Reviewer #1 (Public review):

Summary:

Lai and Doe address the integration of spatial information with temporal patterning and genes that specify cell fate. They identify the Forkhead transcription factor Fd4 as a lineage-restricted cell fate regulator that bridges transient spatial transcription factors to terminal selector genes in the developing Drosophila ventral nerve cord. The experimental evidence convincingly demonstrates that Fd4 is both necessary for late-born NB7-1 neurons, but also sufficient to transform other neural stem cell lineages toward the NB7-1 identity. This work addresses an important question that will be of interest to developmental neurobiologists: How cell identities defined by initial transient developmental cues can be maintained in the progeny cells, even if the molecular mechanism remains to be investigated. In addition, the study proposes a broader concept of lineage identity genes that could be utilized in other lineages and regions in the Drosophila nervous system and in other species.

Strengths:

While the spatial factors patterning the neuroepithelium to define the neuroblast lineages in the Drosophila ventral nerve cord are known, these factors are sometimes absent or not required during neurogenesis. In the current work, Lai and Doe identified Fd4 in the NB7-1 lineage that bridges this gap and explains how NB7-1 neurons are specified after Engrailed (En) and Vnd cease their expression. They show that Fd4 is transiently co-expressed with En and Vnd and are present in all nascent NB7-1 progenies. They further demonstrate that Fd4 is required for later-born NB7-1 progenies and sufficient for the induction of NB7-1 markers (Eve and Dbx) while repressing markers of other lineages when force-expressed in neural progenitors, e.g. in the NB5-6 lineage and in the NB7-3 lineage. They also demonstrate that, when Fd4 is ectopically expressed in NB7-3 and NB5-6 lineages, this leads to the ectopic generation of dorsal muscle-innervating neurons. The inclusion of functional validation using axon projections demonstrates that the transformed neurons acquire appropriate NB7-1 characteristics beyond just molecular markers. Quantitative analyses are thorough and well-presented for most experiments.

Original weaknesses and potential extensions:

(1) While Fd4 is required and sufficient for several later-born NB7-1 progeny features, a comparison between early-born (Hb/Eve) and later-born (Run/Eve) appears missing for pan-progenitor gain of Fd4 (with sca-Gal4; Figure 4) and for the NB7-3 lineage (Figure 6). Having a quantification for both could make it clearer whether Fd4 preferentially induces later-born neurons or is sufficient for NB7-1 features without temporal restriction.

(2) Fd4 and Fd5 are shown to be partially redundant, as Fd4 loss of function alone does not alter the number of Eve+ and Dbx+ neurons. This information is critical and should be included in Figure 3.

(3) Several observations suggest that lineage identity maintenance involves both Fd4-dependent and Fd4-independent mechanisms. In particular, the fact that fd4-Gal4 reporter remains active in fd4/fd5 mutants even after Vnd and En disappear indicates that Fd4's own expression, a key feature of NB7-1 identity, is maintained independently of Fd4 protein. This raises questions about what proportion of lineage identity features require Fd4 versus other maintenance mechanisms, which deserves discussion.

(4) Similarly, while gain of Fd4 induces NB7-1 lineage markers and dorsal muscle innervation in NB5-6 and NB7-3 lineages, drivers for the two lineages remain active despite the loss of molecular markers, indicating some regulatory elements retain activity consistent with their original lineage identity. It is therefore important to understand the degree of functional conversion in the gain-of-function experiments. Sparse labeling of Fd4 overexpressing NB5-6 and NB7-3 progenies, as what was done in Seroka and Doe (2019) would be an option.

(5) The less-penetrant induction of Dbx+ neurons in NB5-6 with Fd4-overexpression is interesting. It might be worth discussing whether it is a Fd4 feature or a NB5-6 feature by examining Dbx+ neuron number in NB7-3 with Fd4-overexpression.

(6) It is logical to hypothesize that spatial factors specify early-born neurons directly so only late-born neurons require Fd4, but it was not tested. The model would be strengthened by examining whether Fd4-Gal4-driven Vnd rescues the generation of later-born neurons in fd4/fd5 mutants.

(7) It is mentioned that Fd5 is not sufficient for the NB7-1 lineage identity. The observation is intriguing in how similar regulators serve distinct roles, but the data are not shown. The analysis in Figure 4 should be performed for Fd5 as supplemental information.

Comments on latest version:

We appreciate the thorough revision and the detailed point-by-point responses. Overall, the updated manuscript has addressed the main issues we raised previously, especially around the potential potency differences of Fd4 along the birth order axis and possible redundancy with Vnd in early-born neurons. The additional data are convincing and presented clearly, with figures and supplements that are informative and appropriately labeled.

We noticed one remaining point that could be considered, the necessary-and-sufficient phrasing for Fd4 regulating NB7-1 fates. Given the possible redundancy among Fd4/5 and Vnd and the fact that early-born outputs (U1-3, Figure 3F) are not dependent on Fd4/5, we suggest revising this claim and either (a) limit the claim to necessary and sufficient for late-born NB7-1 progeny identity, or (b) frame Fd4 as sufficient for NB7-1 program induction while being required but redundant (e.g., with Vnd) for early-born features, rather than universally necessary/sufficient across the entire lineage output.

Regarding the lack of phenotype of single Fd4/5 mutants and Fd5 gain of function, we still encourage the authors to include the fd4 and fd5 single-mutant negative results as a brief supplemental item (e.g., a representative panel plus a simple quantification on Eve and Dbx would be sufficient). This would strengthen transparency, remove "data not shown" statements that are not necessary when these data can be presented as supplementary data with no space limitation, and make it easier for readers to evaluate redundancy claims.

Overall, we view the work as substantially complete and appreciate its contribution and conceptual framing. We have updated our public review to reflect the current version and the authors' efforts to address the major points raised in the prior round.

Reviewer #1 (Public review):

Summary:

This study aims to address an important and timely question: how does the mesoscale architecture of cortical and subcortical circuits reorganize during sensorimotor learning? By using high-density, chronically implanted ultra-flexible electrode arrays, the authors track spiking activity across ten brain regions as mice learn a visual Go/No-Go task. The results indicate that learning leads to more sequential and temporally compressed patterns of activity during correct rejection trials, alongside changes in functional connectivity ranks that reflect shifts in the relative influence of visual, frontal, and motor areas throughout learning. The emergence of a more task-focused subnetwork is accompanied by broader and faster propagation of stimulus information across recorded regions.

Strengths:

A clear strength of this work is its recording approach. The combination of stable, high-throughput multi-region recordings over extended periods represents a significant advance for capturing learning-related network dynamics at the mesoscale. The conceptual framework is well motivated, building on prior evidence that decision-relevant signals are widely distributed across the brain. The analysis approach, combining functional connectivity rankings with information encoding metrics is well motivated but needs refinement. These results provide some valuable evidence of how learning can refine both the temporal precision and the structure of interregional communication, offering new insights into circuit reconfiguration during learning.

Weaknesses:

Several important aspects of the evidence remain incomplete. In particular, it is unclear whether the reported changes in connectivity truly capture causal influences, as the rank metrics remain correlational and show discrepancies with the manipulation results. The absolute response onset latencies also appear slow for sensory-guided behavior in mice, and it is not clear whether this reflects the method used to define onset timing or factors such as task structure or internal state. Furthermore, the small number of animals, combined with extensive repeated measures, raises questions about statistical independence and how multiple comparisons were controlled. The optogenetic experiments, while intended to test the functional relevance of rank-increasing regions, leave it unclear how effectively the targeted circuits were silenced. Without direct evidence of reliable local inhibition, the behavioral effects or lack thereof are difficult to interpret.

Reviewer #1 (Public review):

Summary:

The author's goal was to arrest PsV capsids on the extracellular matrix using cytochalasin D. The cohort was then released and interaction with the cell surface, specifically with CD151 was assessed.

The model that fragmented HS associated with released virions mediates the dominant mechanism of infectious entry has only been suggested by research from a single laboratory and has not been verified in the 10+ years since publication. The authors are basing this study on the assumption that this model is correct, and these data are referred to repeatedly as the accepted model despite much evidence to the contrary. The discussion in lines 65-71 concerning virion and HSPG affinity changes is greatly simplified. The structural changes in the capsid induced by HS interaction and the role of this priming for KLK8 and furin cleavage has been well researched. Multiple laboratories have independently documented this. If this study aims to verify the shedding model, additional data needs to be provided.

Note on revisions:

The authors did an excellent job in their revision to include data from the effect of proteolytic priming on their observed virion transfer to the cell body. All other minor issues were addressed adequately.

The work could be especially critical to understanding the process of in vivo infection.

Reviewer #1 (Public review):

Summary:

The authors aimed to examine how the covariation between cognition (represented by a g-factor based on 12 features of 11 cognitive tasks) and mental health (represented by 133 diverse features) is reflected in MR-based neural markers of cognition, as measured through multimodal neuroimaging (structural, rsfMRI and diffusion MR). To integrate multiple neuroimaging phenotypes across MRI modalities the authors used a so-called a stacking approach, which employs two levels of machine learning. First, they build a predictive model from each neuroimaging phenotype to predict a target variable. Next, in the stacking level, they use predicted values (i.e., cognition predicted from each neuroimaging phenotype) from the first level as features to predict the target variable. To quantify the contribution of the neural indicators of cognition explaining the relationship between cognition and mental health, they conducted commonality analyses. Results showed that when they stacked neuroimaging phenotypes within dwMRI, rsMRI, and sMRI, they captured 25.5%, 29.8%, and 31.6% of the predictive relationship between cognition and mental health, respectively. By stacking all 72 neuroimaging phenotypes across three MRI modalities, they enhanced the explanation to 48%. Age and sex shared substantial overlapping variance with both mental health and neuroimaging in explaining cognition, accounting for 43% of the variance in the cognition-mental health relationship.

Strengths:

(1) Big study population (UK Biobank with 14000 subjects)

(2) Description of methods (including Figure 1) is helpful in understanding the approach

(3) Final manuscript improved after revision

Weaknesses:

(1) The relevance of the question is now better described, but the impact of the work is more of conceptual value than of direct clinical value.

(2) The discussion on the interpretation of the positive and negative PLRS loadings is now further explained, but remains a bit counterintuitive.

Note: the computational aspects of the methods fall beyond my expertise.

Joint Public Review:

In this study, the authors introduce CellCover, a gene panel selection algorithm that leverages a minimal covering approach to identify compact sets of genes with high combinatorial specificity for defining cell identities and states. This framework addresses a key limitation in existing marker selection strategies, which often emphasize individually strong markers while neglecting the informative power of gene combinations. The authors demonstrate the utility of CellCover through benchmarking analyses and biological applications, particularly in uncovering previously unresolved cell states and lineage transitions during neocorticogenesis.

The major strengths of the work include the conceptual shift toward combinatorial marker selection, a clear mathematical formulation of the minimal covering strategy, and biologically relevant applications that underscore the method's power to resolve subtle cell-type differences. The authors' analysis of the Telley et al. dataset highlights intriguing cases of ribosomal, mitochondrial, and tRNA gene usage in specific cortical cell types, suggesting previously underappreciated molecular signatures in neurodevelopment. Additionally, the observation that outer radial glia markers emerge prior to gliogenic progenitors in primates offers novel insights into the temporal dynamics of cortical lineage specification.

However, several aspects of the study would benefit from further elaboration. First, the interpretability of gene panels containing individually lowly expressed genes but high combinatorial specificity could be improved by providing clearer guidelines or illustrative examples. Second, the utility of CellCover in identifying rare or transient cell states should be more thoroughly quantified, especially under noisy conditions typical of single-cell datasets. Third, while the findings on unexpected gene categories are provocative, they require further validation - either through independent transcriptomic datasets or orthogonal methods such as immunostaining or single-molecule FISH-to confirm their cell-type-specific expression patterns.

Specifically, the manuscript would benefit from further clarification and additional validation in the following areas:

• A more in-depth explanation of marker panel applications is needed. Specifically, how should users interpret gene panels where individual genes show only moderate or low expression levels, but the combination provides high specificity? Providing a concrete example, along with guidelines for interpreting such combinatorial signatures, would enhance the practical utility of the method.

• Further quantification of CellCover's sensitivity in detecting rare cell subtypes or states would strengthen the evaluation of its performance. Additionally, it would be helpful to assess how CellCover performs under noisy conditions, such as low cell numbers or read depths, which are common challenges in scRNA-seq datasets.

• It is intriguing and novel that CellCover analysis of the dataset from Telley et al. suggests cell-type-specific expression of ribosomal, mitochondrial, or tRNA genes. These findings would be significantly strengthened by additional validation. For example, the reported radial glia-specific expression of Rps18-ps3 and Rps10-ps1, as well as the postmitotic neuron-specific expression of mt-Tv and mt-Nd4l, should be corroborated using independent scRNA-seq or spatial transcriptomic datasets of the developing neocortex. Alternatively, these expression patterns could be directly examined through immunostaining or single-molecule FISH analysis.

• The observation that outer radial glia (oRG) markers are expressed in neural progenitors before the emergence of gliogenic progenitors in primates and humans is compelling. This could be further supported by examining the temporal and spatial expression patterns of early oRG-specific markers versus gliogenic progenitor markers in recent human spatial transcriptomic datasets - such as the one published by Xuyu et al. (PMID: 40369074) or Wang et al. (PMID: 39779846).

Summary:

Overall, this work provides a conceptually innovative and practically useful method for cell type classification that will be valuable to the single-cell and developmental biology communities. Its impact will likely grow as more researchers seek scalable, interpretable, and biologically informed gene panels for multimodal assays, diagnostics, and perturbation studies.

Reviewer #1 (Public review):

MPRAs are a high-throughput and powerful tool for assaying the regulatory potential of genomic sequences. However, linking MPRA-nominated regulatory sequences to their endogenous target genes, and identifying the more specific functional regions within these sequences can be challenging. MPRAs that tile a genomic region, and saturation mutagenesis-based MRPAs can help to address these challenges. In this work, Tulloch et al. describe a streamlined MPRA system for the identification and investigation of the regulatory elements surrounding a gene of interest with high resolution. The use of BACs covering a locus of interest to generate MPRA libraries allows for an unbiased, and high-coverage assessment of a particular region. Follow up degenerate MPRAs, where each nucleotide in the nominated sequences are systematically mutated, then can point to key motifs driving their regulatory activity. The authors present this MPRA platform as straightforward, easily customizable, and less time- and resource-intensive than traditional MPRA designs. They demonstrate the utility of their design in the context of the developing mouse retina, where they first use the LS-MPRA to identify active regulatory elements for select retinal genes, followed by d-MPRA which allowed them to dissect the functional regions within those elements and nominate important regulatory motifs. These assays were able to recapitulate some previously known cis-regulatory modules (CRMs), as well as identify some new potential regulatory regions. Follow up experiments assessing co-localization of the gene of interest with the CRM-linked GFP reporter in the target cells, and CUT&RUN assays to confirm transcription factor binding to nominated motifs provided support linking these CRMs to the genes of interest. Overall, this method appears flexible and could be an easy to implement tool for other investigators aiming to study their locus of interest with high resolution.

Strengths:

(1) The method of fragmenting BACs allows for high, overlapping coverage of the region of interest.

(2) The d-MPRA method was an efficient way to identify key functional transcription factor motifs, and nominate specific transcription factor-driven regulatory pathways that could be studied further.

(3) Additional assays like co-expression analyses using the endogenous gene promoter, and use of the Notch inhibitor in the case of Olig2, helped correlate the activity of the CRMs to the expression of the gene of interest, and distinguish false positives from the initial MPRA.

(4) The use of these assays across different time points, tissues, and even species demonstrated that they can be used across many contexts to identify both common and divergent regulatory mechanisms for the same gene.

Weaknesses:

(1) The LS-MPRA assay most strongly identified promoters, which are not usually novel regulatory elements you would try to discover, and the signal to noise ratio for more TSS-distal, non-promoter regulatory elements was usually high, making it difficult to discriminate lower activity CRMs, like enhancers, from the background. For example, NR2 and NR3 in Figure 3 have very minimal activity peaks (NR3 seems non-existent). The ex vivo data in Figure 2 is similarly noisy. Is there a particular metric or calculation that was or could be used to quantitatively or statistically call a peak above the background? The authors mention in the discussion some adjustments that could reduce the noise, such as increased sequencing depth, which I think is needed to make these initial LS-MPRA results and the benchmarking of this assay more convincing and impactful.

Reviewer #1 (Public review):

Summary:

The authors considered the mechanism underlying previous observations that H2A.Z is preferentially excluded from methylated DNA regions. They considered two non-mutually exclusive mechanisms. First, they tested the hypothesis that nucleosomes containing both methylated DNA and H2A.Z might be intrinsically unstable due to their structural features. Second, they explored the possibility that DNA methylation might impede SRCAP-C from efficiently depositing H2A.Z onto these DNA methylated regions.

Their structural analyses revealed subtle differences between H2A.Z-containing nucleosomes assembled on methylated versus unmethylated DNA. To test the second hypothesis, the authors allowed H2A.Z assembly on sperm chromatin in Xenopus egg extracts and mapped both H2A.Z localization and DNA methylation in this transcriptionally inactive system. They compared these data with corresponding maps from a transcriptionally active Xenopus fibroblast cell line. This comparison confirmed the preferential deposition or enrichment of H2A.Z on unmethylated DNA regions, an effect that was much more pronounced in the fibroblast genome than in sperm chromatin. Furthermore, nucleosome assembly on methylated versus unmethylated DNA, along with SRCAP-C depletion from Xenopus egg extracts, provided a means to test whether SRCAP-C contributes to the preferential loading of H2A.Z onto unmethylated DNA.

Strengths:

The strength and originality of this work lie in its focused attempt to dissect the unexplained observation that H2A.Z is excluded from methylated genomic regions.

Weaknesses:

The study has two weaknesses. First, although the authors identify specific structural effects of DNA methylation on H2A.Z-containing nucleosomes, they do not provide evidence demonstrating that these structural differences lead to altered histone dynamics or nucleosome instability. Second, building on the elegant work of Berta and colleagues (cited in the manuscript), the authors implicate SRCAP-C in the selective deposition of H2A.Z at unmethylated regions. Yet the role of SRCAP-C appears only partial, and the study does not address how the structural or molecular consequences of DNA methylation prevent efficient H2A.Z deposition. Finally, additional plausible mechanisms beyond the two scenarios the authors considered are not investigated or discussed in the manuscript.

Reviewer #1 (Public review):

Summary:

This study investigates whether prediction error extends beyond lower-order sensory-motor processes to include higher-order cognitive functions. Evidence is drawn from both task-based and resting-state fMRI, with addition of resting-state EEG-fMRI to examine power spectral correlates. The results partially support the existence of dissociable connectivity patterns: stronger ventral-dorsal connectivity is associated with high prediction error, while posterior-anterior connectivity is linked to low prediction error. Furthermore, spontaneous switching between these connectivity patterns was observed at rest and correlated with subtle intersubject behavioral variability.

Strengths:

Studying prediction error from the lens of network connectivity provides new insights into predictive coding frameworks. The combination of various independent datasets to tackle the question adds strength, including two well-powered fMRI task datasets, resting-state fMRI interpreted in relation to behavioral measures, as well as EEG-fMRI.

