Reviewer #2 (Public Review):

The contribution of glial cells to the pathogenesis of amyotrophic lateral sclerosis (ALS) is of substantial interest and the investigators have contributed significantly to this emerging field via prior publications. In the present study, authors use a SOD1G93A mouse model to elucidate the role of astrocyte ephrinB2 signaling in ALS disease progression. Erythropoietin-producing human hepatocellular receptors (Ephs) and the Eph receptor-interacting proteins (ephrins) signaling is an important mediators of signaling between neurons and non-neuronal cells in the nervous system. Recent evidence suggests that dysregulated Eph-ephrin signaling in the mature CNS is a feature of neurodegenerative diseases. In the ALS model, upregulated Eph4A expression in motor neurons has been linked to disease pathogenesis. In the present study, authors extend previous findings to a new class of ephrinB2 ligands. Urban et al. hypothesize that upregulated ephrinB2 signaling contributes to disease pathogenesis in ALS mice. The authors successfully test this hypothesis and their results generally support their conclusion.

Major strengths of this work include a robust study design, a well-defined translational model, and complementary biochemical and experimental methods such that correlated findings are followed up by interventional studies. Authors show that ephrinB2 ligand expression is progressively upregulated in the ventral horn of the cervical and lumbar spinal cord through pre-symptomatic to end stages of the disease. This novel association was also observed in lumbar spinal cord samples from post-mortem samples of human ALS donors with a SOD1 mutation. Further, they use a lentiviral approach to drive knock-down of ephrinB2 in the central cervical region of SOD1G93A mice at the pre-symptomatic stage. Interestingly, in spite of using a non-specific promoter, authors note that the lentiviral expression was preferentially driven in astrocytes.

Since respiratory compromise is a leading cause of morbidity in the ALS population, the authors proceed to characterize the impact of ephrinB2 knockdown on diaphragm muscle output. In mice approaching the end stage of the disease, electrophysiological recordings from the diaphragm muscle show that animals in the knock-down group exhibited a ~60% larger amplitude. This functional preservation of diaphragm function was also accompanied with the preservation of diaphragm neuromuscular innervation. However, it must be noted that this cervical ephrinB2 knockdown approach had no impact on disease onset, disease duration, or animal survival. Furthermore, there was no impact of ephrinB2 knockdown on forelimb or hindlimb function. This is an expected result, given the fairly focal approach of ephrinB2 knockdown in C3-C5 spinal segments.

The major limitation of the study is the conclusion that the preservation of diaphragm output following ephrinB2 knockdown in SOD1 mice is mediated primarily (if not entirely) by astrocytes. The authors present convincing evidence that a reduction in ephrinB2 is observed in local astrocytes (~56% transduction) following the intraspinal injection of the lentivirus. However, the proportion of cell types assessed for transduction with the lentivirus in the spinal cord was limited to neurons, astrocytes, and oligodendrocyte lineage cells. Microglia comprise a large proportion of the glial population in the spinal grey matter and have been shown to associate closely with respiratory motor pools. This cell type, amongst the many other that comprise the ventral gray matter, have not been investigated in this study. Nonetheless, there is convincing evidence to suggest astrocytes play a significant role, as compared to oligodendrocytes in promoting ALS pathogenesis.

In summary, this study by Urban et al. provides a valuable framework for Eph-Ephrin signaling mechanisms imposing pathological changes in an ALS mouse model. The role of glial cells in ALS pathology is a very exciting and upcoming field of investigation. The current study proposes a novel astrocyte-mediated mechanism for the propagation of disease that may eventually help to identify potential therapeutic targets.

Reviewer #2 (Public Review):

Summary:<br /> This manuscript by Martin-Flores et al. examines the role of DKK3 in Alzheimer's disease, focusing on the regulation of synaptic number. Using human AD brain databases and tissue samples, the authors demonstrate increased levels of DKK3 protein and mRNA in the brains of AD patients. DKK3 is expressed in excitatory neurons in WT mouse brains and accumulates at atrophic neurites around amyloid plaques in AD mouse brains. Interestingly, the secretion of DKK3 appears to be regulated by NMDAR antagonists, as well as chemical LTD. Through gain and loss of function studies, the authors reveal that DKK3 regulates the number of both excitatory and inhibitory synapses with distinct downstream pathways. Finally, the authors investigate the contribution of DKK3 to synaptic changes in AD and find that DKK3 loss of function rescues both excitatory and inhibitory synaptic defects, resulting in improved memory function in J20 mice.

Strengths:<br /> Overall, the data is clearly presented and deals with the novel roles of DKK3 in controlling excitatory and inhibitory synapses. The finding that shRNA expression of DKK3 in AD model mice rescues synaptic phenotypes and memory impairment is potentially interesting and may provide a new strategy for AD treatment.

Weaknesses:<br /> There are no major weaknesses.

Reviewer #3 (Public Review):

Summary:<br /> Onck and co-workers present in this work the identification of binding partners and sites of polyPR on various nuclear transport components and elucidate how polyPR might potentially influence the transport process. It's interesting to note that some interaction sites on transport components also serve as their inherent/functional binding sites (Figure 3). The difference in the effects between short polyPR (PR7) and long polyPR (PR50) is also evident, although the authors might need to clarify the mechanisms better. Overall, I find this manuscript well organized and concisely written, and it would greatly enhance our understanding of the toxicity induced by polyPR.

Strengths:<br /> The 1-bead per atom force field model used in the study is well-tuned for studying the interactions between polyPR and proteins, as the essential cation-pi interactions (between Arg and Phe/Tyr/Trp) was included using a 8-6 LJ model.

Weaknesses:<br /> To cite the author's response: "At the moment, accurately capturing the binding of NCT components to their native binding targets and the competition with polyPR are best resolved by all-atom molecular dynamics simulations, which come with significant computational demands. This level of detail and computation-intensive analyses is beyond the scope of the current study."

Reviewer #2 (Public Review):

Summary:<br /> Chang et al. investigate neuronal activity firing patterns across various cortical regions in an interesting context-dependent tactile vs visual detection task, developed previously by the authors (Chevee et al., 2021; doi: 10.1016/j.neuron.2021.11.013). The authors report the important involvement of a medial frontal cortical region (MM, probably a similar location to wM2 as described in Esmaeili et al., 2021 & 2022; doi: 10.1016/j.neuron.2021.05.005; doi: 10.1371/journal.pbio.3001667) in mice for determining task rules.

Strengths:<br /> The experiments appear to have been well carried out and the data well analysed. The manuscript clearly describes the motivation for the analyses and reaches clear and well-justified conclusions. I find the manuscript interesting and exciting!

Weaknesses:<br /> I did not find any major weaknesses.

Reviewer #2 (Public Review):

Summary:<br /> The authors' long-term goals are to understand the utility of precisely phased cortex stimulation regimes on recovery of function after spinal cord injury (SCI). In prior work, the authors explored the effects of contralesion cortex stimulation. Here, they explore ipsilesion cortex stimulation in which the corticospinal fibers that cross at the pyramidal decussation are spared. The authors explore the effects of such stimulation in intact rats and rats with a hemisection lesion at the thoracic level ipsilateral to the stimulated cortex. The appropriately phased microstimulation enhances contralateral flexion and ipsilateral extension, presumably through lumbar spinal cord crossed-extension interneuron systems. This microstimulation improves weight bearing in the ipsilesion hindlimb soon after injury, before any normal recovery of function would be seen. The contralateral homologous cortex can be lesioned in intact rats without impacting the microstimulation effect on flexion and extension during gait. In two rats ipsilateral flexion responses are noted, but these are not clearly demonstrated to be independent of the contralateral homologous cortex remaining intact.

Strengths:<br /> This paper adds to prior data on cortical microstimulation by the laboratory in interesting ways. First, the strong effects of the spared crossed fibers from the ipsi-lesional cortex in parts of the ipsi-lesion leg's step cycle and weight support function are solidly demonstrated. This raises the interesting possibility that stimulating the contra-lesion cortex as reported previously may execute some of its effects through callosal coordination with the ipsi-lesion cortex tested here. This is not fully discussed by the authors but may represent a significant aspect of these data. The authors demonstrate solidly that ablation of the contra-lesional cortex does not impede the effects reported here. I believe this has not been shown for the contra-lesional cortex microstimulation effects reported earlier, but I may be wrong.

Effects and neuroprosthetic control of these effects are explored well in the ipsi-lesion cortex tests here.

Weaknesses:<br /> Some data is based on very few rats. For example (N=2) for ipsilateral flexion effects of microstimulation. N=3 for homologous cortex ablation, and only ipsi extension is tested it seems. There is no explicit demonstration that the ipsilateral flexion effects in only 2 rats reported can survive the contra-lateral cortex ablation.

Some improvements in clarity and precision of descriptions are needed, as well as fuller definitions of terms and algorithms.

Likely Impacts:<br /> This data adds in significant ways to prior work by the authors, and an understanding of how phased stimulation in cortical neuroprosthetics may aid in recovery of function after SCI, especially if a few ambiguities in writing and interpretation are fully resolved.

Reviewer #2 (Public Review):

Summary:<br /> This is a fundamental and elegant study showing the role of BMP signaling in cerebellar development. This is an important question because there are multiple diseases, including aggressive childhood cancers, which involve granule cell precursors. Thus understanding of the factors that govern the formation of the granule cell layer is important both from a basic science and a disease perspective.

Overall, the manuscript is clear and well-written. The figures are extremely clear, wonderfully informative, and overall quite beautiful.

Figures 1-3 show the experimental design and report how BMP activity is altered over development in both the chick and the human developing cerebellum. Both data are very impressive and convincing.

They then go on to modulate BMP activity in the developing chick, using a complex electroporation paradigm that allows them to label cells with GFP as well as with cell-specific reporters of BMP activity levels. They bidirectionally modulate BMP levels and then can look at both cell-specific and non-specific alterations in the formation of the external and internal granule cell layer, across different developmental timepoints. These are really elegant and rigorous experiments, as they look at both sagittal and transverse sections to collect this data. This makes the data extremely compelling. With these rigorous techniques, they show that BMP signaling serves more than one function across development: it is involved in the initial tangential migration from the rhombic lip, but at a later time, both up- and down-regulation of BMP activity reduces the density of amplifying cells in the external granule cell layer.

Strengths:<br /> Overall, I think the paper is interesting and important and the data is strong. The use of both chick and human tissue strengthens the findings. They are extremely rigorous, analyzing data from multiple planes at multiple ages, which also really strengthens their findings. The dual electroporation approach is extremely elegant, providing beautiful visual representations of their findings.

Weaknesses:<br /> I find no significant weaknesses.

Reviewer #2 (Public Review):

Summary:

H2S is a gas that is toxic to many animals and causes avoidance in animals such as C. elegans. The authors show that H2S increases the frequency of turning and the speed of locomotion. The response was shown to be modulated by a number of neurons and signaling pathways as well as by ambient oxygen concentrations. The long-term adaptation involved gene expression changes that may be related to iron homeostasis as well as the homeostasis of mitochondria.

Strengths:

Overall, the authors provide many pieces that will be important for solving how H2S signals through neuronal circuits to change gene expression and physiological programs. The experiments rely mostly on a behavioral assay that measures the increase of locomotion speed upon exposure to H2S. This assay is then combined with manipulations of environmental factors, different wild-type strains, and mutants. The mutants analyzed were obtained as candidates from the literature and from transcriptional profiling that the authors carried out in worms that were exposed to H2S. These studies imply several genetic signaling pathways, some neurons, and metabolism-related factors in the response to H2S. Hence the data provided should be useful for the field.

Weaknesses:

On the other hand, many important aspects of the underlying mechanisms remain unsolved and the reader is left with many loose ends. For example, it is not clear how H2S is actually sensed, how sensory neurons are activated and signal to downstream circuits, and what the role of ciliated and RMG neurons is in this circuit. It remains unclear how signals lead to gene expression and physiological changes such as metabolic rewiring. Solving all this would clearly be beyond the scope of a single manuscript. Yet, the manuscript also does not focus on understanding one of these central aspects and rather is all over the place, which makes it harder to understand for readouts that are not in this core field. Multiple additional methods and approaches exist to dig deeper into these mechanisms in the future, such as neuronal calcium imaging, optogenetics, and metabolic analysis. To generate a story that will be interesting to a broad readership substantial additional experimentation would be required. Further, in the current manuscript, it is often difficult to understand the rationales of the experiments, why they were carried out, and how to place them into a context. This could be improved in terms of documentation, narration/explanation, and visualization.

Reviewer #2 (Public Review):

Summary:<br /> Authors hypothesized that modulation of KNa1.1 channel specifically in inhibitory interneurons contributes to the hyperactivity of neurons in the peripheral cortex at the lesion site, enhances seizure susceptibility to PTZ-induced seizures, and promotes the occurrence of PTE. They test this hypothesis in a mouse model of TBI induced by controlled cortical impact in wild-type and kcnt1 knock-out (KO) mice. The authors performed a series of experiments including behavioral assessment, electrographic recordings in vivo and in vitro, western blotting, and immunofluorescence imaging with the goal of investigating the contributory role of KNa1.1 channel to post-traumatic epileptogenesis.

Strengths:<br /> The hypothesis is innovative, focusing on the specific role of the KNa1.1 channel in the development of PTE post-TBI. The use of a comprehensive set of techniques, including EEG, whole cell patch clamp, western blot, immunofluorescence imaging, and behavioral assessments, provides a diverse data set. The study makes initial steps in correlating specific molecular changes with functional outcomes in TBI models, offering potential pathways for therapeutic intervention.

Weaknesses:<br /> 1) The study presents interesting findings on early changes in protein expression and electrophysiological properties following TBI. However, I would like to draw attention to the timeline of EEG and cellular assessments that require further clarification or consideration. The patch clamp recordings and other assays were conducted within 14 days post-TBI, while EEG recordings with or without PTZ testing were performed at 3 months post-injury. This temporal gap leaves a period where changes in electrophysiological properties and PTE status are not accounted for. Since epileptogenesis post-TBI involves a dynamic process spanning from hyperacute and acute phases to chronic development, capturing these changes continuously or at least at more frequent intervals (on and off bi-weekly) could provide a more comprehensive understanding of this progression. In the current study design, the one-week duration of EEG recordings at the 3-month timepoint raises the possibility that some seizures might have occurred undetected between the early post-injury phase and the EEG recording period. This gap could potentially affect the interpretation of results, especially when correlating early post-injury cellular changes with later seizure activity and thresholds and hence is a significant limitation to data interpretation. Experiments using western blots, immunofluorescence, and patch clamp were done at an early timepoint hence the relevance of these datasets to PTE status outcome is not established.

2) While referencing Nichols et al., 2015, to justify the 14-day timeline for characterizing seizures is understandable, it is important to consider differences in animal models (juvenile rats in Nichols vs. adult mice in the present study) which might influence the generalizability of the findings.

3) Behavior: Authors performed behavioral assays using the rotarod technique evaluating the hanging time of mice with different severity of TBI (mild, moderate, severe). The purpose of the testing is explained as 'to sort out an appropriate TBI model'. The authors also measured mortality rates 'to attain a stable model'. It is not clear what is assumed by the terms 'appropriate' or 'stable' model. Furthermore, the relevance of this to post-traumatic epileptogenesis is unclear. Additionally, the mortality in the Sham group within 2 weeks of craniectomy is not explained.

4) Seizure assessment: authors report seizure severity in PTZ-induced seizures but no mention about the severity of spontaneous seizures between different TBI severity modalities. When characterizing the PTZ-induced seizures, the mild TBI group does not have generalized seizures. Does this mean that al all 6 tested animals in the mild TBI group had exclusively focal seizures? What about the spontaneous seizure occurrence: were all seizures generalized or were any focal too? Did that differ between mild, moderate, and severe TBI?

5) Experiments with KCNT1 KO mice: in all experiments with a mutant mouse line, authors only used them in TBI group. Without the Sham group, it is difficult to discern whether any observed changes in seizure susceptibility in the KCNT1 KO TBI group are due to gene deletion, the TBI, or a combination of both. This group would provide a crucial comparison point to isolate the effects of the KCNT1 knockout from those of TBI. This limits the ability to make comprehensive conclusions about the role of the KCNT1 gene in seizure susceptibility following TBI.

6) While the current study showed interesting data about the KNa1.1 changes early after TBI, the study design and disconnect between early and late electrophysiology experiments timeline, does not establish a correlative or causative link between KNa1.1 and post-traumatic epileptogenesis since it remained unresolved whether KCNT1 KO mice developed no PTE (or less severe/ less frequent seizures at 3 months) compared with WT mice and what are the seizure properties of KCNT1 KO Sham mice compared to WT TBI and Sham groups. The hypothesis was that modulation of KNa1.1 channel specifically in inhibitory interneurons contributes to the hyperactivity of neurons in the peripheral cortex at the lesion site, enhances seizure susceptibility to PTZ-induced seizures, and promotes the occurrence of PTE. The part about 'promotes the occurrence of PTE' was not established.

7) NeuN is not the best marker of neurons in the context of TBI since TBI affects its expression patterns which will influence the interpretation of co-localization results. Unlike NeuN, Nissl staining is less likely to be affected by factors that alter protein expression, such as TBI. Therefore, it can be a more stable marker for identifying neurons in injured brain tissue.

8) Statistics: Authors report only SEM, which shows the precision of the mean and it will decrease as the sample size increases and does not reflect the data variability.

Reviewer #2 (Public Review):

In this study, Leighton et al performed remarkable experiments by combining in-vivo patch-clamp recording with two-photon dendritic Ca2+ imaging. The voltage-clamp mode is a major improvement over the pioneer versions of this combinatorial experiment that has led to major breakthroughs in the neuroscience field for visualizing and understanding synaptic input activities in single cells in-vivo (sharp electrodes: Svoboda et al, Nature 1997, Helmchen et al, Nature Neurosci 1999; whole-cell current-clamp: Jia et al, Nature 2010, Chen et al, Nature 2011. I suggest that these papers would be cited). This is because in voltage-clamp mode, despite the full control of membrane voltage in-vivo not being realistic, is nevertheless most effective in preventing back-propagation action potentials, which would severely confound the measurement of individual synaptically-induced Ca2+ influx events. Furthermore, clamping the cell body at a strongly depolarized potential (here the authors did -30mV) also facilitates the detection of synaptically-induced Ca2+ influx. As a result, the authors successfully recorded high-quality Ca2+ imaging data that can be used for precise analysis. To date, even in view of the rapid progress of voltage-sensitive indicators and relevant imaging technologies in recent years, this very old 'art' of combining single-cell electrophysiology and two-photon imaging (ordinary, raster-scanned, video-rate imaging) of Ca2+ signals still enables measurements of the best-level precision.

On the other hand, the interpretation of data in this study is a bit narrow-minded and lacks a comprehensive picture. Some suggestions to improve the manuscript are as follows:

1. The authors made a segregation of 'spine synapse' and 'shaft synapse' based solely on the two-photon images in-vivo. However, caution shall be taken here, because the optical resolution under in-vivo imaging conditions like this cannot reliably tell apart whether a bright spot within or partially overlapping a segment of the dendrite is a spine on top of (or below) it. Therefore, what the authors consider as a 'shaft synapse' (by detecting Ca2+ hotspots) has an unknown probability of being just a spine on top or below the dendrite. If there is other imaging data of higher axial resolution to validate or calibrate, the authors shall take some further considerations or analysis to check the consistency of their data, as the authors do need such a segregation between spine and shaft synapses to show how they evolve over the brain development stages.

2. The use of terminology 'bursts of spontaneous inputs' for describing voltage-clamp data seems improper. Conventionally, 'burst' refers to suprathreshold spike firing events, but here, the authors use 'burst' to refer to inward synaptic currents collected at the cell body. Not every excitatory synaptic input (or ensemble of inputs) activation will lead to spike firing under naturalistic conditions, therefore, these two concepts are not equivalent. It is recommended to use 'barrage of inputs' instead of 'burst of inputs'. Imagine a full picture of the entire dendritic tree, the fact that the authors could always capture spontaneous Ca2+ events here and there within a few pieces of dendrites within an arbitrary field-of-view suggests that, the whole dendritic tree must have many more such events going on as a barrage while the author's patch electrode picks up the summed current flow from the whole dendritic tree.

3. Following the above issue, an analysis of the temporal correlation between synaptic (not segregating 'spine' or 'shaft') Ca2+ events and EPSCs is absent. Again, the authors drew arbitrary time windows to clump the events for statistical analysis. However, the demonstrated example data already shows that the onset times of individual synaptic Ca2+ events do not necessarily align with the beginning of a 'barrage' inward current event.

4. The authors claim that "these observations indicate that the activity patterns investigated here are not or only slightly affected by low-level anesthesia". It would be nice to show some of the recordings in this work without any anesthesia to support this claim.

Reviewer #2 (Public Review):

Summary: The study by Jaime-Tobon & Moser is a truly major effort to bridge the gap between classical observations on how auditory neurons respond to sounds and the synaptic basis of these phenomena. The so-called spiral ganglion neurons (SGNs) are the primary auditory neurons connecting the brain with hair cells in the cochlea. They all respond to sounds increasing their firing rates, but also present multiple heterogeneities. For instance, some present a low threshold to sound intensity, whereas others have high threshold. This property inversely correlates with the spontaneous rate, i.e., the rate at which each neuron fires in the absence of any acoustic input. These characteristics, along with others, have been studied by many reports over the years. However, the mechanisms that allow the hair cells-SGN synapses to drive these behaviors are not fully understood.

Strengths:<br /> The level of experimental complexity described in this manuscript is unparalleled, producing data that is hardly found elsewhere. The authors provide strong proof for heterogeneity in transmitter release thresholds at individual synapses and they do so in extremely complex experimental settings. In addition, the authors found other specific differences such as in synaptic latency and max EPSCs. A reasonable effort is put into bridging these observations with those extensively reported in in vivo SGNs recordings. Similarities are many and differences are not particularly worrying as experimental conditions cannot be perfectly matched, despite the authors' efforts in minimizing them.

Weaknesses:<br /> Some concern surges in relation to mismatches with previous reports of IHC-SGN synapses function. EPSCs at these synapses present a peculiar distribution of amplitudes, shapes, and rates. These characteristics are well-established and some do not seem to be paralleled in this study. Here, amplitude distributions are drastically shifted to smaller values, and rates of events are very low, all compared with previous evidence. The reasons for these discrepancies are unclear. The rate at which spontaneous EPSCs appear is an especially sensitive matter. A great part of the conclusions relies on the definition of which of the SGNs (or should say synapses) belong to the low end and which to the high end in the spectrum of spontaneous rates. The data presented by the authors seem a bit off and the criteria used to classify recordings are not well justified. The authors should clarify the origin of these differences since they do not seem to come from obvious reasons such as animal ages, recording techniques, mouse strain, or even species.

Reviewer #2 (Public Review):

Summary:

In this paper, Sang et al. set out to identify gustatory receptors involved in salt taste sensation in Drosophila melanogaster. In a two-choice assay screen of 30 Ir mutants, they identified that Ir60b is required for avoidance of high salt. In addition, they demonstrate that activation of Ir60b neurons is sufficient for gustatory avoidance using either optogenetics or TRPV1 to specifically activate Ir60b neurons. Then, using tip recordings of labellar gustatory sensory neurons and proboscis extension response behavioral assays in Ir60b mutants, the authors demonstrate that Ir60b is dispensable for labellar taste neuron responses to high salt and the suppression of proboscis extension by high salt. Since external gustatory receptor neurons (GRNs) are not implicated, they look at Poxn mutants, which lack external chemosensory sensilla but have intact pharyngeal GRNs. High salt avoidance was reduced in Poxn mutants but was still greater than Ir60b mutants, suggesting that pharyngeal gustatory sensory neurons alone are sufficient for high salt avoidance. The authors use a new behavioral assay to demonstrate that Ir60b mutants ingest a higher volume of sucrose mixed with high salt than control flies do, suggesting that the action of Ir60b is to limit high salt ingestion. Finally, they identify that Ir60b functions within a single pair of gustatory sensory neurons in the pharynx, and that these neurons respond to high salt but not bitter tastants.

Strengths:

A great strength of this paper is that it rigorously corroborates previously published studies that have implicated specific Irs in salt taste sensation. It further introduces a new role for Ir60b in limiting high salt ingestion, demonstrating that Ir60b is necessary and sufficient for high salt avoidance and convincingly tracing the action of Ir60b to a particular subset of gustatory receptor neurons. Overall the authors have achieved their aim by identifying a new gustatory receptor involved in limiting high salt ingestion. They use rigorous genetic, imaging, and behavioral studies to achieve this aim, often confirming a given conclusion with multiple experimental approaches. They have further done a great service to the field by replicating published studies and corroborating the roles of a number of other Irs in salt taste sensation. An aspect of this study that merits further investigation is how the same gustatory receptor neurons and Ir in the pharynx can be responsible for regulating the ingestion of both appetitive (sugar) and aversive tastants (high salt).

Weaknesses:

There are several weaknesses that, if addressed, could greatly improve this work.<br /> 1) The authors combine the results and discussion but provide a very limited interpretation of their results. More discussion of the results would help to highlight what this paper contributes, how the authors interpret their results, and areas for future study.<br /> 2) The authors rename previously studied populations of labellar GRNs to arbitrary letters, which makes it difficult to understand the experiments and results in some places. These GRN populations would be better referred to according to the gustatory receptors they are known to express.<br /> 3) The conclusion that GRNs responsible for high salt aversion may be inhibited by those that function in low salt attraction is not well substantiated. This conclusion seems to come from the fact that overexpression of Ir60b in salt attraction and salt aversion sensory neurons still leads to salt aversion, but there need not be any interaction between these two types of sensory neurons if they act oppositely on downstream circuits.<br /> 4) The authors rely heavily on a new Droso-X behavioral apparatus that is not sufficiently described here or in the previous paper the authors cite. This greatly limits the reader's ability to interpret the results.

Reviewer #2 (Public Review):

Summary:<br /> McSwiggen et al present a high throughput platform for SPT that allows them to identify pharmaceutics interactions with the diffusional behavior of receptors and in turn to identify potent new ligands and cellular mechanisms. The manuscript is well written, it provides a solid new mentor and a proper experimental foundation

Strengths:<br /> The method capitalizes and extends to existing high throughput toolboxes and is directly applied to multiple receptors and ligands. The outcomes are important and relevant for society. 10^6 cells and >400 ligands per is a significant achievement.

The method can detect functionally relevant changes in transcription factor dynamics and accurately differentiate the ligand/target specificity directly within the cellular environment. This will be instrumental in screening libraries of compounds to identify starting points for the development of new therapeutics. Identifying hitherto unknown networks of biochemical signaling pathways will propel the field of single-particle live cell and quantitative microscopy in the area of diagnostics. The manuscript is well-written and clearly conveys its message.

Weaknesses:<br /> There are a few elements, that if rectified would improve the claims of the manuscript.

The authors claim that they measure receptor dynamics. In essence, their readout is a variation in diffusional behavior that correlates to ligand binding. While ligand binding can result in altered dynamics or /and shift in conformational equilibrium, SPT is not recording directly protein structural dynamics, but their effect on diffusion. They should correct and elaborate on this.

