Reviewer #3 (Public review):

The manuscript by Barrett et al. "Integrating bulk and single cell RNA-seq refines transcriptomic profiles of individual C. elegans neurons" presents a comprehensive approach to integrating bulk RNA-seq and single-cell RNA-seq (scRNA-seq) data to refine transcriptomic profiles of individual C. elegans neurons. The study addresses the limitations of scRNA-seq, such as the under-detection of lowly expressed and non-polyadenylated transcripts, by leveraging the sensitivity of bulk RNA-seq. The authors deploy a computational method, LittleBites, to remove non-neuronal contamination in bulk RNA-seq, that aims to enhance specificity while preserving the sensitivity advantage of bulk sequencing. Using this approach, the authors identify lowly expressed genes and non-coding RNAs (ncRNAs), many of which were previously undetected in scRNA-seq data.

Overall, the study provides high-resolution gene expression data for 53 neuron classes, covering a wide range of functional modalities and neurotransmitter usage. The integrated dataset and computational tools are made publicly available, enabling community-driven testing of the robustness and reproducibility of the study. Nevertheless, while the study represents a relevant contribution to the field, certain aspects of the work require further refinement to ensure the robustness and rigor necessary for peer-reviewed publication. Below, I outline the areas where improvements are needed to strengthen the overall impact and reliability of the findings.

(1) The study relies on thresholding to determine whether a gene is expressed or not. While this is a common practice, the choice of threshold is not thoroughly justified. In particular, the choice of two uniform cutoffs across protein-encoding RNAs and of one distinct threshold for non-coding RNAs is somewhat arbitrary and has several limitations. This reviewer recommends the authors attempt to use adaptive threshold-methods that define gene expression thresholds on a per-gene basis. Some of these methods include GiniClust2, Brennecke's variance modeling, HVG in Seurat, BASiCS, and/or MAST Hurdle model for dropout correction.

(2) Most importantly, the study lacks independent experimental validation (e.g., qPCR, smFISH, or in situ hybridization) to confirm the expression of newly detected lowly expressed genes and non-coding RNAs. This is particularly important for validating novel neuronal non-coding RNAs, which are primarily inferred from computational approaches.

(3) The novel biology is somewhat limited. One potential area of exploration would be to look at cell-type specific alternative splicing events.

(4) The integration method disproportionately benefits neuron types with limited representation in scRNA-seq, meaning well-sampled neuron types may not show significant improvement. The authors should quantify the impact of this bias on the final dataset.

(5) The authors employ a logit transformation to model single-cell proportions into count space, but they need to clarify its assumptions and potential pitfalls (e.g., how it handles rare cell types).

(6) The LittleBites approach is highly dependent on the accuracy of existing single-cell references. If the scRNA-seq dataset is incomplete or contains classification biases, this could propagate errors into the bulk RNA-seq data. The authors may want to discuss potential limitations and sensitivity to errors in the single-cell dataset, and it is critical to define minimum quality parameters (e.g. via modeling) for the scRNAseq dataset used as reference.

(7) Also very important, the LittleBites method could benefit from a more intuitive explanation and schematic to improve accessibility for non-computational readers. A supplementary step-by-step breakdown of the subtraction process would be useful.

(8) In the same vein, the ROC curves and AUROC comparisons should have clearer annotations to make results more interpretable for readers unfamiliar with these metrics.

(9) Finally, after the correlation-based decontamination of the 4,440 'unexpressed' genes, how many were ultimately discarded as non-neuronal?<br /> a) Among these non-neuronal genes, how many were actually known neuronal genes or components of neuronal pathways (e.g., genes involved in serotonin synthesis, synaptic function, or axon guidance)?<br /> b) Conversely, among the "unexpressed" genes classified as neuronal, how many were likely not neuron-specific (e.g., housekeeping genes) or even clearly non-neuronal (e.g., myosin or other muscle-specific markers)?

(10) To increase transparency and allow readers to probe false positives and false negatives, I suggest the inclusion of:<br /> a) The full list of all 4,440 'unexpressed' genes and their classification at each refinement step. In that list flag the subsets of genes potentially misclassified, including:<br /> - Neuronal genes wrongly discarded as non-neuronal.<br /> - Non-neuronal genes wrongly retained as neuronal.<br /> b) Add a certainty or likelihood ranking that quantifies confidence in each classification decision, helping readers validate neuronal vs. non-neuronal RNA assignments.<br /> This addition would enhance transparency, reproducibility, and community engagement, ensuring that key neuronal genes are not erroneously discarded while minimizing false positives from contaminant-derived transcripts.

Reviewer #3 (Public review):

Summary

Across species, dopamine release carries out seemingly diverse functions, like reinforcing memories and regulating locomotion and flight. However, whether distinct dopaminergic neurons (DANs) are allocated for each function is not clear. In this study, Toshima et al. have used the numerically simple organization of the Drosophila larval brain to answer this question. They use optogenetic activation to systematically stimulate a small set of DANs, individually and collectively, and study the effect on diverse functions such as memory formation, retrieval, and locomotion. They find that singly or collectively, DL1 DANs can induce punishment and/or safety memory formation and retrieval. DANs can even gate the expression of memory. Finally, the same DANs also modulate locomotion in the larvae. The authors speculate that dopaminergic neurons in other species may also share such overlapping functions. Their findings are nicely summarised in Figure 9.

Strengths

The study comprehensively activates the neurons in the DL1 cluster in a systematic manner. Individual and collective stimulation of the Dl1 DANs has been conducted to assess the induction and gating of aversive punishment memory, safety memory, and acute locomotion.

Specific adult Drosophila DANs are known to induce dual behaviors and functions. The same MP1/y1pedc DANs are recognized for gating appetitive memory expression and representing aversive teaching signals downstream of sensory stimuli such as electric shocks, bitter tastes, and heat. Neurons in the PPL1 cluster regulate adult flight and food-seeking behavior. The authors deserve credit for conducting an organized examination of dopaminergic neuron functions in larvae, which makes their findings more comparable and facilitates the proposal of a holistic model.

They have provided substantial evidence for their findings and frequently presented replicated behavioral data sets. They have been transparent about results that were difficult to explain. Additionally, they have provided an impressive body of supporting data to strengthen their main findings.

Weaknesses

The larvae exhibit directed locomotory action to express punishment or safety memory. If the larvae did not move, we would not be able to assess memory function. Hence, functional activation of DANs could result in one action, which seems like two different functions of memory expression and locomotion. It can also be argued that activation of DANs represents a teaching signal to the KCs, and then eventually, downstream of the MBONs, it results in locomotion modulation. Hence, the seeming functional diversity could be a function of different downstream neuronal pathways and not molecular context-dependent diversity inside dopaminergic neurons. The authors should address this possibility or point out the fallacy in the above argument.

The finding that activation of TH-GAL4 conveys aversive valence and R58E02-GAL4 conveys appetitive valence seems redundant (Figure 6). I understand they say this in the context of locomotion. However, they may not have mentioned similar findings in adults. In adults, artificial activation of DANs covered by the same GAL4 lines acts as aversive and appetitive teaching signals for memory formation. These references should be cited appropriately in the results and discussion if not currently included.

The evidence for the role of dopamine (Figure 7) can be bolstered by using other available RNAi lines against TH. A valium20 vector-based shRNA line is recommended. The current evidence is based mainly on non-specific pharmacological intervention with 3IY.

Reviewer #3 (Public review):

Summary:

This study successfully identified genetic loci associated with various traits by generating large-scale long-read sequencing data from a diverse set of samples. This study is significant because it not only produces large-scale long-read genome sequencing data but also demonstrates its application in actual genetics research. Given its potential utility in various fields, this study is expected to make a valuable contribution to the academic community and to this journal. However, there are several critical aspects that could be improved. Below are specific comments for consideration.

Strengths:

Producing high-quality, large-scale variant datasets and imputation datasets

Weaknesses:

(1) Data availability

Currently, it appears that only the Genomic Lens SV Panel is available on the webpage described in the Data Availability section. It is unclear whether the authors intend to release the raw sequencing data. Since the study utilized samples from the 1000 Genomes Project, there should be no restriction on making the data publicly accessible. Given this, would the authors consider making the raw sequencing reads publicly available? If so, NCBI SRA or EBI ENA would be the most appropriate repositories for data deposition. I strongly encourage the authors to consider public data release.

Additionally, accessing the Genomic Lens SV Panel data does not seem straightforward. The manuscript should provide a more detailed description of how researchers can access and utilize these data. In my opinion, the best approach would be to upload the variant data (VCF files) to a public database such as the European Variation Archive (EVA) hosted by EBI.

I strongly request that the authors publicly deposit the variant data. At a minimum:

a) The joint genotype data for all 888 samples from the 1000 Genomes Project must be publicly available.<br /> b) For the UK Biobank samples, at least allele frequency data should be disclosed.

Since eLife has a well-established data-sharing policy, compliance with these guidelines is essential for publication in this journal.

(2) Long-read sequencing data quality

While the manuscript presents N50 read length and mean or median read base quality for each sample in a table, it would be highly beneficial to visualize these data in figures as well. A violin plot or similar visualization summarizing these distributions would significantly improve data presentation.

Notably, the base quality of ONT long-read sequencing data appears lower than expected. This may be attributed to the use of pore version 9.4.1, but the unexpectedly low base quality still warrants attention. It would be helpful to include a small figure within Figure 2 to illustrate this point. A visual representation of read length distribution and base quality distribution would strengthen the manuscript.

(3) Variant detection precision, recall, and F1 score

This study focuses on insertions and deletions (indels) {greater than or equal to}50 bp, but it remains unclear how well variants <50 bp are detected. I am particularly interested in the precision, recall, and F1 score for variants between 5-49 bp.

While ONT base quality is relatively low, single-base variants are challenging to analyze, but variants {greater than or equal to}5 bp should still be detectable as their read accuracy is still approximately 90%, making analysis feasible. Given that Sniffles supports the detection of variants as small as 1 bp, I strongly encourage the authors to conduct an additional analysis.

A simple two-category classification (e.g., 5-49 bp and {greater than or equal to}50 bp) should suffice. Additionally, a comparative analysis with HiFi and short-read sequencing data would be highly valuable. If possible, I strongly recommend that all detected variants {greater than or equal to}5 bp be made publicly available as VCF files.

(4) Assembly-based methods

Given the low read accuracy and low sequencing depth in this dataset, it is understandable that genome assembly is challenging. However, the latest high-quality human genome datasets-such as those produced by the Human Pangenome Reference Consortium (HPRC)-demonstrate that assembly-based approaches provide significant advantages, particularly for resolving complex and long structural variants.

Since HPRC data also utilize 1000 Genomes Project samples, it would be highly informative to compare the accuracy of ONT sequencing in this study with HPRC's assembly-based genome data. The recent publication on 47 HPRC samples provides a valuable reference for such a comparison. Given its relevance, the authors should consider providing a comparative analysis with HPRC data.

References:

(1) A draft human pangenome reference<br /> https://www.nature.com/articles/s41586-023-05896-x

(2) The Human Pangenome Project: a global resource to map genomic diversity<br /> https://www.nature.com/articles/s41586-022-04601-8

(3) A pangenome reference of 36 Chinese populations<br /> https://www.nature.com/articles/s41586-023-06173-7

(4) Long-read sequencing of 3,622 Icelanders provides insight into the role of structural variants in human diseases and other traits<br /> https://www.nature.com/articles/s41588-021-00865-4

(5) Increased mutation and gene conversion within human segmental duplications<br /> https://www.nature.com/articles/s41586-023-05895-y

(6) Structural polymorphism and diversity of human segmental duplications<br /> https://www.nature.com/articles/s41588-024-02051-8

(7) Highly accurate Korean draft genomes reveal structural variation highlighting human telomere evolution<br /> https://academic.oup.com/nar/article/53/1/gkae1294/7945385

Reviewer #4 (Public review):

Summary:

This manuscript is a descriptive study of circulating T follicular helper (cTfh) responses to PfSEA -1A or PfGARP (targets of new antimalaria vaccine candidates) in PBMCs from a convenience sample of children (7 yrs of age) and adults living in a malaria holo endemic Kenya using multiparameter flow cytometry and clustering analysis. This cell type promotes B cell production of long-lived antimalarial antibodies to provide protection against malaria. They find that children had a wider cTFH cytokine and TF profile cellular response in comparison to adults who responded to both antigens but had a narrower response profile.

Strengths:

Carefully done study, very detailed, nice summary model at the end of the paper. The revision provides requested clarification on a number of issues, including CD40L expression which was not differentially expressed between groups. They add additional data into the supplemental files, including IL4 and IL21 data by presenting the cytoplots.

Weaknesses:

To know the significance of these cTfh cells for long-term protection of malaria requires functional and transfer experiments in animal models which is outside the scope of this work.

Reviewer #3 (Public review):

Summary:

This manuscript describes the characterization of mycobacterial cytoskeleton protein Wag31, examining its role in orchestrating protein-lipid and protein-protein interactions essential for mycobacterial survival. The most significant finding is that Wag31, which directs polar elongation and maintains the intracellular membrane domain, was revealed to have membrane tethering capabilities.

Strengths:

The authors provided a detailed analysis of Wag31 domain architecture, revealing distinct functional roles: the N-terminal domain facilitates lipid binding and membrane tethering, while the C-terminal domain mediates protein-protein interactions. Overall, this study offers a robust and new understanding of Wag31 function.

Weaknesses:

The authors did not address some of the comments. The following concerns should be addressed.

• As far as I can tell, authors did not address my prior comments on Line 270, which is Line 280 in the revised manuscript: the N-terminal region is important for lipid homeostasis, but the statement in Line 270, "the maintenance of lipid homeostasis by Wag31 is a consequence of its tethering activity" requires additional proof. Please indicate the page and line numbers in the revised manuscript so that I can identify the specific changes the authors made.

• Since this pull-down assay was conducted by mixing E. coli lysate expressing Wag31 and Msm lysate expression Wag31 interactors like MurG, it is possible that the interactions are not direct. Authors acknowledge that this is a valid point, and indicated that they "will describe this caveat in the revised manuscript". I have difficulty finding where this revision was made. Please indicate the page and line numbers.

Reviewer #3 (Public review):

Summary:

In the present work Deganutti et al. report a structural study on GPCR functional dynamics using a computational approach called supervised molecular dynamics.

Strengths:

The study has the potential to provide novel insight into GPCR functionality. An example is the interaction between D344 and R385 identified during the Gs coupling by GLP-1R. However, validation of the findings, even computationally through for instance in silico mutagenesis study, is advisable.

Weaknesses:

No significant advance of the existing structural data on GPCR and GPCR/G protein coupling is provided. Most of the results are reproductions of the previously reported structures.

Reviewer #3 (Public review):

Summary:

In this study the authors set out to investigate whether GPRC6A mediates kokumi taste initiated by the amino acid L-ornithine. They used Wistar rats, a standard laboratory strain, as the primary model and also performed an informative taste test in humans, in which miso soup was supplemented with various concentrations of L-ornithine. The findings are valuable and overall the evidence is solid. L-Ornithine should be considered to be a useful test substance in future studies of kokumi taste and the class C G protein coupled receptor known as GPRC6A (C6A) along with its homolog, the calcium-sensing receptor (CaSR) should be considered candidate mediators of kokumi taste. The researchers confirmed in rats their previous work on Ornithine and C6A in mice (Mizuta et al Nutrients 2021).

Strengths:

The overall experimental design is solid based on two bottle preference tests in rats. After determining the optimal concentration for L-Ornithine (1 mM) in the presence of MSG, it was added to various tastants including: inosine 5'-monophosphate; monosodium glutamate (MSG); mono-potassium glutamate (MPG); intralipos (a soybean oil emulsion); sucrose; sodium chloride (NaCl; salt); citric acid (sour) and quinine hydrochloride (bitter). Robust effects of ornithine were observed in the cases of IMP, MSG, MPG and sucrose; and little or no effects were observed in the cases of sodium chloride, citric acid; quinine HCl. The researchers then focused on the preference for Ornithine-containing MSG solutions. Inclusion of the C6A inhibitors Calindol (0.3 mM but not 0.06 mM) or the gallate derivative EGCG (0.1 mM but not 0.03 mM) eliminated the preference for solutions that contained Ornithine in addition to MSG. The researchers next performed transections of the chord tympani nerves (with sham operation controls) in anesthetized rats to identify a role of the chorda tympani branches of the facial nerves (cranial nerve VII) in the preference for Ornithine-containing MSG solutions. This finding implicates the anterior half-two thirds of the tongue in ornithine-induced kokumi taste. They then used electrical recordings from intact chorda tympani nerves in anesthetized rats to demonstrate that ornithine enhanced MSG-induced responses following the application of tastants to the anterior surface of the tongue. They went on to show that this enhanced response was insensitive to amiloride, selected to inhibit 'salt tastant' responses mediated by the epithelial Na+ channel, but eliminated by Calindol. Finally they performed immunohistochemistry on sections of rat tongue demonstrating C6A positive spindle-shaped cells in fungiform papillae that partially overlapped in its distribution with the IP3 type-3 receptor, used as a marker of Type-II cells, but not with (i) gustducin, the G protein partner of Tas1 receptors (T1Rs), used as a marker of a subset of type-II cells; or (ii) 5-HT (serotonin) and Synaptosome-associated protein 25 kDa (SNAP-25) used as markers of Type-III cells.

At least two other receptors in addition to C6A might mediate taste responses to ornithine: (i) the CaSR, which binds and responds to multiple L-amino acids (Conigrave et al, PNAS 2000), and which has been previously reported to mediate kokumi taste (Ohsu et al., JBC 2010) as well as responses to Ornithine (Shin et al., Cell Signaling 2020); and (ii) T1R1/T1R3 heterodimers which also respond to L-amino acids and exhibit enhanced responses to IMP (Nelson et al., Nature 2001). These alternatives are appropriately discussed and, taken together, the experimental results favor the authors' interpretation that C6A mediates the Ornithine responses. The authors provide preliminary data in Suppl. 3 for the possibility of co-expression of C6A with the CaSR.

In the Discussion, the authors consider the potential effects of kokumi substances on the threshold concentrations of key tastants such as glutamate, arguing that extension of taste distribution to additional areas of the mouth (previously referred to as 'mouthfulness') and persistence of taste/flavor responses (previously referred to as 'continuity') could arise from a reduction in the threshold concentrations of umami and other substances that evoke taste responses. This concept may help to design future experiments.

Weaknesses:

The authors point out that animal models pose some difficulties of interpretation in studies of taste and raise the possibility in the Discussion that umami substances may enhance the taste response to ornithine (Line 271, Page 9).

The status of one of the compounds used as an inhibitor of C6A, the gallate derivative EGCG, as a potential inhibitor of the CaSR or T1R1/T1R3 is unknown. It would have been helpful to show that a specific inhibitor of the CaSR failed to block the ornithine response.

It would have been helpful to include a positive control kokumi substance in the two bottle preference experiment (e.g., one of the known gamma glutamyl peptides such as gamma-glu-Val-Gly or glutathione), to compare the relative potencies of the control kokumi compound and Ornithine, and to compare the sensitivities of the two responses to C6A and CaSR inhibitors.

quote via the reliable u/ahelper

https://old.reddit.com/r/typewriters/comments/1jvgm5z/feed_pawl_not_engaging_ratchet/

Reviewer #3 (Public review):

Summary:

This study uses a combination of single-cell RNA-Seq to globally profile changes in gene expression in adult P23H transgenic zebrafish, which show progressive rod photoreceptor degeneration, along with age-matched controls. As expected, mitotically active retinal progenitors are identified in both conditions, the increased number of both progenitors and immature rods are observed. DrivAER-mediated gene regulatory network analysis in retinal progenitors, photoreceptor precursors, and mature rod photoreceptors respectively identified e2f1-3, prdm1a, and sp1 as top predicted transcriptional regulators of gene expression specific to these cell types. Finally, morpholino-mediated knockdown of these transcription factors led to expected defects in proliferation and rod differentiation.

Strengths:

Overall, this is a rigorous study that is convincingly executed and well-written. The data presented here will be a useful addition to existing single-cell RNA-Seq datasets obtained from regenerating zebrafish retina.

Weaknesses:

Multiple similar studies have been published and it is something of a missed opportunity in terms of identifying novel mechanisms of rod photoreceptor regeneration. Several other recent studies have used both single-cell RNA and ATAC-Seq to analyze gene regulatory networks that regulate neurogenesis in zebrafish retina following acute photoreceptor damage (Hoang, et al. 2020; Celloto, et al. 2023; Lyu, et al. 2023; Veen, et al 2023) or in other genetic models of progressive photoreceptor dystrophy such cep290 mutants (Fogerty, et al. 2022).

The gene regulatory network analysis here would also benefit from the addition of matched scATAC-Seq data, which would allow the use of more powerful tools such as Scenic+ (Bravo and de Winter, et al. 2023). It would also benefit from integration with single-cell multiome data from developing retinas (Lyu, et al. 2023). The genes selected for functional analysis here are all either robustly expressed in retinal progenitor cells (ef1-3 and aurka) or in developing rods (prdm1a), so it is not really surprising that defects are observed. Identification of factors that selectively regulate rod photoreceptor regeneration, rather than those that regulate both development and regeneration, would provide additional novelty. This would also potentially allow the use of animal mutants for candidate genes, rather than exclusively relying on morphant analysis, which may have off-target effects.

The description of the time points analyzed is vague, stating only that "fish from 6 to 12 months of age were analyzed". Since photoreceptor degeneration is progressive, it is unclear how progenitor behavior changes over time, or how the gene expression profile of other cell types such as microglia, cones, or surviving rods is altered by disease progression. Most similar studies address this by analyzing multiple time points from specific ages or times post-injury.

Reviewer #3 (Public review):

Summary:

The paper by Li et al. describes the crystal structure of a complex of Sld3-Cdc45-binding domain (CBD) with Cdc45 and a model of the dimer of an Sld3-binding protein, Sld7, with two Sld3-CBD-Cdc45 for the tethering. In addition, the authors showed the genetic analysis of the amino acid substitution of residues of Sld3 in the interface with Cdc45 and biochemical analysis of the protein interaction between Sld3 and Cdc45 as well as DNA binding activity of Sld3 to the single-strand DNAs of the ARS sequence.

Strengths:

The authors provided a nice model of an intermediate step in the assembly of an active Cdc45-MCM-GINS (CMG) double hexamers at the replication origin, which is mediated by the Sld3-Sld7 complex. The dimer of the Sld3-Sld7 complexes tethers two MCM hexamers together for the recruitment of GINS-Pol epsilon on the replication origin.

Weaknesses:

The biochemical analysis should be carefully evaluated with more quantitative ways to strengthen the authors' conclusion even in the revised version.

Reviewer #3 (Public review):

In this paper, Sandkuhler et al. reassessed the role of TANGO2 as a heme chaperone proposed by Sun et al in a recently published paper (https://doi.org/10.1038/s41586-022-05347-z) by partially repeating and failing to replicate experiments therein. Overall, Sandkuhler et al. conclude that the heme-related roles of TANGO2 had been overemphasized by Sun et al. especially because the hrg9 gene does not exclusively respond to different regimens of heme synthesis/uptake but is susceptible to a greater extent to, for example, oxidative stress.

In recent years, the discussion around the heme-related roles of TANGO2 has been tantalizing but is still far from a definitive consensus. Discrepancies between results and their interpretation are a testament to how challenging and ambitious the understanding of TANGO2 and the phenotypes associated with TANGO2 defects are. Overall, the work presented by Sandkuhler et al. in this manuscript challenges the recent developments in the field and promotes the continuous characterisation of TANGO2 in relation to heme homeostasis.

A few comments and questions:

(1) The authors stress - with evidence provided in this paper or indicated in the literature - that the primary role of TANGO2 and its homologues is unlikely to be related to heme trafficking, arguing that observed effects on heme transport are instead downstream consequences of aberrant cellular metabolism. But in light of a mounting body of evidence (referenced by the authors) connecting more or less directly TANGO2 to heme trafficking and mobilization, it is recommended that the authors comment on how they think TANGO2 could relate to and be essential for heme trafficking, albeit in a secondary, moonlighting capacity. This would highlight a seemingly common theme in emerging key players in intracellular heme trafficking, as it appears to be the case for GAPDH - with accumulating evidence of this glycolytic enzyme being critical for heme delivery to several downstream proteins.

(2) The observation - using eat-2 mutants and lawn avoidance behaviour - that survival patterns can be partially explained by reduced consumption, is fascinating. It would be interesting to quantify the two relative contributions.

(3) In the legend to Figure 1A it's a bit unclear what the differently coloured dots represent for each condition. Repeated measurements, worms, independent experiments? The authors should clarify this.

(4) It would help if the entire fluorescence images (raw and processed) for the ZnMP treatments were provided. Fluorescence images would also benefit Figure 1B.

(5) Increasingly, the understanding of heme-dependent roles relies on transient or indirect binding to unsuspected partners, not necessarily relying on a tight affinity and outdating the notion of heme as a static cofactor. Despite impressive recent advancements in the detection of these interactions (for example https://doi.org/10.1021/jacs.2c06104; cited by the authors), a full characterisation of the hemome is still elusive. Sandkuhler et al. deemed it possible but seem to question that heme binding to TANGO2 occurs. However, Sun et al. convincingly showed and characterised TANGO2 binding to heme. It is recommended that the authors comment on this.

Reviewer #3 (Public review):

The role of type-I nNOS neurons is not fully understood. The data presented in this paper addresses this gap through optical and electrophysiological recordings in adult mice (awake and asleep).

This manuscript reports on a study on type-I nNOS neurons in the somatosensory cortex of adult mice, from 3 to 9 months of age. Most data were acquired using a combination of IOS and electrophysiological recordings in awake and asleep mice. Pharmacological ablation of the type-I nNOS populations of cells led to decreased coherence in gamma band coupling between left and right hemispheres; decreased ultra-low frequency coupling between blood volume in each hemisphere; decreased (superficial) vascular responses to sustained sensory stimulus and abolishment of the post-stimulus CBV undershoot. While the findings shed new light on the role of type-I nNOS neurons, the etiology of the discrepancies between current observations and literature observations is not clear and many potential explanations are put forth in the discussion.