Minor Weakness:

The lack of spatial specificity of sensor-level EEG somewhat limits the inferences that can be obtained in terms of how the fMRI network processes and the EEG power fluctuations relate to each other.<br /> While the language no longer suggests a strong overlap of the source of the two signals, several scenarios remain open (e.g., the higher-order fMRI networks being the source of the EEG oscillations, or the networks controlling the EEG oscillations expressed in lower-order cortices, or a third process driving both the observations in fMRI networks and EEG oscillations...) and somewhat weaken interpretability of this section.

Comments on revisions:

My prior recommendations have been mostly addressed.

Questions remaining about the NBS results:

The authors write about the NBS cluster: "Visual examination of the cluster roughly points to the same four posterior-anterior and ventral-dorsal modules identified formally in main-text ". I think it might be good to add quantification, not just visual inspection. The size of the significant NBS cluster should be reported. What proportion of the edges that passed uncorrected threshold and entered NBS were part of the NBS cluster? Put simply, I don't think any edges beyond those passing NBS-based correction should be interpreted or used downstream in the manuscript.

Also, NBS is not typically used by collapsing over effects in two effect directions, but the authors use NBS on the absolute value of Z. I understand the logic of the general manuscript focusing on strength rather than direction, but here I am wondering about the methodological validity. I believe that the editor who is an expert on the methodology may be able to comment on the validity of this approach (as opposed to running two separate NBS analyses for the two directions of effect).

Reviewer #2 (Public review):

This study identifies Visham, an asymmetric structure in developing mouse cysts resembling the Drosophila fusome, an organelle crucial for oocyte determination. Using immunofluorescence, electron microscopy, 3D reconstruction, and lineage labeling, the authors show that primordial germ cells (PGCs) and cysts, but not somatic cells, contain an EMA-rich, branching structure that they named Visham, which remains unbranched in male cysts. Visham accumulates in regions enriched in intercellular bridges, forming clusters reminiscent of fusome "rosettes." It is enriched in Golgi and endosomal vesicles and partially overlaps with the ER. During cell division, Visham localizes near centrosomes in interphase and early metaphase, disperses during metaphase, and reassembles at spindle poles during telophase before becoming asymmetric. Microtubule depolymerization disrupts its formation.

Cyst fragmentation is shown to be non-random, correlating with microtubule gaps. The authors propose that 8-cell (or larger) cysts fragment into 6-cell and 2-cell cysts. Analysis of Pard3 (the mouse ortholog of Par3/Baz) reveals its colocalization with Visham during cyst asymmetry, suggesting that mammalian oocyte polarization depends on a conserved system involving Par genes, cyst formation, and a fusome-like structure.

Transcriptomic profiling identifies genes linked to pluripotency and the unfolded protein response (UPR) during cyst formation and meiosis, supported by protein-level reporters monitoring Xbp1 splicing and 20S proteasome activity. Visham persists in meiotic germ cells at stage E17.5 and is later transferred to the oocyte at E18.5 along with mitochondria and Golgi vesicles, implicating it in organelle rejuvenation. In Dazl mutants, cysts form, but Visham dynamics, polarity, rejuvenation, and oocyte production are disrupted, highlighting its potential role in germ cell development.

Overall, this is an interesting and comprehensive study of a conserved structure in the germline cells of both invertebrate and vertebrate species. Investigating these early stages of germ cell development in mice is particularly challenging. Although primarily descriptive, the study represents a remarkable technical achievement. The images are generally convincing, with only a few exceptions.

Major comments:

(1) Some titles contain strong terms that do not fully match the conclusions of the corresponding sections.

(1a) Article title "Mouse germline cysts contain a fusome-like structure that mediates oocyte development":

The term "mediates" could be misleading, as the functional data on Visham (based on comparing its absence to wild-type) actually reflects either a microtubule defect or a Dazl mutant context. There is no specific loss-of-function of visham only.

(1b) Result title, "Visham overlaps centrosomes and moves on microtubules":

The term "moves" implies dynamic behavior, which would require live imaging data that are not described in the article.

(1c) Result title, "Visham associates with Golgi genes involved in UPR beginning at the onset of cyst formation":

The presented data show that the presence of Visham in the cyst coincides temporally with the expression and activity of the UPR response; the term "associates" is unclear in this context.

(1d) Result title, "Visham participates in organelle rejuvenation during meiosis":

The term "participates" suggests that Visham is required for this process, whereas the conclusion is actually drawn from the Dazl mutant context, not a specific loss-of-function of visham only.

(2) The authors aim to demonstrate that Visham is a fusome-like structure. I would suggest simply referring to it as a "fusome-like structure" rather than introducing a new term, which may confuse readers and does not necessarily help the authors' goal of showing the conservation of this structure in Drosophila and Xenopus germ cells. Interestingly, in a preprint from the same laboratory describing a similar structure in Xenopus germ cells, the authors refer to it as a "fusome-like structure (FLS)" (Davidian and Spradling, BioRxiv, 2025).

Comments on revisions:

The revised manuscript has been clearly improved, and the authors have addressed all of our comments. I would like to point out two minor issues:

(1) As suggested by the reviewers, the authors now use the term fusome instead of visham. However, they also acknowledge that this structure lacks many components of the Drosophila fusome. It may therefore be more appropriate to refer to it as a "mouse fusome" or as a "fusome-like structure (FLS)," as used in Xenopus.

(2) I agree with Reviewer 3 that co-localization between EMA and acTubulin on still images does not convincingly demonstrate that fusome vesicles move along microtubules (Figure S2E).

Reviewer #1 (Public review):

Summary:

The issue of how the brain can maintain serial order of presented items in working memory is a major unsolved question in cognitive neuroscience. It has been proposed that this serial order maintenance could be achieved thanks to periodic reactivations of different presented items at different phases of an oscillation, but the mechanisms by which this could be achieved by brain networks, as well as the mechanisms of read-out, are still unclear. In an influential 2008 paper, the authors have proposed a mechanism by which a recurrent network of neurons could maintain multiple items in working memory, thanks to `population spikes' of populations of neurons encoding for the different items, occurring at alternating times. These population spikes occur in a specific regime of the network and are a result of synaptic facilitation, an experimentally observed type of synaptic short-term dynamics with time scales of order hundreds of ms.

In the present manuscript, the authors extend their model to include another type of experimentally observed short-term synaptic plasticity termed synaptic augmentation, that operates on longer time scales on the order of 10s. They show that while a network without augmentation loses information about serial order, augmentation provides a mechanism by which this order can be maintained in memory thanks to a temporal gradient of synaptic efficacies. The order can then be read out using a read-out network whose synapses are also endowed with synaptic augmentation. Interestingly, the read-out speed can be regulated using background inputs.

Strengths:

This is an elegant solution to the problem of serial order maintenance, that only relies on experimentally observed features of synapses. The model is consistent with a number of experimental observations in humans and monkeys. The paper will be of interest to the broad readership of eLife and I believe it will have a strong impact on the field.

Comments on revisions:

I am happy with how the authors have addressed my comments, and believe the paper can be published in its present form.

Reviewer #1 (Public review):

The authors relate a language model developed to predict whether a given sentence correctly followed another given sentence to EEG recordings in a novel way, showing receptive fields related to widely used TRFs. In these responses (or "regression results"), differences between representational levels are found, as well as differences between attended and unattended speech stimuli, and whether there is hearing loss. These differences are found per EEG channel.

In addition to these novel regression results, which are apparently captured from the EEG specifically around the sentence stimulus offsets, the authors also perform a more standard mTRF analysis using a software package (Eelbrain) and TRF regressors that will be more familiar to researchers adjacent to these topics, which was highly appreciated for its comparative value. Comparing these TRFs with the authors' original regression results, several similarities can be seen. Specifically, response contrasts for attended versus unattended speaker during mixed speech, for the phoneme, syllable, and sentence regressors, are greater for normal-hearing participants than hearing-impaired participants for both analyses, and the temporal and spatial extents of the significant differences are roughly comparable (left-front and 0 - 200 ms for phoneme and syllable, and left and 200 - 300 ms for sentence).

The inclusion of the mTRF analysis is helpful also because some aspects of the authors' original regression results, between the EEG data and the HM-LSTM linguistic model, are less than clear. The authors state specifically that their regression analysis is only calculated in the -100 - 300 ms window around stimulus/sentence offsets. They clarify that this means that most of the EEG data acquired while the participants are listening to the sentences is not analyzed, because their HM-LSTM model implementation represents all acoustic and linguistic features in a condensed way, around the end of the sentence. Thus the regression between data and model only occurs where the model predictions exist, which is the end of the sentences. This is in contrast to the mTRF analysis, which seems to have been done in a typical way, regressing over the entire stimulus time, because those regressors (phoneme onset, word onset, etc.) exist over the entire sentence time. If my reading of their description of the HM-LSTM regression is correct, it is surprising that the regression weights are similar between the HM-LSTM model and the mTRF model.

However, the code that the authors uploaded to OSF seems to clarify this issue. In the file ridge_lstm.py, the authors construct the main regressor matrices called X1 and X2 which are passed to sklearn to do the ridge regression. This ridge regression step is calculated on the continuous 10-minute bouts of EEG and stimuli, and it is calculated in a loop over lag times, from -100 ms to 300 ms lag. These regressor matrices are initialized as zeros, and are then filled in two steps: the HM_LSTM model unit weights are read from numpy files and written to the matrices at one timepoint per sentence (as the authors describe in the text), and the traditional phoneme, syllable, etc. annotations are ALSO read in (from csv files) and written to the matrices, putting 1s at every timepoint of those corresponding onsets/offsets. Thus the actual model regressor matrix for the authors' main EEG results includes BOTH the HM_LSTM model weights for each sentence AND the feature/annotation times, for whichever of the 5 features is being analyzed (phonemes, syllables, words, phrases, or sentences).

So for instance, for the syllable HM_LSTM regression results, the regressor matrix contains: 1) the HM_LSTM model weights corresponding to syllables (a static representation, placed once per sentence offset time), AND 2) the syllable onsets themselves, placed as a row of 1s at every syllable onset time. And as another example, for the word HM_LSTM regression results, the regressor matrix contains: 1) the HM_LSTM model weights corresponding to words (a static representation, placed once per sentence offset time), AND 2) the word onsets themselves, placed as a row of 1s at every word onset time.

If my reading of the code is correct, there are two main points of clarification for interpreting these methods:

First, the authors' window of analysis of the EEG is not "limited" to 400 ms as they say; rather the time dimension of both their ridge regression results and their traditional mTRF analysis is simply lags (400 ms-worth), and the responses/receptive fields are calculated over the entire 10-minute trials. This is the normal way of calculating receptive fields in a continuous paradigm. The authors seem to be focusing on the peri-sentence offset time points because that is where the HM_LSTM model weights are placed in the regressor matrix. Also because of this issue, it is not really correct when the authors say that some significant effect occurred at some latency "after sentence offset". The lag times of the regression results should have the traditional interpretation of lag/latency in receptive field analyses.

Second, as both the traditional linguistic feature annotations and the HM_LSTM model weights are part of the regression for the main ridge regression results here, it is not known what the contribution specifically of the HM_LSTM portion of the regression was. Because the more traditional mTRF analysis showed many similar results to the main ridge regression results here, it seems probable that the simple feature annotations themselves, rather than the HM_LSTM model weights, are responsible for the main EEG results. A further analysis separating these two sets of regressors would shed light on this question.

Reviewer #1 (Public review):

The authors attempted to compare calcium calcium-binding properties of wildtype calreticulin with calreticulin deletion mutant (CRTDel52) associated with myeloproliferative neoplasms.

The researchers conducted their study using advanced techniques. They found almost no difference in calcium binding between the two proteins and observed no impact on calcium signaling, specifically store-operated calcium entry (SOCE). The study also noted an increase in ER luminal calcium-binding chaperone proteins. Surprisingly, the authors selected flow cytometry as a technique for measurements of ER luminal calcium. Considering the limitations of this approach, it would be better to use alternative approaches. This is particularly important as previous reports, using cells from MPN patients, indicate reduced ER luminal calcium and effects on SOCE (Blood, 2020). This issue matters because earlier research with MPN patient cells reported reduced ER luminal calcium levels and altered SOCE (Blood, 2020). How do the authors explain the difference between their results and previous findings about lower ER luminal calcium and changed SOCE in MPN patient cells expressing CRTDel52? Other studies have found that unfolded protein responses are activated in MPN cells with CRTDel52 calreticulin (see Blood, 2021), and increased UPR could account for higher levels of some ER-resident calcium-binding proteins observed here. Overall, it remains unclear how this work improves our understanding of MPN or clarifies calreticulin's role in MPN pathophysiology.

Reviewer #1 (Public review):

Summary:

Sullivan and colleagues examined the modulation of reflexive visuomotor responses during collaboration between pairs of participants performing a joint reaching movement to a target. In their experiments, the players jointly controlled a cursor that they had to move towards narrow or wide targets. In each experimental block, each participant had a different type of target they had to move the joint cursor to. During the experiment, the authors used lateral perturbation of the cursor to test participants' fast feedback responses to the different target types. The authors suggest participants integrate the target type and related cost of their partner into their own movements, which suggests that visuomotor gains are affected by the partner's task.

Strengths:

The topic of the manuscript is very interesting, and the authors are using well-established methodology to test their hypothesis. They combine experimental studies with optimal control models to further support their work. Overall, the manuscript is very timely and shows important findings - that the feedback responses reflect both our and our partner's tasks.

Weaknesses:

However, in the current version of the manuscript, I believe the results could also be interpreted differently, which suggests that the authors should provide further support for their hypothesis and conclusions.

Major Comments:

(1) Results of the relevant conditions:

In addition to the authors' explanation regarding the results, it is also possible that the results represent a simple modulation of the reflexive response to a scaled version of cursor movement. That is, when the cursor is partially controlled by a partner, which also contributes to reducing movement error, it can also be interpreted by the sensorimotor system as a scaling of hand-to-cursor movement. In this case, the reflexes are modulated according to a scaling factor (how much do I need to move to bring the cursor to the target). I believe that a single-agent simulation of an OFC model with a scaling factor in the lateral direction can generate the same predictions as those presented by the authors in this study. In other words, maybe the controller has learned about the nature of the perturbation in each specific context, that in some conditions I need to control strongly, whereas in others I do not (without having any model of the partner). I suggest that the authors demonstrate how they can distinguish their interpretation of the results from other explanations.

(2) The effect of the partner target:

The authors presented both self and partner targets together. While the effect of each target type, presented separately, is known, it is unclear how presenting both simultaneously affects individual response. That is, does a small target with a background of the wide target affect the reflexive response in the case of a single participant moving? The results of Experiment 2, comparing the case of partner- and self-relevant targets versus partner-irrelevant and self-relevant targets, may suggest that the system acted based on the relevant target, regardless of the presence and instructions regarding the self-target.

(3) Experiment instructions:

It is unclear what the general instructions were for the participants and whether the instructions provided set the proposed weighted cost, which could be altered with different instructions.

(4) Some work has shown that the gain of visuomotor feedback responses reflects the time to target and that this is updated online after a perturbation (Cesonis & Franklin, 2020, eNeuro; Cesonis and Franklin, 2021, NBDT; also related to Crevecoeur et al., 2013, J Neurophysiol). These models would predict different feedback gains depending on the distance remaining to the target for the participant and the time to correct for the jump, which is directly affected by the small or large targets. Could this time be used to target instead of explaining the results? I don't believe that this is the case, but the authors should try to rule out other interpretations. This is maybe a minor point, but perhaps more important is the location (& time remaining) for each participant at the time of the jump. It appears from the figures that this might be affected by the condition (given the change in movement lengths - see Figure 3 B & C). If this is the case, then could some of the feedback gain be related to these parameters and not the model of the partner, as suggested? Some evidence to rule this out would be a good addition to the paper - perhaps the distance of each partner at the time of the perturbation, for example. In addition, please analyze the synchrony of the two partners' movements.

Reviewer #1 (Public review):

Summary:

This manuscript aims to test the idea that visual recognition (of faces) is hierarchically organized in the human ventral occipital-temporal cortex (VOTC). The paper proposes that if VOTC has a hierarchical organization, this should be seen in two independent features of the VOTC signal. First, hierarchy assumes that signals along the hierarchy increase in representational complexity. Second, hierarchy assumes a progressive increase in the onset time of the earliest neural response at each level of the hierarchy. To test these predictions, the authors extract high-frequency broadband signals from iEEG electrodes in a very large sample of patients (N=140). They find that face selectivity in these signals is distributed across the VOTC with increasing posterior-anterior face selectivity, hence providing evidence for the first prediction. However, they also find broadband activity to occur concurrently, therefore challenging the view of a serial hierarchy.

Strengths:

(1) The hypothesis (that VOTC is hierarchically organized) and predictions (that hierarchy predicts increases in representational complexity and increases in onset time) were clearly described.

(2) The number of subjects sampled (140) is extremely large for iEEG studies that typically involve <10 subjects. Also, 444 face selective recording contacts provide a very nice sampling of the areas of interest.

Weaknesses:

(1) A control analysis where areas have known differences in response onset should be performed to increase confidence that the proposed analyses would reveal expected results when a difference in response onset was present across areas. From Figure 3, it can be seen that many electrodes are placed in earlier visual areas (V1-V3) that have previously been shown to have earlier broadband responses to visual images compared to VOTC (e.g. Martin et al., 2019, JNeurosci https://doi.org/10.1523/JNEUROSCI.1889-18.2018). The same analyses as in Figures 4 and 5 should be used comparing VOTC to early visual areas to confirm that the analyses would detect that V1-V3 have earlier onsets compared to VOTC.

(2) It is unclear why correlating mean timeseries helps understand how much variance is shared between regions (Figure 4). Any variance between images is lost when averaging time series across all images, and this metric thus overestimates the variance shared between areas. Moreover, the finding that correlating time domain signals across VOTC areas does not differ from correlating signals within an area could be driven by this averaging. For example, if the same analysis was done on electrodes in left and right V1 when half of the images had contrast in the left hemifield and the other half had contrast in the right hemifield, the average signals may correlate extremely well, while this correlation falls apart on a trial-by-trial basis. These analyses therefore need to be evaluated on a trial-by-trial basis.

(3) Previous studies on visual processing in VOTC have shown that evoked potentials are more predictive of the onset of visual stimuli than broadband activity (e.g. Miller et al., 2016, PLOS CB, https://doi.org/10.1371/journal.pcbi.1004660). Testing the prediction from a hierarchical representation that signals along the VOTC increase in onset time should therefore include an evaluation of evoked potential onsets in addition to broadband signals.

(4) Testing the second prediction, that the onset time of processing increases along the VOTC posterior to anterior path, is difficult using the iEEG broadband signal, because from a signal processing perspective, broadband signals are inherently temporally inaccurate, given that they are filtered. Any filtering in the signal introduces a certain level of temporal smoothing. The manuscript should clearly describe the level of temporal smoothing for the filter settings used.

(5) The onsets of neural activity in VOTC are surprisingly early: around 80-100 ms. This is earlier than what has previously been reported. For example, the cited Quian Quiroga et al. (2023) found single neuron responses to have the earlier onset around 125 ms (their Figure 3). Similarly, the cited Jacques et al., 2016b and Kadipasaoglu et al., 2017 papers also observe broadband onsets in VOTC after 100 ms. Understanding the temporal smoothing in the broadband signal, as well as showing that typical evoked potentials have latencies compared to other work, would increase confidence that latencies are not underestimated due to factors in the analysis pipeline.

(6) Understanding the extent to which neural processing in the VOTC is hierarchical is essential for building models of vision that capture processing in the human brain, and the data provides novel insight into these processes.

