurred in both alleles with huntingtin protein and mRNA levels; transcriptomics data was unchanged. In knock-in mice carrying 110 CAG repeats, however, base editing did not work as well for different, mainly technical, reasons.

Strengths:<br /> The authors use state-of-the-art methods and carefully and thoroughly designed experiments. The data support the conclusions drawn. This work is a very valuable translation from the insight gained from large GWAS studies into HD pathogenesis. It rightly emphasises the potential this has as a causal treatment in HD, while the authors also acknowledge important limitations.

Weaknesses:<br /> They could dedicate a little more to discussing several of the mentioned challenges. The reader will better understand where base editing is in HD currently and what needs to be done before it can be considered a treatment option. For instance,

-It is important to clarify what can be gained by examining again the relationship between uninterrupted CAG repeat length and age-at-onset. Could the authors clarify why they do this and what it adds to their already published GWAS findings? What is the n of datasets?<br /> -What do they think an ideal conversion rate would be, and how that could be achieved?<br /> -Is there a dose-effect relationship for base editing, and would it be realistic to achieve the ideal conversion rate in target cells, given the difficulties described by the authors in differentiated neurons from stem cells?<br /> - The liver is a good tool for in-vivo experiments examining repeat instability in mouse models. However, the authors could comment on why they did not examine the brain.<br /> - Is there a limit to judging the effects of base editing on somatic instability with longer repeats, given the difficulties in measuring long CAG repeat expansions?<br /> - Given the methodological challenges for assessing HTT fragments, are there other ways to measure the downstream effects of base editing rather than extrapolate what it will likely be?<br /> - Sequencing errors could mask low-level, but biologically still relevant, off-target effects (such as gRNA-dependent and gRNA-independent DNA, Off-targets, RNA off-targets, bystander editing). How likely is that?<br /> - How worried are the authors about immune responses following base editing? How could this be assessed?

Reviewer #3 (Public Review):

This research addresses a critical challenge in malaria research, specifically how to effectively access the highly polymorphic var gene family using short-read sequence data. The authors successfully tackled this issue by introducing an optimization of their original de novo assembler, which notably more than doubled the N50 metric and greatly improved the assembly of var genes.

The most intriguing aspect of this study lies in its methodologies, particularly the longitudinal analysis of assembled var transcripts within subjects. This approach allows for the construction of an unbiased var repertoire for each individual, free from the influence of a reference genome or other samples. These sample-specific var gene repertoires are then tracked over time in culture to evaluate the reliability of using cultured samples for inferences about in vivo expression patterns. The findings from this analysis are thought-provoking. While the authors conclude that culturing parasites can lead to unpredictable transcriptional changes, they also observe that the overall ranking of each var gene remains relatively robust over time. This resilience in the var gene ranking within individuals raises intriguing questions about the mechanisms behind var gene switching and adaptation during short-term culture.

In addition to the var gene-specific analysis, the study also delves into a comparison of ex vivo samples with generation 1 and generation 2 cultured parasites across the core genome. This analysis reveals substantial shifts in expression due to culture adaptation, shedding light on broader changes in the parasite transcriptome during short-term culture.

In summary, this research contributes to our understanding of var gene expression and potentially associations with disease. It emphasizes the importance of improved assembly techniques to access var genes and underscores the challenges of using short-term cultured parasites to infer in vivo characteristics. The longitudinal analysis approach offers a fresh perspective on var gene dynamics within individuals and highlights the need for further investigations into var gene switching and adaptation during culture.

Reviewer #3 (Public Review):

Peng et al. designed a computational framework for identifying pioneer factors using epigenomic data from five cell types. The identification of pioneer factors is important for our understanding of the epigenetic and transcriptional regulation of cells. A computational approach toward this goal can significantly reduce the burden of labor-intensive experimental validation.

The authors have addressed my previous comments.

The main issue identified in this re-review is based on the authors' additional experiments to investigate the reproducibility of the pioneer factors identified in the previous analysis that anchored on H1 ESCs.

The additional analysis that uses the other four cell types (HepG2, HeLa-S3, MCF-7, and K562) as anchors reveals the low reproducibility/concordance and high dependence on the selection of anchor cell type in the computational framework. In particular, now several stem cell related TFs (e.g. ESRRB, POU5F1) are ranked markedly higher when H1 ESC is not used as the anchor cell type as shown in Supplementary Figure 5.

Of note, the authors have now removed the shape labels that denote Yamanaka factors in Figure 2c (revised manuscript) that was presented in the main Figure 2a in the initial submission. The NFYs and ESRRB labels in Supplementary 4a are also removed and the boxplot comparing NFYs and ESRRB with other TF are also removed in this figure. Removing these results effectively hides the issues of the computational framework we identified in this revision. Please justify why this was done.

In summary, these new results reveal significant limitations of the proposed computational framework for identifying pioneer factors. The current identifications appear to be highly dependent on the choice of cell types.

Reviewer #3 (Public Review):

Summary:

This article demonstrates a Pax1-Col11a1-Mmp3 signaling axis associated with adolescent idiopathic scoliosis and finds that estrogen affects this signaling axis. In addition, the authors have identified a new COL11A1 mutation and verified its effect on the Pax1-Col11a1-Mmp3 axis.

Strengths:

1. Col11a1P1335L is verified in multicenter cohorts with high confidence.

2. The article identified a potential pathogenesis of AIS.

Weaknesses:

The SV40-immortalized cell line established from Col11a1fl/fl mouse rib cartilage was applied in the study, and overexpression system was used to confirm that P1335L variant in COL11A1 perturbs its regulation of MMP3. However, due to the absence of P1335L point mutant mice, it cannot be confirmed whether P1335L can actually cause AIS, and the pathogenicity of this mutation cannot be directly verified.

Reviewer #3 (Public Review):

Summary:<br /> This manuscript by Toth et al reveals a conserved phosphorylation site within the RIN4 (RPM1-interacting protein 4) R protein that is exclusive to two of the four nodulating clades, Fabales and Rosales. The authors present persuasive genetic and biochemical evidence that phosphorylation at the serine residue 143 of GmRIN4b, located within a 15-aa conserved motif with a core five amino acids 'GRDSP' region, by SymRK, is essential for optimal nodulation in soybean. While the experimental design and results are robust, the manuscript's discussion fails to clearly articulate the significance of these findings. Results described here are important to understand how the symbiosis signaling pathway prioritizes associations with beneficial rhizobia, while repressing immunity-related signals.

Strengths:<br /> The manuscript asks an important question in plant-microbe interaction studies with interesting findings.

Overall, the experiments are detailed, thorough, and very well-designed. The findings appear to be robust.

The authors provide results that are not overinterpreted and are instead measured and logical.

Weaknesses:<br /> No major weaknesses. However, a well-thought-out discussion integrating all the findings and interpreting them is lacking; in its current form, the discussion lacks 'boldness'. The primary question of the study - how plants differentiate between pathogens and symbionts - is not discussed in light of the findings. The concluding remark, "Taken together, our results indicate that successful development of the root nodule symbiosis requires cross-talk between NF-triggered symbiotic signaling and plant immune signaling mediated by RIN4," though accurate, fails to capture the novelty or significance of the findings, and left me wondering how this adds to what is already known. A clear conclusion, for eg, the phosphorylation of RIN4 isoforms by SYMRK at S143 modulates immune responses during symbiotic interactions with rhizobia, or similar, is needed.

Reviewer #3 (Public Review):

Summary:<br /> Regulated chloroplast breakdown allows plants to modulate these energy-producing organelles, for example during leaf aging, or during changing light conditions. This manuscript investigates how chloroplasts are broken down during light-limiting conditions.

The authors present very nice time-lapse imaging of multiple proteins as buds form on the surface of chloroplasts and pinch away, then associate with the vacuole. They use mutant analysis and autophagy markers to demonstrate that this process requires the ATG machinery, but not dynamin-related proteins that are required for chloroplast division. The manuscript concludes with a discussion of an internally-consistent model that summarizes the results.

Strengths:<br /> The main strength of the manuscript is the high-quality microscopy data. The authors use multiple markers and high-resolution time-lapse imaging to track chloroplast dynamics under light-limiting conditions.

Weaknesses:<br /> The main weakness of the manuscript is the lack of quantitative data. Quantification of multiple events is required to support the authors' claims, for example, claims about which parts of the plastid bud, about the dynamics of the events, about the colocalization between ATG8 and the plastid stroma buds, and the dynamics of this association. Without understanding how often these events occur and how frequently events follow the manner observed by the authors (in the 1 or 2 examples presented in each figure) it is difficult to appreciate the significance of these findings.

Reviewer #3 (Public Review):

The manuscript reports data collected in awake toddlers recording BOLD while watching videos. The authors analyse the BOLD time series using two different statistical approaches, both very complex but do not require any a priori determination of the movie features or contents to be associated with regressors. The two main messages are that 1) toddlers have occipital visual areas very similar to adults, given that an SRM model derived from adult BOLD is consistent with the infant brains as well; 2) the retinotopic organization and the spatial frequency selectivity of the occipital maps derived by applying correlation analysis are consistent with the maps obtained by standard and conventional mapping.

Clearly, the data are important, and the author has achieved important and original results. However, the manuscript is totally unclear and very difficult to follow; the figures are not informative; the reader needs to trust the authors because no data to verify the output of the statistical analysis are presented (localization maps with proper statistics) nor so any validation of the statistical analysis provided. Indeed what I think that manuscript means, or better what I understood, may be very far from what the authors want to present, given how obscure the methods and the result presentation are.

In the present form, this reviewer considers that the manuscript needs to be totally rewritten, the results presented each technique with appropriate validation or comparison that the reader can evaluate.

Reviewer #3 (Public Review):

Summary:

Mao and colleagues generated powerful reagents to genetically analyse chemical communication (CCT) in the brain, and in the process uncovered a function for the CNMa neuropeptide expressed in a subset of DN1p neurons that contributes to the temporal organization of locomotor activity, i.e., the timing of morning anticipation.

Strengths:

The strength of the manuscript relies on the generation/characterization of new tools for conditional targeting a well-defined set of CCT genes along with the design and testing of improved versions of Cas9 for efficient knockout. Such invaluable resources will be of interest to the whole community. The authors employed these tools and intersectional genetics to provide an alternative profiling of clock neurons, which is complementary to the ones already published. Furthermore, they uncovered a role for CNMamide, expressed in two DN1ps, in the timing of morning anticipation.

Weaknesses:

They targeted an extensive set of candidate genes putatively involved in communication (transporters, receptor subunits, neuropeptides, neurotransmitter synthesis, etc); they provide a list of efficient gRNAs to target even a longer list of candidate genes, however, it is not clear if all of those made it into transgenic lines that effectively mediate targeting all chemical transmission genes (as suggested by the authors).

Reviewer #3 (Public Review):

Though it is speculated that gene-environment interactions (GxE) contribute to disease heritability, they remain challenging to detect. Here, the authors use a massively parallel reporter assay in vascular endothelial cells treated with or without caffeine to explore context-specific gene regulation. They use a library of 200-bp candidate regions selected from a variety of genetic studies (eQTL, GWAS) and demonstrate allelic bias in activity across a large proportion, including variants with caffeine-specific allelic effects. The described assays represent a useful approach for examining GxE in complex traits, thus these results are of broad appeal. I have great enthusiasm for the experimental design, including the large library and sample size, testing the MPRA in an appropriate cell type with a relevant stimulus, and interesting functional analyses including transcription factor motif enrichment and comparison to GTEx data. My main critique is that the description of analyses and results lacks the clarity that would aid the reader in interpretation.

1. The abstract states that >43k variants are tested in the library while the methods section states that >43k constructs were tested. Because you tested allele pairs, my expectation is that you would have used ~86k constructs, and at various points, you mention denominators that are higher than 43k. Please address this discrepancy.<br /> 2. Previously, you reported allele-specific expression analysis across many conditions, including caffeine treatment. In that study, you observed high levels of differential expression induced by caffeine treatment (on the order of thousands of genes) with only a modest number of SNPs with allele-specific expression after caffeine treatment. In the current study, you report that only ~800 constructs are differentially active after caffeine treatment which you state as evidence that "caffeine overall increases the activity of the regulatory elements," but this is quite a small number given that you tested tens of thousands of constructs. Later you describe >8k constructs with conditional allele-specific expression. Do you mean that the former subset only displays caffeine effects without allele-specific expression? And taking both studies into account, what do you think accounts for the seeming discrepancies between the relative amount of conditional allele-specific expression measured by RNA-seq vs BiT-STARR-seq?<br /> 3. Your transcription factor motif enrichment analyses are interesting, and would benefit from a further grounding in the biology of the cells you're working with. To this end, what proportion of the transcription factor sets that you use for enrichment are expressed in your cell model? For those that are enriched, are they highly expressed, and does that expression vary with caffeine treatment? You provide some of this information for a specific example (rs228271), but a broader discussion is warranted.<br /> 4. I suggest elaborating on the choice of treatment conditions to provide valuable context. Acute responses to caffeine exposure may vary from chronic exposure. In this study, I think a single acute exposure is more than appropriate for reasons of feasibility and many of the regulatory pathways will be shared between acute and long-term; however, given that CAD is a chronic disease that develops over many years, it would be worthwhile to speculate on longer term effects of caffeine exposure in your model system.

Reviewer #3 (Public Review):

The authors inactivated the MurT-GatD of Mycobacterium bovis BCG using CRISPR interference and found that loss of these enzymes curbs growth but also alters the cell envelope and cell wall composition. As MurT-GatD are required for amidation of D-glutamate residues in the cell wall and amidation is required for cell wall crosslinking, depletion of MurT-GatD leads to envelope defects and increased sensitivity to cell wall-targeting antibiotics. Loss of D-glutamate amidation also leads in the accumulation of cell wall components that are detected by the cellular NOD1-innate immune surveillance system that is normally blind to amidated cell wall components. Such MurT-GatD-depleted BCG cells are more effective in protecting host cells towards infection by Mycobacterium tuberculosis (Mtb) in an in vitro monocyte model, but also in a murine lung infection model of Mtb.

The use of the cellular and animal models gave consistent findings for the recombinant BCG mutant strain in its protective effect against subsequent Mtb infections, importantly occurring in a concentration-dependent manner that correlates with the levels of CRISPR-mediated inhibition.

As no efficient vaccine exists against Mtb and the authors showed the potency of the mutant BCG over WT BCG to vaccinate mice against Mtb, this work identifies MurT-GatD-depleted BCG as a strong new and effective vaccine candidate against Mtb. It is possible that enhanced NOD1-signaling caused by loss of D-glutamate has a general self-adjuvanting effect on BCG bacteria and its conserved surface antigens towards Mtb. Alternatively, Mtb bacteria could alter their cell envelope structure during the course of an infection, rendering them more susceptible to immune responses already entrained by MurT-GatD-depleted BCG.

Reviewer #3 (Public Review):

This paper aims to understand the nature of collaborative hunting. It sets out by first defining simple conditions under which collaborative hunting emerges, which leads to the emergence of a toy environment. The environment itself is simple, K prey chasing a single predator with no occlusions. I find this a little strange, since it was my understanding that collaborative hunting emerges in part because the presence of occlusions allows for more complex strategies that require planning.

That being said, I do think the environment is sufficient for this paper, and I quite enjoyed using it to run some toy experiments. It reminds me of some of the simpler environments from Petting Zoo, a library for multi-agent learning in reinforcement learning.

Once a simple environment was established, the authors fit a reinforcement learning model to the environment. In this case, the model is Q-learning. The predator and prey are treated as separate agents in the environment, each with their own independent Q functions. Each agent gets full observability of the surroundings. As far as I understand, the predators do not share an action space, and so they can only collaborate implicitly by inferring the actions of the other predators. However, there is a version of these experiments wherein the reward function is shared, all agents receiving a 1 when the prey is caught. One limitation of the current work is that it does not consider reinforcement learning methods methods wherein a value function is shared. This is a current dominant strategy in multi-agent RL. See for example OpenAI Five and also Multi-Agent Actor-Critic for Mixed Cooperative-Competitive Environments. Missing these algorithms limits the scope of the work.

Having fit an RL model, the next order of business is to try and search for internal representations in the agent's model that correspond to collaboration. The author's use t-SNE embeddings of the agents last hidden layers in the policy network.

Analyzing these embeddings in Figure 3, we see that there are some representations that correspond to specific types of collaborative behavior, which indicates that the model is indeed learning to encode collaboration. I should note that this is not surprising from an RL perspective. Certainly, we are aware that Multi-Agent actor critic methods can exhibit cooperative behavior. See Emergent tool use from multi-agent interaction where agents jointly learn to push a table together. It is true that earlier work didn't specifically identify the units responsible for this behavior, and I think this work should be lauded for the novelty it brings to this discussion.

A large underlying point of this paper seems to be that we we need to consider these simple toy environments where we can easily train Q-learning, because it is impossible to analyze the behaviors that emerge from real animal behavior. See lines 187-189. This makes sense on the surface, because there are no policy weights in the case of real-world behavior. However, it is unfortunately misleading. It is entirely possible to take existing animal behavior, fit a linear model (or a deep net) to this behavior, and then do t-SNE on this fit model. This is referred to as behavioral cloning. What's more, offline RL makes it entirely possible to fit a Q-function to animal behaviors, in which case the exact same t-SNE analysis can be carried out without ever running Q-learning in the environment. From my perspective, the fact that RL is not needed to carry out the paper's main analysis is the biggest weakness of the paper.

Meanwhile, I do think the comparisons with human players was exceptionally interesting, and I'm glad it was included in this work.

Finally, I would like to speak to the reinforcement learning sections of this paper, as this is my personal area of expertise. I will note that the RL used in this paper is all valid and correct. The descriptions of Q-learning and its modifications are technically accurate. It's worth noting that the performance offered by the Q-learning methods in this paper is not particularly close to optimal. I mean this in two ways. First, cooperative RL methods are much more performant. Second, the Q-learning implementation considered by the author's is far below state of the art standards.

I will also note that, from the perspective of RL, there is no novelty in the paper. Indeed, many Deep Mind papers, including the original Q-learning paper, have similar t-SNE embeddings to try and understand the action space. And works such as Sentiment Neuron and Visualizing and Understanding Recurrent Networks, among many many others, have focused on the problem of understanding the correspondence between network weights and behaviors. Thus, the novelty must come from a biological perspective. Or perhaps from a perspective at the intersection of biology and RL. I do believe this is an area worth further studying.