Reviewer #3 (Public review):

Summary:

In this work, Hathaway and colleagues aim to understand how audiovisual cues at the time of outcome promote the selection of risky choices. A real-life illustration of this effect is used in electronic gambling machines which signal a win with flashing lights and jingles, encouraging the player to keep betting. More specifically, the authors ask whether the cue has to be paired exclusively to wins, or whether it can be paired to both outcomes, or exclusively loss outcomes, or occur randomly. To tackle this question, they employ a version of the Iowa Gambling Task adapted to rats, and test the effect of different rules of cue-outcome associations on the probability of selecting the riskier options; they then test the effect of prior reward devaluation on the task; finally, the optimised computational models on the early phases of the experiment to investigate potential mechanisms underlying the behavioural differences.

Strengths:

The experimental approach is very well thought-out, in particular, the choice of the different task variants covers a wide range of different potential hypotheses. Using this approach, they find that, although rats prefer the optimal choices, there is a shift towards selecting riskier options in the variants of the task where the cue is paired to win outcomes. They analyse this population average shift by showing that there is a concurrent increase in the number of risk-taking individuals in these tasks. They also make the novel discovery that pairing cues with loss outcomes only reduces the tendency for risky decisions.

The computational strategy is appropriate and in keeping with the accepted state of the art: defining a set of candidate models, optimising them, comparing them, simulating the best ones to ensure they replicate the main experimental results, then analysing parameter estimates in the different tasks to speculate about potential mechanisms.

Weaknesses:

There is a very problematic statistical stratagem that involves categorising individuals as either risky or optimal based on their choice probabilities. As a measurement or outcome, this is fine, as previously highlighted in the results, but this label is then used as a factor in different ANOVAs to analyse the very same choice probabilities, which then constitutes a circular argument (individuals categorised as risky because they make more risky choices, make more risky choices...).

A second experiment was done to study the effect of devaluation on risky choices in the different tasks. The results, which are not very clear to understand from Figure 3, would suggest that reward devaluation affects choices in tasks where the win-cue pairing is not present. The authors interpret this result by saying that pairing wins with cues makes the individuals insensitive to reward devaluation. Counter this, if an individual is prone to making risky choices in a given task, this points to an already distorted sense of value as the most rewarding strategy is to make optimal non-risky choices.

While the overall computational approach is excellent, I believe that the choice of computational models is poor. Loss trials come at a double cost, something the authors might want to elaborate more upon, firstly the lost opportunity of not having selected a winning option which is reflected in Q-learning by the fact that r=0, and secondly a waiting period which will affect the overall reward rate. The authors choose to combine these costs by attempting to convert the time penalty into "reward currency" using three different functions that make up the three different tested models. This is a bit of a wasted opportunity as the question when comparing models is not something like "are individuals in the paired win-cue tasks more sensitive to risk? or less sensitive to time? etc" but "what is the best way of converting time into Q-value currency to fit the data?" Instead, the authors could have contrasted other models that explicitly track time as a separate variable (see for example "Impulsivity and risk-seeking as Bayesian inference under dopaminergic control" (Mikhael & Gershman 2021)) or give actions an extra risk bonus (as in "Nicotinic receptors in the VTA promote uncertainty seeking" (Naude et al 2016)). Another weakness of the computational section is the fact, that despite simulations having been made, figure 5 only shows the simulated risk scores and not the different choice probabilities which would be a much more interesting metric by which to judge model validity. In the last section, the authors ask whether the parameter estimates (obtained from optimisation on the early sessions) could be used to predict risk preference. While this is an interesting question to address, the authors give very little explanation as to how they establish any predictive relationship. A figure and more detailed explanation would have been warranted to support their claims.

Reviewer #3 (Public review):

Summary:

This study investigates the computational role of top-down feedback in artificial neural networks (ANNs), a feature that is prevalent in the brain but largely absent in standard ANN architectures. The authors construct hierarchical recurrent ANN models that incorporate key properties of top-down feedback in the neocortex. Using these models in an audiovisual integration task, they find that hierarchical structures introduce a mild visual bias, akin to that observed in human perception, not always compromising task performance.

Strengths:

The study investigates a relevant and current topic of considering top-down feedback in deep neural networks. In designing their brain-like model, they use neurophysiological data, such as externopyramidisation and hierarchical connectivity. Their brain-like model exhibits a visual bias that qualitatively matches human perception.

Weaknesses:

While the model is brain-inspired, it has limited bioplausibility. The model assumes a simplified and fixed hierarchy. In the brain with additional neuromodulation, the hierarchy could be more flexible and more task-dependent.

While the brain-like model showed an advantage in ignoring distracting auditory inputs, it struggled when visual information had to be ignored. This suggests that its rigid bias toward visual processing could make it less adaptive in tasks requiring flexible multimodal integration. It hence does not necessarily constitute an improvement over existing ANNs. It is unclear, whether this aspect of the model also matches human data. In general, there is no direct comparison to human data. The study does not evaluate whether the top-down feedback architecture scales well to more complex problems or larger datasets. The model is not well enough specified in the methods and some definitions are missing.

Reviewer #3 (Public review):

Summary:

This work presents the development, characterization and use of new thin microendoscopes (500µm diameter) whose accessible field of view has been extended by the addition of a corrective optical element glued to the entrance face. Two microendoscopes of different lengths (6.4mm and 8.8mm) have been developed, allowing imaging of neuronal activity in brain regions >4mm deep. An alternative solution to increase the field of view could be to add an adaptive optics loop to the microscope to correct the aberrations of the GRIN lens. The solution presented in this paper does not require any modification of the optical microscope and can therefore be easily accessible to any neuroscience laboratory performing optical imaging of neuronal activity.

Strengths:

(1) The paper is generally clear and well written. The scientific approach is well structured, and numerous experiments and simulations are presented to evaluate the performance of corrected microendoscopes. In particular, we can highlight several consistent and convincing pieces of evidence for the improved performance of corrected microendoscopes:

- PSFs measured with corrected microendoscopes 75µm from the centre of the FOV show a significant reduction in optical aberrations compared to PSFs measured with uncorrected microendoscopes.

- Morphological imaging of fixed brain slices shows that optical resolution is maintained over a larger field of view with corrected microendoscopes compared to uncorrected ones, allowing neuronal processes to be revealed even close to the edge of the FOV.

- Using synthetic calcium data, the authors showed that the signals obtained with the corrected microendoscopes have a significantly stronger correlation with the ground truth signals than those obtained with uncorrected microendoscopes.

(2) There is a strong need for high quality microendoscopes to image deep brain regions in vivo. The solution proposed by the authors is simple, efficient and potentially easy to disseminate within the neuroscience community.

Weaknesses:

Weaknesses that were present in the first version of the paper were carefully addressed by the authors.

Reviewer #3 (Public review):

Summary:

In this manuscript, Nagarajan et al. study the impact of early damage to the anterior cingulate cortex (ACC) on the vocal development of marmoset monkeys. AAC lesions were performed on neonatal marmosets and their vocal patterns and the spectrotemporal features of their calls were analyzed compared to control groups during the first six weeks of life. While the vocal repertoire was not significantly affected by ACC lesions, the authors described notable differences in the social contact call, the phee call. Marmosets with ACC damage made fewer social contact calls, and when they did, these calls were shorter, louder, and monotonic. Additionally, the study revealed that ACC damage in infancy led to permanent alterations in downstream brain areas involved in social vocalizations, such as the amygdala and periaqueductal gray.

Strengths:

This study suggests that the ACC plays a crucial role in the normal development of social vocal behavior in infant marmosets. Studying vocal behavior in marmosets can provide insights into the neural mechanisms underlying human speech and communication disorders due to their similarity in brain structure and social behavior.

The methods are robust and reliable with precise localization of the lesions with neuroimaging and histological examination.

Reviewer #3 (Public review):

Summary:

In this report, the authors test the necessity of prefrontal cortex (specifically, FEF) activity in driving changes in oscillatory power, spike rate, and spike timing of extrastriate visual cortex neurons during a visual spatial working memory (WM) task. The authors recorded LFP and spikes in V4 while macaques remembered a single spatial location over a delay period during which task-irrelevant background gratings were displayed on the screen with varying orientation and contrast. V4 oscillations (in the beta range) scaled with WM maintenance, and the information encoded by spike timing relative to beta band LFP about the task-irrelevant background orientation depended on remembered location. They also compared recorded signals in V4 with and without muscimol inactivation of FEF, demonstrating the importance of FEF input for WM-induced changes in oscillatory amplitude, phase coding, and information encoded about background orientations. Finally, they built a network model that can account for some of these results. Together, these results show that FEF provides meaningful input to visual cortex that is used to alter neural activity, and that these signals can impact information coding of task-irrelevant information during a WM delay.

Strengths:

- Elegant and robust experiment that allows for clear tests for the necessity of FEF activity in WM-induced changes in V4 activity<br /> - Comprehensive and broad analyses of interactions between LFP and spike timing provide compelling evidence for FEF-modulated phase coding of task-irrelevant stimuli at remembered location<br /> - Convincing modeling efforts

Comments on revisions:

I have no further comments for the authors. The revised manuscript appears to have adequately addressed the substantial comments raised in the previous round of review. I especially appreciate the addition of a new supplementary figure analyzing the data when no background stimulus was presented.

Reviewer #3 (Public review):

Summary:

The authors conducted a well-designed experiment, incorporating VR classroom scenes and background sound events, with both control and ADHD participants. They employed multiple neurophysiological measures, such as EEG, eye movements, and skin conductance, to investigate the mechanistic underpinnings of paying attention in class and the disruptive effects of background noise.

The results revealed that individuals with ADHD exhibited heightened sensory responses to irrelevant sounds and reduced tracking of the teacher's speech. Overall, this manuscript presented an ecologically valid paradigm for assessing neurophysiological responses in both control and ADHD groups. The analyses were comprehensive and clear, making the study potentially valuable for the application of detecting attentional deficits.

Strengths:

• The VR learning paradigm is well-designed and ecologically valid.

• The neurophysiological metrics and analyses are comprehensive, and two physiological markers are identified capable of diagnosing ADHD.

• The data shared could serve as a benchmark for future studies on attention deficits in ecologically valid scenarios.

Weaknesses:

• Several results are null results, i.e., no significant differences were found between ADHD and control populations.

Comments on revisions:

The authors have addressed all of my concerns with the original manuscript.

Reviewer #3 (Public review):

Summary:

In the present manuscript, the authors use a few minutes of voltage imaging of CA1 pyramidal cells in head fixed mice running on a track while local field potential (LFPs) are recorded. The authors suggest that synchronous ensembles of neurons are differentially associated with different types of LFP patterns, theta and ripples. The experiments are flawed in that the LFP is not "local" but rather collected the other side of the brain.

Strengths:

The authors use a cutting-edge technique.

Weaknesses:

Although the authors have toned down their claims, the statement in the title ("Synchronous Ensembles of Hippocampal CA1 Pyramidal Neurons Associated with Theta but not Ripple Oscillations During Novel Exploration") is still unsupported.

One could write the same title while voltage imaging one mouse and recording LFP from another mouse.

To properly convey the results, the title should be modified to read "Synchronous Ensembles of Hippocampal CA1 Pyramidal Neurons Associated with Contralateral Theta but not with Contralateral Ripple Oscillations During Novel Exploration"

Without making this change, the title - and therefore the entire work - is misleading at best.

Reviewer #3 (Public review):

Summary:

This paper points out an inconsistency of the roles of the striatal spiny neurons projecting to the indirect pathway (iSPN) and the synaptic plasticity rule of those neurons expressing dopamine D2 receptors, and proposes a novel, intriguing mechanisms that iSPNs are activated by the efference copy of the chosen action that they are supposed to inhibit.

The proposed model was supported by simulations and analysis of the neural recording data during spontaneous behaviors.

Strengths:

Previous models suggested that the striatal neurons learn action values functions, but how the information about the chosen action is fed back to the striatum for learning was not clear. The author pointed out that this is a fundamental problem for iSPNs that are supposed to inhibit specific actions and its synaptic inputs are potentiated with dopamine dips.

The authors proposes a novel hypothesis that iSPNs are activated by efference copy of the selected action which they are supposed to inhibit during action selection. Even though intriguing and seemingly unnatural, the authors demonstrated that the model based on the hypothesis can circumvent the problem of iSPNs learning to disinhibit the actions associated with negative reward errors. They further showed by analyzing the cell-type specific neural recording data by Markowitz et al. (2018) that iSPN activities tend to be anti-correlated before and after action selection.

Weaknesses:

(1) It is not correct to call the action value learning using the externally-selected action as "off-policy." Both off-policy algorithm Q-learning and on-policy algorithm SARSA update the action value of the chosen action, which can be different from the greedy action implicated by the present action values. In standard reinforce learning terminology, on-policy or off-policy is regarding the actions in the subsequent state, whether to use the next action value of (to be) chosen action or that of greedy choice as in equation (7).<br /> It is worth noting that this paper suggested that dopamine neurons encode on-policy TD errors: Morris G, Nevet A, Arkadir D, Vaadia E, Bergman H (2006). Midbrain dopamine neurons encode decisions for future action. Nat Neurosci, 9, 1057-63. https://doi.org/10.1038/nn1743

(2) It is also confusing to contract TD learning and Q-learning, as the latter is considered as on type of TD learning. In the TD error signal by state value function (6) is dependent on the chosen action a_{t-1} implicitly in r_t and s_t based on the reward and state transition function.

(3) It is not clear why interferences of the activities for action selection and learning can be avoided, especially when actions are taken with short intervals or even temporal overlaps. How can the efference copy activation for the previous action be dissociated with the sensory cued activation for the next action selection?

(4) Although it may be difficult to single out the neural pathway that carries the efference copy signal to the striatum, it is desired to consider their requirements and difference possibilities. A major issue is that the time delay from actions to reward feedback can be highly variable.

An interesting candidate is the long-latency neurons in the CM thalamus projecting to striatal cholinergic interneurons, which are activated following low-reward actions:<br /> Minamimoto T, Hori Y, Kimura M (2005). Complementary process to response bias in the centromedian nucleus of the thalamus. Science, 308, 1798-801. https://doi.org/10.1126/science.1109154

(5) In the paragraph before Eq. (3), Eq (1) should be Eq. (2) for the iSPN.

Here are comments back to the authors' replies with the revised version:

(1) I do not agree on the use of inaccurate technical terms. On-policy does not require that the policy is greedy with respect to the actions values, as authors seem to assume here.

In fact, the policy (10) is just a standard soft-max action selection based on the action values by the difference of dSPN and iSPN outputs.

Furthermore, in the immediate reward setting tested in this paper, action values are independent of the policy, so there is no distinction between on-policy vs. off-policy. This is also apparent from the "TD" errors in (19) and (21), where there is no TD.

(2) To really compare the different forms of TD, multi-step RL tasks should be used.

(3) This fundamental limitation should be explicitly documented in the manuscript. This is not just the same as any RL algorithms. Having two action representations within each action step make temporal credit assignment more difficult.

Reviewer #3 (Public review):

Kim, Lognon et al. present an important finding on pro-locomotor effects of optogenetic activation of the A13 region, which they identify as a dopamine-containing area of the medial zona incerta that undergoes profound remodeling in terms of afferent and efferent connectivity after administration of 6-OHDA to the MFB. The authors claim to address a model of PD-related gait dysfunction, a contentious problem that can be difficult to treat by dopaminergic medication or DBS in conventional targets. They make use of an impressive array of technologies to gain insight into the role of A13 remodeling in the 6-OHDA model of PD. The evidence provided is solid and the paper is well written, but there are several general issues that reduce the value of the paper in its current form, and a number of specific, more minor ones. Also some suggestions, that may improve the paper compared to its recent form, come to mind.

The most fundamental issue that needs to be addressed is the relation of the structural to the behavioral findings. It would be very interesting to see whether the structural heterogeneity in afferent/effects projections induced by 6-OHDA is related to the degree of symptom severity and motor improvement during A13 stimulation.

The authors provide extensive interrogation of large-scale changes in the organization of the A13 region afferent and efferent distributions. It remains unclear how many animals were included to produce Fig 4 and 5. Fig S5 suggests that only 3 animals were used, is that correct? Please provide details about the heterogeneity between animals. Please provide a table detailing how many animals were used for which experiment. Were the same animals used for several experiments?

While the authors provide evidence that photoactivation of the A13 is sufficient in driving locomotion in the OFT, this pro-locomotor effect seems to be independent of 6-OHDA induced pathophysiology. Only in the pole test do they find that there seems to be a difference between Sham vs 6-OHDA concerning effects of photoactivation of the A13. Because of these behavioral findings, optogenic activation of A13 may represent a gain of function rather than disease-specific rescue. This needs to be highlighted more explicitly in the title, abstract and conclusion.

The authors claim that A13 may be a possible target for DBS to treat gait dysfunction. However, the experimental evidence provided (in particular lack of disease-specific changes in the OFT) seem insufficient to draw such conclusions. It needs to be highlighted that optogenetic activation does not necessarily have the same effects as DBS (see the recent review from Neumann et al. in Brain: https://pubmed.ncbi.nlm.nih.gov/37450573/). This is important because ZI-DBS so far had very mixed clinical effects. The authors should provide plausible reasons for these discrepancies. Is cell-specificity, that only optogenetic interventions can achieve, necessary? Can new forms of cyclic burst DBS achieve similar specificity (Spix et al, Science 2021)? Please comment.

In a recent study, Jeon et al (Topographic connectivity and cellular profiling reveal detailed input pathways and functionally distinct cell types in the subthalamic nucleus, 2022, Cell Reports) provided evidence on the topographically graded organization of STN afferents and McElvain et al. (Specific populations of basal ganglia output neurons target distinct brain stem areas while collateralizing throughout the diencephalon, 2021, Neuron) have shown similar topographical resolution for SNr efferents. Can a similar topographical organization of efferents and afferents be derived for the A13/ ZI in total?

In conclusion, this is an interesting study that can be improved taking into consideration the points mentioned above.

Reviewer #3 (Public review):

Summary:

The study is well written, and the results are solid and well demonstrated. It shows a field that can be explored for the treatment of CDI

Strengths:

Results are really good, and the CAPE shows a good and promising alternative for treating CDI.

Weaknesses:

Some references are too old or missing.

Comments on revisions:

I have read your study after comments made by all referees, and I noticed that all questions and suggestions addressed to the authors were answered and well explained. Some of the minor and major issues related to the article were also solved. I am satisfied with all the effort given by the authors to improve their manuscript.

Reviewer #3 (Public review):

Summary:

The study uses the food choice task, a well-established method in eating disorder research, particularly in anorexia nervosa. However, it introduces a novel analytical approach - the diffusion decision model - to deconstruct food choices and assess the influence of negative affect on how and when tastiness and healthiness are considered in decision-making among individuals with bulimia nervosa and healthy controls.

Strengths:

The introduction provides a comprehensive review of the literature, and the study design appears robust. It incorporates separate sessions for neutral and negative affect conditions and counterbalances tastiness and healthiness ratings. The statistical methods are rigorous, employing multiple testing corrections.

A key finding - that negative affect induction biases individuals with bulimia nervosa toward prioritizing tastiness over healthiness - offers an intriguing perspective on how negative affect may drive binge eating behaviors.

Weaknesses:

A notable limitation is the absence of a sample size calculation, which, combined with the relatively small sample, may have contributed to null findings. Additionally, while the affect induction method is validated, it is less effective than alternatives such as image or film-based stimuli (Dana et al., 2020), potentially influencing the results.

Another concern is the lack of clarity regarding which specific negative emotions were elicited. This is crucial, as research suggests that certain emotions, such as guilt, are more strongly linked to binge eating than others. Furthermore, recent studies indicate that negative affect can lead to both restriction and binge eating, depending on factors like negative urgency and craving (Leenaerts et al., 2023; Wonderlich et al., 2024). The study does not address this, though it could explain why, despite the observed bias toward tastiness, negative affect did not significantly impact food choices.

Reviewer #3 (Public review):

Summary:

The authors investigated the role of dopaminergic neurons (dopamine transporter expressing, DAT) in the dorsal raphe nucleus (DRN) in regulating social and affective behavior through projections to the central nucleus of the amygdala (CeA), bed nucleus of the stria terminalis (BNST), and the posterior subdivision of the basolateral amygdala. The largest effect observed was in the DRN-DAT projections to the CeA. Augmenting previously published results from this group (Matthews et al., 2016), the comprehensive behavioral analysis relative to social dominance, gene expression analysis, electrophysiological profiling, and in vivo imaging provides novel insights into how DRN-DAT projections to the CeA influence the engagement of social behavior in the contexts of group-housed and socially isolated mice.

Strengths:

Correlational analysis with social dominance is a nice addition to the study. The overall computational analyses performed are well-designed and rigorous.

Weaknesses:

(1) Analysis of dopamine receptor expression did not include Drd3, Drd4, or Drd5 which may provide more insights into how dopamine modulates downstream targets. This is particularly relevant to the BNST projection in which the densest innervation did not robustly co-localize with the expression of either Drd1 or Drd2. It is also possible that dopamine release from DRN-DAT neurons in any or all of these structures modulates neurotransmitter release from inputs to these regions that contain D2 receptors on their terminals.

(2) Although not the focus of this study, without pharmacological blockade of dopamine receptors, it is not possible to assess what the contribution of dopamine is to the behavioral outcomes. Given the co-release of glutamate and GABA from these neurons, it is possible that dopamine plays only a marginal role in the functional connectivity of DRN-DAT neurons. (

(3) Photostimulation parameters used during the behavioral studies (8 pulses of light delivered at 30 Hz for several minutes) could lead to confounding results limiting data interpretation. As shown in Figure 6J, 8 pulses of light delivered at 30 Hz result in a significant attenuation of the EPSC amplitude in the BLP and CeA projection. Thus, prolonged stimulation could lead to significant synaptic rundown resulting in an overall suppression of connectivity in the later stages of the behavioral analyses.

Reviewer #3 (Public review):

Summary:

The major novel finding in this study is that SFSWAP, a splicing factor containing an RS domain but no canonical RNA binding domain, functions as a negative regulator of splicing. More specifically, it promotes retention of specific introns in a wide variety of transcripts including transcripts from the OGT gene previously studied by the Conrad lab. The balance between OGT intron retention and OGT complete splicing is an important regulator of O-GlcNAc expression levels in cells.

Strengths:

An elegant CRISPR knockout screen employed a GFP reporter, in which GFP is efficiently expressed only when the OGT retained intron is removed (so that the transcript will be exported from the nucleus to allow for translation of GFP). Factors whose CRISPR knockdown cause decreased intron retention therefore increase GFP, and these can be identified by sequencing RNA of GFP-sorted cells. SFSWAP was thus convincingly identified as a negative regulator of OGT retained intron splicing. More focused studies of OGT intron retention indicate that it may function by regulating a decoy exon previously identified in the intron, and that this may extend to other transcripts with decoy exons.

Weaknesses:<br /> The mechanism by which SFSWAP represses retained introns is unclear, although some data suggests it can operate (in OGT) at the level of a recently reported decoy exon within that intron. Interesting / appropriate speculation about possible mechanism are provided and will likely be the subject of future studies.

Overall the study is well done and carefully described.

Reviewer #3 (Public review):

In this manuscript, the authors demonstrated the significance of the TRPγ channel in regulating internal TAG levels. They found high TAG levels in TRPγ mutant, which was ascribed to a deficit in the lipolysis process due to the downregulation of brummer (bmm). It was notable that the expression of TRPγ in DH44+ PI neurons, but not dILP2+ neurons, in the brain restored the internal TAG levels and that the knockdown of TRPγ in DH44+ PI neurons resulted in an increase in TAG levels. These results suggested a non-cell autonomous effect of Dh44+PI neurons. Additionally, the expression of the TRPγ channel in Dh44 R2-expressing cells restored the internal TAG levels. The authors, however, did not provide an explanation of how TRPγ might function in both presynaptic and postsynaptic cells in the non-cell autonomous manner to regulate the TAG storage. The authors further determined the effect of TRPγ mutation on the size of lipid droplets (LD) and the lifespan and found that TRPγ mutation caused an increase in the size of LD and a decrease in the lifespan, which were reverted by feeding lipase and metformin. These were creative endeavors, I thought. The finding that DH44+ PI neurons have non-cell autonomous functions in regulating bodily metabolism (mainly sugar/lipid) in addition to directing sugar nutrient sensing and consumption is likely correct, but the paper has many loose ends.

Comments on revisions:

The authors have addressed nearly all of my concerns with additional experiments and explanations.

Reviewer #3 (Public Review):

This is the first report to show a transcriptional factor, foxl2l, is essential for the development of female germs. Without foxl2l, germ cells will be developed into sperms. The report also clearly defined the arrested stage of early germ cells in foxl2l mutants, or stages that is critical for foxl2l to play a role for the further development of female germ cells. Due to lack of cell lineage tracing, the claim of foxl2l suppression of dedifferentiate of progenitor cells to GSC based on the gene expression and cell number changes is weak. In addition, separation of early germ cell types in foxl2l mutant using marker genes from WT may not be optimal.

Reviewer #3 (Public review):

Summary:

Whether and how animals can taste cholesterol is not well understood. The study provides evidence that 1) cholesterol activates a subset of bitter-sensing gustatory receptor neurons (GRNs) in the fly labellum, but not other types of GRNs, 2) flies show aversion to high concentrations of cholesterol, and this is mediated by bitter GRNs, and 3) cholesterol avoidance depends on a specific set of ionotropic receptor (IR) subunits acting in bitter GRNs. The claims of the study are supported by electrophysiological recordings, genetic manipulations, and behavioral readouts.

Strengths:

Cholesterol taste has not been well studied, and the paper provides new insight into this question. The authors took a comprehensive and rigorous approach in several different parts of the paper, including screening the responses of all 31 labellar sensilla, screening a large panel of receptor mutants, and performing misexpression experiments with nearly every combination of the 5 IRs identified. The effects of the genetic manipulations are very clear and the results of electrophysiological and behavioral studies match nicely, for the most part. The appropriate controls are performed for all genetic manipulations.

Weaknesses:

The weaknesses of the study, described below, are relatively minor and do not detract from the main conclusions of the paper.