L 148 What do the authors mean 'No correlation between diffusion and monomeric protein size was observed, highlighting the differences between cellular protein dynamics versus purified systems'. This is not justified by data here or literature reference. How do the authors know these are individual molecules? Intensity distributions or single bleaching steps should be presented.

Along the same lines, the data in Figs 2 and 4 show that not only the immobile fraction is increased but also that the diffusion coefficient of the fast-moving (attributed to free) is reduced. The authors mention this and show an extended Fig 5 but do not provide an explanation. How do potential transient ligand binding and the time-dependent heterogeneity in motion (see comment above) contribute to this? Also, in line 216 the authors write "with no evidence" of transient diffusive states. How do they define transient diffusive states? While there are toolboxes to directly extract the existence and abundance of these either by HMM analysis or temporal segmentation, the authors do not discuss or use them.

The authors discuss the methods for extracting kinetic information of ligand binding by diffusion. They should consider the temporal segmentation of heterogenous diffusion. There are numerous methods published in journals or BioRxiv based on analytical or deep learning tools to perform temporal segmentation. This could elevate their analysis of Kon and Koff.

Reviewer #2 (Public Review):

Summary:

In the present manuscript, Zhang et al utilize single-nuclei RNA-Seq to investigate the heterogeneity of perirenal adipose tissue. The perirenal depot is interesting because it contains both brown and white adipocytes, a subset of which undergo functional "whitening" during early development. While adipocyte thermogenic transdifferentiation has been previously reported, there remain many unanswered questions regarding this phenomenon and the mechanisms by which it is regulated.

Strengths:

The combination of UCP1-lineage tracing with the single nuclei analysis allowed the authors to identify four populations of adipocytes with differing thermogenic potential, including a "whitened" adipocyte (mPRAT-ad2) that retains the capacity to rapidly revert to a brown phenotype upon cold exposure. They also identify two populations of white adipocytes that do not undergo browning with acute cold exposure.

Anatomically distinct adipose depots display interesting functional differences, and this work contributes to our understanding of one of the few brown depots present in humans.

Weaknesses:

The most interesting aspect of this work is the identification of a highly plastic mature adipocyte population with the capacity to switch between a white and brown phenotype. The authors attempt to identify the transcriptional signature of this ad2 subpopulation, however, the limited sequencing depth of single nuclei somewhat lessens the impact of these findings. Furthermore, the lack of any form of mechanistic investigation into the regulation of mPRAT whitening limits the utility of this manuscript. However, the combination of well-executed lineage tracing with comprehensive cross-depot single-nuclei presented in this manuscript could still serve as a useful reference for the field.

Reviewer #2 (Public Review):

This study by Matsuo-Takasaki et al. reported the development of a novel suspension culture system for hiPSC maintenance using Wnt/PKC inhibitors. The authors showed elegantly that inhibition of the Wnt and PKC signaling pathways would repress spontaneous differentiation into neuroectoderm and mesendoderm in hiPSCs, thereby maintaining cell pluripotency in suspension culture. This is a solid study with substantial data to demonstrate the quality of the hiPSC maintained in the suspension culture system, including long-term maintenance in >10 passages, robust effect in multiple hiPSC lines, and a panel of conventional hiPSC QC assays. Notably, large-scale expansion of a clinical grade hiPSC using a bioreactor was also demonstrated, which highlighted the translational value of the findings here. In addition, the author demonstrated a wide range of applications for the IWR1+LY suspension culture system, including support for freezing/thawing and PBMC-iPSC generation in suspension culture format. The novel suspension culture system reported here is exciting, with significant implications in simplifying the current culture method of iPSC and upscaling iPSC manufacturing.

Another potential advantage that perhaps wasn't well discussed in the manuscript is the reported suspension culture system does not require additional ECM to provide biophysical support for iPSC, which differentiates from previous studies using hydrogel and this should further simplify the hiPSC culture protocol.

Interestingly, although several hiPSC suspension media are currently available commercially, the content of these suspension media remained proprietary, as such the signaling that represses differentiation/maintains pluripotency in hiPSC suspension culture remained unclear. This study provided clear evidence that inhibition of the Wnt/PKC pathways is critical to repress spontaneous differentiation in hiPSC suspension culture.

I have several concerns that the authors should address, in particular, it is important to benchmark the reported suspension system with the current conventional culture system (eg adherent feeder-free culture), which will be important to evaluate the usefulness of the reported suspension system. Also, the manuscript lacks a clear description of a consistent robust effect in hiPSC maintenance across multiple cell lines. There are also several minor comments that should be addressed to improve readability, including some modifications to the wording to better reflect the results and conclusions.

Reviewer #2 (Public Review):

Summary:

The authors have developed novel Ovalbumin model (OTII) peptide that can be labeled with a site-specific FlAsH dye to track agonist peptides both in vitro and in vivo. The utility of this tool could allow better tracking of activated polyclonal T cells particularly in novel systems. The authors have provided solid evidence that peptides are functional, capable of activating OTII T cells, and these peptides can undergo trogocytosis by cognate T cells only.

Strengths:<br /> -An extensive array of in vitro and in vivo studies are used to assess peptide functionality.<br /> -Nice use of cutting edge intravital imaging,<br /> -internal controls such as multiple non-cogate T cells were used to improve robustness of the results<br /> -One of the strengths is the direct labeling of the peptide, and the potential utility in other systems.

Weaknesses:<br /> -Peptide labeling specificity and efficiency is not clear. High levels of background labeling. While it was sufficient for demonstrating the system works, it may pose problems depending on the peptide sequence, and/or use at lower dose.<br /> -Only one peptide system was tested, namely OVA323-339 region.<br /> -Limited novel biological findings. This study mostly describes a new tool that may have exciting potential.

Reviewer #2 (Public Review):

Summary:

The goal of this study was to examine the role of FNDC5 in the response of the murine skeleton to either lactation or a calcium-deficient diet. The authors find that female FNDC5 KO mice are somewhat protected from bone loss and osteocyte lacunar enlargement caused by either lactation or a calcium-deficient diet. In contrast, male FNDC5 KO mice lose more bone and have a greater enlargement of osteocyte lacunae than their wild-type controls. Based on these results, the authors conclude that in males irisin protects bone from calcium deficiency but that in females it promotes calcium removal from bone for lactation.

While some of the conclusions of this study are supported by the results, it is not clear that the modest effects of FNDC5 deletion have an impact on calcium homeostasis or milk production.

Specific comments:

1. The authors sometimes refer to FNDC5 and other times to irisin when describing causes for a particular outcome. Because irisin was not measured in any of the experiments, the authors should not conclude that lack of irisin is responsible. Along these lines, is there any evidence that either lactation or a calcium-deficient diet increases the production of irisin in mice?

2. The results of the irisin-rescue experiment shown in figure 2G cannot be appropriately interpreted without normal diet controls. In addition, some evidence that the AAV8-irisin virus actually increased irisin levels in the mice would strengthen the conclusion.

3. There is insufficient evidence to support the idea that the effect of FNDC5 on bone resorption and osteocytic osteolysis is important for the transfer of calcium from bone to milk. Previous studies by others have shown that bone resorption is not required to maintain milk or serum calcium when dietary calcium is sufficient but is critical if dietary calcium is low (Endo. 156:2762-73, 2015). To support the conclusions of the current study, it would be necessary to determine whether FNDC5 is required to maintain calcium levels when lactating mice lack sufficient dietary calcium.

4. The amount of cortical bone loss due to lactation is very similar in both WT and FNDC5 KO mice. The results of the statistical analysis of the data presented in figure 1B are surprising given the very similar effect size of lactation. The key result from the 2-way ANOVA is whether there is an effect of genotype on the effect size of lactation (genotype-lactation interaction). The interaction terms were not provided. Similar concerns are noted for the results shown in figure 1G and H.

5. It is not clear what justifies the term 'primed' or 'activated' for resorption. Is there evidence that a certain level of TRAP expression lowers the threshold for osteocytic osteolysis in response to a stimulus?

Review #2 (Public Review)

In the manuscript Watanuki et al. define the metabolic profile of HSCs in stress/proliferative (myelosuppression with 5-FU), and mitochondrial inhibition and homeostatic conditions. Their conclusions are that during proliferation HSCs rely more on glycolysis (as other cell types) while HSCs in homeostatic conditions are mostly dependent on mitochondrial metabolism. Mitochondrial inhibition is used to demonstrate that blocking mitochondrial metabolism results in similar features of proliferative conditions.

The authors used state-of-the-art technologies that allow metabolic readout in a limited number of cells like rare HSCs. These applications could be of help in the field since one of the major issues in studying HSCs metabolism is the limited sensitivity of the "standard" assays, which make them not suitable for HSC studies.

Reviewer #2 (Public Review):

Summary:<br /> The work by Varadharajan et. al. explored a previously known genetic variant and its pathophysiology in the development of alcohol-associated liver injury. It provides a plausible mechanism for how varying levels of MBOAT7 could impact the lipid metabolomics of the cell, leading to a deleterious phenotype in MBOAT7 knockout. The authors further characterized the impact of the lipidomic changes and raised lysosomal biogenesis and autophagic flux as mechanisms of how MBOAT7 deletion causes the progression of ALD.

Strengths:<br /> Connecting the GWAS data on MBOAT7 variants with plausible pathophysiology greatly enhances the translational relevance of these findings. The global lipidomic profiling of ALD mice is also very informative and may lead to other discoveries related to lipid handling pathways.

Weaknesses:<br /> The rationale of why MBOAT7 metabolites are lower in heavy drinkers than in normal individuals is not well explained. MBOAT7 loss of function drives ALD, but unclear if MBOAT7 deletion also drives preference for alcohol or if alcohol inhibits MBOAT7 function. Presuming most individuals studied here were WT and expressed an appropriate level of MBOAT7?<br /> Also, the discussion of mechanisms of MBOAT7-induced dysregulation of lysosomal biogenesis/autophagy, while very interesting, seems incomplete. It is not clear how MBOAT7 an enzyme involved in membrane phospholipid remodeling increases mTOR which leads to decreased TFEB target gene transcription. Furthermore, given the significant disturbances of global lipidomic profiling in MBOAT7 knockout, many pathways are potentially affected by this deletion. Further in vivo modeling that specifically addresses these pathways (TFEB targeting, mTOR inhibitor) would help strengthen the conclusions of this paper.

Reviewer #2 (Public Review):

Summary:

While a significant portion of immunotherapy research has focused on the pivotal role of T cells in tumor immunity, their effectiveness may be limited by the suppressive nature of the tumor environment. On the other hand, myeloid cells are commonly found within tumors and can withstand these adverse conditions. However, these cells often adopt an immunosuppressive phenotype when infiltrating tumors. Therefore, manipulating myeloid cells could potentially enhance the anti-tumor potential of immunotherapy.

In this manuscript, Farhat-Younes and colleagues have demonstrated that activating the IgM receptor signaling in myeloid cells induces an oxygen burst, the secretion of Granzyme B, and the lysis of adjacent tumor cells. Furthermore, they have outlined a strategy to utilize these features to generate CAR macrophages. However, they have identified a limitation: the expression of scFv in myeloid cells induces ER stress and the degradation of misfolded proteins. To address this issue, chimeric receptors were designed based on the high-affinity FcγRI for IgG. When macrophages transfected with these receptors were exposed to tumor-binding IgG, extensive tumor cell killing, and the release of reactive oxygen species and Granzyme B were observed.

Strengths:<br /> In general, I consider this work to be significant, and the results are compelling. It emphasizes the specific considerations and requirements for successful manipulation in myeloid cells, which could further advance the field of cellular engineering for the benefit of immunotherapy

Weaknesses:

Nevertheless, there are several minor issues that should be addressed:

1- TCR fragments are commonly used to induce ER stress in non-immune cells. Therefore, it would be interesting to investigate whether TCR fragments can be expressed in myeloid cells and if they induce ER stress. Addressing this issue would support the notion that these cells lack the ER chaperones required for folding immunoglobulin variable chains.<br /> 2- It would be valuable to determine whether, after the degradation of scFv fragments by myeloid cells, they are presented on MHC-I and MHC-II.<br /> 3- Some methodological details, such as the vaccination protocol and high-resolution microscopy procedures, are missing from the text.

Reviewer #2 (Public Review):

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

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

The data, for the most part, support the conclusions but I do have concerns about some of the data and the interpretations that should be addressed.

Reviewer #2 (Public Review):

Summary:

This combined experimental-theoretical paper introduces a novel two-domain statistical thermodynamic model (primarily Equation 1) to study allostery in generic systems but focusing here on the tetracycline repressor (TetR) family of transcription factors. This model, building on a function-centric approach, accurately captures induction data, maps mutants with precision, and reveals insights into epistasis between mutations.

Strengths:

The study contributes innovative modeling, successful data fitting, and valuable insights into the interconnectivity of allosteric networks, establishing a flexible and detailed framework for investigating TetR allostery. The manuscript is generally well-structured and communicates key findings effectively.

Weaknesses:

The only minor weakness I found was that I still don't have a better sense into (a) intuition and (b) mathematical derivation of Equation 1, which is so central to the work. I would recommend that the authors provide this early on in the main text.

Reviewer #3 (Public Review):

Summary<br /> In this research advance, the authors purport to show that the unified neutral theory of biodiversity (UNTB) is not a suitable null model for exploring the relationship between macroecological quantities, and additionally that the stochastic logistic growth model (SLM) is a viable replacement. They do this by citing other studies where UNTB was unable to capture individual macroecological quantities, and then demonstrating SLM's strength at predicting the same diversity metrics. They extend this analysis to show SLM's modeling capability at multiple scales of coarse graining, in addition to its failures at predicting these metrics' variances. Finally, authors conduct a similar analysis to Madi et al. (2020) by investigating the relationship between diversity measures within a group and across coarse-grained groups (e.g. genera diversity in one family compared to diversity of families). The authors show that choosing SLM as a null model reveals some previously reported relationships to be no longer "novel", in the sense that the patterns can be adequately captured by the null model. Authors also show that relationships not captured by the null model can be recovered by adding correlations, suggesting interactions are the driving force behind them.

Strengths<br /> 1. Authors make a strong argument that UNTB is not a good null model of macroecological observables and especially relationships between them. Authors convincingly argue that a SLM is a better null since the gamma distribution it predicts is a better description of the empirical Abundance Fluctuation Distributions (AFD).<br /> 2. Authors show that the gamma distribution predicted by SLM is a good fit for the AFD's at many different scales of coarse graining, not just the OTU level as was previously demonstrated. Authors show the same distribution predicted the mean diversity and richness at all scales of coarse graining.<br /> 3. Authors convincingly demonstrate how SLM can be used to test the relevance of interactions to macroecological relationships.

Weaknesses<br /> This reviewer's concerns were convincingly addressed by the revisions.

Overall Impact<br /> The authors present a convincing argument for the use of SLM as a better non-interacting null model for macroecological quantities and relationships.

Reviewer #2 (Public Review):

Summary:

In this study, the authors investigate the effect of ACh on neuronal responses in the auditory cortex of anesthetized rats during an auditory oddball task. The paradigm consisted of two pure tones (selected from the frequency responses at each recording site) presented in a pseudo-random sequence. One tone was presented frequently (the "standard" tone) and the other infrequently (the "deviant" tone). The authors found that ACh enhances the detection of unexpected stimuli in the auditory environment by increasing or decreasing the neuronal responses to deviant and standard tones.

Strengths:

The study includes the use of appropriate and validated methodology in line with the current state-of-the-art, rigorous statistical analysis and the demonstration of the effects of acetylcholine on auditory processing.

Weaknesses:

The study was conducted in anesthetized rats, and further research is needed to determine the behavioral relevance of these findings.

Reviewer #2 (Public Review):

Summary:

This interesting study addresses the ability of Ym1 protein crystals to promote pulmonary type 2 inflammation in vivo, in mice.

Strengths:

The data are extremely high quality, clearly presented, significantly extending previous work from this group on the type 2 immunogenicity of protein crystals.

Weaknesses:

There are no major weaknesses in this study. It would be interesting to see if Ym2 crystals behave similarly to Ym1 crystals in vivo. Some additional text in the Introduction and Discussion would enrich those sections.

Reviewer #2 (Public Review):

Summary:<br /> The work fruitfully adds to the tools to study cannabinoid action and pharmacology specifically, but also this method is applicable to other drugs, in particular, if lipophilic in nature.

Strengths:<br /> The addition of chocolate flavor overcomes aversive reactions which are often experienced in pharmacological treatments, leading to possible caveats in the interpretation of the behavioral outcomes.

Weaknesses:<br /> Certainly, more THC mediated behavioral outcomes could have been tested, but the work presents a proof-of-concept study to investigate acute THC treatment.<br /> It would have been interesting if this application form is also possible for chronic treatment regimen.

Reviewer #3 (Public Review):

Summary: This paper presents evidence of recursive self-embedding in the vocalization structure of orangutans, using fine-grained acoustical analysis. It proves the existence of isochrony nested in isochrony in the motifs produced by a nonhuman vocal system.

Strengths: Very clear written, clear analysis, excellent responses to the Reviewers.

Weaknesses: Jargonous language may be reduced. A video showing the sound as it unfolds and the spectrogram (as in Fig 1A) of the long call could be useful to best exemplify the results.

Reviewer #2 (Public Review):

Summary:<br /> Morucci et al. tested the influence of linguistic prosody long-term priors in forming predictions about simple acoustic rhythmic tone sequences composed of alternating tone duration, by violating context-dependent short-term priors formed during sequence listening. Spanish and Basque participants were selected due to the different rhythmic prosody of the two languages (functor-initial vs. Functor final, respectively), despite a common cultural background. The authors found that neuromagnetic responses to casual tone omissions reflected the linguistic prosody pattern of the participant's dominant language: in Spanish speakers, omission responses were larger to short tones, whereas in Basque speakers, omission responses were larger to long tones. Source localization of these responses revealed this interaction pattern in the left auditory cortex, which the authors interpret as reflecting a perceptual bias due to acoustic cues (inherent linguistic rhythms, rather than linguistic content). Importantly, this pattern was not found when the rhythmic sequence entailed pitch, rather than duration, cues. To my knowledge, this is the first study providing neural signatures of a known behavioral effect linking ambiguous rhythmic tone sequence perceptual organization to linguistic experience.

The conclusions of the study are well supported by the data, albeit weakly by the source analysis, but I have the impression that the rationale of the study and the analyses performed may be missing an important aspect of rhythmic sequence perception, namely the involvement of entrained oscillatory activity to the perceived rhythm, particularly phase alignment to pattern onsets. This view would not change the impact of the results but add depth to their interpretation.

Strengths:<br /> 1) The choice of participants. The bilingual population of the Basque country is perfect for performing studies that need to control for cultural and socio-economic background while having profound linguistic differences. In this sense, having dominant Basque speakers as a sample equates that in Molnar et al. (2016), and thus overcomes the lack of direct behavioral evidence for a difference in rhythmic grouping across linguistic groups. Molnar et al. (2016)'s evidence on the behavioral effect is compelling, and the evidence on neural signatures provided by the present study aligns with it.

2) The experimental paradigm. It is a well-designed acoustic sequence, that considers aspects such as gap length insertion, to be able to analyze omission responses free from subsequent stimulus-driven responses, and which includes a control sequence that uses pitch instead of duration as a cue to rhythmic grouping, which provides a stronger case for the differences found between groups to be due to prosodic duration cues.

3) Data analyses. Sound, state-of-the-art methodology in the event-related field analyses at the sensor level.

Weaknesses:<br /> 1) Despite the evidence provided on neural responses, the main conclusion of the study reflects a known behavioral effect on rhythmic sequence perceptual organization driven by linguistic background (Molnar et al. 2016, particularly). Also, the authors themselves provide a good review of the literature that evidences the influence of long-term priors in neural responses related to predictive activity. Thus, in my opinion, the strength of the statements the authors make on the novelty of the findings may be a bit far-fetched in some instances.

2) Albeit the paradigm is well designed, I fail to see the grounding of the hypotheses laid by the authors as framed under the predictive coding perspective. The study assumes that responses to an omission at the beginning of a perceptual rhythmic pattern will be stronger than at the end. I feel this is unjustified. If anything, omission responses should be larger when the gap occurs at the end of the pattern, as that would be where stronger expectations are placed: if in my language a short sound occurs after a long one, and I perceptually group tone sequences of alternating tone duration accordingly, when I hear a short sound I will expect a long one following; but after a long one, I don't necessarily need to expect a short one, as something else might occur.

3) In this regard, it is my opinion that what is reflected in the data may be better accounted for (or at least, additionally) by a different neural response to an omission depending on the phase of an underlying attentional rhythm (in terms of Large and Jones rhythmic attention theory, for instance) and putative underlying entrained oscillatory neural activity (in terms of Lakatos' studies, for instance). Certainly, the fact that the aligned phase may differ depending on linguistic background is very interesting and would reflect the known behavioral effect.

4) Source localization is performed on sensor-level significant data. The lack of source-level statistics weakens the conclusions that can be extracted. Furthermore, only the source reflecting the interaction pattern is taken into account in detail as supporting their hypotheses, overlooking other sources. Also, the right IFG source activity is not depicted, but looking at whole brain maps seems even stronger than the left. To sum up, source localization data, as informative as it could be, does not strongly support the author's claims in its current state.

Reviewer #2 (Public Review):

Summary:<br /> In this study, Hauser et al investigate the role of amphibian (Xenopus laevis) mast cells in cutaneous immune responses to the ecologically important pathogen Batrachochytrium dendrobatidis (Bd) using novel methods of in vitro differentiation of bone marrow-derived mast cells and in vivo expansion of skin mast cell populations. They find that bone marrow-derived myeloid precursors cultured in the presence of recombinant X. laevis Stem Cell Factor (rSCF) differentiate into cells that display hallmark characteristics of mast cells. They inject their novel (r)SCF reagent into the skin of X. laevis and find that this stimulates the expansion of cutaneous mast cell populations in vivo. They then apply this model of cutaneous mast cell expansion in the setting of Bd infection and find that mast cell expansion attenuates the skin burden of Bd zoospores and pathologic features including epithelial thickness and improves protective mucus production and transcriptional markers of barrier function. Utilizing their prior expertise with expanding neutrophil populations in X. laevis, the authors compare mast cell expansion using (r)SCF to neutrophil expansion using recombinant colony-stimulating factor 3 (rCSF3) and find that neutrophil expansion in Bd infection leads to greater burden of zoospores and worse skin pathology.

Strengths:<br /> The authors report a novel method of expanding amphibian mast cells utilizing their custom-made rSCF reagent. They rigorously characterize expanded mast cells in vitro and in vivo using histologic, morphologic, transcriptional, and functional assays. This establishes solid footing with which to then study the role of rSCF-stimulated mast cell expansion in the Bd infection model. This appears to be the first demonstration of the exogenous use of rSCF in amphibians to expand mast cell populations and may set a foundation for future mechanistic studies of mast cells in the X. laevis model organism.

Weaknesses:<br /> The conclusions regarding the role of mast cell expansion in controlling Bd infection would be stronger with a more rigorous evaluation of the model, as there are some key gaps and remaining questions regarding the data. For example:

1. Granulocyte expansion is carefully quantified in the initial time courses of rSCF and rCSF3 injections, but similar quantification is not provided in the disease models (Figures 3E, 4G, 5D-G). A key implication of the opposing effects of mast cell vs neutrophil expansion is that mast cells may suppress neutrophil recruitment or function. Alternatively, mast cells also express notable levels of csfr3 (Figure 2) and previous work from this group (Hauser et al, Facets 2020) showed rG-CSF-stimulated peritoneal granulocytes express mast cell markers including kit and tpsab1, raising the question of what effect rCSF3 might have on mast cell populations in the skin. Considering these points, it would be helpful if both mast cells and neutrophils were quantified histologically (based on Figure 1, they can be readily distinguished by SE or Giemsa stain) in the Bd infection models.

2. Epithelial thickness and inflammation in Bd infection are reported to be reduced by rSCF treatment (Figure 3E, 5A-B) or increased by rCSF3 treatment (Figure 4G) but quantification of these critical readouts is not shown.

3. Critical time points in the Bd model are incompletely characterized. Mast cell expansion decreases zoospore burden at 21 dpi, while there is no difference at 7 dpi (Figure 3E). Conversely, neutrophil expansion increases zoospore burden at 7 dpi, but no corresponding 21 dpi data is shown for comparison (Figure 4G). Microbiota analysis is performed at a third time point,10 dpi (Figure 5D-G), making it difficult to compare with the data from the 7 dpi and 21 dpi time points. Reporting consistent readouts at these three time points is important to draw solid conclusions about the relationship of mast cell expansion to Bd infection and shifts in microbiota.

4. Although the effect of rSCF treatment on Bd zoospores is significant at 21 dpi (Figure 3E), bacterial microbiota changes at 21 dpi are not (Figure S3B-C). This discrepancy, how it relates to the bacterial microbiota changes at 10 dpi, and why 7, 10, and 21 dpi time points were chosen for these different readouts (Figure 5F-G), is not discussed.

5. The time course of rSCF or rCSF3 treatments relative to Bd infection in the experiments is not clear. Were the treatments given 12 hours prior to the final analysis point to maximize the effect? For example, in Figure 3E, were rSCF injections given at 6.5 dpi and 20.5 dpi? Or were treatments administered on day 0 of the infection model? If the latter, how do the authors explain the effects at 7 dpi or 21 dpi given mast cell and neutrophil numbers return to baseline within 24 hours after rSCF or rCSF3 treatment, respectively?

The title of the manuscript may be mildly overstated. Although Bd infection can indeed be deadly, mortality was not a readout in this study, and it is not clear from the data reported that expanding skin mast cells would ultimately prevent progression to death in Bd infections.

Reviewer #2 (Public Review):

Summary:<br /> This study focuses on the 5-HT3 serotonin receptor, a pentameric ligand-gated ion channel important in chemical neurotransmission. There are many cryo-EM structures of this receptor with diverse ligands bound, however assignment of functional states to the structures remains incomplete. The team applies voltage-clamp fluorometry to measure, at once, both changes in ion channel activity, and changes in fluorescence. Four cysteine mutants were selected for fluorophore labeling, two near the neurotransmitter site, one in the ECD vestibule, and one at the ECD-TMD junction. Agonists, partial agonists, and antagonists were all found to yield similar changes in fluorescence, a proxy for conformational change, near the neurotransmitter site. The strength of the agonist correlated to a degree with propagation of this fluorescence change beyond the local site of neurotransmitter binding. Antagonists failed to elicit a change in fluorescence in the vestibular the ECD-TMD junction sites. The VCF results further turned up evidence supporting intermediate (likely pre-active) states.

Strengths:<br /> The experiments appear rigorous, the problem the team tackles is timely and important, the writing and the figures are for the most part very clear. We sorely need approaches orthogonal to structural biology to annotate conformational states and observe conformational transitions in real membranes- this approach, and this study, get right to the heart of what is missing.

Weaknesses:<br /> The weaknesses in the study itself are overall minor, I only suggest improvements geared toward clarity. What we are still missing is application of an approach like this to annotate the conformation of the part of the receptor buried in the membrane; there is important debate about which structure represents which state, and that is not addressed in the current study.