Reviewer #3 (Public Review):

The authors elucidated the roles of cholecystokinin (CCK)-expressing excitatory neurons, which project from the rhinal cortex to the motor cortex, in motor skill learning. The authors found CCK knock-out mice exhibited learning defects in the pellet reaching task while the baseline success rate of the knock-out mice was similar to that of the wild-type mice. Application of a CCK B receptor (CCKBR) antagonist into the motor cortex lowered the success rate in the motor task. The authors found the population activity which was observed in the in vivo calcium imaging during motor learning was elevated after motor learning, but this increase disappeared in CCK knock-out mice and animals with CCKBR antagonist administration. Anterograde and retrograde viral tracing revealed that CCK-expressing excitatory neurons in the rhinal cortex projected to the motor cortex. Chemogenetic inhibition of the CCK-expressing neurons in the rhinal cortex lowered the ability for motor learning. The application of a CCKBR agonist increased the motor learning ability of CCK knock-out animals as well as long-term potentiation (LTP) observed in the slice of the motor cortex.

However, the manuscript contains several shortcomings:

First, the "Discussion" has several statements that are only supported weakly by the results, for example, ll. 429-431, ll. 432-433, and ll. 447-448. In addition, most of the sentences in this section are not divided into subsections. The paragraphs should be composed in multiple subsections with appropriate subheadings, even though the initial section summarizing the results can lack a subheading.

Second, it would be important that the authors showed which area(s) of the brain is affected by the CCKBR antagonist in the experiments described in ll. 166-206 and Fig. 2. The authors injected the drug into the motor cortex, but the chemical can spread to neighboring cortical areas (e.g. somatosensory cortex) or wider brain regions. If so, the blockade of the CCKBR in the brain areas other than the motor cortex could cause the defects of the motor task learning observed in these experiments. I think it is desirable that such a possibility should be excluded. Conversely, it is possible that the antagonist had an effect on a limited subarea of the motor cortex (e.g. only the primary motor cortex (M1)). In this case, the information about the field altered by the CCKBR blocker would be useful to interpret the results of the learning defects.

Third, the authors need to show bilateral data about their anterograde and retrograde tracking of CCK-expressing neurons in the rhinal cortex. In ll. 290-292, they described as follows: "Both anterograde and retrograde tracking results indicated that CCK-expressing neurons in the rhinal cortex projecting to the motor cortex were asymmetric, showing a preference for the ipsilateral hemisphere." However, they provided only unilateral data for the anterograde (Fig. 4B) and the retrograde (Fig. 4D) experiments.

Fourth, unilateral (contralateral to the dominant forelimb) experiments are needed in the chemogenetic inhibition of the CCK neurons. In ll. 301-338 and Fig. 5, the authors inhibited the CCK -expressing neurons in both hemispheres by injecting the virus into both sides. However, the CCKBR antagonist injection into the motor cortex contralateral to the dominant forelimb caused defects in motor learning ability, as described in ll. 166-206. The authors also observed that the population neuronal activity in the motor cortex contralateral to the dominant forelimb changed in accordance with the improvement of the motor skill in ll. 208-269. Therefore, it may be the case that inhibition of CCK neurons only in the side contralateral to the dominant forelimb - not bilaterally, as the authors did - could cause the lowered ability of motor learning. Such unilateral inhibition can be carried out by unilateral injection of the virus.

In relation to the point above, in the chemogenetic inhibition experiments, it would be important to show which neurons in which cortical area is inhibited. This could be done by examining the distributions of the mCherry-labeled somata in the rhinal cortex using histochemistry.

Fifth, it would be valuable to further examine differences in task performance across sessions and groups. The paragraph in ll. 138-153 needs a comparison of the "miss" rates of CCK-/- animals between Day 1 vs. Day 6 (related to ll. 429- 431). This paragraph also needs comparisons of the "no-grasp" and "drop" rates of CCK-/- animals between Day 1 vs. Day 6 (related to ll. 432- 433). The paragraph in ll. 175-190 needs comparisons of success rates between Day 1 and Day 5/6 within the antagonist group (related to ll. 447-448).

• for: 3 Deg C world - catastrophic

Reviewer #3 (Public Review):

The study by Ngodup and colleagues describes the contribution of sodium leak NALCN conductance on the effects of noradrenaline on cartwheel interneurons of the DCN. The manuscript is very well-written and the experiments are well-controlled. The scope of the study is of high biological relevance and recapitulates a primary finding of the Khaliq lab (Philippart et al., eLife, 2018) in ventral midbrain dopamine neurons, that Gi/o-coupled receptors inhibit NALCN current to reduce neuronal excitability. Together these studies provide unequivocable evidence for NALCN as a downstream target of these receptors.

In re-review of this study, the authors have addressed the concerns sufficiently. This is a very nice study.

Reviewer #3 (Public Review):

Summary:<br /> Much of the literature on attention has focused on static, non-contingent stimuli that can be easily controlled and replicated--a mismatch with the actual day-to-day deployment of attention. The same limitation is evident in the developmental literature, which is further hampered by infants' limited behavioral repertoires and the general difficulty in collecting robust and reliable data in the first year of life. The current study engages young infants as they play with age-appropriate toys, capturing visual attention, cardiac measures of arousal, and EEG-based metrics of cognitive processing. The authors find that the temporal relations between measures are different at age 5 months vs. age 10 months. In particular, at 5 months of age, cardiac arousal appears to precede attention, while at 10 months of age attention processes lead to shifts in neural markers of engagement, as captured in theta activity.

Strengths:<br /> The study brings to the forefront sophisticated analytical and methodological techniques to bring greater validity to the work typically done in the research lab. By using measures in the moment, they can more closely link biological measures to actual behaviors and cognitive stages. Often, we are forced to capture these measures in separate contexts and then infer in-the-moment relations. The data and techniques provide insights for future research work.

Weaknesses:

The sample is relatively modest, although this is somewhat balanced by the sheer number of data points generated by the moment-to-moment analyses. In addition, the study is cross-sectional, so the data cannot capture true change over time. Larger samples, followed over time, will provide a stronger test for the robustness and reliability of the preliminary data noted here. Finally, while the method certainly provides for a more active and interactive infant in testing, we are a few steps removed from the complexity of daily life and social interactions.

Reviewer #3 (Public Review):

Summary:<br /> The authors are looking for a spatially specific functional brain response to visualise non-invasively with 3T (clinical field strength) MRI. They propose a velocity-nulled weighting to remove the signal from draining veins in a submillimeter multiband acquisition.

Strengths:<br /> - This manuscript addresses a real need in the cognitive neuroscience community interested in imaging responses in cortical layers in-vivo in humans.<br /> - An additional benefit is the proposed implementation at 3T, a widely available field strength.

Weaknesses:<br /> - Although the VASO acquisition is discussed in the introduction section, the VN-sequence seems closer to diffusion-weighted functional MRI. The authors should make it more clear to the reader what the differences are, and how results are expected to differ. Generally, it is not so clear why the introduction is so focused on the VASO acquisition (which, curiously, lacks a reference to Lu et al 2013). There are many more alternatives to BOLD-weighted imaging for fMRI. CBF-weighted ASL and GRASE have been around for a while, ABC and double-SE have been proposed more recently.<br /> - The comparison in Figure 2 for different b-values shows % signal changes. However, as the baseline signal changes dramatically with added diffusion weighting, this is rather uninformative. A plot of t-values against cortical depth would be much more insightful.<br /> - Surprisingly, the %-signal change for a b-value of 0 is not significantly different from 0 in the gray matter. This raises some doubts about the task or ROI definition. A finger-tapping task should reliably engage the primary motor cortex, even at 3T, and even in a single participant.<br /> - The BOLD weighted images in Figure 3 show a very clear double-peak pattern. This contradicts the results in Figure 2 and is unexpected given the existing literature on BOLD responses as a function of cortical depth.<br /> - Given that data from Figures 2, 3, and 4 are derived from a single participant each, order and attention affects might have dramatically affected the observed patterns. Especially for Figure 4, neither BOLD nor VN profiles are really different from 0, and without statistical values or inter-subject averaging, these cannot be used to draw conclusions from.<br /> - In Figure 5, a phase regression is added to the data presented in Figure 4. However, for a phase regression to work, there has to be a (macrovascular) response to start with. As none of the responses in Figure 4 are significant for the single participant dataset, phase regression should probably not have been undertaken. In this case, the functional 'responses' appear to increase with phase regression, which is contra-intuitive and deserves an explanation.<br /> - Consistency of responses is indeed expected to increase by a removal of the more variable vascular component. However, the microvascular component is always expected to be smaller than the combination of microvascular+macrovascular responses. Note that the use of %signal changes may obscure this effect somewhat because of the modified baseline. Another expected feature of BOLD profiles containing both micro- and microvasculature is the draining towards the cortical surface. In the profiles shown in Figure 7, this is completely absent. In the group data, no significant responses to the task are shown anywhere in the cortical ribbon.<br /> - Although I'd like to applaud the authors for their ambition with the connectivity analysis, I feel that acquisitions that are so SNR starved as to fail to show a significant response to a motor task should not be used for brain wide directed connectivity analysis.

The claim of specificity is supported by the observation of the double-peak pattern in the motor cortex, previously shown in multiple non-BOLD studies. However, this same pattern is shown in some of the BOLD weighted data, which seems to suggest that the double-peak pattern is not solely due to the added velocity nulling gradients. In addition, the well-known draining towards the cortical surface is not replicated for the BOLD-weighted data in Figures 3, 4, or 7. This puts some doubt about the data actually having the SNR to draw conclusions about the observed patterns.

Reviewer #3 (Public Review):

Summary:<br /> This study studied the neural mechanisms underlying the shift of ocular dominance induced by "dichoptic-backward-movie" adaptation. The study is self-consistent.

Strengths:<br /> The experimental design is solid and progressive (relationship among three studies), and all of the raised research questions were well answered.

The logic behind the neural mechanisms is solid.

The findings regarding the cTMS (especially the position/site can be useful for future medical implications).

Weaknesses:<br /> Why does the "dichoptic-backward-movie" adaptation matter? This part is severely missing. This kind of adaptation is neither intuitive like the classical (Gbison) visual adaptation, nor practical as adaptation as a research paradigm as well as the fundamental neural mechanism. If this part is not clearly stated and discussed, this study is just self-consistent in terms of its own research question. There are tons of "cool" phenomena in which the neural mechanisms are apparent as "FEF controls vision-attention" but never tested using TMS & fMRI, but we all know that this kind of research is just of incremental implications.

Reviewer #3 (Public Review):

Summary:

Through a detailed methodology, the authors demonstrated that within 11 different primates, the shape of the brain matched a fractal of dimension 2.5. They enhanced the universality of this result by showing the concordance of their results with a previous study investigating 70 mammalian brains, and the discordance of their results with other folded objects that are not brains. They incidentally illustrated potential applications of this fractal property of the brain by observing a scale-dependent effect of aging on the human brain.

Strengths:

- New hierarchical way of expressing cortical shapes at different scales derived from the previous report through the implementation of a coarse-graining procedure.<br /> - Positioning of results in comparison to previous works reinforcing the validity of the observation.<br /> - Illustration of scale-dependence of effects of brain aging in the human.

Weaknesses:

- The impact of the contribution should be clarified compared to previous studies (implementation of new coarse graining procedure, dimensionality of primate brain vs previous studies, and brain aging observations).<br /> - The rather small sample sizes, counterbalanced by the strength of the effect demonstrated.<br /> - The use of either averaged or individual brains for the different sub-studies could be made clearer.<br /> - The model discussed hypothetically in the discussion is not very clear, and may not be state-of-the-art (axonal tension driving cortical folding? cf. https://doi.org/10.1115/1.4001683).

Reviewer #3 (Public Review):

Summary:<br /> The high heterogeneity nature of α-synuclein (α-syn) fibrils posed significant challenges in structural reconstruction of the ex vivo conformation. A deeper understanding of the factors influencing the formation of various α-syn polymorphs remains elusive. The manuscript by Frey et al. provides a comprehensive exploration of how pH variations (ranging from 5.8 to 7.4) affect the selection of α-syn polymorphs (specifically, Type1, 2, and 3) in vitro by using cryo-electron microscopy (cryo-EM) and helical reconstruction techniques. Crucially, the authors identify two novel polymorphs at pH 7.0 in PBS. These polymorphs bear resemblance to the structure of patient-derived juvenile-onset synucleinopathy (JOS) polymorph and diseased tissue amplified α-syn fibrils. The manuscript supports the notion that seeding is non-polymorph-specific in the context of secondary nucleation-dominated aggregation, underscoring the irreplaceable role of pH in polymorph formation. Nevertheless, certain areas within the manuscript would benefit from further refinement and elaboration to more robustly substantiate this hypothesis.

Strengths:<br /> This study systematically investigates the effects of environmental conditions and seeding on the structure of α-syn fibrils. It emphasizes the significant influence of environmental factors, especially pH, in determining the selection of α-syn polymorphs. The high-resolution structures obtained through cryo-EM enable a clear characterization of the composition and proportion of each polymorph in the sample. Collectively, this work provides strong support for the pronounced sensitivity of α-syn fibril structures to environmental conditions and systematically categorizes previously reported α-syn fibril structures. Furthermore, the identification of JOS-like polymorph also demonstrates the possibility of in vitro reconstruction of brain-derived α-syn fibril structures.

Weaknesses:<br /> 1. The authors reveal that both Type 1 monofilament fibril polymorph (reminiscent of JOS-like polymorph) and Type 5 polymorph (akin to tissue-amplified-like polymorph) can both form under the same condition. Additionally, this condition also fosters the formation of flat ribbon-like fibril across different batches. Notably, at pH 5.8, variations in experimental groups yield disparate abundance ratios between polymorph 3B and 3C, indicating a degree of instability in fibrillar formation. The variability would potentially pose challenges for replicability in subsequent research. In light of these situations, I propose the following recommendations:

(1) An explicit elucidation of the factors contributing to these divergent outcomes under similar experimental conditions is warranted. This should include an exploration of whether variations in purified protein batches are contributing factors to the observed heterogeneity.

(2) To enhance the robustness of the conclusions, additional replicates of the experiments under the same condition should be conducted, ideally a minimum of three times.

(3) Further investigation into whether different polymorphs formed under the same buffer condition could lead to distinct toxicological and pathology effects would be a valuable addition to the study.

2. The cross-seeding study presented in the manuscript demonstrates the pivotal role of pH conditions in dictating conformation. However, an intriguing aspect that emerges is the potential role of seed concentration in determining the resultant product structure. This raises a critical question: at what specific seed concentration does the determining factor for polymorph selection shift from pH condition to seed concentration? A methodological robust approach to address this should be conducted through a series of experiments across a range of seed concentrations. Such an approach could delineate a clear boundary at which seed concentration begins to predominantly dictate the conformation, as opposed to pH conditions. Incorporating this aspect into the study would not only clarify the interplay between seed concentration and pH conditions, but also add a fascinating dimension to the understanding of polymorph selection mechanisms.

Furthermore, the study prompts additional queries regarding the behavior of cross-seeding production under the same pH conditions when employing seeds of distinct conformation. Evidence from various studies, such as those involving E46K and G51D cross-seeding, suggests that seed structure plays a crucial role in dictating polymorph selection. A key question is whether these products consistently mirror the structure of their respective seeds.

3. In the Results section of "The buffer environment can dictate polymorph during seeded nucleation", the authors reference previous cell biological and biochemical assays to support the polymorph-specific seeding of MSA and PD patients under the same buffer conditions. This discussion is juxtaposed with recent research that compares the in vivo biological activities of hPFF, ampLB as well as LB, particularly in terms of seeding activity and pathology. Notably, this research suggests that ampLB, rather than hPFF, can accurately model the key aspects of Lewy Body Diseases (LBD) (refer to: https://doi.org/10.1038/s41467-023-42705-5). The critical issue here is the need to reconcile the phenomena observed in vitro with those in in-vivo or in-cell models. Given the low seed concentration reported in these studies, it is imperative for the authors to provide a more detailed explanation as to why the possible similar conformation could lead to divergent pathologies, including differences in cell-type preference and seeding capability.

4. In the Method section of "Image processing", the authors describe the helical reconstruction procedure, without mentioning much detail about the 3D reconstruction and refinement process. For the benefit of reproducibility and to facilitate a deeper understanding among readers, the authors should enrich this part to include more comprehensive information, akin to the level of detail found in similar studies (refer to: https://doi.org/10.1038/nature23002).

5. The abbreviation of amino acids should be unified. In the Results section "On the structural heterogeneity of Type 1 polymorphs", the amino acids are denoted using three-letter abbreviation. Conversely, in the same section under "On the structural heterogeneity of Type 2 and 3 structures", amino acids are abbreviated using the one-letter format. For clarity and consistency, it is essential that a standardized format for amino acid abbreviations be adopted throughout the manuscript.

Reviewer #3 (Public Review):

This manuscript focuses on defining the importance of UGGT1/2 in the process of protein degradation within the ER. The authors prepared cells lacking UGGT1, UGGT2, or both UGGT1/UGGT2 (DKO) HCT116 cells and then monitored the degradation of specific ERAD substrates. Initially, they focused on the ER stress sensor ATF6 and showed that loss of UGGT1 increased the degradation of this protein. This degradation was stabilized by deletion of ERAD-specific factors (e.g., SEL1L, EDEM) or treatment with mannose inhibitors such as kifunesine, indicating that this is mediated through a process involving increased mannose trimming of the ATF6 N-glycan. This increased degradation of ATF6 impaired the function of this ER stress sensor, as expected, reducing the activation of downstream reporters of ER stress-induced ATF6 activation. The authors extended this analysis to monitor the degradation of other well-established ERAD substrates including A1AT-NHK and CD3d, demonstrating similar increases in the degradation of destabilized, misfolding protein substrates in cells deficient in UGGT. Importantly, they did experiments to suggest that re-overexpression of wild-type, but not catalytically deficient, UGGT rescues the increased degradation observed in UGGT1 knockout cells. Further, they demonstrated the dependence of this sensitivity to UGGT depletion on N-glycans using ERAD substrates that lack any glycans. Ultimately, these results suggest a model whereby depletion of UGGT (especially UGGT1 which is the most expressed in these cells) increases degradation of ERAD substrates through a mechanism involving impaired re-glucosylation and subsequent re-entry into the calnexin/calreticulin folding pathway.

I must say that I was under the impression that the main conclusions of this paper (i.e., UGGT1 functions to slow the degradation of ERAD substrates by allowing re-entry into the lectin folding pathway) were well-established in the literature. However, I was not able to find papers explicitly demonstrating this point. Because of this, I do think that this manuscript is valuable, as it supports a previously assumed assertion of the role of UGGT in ER quality control. However, there are a number of issues in the manuscript that should be addressed.