(1) The paper does not state what concentrations of cholesterol are present in Drosophila's natural food sources. Are the authors testing concentrations that are ethologically relevant?

(2) The paper does not state or show whether the expression of IR7g, IR51b, and IR56d is confined to bitter GRNs. Bitter-specific expression of at least some of these receptors would be necessary to explain why bitter GRNs but not sugar GRNs (or other GRN types) normally show cholesterol responses.

(3) The authors only investigated the responses of GRNs in the labellum, but GRN responses in the leg may also contribute to the avoidance of cholesterol feeding. Alternatively, leg GRNs might contribute to cholesterol attraction that is unmasked when bitter GRNs are silenced. In support of this possibility, Ahn et al. (2017) showed that Ir56d functions in sugar GRNs of the leg to promote appetitive responses to fatty acids.

(4) The authors might consider using proboscis extension as an additional readout of taste attraction or aversion, which would help them more directly link the labellar GRN responses to a behavioral readout. Using food ingestion as a readout can conflate the contribution of taste with post-ingestive effects, and the regulation of food ingestion also may involve contributions from GRNs on multiple organs, whereas organ-specific contributions can be dissociated using proboscis extension. For example, does presenting cholesterol on the proboscis lead to aversive responses in the proboscis extension assay (e.g., suppression of responses to sugar)? Does this aversion switch to attraction when bitter GRNs are silenced, as with the feeding assay?

(5) The authors claim that the cholesterol receptor is composed of IR25a, IR76b, IR56d, and either IR7g or IR51b. While the authors have shown that IR25a and IR76b are each required for cholesterol sensing, they did not show that both are required components of the same receptor complex. If the authors are relying on previous studies to make this assumption, they should state this more clearly. Otherwise, I think further misexpression experiments may be needed where only IR25a or IR76b, but not both, are expressed in GRNs.

Reviewer #3 (Public review):

Hon et al. investigated the role of BNST CRF signaling in modulating phasic and sustained fear in male and female mice. They found that partial and full fear conditioning had similar effects in both sexes during conditioning and during recall. However, males in the partially reinforced fear conditioning group showed enhanced acoustic startle, compared to the fully reinforced fear conditioning group, an effect not seen in females. Using fiber photometry to record calcium activity in all BNST neurons, the authors show that the BNST was responsive to foot shock in both sexes and both conditioning groups. Shock response increased over the session in males in the fully conditioned fear group, an effect not observed in the partially conditioned fear group. This effect was not observed in females. Additionally, tone onset resulted in increased BNST activity in both male groups, with the tone response increasing over time in the fully conditioned fear group. This effect was less pronounced in females, with partially conditioned females exhibiting a larger BNST response. During recall in males, BNST activity was suppressed below baseline during tone presentations and was significantly greater in the partially conditioned fear group. Both female groups showed an enhanced BNST response to the tone that slowly decayed over time. Next, they knocked CRF in the BNST to examine its effect on fear conditioning, recall and anxiety-like behavior after fear. They found no effect of the knockdown in either sex or group during fear conditioning. During fear recall, BNST CRF knockdown lead to an increase in freezing in only the partially conditioned females. In the anxiety-like behavior tasks, BNST CRF knockdown lead to increased anxiolysis in the partially reinforced fear male, but not in females. Surprisingly, BNST CRF knockdown increased startle response in fully conditioned, but not partially conditioned males. An effect not observed in either female group. In a final set of experiments, the authors single photon calcium imaging to record BNST CRF cell activity during fear conditioning and recall. Approximately, 1/3 of BNST CRF cells were excited by shock in both sexes, with the rest inhibited and no differences were observed between sexes or group during fear conditioning. During recall, BNST CRF activity decreased in both sexes, an effect pronounced in male and female fully conditioned fear groups.

Overall, these data provide novel, intriguing evidence in how BNST CRF neurons may encode phasic and sustained fear differentially in males and females. The experiments were rigorous. My biggest concerns I have regard the interpretations and some conclusions from this data set, which I have stated below.

(1) It was surprising to see minimal and somewhat conflicting behavioral effects due to BNST CRF knockdown. The authors provide a representative image and address this in the conclusion. They mention the role of local vs projection CRF circuits as well as the role of GABA. I don't think those experiments are necessary for this manuscript. However, it may be worthwhile to see through in situ hybridization or IHC, to see BNST CRF levels after both full and partial conditioned fear paradigms. Additionally, it would help to see a quantification of the knockdown of the animals. The authors can add a figure showing deltaF/F changes from control.

(2) Related to the previous point, it was surprising to see an effect of the CRF deletion in the full fear group compared to the partial fear in the acoustic startle task. To strengthen the conclusion about differential recruitment of CRF during phasic and sustained fear, the experiment in my previous point could help elucidate that. Conversely, intra-BNST administration of a CRF antagonist into the BNST before the acoustic startle after both conditioning tasks could also help. Or patch from BNST CRF neurons after the conditioning tasks to measure intrinsic excitability. Not all these experiments are needed to support the conclusion, it's some examples.

(3) In Figure 5 F and K, the authors report data combined for both part and full fear conditioning. Were there any differences between the number of excited or inhibited neurons b/t the conditioning groups? Also, can the authors separate male and female traces in Fig 5 E and P?

(4) Also, regarding the calcium imaging data, what was the average length of a transient induced by shock? Were there any differences between the sexes?

Reviewer #3 (Public review):

The authors have responded very thoughtfully to many of the points raised, and the revised manuscript will make a useful contribution to our understanding of some of the computations performed by area PF. In particular, the investigators' addition of analyses of peak activations, their additional clarifications that area PF is likely to be part of a larger network concerned with technical reasoning, and their responses to the reviewers' concerns about differential task difficulty have strengthened the conclusions that can be drawn from the study.

The authors' response does not completely mitigate the concern noted by all 3 reviewers that the control tasks were easier than their corresponding experimental tasks (for everything but the fluid cognition task). The specific trouble with this issue can be appreciated by looking at Figure 4A, for example, which shows that area PF was activated for many individuals in both the control task and the experimental mechanical problem-solving task, but more so for the latter. Since the experimental task was harder (and more trial time was likely spent on task trying to solve it), the concern remains that area PF was driven harder by the experimental task in part due to the more challenging nature of that task.

The revised manuscript counters that the fluid cognition task was also harder than its control condition, yet did not activate PF more than its control condition. But this response seems to sidestep the central point of the reviewers' concerns: the fundamental computations that underlie the technical reasoning tasks may also be present in the respective (non technical-reasoning-based) control tasks and drive area PF activations to greater or lesser degrees based on how much they tax those computations. The fact that the fluid cognition experimental task and control task are not differentially difficult does not mitigate this concern, it just suggests that neither of those tasks tap the same fundamental computations, whatever they may be. (As an added note, Figures 2 and 4 show that both the PHYS-only and INT+PHYS mentalizing tasks only weakly activated PF, and both of these tasks were easier than the other technical cognition tasks).

The new ROI analysis with removal of subjects who performed below 50% in the revised manuscript is somewhat helpful, but there are two remaining issues: 1) chance performance is defined by a binomial test in this case, so scores somewhat above 50% may still be at chance depending on the number of items, and thus there may have been subjects who were not removed who could not perform the tasks; 2) it would have been convincing to include accuracy as a covariate in the modeling of BOLD parameter estimates for the remaining above-chance subjects to ensure that all reported effects remain once differential task difficulty is taken into account. It also appears that the legend for Figure S2, which indicates that the figure includes just subjects who performed at or below 50%, may not be correct; does the figure instead show data from subjects who performed at or above 50%?

Despite these remaining concerns, there are many aspects of this revised study that render it a useful contribution that will likely spur further research in this very interesting area.

Reviewer #3 (Public review):

Summary:

The manuscript by Kaya et al. explores the effects of feeding on sharp wave-ripples (SWRs) in the hippocampus, which could reveal a better understanding of how metabolism is regulated by neural processes. Expanding on prior work that showed that SWRs trigger a decrease in peripheral glucose levels, the authors further tested the relationship between SWRs and meal consumption by recording LFPs from the dorsal CA1 region of the hippocampus before and after meal consumption. They found an increase in SWR magnitude during sleep after food intake, in both food-restricted and ad libitum fed conditions. Using fiber photometry to detect GABAergic neuron activity in the lateral hypothalamus, they found increased activity locked to the onset of SWRs. They conclude that the animal's satiety state modulates the amplitude and rate of SWRs, and that SWRs modulate downstream circuits involved in regulating feeding.

The authors have addressed prior requests for revision and clarification, and provide a convincing case for SWRs being modulated by satiety state. These experiments provide an important step forward in understanding how metabolism is regulated in the brain. The study will likely be of great interest in the field of learning and memory while carrying broader implications for understanding brain-body physiology.

Reviewer #3 (Public review):

Summary:

The authors present a study building on their previous work on activation of the general stress response phosphatase, RsbU, from Bacillus subtilis. Using computed structural models of the RsbU dimer the authors map previously identified activating mutations onto the structure and suggest further protein variants to test the role of the predicted linker helix and the interaction with RsbT on the activation of the phosphatase activity.

Using in vivo and in vitro activity assays, the authors demonstrate that linker variants can constitutively activate RsbU and increase the affinity of the protein for RsbT, thus showing a link between the structure of the linker region and RsbT binding.

Small angle X-ray scattering experiments on RsbU variants alone, and in complex with RsbT show structural changes consistent with a decreased flexibility of the RsbU protein, which are hypothesised to indicate an disorder-order transition in the linker when RsbT binds. This interpretation of the data is consistent with the biochemical data presented by the authors.

Further computed structure models are presented for other protein phosphates from different bacterial species and the authors propose a model for phosphatase activation by partner binding. They compare this to the activation mechanisms proposed for histidine kinase two-component systems and GGDEF proteins and suggest the individual domains could be swapped to give a toolkit of modular parts for bacterial signalling.

Strengths:

The key mutagenesis data is presented with two lines of evidence to demonstrate RsbU activation - in vivo sigma-b activation assays utilising a beta-galactosidase reporter and in vitro activity assays against the RsbV protein, which is the downstream target of RsbU. These data support the hypothesis for RsbT binding to the RsbU linker region as well as the dimerisation domain to activate the RsbU activity.

Weaknesses:

Small angle scattering curves are difficult to unambiguously interpret, but the authors present good interpretations that fit with the biochemical data presented. These interpretations should be considered as models for future testing with other methods - hydrogen/deuterium exchange mass spectrometry, would be a good additional method to use, as exchange rates in the linker region would be affected significantly by the disorder/order transition on RsbT binding.

The interpretation of the computed structure models is provided with a few caveats related to the bias in the models returned by AlphaFold2. For the full-length models of RsbU and other phosphatase proteins, the relationship of the domains to each other is likely to be the least reliable part of the models - this is apparent from the PAE plots shown in supplementary figure 8.

Comments on revisions:

The authors have addressed the review comments satisfactorily for this manuscript to stand as a version of record.

Reviewer #3 (Public review):

This study investigates the characteristics of the autofluorescence signal excited by 740 nm 2-photon excitation, in the range of 420-500 nm, across the Drosophila brain. The fluorescence lifetime (FL) appears bi-exponential, with a short 0.4 ns time constant followed by a longer decay. The lifetime decay and the resulting parameter fits vary across the brain. The resulting maps reveal anatomical landmarks, which simultaneous imaging of genetically encoded fluorescent proteins helps to identify. Past work has shown that the autofluorescence decay time course reflects the balance of the redox enzyme NAD(P)H vs. its protein-bound form. The ratio of free-to-bound NADPH is thought to indicate relative glycolysis vs. oxidative phosphorylation, and thus shifts in the free-to-bound ratio may indicate shifts in metabolic pathways. The basics of this measure have been demonstrated in other organisms, and this study is the first to use the FLIM module of the STELLARIS 8 FALCON microscope from Leica to measure autofluorescence lifetime in the brain of the fly. Methods include registering the brains of different flies to a common template and masking out anatomical regions of interest using fluorescence proteins.

The analysis relies on fitting an FL decay model with two free parameters, f_free and t_bound. F_free is the fraction of the normalized curve contributed by a decaying exponential with a time constant of 0.4 ns, thought to represent the FL of free NADPH or NADH, which apparently cannot be distinguished. T_bound is the time constant of the second exponential, with scalar amplitude = (1-f_free). The T_bound fit is thought to represent the decay time constant of protein-bound NADPH but can differ depending on the protein. The study shows that across the brain, T_bound can range from 0 to >5 ns, whereas f_free can range from 0.5 to 0.9 (Figure 1a). These methods appear to be solid, the full range of fits are reported, including maximum likelihood quality parameters, and can be benchmarks for future studies.

The authors measure the properties of NADPH-related autofluorescence of Kenyon Cells (KCs) of the fly mushroom body. The results from the three main figures are:

(1) Somata and calyx of mushroom bodies have a longer average tau_bound than other regions (Figure 1e);

(2) The f_free fit is higher for the calyx (input synapses) region than for KC somata (Figure 2b);

(3) The average across flies of average f_free fits in alpha/beta KC somata decreases from 0.734 to 0.718. Based on the first two findings, an accurate title would be "Autofluorecense lifetime imaging reveals regional differences in NADPH state in Drosophila mushroom bodies."

The third finding is the basis for the title of the paper and the support for this claim is unconvincing. First, the difference in alpha/beta f_free (p-value of 4.98E-2) is small compared to the measured difference in f_free between somas and calyces. It's smaller even than the difference in average soma f_free across datasets (Figure 2b vs c). The metric is also quite derived; first, the model is fit to each (binned) voxel, then the distribution across voxels is averaged and then averaged across flies. If the voxel distributions of f_free are similar to those shown in Supplementary Figure 2, then the actual f_free fits could range between 0.6-0.8. A more convincing statistical test might be to compare the distributions across voxels between alpha/beta vs alpha'/beta' vs. gamma KCs, perhaps with bootstrapping and including appropriate controls for multiple comparisons.

I recommend the authors address two concerns. First, what degree of fluctuation in autofluorescence decay can we expect over time, e.g. over circadian cycles? That would be helpful in evaluating the magnitude of changes following conditioning. And second, if the authors think that metabolism shifts to OXPHOS over glycolosis, are there further genetic manipulations they could make? They test LDH knockdown in gamma KCs, why not knock it down in alpha/beta neurons? The prediction might be that if it prevents the shift to OXPHOS, the shift in f_free distribution in alpha/beta KCs would be attenuated. The extensive library of genetic reagents is an advantage of working with flies, but it comes with a higher standard for corroborating claims.

FLIM as a method is not yet widely prevalent in fly neuroscience, but recent demonstrations of its potential are likely to increase its use. Future efforts will benefit from the description of the properties of the autofluorescence signal to evaluate how autofluorescence may impact measures of FL of genetically engineered indicators.

Reviewer #3 (Public review):

Summary:

The authors describe important new biochemical elements in the synthesis of a class of critical developmental signaling molecules, BMP4. They also present a highly detailed description of developmental anomalies in mice bearing known human mutations at these specific elements.

Strengths:

This paper presents exceptionally detailed descriptions of pathologies occurring in BMP4 mutant mice. Novel findings are shown regarding the interaction of propeptide phosphorylation and convertase cleavage, both of which will move the field forward. Lastly, a provocative hypothesis regarding furin access to cleavage sites is presented, supported by Alphafold predictions.

Reviewer #3 (Public review):

Summary:

The manuscript by Chang et al. aims to investigate how the behavioral relevance of auditory and visual stimuli influences the way in which the primary auditory cortex encodes auditory, visual and audiovisual information. The main results is that behavioral training induces an increase in the encoding of auditory and visual information and in multisensory enhancement that is mainly related to the choice located contralaterally with respect to the recorded hemisphere.

Strengths:

The manuscript reports the results of an elegant and well planned experiment meant to investigate if auditory cortex encodes visual information and how learning shapes visual responsiveness in auditory cortex. Analyses are typically well done and properly address the questions raised

Weaknesses:

The authors have addressed most of my comments satisfactorily. However, I am still not convinced by the authors' claim that the use of LED should lead to visually-evoked responses with faster dynamics compared to the use of normal screens. In fact, previous studies using screen-emitted flashed did not report such faster dynamics. Visually-evoked responses in V1 (which are expected to occur earlier than A1) typically do not show onset latencies faster than 40 ms, and have a peak latency of about 100-120 ms. The dynamics shown in the new supplementary Fig. 2 are still faster than this, and thus should be explained. The authors' claim is in fact not supported by cited literature. The authors should at least provide evidence that a similar effect has been observed previously, or otherwise collect evidence themselves. In the absence of such evidence, I remain dubious about the visual nature of the observed activity, especially since, in contrast with what the authors say elsewhere in the rebuttal, involuntary motor reaction to (at least auditory) stimuli can be extremely fast (<40 ms; Clayton et al. 2024) and might thus potentially, at least partially, explain the observed "visual" response.

Reviewer #3 (Public review):

Summary:

This manuscript by Bergheim et al investigates the molecular and developmental dynamics of the matrisome, a set of gene products that comprise the extra cellular matrix, in the sea anemone Nematostella vectensis using transcriptomic and proteomic approaches. Previous work has examined the matrisome of the hydra, a medusozoan, but this is the first study to characterize the matrisome in an anthozoan. The major finding of this work is a description of the components of the matrisome in Nematostella, which turns out to be more complex than that previously observed in hydra. The authors also describe remodeling of the extra cellular matrix that occurs in the transition from larva to primary polyp, and from primary polyp to adult. The authors interpret these data to support previously proposed (Steinmetz et al. 2017) homology between the cnidarian endoderm with the bilaterian mesoderm.

Strengths:

The data described in this work are comprehensive (but see important considerations of reviewer #1) combining both transcriptome and proteomic interrogation of key stages in the life history of Nematostella and are of value to the community.

Weaknesses:

The authors offer numerous evolutionary interpretations of their results that I believe are unfounded. The main problem with extending these results, together with previous results from hydra, into an evolutionary synthesis that aims to reconstruct the matrisome of the ancestral cnidarian is that we are considering data from only two species. I agree with the authors' depiction of hydra as "derived" relative to other medusozoans and see it as potentially misleading to consider the hydra matrisome as an exemplar for the medusozoan matrisome. Given the organismal and morphological diversity of the phylum, a more thorough comparative study that compares matrisome components across a selection of anthozoan and medusozoan species using formal comparative methods to examine hypotheses is required.<br /> Specifically, I question the author's interpretation of the evolutionary events depicted in this statement:

"The observation that in Hydra both germ layers contribute to the synthesis of core matrisome proteins (Epp et al. 1986; Zhang et al. 2007) might be related to a secondary loss of the anthozoan-specific mesenteries, which represent extensions of the mesoglea into the body cavity sandwiched by two endodermal layers."<br /> Anthozoans and medusozoans are evolutionary sisters. Therefore, secondary loss of "anthozoan-like mesenteries" in hydrozoans is at least as likely as the gain of this character state in anthozoans. By extension, there is no reason to prefer the hypothesis that the state observed in Nematostella, where gastroderm is responsible for the synthesis of the core matrisome components, is the ancestral state of the phylum.<br /> Moreover, the fossil evidence provided in support of this hypotheses (Ou et al. 2022)is not relevant here because the material described in that work is of a crown group anthozoan, which diversified well after the origin of Anthozoa. The phylogenetic structure of Cnidaria has been extensively studied using phylogenomic approaches and is generally well supported(Kayal et al. 2018; DeBiasse et al. 2024). Based on these analyses, anthozoans are not on a "basal" branch, as the authors suggest. The structure of cnidarian phylogeny bifurcates with Anthozoa forming one clade and Medusozoa forming the other. From the data reported by Bergheim and co-workers, it is not possible to infer the evolutionary events that gave rise to the different matrisome states observed in Nematostella (an anthozoan) and hydra (a medusozoan).<br /> Furthermore, I take the observation in Fig 5 that anthozoan matrisomes generally exhibit a higher complexity than other cnidarian species to be more supportive of a lineage specific expansion of matrisome components in the Anthozoa, rather than those components being representative of an ancestral state for Cnidaria. Whatever the implication, I take strong issue with the statement that "the acquisition of complex life cycles in medusozoa, that are distinguished by the pelagic medusa stage, led to a secondary reduction in the matrisome repertoire." There is no causal link in any of the data or analyses reported by Bergheim and co-workers to support this statement and, as stated above, while we are dealing with limited data, insufficient to address this question, it seems more likely to me that the matrisome expanded in anthozoans, contrasting with the authors conclusions. While the discussion raises many interesting evolutionary hypotheses related to the origin of the cnidarian matrisome, which is of vital interest if we are to understand the origin of the bilaterian matrisome, a more thorough comparative analysis, inclusive of a much greater cnidarian species diversity, is required if we are to evaluate these hypotheses.

DeBiasse MB, Buckenmeyer A, Macrander J, Babonis LS, Bentlage B, Cartwright P, Prada C, Reitzel AM, Stampar SN, Collins A, et al. 2024. A Cnidarian Phylogenomic Tree Fitted With Hundreds of 18S Leaves. Bulletin of the Society of Systematic Biologists [Internet] 3. Available from: https://ssbbulletin.org/index.php/bssb/article/view/9267

Epp L, Smid I, Tardent P. 1986. Synthesis of the mesoglea by ectoderm and endoderm in reassembled hydra. J Morphol [Internet] 189:271-279. Available from: https://pubmed.ncbi.nlm.nih.gov/29954165/

Kayal E, Bentlage B, Sabrina Pankey M, Ohdera AH, Medina M, Plachetzki DC, Collins AG, Ryan JF. 2018. Phylogenomics provides a robust topology of the major cnidarian lineages and insights on the origins of key organismal traits. BMC Evol Biol [Internet] 18:1-18. Available from: https://bmcecolevol.biomedcentral.com/articles/10.1186/s12862-018-1142-0

Ou Q, Shu D, Zhang Z, Han J, Van Iten H, Cheng M, Sun J, Yao X, Wang R, Mayer G. 2022. Dawn of complex animal food webs: A new predatory anthozoan (Cnidaria) from Cambrian. The Innovation 3:100195.

Steinmetz PRH, Aman A, Kraus JEM, Technau U. 2017. Gut-like ectodermal tissue in a sea anemone challenges germ layer homology. Nature Ecology & Evolution 2017 1:10 [Internet] 1:1535-1542. Available from: https://www.nature.com/articles/s41559-017- 0285-5

Zhang X, Boot-Handford RP, Huxley-Jones J, Forse LN, Mould AP, Robertson DL, Li L, Athiyal M, Sarras MP. 2007. The collagens of hydra provide insight into the evolution of metazoan extracellular matrices. J Biol Chem [Internet] 282:6792-6802. Available from: https://pubmed.ncbi.nlm.nih.gov/17204477/

Reviewer #3 (Public review):

The study aimed to address a fundamental question in T. cruzi and Chagas disease biology - how much variation is there in gene expression between individual parasites? This is particularly important with respect to the surface protein-encoding genes, which are mainly from massive repetitive gene families with 100s to 1000s of variant sequences in the genome. There is very little direct evidence for how the expression of these genes is controlled. The authors conducted a single-cell RNAseq experiment of in vitro cultured parasites with a mixture of amastigotes and trypomastigotes. Most of the analysis focused on the heterogeneity of gene expression patterns amongst trypomastigotes. They show that heterogeneity was very high for all gene classes, but surface-protein encoding genes were the most variable. In the case of the trans-sialidase gene family, many sequence variants were only detected in a small minority of parasites. The biology of the parasite (e.g. extensive post-transcriptional regulation) and potential technical caveats (e.g. high dropout rates across the genome) make it difficult to infer what this might mean for actual protein expression on the parasite surface.

(1) Limit of detection and gene dropouts

An average of ~1100 genes are detected per parasite which indicates a dropout rate of over 90%. It appears that RNA for the "average" single copy 'core' gene is only detected in around 3% of the parasites sampled (Figure 2c: ~100 / 3192). This may be comparable with some other trypanosome scRNAseq studies, but this still seems to be a major caveat to the interpretation that high cell-to-cell variability in gene expression is explained by biological rather than technical factors. The argument would be more convincing if the dropout rates and expression heterogeneity were minimal for well-known highly expressed genes e.g. tubulin, GAPDH, and ribosomal RNAs. Admittedly, in their Final Remarks, the authors are very cautious in their interpretation, but it would be good to see a more thorough discussion of technical factors that might explain the low detection rates and how these could be tested or overcome in future work.

(2) Heterogeneity across the board

The authors focus on the relative heterogeneity in RNA abundance for surface proteins from the multicopy gene families vs core genes. While multicopy gene sequences do show more cell-to-cell variability, the differences (Figure 2D) are roughly average Gini values of 0.99 vs 0.97 (single copy) or 0.95 (ribosomal). Other studies that have applied similar approaches in other systems describe Gini values of < 0.2-0.25 for evenly expressed "housekeeping" genes (PMIDs 29428416, 31784565). Values observed here of >0.9 indicate that the distribution for all gene classes is extremely skewed and so the biological relevance of the comparison is uncertain.

Nevertheless, this study does provide some tantalising evidence that the expression of surface genes may vary substantially between individual parasites in a single clonal population. The study is also amongst the very first to apply scRNAseq to T. cruzi, so the broader data set will be an important resource for researchers in the field.

Reviewer #3 (Public review):

Summary:

The authors aim to develop glmSMA, a network-regularized linear model that accurately infers spatial gene expression patterns by integrating single-cell RNA sequencing data with spatial transcriptomics reference atlases. Their goal is to reconstruct the spatial organization of individual cells within tissues, overcoming the limitations of existing methods that either lack spatial resolution or sensitivity.

Strengths:

(1) Comprehensive Benchmarking:

Compared against CellTrek and Novosparc, glmSMA consistently achieved lower Kullback-Leibler divergence (KL divergence) scores, indicating better cell assignment accuracy.

Outperformed CellTrek in mouse cortex mapping (90% accuracy vs. CellTrek's 60%) and provided more spatially coherent distributions.

(2) Experimental Validation with Multiple Real-World Datasets:

The study used multiple biological systems (mouse brain, Drosophila embryo, human PDAC, intestinal villus) to demonstrate generalizability.