For additional context, a schematic figure of the hierarchical view and a more parallel system described in the paragraph on models of visual recognition (lines 553) would help the reader interpret and understand the implications of the paper.

Reviewer #1 (Public review):

Summary:

In this study, the authors elegantly combined latent variable models (i.e., HMM, GPFA and dynamical system models) with a calcium imaging observation model (i.e., latent Poisson spiking and autoregressive calcium dynamics (AR)).

Strengths:

Integrating a calcium observation model into existing latent variable models improves significantly the inference of latent neural states compared to existing approaches such as spike deconvolution or Gaussian assumptions.<br /> The authors also provide an open-source access to their method for direct application to calcium imaging data analysis.

Weaknesses:

As acknowledged by the authors, their method is dependent on the quality of calcium trace extraction from fluorescence videos. It should be noted that this limitation applies to alternative strategies.

While the contribution of this study should prove useful for researchers using calcium imaging, the novelty is limited, as it consists of an integration of the calcium imaging model from Ganmor et al. 2016 with existing LVM frameworks.

Reviewer #1 (Public review):

I read this paper with great interest based on my experience in insect sciences. I have some minor comments (and recommendations) that I believe the authors should address.

(1) The paper has an original biological question that is overly broad and mechanistically ambitious. The central biological question, namely how CLas infection enhances fecundity of Diaphorina citri via dopamine signaling, is clearly stated and well motivated by previous literature. However, my advice to the authors is that, while the general question is clear, the manuscript attempts to answer multiple mechanistic layers simultaneously. As a result, I feel that the biological narrative becomes diffuse, especially in later sections where DA, miRNA regulation, AKH signaling, and JH signaling are all proposed as parts of a single linear cascade. In summary, my key concern is that the paper often moves from correlation to causal hierarchy without fully disentangling whether these pathways act sequentially, in parallel, or redundantly. A more explicitly framed primary hypothesis (e.g., "DA-DcDop2 is necessary and sufficient for CLas-induced fecundity") may improve conceptual clarity.

(2) On the novelty of the data, I feel they are moderately novel, with substantial confirmatory components. If I am correct, the novel contributions include the identification of DcDop2 as the DA receptor responsive to CLas infection in D. citri, the discovery that miR-31a directly targets DcDop2, which is supported by luciferase assays and RIP, and thirdly, the integration of dopamine signaling into the already-described CLas-AKH-JH-fecundity framework. My advice to the authors is to focus more on the manuscript's novelty, which lies more in pathway integration than in discovering fundamentally new biological phenomena. This is appropriate for a mechanistic paper, but should be framed as an extension of existing models rather than a paradigm shift.

(3) On the conclusions, I recommend that the authors modify their statements a little. I feel that there are some overstated or insufficiently supported claims. For instance, the assertion that CLas "hijacks" the DA-DcDop2-miR-31a-AKH-JH cascade implies direct pathogen manipulation, but no CLas-derived effector or mechanism is identified. Also that the model suggests a linear signaling hierarchy, but the data largely show correlation and partial dependency rather than strict epistasis. In third, the term "mutualistic interaction" may be too strong, as host fitness costs outside fecundity (e.g., longevity, immunity) are not evaluated. In conclusion, I confirm that the data support a functional association, but mechanistic causality and evolutionary interpretation are somewhat overstated.

Reviewer #1 (Public review):

Summary:

Large language models (LLMs) have been developed rapidly in recent years and are already contributing to progress across scientific fields. The manuscript tries to address a specific question: whether LLMs can accurately infer signaling networks from gene lists. However, the evaluation is inadequate due to four major weaknesses described below. Despite these limitations, the authors conclude that current general-purpose LLMs lack adequate accuracy, which is already widely recognized. Its key contribution should instead be to provide concrete recommendations for the development of specialized LLMs for this task, which is completely absent. Developing such specific LLMs would be highly valuable, as they could substantially reduce the time required by researchers to analyze signaling networks.

Strengths:

The manuscript raises a good question: whether current LLMs can accurately generate signaling networks from gene lists.

Weaknesses:

(1) The authors evaluate LLM performance using only three signaling networks: "hypertrophy", "fibroblast", and "mechanosignaling". Given the large number of well-established signaling pathways available, this is not a comprehensive assessment. Moreover, the analysis need not be restricted to signaling networks. Other network types, including metabolic and transcriptional regulatory networks, are already accessible in well-known databases such as KEGG, Reactome, BioCyc, WikiPathways, and Pathway Commons. Including these additional networks would substantially strengthen the evaluation.

(2) In LLM evaluation, the authors use the gene lists that exactly match those in their "ground truth" networks, thereby fixing the set of nodes and evaluating only the predicted edges. However, in practical research, the relevant genes or nodes are not fully known. A more realistic assessment would therefore include gene lists with both genes present in the ground-truth network and additional genes absent from it, to evaluate the ability of the LLM to exclude irrelevant genes.

(3) The authors report only the recall/sensitivity of the LLM, without assessing specificity. In practical applications, if an LLM generates a large number of incorrect interactions that greatly exceed the correct ones, researchers may be misled or may lose confidence in the LLM output. Therefore, a comprehensive evaluation must include both sensitivity and specificity. Furthermore, it would be informative to check whether some of the "false positives" might in fact represent biologically plausible interactions that are absent from the manually curated "ground truth". Manually generated "ground truth" can overlook genuine interactions, and the ability of LLMs to recover such missing edges could be particularly valuable. This may even represent one of the most important potential contributions of LLMs.

(4) It is widely known that applying differential equation models to highly complex biological networks, such as the three networks in the manuscript, is meaningless, because these systems involve a large number of parameters whose values can drastically alter the results. As Richard Feynman once said: "with four parameters I can fit an elephant, and with five I can make him wiggle his trunk." Thus, the evaluation of LLMs on "logic-based differential equation models" does not make much sense.

A recent patient I have is a middle-aged female with respiratory failure, chronic COPD, pre-diabetes that is diet-controlled, and a slow-healing wound on her forearm. Her normal random blood glucose before lunch is around 100-120 mg/dL; it is now 190-210 mg/dL. She recently had bronchitis and needs corticosteroid therapy. This patient demonstrates how chronic physiological stress, combined with necessary medical intervention, can interact and alter clinical outcomes. Her chronic illness and acute bronchitis treatment with corticosteroids stimulates the sympathetic nervous system to increase the cortisol effects. The cortisol effects promote glucogenesis and insulin resistance. This elevated glycemic state impairs wound healing by reducing leukocyte function and collagen synthesis, contributing to the staling of her arm wound. The increased blood glucose also triggers overstimulation of mitochondrial respiration, leading to increased metabolic output. I noticed an increase in her respiratory rate from 16 to 19-20 and in oxygen usage from 2L to 3L to offset the metabolic output. The patient stated she hasn’t been sleeping well due to increased oxygen requirements and a higher respiratory rate. The combination of chronic illness, acute bronchitis, and medical intervention creates a domino effect that delays the patient from healing and maintaining homeostasis.

Reviewer #1 (Public review):

Summary:

The authors use methylphenidate (MPH) administration after learning a Pavlovian-to-instrumental transfer (PIT) task to parse decision making from instrumental influences. While the main pharmacological effects were null, individual differences in working memory ability moderated the tendency of MPH to boost cognitive control in order to override PIT-biased instrumental learning. Importantly, this working memory moderator had symmetrical effects in appetite and aversive conditions, and these patterns replicated within each valence condition across different values of gain/loss (Fig S1c), suggesting a reliable effect that is generalized across instances of Pavlovian influence.

Strengths:

The idea of using pharmacological challenge after learning but prior to transfer is a novel technique that highlights the influence of catecholamines on the expression of learning under Pavlovian bias, and importantly it dissociates this decision feature from the learning of stimulus-outcome or action-outcome pairings.

Comments on revisions:

I have no further recommendations or concerns.

Reviewer #1 (Public review):

This manuscript discusses from a theory point of view he mechanisms underlying the formation of specialized or mixed factories. To investigate this, a chromatin polymer model was developed to mimic the chromatin binding-unbinding dynamics of various complexes of transcription factors (TFs).

The model revealed that both specialized (i.e., demixed) and mixed clusters can emerge spontaneously, with the type of cluster formed primarily determined by cluster size. Non-specific interactions between chromatin and proteins were identified as the main factor promoting mixing, with these interactions becoming increasingly significant as clusters grow larger.

These findings, observed in both simple polymer models and more realistic representations of human chromosomes, reconcile previously conflicting experimental results. Additionally, the introduction of different types of TFs was shown to strongly influence the emergence of transcriptional networks, offering a framework to study transcriptional changes resulting from gene editing or naturally occurring mutations.

Overall I think this is an interesting paper discussing a valuable model of how chromosome 3D organisation is linked to transcription.

Comments on revisions: It's a good paper.

Reviewer #1 (Public review):

In this manuscript, Aghabi et al. present a comprehensive characterization of ZFT, a metal transporter located at the plasma membrane of the eukaryotic parasite Toxoplasma gondii. The authors provide convincing evidence that ZFT plays a crucial role in parasite fitness, as demonstrated by the generation of a conditional knock-down mutant cell line, which exhibits a marked impact on mitochondrial respiration, a process dependent on several iron-containing proteins. Consistent with previous reports, the authors also show that disruption of mitochondrial metabolism leads to conversion into the persistent bradyzoite stage.

The study then employed advanced techniques, such as inductively coupled plasma-mass spectrometry (ICP-MS) and X-ray fluorescence microscopy (XFM), to demonstrate that ZFT depletion results in reduced parasite-associated metals, particularly iron and zinc. Additionally, the authors show that ZFT expression is modulated by the availability of these metals, although defects in the transporter could not be compensated by exogenous addition of iron or zinc. Finally, the authors used heterologous expression of ZFT in Xenopus oocytes and yeast mutants, highlighting the dual substrate specificity of the transporter. The ability of ZFT to transport both iron and zinc is thus supported by two experimental approaches in heterologous systems. First by demonstrating ZFT ability to transport zinc, as the expression of Toxoplasma ZFT can compensate for a lack of zinc transport in yeast. Then, by showing the ability of ZFT to transport iron, as assessed in the Xenopus oocytes model. Furthermore, phenotypic analyses suggest defects in iron availability upon ZFT depletion, particularly with regard to Fe-S mitochondrial proteins and mitochondrial function.

Overall, the manuscript provides a solid, well-rounded argument for ZFT's role in metal transport, using a combination of complementary approaches. The converging evidence, including changes in metal concentrations upon ZFT depletion, data on metal transport obtained in heterologous systems, and phenotypic changes linked to iron deficiency, presents a convincing case. Given that metal acquisition remains largely uncharacterized in Toxoplasma, this manuscript provides an important first step in identifying a metal transporter in these parasites, and the data presented are generally convincing and insightful.

Comments on revisions:

The revised manuscript has successfully addressed all of the key points raised in the initial review. Notably, the metal transport experiments in Xenopus oocytes now provide compelling evidence supporting the role of ZFT function. I congratulate the authors on their efforts and have no further concerns to raise.

Reviewer #1 (Public review):

Summary and Strengths:

This manuscript presents a thoughtful and well-executed analysis of how S. aureus adapts to disulfide stress using a redox-sensitive regulator, Spx, as a lynchpin to coordinate nutrient uptake, redox balance, and growth. The work is strengthened by a systematic and complementary experimental approach that combines genetic, biochemical, and physiological measurements. The authors carefully test alternative explanations and build a coherent model linking stress sensing to downstream metabolic consequences. Several results, particularly those connecting cysteine uptake to growth defects, provide convincing support for the proposed trade-off. Overall, the authors largely achieve their aims, and the evidence generally supports the central conclusions. The conceptual framework and experimental approaches should be of broad interest to researchers studying S. aureus physiology and pathogenesis and to those studying bacterial stress responses and metabolic trade-offs.

Weaknesses:

Clarifying several interpretive points would further strengthen confidence in the proposed model. Some conclusions rely on data presentations or experimental designs that are not immediately clear to the reader. In particular, aspects of the protein stability analysis, global regulatory comparisons, and assays linking cysteine uptake to iron limitation would benefit from clearer justification and more precise interpretation. In addition, certain conclusions could be more carefully framed to reflect partial rather than complete rescue effects.

Reviewer #1 (Public review):

Summary:

This study uses a novel DNA origami nanospring to measure the stall force and other mechanical parameters of the kinesin-3 family member, KIF1A, using light microscopy. The key is to use SNAP tags to tether a defined nanospring between a motor-dead mutant of KIF5B and the KIF1A to be integrated. The mutant KIF5B binds tightly to a subunit of the microtubule without stepping, thus creating resistance to the processive advancement of the active KIF1A. The nanospring is conjugated with 124 Cy3 dyes, which allows it to be imaged by fluorescence microscopy. Acoustic force spectroscopy was used to measure the relationship between the extension of the NS and force as a calibration. Two different fitting methods are described to measure the length of the extension of the NS from its initial diffraction-limited spot. By measuring the extension of the NS during an experiment, the authors can determine the stall force. The attachment duration of the active motor is measured from the suppression of lateral movement that occurs when the KIF1A is attached and moving. There are numerous advantages of this technology for the study of single molecules of kinesin over previous studies using optical tweezers. First, it can be done using simple fluorescence microscopy and does not require the level of sophistication and expense needed to construct an optical tweezer apparatus. Second, the force that is experienced by the moving KIF1A is parallel to the plane of the microtubule. This regime can be achieved using a dual beam optical tweezer set-up, but in the more commonly used single-beam set-up, much of the force experienced by the kinesin is perpendicular to the microtubule. Recent studies have shown markedly different mechanical behaviors of kinesin when interrogated by the two different optical tweezer configurations. The data in the current manuscript are consistent with those obtained using the dual-beam optical tweezer set-up. In addition, the authors study the mechanical behavior of several mutants of KIF1A that are associated with KIF1A-associated neurological disorder (KAND).

Strengths:

The technique should be cheaper and less technically challenging than optical tweezer microscopy to measure the mechanical parameters of molecular motors. The method is described in sufficient detail to allow its use in other labs. It should have a higher throughput than other methods.

Weaknesses:

The experimenter does not get a "real-time" view of the data as it is collected, which you get from the screen of an optical tweezer set-up. Rather, you have to put the data through the fitting routines to determine the length of the nanospring in order to generate the graphs of extension (force) vs time. No attempts were made to analyze the periods where the motor is actually moving to determine step-size or force-velocity relationships.

Comments on revisions:

I am satisfied with the revision made by the authors in response to my first round of criticisms.

Reviewer #1 (Public review):

Summary:

In this manuscript, Blanco-Ameijeiras et al. present an organoid-based model of the caudal neural tube that builds upon established principles from embryonic development and prior organoid work. By systematically testing and refining signaling conditions, the authors generate caudal progenitor populations that self-organize into neuroepithelia with molecular features consistent with secondary neurulation. Bulk-RNA sequencing supports the emergence of caudal neural identities, and the authors further examine cellular features such as apico-basal polarity and interkinetic nuclear migration. Finally, they provide evidence for a conserved, YAP-dependent mechanism of tube formation specific to secondary neurulation. The manuscript provides valuable methodological resources, including troubleshooting guidance that will be especially useful for the field. While this work represents a significant advance toward modeling human spinal cord development - particularly the process of secondary neurulation - the claims of complete caudalization and full AP-axis representation require additional experimental support and clarification.

Strengths:

(1) Methodological clarity and transparency: The first figure and accompanying text provide an exemplary explanation of protocol optimization and troubleshooting. This transparency - showing approaches that failed as well as those that succeeded - sets a high standard for reproducibility and will be highly beneficial to laboratories aiming to adopt or build upon this model.

(2) Testing across multiple cell lines: Multiple hPSC and hiPSC lines were evaluated, strengthening the robustness and generalizability of the reported protocol.

(3) Biological relevance: The focus on secondary neurulation fills a notable gap in current human organoid models of spinal cord development. The identification of YAP-dependent mechanisms in tube formation is a valuable insight with potential translational relevance.

(4) Resource creation: The detailed parameters and signaling regimes will serve as a resource for the spinal cord and organoid communities.

Weaknesses:

(1) The manuscript over-interprets bulk RNA-seq data to make strong claims on the organoid AP patterning and caudalization. Bulk sequencing provides population-level averages and cannot confirm that individual organoids represent discrete AP levels. To support claims of generating every AP identity, the authors must perform staining or in situ hybridization for HOX genes on individual organoids. Further, the current interpretation of CDX2 as marking "very distal" identity is inaccurate in vitro; CDX2 marks caudal progenitors across the spinal cord axis. The language should be revised accordingly.

(2) The claim of being the first organoid system to model secondary neurulation overlooks prior work showing HOXC9 in human organoids (Xue et al., Nature 2024; Libby et al., Development 2021), which would reflect the beginning of secondary neurulation. While this system may indeed be the first isolated secondary neurulation organoid model that expresses HOXD9/10 - a meaningful advance - bulk RNA-seq alone is insufficient to support the exclusivity of this claim. Additional single-organoid-level spatial analyses (via immunofluorescence of in situ hybridisation) and frequency quantification of regional identities are required to fully characterize the system.

(3) Similarly, as written, there are overstatements taken from the bulk RNA sequencing to determine dorsal-ventral identity. Although dorsal markers are present, the dataset also contains ventral-associated genes (PAX6, SP8, NKX6-1, NKX6-2, PRDM12). To claim a "dorsal-only" identity, the authors should perform PAX7 immunostaining to demonstrate dorsalization of the entire organoid tissue.

(4) The studies identifying YAP as a key driver of lumen fusion in Figure 6 are important and should be extended to the apical organoid system to demonstrate that this is truly a feature of secondary neurulation.

Reviewer #1 (Public review):

Summary

In this study, the authors have performed tissue-specific ribosome pulldown to identify gene expression (translatome) differences in the anterior vs posterior cells of the C. elegans intestine. They have performed this analysis in fed and fasted states of the animal. The data generated will be very useful to the C. elegans community, and the role of pyruvate shown in this study will result in interesting follow-up investigations.

However, several strong claims made in the study are solely based on in silico predictions and are not supported by experimental evidence.

Strengths:

Several studies in the past have predicted different functions of the anterior (INT1) vs posterior (INT2-9) epithelial cells of the C. elegans intestine based on their anatomy and ultrastructure, but detailed characterization of differences in gene expression between these cell types (and whether indeed these are different 'cell types') was lacking prior to this study. The genes and drivers identified to be exclusively expressed in the anterior vs posterior segments of the intestine will be very helpful to selectively modulate different parts of the C. elegans intestine in future studies.

Another strength of this study is the careful experimental design to test how the anterior vs posterior cell types of the intestine respond differently to food deprivation and recovery after return to food. These comparisons between 'states' of a cell in different physiological conditions are difficult to pick up in single-cell analyses due to low sequencing depth, which can fail to identify subtle modulation of gene expression.

The TRAP-associated bulk RNA-seq approach used in this study is more suitable for such comparisons and provides additional information on post-transcriptional regulation during metabolic stress.

A key finding of this study is that pyruvate levels modulate the translation state of anterior intestinal cells during fasting. Characterization of pyruvate metabolism genes, especially of the enzymes involved in its mitochondrial breakdown, provides novel insights into how gut epithelial cells respond to the acute absence of food.