Notably, the focus on well-established, trafficking-deficient ERAD substrates, while a traditional approach to studying these types of processes, limits our understanding of global ER quality control of proteins that are trafficked to downstream secretory environments where proteins can be degraded through multiple mechanisms. For example, in Figure 1-Figure Supplement 2, UGGT1/2 knockout does not seem to increase the degradation of secretion-competent proteins such as A1AT or EPO, instead appearing to stabilize these proteins against degradation. They do show reductions in secretion, but it isn't clear exactly how UGGT loss is impacting ER Quality Control of these more relevant types of ER-targeted secretory proteins.

Lastly, I don't understand the link between UGGT, ATF6 degradation, and ATF6 activation. I understand that the idea is that increased ATF6 degradation afforded by UGGT depletion will impair activation of this ER stress sensor, but if that is the case, how does UGGT2 depletion, which only minimally impacts ATF6 degradation (Fig. 1), impact activation to levels similar to the UGGT1 knockout (Fig 4)? This suggests UGGT1/2 may serve different functions beyond just regulating the degradation of this ER stress sensor. Also, the authors should quantify the impaired ATF6 processing shown in Fig 4B-D across multiple replicates.

Ultimately, I do think the data support a role for UGGT (especially UGGT1) in regulating the degradation of ERAD substrates, which provides experimental support for a role long-predicted in the field. However, there are a number of ways this manuscript could be strengthened to further support this role, some of which can be done with data they have in hand (e.g., the stats) or additional new experiments.

Reviewer #3 (Public Review):

In their paper entitled "Fear conditioning biases olfactory stem cell receptor fate" Liff et al. address the still enigmatic (and quite fascinating) phenomenon of intergenerationally inherited changes in the olfactory system in response to odor-dependent fear conditioning.

In the abstract / summary, the authors raise expectations that are not supported by the data. For example, it is claimed that "increases in F0 were due to biased stem cell receptor choice." While an active field of study that has seen remarkable progress in the past decade, olfactory receptor gene choice and its relevant timing in particular is still unresolved. Here, Liff et al., do not pinpoint at what stage during differentiation the "biased choice" is made.

Similarly, the concluding statement that the study provides "insight into the heritability of acquired phenotypes" is somewhat misleading. The experiments do not address the mechanisms underlying heritability.

The statement that "the percentage of newborn M71 cells is 4-5 times that of MOR23 may simply reflect differences in the birth rates of the two cell populations" should, if true, result in similar differences in the occurrence of mature OSNs with either receptor identity. According to Fig. 1H & J, however, this is not the case.

An important result is that Liff et al., in contrast to results from other studies, "do not observe the inheritance of odor-evoked aversion to the conditioned odor in the F1 generation." This discrepancy needs to be discussed.

The authors speculate that "the increase in neurons responsive to the conditioned odor could enhance the sensitivity to, or the discrimination of, the paired odor in F0 and F1. This would enable the F1 population to learn that odor predicts shock with fewer training cycles or less odorant when trained with the conditioned odor." This is a fascinating idea that, in fact, could have been readily tested by Liff and coworkers. If this hypothesis were found true, this would substantially enhance the impact of the study for the field.

Reviewer #3 (Public Review):

Summary:<br /> The authors food-deprived male and female mice and observed a much stronger reduction of leptin levels, energy consumption in the visual cortex, and visual coding performance in males than females. This indicates a sex-specific strategy for the regulation of the energy budget in the face of low food availability.

Strengths:<br /> This study extends a previous study demonstrating the effect of food deprivation on visual processing in males, by providing a set of clear experimental results, demonstrating the sex-specific difference. It also provides hypotheses about the strategy used by females to reduce energy budget based on the literature.

Weaknesses:<br /> The authors do not provide evidence that females are not impacted by visually guided behaviors contrary to what was shown in males in the previous study.

Reviewer #3 (Public Review):

Summary:<br /> Zhang et al sought to use spatial transcriptomics and single-nucleus RNA sequencing to classify human spinal cord neurons. The authors reported 17 clusters on 10x Visium slides (6 donors) and 21 clusters by single-nucleus sequencing (9 donors). The authors tried to compare the results to those reported in mice and claimed similar patterns with some differing genes.

Strengths:<br /> The manuscript provides a valuable database for the molecular and cellular organization of adult human spinal cords in addition to published datasets (Andersen, et al. 2023; Yadav, et al. 2023).

Weaknesses:<br /> The results are largely observatory and lack quantitative analysis. Moreover, the assertions regarding the sex differences in motor neurons and the potential interactions between DRG and spinal cord neuronal subclusters appear preliminary and necessitate more rigorous validation.

Reviewer #3 (Public Review):

Summary and strengths<br /> The manuscript investigated the factors related to understudied genes in biomedical research. It showed that understudied are largely abandoned at the writing stage and identified biological and experimental factors associated with selection of highlighted genes.

It is very important for the research community to recognize the systematic bias in research of human genes and take precautions when designing experiments and interpreting results. The authors have tried to profile this issue comprehensively and promoted more awareness and investigation of understudied genes.

Weaknesses<br /> Regarding result section 1 "Understudied genes are abandoned at synthesis/writing stage", the figures are not clear and do not convey the messages written in the main text. For example, in Figure 1B, figure S5 and S6,<br /> - There is no "numbers to the right of each box plot".<br /> - Do these box plots only show understudied genes? How many genes are there in each box plot? The definition and numbers of understudied genes are not clear.<br /> - "We found that hit genes that are highlighted in the title or abstract are strongly over-represented among the 20% highest-studied genes in all biomedical literature (Figure 1B)". This is not clear from the figure.

Regarding result section 2 "Subsequent reception by other scientists does not penalize studies on understudied genes", the authors showed in figure 2 that there is a negative correlation between articles per gene before 2015 and median citations to articles published in 2015. Another explanation could be that for popular genes, there are more low-quality articles that didn't get citations, not necessarily that less popular genes attract more citations.

Regarding result section 3 "Identification of biological and experimental factors associated with selection of highlighted genes", in Figure 3 and table s2, the author stated that "hits with a compound known to affect gene activity are 5.114 times as likely to be mentioned in the title/abstract in an article using transcriptomics", The number 5.144 comes out of nowhere both in the figure and the table. In addition, figure 4 is not informative enough to be included as a main figure.

Reviewer #3 (Public Review):

Summary:<br /> In this manuscript, Schembri et al performed a molecular analysis by WGS of 52 E. coli strains identified as "causing neonatal meningitis" from several countries and isolated from 1974 to 2020. Sequence types, virulence genes content as well as antibiotic-resistant genes are depicted. In the second part, they also described three cases of relapse and analysed their respective strains as well as the microbiome of three neonates during their relapse. For one patient the same E. coli strain was found in blood and stool (this patient had no meningitis). For two patients microbiome analysis revealed a severe dysbiosis.

Major comments:<br /> Although the authors announce in their title that they study E. coli that cause neonatal meningitis and in methods stipulate that they had a collection of 52 NMEC, we found in Supplementary Table 1, 29 strains (threrefore most of the strains) isolated from blood and not CSF. This is a major limitation since only strains isolated from CSF can be designated with certainty as NMEC even if a pleiocytose is observed in the CSF. A very troubling data is the description of patient two with a relapse infection. As stated in the text line 225, CSF microscopy was normal and culture was negative for this patient! Therefore it is clear that patient without meningitis has been included in this study.

Another major limitation (not stated in the discussion) is the absence of clinical information on neonates especially the weeks of gestation. It is well known that the risk of infection is dramatically increased in preterm neonates due to their immature immunity. Therefore E. coli causing infection in preterm neonates are not comparable to those causing infection in term neonates notably in their virulence gene content. Indeed, it is mentioned that at least eight strains did not possess a capsule, we can speculate that neonates were preterm, but this information is lacking. The ages of neonates are also lacking. The possible source of infection is not mentioned, notably urinary tract infection. This may have also an impact on the content of VF.

Sequence analysis reveals the predominance of ST95 and ST1193 in this collection. The high incidence of ST95 is not surprising and well previously described, therefore, the concluding sentence line 132 indicating that ST95 E. coli should exhibit specific virulence features associated with their capacity to cause NM does not add anything. On the contrary, the high incidence of ST1193 is of interest and should have been discussed more in detail. Which specific virulence factors do they harbor? Any hypothesis explaining their emergence in neonates? In the paragraph depicted the VF it is only stated that ST95 contained significantly more VF than the ST1193 strains. And so what? By the way "significantly" is not documented: n=?, p=?<br /> The complete sequence of 18 strains is not clear. Results of Supplementary Table 2 are presented in the text and are not discussed.

46 years is a very long time for such a small number of strains, making it difficult to put forward epidemiological or evolutionary theories. In the analysis of antibiotic resistance, there are no ESBLs. However, Ding's article (reference 34) and other authors showed that ESBLs are emerging in E. coli neonatal infection. These strains are a major threat that should be studied, unfortunately, the authors haven't had the opportunity to characterize such strains in their manuscript.

Second part of the manuscript:<br /> The three patients who relapsed had a late neonatal infection (> 3 days) with respective ages of 6 days, 7 weeks, and 3 weeks. We do not know whether they are former preterm newborns (no term specified) or whether they have received antibiotics in the meantime.

Patient 1: Although this patient had a pleiocytose in CSF, the culture was negative which is surprising and no explanation is provided. Therefore, the diagnosis of meningitis is not certain. Pleiocytose without meningitis has been previously described in neonates with severe sepsis.

Line 215: no immunological abnormalities were identified (no details are given).

Patient 2: This patient had a recurrence of bacteremia without meningitis (line 225: CSF microscopy was normal and culture negative!). This case should be deleted.

Patient 3: This patient had two relapses which is exceptional and may suggest the existence of a congenital malformation or a neurological complication such as abscess or empyema therefore, "imaging studies" should be detailed.

The authors suggest a link between intestinal dysbiosis and relapse in three patients. However, the fecal microbiomes of patients without relapse were not analysed, so no comparison is possible. Moreover, dysbiosis after several weeks of antibiotic treatment in a patient hospitalized for a long time is not unexpected. Therefore, it's impossible to make any assumption or draw any conclusion. This part of the manuscript is purely descriptive. Finally, the authors should be more prudent when they state in line 289 "we also provide direct evidence to implicate the gut as a reservoir [...] antibiotic treatment". Indeed the gut colonization of the mothers with the same strain may be also a reservoir (as stated in the discussion line 336).

Finally, the authors do not discuss the potential role of ceftriaxone vs cefotaxime in the dysbiosis observed. Ceftriaxone may have a major impact on the microbiota due to its digestive elimination.

Reviewer #3 (Public Review):

In this manuscript, Magnuson and colleagues investigate the meiotic functions of ARID1A, a putative DNA binding subunit of the SWI/SNF chromatin remodeler BAF. The authors develop a germ cell specific conditional knockout (cKO) mouse model using Stra8-cre and observe that ARID1A-deficient cells fail to progress beyond pachytene, although due to inefficiency of the Stra8-cre system the mice retain ARID1A-expressing cells that yield sperm and allow fertility. Because ARID1A was found to accumulate at the XY body late in Prophase I, the authors suspected a potential role in meiotic silencing and by RNAseq observe significant misexpression of sex-linked genes that typically are silenced at pachytene. They go on to show that ARID1A is required for exclusion of RNA PolII from the sex body and for limiting promoter accessibility at sex-linked genes, consistent with a meiotic sex chromosome inactivation (MSCI) defect in cKO mice. The authors proceed to investigate the impacts of ARID1A on H3.3 deposition genome-wide. H3.3 is known be regulated by ARID1A and is linked to silencing, and here the authors find that upon loss of ARID1A, overall H3.3 enrichment at the sex body as measured by IF failed to occur, but H3.3 was enriched specifically at transcriptional start sites of sex-linked genes that are normally regulated by ARID1A. The results suggest that ARID1A normally prevents H3.3 accumulation at target promoters on sex chromosomes and based on additional data, restricts H3.3 to intergenic sites. Finally, the authors present data implicating ARID1A and H3.3 occupancy in DSB repair, finding that ARID1A cKO leads to a reduction in focus formation by DMC1, a key repair protein. Overall the paper provides new insights into the process of MSCI from the perspective of chromatin composition and structure, and raises interesting new questions about the interplay between chromatin structure, meiotic silencing and DNA repair.

In general the data are convincing. The conditional KO mouse model has some inherent limitations due to incomplete recombination and the existence of 'escaper' cells that express ARID1A and progress through meiosis normally. This reviewer feels that the authors have addressed this point thoroughly and have demonstrated clear and specific phenotypes using the best available animal model. The data demonstrate that the mutant cells fail to progress past pachytene, although it is unclear whether this specifically reflects pachytene arrest, as accumulation in other stages of Prophase also is suggested by the data in Table 1. The western blot showing ARID1A expression in WT vs. cKO spermatocytes (Fig. S2) is supportive of the cKO model but raises some questions. The blot shows many bands that are at lower intensity in the cKO, at MWs from 100-250kDa. The text and accompanying figure legend have limited information. Are the various bands with reduced expression different isoforms of ARID1A, or something else? What is the loading control 'NCL'? How was quantification done given the variation in signal across a large range of MWs?

An additional weakness relates to how the authors describe the relationship between ARID1A and DNA damage response (DDR) signaling. The authors don't see defects in a few DDR markers in ARID1A CKO cells (including a low resolution assessment of ATR), suggesting that ARID1A may not be required for meiotic DDR signaling. However, as previously noted the data do not rule out the possibility that ARID1A is downstream of DDR signaling and the authors even indicate that "it is reasonable to hypothesize that DDR signaling might recruit BAF-A to the sex chromosomes." It therefore is difficult to understand why the authors continue to state that "...the mechanisms underlying ARID1A-mediated repression of the sex-linked transcription are mutually exclusive to DDR pathways regulating sex body formation" (p. 8) and that "BAF-A-mediated transcriptional repression of the sex chromosomes occurs independently of DDR signaling" (p. 16). The data provided do not justify these conclusions, as a role for DDR signaling upstream of ARID1A would mean that these mechanisms are not mutually exclusive or independent of one another.

A final comment relates to the impacts of ARID1A loss on DMC1 focus formation and the interesting observation of reduced sex chromosome association by DMC1. The authors additionally assess the related recombinase RAD51 and suggest that it is unaffected by ARID1A loss. However, only a single image of RAD51 staining in the cKO is provided (Fig. S11) and there are no associated quantitative data provided. The data are suggestive but it would be appropriate to add a qualifier to the conclusion regarding RAD51 in the discussion which states that "...loss of ARID1a decreases DMC1 foci on the XY chromosomes without affecting RAD51" given that the provided RAD51 data are not rigorous. In the long-term it also would be interesting to quantitatively examine DMC1 and RAD51 focus formation on autosomes as well.

Reviewer #3 (Public Review):

Summary<br /> The researchers aim add to the literature on faculty career pathways with particular attention to how gender disparities persist in the career and funding opportunities of researchers. The researchers also examine aspects of institutional prestige that can further amplify funding and career disparities. While some factors about individuals' pathways to faculty lines are known, including the prospects of certain K award recipients, the current study provides the only known examination of the K99/R00 awardees and their pathways.

Strengths<br /> The authors establish a clear overview of the institutional locations of K99 and R00 awardees and the pathways for K99-to-R00 researchers and the gendered and institutional patterns of such pathways. For example, there's a clear institutional hierarchy of hiring for K99/R00 researchers that echo previous research on the rigid faculty hiring networks across fields, and a pivotal difference in the time between awards that can impact faculty careers. Moreover, there's regional clusters of hiring in certain parts of the US where multiple research universities are located. Moreover, documenting the pathways of HBCU faculty is an important extension of the study by Wapman et al. (2022: https://www.nature.com/articles/s41586-022-05222-x), and provides a more nuanced look at the pathways of faculty beyond the oft-discussed high status institutions. (However, there is a need for more refinement in this segment of the analyses). Also, the authors provide important caveats throughout the manuscript about the study's findings that show careful attention to the complexity of these patterns and attempting to limit misinterpretations of readers.

Weaknesses<br /> The authors have addressed my recommendations in the previous review round in a satisfactory way.

Reviewer #3 (Public Review):

Summary:<br /> This work aims to understand the contribution of microglia to anesthesia induced by general anesthetics. The authors report that ablation of microglia shortens anesthesia, manifested by the delay of anesthesia induction and the early anesthesia emergence. They show that microglial depletion suppresses activity in the neuronal network of anesthesia-activated brain regions but enhances activity in emergence-activated brain regions. Based on these findings, the authors suggest microglia facilitate and stabilize the anesthesia status. To elucidate the underlying mechanism, they further tested the potential contribution of microglia-mediated dendritic spine plasticity and microglial P2Y12-Ca2+ signaling, and identified the latter as a critical pathway through which microglia regulate anesthesia.

Strengths:<br /> A major strength of this study is the systematic experimental design, which includes multiple anesthetics and complementary approaches, leading to very compelling data. As a result, a significant contribution of microglia in instating and maintaining the state of anesthesia is convincingly established. In addition, the results also shed light on the potential underlying microglial mechanistic. The findings are of relevance to both medical practice and basic understanding of microglial biology and neuron-glia interactions.

Weaknesses:<br /> The study produces a large amount of data that is in general cohesive and support the main conclusions, but more thorough considerations on some of their findings may be helpful, as exemplified by the following:

1) the effect of microglial ablation on chloral hydrate-induced RORR in Fig. 1B appears to be not the same as other anesthetics. what does this mean?

2) Macrophage ablation impedes anesthesia emergence from pentobarbital (Fig. 3C). how may this occur?

3) examination of the potential effect of microglial depletion on dendritic spine density is interesting but the experimental design does not seem to align well with the PPR and eEPSC data, which indicate a reduction in presynaptic release (Fig.10E) and increase of postsynaptic function (Fig. 10H), respectively. The PPR data seems to suggest a presynaptic effect of microglia; ablation.

Reviewer #3 (Public Review):

Perrodin, Verzat and Bendor describe the response of female mice to the playback of male mouse ultrasonic songs. The experiments were performed in a Y-maze-like apparatus with two acoustically separate response chambers. Sounds were presented in 4 trials, alternating strictly between the left and right branches of the Y. Cumulative dwell time in the two chambers was measured, and used as an index of female preference. They first show, consistent with previous observations, that female mice will spend more time near a speaker playing a male mouse song than near a speaker playing nothing. They then performed several manipulations-time reversals, syllable order randomization, phase scrambled replacement, pure tone replacement, and 'hyper-regular' inter-syllable-intervals-which female mice did not discriminate from the normal song in this assay. Finally, they show that females spent more time near normal songs than near songs with more variable inter-syllable-intervals

The authors' approach to the problem was ethologically sensible -- females were tested in proestrus and estrus, the male odor was used to increase motivation, mouse handling was with tube transfers to reduce stress, mice were age-matched across conditions, and experiments were conducted in the dark (active) phase. In addition, animals were habituated to handling and to the apparatus.