Validation through correlation analyses, Pearson's coefficient, and KL divergence support the accuracy of glmSMA's predictions.

Weaknesses:

(1) The accuracy of glmSMA depends on the selection of marker genes, which might be limited by current FISH-based reference atlases.

(2) glmSMA operates under the assumption that cells with similar gene expression profiles are likely to be physically close to each other in space which not be true under various heterogeneous environments.

Reviewer #3 (Public review):

Overall, this is an outstanding paper. It presents a novel approach to estimating rotavirus vaccine efficacy; is clearly written and presented; and has implications for this vaccine specifically as well as type-specific vaccine evaluation more generally. The analytical framework is a creative and there is rigorous use of data and statistical approaches. It has long been argued that rotavirus immunity/vaccine performance operates beyond the scale of G/P genotyping. This paper is the first to demonstrate that convincingly, using data on all 11 viral genes and whole genome sequence analysis. I have only minor comments that I recommend should be addressed.

Reviewer #3 (Public review):

Summary:

This study addressed the TCR pairing types and CDR3 characteristics of Treg cells. By analyzing scRNA and TCR-seq data, it claims that 10-20% of dual TCR Treg cells exist in mouse lymphoid and non-lymphoid tissues and suggests that dual TCR Treg cells in different tissues may play complex biological functions.

Strengths:

The study addresses an interesting question of how dual-TCR-expressing Treg cells play roles in tissues.

Weaknesses:

This study is inadequate, particularly regarding data interpretation, statistical rigor, and the discussion of the functional significance of Dual TCR Tregs.

Major Comments:

(1) Definition of Dual TCR and Validity of Doublet Removal<br /> This study analyzes Treg cells with Dual TCR, but it is not clearly stated how the possibility of doublet cells was eliminated. The authors mention using DoubletFinder for detecting doublets in scRNA-seq data, but is this method alone sufficient?<br /> We strongly recommend reporting the details of doublet removal and data quality assessment in the Supplementary Data.

(2) Inconsistency in the Proportion of Dual TCR T Cells in the Skin Across Figures<br /> In Figure 3D, the proportion of Dual TCR T cells (A1+A2+B1+B2) in the skin is reported to be very high compared to other tissues. However, in Figure 4C, the proportion appears lower than in other tissues, which may be due to contamination by non-Tregs. The authors should clarify why it was necessary to include non-Tregs as a target for analysis in this study. Additionally, the sensitivity of scRNA-seq and TCR-seq may vary between tissues and may also be affected by RNA quality and sequencing depth in skin samples, so the impact of measurement bias should be assessed.

(3) Issue of Cell Contamination<br /> In Figure 2A, the data suggest a high overlap between blood, kidney, and liver samples, likely due to contamination. Can the authors effectively remove this effect? If the dataset allows, distinguishing between blood-derived and tissue-resident Tregs would significantly enhance the reliability of the findings. Otherwise, it would be difficult to separate biological signals from contamination noise, making interpretation challenging.

(4) Inconsistency Between CDR3 Overlap and TCR Diversity<br /> The manuscript states that Single TCR Tregs have a higher CDR3 overlap, but this contradicts the reported data that Dual TCR Tregs exhibit lower TCR diversity (higher 1/DS score). Typically, when TCR diversity is low (i.e., specific clones are concentrated), CDR3 overlap is expected to increase. The authors should carefully address this discrepancy and discuss possible explanations.

(5) Functional Evaluation of Dual TCR Tregs<br /> This study indicates gene expression differences among tissue-resident Dual TCR T cells, but there is no experimental validation of their functional significance. Including functional assays, such as suppression assays or cytokine secretion analysis, would greatly enhance the study's impact.

(6) Appropriateness of Statistical Analysis<br /> When discussing increases or decreases in gene expression and cell proportions (e.g., Figure 2D), the statistical methods used (e.g., t-test, Wilcoxon, FDR correction) should be explicitly described. They should provide detailed information on the statistical tests applied to each analysis.

Reviewer #3 (Public review):

Summary:

Mancl et al. report four Cryo-EM structures of glycosylated and soluble Angiotensin-I converting enzyme (sACE) dimer. This moves forward the structural understanding of ACE, as previous analysis yielded partially denatured or individual ACE domains. By performing a heterogeneity analysis, the authors identify three structural conformations (open, intermediate open, and closed) that define the openness of the catalytic chamber and structural features governing the dimerization interface. They show that the dimer interface of soluble ACE consists of an N-terminal glycan and protein-protein interaction region, as well as C-terminal protein-protein interactions. Further heterogeneity mining and all-atom molecular dynamic simulations show structural rearrangements that lead to the opening and closing of the catalytic pocket, which could explain how ACE binds its substrate. These studies could contribute to future drug design targeting the active site or dimerization interface of ACE.

Strengths:

The authors make significant efforts to address ACE denaturation on cryo-EM grids, testing various buffers and grid preparation techniques. These strategies successfully reduce denaturation and greatly enhance the quality of the structural analysis. The integration of cryoDRGN, 3DVA, RECOVAR, and all-atom simulations for heterogeneity analysis proves to be a powerful approach, further strengthening the overall experimental methodology.

Weaknesses:

In general, the findings are supported by experimental data, but some experimental details and approaches could be improved. For example, CryoDRGN analysis is limited to the top 5 PCA components for ease of comparison with cryoSPARC 3DVA, but wouldn't an expansion to more components with CryoDRGN potentially identify further conformational states? The authors also say that they performed heterogeneity analysis on both datasets but only show data for one. The results for the first dataset should be shown and can be included in supplementary figures. In addition, the authors mention that they were not successful in performing cryoSPARC 3DFLex analysis, but they do not show their data or describe the conditions they used in the methods section. These data should be added and clearly described in the experimental section.

Some cryo-EM data processing details are missing. Please add local resolution maps, box sizes, and Euler angle distributions and reference the initial PDB model used for model building.

Reviewer #3 (Public review):

Summary:

The study titled "Zinc is a Key Regulator of the Sperm-Specific K+ Channel (Slo3) Function" aims to investigate the role of intracellular zinc in sperm capacitation and its regulation of the sperm-specific Slo3 potassium channel. Capacitation is a crucial physiological process that enables sperm to fertilize an egg, and membrane hyperpolarization through Slo3 activation is a well-established event in this process. The authors propose that intracellular zinc dynamically decreases during capacitation and inhibits Slo3-mediated K⁺ currents, thereby playing a regulatory role in sperm function.

Strengths:

(1) Novel Contribution to Sperm Physiology.

The study provides new insights into how zinc dynamics contribute to sperm capacitation, specifically through its direct inhibition of Slo3 activity.<br /> Previous research has focused primarily on extracellular zinc's effect on sperm function; this work expands the discussion to intracellular zinc regulation, an area with limited prior investigation.

(2) Strong Electrophysiological Evidence.

The study employs inside-out patch-clamp recordings in Xenopus oocytes to demonstrate zinc's direct inhibition of Slo3 currents.<br /> The observed slow dissociation of zinc from Slo3 suggests a long-lasting regulatory effect, adding to the understanding of ion channel modulation in sperm cells.

(3) Molecular Mechanistic Insights

Using Molecular Dynamics (MD) simulations and mutagenesis, the authors identify potential zinc-binding sites within Slo3's voltage-sensing domain (VSD), particularly E169 and E205.

These computational predictions are supported by electrophysiological recordings, strengthening the argument that zinc directly binds and inhibits Slo3.

(4) Physiological Relevance and Functional Implications

The study suggests that zinc inhibition of Slo3 could contribute to sperm motility regulation during capacitation.

The authors provide sperm motility assays as supporting evidence, showing that zinc chelation affects motility only after capacitation has begun, suggesting a dynamic role of intracellular zinc in the capacitation process.

Weaknesses:

While the study presents compelling electrophysiological data and molecular insights, there are several critical gaps that must be addressed before fully supporting the physiological relevance of the findings.

(1) The authors should measure the effects in sperm cells using the patch-clamp technique to directly record Slo3 currents. By normalizing Slo3 currents to cell capacitance at different intracellular zinc concentrations, the authors can quantitatively assess the extent of Slo3 inhibition by zinc and strengthen the physiological relevance of their findings.

(2) Lack of Controls in Non-Capacitated Sperm

The claim that zinc is exported from sperm during capacitation needs stronger experimental validation.

The authors did not include a control group of non-capacitated sperm in key fluorescence imaging experiments, making it difficult to confirm that the observed zinc decrease is capacitation-specific rather than a general zinc redistribution process.

To strengthen this conclusion, experiments should be performed in non-capacitating conditions to determine whether intracellular zinc levels remain unchanged.

(3) Unclear Role of Zinc in Physiological Capacitation

The study clearly demonstrates zinc inhibition of Slo3 but does not sufficiently establish how this affects capacitation at a functional level.

Additional motility and capacitation markers should be analyzed to confirm that zinc influences sperm behavior beyond Slo3 inhibition.

(4) Insufficient Data on Zinc-Slo3 Specificity

The authors should consider using quinidine, a known washable Slo3 inhibitor, to confirm that zinc acts specifically on Slo3 channels rather than other endogenous ion channels.

The study would benefit from including washout controls in the inside-out patch-clamp recordings, as seen in Figure 3-Supplement 1, to confirm that zinc inhibition is reversible or long-lasting.

(5) Missing Discussion of Zinc's Role in CatSper Regulation

The study focuses solely on Slo3 but does not mention CatSper, the principal Ca²⁺ channel essential for sperm capacitation.

Zinc has been reported to inhibit CatSper activity, which could significantly impact sperm function.

The discussion should address whether zinc's effect on Slo3 represents a broader regulatory mechanism influencing multiple ion channels during capacitation.

Final Assessment

This work presents important findings on zinc regulation of Slo3 channels, supported by strong electrophysiological and molecular analyses. However, the physiological relevance of these findings remains unclear due to missing controls, and needs additional functional assays. Addressing these issues would significantly enhance the manuscript's scientific rigor and impact.

Reviewer #3 (Public review):

Summary:

This important study combines comparative genomics with other validation methods to identify the factors that mediate genome size evolution in Sordariomycetes fungi and their relationship with lifestyle. The study provides insights into genome architecture traits in this Ascomycete group, finding that, rather than transposons, the size of their genomes is often influenced by gene gain and loss. With an excellent dataset and robust statistical support, this work contributes valuable insights into genome size evolution in Sordariomycetes, a topic of interest to both the biological and bioinformatics communities.

Strengths:

This study is complete and well-structured.

Bioinformatics analysis is always backed by good sampling and statistical methods. Also, the graphic part is intuitive and complementary to the text.

Weaknesses:

The work is great in general, I just had issues with the Figure 1B interpretation.

I struggled a bit to find the correspondence between this sentence: "Most genomic features were correlated with genome size and with each other, with the strongest positive correlation observed between the size of the assembly excluding repeats and the number of genes (Figure 1B)." and the Figure 1B. Perhaps highlighting the key p values in the figure could help.

Reviewer #3 (Public review):

Summary:

The authors have developed an interactive knowledge-base that uses crowdsourcing information on antibodies and reagents for immunofluorescence imaging.

Strengths:

The authors provide an extremely relevant and needed interphase for a community-based IF reagent and protocol knowledgebase, and a well-built interface. All the links on their website work, the information provided, reagents, datasets, videos, and protocols are very informative. The instructions for the community researchers to contribute are clear and they provide detailed instructions on how to technically proceed.

Weaknesses:

Reporting of the validation of antibodies could be improved. To increase public participation they suggest reducing the amount of details that one needs to submit to claim that something does not work. However, in our experience, this information is critical to be shared with the community.

Reviewer #3 (Public review):

Summary:

This study by Park and colleagues investigated how the medial prefrontal cortex (mPFC) influences behavior and hippocampal place cell activity during a two-frame active place avoidance task in rats. Rats learned to avoid the location of mild shock within a rotating arena, with the shock zone being defined relative to distal cues in the room. Permanent chemical lesions of the mPFC did not impair the ability to avoid the shock zone by using the distal cues and ignoring proximal cues in the arena. In parallel, hippocampal place cells alternated between two spatial tuning patterns, one anchored to the distal cues and the other to the proximal cues, and this alteration was not affected by the mPFC lesion. Based on these findings, the authors argue that the mPFC is not essential for differentiating between task-relevant and irrelevant information.

Strengths:

This study was built on substantial work by the Fenton lab that validated their two-frame active place avoidance task and provided sound theoretical and analytical foundations. Additionally, the effectiveness of mPFC lesions was validated by several measures, enabling the authors to base their argument on the lack of lesion effects on behavior and place cell dynamics.

Weaknesses:

The authors define cognitive control as "the ability to judiciously use task-relevant information while ignoring salient concurrent information that is currently irrelevant for the task." (Lines 77-78). This definition is much simpler than the one by Miller and Cohen: "the ability to orchestrate thought and action in accordance with internal goals (Ref. 1)" and by Robbins: "processes necessary for optimal scheduling of complex sequence of behaviour." (Dalley et al., 2004, PMID: 15555683). Differentiating between task-relevant and irrelevant information is required in various behavioral tasks, such as differential learning, reversal learning, and set-shifting tasks. Previous rodent behavioral studies have shown that the integrity of the mPFC is necessary for set-shifting but not for differential or reversal learning (e.g., Enomoto et al., 2011, PMID: 21146155; Cho et al., 2015, PMID: 25754826). In the present task design, the initial training is a form of differential learning between proximal and distal cues, and the conflict training is akin to reversal learning. Therefore, the lack of lesion effects is somewhat expected. It would be interesting to test whether mPFC lesions impair set-shifting in their paradigm (e.g., the shock zone initially defined by distal cues and later by proximal cues). If the mPFC lesions do not impair this ability and associated hippocampal place dynamics, it will provide strong support for the authors' local-computation hypothesis.

Comments on revisions:

The authors fully addressed my comments. I do not have any additional suggestions.

Reviewer #3 (Public review):

Summary:

Obray et al. investigate the long-lasting effects of adolescent intermittent ethanol (AIE) in rats, a model of alcohol dependence, on a neural circuit within prefrontal cortex. The studies are focused on inputs from the basolateral amygdala (BLA) onto parvalbumin (PV) interneurons and pyramidal cells that project to the periaqueductal gray (PAG). The authors found that AIE increased BLA excitatory drive onto parvalbumin interneurons and increased BLA feedforward inhibition onto PAG-projecting neurons.

Strengths:

Fully powered cohorts of male and female rodents are used, and the design incorporates both AIE and an acute pain model. The authors used several electrophysiological techniques to assess synaptic strength and excitability from a few complimentary angles. The design and statistical analysis are sound, and the evidence supporting synaptic changes following AIE results is convincing. The authors have also revised the Discussion to assimilate the findings within prior work out of their lab and others.

Weaknesses:

(1) There is incomplete evidence supporting some of the conclusions drawn in this manuscript. The authors claim the changes in feedforward inhibition onto pyramidal cells are due to the changes in parvalbumin interneurons; however, the authors did not determine that PV cells mediate the feedforward BLA op-IPSCs and changes following AIE (this would require a manipulation to reduce/block PV-IN activity). This limitation in results and interpretation is important because prior work shows BLA-PFC feedforward IPSCs can be driven by somatostatin cells. Cholecystokinin cells are also abundant basket cells in PFC and have been recently shown to mediate feedforward inhibition from thalamus and ventral hippocampus, so it's also possible that CCK cells are involved in the effects observed here

(2) The authors conclude that the changes in this circuit likely mediate long-lasting hyperalgesia, but this is not addressed experimentally. In some ways, the focused nature of the study is a benefit in this regard, as there is extensive prior literature linking this circuit with pain behaviors in alternative models (e.g., SNI), but it should be noted that these studies have not assessed hyperalgesia stemming from prior alcohol exposure. While the current studies do not include a causative behavioral manipulation, the strength of the association between BLA-PL-PAG function and hyperalgesia could be bolstered by with current data if there were relationships detected between electrophysiological properties and hyperalgesia.

(3) It should be noted that asEPSC frequency can also reflect changes in number of functional/detectable synapses. This measurement is also fairly susceptible to differences in inter-animal differences in ChR2 expression. There are other techniques for assessing presynaptic release probability (e.g., PPR, MK-801 sensitivity) that would improve the interpretation of these studies if that is intended to be a point of emphasis.

Reviewer #3 (Public review):

Mondal et al. use computational modeling to investigate how activity-dependent shifts in voltage-dependent (in)activation curves can complement activity-dependent changes in ion channel conductance to support homeostatic plasticity. While changes in the voltage-dependent properties of ion channels are known to modulate neuronal excitability, their role as a homeostatic plasticity mechanism interacting with channel conductance has been largely unexplored. The results presented here demonstrate that activity-dependent regulation of voltage-dependent properties can interact with plasticity in channel conductance to allow neurons to attain and maintain target activity patterns, in this case, intrinsic bursting. These results also show that the rate of channel voltage-dependent shifts can influence steady-state parameters reached as the model stabilizes into a stable intrinsic bursting state. That is, the rate of these modifications shapes the range of channel conductances and half-(in)activation parameters as well as activity characteristics such as burst period and duration. A major conclusion of the study is that altering the timescale of channel voltage dependence can seamlessly shift a neuron's activity characteristics, a mechanism that the authors argue may be employed by neurons to adapt to perturbations. While the study's conclusions are mostly well-supported, additional analyses, and simulations are needed.

(1) A main conclusion of this study is that the speed at which (in)activation dynamics change determines the range of possible electrical patterns. The authors propose that neurons may dynamically regulate the timescale of these changes (a) to achieve alterations in electrical activity patterns, for example, to preserve the relative phase of neuronal firing in a rhythmic network, and (b) to adapt to perturbations. The results presented in Figure 4 clearly demonstrate that the timescale of (in)activation modifications impacts the range of activity patterns generated by the model as it transitions from an initial state of no activity to a final steady-state intrinsic burster. This may have important implications for neuronal development, as discussed by the authors.

However, the authors also argue that the model neuron's dynamics - such as period, and burst duration, etc - could be dynamically modified by altering the timescale of (in)activation changes (Figure 6 and related text). The simulations presented here, however, do not test whether modifications in this timescale can shift the model's activity features once it reaches steady state. In fact, it is unlikely that this would be the case since, at steady-state, calcium targets are already satisfied. It is likely, however, as the authors suggest, that the rate at which (in)activation dynamics change may be important for neuronal adaptation to perturbations, such as changes in temperature or extracellular potassium. Yet, the results presented here do not examine how modifying this timescale influences the model's response to perturbations. Adding simulations to characterize how alterations in the rate of (in)activation dynamics affect the model's response to perturbations-such as transiently elevated extracellular potassium (Figure 5) - would strengthen this conclusion.

(2) Another key argument in this study is that small, coordinated changes in channel (in)activation contribute to shaping neuronal activity patterns, but that, these subtle effects may be obscured when averaging across a population of neurons. This may be the case; however, the results presented don't clearly demonstrate this point. This point would be strengthened by identifying correlations, if they exist, between (in)activation curves, conductance, and the resulting bursting patterns of the models for the simulations presented in Figure 2 and Figure 4, for example. Alternatively, or additionally, relationships between (in)activation curves could be probed by perturbing individual (in)activation curves and quantifying how the other model parameters compensate, which could clearly illustrate this point.

Reviewer #3 (Public review):

Summary

This manuscript, from the developers of the novel DREADD-selective agonist DCZ (Nagai et al., 2020), utilizes a unique dataset where multiple PET scans in a large number of monkeys, including baseline scans before AAV injection, 30-120 days post-injection, and then periodically over the course of the prolonged experiments, were performed to access short- and long-term dynamics of DREADD expression in vivo, and to associate DREADD expression with the efficacy of manipulating the neuronal activity or behavior. The goal was to provide critical insights into the practicality and design of multi-year studies using chemogenetics and to elucidate factors affecting expression stability.

Strengths are systematic quantitative assessment of the effects of both excitatory and inhibitory DREADDs, quantification of both the short-term and longer-term dynamics, a wide range of functional assessment approaches (behavior, electrophysiology, imaging), and assessment of factors affecting DREADD expression levels, such as serotype, promoter, titer (concentration), tag, and DREADD type.

Minor weaknesses are related to a few instances of suboptimal phrasing, and some room for improvement in time course visualization and quantification. These would be easily addressed in a revision.

These findings will undoubtedly have a very significant impact on the rapidly growing but still highly challenging field of primate chemogenetic manipulations. As such, the work represents an invaluable resource for the community.

Reviewer #3 (Public review):

A recent bioRxiv paper from Craig Hunter's lab (Gainey et al. 2024) puts into question several manuscripts that report that pathogen avoidance by the nematode C. elegans to the pathogenic bacteria, Pseudomonas aeruginosa, for several generations after initial exposure is not robust nor repeatable. From the Hunter lab publication, the authors tried to eliminate genetic drift of the pathogenic bacterial strains and C. elegans, as well as several experimental conditions, including assay temperature conditions and the effect of light.

The papers (Moore et al. 2019, Kaletsky et al. 2020, Moore et al. 2021 and Sengupta et al. 2024) that the Gainey et al. manuscript brings into question discovered that Pseudomonas aeruginosa can produce a small RNA (sRNA), P11, that is necessary and sufficient for pathogen avoidance of the future generation of C. elegans (up to F4 generation). The Gainey et al. manuscript does not assess the status of P11 production in their work.

Here, the Murphy group has made several new discoveries that highlight the differences with the work performed in the Hunter lab. One, the assay used to test attraction and avoidance of C. elegans for pathogenic bacteria differs amongst the two groups. In the Murphy lab papers, and many others in this field, the assay is established whereby worms can decide between spots of non-pathogenic bacteria (E. coli) or pathogenic (P. aeruginosa) on a single plate separated by a few centimeters. Also included in each spot is an aliquot of NaN3 to freeze the animals upon entry into their first bacterial choice. C. elegans will initially choose the pathogenic bacteria as its first choice and then learn to avoid the pathogenic spot thereafter. Therefore, establishing this first baseline attraction point is essential for determining future avoidance events. The Hunter lab did not use NaN3 and instead relied upon moving plates to 4°C to slow the worm's movements to count the population. Furthermore, the Hunter lab allowed the "choice" to proceed for an hour before moving to 4°C, making capture of the initial attraction phase of the choice assay difficult to discern since the worms could move freely from their initial choice due to the lack of the paralyzing NaN3.

The second major advance that the Murphy group has found is that the growth of P. aeruginosa prior to being used for the choice assay is critical. Growth on plates at 25°C, but not 20°C on plates or in liquid at 37°C, can produce the transgenerational inheritance of pathogen avoidance. Interestingly, P11 is only produced by P. aeruginosa at 25°C grown on plates. The Hunter group grew the Pseudomonas bacteria at 37°C in liquid with gentle shaking and then spotted onto assay plates followed by growth for 2 days at 25°C and then equilibrated to room temperature before the choice assay. The Hunter lab did not check the status of P11 production in any of their experiments.

The results from the Murphy group are solid and they go on to find genetic requirements in C. elegans required for the transgenerational response to P. aeruginosa and P11. Furthermore, they repeat their results with additional members of the Pseudomonas clade and find the same transgenerational avoidance response and new sRNAs responsible for the avoidance response to the newly tested Pseudomonas members.

Overall, the discrepancies between the Hunter work and the numerous papers for the Murphy group would tend to complicate this area of research. However, this eLife paper plainly illustrates the straightforward nature of the experimental setup and reconfirms the necessary and sufficient nature of P11 in orchestrating the multigenerational response to pathogenic Pseudomonas. It appears that ensuring the production of P11 from the Pseudomonas culture and ensuring that the assay captures the initial bacterial choice are essential to observe the transgenerational inheritance of the avoidance phenotype.

Reviewer #3 (Public review):

Summary:

To explore the diverse nature of somatosensation, Parkes et al. established and characterized a system for precise cutaneous stimulation of mice as they walk and run in naturalistic settings. This paper provides a framework for real-time body part tracking and targeted optical stimuli with high precision, ensuring reliable and consistent cutaneous stimulation. It can be adapted in somatosensation labs as a general technique to explore somatosensory stimulation and its impact on behavior, enabling rigorous investigation of behaviors that were previously difficult or impossible to study.

Strengths:

The authors characterized the closed-loop system to ensure that it is optically precise and can precisely target moving mice. The integration of accurate and consistent optogenetic stimulation of the cutaneous afferents allows systematic investigation of somatosensory subtypes during a variety of naturalistic behaviors. Although this study focused on nociceptors innervating the skin (Trpv1::ChR2 animals), this setup can be extended to other cutaneous sensory neuron subtypes, such as low-threshold mechanoreceptors and pruriceptors. This system can also be adapted for studying more complex behaviors, such as the maze assay and goal-directed movements.

Weaknesses:

Although the paper has strengths, its weakness is that some behavioral outputs could be analyzed in more detail to reveal different types of responses to painful cutaneous stimuli. For example, paw withdrawals were detected after optogenetically stimulating the paw (Figures 3E and 3F). Animals exhibit different types of responses to painful stimuli on the hind paw in standard pain assays, such as paw lifting, biting, and flicking, each indicating a different level of pain. Improving the behavioral readouts from body part tracking would greatly strengthen this system by providing deeper insights into the role of somatosensation in naturalistic behaviors. Additionally, if the laser spot size could be reduced to a diameter of 2 mm², it would allow the activation of a smaller number of cutaneous afferents, or even a single one, across different skin types in the paw, such as glabrous or hairy skin.

Reviewer #3 (Public review):

Summary:

In this study, the authors aimed to investigate if hemodynamic occlusion contributes to fluorescent signals measured with two-photon microscopy. For this, they image the activity-independent fluorophore GFP in 2 different cortical areas, at different cortical depths and in different behavioral conditions. They compare the evoked fluorescent signals with those obtained with calcium sensors and neuromodulator sensors and evaluate their relationship to vessel diameter as a readout of blood flow.<br /> They find that GFP fluorescence transients are comparable to GCaMP6f stimuli-evoked signals in amplitude, although they are generally smaller. Yet, they are significant even at the single neuronal level. They show that GFP fluorescence transients resemble those measured with the dopamine sensor GRAB-DA1m and the serotonin sensor GRAB-5HT1.0 in amplitude an nature, suggesting that signals with these sensors are dominated by hemodynamic occlusion. 
Moreover, the authors perform similar experiments with wide-field microscopy which reveals the similarity between the two methods in generating the hemodynamic signals. Together the evidence presented calls for the development and use of high dynamic range sensors to avoid measuring signals that have another origin from the one intended to measure. In the meantime, the evidence highlights the need to control for those artifacts such as with the parallel use of activity independent fluorophores.