Weaknesses:

Unlike previous TRAP-seq studies (PMID: 30580965, 36044259, 36977417) that reported sequencing data for both input and IP samples, this study only reports the sequencing data for IP samples. Since biochemical pulldowns are variable across replicates, it is difficult to know if the observed differences between different conditions are due to biological factors or differences in IP efficiency. More importantly, since two different TRAP lines were utilized in this study and a large proportion of the results focus on the differences between the translational profiles of INT1 vs INT2-9 cells, it is essential to know if the IP worked with similar efficiency for both TRAP strains that likely have different expression levels of the HA-tagged ribosomal protein. One way to estimate this would be to perform qRT-PCR of genes that are known to be enriched in all intestinal cells and determine whether their fold-enrichment over housekeeping genes (normalized to input) is similar in INT1 vs INT2-9 TRAP strains and across the fed vs fasted conditions. The authors, in fact, mention variability across biological replicates, due to which certain replicates were excluded from their WGCNA analysis.

It appears that GFP expression is also detectable in INT2 (in addition to strong expression in INT1 in Fig.1A). Compared to INT3-9, which looks red, INT2 cells appear yellow, suggesting that the expression patterns of the two TRAP drivers are not mutually exclusive, which changes the interpretation of many of the results described in the study.

Some parts of the study overemphasize the differences between the INT1 vs INT2-9 cell types, which is a biased representation of the results. For example, the authors specifically point out that 270 genes are differentially expressed in opposite directions in INT1 vs INT2-9 cell types during acute (30 min) fasting without mentioning the 1,268 genes that are differentially expressed in the same direction. They also do not mention here that 96% of the genes are differentially expressed in the same direction in INT1 and INT2-9 cell types after prolonged (180 min) fasting, suggesting that the divergent translational responses of these cell types are only observed in the first 30 minutes of food deprivation. Similar results have also been reported for the effect of fasting on locomotory and feeding behaviors, where 30 min of fasting produces more variable effects, which become more consistent after longer periods of fasting (PMID: 36083280). Hence, the effects of brief food deprivation should be interpreted with caution.

Many of the interpretations of this study primarily rely on pathway enrichment analyses, which are based on the known function of genes. The function of uncharacterized genes that were found to be differentially expressed in INT1 vs INT2-9 cell types, e.g., the ShKT proteins, was not explored in this study. In addition, overreliance on pathway enrichment tools (instead of functional validation) has resulted in several conflicting findings. For example, one of the main messages of this study is that INT1 cells specialize in immune and stress response in response to fasting, which relies on pathway analysis in Figs 5E and 5F. However, pathway analysis at a different time point (shown in Figure S5A) indicates that INT2-9 cells show a much stronger increase in translation of stress and pathogen-responsive genes compared to INT1 cells. Hence, some of the results should be interpreted as different translational effects in INT1 vs INT2-9 cells after different lengths of food deprivation, without making broad claims about selective pathways being affected only in specific cell types.

The authors have compared their TRAP-seq results with genes enriched in the anterior and posterior intestine clusters from a previously published whole-animal adult scRNA dataset (PMID: 37352352). They claim that their TRAP-seq results are in agreement with the findings of the scRNA study. However, among the 10 genes from the 'posterior intestine' scRNA cluster in Fig.S1E, six are downregulated in the INT1 vs INT2-9 comparison, while four are upregulated. Hence, there is no clear agreement between the two studies in terms of the top enriched genes in the anterior vs posterior intestine, which should be considered for cross-study comparisons in the future.

The authors describe in the manuscript that they have performed INT1-specific RNAi for two C-type lectin genes that are upregulated during fasting. Due to a recent expansion of C-type lectin genes in C. elegans, there is a high chance of off-target effects of RNAi that is designed for members of this gene family. More trustworthy results could have been obtained using CRISPR-based loss-of-function alleles for these genes, one of which is publicly available. Also, the authors do not provide any explanation for why knockdown of these stress-response genes, which are activated in INT1 cells in response to food deprivation, results in improved resistance to pathogens. This, in fact, suggests a role of INT1 cells in increasing pathogen susceptibility, and not pathogen resistance, during food deprivation.

Many of the studies in this field (e.g., references 2-4 in this article) have investigated the effects of food deprivation ranging from 4 hr to 24 hr, which results in activation of starvation responses in C. elegans. In contrast, the authors have used shorter time periods of fasting (30 min and 180 min), and most of their follow-up experiments have used 30 min of food deprivation. Previous work has shown that the effects of food deprivation can either accumulate over time (i.e., the effect gets stronger with longer food deprivation) or can be transient (i.e., only observed briefly after removal of food and not observed during long-term food deprivation). Starvation-induced transcription factors such as DAF-16/FoxO and HLH-30 show strong translocation to the nucleus only after 30 min of fasting. Though gene expression changes in all stages of food deprivation are of biological relevance, the authors have missed the opportunity to explore whether increased INS-7 secretion from the anterior intestine is dependent on these starvation-induced transcription factors (which can be easily tested using loss-of-function alleles) or is due to other fast-acting regulatory mechanisms induced due to the absence of food contents in the gut lumen. A previous study (PMID: 40991693) has shown that DAF-16 activation during prolonged starvation shuts down insulin peptide secretion from the intestinal epithelial cells. Hence, it is not clear if increased INS-7 secretion is only a feature of short-term food deprivation or is also a signature of long-term starvation (e.g., at 8 hr or 16 hr timepoints). Since most of the INS-7 secretion data in this study are for 30 min of fasting, it remains unknown whether the discovered regulators of INS-7 secretion can be generalized for extended food deprivation that triggers major metabolic changes, such as fat loss (e.g., conditions shown in Figure 1D).

Two previous studies (PMID: 18025456, 40991693) have shown a strong reduction in the expression of ins-7 in the anterior intestine using GFP-based reporters (both promoter fusions and endogenous CRISPR-generated) and in whole-animal RNA-seq data from starved animals. These results are in contrast to the increased INS-7 secretion from INT1 cells during fasting that is reported in this study. The authors here have reported that INS-7 translation is higher in INT1 compared to INT2-9 during fed, acute fasted, and chronic fasted conditions, but they have not shown whether INS-7 translation is upregulated during acute and chronic fasting in INT1 cells in their TRAP-seq analysis. Knowing whether increased INS-7 secretion during acute fasting is due to increased transcription, translation, or secretion of INS-7 is crucial to resolve the discrepancy between these studies.

Reviewer #1 (Public review):

Summary:

The authors Hall et al. establish a purification method for snake venom metalloproteinases (SVMPs). By generating a generic approach to purify this divergent class of recombinant proteins, they enhance the field's accessibility to larger quantities of SVMPs with confirmed activity and, for some, characterized kinetics. In some cases, the recombinant protein displayed comparable substrate specificity and substrate recognition compared to the native enzyme, providing convincing evidence of the authors' successful recombinant expression strategy. Beyond describing their route towards protein purification, they further provide evidence for self-activation upon Zn2+ incubation. They further provide insights on how to design high-throughput screening (HTS) methods for drug discovery and outline future perspectives for the in-depth characterization of these enzyme classes to enable the development of novel biomedical applications.

Strengths:

The study is well-presented and structured in a compelling way. The purification strategy results in highly pure protein products, well characterized by size exclusion chromatography, SDS page as well as confirmed by mass spectrometry analysis. Further, a significant portion of the manuscript focuses on enzyme activity, thereby validating function. Particularly convincing is the comparability between recombinant vs. native enzymes; this is successfully exemplified by insulin B digestion. By testing the fluorogenic substrate, the authors provide evidence that their production method of recombinant protein can open up possibilities in HTS. Since their purification method can be applied to three structurally variable SVMP classes, this demonstrates the robust nature of the approach.

Weaknesses:

The universal applicability of the approach could be emphasized more clearly. The potential for this generic protocol for recombinant SVMP zymogen production to be adapted to other SVMPs is somewhat obscured by the detailed optimization steps. A general schematic overview would strengthen the manuscript, presented as a final model, to illustrate how this strategy can be extended to other targets with similar features. Such a schematic might, for example, outline the propeptide fusion design, including its tags, relevant optimizations during expression, lysis, purification (e.g., strategies for metal ion removal and maintenance of protease inactivity), as well as the controllable auto-activation.

The product obtained from the purification protocol appears to be a heterogeneous mixture of self-activated and intact protein species. The protocol would benefit from improved control over the self-activation process. The Methods section does not indicate whether residual metal ions were attempted to be removed during the purification, which could influence premature activation. Additionally, it has not been discussed whether the shift to pH 8 in the purification process is necessary from the initial steps onwards, given that a lower pH would be expected to maintain enzyme latency.

The characterization of PIII activity using the fluorogenic peptide effectively links the project to its broader implications for drug design. However, the absence of comparable solutions for PI and PII classes limits the overall scope and impact of the finding.

Overall, the authors successfully purified active SVMP proteins of all three structurally diverse classes in high quality and provided convincing evidence throughout the manuscript to support their claims. The described method will be of use for a broader community working with self-activating and cytotoxic proteases.

Reviewer #1 (Public review):

Summary:

In this manuscript, Ampartzidis et al. report the establishment of an iPSC-derived neuroepithelial model to examine how mutations from spina bifida patients disrupt fundamental cellular properties that underlie neural tube closure. The authors utilize an adherent neural induction protocol that relies on dual SMAD inhibition to differentiate three previously established iPSC lines with different origins and reprogramming methods. The analysis is comprehensive and outstanding, demonstrating reproducible differentiation, apical-basal elongation, and apical constriction over an 8-day period among the 3 lines. In inhibitor studies, it is shown that apical constriction is dependent on ROCK and generates tension, which can be measured using an annular laser ablation assay. Since this pathway is dependent on PCP signaling, which is also implicated in neural tube defects, the authors investigated whether VANGL2 is required by generating 2 lines with a pathogenic patient-derived sequence variant. Both lines showed reduced apical constriction and reduced tension in the laser ablation assays. The authors then established lines obtained from amniocentesis, including 2 control and 2 spina bifida patient-derived lines. These remarkably exhibited different defects. One line showed defects in apical-basal elongation, while the other showed defects in neural differentiation. Both lines were sequenced to identify candidate variants in genes implicated in NTDs. While no smoking gun was found in the line that disrupts neural differentiation (as is often the case with NTDs), compound heterozygous MED24 variants were found in the patient whose cells were defective in apical-basal elongation. Since MED24 has been linked to this phenotype, this finding is especially significant.

Some details are missing regarding the method to evaluate the rigor and reproducibility of the study.

Major Comments:

It is mentioned throughout the manuscript that 3 plates were evaluated per line. I believe these are independently differentiated plates. This detail is critical concerning rigor and reproducibility. This should be clearly stated in the Methods section and in the first description of the experimental system in the Results section for Figure 1.

For the patient-specific lines - how many lines were derived per patient?

Was the Vangl2 variant introduced by prime editing? Base editing? The details of the methods are sparse.

Significance:

This paper is significant not only for verifying the cell behaviors necessary for neural tube closure in a human iPSC model, but also for establishing a robust assay for the functional testing of NTD-associated sequence variants. This will not only demonstrate that sequence variants result in loss of function but also determine which cellular behaviors are disrupted.

Reviewer #1 (Public review):

Summary:

This work addresses a key question in cell signalling, how does the membrane composition affect the behaviour of a membrane signalling protein? Understanding this is important, not just to understand basic biological function but because membrane composition is highly altered in diseases such as cancer and neurodegenerative disease. Although parts of this question have been addressed on fragments of the target membrane protein, EGFR, used here, Srinivasan et al. harness a unique tool, membrane nanodisks, which allow them to probe full length EGFR in vitro in great detail with cutting-edge fluorescent tools. They find interested impacts on EGFR conformation in differently charged and fluid membranes, explaining previously identified signalling phenotypes.

Strengths:

The nanodisk system enables full length EGFR to be studied in vitro and in a membrane with varying lipid and cholesterol concentrations. The authors combine this with single-molecule FRET utilising multiple pairs of fluorophores at different places on the protein to probe different conformational changes in response to EGF binding under different anionic lipid and cholesterol concentrations. They further support their findings using molecular dynamics simulations which help uncover the full atomistic detail of the conformations they observe.

Weaknesses:

Much of the interpretation of the results comes down to a bimodal model of an 'open' and 'closed' state between the intracellular tail of the protein and the membrane. Some of the data looks like a bimodal model is appropriate but not all. The authors have just this bimodal model statistically and although adding a third component is a better fit, I agree with the authors that it cannot be justified statistically, given the data. Further work beyond the scope of this study would be needed to try to define further states.

Reviewer #1 (Public review):

Summary:

This study identifies a mechanism responsible for the accumulation of the MET receptor in invadopodia, following stimulation of Triple-negative breast cancer (TNBC) cells with HGF. HGF-driven accumulation and activation of MET in invadopodia causes the degradation of the extracellular matrix, promoting cancer cell invasion, a process here investigated using gelatin-degradation and spheroid invasion assays.

Mechanistically, HGF stimulates the recycling of MET from RAB14-positive endodomes to invadopodia, increasing their formation. At invadopodia, MET induces matrix degradation via direct binding with the metalloprotease MT1-MMP. The delivery of MET from the recycling compartment to invadopodia is mediated by RCP, which facilitates the colocalization of MET to RAB14 endosomes. In this compartment, HGF induces the recruitment of the motor protein KIF16B, promoting the tubulation of the RAB14-MET recycling endosomes to the cell surface. This pathway is critical for the HGF-driven invasive properties of TNBC cells, as it is impaired upon silencing of RAB14.

Strengths:

The study is well-organized and executed using state-of-the-art technology. The effects of MET recycling in the formation of functional invadopodia are carefully studied, taking advantage of mutant forms of the receptor that are degradation-resistant or endocytosis-defective.

Data analyses are rigorous, and appropriate controls are used in most of the assays to assess the specificity of the scored effects. Overall, the quality of the research is high.

The conclusions are well-supported by the results, and the data and methodology are of interest for a wide audience of cell biologists.

Weaknesses:

The role of the MET receptor in invadopodia formation and cancer cell dissemination has been intensively studied in many settings, including triple-negative breast cancer cells. The novelty of the present study mostly consists of the detailed molecular description of the underlying mechanism based on HGF-driven MET recycling. The question of whether the identified pathway is specific for TNBC cells or represents a general mechanism of HGF-mediated invasion detectable in other cancer cells is not addressed or at least discussed.

Reviewer #1 (Public review):

Summary:

GPCRs affect the EV-miRNA cargoes

Strengths:

Novel idea of GPCRs-mediated control of EV loading of miRNAs

Weaknesses:

Incomplete findings failed to connect and show evidence of any physiological parameters that are directly related to the observed changes. The mechanical detail is completely lacking.

Comments on revisions:

The revised version of the manuscript falls short of the required standard by lacking additional experiments. Some of the conditions for acceptability could have been met only through clarifying uncertainties via further experiments, which, unfortunately, have not been conducted.

Reviewer #1 (Public review):

Significance:

While most MAVEs measure overall function (which is a complex integration of biochemical properties, including stability), VAMP-seq-type measurements more strongly isolate stability effects in a cellular context. This work seeks to create a simple model for predicting the response for a mutation on the "abundance" measurement of VAMP-seq.

Public Review:

Of course, there is always another layer of the onion, VAMP-seq measures contributions from isolated thermodynamic stability, stability conferred by binding partners (small molecule and protein), synthesis/degradation balance (especially important in "degron" motifs), etc. Here the authors' goal is to create simple models that can act as a baseline for two main reasons:

(1) how to tell when adding more information would be helpful for a global model;

(2) how to detect when a residue/mutation has an unusual profile indicative of an unbalanced contribution from one of the factors listed above.

As such, the authors state that this manuscript is not intended to be a state-of-the-art method in variant effect prediction, but rather a direction towards considering static structural information for the VAMP-seq effects. At its core, the method is a fairly traditional asymmetric substitution matrix (I was surprised not to see a comparison to BLOSUM in the manuscript) - and shows that a subdivision by burial makes the model much more predictive. Despite only having 6 datasets, they show predictive power even when the matrices are based on a smaller number. Another success is rationalizing the VAMPseq results on relevant oligomeric states.

Comments on revision:

We have no further comments on this manscript.

Reviewer #1 (Public review):

Summary:

The authors clearly demonstrate that overexpressed Dcp-1, but not Drice, is activated without canonical apoptosome components. Using TurboID-based proximity labeling, they revealed distinct proximal proteomes, among which Sirtuin 1, an Atg8a deacetylase, which promotes autophagy, was specifically required for Dcp-1 activation. Additionally, the show that autophagy-related genes, including Bcl-2 family members Debcl and Buffy, are required for Dcp-1 activation.

Using structure-based prediction using AlphaFold3, they identified that Bruce, an autophagy-regulated inhibitor of apoptosis, acts as a Dcp-1-specific regulator acting outside the apoptosome-mediated pathway. Finally, they show that Bruce suppresses wing tissue growth. These findings indicate that non-lethal Dcp-1 activity is governed by the autophagy-Bruce axis, enabling distinct non-lethal functions independent of cell death.

Strengths:

This is an excellent paper with very good structure, excellent quality data and analysis.

Weaknesses:

This reviewer did not identify any weaknesses or recommendations for revision.

Reviewer #1 (Public review):

Summary:

The authors aimed to overcome a major technical limitation in pancreatic slice research - the inefficient viral transduction of dense, enzyme-active human pancreas tissue - while maintaining tissue integrity and physiological responsiveness. They developed a modified culture and infection protocol that incorporates gentle orbital agitation, removal of protease inhibitors, and physiological temperature during adenoviral transduction. This method increased transduction efficiency by approximately threefold without impairing insulin secretion or calcium signaling responses.

Strengths:

The study's major strengths are its clear methodological innovation, experiment optimization, and multiparametric validation. The authors provide compelling evidence that their approach enhances the expression of genetically encoded calcium indicators (GCaMP6m) and integrators (CaMPARI2), preserving both endocrine and exocrine cell functionality. The demonstration of targeted biosensor expression in β-cells and multiplexed imaging of redox and calcium dynamics highlights the versatility of the system. The CaMPARI2-based approach is particularly impactful, as it decouples maximum calcium response assessment from real-time imaging, thereby increasing throughput and reducing bias. The authors successfully apply the technique to samples from non-diabetic, T1D, and T2D donors, revealing disease-relevant alterations in β-cell calcium responses consistent with known physiological dysfunctions. The analysis of islet size versus calcium response further underscores the utility of this platform for probing structure-function relationships in situ.

Weaknesses:

The primary limitations are a lack of live/dead assessment to differentiate viability-related effects from methodological improvements, a lack of quantification of the transduction efficiency (while relative efficiency is clearly increased, it is not shown what is absolute efficiency is), lack of IF confirmation of the cell-specific transduction efficiency. These limitations, however, do not detract from the overall strength of the technical advance.

Overall, this work offers a convincing and practical advance for the diabetes and islet biology community. It substantially improves the toolkit available for live human pancreas studies and will likely catalyze further mechanistic investigations of islet heterogeneity, disease progression, and therapeutic response.

Reviewer #1 (Public review):

Liu, Li, Ge, and colleagues use whole genome sequence data to estimate the recombination landscape of domesticated chickens and their wild ancestor, Red Junglefowl. They compare landscapes estimated using the deep learning method RelERNN (Adrion et al. 2020) to understand the consequences of domestication for the evolution of recombination. The authors build on previous work in tomato, maize, and other domesticated species to examine how recombination rate and patterning evolve under the demography and selection pressures of domestication. They do so by comparing estimates of local recombination rates across chromosomes and populations, asking if/how well certain sequence and chromatin-based predictors predict recombination rate, and testing for an association between recombination rate and the proportion of introgressed ancestry from Red Junglefowl.