The acoustics were very good. The acoustic structure of the vocal signals was well described. Specific ranges of dB SPL were reported, speaker flatness was evaluated, the sound amplitude was matched in manipulated and unmanipulated songs, and playback onset timing jittered randomly between manipulated and unmanipulated signals.

I think it is a reasonable result. My concerns are the following:

1) The authors use "approach" as it has been used in other publications, but what is actually measured is dwell time. Pomerantz et al, 1983 observed that female mice approached mute and singing males the same number of times (e.g. approached both at the same rate), but spent more time with the singing than the mute male. Their use of "approach" to describe dwell time was a bit confusing to me, but sticking with the way the literature is defensible. However, they also refer to the assay as a "place preference assay", which I found confusing.

2) I am a bit worried about their method of removing side bias (29% of trials). It certainly seems like a reasonable thing to exclude mice that simply picked one side or the other, but, because the stimulus always alternated between the sides, this exclusion of mice exhibiting a side bias is also excluding, specifically, behavior that would be incorrect.

3) Given the observation by Hammerschmidt et al, 2009, that female mice would only discriminate male songs in a playback assay on the first presentation, it is important to know whether females were used across the different manipulations. How many conditions did each female experience? How often did a female display positive discrimination in a condition after having displayed no discrimination?

Specific comments:

1) For Figure 2L

The heat map legend is labeled "Towards" indicating a motion towards either the speaker playing the song or the silent speaker. However, there is nothing in the methods that indicates that the direction of movement was ever measured. I may have missed it, but I can't figure out how this heat map was generated and what it represents. The figure legend states: "Normalized temporal profiles of approach behaviour to mouse songs vs silence over the course of 4 sound presentation trials (x-axis, coloured bars) for each of the behavioural sessions (y-axis, each animal is one line, n = 29), calculated as in I. Sessions (lines) are ordered by the amplitude of their last element." 2I states " I. Temporal profile of approach behaviour over the four sound presentation trials in the example session in C, calculated as the cumulative sum of time in the intact song playback (positively weighted) vs silent (negatively weighted) speaker zone." I interpret this to mean that "Towards" is an inaccurate description of what is being plotted, as there is no motion, only dwell time.

References

K. Hammerschmidt, K. Radyushkin, H. Ehrenreich & J. Fischer (2009) Female mice respond to male ultrasonic 'songs' with approach behavior. Biol. Lett. 5:589-592.

Pomerantz, S.M., Nunez, A.A. & Bean, J (1983) Female behavior is affected by male ultrasonic vocalizations in house mouse. Physiol. Behav. 31:91-96.

Reviewer #3 (Public Review):

In this revised manuscript, Urtecho et al., present an updated version of their earlier submission. They characterized thousands of promoter sequences in E. coli using a massively-parallel reporter assay and built a number of computational models to classify active from inactive promoters or associate the sequence to promoter expression/strength. As eluded in the earlier review cycle, the amount of experimental, bioinformatics, and analytical work presented here is astounding.

Identifying promoters and associating genomic (or promoter) sequences to promoter strength is nontrivial. Authors report challenges in achieving this grand goal even with the state-of-the-art characterization technology used here. Nevertheless, the experimental work, analytic workflow, and data resource presented here will serve as a milestone for future researchers.

Reviewer #3 (Public Review):

Summary:<br /> In Hunter, Coulson et al, the authors seek to expand our understanding of how neural activity during developmental critical periods might control the function of the nervous system later in life. To achieve increased excitation, the authors build on their previous results and apply picrotoxin 17-19 hours after egg-laying, which is a critical period of nervous system development. This early enhancement of excitation leads to multiple effects in third-instar larvae, including prolonged recovery from electroshock, increased synchronization of motor neuron networks, and increased AP firing frequency. Using optogenetics and whole-cell patch clamp electrophysiology, the authors elegantly show that picrotoxin-induced over-excitation leads to increased strength of excitatory inputs, and not loss of inhibitory inputs. To enhance inhibition, the authors chose an approach that involved stimulation of mechanosensory neurons; this counteracts picrotoxin-induced signs of increased excitation. This approach to enhancing inhibition requires further validation.

Strengths:<br /> • The authors confirm their previous results and show that 17-19 hours after egg laying is a critical period of nervous system development.<br /> • Using Ca2+/Sr2+ substitutions, the authors demonstrate that synaptic connections between A18a & aCC show increased mEPSP amplitudes. The authors show that this aCC input is what is driving enhanced excitation.<br /> • The authors demonstrate that the effects of over-excitation attributed to picrotoxin exposure are generalizable and also occur in bss mutant flies.

Weaknesses:<br /> • The authors build on their previous work and argue that the critical period (17-19h after egg-laying) is a uniquely sensitive period of development. Establishing the developmental window of the critical period is important for the present study. The present study would benefit from demonstrating that exposure to picrotoxin at L1 or L2 do not lead to changes in induced seizure at L3. This would further the authors hypothesis of the criticality of the 17-19h AEL period.<br /> • The ch-related experiments require further controls and explanation. Regarding experiments in Fig 6, what is the effect of ch neuron stimulation alone on time lag and AP frequency? The authors report related pilot experiments have been performed; the present study would be strengthened with inclusion of these data.

Reviewer #3 (Public Review):

Summary:<br /> This manuscript reports an experiment that compared groups of rats acquisition and performance of a Pavlovian bi-conditional discrimination, in which the presence of one cue, A, signals that the presentation of one CS, X, will be followed by a reinforcer and a second CS, Y, will be nonreinforced. Periods of cue A alternated with periods of cue B, which signaled the opposite relationship, cue X is nonreinforced, and cue Y is reinforced. This is a conditional discrimination problem in which the rats learned to approach the food cup in the presence of each CS conditional on the presence of the third background cue. The comparison groups consisted of the same conditional discrimination with the exception that each CS was paired with a different reinforcer. This makes the problem easier to solve as the background is now priming a differential outcome. A third group received simple discrimination training of X reinforced and Y nonreinforced in cues A and B, and the final group was trained with X and Y reinforced on half the trials (no discrimination). The results were clear that the latter two discrimination learning procedures resulted in rapid learning in comparison to the first. Rats required about 3 times as many 4-session blocks to acquire the bi-conditional discrimination than the other two discrimination groups. Within the biconditional discrimination group, female and male rats spent the same amount of time in the food cup during the rewarded CS, but females spent more time in the food cup during CS- than males. The authors interpret this as a deficit in discrimination performance in females on this task and use a measure that exaggerates the difference in CS+ and CS_ responding (a discrimination ratio) to support their point. When tested after acute restraint stress, the male rats spent less time in the food cup during the reinforced CS in comparison to the female rats, but did not lose discrimination performance entirely. The was also some evidence of more fos-positive cells in the orbitofrontal cortex in females, but this difference was of degree.

Overall, I think the authors were successful in documenting performance on the biconditional discrimination task. Showing that it is more difficult to perform than other discriminations is valuable and consistent with the proposal that accurate performance requires encoding of conditional information (which the authors refer to as "context"). There is evidence that female rats spend more time in the food cup during CS-, but I hesitate to agree that this is an important sex difference. There is no cost to spending more time in the food cup during CS- and they spend much less time there than during CS+. Males and females also did not differ in their CS+ responses, suggesting similar levels of learning. A number of factors could contribute to more food cup time in CS-, such as smaller body size and more locomotor activity. The number of food cup entries during CS+ and CS- was not reported here. Nevertheless, I think the manuscript will make a useful contribution to the field and hopefully lead readers to follow up on these types of tasks.

One area for development would be to test the associative properties of the cues controlling the conditional discrimination, can they be shown to have the properties of Pavlovian occasion-setting stimuli? Such work would strengthen the justification/rationale for using the terms "context" and "occasion setter" to refer to these stimuli in this task in the way the authors do in this paper.

Strengths:<br /> - Nicely designed and conducted experiment.<br /> - Documents performance difference by sex.

Weaknesses:<br /> - Overstatement of sex differences.<br /> - Inconsistent, confusing, and possibly misleading use of terms to describe/imply the underlying processes contributing to performance.

Reviewer #3 (Public Review):

Summary:<br /> This manuscript represents a technological development- specifically a micrococcal nuclease chromatin capture approach, termed MChIP-C to identify promoter-centered chromatin interactions at single nucleosome resolution via a specific protein, similar to HiChIP, ChIA-PET, etc.. In general, the manuscript is technically well done. Two major issues raise concerns that need to be addressed. First, it does not appear that novel chromatin interactions identified by MChIP-C which were missed by other approaches such as HiChIP, were validated. This is central to the argument of "improved" sensitivity, which is one of the key factors to assess sensitivity. Second is the question of resolution. Because the authors focus on a histone mark (H3K4me3) it is unclear whether the resolution of the assay truly exceeds other approaches, especially microC. These two issues are not completely supported by the data provided.

Strengths:<br /> 1) The method appears to hold promise to improve both the sensitivity and resolution of protein-centered chromatin capture approaches.

Weaknesses:<br /> 1) Specific validation experiments to demonstrate the identification of previously missed novel interactions are missing.

2) It is unclear if the resolution is really superior based on the data provided.

3) It is unclear how much advantage the approach has, especially compared to existing approaches such as HiChIP< since sequencing depth as a variable is not adequately addressed.

Reviewer #3 (Public Review):

Summary:<br /> A central question in ecology is: Why are there so many species? This question gained heightened interest after the development of influential models in theoretical ecology in the 1960s, demonstrating that under certain conditions, two consumer species cannot coexist on the same resource. Since then, several mechanisms have been shown to be capable of breaking the competitive exclusion principle (although, we still lack a general understanding of the relative importance of the various mechanisms in promoting biodiversity).

One mechanism that allows for breaking the competitive exclusion principle is predator interference. The Beddington-DeAngelis is a simple model that accounts for predator interference in the functional response of a predator. The B-D model is based on the idea that when two predators encounter one another, they waste some time engaging with one another which could otherwise be used to search for resources. While the model has been influential in theoretical ecology, it has also been criticized at times for several unusual assumptions, most critically, that predators interfere with each other regardless of whether they are already engaged in another interaction. However, there has been considerable work since then which has sought either to find sets of assumptions that lead to the B-D equation or to derive alternative equations from a more realistic set of assumptions (Ruxton et al. 1992; Cosner et al. 1999; Broom et al. 2010; Geritz and Gyllenberg 2012). This paper represents another attempt to more rigorously derive a model of predator interference by borrowing concepts from chemical reaction kinetics (the approach is similar to previous work: Ruxton et al. 1992). The main point of difference is that the model in the current manuscript allows for 'chasing pairs', where a predator and prey engage with one another to the exclusion of other interactions, a situation Ruxton et al. (1992) do not consider. While the resulting functional response is quite complex, the authors show that under certain conditions, one can get an analytical expression for the functional response of a predator as a function of predator and resource densities. They then go on to show that including intraspecific interference allows for the coexistence of multiple species on one or a few resources, and demonstrate that this result is robust to demographic stochasticity.

Strengths:<br /> I appreciate the effort to rigorously derive interaction rates from models of individual behaviors. As currently applied, functional responses (FRs) are estimated by fitting equations to feeding rate data across a range of prey or predator densities. In practice, such experiments are only possible for a limited set of species. This is problematic because whether a particular FR allows stability or coexistence depends on not just its functional form, but also its parameter values. The promise of the approach taken here is that one might be able to derive the functional response parameters of a particular predator species from species traits or more readily measurable behavioral data.

Weaknesses:<br /> The main weakness of this paper is that it devotes the vast majority of its length to demonstrating results that are already widely known in ecology. We have known for some time that predator interference can relax the CEP (e.g., Cantrell, R. S., Cosner, C., & Ruan, S. 2004).

While the model presented in this paper differs from the functional form of the B-D in some cases, it would be difficult to formulate a model that includes intraspecific interference (that increases with predator density) that does not allow for coexistence under some parameter range. Thus, I find it strange that most of the main text of the paper deals with demonstrating that predator interference allows for coexistence, given that this result is already well known. A more useful contribution would focus on the extent to which the dynamics of this model differ from those of the B-D model.

The formulation of chasing-pair engagements assumes that prey being chased by a predator are unavailable to other predators. For one, this seems inconsistent with the ecology of most predator-prey systems. In the system in which I work (coral reef fishes), prey under attack by one predator are much more likely to be attacked by other predators (whether it be a predator of the same species or otherwise). I find it challenging to think of a mechanism that would give rise to chased prey being unavailable to other predators. The authors also critique the B-D model: "However, the functional response of the B-D model involving intraspecific interference can be formally derived from the scenario involving only chasing pairs without predator interference (Wang and Liu, 2020; Huisman and De Boer, 1997) (see Eqs. S8 and S24). Therefore, the validity of applying the B-D model to break the CEP is questionable.".

However, the way "chasing pairs" are formulated does result in predator interference because a predator attacking prey interferes with the ability of other predators to encounter the prey. I don't follow the author's logic that B-D isn't a valid explanation for coexistence because a model incorporating chasing pairs engagements results in the same functional form as B-D.

More broadly, the specific functional form used to model predator interference is of secondary importance to the general insight that intraspecific interference (however it is modeled) can allow for coexistence. Mechanisms of predator interference are complex and vary substantially across species. Thus it is unlikely that any one specific functional form is generally applicable.

Reviewer #3 (Public Review):

In this study, Gumaste et al. aim to determine whether mice can discriminate odor intermittency and whether the olfactory bulb encodes intermittency. Using a Go/No-Go task, the study first showed that mice can be trained to discriminate odor stimuli with a low versus high intermittency value. Next, the authors demonstrated that early olfactory processing in the OSNs and mitral/tufted cells encodes intermittency. Through calcium imaging of olfactory bulb glomeruli, they obtained the glomerular response properties across intermittency and demonstrated the effects of sniff frequency on the glomerular representation of intermittency. Although the results are expected based on previous literature, they do lend support to the notion that intermittency can be used for odor-guided navigation.

Strengths:

The counterbalanced olfactometer used in this study keeps the air flow constant while odor concentration changes. This design is very useful for experiments in which odor delivery needs to be precisely controlled.

In a Go/No-Go task, mice were successfully trained to discriminate CS+ versus CS- odor stimuli with high versus low intermittency values in three different stimulus types (termed naturalistic, binary naturalistic, and square wave).

The olfactory bulb glomerular activity (from either olfactory sensory neurons or mitral/tufted cells) was monitored while mice performing the behavioral tasks, supporting that intermittency coding could arise from early olfactory processing.

Weaknesses:

Alternative interpretations of the behavioral outcome could be better discussed. For instance, the odors delivered with high intermittency values may lead to higher odor concentrations that olfactory sensory neurons encounter in the mucus. Mice might discriminate the total amount of odors present in the mucus rather than intermittency.

The conclusion that intermittency encoding is odor specific and depends on the spatial patterning/intrinsic glomerular properties is only based on two odorants used in this study.

Reviewer #3 (Public Review):

This manuscript describes a multiplexed approach for the identification of transcriptional features of neurons projecting to specific target areas at the single-cell level. This approach, called MERGE-seq, begins with multiplexed retrograde tracing by injecting distinctly barcoded rAAV-retro viruses into different target areas. The transcriptomes and barcoding of neurons in the source area are then characterized by single-cell RNA sequencing (scRNAseq) on the 10xGenomics platform. The projection targets of barcoded neurons in the source area can be inferred by matching the detected barcodes to the barcode sequences to of rAAV-retro viruses injected into the target areas.

The authors validated their approach by injecting five rAAV-retro GFP viruses, each encoding a different barcode, into five known targets of the ventromedial prefrontal cortex (vmPFC). The transcriptomes and barcoding of vmPFC neurons were then analyzed by scRNA-seq with or without enrichment of retrogradely labeled neurons based on GFP fluorescence. The authors confirmed the previously described heterogeneity of vmPFC neurons. In addition, they showed that most transcriptionally defined cell types project to multiple targets and that the five targets received projections from multiple transcriptomic types. The authors further characterized the transcriptomic features of barcoded vmPFC neurons with different projection patterns and defined Pou3f1 as a marker gene of neurons extending collateral branches to the dorsomedial striatum and lateral hypothalamus.

Overall, the results of the manuscript are convincing: the transcriptomic vmPFC cell types defined by scRNAseq in this study appear to correlate well with previous studies, the bifurcated projection patterns inferred by barcoding are validated using dual-color retro-AAV tracing, and marker genes for projection-specific cell subclasses are validated in retrogradely labeled vmPFC using RNA FISH for marker detection.

The concept of combining retrograde tracing and scRNAseq is not new. Previous studies have applied recombinase-expressing viruses capable of retrograde labeling, such as CAV, rabies virus, and AAV2-Retro, to retrogradely label and induce the expression of fluorescence markers in projection neurons, therefore facilitating enrichment and analysis of neurons projecting to a specific target. Multiplexed analysis can be achieved with the combination of different reporter viruses or viruses expressing different recombinases and appropriate reporter mouse lines. The advantages of MERGE-seq include that no transgenic lines are required and that it could be applied at even higher levels of multiplexity.

However, previously existing datasets that have already profiled this region with scRNAseq have not been utilized to their full extent. Therefore, for the proper context with prior literature, bioinformatic integration of these scRNAseq and prior scRNAseq data is needed.

Moreover, robust detection of barcodes in neurons labeled by barcoded AAV-retro viruses remains a challenge. The authors should clearly discuss the difficulties with barcode detection in this approach, as well as discuss potential solutions, which are important for others interested in its approach.

While this study is limited to the five known targets of vmPFC, the results suggest that MERGE-seq is a valuable tool that could be used in the future to characterize projection targets and transcriptomes of neurons in a multiplexed manner. As MERGE-seq uses AAVs to deliver barcodes, this method has the potential for application in model organisms for which transgenic lines are not available. Further improvements in experimental design and data analysis should be considered when applying MERGE-seq to poorly characterized source areas or with increased multiplexity of target areas.

In summary, this is a valuable approach, but the authors should clearly provide the context for their study within the existing literature, transparently discuss the limitations of MERGE-seq, as well as suggest improvements for the future.

Reviewer #3 (Public Review):

Male seminal fluid proteins play a crucial role in fertility and influence female physiology and behavior after mating. Brown et al. have discovered a new reproductive function for odorant-binding proteins (Obps) in Drosophila. The study shows that Obp56g is expressed in male reproductive tissues that produce seminal fluid proteins and is required for the formation of the mating plug in the mated female. The study demonstrates that RNAi knockdown and CRISPR/Cas9-generated mutations in Obp56g result in a defective mating plug, reduced sperm storage, and subsequent effects on female post-mating responses. The research also suggests that Obp56g has been co-opted for a reproductive function over evolutionary time, as supported by functional and comparative RNAseq data across Drosophila species. Finally, the study reports expression shifts, duplication, and divergence in the evolution of these seminal protein genes.