Reviewer #2 (Public Review):

Summary:<br /> The authors have developed a comprehensive set of tools to describe dynamics within a single time-series or across multiple time-series. The motivation is to better understand interacting networks within the human brain. The time-series used here are from direct estimates of the brain's electrical activity; however the tools have been used with other metrics of brain function and would be applicable to many other fields.

Strengths:<br /> The methods described are principled, based on generative probabilistic models.<br /> This makes them compact descriptors of the complex time-frequency data.<br /> Few initial assumptions are necessary in order to reveal this compact description.<br /> The methods are well described and demonstrated within multiple peer reviewed articles.<br /> This toolbox will be a great asset to the brain imaging community.

Weaknesses:<br /> The only question I had (originally) was how to objectively/quantitatively compare different network models. This has now been addressed by the authors in the latest revision.

Reviewer #2 (Public Review):

Summary:<br /> The authors build a gene expression model based on histone post-translational modifications and find that H3K27ac is correlated with gene expression. They proceed to perturb H3K27ac at 8 gene promoters, and measure gene expression changes to test their model.

Strengths:<br /> The combination of multiple methods to model expression, along with utilizing 6 histone datasets in 13 cell types allowed the authors to build a model that correlates between 0.7-0.79 with gene expression. This group also utilized a tool they are experts in, dCas9-p300 fusions to perturb H3K27ac and monitor gene expression to test their model. Ranked correlations showed some support for the predictions after the perturbation of H3K27ac.

Weaknesses:<br /> The perturbation of only 8 genes, and the only readout being qPCR-based gene expression, as opposed to including H3K27ac, weakened their validation of the computational model. Likewise, the use of six genes that were not expressed being most activated by dCas9-p300 might weaken the correlations vs. looking at a broad range of different gene expressions as the original model was trained on.

Reviewer #2 (Public Review):

Summary:<br /> This manuscript characterizes a chemoattractant response to human serum by pathogenic bacteria, focusing on pathogenic strains of Salmonella enterica (Se). The researchers conducted the chemotaxis assays using a micropipette injection method that allows real-time tracking of bacterial population densities. They found that clinical isolates of several Se strains present a chemoattractant response to human serum. The specific chemoattractant within the serum is identified as L-serine, a highly characterized and ubiquitous chemoattractant, that is sensed by the Tsr receptor. They further show that chemoattraction to serum is impaired with a mutant strain devoid of Tsr. X-ray crystallography is then used to determine the structure of L-serine in the Se Tsr ligand binding domain, which differs slightly from a previously determined structure of a homologous domain. They went on to identify other pathogens that have a Tsr domain through a bioinformatics approach and show that these identified species also present a chemoattractant response to serum.

Strengths and Weaknesses:<br /> This study is well executed and the experiments are clearly presented. These novel chemotaxis assays provide advantages in terms of temporal resolution and the ability to detect responses from small concentrations. That said, it is perhaps not surprising these bacteria respond to serum as it is known to contain high levels of known chemoattractants, serine certainly, but also aspartate. In fact, the bacteria are shown to respond to aspartate and the tsr mutant is still chemotactic. The authors do not adequately support their decision to focus exclusively on the Tsr receptor. Tsr is one of the chemoreceptors responsible for observed attraction to serum, but perhaps, not the receptor. Furthermore, the verification of chemotaxis to serum is a useful finding, but the work does not establish the physiological relevance of the behavior or associate it with any type of disease progression. I would expect that a majority of chemotactic bacteria would be attracted to it under some conditions. Hence the impact of this finding on the chemotaxis or medical fields is uncertain.

The authors also state that "Our inability to substantiate a structure-function relationship for NE/DHMA signaling indicates these neurotransmitters are not ligands of Tsr." Both norepinephrine (NE) and DHMA have been shown previously by other groups to be strong chemoattractants for E. coli (Ec), and this behavior was mediated by Tsr (e.g. single residue changes in the Tsr binding pocket block the response). Given the 82% sequence identity between the Se and Ec Tsr, this finding is unexpected (and potentially quite interesting). To validate this contradictory result the authors should test E. coli chemotaxis to DHMA in their assay. It may be possible that Ec responds to NE and DHMA and Se doesn't. However, currently, the data is not strong enough to rule out Tsr as a receptor to these ligands in all cases. At the very least the supporting data for Tsr being a receptor for NE/DHMA needs to be discussed.

The authors also determine a crystal structure of the Se Tsr periplasmic ligand binding domain bound to L-Ser and note that the orientation of the ligand is different than that modeled in a previously determined structure of lower resolution. I agree that the SeTsr ligand binding mode in the new structure is well-defined and unambiguous, but I think it is too strong to imply that the pose of the ligand in the previous structure is wrong. The two conformations are in fact quite similar to one another and the resolution of the older structure, is, in my view, insufficient to distinguish them. It is possible that there are real differences between the two structures. The domains do have different sequences and, moreover, the crystal forms and cryo-cooling conditions are different in each case. It's become increasingly apparent that temperature, as manifested in differential cooling conditions here, can affect ligand binding modes. It's also notable that full-length MCPs show negative cooperativity in binding ligands, which is typically lost in the isolated periplasmic domains. Hence ligand binding is sensitive to the environment of a given domain. In short, the current data is not convincing enough to say that a previous "misconception" is being corrected.

Reviewer #2 (Public Review):

Greve et al. investigated the effects of a disease-associated gamma-actin mutation (E334Q) on actin filament polymerization, association of selected actin-binding proteins, and myosin activity. Recombinant wildtype and mutant proteins expressed in sf9 cells were found to be folded and stable, and the presence of the mutation altered a number of activities. Given the location of the mutation, it is not surprising that there are changes in polymerization and interactions with actin binding proteins. Nevertheless, it is important to quantify the effects of the mutation to better understand disease etiology. Some weaknesses were identified in the paper as discussed below.

Throughout the paper, the authors report average values and the standard-error-of-the-mean (SEM) for groups of three experiments. Reporting the SEM is not appropriate or useful for so few points, as it does not reflect the distribution of the data points. When only three points are available, it would be better to just show the three different points. Otherwise, plot the average and the range of the three points.

The description and characterization of the recombinant actin is incomplete. Please show gels of purified proteins. This is especially important with this preparation since the chymotrypsin step could result in internally cleaved proteins and altered properties, as shown by Ceron et al (2022). The authors should also comment on N-terminal acetylation of actin.

The authors do not use the best technique to assess actin polymerization parameters. Although the TIRF assay is excellent for some measurements, it is not as good as the standard pyrene-actin assays that provide critical concentration, nucleation, and polymerization parameters. The authors use pyrene-actin in other parts of the paper, so it is not clear why they don't do the assays that are the standard in the actin field.

The authors' data suggest that, while the binding of cofilin-1 to both the WT and mutant actins remains similar, the major defect of the E334Q actin is that it is not as readily severed/disassembled by cofilin. What is missing is a direct measurement of the severing rate (number of breaks per second) as measured in TIRF.

Figure 4 shows that the E334Q mutation increases rather than decreases the number of filaments that spontaneously assemble in the TIRF assay, but it is unclear how reduced severing would lead to increased filament numbers, rather, the opposite would be expected. A more straightforward approach would be to perform experiments where severing leads to more nuclei and therefore enhances the net bulk assembly rate.

Figure 5 A: in the pyrene disassembly assay, where actin is diluted below its critical concentration, cofilin enhances the rate of depolymerization by generating more free ends. The E334Q mutation leads to decreased cofilin-induced severing and therefore lower depolymerization. While these data seem convincing, it would be better to present them as an XY plot and fit the data to lines for comparison of the slopes.

Figure 5 B and C: the cosedimentation data do not seem to help elucidate the underlying mechanism. While the authors report statistical significance, differences are small, especially for gel densitometry measurements where the error is high, which suggests that there may be little biological significance. Importantly, example gels from these experiments should be shown, if not the complete set included in the supplement. In B, the higher cofilin concentrations would be expected to stabilize the filaments and thus the curve should be U-shaped.

Figure 5 D: these data show that the binding of cofilin to WT and E334Q actin is approximately the same, with the mutant binding slightly more weakly. It would be clearer if the two plots were normalized to their respective plateaus since the difference in arbitrary units distracts from the conclusion of the figure. If the difference in the plateaus is meaningful, please explain.

Figure 6: It is assumed that the authors are trying to show in this figure that cofilin binds both actins approximately the same but does not sever as readily for E334Q actin. The numerous parameters measured do not directly address what the authors are actually trying to show, which presumably is that the rate of severing is lower for E334Q than WT. It is therefore puzzling why no measurement of severing events per second per micron of actin in TIRF is made, which would give a more precise account of the underlying mechanism.

Actin-activated steady-state ATPase data of the NM2A with mutant and WT actin would have been extremely useful and informative. The authors show the ability to make these types of measurements in the paper (NADH assay), and it is surprising that they are not included for assessing the myosin activity. It may be because of limited actin quantities. If this is the case, it should be indicated.

(line 310) The authors state that they "noticed increased rapid dissociation and association events for E334Q filaments" in the motility assay. This observation motivates the authors to assess actin affinities of NM2A-HMM. Although differences in rigor and AM.ADP affinities are found between mutant and wt actins, the actin attachment lifetimes (many minutes) are unlikely to be related to the rapid association and dissociation event seen in the motility assay. Rather, this jiggling is more likely to be related to a lower duty ratio of the myosins, which appears to be the conclusion reached for the myosin-V data. These points should be clarified in the text.

(line 327) The authors report that the 1/K1 value is unchanged. There are no descriptions of this experiment in the paper. I am assuming the authors measured the ATP-induced dissociation of actomyosin and determined ATP affinity (K1) from this experiment. If this is the case, they should describe the experiment and show the data, provide a second-order rate constate for ATP binding, and report the max rate of dissociation (k2). This is a kinetic experiment done frequently by this group, so the absence of these details is surprising.

Reviewer #2 (Public Review):

Summary:<br /> In this new paper, the authors used biochemical, structural, and biophysical methods to elucidate the mechanisms by which IP4, the PIP3 headgroup, can induce an autoinhibit form of P-Rex1 and propose a model of how PIP3 can trigger long-range conformational changes of P-Rex1 to relieve this autoinhibition. The main findings of this study are that a new P-Rex1 autoinhibition is driven by an IP4-induced binding of the PH domain to the DH domain active site and that this autoinhibited form is stabilized by two key interactions between DEP1 and DH and between PH and IP4P 4-helix bundle (4HB) subdomain. Moreover, they found that the binding of phospholipid PIP3 to the PH domain can disrupt these interactions to relieve P-Rex1 autoinhibition.

Strengths:<br /> The study provides good evidence that binding of IP4 to the P-Rex1 PH domain can make the two long-range interactions between the catalytic DH domain and the first DEP domain and between the PH domain and the C-terminal IP4P 4HB subdomain that generate a novel P-Rex1 autoinhibition mechanism. This valuable finding adds an extra layer of P-Rex1 regulation (perhaps in the cytoplasm) to the synergistic activation by phospholipid PIP3 and the heterotrimeric Gbeta/gamma subunits at the plasma membrane. Overall, this manuscript's goal sounds interesting, the experimental data were carried out carefully and reliably.

Reviewer #2 (Public Review):

Summary:<br /> The study by Yeo and co-authors addresses a long-lasting issue about botulinum neurotoxin (BoNT) intoxication. The current view is that the toxin binds to its receptors at the axon terminus by its HCc domain and is internalized in recycled neuromediator vesicles just after the release of the neuromediators. Then, the HCn domain assists the translocation of the catalytic light chain (LC) of the toxin through the membrane of these endocytic vesicles into the cytosol of the axon terminus. There, the LC cleaves its SNARE substrate and blocks neurosecretion. However, other views involving kinetic aspects of intoxication suggest that the toxin follows the retrograde axonal transport up to the nerve cell body and then back to the nerve terminus before cleaving its substrate.

In the current study, the authors claim that the BoNT/A (isotype A of BoNT) not only progresses to the cell body but once there, follows the retrograde transport trafficking pathway in a retromer-dependent fashion, through the Golgi apparatus, until reaching the endoplasmic reticulum. Next, the LC dissociates from the HC (a process not studied here) and uses the translocon Sec61 machinery to retro-translocate into the cytosol. Only then, does the LC traffic back to the nerve terminus following the anterograde axonal transport. Once there, LC cleaves its SNARE substrate (SNAP25 in the case of BoTN/A) and blocks neurosecretion.

To reach their conclusion, Yeo and co-authors use a combination of engineered tools: a cell line able to differentiate into neurons (ReNcell VN), a reporter dual fluorescent protein derived from SNAP25, the substrate of BoNT/A (called SNAPR), the use of either native BoNT/A or a toxin to which three fragment 11 of the reporter fluorescent protein Neon Green (mNG) are fused to the N-terminus of the LC (BoNT/A-mNG11x3), and finally ReNcell VN transfected with mNG1-10 (a protein consisting of the first 10 beta strands of the mNG).

SNAPR is stably expressed all over in the ReNcell VN. SNAPR is yellow (red and green) when intact and becomes red only when cleaved by BoNT/A LC, the green tip being degraded by the cell. When the LC of BoNT/A-mNG11x3 reaches the cytosol in ReNcell VN transfected by mNG1-10, the complete mNG is reconstituted and emits a green fluorescence.

In the first experiment, the authors show that the catalytic activity of the LC appears first in the cell body of neurons where SNAPR is cleaved first. This phenomenon starts 24 hours after intoxication and progresses along the axon towards the nerve terminus during an additional 24 hours. In a second experiment, the authors intoxicate the ReNcell VN transfected by mNG1-10 using the BoNT/A-mNG11x3. The fluorescence appears also first in the soma of neurons, then diffuses in the neurites in 48 hours. The conclusion of these two experiments is that translocation occurs first in the cell body and that the LC diffuses in the cytosol of the axon in an anterograde fashion.

In the second part of the study, the authors perform a siRNA screen to identify regulators of BoNT/A intoxication. Their aim is to identify genes involved in intracellular trafficking of the toxin and translocation of the LC. Interestingly, they found positive and negative regulators of intoxication. Regulators could be regrouped according to the sequential events of intoxication. Genes affecting binding to the cell-surface receptor (SV2) and internalization. Genes involved in intracellular trafficking. Genes involved in translocation such as reduction of the disulfide bond linking the LC to the HC and refolding in the cytosol. Genes involved in signaling such as tyrosine kinases and phosphatases. All these groups of genes may be consistent with the current view of BoNT intoxication within the nerve terminus. However, two sets of genes were particularly significant to reach the main conclusion of the work and definitely constitute an original finding important to the field. One set of genes consists of those of the retromer, and the other relates to the Sec61 translocon. This should indicate that once endocytosed, the BoNT traffics from the endosomes to the Golgi apparatus, and then to the ER. Ultimately, the LC should translocate from the ER lumen to the cytosol using the Sec61 translocon. The authors further control that the SV2 receptor for the BoNT/A traffics along the axon in a retromer-dependent fashion and that BoNT/A-mNG11x3 traverses the Golgi apparatus by fusing the mNG1-10 to a Golgi resident protein.

Strengths:<br /> The findings in this work are convincing. The experiments are carefully done and are properly controlled. In the first part of the study, both the activity of the LC is monitored together with the physical presence of the toxin. In the second part of the work, the most relevant genes that came out of the siRNA screen are checked individually in the ReNcell VN / BoNT/A reporter system to confirm their role in BoNT/A trafficking and retro-translocation.

These findings are important to the fields of toxinology and medical treatment of neuromuscular diseases by BoNTs. They may explain some aspects of intoxication such as slow symptom onset, aggravation, and appearance of central effects.

Weaknesses:<br /> The findings antagonize the current view of the intoxication pathway that is sustained by a vast amount of observations. The findings are certainly valid, but their generalization as the sole mechanism of BoNT intoxication should be tempered. These observations are restricted to one particular neuronal model and engineered protein tools. Other models such as isolated nerve/muscle preparations display nerve terminus paralysis within minutes rather than days. Also, the tetanus neurotoxin (TeNT), whose mechanism of action involving axonal transport to the posterior ganglia in the spinal cord is well described, takes between 5 and 15 days. It is thus possible that different intoxication mechanisms co-exist for BoNTs or even vary depending on the type of neurons.

Although the siRNA experiments are convincing, it would be nice to reach the same observations with drugs affecting the endocytic to Golgi to ER transport (such as Retro-2, golgicide or brefeldin A) and the Sec61 retrotranslocation (such as mycolactone). Then, it would be nice to check other neuronal systems for the same observations.

Reviewer #2 (Public Review):

Summary:<br /> This study analyses camera trapping information on the occurrence of forest mammals along a gradient of human modification of the environment. The key hypotheses are that human disturbance squeezes wildlife into a smaller area or their activity into only part of the day, leading to increased co-occurrence under modification. The method used is joint species distribution modelling (JSDM).

Strengths:<br /> The data source seems to be very nice, although since very little information is presented, this is hard to be sure of. Also, the JSDM approach is, in principle, a nice way of simultaneously analysing the data.

Weaknesses:<br /> The manuscript suffers from a mismatch of hypotheses and methods at two different levels.

1) At the lower level, we first need to understand what the individual species do and "like" (their environmental niche). That information is not presented, and the methods suggest that the representation of each species in the JSDM is likely to be extremely poor.

2) The hypothesis clearly asks for an analysis of the statistical interaction between human disturbance and co-occurrence. Yet, the model is not set up this way, and the authors thus do a lot of indirect exploration, rather than direct hypothesis testing.

Even when the focus is not the individual species, but rather their association, we need to formulate what the expectation is. The hypotheses point towards presenting the spatial and the temporal niche, and how it changes, species for species, under human disturbance. To this, one can then add the layer of interspecific associations.

The change in activity and space use can be analysed much simpler, by looking at the activity times and spatial distribution directly. It remains unclear what the contribution of the JSDM is, unless it is able to represent this activity and spatial information, and put it in a testable interaction with human disturbance.

The topic is actually rather complicated. If biotic interactions change along the disturbance gradient, then observed data are already the outcome of such changed interactions. We thus cannot use the data to infer them! But we can show, for each species, that the habitat preferences change along the disturbance gradient - or not, as the case may be.

Then, in the next step, one would have to formulate specific hypotheses about which species are likely to change their associations more, and which less (based e.g. on predator-prey or competitive interactions). The data and analyses presented do not answer any of these issues.

Another more substantial point is that, according to my understanding of the methods, the per-species models are very inappropriate: the predictors are only linear, and there are no statistical interactions (L374). There is no conceivable species in the world whose niche would be described by such an oversimplified model.

We have no idea of even the most basic characteristics of the per-species models: prevalences, coefficient estimates, D2 of the model, and analysis of the temporal and spatial autocorrelation of the residuals, although they form the basis for the association analysis! Why are times of day and day of the year not included as predictors IN INTERACTION with niche predictors and human disturbance, since they represent the temporal dimension on which niches are hypothesised to change?

Also, all correlations among species should be shown for the raw data and for the model residuals: how much does that actually change and can thus be explained by the niche models?

The discussion has little to add to the results. The complexity of the challenge (understanding a community-level response after accounting for species-level responses) is not met, and instead substantial room is given to general statements of how important this line of research is. I failed to see any advance in ecological understanding at the community level.

Reviewer #2 (Public Review):

Allison Coté et al. investigated the ordering and spatial distribution of nascent transcripts in several cells using smFISH, expansion microscopy, and live-cell imaging. They find that pre-mRNA splicing occurs post-transcriptionally at the clouds around the transcription start site, termed the transcription site proximal zone. They show that pre-mRNA may undergo continuous splicing when they pass through the zone after transcription. These data suggest a unifying model for explaining previously reported co-transcriptional splicing events and provide a direction for further study of the nature of the slow-moving zone around the transcription start site.

This paper is well-written. The findings are very important, and the data supports the conclusions well. However, some aspects of the image and description need to be clarified and revised.

1) The sentence "By distinguishing the separate fluorescent signals from probes bound to exons and introns, we could visualize splicing intermediates (represented by colocalized intron and exon spots) relative to the site of transcription (represented by bright colocalized intron and exon spots) and fully spliced products (represented by exon spots alone)." is accidentally repeated twice, one of them should be deleted.<br /> 2) The authors describe Figure 4E and 4F results in the main text as that "we performed RNA FISH simultaneously with immunofluorescence for SC35, a component of speckles, and saw that these compartmentalized pre-mRNA did indeed appear near nuclear speckles both before (Supplementary Figure 6C) and after (Figure 4E) splicing inhibition." However, no SC35 staining is shown in the Figure 4E. A similar situation happened in describing Figure 4F.

Reviewer #2 (Public Review):

Lin et al attempt to examine the role of lncRNAs in human evolution in this manuscript. They apply a suite of population genetics and functional genomics analyses that leverage existing data sets and public tools, some of which were previously built by the authors, who clearly have experience with lncRNA binding prediction. However, I worry that there is a lack of suitable methods and/or relevant controls at many points and that the interpretation is too quick to infer selection. While I don't doubt that lnc RNAs contribute to the evolution of modern humans, and certainly agree that this is a question worth asking, I think this paper would benefit from a more rigorous approach to tackling it.

I thank the authors for their revisions to the manuscript; however, I find that the bulk of my comments have not been addressed to my satisfaction. As such, I am afraid I cannot say much more than what I said last time, emphasising some of my concerns with regards to the robustness of some of the analyses presented. I appreciate the new data generated to address some questions, but think it could be better incorporated into the text - not in the discussion, but in the results.

Reviewer #2 (Public Review):

In this manuscript the authors generate an annotated brain atlas for the prairie vole, which is a widely studied organism. This species has a suite of social behaviors that are difficult or impossible to study in conventional rodents, and has attracted a large community of researchers. The atlas is impressive and will be a fantastic resource. The authors use this atlas to examine brain-wide c-fos expression in prairie voles that were paired with same sex or opposite sex vole across multiple timepoints. In some sense the design resembles PET studies done in primates that take whole brain scans after an important behavioral experience. The authors observed increased c-fos expression across a network of brain regions that largely corresponds with the previous literature. The study design captured several novel observations including that c-fos expression in some regions correlate strongly between males and females during pair bond formation and mating, suggesting synchrony in neural activity. The authors address an important caveat that c-fos provides a snapshot of neural activity and that important populations of neurons could be active and not express c-fos. Thus observed correlations are likely to be robust, but that the absence of differences (in say accumbens) may just reflect the limits of c-fos estimation of neural activity. Similarly, highly coordinated neural activity between males and females might still be driven by different mechanisms if different cell types were activated within a specific region. The creation of this resource and it's use in a well designed study is an important accomplishment.

Reviewer #2 (Public Review):

Summary:<br /> The authors describe a novel ML approach to predict binding between MHC-bound peptides and T-Cell receptors. Such approaches are particularly useful for predicting the binding of peptide sequences with low similarity when compared to existing data sets. The authors focus on improving dataset quality and optimizing model architecture to achieve a pan-specific predictive model in hopes of achieving a high-precision model for novel peptide sequences.

Strengths:<br /> Since assuring the quality of training datasets is the first major step in any ML training project, the extensive human curation, computational analysis, and enhancements made in this manuscript represent a major contribution to the field. Moreover, the systematic approach to testing redundancy reduction and data augmentation is exemplary, and will significantly help future research in the field.

The authors also highlight how their model can identify outliers and how that can be used to improve the model around known sequences, which can help the creation and optimization of future datasets for peptide binding.

The new models presented here are novel and built using paired α/β TCR sequence data to predict peptide-specific TCR binding, and have been extensively and rigorously tested.

Weaknesses:<br /> Achieving an accurate pan-specific model is an ambitious goal, and the authors have significant difficulties when trying to achieve non-random performance for the prediction of TCR binding to novel peptides. This is the most challenging task for this kind of model, but also the most desirable when applying such models to biotechnological and bioengineering projects.

The manuscript is a highly technical and extremely detailed computational work, which can make the achievements and impact of the work hard to parse for application-oriented researchers.<br /> The authors briefly mention real-world use cases for TCR specificity predictions, but do not contextualize the work into possible applications.

Reviewer #2 (Public Review):

Summary:

This paper nicely introduces WormPsyQi, an imaging analysis pipeline that effectively quantifies synaptically localized fluorescent signals in C. elegans through high-throughput automation. This toolkit is particularly valuable for the analysis of densely packed regions in 3D space, such as the nerve ring. The authors applied WormPsyQi to various aspects, including the examination of sexually dimorphic synaptic connectivity, presynaptic markers in eight head neurons, five GRASP reporters, electrical synapses, the enteric nervous system, and developmental synapse comparisons. Furthermore, they validated WormPsyQi's accuracy by comparing its results to manual analysis.

Strengths:

Overall, the experiments are well done, and their toolkit demonstrates significant potential and offers a valuable resource to the C. elegans community. This will expand the range of possibilities for studying synapses in C. elegans.

Reviewer #2 (Public Review):

Summary:<br /> Developing a mechanical model of C. elegans is difficult to do from basic principles because it moves at a low (but not very small) Reynolds number, is itself visco-elastic, and often is measured moving at a solid/liquid interface. The ElegansBot is a good first step at a kinetic model that reproduces a wide range of C. elegans motiliy behavior.

Strengths:<br /> The model is general due to its simplicity and likely useful for various undulatory movements. The model reproduces experimental movement data using realistic physical parameters (e.g. drags, forces, etc). The model is predictive (semi?) as shown in the liquid-to-solid gait transition. The model is straightforward in implementation and so likely is adaptable to modification and addition of control circuits.

Weaknesses:<br /> Since the inputs to the model are the actual shape changes in time, parameterized as angles (or curvature), the ability of the model to reproduce a realistic facsimile of C. elegans motion is not really a huge surprise.

The authors do not include some important physical parameters in the model and should explain in the text these assumptions. 1) The cuticle stiffness is significant and has been measured [1]. 2) The body of C. elegans is under high hydrostatic pressure which adds an additional stiffness [2]. 3) The visco-elasticity of C. elegans body has been measured. [3]

There is only a very brief mention of proprioception. The lack of inclusion of proprioception in the model should be mentioned and referenced in more detail in my opinion.

These are just suggested references. There may be more relevant ones available.

1. Rahimi M, Sohrabi S, Murphy CT. Novel elasticity measurements reveal C. elegans cuticle stiffens with age and in a long-lived mutant. Biophys J. 2022 Feb 15;121(4):515-524. doi: 10.1016/j.bpj.2022.01.013. Epub 2022 Jan 19. PMID: 35065051; PMCID: PMC8874029.

2. Park SJ, Goodman MB, Pruitt BL. Analysis of nematode mechanics by piezoresistive displacement clamp. Proc Natl Acad Sci U S A. 2007 Oct 30;104(44):17376-81. doi: 10.1073/pnas.0702138104. Epub 2007 Oct 25. PMID: 17962419; PMCID: PMC2077264.

3. Backholm M, Ryu WS, Dalnoki-Veress K. Viscoelastic properties of the nematode Caenorhabditis elegans, a self-similar, shear-thinning worm. Proc Natl Acad Sci U S A. 2013 Mar 19;110(12):4528-33. doi: 10.1073/pnas.1219965110. Epub 2013 Mar 4. PMID: 23460699; PMCID: PMC3607018.