This study provides evidence for the hypothesis that recombination evolves rapidly in domesticated lineages -- so much so that we see little hotspot sharing between breeds in the present-day! Strengths of the paper include the collection/analysis of data from several domesticated sub-populations and efforts to control for demography and structure in the inference of recombination landscapes (given the challenges of some methods under non-equilibrium demography: https://academic.oup.com/mbe/article/35/2/335/4555533). It is also reassuring to see patterns that have been thoroughly established (e.g., the negative relationship between recombination rate and chromosome size) validated.

However, I have concerns about the data and methodology.

(1) My main concern is that the demographic and recombination rate estimates inferred using ~20 whole genomes are likely quite variable and, without quantification of the uncertainty or systematic assessment of the possible biases in the methodology, it is difficult to have confidence in analyses which make use of the RelERNN landscapes.

(a) Similar studies in rye (https://academic.oup.com/mbe/article/39/6/msac131/6605708) and tomato (https://academic.oup.com/mbe/article/39/1/msab287/6379725) used data from far more individuals (916 individuals split up into populations of size 50 for rye, >75 samples for tomato) to infer recombination maps and conduct downstream analyses. Studies in human genetics make use of an even greater number! The evidence (Lines 189-196 of the main text) that the sample size is sufficient to capture fine-scale variation in recombination is weak. In particular, correlations between the true and estimated recombination rate are based on *equilibrium* demography at sample sizes of 5, 10, and 20, yet used draw the inference "20 samples per population are sufficient to reconstruct their recombination landscapes" under the *non-equilibrium* demography (inferred using SMC+).

(b) RelERNN learns the recombination landscape by using several signatures (the decay of linkage disequilibrium and, as described in https://academic.oup.com/genetics/advance-article-abstract/doi/10.1093/genetics/iyaf108/8157390, choppiness of the allele frequency spectrum) left in present-day genomes. Both signatures depend strongly on local SNP density. It does not seem the effect of SNP density on the inferred recombination rate is examined, despite the potential for correlated noise in inferred recombination rate (in SNP-sparse regions of the genome) to confound downstream inference.

(c) It is unclear if the demographic histories for chickens (Figure S6) broadly match what have been previously estimated from whole-genome data, or if a large class of demographic models are compatible with the data (i.e., confidence intervals for the demographic histories are quite large). In Figure S6, its bottlenecks are somewhat weak and affect only a couple of the groups, despite the history of domestication and the expectation that effective sizes vary more widely. The groups affected (LX and WL) are those that have the weakest correlations between recombination rate under the equilibrium and non-equilibrium demographic models.

(2) The authors test for the effects of chromatin modifications, GC content, etc using correlations between local recombination rate and the features individually. However, joint inference of the effects under a GLM (the distribution of recombination rates is probably better described by, e.g., a Gamma distribution) would permit more straightforward causal inference, given, e.g., the potential effects of chromatin marks on deleterious mutation accumulation. I recognize this likely would not change the direction or significance of the effects in question, but it is worth noting given readers who may want to learn something from the effect sizes and the nature of causes and effects is difficult to disentangle without a multivariate approach.

Overall:

Previous work on recombination landscape evolution in birds (namely, the zebra finch and long-tailed finch; Singhal & Leffler 2015) has shown that many hotspots, i.e., small stretches of the genome that experience rates of crossing over that are much higher than the genome-wide average, are conserved over tens of millions of years of evolution. Work in tomato, maize, rye, and other flowering plants with histories of domestication have shown that hotspots can be dynamic. The results of Liu, Li, Ge, and colleagues complement those analyses and will, therefore, be of interest to those working on the evolution of recombination. Additionally, the finding that minor parent ancestry is negatively associated with recombination is interesting to an otherwise general rule in evolutionary biology. Finally, it is quite exciting to see recombination maps inferred using RelERNN, and in a demography-aware fashion!

That all said, it is difficult to have certainty in the results due to the relatively limited sample size for each of the populations, the lack of control for SNP density, the uncertainty in both recombination maps and demographic histories, and the lack of a joint modelling framework to carefully tease apart effects that are reported in isolation.

Reviewer #1 (Public review):

Summary:

These authors have developed a method to induce MI or MII arrest. While this was previously possible in MI, the advantage of the method presented here is it works for MII, and chemically inducible because it is based on a system that is sensitive to the addition of ABA. Depending on when the ABA is added, they achieve a MI or MII delay. The ABA promotes dimerizing fragments of Mps1 and Spc105 that can't bind their chromosomal sites. The evidence that the MI arrest is weaker than the MII arrest is convincing and consistent with published data and indicating the SAC in MI is less robust than MII or mitosis. The authors use this system to find evidence that the weak MI arrest is associated with PP1 binding to Spc105. This is a nice use of the system.

The remainder of the paper uses the SynSAC system to isolate populations enriched for MI or MII stages and conduct proteomics. This shows a powerful use of the system, but more work is needed to validate these results, particularly in normal cells.

Overall, the most significant aspect of this paper is the technical achievement, which is validated by the other experiments. They have developed a system and generated some proteomics data that maybe useful to others when analyzing kinetochore composition at each division.

Reviewer #1 (Public review):

Summary:

The authors performed an elegant investigation to clarify the roles of CHD4 in chromatin accessibility and transcription regulation. In addition to the common mechanisms of action through nucleosome repositioning and opening of transcriptionally active regions, the authors considered here a new angle of CHD4 action through modulating the off rate of transcription factor binding. Their suggested scenario is that the action of CHD4 is context-dependent and is different for highly-active regions vs low-accessibility regions.

Strengths:

This is a very well-written paper that will be of interest to researchers working in this field. The authors performed large work with different types of NGS experiments and the corresponding computational analyses. The combination of biophysical measurements of the off-rate of protein-DNA binding with NGS experiments is particularly commendable.

Comments on revised version:

The authors have addressed all my points

Reviewer #1 (Public review):

Summary:

The article presents the details of the high-resolution light-sheet microscopy system developed by the group. In addition to presenting the technical details of the system, its resolution has been characterized and its functionality demonstrated by visualizing subcellular structures in a biological sample.

Strengths:

The article includes extensive supplementary material that complements the information in the main article.

Live imaging has been incorporated, as requested, increasing the value of the paper.

Weaknesses:

None

Reviewer #1 (Public review):

Summary:

ZMAT3 is a p53 target gene that the Lal group and others have shown is important for p53-mediated tumor suppression, and which plays a role in the control of RNA splicing. In this manuscript Lal and colleagues perform quantitative proteomics of cells with ZMAT3 knockout and show that the enzyme hexokinase HKDC1 is the most upregulated protein. Mechanistically, the authors show that ZMAT3 does not appear to directly regulate the expression of HKDC1; rather, they show that the transcription factor c-JUN was strongly enriched in ZMAT3 pull-downs in IP-mass spec experiments, and they perform IP-western to demonstrate an interaction between c-JUN and ZMAT3. Importantly, the authors demonstrate, using ChIP-qPCR, that JUN is present at the HKDC1 gene (intron 1) in ZMAT3 WT cells, and showed markedly enhanced binding in ZMAT3 KO cells. The data best fit a model whereby p53 transactivates ZMAT3, leading to decreased JUN binding to the HKDC1 promoter, and altered mitochondrial respiration. The data are novel, compelling and very interesting.

Comments on revisions:

The authors have done a thorough job addressing my comments. This manuscript is quite strong and will be highly cited for its novelty and rigor.

Reviewer #2 (Public review):

In the original review of this manuscript, I noted that this study provides the first evidence that alteration of the Hox code in neck lateral plate mesoderm is sufficient for ectopic forelimb budding. Their finding that ectopic expression of Hoxa6 or Hoxa7 induces wing budding at neck level, a demonstration of sufficiency, is of major significance. The experiments used to test the necessity of specific Hox genes for limb budding involved overexpression of dominant negative constructs, and there were questions about whether the controls were well designed. The reviewers made several suggestions for additional experiments that would address their concerns. In their responses to those comments, the authors indicated that they would conduct those experiments, and they acknowledged the requests for further discussion of a few points.

In the revised version of the manuscript, the authors have provided additional RNA-seq data in Table 3, which lists 221 genes that are shared between the Hoxa6-induced limb bud and normal wing bud but not the neck. This shows that the ectopic limb bud has a limb-like character. The authors also expanded the discussion of their results in the context of previous work on the mouse. These changes have improved the paper.

The authors elected not to conduct the co-transfection experiments that were suggested to test the ability of Hoxa4/a5 to block the limb-inducing ability of Hoxa6/a7. They also chose not to conduct the additional control experiments that were suggested for the dominant negative studies. The authors' justification for not conducting these experiments is provided in the responses to reviewers.

The paper is improved over the previous version, but the conclusions, particularly regarding the dominant negative experiments, would have been strengthened by the additional experiments that were recommended by the reviewers. Under the current publishing model for eLife, it is the authors' prerogative to decide whether to revise in accordance with the reviewers' suggestions. Therefore, it seems to me that this version of the manuscript is the definitive version that the authors want to publish, and that eLife should publish it together with the reviewers' comments and the authors' responses.

Reviewer #1 (Public review):

Summary:

In the manuscript submission by Zhao et al. entitled, "Cardiac neurons expressing a glucagon-like receptor mediate cardiac arrhythmia induced by high-fat diet in Drosophila" the authors assert that cardiac arrhythmias in Drosophila on a high fat diet is due in part to adipokinetic hormone (Akh) signaling activation. High fat diet induces Akh secretion from activated endocrine neurons, which activate AkhR in posterior cardiac neurons. Silencing or deletion of Akh or AkhR blocks arrhythmia in Drosophila on high fat diet. Elimination of one of two AkhR expressing cardiac neurons results in arrhythmia similar to high fat diet.

Strengths:

The authors propose a novel mechanism for high fat diet induced arrhythmia utilizing the Akh signaling pathway that signals to cardiac neurons.

Reviewer #1 (Public review):

Summary:

This work revisits a substantial part of the published literature in the field of Drosophila innate immunity from 1959 to 2011. The strategy has been to restrain the analysis to some 400 articles and then to extract a main claim, two to four major claims and up to four minor claims totaling some 2000 claims overall. The consistency of these claims with the current state-of-the-art has been evaluated and reported on a dedicated Web site known as ReproSci and also in the text as well as in the 28 Supplements that report experimental verification, direct or indirect, e.g., using novel null mutants unavailable at the time, of a selected set of claims made in several articles. Of note, this review is mostly limited to the manuscript and its associated supplements and does not integrally cover the ReproSci website.

Strengths:

One major strength of this article is that it tackles the issue of reproducibility/consistency on a large scale. Indeed, while many investigators have some serious doubts about some results found in the literature, few have the courage, or the means and time, to seriously challenge studies, especially if published by leaders in the field. The Discussion adequately states the major limitations of the ReproSci approach, which should be kept in mind by the reader to form their own opinion.

This study also allows investigators not familiar with the field to have a clearer understanding of the questions at stake and to derive a more coherent global picture that allows them to better frame their own scientific questions. Besides a thorough and up-to-date knowledge of the literature used to assess the consistency of the claims with our current knowledge, a merit of this study is the undertaking of independent experiments to address some puzzling findings and the evidence presented is often convincing, albeit one should keep in mind the inherent limitations as several parameters are difficult to control, especially in the field of infections, as underlined by the authors themselves. Importantly, some work of the lead author has also been re-evaluated (Supplements S2-S4). Thus, while utmost caution should be exerted, and often is, in challenging claims, even if the challenge eventually proves to be not grounded, it is valuable to point out potential controversial issues to the scientific community.

While this is not a point of this review, it should be acknowledged that the possibility to post comments on the ReproSci website will allow further readjustments by the community in the appreciation of the literature and also of the ReproSci assessments themselves and of its complementary additional experiments.

Weaknesses:

Challenging the results from articles is, by its very nature, a highly sensitive issue, and utmost care should be taken when challenging claims. While the authors generally acknowledge the limitations of their approach in the main text and Supplements, there are a few instances where their challenges remain questionable and should be reassessed. This is certainly the case for Supplement S18, for which the ReproSci authors make a claim for a point that was not made in the publication under scrutiny. The authors of that study (Ramet et al., Immunity, 2001) never claimed that scavenger receptor SR-CI is a phagocytosis receptor, but that it is required for optimal binding of S2 cells to bacteria. Westlake et al. here have tested for a role of this scavenger receptor in phagocytosis, which had not been tested by Ramet et al. Thus, even though the ReproSci study brings additional knowledge to our understanding of the function of SR-CI by directly testing its involvement in phagocytosis by larval hemocytes, it did not address the major point of the Ramet et al. study, SR-CI binding to bacteria, and thus inappropriately concludes in Supplement S18 that "Contrary to (Ramet et al., 2001, Saleh et al., 2006), we find that SR-CI is unlikely to be a major Drosophila phagocytic receptor for bacteria in vivo." It follows that the results of Ramet et al. cannot be challenged by ReproSci as it did not address this program. Of note, Saleh et al. (2006) also mistakenly stated that SR-CI impaired phagocytosis in S2 cells and could be used as a positive control to monitor phagocytosis in S2 cells. Their assay appears to have actually not monitored phagocytosis but the association of FITC-labeled bacteria to S2 cells by FACS, as they did not mention quenching the fluorescence of bacteria associated with the surface with Trypan blue.

The inference method to assess the consistency of results with current knowledge also has limitations that should be better acknowledged. At times, the argument is made that the gene under scrutiny may not be expressed at the right time according to large-scale data or that the gene product was not detected in the hemolymph by a mass-spectrometry approach. While being in theory strong arguments, some genes, for instance, those encoding proteases at the apex of proteolytic activation cascades, need not necessarily be strongly expressed and might be released by a few cells. In addition, we are often lacking relevant information on the expression of genes of interest upon specific immune challenges such as infections with such and such pathogens.

As regards mass spectrometry, there is always the issue of sensitivity that limits the force of the argument. Our understanding of melanization remains currently limited, and methods are lacking to accurately measure the killing activity associated with the triggering of the proPO activation cascade. In this study, the authors monitor only the blackening reaction of the wound site based on a semi-quantitative measurement. They are not attempting to use other assays, such as monitoring the cleavage of proPOs into active POs or measuring PO enzymatic activity. These techniques are sometimes difficult to implement, and they suffer at times from variability. Thus, caution should be exerted when drawing conclusions from just monitoring the melanization of wounds.

Likewise, the study of phagocytosis is limited by several factors. As most studies in the field focus on adults, the potential role of phagocytosis in controlling Gram-negative bacterial infections is often masked by the efficiency of the strong IMD-mediated systemic immune response mediated by AMPs (Hanson et al, eLife, 2019). This problem can be bypassed in rare instances of intestinal infections by Gram-negative bacteria such as Serratia marcescens (Nehme et al., PLoS Pathogens, 2007) or Pseudomonas aeruginosa (Limmer et al. PNAS, 2011), which escape from the digestive tract into the hemocoel without triggering, at least initially, the systemic immune response. It is technically feasible to monitor bacterial uptake in adults by injecting fluorescently labeled bacteria and subsequently quenching the signal from non-ingested bacteria. Nonetheless, many investigators prefer to resort to ex vivo assays starting from hemocytes collected from third-instar wandering larvae as they are easier to collect and then to analyze, e.g., by FACS. However, it should be pointed out that these hemocytes have been strongly exposed to a peak of ecdysone, which may alter their properties. Like for S2 cells, it is thus not clear whether third-instar larval hemocytes faithfully reproduce the situation in adults. The phagocytic assays are often performed with killed bacteria. Evidence with live microorganisms is better, especially with pathogens. Assays with live bacteria require however, an antibody used in a differential permeabilization protocol. Furthermore, the killing method alters the surface of the microorganisms, a key property for phagocytic uptake. Bacterial surface changes are minimal when microorganisms are killed by X-ray or UV light. These limitations should be kept in mind when proceeding to inference analysis of the consistency of claims. Eater illustrates this point well. Westlake et al. state that:" [...] subsequent studies showed that a null mutation of eater does not impact phagocytosis". The authors refer here to Bretscher et al., Biology Open, 2015, in which binding to heat-killed E. coli was assessed in an ex vivo assay in third instar larvae. In contrast, Chung and Kocks (JBC, 2011) tested whether the recombinant extracellular N-terminal ligand-binding domain was able to bind to bacteria. They found that this domain binds to live Gram-positive bacteria but not to live Gram-negative bacteria. For the latter, killing bacteria with ethanol or heating, but not by formaldehyde treatment, allowed binding. More importantly, Chung and Kocks documented a complex picture in which AMPs may be needed to permeabilize the Gram-negative bacterial cell wall that would then allow access of at least the recombinant secreted Eater extracellular domain to peptidoglycan or peptidoglycan-associated molecules. Thus, the systemic Imd-dependent immune response would be required in vivo to allow Eater-dependent uptake of Gram-negative bacteria by adult hemocytes. In ex vivo assays, any AMPs may be diluted too much to effectively attack the bacterial membrane. A prediction is then that there should be an altered phagocytosis of Gram-negative bacteria in IMD-pathway mutants, e.g., an imd null mutant but not the hypomorphic imd[1] allele. This could easily be tested by ReproSci using the adult phagocytosis assay used by Kocks et al, Cell, 2005. At the very least, the part on the role of Eater in phagocytosis should take the Chung &Kocks study into account, and the conclusions modulated.

Another point is that some mutant phenotypes may be highly sensitive to the genetic background, for instance, even after isogenization in two different backgrounds. In the framework of a Reproducibility project, there might be no other option for such cases than direct reproduction of the experiment as relying solely on inference may not be reliable enough.

With respect to the experimental part, some minor weaknesses have been noted. The authors rely on survival to infection experiments, but often do not show any control experiments with mock-challenged or noninfected mutant fly lines. In some cases, monitoring the microbial burden would have strengthened the evidence. For long survival experiments, a check on the health status of the lines (viral microbiota, Wolbachia) would have been welcome. Also, the experimental validation of reagents, RNAi lines, or KO lines is not documented in all cases.

Reviewer #1 (Public review):

Summary:

This paper describes an application of the high-resolution cryo-EM 2D template matching technique to sub-50kDa complexes. The paper describes how density for ligands can be reconstructed without having to process cryo-EM data through the conventional single particle analysis pipelines.

Strengths:

This paper contributes additional data (alongside other papers by the same authors) to convey the message that high-resolution 2D template matching is a powerful alternative for cryo-EM structure determination. The described application to ligand density reconstruction, without the need for extensive refinements, will be of interest to the pharmaceutical industry, where often multiple structures of the same protein in complex with different ligands are solved as part of their drug development pipelines. Improved insights into which particles contribute to the best ligand density are also highly valuable and transferable to other applications of the same technique.

Weaknesses:

Although the convenient visualisation of small molecules bound to protein targets of a known structure would be relevant for the pharmaceutical industry, the evidence described for the claim that this technique "significantly" improves alignment of reconstruction of small complexes is incomplete. The authors are encouraged to better evaluate the effects of model bias on the reconstructed densities in a revised paper.

It is fascinating that Whatley is commending Jane Austin for covert didactic narratives. To have the moral lessons being in arm's grasp, if only, the individual seeks it out. Though, if I was to critique this rationale, to suggest that this methodology is "conformed more closely to real life" not evidently true. Often times, the big moral lessons in real life become loud and clear with great consequences. Beyond the critique, it is fascinating that Jane Austen wrote works with social realism predating the Realism literary period. Revolutionary and "novel" in application.