Overall, the study represents a significant contribution to our understanding of seminal proteins and their reproductive function. The creation of novel Obp mutants using CRISPR/Cas9 technology is a valuable resource for future research in the Drosophila community. The manuscript successfully conveys the key findings and their potential implications for the field. However, to reinforce the study's conclusions, more quantitative data is necessary. Furthermore, improving the statistical analysis and incorporating additional genetic controls would enhance the quality of the study and provide a stronger foundation for its conclusions.

Reviewer #3 (Public Review):

This manuscript offers a novel account of history biases in perceptual decisions in terms of bounded rationality, more specifically in terms of finite resources strategy. Bridging two works of literature on the suboptimalities of human decision-making (cognitive biases and bounded rationality) is very valuable per se; the theoretical framework is well derived, building upon the authors' previous work; and the choice of experiment and analysis to test their hypothesis is adequate. However, I do have important concerns regarding the work that do not enable me to fully grasp the impact of the work. Most importantly, I am not sure whether the hypothesis whereby inference is biased towards avoiding high precision posterior is equivalent or not to the standard hypothesis that inference "leaks" across time due to the belief that the environment is not stationary. This and other important issues are detailed below. I also think that the clarity and architecture of the manuscript could be greatly improved.

1. At this point it remains unclear what is the relationship between the finite resources hypothesis (the only bounded rationality hypothesis supported by the data) and more standard accounts of historical effects in terms of adaptation to a (believed to be) changing environment. The Discussion suggests that the two approaches are similar (if not identical) at the algorithmic level: in one case, the posterior belief is stretched (compared to the Bayesian observer for stationary environments) due to precision cost, in other because of possible changes in the environment. Are the two formalisms equivalent? Or could the two accounts provide dissociable predictions for a different task? In other words, if the finite resources hypothesis is not meant to be taken as brain circuits explicitly minimizing the cost (as stated by the authors), and if it produces the same type of behavior as more classical accounts: is the hypothesis testable experimentally?

2. The current analysis of history effects may be confounded by effects of the motor responses (independently from the correct response), e.g. a tendency to repeat motor responses instead of (or on top of) tracking the distribution of stimuli.

3. The authors assume that subjects should reach their asymptotic behavior after passively viewing the first 200 trials but this should be assessed in the data rather than hypothesized. Especially since the subjects are passively looking during the first part of the block, they may well pay very little attention to the statistics.

4. The experiment methods are described quite poorly: when is the feedback provided? What is the horizontal bar at the bottom of the display? What happens in the analysis with timeout trials and what percentage of trials do they represent? Most importantly, what were the subjects told about the structure of the task? Are they told that probabilities change over blocks but are maintained constant within each block?

Reviewer #3 (Public Review):

In this study, Yang et al. address a fundamental question of the role of dorsal striatum in neural coding of gait. The authors study the respective roles of D1 and D2 MSNs by linking their balanced activity to detailed gait parameters. In addition, they put in parallel the striatal activity related to whole-body measures such as initiation/cessation of movement or body speed. They are using an elegant combination of high-resolution single-limb motion tracking, identification of bouts of movements, and electrophysiological recordings of striatal neurons to correlate those different parameters. Subpopulations of striatal output neurons (D1 and D2 expressing neurons) are identified in neural recordings with optogenetic tagging. Those complementary approaches show that a subset of striatal neurons have phase-locked activity to individual limbs. In addition, more than a third of MSNs appear to encode all three aspects of motor behavior addressed here, initiation/cessation of movement, body speed, and gait. This activity is balanced between D1 and D2 neurons, with a higher activity of D1 neurons only for movement initiation. Finally, alterations of gait, and the associated striatal activity, are studied in a mouse model of Parkinson's Disease, using 6-OHDA lesions in the medial forebrain bundle (MFB). In the 6OHDA mice, there is an imbalance toward D2 activity.

Strengths:<br /> There is a long-standing debate on the respective role of D1 and D2 MSNs on the control of movement. This study goes beyond prior work by providing detailed quantification of individual limb kinematics, in parallel with whole-body motion, and showing a high proportion of MSNs to be phase-locked to precise gait cycle and also encoding whole-body motion. The temporal resolution used here highlights the preferential activity of D1 MSN at the movement starts, whereas previous studies described a more balanced involvement. Finally, they reveal neural mechanisms of dopamine depletion-induced gait alterations, with a preponderant phase-locked activity of D2 neurons. The results are convincing, and the methodology supports the conclusions presented here.

Weaknesses:<br /> Some more detailed explanations would improve the clarity of the results in the corresponding section. Analysis of the 6OHDA experiments could be expanded to extract more relevant information.

Reviewer #3 (Public Review):

The original research article, titled "mitoBKCa is functionally expressed in murine and human breast cancer cells and promotes metabolic reprogramming" by Bischof et al, has demonstrated the underlying molecular mechanisms of alterations in the function of Ca2+ activated K+ channel of large conductance (BKCa) in the development and progression of breast cancer. The authors also proposed that targeting mitoBKCa in combination with established anti-cancer approaches, could be considered as a novel treatment strategy in breast cancer treatment.

The paper is clearly written, and the reported results are interesting.

Strengths:

Rigorous biophysical experimental proof in support of the hypothesis.

Weaknesses:

A combinatorial synergistic study is missing.

Reviewer #3 (Public Review):

Summary:

The authors try to elucidate the molecular mechanisms underlying the intra-organ crosstalks that perpetuate intestinal permeability and inflammation.

Strengths:

This study identifies a hepatocyte-specific rela/stat3 network as a potential therapeutic target for intestinal diseases via the gut-liver axis using both murine models and human samples.

Weaknesses:

1. The mechanism by which DSS administration induces the activation of the Rela and Stat3 pathways and subsequent modification of the bile acid pathway remains clear. As the authors state, intestinal bacteria are one candidate, and this needs to be clarified. I recommend the authors investigate whether gut sterilization by administration of antibiotics or germ-free condition affects 1. the activation of the Rela and Stat3 pathway in the liver by DSS-treated WT mice and 2. the reduction of colitis in DSS-treated relaΔhepstat3Δhep mice.

2. It has not been shown whether DSS administration causes an increase in primary bile acids, represented by CDCA, in the colon of WT mice following activation of the Rela and Stat3 pathways, as demonstrated in Figure 6.

3. The implications of these results for IBD treatment, especially in what ways they may lead to therapeutic intervention, need to be discussed.

Reviewer #3 (Public Review):

Summary:<br /> This paper presents convincing data from technically demanding dual whole-cell patch recordings of stellate cells in medial entorhinal cortex slice preparations during optogenetic stimulation of PV+ interneurons. The authors show that the patterns of postsynaptic activation are consistent with dual recorded cells close to each other receiving shared inhibitory input and sending excitatory connections back to the same PV neurons, supporting a circuitry in which clusters of stellate cells and PV+IN interact with each other with much weaker interactions between clusters. These data are important to our understanding of the dynamics of functional cell responses in the entorhinal cortex. The experiments and analysis are quite complex and would benefit from some revisions to enhance clarity.

Strengths:<br /> These are technically demanding experiments, but the authors show quite convincing differences in the correlated response of cell pairs that are close to each other in contrast to an absence of correlation in other cell pairs at a range of relative distances. This supports their main point of demonstrating anatomical clusters of cells receiving shared inhibitory input.

Weaknesses:<br /> The overall technique is complex and the presentation could be more clear about the techniques and analysis. In addition, due to this being a slice preparation they cannot directly relate the inhibitory interactions to the functional properties of grid cells which was possible in the 2-photon in vivo imaging experiment by Heys and Dombeck, 2014.

Reviewer #3 (Public Review):

The lateral cortex of the inferior colliculus (LC) is a region of the auditory midbrain noted for receiving both auditory and somatosensory input. Anatomical studies have established that somatosensory input primarily impinges on "modular" regions of the LC, which are characterized by high densities of GABAergic neurons, while auditory input is more prominent in the "matrix" regions that surround the modules. However, how auditory and somatosensory stimuli shape activity, both individually and when combined, in the modular and matrix regions of the LC has remained unknown.

The major obstacle to progress has been the location of the LC on the lateral edge of the inferior colliculus where it cannot be accessed in vivo using conventional imaging approaches. The authors overcame this obstacle by developing methods to implant a microprism adjacent to the LC. By redirecting light from the lateral surface of the LC to the dorsal surface of the microprism, the microprism enabled two-photon imaging of the LC via a dorsal approach in anesthetized and awake mice. Then, by crossing GAD-67-GFP mice with Thy1-jRGECO1a mice, the authors showed that they could identify LC modules in vivo using GFP fluorescence while assessing neural responses to auditory, somatosensory, and multimodal stimuli using Ca2+ imaging. Critically, the authors also validated the accuracy of the microprism technique by directly comparing results obtained with a microprism to data collected using conventional imaging of the dorsal-most LC modules, which are directly visible on the dorsal IC surface, finding good correlations between the approaches.

Through this innovative combination of techniques, the authors found that matrix neurons were more sensitive to auditory stimuli than modular neurons, modular neurons were more sensitive to somatosensory stimuli than matrix neurons, and bimodal, auditory-somatosensory stimuli were more likely to suppress activity in matrix neurons and enhance activity in modular neurons. Interestingly, despite their higher sensitivity to somatosensory stimuli than matrix neurons, modular neurons in the anesthetized prep were far more responsive to auditory stimuli than somatosensory stimuli (albeit with a tendency to have offset responses to sounds). This suggests that modular neurons should not be thought of as primarily representing somatosensory input, but rather as being more prone to having their auditory responses modified by somatosensory input. However, this trend was reversed in the awake prep, where modular neurons became more responsive to somatosensory stimuli than auditory stimuli. Thus, to this reviewer, the most intriguing result of the present study is the dramatic extent to which neural responses in the LC changed in the awake preparation. While this is not entirely unexpected, the magnitude and stimulus specificity of the changes caused by anesthesia highlight the extent to which higher-level sensory processing is affected by anesthesia and strongly suggest that future studies of LC function should be conducted in awake animals.

Together, the results of this study expand our understanding of the functional roles of matrix and module neurons by showing that responses in LC subregions are more complicated than might have been expected based on anatomy alone. The development of the microprism technique for imaging the LC will be a boon to the field, finally enabling much-needed studies of LC function in vivo. The experiments were well-designed and well-controlled, and the limitations of two-photon imaging for tracking neural activity are acknowledged. Appropriate statistical tests were used. There are three main issues the authors should address, but otherwise, this study represents an important advance in the field.

1) Please address whether the Thy1 mouse evenly expresses jRGECO1a in all LC neurons. It is known that these mice express jRGECO1a in subsets of neurons in the cerebral cortex, and similar biases in the LC could have biased the results here.

2) I suggest adding a paragraph or two to the discussion to address the large differences observed between the anesthetized and awake preparations. For example, somatosensory responses in the modules increased dramatically from 14.4% in the anesthetized prep to 63.6% in the awake prep. At the same time, auditory responses decreased from 52.1% to 22%. (Numbers for anesthetized prep include auditory responses and somatosensory + auditory responses.). In addition, the tonotopy of the DC shifted in the awake condition. These are intriguing changes that are not entirely expected from the switch to an awake prep and therefore warrant discussion.

3) For somatosensory stimuli, the authors used whisker deflection, but based on the anatomy, this is presumably not the only somatosensory stimulus that affects LC. The authors could help readers place the present results in a broader context by discussing how other somatosensory stimuli might come into play. For example, might a larger percentage of modular neurons be activated by somatosensory stimuli if more diverse stimuli were used?

Reviewer #3 (Public Review):

Lee, Kyungtae and colleagues have discovered and mapped out alpha-arrestin interactomes in both human and Drosophila through the affinity purification/mass spectrometry and the SAINTexpress method. Their work revealed highly confident interactomes, consisting of 390 protein-protein interactions (PPIs) between six human alpha-arrestins and 307 preproteins, as well as 740 PPIs between twelve Drosophila alpha-arrestins and 467 prey proteins.

To define and characterize these identified alpha-arrestin interactomes, the team employed a variety of widely recognized bioinformatics tools. These analyses included protein domain enrichment analysis, PANTHER for protein class enrichment, DAVID for subcellular localization analysis, COMPLEAT for the identification of functional complexes, and DIOPT to identify evolutionary conserved interactomes. Through these assessments, they not only confirmed the roles and associated functions of known alpha-arrestin interactors, such as ubiquitin ligase and protease, but also unearthed unexpected biological functions in the newly discovered interactomes. These included involvement in RNA splicing and helicase, GTPase-activating proteins, and ATP synthase.

The authors carried out further study into the role of human TXNIP in transcription and epigenetic regulation, as well as the role of ARRDC5 in osteoclast differentiation. It is particularly commendable that the authors conducted comprehensive testing of TXNIP's role in HDAC2 in gene expression and provided a compelling model while revising the manuscript. Additionally, the quantification of the immunocytochemistry data presented in Figure 6 convincingly supports the authors' hypothesis.

Overall, this study holds important value, as the newly identified alpha-arrestin interactomes are likely aiding functional studies of this protein group and advance alpha-arrestin research.

Reviewer #3 (Public Review):

Summary:<br /> The paper makes a convincing argument that physical interactions of proteins do not cause substantial evolutionary co-variation.

Strengths:<br /> The presented analyses are reasonable and look correct and the conclusions make sense.

Weaknesses:<br /> The overall problem of the analysis is that nobody who has followed the literature on evolutionary rate variation over the last 20 years would think that physical interactions are a major cause of evolutionary rate variation. First, there have been probably hundreds of studies showing that gene expression level is the primary driver of evolutionary rate variation (see, for example, [1]). The present study doesn't mention this once. People can argue the causes or the strength of the effect, but entirely ignoring this body of literature is a serious lack of scholarship. Second, interacting proteins will likely be co-expressed, so the obvious null hypothesis would be to ask whether their observed rates are higher or lower than expected given their respective gene expression levels. Third, protein-protein interfaces exert a relatively weak selection pressure so I wouldn't expect them to play much role in the overall evolutionary rate of a protein.

On point 3, the authors seem confused though, as they claim a co-evolving interface would evolve *faster* than the rest of the protein (Figure 1, caption). Instead, the observation is they evolve slower (see, for example, [2]). This makes sense: A binding interface adds additional constraint that reduces the rate at which mutations accumulate. However, the effect is rather weak.

All in all, I'm fine with the analysis the authors perform, and I think the conclusions make sense, but the authors have to put some serious effort into reading the relevant literature and then reassess whether they are actually asking a meaningful question and, if so, whether they're doing the best analysis they could do or whether alternative hypotheses or analyses would make more sense.

[1] https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4523088/<br /> [2] https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4854464/

Reviewer #3 (Public Review):

Summary:<br /> The protein kinase, Aurora B, is a critical regulator of mitosis and cytokinesis in eukaryotes, exhibiting a dynamic localisation. As part of the Chromosomal Passenger Complex (CPC), along with the Aurora B activator, INCENP, and the CPC localisation module comprised of Borealin and Survivin, Aurora B travels from the kinetochores at metaphase to the spindle midzone at anaphase, which ensures its substrates are phosphorylated in a time- and space-dependent manner. In the kinetoplastid parasite, T. brucei, the Aurora B orthologue (AUK1), along with an INCENP orthologue known as CPC1, and a kinetoplastid-specific protein CPC2, also displays a dynamic localisation, moving from the kinetochores at metaphase to the spindle midzone at anaphase, to the anterior end of the newly synthesised flagellum attachment zone (FAZ) at cytokinesis. However, the trypanosome CPC lacks orthologues of Borealin and Survivin, and T. brucei kinetochores also have a unique composition, being comprised of dozens of kinetoplastid-specific proteins (KKTs). Of particular importance for this study are KKT7 and the KKT8 complex (comprising KKT8, KKT9, KKT11, and KKT12). Here, Ballmer and Akiyoshi seek to understand how the CPC assembles and is targeted to its different locations during the cell cycle in T. brucei.

Strengths & Weaknesses:<br /> Using immunoprecipitation and mass-spectrometry approaches, Ballmer and Akiyoshi show that AUK1, CPC1, and CPC2 associate with two orphan kinesins, KIN-A and KIN-B, and with the use of endogenously expressed fluorescent fusion proteins, demonstrate for the first time that KIN-A and KIN-B display a dynamic localisation pattern similar to other components of the CPC. Most of these data provide convincing evidence for KIN-A and KIN-B being bona fide CPC proteins, although the evidence that KIN-A and KIN-B translocate to the anterior end of the new FAZ at cytokinesis is weak - the KIN-A/B signals are very faint and difficult to see, and cell outlines/brightfield images are not presented to allow the reader to determine the cellular location of these faint signals (Fig S1B).

They then demonstrate, by using RNAi to deplete individual components, that the CPC proteins have hierarchical interdependencies for their localisation to the kinetochores at metaphase. These experiments appear to have been well performed, although only images of cell nuclei were shown (Fig 2A), meaning that the reader cannot properly assess whether CPC components have localised elsewhere in the cell, or if their abundance changes in response to depletion of another CPC protein.

Ballmer and Akiyoshi then go on to determine the kinetochore localisation domains of KIN-A and KIN-B. Using ectopically expressed GFP-tagged truncations, they show that coiled-coil domains within KIN-A and KIN-B, as well as a disordered C-terminal tail present only in KIN-A, but not the N-terminal motor domains of KIN-A or KIN-B, are required for kinetochore localisation. These data are strengthened by immunoprecipitating CPC complexes and crosslinking them prior to mass spectrometry analysis (IP-CLMS), a state-of-the-art approach, to determine the contacts between the CPC components. Structural predictions of the CPC structure are also made using AlphaFold2, suggesting that coiled coils form between KIN-A and KIN-B, and that KIN-A/B interact with the N termini of CPC1 and CPC2. Experimental results show that CPC1 and CPC2 are unable to localise to kinetochores if they lack their N-terminal domains consistent with these predictions. Altogether these data provide convincing evidence of the protein domains required for CPC kinetochore localisation and CPC protein interactions. However, the authors also conclude that KIN-B plays a minor role in localising the CPC to kinetochores compared to KIN-A. This conclusion is not particularly compelling as it stems from the observation that ectopically expressed GFP-NLS-KIN-A (full length or coiled-coil domain + tail) is also present at kinetochores during anaphase unlike endogenously expressed YFP-KIN-A. Not only is this localisation probably an artifact of the ectopic expression, but the KIN-B coiled-coil domain localises to kinetochores from S to metaphase and Fig S2G appears to show a portion of the expressed KIN-B coiled-coil domain colocalising with KKT2 at anaphase. It is unclear why KIN-B has been discounted here.