Strengths:

- Comprehensive study comparing different cortical regions in diverse behavioral settings in controlled conditions.<br /> - Comparison to the state-of-the-art, i.e. what has been demonstrated with wide-field microscopy.<br /> - Comparison to diverse activity-dependent sensors, including the widely used GCaMP.

Comments on revisions:

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

Reviewer #3 (Public review):

Summary:

This study provides evidence that the protein Treacle plays an essential role in the structure and function of the fibrillar center (FC) of the nucleolus, which is surrounded by the dense fibrillar component (DFC) and the granular component (GC). The authors provide new evidence that, like the DFC and GC, the functional FC compartment involves a biomolecular condensate that contains Treacle as a key component. Treacle is essential to transcription of the rDNA as well as proper rRNA processing that the authors tie to a role in maintaining separation of FC components from the DFC. In vitro and in vivo experiments highlight that Treacle is itself capable of undergoing condensation in a manner that depends on concentration and charge-charge interactions, but is not affected by 1,6 hexanediol, which disrupts weak hydrophobic interactions. Attempting to generate separation-of-function mutants, the authors provide further evidence of complex interactions that drive proper condensation in the FC mediated by both the central repeat (low-complexity, likely driving the condensation) and C-terminal domain (which appears to target the specificity of the condensation to the proper location). Using mutant forms of Treacle defective in condensation, the authors provide evidence that these same protein forms are also disrupted in supporting Treacle's functions in rDNA transcription and rRNA processing. Last, the authors suggest that cells lacking Treacle are defective in the DNA damage response at the rDNA in response to VP16.

Strengths:

In general, the data are of high quality, the experiments are well-designed and the findings are carefully interpreted. The findings of the work complement prior high-impact studies of the DFC and GC that have identified constituent proteins as the lynchpins of the biomolecular condensates that organize the nucleolus into its canonical three concentric compartment structure and are therefore likely to be of broad interest. The attempts to generate separation-of-function mutants to dissect the contribution of condensation to Treacle function are ambitious and critical to demonstrating the relevance of this property to the biology of the FC. The complementarity of the methods applied to investigate Treacle function are appropriate and the findings integrate well towards a compelling narrative.

Weaknesses:

While the separation of function mutants of Treacle are a major strength of the work, further studies will be required to fully explore the relevance of Treacle condensation to the stability of the rDNA repeats.

Reviewer #3 (Public review):

Summary:

This paper seeks to identify underlying mechanisms contributing to memory deficits observed in Alzheimer's disease (AD) mouse models. By understanding these mechanisms, they hope to uncover insights into subtle cognitive changes early in AD to inform interventions for early-stage decline.

Strengths:

The paper provides a comprehensive exploration of memory deficits in an AD mouse model, covering the early and late stages of the disease. The experimental design was robust, confirming age-dependent increases in Aβ plaque accumulation in the AD model mice and using multiple behavior tasks that collectively highlighted difficulties in maintaining multiple competing memory cues, with deficits most pronounced in older mice.

In the fear acquisition, extinction, and reinstatement task, AD model mice exhibited a significantly higher fear response after acquisition compared to controls, as well as a greater drop in fear response during reinstatement. These findings suggest that AD mice struggle to retain the fear memory associated with the conditioned stimulus, with the group differences being more pronounced in the older mice.

In the reversal Barnes maze task, the AD model mice displayed a tendency to explore the maze perimeter rather than the two potential target holes, indicating a failure to integrate multiple memory cues into their strategy. This contrasted with the control mice, which used the more confirmatory strategy of focusing on the two target holes. Despite this, the AD mice were quicker to reach the target hole, suggesting that their impairments were specific to memory retrieval rather than basic task performance.

The authors strengthened their findings by analyzing their data with a leading computational model, which describes how animals balance competing memories. They found that AD mice showed somewhat of a contradiction: a tendency to both treat trials as more alike than they are (lower α) and similar stimuli as more distinct than they are (lower σx) compared to controls.

Weaknesses:

While conceptually solid, the model struggles to fit the data and to support the key hypothesis about AD mice's ability to retain competing memories. These issues are evident in Figure 3:

(1) The model misses key trends in the data, including the gradual learning of fear in all groups during acquisition, the absence of a fear response at the start of the experiment, the increase in fear at the start of day 2 of extinction (especially in controls), and the more rapid reinstatement of fear observed in older controls compared to acquisition.

(2) The model attributes the higher fear response in controls during reinstatement to a stronger association with the context from the unsignaled shock phase, rather than to any memory of the conditioned stimulus from acquisition.

These issues lead to potential overinterpretation of the model parameters. The differences in α and σx are being used to make claims about cognitive processes (e.g., overgeneralization vs. overdifferentiation), but the model itself does not appear to capture these processes accurately.

The authors could benefit from a model that better matches the data and that can capture the retention and recollection of a fear memory across phases.

Conclusion:

Overall, the data support the authors' hypothesis that AD model mice struggle to retain competing memories, with the effect becoming more pronounced with age. While I believe the right computational model could highlight these differences, the current model falls short in doing so.

Reviewer #3 (Public review):

Summary:

The authors record from the ACC during a task in which animals must switch contexts to avoid shock as instructed by a cue. As expected, they find neurons that encode context, with some encoding of actions prior to the context, and encoding of neurons post-action. The primary novelty of the task seems to be dynamically encoding action-outcome in a discrimination-avoidance domain, while this is traditionally done using operant methods. While I'm not sure that this task is all that novel, I can't recall this being applied to the frontal cortex before, and this extends the well-known action/context/post-context encoding of ACC to the discrimination-avoidance domain.

While the analysis is well done, there are several points that I believe should be elaborated upon. First, I had questions about several details (see point 3 below). Second, I wonder why the authors downplayed the clear action coding of ACC ensembles. Third, I wonder if the purported 'novelty' of the task (which I'm not sure of) and pseudo-debate on ACC's role undermines the real novelty - action/context/outcome encoding of ACC in discrimination-avoidance and early learning.

Strengths:

Recording frontal cortical ensembles during this task is particularly novel, and the analyses are sophisticated. The task has the potential to generate elegant comparisons of action and outcome, and the analyses are sophisticated.

Weaknesses:

I had some questions that might help me understand this work better.

(1) I wonder if the field would agree that there is a true 'debate' and 'controversy' about the ACC and conflict monitoring, or if this is a pseudodebate (Line 34). They cite 2 very old papers to support this point. I might reframe this in terms of the frontal cortex studying action-outcome associations in discrimination-avoidance, as the bulk of evidence in rodents comes from overtrained operant behavior, and in humans comes from high-level tasks, and humans are unlikely to get aversive stimuli such as shocks.

(2) Does the purported novelty of the task undermine the argument? While I don't have an exhaustive knowledge of this behavior, the novelty involves applying this ACC. There are many paradigms where a shock triggers some action that could be antecedents to this task.

(3) The lack of details was confusing to me:

a) How many total mice? Are the same mice in all analyses? Are the same neurons? Which training day? Is it 4 mice in Figure 3? Five mice in line 382? An accounting of mice should be in the methods. All data points and figures should have the number of neurons and mice clearly indicated, along with a table. Without these details, it is challenging to interpret the findings.

b) How many neurons are from which stage of training? In some figures, I see 325, in some ~350, and in S5/S2B, 370. The number of neurons should be clearly indicated in each figure, and perhaps a table.

c) Were the tetrodes driven deeper each day? The depth should be used as a regressor in all analyses?

d) Was is really ACC (Figure 2A)? Some shanks are in M2? All electrodes from all mice need to be plotted as a main figure with the drive length indicated.

e) It's not clear which sessions and how many go into which analysis

f) How many correct and incorrect trials (<7?) are there per session?

g) Why 'up to 10 shocks' on line 358? What amplitudes were tried? What does scrambled mean?

(4) Why do the authors downplay pre-action encoding? It is clearly evident in the PETHs, and the classifiers are above chance. It's not surprising that post-shuttle classification is so high because the behavior has occurred. This is most evident in Figure S2B, which likely should be a main figure.

(5) The statistics seem inappropriate. A linear mixed effects model accounting for between-mouse variance seems most appropriate. Statistical power or effect size is needed to interpret these results. This is important in analyses like Figure 7C or 6B.

(6) Better behavioral details might help readers understand the task. These can be pulled from Figures S2 and S5. This is particularly important in a 'novel' task.

(7) Can the authors put post-action encoding on the same classification accuracy axes as Figure 6B? It'd be useful to compare.

(8) What limitations are there? I can think of several - number of animals, lack of causal manipulations, ACC in rodents and humans.

Minor:

(1) Each PCA analysis needs a scree plot to understand the variance explained.

(2) Figure 4C - y and x-axes have the same label?

(3) What bin size do the authors use for machine learning (Not clear from line 416)?

(4) Why not just use PCA instead of 'dimension reduction' (of which there are many?)

(5) Would a video enhance understanding of the behavior?

Reviewer #3 (Public review):

This work aims to establish cell-type specific changes in gene expression upon exposure to different flavors of commercial e-cigarette aerosols compared to control or vehicle. Kaur et al. conclude that immune cells are most affected, with the greatest dysregulation found in myeloid cells exposed to tobacco-flavored e-cigs and lymphoid cells exposed to fruit-flavored e-cigs. The up-and-down-regulated genes are heavily associated with innate immune response. The authors suggest that a Ly6G-deficient subset of neutrophils is found to be increased in abundance for the treatment groups, while gene expression remains consistent, which could indicate impaired function. Increased expression of CD4+ and CD8+ T cells along with their associated markers for proliferation and cytotoxicity is thought to be a result of activation following this decline in neutrophil-mediated immune response.

Strengths:

(1) Single-cell sequencing data can be very valuable in identifying potential health risks and clinical pathologies of lung conditions associated with e-cigarettes considering they are still relatively new.

(2) Not many studies have been performed on cell-type specific differential gene expression following exposure to e-cig aerosols.

(3) The assays performed address several factors of e-cig exposure such as metal concentration in the liquid and condensate, coil composition, cotinine/nicotine levels in serum and the product itself, cell types affected, which genes are up- or down-regulated and what pathways they control.

(4) Considerations were made to ensure clinical relevance such as selecting mice whose ages corresponded with human adolescents so that the data collected was relevant.

Weaknesses:

(1) The exposure period of 1 hour a day for 5 days is not representative of chronic use and this time point may be too short to see a full response in all cell types. The experimental design is not well-supported based on the literature available for similar mouse models.

(2) Several claims lack supporting evidence or use data that is not statistically significant. In particular, there were no statistical analyses to compare results across sex, so conclusions stating there is a sex bias for things like Ly6G+ neutrophil percentage by condition are observational.

(3) Statistical analyses lack rigor and are not always displayed with the most appropriate graphical representation.

(4) Overall, the paper and its discussion are relatively limited and do not delve into the significance of the findings or how they fit into the bigger picture of the field.

(5) The manuscript lacks validation of findings in tissue by other methods such as staining.

(6) This paper provides a foundation for follow-up experiments that take a closer look at the effects of e-cig exposure on innate immunity. There is still room to elaborate on the differential gene expression within and between various cell types.

Reviewer #3 (Public review):

Summary:

In this study, Benedikt et al. sought to understand how adolescents and adult mice differ in auditory cortical processing, performance on a go/nogo sound-guided task, and learning. They report that behavioral performance is superior in adults. They also report that neuronal representations of both the acoustic stimulus and behavioral choice are weaker and sluggish in adolescents compared to adults and that these differences were larger in expert mice than in novices. The neural basis of adolescent auditory cognition is an important topic (both clinically and from a basic science perspective) and vastly understudied. However, many aspects of the study fell short, thereby undermining the primary conclusions drawn by the authors. My major concerns are as follows:

(1) The authors report that "adolescent mice showed lower auditory discrimination performance compared to adults" and that this performance deficit was due to (among other things) "weaker cognitive control". I'm not fully convinced of this interpretation, for a few reasons. First, the adolescents may simply have been thirstier, and therefore more willing to lick indiscriminately. The high false alarm rates in that case would not reflect a "weaker cognitive control" but rather, an elevated homeostatic drive to obtain water. Second, even the adult animals had relatively high (~40%) false alarm rates on the freely moving version of the task, suggesting that their behavior was not particularly well controlled either. One fact that could help shed light on this would be to know how often the animals licked the spout in between trials. Finally, for the head-fixed version of the task, only d' values are reported. Without the corresponding hit and false alarm rates (and frequency of licking in the intertrial interval), it's hard to know what exactly the animals were doing.

(2) There are some instances where the citations provided do not support the preceding claim. For example, in lines 64-66, the authors highlight the fact that the critical period for pure tone processing in the auditory cortex closes relatively early (by ~P15). However, one of the references cited (ref 14) used FM sweeps, not pure tones, and even provided evidence that the critical period for this more complex stimulus occurred later in development (P31-38). Similarly, on lines 72-74, the authors state that "ACx neurons in adolescents exhibit high neuronal variability and lower tone sensitivity as compared to adults." The reference cited here (ref 4) used AM noise with a broadband carrier, not tones.

(3) Given that the authors report that neuronal firing properties differ across auditory cortical subregions (as many others have previously reported), why did the authors choose to pool neurons indiscriminately across so many different brain regions? And why did they focus on layers 5/6? (Is there some reason to think that age-related differences would be more pronounced in the output layers of the auditory cortex than in other layers?)

Reviewer #3 (Public review):

Summary:

Here the authors describe the role of mORs in synaptic glutamate release from substance P and cholinergic neurons in the medial habenula to the interpeduncular nucleus (IPN) circuit in adult mice. They show that mOR activation reduces evoked glutamate release from substance P neurons yet increases evoked glutamate release and Ach release from cholinergic neurons. Unlike glutamate release, Ach release is only detected when potassium channels are blocked with 4-AP or dendrotoxin, implicating Kv1.2. The authors also report a previously unidentified glutamatergic input to IPR mediated from SP neurons and describe the developmental timing of mOR-facilitation in adolescent mice.

Strengths:

(1) The experiments provide new insight into the role of mORs in controlling evoked glutamate release in a circuit with high levels of mORs and established roles in relevant behaviors.

(2) The experimental design is generally rigorous, and the results are clear-cut. The conclusions are largely supported by the data.

(3) The findings will be of interest to those working in the field.

Weaknesses:

(1) The mechanistic underpinnings of the most interesting results are not pursued. For example, the experiments do not provide new insight into the differential effects of evoked and spontaneous glutamate/Ach release by Gi/o coupled mORs, nor the differential threshold for glutamate versus Ach release.

(2) The significance of the ratio of AMPA versus nACh EPSCs shown in Figure 6 is unclear since nAChR EPSCs measured in the K+ channel blockers are compared to AMPA EPSCs in control (presumably 4-AP would also increase AMPA EPSCs).

(3) The authors note that blocking Kv1 channels typically enhances transmitter release by slowing action potential repolarization. The idea that Kv1 channels serve as a brake for Ach release in this system would be strengthened by showing that these channels are the target of neuromodulators or that they contribute to activity-dependent regulation that allows the brake to be released.

Reviewer #3 (Public review):

Summary:

Chatzis et al showed that β-glucan trained macrophages have decreased phagocytic activity of apoptotic tumor cells and that is accompanied by lower levels of secreted IL-1β using a mouse model.

Strengths:

This finding has a potential impact on designing new cancer immunotherapeutic approaches by targeting macrophage efferocytosis.

Weaknesses:

Whether this finding could be applied to other scenarios is underdetermined.

(1) Does the decrease of efferocytosis also occur in human monocytes/macrophages after training?

(2) Both β-glucan and BCG are well-trained innate immunity agents, the authors showed that β-glucan decreased efferocytosis via IL-1 β, so it is interesting to know whether BCG has a similar effect.

Reviewer #3 (Public review):

Summary:

Chow-Wing-Bom et al. introduce an innovative wide-field visual stimulation setup for 3T experiments that enables stimulation up to a diameter of 40{degree sign} visual angle while allowing continuous gaze tracking. Using this setup, the authors systematically investigate contrast sensitivity across the visual field by presenting subjects with sinusoidal gratings varying in contrast and spatial frequency. Their findings confirm the expected organization of contrast sensitivity, demonstrating a preference for high spatial frequencies in the central field and lower frequencies in the periphery. They also extend these measurements to eccentricities up to 20{degree sign}, which exceeds previous fMRI-based reports. Moreover, the study explores the potential of using contrast sensitivity calculations as a method for detecting visual field defects, as demonstrated in both a healthy subject with an artificial, ring-shaped scotoma and a patient with LHON.

Strengths:

(1) The manuscript is well written and provides comprehensive methodological details, ensuring high transparency and reproducibility.

(2) The visual stimulation setup represents a significant technical advance by enabling wide-field stimulation with continuous eye tracking, which is crucial for both research and potential clinical applications.

(3) The study confirms established findings regarding the organization of contrast sensitivity while extending them to a larger eccentricity range.

(4) The efforts to establish a measure for visual field losses align with current efforts to develop objective alternatives to conventional perimetry.

Weaknesses:

(1) The authors should more strongly emphasize their findings on the organization of contrast sensitivity, particularly in light of the stimulation extent provided by the wide-field setup.

(2) Certain methodological aspects require further clarification, particularly regarding the correction of eccentricity values from the Benson atlas. It's not clear which V1 masks are used for the specific analysis which could have a substantial impact on the reported differences between the two approaches of pRF mapping and atlas-based pRF parameters.

(3) Minor inconsistencies in reporting, e.g., the introduction of a second session in the Results section.

(4) The conclusion that high-contrast patterns as in pRF mapping are not optimal to test for subtle but potentially clinically relevant changes in the visual field coverage is very valid. The suggested use of contrast sensitivity can therefore be a potentially well-suited parameter for estimating visual field losses. The presented work is an interesting starting point and the proposed method of using contrast sensitivity as a measure for partial vision loss should further be explored.

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for - program event selection - 2025 - April 3 - 1-4pm GMT - Skoll World Forum - Project Dandelion: Women, Food and the Climate Future - Agrosphere Systems - relevant to

for - program event selection - 2025 - April 3 - 2-3:15pm GMT - Skoll World Forum - Big Bet Philanthropy - Stop Reset Go - TPF - LCE - relevant to - event time conflict - with - Project Dandelion

for - program event selection - 2025 - April 3 - 2-3:15pm GMT - Skoll World Forum - Intergenerational Wisdom - Stop Reset Go - Deep Humanity - LCE - relevant to - event time conflict - with - Project Dandelion

for - program event selection - 2025 - April 3 - 2-3:15pm GMT - Skoll World Forum - Local Leadership - Stop Reset Go - Cosmolocal Production - TPF - LCE - relevant to - event time conflict - with - Project Dandelion

for - program event selection - 2025 - April 3 - 2-3:15pm GMT - Skoll World Forum - Delegate Led Discussion - Strategies for Action and Care in Closing Civic Space - Stop Reset Go - Indyweb autonomy - relevant to - event time conflict - with - Project Dandelion

for - program event selection - 2025 - April 3 - 2-3:15pm GMT - Skoll World Forum - Delegate Led Discussion - Tuning In: Music, Deep Listening - Stop Reset Go - Deep Humanity BEing journeys - relevant to - event time conflict - with - Project Dandelion

for - program event selection - 2025 - April 2 - 2-3:15pm GMT - Skoll World Forum - The Changing State of AI, Media - Indyweb - Stop Reset Go - TPF - Eric's project - Skoll's Participatory Media project - relevant to - adjacency - indyweb - Stop Reset Go - participatory news - participatory movie and tv show reviews - Eric's project - Skoll's Particiipatory Media - event time conflict - with - Leadership in Alien Times

adjacency - between - Skoll's Participatory Media project - Global Witness - Indyweb - Stop Reset Go's participatory news idea - Stop Reset Go's participatory movie and TV show review idea - Eric's media project - adjacency relationship - Participatory media via Indyweb and idea of participatory news and participatory movie and tv show reviews - might be good to partner with Skoll Foundation's Participatory Media group

for - program event selection - 2025 - April 2 - 2-3:15pm GMT - Skoll World Forum - Fail Loud: Collaboration - Indyweb - Stop Reset Go - TPF - LCE - relevant to

for - program event selection - 2025 - April 2 - 2-3:30pm GMT - Skoll World Forum - Leadership in Alien Times - Stop Reset Go - Deep Humanity - LCE - transition - relevant to - event time conflict - with Building Comfort with Discomfort - solution - watch one live and the other recorded

for - program event selection - 2025 - April 2 - 2-3:30 pm GMT - Skoll World Forum - Comfort with Discomfort: Practices for Lasting Social Change - Stop Reset Go - Deep Humanity - Common Human Denominators - LCE - relevant to - event time conflict - with - Leadership in Alien Times

Reviewer #3 (Public Review):

In their manuscript, Umetani, et al. address the question of the origin of persister bacteria using single-cell approaches. Persistence refers to a physiological state where bacteria are less sensitive to antibiotherapy, although they have not acquired a resistance mutation; importantly, the concept of persistence has been refined in the past decade to distinguish it from tolerance where bacteria are only transiently insensitive. Since persister cells are very rare in growing populations (typically 1e-5 or 1e-6), it is very challenging to observe them directly. It had been proposed that individual cells surviving antibiotics are not growing at the start of the treatment, but recent studies (nicely reviewed in the introduction) where persister bacteria were observed directly do not support this link. Following a similar line, the authors nonetheless still aim at "investigating whether non-growing cells are predominantly responsible for bacterial persistence". Based on new experimental data, they claim the contrary that most surviving cells were "actively growing before drug exposure" and that their work "reveals diverse survival pathways underlying antibiotic persistence".

The main strengths of the manuscript are in my opinion:

- To report on direct observation of E. coli persisters to ampicillin (200µg/mL) in 5 different growth media (typically 20 persisters or more per condition, one condition with 12 only), which constitutes without a doubt an experimental tour de force.

- To aim at bridging the population level and the single-cell level by measuring relevant variables for each and analyzing them jointly.

- To demonstrate that in most conditions a large fraction of surviving cells was actively growing before drug exposure.

In addition, although it is well-known that E. coli doesn't need to maintain its rod shape for surviving and dividing, I found very remarkable in their data the extent to which morphology can be affected in persister cells and their progeny, since this really challenges our understanding of E. coli's "lifestyle" (these swimming amoeba-like cells in Supp Video 11 are mind-blowing!).

Unfortunately, these positive aspects are counter-balanced by several shortcomings in the way experiments are analyzed and interpreted, which I explain below. Moreover, the manuscript is written in a way that makes it very hard to find important information on how experiments are done and is likely to leave the reader with an impression of confusion about what the main findings actually are.

My major concerns are the following:

(1) The main interpretation framework proposed by the authors is to assess whether cells not growing before drug exposure (so-called "dormant") are more or less likely to survive the treatment than growing ones ("non-dormant"). Fig 2A and Fig 3G show the main conclusions of the article from this perspective, that growing cells can survive the treatment and that the fraction of persisters in a given condition is not explained by the fraction of "dormant" cells, respectively. With this analysis, the authors essentially assume that "dormant" cells are of the same type in their different conditions, which ignores the progress in this field over the last decade (Balaban et al. 2019). I argue on the contrary that the observation of "diverse modes of survival in antibiotic persistence" is expected from their experimental design. In particular, the sensitivity of E. coli to beta-lactams such as ampicillin is expected to be much lower during the lag out of the stationary phase, a phenomenon which has been coined "tolerance"; hence in the Late Stationary condition, two subpopulations coexist for which different response to ampicillin is expected. I propose steps toward a more compelling interpretation of the experimental data. Should this point be taken seriously by the authors, it, unfortunately, implies a major rewriting of the article, including its title.

(2) The way the authors describe their experiments with bacteria in the stationary phase is very problematic. For instance, they write that they "sampled cells from early and late stationary phases (...) and exposed them to 200 μg/mL of Amp in both batch and single-cell cultures." For any reader in a hurry (hence skipping methods and/or supplementary figure), this leads to believe that bacteria sampled in the stationary phase were exposed to the drug right away (either by adding the drug to the stationary phase sample, or more classically by transferring cells to fresh media with antibiotics). However, it turns out that, after sampling and loading in the microfluidic device, bacteria are grown 2 h in LB (or 4 h in M9) - I don't know what to think of such a blatant omission. The names chosen for each condition should reflect their most important aspects, here "stationary" is simply not appropriate - maybe something like "post early stationary" instead. In any case, I believe that this point highlights further the misconception pointed out in 1 and implies that the average reader will be at best confused, and probably misled.

(3) Figures 4 and 5 are of very minor significance, and the methodology used in Fig 4 is questionable. The authors measure the abundance of an Rpos-mCherry translational fusion because its "high expression has been suggested to predict persistence". The rationale for this (that an RpoS-mCherry fusion would be a proxy for intracellular ppGpp levels, and in turn predict persistence) has never been firmly established, and the standards used in the article where this reporter was introduced (Maisonneuve, Castro-Camargo, and Gerdes 2013) are notoriously low (which eventually led to its retraction) - I don't know what to think of the fact that the authors cite a review by this group rather than their retracted article. While transcriptional fusions of promoters regulated by RpoS have been proposed to measure its regulatory activity (Patange et al. 2018), the combination of self-regulation and complex post-translational regulation of rpoS makes the physical meaning of the reporter used here completely unclear. Moreover, this translational fusion is introduced without doing any of the necessary controls to demonstrate that the activity of RpoS is not impaired by the addition of the fluorescent protein. Fig 5 simply reports the existence of persisters to ciprofloxacin growing before the treatment. This might be a new observation but it is not unexpected given that a similar observation has been made with a similar drug, ofloxacin (Goormaghtigh and van Melderen 2019), as pointed out in the introduction. There is no further quantitative claim on this.