Reviewer #2 (Public Review):

In this study, Hernandez-Hernandez et al developed a gender-dependent mathematical model of arterial myocytes based on a previous model and new experimental data. The ionic currents of the model and its sex difference were formulated based on patch clamp experimental data, and the model properties were compared with single cell and tissue scale experimental results. This is a study that is of importance for the modeling field as well as for experimental physiology.

Reviewer #2 (Public Review):

Summary:<br /> The authors are studying the behavioral response to pathogen exposure. They and others have previously describe the role that the G-protein coupled receptors in the nervous system plays in detecting pathogens, and initiating behavioral patterns (e.g. avoidance/learned avoidance) that minimize contact. The authors study this problem in C. elegans, which is amenable to genetic and cellular manipulations and allow the authors to define cellular and signaling mechanisms. This paper extends the original idea to now implicate signaling and transcriptional pathways within a particular neuron (ASJ) and the gut in mediating avoidance behaviour.

Strengths:<br /> The work is rigorous and elegant and the data are convincing. The authors make superb use of mutant strains in C. elegans, as well tissue specific gene inactivation and expression and genetic methods of cell ablation. to demonstrate how a gene, NPR15 controls behavioral changes in pathogen infection. The results suggest that ASJ neurons and the gut mediate such effects. I expect the paper will constitute an important contribution to our understanding of how the nervous system coordinates immune and behavioral responses to infection.

Reviewer #2 (Public Review):

This is a nice story about auricular chondrocyte maintenance, its molecular mechanism, and the role of the BMP 1 receptor in microtia disease conditions. A detailed analysis of different parts of the ear, their proliferation, and their differentiation condition with histological and immunofluorescence analysis strengthens the evidence. Further validation with patient sample RNA-Seq also helps the study end with an informative story.

From the public point of view, I want to say that the authors want to explain how auricular chondrocytes differ from growth plates or other chondrocytes. The authors show that Prxx1 is a good marker to differentiate auricular chondrocytes from different types of chondrocytes, which I doubt because other chondrocytes have an expression of Prxx1 at a lower level.

Another thing the authors mention is that microtia conditions develop through reduced size without affecting proliferation and apoptosis. The authors never provide any evidence about how the ablation of Bmpr1a affects the size, protein trafficking, and ECM organization.

Crosstalk between BMP-PKA in auricular chondrocytes and switching the chondrocytes' cell fate in osteoblast cells are not entirely stable by these studies for physiological functions.

Reviewer #3 (Public Review):

Summary:<br /> The authors set out to characterize the anatomical connectivity profile and the functional responses of chandelier cells (ChCs) in the mouse primary visual cortex. Using retrograde rabies tracing, optogenetics, and in vitro electrophysiology, they found that the primary source of input to ChCs are local layer 5 pyramidal cells, as well as long-range thalamic and cortical connections. ChCs provided input to local layer 2/3 pyramidal neurons, but did not receive reciprocal connections.

With two-photon calcium imaging recordings during passive viewing of drifting gratings, the authors showed that ChCs exhibit weakly selective visual responses, high correlations within their own population, and strong responses during periods of arousal (assessed by locomotion and pupil size). These results were replicated and extended in experiments with natural images and prediction of receptive field structure using a convolutional neural network.

Furthermore, the authors employed a learned visuomotor task in a virtual corridor to show that ChCs exhibit strong responses to mismatches between visual flow and locomotion, locomotion-related activation (similar to what was shown above), and visually-evoked suppression. They also showed the existence of two clusters of pyramidal neurons with functionally different responses - a cluster with "classically visual" responses and a cluster with locomotion- and mismatch-driven responses (the latter more correlated with ChCs). Comparing naive and trained mice, the authors found that visual responses of ChCs are suppressed following task learning, accompanied by a shortening of the axon initial segment (AIS) of pyramidal cells and an increase in the proportion of AIS contacted by ChCs. However, additional controls would be required to identify which component(s) of the experimental paradigm led to the functional and anatomical changes observed.

Strengths:<br /> The authors bring a comprehensive, state-of-the-art methodology to bear, including rabies tracing, in vivo two-photon calcium imaging, in vitro electrophysiology, optogenetics and chemogenetics, and deep neural networks. Their analyses and statistical tests are sound and for the most part, support their claims. Their results are in line with previous findings and extend them to the primary visual cortex.

Weaknesses:<br /> - Some of the results (e.g. arousal-related responses) are not entirely surprising given that similar results exist in other cortical areas.

Reviewer #2 (Public Review):

Summary:<br /> Nakai-Futatsugi et al. present a novel method to analyze the correlation between the degree of pigmentation and the gene expression profile of human-induced pluripotent stem cell-derived RPE (iPSC-RPE) cells at the single cell level. This was achieved with the use of ALPS (Automated Live imaging and cell Picking System), an invention developed by the same authors. Briefly, it allows one to choose and photograph a specific cell from a culture dish and proceed to single-cell digital RNA-seq. The authors identify clusters of cells that present differential gene expression, but this shows no association with the degree of pigmentation of the cells. Further data analysis allowed the authors to correlate the degree of pigmentation to some degree with the expression of complement and lysosome-related genes.

Strengths:<br /> An important amount of data related to gene expression and heterogeneity of the iPSC-RPE population has been generated in this work.

Weaknesses:<br /> However, the justification of the analysis, and the physiological relevance of the hypothesis and the findings could be strengthened.

Importantly, I fail to grasp from the introduction what is the previous evidence that leads to the hypothesis. Why would color intensity be related to the quality of cell transplantation? In fact, cell transplantation is not evaluated at all in this work. The authors mention "quality metrics for clinical use", but this concept is not further explained. Neither is the concept of "sufficient degree of pigmentation" explained.

On the other hand, the positive correlation of cluster formation with complement and lysosome-related genes is not discussed.

As a consequence, it is very difficult to evaluate the impact of these findings on the field.

Reviewer #2 (Public Review):

This paper introduces a new model that aims to explain the generators of temporal decoding matrices (TGMs) in terms of underlying signal properties. This is important because TGMs are regularly used to investigate neural mechanisms underlying cognitive processes, but their interpretation in terms of underlying signals often remains unclear. Furthermore, neural signals are often variant over different instances of stimulation despite behaviour being relatively stable. The author aims to tackle these concerns by developing a generative model of electrophysiological data and then showing how different parameterizations can explain different features of TGMs. The developed technique is able to capture empirical observations in terms of fundamental signal properties. Specifically, the model shows that complexity is necessary in terms of spatial configuration, frequencies and latencies to obtain a TGM that is comparable to empirical data.

The major strength of the paper is that the novel technique has the potential to further our understanding of the generators of electrophysiological signals which are an important way to understand brain function. The paper clearly outlines how the method can be used to capture empirical data. Furthermore, the used techniques are state-of-the-art and the developed model is publicly shared in open source code.

On the other hand, there is no unambiguous mapping between neurobiological mechanisms and different signal generators, making it hard to draw firm conclusions about neural underpinnings based on this analysis.

Reviewer #2 (Public Review):

This manuscript by Petersen and colleagues investigates the mechanistic underpinnings of activation of the ion channel TREK-1 by mechanical inputs (fluid shear or membrane stretch) applied to cells. Using a combination of super-resolution microscopy, pair correlation analysis and electrophysiology, the authors convincingly show that the application of shear to a cell can lead to changes in the distribution of TREK-1 and the enzyme PhospholipaseD2 (PLD2), relative to lipid domains defined by either GM1 or PIP2. The activation of TREK-1 by mechanical stimuli was shown to be sensitized by the presence of PLD2, but not a catalytically inactive xPLD2 mutant. In addition, the activity of PLD2 is increased when the molecule is more associated with PIP2, rather than GM1 defined lipid domains. The presented data do not exclude direct mechanical activation of TREK-1, rather suggest a modulation of TREK-1 activity, increasing sensitivity to mechanical inputs, through an inherent mechanosensitivity of PLD2 activity. The authors additionally demonstrate that cellular uptake of cholesterol inhibits TREK-1 activation and, in ex vivo studies, that depletion of cholesterol from astrocytes reduces correlation of TREK-1 and G1 lipids in mouse brain slices. In vivo studies, using Drosophila melanogaster behavioural assays, were used to demonstrate that disrupting PLD2 altered behavioural responses to mechanical and electrical inputs. These data demonstrate that manipulation of PLD2 analogue in the fly can alter sensory transduction, suggesting that PLD functions to regulate sensitivity to mechanical force. However, as the authors note, there is no TREK-1 homologue in this organism: thus the identity of the downstream effectors of PLD in D. melanogaster remain unknown. This work will be of interest to the growing community of scientists investigating the myriad mechanisms that can tune mechanical sensitivity of cells, providing valuable insight into the role of functional PLD2 in sensitizing TREK-1 activation in response to mechanical inputs, in some cellular systems.

The authors convincingly demonstrate that, post application of shear, an alteration in the distribution of TREK-1 and mPLD2 (in HEK293T cells) from being correlated with GM1 defined domains (no shear) to increased correlation with PIP2 defined membrane domains (post shear). The association of TREK-1 with PIP2 required functional mPLD2. These data were generated using super-resolution microscopy to visualise, at sub diffraction resolution, the localisation of labelled protein, compared to labelled lipids. The use of super-resolution imaging enabled the authors to visualise changes in cluster association that would not have been achievable with diffraction limited microscopy.

This work provides further evidence of the astounding flexibility of mechanical sensing in cells. By outlining how mechanical activation of TREK-1 can be sensitised by mechanical regulation of PLD2 activity, the authors highlight a mechanism by which TREK-1 sensitivity could be regulated under distinct physiological conditions.

Reviewer #2 (Public Review):

In their submitted manuscript, Blin et al. describe differences in the olfactory-driven behaviors of river-dwelling surface forms and cave-dwelling blind forms of the Mexican tetra, Astyanax mexicanus. They provide a dataset of unprecedented detail, that compares not only the behaviors of the two morphs but also that of a significant number of F2 hybrids, therefore also demonstrating that many of the differences observed between the two populations have a clear (and probably relatively simple) genetic underpinning.

To complete the monumental task of behaviorally testing 425 six-week-old Astyanax larvae, the authors created a setup that allows for the simultaneous behavioral monitoring of multiple larvae and the infusion of different odorants without introducing physical perturbations into the system, thus biasing the responses of cavefish that are particularly fine-tuned for this sensory modality. During the optimization of their protocol, the authors also found that for cave-dwelling forms one hour of habituation was insufficient and a full 24 hours were necessary to allow them to revert to their natural behavior. It is also noteworthy that this extremely large dataset can help us see that population averages of different morphs can mask quite significant variations in individual behaviors.

Testing with different amino-acids (applied as relevant food-related odorant cues) shows that cavefish are alanine- and histidine-specialists, while surface fish elicit the strongest behavioral responses to cysteine. It is interesting that the two forms also react differently after odor detection: while cave-dwelling fish decrease their locomotory activity, surface fish increase it. These differences are probably related to different foraging strategies used by the two populations, although, as the observations were made in the dark, it would be also interesting to see if surface fish elicit the same changes in light as well.

Further work will be needed to pinpoint the exact nature of the genetic changes that underlie the differences between the two forms. Such experimental work will also reveal how natural selection acted on existing behavioral variations already present in the SF population.

It will be equally interesting, however, to understand what lies behind the large individual variation of behaviors observed both in the case surface and cave populations. Are these differences purely genetic, or perhaps environmental cues also contribute to their development? Does stochasticity provided by the developmental process has also a role in this? Answering these questions will reveal if the evolvability of Astyanax behavior was an important factor in the repeated successful colonization of underground caves.

Reviewer #2 (Public Review):

The mechanisms that mediate female aggression remain poorly understood. Chiu, Schretter, and colleagues, employed circuit dissection techniques to tease apart the specific roles of particular doublesex and fruitless expressing neurons in the fly Drosophila in generating a persistent aggressive state. They find that activating the fruitless positive alPg neurons, generated an aggressive state that persisted for >10min after the stimulation ended. Similarly, activating the doublesex positive pC1de neurons also generated a peristent state. Activating pC1d or pC1e individually did not induce a persistent state. Interestingly, while neural activation of alPGs and pC1d+e neurons induced a persistent behavioural states it did not induce persistent activity in the neurons being activated.

The authors have revised the manuscript in accordance with comments of the reviewers. The conclusions of this paper are by and large well supported by the data. These data will be a useful addition to the literature on the circuit basis of female aggression, and open up intriguing avenues for further studies to explore.

Reviewer #2 (Public Review):

In this study, the authors describe a pipeline to sequence expressed var genes from RNA sequencing that improves on a previous one that they had developed. Importantly, they use this approach to determine how var gene expression changes with short-term culture. Their finding of shifts in the expression of particular var genes is compelling and casts some doubt on the comparability of gene expression in short-term culture versus var expression at the time of participant sampling.

Other studies have relied on short-term culture to understand var gene expression in clinical malaria studies. This study indicates the need for caution in over-interpreting findings from these studies.

We appreciate the careful attention of the authors to our comments and the edits that have been made. One additional suggestion that would be helpful to readers is to include in Table S1 the new approach described in the manuscript. This will provide the reader a direct means of comparing what the authors have done to past work.

Reviewer #2 (Public Review):

In this study, a minimalist setup was used to investigate the selectivity of the nuclear pore complex as a function of its diameter. To this end, a series of solid-state pores in a free-standing palladium membrane were designed and attached to a PDMS-based fluid cell that could be mounted on a confocal microscope. In this way, the frequency of translocation events could be measured in an unbiased manner. Furthermore, the pores were designed to exhibit the key properties of the nuclear pore complex: (i) the size of the pore, (ii) disordered FG Nups specifically located in the central channel; (ii) transport receptors that can shuttle through the central channel by binding to the FG-Nups. Additionally, such system offered the advantage of monitoring the translocation of multiple fluorescently labeled molecules (e.g. Kap95 and BSA) simultaneously and under well-controlled conditions.

The authors were able to demonstrate convincingly that the pore selectivity depends on the pore diameter, the FG Nup layer organization within the pore and the transport receptors concentration that can specifically interact with FG Nups. It was shown that the pores coated with FG Nups (e.g. Nsp1 in this case) and smaller than 50-60 nm are highly selective and such selectivity is increasing with the decrease of the pore diameter. Also, it was shown that the pore selectivity moderately enhances at the high Kap95 concentration (1 µM). Importantly, it was also shown that the selectivity is becoming negligible for the pores, which are larger than 60-75 nm.

The experimental data are well supported by coarse-grained modelling of Nsp1-coated pores, and the theoretical prediction correlates qualitatively with the experimentally obtained data.

Reviewer #2 (Public Review):

This study explores the breadth of effects of one important metabolite, azelaic acid, on marine microbes, and reveals in-depth its pathway of uptake and catabolism in one model bacterial strain. This compound is known to be widely produced by phytoplankton and plants, and to have complex effects on associated microbiomes.

This work uses transcriptomics to assay the response of two strains that show contrasting responses to the metabolite: one catabolizes the compound and assimilates the carbon, while the other shows growth inhibition and stress response. A highly induced TRAP transporter, adjacent to a previously identified regulator, is inferred to be the specific uptake system for azelaic acid, though this function was not directly tested via genetic or biochemical methods. Nevertheless, this is a significant finding that will be useful for exploring the distribution of azelaic acid uptake capability across metagenomes and other bacteria.

The authors use pulse-chase style metabolomics experiments to beautifully demonstrate the fate of azelaic acid through catabolic pathways. They also measure an assimilation rate per cell, though it remains unclear how this measured rate relates to natural systems. The metabolomics approach is an elegant way to show carbon flux through cells, and could serve as a model for future studies.

The study seeks to extend the results from two model strains to complex communities, using seawater mesocosm experiments and soil/Arabidopsis experiments. The seawater experiments show a community shift in mesocosms with added azelaic acid. The mechanisms for the shift were not determined in this study; further work is necessary to demonstrate which community members are directly assimilating the compound, benefitting indirectly, or experiencing inhibition. The authors also took the unusual and creative step of performing similar experiments in a soil - Arabidopsis system. I admire the authors' desire to identify unifying themes across ecosystems. The parallels are intriguing, and future experiments could determine the different modes of action in aquatic vs terrestrial microbial communities.

This work is a nice illustration of how we can begin to tease apart the effects of chemical currencies on marine ecosystems. A key strength of this work is the combination of transcriptomics and metabolomics methods, along with assaying the impacts of the metabolite on model strains of bacteria and whole communities. Given the sheer number of compounds that probably play critical roles in community interactions, a key challenge for the field will be navigating the tradeoffs between breadth and depth in future studies of metabolite impacts. This study offers a good compromise and will be a useful model for future studies.

Reviewer #2 (Public Review):

In this study, the authors utilize a compendium of public genomic data to identify transcription factors (TF) that can identify their DNA binding motifs in the presence of nuclosome-wrapped chromatin and convert the chromatin to open chromatin. This class of TFs are termed Pioneer TFs (PTFs). A major strength of the study is the concept, whose premise is that motifs bound by PTFs (assessed by ChIP-seq for the respective TFs) should be present in both "closed" nucleosome wrapped DNA regions (measured by MNase-seq) as well as open regions (measured by DNAseI-seq) because the PTFs are able to open the chromatin. Use of multiple ENCODE cell lines, including the H1 stem cell line, enabled the authors to assess if binding at motifs changes from closed to open. Typical, non-PTF TFs are expected to only bind motifs in open chromatin regions (measured by DNaseI-seq) and not in regions closed in any cell type. This study contributes to the field a validation of PTFs that are already known to have pioneering activity and presents an interesting approach to quantify PTF activity.

For this reviewer, there were a few notable limitations. One was the uncertainty regarding whether expression of the respective TFs across cell types was taken into account. This would help inform if a TF would be able to open chromatin. Another limitation was the cell types used. While understandable that these cell types were used, because of their deep epigenetic phenotyping and public availability, they are mostly transformed and do not bear close similarity to lineages in a healthy organism. Next, the methods used to identify PTFs were not made available in an easy-to-use tool for other researchers who may seek to identify PTFs in their cell type(s) of interest. Lastly, some terms used were not defined explicitly (e.g., meaning of dyads) and the language in the manuscript was often difficult to follow and contained improper English grammar.

Reviewer #2 (Public Review):

Summary:

In this manuscript, Yu and colleagues sought to identify new susceptibility genes for adolescent idiopathic scoliosis (AIS). The significance of this work is high, especially given the still large knowledge gap of the mechanistic underpinnings for AIS. In this multidisciplinary body of work, the authors first performed a genetic association study of AIS case-control cohorts (combined 9,161 cases and 80,731 controls) which leveraged common SNPs in 1027 previously defined matrisome genes. Two nonsynonymous variants were found to be significantly associated with AIS: MMP14 p.Asp273Asn and COL11A1 p.Pro1153Leu, the latter of which had the more robust association and remained significant when females were tested independent of males. Next, the authors followed a series of functional validation experiments to support biological involvement of COL11A1 p.Pro1153Leu in AIS through expression, biochemical, and histological studies in physiologically relevant cell and mouse models. Together, the authors propose a hitherto unreported model for AIS that involves the interplay of the COL11A1 susceptibility locus with estrogen signaling to alter a Pax1-Col11a1-Mmp3 signaling axis at the growth plate.

Strengths:

The manuscript is clearly written and follows a series of logical steps toward connecting multiple matrisome genes and putative AIS effectors in a new framework of pathomechanism. The multidisciplinary nature of the work makes it a strong body of work wherein multiple models offer multiple lines of supportive data. Thus, this manuscript remains an important multidisciplinary study of the genetic and functional basis of adolescent idiopathic scoliosis (AIS). To the benefit of the overall manuscript quality, the reviewers have addressed most concerns to satisfaction. Please include the list of three rare missense variants mentioned in the response to reviewers as a supplementary table. Please also include methods for the SKATO rare variant burden analysis.

Reviewer #2 (Public Review):

Summary:<br /> In Ferrareti et al. they identify adaptively introgressed genes using VolcanoFinder and then identify pathways enriched for adaptively introgressed genes. They also use a signet to identify pathways that are enriched for Denisovan alleles. The authors find that angiogenesis and nitric oxide induction are enriched for archaic introgression.

Strengths:<br /> Most papers that have studied the genetic basis of high altitude (HA) adaptation in Tibet have highly emphasized the role of a few genes (e.g. EPAS1, EGLN1), and in this paper, the authors look for more subtle signals in other genes (e.g EP300, NOS 2) to investigate how archaic introgression may be enriched at the pathway level.

Looking into the biological functions enriched for Denisovan introgression in Tibetans is important for characterizing the impact of Denisovan introgression.

Weaknesses:<br /> The manuscript lacks details or justification about how/why some of the analyses were performed. Below are some examples where the authors could provide additional details.

The authors made specific choices in their window analysis. These choices are not justified or there is no comment as to how results might change if these choices were perturbed. For example, in the methods, the authors write "Then, the genome was divided into 200 kb windows with an overlap of 50 kb and for each of them we calculated the ratio between the number of significant SNVs and the total number of variants."

Additional information is needed for clarity. For example, "we considered only protein-protein interactions showing confidence scores {greater than or equal to} 0.7 and the obtained protein frameworks were integrated using information available in the literature regarding the functional role of the related genes and their possible involvement in high-altitude adaptation." What do the confidence scores mean? Why 0.7?

In the method section (Identifying gene networks enriched for Denisovan-like derived alleles), the authors write "To validate VolcanoFinder results by using an independent approach". Does this mean that for signet the authors do not use the regions identified as adaptively introgressed using volcanofinder? I thought in the original signet paper, the authors used a summary describing the amount of introgression of a given region.

Later, the authors write "To do so, we first compared the Tibetan and Denisovan genomes to assess which SNVs were present in both modern and archaic sequences. These loci were further compared with the ancestral reconstructed reference human genome sequence (1000 Genomes Project Consortium et al., 2015) to discard those presenting an ancestral state (i.e., that we have in common with several primate species)." It is not clear why the authors are citing the 1000 genomes project. Are they comparing with the reference human genome reference or with all populations in the 1000 genomes project? Also, are the authors allowing derived alleles that are shared with Africans? Typically, populations from Africa are used as controls since the Denisovan introgression occurred in Eurasia.

The methods section for Figures 4B, 4C, and 4D is a little hard to understand. What is the x-axis on these plots? Is it the number of pairwise differences to Denisovan? The caption is not clear here. The authors mention that "Conversely, for non-introgressed loci (e.g., EGLN1), we might expect a remarkably different pattern of haplotypes distribution, with almost all haplotype classes presenting a larger proportion of non-Tibetan haplotypes rather than Tibetan ones." There is clearly structure in EGLN1. There is a group of non-Tibetan haplotypes that are closer to Denisovan and a group of Tibetan haplotypes that are distant from Denisovan...How do the authors interpret this?

In the original signet paper (Guoy and Excoffier 2017), they apply signet to data from Tibetans. Zhang et al. PNAS (2021) also applied it to Tibetans. It would be helpful to highlight how the approach here is different.

Reviewer #2 (Public Review):

In the manuscript by Rajan et al., the authors have highlighted the direct interaction between Dbp5 and tRNA, wherein Dbp5 serves as a mediator for tRNA export. This export process is subject to spatial regulation, as Dbp5 ATPase activation occurs specifically at nuclear pore complexes. Notably, this regulation is independent of the Los1-mediated pre-tRNA export route and instead relies on Gle1. The manuscript is well constructed and nicely written.

Reviewer #2 (Public Review):

In their study, Stajich and co-authors present a new 1.03 Gb genome assembly for an isolate of the fungal insect parasite Entomophthora muscae (Entomophthoromycota phylum, isolated from Drosophila hydei). Many species of the Entomophthoromycota phylum are specialised insect pathogens with relatively large genomes for fungi, with interesting yet largely unexplored biology. The authors compare their new E. muscae assembly to those of other species in the Entomophthorales order and also more generally to other fungi. For that, they first focus on repetitive DNA (transposons) and show that Ty3 LTRs are highly abundant in the E. muscae genome and contribute to ~40% of the species' genome, a feature that is shared by closely related species in the Entomophthorales. Next, the authors describe the major differences in protein content between species in the genus, focusing on functional domains, namely protein families (pfam), carbohydrate-active enzymes, and peptidases. They highlight several protein families that are overrepresented/underrepresented in the E. muscae genome and other Entomophthorales genomes. The authors also highlight differences in components of the circadian rhythm, which might be relevant to the biology of these insect-infecting fungi. To gain further insights into E. muscae specificities, the authors identify orthologous proteins among four Entomophthorales species. Consistently with a larger genome and protein set in E. muscae, they find that 21% of the 17,111 orthogroups are specific to the species. To finish, the authors examine the consistency between methods for species delineation in the genus using molecular (ITS + 28S) or morphological data (# of nuclei per conidia + conidia size) and highlight major incongruences between the two.

Although most of the methods applied in the frame of this study are appropriate with the scripts made available, I believe there are some major discrepancies in the datasets that are compared which could undermine most of the results/conclusions. More precisely, most of the results are based on the comparison of protein family content between four Entomophthorales species. As the authors mention on page 5, genome (transcriptome) assembly and further annotation procedures can strongly influence gene discovery. Here, the authors re-annotated two assemblies using their own methods and recovered between 30 and 60% more genes than in the original dataset, but if I understand it correctly, they perform all downstream comparative analyses using the original annotations. Given the focus on E. muscae and the small sample size (four genomes compared), I believe performing the comparisons on the newly annotated assemblies would be more rigorous for making any claim on gene family variation.

The authors also investigate the putative impact of repeat-induced point mutation on the architecture of the large Entomophthorales genomes (for three of the eight species in Figure 1) and report low RIP-like dinucleotide signatures despite the presence of RID1 (a gene involved in the RIP process in Neurospora crassa) and RNAi machinery. They base their analysis on the presence of specific PFAM domains across the proteome of the three Entomophthorales species. In the case of RID1, the authors searched for a DNA methyltransferase domain (PF00145), however other proteins than RID1 bear such functional domain (DNMT family) so that in the current analysis it is impossible to say if the authors are actually looking at RID1 homologs (probably not, RID1 is monophyletic to the Ascomycota I believe). Similar comments apply to the analysis of components of the RNAi machinery. A more reliable alternative to the PFAM analysis would be to work with full protein sequences in addition to the functional domains.

Reviewer #2 (Public Review):

Summary:<br /> The study by Toth et al. investigates the role of RIN4, a key immune regulator, in the symbiotic nitrogen fixation process between soybean and rhizobium. The authors found that SymRK can interact with and phosphorylate GmRIN4. This phosphorylation occurs within a 15 amino acid motif that is highly conserved in N-fixation clades. Genetic studies indicate that GmRIN4a/b play a role in root nodule symbiosis. Based on their data, the authors suggest that RIN4 may function as a key regulator connecting symbiotic and immune signaling pathways.

Overall, the conclusions of this paper are well supported by the data, although there are a few areas that need clarification.

Strengths:<br /> • This study provides important insights by demonstrating that RIN4, a key immune regulator, is also required for symbiotic nitrogen fixation.<br /> • The findings suggest that GmRIN4a/b could mediate appropriate responses during infection, whether it is by friendly or hostile organisms.