Next, using a mixture of RNAi depletion and LacI-LacO recruitment experiments, the authors show that kinetochore proteins KKT7 and KKT9 are required for AUK1 to localise to kinetochores (other KKT8 complex components were not tested here) and that all components of the KKT8 complex are required for KIN-A kinetochore localisation. Further, both KKT7 and KKT8 were able to recruit AUK1 to an ectopic locus in the S phase, and KKT7 recruited KKT8 complex proteins, which the authors suggest indicates it is upstream of KKT8. However, while these experiments have been performed well, the reciprocal experiment to show that KKT8 complex proteins cannot recruit KKT7, which could have confirmed this hierarchy, does not appear to have been performed. Further, since the LacI fusion proteins used in these experiments were ectopically expressed, they were retained (artificially) at kinetochores into anaphase; KKT8 and KIN-A were both able to recruit AUK1 to LacO foci in anaphase, while KKT7 was not. The authors conclude that this suggests the KKT8 complex is the main kinetochore receptor of the CPC - while very plausible, this conclusion is based on a likely artifact of ectopic expression, and for that reason, should be interpreted with a degree of caution.

Further IP-CLMS experiments, in combination with recombinant protein pull-down assays and structural predictions, suggested that within the KKT8 complex, there are two subcomplexes of KKT8:KKT12 and KKT9:KKT11, and that KKT7 interacts with KKT9:KKT11 to recruit the remainder of the KKT8 complex. The authors also assess the interdependencies between KKT8 complex components for localisation and expression, showing that all four subunits are required for the assembly of a stable KKT8 complex and present AlphaFold2 structural modelling data to support the two subcomplex models. In general, these data are of high quality and convincing with a few exceptions. The recombinant pulldown assay (Fig. 4H) is not particularly convincing as the 3rd eluate gel appears to show a band at the size of KKT11 (despite the labelling indicating no KKT11 was present in the input) but no pulldown of KKT9, which was present in the input according to the figure legend (although this may be mislabeled since not consistent with the text). The text also states that 6HIS-KKT8 was insoluble in the absence of KKT12, but this is not possible to assess from the data presented. It is also surprising that data showing the effects of KKT8, KKT9, and KKT12 depletion on KKT11 localisation and abundance are not presented alongside the reciprocal experiments in Fig S4G-J.

The authors also convincingly show that AlphaFold2 predictions of interactions between KKT9:KKT11 and a conserved domain (CD1) in the C-terminal tail of KIN-A are likely correct, with CD1 and a second conserved domain, CD2, identified through sequence analysis, acting synergistically to promote KIN-A kinetochore localisation at metaphase, but not being required for KIN-A to move to the central spindle at anaphase. They then hypothesise that the kinesin motor domain of KIN-A (but not KIN-B which is predicted to be inactive based on non-conservation of residues key for activity) determines its central spindle localisation at anaphase through binding to microtubules. In support of this hypothesis, the authors show that KIN-A, but not KIN-B can bind microtubules in vitro and in vivo. However, ectopically expressed GFP-NLS fusions of full-length KIN-A or KIN-A motor domain did not localise to the central spindle at anaphase. The authors suggest this is due to the GPF fusion disrupting the ATPase activity of the motor domain, but they provide no evidence that this is the case. Instead, they replace endogenous KIN-A with a predicted ATPase-defective mutant (G209A), showing that while this still localises to kinetochores, the kinetochores were frequently misaligned at metaphase, and that it no longer concentrates at the central spindle (with concomitant mis-localisation of AUK1), causing cells to accumulate at anaphase. From these data, the authors conclude that KIN-A ATPase activity is required for chromosome congression to the metaphase plate and its central spindle localisation at anaphase. While potentially very interesting, these data are incomplete in the absence of any experimental data to show that KIN-A possesses ATPase activity or that this activity is abrogated by the G209A mutation, and the conclusions of this section are rather speculative.

Impact:<br /> Overall, this work uses a wide range of cutting-edge molecular and structural predictive tools to provide a significant amount of new and detailed molecular data that shed light on the composition of the unusual trypanosome CPC and how it is assembled and targeted to different cellular locations during cell division. Given the fundamental nature of this research, it will be of interest to many parasitology researchers as well as cell biologists more generally, especially those working on aspects of mitosis and cell division, and those interested in the evolution of the CPC.

Reviewer #3 (Public Review):

Summary:<br /> This study investigates the continuous effect of MetS components - namely, obesity, arterial hypertension, dyslipidemia, and insulin resistance - on cortical thickness. It also examines the spatial correlations between MetS effects on cortical thickness with brain cellular and network topological attributes. Additionally, the authors attempt to explore the complex interplay among MetS, cognitive function, and cortical thickness.

The results reveal a latent relationship between MetS and cortical thickness based on a clinical-anatomical dimension. Furthermore, the effect of MetS on cortical thickness is linked to local cell types and network topological attributes. These findings suggest that the authors achieved most, though not all, of their research objectives.

The conclusions are mostly well supported by data and results. However, the use of "was governed by" in the conclusion section suggests a causal relationship. This phrasing is inappropriate given that the study primarily employs correlational analyses.

Strengths<br /> The study presents several strengths:

This study undertakes a comprehensive assessment encompassing the full range of MetS components, such as obesity or arterial hypertension, rather than adopting a case-control study approach (categorizing participants into MetS or non-MetS groups) as seen in some previous research. Utilizing Partial Least Squares (PLS) for correlational analysis effectively addresses issues of multicollinearity (or high covariance among MetS components) and explores the relationship between MetS and brain morphology.

The study leverages two datasets, examining a large sample size of 40,087 individuals. This substantial sample potentially aids in identifying nuanced and underexplored brain anomalies. By incorporating high-quality MRI images, standardized data, and statistical analysis procedures, as well as sensitivity analyses, the results gain robustness, which addresses the limitations of small samples and low reproducibility.

In the context of MetS, this research uniquely employs the concept of imaging transcriptomics, i.e. virtual histology analysis. This approach allows the study to explore intricate relationships between cellular types and cortical thickness anomalies.

Weaknesses<br /> While this work has foundational strengths, the analyses and data seem inadequate to fully support the key claim and analysis. In particular:

After a thorough review of the methods and results sections, I found no direct or strong evidence supporting the authors' claim that the identified latent variables were related to more severe MetS to worse cognitive performance. While a sub-group comparison was conducted, it did not adequately account for confounding factors such as educational level. Additionally, the strength of evidence from such a sub-group comparison is substantially weaker than that from randomized controlled trials or longitudinal cohort studies. Therefore, it is inaccurate for the authors to assert a direct relationship between MetS and cognitive function based on the presented data. A more appropriate research design or data analysis approach, such as mediation analysis, can be employed to address this issue.

The use of the imaging transcriptomics pipeline (virtual histology analysis) to explore the microscale associations with MetS effects on the brain is commendable and has shown promising results. Nevertheless, variations in gene sets may introduce a degree of heterogeneity in the results (Seidlitz, et al., 2020; Martins et al., 2021). Consequently, further validation or exploratory analyses utilizing different gene sets can yield more compelling results and conclusions.

• for: GS3, Global System Three transition, mutual coordination economics

• paraphrase

  • GS3 will be more difficult than GS2
  • social contract needs to be updated to include
    • new relation with nature and non-human beings
    • stronger multilateral relasionships to protect the planet
  • In Michel's view, a cosmolocal coordination will be required
  • The alternative is coercive eco-fascism to prevent massive ecological damage while we continue to overconsume planetary resources
  • definition: mutual coordination economics
    • an economic system that maximizes freedom of choice within earth system boundaries with minimal coercion
    • it is a new synthesis of markets, states and commons via decentralized p2p networks

Reviewer #3 (Public Review):

Summary: The present study sought to investigate the role ERα expressed in Gabaergic neurons of the rostral periventricular aspect of the third ventricle (RP3V) and medial preoptic nucleus (MPN) in the positive feedback using genetically driven Crispr-Cas9 mediated knockdown of ESR1 in VGAT expressing neurons. ESR1 Knockdown in preoptic gabaergic neurons led to an absence of LH surge and acyclicity when associated with severely reduced kisspeptin (Kp) expression suggesting that a subpopulation of neurons co-expressing Kp and VGAT are key for LH surge since total absence of Kp is associated with an absence of GnRH neuron activation and reduced LH surge. Although the implication of kisspeptin neurons was highly suspected already, the novelty of these results lies in the fact that estrogen signaling is necessary in only a selected fraction of them to maintain both regular cycles and LH surge capacity.

Strengths:<br /> Remarkable aspects of this study are, its dataset which allowed them to segregate animals based on distinct neuronal phenotype matching specific physiological outcomes, the transparency in reporting the results (e.g. all statistical values being reported, all grouping variables being clearly defined, clarity about animals that were excluded and why) and the clarity of the writing. Another remarkable feature of this work lies in the analysis of the dataset. As opposed to the cre-lox approach which theoretically allows for the complete ablation of specific neuronal populations, but may lack specificity regarding timing of action and location, genetically driven in vivo Crispr-Cas9 editing offers both temporal and neuroanatomic selectivity but cannot achieve a complete knock down. This approach based on stereotaxic delivery of the AAV encoded guide RNAs comes with inevitable variability in the location where gene knockdown is achieved. By adjusting their original grouping of the animals based on the evaluation of the extent of kisspeptin expression in the target region, the authors obtained a much clearer and interpretable picture. Although only few animals (n=4) displayed absent kisspeptin expression, the convergence of observations suggesting a central impairment of the reproductive axis is convincing. Finally, the observation that the pulsatile secretion of LH is maintained in the absence of Kp expression in the RP3V lends support to the notion that LH surge and pulsatility are regulated independently by distinct neuronal populations, a model put forward by corresponding author a few years ago.

Reviewer #3 (Public Review):

The main problem with the work is that the results are only descriptive and do not allow any inferences or conclusions about the importance of the function of G4 structures. The discussion and conclusions are poor. The results are preliminary and in order to try to make the analysis more interesting, it should be further extended and the data must be explored in a much greater depth.

Reviewer #3 (Public Review):

Summary:<br /> In this manuscript, Chiolo and colleagues adapt a Drosophila induced-DSB repair outcome assay to the spermatogonia. In order to compare the outcomes in H3K9me-rich centromeric heterochromatin with a euchromatic site they use a cross to a silencing mutant to reveal the sequence changes in the reporter, which otherwise are not expressed. The authors corroborate that homologous recombination (HR) is up-regulated in this chromatin context, consistent with prior studies. Applying sequencing to mutagenic products the authors reveal context-dependent preferences in mutagenic end joining pathways and mechanisms, although these seem less categorical in terms of hetero- and euchromatin and instead sensitive to more subtle aspects of the local chromatin landscape. One theme, however, is that the microhomologies used for synthesis-dependent end joining are nearer to the induced DSB in heterochromatin than seen for the euchromatic DSB.

Strengths:<br /> 1. The use of the mitotically active spermatogonia and transient expression of the I-SceI to induce the DSB mitigates some caveats of prior experimental approaches including the fact that the cells are universally mitotically active. This approach also enables the outcomes to be assayed in the next generation, which is necessary for reporters expressed within heterochromatin. Thus, this is a technological tool that will be useful to other groups.

2. The observations suggest that MMEJ within heterochromatin (inferred to be Pol theta-dependent) prefers to use microhomologies close to the DSB. This suggests that either DSB end resection or RPA loading/removal is modulated by chromatin context, which is a new finding.

Weaknesses:<br /> 1. The observation that HR is preferred in heterochromatin has been documented in many prior systems.

2. Although the conclusions of the authors are well-supported by the data, the study is somewhat limited in mechanistic detail and would be strengthened by additional use of the genetic tools in the model system, particularly with regard to whether the preference for using microhomologies near the DSB in heterochromatin arises due to modulation of resection or RPA loading stability (the latter is the preferred interpretation of the authors, but goes untested). Nucleosome stability, presence of HP1, etc. seem attractive.

3. Given the variability observed for EJ pathway usage at the four heterochromatic genomic sites probed in the manuscript there is some concern that a single euchromatic site may not be sufficient for rigorous comparisons. This is particularly true because there seems to be little transcription at the "euchromatic" region (Fig. S5). Given that we do not know what matters to dictate the outcomes (epigenetic modifications and/or transcriptional status), this is concerning.

4. (Minor) Some caution should be stated in comparing the HR frequency between this system (low single digits) and prior induction/tissue systems (~20%) because the time domain of cut and repair cycles is vastly different.

5. (Minor) While there are certainly strengths to using the spermatogonia system, one also wonders if it might not have some unique biology given the importance of maintaining genome integrity in this tissue (e.g. the piRNA pathways to repress transposon mobilization). A comment on this point would be welcomed.

6. (Minor) The authors argue that alt-EJ is less mutagenic as a consequence of the observed use of microhomologues closer to the DSB, but what they really mean perhaps is that less sequence is lost? A mutagenic outcome can be equally deleterious in other cases if 1, 5, or 20+ bps are lost, depending on the context.

Reviewer #3 (Public Review):

Summary:

Gaynes et al. investigated the presynaptic and postsynaptic mechanisms of starburst amacrine cell (SAC) direction selectivity in the mouse retina by computational modeling and glutamate sensitivity (iGluSnFR) imaging methods. Using the SAC computational simulation, the authors initially tested bipolar cell contributions (space-time wiring model, presynaptic effect) and SAC axial resistance contributions (postsynaptic effect) to the SAC DS. Then, the authors conducted two-photon iGluSnFR imaging from SACs to examine the presynaptic glutamate release and found seven clusters of ON-responding and six clusters of OFF-responding bipolar cells. They were categorized based on their response kinetics: delay, onset phase, decay time, and others. Finally, the authors used cluster data to reconstruct bipolar cell inputs to SACs that generate direction selectivity. They concluded that presynaptic effects through the space-time wiring model only account for a fraction of SAC DS.

The article has many interesting findings, and the data presentation is superb. Strengths and weaknesses are summarized below.

Major Strengths:

The authors utilized solid technology to conduct computational modeling with Neuron software and a machine-learning approach based on evolutionary algorithms. Results are effectively and thoroughly presented.

The space-time wiring model was evaluated by changing bipolar cell response properties in the proximal and distal SAC dendrites. Many response parameters in bipolar cells are compared, and DSI is compared in Figure 3. These parameter comparisons are valuable to the field.

Two-photon microscopy was used to measure the bipolar cell glutamate outputs onto SACs by conducting iGluSnFR imaging. All the data sets, including images and transients, are elegantly presented. The authors analyzed the response based on various parameters, which generated more than several response clusters. The clustering is convincing.

Major Weaknesses:

The computational modeling demonstrates intriguing results: SAC dendritic morphology produces dendritic isolation, and a massive input overcomes the dendritic isolation (Figure 1). This modeling seems to be generated by basic dendritic cable properties. However, it has been reported that SAC dendrites express Kv3 and voltage-gated Ca channels. Are they incorporated into this model? If not, how about comparing these channel contributions?

In Figure 9 the authors generated the bipolar cell cluster alignment based on the space-time wiring model. The space-time wiring model has been proposed based on the EM study that distinct types of bipolar cells synapse on distinct parts of SAC dendrites (Green et al 2016, Kim et al 2014). While this is one of the representative Reicardt models, it is not fully agreed upon in the field (see Stincic et al 2016). Therefore, the authors' approach might be only hypothetical without concrete evidence for geographical cluster distributions. Is there any data suggesting each cluster's location on the SAC dendrites? I assume that the iGluSnFR imaging was conducted on the SAC dendritic network, which does not provide geographical information. How about injecting the iGluSnFR-AAV at a lower titer, which labels only some SACs in a tissue? This method may reveal each cluster's location on SAC dendrites.

The authors found that there are seven ON clusters and six OFF clusters, which are supposed to be bipolar cell terminals. However, bipolar cells reported to provide synaptic inputs are T-7, T-6, and multiple T-5s for ON SACs and T-1, T-2, and T-3s for OFF SACs. The number of types is less than the number of clusters. Is there a possibility of clusters belonging to glutamatergic amacrine cells? Please provide a discussion regarding the relations between clusters and cell types.

In Figure 5B, representative traces are shown responding to moving bars in horizontal directions. These did not show different responses to two directional stimuli. Is there any directional preference from other ROIs? Yonehara's group recently exhibited the bipolar cells' direction selectivity (Matsumoto et al 2021). Did you see any correlations with their results? Please discuss.

Reviewer #3 (Public Review):

Summary: The manuscript by Ryan and colleagues uses a well-established object recognition task to examine memory retrieval and forgetting. They show that memory retrieval requires activation of the acquisition engram in the dentate gyrus and failure to do so leads to forgetting. Using a variety of clever behavioural methods, the authors show that memories can be maintained and retrieval slowed when animals are reared in environmental enrichment and that normally retrieved memories can be forgotten if exposed to the environment in which the expected objects are no longer presented. Using a series of neural methods, the authors also show that activation or inhibition of the acquisition engram is key to memory expression and that forgetting is due to Rac1.

Strengths:<br /> This is an exemplary examination of different conditions that affect successful retrieval vs forgetting of object memory. Furthermore, the computational modelling that captures in a formal way how certain parameters may influence memory provides an important and testable approach to understanding forgetting.<br /> The use of the Rescorla-Wagner model in the context of object recognition and the idea of relevance being captured in negative prediction error are novel (but see below).<br /> The use of gain and loss of function approaches are a considerable strength and the dissociable effects on behaviour eliminate the possibility of extraneous variables such as light artifacts as potential explanations for the effects.

Weaknesses:<br /> Knowing what process (object retrieval vs familiarity) governed the behavioural effect in the present investigation would have been of even greater significance.

The impact of the paper is somewhat limited by the use of only one sex.

While relevance is an interesting concept that has been operationalized in the paper, it is unclear how distinct it is from extinction. Specifically, in the case where the animals are exposed to the context in the absence of the object, the paper currently expresses this as a process of relevance - the objects are no longer relevant in that context. Another way to think about this is in terms of extinction - the association between the context and the objects is reduced results in a disrupted ability of the context to activate the object engram.

Reviewer #3 (Public Review):

Summary:<br /> Nguyen et al show data indicating that the vomeronasal organ (VNO) and ventromedial hypothalamus (VMH) are part of a circuit that elicits defensive responses induced by predator odors. They also show that using fresh or old predator saliva may be a method to change the perceived imminence of predation. The authors also identify a family of VNO receptors that are activated by cat saliva. Next, the authors show how different components of this defensive circuit are activated by saliva, as measured by fos expression. Though interesting, the findings are not all integrated into a single narrative, and some of the results are only replications of earlier findings using modern methods. Overall, these findings provide incremental advance.