SIDE NOTE: I hope Whatley lived long enough to see the emergence of the Realism literary period. Given this was written in 1818, I hope he lived 22 years to at least see prevalence of Realism as that seems to be his fascination.

Reviewer #1 (Public review):

Summary:

Fungal survival and pathogenicity rely on the ability to undergo reversible morphological transitions, which is often linked to nutrient availability. In this study, the authors uncover a conserved connection between glycolytic activity and sulfur amino acid biosynthesis that drives morphogenesis in two fungal model systems. By disentangling this process from canonical cAMP signaling, the authors identify a new metabolic axis that integrates central carbon metabolism with developmental plasticity and virulence.

Strengths:

The study integrates different experimental approaches, including genetic, biochemical, transcriptomic and morphological analyses and convincingly demonstrates that perturbations in glycolysis alters sulfur metabolic pathways and thus impacts pseudohyphal and hyphal differentiation. Overall, this work offers new and important insights into how metabolic fluxes are intertwined with fungal developmental programs and therefore opens new perspectives to investigate morphological transitioning in fungi.

Importantly, in the revised version the authors now substantiate the transcriptomic findings by RT-qPCR analyses in the pfk1ΔΔ and adh1ΔΔ strains, demonstrating that genetic disruption of glycolytic flux generally mirrors the effects of 2-deoxyglucose treatment. The manuscript's discussion has also been strengthened by explicitly addressing why cysteine and methionine differ in their ability to rescue filamentation in S. cerevisiae versus C. albicans, highlighting species-specific differences in sulfur uptake and transsulfuration pathways.

Overall, this revised manuscript provides compelling evidence for a previously unrecognized coupling between glycolysis and sulfur metabolism that shapes fungal morphogenesis and virulence. It opens new perspectives on metabolic control of fungal development and raises interesting mechanistic questions for future work.

Comments on revisions:

The authors have incorporated all of my suggested changes and addressed all raised concerns.

Joint Public Review:

In this work, the authors present DeepTX, a computational tool for studying transcriptional bursting using single-cell RNA sequencing (scRNA-seq) data and deep learning. The method aims to infer transcriptional burst dynamics-including key model parameters and the associated steady-state distributions-directly from noisy single-cell data. The authors apply DeepTX to datasets from DNA damage experiments, revealing distinct regulatory patterns: IdU treatment in mouse stem cells increases burst size, promoting differentiation, while 5FU alters burst frequency in human cancer cells, driving apoptosis or survival depending on dose. These findings underscore the role of burst regulation in mediating cell fate responses to DNA damage.

The main strength of this study lies in its methodological contribution. DeepTX integrates a non-Markovian mechanistic model with deep learning to approximate steady-state mRNA distributions as mixtures of negative binomial distributions, enabling genome-scale parameter inference with reduced computational cost. The authors provide a clear discussion of the framework's assumptions, including reliance on steady-state data and the inherent unidentifiability of parameter sets, and they outline how the model could be extended to other regulatory processes.

The revised manuscript addresses the original concerns raised by the reviewers, particularly those related to sample size requirements, distributional assumptions, and the biological interpretation of the inferred parameters. The authors have also included an extensive discussion of the limitations of the methodological framework, including the constraints associated with relying on snapshot data, as well as a broader contextualisation of DeepTX within the landscape of existing tools that link mechanistic modelling and single-cell transcriptomics.

Overall, this work represents a valuable contribution to the integration of mechanistic models with high-dimensional single-cell data. It will be of interest to researchers in systems biology, bioinformatics, and computational modelling.

Comments on revisions:

We thank the authors for their thorough revision and for carefully addressing the points raised in the previous review. At this stage, the reviewers have no further concerns.

Reviewer #1 (Public review):

Summary:

The paper by Graff et al. investigates the function of foxf2 in zebrafish to understand the progression of cerebral small vessel disease. The authors use a partial loss of foxf2 (zebrafish possess two foxf2 genes, foxf2a and foxf2b, and the authors mainly analyze homozygous mutants in foxf2a) to investigate the role of foxf2 signaling in regulating pericyte biology. The find that the number of pericytes is reduced in foxf2a mutants and that the remaining pericytes display alterations in their morphologies. The authors further find that mutant animals can develop to adulthood but that in adult animals, both endothelial and pericyte morphologies are affected. They also show that mutant pericytes can partially repopulate the brain after genetic ablation.

Strengths:

The paper is well written and easy to follow. The authors now include pericyte marker gene analysis and solid quantifications of the observed phenotypes.

Weaknesses:

None left.

Reviewer #1 (Public review):

Summary:

The manuscript presents a robust set of experiments that provide new insights into the role of STN neurons during active and passive avoidance tasks. These forms of avoidance have received comparatively less attention in the literature than the more extensively studied escape or freezing responses, despite being extremely relevant to human behaviour and more strongly influenced by cognitive control.

Strengths:

Understanding the neural infrastructure supporting avoidance behaviour would be a fundamental milestone in neuroscience. The authors employ sophisticated methods to delineate the role of STN neurons during avoidance behaviours. The work is thorough and the evidence presented is compelling. Experiments are carefully constructed, well-controlled, and the statistical analyses are appropriate.

Reviewer #1 (Public review):

This manuscript used deep learning to highlight the role of inhibition in shaping selectivity in primary and higher visual cortex. The findings hint at hitherto unknown axes of structured inhibition operating in cortical networks with a potentially key role in object recognition.

The multi-species approach of testing the model in macaque and mouse is excellent, as it improves the chances that the observed findings are a general property of mammalian visual cortex. However, it would be useful to delineate any notable differences between these species, which are to be expected given their lifestyle.

The overall performance of the model appears to be excellent in V1, with over 80% performance, but it falls substantially in V4. It would be important to consider the implications of this finding; for example, in the context of studying temporal lobe structures that are central to recognizing objects. Would one expect that model performance decreases further here, and what measures could be taken to avoid this? Or is this type of model better restricted to V1 or even LGN?

While the manuscript delineates novel axes of inhibitory interactions, it remains unclear what exactly these axes are and how they arise. What are the steps that need to be taken to make progress along these lines?

Reviewer #1 (Public review):

Wang, Zhou et al. investigated coordination between the prefrontal cortex (PFC) and the hippocampus (Hp), during reward delivery, by analyzing beta oscillations. Beta oscillations are associated with various cognitive functions, but their role in coordinating brain networks during learning is still not thoroughly understood. The authors focused on the changes in power, peak frequencies, and coherence of beta oscillations in two regions when rats learn a spatial task over days. Inconsistent with the authors' hypothesis, beta oscillations in those two regions during reward delivery were not coupled in spectral or temporal aspects. They were, however, able to show reverse changes in beta oscillations in PFC and Hp as the animal's performance got better. The authors were also able to show a small subset of cell populations in PFC that are modulated by both beta oscillations in PFC and sharp wave ripples in Hp. A similarly modulated cell population was not observed in Hp. These results are valuable in pointing out distinct periods during a spatial task when two regions modulate their activity independently from each other.

The authors included a detailed analysis of the data to support their conclusions. However, some clarifications would help their presentation, as well as help readers to have a clear understanding.

(1) The crucial time point of the analysis is the goal entry. However, it needs a better explanation in the methods or in figures of what a goal entry in their behavioral task means.

(2) Regarding Figure 2, the authors have mentioned in the methods that PFC tetrodes have targeted both hemispheres. It might be trivial, but a supplementary graph or a paragraph about differences or similarities between contralateral and ipsilateral tetrodes to Hp might help readers.

(3) The authors have looked at changes in burst properties over days of training. For the coincidence of beta bursts between PFC and Hp, is there a change in the coincidence of bursts depending on the day or performance of the animal?

(4) Regarding the changes in performance through days as well as variance of the beta burst frequency variance (Figures 3C and 4C); was there a change in the number of the beta bursts as animals learn the task, which might affect variance indirectly?

(5) In the behavioral task, within a session, animals needed to alternate between two wells, but the central arm (1) was in the same location. Did the authors alternate the location of well number 1 between days to different arms? It is possible that having well number 1 in the same location through days might have an effect on beta bursts, as they would get more rewards in well number 1?

(6) The animals did not increase their performance in the F maze as much as they increased it in the Y maze. It would be more helpful to see a comparison between mazes in Figure 5 in terms of beta burst timing. It seems like in Y maze, unrewarded trials have earlier beta bursts in Y maze compared to F maze. Also, is there a difference in beta burst frequencies of rewarded and unrewarded trials?

(7) For individual cell analysis, the authors recorded from Hp and the behavioral task involved spatial learning. It would be helpful to readers if authors mention about place field properties of the cells they have recorded from. It is known that reward cells firing near reward locations have a higher rate to participate in a sharp wave ripple. Factoring in the place field properties of the cells into the analysis might give a clearer picture of the lack of modulation of HP cells by beta and sharp wave ripples.

Reviewer #1 (Public review):

Summary:

The authors set out to understand how animals respond to visible light in an animal without eyes. To do so they used the C. elegans model, which lacks eyes, but nonetheless exhibits robust responses to visible light at several wavelengths. Here, the authors report a promoter that is activated by visible light and independent of known pathways of light resposnes.

Strengths:

The authors convincingly demonstrate that visible light activates the expression of the cyp-14A5 promoter driven gene expression in a variety of contexts and report the finding that this pathway is activated via the ZIP-2 transcriptionally regulated signaling pathway.

Weaknesses:

Because the ZIP-2 pathway has been reported to activated predominantly by changes in the bacterial food source of C. elegans -- or exposure of animals to pathogens -- it remains unclear if visible light activates a pathway in C. elegans (animals) or if visible light potentially is sensed by the bacteria on the plate which also lack eyes. Specifically, it is possible that the the plates are seeded with excess E. coli, that E. coli is altered by light in some way and in this context alters its behavior in such a way that activates a known bacterially responsive pathway in the animals. Consistent with this possibility the authors found that heat-killed bacteria prevented the reporter activation in animals. This weakness would not affect the ability to use this novel discovery as a tool, which would still be useful to the field.

Reviewer #1 (Public review):

Aw et al. have proposed that utilizing stability analysis can be useful for fine-mapping of cross populations. In addition, the authors have performed extensive analyses to understand the cases where the top eQTL and stable eQTL are the same or different via functional data.

Comments on revisions:

The authors have answered all my concerns.

Reviewer #1 (Public review):

While the structure of the melibiose permease in both outward and inward-facing forms has been solved previously, there remains unanswered questions regarding its mechanism. Hariharan et al set out to address this with further crystallographic studies complemented with ITC and hydrogen deuterium exchange (HDX) mass spectrometry. They first report 4 different crystal structures of galactose derivatives to explore molecular recognition showing that the galactose moiety itself is the main source of specificity. Interestingly, they observe a water-mediated hydrogen bonding interaction with the protein and suggest that this water molecule may be important in binding.

The results from the crystallography appear sensible, though the resolution of the data is low with only the structure with NPG better than 3Å. Support for the conclusion of the water molecule in the binding site, as interpreted from the density, is given by MD studies.

The HDX also appears to be well done and is explained reasonably well in the revision.

Reviewer #1 (Public review):

Summary:

The authors analyze transcription in single cells before and after 4000 rads of ionizing radiation. They use Seuratv5 for their analyses, which allows them to show that most of the genes cluster along the proximal-distal axis. Due to the high heterogeneity in the transcripts, they use the Herfindahl-Hirschman index (HHI) from Economics, which measures market concentration. Using the HHI, they find that genes involved in several processes (like cell death, response to ROS, DNA damage response (DDR)) are relatively similar across clusters. However, ligands activating the JAK/STAT, Pvr, and JNK pathways and transcription factors Ets21C and dysf are upregulated regionally. The JAK/STAT ligands Upd1,2,3 require p53 for their upregulation after irradiation, but the normal expression of Upd1 in unirradiated discs is p53-independent. This analysis also identified a cluster of cells that expressed tribbles, encoding a factor that downregulates mitosis-promoting String and Twine, that appears to be G2/M arrested and expressed numerous genes involved in apoptosis, DDR, the aforementioned ligands and TFs. As such, the tribbles-high cluster contains much of the heterogeneity.

Strengths:

(1) The authors have used robust methods for rearing Drosophila larvae, irradiating wing discs and analyzing the data with Seurat v5 and HHI.<br /> (2) These data will be informative for the field.<br /> (3) Most of the data is well-presented.<br /> (4) The literature is appropriately cited.

Weaknesses

The authors have addressed my concerns in the revised article.

Reviewer #1 (Public review):

Summary:

Negreira, G. et al clearly presented the challenges of conducting genomic studies in unicellular pathogens and of addressing questions related to the balance between genome integrity and instability, pivotal for survival under the stressful conditions these organisms face and for their evolutionary success. This underlies the need for powerful approaches to perform single-cell DNA analyses suited to the small and plastic Leishmania genome. Accordingly, their goal was to develop such a novel method and demonstrate its robustness.

In this study, the authors combined semi-permeable capsules (SPCs) with primary template-directed amplification (PTA) and adapted the system to the Leishmania genome, which is about 100 times smaller than the human genome and exhibits remarkable plasticity and mosaic aneuploidy. Given the size and organization of the Leishmania genome, the challenges were substantial; nevertheless, the authors successfully demonstrated that PTA not only works for Leishmania but also represents a significantly improved whole-genome amplification (WGA) method compared with standard approaches. They showed that SPCs provide a superior alternative for cell encapsulation, increasing throughput. The methodology enabled high-resolution karyotyping and the detection of fine-scale copy number variations (CNVs) at the single-cell level. Furthermore, it allowed discrimination between genotypically distinct cells within mixed populations.

Strengths:

This is a high-impact study that will likely contribute to our understanding of DNA replication and the genetic plasticity of Leishmania, including its well-documented aneuploidy, somy variations, CNVs, and SNPs - all key elements for elucidating various aspects of the parasite's biology, such as genome evolution, genetic exchange, and mechanisms of drug resistance.

Overall, the authors clearly achieved their objectives, providing a solid rationale for the study and demonstrating how this approach can advance the investigation of Leishmania's small, plastic genome and its frequent natural strain mixtures within hosts. This methodology may also prove valuable for genomic studies of other single-celled organisms.

Weaknesses:

The discussion section could be enriched to help readers understand the significance of the work, for instance, by more clearly pointing out the obstacles to a better understanding of DNA replication in Leishmania. Or else, when they discuss the results obtained at the level of nucleotide information and the relevance of being able to compare, in their case, the two strains, they could refer to the implications of this level of precision to those studying clonal strains or field isolates, drug resistance or virulence in a more detailed way.

1 вопрос

Reviewer #1 (Public review):

Summary:

This study is an evaluation of patient variants in the kidney isoform of AE1 linked to distal renal tubular acidosis. Drawing on observations in the mouse kidney, this study extends findings to autophagy pathways in a kidney epithelial cell line.

Strengths:

Experimental data are convincing and nicely done.

The revised manuscript incorporates most of the reviewer recommendations and presents a more cohesive story that is easier to read and assess. The data are convincing, of suitable quality and nicely presented. Statistical evaluation is rigorous. The link between kAE1 mutants and cell metabolism and autophagy is novel and provides insights on pathological observations in dRTA.

Reviewer #1 (Public review):

Lahtinen et al. evaluated the association between polygenic scores and mortality. This question has been intensely studied (Sakaue 2020 Nature Medicine, Jukarainen 2022 Nature Medicine, Argentieri 2025 Nature Medicine), where most studies use PRS as an instrument to attribute death to different causes. The presented study focuses on polygenic scores of non-fatal outcomes and separates the cause of death into "external" and "internal". The majority of the results are descriptive, and the data doesn't have the power to distinguish effect sizes of the interesting comparisons: (1) differences between external vs. internal (2) differences between PGI effect and measured phenotype.

Comments on revised version:

The authors answered my concerns well. I don't have any further comments.

Reviewer #1 (Public review):

Summary:

Carloni et al. comprehensively analyze which proteins bind repetitive genomic elements in Trypanosoma brucei. For this, they perform mass spectrometry on custom-designed, tagged programmable DNA-binding proteins. After extensively verifying their programmable DNA-binding proteins (using bioinformatic analysis to infer target sites, microscopy to measure localization, ChIP-seq to identify binding sites), they present, among others, two major findings: 1) 14 of the 25 known T. brucei kinetochore proteins are enriched at 177bp repeats. As T. brucei's 177bp repeat-containing intermediate-sized and mini-chromosomes lack centromere repeats but are stable over mitosis, Carloni et al. use their data to hypothesize that a 'rudimentary' kinetochore assembles at the 177bp repeats of these chromosomes to segregate them. 2) 70bp repeats are enriched with the Replication Protein A complex, which, notably, is required for homologous recombination. Homologous recombination is the pathway used for recombination-based antigenic variation of the 70bp-repeat-adjacent variant surface glycoproteins.

Strengths and Weaknesses:

The manuscript was previously reviewed through Review Commons. As noted there, the experiments are well controlled, the claims are well supported, and the methods are clearly described. The conclusions are convincing. All concerns I raised have been addressed except one (minor point #8):

"The way the authors mapped the ChIP-seq data is potentially problematic when analyzing the same repeat type in different genomic regions. Reads with multiple equally good mapping positions were assigned randomly. This is fine when analyzing repeats by type, independent of genomic position, which is what the authors do to reach their main conclusions. However, several figures (Fig. 3B, Fig. 4B, Fig. 5B, Fig. 7) show the same repeat type at specific genomic locations." Due to the random assignment, all of these regions merely show the average signal for the given repeat. I find it misleading that this average is plotted out at "specific" genomic regions.<br /> Initially, I suggested a workaround, but the authors clarified why the workaround was not feasible, and their explanation is reasonable to me. That said, the figures still show a signal at positions where they can't be sure it actually exists. If this cannot be corrected analytically, it should at least be noted in the figure legends, Results, or Discussion.

Importantly, the authors' conclusions do not hinge on this point; they are appropriately cautious, and their interpretations remain valid regardless.

Significance:

This work is of high significance for chromosome/centromere biology, parasitology, and the study of antigenic variation. For chromosome/centromere biology, the conceptual advancement of different types of kinetochores for different chromosomes is a novelty, as far as I know. It would certainly be interesting to apply this study as a technical blueprint for other organisms with mini-chromosomes or chromosomes without known centromeric repeats. I can imagine a broad range of labs studying other organisms with comparable chromosomes to take note of and build on this study. For parasitology and the study of antigenic variation, it is crucial to know how intermediate- and mini-chromosomes are stable through cell division, as these chromosomes harbor a large portion of the antigenic repertoire. Moreover, this study also found a novel link between the homologous repair pathway and variant surface glycoproteins, via the 70bp repeats. How and at which stages during the process, 70bp repeats are involved in antigenic variation is an unresolved, and very actively studied, question in the field. Of course, apart from the basic biological research audience, insights into antigenic variation always have the potential for clinical implications, as T. brucei causes sleeping sickness in humans and nagana in cattle. Due to antigenic variation, T. brucei infections can be chronic.

Comments on revised version:

All my recommendations have been addressed.