(4) The authors don't mention the dead volume nor the speed of media exchange in their device. Hopefully, it is short compared to the duration of the treatment; however, it is challenging to remove all antibiotics after the treatment and only 1e-3 or 1e-4 of the treatment concentration is already susceptible to affecting regrowth in fresh media. If this is described in another article, it would be worth adding a comment in the main text.

(5) Fig 2A supports the main finding that a significant fraction of bacteria surviving the treatment are growing before drug exposure, but it uses a poorly chosen representation.<br /> - In order to compare between conditions, one would like to see the fraction of each type in the population.<br /> - The current representation (of a fraction of each type among surviving cells) requires a side-by-side comparison with a random sample (which will practically be equivalent to the fraction of each type among killed cells) in order to be informative.

Reviewer #3 (Public review):

Summary:

This study by Tetenborg S et al. identifies proteins that are physically closely associated with gap junctions in retinal neurons of mice and zebrafish using BioID, a technique that labels and isolates proteins proximal to a protein of interest. These proteins include scaffold proteins, adhesion molecules, chemical synapse proteins, components of the endocytic machinery, and cytoskeleton-associated proteins. Using a combination of genetic tools and meticulously executed immunostaining, the authors further verified the colocalizations of some of the identified proteins with connexin-positive gap junctions. The findings in this study highlight the complexity of gap junctions. Electrical synapses are abundant in the nervous system, yet their regulatory mechanisms are far less understood than those of chemical synapses. This work will provide valuable information for future studies aiming to elucidate the regulatory mechanisms essential for the function of neural circuits.

Strengths:

A key strength of this work is the identification of novel gap junction-associated proteins in AII amacrine cells and photoreceptors using BioID in combination with various genetic tools. The well-studied functions of gap junctions in these neurons will facilitate future research into the functions of the identified proteins in regulating electrical synapses.

Weaknesses:

I do not see major weaknesses in this paper. A minor point is that, although the immunostaining in this study is beautifully executed, the quantification to verify the colocalization of the identified proteins with gap junctions is missing. In particular, endocytosis component proteins are abundant in the IPL, making it unclear whether their colocalization with gap junction is above chance level (e.g. EPS15l1, HIP1R, SNAP91, ITSN in Figure 3B).

Reviewer #3 (Public review):

Summary:

The authors provide an in-depth analysis of the function of Numb in adult Drosophila midgut. Based on RNAi combinations and double mutant clonal analyses, they propose that Numb has a function in inhibiting Notch pathway to maintain intestinal stem cells, and is a backup mechanism with BMP pathway in maintaining midgut stem cell mediated homeostasis.

Strengths:

Overall, this is a carefully constructed series of experiments, and the results and statistical analyses provides believable evidence that Numb has a role, albeit weak compared to other pathways, in sustaining ISC and in promoting regeneration especially after damage by bleomycin, which may damage enterocytes and therefore disrupt BMP pathway more. The results overall support their claim.

The data are highly coherent, and support a genetic function of Numb, in collaborating with BMP signaling, to maintain the number and proliferative function of ISCs in adult midguts. The authors used appropriate and sophisticated genetic tools of double RNAi, mutant clonal analysis and dual marker stem cell tracing approaches to ensure the results are reproducible and consistent. The statistical analyses provide confidence that the phenotypic changes are reliable albeit weaker than many other mutants previously studied.

Weaknesses:

In the absence of Numb itself, the midgut has a weak reduction of ISC number (Fig. 3 and 5), as well as weak albeit not statistically significant reduction of ISC clone size/proliferation. I think the authors published similar experiments with BMP pathway mutants. The mad1-2 allele used here as stated below may not be very representative of other BMP pathway mutants. Therefore, it could be beneficial to compare the number of ISC number and clone sizes between other BMP experiments to provide the readers a clearer picture how these two pathways individually contribute (stronger/weaker effects) to the ISC number and gut homeostasis.

The main weakness of this manuscript is the analysis of the BMP pathway components, especially the mad1-2 allele. The mad RNAi and mad1-2 alleles (P insertion) are supposed to be weak alleles and that might be suitable for genetic enhancement assays here together with numb RNAi. However, the mad1-2 allele, and sometime the mad RNAi, showed weakly increased ISC clone size. This is kind of counter-intuitive that they should have a similar ISC loss and ISC clone size reduction.

A much stronger phenotype was observed when numb mutants were subject to treatment of tissue damaging agents Bleomycin, which causes damage in different ways than DSS. Bleomycin as previously shown to be causing mainly enterocyte damage, and therefore disrupt BMP signaling from ECs more likely. Therefore, this treatment together with loss of numb led to highly significant reduction of ISC in clones and reduction of clone size/proliferation. One improvement is that it is not clear whether the authors discussed the nature of the two numb mutant alleles used in this study and the comparison to the strength of the RNAi allele. Because the phenotypes are weak, and more variable, the use of specific reagents is important.

Furthermore, the use of possible activating alleles of either or both pathways to test genetic enhancement or synergistic activation will provide strong support for the claims.

For the revision, the authors have provided detailed responses, comments, and a revised manuscript that together satisfactorily answer all my questions. The manuscript read well and the flow of information is quite clear. I do not have further concerns and support the manuscript moving forward.

Reviewer #3 (Public review):

Summary:

This work describes how two chemosensory neurons in C. elegans drive opposite behaviors in response to a volatile cue. Because they have different concentration dependencies, this leads to different behavioral responses (attraction at low concentration and repulsion at high concentration). It has been known that many odorants that are attractive at low concentrations are aversive at high concentrations, and the implicated neurons (at least AWC for attraction and ASH for repulsion) have been well established. Nonetheless, studying behavior and neural responses in a common context (odor pulses, as opposed to gradients) provides a clear picture of how these sensory neurons may guide the dose-dependent response by separately modulating odor entry and odor exit behaviors.

Strengths:

(1) There is good evidence that worms are attracted to low concentrations and repelled by high concentrations of 1-oct. Calcium imaging also makes it clear that dose dependence is stronger for ASH than AWC.

(2) There is good evidence for conc. dependent responses via ASH (Figure 4E) and attractive inhibition via tonic IAA (Figure 7A).

(3) This work presents calcium imaging and behavior with the same stimulus (sudden pulses in volatile odor concentration), while previous studies often focus on using neuronal responses to pulses to understand the navigation of gentle gradients.

Weaknesses:

(1) It is not clear precisely how important AWC is (compared to other cells) for the attractive response, though the presence of odor-off behavior implicates it. This could be resolved by looking at additional mutants (tax-4 is broad).

(2) Relatedly, dose-dependent chemotaxis data (Figure 4C, D) should be provided for osm-9 animals to get a sense of the degree to which dose-dependence is explained by ASH.

(3) Figure 4A, B should include average traces with errors, as there are several ways the responses can vary across conditions.

(4) The data in Figure 6G does not appear to have error bars. Also, it would help to include a more conventional demonstration of AIB responding to stimuli (e.g. averaging stimulus-aligned responses as a percent of the fluorescence value at stimulus onset to perform the desired subtraction). Subtracted calcium traces are harder to interpret. As it stands, the evidence that sensory signals are persisting in AIB and not being shunted by proprioceptive feedback in microfluidic devices is not strong.

• 看不懂
• 文字愛康可V2一起提供，但計算邏輯需一致
• 當有多檻優惠，只顯示最接近購物車金額門檻

Reviewer #3 (Public review):

Summary:

The authors submitted a second revised manuscript that reports findings from a series of experiments suggesting that bovine oviductal fluid and species-specific oviductal glycoprotein (OVGP1 or oviductin) from bovine, murine, or human sources modulate the species specificity of bovine and murine oocytes.

Strengths:

The study reported in the manuscript deals with an important topic of interest in reproductive biology.

Weaknesses:

The authors submitted a second revised manuscript. Some of the previous questions are considered inadequate. There are still several problematic issues that require the authors' attention.

Reviewer #3 (Public review):

Summary:

Franchet et al. sought to characterize the impact of Nora virus on host lifespan and sensitivity to a variety of infectious or stressful treatments. Through careful and rigorous analyses, they provide evidence that the Nora virus greatly impacts fly survival to infection, overall lifespan, and intestinal integrity. The authors have been thorough and rigorous, and the experimental evidence including proper isolation of the virus and Koch's Postulate reinoculation of the organism is excellent. The additional work is valuable and to the gold standard of the field, characterizing the pathology of the gut, including data showing gut leakage, the presence of the virus in the intestinal stem cells, and the importance of stem cell proliferation for virus replication and spread using elegant genetic tools to block stem cell proliferation or enterocyte death.

Strengths:

The authors have been rigorous and careful. The initial finding is presented through the lens of two related strains differing in virus infection. From there, the authors characterized the virus and isolated a purified culture, which they used to reinoculate a cleared strain to demonstrate proper Koch's Postulate satisfaction. The authors have also probed various parameters in terms of dietary importance in relevant conditions for many experiments. The additional work to characterize the pathology of the gut is compelling, using genetic tools to block or allow intestinal stem cell proliferation and enterocyte death through JAK-STAT and JNK signalling alongside the tracing of virus presence using a Nora virus antibody. JAK-STAT and JNK are previously described as regulators of these processes, making these tools appropriate and convincing. It is also interesting to see good evidence that the virus itself is damaging, rather than simply permitting coinfection by gut microbes (which does happen).

Weaknesses:

The claim that Dcr2 is not abundant in ISCs because the protein is not stable is logically consistent and reasonable. Perhaps I missed this, but the authors could additionally knock down or use somatic CRISPR to delete Dcr2 in ISCs to test whether a lack of Dcr2 underlies sensitivity. In this experiment, the expectation would be that depleting Dcr2 in ISCs genetically would make little difference to susceptibility overall compared to controls. This is not an essential experiment request.

Reviewer #3 (Public review):

Summary:

This is an interesting investigation of the benefits of perceiving control and its impact on the subjective experience of stress. To assess a subjective sense of control, the authors introduce a novel wheel-stopping (WS) task where control is manipulated via size and speed to induce low and high control conditions. The authors demonstrate that the subjective sense of control is associated with experienced subjective stress and individual differences related to mental health measures. In a second experiment, they further show that an increased sense of control buffers subjective stress induced by a trier social stress manipulation, more so than a more typical stress buffering mechanism of watching neutral/calming videos.

Strengths:

There are several strengths to the manuscript that can be highlighted. For instance, the paper introduces a new paradigm and a clever manipulation to test an important and significant question. Additionally, it is a well-powered investigation that allows for confidence in replicability and the ability to show both high internal consistency and high external validity with an interesting set of individual difference analyses. Finally, the results are quite interesting and support prior literature while also providing a significant contribution to the field with respect to understanding the benefits of perceiving control.

Weaknesses:

There are also some questions that, if addressed, could help our readership.

(1) A key manipulation was the high-intensity stressor (Anticipatory TSST signal), which was measured via subjective ratings recorded on a sliding scale at different intervals during testing. Typically, the TSST conducted in the lab is associated with increases in cortisol assessments and physiological responses (e.g., skin conductance and heart rate). The current study is limited to subjective measures of stress, given the online nature of the study. Since TSST online may also yield psychologically different results than in the lab (i.e., presumably in a comfortable environment, not facing a panel of judges), it would be helpful for the authors to briefly discuss how the subjective results compare with other examples from the literature (either online or in the lab). The question is whether the experienced stress was sufficiently stressful given that it was online and measured via subjective reports. The control condition (low intensity via reading recipes) is helpful, but the low-intensity stress does not seem to differ from baseline readings at the beginning of the experiment.

(2) The neutral videos represent an important condition to contrast with WS, but it raises two questions. First, the conditions are quite different in terms of experience, and it is interesting to consider what another more active (but not controlled per se) condition would be in comparison to the WS performance. That is, there is no instrumental action during the neutral video viewing (even passive ratings about the video), and the active demands could be an important component of the ability to mitigate stress. Second, the subjective ratings of the stress of the neutral video appear equivalent to the win condition. Would it have been useful to have a high arousal video (akin to the loss condition) to test the idea that experience of control will buffer against stress? That way, the subjective stress experience of stress would start at equivalent points after WS3.

(3) For the stress relief analysis, the authors included time points 2 and 3 (after the stressor and debrief) but not a baseline reading before stress. Given the potential baseline differences across conditions, can this decision be justified in the manuscript?

(4) Is the increased control experience during the losses condition more valuable in mitigating experienced stress than the win condition?

(5) The subjective measure of control ("how in control do you feel right now") tends to follow a successful or failed attempt at the WS task. How much is the experience of control mediated by the degree of experienced success/schedule of reinforcement? Is it an assessment of control or, an evaluation of how well they are doing and/or resolution of uncertainty? An interesting paper by Cockburn et al. 2014 highlights the potential for positive prediction errors to enhance the desire for control.

(6) While the authors do a very good job in their inclusion and synthesis of the relevant literature, they could also amplify some discussion in specific areas. For example, operationalizing task controllability via task difficulty is an interesting approach. It would be useful to discuss their approach (along with any others in the literature that have used it) and compare it to other typically used paradigms measuring control via presence or absence of choice, as mentioned by the authors briefly in the introduction.

(7) The paper is well-written. However, it would be useful to expand on Figure 1 to include a) separate figures for study 1 (currently not included) and 2, and b) a timeline that includes the measurements of subjective stress (incorporated in Figure 1). It would also be helpful to include Figure S4 in the manuscript.

Reviewer #3 (Public review):

The authors explore the role of Rec domains in a thermophilic Cas9 enzyme. They report on the crystal structure of part of the recognition lobe, its dynamics from NMR spin relaxation and relaxation-dispersion data, its interaction mode with guide RNA, and the effect of two single-point mutations hypothesised to enhance specificity. They find that mutations have small effects on Rec domain structure and stability but lead to significant rearrangement of micro- to milli-second dynamics which does not translate into major changes in guide RNA affinity or DNA cleavage specificity, illustrating the inherent tolerance of GeoCas9. The work can be considered as a first step towards understanding motions in GeoCas9 recognition lobe, although no clear hotspots were discovered with potential for future rational design of enhanced Cas9 variants.

Strengths:

- Detailed biophysical and structural investigation, despite a few technical limitations inherent with working with complex targets, provides converging evidence that molecular dynamics embedded in the recognition lobes allow GeoCas9 to operate on a broad range of substrates.<br /> - Since the authors and others have shown that substrate specificity is dictated by equivalent hotspot mutations in other Cas9 variants, we are one step closer to understanding this phenomenon.

Weaknesses:

- Since the mutations investigated here do not significantly affect substrate binding or enzymatic activity, it is difficult to rationalize anything for enzyme engineering at this point.<br /> - Further investigation of the determinants of the observed dynamic modes, and follow-up with rationally designed mutations would hopefully allow to create a real model of the mechanism, but I do understand that this goes beyond the scope of this study.

Reviewer #3 (Public review):

Summary:

The data and experiments presented in that study convincingly show that a subpopulation of endothelial cells undergo transformation into pericyte-like cells after stroke in mice. These so-called "E-pericytes" are protective and might present a new target for stroke recovery. The authors used a huge battery of different techniques and modified signaling pathways and cellular interactions using several genetic and pharmacological tools to show that TGFbeta and EndoMT are causes of this transformation.

Strengths:

The amount of different genetic and pharmacological approaches in combination with sophisticated techniques such as single-cell RNAseq is impressive and convincing. The results support their conclusions and the authors achieved their aims. The findings will strongly impact the field of cerebrovascular recovery after stroke and might open up new therapeutic targets.

Weaknesses:

The written and graphic presentation of the findings needs substantial improvement. Language editing is strongly recommended (there are a lot of spelling and grammatical errors in the text and illustrations, including legends).

Reviewer #3 (Public review):

Summary:

In this manuscript, Franco and colleagues describe careful analyses of Salmonella chemotactic behavior in the presence of conflicting environmental stimuli. By doing so, the authors describe that this human pathogen integrates signals from a chemoattractant and a chemorepellent into an intermediate "chemohalation" phenotype.

Strengths:

The study was clearly well-designed and well-executed. The methods used are appropriate and powerful. The manuscript is very well written and the analyses are sound. This is an interesting area of research and this work is a positive contribution to the field.

Weaknesses:

Although the authors do a great job in discussing their data and the observed bacterial behavior through the lens of chemoattraction and chemorepulsion to serine and indole specifically, the manuscript lacks, to some extent, a deeper discussion on how other effectors may play a role in this phenomenon. Specifically, many other compounds in the mammalian gut are known to exhibit bioactivity against Salmonella. This includes compounds with antibacterial activity, chemoattractants, chemorepellers, and chemical cues that control the expression of invasion genes. Therefore, authors should be careful when making conclusions regarding the effect of these 2 compounds on invasive behavior. It is important that the word invasion is used in the manuscript only in its strictest sense, the ability displayed by Salmonella to enter non-phagocytic host cells. With that in mind, authors should discuss how other signals that feed into the control of Salmonella invasion can be at play here.

Reviewer #3 (Public review):

Summary:

The authors describe a model to mimic bat echolocation behavior and flight under high-density conditions and conclude that the problem of acoustic jamming is less severe than previously thought, conflating the success of their simulations (as described in the manuscript) with hard evidence for what real bats are actually doing. The authors base their model on two species of bats that fly at "high densities" (defined by the authors as colony sizes from tens to tens of thousands of individuals and densities of up to 33.3 bats/m2), Pipistrellus kuhli and Rhinopoma microphyllum. This work fits into the broader discussion of bat sensorimotor strategies during collective flight, and simulations are important to try to understand bat behavior, especially given a lack of empirical data. However, I have major concerns about the assumptions of the parameters used for the simulation, which significantly impact both the results of the simulation and the conclusions that can be made from the data. These details are elaborated upon below, along with key recommendations the authors should consider to guide the refinement of the model.

Strengths:

This paper carries out a simulation of bat behavior in dense swarms as a way to explain how jamming does not pose a problem in dense groups. Simulations are important when we lack empirical data. The simulation aims to model two different species with different echolocation signals, which is very important when trying to model echolocation behavior. The analyses are fairly systematic in testing all ranges of parameters used and discussing the differential results.

Weaknesses:

The justification for how the different foraging phase call types were chosen for different object detection distances in the simulation is unclear. Do these distances match those recorded from empirical studies, and if so, are they identical for both species used in the simulation? What reasoning do the authors have for a bat using the same call characteristics to detect a cave wall as they would for detecting a small insect? Additionally, details on the signal creation are also absent, but based on the sample spectrogram in Figure 2A, it appears that the authors used a synthetic linear FM chirp characterized by the call parameters. This simplification of the echolocation signals for these species is not representative of the true emitted signals, which are nonlinear FM for not only the species used within this simulation--PK (Schnitzler et al., 1987; Kalko and Schnitzler 1993 and RM (Schmidt and Joermann 1986)-but also for many other bat species that form large aggregations and undergo dense emergence. Furthermore, echolocation calls of bats emitted during dense emergence flights (see Gillam et al 2010) can be very much different from those emitted during foraging calls, so limiting the simulation to foraging calls may not be valid. Why did the authors not use actual waveforms of calls produced by these species during dense emergence to use biologically relevant signals in their simulation?

The two species modeled have different calls. In particular, the bandwidth varies by a factor of 10, meaning the species' sonars will have different spatial resolutions. Range resolution is about 10x better for PK compared to RM, but the authors appear to use the same thresholds for "correct detection" for both, which doesn't seem appropriate. Also, the authors did not mention incorporating/correcting for/exploiting Doppler, which leads me to assume they did not model it.

The success of the simulation may very well be due to variation in the calls of the bats, which ironically enough demonstrates the importance of a jamming avoidance response in dense flight. This explains why the performance of the simulation falls when bats are not able to distinguish their own echoes from other signals. For example, in Figure C2, there are calls that are labeled as conspecific calls and have markedly shorter durations and wider bandwidths than others. These three phases for call types used by the authors may be responsible for some (or most) of the performance of the model since the correlation between different call types is unlikely to exceed the detection threshold. But it turns out this variation in and of itself is what a jamming avoidance response may consist of. So, in essence, the authors are incorporating a jamming avoidance response into their simulation.

The authors claim that integration over multiple pings (though I was not able to determine the specifics of this integration algorithm) reduces the masking problem. Indeed, it should: if you have two chances at detection, you've effectively increased your SNR by 3dB.

They also claim - although it is almost an afterthought - that integration dramatically reduces the degradation caused by false echoes. This also makes sense: from one ping to the next, the bat's own echo delays will correlate extremely well with the bat's flight path. Echo delays due to conspecifics will jump around kind of randomly. However, the main concern is regarding the time interval and number of pings of the integration, especially in the context of the bat's flight speed. The authors say that a 1s integration interval (5-10 pings) dramatically reduces jamming probability and echo confusion. This number of pings isn't very high, and it occurs over a time interval during which the bat has moved 5-10m. This distance is large compared to the 0.4m distance-to-obstacle that triggers an evasive maneuver from the bat, so integration should produce a latency in navigation that significantly hinders the ability to avoid obstacles. Can the authors provide statistics that describe this latency, and discussion about why it doesn't seem to be a problem?

The authors are using a 2D simulation, but this very much simplifies the challenge of a 3D navigation task, and there is an explanation as to why this is appropriate. Bat densities and bat behavior are discussed per unit area when realistically it should be per unit volume. In fact, the authors reference studies to justify the densities used in the simulation, but these studies were done in a 3D world. If the authors have justification for why it is realistic to model a 3D world in a 2D simulation, I encourage them to provide references justifying this approach.

The focus on "masking" (which appears to be just in-band noise), especially relative to the problem of misassigned echoes, is concerning. If the bat calls are all the same waveform (downsweep linear FM of some duration, I assume - it's not clear from the text), false echoes would be a major problem. Masking, as the authors define it, just reduces SNR. This reduction is something like sqrt(N), where N is the number of conspecifics whose echoes are audible to the bat, so this allows the detection threshold to be set lower, increasing the probability that a bat's echo will exceed a detection threshold. False echoes present a very different problem. They do not reduce SNR per se, but rather they cause spurious threshold excursions (N of them!) that the bat cannot help but interpret as obstacle detection. I would argue that in dense groups the mis-assignment problem is much more important than the SNR problem.

The criteria set for flight behavior (lines 393-406) are not justified with any empirical evidence of the flight behavior of wild bats in collective flight. How did the authors determine the avoidance distances? Also, what is the justification for the time limit of 15 seconds to emerge from the opening? Instead of an exit probability, why not instead use a time criterion, similar to "How long does it take X% of bats to exit?" What is the empirical justification for the 1-10 calls used for integration? The "average exit time for 40 bats" is also confusing and not well explained. Was this determined empirically? From the simulation? If the latter, what are the conditions? Does it include masking, no masking, or which species?

Reviewer #3 (Public review):

Summary:

This paper identifies GTSE1 as a substrate of cyclin D1-CDK4/6 complexes when cyclin D1 is significantly over-expressed (as is common in cancers) rather than its endogenous level. GTSE is stabilized by phosphorylation and GTSE1 correlates with cancer prognosis, probably through an effect on cell proliferation.

Strengths:

There are few bonafide cyclin D1-Cdk4/6 substrates identified to be important in vivo so GTSE1 represents a potentially important finding for the field. Currently, the only cyclin D1 substrates involved in proliferation are the Rb family proteins.

Weaknesses:

GTSE1 is not a 'normal' target of cyclin D1-Cdk4/6, but rather only a target in a pathological situation.

Reviewer #3 (Public review):

This paper describes a new mechanism for the clearance of protein aggregates associated to endoplasmic reticulum re-organization that occurs during mitosis.

Experimental data showing clearance of protein aggregates during mitosis is solid, statistically significant, and very interesting. The authors made several new experiments included in the revised version to address the concerns raised by reviewers. A new proteomic analysis, co-localization of the aggregates with the ER membrane Sec61beta protein, expression of the aggregate-prone protein in the nucleus does not result in accumulation of aggregates, detection of protein aggregates in the insoluble faction after cell disruption and mostly importantly knockdown of ATL proteins involved in the organization of ER shape and structure impaired the clearance mechanism. This last observation addresses one of the weakest points of the original version which was the lack of experimental correlation between ER structure capability to re-shape and the clearance mechanism.

In conclusion, this new mechanism of protein aggregate clearance from the ER was not completely understood in this work but the manuscript presented, particularly in the revised version, an ensemble of solid observations and mechanistic information to scaffold future studies that clarify more details of this mechanism. As stated by the authors: "How protein aggregates are targeted and assembled into the intranuclear membranous structure waits for future investigation". This new mechanism of aggregate clearance from the ER is not expected to be fully understood in a single work but this paper may constitute one step to better comprehend the cell capability to resolve protein aggregates in different cell compartments.

Reviewer #3 (Public review):

Summary:

Transcriptionally silent HIV-1 genomes integrated in the host`s genome represent the main obstacle for an HIV-1 cure. Therefore, agents aimed at promoting HIV transcription, the so-called latency reactivating agents (LRAs) might represent useful tools to render these hidden proviruses visible to the immune system. The authors successfully identified, through multiple techniques, INTS12, a component of the Integrator complex involved in 3' processing of small nuclear RNAs U1 and U2, as a factor promoting HIV-1 latency and hindering elongation of the HIV RNA transcripts. This factor hinders the activity of a previously identified combination of LRAs, one of which, AZD5582, has been validated in the macaque model for HIV persistence during therapy (https://pubmed.ncbi.nlm.nih.gov/37783968/). The other compound, I-BET151, is known to synergize with AZD5582, and is a inhibitor of BET, factors counteracting elongation of RNA transcripts.<br /> Therefore, INTS12 maight represent a target for future LRAs-

Strengths:

Findings were confirmed through multiple screens and multiple techniques. The authors successfully mapped the identified HIV silencing factor at the HIV promoter, Silencing of INTS12 increases the activity of small-molecule HIV latency-reversing agents such as the histone deacetylase inhibitor vorinostat. Knockdown of INTS12 does not induce toxic effects in the cells, thus rendering it a candidate a drug discovery campaign aimed at finding new agents for an HIV/AIDS cure.

Weaknesses:

A caveat is that the impact of INTS12 in diverse T cell functions or other in vivo functions is not yet known, but the authors acknowledge this in the revised discussion.