Strengths:<br /> 1 Predator saliva is a stimulus of high ethological relevance<br /> 2 The authors performed a careful quantification of fos induction across the anterior-posterior axis in Figure 6.

Weaknesses:<br /> 1 It is unclear if fresh and old saliva indeed alter the perceived imminence predation, as claimed by the authors. Prior work indicates that lower imminence induces anxiety-related actions, such as re-organization of meal patterns and avoidance of open spaces, while slightly higher imminence produces freezing. Here, the authors show that fresh and old predator saliva only provoke different amounts of freezing, rather than changing the topography of defensive behaviors, as explained above. Another prediction of predatory imminence theory would be that lower imminence induced by old saliva should produce stronger cortical activation, while fresh saliva would activate the amygdala, if these stimuli indeed correspond to significantly different levels of predation imminence.

2 It is known that predator odors activate and require AOB, VNO, and VMH, thus replications of these findings are not novel, decreasing the impact of this work.

3 There is a lack of standard circuit dissection methods, such as characterizing the behavioral effects of increasing and decreasing the neural activity of relevant cell bodies and axonal projections, significantly decreasing the mechanistic insights generated by this work.

4 The correlation shown in Figure 5c may be spurious. It appears that the correlation is primarily driven by a single point (the green square point near the bottom left corner). All correlations should be calculated using Spearman correlation, which is non-parametric and less likely to show a large correlation due to a small number of outliers. Regardless of the correlation method used, there are too few points in Figure 5c to establish a reliable correlation. Please add more points to 5c.

5 Some of the findings are disconnected from the story. For example, the authors show that V2R-A4-expressing cells are activated by predator odors. Are these cells more likely to be connected to the rest of the predatory defense circuit than other VNO cells?

6 Were there other behavioral differences induced by fresh compared to old saliva? Do they provoke differences in stretch-attend risk evaluation postures, number of approaches, the average distance to odor stimulus, the velocity of movements towards and away from the odor stimulus, etc?

Reviewer #3 (Public Review):

Summary: In this manuscript, Mure et al. describe interactions between diet, microbiome, and host development using Drosophila as a model. By characterizing microbial communities in food sources and animals, the authors showed that microbial community dynamics in the food source is critical for host development.

Strengths: This is a very interesting study where authors managed to tackle a difficult question in an elegant manner. How the interactions between different microbial species within the microbiome shape host physiology is an area of great interest but equally challenging due to the complexity of intercellular interactions in complex, host-associated microbial communities. By using a simplified model and interrogating not only microbe-microbe and host-microbe interactions, but also the role played by diet, authors were able to identify significant interactions during fly development.

Weaknesses: All weaknesses observed in the original manuscript have been corrected in the current version.

Exercise 19.5.1 The voltage will be given to us correct?

Exercise 19.3.7 What would the answer look like if both electrodes are consumed?

Exercise 19.2.1b Does it matter which side these are displayed? Mine tend to be on the opposite sides

Exercise 19.23 Similar to our last Quiz Question

Equation put on index card

Write equation on index card, will be on exam

19.3.4 Cathode is reducing and an anode is oxidating

Quiz Question, will be on exam

• for: visualizations - sea level rise at 3 Deg C

• comment

  • Look to canal cities like Venice or Amsterdam for inspiration because if it cities are salvagable, parts of them will become canal cities.

Reviewer #3 (Public Review):

In this article, Faisal et. al., use a combinatorial approach to look at the mechanisms of HIV-capsid inhibition by the highly potent drug Lenacepavir (LEN). The authors conclude that LEN induces capsid opening, but hyper-stabilizes the remaining capsid lattice during the early stages, and adversely affects the assembly of capsids during late stages of HIV-1 infection. Additionally, they suggest that hyper-stabilization effects of LEN on the capsid-lattice are induced by a low occupancy of this highly potent drug, while less potent inhibitors like PF74 need high occupancy on the lattice to induce similar effects. Taken together their findings shine a light on the importance of the capsid binding pocket targeted by multiple inhibitors including LEN, PF74, BI-2, and host-factor CPSF6 on overall capsid assembly, its stability in cells, and its role in HIV-1 infection.

Strengths:<br /> 1. Combinatorial approach using single-molecule imaging, cryoET and cellular assays show the adverse effects of LEN on HIV-1 capsid assembly, capsid disassembly, and block to virus infectivity.<br /> 2. Several novel insights are obtained in this paper, including the cryoET-data showing 2-layers of capsid formation in the presence of LEN. CPSF6-peptide binding to capsids, and their effect on stability.

Weakness:<br /> 1. Interpretation of the capsid stability data is focused on single virus traces rather than population analysis, which might paint a different picture of the conclusions.<br /> 2. The description and interpretation of the data in the results sections and the conclusions are inconsistent, and somewhat confusingly presented for the general non-expert audience.

Reviewer #3 (Public Review):

To identify direct targets of BMP signal in Nematostella, the authors performed ChIP-seq using an antibody against phosphorylated SMAD1/5 (pSMAD1/5) at late gastrula and late planula stages. In accordance with the highly dynamic BMP activity detected using immunofluorescence, pSMAD1/5 binding profiles change drastically as the larvae develop, with only a fraction of target genes shared between these two time points. The authors then followed up with RNA-seq in control versus BMP2/4 KD embryos and identified significant expression changes in many transcription factors and signaling molecules, including the Gbx-Hox genes, which are known to regulate endoderm patterning. These results, in conjunction with a thorough validation using in situ hybridization, strongly support the authors' claim that the BMP signal in Nematostella directly controls a small set of second-tier targets which in turn execute the morphogenic functions.

Next, the authors explored the conservation of BMP downstream targets by intersecting their candidate list with two published datasets from Drosophila (2-3hpf) and Xenopus (NF20 stage). Results from such an analysis should be taken with a grain of salt, as the developmental time points and biological context examined here are not necessarily comparable. Furthermore, whole genome duplication in vertebrates means multiple copies of transcription factors and signaling molecules belonging to the same family exist in Xenopus, making a homology-based comparison difficult. A handful of shared targets were identified between different species, although no statics were provided to support the significance of such an observation.

The authors then focused on Zswim4-6, one of the identified BMP targets with a high pSMAD1/5 enrichment level, and dissected its regulatory properties on BMP activity. Using complimentary knockdown and overexpression experiments, the authors rigorously demonstrated that Zswim4-6 is crucial to maintaining the proper pSMAD1/5 gradient at the late gastrula stage. By ectopically overexpressing a GFP tagged form of Zswim4-6, the authors performed low input ChIP-qPCR and confirmed that Zswim4-6 selectively binds to a regulatory region of a BMP-repressed gene, suggesting it may function as a co-repressor for certain BMP targets.<br /> Lastly, the authors examined the effect of Zswim5, a bilaterian homolog of Zswim4-6, during zebrafish D-V axis establishment. Overexpression of Zswim5 leads to a dampened pSMAD1/5 gradient and dorsalization of the fish larvae, hinting at the possibility that Zswim5 may function as a BMP modulator in zebrafish as well.

Overall, despite certain caveats, the experimental evidence supports the claims from the authors that Zswim4-6 is directly activated by and reciprocally modulates the BMP activity in Nematostella. The work presented here opens exciting possibilities to further dissect the gene regulatory networks downstream of the cnidarian BMP signaling pathway and expands our knowledge on the evolution of a bilaterally symmetric body plan.

Reviewer #3 (Public Review):

The study is interesting and the results are informative in how well people can report colors of two superimposed dot clouds. It reveals that there are trade-offs between reporting two colors. However, I have a few basic but major concerns with the present study and its conclusions about people's abilities to continuously track color values and the rate at which attention may be allocated across the two streams which I am outlining below.

1) The first concern regards the task that was used to measure continuous tracking of feature values, which in my view is ambiguous in whether it truly assesses active tracking of features or rather short-term memory of the last-seen colors. Specifically, participants were viewing two colored dot clouds that then turned gray, and were asked to report each of the colors they saw using continuous report. The test usually occurred after 6-8s (in Exp. 1 &2), so while not completely predictable, participants could easily perform the task without tracking both feature streams continuously and simply perform the color report based on the very last colors they saw. In other words, it does not seem necessary to know which color belonged to which stream, or what color it was before, to perform the task successfully. Thus, it is unclear to what extent this task is actually measuring active tracking, the same way tracking of spatial locations in multiple-object tracking tasks has been studied, which is the literature that the authors are trying to draw parallels to. In multiple-object tracking tasks, targets and nontarget objects look identical and so to keep track of which of the moving objects are targets, participants need to attend to them actively and selectively. (Similarly, the original feature-tracking study by Blaser et al., at least in their main experiment, people were asked to track an object superimposed on a second object which required continuous and selective tracking of that object).

2) The main claim that tracking two colors relies on a shared and strictly limited resource is primarily based on the relation between the two responses people give, such that the first response about one color tends to be higher accuracy than for the second response of the other color across participants. In my view, this is a relatively weak version of looking at trade-offs in resources, and it would have been more compelling to show such trade-offs at a single-trial level, or assess them with well-established methods that have been developed to look at attentional bottlenecks such as attention-operating characteristics that allow quantifying the cost of adding an additional task in a precise and much more direct manner.

3) Finally, the data of the last experiment is taken as evidence that feature-based selection oscillates at 1Hz between the two streams. This is based on response errors changing across time points with respect to an exogenous cue that is thought to "reset" attentional allocation to one stream. Only one of three data sets (which uses relatively sparse temporal sampling) shows a significant interaction between cue and time, and given that there was no a priori prediction of when such interaction should occur, this result begs for a replication to ensure that this is not a false positive result. Furthermore, based on the analyses done in the paper, it may very well be the case that the presumed "switching rate" is entirely non-oscillatory based on a recent very important paper by Geoffrey Brookshire (2022, Nature Human Behavior) that demonstrates that frequency analysis are not just sensitive to periodic but also aperiodic temporal structures. The paper also has a series of suggested analyses that could be used here to further test the current conclusions.

Reviewer #3 (Public Review):

This paper studies the role of the core PCP pathway on tissue morphogenesis of the Drosophila pupil wing. The authors used three different core PCP mutants to compare the cell dynamics with the wild type and conclude that core PCP does not guide the global patterns of cell dynamics during pupal wing morphogenesis. They use the previously published "triangle method" to extract modes of deformation (total shear, cell elongation, cell rearrangements) and find that they are the same (to within error) in the core PCP mutants. Moreover, the global shape of the wing at the end of the process is nearly the same, too.

Using laser ablation and a rheological model, the paper also investigates the effect of the core PCP pathway on the short-time mechanical properties of the tissue. The authors find that the short-time mechanical response is different in core PCP mutants. This is surprising, as most researchers in the field assume that the short-time recoil velocity is a proxy for tissue mechanics, and therefore also predictive of global tissue deformations. So the observation that the short-time recoils are different, while the global response is the same, is important for the field to understand.

A challenge with the paper as written is that it does not clearly explain how to reconcile these two observations, stating in the discussion that "the proportionality factor [which relates short-time recoil to tissue mechanics] can depend on the genotype and can change in time". It is possible that the data and model in the paper could be used to make a more convincing and clear statement.

The paper is conceptually interesting, methodologically sound, and likely impactful to the broad area of tissue mechanics and mechanobiology.

Reviewer #3 (Public Review):

In this study, the authors present the first comprehensive transcriptome map of the human locus coeruleus using two independent but complementary approaches, spatial transcriptomics and single-nucleus RNA sequencing. Several canonical features of locus coeruleus neurons that have been described in rodents were conserved, but potentially important species differences were also identified. This work lays the foundation for future descriptive and experimental approaches to understanding the contribution of the locus coeruleus to healthy brain function and disease.

This study has many strengths. It is the first reported comprehensive map of the human LC transcriptome and uses two independent but complementary approaches (spatial transcriptomics and snRNA-seq). Some of the key findings confirmed what has been described in the rodent LC, as well as some intriguing potential genes and modules identified that may be unique to humans and have the potential to explain LC-related disease states. The main limitations of the study were acknowledged by the authors and include the spatial resolution probably not being at the single cell level and the relatively small number of samples (and questionable quality) for the snRNA-seq data. Overall, the strengths greatly outweigh the limitations. This dataset will be a valuable resource for the neuroscience community, both in terms of methodology development and results that will no doubt enable important comparisons and follow-up studies.

Reviewer #3 (Public Review):

In this manuscript, the authors define the developmental trajectory resulting in a diverse mTEC compartment. Using a variety of approaches, including a novel CCL21-fate mapping model, data is presented to argue that embryonic CCL21-expressing thymocyte attracting mTECs naturally convert to into self-antigen displaying mTEC subsets, including Aire+ mTECs and thymic tuft cells. Perhaps somewhat surprisingly, a large fraction of cTECs were also marked for having expressed CCL21, suggesting that there exists some conversion of mTEC (progenitors) into cTEC, a developmentally interesting observation that could be followed up later. Overall, the experimental setup, writing, and conclusions, are all outstanding.

Reviewer #3 (Public Review):

Summary: Despite being preventable and treatable, cervical cancer remains the second most common cause of cancer death globally. This cancer, and associated deaths, occur overwhelmingly in low- and middle-income countries (LMIC), reflecting a lack of access to vaccination, screening and treatment services. Cervical screening is the second pillar in the WHO strategy to eliminate cervical cancer as a public health problem and will be critical in delivering early gains in cervical cancer prevention as the impact of vaccination will not be realized for several decades. However, screening strategies implemented in high income countries are not feasible or affordable in LMICs. This ambitious multi-center study aims to address these issues by developing and systematically evaluating a novel approach to cervical screening. The approach, based on primary screening with self-collected specimens for HPV testing, is focused on optimizing triage of people in whom HPV is detected, so that sensitivity for the detection of pre-cancer and cancer is maximized while treatment of people without pre-cancer or cancer is minimized.

Strengths:

The triage proposed for this study builds on the authors' previously published work in designing the ScreenFire test to appropriately group the 13 detected genotypes into four channels and to develop automated visual evaluation (AVE) of images of the cervix, taken by health workers.

The move from mobile telephone devices to a dedicated device to acquire and evaluate images, overcomes challenges previously encountered whereby updates of mobile phone models required retraining of the AVE algorithm.

The separation of the study into two phases, an efficacy phase in which screen positive people will be triaged and treated according to local standard of care and the performance of AVE will be evaluated against biopsy outcomes will be followed by the second phase in which the effectiveness, cost-effectiveness, feasibility and acceptability will be evaluated.

The setting in a range of low resource settings which are geographically well spread and reflective of where the global cancer burden is highest.

Weaknesses:

Potential ascertainment bias due to the lack of specified biopsy (such as small four quadrant biopsies or small biopsies across the transformation zone) when aceto-white areas are not identified. This has the potential lead to lead to an over-estimate of sensitivity of the triage approach, particularly in the setting of VIA as compared to colposcopy. While the authors specify endocervical sampling in this setting, using curette or brush (for cytology), this may not be as sensitive unless clinicians are experienced in endocervical curette procedures.

Reviewer #3 (Public Review):

Summary:<br /> The authors focus on the role of formin-like protein 2 in the mouse oocyte, which could play an important role in actin filament dynamics. The cytoskeleton is known to influence a number of cellular processes from transcription to cytokinesis. The results show that downregulation of FMNL2 affects spindle migration with resulting abnormalities in cytokinesis in oocyte meiosis I.

Weaknesses:<br /> The overall description of methods and figures is overall dismissively poor. The description of the sample types and number of replicate experiments is impossible to interpret throughout, and the quantitative analysis methods are not adequately described. The number of data points presented is unconvincing and unlikely to support the conclusions. On the basis of the data presented, the conclusions appear to be preliminary, overstated, and therefore unconvincing.

Reviewer #3 (Public Review):

In this improved version of the manuscript, Chang et al set out to find direct interactions with the Eph-B2 receptor, as our knowledge of its function/regulation is still incomplete. Using proteomic analysis of Hela cells expressing EPHB2, they identified MYCBP2 a potential binder, which they then confirm using extensive biochemical analyses, an interaction that seems to be negatively affected by binding of ephrin-B2 (but not B1). Furthermore, they find that FBXO45, a known MYCBP2 interaction, strongly facilitates its binding to EPHB2. Intriguingly, these interactions depend on the extracellular domains of EPHB2, suggesting the involvement of additional proteins as MYCBP2 is thought to be a cytoplasmic protein. Finally, they find that, in contrast to what could be expected given the known function of MYCBP2 as a ubiquitin E3 ligase, it actually positively regulates EPHB2 protein stability, and function.

The strength of this manuscript is the extensive biochemical analysis of the EPHB2/MYCBP2/FBXO43 interactions. The vast majority of the conclusions are supported by the data.

The attempt to extend the study to an in vivo animal using the worm is important, however the additive insight is, unfortunately, minimal.

Reviewer #3 (Public Review):

Summary:

In this manuscript, Krause and colleagues identify miR-182 as diabetes-associated microRNA: miR-182 is increased in bariatric surgery patients with versus without T2D; miR-182 was the only microRNA associated with three metabolic traits; miR-182 levels were associated with increased body weight in mice under different dietary manipulations; overexpression in Hep-G2 led to a decrease in LRP6; and overexpression in HFD fed mice led to increased insulin and liver TG. The manuscript provides a potentially useful resource for microRNA expression in human livers, though the functional importance of miR-182 remains unclear.

Strengths:

The use of human tissues and good sample sizes is strong.

Weaknesses:

The study is primarily correlative; the in vivo overexpression is non-physiological; and the mechanisms by which miR-182 exerts its effects are not rigorously tested.

Reviewer #3 (Public Review):

In this work, Kita et al., aim to understand the activation mechanisms of the kinesin-3 motors KLP-6 and UNC-104 from C. elegans. As many other motor proteins involved in intracellular transport processes, KLP-6 and UNC-104 motors suppress their ATPase activities in the absence of cargo molecules. Relieving the autoinhibition is thus a crucial step that initiates directional transport of intracellular cargo. To investigate the activation mechanisms, the authors make use of mass photometry to determine the oligomeric states of the full length KLP-6 and the truncated UNC-104(1-653) motors at sub-micromolar concentrations. While full length KLP-6 remains monomeric, the truncated UNC-104(1-653) displays a sub-population of dimeric motors that is much more pronounced at high concentrations, suggesting a monomer-to-dimer conversion. The authors push this equilibrium towards dimeric UNC-104(1-653) motors solely by introducing a point mutation into the coiled-coil domain and ultimately unleash a robust processivity of the UNC-104 dimer. The authors find that the same mechanistic concept does not apply to the KLP-6 kinesin-3 motor, suggesting an alternative activation mechanism of the KLP-6 that remains to be resolved. The present study encourages further dissection of the kinesin-3 motors with the goal of uncovering the main factors needed to overcome the 'self-inflicted' deactivation.