Reviewer #1 (Public review):

Summary:

The authors assess the role of map3k1 in adult Planaria through whole body RNAi for various periods of time. The authors' prior work has shown that neoblasts (stem cells that can regenerate the entire body) for various tissues are intermingled in the body. Neoblasts divide to produce progenitors that migrate within a "target zone" to the "differentiated target tissues" where they differentiate into a specific cell type. Here the authors show that map3k1-i animals have ectopic eyes that form along the "normal" migration path of eye progenitors, ectopic neurons and glands along the AP axis and pharynx in ectopic anterior positions. The rest of the study shows that positional information is largely unaffected by loss of map3k1. However, loss of map3k1 leads to premature differentiated of progenitors along their normal migratory route. They also show that "long-term" whole body depletion of map3k1 results in mis-specified organs and teratomas. In short, this study convincingly demonstrates that in planaria, map3k1 maintains progenitor cells in an undifferentiated state, preventing premature fate commitment until they encounter the appropriate signals, either positional cues within a designated region or contact-dependent inputs from surrounding tissues.

Strengths:

(1) The study has appropriate controls, sample sizes and statistics.

(2) The work is high-quality.

(3) The conclusions are supported by the data.

(4) Planaria is a good system to analyze the function of map3k1, which exists in mammals but not other invertebrates.

Weaknesses:

None noted.

Reviewer #1 (Public review):

Summary:

This manuscript by Joshi and colleagues demonstrates that the precise theta-phase timing of spikes is causal for CA1 hippocampal theta sequences during locomotion on a linear track and is necessary for learning the cognitively demanding outbound component of a hippocampus-dependent alternation task (W-maze), independently of replay during immobility. To reach these conclusions, the authors developed a theta-phase-specific, closed-loop manipulation that used optogenetic activation of medial septal parvalbumin (PV) interneurons at the ascending phase of theta during locomotion. This protocol preserved immobility periods, allowing a clean and elegant dissociation from SWR-associated replay.

The manuscript is well written and was a pleasure to read. The work described is of high quality and introduces several notable advances to the field:

(a) It extends prior studies that manipulated theta oscillations by examining precise temporal structure (specifically theta sequences) rather than only LFP features.

(b) The closed-loop manipulation enabled dissociation between deficits in theta sequences during a behavioural task and SWR-associated replay activity.

(c) As controls, the authors included rats with suboptimal viral transduction or optic-fibre placement, and, within subjects, both stimulation-on (stim-on) and stimulation-off (stim-off) trials. Notably, sequence disruption persisted into stim-off periods within the same session.

Overall, this is a strong manuscript that will provide valuable insights to the field. I have only minor comments:

(1) As the authors note, it is striking that both behavioural performance and spike patterns are altered during stim-off trials. They propose that "disruption of theta sequences during the initial experience in an environment is sufficient to have lasting effects," implying that rapid, experience-dependent plasticity is driven by sequential firing. Does this imply that if rats were previously trained on the task, subsequent stim-on and stim-off trials would yield different outcomes, with stim-off trials showing improved performance and intact theta sequences? For example, if the sequence of one-third stim-on, one-third stim-off, one-third stim-on were inverted to off-on-off, would theta sequences be expected to emerge, disappear, and potentially re-emerge? While I am not asking for additional experiments, I think the discussion could be extended in this aspect.

Alternatively, could the number of stim-off trials (one third of the total) be insufficient to support learning/induce plasticity? In the controls, ~50-100 trials appear necessary to achieve high performance.

(2) In line with the point above, the authors characterise the behavioural changes induced by MS optogenetic stimulation specifically as a "learning deficit," as rats failed to improve across 300 trials in an initially novel environment (W-maze). While they present this as complementary to prior demonstrations of impaired performance on previously learned tasks (Zutshi et al., 2018; Quirk et al., 2021; Etter et al., 2023; Petersen et al., 2020), an alternative interpretation is a working-memory deficit. This would produce the same behavioural pattern, with reference memory (the less cognitively demanding trials) remaining intact despite stimulation and concomitant changes in theta sequences. This interpretation would also be consistent with work in certain disease models, where reduced synaptic plasticity and working-memory deficits co-occur with preserved place coding despite impaired theta sequences (e.g., Viana da Silva et al., 2024; Donahue et al., 2025).

(3) It was not immediately clear whether SWR-associated activity was derived from the interleaved ~15-min rest sessions in a rest box, or from periods of immobility or reward consumption in the maze (aSWR, as in Jadhav et al 2012). Regardless, it would be informative to compare aSWR events within the maze to rest-box SWRs that may occur during more prolonged slow-wave episodes (even if not full sleep). This contrasts with Liu et al. (2024), who analysed replay during ~1.5-h sleep sessions.

Reviewer #1 (Public review):

Summary:

This study examines the role of the long non-coding RNA Dreg1 in regulating Gata3 expression and ILC2 development. Using Dreg1-deficient mice, the authors show a selective loss of ILC2s but not T or NK cells, suggesting a lineage-specific requirement for Dreg1. By integrating public chromatin and TF-binding datasets, they propose a Tcf1-Dreg1-Gata3 regulatory axis. The topic is relevant for understanding epigenetic regulation of ILC differentiation.

Strengths:

(1) Clear in vivo evidence for a lineage-specific role of Dreg1.

(2) Comprehensive integration of genomic datasets.

(3) Cross-species comparison linking mouse and human regulatory regions.

Weaknesses:

(1) Mechanistic conclusions remain correlative, relying on public data.

(2) Lack of direct chromatin or transcriptional validation of Tcf1-mediated regulation.

(3) Human enhancer function is not experimentally confirmed.

(4) Insufficient methodological detail and limited mechanistic discussion.

Reviewer #1 (Public review):

Summary:

The authors provide a resource to the systems neuroscience community by offering their Python-based CLoPy platform for closed-loop feedback training. In addition to using neural feedback, as is common in these experiments, they include a capability to use real-time movement extracted from DeepLabCut as the control signal. The methods and repository are detailed for those who wish to use this resource. Furthermore, they demonstrate the efficacy of their system through a series of mesoscale calcium imaging experiments. These experiments use a large number of cortical regions for the control signal in the neural feedback setup, while the movement feedback experiments are analyzed more extensively. The revised preprint has improved substantially upon the previous submission.

Strengths:

The primary strength of the paper is the availability of their CLoPy platform. Currently, most closed-loop operant conditioning experiments are custom built by each lab, and carry a relatively large startup cost to get running. This platform lowers the barrier to entry for closed-loop operant conditioning experiments, in addition to making the experiments more accessible to those with less technical expertise.

Another strength of the paper is the use of many different cortical regions as control signals for the neurofeedback experiments. Rodent operant conditioning experiments typically record from the motor cortex, and maybe one other region. Here, the authors demonstrate that mice can volitionally control many different cortical regions not limited to those previously studied, recording across many regions in the same experiment. This demonstrates the relative flexibility of modulating neural dynamics, including in non-motor regions.

Finally, adapting the closed-loop platform to use real-time movement as a control signal is a nice addition. Incorporating movement kinematics into operant conditioning experiments has been a challenge due to the increased technical difficulties of extracting real-time kinematic data from video data at a latency where it can be used as a control signal for operant conditioning. In this paper, they demonstrate that the mice can learn the task using their forelimb position, at a rate that is quicker than the neurofeedback experiments.

Weaknesses:

Many of the original weaknesses have been addressed in the revised preprint.

While the dataset contains an impressive amount of animals and cortical regions for the neurofeedback experiment, my excitement for these experiments is tempered by the relative incompleteness of the dataset.

Additionally, adoption of the platform may be hindered by the absence of a tutorial on how to run a session.

Reviewer #1 (Public review):

Summary:

Here Bansal et al., present a study on the fundamental blood and nectar feeding behaviors of the critical disease vector, Anopheles stephensi. The study encompasses not just the fundamental changes in blood feeding behaviors of the crucially understudied vector, but then use a transcriptomic approach to identify candidate neuromodulation path ways which influence blood feeding behavior in this mosquito species. The authors then provide evidence through RNAi knockdown of candidate pathways that the neuromodulators sNPF and Rya modulate feeding either via their physiological activity in the brain alone or through joint physiological activity along the brain-gut axis (but critically not the gut alone). Overall, I found this study to be built on tractable, well-designed behavioral experiments.

Their study begins with a well-structured experiment to assess how the feeding behaviors of A. stephensi changes over the course of its life history and in response to its age, mating and oviposition status. The authors are careful and validate their experimental paradigm in the more well-studied Ae. aegypti, and are able to recapitulate the results of prior studies which show that mating is pre-requisite for blood feeding behaviors in Ae. aegypt. Here they find A. stephensi like another Anopheline mosquitoes has a more nuanced regulation of its blood and nectar feeding behaviors.

The authors then go on to show in a Y- maze olfactometer that to some degree, changes in blood feeding status depend on behavioral modulation to host-cues, and this is not likely to be a simple change to the biting behaviors alone. I was especially struck by the swap in valence of the host-cues for the blood-fed and mated individuals which had not yet oviposited. This indicates that there is a change in behavior that is not simply desensitization to host-cues while navigating in flight, but something much more exciting happening.

The authors then use a transcriptomic approach to identify candidate genes in the blood feeding stages of the mosquito's life cycle to identify a list of 9 candidates which have a role in regulating the host-seeking status of A. stephensi. Then through investigations of gene knockdown of candidates they identify the dual action of RYa and sNPF and candidate neuromodulators of host-seeking in this species. Overrall, I found the experiments to be well-designed. I found the molecular approach to be sound. While I do not think the molecular approach is necessarily an all-encompassing mechanism identification (owing mostly to the fact that genetic resources are not yet available in A. stephensi as they are in other dipteran models), I think it sets up a rich lines of research questions for the neurobiology of mosquito behavioral plasticity and comparative evolution of neuromodulator action.

Strengths:

I am especially impressed by the authors' attention to small details in the course of this article. As I read and evaluated this article I continued to think how many crucial details I may have missed if I were the scientist conducting these experiments. That attention to detail paid off in spades and allowed the authors to carefully tease apart molecular candidates of blood-seeking stages. The authors top down approach to identifying RYamide and sNPF starting from first principles behavioral experiments is especially comprehensive. The results from both the behavioral and molecular target studies will have broad implications for the vectorial capacity of this species and comparative evolution of neural circuit modulation.

I believe the authors have adequately addressed all of my concerns; however, I think an accompanying figure to match the explained methods of the tissue-specific knockdown would help readers. The methods are now explicitly written for the timing and concentrations required to achieve tissue-specific knockdown, but seeing the data as a supplement would be especially reassuring given the critical nature of tissue-specific knockdown to the final interpretations of this paper.

Reviewer #1 (Public review):

Bredenberg et al. aim to model some of the visual and neural effects of psychedelics via the Wake-Sleep algorithm. This is an interesting study with findings that challenge certain mainstream ideas in psychedelic neuroscience.

While some of my concerns have been addressed in revision, I am still not convinced that this model applies to 5-HT2A hallucinogens, as opposed to a pharmacologically distinct hallucinogen. I think it is important to justify which class of hallucinogens this model applies to and distinguish it from other hallucinogens. While some researchers tend to group several hallucinogens together (e.g., 5-HT2A agonists, NMDA antagonists, kappa-opioids agonists), I'm not convinced this is warranted, when they have distinct subjective and cognitive effects (including quite different visual distortions, and again I point out that the kappa-opioid agonist salvinorin A, which is referred to as an "oneirogen," has been described as particularly dream-like, perhaps more so than 5-HT2A hallucinogens), as well as some differences in therapeutic outcomes (ketamine seems to not have as persisting of therapeutic effects, and kappa-opioid agonist have yet to be shown to be therapeutic). Their use patterns highlight this (e.g., 5-HT2A drugs are used less in non-festival/rave social settings compared to NMDA drugs like ketamine, which can be used frequently enough to the point of abuse; kappa-opioid agonists have quite mixed effects in terms of pleasurable outcomes, thereby rarely being used/abused and almost never to my knowledge being used recreationally).

In sum, more is needed to justify the claim that this work applies to 5-HT2A drugs in particular.

Reviewer #1 (Public review):

Summary:

The image analysis pipeline is tested in analysing microscopy imaging data of gastruloids of varying sizes, for which an optimised protocol for in toto image acquisition is established based on whole mount sample preparation using an optimal refractive index matched mounting media, opposing dual side imaging with two-photon microscopy for enhaced laser penetration, dual view registration and weighted fusion for improved in toto sample data representation. For enhanced imaging speed in a two-photon microscope, parallel imaging was used and the authors performed spectral unmixing analysis to avoid issues of signal cross-talk.

In the image analysis pipeline image, different pre-treatments are done dependent on the analysis to be performed (for nuclear segmentation - contrast enhancement and normalisation; for quantitative analysis of gene expression - corrections for optical artifacts inducing signal intensity variations). Stardist3D was used for the nuclear segmentation. The study analyses in toto properties of gastruloid nuclear density, patterns of cell division, morphology, deformation and gene expression.

Strengths:

The methods developed are sound, well described and well validated, using a sample challenging for microscopy, gastruloids. Many of the established methods are very useful (e.g. registration, corrections, signal normalisation, lazy loading bioimage visualisation, spectral decomposition analysis), facilitate the development of quantitative research and would be of interest to the wide scientific community.

Comments on revisions:

I am happy with the job the authors have done with the revision. No further comments.

Reviewer #1 (Public review):

Summary:

This paper investigates the potential link between amygdala volume and social tolerance in multiple macaque species. Through a comparative lens, the authors considered tolerance grade, species, age, sex, and other factors that may contribute to differing brain volumes. They found that amygdala, but not hippocampal, volume differed across tolerance grades such that high-tolerance species showed larger amygdala than low-tolerance species of macaques. They also found that less tolerant species exhibited increases in amygdala volume with age, while more tolerant species showed the opposite. Given their wide range of species with varied biological and ecological factors, the authors' findings provide new, important evidence for changes in amygdala volume in relation to social tolerance grades. Contributions from these findings will greatly benefit future efforts in the field to characterize brain regions critical for social and emotional processing across species.

(1) This study demonstrates a concerted and impressive effort to comparatively examine neuroanatomical contributions to sociality in monkeys. The authors impressively collected samples from 12 macaque species with multiple datapoints across species age, sex, and ecological factors. Species from all four social tolerance grades were present. Further, the age range of the animals is noteworthy, particularly the inclusion of individuals over 20 years old.

(2) This work is the first to report neuroanatomical correlates of social tolerance grade in macaques in one coherent study. Given the prevalence of macaques as a model of social neuroscience, considerations of how socio-cognitive demands are impacted by the amygdala are highly important. The authors' findings will certainly inform future studies on this topic.

(3) The methodology and supplemental figures for acquiring brain MRI images are nicely detailed. Clear information on these parameters is crucial for future comparative interpretations of sociality and brain volume, and the authors do an excellent job of describing this process in full.

(4) The following comments were brought up during the review. In their revision, the authors have sufficiently addressed all of these comments by providing detailed responses and updating their manuscript. First, the revision clarified how much one could draw conclusions about "nature vs. nurture" from this study. Second, the revision also clarified the contributions of very young and very old animals in their correlations. Third, in their revision, the authors expanded on how their results could be interpreted in the context of multiple behavioral traits by Thierry (2021) by providing more detailed descriptions. Finally, during the revision, the authors clarified that both intolerant and tolerant species experience complex socio-cognitive demands and highlighted that socio-cognitive challenges arise across the tolerance spectrum under different behavioral demands.

as children grow are they not in a stage of metamorphosis with changing the way they think and interact in daily life growing and shedding the adolescent Self?

Reviewer #1 (Public review):

Summary:

The manuscript by Hensley and Yildez studies the mechanical behavior of kinesin under conditions where the z-component of the applied force is minimized. This is accomplished by tethering the kinesin to the trapped bead with a long double stranded DNA segment as opposed to directly binding the kinesin to the large bead. It complements several recent studies that have used different approaches to looking at the mechanical properties of kinesin under low z-force loads. The study shows that much of the mechanical information gleaned from the traditional "one bead" with attached kinesin approach was probably profoundly influenced by the direction of the applied force. The authors speculate that when moving small vesicle cargos (particularly membrane bound ones) the direction of resisting force on the motor has much less of a z-component than might be experience if the motor were moving large organelles like mitochondria.

Strengths:

The approach is sound and provides an alternative method to examine the mechanics of kinesin under conditions where the z-component of the force is lessened. The data show that kinesin has very different mechanical properties compared to those extensively reported with using the "single-bead" assay where the molecule is directly coupled to a large bead which is then trapped.

Weaknesses:

The sub stoichiometry binding of kinesins to the multivalent DNA complicates the interpretation of the data.

Comments on revisions:

The authors have addressed my concerns.

Reviewer #1 (Public review):

The authors have conducted substantial additional analyses to address the reviewers' comments. However, several key points still require attention. I was unable to see the correspondence between the model predictions and the data in the added quantitative analysis. In the rebuttal letter, the delta peak speed time displays values in the range of [20, 30] ms, whereas the data were negative for the 45{degree sign} direction. Should the reader directly compare panel B of Figure 6 with Figure 1E? The correspondence between the model and the data should be made more apparent in Figure 6. Furthermore, the rebuttal states that a quantitative prediction was not expected, yet it subsequently argues that there was a quantitative match. Overall, this response remains unclear.

A follow-up question concerns the argument about strategic slowing. The authors argue that this explanation can be rejected because the timing of peak speed should be delayed, contrary to the data. However, there appears to be a sign difference between the model and the data for the 45{degree sign} direction, which means that it was delayed in this case. Did I understand correctly? In that regard, I believe that the hypothesis of strategic slowing cannot yet be firmly rejected and the discussion should more clearly indicate that this argument is based on some, but not all, directions. I agree with the authors on the importance of the mass underestimation hypothesis, and I am not particularly committed to the strategic slowing explanation, but I do not see a strong argument against it. If the conclusion relies on the sign of the delta peak speed, then the authors' claims are not valid across all directions, and greater caution in the interpretation and discussion is warranted. Regarding the peak acceleration time, I would be hesitant to draw firm conclusions based on differences smaller than 10 ms (Figures R3 and 6D).

The authors state in the rebuttal that the two hypotheses are competing. This is not accurate, as they are not mutually exclusive and could even vary as a function of movement direction. The abstract also claims that the data "refutes" strategic slowing, which I believe is too strong. The main issue is that, based on the authors' revised manuscript, the lack of quantitative agreement between the model and the data for the mass underestimation hypothesis is considered acceptable because a precise quantitative match is not expected, and the predictions overall agree for some (though not all) directions and phases (excluding post-in). That is reasonable, but by the same logic, the small differences between the model prediction and the strategic slowing hypothesis should not be taken as firm evidence against it, as the authors seem to suggest. In practice, I recommend a more transparent and cautious interpretation to avoid giving readers the false impression that the evidence is decisive. The mass underestimation hypothesis is clearly supported, but the remaining aspects are less clear, and several features of the data remain unexplained.

Reviewer #1 (Public review):

Summary:

In the manuscript "Conformational Variability of HIV-1 Env Trimer and Viral Vulnerability", the authors study the fully glycosylated HIV-1 Env protein using an all-atom forcefield. It combines long all-atom simulations of Env in a realistic asymmetric bilayer with careful data analysis. This work clarifies how the CT domain modulates the overall conformation of the Env ectodomain and characterizes different MPER-TMD conformations. The authors also carefully analyze the accessibility of different antibodies to the Env protein.

Strengths:

This paper is state-of-the-art, given the scale of the system and the sophistication of the methods. The biological question is important, the methodology is rigorous, and the results will interest a broad audience.