Weaknesses:<br /> • The study did not explore the immune response in the rin4 mutant. Therefore, it remains unknown how GmRIN4a/b distinguishes between friend and foe.

Reviewer #2 (Public Review):

This manuscript proposed a new link between the formation of chloroplast budding vesicles (Rubisco-containing bodies [RCBs]) and the development of chloroplast-associated autophagosomes. The authors' previous work demonstrated two types of autophagy pathways involved in chloroplast degradation, including piecemeal degradation of partial chloroplast and whole chloroplast degradation. However, the mechanisms underlying piecemeal degradation are largely unknown, particularly regarding the initiation and release of the budding structures. Here, the authors investigated the progression of piecemeal-type chloroplast trafficking by visualizing it with a high-resolution time-lapse microscope. They provide evidence that autophagosome formation is required for the initiation of chloroplast budding, and that stromule formation is not correlated with this process. In addition, the authors also demonstrated that the release of chloroplast-associated autophagosome is independent of a chloroplast division factor, DRP5b.

Overall, the findings are interesting, and in general, the experiments are very well executed. Although the mechanism of how Rubisco-containing bodies are processed is still unclear, this study suggests that a novel chloroplast division machinery exists to facilitate chloroplast autophagy, which will be valuable to investigate in the future.

Reviewer #2 (Public Review):

Summary:<br /> The manuscript by Knights et al set out to identify the specific immune cells and their contribution to the development of osteoarthritis. They performed a comprehensive analysis of scRNA-seq and flow cytometry using different stages of the PTOA model and sought to identify specific synovial macrophages in OA. Computational analysis revealed that M-CSF signaling in synovium plays an important role in stromal-immune crosstalk in OA. They also found that four transcription factors including Pu.1, Cebp-alpha, Cebp-beta, and Jun regulate the differentiation of monocytes into pro-inflammatory synovial macrophages in OA.

Strengths:<br /> The main strength of this study is the profiling of immune cells which will be a valuable resource for better understanding the pathogenesis of OA. The work is technically sound, and the level of analysis of gene expression, clustering, cell-cell communication, and dynamic changes in gene modules over time is state-of-the-art.

The reviewer appreciates that the authors uncovered the transcriptional network that regulates the differentiation of synovial macrophages in OA. In addition, the identification of M-CSF signaling as a major crosstalk axis in OA development is also intriguing.

Weaknesses:<br /> Although the scRNA-seq analysis of immune cells in OA is quite convincing, the data has been rather descriptive and superficial at this stage. The authors did not show the in vivo significance of their findings in OA development.

Reviewer #2 (Public Review):

Summary:

The study introduces BRAID, a novel approach for targeting drugs to specific cell types, addressing the challenges of pleiotropic drug actions. Unlike existing methods, this one involves breaking a protein drug molecule into inactive parts that are then put back together using a bridging receptor on the target cell. The individual components of this assembly are not required to be together, thereby affording it a degree of flexibility. The authors applied this idea to the WNT/-catenin signaling pathway by splitting a WNT mimic into two parts with FZD and LRP binding domains and bridging receptors. This combined method, which is called SWIFT, showed that WNT signaling was turned on in target cells, showing that cell-specific targeting is. The technique shows promise for the development of therapeutics, as it provides a way to more precisely target signaling pathways.

The authors have effectively elucidated their strategy through visually appealing diagrams, providing clear and thorough visual aids that facilitate comprehension of the concept. In addition, the authors have provided convincing evidence that the C-terminal region of FGF21 is essential for the binding process. Their meticulous and thorough presentation of experimental results emphasizes the significance of this specific binding domain and validates their findings.

Strengths:

BRAID, a novel cell targeting method, divides an active drug molecule into inactive components formed by a bridging receptor. This novel approach to cell-specific drug action may reduce systemic toxicity.

The SWIFT approach successfully targets cells in the WNT/β-catenin signaling pathway. The approach activates WNT signaling only in target cells (hepatocytes), proving its specificity.

The study indicates that the BRAID approach can target various signaling systems beyond WNT/β-catenin, indicating its versatility. Therapeutic development may benefit from this adaptability.

Weaknesses:

The study shows the SWIFT approach works in vitro using cell lines, primary human hepatocytes, and human intestinal organoids, but it lacks in vivo animal model or clinical validation. I believe future studies will determine this aspect.

The success of SWIFT depends on the presence and expression of the bridging receptor (βKlotho) on target cells. The approach may fail if the target receptor is not expressed.

Reviewer #2 (Public Review):

Zirin, Jusiak, and Lopes et al presented an efficient pipeline for making LexA-GAD and QF2 drivers. The tools can be combined with a large collection of existing GAL4 drivers for a dual genetic control of two cell populations. This is essential when studying inter-organ communications since most of the current genetic drivers are biased toward the expression of the central nervous system. In this manuscript, the authors described the methodology for efficiently generating T2A-LexA-GAD and T2A-QF2 knock-ins by CRISPR, targeting a number of genes with known tissue-specific expression patterns. The authors then validated and compared the expression of double as well as single drivers and found the tissue-specific expression results were largely consistent as expected. Finally, a collection of plasmids for LexA-GAD and QF,2 as well as the corresponding LexAop and QUAS plasmids were generated to facilitate the expansion of these tool kits. In general, this study will be of considerable interest to the fly community and the resources can be readily generalized to make drivers for other genes. I believe this toolkit will have a significant, immediate impact on the fly community.

Reviewer #2 (Public Review):

In this manuscript, Chen et al. determined the structural basis for pre-RNA processing by Las1-Grc3 endoribonuclease and polynucleotide kinase complexes from S. cerevisiae (Sc) and C. jadinii (Cj). Using a robust set of biochemical assays, the authors identify that the sc- and CjLas1-Grc3 complexes can cleave the ITS2 sequence in two specific locations, including a novel C2' location. The authors then determined X-ray crystallography and cryo-EM structures of the ScLas1-Grc3 and CjLas1-Grc3 complexes, providing structural insight that is complimentary to previously reported Las1-Grc3 structures from C. thermophilum (Pillon et al., 2019, NSMB). The authors further explore the importance of multiple Las1 and Grc3 domains and interaction interfaces for RNA binding, RNA cleavage activity, and Las1-Grc3 complex formation. Finally, evidence is presented that indicates Las1 undergoes a conformational change upon Grc3 binding that stabilizes the Las1 HEPN active site, providing a possible rationale for the stimulation of Las1 cleavage by Grc3.

In the revised manuscript, the authors have made significant efforts towards addressing initial reviewer comments. This includes further clarification for key biochemical experiments, significant improvement in structural model quality, and additional structural analysis that further strengthens major conclusions in the manuscript. Overall, the authors conclusions are now well supported by the biochemical and structural data provided.

Reviewer #2 (Public Review):

Summary:<br /> This manuscript shows evidence from a dataset with awake movie-watching in infants, that the infant brain contains areas with distinct functions, consistent with previous studies using resting state and awake task-based infant fMRI. However, substantial new analyses would be required to support the novel claim that movie-watching data in infants can be used to identify retinotopic areas or to capture within-area functional organization.

Strengths:<br /> The authors have collected a unique dataset: the same individual infants both watched naturalistic animations and a specific retinotopy task. These data position the authors to test their novel claim, that movie-watching data in infants can be used to identify retinotopic areas.

Weaknesses:<br /> To claim that movie-watching data can identify retinotopic regions, the authors should provide evidence for two claims:

- Retinotopic areas defined based only on movie-watching data, predict retinotopic responses in independent retinotopy-task-driven data.

- Defining retinotopic areas based on the infant's own movie-watching response is more accurate than alternative approaches that don't require any movie-watching data, like anatomical parcellations or shared response activation from independent groups of participants.

Both of these analyses are possible, using the (valuable!) data that these authors have collected, but these are not the analyses that the authors have done so far. Instead, the authors report the inverse of (1): regions identified by the retinotopy task can be used to predict responses in the movies. The authors report one part of (2), shared responses from other participants can be used to predict individual infants' responses in the movies, but they do not test whether movie data from the same individual infant can be used to make better predictions of the retinotopy task data, than the shared response maps.

So to be clear, to support the claims of this paper, I recommend that the authors use the retinotopic task responses in each individual infant as the independent "Test" data, and compare the accuracy in predicting those responses, based on:

- The same infant's movie-watching data, analysed with MELODIC, when blind experimenters select components for the SF and meridian boundaries with no access to the ground-truth retinotopy data.<br /> - Anatomical parcellations in the same infant.<br /> - Shared response maps from groups of other infants or adults.<br /> - (If possible, ICA of resting state data, in the same infant, or from independent groups of infants).

Or, possibly, combinations of these techniques.

If the infant's own movie-watching data leads to improved predictions of the infant's retinotopic task-driven response, relative to these existing alternatives that don't require movie-watching data from the same infant, then the authors' main claim will be supported.

The proposed analysis above solves a critical problem with the analyses presented in the current manuscript: the data used to generate maps is identical to the data used to validate those maps. For the task-evoked maps, the same data are used to draw the lines along gradients and then test for gradient organization. For the component maps, the maps are manually selected to show the clearest gradients among many noisy options, and then the same data are tested for gradient organization. This is a double-dipping error. To fix this problem, the data must be split into independent train and test subsets.

Reviewer #2 (Public Review):

In this study, Mao and co-workers deliver a substantial suite of genetic tools in support of the senior author's recent proposal to create a "chemoconnectomic" tool kit for the expression mapping and conditional disruption of specific neurotransmitter systems with fly neurons of interest. Specifically, they describe the creation of two toolsets for recombination-based and CRISPR/Cas9-based conditional knockouts of genes supporting neurotransmitter and neuromodulator function and Flp-Out and Split-LexA toolkit for the examination of gene expression within defined subsets of neurons. The authors report the creation of conditional genetic tools for the disruption/mapping of approximately 200 chemoconnectomic gene products, an examination of the general effectiveness of these tools in the fly brain, and apply them to the circadian clock network in an attempt to reveal new information regarding the transmitter/modulator systems involved in daily behavioral timing. The authors provide clear evidence of the effectiveness of the new methods along with a transparent assessment of the variability of the tools. In addition, they present evidence that the neuro peptide CNMa influences the morning peak of daily activity in the fly by regulating the timing of activity increases in anticipation of dawn.

A major strength of the study is the transparent assessment of the effectiveness and variability of the conditional genetic approaches developed by the authors. The authors have largely achieved their aims and the study therefore represents a major delivery on the promise of chemoconnectomics made by the senior author in 2019 (Neuron, Vol. 101, p. 876). Though there are some concerns about the variability of knockout effectiveness, off-target effects of the knockout strategies, and (especially) the accuracy of the gene expression approach, the tools created for this study will almost certainly be useful for the field and support a great deal of future work.

Reviewer #2 (Public Review):

In "Characterization of caffeine response regulatory variants in vascular endothelial cells", Boye et. al. employ a massively parallel reporter assay, bi-allelic targeted STARR-seq (BiT-STARR-seq), to characterize how non-coding variants affect gene expression in HUVECs after treatment with caffeine. After measuring the differential activity of the individual MPRA constructs in their cells, they test for both allele-specific effects (ASE) in each condition. They likewise test for conditional allele-specific effects (cASE). The authors identify an enrichment cASE variants with stronger allelic effects in caffeine vs control conditions and use a combination of transcription factor motif identification, open chromatin enrichment, caffeine response factor binding site identification, and eQTL fine-mapping to identify 25 SNPs that meet their selection criteria. The authors finally highlight one example SNP from this set, rs22871, as a potential candidate for further analysis.

Reviewer #2 (Public Review):

In this manuscript, Shaku and colleagues investigated if the deletion of the enzymatic pair MurT-GatD from Mycobacterium bovis BCG leads to more effective immune activation and protection against tuberculosis disease. MurT-GatD are enzymes implicated in the amidation of peptidoglycan sidechains, an immune evasion mechanism used by virulent mycobacteria to avoid recognition by the pathogen recognition receptor NOD-1.<br /> Using CRISPRi, the authors show that D-glutamate diaminopimelate (iE-DAP) gets unmasked in BCG when MurT-GatD are deleted. They call the resulting recombinant BCG strain in which the induction of the CRISPRi construct is achieved via anhydrotetracycline, BCG::iE-DAP.<br /> Subsequently, the authors characterize the growth kinetics of the strain and show that MurT-GatD deletion results in cell wall defects (as expected) and increased susceptibility to antibiotics. They use in vitro assays with bone marrow-derived macrophages to show that rBCG::iE-DAP leads to an enhanced 'training effect' of the macrophages and increased killing of subsequent Mtb infection. They go on to show that the growth of the rBCG strain can be inhibited both in vitro and in vivo via the addition of doxycycline. Finally, the authors vaccinate Balb/c mice with wildtype BCG or their rBCG strain, deliver doxycycline via oral gavage, and challenge mice with Mycobacterium tuberculosis 6 weeks later. At 4 and 8 weeks after M. tuberculosis infection the mice get assessed for bacterial burden and histopathology. They show that rBCG::iE-DAP leads to reduced bacterial burden, but increased pathology in the lung compared to parental BCG.

The conclusions of this paper are mostly supported by data, but the in vivo protection results against TB need to be clarified and extended.

Strength:<br /> The authors demonstrate an important new pathway by which to improve immunogenicity of BCG - the unmasking of DAP. This is an exciting finding and could lead to the improvement of multiple existing rBCG strains.<br /> The authors also show a rigorous characterization of the rBCG strain and robust in vitro data, demonstrating the effect of MuRT-GatD deletion on cell wall morphology, antibiotic susceptibility and immune training of macrophages.

Weaknesses:<br /> The in vivo part of the manuscript is much weaker than the in vitro findings, and the in vivo experiments are only performed with 5 mice per group and time-point in one single experiment. Scientific standards require that each experiment is repeated at least once to show reproducibility and robustness. The low number of mice for the in vivo experiments also don't allow for strong statistical power.

Reviewer #2 (Public Review):

This paper demonstrates that model-free reinforcement learning, with relatively small networks, is sufficient to observe collaborative hunting in predator prey environments. The paper then studies the conditions under which collaborative hunting emerges (namely, difficulty of hunting and sharing of the spoils) which is an interesting question to study and the paper contains a fascinating study in which a human is tasked with controlling the prey. However, the simplicity of the environment, a 2-d particle world with simple dynamics, makes it unclear how generalizable the results are and the results rely heavily on visual interpretation of t-SNE plots rather than more direct metrics.

Strengths:<br /> - The distinct behaviors uncovered between the predators in shared vs. not-shared reward are quite interesting!<br /> - The realization that the ability of deep RL models to solve predator-prey problems has implication for models of what is needed for collaborative hunting is clever.

Weaknesses:<br /> - The paper seems to make a claim that since this problem is solvable with model-free learning or a model-free decision tree, complicated cognition is not needed for collaborative hunting. However, the settings under which this hunting is done is exceedingly simple and it is possible that in more complex settings such as more partially observable settings or settings where the capabilities of the partners are unknown then more complicated forms of cognition might still be needed.<br /> - The problem is fully observed (I think), so there may be one uniquely good strategy that the predators can use that will work successfully against all prey. If this is the case, the human studies are of limited value, they are just confirming that the problem has a near-deterministic solution on the part of the predators.

Reviewer #2 (Public Review):

In this interesting work on the neuropharmacological effects of ketamine, the authors conducted a pharmacological functional magnetic resonance imaging (fMRI) study in 40 healthy participants receiving bolus and constant infusion of ketamine during resting-state fMRI. Data were preprocessed with the human connectome-based standard pipeline previously successfully used by the lab (FS parcellation and application of an atlas published by the group, HCP pipeline, FSL, global brain connectivity with and without global-signal regression). Briefly, GBC and principle component maps of the positive and negative syndrome scale (PANSS) were related to somatostatin and parvalbumin cortical gene expression patterns. In addition, the authors compared the effective dimensionality, i.e. eigenvalues of covariance matrices of drug vs. placebo, and found higher complexity of responses in ketamine vs. LSD and psilocybin, which is very interesting. Also, there was substantial inter-individual variation in behavioral and neurobehavioral results, which was captured by PC and GBC maps. In supplementary results, the authors also showed that the principle component PS1 highly correlated with the fMRI global signal.

Although a complex set of analyses is presented, the paper is written very clearly and understandable. The authors did a good job of outlining the steps of their analyses in supplemental diagrams and the source code is provided. As a general remark, I consider the main strength of this work, to acknowledge the very diverse inter-individual variation of ketamine's effects and to use advanced methodological approaches to disentangle these.

Since the drug also exhibits strong variation in clinical antidepressant responses, the methodology applied here will very likely yield interesting results applied in clinical datasets of patients with major depressive disorder.

Reviewer #2 (Public Review):

The authors set out to study the potent HIV capsid inhibitor lenacapavir (LEN) and how it alters capsid stability. They use a previously developed single-molecule fluorescence imaging assay to take two measurements of individual viral particles over time: 1) they track the release of GFP from GFP-loaded particles to determine whether the capsid is intact or open, and 2) they track the disassembly of the capsid lattice by measuring the signal intensity of a capsid binding fluorophore (AF568-CypA), which diminishes as the capsid lattice subunits disassociate.

As in their previous work, the authors report that most of their capsids are "leaky" and rapidly lose GFP after the viral membrane is permeabilized, followed by disassembly of the capsid lattice. A subset of capsids maintain GFP signal for various periods of time until they spontaneously "open," and a smaller subset remains closed for the entire length of the imaging experiment (typically 30 min). Interestingly, the authors find that LEN has two effects in this assay: it not only promotes a more rapid release of GFP (interpreted to mean loss of capsid integrity), but it also prevents the capsid lattice from disassembling after opening. As expected, the cellular cofactor IP6 (which stabilizes capsids in cells and in vitro) was found to protect against capsid rupture and counteracted the effects of LEN (although high concentrations of LEN could override any protective effects of IP6).

Their single-molecule experiments are nicely buttressed by in vitro assembly reactions of purified CA protein, with IP6 promoting cone formation and LEN promoting aberrant assembly into tubes. The authors go further to test the kinetics of LEN's effects on HIV infection and reverse transcription, and they perform experiments in comparison to other factors that target the FG binding pocket (BI-2, PF-74, and a peptide from the host factor CPSF6). They find that LEN works differently than these other capsid binders, and stabilizes the lattice structure much more effectively, which the authors suggest is due to how well LEN bridges between CA-CA monomers and rigidifies CA hexamers.

It's particularly interesting that the results of their kinetic studies indicate that LEN's effects on capsid strain (which may ultimately promote rupture) may not happen immediately, but instead, take time to build as the drug occupies more and more binding sites. The authors estimate that roughly 30% of binding sites need to be occupied by LEN to reach half-maximal inhibition of infection, and based on their binding curves, it may take ~20h to reach this level of occupancy in the presence of sub nM concentrations of LEN. Although other mechanisms in addition to catastrophic rupture of capsids are likely at play during inhibition of infection (such as inhibition of host factor binding), these kinetics support previous reports that the most potent functions of capsid inhibition occur at or between the steps of nuclear entry and integration.

It is important to note that although in vitro uncoating assays can help us understand the physical nature of HIV capsid and capsid inhibitor interactions, the assays in this paper might not accurately model the capsid dynamics that are experienced in a cell during infection. The authors report that more than half of their capsids are "leaky" at the start of their assay, but this could be an artifact of the experimental system. Several groups have now demonstrated that capsids remain intact or largely intact for several hours after infection. Thus, while their method is valuable to the research community and can provide insight into capsid stability (and how it can be influenced by capsid binding factors), the authors should be cautious about using pore-forming proteins to permeabilize the virion and interpreting the release of GFP in their single-molecule fluorescence system as an accurate reflection of HIV dynamics in vivo.

In this regard, it would be helpful to establish whether the pore-forming proteins used in vitro to permeabilize the virus membrane have an impact on capsid integrity. It's possible that the concentration of pore-forming proteins used in this paper (200nM) actually promotes "leaky" capsids and rapid opening of capsids in vitro, whereas capsids in their native state in the cytoplasm could remain mostly intact until disrupted by host factors and/or small molecules. Determining whether lower concentrations of DLY/SLO (or PFO as used in Marquez et al., 2018) change the ratio of leaky to closed capsids, or delay the time to capsid opening (either in the presence of IP6 or in the presence of LEN) would be informative. It may be possible to optimize the concentration of pore-forming proteins (and other buffer constituents) to achieve permeabilization of the membrane with minimal disruption to capsid integrity, which could approximate conditions within the cell.

Experiments with capsid mutations that stabilize or destabilize the lattice structure (and exhibit different sensitivities to IP6) could help support the authors' conclusions, as would testing mutations that confer resistance to LEN (e.g. Q67H+N74D, M66I, etc...). It would be of great interest to find if CA mutations affect either GFP release or the CypA paint signal, and whether resistance mutations mitigate the effects of LEN in single-molecule experiments.

The discussion section of this paper is expertly written and places the work into the larger context of HIV research. The authors have thoughtfully analyzed their experiments with capsid inhibitors in relation to kinetics, occupancy, the potential for rigidification, and cofactor binding. They offer reasonable explanations for how LEN exhibits opposing effects on the HIV capsid at high occupancy through inducing capsid rupture while simultaneously preventing the dissociation of CA subunits. Many lines of evidence are now converging on the concept that the capsid evolved to be stable enough to protect its contents, yet flexible enough to navigate the steps of reverse transcription, nuclear entry, and uncoating. With this paper, the authors make a strong case that LEN functions as an antiviral, at least in part, through engaging "lethal hyperstabilization" of the capsid, promoting rigid lattice formations that are incompatible with closed cone structures.

Reviewer #2 (Public Review):

The core planar cell polarity (PCP) pathways are known to control tissue morphogenesis in vertebrates and also in a number of developing tissues in the fruitfly Drosophila. However, it has long been observed that beyond effects on hair polarity, core PCP activity does not have dramatic effects on Drosophila wing morphogenesis. Here the authors carry out detailed quantitative studies of cell behaviors in flies mutant for core PCP genes during pupal wing morphogenesis between about 16 to 32 hours of pupal life to further try to determine if core PCP activity affects cell behaviors in the wing.

Their overall conclusion is that there is no effect on tissue morphogenesis. However, the number of wings looked at for each genotype is low due to the enormous amount of work required to analyze the cell behaviors on an entire wing surface over 16 hours of development. Thus, rigorous statistics cannot be applied to support the statement that there is no change in morphogenesis. Moreover, by eye, the average cell behaviors do appear different and the authors themselves say there are subtle differences. They also note that adult wings have a change in size. Also, a previous publication suggested a change in cell arrangements at the late stages of the period studied (Sugimura & Ishihara 2013).

Interestingly, the authors do report a change in local mechanical properties of the tissue in flies with altered core PCP pathway activity, by using laser ablation to study tissue rheology. This seems to support the view that there could be a subtle change in tissue morphogenesis.

Ultimately, this is a valuable set of results that help to clarify core PCP pathway function in Drosophila tissues. It clearly demonstrates effects on tissue mechanics, but also indicates that this does not result in gross changes in tissue morphogenesis - the latter being consistent with previous observations.

DOI: 10.1016/j.neuron.2023.11.008

Resource: ZFIN_ZDB-ALT-200915-2

Curator: @evieth

SciCrunch record: RRID:ZFIN_ZDB-ALT-200915-2

What is this?

Reviewer #2 (Public Review):

In the present study, Liu et al present an analysis of benign and HCC liver samples which were subjected to a new technology (LOOP-Seq) and paired WES. By integrating these data, the authors find isoforms, fusions and mutations which uniquely cluster within HCC samples, such as in the HLA locus, which serve as candidate leads for further investigation. The main appeal of the study is in the potential of LOOP-Seq as a method to present isoform-resolved data without actually performing long-read sequencing.

Comments on revised version:

I made several comments on the previous version which have been adequately addressed.

Reviewer #2 (Public Review):

This is a very interesting paper with several important findings related to the working mechanism of the cartwheel cells (CWC) in the dorsal cochlear nucleus (DCN). These cells generate spontaneous firing that is inhibited by the activation of α2-adrenergic receptors, which also enhances the synaptic strength in the cells, but the mechanisms underlying the spontaneous firing and the dual regulation by α2-adrenergic receptor activation have remained elusive. By recording these cells with the NALCN sodium-leak channel conditionally knocked, the authors discovered that both the spontaneous firing and the regulation by noradrenaline (NA) require NALCN. Mechanistically, the authors found that activation of the adrenergic receptor or GABAB receptor inhibits NALCN. Interestingly, these receptor activations also suppress the low [Ca2+] "activation" of NALCN currents, suggesting crosstalk between the pathways. The finding of such dominant contribution of the NALCN conductance to the regulation of firing by NA is somewhat surprising considering that NA is known to regulate K+ conductances in many other neurons.

The studies reveal the molecular mechanisms underlying well known regulations of the neuronal processes in the auditory pathway. The results will be important to the understanding of auditory information processing in particular, and, more generally, to the understanding of the regulation of inhibitory neurons and ion channels. The results are convincing and are clearly presented.

In this revision, the authors have satisfactorily addressed all my previous comments.

Reviewer #2 (Public Review):

Summary:<br /> This manuscript explores infants' attention patterns in real-world settings and their relationship with autonomic arousal and EEG oscillations in the theta frequency band. The study included 5- and 10-month-old infants during free play. The results showed that the 5-month-old group exhibited a decline in HR forward-predicted attentional behaviors, while the 10-month-old group exhibited increased theta power following shifts in gaze, indicating the start of a new attention episode. Additionally, this increase in theta power predicted the duration of infants' looking behavior.

Strengths:<br /> The study's strengths lie in its utilization of advanced protocols and cutting-edge techniques to assess infants' neural activity and autonomic arousal associated with their attention patterns, as well as the extensive data coding and processing. Overall, the findings have important theoretical implications for the development of infant attention.

Weaknesses:<br /> Certain methodological procedures require further clarification, e.g., details on EEG data processing. Additionally, it would be beneficial to eliminate possible confounding factors and consider alternative interpretations, e,g., whether the differences observed between the two age groups were partly due to varying levels of general arousal and engagement during the free play.

Reviewer #2 (Public Review):

In this paper, Portillo-Ledesma et al. study chromatin organization in the length scale of a gene, simulating the polymer at nucleosome resolution. The authors have presented an extensive simulation study with an excellent model of chromatin. The model has linker DNA and nucleosomes with all relevant interactions (electrostatics, tails, etc). Authors simulate 10 to 26 kb chromatin with varying linker lengths, linker histones (LH), and acetylated tails. The authors then study the effect of a transcription factor (TF) Myc: Max binding. The critical physical feature of the TF in the model is that it binds to the linker region and bends the DNA to make loops/intra-chromatin contacts. Authors systematically investigate the interplay between different variables such as linker DNA length, LH density, and the TF concentration in determining chromatin compaction and 3D organization.