Reviewer #3 (Public Review):

In this study, Kierdorf and colleagues investigated the function of hemocytes in oxidative stress response and found that non-canonical DNA damage response (DDR) is critical for controlling JNK activity and the expression of cytokine unpaired3. Hemocyte-mediated expression of upd3 and JNK determines the susceptibility to oxidative stress and systemic energy metabolism required for animal survival, suggesting a new role for hemocytes in the direct mediation of stress response and animal survival.

In the revised manuscript, the authors provide additional evidence to support the role of DNA damage-modulated cytokine release by hemocytes during oxidative stress responses and strengthen the connection between DNA damage and the regulation of upd3 release from hemocytes. The authors have also included new analyses to emphasize the significance of hemocytes in the regulation of energy during oxidative stress. Following the reviewers' suggestions, the authors made improvements to the manuscript and the graphical abstract to better display their findings. Overall, the revised manuscript makes it easier to understand the main points, flows better, and is supported by convincing data and analysis throughout.

Reviewer #3 (Public Review):

Summary:<br /> The manuscript by Coberski et al describes a combined experimental and computational study aimed to shed light on the catalytic mechanism in a methyltransferase that transfers a methyl group from S-adenosylmethionine (SAM) to a substrate adenosine to form N6-methyladenosine (m6A).

Strengths:<br /> The authors determine crystal structures in complex with so-called bi-substrate analogs that can bridge across the SAM and adenosine binding sites and mimic a transition state or intermediate of the methyl-transfer reaction. The crystal structures suggest dynamical motions of the substrate(s) that are examined further using classical MD simulations. The authors then use QM/MM calculations to study the methyl-transfer process. Together with biochemical assays of ligand/substrate binding and enzyme turnover, the authors use this information to suggest what the key steps are in the catalytic cycle. The manuscript is in most places easy to read.

Weaknesses:<br /> My main suggestion for the authors is that they show better how their conclusions are supported by the data. This includes how the electron density maps for example support the key interactions and water molecules in the active site and a better error analysis of the computational analyses.

Reviewer #3 (Public Review):

Summary:<br /> The authors were trying to show that a novel neuronal metallothionein of poorly defined function, GIF/MT3, is actually heavily persulfidated in both the Zn-bound and apo (metal-free) forms of the molecule as purified from a heterologous or native host. Evidence in support of this conclusion is compelling, with both spectroscopic and mass spectrometry evidence strongly consistent with this general conclusion. The authors would appear to have achieved their aims.

Strengths:<br /> The analytical data are compelling in support of the author's primary conclusions are strong. The authors also provide some modeling evidence that strongly supports the contention that MT3 (and other MTs) can readily accommodate sulfane sulfur on each of the 20 cysteines in the Zn-bound structure, with little perturbation of the structure. This is not the case with Cys trisulfides, which suggests that the persulfide-metallated state is clearly positioned at lower energy relative to the immediately adjacent thiolate- or trisulfidated metal coordination complexes.

Weaknesses:<br /> The biological significance of the findings is not entirely clear. On the one hand, the analytical data are clearly solid (albeit using a protein derived from a bacterial over-expression experiment), and yes, it's true that sulfane S can protect Cys from overoxidation, but everything shown in the summary figure (Fig. 8D) can be done with Zn release from a thiol by ROS, and subsequent reduction by the Trx/TR system. In addition, it's long been known that Zn itself can protect Cys from oxidation. I view this as a minor weakness that will motivate follow-up studies. Fig. 1 was incomplete in its discussion and only suggests that a few S atoms may be covalently bound to MT3 as isolated. This is in contrast to the sulfate S "release" experiment, which I find quite compelling.

Impact:<br /> The impact will be high since the finding is potentially disruptive to the metals in the biology field in general and the MT field for sure. The sulfane sulfur counting experiment (the HPE-IAM electrophile trapping experiment) may well be widely adopted by the field. Those of us in the metals field always knew that this was a possibility, and it will interesting to see the extent to which metal-binding thiolates broadly incorporate sulfate sulfur into their first coordination shells.

Reviewer #3 (Public Review):

Summary:<br /> This manuscript describes some biochemical experiments on the crucial virulence factor EsxA (ESAT-6) of Mycobacterium tuberculosis. EsxA is secreted via the ESX-1 secretion system. Although this system is recognized to be crucial for virulence the actual mechanisms employed by the ESX-1 substrates are still mostly unknown. The EsxA substrate is attracting the most attention as the central player in virulence, especially phagosomal membrane disruption. EsxA is secreted as a dimer together with EsxB. The authors show that EsxA is also able to form homodimers and even tetramers, albeit at very low pH (below 5). Furthermore, the addition of a nanobody that specifically binds EsxA blocks intracellular survival, as well as if the nanobody is produced in the cytosol of the infected macrophages.

Strengths:<br /> -Decent biochemical characterization of EsxA and identification of a new and interesting tool to study the function of EsxA (nanobody).

-The manuscript is well-written.

Weaknesses:<br /> The findings are not critically evaluated using extra experiments or controls.

For instance, tetrameric EsxA in itself is interesting and could reveal how EsxA works. But one would say that this is a starting point to make small point mutations that specifically affect tetramer formation and then evaluate what the effect is on phagosomal membrane lysis. Also one would like to see experiments to indicate whether these structures can be produced under in vitro conditions, especially because it seems that this mainly happens when the pH is lower than 5, which is not normally happening in phagosomes that are loaded with M. tuberculosis.

Also, the fact that the addition of the nanobody, either directly to the bacteria or produced in the cytosol of macrophages is interesting, but again it is the starting point for further experimentation. As a control, one would like to see the effect on an Esx-1 secretion mutant. Furthermore, does cytosolic production or direct addition of the nanobody affect phagosomal escape? What happens if an EsxA mutant is produced that does not bind the nanobody?

Finally, it is a bit strange that the authors use a non-native version of esxA that has not only an additional His-tag but also an additional 12 amino acids, which makes the protein in total almost 20% bigger. Of course, these additions do not have to alter the characteristics, but they might. On the other hand, they easily discard the natural acetylation of EsxA by mycobacteria itself (proven for M. marinum) as not relevant for the function because it might not happen in (the close homologue) M. tuberculosis.

Reviewer #3 (Public Review):

Summary:

This article demonstrates a Pax1-Col11a1-Mmp3 signaling axis associated with adolescent idiopathic scoliosis and finds that estrogen affects this signaling axis. In addition, the authors have identified a new COL11A1 mutation and verified its effect on the Pax1-Col11a1-Mmp3 axis.

Strengths:

1. Col11a1P1335L is verified in multicenter cohorts with high confidence.

2. The article identified a potential pathogenesis of AIS.

Weaknesses:

The SV40-immortalized cell line established from Col11a1fl/fl mouse rib cartilage was applied in the study, and overexpression system was used to confirm that P1335L variant in COL11A1 perturbs its regulation of MMP3. However, due to the absence of P1335L point mutant mice, it cannot be confirmed whether P1335L can actually cause AIS, and the pathogenicity of this mutation cannot be directly verified.

Reviewer #3 (Public Review):

Summary:

In this study, Warfvinge and colleagues use CITE-seq to interrogate how CML stem cells change between diagnosis and after one year of TKI therapy. This provides important insight into why some CML patients are "optimal responders" to TKI therapy while others experience treatment failure. CITE-seq in CML patients revealed several important findings. First, substantial cellular heterogeneity was observed at diagnosis, suggesting that this is a hallmark of CML. Further, patients who experienced treatment failure demonstrated increased numbers of primitive cells at diagnosis compared to optimal responders. This finding was validated in a bulk gene expression dataset from 59 CML patients, in which it was shown that the proportion of primitive cells versus lineage-primed cells correlates to treatment outcome. Even more importantly, because CITE-seq quantifies cell surface protein in addition to gene expression data, the authors were able to identify that BCR/ABL+ and BCR/ABL- CML stem cells express distinct cell surface markers (CD26+/CD35- and CD26-/CD35+, respectively). In optimal responders, BCR/ABL- CD26-/CD35+ CML stem cells were predominant, while the opposite was true in patients with treatment failure. Together, these findings represent a critical step forward for the CML field and may allow more informed development of CML therapies, as well as the ability to predict patient outcomes prior to treatment.

Strengths:

This is an important, beautifully written, well-referenced study that represents a fundamental advance in the CML field. The data are clean and compelling, demonstrating convincingly that optimal responders and patients with treatment failure display significant differences in the proportion of primitive cells at diagnosis, and the ratio of BCR-ABL+ versus negative LSCs. The finding that BCR/ABL+ versus negative LSCs display distinct surface markers is also key and will allow for a more detailed interrogation of these cell populations at a molecular level.

Weaknesses:

CITE-seq was performed in only 9 CML patient samples and 2 healthy donors. Additional samples would greatly strengthen the very interesting and notable findings.

Reviewer #3 (Public Review):

Peng et al. designed a computational framework for identifying pioneer factors using epigenomic data from five cell types. The identification of pioneer factors is important for our understanding of the epigenetic and transcriptional regulation of cells. A computational approach toward this goal can significantly reduce the burden of labor-intensive experimental validation.

The authors have addressed my previous comments.

The main issue identified in this re-review is based on the authors' additional experiments to investigate the reproducibility of the pioneer factors identified in the previously analysis that anchored on H1 ESCs.

The additional analysis that uses the other four cell types (HepG2, HeLa-S3, MCF-7, and K562) as anchors reveals the low reproducibility/concordance and high dependence on the selection of anchor cell type in the computational framework. In particular, now several stem cell related TFs (e.g. ESRRB, POU5F1) are ranked markedly higher when H1 ESC is not used as the anchor cell type as shown in Supplementary Figure 5.

Of note, the authors have now removed the shape labels that denote Yamanaka factors in Figure 2c (revised manuscript) that was presented in the main Figure 2a in the initial submission. The NFYs and ESRRB labels in Supplementary 4a are also removed and the boxplot comparing NFYs and ESRRB with other TF are also removed in this figure. Removing these results effectively hides the issues of the computational framework we identified in this revision. Please justify why this was done.

In summary, these new results reveal significant limitations of the proposed computational framework for identifying pioneer factors. The current identifications appear to be highly dependent on the choice of cell types.

Reviewer #3 (Public Review):

The authors introduce two new concepts for antimicrobial resistance borrowed from pharmacology, "variant vulnerability" (how susceptible a particular resistance gene variant is across a class of drugs) and "drug applicability" (how useful a particular drug is against multiple allelic variants). They group both terms under an umbrella term "drugability". They demonstrate these features for an important class of antibiotics, the beta-lactams, and allelic variants of TEM-1 beta-lactamase. In the revised version, they investigate a second drug class that targets dihydrofolate reductase in Plasmodium (the causative agent of malaria).

The strength of the result is in its conceptual advance and that the concepts seem to work for beta-lactam resistance and DHFR inhibitors in a protozoan. However, I do not necessarily see the advance of lumping both terms under "drugability", as this adds an extra layer of complicaton in my opinion.

I think that the utility of the terms will be more comprehensively demonstrated by using examples across a breadth of drug classes classes and/or resistance genes. For instance, another good bacterial model with published data might have been trimethoprim resistance, which arises through point mutations in the folA gene (although, clinical resistance tends to be instead conferred by a suite of horizontally acquired dihydrofolate reductase genes, which are not so closely related as the TEM variants explored here).

The impact of the work on the field depends on a more comprehensive demonstration of the applicability of these new concepts to other drugs. This would be demonstrated in future work.

Reviewer #3 (Public Review):

Summary:<br /> The authors have undertaken a study to rigorously characterize the possible role of eIF2A in regulating translation in yeast. The authors test for the role of eIF2A in the absence or presence of cellular stress and conclude that eIF2A does not play any significant role in regulating translation initiation in yeast.

Strengths:<br /> The authors have used rigorous experimental approaches, including genome-wide ribosome profiling analysis in the absence or presence of stress, to show that eIF2A does not function in translation initiation on most mRNAs in yeast. Interestingly, the authors do identify a small number of mRNAs that possess some eIF2A dependency, so they constructed reporters to rigorously test them. One mRNA, HKR1, appears to possess a degree of eIF2A-dependent translation regulation.

Weaknesses:<br /> While no role of eIF2A in translation initiation is apparent, the authors do not determine what function eIF2A does play in yeast. Whether it plays a role in regulating translation in a different stress response is not determined.

Reviewer #3 (Public Review):

The manuscript from Mandal et al. aims to show that the actin cytoskeleton is the key mechanosensitive element in cytotoxic T lymphocytes, enabling them to discriminate between target cells of different cortical stiffness. They further examine whether WASP activation is sensitive to substrate stiffness, and thus modulates actin polymerization and early T cell signaling in a mechanosensitive manner. Overall, the mechanosensitivity of CTLs has attracted a lot of attention in the last few years and this study explores new and interesting facets. The manuscript asks an important question regarding the mechanisms underlying the stiffness dependent response observed in T cells. The authors have used a variety of techniques ranging from mouse models and in vivo studies, cell biological manipulations and biophysical measurements which is commendable. Their work suggests that the actin cytoskeleton regulated by WASP plays a key role in mechanosensitivity - which is an intriguing finding.

While this manuscript has wide-ranging experiments and interesting results, a number of points need to be carefully addressed to support the central claims.

The first major issue is that the irreversible actin inhibitor myca can have a number of non-specific effects on CTL activation. It is not clear that the effects observed are due to the change in stiffness alone. Since Myca depolymerizes actin, the B16 target cells would have altered MHC mobility or impaired receptor-ligand engagement - which might affect actin foci formation and signaling. There is also no gain of function experiment, wherein the stiffness of the target cell is enhanced. Moreover, there are two populations in both the control and myca-treated Young's modulus histograms for B16 cells. Are these sub-populations fundamentally different in their cytoskeletal organization? This can also confound or introduce variability in results on stiffness-dependence of CTL function, given the second sub-population of Myca-treated cells overlaps with the first sub-population of control cells. The authors need to provide a justification for these.

Secondly, the WASP knockout still shows mechanosensitivity but at reduced force levels (Fig. 3B). Similarly, other measures (Fig. 3) still show increases with stiffness. Thus, it is not clear whether WASP is necessary for mechanosensing but simply for maintaining force levels and (expectedly) lower actin levels and foci in the WASP knockout. In fact, Fig 3 implies WASP is required for signaling and not for mechanosensing, undermining the main claim of the paper. At the very least, ANOVA or factor analysis (stiffness x WASP) needs to be done to demonstrate the requirement of WASP for CTL mechanosensitivity.

Third, there are some concerns regarding the traction force microscopy. The authors do not present key details in the manuscript about the methods used. Secondly, the traction values are entirely too high compared to reported values in the literature for CTLs. A back-of-the-envelope calculation of the total force yields ~30 nN for wild-type cells) on 10 kPa gels, which is about an order of magnitude higher than reported values (Tamzalit et al. 2020, Hui et al. 2017, Bashour et al. 2014, Pathni et al. 2022). The authors should clearly demonstrate and justify that their measured values are reasonable and accurate. The lack of representative movies and displacement maps used for the traction force measurements make it hard to evaluate the results. Typical bead displacements for CTLs on softer gels are on the order of 1 micron (Mustapha et al. 2022), which should decrease to 0.1 micron or less on 50 kPa gels. These would make the tractions hard to estimate accurately. The authors should evaluate and show the displacements underneath the cell and outside the cell boundaries to give estimates of the noise floor for tractions. Finally, there is no discussion of how the tractions were calculated from the displacements - was Fourier Transform or Finite element method used? What is the noise level of the measurements and how were the traction estimates regularized?

Fourth, many of the plots in the manuscripts are not accompanied by representative images to show how these aspects (distribution of actin and signaling markers for example) change qualitatively under different conditions (e.g. stiffness). Details of analysis and quantification need to be provided for a clearer understanding of the results and interpretations. All figures and captions should include information about the number of cells and experiments. Along these lines, there is very little detail in the methods, statistical power, calculations are not mentioned, there is little description of the pmel-1 knockout mouse, all of which make it hard to evaluate the soundness of the results.

Finally, the study as presented, doesn't conclusively show that WASP is required for mechanosensitive CTL function. The results presented show that WASP is required for early and longer-term signaling events and cytolytic activity, and that knocking out WASP reduces early TCR signaling, actin foci formation in response to substrate stiffness. To make the claim of WASP-mediated regulation of CTL mechanosensitivity stronger, it would be helpful to see how WASP knockout affects CTL killing in response to softened and (possibly) stiffened B16 targets.

Reviewer #3 (Public Review):

The authors investigate the role of commensal microbes and molecules in the antigen presentation pathway in the development and phenotype of CD8 T cells specific for the Qa-1b-restricted peptide FL9 (QFL). The studies track both endogenous QFL-specific T cells and utilize a recently generated TCR transgenic model. The authors confirm that QFL-specific T cells in the spleen and small intestine intraepithelial lymphocyte (IEL) pool show an antigen-experienced phenotype as well as unique phenotypic and innate-like functional traits, especially among CD8+ T cells expressing Va3.2+ TCRs. They find that deficiency in the TAP transporter leads to almost complete loss of QFL-specific T cells but that loss of either Qa1 or the ERAAP aminopeptidase does not impact QFL+ T cell numbers but does cause them to maintain a more conventional, naïve-like phenotype. In germ-free (GF) mice, the QFL-specific T cells are present at similar numbers and with a similar phenotype to SPF animals, but in older animals (>18w) there is a notable loss of IEL QFL-specific cells. This drop can be avoided by neonatal colonization of GF mice with the commensal microbe Pediococcus pentosaceus but not a different commensal, Lactobacillus johnsonii, and the authors show that P. pentosaceus encodes a peptide that weakly stimulates QFL-specific T cells, while the homologous peptide from L. johnsonii does not stimulate such cells.

This study provides new insights into the way in which the differentiation, phenotype, and function of CD8+ T cells specific for Qa-1b/FL9 is regulated by peptide processing and Qa1 expression, and by interactions with the microbiota. The approaches are well designed, the data compelling, and the interpretation, for the most part, appropriate.

The response to several of my concerns involved reference to a different manuscript from the authors (which has not been through peer review), and for point #3, it would have been useful to provide experimental evidence (e.g., competitive inhibition assays) to justify their hypothesis that P4 serves as a TCR contact while P6 may be a Qa-1b contact residue. Nevertheless, the authors have made considerable efforts to clarify their approaches and interpretation, which strengthens the manuscript.