Reviewer #3 (Public review):

Summary:

In this study, Sanchez-Leon et al. combined extracellular recordings of Purkinje cell activity in awake and anesthesized mice with juxtacellular recordings and Purkinje cell staining to link Purkinje cell orientation to their stimulation response. The authors find a relationship between neuron orientation and firing rate, dependent on stimulation type (anodal/cathodal). They also show effects of stimulation intensity and rebound effects.

Strengths:

Overall, the work is methodologically sound and the manuscript well written. The authors have taken great care to explain their rationale and methodological choices.

Weaknesses:

My only reservation is the lack of reporting of the precise test statistics, p-values and multiple comparison corrections. The work would benefit from adding this and other information.

Reviewer #3 (Public review):

Summary:

Wang and van Ede investigate whether and how attention re-orients within visual working memory following expected and unexpected centrally presented memory tests. Using a combination of spatial modulations in neural activity (EEG-alpha lateralization) and gaze bias quantified as time courses of microsaccade rate, the authors examined how retro cues with varying levels of reliability influence attentional deployment and subsequent memory performance. The conclusion is that attentional re-orienting occurs within visual working memory, even when tested centrally, with distinct patterns following expected and unexpected tests. The findings provide new value for the field and are likely of broad interest and impact, by highlighting working memory as an action-bound process (in)dependent on (an ambiguous) past.

Strengths:

The study uniquely integrates behavioral data (accuracy and reaction time), EEG-alpha activity, and gaze tracking to provide a comprehensive analysis of attentional re-orienting within visual working memory. As typical for this research group, the validity of the findings follows from the task design that effectively manipulates the reliability of retro cues and isolates attentional processes related to memory tests. The use of well-established markers for spatial attention (i.e. alpha lateralization) and more recently entangled dependent variable (gaze bias) is commendable. Utilizing these dependent metrics, the concise report presents a thorough analysis of the scaling effects of cue reliability on attentional deployment, both at the behavioral and neural levels. The clear demonstration of prolonged attentional deployment following unexpected memory tests is particularly noteworthy, although there are no significant time clusters per definition as time isn't a factor in a statistical sense, the jackknife approach is convincing. Overall, the evidence is compelling, allowing the conclusion of a second stage of internal attentional deployment following both expected and unexpected memory tests, highlighting the importance of memory verification and re-orienting processes.

Weaknesses:

I want to stress upfront that these are not specific to the presented work and do not affect my recommendation to offer the report to the public in its present form.

The sample size is consistent with previous studies, a larger sample could enhance the generalizability and robustness of the findings. The authors acknowledge high noise levels in EEG-alpha activity, which may affect the reliability of this marker. This is a general issue in non-invasive electrophysiology that cannot be handled by the authors but an interested reader should be aware of it. Effectively, the sensitivity of the gaze analysis appears "better" in part due to the better SNR. The latter also sets the boundaries for single trial analyses as the authors correctly mention. In terms of generalizability, I am convinced that the main outcome will likely generalize to different samples and stimulus types. Yet, as typical for the field, future research could explore different contexts and task demands to validate and extend the findings. The authors provide here how and why (including sharing of data and code).

Comments on revisions:

Really nice work, Thank you!

Reviewer #3 (Public review):

Li, Zhang, Wu and colleagues describe a new role for nuclear IDH1 in erythroid differentiation. IDH1 depletion results in a terminal erythroid differentiation defect with polychromatic and orthochromatic erythroblasts showing abnormal nuclei, nuclear condensation defects and an increased proportion of euchromatin, as well as enucleation defects. Using ChIP-seq for the histone modifications H3K79me3, H3K27me2 and H3K9me3, as well as ATAC-seq and RNA-seq in primary CD34-derived erythroblasts, the authors elucidate SIRT1 as a key dysregulated gene that is upregulated upon IDH1 knockdown. They furthermore show that chemical inhibition of SIRT1 partially rescues the abnormal nuclear morphology and enucleation defect during IDH1-deficient erythroid differentiation. The phenotype of delayed erythroid maturation and enucleation upon IDH1 shRNA-mediated knockdown was described in the group's previous co-authored study (PMID: 33535038). The authors describe this new role of IDH1 as non-canonical, but more experiments will be needed to determine whether this function of IDH1 in chromatin organization is secondary to its enzymatic-metabolic role. On the other hand, while the dependency of IDH1 mutant cells on NAD+ as well as a cell survival benefit upon SIRT1 inhibition has already been shown (see, e.g, PMID: 26678339, PMID: 32710757), previous studies focused on cancer cell lines and did not look at a developmental differentiation process, which makes this study interesting.

The authors had initially hypothesized that IDH1 has a role in the nucleus independent of its enzymatic function, which is interesting but was not supported by the presented experiments. In the revised manuscript, the authors decided to just focus on the nuclear role of IDH1. To this end, they present a system in HUDEP-2 cells harboring a CRISPR/Cas9-mediated IDH1 knockout and overexpression of an IDH1 construct containing a nuclear export signal. While they only use this system in some of their experiments, they mostly use a global IDH1 shRNA knockdown approach is employed, which will affect both forms of IDH1, cytoplasmic and nuclear. Future work using their system that specifically depletes nuclear IDH1 could further delineate changes of the chromatin landscape upon loss of nuclear IDH1 and also address how loss of nuclear IDH1 affects the part of the TCA cycle that has recently been shown to be present in the nucleus (PMID: 36044572).

Reviewer #3 (Public review):

The paper addresses pivotal questions concerning the multifaceted functions of oyster hemocytes by integrating single-cell RNA sequencing (scRNA-seq) data with analyses of cell morphology, transcriptional profiles, and immune functions. In addition to investigating granulocyte cells, the study delves into the potential roles of blast and hyalinocyte cells. A key discovery highlighted in this research is the identification of cell types engaged in antimicrobial activities, encompassing processes such as phagocytosis, intracellular copper accumulation, oxidative bursts, and antimicrobial peptide synthesis.

A particularly intriguing aspect of the study lies in the exploration of hemocyte lineages, warranting further investigation, such as employing scRNA-seq on embryos at various developmental stages.

Reviewer #3 (Public review):

There is an interesting mathematical connection - an "isomorphism"-between Price's equation and least-squares linear regression. Some people have misinterpreted this connection as meaning that there is a generality-limiting assumption of linearity within Price's equation, and hence that Hamilton's rule-which is derived from Price's equation-provides only an approximation of the action of natural selection. This is in contrast to the majority view that Hamilton's rule is a fully general and exact result.

To briefly give some mathematical details: Price's equation defines the action of natural selection in relation to a trait of interest as the covariance between fitness w and the genetic breeding value g for the trait, i.e. cov(w,g); this is a fully general result that applies exactly to any arbitrary set of (g,w) data; without any loss of generality this covariance can be expressed as the product of genetic variance var(g) and a coefficient b(w,g), the coefficient simply being defined as b(w,g) = cov(w,g)/var(g) for all var(g) > 0; it happens that if one fits a straight line to the same (g,w) data by means of least-squares regression then the slope of that line is equal to b(w,g).

All of this has already been discussed, repeatedly, in the literature.

Now turn to the present paper: the first sentence of the Abstract says "The generality of Hamilton's rule is much debated", and then the next sentence says "In this paper, I show that this debate can be resolved by constructing a general version of Hamilton's rule". But immediately it's clear that this isn't really resolving the debate, what this paper is actually doing is asserting the correctness of the minority view (i.e. that Hamilton's rule as it currently stands is not a general result) and then attempting to build a more general form of Hamilton's rule upon that shaky foundation. Predictably, the paper erroneously interprets the standard formulation of Hamilton's rule as a linear approximation and develops non-linear extensions to improve the goodness of fit for a result that is already exactly correct.

This is not a convincing contribution. It will not change minds or improve understanding of the topic.

Nor is it particularly novel. Smith et al (2010, "A generalisation of Hamilton's rule for the evolution of microbial cooperation" Science 328, 1700-1703) similarly interpreted Hamilton's rule as a linear model and provided a corresponding polynomial expansion - usefully fitting the model to microbial data so as to learn something about the costs and benefits of cooperation in an empirical setting. it's odd that this paper isn't cited here.

Reviewer #3 (Public review):

Kinesin-1 is a dimeric motor protein that transports cargo along microtubules. Its movement relies on the ability of its two catalytic motor domains (heads) to couple microtubule interactions with directional conformational changes and ATP turnover in a coordinated, alternating manner. The kinetics of these processes in each head are tightly regulated (gated) to ensure that at least one motor domain remains bound to the microtubule at all times, preventing detachment.

Niitani et al. investigated the gating mechanism by focusing on the role of the neck linker, a flexible region extending from the motor domain's C-terminus that undergoes conformational changes during stepping. They examined how the neck linker differentially regulates the microtubule affinity and ATP turnover of the front and rear heads. To do this, they designed cross-linkable monomeric motor domains mimicking the conformations of the front and rear heads and employed a combination of pre-steady-state and single-molecule analyses to measure ATP-binding and microtubule-detachment kinetics. Additionally, they studied a kinesin heterodimer with a locked rear head conformation to distinguish the kinetic properties of the front and rear heads within an active dimer.

ATP binding rates were measured using stopped-flow experiments with mant-ATP and nucleotide-free kinesin-microtubule complexes. The results showed that crosslinking the neck linker in the forward-pointing conformation (mimicking the rear head) reduced the ATP dissociation rate, while crosslinking it in the rear-pointing conformation (mimicking the front head) had no significant effect on ATP binding kinetics. ATP dissociation from the rear head was further examined using a kinesin mutant (E236A) that stabilizes the ATP-bound state by significantly slowing ATP hydrolysis.

To assess how neck-linker orientation affects microtubule attachment, the authors monitored turbidity changes after rapidly mixing nucleotide-free, crosslinked kinesin-microtubule complexes with ATP in a stopped-flow apparatus. Their findings demonstrated that the forward-oriented neck linker in the rear head promotes microtubule detachment, whereas the backward-oriented neck linker in the front head reduces detachment rates.

These results indicate that neck-linker conformation governs gating of microtubule affinity and nucleotide binding. Moreover, they show that even partial docking of the neck linker onto the head is sufficient to partially open the gating mechanism. To further investigate the role of neck linker tension, the authors created kinesin dimers with neck linker insertions of varying lengths. Microtubule detachment kinetics and ATPase activity assays revealed that ATP turnover in the rear head is significantly affected by the degree of forward tension applied to its neck linker.

Overall, Niitani et al. build upon previous kinesin gating models by introducing a neck-linker tension-based ATP binding affinity mechanism. Their findings provide a mechanistic basis for recent cryo-EM observations for kinesin-1 and kinesin-3 (KIF14) and distinguish the specific roles of neck linker tension in the front and rear heads in regulating ATP binding, hydrolysis, and microtubule detachment. This study is biochemically rigorous and makes an important contribution, though direct structural validation (e.g., cryo-EM snapshots of crosslinked or mutant kinesins bound to microtubules) would further strengthen their conclusions and clarify the asymmetry in ATP affinity between the front and rear heads.

Reviewer #3 (Public review):

Summary:

This paper presents a method for reconstructing input videos shown to a mouse from the simultaneously recorded visual cortex activity (two-photon calcium imaging data). The publicly available experimental dataset is taken from a recent brain-encoding challenge, and the (publicly available) neural network model that serves to reconstruct the videos is the winning model from that challenge (by distinct authors). The present study applies gradient-based input optimization by backpropagating the brain-encoding error through this selected model (a method that has been proposed in the past, with other datasets). The main contribution of the paper is, therefore, the choice of applying this existing method to this specific dataset with this specific neural network model. The quantitative results appear to go beyond previous attempts at video input reconstruction (although measured with distinct datasets). The conclusions have potential practical interest for the field of brain decoding, and theoretical interest for possible future uses in functional brain exploration.

Strengths:

The authors use a validated optimization method on a recent large-scale dataset, with a state-of-the-art brain encoding model. The use of an ensemble of 7 distinct model instances (trained on distinct subsets of the dataset, with distinct random initializations) significantly improves the reconstructions. The exploration of the relation between reconstruction quality and the number of recorded neurons will be useful to those planning future experiments.

Weaknesses:

The main contribution is methodological, and the methodology combines pre-existing components without any new original components. The movie reconstructions include a learned "transparency mask" to concentrate on the most informative area of the frame; it is not clear how this choice impacts the comparison with prior experiments. Did they all employ this same strategy? If not, shouldn't the quantitative results also be reported without masking, for a fair comparison?

Reviewer #3 (Public review):

Summary:

This well-powered study tested the effects of hunger on value-based dietary decision-making. The main hypothesis was that attentional mechanisms guide choices toward unhealthier and tastier options when participants are hungry and are in the fasted state compared to satiated states. Participants were tested twice - in a fasted state and in a satiated state after consuming a protein shake. Attentional mechanisms were measured during dietary decision-making by linking food choices and reaction times to eye-tracking data and mathematical drift-diffusion models. The results showed that hunger makes high-conflict food choices more taste-driven and less health-driven. This effect was formally mediated by relative dwell time, which approximates attention drawn to chosen relative to unchosen options. Computational modeling showed that a drift-diffusion model, which assumed that food choices result from a noisy accumulation of evidence from multiple attributes (i.e., taste and health) and discounted non-looked attributes and options, best explained observed choices and reaction times.

Strengths:

This study's findings are valuable for understanding how energy states affect decision-making and provide an answer to how hunger can lead to unhealthy choices. These insights are relevant to psychology, behavioral economics, and behavioral change intervention designs.

The study has a well-powered sample size and hypotheses were pre-registered. The analyses comprised classical linear models and non-linear computational modeling to offer insight into putative cognitive mechanisms.

In summary, the study advances the understanding of the links between energy states and value-based decision-making by showing that depleting is powerful for shaping the formation of food preferences. Moreover, the computational analysis part offers a plausible mechanistic explanation at the algorithmic level of observed effects.

Weaknesses:

Some parts of the positioning of the hunger state manipulation and the interpretation of its effects could be improved.

On the positioning side, it does not seem like a 'bad' decision to replenish energy states when hungry by preferring tastier, more often caloric options. In this sense, it is unclear whether the observed behavior in the fasted state is a fallacy or a response to signals from the body. The introduction does mention these two aspects of preferring more caloric food when hungry. However, some ambiguity remains about whether the study results indeed reflect suboptimal choice behavior or a healthy adaptive behavior to restore energy stores.

On the interpretation side, previous work has shown that beliefs about the nourishing and hunger-killing effectiveness of drinks or substances influence subjective and objective markers of hunger, including value-based dietary decision-making, and attentional mechanisms approximated by computational models and the activation of cognitive control regions in the brain. The present study shows differences between the protein shake and a natural history condition (fasted, state). This experimental design, however, cannot rule between alternative interpretations of observed effects. Notably, effects could be due to (a) the drink's active, nourishing ingredients, (b) consuming a drink versus nothing, or (c) both.

Reviewer #3 (Public review):

In general, although the authors interpret their results as pointing towards a possible role of BDNF in dentin regeneration, the results are over-interpreted due to the lack of proper controls and focus on TrkB expression, but not its isoforms in inflammatory processes. Surprisingly, the authors do not study the possible role of p75 in this process, which could be one of the mechanisms intervening under inflammatory conditions.

(1) The authors claim that there are two Trk receptors for BDNF, TrkA and TrkB. To date, I am unaware of any evidence that BDNF binds to TrkA to activate it. It is true that two receptors have been described in the literature, TrkB and p75 or NGFR, but the latter is not TrkA despite its name and capacity to bind NGF along with other neurotrophins. It is crucial for the authors to provide a reference stating that TrkA is a receptor for BDNF or, alternatively, to correct this paragraph.

(2) The authors discuss BDNF/TrkB in inflammation. Is there any possibility of p75 involvement in this process?

(3) The authors present immunofluorescence (IF) images against TrkB and pTrkB in the first figure. While they mention in the materials and methods section that these antibodies were generated for this study, there is no proof of their specificity. It should be noted that most commercial antibodies labeled as anti-TrkB recognize the extracellular domain of all TrkB isoforms. There are indications in the literature that pathological and excitotoxic conditions change the expression levels of TrkB-Fl and TrkB-T1. Therefore, it is necessary to demonstrate which isoform of TrkB the authors are showing as increased under their conditions. Similarly, it is essential to prove that the new anti-p-TrkB antibody is specific to this Trk receptor and, unlike other commercial antibodies, does not act as an anti-phospho-pan-Trk antibody.

(4) I believe this initial conclusion could be significantly strengthened, without opening up other interpretations of the results, by demonstrating the specificity of the antibodies via Western blot (WB), both in the presence and absence of BDNF and other neurotrophins, NGF, and NT-3. Additionally, using WB could help reinforce the quantification of fluorescence intensity presented by the authors in Figure 1. It's worth noting that the authors fixed the cells with 4% PFA for 2 hours, which can significantly increase cellular autofluorescence due to the extended fixation time, favoring PFA autofluorescence. They have not performed negative controls without primary antibodies to determine the level of autofluorescence and nonspecific background. Nor have they indicated optimizing the concentration of primary antibodies to find the optimal point where the signal is strong without a significant increase in background. The authors also do not mention using reference markers to normalize specific fluorescence or indicating that they normalized fluorescence intensity against a standard control, which can indeed be done using specific signal quantification techniques in immunocytochemistry with a slide graded in black-and-white intensity controls. From my experience, I recommend caution with interpretations from fluorescence quantification assays without considering the aforementioned controls.

(5) In Figure 2, the authors determine the expression levels of TrkA and TrkB using qPCR. Although they specify the primers used for GAPDH as a control in materials and methods, they do not indicate which primers they used to detect TrkA and TrkB transcripts, which is essential for determining which isoform of these receptors they are detecting under different stimulations. Similarly, I recommend following the MIQE guidelines (Minimum Information for Publication of Quantitative Real-Time PCR experiments), so they should indicate the amplification efficiency of their primers, the use of negative and positive controls to validate both the primer concentration used, and the reaction, the use of several stable reference genes, not just one.

(6) Moreover, the authors claim they are using the same amounts of cDNA for qPCRs since they have quantified the amounts using a Nanodrop. Given that dNTPs are used during cDNA synthesis, and high levels remain after cDNA synthesis from mRNA, it is not possible to accurately measure cDNA levels without first cleaning it from the residual dNTPs. Therefore, I recommend that the authors clarify this point to determine how they actually performed the qPCRs. I also recommend using two other reference genes like 18S and TATA Binding Protein alongside GAPDH, calculating the geometric mean of the three to correctly apply the 2^-ΔΔCt formula.

(7) Similarly, given that the newly generated antibodies have not been validated, I recommend introducing appropriate controls for the validation of in-cell Western assays.

(8) The authors' conclusion that TrkB levels are minimal (Figure 2E) raises questions about what they are actually detecting in the previous experiments might not be the TrkB-Fl form. Therefore, it is essential to demonstrate beyond any doubt that both the antibodies used to detect TrkB and the primers used for qPCR are correct, and in the latter case, specify at which cycle (Ct) the basal detection of TrkB transcripts occurs. Treatment with TNF-alpha for 14 days could lead to increased cell proliferation or differentiation, potentially increasing overall TrkB transcript levels due to the number of cells in culture, not necessarily an increase in TrkB transcripts per cell.

(9) Overall, there are reasonable doubts about whether the authors are actually detecting TrkB in the first three images, as well as the phosphorylation levels and localization of this receptor in the cells. For example, in Figure 3 A to J, it is not clear where TrkB is expressed, necessitating better resolution images and a magnified image to show in which cellular structure TrkB is expressed.

(10) In Figure 4, the authors indicate they have generated cells overexpressing BDNF after recombination using CRISPR technology. However, the WB they show in Figure 4B, performed under denaturing conditions, displays a band at approximately 28kDa. This WB is absolutely incorrect with all published data on BDNF detection via this technique. I believe the authors should demonstrate BDNF presence by showing a WB with appropriate controls and BDNF appearing at 14kDa to assume they are indeed detecting BDNF and that the cells are producing and secreting it. What antibodies have been used by the authors to detect BDNF? Have the authors validated it? There are some studies reporting the lack of specificity of certain commercial BDNF antibodies, therefore it is necessary to show that the authors are convincingly detecting BDNF.

(11) While the RNA sequencing data indicate changes in gene expression in cells treated with TNFalpha+CTX-B compared to control, the authors do not show a direct relationship between these genetic modifications with the rest of their manuscript's argument. I believe the results from these RNA sequencing assays should be put into the context of BDNF and TrkB, indicating which genes in this signaling pathway are or are not regulated, and their importance in this context.

Reviewer #3 (Public review):

Summary:

Soffers et al. developed a comprehensive genetic toolkit that enables researchers to access neuronal hemilineages during developmental and adult time points using scRNA-seq analysis to guide gene cassette exchange-based or CRISPR-based tool building. Currently, research groups studying neural circuit development are challenged with tying together findings in the development and mature circuit function of hemilineage-related neurons. Here, authors leverage publicly available scRNA-seq datasets to inform the development of a split-Gal4 library that targets 32 of 34 hemilineages in development and adult stages. The authors demonstrated that the split-Gal4 library, or genetic toolkit, can be used to assess the functional roles, neurotransmitter identity, and morphological changes in targeted cells. The tools presented in this study should prove to be incredibly useful to Drosophila neurobiologists seeking to link neural developmental changes to circuit assembly and mature circuit function. Additionally, some hemilineages have more than one split-Gal4 combination that will be advantageous for studies seeking to disrupt associated upstream genes.

Strengths:

Informing genetic tool development with publicly available scRNA-seq datasets is a powerful approach to creating specific driver lines. Additionally, this approach can be easily replicated by other researchers looking to generate similar driver lines for more specific subpopulations of cells, as mentioned in the Discussion.

The unification of optogenetic stimulation data of 8B neurons and connectomic analysis of the Giant-Fiber-induced take-off circuit was an excellent example of the utility of this study. The link between hemilineage-specific functional assays and circuit assembly has been limited by insufficient genetic tools. The tools and data present in this study will help better understand how collections of hemilineages develop in a genetically constrained manner to form circuits amongst each other selectively.

Weaknesses:

Although cell position, morphology (to some extent), and gene expression are good markers to track cell identity across developmental time, there are genetic tools available that could have been used to permanently label cells that expressed genes of interest from birth, ensuring that the same cells are being tracked in fixed tissue images.

Although gene activation is a good proxy for assaying neurochemical features, relying on whether neurochemical pathway genes are activated in a cell to determine its phenotype can be misleading given that the Trojan-Gal4 system commandeers the endogenous transcriptional regulation of a gene but not its post-transcriptional regulation. Therefore, neurochemical identity is best identified via protein detection. (strong language used in this section of the paper).

The authors mainly rely on the intersectional expression of transcription factors to generate split-Gal4 lines and target hemilineages specifically. However, the Introduction (Lines 97-99) makes a notable point about how driver lines in the past, which have also predominantly relied on the regulatory sequences of transcription factors, lack the temporal stability to investigate hemilineages across time. This point seems to directly conflict with the argument made in the Results (Lines 126-127) that states that most transcription factors are stably expressed in hemilineage neurons that express them. It is generally known that transcription factors can be expressed stably or transiently depending on the context. It is unclear how using the genes of transcription factors in this study circumvents the issue of creating temporally stable driver lines.

Reviewer #3 (Public review):

Summary:

This paper presents evidence from three behavioral experiments that causal impressions of "launching events", in which one object is perceived to cause another object to move, depend on motion direction-selective processing. Specifically, the work uses an adaptation paradigm (Rolfs et al., 2013), presenting repetitive patterns of events matching certain features to a single retinal location, then measuring subsequent perceptual reports of a test display in which the degree of overlap between two discs was varied, and participants could respond "launch" or "pass". The three experiments report results of adapting to motion direction, motion speed and "object identity", and examine how the psychometric curves for causal reports shift in these conditions depending on the similarity of adapter and test. While causality reports in the test display were selective for motion direction (Experiment 1), they were not selective for adapter-test speed differences (Experiment 2) nor for changes in object identity induced via color swap (Experiment 3). These results support the notion of a biological implementation of causality perception in the visual system, possibly even independently of computations of object identity.

Strengths:

The setup of the research question and hypotheses are exceptional. The authors thoroughly discuss relevant literature to clearly link their launch/pass paradigm to impressions of causality, strengthening their hypothesis and conclusions. The experiments are carefully performed (appropriate equipment, careful control of eye movements). The slip adaptor is a really nice control condition and effectively mitigates the need to control for motion direction with a drifting grating or similar. Participants were measured with sufficient precision, and a power curve analysis was conducted to determine the sample size. Data analysis and statistical quantification is appropriate. Data and analysis code will be shared on publication, in keeping with open science principles. The paper is concise and well written.

Weaknesses:

I would like to emphasise that in the employed paradigm and previously conducted similar study, the only report options are "launch" or "pass". As pointed out by the authors' reply, the adaptation to launches seems to be a highly specific process and likely is a consequence of the causal interaction between the objects. I would nonetheless be interested to see which of the stimulus features driving the adaptation effect observed here are relevant/irrelevant to subjective causal impressions in an experiment.

References:

Rolfs, M., Dambacher, M., & Cavanagh, P. (2013). Visual Adaptation of the Perception of Causality. Current Biology, 23(3), 250-254. https://doi.org/10.1016/j.cub.2012.12.017

Reviewer #3 (Public review):

The preprint by Yadav et al. describes a new setup to quantify a number of aggression and mating behaviors in Drosophila melanogaster. The investigation of these behaviors requires the analysis of a large number of videos to identify each kind of behavior displayed by a fly. Several approaches to automatize this process have been published before, but each of them has its limitations. The authors set out to develop a new setup that includes very low-cost, easy-to-acquire hardware and open-source machine-learning classifiers to identify and quantify the behavior.

Strengths:

(1) The study demonstrates that their cheap, simple, and easy-to-obtain hardware works just as well as custom-made, specialized hardware for analyzing aggression and mating behavior. This enables the setup to be used in a wide range of settings, from research with limited resources to classroom teaching.

(2) The authors used previously published software to train new classifiers for detecting a range of behaviors related to aggression and mating and to make them freely available. The classifiers are very positively benchmarked against a manually acquired ground truth as well as existing algorithms.