The manuscript is well-written and is a relevant study with many useful results. The biggest strength of the work is the fact that the authors start with a relevant model that incorporates well-known biophysical properties of DNA, nucleosomes, linker histones, and the transcription factor Myc:Max. One of the novel results is the demonstration of how linker lengths play an important role in chromatin compaction (measured by computing packing ratio) in the presence of DNA-bending TFs. As the TF concentration increases, chromatin with short linker lengths does not compact much (only a small change in packing ratio). If the linker lengths are long, a higher percentage of TFs leads to an increase in packing ratio (higher compaction). Authors further show that TFs are able to compact Life-like chromatin fiber with linker length taken from a realistic distribution. The authors compute inter-nucleosomal contact maps from their simulated configurations and show that the map has features similar to what is observed in Hi-C/Micro-C experiments. Authors study the compaction of the Eed gene locus and show that TF binding leads to the formation of small domains known as micro-domains. Authors have predicted many relevant and testable quantities. Many of the results agree with known experiments like the formation of the micro-domains. Hence, the conclusions made in this study are justified - they follow from the simulation results.

Reviewer #2 (Public Review):

Summary:<br /> In this paper, the authors explore the role of the Homeodomain Transcription Factor Bsh in the specification of Lamina neuronal types in the optic lobe of Drosophila. Using the framework of terminal selector genes and compelling data, they investigate whether the same factor that establishes early cell identity is responsible for the acquisition of terminal features of the neuron (i.e., cell connectivity and synaptogenesis).

The authors convincingly describe the sequential expression and activity of Bsh, termed here as 'primary HDTF', and of Ap in L4 or Pdm3 in L5 as 'secondary HDTFs' during the specification of these two neurons. The study demonstrates the requirement of Bsh to activate either Ap and Pdm3, and therefore to generate the L4 and L5 fates. Moreover, the authors show that in the absence of Bsh, L4 and L5 fates are transformed into a L1 or L3-like fates.

Finally, the authors used DamID and Bsh:DamID to profile the open chromatin signature and the Bsh binding sites in L4 neurons at the synaptogenesis stage. This allows the identification of putative Bsh target genes in L4, many of which were also found to be upregulated in L4 in a previous single-cell transcriptomic analysis. Among these genes, the paper focuses on Dip-β, a known regulator of L4 connectivity. They demonstrate that both Bsh and Ap are required for Dip-β, forming a feed-forward loop. Indeed, the loss of Bsh causes abnormal L4 synaptogenesis and therefore defects in several visual behaviors.

The authors also propose the intriguing hypothesis that the expression of Bsh expanded the diversity of Lamina neurons from a 3 cell-type state to the current 5 cell-type state in the optic lobe.

Strengths:<br /> Overall, this work presents a beautiful practical example of the framework of terminal selectors: Bsh acts hierarchically with Ap or Pdm3 to establish the L4 or L5 cell fates and, at least in L4, participates in the expression of terminal features of the neuron (i.e., synaptogenesis through Dip-β regulation).

The hierarchical interactions among Bsh and the activation of Ap and Pdm3 expression in L4 and L5, respectively, are well established experimentally. Using different genetic drivers, the authors show a window of competence during L4 neuron specification during which Bsh activates Ap expression. Later, as the neuron matures, Ap becomes independent of Bsh. This allows the authors to propose a coherent and well-supported model in which Bsh acts as a 'primary' selector that activates the expression of L4-specific (Ap) and L5-specific (Pdm3) 'secondary' selector genes, that together establish neuronal fate.

Importantly, the authors describe a striking cell fate change when Bsh is knocked down from L4/L5 progenitor cells. In such case, L1 and L3 neurons are generated at the expense of L4 and L5. The paper demonstrates that Bsh in L4/L5 represses Zfh1, which in turn acts as the primary selector for L1/L3 fates. These results point to a model where the acquisition of Bsh during evolution might have provided the grounds for the generation of new cell types, L4 and L5, expanding lamina neuronal diversity for a more refined visual behaviors in flies. This is an intriguing and novel hypothesis that should be tested from an evo-devo standpoint, for instance by identifying a species when L4 and L5 do not exist and/or Bsh is not expressed in L neurons.

To gain insight into how Bsh regulates neuronal fate and terminal features, the authors have profiled the open chromatin landscape and Bsh binding sites in L4 neurons at mid-pupation using the DamID technique. The paper describes a number of genes that have Bsh binding peaks in their regulatory regions and that are differentially expressed in L4 neurons, based on available scRNAseq data. Although the manuscript does not explore this candidate list in depth, many of these genes belong to classes that might explain terminal features of L4 neurons, such as neurotransmitter identity, neuropeptides or cytoskeletal regulators. Interestingly, one of these upregulated genes with a Bsh peak is Dip-β, an immunoglobulin superfamily protein that has been described by previous work from the author's lab to be relevant to establish L4 proper connectivity. This work proves that Bsh and Ap work in a feed-forward loop to regulate Dip-β expression, and therefore to establish normal L4 synapses. Furthermore, Bsh loss of function in L4 causes impairs visual behaviors.

Weaknesses:<br /> ● The last paragraph of the introduction is written using rhetorical questions and does not read well. I suggest rewriting it in a more conventional direct style to improve readability.

● A significant concern is the way in which information is conveyed in the Figures. Throughout the paper, understanding of the experimental results is hindered by the lack of information in the Figure headers. Specifically, the genetic driver used for each panel should be adequately noted, together with the age of the brain and the experimental condition. For example, R27G05-Gal4 drives early expression in LPCs and L4/L5, while the 31C06-AD, 34G07-DBD Split-Gal4 combination drives expression in older L4 neurons, and the use of one or the other to drive Bsh-KD has dramatic differences in Ap expression. The indication of the driver used in each panel will facilitate the reader's grasp of the experimental results.

● Bsh role in L4/L5 cell fate:<br /> o It is not clear whether Tll+/Bsh+ LPCs are the precursors of L4/L5. Morphologically, these cells sit very close to L5, but are much more distant from L4.<br /> o Somatic CRISPR knockout of Bsh seems to have a weaker phenotype than the knockdown using RNAi. However, in several experiments down the line, the authors use CRISPR-KO rather than RNAi to knock down Bsh activity: it should be explained why the authors made this decision. Alternatively, a null mutant could be used to consolidate the loss of function phenotype, although this is not strictly necessary given that the RNAi is highly efficient and almost completely abolishes Bsh protein.<br /> o Line 102: Rephrase "R27G05-Gal4 is expressed in all LPCs and turned off in lamina neurons" to "is turned off as lamina neurons mature", as it is kept on for a significant amount of time after the neurons have already been specified.<br /> o Line 121: "(a) that all known lamina neuron markers become independent of Bsh regulation in neurons" is not an accurate statement, as the markers tested were not shown to be dependent on Bsh in the first place.<br /> o Lines 129-134: Make explicit that the LPC-Gal4 was used in this experiment. This is especially important here, as these results are opposite to the Bsh Loss of Function in L4 neurons described in the previous section. This will help clarify the window of competence in which Bsh establishes L4/L5 neuronal identities through ap/pdm3 expression.

● DamID and Bsh binding profile:<br /> ○ Figure 5 - figure supplement 1C-E: The genotype of the Control in (C) has to be described within the panel. As it is, it can be confused with a wild type brain, when it is in fact a Bsh-KO mutant.<br /> ○ It Is not clear how L4-specific Differentially Expressed Genes were found. Are these genes DEG between Lamina neurons types, or are they upregulated genes with respect to all neuronal clusters? If the latter is the case, it could explain the discrepancy between scRNAseq DEGs and Bsh peaks in L4 neurons.

● Dip-β regulation:<br /> ○ Line 234: It is not clear why CRISPR KO is used in this case, when Bsh-RNAi presents a stronger phenotype.<br /> ○ Figure 6N-R shows results using LPC-Gal4. It is not clear why this driver was used, as it makes a less accurate comparison with the other panels in the figure, which use L4-Split-Gal4. This discrepancy should be acknowledged and explained, or the experiment repeated with L4-Split-Gal4>Ap-RNAi.<br /> ○ Line 271: It is also possible that L4 activity is dispensable for motion detection and only L5 is required.

● Discussion: It is necessary to de-emphasize the relevance of HDTFs, or at least acknowledge that other, non-homeodomain TFs, can act as selector genes to determine neuronal identity. By restricting the discussion to HDTFs, it is not mentioned that other classes of TFs could follow the same Primary-Secondary selector activation logic.

Reviewer #2 (Public Review):

Summary:

In this work, the authors explore how Notch activity acts together with Bsh homeodomain transcription factors to establish L4 and L5 fates in the lamina of the visual system of Drosophila. They propose a model in which differential Notch activity generates different chromatin landscapes in presumptive L4 and L5, allowing the differential binding of the primary homeodomain TF Bsh (as described in the co-submitted paper), which in turn activate downstream genes specific to either neuronal type. The requirement of Notch for L4 vs. L5 fate is well supported, and complete transformation from one cell type into the other is observed when altering Notch activity. However, the role of Notch in creating differential chromatin landscapes is not directly demonstrated. It is only based on correlation, but it remains a plausible and intriguing hypothesis.

Strengths:<br /> The authors are successful in characterizing the role of Notch to distinguish between L4 and L5 cell fates. They show that the Notch pathway is active in L4 but not in L5. They identify L1, the neuron adjacent to L4 as expressing the Delta ligand, therefore being the potential source for Notch activation in L4. Moreover, the manuscript shows molecular and morphological/connectivity transformations from one cell type into the other when Notch activity is manipulated.

Using DamID, the authors characterize the chromatin landscape of L4 and L5 neurons. They show that Bsh occupies distinct loci in each cell type. This support their model that Bsh acts as a primary selector gene in L4/L5 that activates different target genes in L4 vs L5 based on the differential availability of open chromatin loci.

Overall, the manuscript presents an interesting example of how Notch activity cooperates with TF expression to generate diverging cell fates. Together with the accompanying paper, it helps thoroughly describe how lamina cell types L4 and L5 are specified and provides an interesting hypothesis for the role of Notch and Bsh in increasing neuronal diversity in the lamina during evolution.

Weaknesses:<br /> Differential Notch activity in L4 and L5:<br /> ● The manuscript focuses its attention on describing Notch activity in L4 vs L5 neurons. However, from the data presented, it is very likely that the pool of progenitors (LPCs) is already subdivided into at least two types of progenitors that will rise to L4 and L5, respectively. Evidence to support this is the activity of E(spl)-mɣ-GFP and the Dl puncta observed in the LPC region. Discussion should naturally follow that Notch-induced differences in L4/L5 might preexist L1-expressed Dl that affect newborn L4/L5. Therefore, the differences between L4 and L5 fates might be established earlier than discussed in the paper. The authors should acknowledge this possibility and discuss it in their model.<br /> ● The authors claim that Notch activation is caused by L1-expressed Delta. However, they use an LPC driver to knock down Dl. Dl-KD should be performed exclusively in L1, and the fate of L4 should be assessed.<br /> ● To test whether L4 neurons are derived from NotchON LPCs, I suggest performing MARCM clones in early pupa with an E(spl)-mɣ-GFP reporter.<br /> ● The expression of different Notch targets in LPCs and L4 neurons may be further explored. I suggest using different Notch-activity reporters (i.e., E(spl)-GFP reporters) to further characterize these differences. What cause the switch in Notch target expression from LPCs to L4 neurons should be a topic of discussion.

Notch role in establishing L4 vs L5 fates:<br /> ● The authors describe that 27G05-Gal4 causes a partial Notch Gain of Function caused by its genomic location between Notch target genes. However, this is not further elaborated. The use of this driver is especially problematic when performing Notch KD, as many of the resulting neurons express Ap, and therefore have some features of L4 neurons. Therefore, Pdm3+/Ap+ cells should always be counted as intermediate L4/L5 fate (i.e., Fig3 E-J, Fig3-Sup2), irrespective of what the mechanistic explanation for Ap activation might be. It's not accurate to assume their L5 identity. In Fig4 intermediate-fate cells are correctly counted as such.<br /> ● Lines 170-173: The temporal requirement for Notch activity in L5-to-L4 transformation is not clearly delineated. In Fig4-figure supplement 1D-E, it is not stated if the shift to 29{degree sign}C is performed as in Fig4-figure supplement 1A-C.<br /> ● Additionally, using the same approach, it would be interesting to explore the window of competence for Notch-induced L5-to-L4 transformation: at which point in L5 maturation can fate no longer be changed by Notch GoF?

L4-to-L3 conversion in the absence of Bsh<br /> ● Although interesting, the L4-to-L3 conversion in the absence of Bsh is never shown to be dependent on Notch activity. Importantly, L3 NotchON status is assumed based on their position next to Dl-expressing L1, but it is not empirically tested. Perhaps screening Notch target reporter expression in the lamina, as suggested above, could inform this issue.<br /> ● Otherwise, the analysis of Bsh Loss of Function in L4 might be better suited to be included in the accompanying manuscript that specifically deals with the role of Bsh as a selector gene for L4 and L5.

Different chromatin landscape in L4 and L5 neurons<br /> ● A major concern is that, although L4 and L5 neurons are shown to present different chromatin landscapes (as expected for different neuronal types), it is not demonstrated that this is caused by Notch activity. The paper proves unambiguously that Notch activity, in concert with Bsh, causes the fate choice between L4 and L5. However, that this is caused by Notch creating a differential chromatin landscape is based only in correlation (NotchON cells having a different profile than NotchOFF). Although the authors are careful not to claim that differential chromatin opening is caused directly by Notch, this is heavily suggested throughout the text and must be toned down.<br /> e.g.: Line 294: "With Notch signaling, L4 neurons generate distinct open chromatin landscape" and Line 298: "Our findings propose a model that the unique combination of HDTF and open chromatin landscape (e.g. by Notch signaling)" . These claims are not supported well enough, and alternative hypotheses should be provided in the discussion. An alternative hypothesis could be that LPCs are already specified towards L4 and L5 fates. In this context, different early Bsh targets in each cell type could play a pioneer role generating a differential chromatin landscape.

● The correlation between open chromatin and Bsh loci with Differentially Expressed genes is much higher for L4 than L5. It is not clear why this is the case, and should be discussed further by the authors.

Reviewer #2 (Public Review):

This study developed a setup for laminar fMRI at 3T that aimed to get the best from all worlds in terms of brain coverage, temporal resolution, sensitivity to detect functional responses, and spatial specificity. They used a gradient-echo EPI readout to facilitate sensitivity, brain coverage and temporal resolution. The former was additionally boosted by NORDIC denoising and the latter two were further supported by parallel-imaging acceleration both in-plane and across slices. The authors evaluated whether the implementation of velocity-nulling (VN) gradients could mitigate macrovascular bias, known to hamper the laminar specificity of gradient-echo BOLD.

The setup allows for 0.9 mm isotropic acquisitions with large coverage at a reasonable TR (at least for block designs) and the fMRI results presented here were acquired within practical scan-times of 12-18 minutes. Also, in terms of the availability of the method, it is favorable that it benefits from lower field strength (additional time for VN-gradient implementation, afforded by longer gray matter T2*).

The well-known double peak feature in M1 during finger tapping was used as a test-bed to evaluate the spatial specificity. They were indeed able to demonstrate two distinct peaks in group-level laminar profiles extracted from M1 during finger tapping, which was largely free from superficial bias. This is rather intriguing as, even at 7T, clear peaks are usually only seen with spatially specific non-BOLD sequences. This is in line with their simple simulations, which nicely illustrated that, in theory, intravascular macrovascular signals should be suppressible with only minimal suppression of microvasculature when small b-values of the VN gradients are employed. However, the authors do not state how ROIs were defined making the validity of this finding unclear; were they defined from independent criteria or were they selected based on the region mostly expressing the double peak, which would clearly be circular? In any case, results are based on a very small sub-region of M1 in a single slice - it would be useful to see the generalizability of superficial-bias-free BOLD responses across a larger portion of M1.

As repeatedly mentioned by the authors, a laminar fMRI setup must demonstrate adequate functional sensitivity to detect (in this case) BOLD responses. The sensitivity evaluation is unfortunately quite weak. It is mainly based on the argument that significant activation was found in a challenging sub-cortical region (LGN). However, it was a single participant, the activation map was not very convincing, and the demonstration of significant activation after considerable voxel-averaging is inadequate evidence to claim sufficient BOLD sensitivity. How well sensitivity is retained in the presence of VN gradients, high acceleration factors, etc., is therefore unclear. The ability of the setup to obtain meaningful functional connectivity results is reassuring, yet, more elaborate comparison with e.g., the conventional BOLD setup (no VN gradients) is warranted, for example by comparison of tSNR, quantification and comparison of CNR, illustration of unmasked-full-slice activation maps to compare noise-levels, comparison of the across-trial variance in each subject, etc. Furthermore, as NORDIC appears to be a cornerstone to enable submillimeter resolution in this setup at 3T, it is critical to evaluate its impact on the data through comparison with non-denoised data, which is currently lacking.

The proposed setup might potentially be valuable to the field, which is continuously searching for techniques to achieve laminar specificity in gradient echo EPI acquisitions. Nonetheless, the above considerations need to be tackled to make a convincing case.

Reviewer #2 (Public Review):

Summary<br /> Song et al investigate the role of the frontal eye field (FEF) and the intraparietal sulcus (IPS) in mediating the shift in ocular dominance (OD) observed after a period of dichoptic stimulation during which attention is selectively directed to one eye. This manipulation has been previously found to transiently shift OD in favor of the unattended eye, similar to the effect of short-term monocular deprivation. To this aim, the authors combine psychophysics, fMRI, and transcranial magnetic stimulation (TMS). In the first experiment, the authors determine the regions of interest (ROIs) based on the responses recorded by fMRI during either dichoptic or binocular stimulation, showing selective recruitment of the right FEF and IPS during the dichoptic condition, in line with the involvement of eye-based attention. In a second experiment, the authors investigate the causal role of these two ROIs in mediating the OD shift observed after a period of dichoptic stimulation by selectively inhibiting with TMS (using continuous theta burst stimulation, cTBS), before the adaptation period (50 min exposure to dichoptic stimulation). They show that, when cTBS is delivered on the FEF, but not the IPS or the vertex, the shift in OD induced by dichoptic stimulation is reduced, indicating a causal involvement of the FEF in mediating this form of short-term plasticity. A third control experiment rules out the possibility that TMS interferes with the OD task (binocular rivalry), rather than with the plasticity mechanisms. From this evidence, the authors conclude that the FEF is one of the areas mediating the OD shift induced by eye-selective attention.

Strengths<br /> 1. The experimental paradigm is sound and the authors have thoroughly investigated the neural correlates of an interesting form of short-term visual plasticity combining different techniques in an intelligent way.

2. The results are solid and the appropriate controls have been performed to exclude potential confounds.

3. The results are very interesting, providing new evidence both about the neural correlates of eye-based attention and the involvement of extra-striate areas in mediating short-term OD plasticity in humans, with potential relevance for clinical applications (especially in the field of amblyopia).

Weaknesses<br /> 1. Ethics: more details about the ethics need to be included in the manuscript. It is only mentioned for experiment 1 that participants "provided informed consent in accordance with the Declaration of Helsinki. This study was approved by the Institutional Review Board of the Institute of Psychology, Chinese Academy of Sciences". (Which version of the Declaration of Helsinki? The latest version requires the pre-registration of the study. The code of the approved protocol together with the code and date of the approval should be provided.) There is no mention of informed consent procedures or ethics approval for the TMS experiments. This is a huge concern, especially for brain stimulation experiments!

2. Statistics: the methods section should include a sub-section describing in detail all the statistical analyses performed for the study. Moreover, in the results section, statistical details should be added to support the fMRI results. In the current version of the manuscript, the claims are not supported by statistical evidence.

3. Interpretation of the results: the TMS results are very interesting and convincing regarding the involvement of the FEF in the build-up of the OD shift induced by dichoptic stimulation, however, I am not sure that the authors can claim that this effect is related to eye-based attention, as cTBS has no effect on the blob detection task during dichoptic stimulation. If the FEF were causally involved in eye-based attention, one would expect a change in performance in this task during dichoptic stimulation, perhaps a similar performance for the unattended and attended eye. The authors speculate that the sound could have an additional role in driving eye-based attention, which might explain the lack of effect for the blob discrimination task, however, this hypothesis has not been tested.

4. Writing: in general, the manuscript is well written, but clarity should be improved in certain sections.

a. fMRI results: the first sentence is difficult to understand at first read, but it is crucial to understand the results, please reformulate and clarify.

b. Experiment 3: the rationale for experiment one should be straightforward, without a long premise explaining why it would not be necessary.

c. Discussion: the language is a bit familiar here and there, a more straightforward style should be preferred (one example: p.19 second paragraph).

5. Minor: the authors might consider using the term "participant" or "observer" instead of "subject" when referring to the volunteers who participated in the study.

Reviewer #2 (Public Review):

Summary:<br /> This study by Tünte et al. investigated the development of interoceptive sensitivity in the first year of life, focusing specifically on cardiac and respiratory sensitivity in infants aged 3, 9, and 18 months. The research employed a previously developed experimental paradigm in the cardiac domain and adapted it for a novel paradigm in the respiratory domain. This approach assessed infants' cardiac and respiratory sensitivity based on their preferential-looking behavior toward visuo-auditory stimuli displayed on a monitor, which moved either in sync or out of sync with the infants' own heartbeats or breathing. The results for the cardiac domain showed that infants, across all age groups, preferred stimuli moving synchronously rather than asynchronously with their heartbeat, suggesting the presence of cardiac sensitivity as early as 3 months of age. However, it is noteworthy that the direction of this preference contradicts a previous study, which found that 5-month-old infants looked longer at stimuli moving asynchronously, rather than synchronously, with their heartbeat (Maister et al., 2017). In the respiratory domain, only the younger age group(s) of infants showed a preference for stimuli presented synchronously with their breathing, unlike the 18-month-olds. The authors conducted various statistical analyses to thoroughly examine the obtained data, an effort that provides deeper insights and is valuable for future research in this field.

Strengths:<br /> Few studies have explored the early development of interoception, making the replication of the original study by Maister et al. (2017) particularly valuable. Beyond replication, this study expands the investigation into the respiratory domain, significantly enhancing our understanding of interoceptive development. The provision of longitudinal and cross-sectional data from infants at 3, 9, and 18 months of age is instrumental in understanding their developmental trajectory.

Weaknesses:<br /> (1) My primary concern is that this study did not counterbalance the conditions of the first trial in both iBEAT and iBREATH tests for the 9-month and 18-month age groups. In these tests, the first trial invariably involved a synchronous stimulus. I believe that the order of trials can significantly influence an infant's looking duration, and this oversight could potentially impact the results, especially where a marked preference for synchronous stimuli was observed among infants.<br /> (2) The analysis indicated that the study's sample size was too small to effectively assess the effects within each age group. This limitation fundamentally undermines the reliability of the findings.<br /> (3) The authors attribute the infants' preferential-looking behavior solely to the effects of familiarity and novelty. However, the meaning of "familiarity" in relation to external stimuli moving in sync with an infant's heartbeat or breathing is not clearly defined. A deeper exploration of the underlying mechanisms driving this behavior, such as from the perspectives of attention and perception, is necessary.

Reviewer #2 (Public Review):

In this manuscript, Wang and colleagues analyze the shapes of cerebral cortices from several primate species, including subgroups of young and old humans, to characterize commonalities in patterns of gyrification, cortical thickness, and cortical surface area. The work builds on the scaling law introduced previously by co-author Mota, and Herculano-Houzel. The authors state that the observed scaling law shares properties with fractals, where shape properties are similar across several spatial scales. One way the authors assess this is to perform a "cortical melting" operation that they have devised on surface models obtained from several primate species. The authors also explore differences in shape properties between the brains of young (~20 year old) and old (~80) humans. My main criticism of this manuscript is that the findings are presented in too abstract a manner for the scientific contribution to be recognized.

1. The series of operations to coarse-grain the cortex illustrated in Figure 1, constitute a novel procedure, but it is not strongly motivated, and it produces image segmentations that do not resemble real brains. The process to assign voxels in downsampled images to cortex and white matter is biased towards the former, as only 4 corners of a given voxel are needed to intersect the original pial surface, but all 8 corners are needed to be assigned a white matter voxel (section S2). This causes the cortical segmentation, such as the bottom row of Figure 1B, to increase in thickness with successive melting steps, to unrealistic values. For the rightmost figure panel, the cortex consists of several 4.9-sided voxels and thus a >2 cm thick cortex. A structure with these morphological properties is not consistent with the anatomical organization of a typical mammalian neocortex.

2. For the comparison between 20-year-old and 80-year-old brains, a well-documented difference is that the older age group possesses more cerebral spinal fluid due to tissue atrophy, and the distances between the walls of gyri becomes greater. This difference is born out in the left column of Figure 4c. It seems this additional spacing between gyri in 80-year-olds requires more extensive down-sampling (larger scale values in Figure 4a) to achieve a similar shape parameter K as for the 20-year-olds. A case could be made that the familiar way of describing brain tissue - cortical volume, white matter volume, thickness, etc. - is a more direct and intuitive way to describe differences between young and old adult brains than the obscure shape metric described in this manuscript. At a minimum, a demonstration of an advantage of the Figure 4a and 4b analyses over current methods for interpreting age-related differences would be valuable.

3. In Discussion lines 199-203, it is stated that self-similarity, operating on all length scales, should be used as a test for existing and future models of gyrification mechanisms. First, the authors do not show, (and it would be surprising if it were true) that self-similarity is observed for length scales smaller than the acquired MRI data for any of the datasets analyzed. The analysis is restricted to coarse (but not fine)-graining. Therefore, self-similarity on all length scales would seem to be too strong a constraint. Second, it is hard to imagine how this test could be used in practice. Specific examples of how gyrification mechanisms support or fail to support the generation of self-similarity across any length scale, would strengthen the authors' argument.

Some additional, specific comments are as follows:

4. The definition of the term A_e as the "exposed surface" was difficult to follow at first. It might be helpful to state that this parameter is operationally defined as the convex hull surface area. Also, for the pial surface, A_t, there are several who advocate instead for the analysis of a cortical mid-thickness surface area, as the pial surface area is subject to bias depending on the gyrification index and the shape of the gyri. It would be helpful to understand if the same results are obtained from mid-thickness surfaces.

5. In Figure 2c, the surfaces get smaller as the coarse-graining increases, making it impossible to visually assess the effects of coarse-graining on the shapes. Why aren't all cortical models shown at the same scale?

6. Text in Section 3.2 emphasizes that K is invariant with scale (horizontal lines in Figure 3), and asserts this is important for the formation of all cortices. However, I might be mistaken, but it appears that K varies with scale in Figure 4a, and the text indicates that differences in the S dependence are of importance for distinguishing young vs. old brains. Is this an inconsistency?

Reviewer #2 (Public Review):

Summary:<br /> Yan, Hu, and colleagues introduce BADGERS, a new method for biobank-wide scanning to find associations between a phenotype of interest, and the genetic component of a battery of candidate phenotypes. Briefly, BADGERS capitalizes on publicly available weights of genetic variants for a myriad of traits to estimate polygenic risk scores for each trait, and then identify associations with the trait of interest. Of note, the method works using summary statistics for the trait of interest, which is especially beneficial for running in population-based cohorts that are not enriched for any particular phenotype (ie. with few actual cases of the phenotype of interest).

Here, they apply BADGERS on Alzheimer's disease (AD) as the trait of interest, and a battery of circa 2,000 phenotypes with publicly available precalculated genome-wide summary statistics from the UK Biobank. They run it on two AD cohorts, to discover at least 14 significant associations between AD and traits. These include expected associations with dementia, cognition (educational attainment), and socioeconomic status-related phenotypes. Through multivariate modelling, they distinguish between (1) clearly independent components associated with AD, from (2) by-product associations that are inflated in the original bivariate analysis. Analyses stratified according to APOE inclusion show that this region does not seem to play a role in the association of some of the identified phenotypes. Of note, they observe overlap but significant differences in the associations identified with BADGERS and other Mendelian randomization (MR), hinting at BADGERS being more powerful than classical top variant-based MR approaches. They then extend BADGERS to other AD-related phenotypes, which serves to refine the hypotheses about the underlying mechanisms accounting for the genetic correlation patterns originally identified for AD. Finally, they run BADGERS on a pre-clinical cohort with mild cognitive impairment. They observe important differences in the association patterns, suggesting that this preclinical phenotype (at least in this cohort) has a different genetic architecture than general AD.

Strengths:<br /> BADGERS is an interesting new addition to a stream of attempts to "squeeze" biobank data beyond pure association studies for diagnosis. Increasingly available biobank cohorts do not usually focus on specific diseases. However, they tend to be data-rich, opening for deep explorations that can be useful to refine our knowledge of the latent factors that lead to diagnosis. Indeed, the possibility of running genetic correlation studies in specific sub-settings of interest (e.g. preclinical cohorts) is arguably the most interesting aspect of BADGERS. Classical methods like LDSC or two-sample MR capitalize on publicly available summary statistics from large cohorts, or having access to individual genotype data of large cohorts to ensure statistical power. Seemingly, BADGERS provides a balanced opportunity to dissect the correlation between traits of interest in settings with small sample size in which other methods do not work well.

Weaknesses:<br /> However, the increased statistical power is just hinted, and for instance, they do not explore if LDSC would have identified these associations. Although I suspect that is the case, this evidence is important to ensure that the abovementioned balance is right. Finally, as discussed by the authors, the reliance on polygenic risk scoring necessarily undermines the causality evidence gained through BADGERS. In this sense, BADGERS provides an alternative to strict instrumental-variable based analysis, which can be particularly useful to generate new mechanistic hypotheses.

In summary, after 15 years of focus on diagnosis that would require having individual access to large patient cohorts, BADGERS can become an excellent tool to dig into trait heterogeneity, especially if it turns out to be more powerful than other available methodologies.

Reviewer #2 (Public Review):

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

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

Weaknesses:<br /> The paper contains multiple instances of non-scientific language, as indicated below. It would also benefit from additional details on the cryo-EM structure determination in the Methods and inclusion of commonly accepted requirements for cryo-EM structures, like examples of 2D class averages, raw micrographs, and FSC curves (between half-maps as well as between rigid-body fitted (or refined) atomic models of the different polymorphs and their corresponding maps). In addition, cryo-EM maps for the control experiments F1 and F2 should be presented in Figure 9.

Reviewer #2 (Public Review):

In this study, Ninagawa et al., shed light on UGGT's role in ER quality control of glycoproteins. By utilizing UGGT1/UGGT2 DKO cells, they demonstrate that several model misfolded glycoproteins undergo early degradation. One such substrate is ATF6alpha where its premature degradation hampers the cell's ability to mount an ER stress response.

While this study convincingly demonstrates early degradation of misfolded glycoproteins in the absence of UGGTs, my major concern is the need for additional experiments to support the "tug of war" model involving UGGTs and EDEMs in influencing the substrate's fate - whether misfolded glycoproteins are pulled into the folding or degradation route. Specifically, it would be valuable to investigate how overexpression of UGGTs and EDEMs in WT cells affects the choice between folding and degradation for misfolded glycoproteins. Considering previous studies indicating that monoglucosylation influences glycoprotein solubility and stability, an essential question is: what is the nature of glycoproteins in UGGTKO/EDEMKO and potentially UGGT/EDEM overexpression cells? Understanding whether these substrates become more soluble/stable when GM9 versus mannose-only translation modification accumulates would provide valuable insights.

The study delves into the physiological role of UGGT, but is limited in scope, focusing solely on the effect of ATF6alpha in UGGT KO cells' stress response. It is crucial for the authors to investigate the broader impact of UGGT KO, including the assessment of basal ER proteotoxicity levels, examination of the general efflux of glycoproteins from ER, and the exploration of the physiological consequences due to UGGT KO. This broader perspective would be valuable for the wider audience. Additionally, the marked increase in ATF4 activity in UGGTKO requires discussion, which the authors currently omit.

The discussion section is brief and could benefit from being a separate section. It is advisable for the authors to explore and suggest other model systems or disease contexts to test UGGT's role in the future. This expansion would help the broader scientific community appreciate the potential applications and implications of this work beyond its current scope.

Reviewer #2 (Public Review):

I would like to express my appreciation for the authors' dedication to revising the manuscript. It is evident that they have thoughtfully addressed numerous concerns I previously raised, significantly contributing to the overall improvement of the manuscript.

My primary concern regarding the authors' framing of their findings within the realm of habitual and goal-directed action control persists. I will try explain my point of view and perhaps clarify my concerns.<br /> While acknowledging the historical tendency to equate procedural learning with habits, I believe a consensus has gradually emerged among scientists, recognizing a meaningful distinction between habits and skills or procedural learning. I think this distinction is crucial for a comprehensive understanding of human action control. While these constructs share similarities, they should not be used interchangeably. Procedural learning and motor skills can manifest either through intentional and planned actions (i.e., goal-directed) or autonomously and involuntarily (habitual responses).

Watson et al. (2022) aptly detailed my concerns in the following statements: "Defining habits as fluid and quickly deployed movement sequences overlaps with definitions of skills and procedural learning, which are seen by associative learning theorists as different behaviours and fields of research, distinct from habits."<br /> "...the risk of calling any fluid behavioural repertoire 'habit' is that clarity on what exactly is under investigation and what associative structure underpins the behaviour may be lost."<br /> I strongly encourage the authors, at the very least, to consider Watson et al.'s (2022) suggestion: "Clearer terminology as to the type of habit under investigation may be required by researchers to ensure that others can assess at a glance what exactly is under investigation (e.g., devaluation-insensitive habits vs. procedural habits)", and to refine their terminology accordingly (to make this distinction clear). I believe adopting clearer terminology in these respects would enhance the positioning of this work within the relevant knowledge landscape and facilitate future investigations in the field.

Regarding the authors' use of Balleine and Dezfouli's (2018) criteria to frame recorded behavior as habitual, as well as to acknowledgment the study's limitations, it's important to highlight that while the authors labeled the fourth criterion (which they were not fulfilling) as "resistance to devaluation," Balleine and Dezfouli define it as "insensitive to changes in their relationship to their individual consequences and the value of those consequences." In my understanding, this definition is potentially aligned with the authors' re-evaluation test, namely, it is conceptually adequate for evaluating the fourth criterion (which is the most accepted in the field and probably the one that differentiate habits from skills). Notably, during this test, participants exhibited goal-directed behavior.

The authors characterized this test as possibly assessing arbitration between goal-directed and habitual behavior, stating that participants in both groups "demonstrated the ability to arbitrate between prior automatic actions and new goal-directed ones." In my perspective, there is no justification for calling it a test of arbitration. Notably, the authors inferred that participants were habitual before the test based on some criteria, but then transitioned to goal-directed behavior based on a different criterion. While I agree with the authors' comment that: "Whether the initiation of the trained motor sequences in experiment 3 (arbitration) is underpinned by an action-outcome association (or not) has no bearing on whether those sequences were under stimulus-response control after training (experiment 1)." they implicitly assert a shift from habit to goal-directed behavior without providing evidence that relies on the same probed mechanism.<br /> Therefore, I think it would be more cautious to refer to this test as solely an outcome revaluation test. Again, the results of this test, if anything, provide evidence that the fourth criterion was tested but not met, suggesting participants have not become habitual (or at least undermines this option).

Reviewer #2 (Public Review):

SUMMARY:<br /> In this manuscript, Ger and colleagues propose two complementary analytical methods aimed at quantifying the model misspecification and irreducible stochasticity in human choice behavior. The first method involves fitting recurrent neural networks (RNNs) and theoretical models to human choices and interpreting the better performance of RNNs as providing evidence of the misspecifications of theoretical models. The second method involves estimating the number of training iterations for which the fitted RNN achieves the best prediction of human choice behavior in a separate, validation data set, following an approach known as "early stopping". This number is then interpreted as a proxy for the amount of explainable variability in behavior, such that fewer iterations (earlier stopping) correspond to a higher amount of irreducible stochasticity in the data. The authors validate the two methods using simulations of choice behavior in a two-stage task, where the simulated behavior is generated by different known models. Finally, the authors use their approach in a real data set of human choices in the two-stage task, concluding that low-IQ subjects exhibit greater levels of stochasticity than high-IQ subjects.

STRENGTHS:<br /> The manuscript explores an extremely important topic to scientists interested in characterizing human decision-making. While it is generally acknowledged that any computational model of behavior will be limited in its ability to describe a particular data set, one should hope to understand whether these limitations arise due to model misspecification or due to irreducible stochasticity in the data. Evidence for the former suggests that better models ought to exist; evidence for the latter suggests they might not.

To address this important topic, the authors elaborate carefully on the rationale of their proposed approach. They describe a variety of simulations - for which the ground truth models and the amount of behavioral stochasticity are known - to validate their approaches. This enables the reader to understand the benefits (and limitations) of these approaches when applied to the two-stage task, a task paradigm commonly used in the field. Through a set of convincing analyses, the authors demonstrate that their approach is capable of identifying situations where an alternative, untested computational model can outperform the set of tested models, before applying these techniques to a realistic data set.

WEAKNESSES:<br /> The most significant weakness is that the paper rests on the implicit assumption that the fitted RNNs explain as much variance as possible, an assumption that is likely incorrect and which can result in incorrect conclusions. While in low-dimensional tasks RNNs can predict behavior as well as the data-generating models, this is not *always* the case, and the paper itself illustrates (in Figure 3) several cases where the fitted RNNs fall short of the ground-truth model. In such cases, we cannot conclude that a subject exhibiting a relatively poor RNN fit necessarily has a relatively high degree of behavioral stochasticity. Instead, it is at least conceivable that this subject's behavior is generated precisely (i.e., with low noise) by an alternative model that is poorly fit by an RNN - e.g., a model with long-term sequential dependencies, which RNNs are known to have difficulties in capturing.

These situations could lead to incorrect conclusions for both of the proposed methods. First, the model misspecification analysis might show equal predictive performance for a particular theoretical model and for the RNN. While a scientist might be inclined to conclude that the theoretical model explains the maximum amount of explainable variance and therefore that no better model should exist, the scenario in the previous paragraph suggests that a superior model might nonetheless exist. Second, in the early-stopping analysis, a particular subject may achieve optimal validation performance with fewer epochs than another, leading the scientist to conclude that this subject exhibits higher behavioral noise. However, as before, this could again result from the fact that this subject's behavior is produced with little noise by a different model. Admittedly, the existence of such scenarios *in principle* does not mean that such scenarios are common, and the conclusions drawn in the paper are likely appropriate for the particular examples analyzed. However, it is much less obvious that the RNNs will provide optimal fits in other types of tasks, particularly those with more complex rules and long-term sequential dependencies, and in such scenarios, an ill-advised scientist might end up drawing incorrect conclusions from the application of the proposed approaches.

In addition to this general limitation, the paper also makes a few additional claims that are not fully supported by the provided evidence. For example, Figure 4 highlights the relationship between the optimal epochs and agent noise. Yet, it is nonetheless possible that the optimal epoch is influenced by model parameters other than inverse temperature (e.g., learning rate). This could again lead to invalid conclusions, such as concluding that low-IQ is associated with optimal epoch when an alternative account might be that low-IQ is associated with low learning rate, which in turn is associated with optimal epoch. Yet additional factors such as the deep double-descent (Nakkiran et al., ICLR 2020) can also influence the optimal epoch value as computed by the authors.

An additional issue is that Figure 4 reports an association between optimal epoch and noise, but noise is normalized by the true minimal/maximal inverse-temperature of hybrid agents (Eq. 23). It is thus possible that the relationship does not hold for more extreme values of inverse-temperature such as beta=0 (extremely noisy behavior) or beta=inf (deterministic behavior), two important special cases that should be incorporated in the current study. Finally, even taking the association in Figure 4 at face value, there are potential issues with inferring noise from the optimal epoch when their correlation is only r~=0.7. As shown in the figures, upon finding a very low optimal epoch for a particular subject, one might be compelled to infer high amounts of noise, even though several agents may exhibit a low optimal epoch despite having very little noise.

APPRAISAL AND DISCUSSION:<br /> Overall, the authors propose a novel method that aims to solve an important problem, but whose generality might be limited only to special cases. In the future, it would be beneficial to test the proposed approach in a broader setting, including simulations of different tasks, different model classes, different model parameters, and different amounts of behavioral noise. Nonetheless, even without such additional work, the proposed methods are likely to be used by cognitive scientists and neuroscientists interested in assessing the quality and limits of their behavioral models.

Reviewer #2 (Public Review):

Summary:<br /> This is an interesting and well-written manuscript that seeks to detail the performance of two human psychophysical experiments designed to look at the relative contributions of transient and sustained components of a multisensory (i.e., audiovisual) stimulus to their integration. The work is framed within the context of a model previously developed by the authors and is now somewhat revised to better incorporate the experimental findings. The major takeaway from the paper is that transient signals carry the vast majority of the information related to the integration of auditory and visual cues, and that the Multisensory Correlation Detector (MCD) model not only captures the results of the current study but is also highly effective in capturing the results of prior studies focused on temporal and causal judgments.

Strengths:<br /> Overall the experimental design is sound and the analyses are well performed. The extension of the MCD model to better capture transients makes a great deal of sense in the current context, and it is very nice to see the model applied to a variety of previous studies.

Weaknesses:<br /> My one major issue with the paper revolves around its significance. In the context of a temporal task(s), is it in any way surprising that the important information is carried by stimulus transients? Stated a bit differently, isn't all of the important information needed to solve the task embedded in the temporal dimension? I think the authors need to better address this issue to punch up the significance of their work.

In a more minor comment, I think there also needs to be a bit more effort into articulating the biological plausibility/potential instantiations of this sustained versus transient dichotomy. As written, the paper suggests that these are different "channels" in sensory systems, when in reality many neurons (and neural circuits) carry both on the same lines.

Reviewer #2 (Public Review):

Maurer et al investigated the contribution of GAD2+ neurons in the preoptic area (POA), projecting to the tuberomammillary nucleus (TMN), to REM sleep regulation. They applied an elegant design to monitor and manipulate the activity of this specific group of neurons: a GAD2-Cre mouse, injected with retrograde AAV constructs in the TMN, thereby presumably only targeting GAD2+ cells projecting to the TMN. Using this set-up in combination with technically challenging techniques including EEG with photometry and REM sleep deprivation, the authors found that this cell-type studied becomes active shortly (≈40sec) prior to entering REM sleep and remains active during REM sleep. Moreover, optogenetic inhibition of GAD2+ cells inhibits REM sleep by a third and also impairs the rebound in REM sleep in the following hour. Despite a few reservations or details that would benefit from further clarification (outlined below), the data makes a convincing case for the role of GAD2+ neurons in the POA projecting to the TMN in REM sleep regulation.

The authors found that optogenetic inhibition of GAD2+ cells suppressed REM sleep in the hour following the inhibition (e.g. Fig2 and Fig4). If the authors have the data available, it would be important to include the subsequent hours in the rebound time (e.g. from ZT8.5 to ZT24) to test whether REM sleep rebound remains impaired, or recovers, albeit with a delay.

REM sleep is under tight circadian control (e.g. Wurts et al., 2000 in rats; Dijk, Czeisler 1995 in humans). To contextualize the results, it would be important to mention that it is not clear if the role of the manipulated neurons in REM sleep regulation hold at other circadian times of the day.

The effect size of the REM sleep deprivation using the vibrating motor method is unclear. In FigS4-D, the experimental mice reduce their REM sleep to 3% whereas the control mice spend 6% in REM sleep. In Fig4, mice are either subjected to REM sleep deprivation with the vibrating motor (controls), or REM sleep deprivations + optogenetics (experimental mice). The control mice (vibrating motor) in Fig4 spend 6% of their time in REM sleep, which is double the amount of REM sleep compared to the mice receiving the same treatment in FigS4-D. Can the authors clarify the origin of this difference in the text?

Reviewer #2 (Public Review):

Summary:<br /> The authors examined inherited changes to the olfactory epithelium produced by odor-shock pairings. The manuscript demonstrates that odor fear-conditioning biases olfactory bulb neurogenesis toward more production of the olfactory sensory neurons engaged by the odor-shock paring. Further, the manuscript reveals that this bias remains in first-generation male and female progeny produced by trained parents. Surprisingly, there was a disconnect between the increased morphology of the olfactory epithelium for the conditioned odor and the response to odor presentation. The expectation based on previous literature and the morphological results was that F1 progeny would also show an aversion to the odor stimulus. However, the authors found that F1 progeny were not more sensitive to the odor compared to littermate controls.

Strengths:<br /> The manuscript includes conceptual innovation and some technical innovation. The results validate previous findings that were deemed controversial in the field, which is a major strength of the work. Moreover, these studies were conducted using a combination of genetically modified animals and state-of-the-art imaging techniques, highlighting the rigorous nature of the research. Lastly, the authors provide novel mechanistic details regarding the remodeling of the olfactory epithelium, demonstrating that biased neurogenesis, as opposed to changes in survival rates, account for the increase in odorant receptors after training.

Weaknesses:<br /> The main weakness is the disconnect between the morphological changes reported and the lack of change in aversion to the odorant in F1 progeny. The authors also do not address the mechanisms underlying the inheritance of the phenotype, which may lie outside of the scope of the present study.

Reviewer #2 (Public Review):

Summary:<br /> The work of Volotsky et al presented here shows that adult archerfish are able to adjust their shooting in response to their own visual feedback, taking consistent alterations of their shot, here by an air flow, into account. The evidence provided points to an internal mechanism of shooting adaptation that is independent of external cues, such as wind. The authors provide evidence for this by forcing the fish to shoot from 2 different orientations to the external alteration of their shots (the airflow). This paper thus provides behavioral evidence of an internal correction mechanism, that underlies adaptive motor control of this behavior. It does not provide direct evidence of refractory index-associated shoot adjustance.

Strengths:<br /> The authors have used a high number of trials and strong statistical analysis to analyze their behavioral data.

Weaknesses:<br /> While the introduction, the title, and the discussion are associated with the refraction index, the latter was not altered, and neither was the position of the target. The "shot" was altered, this is a simple motor adaptation task and not a question related to the refractory index. The title, abstract, and the introduction are thus misleading. The authors appear to deduce from their data that the wind is not taken into account and thus conclude that the fish perceive a different refractory index. This might be based on the assumption that fish always hit their target, which is not the case. The airflow does not alter the position of the target, thus the airflow does not alter the refractive index. The fish likely does not perceive the airflow, thus alteration of its shooting abilities is likely assumed to be an "internal problem" of shooting. I am sorry but I am not able to understand the conclusion they draw from their data.

Reviewer #2 (Public Review):

Summary:<br /> In this study, the authors wanted to test if using a shared relational structure by a sequence of colors in locations can be leveraged to reorganize and compress information.

Strength:<br /> They applied machine learning to EEG data to decode the neural mechanism of reinstatement of visual stimuli at recall. They were able to show that when the location of colors is congruent with the semantically expected location (for example, green is closer to blue-green than purple) the related color information is reinstated at the probed location. This reinstatement was not present when the location and color were not semantically congruent (meaning that x displacement in color ring location did not displace colors in the color space to the same extent) and semantic knowledge of color relationship could not be used for reducing the working memory load or to benefit encoding and retrieval in short term memory.

Weakness:<br /> The experiment and results did not address any reorganization of information or neural mechanism of working memory (that would be during the gap between encoding and retrieval). There was also a lack of evidence to rule out that the current observation can be addressed by schematic abstraction instead of the utilization of a cognitive map.<br /> The likely impact of the initial submission of the study would be in the utility of the methods that would be helpful for studying a sequence of stimuli at recall. The paper was discussed in a narrow and focused context, referring to limited studies on cognitive maps and replay. The bigger picture and long history of studying encoding and retrieval of schema-congruent and schema-incongruent events is not discussed.

Reviewer #2 (Public Review):

Summary:<br /> Padamsey et al build up on previous significant work from the same group which demonstrated robust changes in the visual cortex in male mice from long-term (2-3 weeks) food restriction. Here, the authors extend this finding and reveal striking sex-specific differences in the way the brain responds to food restriction. The measures included the whole-body measure of serum leptin levels, and V1-specific measures of activity of key molecular players (AMPK and PPARα), gene expression patterns, ATP usage in V1, and the sharpness of visual stimulus encoding (orientation tuning). All measures supported the conclusion that the female mouse brain (unlike in males) does not change its energy usage and cortical functional properties on comparable food restriction.

While the effect of food restriction on more peripheral tissue such as muscle and bones has been well studied, this result contributes to our understanding of how the brain responds to food restriction. This result is particularly significant given that the brain consumes a large fraction of the body's energy consumption (20%), with the cortex accounting for half of that amount. The sex-specific differences found here are also relevant for studies using food restriction to investigate cortical function.

Strengths:<br /> The study uses a wide range of approaches mentioned above which converge on the same conclusion, strengthening the core claim of the study.

Weaknesses:<br /> Since the absence of a significant effect does not prove the absence of any changes, the study cannot claim that the female mouse brain does not change in response to food restriction. However, the authors do not make this claim. Instead, they make the well-supported claim that there is a sex-specific difference in the response of V1 to food restriction.

Reviewer #2 (Public Review):

Summary:<br /> In this paper, the authors generated a comprehensive dataset of human spinal cord transcriptome using single-cell RNA sequencing and the Visium spatial transcriptomics platform. They employed Visium data to determine the spatial orientation of each cell type. Using single-cell RNA sequencing data, they identified differentially expressed genes by comparing human and mouse samples, as well as male and female samples.

Strengths:<br /> This study offers a thorough exploration of both cellular and spatial heterogeneity within the human spinal cord. The resulting atlas datasets and analysis findings represent valuable resources for the neuroscience community.

Weaknesses:<br /> The analysis of spatial transcriptomics data was conducted as it is single-cell RNAseq data. However, there are established tools for effectively integrating these two types of data. The incorporation of deconvolution methods could enhance the characterization of each spot's cell type composition.

Reviewer #2 (Public Review)

Summary and strengths<br /> In this manuscript the authors analyse the trajectory of understudied genes (UGs) from experiment to publication and study the reasons for why UGs remain underrepresented in the scientific literature. They show that UGs are not underrepresented in experimental datasets, but in the titles and abstracts of the manuscripts reporting experimental data as well as subsequent studies referring to those large-scale studies. They also develop an app that allows researchers to find UGs and their annotation state. Overall, this is a timely article that makes an important contribution to the field. It could help to boost the future investigation of understudied genes, a fundamental challenge in the life sciences. It is concise and overall well-written, and I very much enjoyed reading it. However, there are a few points that I think the authors should address.

Weaknesses<br /> The authors conclude that many UGs "are lost" from genome-wide assay at the manuscript writing stage. If I understand correctly, this is based on gene names not being reported in the title or abstract of these manuscripts. However, for genome-wide experiments, it would be quite difficult for authors to mention large numbers of understudied genes in the abstract. In contrast, one might highlight the expected behaviour of a well-studied protein simply to highlight that the genome-wide study provides credible results. Could this bias the authors' conclusions and, if so, how could this be addressed? For example, would it be worth to normalise studies based on the total number of genes they cover?

Figure 1B is confusing in its present form. I think the plot and/or the legend need revising. For example, what "numbers to the right of each box plot" are the authors referring to? Also, I assume that the filled boxes are understudied genes and the empty/white box is "all genes", but that's not explained in the legend. In the main text, the figure is referred to with the sentence "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 ". I cannot follow how the figure shows this. My interpretation is that the y-axis is not showing the number of articles, but represents the percentage of articles mentioning a gene in the title/abstract, displayed on a log scale. If so, perhaps a better axis labels and legend text could be sufficient. But then one would also need to somehow connect this to the statement in the main text about the 20% highest-studied genes (a dashed line?). Alternatively, the authors could consider other ways of plotting these data, e.g. simply plotting the "% of publication in which a gene appears" from 0-100% or so.

Reviewer #2 (Public Review):

Summary:<br /> In this report, the authors used solution-based single-molecule FRET and low-resolution cryo-EM to investigate the interactions between the substrate-binding domains of the ABC-importer OpuA from Lactococcus lactis. Based on their results, the authors suggest that the SBDs interact in an ionic strength-dependent manner.

Strengths:<br /> The strength of this manuscript is the uniqueness and importance of the scientific question, the adequacy of the experimental system (OpuA), and the combination of two very powerful and demanding experimental approaches.

Weaknesses:<br /> A demonstration that the SBDs physically interact with one another and that this interaction is important for the transport mechanism will greatly strengthen the claims of the authors. The relation to cooperativity is also unclear.

Reviewer #2 (Public Review):

Summary:<br /> The Meiri group previously showed that Notch1-activated human T-ALL cell lines are sensitive to a cannabis extract in vitro and in vivo (Ref. 32). In that article, the authors showed that Extract #12 reduced NICD expression and viability, which was partially rescued by restoring NICD expression. Here, the authors have identified three compounds of Extract #12 (CBD, 331-18A, and CBDV) that are responsible for the majority of anti-leukemic activity and NICD reduction. Using a pharmacological approach, the authors determined that Extract #12 exerted its anti-leukemic and NICD-reducing effects through the CB2 and TRPV1 receptors. To determine the mechanism, the authors performed RNA-seq and observed that Extract #12 induces ER calcium depletion and stress-associated signals -- ATF4, CHOP, and CHAC1. Since CHAC1 was previously shown to be a Notch inhibitor in neural cells, the authors assume that the cannabis compounds repress Notch S1 cleavage through CHAC1 induction. The induction of stress-associated signals, Notch repression, and anti-leukemic effects were reversed by the integrated stress response (ISR) inhibitor ISRIB. Interestingly, combining the 3 cannabinoids gave synergistic anti-leukemic effects in vitro and had growth-inhibitory effects in vivo.

Strengths:<br /> 1. The authors show novel mechanistic insights that cannabinoids induce ER calcium release and that the subsequent integrated stress response represses activated NOTCH1 expression and kills T-ALL cells.

2. This report adds to the evidence that phytocannabinoids can show a so-called "entourage effect" in which minor cannabinoids enhance the effect of the major cannabinoid CBD.

3. This report dissects the main cannabinoids in the previously described Extract #12 that contribute to T-ALL killing.

4. The manuscript is clear and generally well-written.

5. The data are generally high quality and with adequate statistical analyses.

6. The data generally support the authors' conclusions. The exception is the experiments related to Notch.

7. The authors' discovery of the role of the integrated stress response might explain previous observations that SERCA inhibitors block Notch S1 cleavage and activation in T-ALL (Roti Cancer Cell 2013). The previous explanation by Roti et al was that calcium depletion causes Notch misfolding, which leads to impaired trafficking and cleavage. Perhaps this explanation is not entirely sufficient.