(3) The study demonstrates the applicability of the setup (hardware and classifiers) to common methods in the field by confirming a number of expected phenotypes with their setup.

Weaknesses:

(1) When measuring the performance of the duration-based classifiers, the authors count any bout of behavior as true positive if it overlaps with a ground-truth positive for only 1 frame - despite the minimal duration of a bout is 10 frames, and most bouts are much longer. That way, true positives could contain cases that are almost totally wrong as long there was an overlap of a single frame. For the mating behaviors that are classified in ongoing bouts, I think performance should be evaluated based on the % of correctly classified frames, not bouts.

(2) In the methods part, only one of the pre-existing algorithms (MateBook), is described. Given that the comparison with those algorithms is a so central part of the manuscript, each of them should be briefly explained and the settings used in this study should be described.

Taken together, this work can greatly facilitate research on aggression and mating in Drosophila. The combination of low-cost, off-the-shelf hardware and open-source, robust software enables researchers with very little funding or technical expertise to contribute to the scientific process and also allows large-scale experiments, for example in classroom teaching with many students, or for systematic screenings.

Reviewer #3 (Public review):

Summary:

The paper by Chang-Gonzalez et al. is a molecular dynamics (MD) simulation study of the dynamic recognition (load-induced catch bond) by the T cell receptor (TCR) of the complex of peptide antigen (p) and the major histocompatibility complex (pMHC) protein. The methods and simulation protocols are essentially identical as those employed in a previous study by the same group (Chang-Gonzalez et al., eLife 2024). In the current manuscript the authors compare the binding of the same pMHC complex to two different TCRs, B7 and A6 which was investigated in the previous paper. While the binding is more stable for both TCRs under load (of about 10-15 pN) than in the absence of load, the main difference is that B7 shows a smaller amount of stable contacts with the pMHC than A6.

Strengths:

The topic is interesting because of the relevance of mechanosensing in biological processes including cellular immunology. The MD simulations provide strong evidence that different TCRs can respond mechanically in a different way upon binding the same pMHC complex. These findings are useful for interpreting how mechanical force is employed for modulating different function of T cells.

Reviewer #3 (Public review):

Summary:

Bos et al study a computational model of cortical circuits with excitatory (E) and two subtypes of inhibition - parvalbumin (PV) and somatostatin (SOM) expressing interneurons. They perform stability and gain analysis of simplified models with nonlinear transfer functions when SOM neurons are perturbed. Their analysis suggests that in a specific setup of connectivity, instability and gain can be untangled, such that SOM modulation leads to both increase in stability and gain, in contrast to the typical direction in neuronal networks where increased gain results in decreased stability.

Strengths:

- Analysis of the canonical circuit in response to SOM perturbations. Through numerical simulations and mathematical analysis, the authors have provided a rather comprehensive picture of how SOM modulation may affect response changes.<br /> - Shedding light on two opposing circuit motifs involved in the canonical E-PV-SOM circuitry - namely, direct inhibition (SOM -> E) vs disinhibition (SOM -> PV -> E). These two pathways can lead to opposing effects, and it is often difficult to predict which one results from modulating SOM neurons. In simplified circuits, the authors show how these two motifs can emerge and depend on parameters like connection weights.<br /> - Suggesting potentially interesting consequences for cortical computation. The authors suggest that certain regimes of connectivity may lead to untangling of stability and gain, such that increases in network gain are not compromised by decreasing stability. They also link SOM modulation in different connectivity regimes to versatile computations in visual processing in simple models.

Weaknesses:

- Computationally, the analysis is solid, but it's very similar to previous studies (del Molino et al, 2017). Many studies in the past few years have done the perturbation analysis of a similar circuitry with or without nonlinear transfer functions (some of them listed in the references). This study applies the same framework to SOM perturbations, which is a useful computational analysis, in view of the complexity of the high-dimensional parameter space.<br /> - A general weakness of the paper is a lack of direct comparison to biological parameters or experiments. How different experiments can be reconciled by the results obtained here, and what new circuit mechanisms can be revealed? In its current form, the paper reads as a general suggestion that different combinations of gain modulation and stability can be achieved in a circuit model equipped with many parameters (12 parameters). This is potentially interesting but not surprising, given the high dimensional space of possible dynamical properties. A more interesting result would have been to relate this to biology, by providing reasoning why it might be relevant to certain circuits (and not others), or to provide some predictions or postdictions, which are currently not very strong in the manuscript.<br /> - Tuning curves are simulated for an individual orientation (same for all neurons), not considering the heterogeneity of neuronal networks with multiple orientation selectivity (and other visual features) - making the model too simplistic.

Reviewer #3 (Public review):

Summary:

This well-powered study tested the effects of hunger on value-based dietary decision-making. The main hypothesis was that attentional mechanisms guide choices toward unhealthier and tastier options when participants are hungry, and are in the fasted state compared to satiated states. Participants were tested twice - in a fasted state and in a satiated state after consuming a protein shake. Attentional mechanisms were measured during dietary decision-making by linking food choices and reaction times to eye-tracking data and mathematical drift-diffusion models. The results showed that hunger makes high-conflict food choices more taste-driven and less health-driven. This effect was formally mediated by relative dwell time, which approximates attention drawn to chosen relative to unchosen options. Computational modeling showed that a drift-diffusion model, which assumed that food choices result from a noisy accumulation of evidence from multiple attributes (i.e., taste and health) and discounted non-looked attributes and options, best explained observed choices and reaction times.

Strengths:

This study's findings are valuable for understanding how energy states affect decision-making and provide an answer to how hunger can lead to unhealthy choices. These insights are relevant to psychology, behavioral economics, and behavioral change intervention designs.

The study has a well-powered sample size and hypotheses were pre-registered. The analyses comprised classical linear models and non-linear computational modeling to offer insight into putative cognitive mechanisms.

In summary the study advances the understanding of the links between energy states and value-based decision-making by showing that depleting is powerful for shaping the formation of food preferences. Moreover, the computational analysis part offers a plausible mechanistic explanation at the algorithmic level of observed effects.

Weaknesses:

Some parts of the positioning of the hunger state manipulation and the interpretation of its effects could be improved.

On the positioning side, it does not seem like a 'bad' decision to replenish energy states when hungry by preferring tastier, more often caloric options. In this sense, it is unclear whether the observed behavior in the fasted state is a fallacy or a response to signals from the body. The introduction does mention these two aspects of preferring more caloric food when hungry. However, some ambiguity remains about whether the study results indeed reflect suboptimal choice behavior or a healthy adaptive behavior to restore energy stores.

On the interpretation side, previous work has shown that beliefs about the nourishing and hunger-killing effectiveness of drinks or substances influence subjective and objective markers of hunger, including value-based dietary decision-making, and attentional mechanisms approximated by computational models and the activation of cognitive control regions in the brain. The present study shows differences between the protein shake and a natural history condition (fasted, state). This experimental design, however, cannot rule between alternative interpretations of observed effects. Notably, effects could be due to (a) the drink's active, nourishing ingredients, (b) to consuming a drink versus nothing, or (c) both.

Comments on revisions:

The authors addressed all my comments appropriately and I have no further requests. Thank you for the added discussion of findings and extra analyses.

Reviewer #3 (Public Review):

Compared to the pyramidal cells of the CA1 and CA3 regions of the hippocampus, and the granule cells of the dentate gyrus (DG), the computational role(s) of mossy cells of the DG have received much less attention over the years and are consequently not well understood. Mossy cells receive feedforward input from granule cells and feedback from CA3 cells. One significant factor is the compression of the large number of CA3 cells that input onto a much smaller population of mossy cells, which then send feedback connections to the granule cell layer. The present paper seeks to understand this compression in terms of neural coding, and asks whether the subthreshold activity of a small number of mossy cells can predict above chance levels the shapes of individual SWs produced by the CA3 cells. Using elegant multielectrode intracellular recordings of mossy cells, the authors use deep learning networks to show that they can train the network to "predict" the shape of a SW that preceded the intracellular activity of the mossy cells. Putatively, a single mossy cell can predict the shape of SWs above chance. These results are interesting, but there are some conceptual issues and questions about the statistical tests that must be addressed before the results can be considered convincing.

Strengths<br /> (1) The paper uses technically challenging techniques to record from multiple mossy cells at the same time, while also recording SWs from the LFP of the CA3 layer. The data appear to be collected carefully and analyzed thoughtfully.<br /> (2) The question of how mossy cells process feedback input from CA3 is important to understand the role of this feedback pathway in hippocampal processing.<br /> (3) Given the concerns expressed below about proper statistical testing are resolved, the data appear supportive of the main conclusions of the authors and suggest that, to some degree, the much smaller population of mossy cells can conserve the information present in the larger population of CA3 cells, presumably by using a more compressed, dense population code.

Weaknesses<br /> (4) Some of the statistical tests appear inappropriate because they treat each CA3 SW and associated Vm from a mossy cell as independent samples. This violates the assumptions of statistical tests such as the Kolmogorov-Smirnov tests of Figure 3C and Fig 3E. Although there is large variability among the SWs recorded and among the Vm's, they cannot be considered independent measurements if they derive from the same cell and same recording site of an individual animal. This becomes especially problematic when the number of dependent samples adds up to the tens of thousands, providing highly inflated numbers of samples that artificially reduce the p values. Techniques such as mixed-effects models are being increasingly used to factor out the effects of within cell and within animal correlations in the data. The authors need to do something similar to factor out these contributions in order to perform statistical tests, throughout the manuscript when this problem occurs.<br /> (5) A separate statistical problem occurs when comparing real data against a shuffled, surrogate data set. From the methods, I gather that Figure 3C combined data from 100 surrogate shuffles to compare to the real data. It is inappropriate to do a classic statistical test of data against such shuffles, because the number of points in the pooled surrogate data sets are not true samples from a population. It is a mathematical certainty that one can eventually drive a p value to < 0.05 just by increasing the number of shuffles sufficiently. Thus, the p value is determined by the number of computer shuffles allowed by the time and processing power of a computer, rather than by sampling real data from the population. Figures such as 4C and 5A are examples that test data against shuffle appropriately, as a single value is determined to be within or outside the 95% confidence interval of the shuffle, and this determination is not directly affected by the number of shuffles performed.<br /> (6) The last line of the Discussion states that this study provides "important insights into the information processing of neural circuits at the bottleneck layer," but it is not clear what these insights are. If the statistical problems are addressed appropriately, then the results do demonstrate that the information that is reflected in SWs can be reconstructed by cells in the MC bottleneck, but it is not certain what conceptual insights the authors have in mind. They should discuss more how these results further our understanding of the function of the feedback connection from CA3 to the mossy cells, discuss any limitations on their interpretation from recording LFPs rather than the single-unit ensemble activity (where the information is really encoded).<br /> 7) In Figure 1C, the maximum of the MC response on the first inset precedes the SW, and the onset of the Vm response may be simultaneous with SW. This would suggest that the SW did not drive the mossy cell, but this was a coincident event. How many SW-mossy cell recordings are like this? Do the authors have a technical reason to believe that these are events in which the mossy cell is driven by the CA3 cells active during the SW?

Reviewer #3 (Public review):

Summary:

Predicting how two different drugs act together by looking at their specific gene targets and pathways is crucial for understanding the biological significance of drug combinations. This study incorporates drug-specific pathway activation scores (PASs) to estimate synergy scores as one of the key advancements for synergy prediction. The new algorithm, Drug synergy Interaction Prediction (DIPx), developed in this study, uses gene expression, mutation profiles, and drug synergy data to train the model and predict synergy between two drugs. Comprehensive comparisons with another best-performing algorithm, TAIJI-M, highlight the potential of its capabilities.

Strengths:

DIPx uses target and driver genes to elucidate pathway activation scores (PASs) to predict drug synergy. This approach integrates gene expression, mutation profiles, and drug synergy data to capture information about the functional interactions between drug targets, thereby providing a potential biological explanation for the synergistic effects of combined drugs. DIPx's performance was tested using the AstraZeneca-Sanger (AZS) DREAM Challenge dataset, especially in Test Set 1, where the Spearman correlation coefficient between predicted and observed drug synergy was 0.50 (95% CI: 0.47-0.53). DIPx's ability to handle novel combinations, as evidenced by its performance in Test Set 2, indicates its potential for predictions of new and untested drug combinations.

Weaknesses:

While the DIPx algorithm shows promise in predicting drug synergy based on pathway activation scores, it's essential to consider its limitations. One limitation is that the availability of training data for specific drug combinations may influence its predictive capability. Further testing and experimental validation of the predictions in future studies would be necessary to fully assess the algorithm's generalizability and robustness.

Reviewer #4 (Public review):

Summary:

In this study, the authors explore the neural dynamics of mirror neurons in the premotor cortex, focusing on the relationship between neural activity during action execution and observation. The study presents a rich dataset from three monkeys, with recordings from two regions per monkey. The authors use a method to analyze instantaneous neural subspaces and track their temporal evolution. Consistent with prior literature, they report that execution and observation subspaces remain largely distinct throughout the trial. However, after applying canonical correlation analysis, they observe a notable alignment between execution and observation activities, suggesting the presence of shared neural codes. The study is well-designed, and the analyses are thoroughly documented, occasionally overly so in the main text. While most findings are compelling, I find the conclusions drawn from Figure 8 less convincing. Specifically, I am skeptical about the application of CCA in this context and the subsequent interpretations regarding execution-observation similarity, which is a central claim of the manuscript.

• The authors cite Safaie et al. 2023 as a precedent for applying CCA to align neural population dynamics. However, in that study, CCA was used to align neural dynamics across different animals, a justifiable approach given that neural trajectories exist in separate neural state spaces for each animal. Here, CCA is applied to align execution and observation activities within the same neural state space of the same MNs. I find this application of CCA less well-justified, as it may overestimate execution-observation similarity.<br /> • The control conditions presented in Figures 8C and 8D are somewhat reassuring, as they show that the similarity introduced by CCA is not universally high. However, these controls appear to be limited to the Hold epoch. It remains unclear whether the same holds true for the Go and Movement epochs.<br /> • In Figure 5, the authors display low-dimensional representations of four objects across task epochs during execution (A) and observation (B). The diagonals of the matrices reveal clear differences between execution and observation configurations across all four epochs. The authors suggest using CCA to align these configurations; however, this alignment seems to require time-specific application of CCA for each epoch (as demonstrated in Figure 8 for the Hold epoch). The need for time-specific adjustments likely depends on the fact that execution and observation subspaces are continuously shifting over time (as authors show in Figure 4), but this approach appears to be a strained attempt to demonstrate similarity between execution and observation codes.<br /> • The authors themselves offer an alternative hypothesis (line 730): that "PM MN population activity during action observation, rather than representing movements made by another individual similar to one's own movements, instead may represent different movements one might execute oneself in response to those made by another individual". This interpretation appears more congruent with the data presented.<br /> • In the end, I am left with a sense of ambiguity: which analysis should be considered more reliable, the negligible correspondence between execution and observation activity depicted in Figure 7, or the considerable similarity shown in Figure 8? The authors should address this apparent contradiction and provide a clearer discussion to reconcile these findings.

Reviewer #3 (Public review):

Summary:

In this paper, Tang et al report the discovery of a Glycoslyceramide synthase gene, GlcT, which they found in a genetic screen for mutations that generate tumorous growth of stem cells in the gut of Drosophila. The screen was expertly done using a classic mutagenesis/mosaic method. Their initial characterization of the GlcT alleles, which generate endocrine tumors much like mutations in the Notch signaling pathway, is also very nice. Tang et al checked other enzymes in the glycosylceramide pathway and found that the loss of one gene just downstream of GlcT (Egh) gives similar phenotypes to GlcT, whereas three genes further downstream do not replicate the phenotype. Remarkably, dietary supplementation with a predicted GlcT/Egh product, Lactosyl-ceramide, was able to substantially rescue the GlcT mutant phenotype. Based on the phenotypic similarity of the GlcT and Notch phenotypes, the authors show that activated Notch is epistatic to GlcT mutations, suppressing the endocrine tumor phenotype and that GlcT mutant clones have reduced Notch signaling activity. Up to this point, the results are all clear, interesting, and significant. Tang et al then go on to investigate how GlcT mutations might affect Notch signaling, and present results suggesting that GlcT mutation might impair the normal endocytic trafficking of Delta, the Notch ligand. These results (Fig X-XX), unfortunately, are less than convincing; either more conclusive data should be brought to support the Delta trafficking model, or the authors should limit their conclusions regarding how GlcT loss impairs Notch signaling. Given the results shown, it's clear that GlcT affects EE cell differentiation, but whether this is via directly altering Dl/N signaling is not so clear, and other mechanisms could be involved. Overall the paper is an interesting, novel study, but it lacks somewhat in providing mechanistic insight. With conscientious revisions, this could be addressed. We list below specific points that Tang et al should consider as they revise their paper.

Strengths:

The genetic screen is excellent.

The basic characterization of GlcT phenotypes is excellent, as is the downstream pathway analysis.

Weaknesses:

(1) Lines 147-149, Figure 2E: here, the study would benefit from quantitations of the effects of loss of brn, B4GalNAcTA, and a4GT1, even though they appear negative.

(2) In Figure 3, it would be useful to quantify the effects of LacCer on proliferation. The suppression result is very nice, but only effects on Pros+ cell numbers are shown.

(3) In Figure 4A/B we see less NRE-LacZ in GlcT mutant clones. Are the data points in Figure 4B per cell or per clone? Please note. Also, there are clearly a few NRE-LacZ+ cells in the mutant clone. How does this happen if GlcT is required for Dl/N signaling?

(4) Lines 222-225, Figure 5AB: The authors use the NRE-Gal4ts driver to show that GlcT depletion in EBs has no effect. However, this driver is not activated until well into the process of EB commitment, and RNAi's take several days to work, and so the author's conclusion is "specifically required in ISCs" and not at all in EBs may be erroneous.

(5) Figure 5C-F: These results relating to Delta endocytosis are not convincing. The data in Fig 5C are not clear and not quantitated, and the data in Figure 5F are so widely scattered that it seems these co-localizations are difficult to measure. The authors should either remove these data, improve them, or soften the conclusions taken from them. Moreover, it is unclear how the experiments tracing Delta internalization (Fig 5C) could actually work. This is because for this method to work, the anti-Dl antibody would have to pass through the visceral muscle before binding Dl on the ISC cell surface. To my knowledge, antibody transcytosis is not a common phenomenon.

(6) It is unclear whether MacCer regulates Dl-Notch signaling by modifying Dl directly or by influencing the general endocytic recycling pathway. The authors say they observe increased Dl accumulation in Rab5+ early endosomes but not in Rab7+ late endosomes upon GlcT depletion, suggesting that the recycling endosome pathway, which retrieves Dl back to the cell surface, may be impaired by GlcT loss. To test this, the authors could examine whether recycling endosomes (marked by Rab4 and Rab11) are disrupted in GlcT mutants. Rab11 has been shown to be essential for recycling endosome function in fly ISCs.

(7) It remains unclear whether Dl undergoes post-translational modification by MacCer in the fly gut. At a minimum, the authors should provide biochemical evidence (e.g., Western blot) to determine whether GlcT depletion alters the protein size of Dl.

(8) It is unfortunate that GlcT doesn't affect Notch signaling in other organs on the fly. This brings into question the Delta trafficking model and the authors should note this. Also, the clonal marker in Figure 6C is not clear.

(9) The authors state that loss of UGCG in the mouse small intestine results in a reduced ISC count. However, in Supplementary Figure C3, Ki67, a marker of ISC proliferation, is significantly increased in UGCG-CKO mice. This contradiction should be clarified. The authors might repeat this experiment using an alternative ISC marker, such as Lgr5.

Reviewer #3 (Public review):

Summary:

Fleming et al sought to better understand DNAJC7's function in motor neurons as mutations in this gene have been associated with amyotrophic lateral sclerosis (ALS). The research question is relevant and important. The authors use an induced pluripotent stem cell (iPSC) line to derive motor neurons (iMNs) finding that DNAJC7 interacts with RNA-binding proteins (RBP) in wild-type cells and a truncated mutant DNAJC7[R156*] disrupts the RBP, hnRNPU, by promoting its accumulation into insoluble fractions. Given that DNAJC7 is predicted to regulate stress responses, the authors then find that DNAJC7[R156*] expression sensitizes the iMNs to proteosomal stress by disrupting the expression of the key heat stress response regulator, HSF1. These findings support that loss-of-function mutations in DNAJC7 will indeed sensitize motor neurons to proteotoxic stress, potentially driving ALS. The association with RBPs, which routinely are found to be disrupted in ALS, is of interest and warrants further study.

Strengths:

(1) The research question is relevant and important. The authors provide interesting data that DNAJC7 mutations impact two important features in ALS, the dysregulation of RNA binding proteins and the sensitivity of motor neurons to proteotoxic stress.

(2) The authors provide solid data to support their findings and the assays are appropriate.

Weaknesses:

(1) The authors rely on a single iPSC line throughout the text, using the same line to make the mutation-carrying cells. iPSCs are highly variable and at minimum 3 lines, typically 5 lines, should be used to define consistent findings. This work would be greatly strengthened if 3 or more lines were used to confirm consistent effects. This is particularly concerning given that iPSCs were differentiated using growth factors versus genetic induction. Growth-factor-based differentiations are more variable.

(2) The authors argue that HSF1 and its targets are downregulated in sporadic ALS and mutant C9orf72 ALS. The first concern is that these transcriptomics data were derived from cortical tissue which does not contain motor neurons (Pineda et al. 2024 Cell 187: 1971-1989.e1916). The second concern is that the inclusion of C9orf72 mutant tissue is not well justified as (1) this mutation is associated with an upregulation of HSF1 and its targets in patients (Mordes et al, Acta Neuropathol Commun 2018 6(1):55; Lee et al Neuron 2023 111(9):1381-1390) and (2) the C9orf72 mutation is associated with a ALS/FTD spectrum disorder defined by TDP-43 pathology. Disease mechanisms associated with this spectrum disorder may not overlap with traditional ALS which is typically defined by SOD1 pathology.

(3) As a whole, the findings are mechanistically disjointed, and additional experiments or discussion would help to connect the dots a bit more.

Reviewer #3 (Public review):

ZSS has been widely used in Traditional Chinese Medicine as a sleep-promoting herb. This study tests the effects of ZSS powder and extracts on AD, PD, and aging, and broad protective effects were revealed in mice.

However, this work did not include a mechanistic study or target data on ZSS were included, and PK data were also not involved. Mechanisms or targets and PK study are suggested. A human PK study is preferred over mice or rats. E.g. which main active ingredients and the concentration in plasma, in this context, to study the pharmacological mechanisms of ZSS.

Reviewer #3 (Public review):

Summary:

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

Strengths:

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

Weaknesses:

- The comparison in Figure 4 for different b-values shows % signal changes. However, as the baseline signal changes with added diffusion weighting, this is rather uninformative. A plot of t-values against cortical depth would be more insightful.<br /> - Surprisingly, the %-signal change for a b-value of 0 is below 1% for 3/4 participants, even at the cortical surface. This raises some doubts about the task or ROI definition. A finger-tapping task should reliably engage the primary motor cortex, even at 3T, and even in individual participants.<br /> - The double peak patter in the BOLD weighted images in Figure 4 is unexpected given the existing literature on BOLD responses as a function of cortical depth.<br /> - Although I'd like to applaud the authors for their ambition with the connectivity analysis, the low significance threshold used in these maps (z=1,64) leads to concerns about the SNR of the underlying data.

I remain unconvinced of the conclusion that the developed VN fMRI exhibited layer specificity - the double peak which is taken as a marker of specificity is not absent in the BOLD responses either, and overall BOLD and VN response profiles as a function of cortical depth are quite similar.

Reviewer #3 (Public review):

In this manuscript, Millard et al. investigate the effects of nicotine on pain sensitivity and peak alpha frequency (PAF) in resting state EEG. To this end, they ran a randomized, double-blind, placebo-controlled experiment involving 62 healthy adults that received either 4 mg nicotine gum (n=29) or placebo (n=33). Prolonged heat and pressure were used as pain models. Resting state EEG and pain intensity (assessed with a visual analog scale) were measured before and after the intervention. Additionally, several covariates (sex at birth, depression and anxiety symptoms, stress, sleep quality, among others) were recorded. Data was analyzed using ANCOVA-equivalent two-wave latent change score models, as well as repeated measures analysis of variance. Results do not show experimentally relevant changes of PAF or pain intensity scores for neither of the prolonged pain models due to nicotine intake.

The main strengths of the manuscript are its solid conceptual framework and the thorough experimental design. The researchers make a good case in the introduction and discussion for the need to further investigate the association of PAF and pain sensitivity. Furthermore, they proceed to carefully describe every aspect of the experiment in great detail, which is excellent for reproducibility purposes. Finally, they analyze the data from different and provide an extensive report of their results.

There are relevant weaknesses to highlight. Firstly, authors preregistered the study and the analysis plan, but the preregistration does not contain an estimation of the expected effect sizes or the rationale for the selected the sample size. Furthermore, the authors interpret their results in a way that is not supported by the evidence (which is notorious in the abstract and the first paragraph of the discussion). Even though some of the differences are statistically significant (e.g., global PAF, pain intensity ratings during heat pain), these differences are far from being experimentally or clinically relevant. The effect sizes observed are not sufficiently large to consider that pain sensitivity was modulated by the nicotine intake, which puts into question all the answers to the research questions posed in the study. The authors attempt to nuance this throughout the discussion, but in a way that is not compatible with the main claims.

https://youtu.be/TwAJO7uDwJg?si=UfRBFcai-IgZDG4B&t=120

Reviewer #3 (Public review):

In the report entitled "CXXC-finger protein 1 associates with FOXP3 to stabilize homeostasis and suppressive functions of regulatory T cells", the authors demonstrated that Cxxc1-deletion in Treg cells leads to the development of severe inflammatory disease with impaired suppressive function. Mechanistically, CXXC1 interacts with Foxp3 and regulates the expression of key Treg signature genes by modulating H3K4me3 deposition. Their findings are interesting and significant.

Comments on revisions:

In the revised manuscript, the authors have responded well to all the concerns reviewers raised. The manuscript has further improved.