Weaknesses:<br /> 1. Given the authors' previous Cancer Communications paper on the anti-leukemic effects and mechanism of Extract #12, the significance of the current manuscript is reduced.

2. It would be important to connect the authors' findings and a wealth of literature on the role of ER calcium/stress on Notch cleavage, folding, trafficking, and activation.

3. There is an overreliance on the data on a single cell line -- MOLT4. MOLT4 is a good initial choice as it is Notch-mutated, Notch-dependent, and representative of the most common T-ALL subtype -- TAL1. However, there is no confirmatory data in other TAL1-positive T-ALLs or interrogation of other T-ALL subtypes.

4. Fig. 6H. The effects of the cannabinoid combination might be statistically significant but seem biologically weak.

5. Fig. 3. Based on these data, the authors conclude that the cannabinoid combination induces CHAC1, which represses Notch S1 cleavage in T-ALL cells. The concern is that Notch signaling is highly context-dependent. CHAC1 might inhibit Notch in neural cells (Refs. 34-35), but it might not do this in a different context like T-ALL. It would be important to show evidence that CHAC1 represses S1 cleavage in the T-ALL context. More importantly, Fig. 3H clearly shows the cannabinoid combination inducing ATF4 and CHOP protein expression, but the effects on CHAC1 protein do not seem to be satisfactory as a mechanism for Notch inhibition. Perhaps something else is blocking Notch expression?

6. Fig. 4B-C/S5D-E. These Western blots of NICD expression are consistent with the cannabinoid combination blocking Furin-mediated NOTCH1 cleavage, which is reversed by ISR inhibition. However, there are many mechanisms that regulate NICD expression. To support their conclusion that the effects are specifically Furin-medated, the authors should probe full-length (uncleaved) NOTCH1 in their Western blots.

7. Fig. S4A-B. While these pharmacologic data are suggestive that Extract #12 reduces NICD expression through the CB2 receptor and TRPV1 channel, the doses used are very high (50uM). To exclude off-target effects, these data should be paired with genetic data to support the authors' conclusions.

Reviewer #2 (Public Review):

Summary:<br /> In this work, the authors present a robust genomic dataset profiling 58 isolates of neonatal meningitis-causing E. coli (NMEC), the largest such cohort to be profiled to date. The authors provide genomic information on virulence and antibiotic resistance genomic markers, as well as serotype and capsule information. They go on to probe three cases in which infants presented with recurrent febrile infection and meningitis and provide evidence indicating that the original isolate is likely causing the second infection and that an asymptomatic reservoir exists in the gut. Accompanying these results, the authors demonstrate that gut dysbiosis coincides with the meningitis.

Strengths:<br /> The genomics work is meticulously done, utilizing long-read sequencing.<br /> The cohort of isolates is the largest to be sampled to date.<br /> The findings are significant, illuminating the presence of a gut reservoir in infants with repeating infection.

Weaknesses:<br /> Although the cohort of isolates is large, there is no global representation, entirely omitting Africa and the Americas. This is acknowledged by the group in the discussion, however, it would make the study much more compelling if there was global representation.

Reviewer #2 (Public Review):

The authors tried to characterize the function of the SWI/SNF remodeler family, BAF, in spermatogenesis. The authors focused on ARID1A, a BAF-specific putative DNA binding subunit, based on gene expression profiles. The study has several serious issues with the data and interpretation. The conditional deletion mouse model of ARIDA using Stra8-cre showed inefficient deletion; spermatogenesis did not appear to be severely compromised in the mutants. Using this data, the authors claimed that meiotic arrest occurs in the mutants. This is obviously a misinterpretation. In the later parts, the authors performed next-gen analyses, including ATAC-seq and H3.3 CUT&RUN, using the isolated cells from the mutant mice. However, with this inefficient deletion, most cells isolated from the mutant mice appeared not to undergo Cre-mediated recombination. Therefore, these experiments do not tell any conclusion pertinent to the Arid1a mutation. Furthermore, many of the later parts of this study focus on the analysis of H3.3 CUT&RUN. However, Fig. S7 clearly suggests that the H3.3 CUT&RUN experiment in the wild-type simply failed. Thus, none of the analyses using the H3.3 CUT&RUN data can be interpreted. Overall, I found that the study does not have rigorous data, and the study is not interpretable. If the author wishes to study the function of ARID2 in spermatogenesis, they may need to try other cre-lines to have more robust phenotypes, and all analyses must be redone using a mouse model with efficient deletion of ARID2.

In this revised manuscript, the authors did not make any efforts to address my major criticisms, and I do not see any improvement. I only found the responses to 4 points, but I do not see any response to other major and minor comments. I understand the challenge (~70 deletion efficiency in the mutants) in this study. However, the inefficient deletion of ARID1A in this mouse model does not allow any detailed analysis in a quantitative manner.

Reviewer #2 (Public Review):

This manuscript by Port and colleagues describes rigorous experiments that provide a wealth of virologic, respiratory physiology, and particle aerodynamic data pertaining to aerosol transmission of SARS-CoV-2 between infected Syrian hamsters. The data is particularly significant because infection is compared between alpha and delta variants, and because viral load is assessed via numerous assays (gRNA, sgRNA, TCID) and in tissues as well as the ambient environment of the cage. The paper will be of interest to a broad range of scientists including infectious diseases physicians, virologists, immunologists and potentially epidemiologists.

Reviewer #2 (Public Review):

Summary and strengths<br /> Early career funding success has an immense impact on later funding success and faculty persistence, as evidenced by well-documented "rich-get-richer" or "Matthew effect" phenomena in science (e.g., Bol et al., 2018, PNAS). In this study the authors examined publicly available data on the distribution of the National Institutes of Health's K99/R00 awards - an early career postdoc-to-faculty transition funding mechanism - and showed that although 89% of K99 awardees successfully transitioned into faculty, disparities in subsequent R01 grant obtainment emerged along three characteristics: researcher mobility, gender, and institution. Men who moved to a top-25 NIH funded institution in their postdoc-to-faculty transition experienced the shortest median time to receiving a R01 award, 4.6 years, in contrast to the median 7.4 years for women working at less well-funded schools who remained at their postdoc institutions.

Amongst the three characteristics, the finding that researcher mobility has the largest effect on subsequent funding success is key and novel. Other data supplement this finding: for example, although the total number of R00 awards has increased, most of this increase is for awards to individuals moving to different institutions. In 2010, 60% of R00 awards were activated at different institutions compared to 80% in 2022. These findings enhance previous work on the relationship between mobility and ones' access to resources, collaborators, or research objects (e.g., Sugimoto and Larivière, 2023, Equity for Women in Science (Harvard University Press)).

These results empirically demonstrate that even after receiving a prestigious early career grant, researchers with less mobility belonging to disadvantaged groups at less-resourced institutions continue to experience barriers that delay them from receiving their next major grant. This result has important policy implications aimed at reducing funding disparities - mainly that interventions that focus solely on early career or early stage investigator funding alone will not achieve the desired outcome of improving faculty diversity.

The authors also highlight two incredible facts: No postdoc at a historically Black college or university (HBCU) has been awarded a K99 since the program's launch. And out of all 2,847 R00 awards given thus far, only two have been made to faculty at HBCUs. Given the track record of HBCUs for improving diversity in STEM contexts, this distribution of awards is a massive oversight that demands attention.

At no fault of the authors, the analysis is limited to only examining K99 awardees and not those who applied but did not receive the award. This limitation is solely due to the lack of data made publicly available by the NIH. If this data were available, this study would have been able to compare the trajectory of winners versus losers and therefore could potentially quantify the impact of the award itself on later funding success, much like the landmark paper by Bol et al. (PNAS; 2018) that followed the careers of an early career grant scheme in the Netherlands. Such an analysis would also provide new insights that would inform policy.

Although data on applications versus awards for the K99/R00 mechanism are limited, there exists data for applicant race and ethnicity for the 2007-2017 period, which were made available by a Freedom of Information Act request through the now defunct Rescuing Biomedical Research Initiative (https://web.archive.org/web/20180723171128/http://rescuingbiomedicalresearch.org/blog/examining-distribution-k99r00-awards-race/). These results are highly relevant given the discussion of K99 award impacts on the sociodemographic composition of U.S. biomedical faculty. During the 2007-2017 period, the K99 award rate for white applicants was 31% compared to 26.7% for Asian applicants and 16.2% for Black applicants. In terms of award totals, these funding rates amount to 1,384 awards to white applicants, 610 to Asian applicants, and 25 to Black applicants. However, the work required to include these data may be beyond the scope of the study.

The conclusions are well-supported by the data, and limitations of the data and the name-gender matching algorithm are described satisfactorily.

Reviewer #2 (Public Review):

In this manuscript, He et al. have found that delayed anesthesia induction and early anesthesia emergence were observed in microglia-depleted mice. They also showed that neuronal activities were differentially regulated by microglia depletion, possibly via suppressing the neuronal network of anesthesia-activated brain regions and activating emergence-activated brain regions. Mechanistically, this influence was found to be dependent on the activation of microglial P2Y12 receptors and subsequent calcium influx. These findings contribute to a better understanding of the role microglia play in regulating anesthesia and shed light on the underlying mechanisms involved. Nonetheless, there are still some aspects that require further investigation and clarification.

1. In Figure 3A the authors used IBA1 to represent microglia, and the corresponding description is 'brain microglia were not influenced'. However, IBA1 is not a specific biomarker for brain resident microglia. It's recommended to use other biomarkers, such as TMEM119 and P2RY12 to better examine the efficiency of microglial depletion.<br /> 2. In Figure 7, 8 and 9 the authors stated that they aim to investigate the impacts microglia exert on neuronal activity. However, using only c-Fos is not sufficient to represent neuron. The authors are supposed to combine c-Fos with other specific biomarkers for neuron to better validate their conclusions.<br /> 3. In Figure 11 the authors use C1qa-/- transgenic mice and draw the conclusion 'microglia mediated anesthesia modulation does not result from spine pruning'. However, as C1q contains multiple subtypes, I have some reservations regarding whether the authors' conclusion is entirely warranted based solely on the knockout of a single subtype of C1q.<br /> 4. In Figure 14E the authors showed that expression levels of Stim1 is significantly down-regulated in CX3CR1CreER::STIM1fl/fl mouse brains. While this is not incorrect, I would suggest the authors sort microglia with FACS or MACS to perform q-RT-PCR and examine the expression levels of Stim1 since the Cre-LoxP system here is microglia specific.<br /> 5. The flow of the manuscript should have been improved. For instance, the results of repopulated microglia in Figure 1B was described even after Figure 2 and 3, which makes the manuscript a little confusing. Additionally, in Figure 14, it would be beneficial to provide a more comprehensive introduction to molecules such as hM3Dq and Stim1 to improve the clarity and readability of the result descriptions.

Reviewer #2 (Public Review):

Summary:<br /> A bidirectional occasion-setting design is used to examine sex differences in the contextual modulation of reward-related behaviour. It is shown that females are slower to acquire contextual control over cue-evoked reward seeking. However, once established, the contextual control over behaviour was more robust in female rats (i.e., less within-session variability and greater resistance to stress) and this was also associated with increased OFC activation.

Strengths:<br /> The authors use sophisticated behavioural paradigms to study the hierarchical contextual modulation of behaviour. The behavioural controls are particularly impressive and do, to some extent, support the specificity of the conclusions. The analyses of the behavioural data are also elegant, thoughtful, and rigorous.

Weaknesses:<br /> My primary concern is that the authors' claim of sex differences in context-dependent discrimination behaviour is not fully supported by their data.

First, the basic behavioural effect does not seem to replicate across experiments. The authors first show sex differences in the % time in food port and the discrimination ratio (Figures 1 and 2) such that males show better context-dependent discrimination than females (group ctx-dep O1). However, this difference is not observed in the baseline condition group in the next experiment, which investigates the effect of acute stress on context-gated reward seeking: "In Figure 4, we observe no difference between males versus females in group "ctx-dep O1".

Second, I am not fully convinced by the authors' assertion that the results are specific to the contextual modulation process. The authors' main conclusions are derived from comparing a group trained with the differential outcome procedure (group cxt-dep O1/O2) and a group with the non-differential outcome procedure (group cxt-dep O1). However, importantly, a different number of training sessions was used for ctx-dep O1/O2 and ctx-dep O1. Is it not possible that sex differences could have emerged with additional training in the cxt-dep O1/O2 group? Moreover, the authors also seem to assume that rats are not using a contextual strategy in the context-dep O1/O2 condition (i.e., rats use instead distinct context-outcome associations) but what is the evidence for this? Also, the authors argue that the impact of stress is specific to the hierarchical contextual modulation of behaviour however inspection of Figure 4A suggests that there may also be an effect of stress on the context-dependent O1/O2 group.

I also had some minor issues with how the authors interpreted some of the findings. First, it is shown that recent rewards disrupt contextual control of reward seeking in male, but not female, rats. That is, in males, prior reward increased the probability of responding on subsequent non-rewarded trials but trial history had no effect in females. How do the authors reconcile this finding with the quicker acquisition and better discrimination that is observed in males? It is not evident to me how males can have difficulty inhibiting responding to non-rewarded cues following recent reward yet still show better discrimination throughout training.

Finally, the authors argue that the contextual control over behaviour was more robust in female rats as females show less within-session variability and greater resistance to stress. What evidence is there that the restraint stress procedure causes a similar stress response in both sexes?

Reviewer #2 (Public Review):

This work introduces PLMGraph-Inter, a new deep-learning approach for predicting inter-protein contacts, which is crucial for understanding protein-protein interactions. Despite advancements in this field, especially driven by AlphaFold, prediction accuracy and efficiency in terms of computational cost) still remains an area for improvement. PLMGraph-Inter utilizes invariant geometric graphs to integrate the features from multiple protein language models into the structural information of each subunit. When compared against other inter-protein contact prediction methods, PLMGraph-Inter shows better performance which indicates that utilizing both sequence embeddings and structural embeddings is important to achieve high-accuracy predictions with relatively smaller computational costs for the model training.

The conclusions of this paper are mostly well supported by data, but test examples should be revisited with a more strict sequence identity cutoff to avoid any potential information leakage from the training data. The main figures should be improved to make them easier to understand.

1) The sequence identity cutoff to remove redundancies between training and test set was set to 40%, which is a bit high to remove test examples having homology to training examples. For example, CDPred uses a sequence identity cutoff of 30% to strictly remove redundancies between training and test set examples. To make their results more solid, the authors should have curated test examples with lower sequence identity cutoffs, or have provided the performance changes against sequence identities to the closest training examples.

2) Figures with head-to-head comparison scatter plots are hard to understand as scatter plots because too many different methods are abstracted into a single plot with multiple colors. It would be better to provide individual head-to-head scatter plots as supplementary figures, not in the main figure.

3) The authors claim that PLMGraph-Inter is complementary to AlphaFold-multimer as it shows better precision for the cases where AlphaFold-multimer fails. To strengthen the point, the qualities of predicted complex structures via protein-protein docking with predicted contacts as restraints should have been compared to those of AlphaFold-multimer structures.

4) It would be interesting to further analyze whether there is a difference in prediction performance depending on the depth of multiple sequence alignment or the type of complex (antigen-antibody, enzyme-substrates, single species PPI, multiple species PPI, etc).

Reviewer #2 (Public Review):

In this work, Urtecho et al. use genome-integrated massively parallel reporter assays (MPRAs) to catalog the locations of promoters throughout the E. coli genome. Their study uses four different MPRA libraries. First, they assayed a library containing 17,635 promoter regions having transcription start sites (TSSs) previously reported by three different sources. They found that 2,760 of these regions exhibited transcription above an experimentally determined threshold. Second, they assayed a library using sheared E. coli genome fragments. This library allowed the authors to systematically identify candidate promoter regions throughout the genome, some of which had not been identified before. Additionally, by performing experiments with this library under different growth conditions, the authors were able to identify promoters with condition-dependent activity. Third, to improve the resolution at which they were able to identify transcription start sites, the authors assayed a library that tiled all candidate promoter regions identified using the genomic fragments library. Data from the tiled library allowed the authors to identify minimal promoter regions. Fourth, the authors assayed a scanning mutagenesis library in which they systematically scrambled individual 10 bp windows within 2,057 previously identified active promoters at 5 bp intervals. After validation with known promoters, this approach allowed the authors to identify novel functional elements within regulatory regions. Finally, the authors fit multiple machine learning models to their data with the goal of predicting promoter activity from DNA sequences.

The work by Urtecho et al. provides an important resource for researchers studying bacterial transcriptional regulation. Despite decades of study, a comprehensive catalogue of E. coli promoters is still lacking. The results of Urtecho et al. provide a state-of-the-art atlas of promoters in the E. coli genome that is readily accessible through the website, http://ecolipromoterdb.com. The authors' work also provides an important demonstration of the power of genome-integrated MPRAs. Unlike many MPRA-based studies, the authors use the results of their initial MPRAs to design follow-up MPRAs, which they then carry out. Finally, the scanning mutagenesis MPRAs the authors perform provide valuable data that could lead to the discovery of novel transcription factor binding sites and other functional regulatory sequence elements.

Below I provide two major critiques and some minor critiques of the paper. The purpose of these critiques is simply to help the authors improve the quality of the manuscript.

Major points:<br /> 1. Ultimately, a comprehensive atlas of E. coli promoters should include nucleotide resolution TSS data, which is not present in the MPRA datasets reported by Urtecho et al.. The authors do use some methods to narrow down the positions of TSSs, but these methods do not provide the resolution one would ideally like to see in a TSS atlas. I understand that acquiring single-nucleotide-resolution data is beyond the scope of this manuscript, but it still might make sense for the authors to discuss this limitation in the Discussion section.

2. The authors should clarify which points in the Results section are novel conclusions or observations, and which points are simply statements that prior conclusions or observations were confirmed. This distinction can be unclear at times.

Minor points:<br /> 1. Line 200-203: "We conclude that inactive TSS-associated promoters lack -35 elements but may become active in growth conditions where additional transcription factors mobilize and facilitate RNAP positioning in the absence of a -35 motif." Making this type of mechanistic observations from the slight difference observed in the enrichment analysis seems too speculative to me. Also, I do not understand how the discrepancies can be explained in terms of transcription factor differences. If the previous studies from which the annotated TSS were extracted were also performed during the log phase in rich media, why would the transcription factors present be different?

2. Line 224-226: "Active TSSs not overlapping a candidate promoter region generally exhibited weak activity, which may indicate that greater sensitivity is achieved through testing of oligo-array synthesized regions (Figure S3)." The authors should clarify this statement. In particular, it is mechanistically unclear why one library would be more sensitive than another if they contain similar sequences.

3. Figure 2B. The authors should clarify that the heights of the arrows correspond to TSS activity as assayed by one library and that the pile-up plots represent promoter activity as assayed by a different library.

4. Line 255-257: "We also observed an enrichment for 150 bp minimal promoter regions, although these were generally weak indicating that our resolution is limited when tiling weaker promoters." The authors should clarify whether the peak at 150 bp is an artifact of using oligos containing 150 bp tiles to construct the library. Also, the authors should clarify why there are some minimal promoters with lengths > 150 bp when the length of the tiles was 150 bp.

5. Line 262 refers to "Supplementary Table 1", but I was not able to find this table in the supplement.

6. Line 324-325: "We used a σ70 PWM to identify the highest-scoring σ70 motifs within intragenic promoters and determined their relative coding frames". I find the term "relative coding frame" here to be unclear; the authors should clarify what they mean.

7. Figure 3 C , D: The authors should use the same terminology in the plots and the methods section describing them. They should also clarify how the values plotted in C and D were computed.

8. Line 329-332: "The observed depletion of -35 motifs positioned in the +2 reading frame and -10 motifs in the +1 reading frame is likely due to the fact that the canonical sequences for these motifs would create stop codons within the protein if placed at these positions." The definition of the reading frame here is unclear. Do the authors mean that the 0 frame is defined as occurring when the hexamer exactly overlaps 2 codons, the +1 frame is when the hexamer is shifted 1 nt downstream of that position, and the +2 frame is when the hexamer is shifted 2 nt downstream of that position?

9. Line 538-539: "We performed hyperparameter tuning for a three-layer CNN and achieved an AUPRC =0.44." The authors should explicitly describe the architecture used for the CNN, and perhaps include a diagram of this architecture. In addition, the authors should clarify the mathematical forms of the other methods tested.

10. Line 1204-1205: "We standardized all datasets as detailed above in 'Universal Promoter Expression Quantification and Activity Thresholding'". That title does not appear before in the text. I believe the appropriate subsection is called "Standardizing Promoter Expression Quantification and Activity Thresholding".

11. Line 1265-1266: "We include a k-mer if the absolute correlation with expression is greater than the 'random' k-mer frequency, resulting in 4800/5440 filtered k-mers." It is unclear to me which two correlations are being compared. Please clarify. For example, would this be accurate: "We include a k-mer if the absolute correlation of its frequency with expression is greater than the absolute correlation of its 'random' frequency with expression"?

Reviewer #2 (Public Review):

In this manuscript, Xie et al presented a new method derived from PORE-C, SCA-seq, for simultaneously measuring chromatin accessibility, genome 3D and CpG DNA methylation. SCA-seq provides a useful tool to the scientific communities to interrogate the genome structure-function relationship.

The revised manuscript has clarified almost of the concerns raised in the previous round of review, though I still have two minor concerns,

1) In fig 2a, there is no number presented in the Venn diagram (although the left panel indeed showed the numbers of the different categories, including the numbers in the right panel would be more straightforward).

2) The authors clarified the discrepancy between sfig 7a and sfig 7g. However, the remaining question is, why is there a big difference in the percentage of the cardinality count of concatemers of the different groups between the chr7 and the whole genome?

Reviewer #2 Public Review

The authors wish to apply established psychophysical methods to the study of number. Specifically, they wish to test the hypothesis - supported by their previous work - that human sensorimotor processes are tuned to specific number ranges. In a novel set of tasks, they ask participants to tap a button N times (either fast or slow), where N varies between 8 and 32 across trials. As I understood it, they then computed the Weber fraction (WF) for each participant for each number and correlated those values across participants and numbers. They find stronger correlations for nearby numbers than for distant numbers and interpret this as evidence of sensorimotor tuning functions. Two other analyses - cluster analyses and principal component analyses (PCA) - suggest that participants' performance relied on at least 2 mechanisms, one for encoding low numbers of taps (around 10) and another for encoding larger numbers (around 27).

Strengths

Individual differences can be a rich source of scientific insight and I applaud the authors for taking them seriously, and for exploring new avenues in the study of numerical cognition.

Weaknesses

Inter-subject-correlation<br /> The experiment "is based on the idea that interindividual variability conveys information that can reveal common sensory processes (Peterzell & Kennedy, 2016)" but I struggled to understand the logic of this technique. The authors explain it most clearly when they write "Regions of high intercorrelation between neighbouring stimuli intensity can be interpreted to imply that sets of stimuli are processed by the same (shared) underlying channel. This channel, while responding relatively more to its preferred stimulus, will also be activated by neighbouring stimuli that although slightly different from the preferred intensity, are nevertheless included in the same response distribution." As I understood it, the correlations are performed "between participants, for all targets values" - meaning that they are measuring the extent to which different participants' WFs vary together. But why is this a good measure of channels? This analysis seems to assume that if people have channels for numerical estimation, they will have the same channels, tuned to the same numerical ranges. But this is an empirical question - individual participants could have wildly different channels, and perhaps different numbers of channels (even in the tested range). If they do, then this between-subject analysis would mask these individual differences (despite the subtitle).

Different channels<br /> I had trouble understanding much of the analyses, and this may account for at least some of my confusion. That said, as I understand it, the results are meant to provide "evidence that tuned mechanisms exist in the human brain, with at least two different tunings" because of the results of the clustering analysis and PCA. However, as the authors acknowledge, "PCA aims to summarize the dataset with the minimal number of components (channels). We can therefore not exclude the possible existence of more than two (perhaps not fully independent) channels." So I believe this technique does not provide more evidence for the existence of 2 channels as for the existence of 4 or 8 or 11 channels, the upper bound for a task testing 11 different numbers. If we can conclude that people may have one channel per number, what does "channel" mean?

Several other questions arose for me when thinking through this technique. If people did have two channels (at least in this range), why would they be so broad? Why would they be centered so near the ends of the tested range? Can such effects be explained by binning on the part of the participants, who might have categorized each number (knowingly or not) as either "small" or "large"? Whereas the experiment tested numbers 8-32, numbers are infinite - How could a small number of channels cover an infinite set? Or even the set 8-10,000? More broadly, I was unsure what advantages channels would have - that is - how in principle would having distinct channels for processing similar stimuli improve (rather than impede) discrimination abilities?

No number perception<br /> I was uncertain about the analogy to studies of other continuous dimensions like spatial frequency, motion, and color. In those studies, participants view images with different spatial frequency, motion, or color - the analogy would be to see dot arrays containing different numbers of dots. Instead, here participants read written numerals (like "19"), symbols which themselves do not have any numerical properties to perceive. How does that difference change the interpretation of the effects? One disadvantage of using numerals is that they introduce a clear discontinuity: Our base-10 numerical system artificially chunks integers into decades, potentially causing category-boundary effects in people's reproductions.

Sensorimotor<br /> The authors wished to test for "sensorimotor mechanisms selective to numerosity" but it's not clear what makes their effects sensorimotor (or selective to numerosity, see below). It's true they found effects using a tapping task (which like all behavior is sensorimotor), but it's not clear that this effect is specific to sensorimotor number reproduction. They might find similar effects for numerical comparison or estimation tasks. Such findings would suggest the effect may be a general feature of numerical cognition across modalities.

Specific to numbers<br /> The authors argue that their effects are "number selective" but they do not provide compelling evidence for this selectivity. In principle, their main findings could be explained by the duration of tapping rather than the number of taps. They argue this is unlikely for two reasons. The first reason is that the overall pattern of results was unchanged across the fast and slow tapping conditions, but differences in duration were confounded with numerosity in both conditions, so the comparison is uninformative. (Given this, I am not sure what we stand to learn by comparing the two tapping speeds.) The second reason is that temporal reproduction was less precise in their control condition than numerical reproduction, but this logic is unclear: Participants could still use duration (or some combination of speed and duration) as a helpful cue to numerosity, even if their duration reproductions were imperfect.

If the authors wish to test the role of duration, they might consider applying the same analytical techniques they use for numbers to their duration data. Perhaps participants show similar evidence for duration-selective channels, in the absence of number, as they do for other non-numerical domains (like spatial frequency).

Theories of numerical cognition. An expansive literature on numerical cognition suggests that many animals, human children, and adults across cultures have two systems for representing numerosity without counting - one that can represent the exact cardinality of sets smaller than about 4 and another that represents the approximate number of larger sets (but see Cheyette & Piantadosi, 2020). The current paper would benefit from better relating its findings to this long lineage of theories and findings in numerical approximation across cultures, ages, and species.