Weaknesses:

The manuscript lacks a discussion of previous studies. The authors should consider addressing or comparing their work with the following points:

(1) Tilting of the Env ectodomain has also been reported in previous experimental and theoretical work:

https://doi.org/10.1101/2025.03.26.645577

(2) A previous all-atom simulation study has characterized the conformational heterogeneity of the MPER-TMD domain:

https://doi.org/10.1021/jacs.5c15421

(3) Experimental studies have shown that MPER-directed antibodies recognize the prehairpin intermediate rather than the prefusion state:

https://doi.org/10.1073/pnas.1807259115

(4) How does the CT domain modulate the accessibility of these antibodies studied? The authors are in a strong position to compare their results with the following experimental study:

https://doi.org/10.1126/science.aaa9804

Reviewer #1 (Public review):

Summary:

The authors present a novel usage of fluorescence life-time imaging microscopy (FLIM) to measure NAD(P)H autofluorescence in the Drosophila brain, as a proxy for cellular metabolic/redox states. This new method relies on the fact that both NADH and NADPH are autofluorescent, with a different excitation lifetime depending on whether they are free (indicating glycolysis) or protein-bound (indicating oxidative phosphorylation). The authors successfully use this method in Drosophila to measure changes in metabolic activity across different areas of the fly brain, with a particular focus on the main center for associative memory: the mushroom body.

Strengths:

The authors have made a commendable effort to explain the technical aspects of the method in accessible language. This clarity will benefit both non-experts seeking to understand the methodology and researchers interested in applying FLIM to Drosophila in other contexts.

Weaknesses:

Despite being statistically significant, the learning-induced change in f-free in α/β Kenyon cells is minimal (a decrease from 0.76 to 0.73, with a high variability). It is unclear whether this small effect represents a meaningful shift in neuronal metabolic state.

Whether this method can be valuable to examine the effects of long-term memory (after spaced or massed conditioning) remains to be established.

Reviewer #1 (Public review):

Summary:

This study investigates how individuals with chronic temporomandibular disorder (TMD) learn from uncertain rewards, using a probabilistic three-armed bandit task and computational modelling. The authors aim to identify whether people living with chronic pain show altered learning under uncertainty and how such differences might relate to psychological symptoms.

Strengths:

The work addresses an important question about how chronic pain may influence cognition and motivation. The task design is appropriate for probing adaptive learning, and the modelling approach is novel. The findings of altered uncertainty updating in the TMD group are interesting.

Weaknesses:

Several aspects of the paper limit the strength of the conclusions. The group differences appear only in model-derived parameters, with no corresponding behavioural differences in task performance. Model parameters do not correlate with pain severity, making the proposed mechanistic link between pain and learning speculative. Some of the interpretations extend beyond what the data can directly support.

Reviewer #1 (Public review):

Summary:

This manuscript by Wang et al. reports the potential involvement of an asymmetric neurocircuit in the sympathetic control of liver glucose metabolism.

Strengths:

The concept that the contralateral brain-liver neurocircuit preferentially regulates each liver lobe may be interesting.

Weaknesses:

However, the experimental evidence presented did not support the study's central conclusion.

(1) Pseudorabies virus (PRV) tracing experiment:<br /> The liver not only possesses sympathetic innervations but also vagal sensory innervations. The experimental setup failed to distinguish whether the PRV-labeling of LPGi (Lateral Paragigantocellular Nucleus) is derived from sympathetic or vagal sensory inputs to the liver.

(2) Impact on pancreas:<br /> The celiac ganglia not only provide sympathetic innervations to the liver but also to the pancreas, the central endocrine organ for glucose metabolism. The chemogenetic manipulation of LPGi failed to consider a direct impact on the secretion of insulin and glucagon from the pancreas.

(3) Neuroanatomy of the brain-liver neurocircuit:<br /> The current study and its conclusion are based on a speculative brain-liver sympathetic circuit without the necessary anatomical information downstream of LPGi.

(4) Local manipulation of the celiac ganglia:<br /> The left and right ganglia of mice are not separate from each other but rather anatomically connected. The claim that the local injection of AAV in the left or right ganglion without affecting the other side is against this basic anatomical feature.

Reviewer #1 (Public review):

Summary:

In this paper, the authors investigate the effects of Miro1 on VSMC biology after injury. Using conditional knockout animals, they provide the important observation that Miro1 is required for neointima formation. They also confirm that Miro1 is expressed in human coronary arteries. Specifically, in conditions of coronary diseases, it is localized in both media and neointima and, in atherosclerotic plaque, Miro1 is expressed in proliferating cells.

However, the role of Miro1 in VSMC in CV diseases is poorly studied and the data available are limited; therefore, the authors decided to deepen this aspect. The evidence that Miro-/- VSMCs show impaired proliferation and an arrest in S phase is solid and further sustained by restoring Miro1 to control levels, normalizing proliferation. Miro1 also affects mitochondrial distribution, which is strikingly changed after Miro1 deletion. Both effects are associated with impaired energy metabolism due to the ability of Miro1 to participate in MICOS/MIB complex assembly, influencing mitochondrial cristae folding. Interestingly, the authors also show the interaction of Miro1 with NDUFA9, globally affecting super complex 2 assembly and complex I activity.<br /> Finally, these important findings also apply to human cells and can be partially replicated using a pharmacological approach, proposing Miro1 as a target for vasoproliferative diseases.

Strengths:

The discovery of Miro1 relevance in neointima information is compelling, as well as the evidence in VSMC that MIRO1 loss impairs mitochondrial cristae formation, expanding observations previously obtained in embryonic fibroblasts.<br /> The identification of MIRO1 interaction with NDUFA9 is novel and adds value to this paper. Similarly, the findings that VSMC proliferation requires mitochondrial ATP support the new idea that these cells do not rely mostly on glycolysis.

The revised manuscript includes additional data supporting mitochondrial bioenergetic impairment in MIRO1 knockout VSMCs. Measurements of oxygen consumption rate (OCR), along with Complex I (ETC-CI) and Complex V activity, have been added and analyzed across multiple experimental conditions. Collectively, these findings provide a more comprehensive characterization of the mitochondrial functional state. Following revision, the association between MIRO1 deficiency and impaired Complex I activity is more robust.

Although the precise molecular mechanism of action remains to be fully elucidated, in this updated version, experiments using a MIRO1 reducing agent are presented with improved clarity

Although some limitations remain, the authors have addressed nearly all the concerns raised, and the manuscript has substantially improved

Weaknesses:

Figure 6: The authors do not address the concern regarding the cristae shape; however, characterization of the cristae phenotype with MIRO1 ΔTM would have strengthened the mechanistic link between MIRO1 and the MIB/MICOS complex

Although the authors clarified their reasoning, they did not explore in vivo validation of key biochemical findings, which represents a limitation of the current study. While their justification is acknowledged, at least a preliminary exploratory effort could have been evaluated to reinforce the translational relevance of the study.

Finally, in line with the explanations outlined in the rebuttal, the Discussion section should mention the limits of MIRO1 reducer treatment.

Joint Public Review:

Quite obviously, the brain encodes "time", as we are able to tell if something happened before or after something else. How this is done, however, remains essentially not understood. In the context of Working Memory tasks, many experiments have shown that the neural activity during the retention period "encodes" time, besides the stimulus to be remembered; that is, the time elapsed from stimulus presentation can be reliably inferred from the recordings, even if time per se is not important for the task. This implies 'mixed selectivity', in the weak sense of neural activity varying with both stimulus identity and time elapsed (since presentation).

In this paper, the authors investigate the implications of a specific form of such mixed selectivity, that is, conjunctive coding of what (stimulus) and when (time) at the single-neuron level, on the resulting dynamics of the population activity when 'viewed' through linear dimensionality-reduction techniques, essentially Principal Component Analysis (PCA). The theoretical/modeling results presented provide a useful guide to the interpretation of the experimental results; in particular, with respect to what can, or cannot, be rightfully inferred from those experimental results (using PCA-like techniques). The results are essentially theoretical in nature; there are, however, some conclusions that require a more precise justification, in my opinion. More generally, as the authors themselves discuss in the paper, it is not clear how to generalize this coding scheme to more complicated, but behaviorally and cognitively relevant, situations, such as multi-item WM or WM for sequences.

(1) It is unclear to me how the conjunctive code that the authors use (i.e., Equation (3)) is constrained by the theoretical desiderata (i.e., compositionality) they list, or whether it is simply an ansatz, partly motivated by theoretical considerations and experimental observations.

The "what" part: What the authors mean by "relationships" between stimuli is never clearly defined. From their argument (and from Figure 1b), it would seem that what they mean is "angles" between population vectors for all pairs of stimuli. If this is so, then the effect of the passing time can only amount to a uniform rescaling of the components of the population vector (i.e., it must be a similarity transformation; rotations are excluded, if the linear-decoder vectors are to be time-independent); the scaling factor, then, must be a strictly monotonous function of time (increasing or decreasing), if one is to decode time. In other words, the "when" receptive fields must be the same for all neurons.

The "when" part: The condition, \tau_3=\tau_1+\tau_2, does not appear to be used at all. In fact, it is unclear (to me at least) whether the model, as it is formulated, is able to represent time intervals between stimuli.

(2) For the specific case considered, i.e., conjunctive coding, it would seem that one should be able to analytically work out the demixed PCA (see Kobak et al., 2016). More generally, it seems interesting to compare the results of the PCA and the demixed PCA in this specific case, even just using synthetic data.

(3) In the Section "Dimensionality of neural trajectories...", there is some claim about how the dimensionality of the population activity goes up with the observation window T, backed up by numerical results that somehow mimic the results of Cueva et al. (2020) on experimental data. Is this a result that can be formally derived? Related to this point, it would be useful to provide a little more justification for Equation (17). Naively, one would think that the correlation matrix of the temporal component is always full-rank nominally, but that one can get excellent low-rank approximations (depending on T, following your argument).

Reviewer #1 (Public review):

Summary:

In the manuscript "Pathogen-Phage Geomapping to Overcome Resistance," Do et al. present an impressive demonstration of using geographical sampling and metagenomics to guide sample choice for enrichment in human-associated microbes and the pathogen of interest to increase the chances of success for isolating phages active against highly resistant bacterial strains. The authors document many notable successes (17!) with highly resistant bacterial isolates and share a thoughtfully structured phage discovery effort, potentially opening the door to similar geomapping efforts across the field. While the work is methodologically strong and valuable for the community, there are a few areas where additional clarification and analysis could better align the claims with the data presented.

Strengths:

(1) The manuscript describes a well-executed and transparent example of overcoming a major obstacle in therapeutic virus identification, providing a practical success story that will resonate with researchers in microbiology and medicine.

(2) Many phage researchers have anecdotally experienced a similar phenomenon, that a particular wastewater treatment plant always seems to have the pathogens you need. Quantifying this with metagenomics modernizes and adds evidence to this phenomenon in a way that could help researchers reproduce this success in a methodical way.

(3) The methodology of combining environmental sampling, viral screening, and host-range analysis is clearly articulated and reproducible, offering a valuable blueprint for others in the field.

(4) The data are presented with appropriate analytical rigor, and the results include robust sequencing and metagenomic profiling that deepen understanding of local viral communities.

(5) The 17 successes yielding 35 phages have a lot of phylogenetic novelty beyond what the Tailor labs have typically found with previous methods.

(6) The work highlights a practical and innovative solution to an increasingly important clinical problem, supporting the development of personalized antiviral strategies.

Weaknesses:

(1) The central concept of geomapping as a broadly applicable strategy is wonderfully supported by the 17 successes documented in the paper. While this is actually, of course, a strength, the study does not include a comparative analysis across multiple sites with varying sampling outcomes for different bacterial types, which would be necessary to validate this claim more generally.

(2) Some elements, such as beta diversity comparisons and the metagenomics analysis of viral dark matter, would benefit from additional statistical analysis and clearer context.

(3) Claims about therapeutic cocktails would be better framed as speculative and/or moved to the discussion section.

(4) The manuscript could be strengthened by elaborating on the scope and composition of the phage and bacterial isolate collections, which are important for interpreting the broader significance of the findings.

Reviewer #1 (Public review):

Summary:

In this study, the authors trained rats on a "figure 8" go/no-go odor discrimination task. Six odor cues (3 rewarded and 3 non-rewarded) were presented in a fixed temporal order and arranged into two alternating sequences that partially overlap (Sequence #1: 5⁺-0⁻-1⁻-2⁺; Sequence #2: 3⁺-0⁻-1⁻-4⁺) --forming an abstract figure-8 structure of looping odor cues.

This task is particularly well-suited for probing representations of hidden states, defined here as the animal's position within the task structure beyond superficial sensory features. Although the task can be solved without explicit sequence tracking, it affords the opportunity to generalize across functionally equivalent trials (or "positions") in different sequences, allowing the authors to examine how OFC representations collapse across latent task structure.

Rats were first trained to criterion on the task and then underwent 15 days of self-administration of either intravenous cocaine (3 h/day) or sucrose. Following self-administration, electrodes were implanted in lateral OFC, and single-unit activity was recorded while rats performed the figure-8 task.

Across a series of complementary analyses, the authors report several notable findings. In control animals, lOFC neurons exhibit representational compression across corresponding positions in the two sequences. This compression is observed not only in trial/positions involving overlapping odor (e.g., Position 3 = odor 1 in sequence 1 vs sequence 2), but also in trials/positions involving distinct, sequence-specific odors (e.g., Position 4: odor 2 vs odor 4) --indicating generalization across functionally equivalent task states. Ensemble decoding confirms that sequence identity is weakly decodable at these positions, consistent with the idea that OFC representations collapse incidental differences in sensory information into a common latent or hidden state representation. In contrast, cocaine-experienced rats show persistently stronger differentiation between sequences, including at overlapping odor positions.

Strengths:

Elegant behavioral design that affords the detection of hidden-state representations.

Sophisticated and complementary analytical approaches (single-unit activity, population decoding, and tensor component analysis).

Weaknesses:

The number of subjects is small --can't fully rule out idiosyncratic, animal-specific effects.

Comments

(1) Emergence of sequence-dependent OFC representations across learning.

A conceptual point that would benefit from further discussion concerns the emergence of sequence-dependent OFC activity at overlapping positions (e.g., position P3, odor 1). This implies knowledge of the broader task structure. Such representations are presumably absent early in learning, before rats have learned the sequence structure. While recordings were conducted only after rats were well trained, it would be informative if the authors could comment on how they envision these representations developing over learning. For example, does sequence differentiation initially emerge as animals learn the overall task structure, followed by progressive compression once animals learn that certain states are functionally equivalent? Clarifying this learning-stage interpretation would strengthen the theoretical framing of the results.

(2) Reference to the 24-odor position task

The reference to the previously published 24-odor position task is not well integrated into the current manuscript. Given that this task has already been published and is not central to the main analyses presented here, the authors may wish to a) better motivate its relevance to the current study or b) consider removing this supplemental figure entirely to maintain focus.

(3) Missing behavioral comparison

Line 117: the authors state that absolute differences between sequences differ between cocaine and sucrose groups across all three behavioral measures. However, Figure 1 includes only two corresponding comparisons (Fig. 1I-J). Please add the third measure (% correct) to Figure 1, and arrange these panels in an order consistent with Figure 1F-H (% correct, reaction time, poke latency).

(4) Description of the TCA component

Line 220: authors wrote that the first TCA component exhibits low amplitude at positions P1 and P4 and high amplitude at positions P2 and P3. However, Figure 3 appears to show the opposite pattern (higher magnitude at P1 and P4 and lower magnitude at P2 and P3). Please check and clarify this apparent discrepancy. Alternatively, a clearer explanation of how to interpret the temporal dynamics and scaling of this component in the figure would help readers correctly understand the result.

(5) Sucrose control<br /> Sucrose self-administration is a reasonable control for instrumental experience and reward exposure, but it means that this group also acquired an additional task involving the same reinforcer. This experience may itself influence OFC representations and could contribute to the generalization observed in control animals. A brief discussion of this possibility would help contextualize the interpretation of cocaine-related effects.

(6) Acknowledge low N

The number of rats per group is relatively low. Although the effects appear consistent across animals within each group, this sample size does not fully rule out idiosyncratic, animal-specific effects. This limitation should be explicitly acknowledged in the manuscript.

(7) Figure 3E-F: The task positions here are ordered differently (P1, P4, P2, P3) than elsewhere in the paper. Please reorder them to match the rest of the paper.

Reviewer #1 (Public review):

Summary:

This study makes a significant and timely contribution to the field of attention research. By providing the first direct neuroimaging evidence for the integration-segregation theory of exogenous attention, it fills a critical gap in our understanding of the neural mechanisms underlying inhibition of return (IOR). The authors employ a carefully optimized cue-target paradigm combined with fMRI to elegantly dissociate the neural substrates of cue-target integration from those of segregation, thereby offering compelling support for the integration-segregation account. Beyond validating a key theoretical hypothesis, the study also uncovers an interaction between spatial orienting and cognitive conflict processing, suggesting that exogenous attention modulates conflict processing at both semantic and response levels. This finding shed new light on the neural mechanisms that connect exogenous attentional orienting with cognitive control.

Strengths:

The experimental design is rigorous, the analyses are thorough, and the interpretation is well grounded in the literature. The manuscript is clearly written, logically structured, and addresses a theoretically important question. Overall, this is an excellent, high-impact study that advances both theoretical and neural models of attention.

Weaknesses:

While this study addresses an important theoretical question and presents compelling neuroimaging findings, a few additional details would help improve clarity and interpretation. Specifically, more information could be provided regarding the experimental conditions (SI and RI), the justification for the criteria used for excluding behavioral trials, and how the null condition was incorporated into the analyses. In addition, given the non-significant interaction effect in the behavioral results, the claim that the behavioral data "clearly isolated" distinct semantic and response conflict effects should be phrased more cautiously.

Reviewer #1 (Public review):

Summary:

Fahdan et al. present a study investigating the molecular programs underlying axon initial growth and regrowth in Drosophila mushroom body (MB) neurons. The authors leverage the fact that different Kenyon cell (KC) subtypes undergo distinct axonal events on the same developmental timeline: γ KCs prune and then regrow their axons during early pupation, whereas α/β KCs extend their axons for the first time during the same pupal period. Using bulk Smart-seq2 RNA sequencing across six developmental time points, the authors identify genes enriched during γ KC regrowth and α/β KC initial outgrowth, and subsequently perform an RNAi screen to determine which candidates are functionally required for these processes.

Among these, they focus on Pmvk, a key enzyme in the mevalonate pathway. Both RNAi knockdown and a CRISPR-generated mutant produce strong γ KC regrowth defects. Knockdown of other mevalonate pathway components (Hmgcr, Mvk) partially recapitulates this phenotype. The authors propose that Pmvk promotes axonal regrowth through effects on the TOR pathway.

Overall, this work identifies new molecular players in developmental axon remodeling and provides intriguing evidence connecting Pmvk to γ KC regrowth.

While the Pmvk knockdown and loss-of-function data are compelling, the evidence that the mevalonate pathway broadly regulates γ KC axon regrowth is less clear. RNAi knockdown of enzymes upstream of Pmvk (Hmgcr, Mvk) produces only mild phenotypes, and knockdown of several downstream enzymes produces no phenotype. The authors attribute this discrepancy to the possibility of weak RNAi constructs, which is plausible but not fully demonstrated. It would be helpful for the authors to discuss alternative explanations, including non-canonical roles for Pmvk that may not require the full pathway, and clarify the extent to which the current data support the conclusion that the mevalonate pathway, rather than Pmvk specifically, is a core regulator of regrowth.

It is not clear from the Methods whether γ KCs and α/β KCs were sorted from the same brains using orthogonal binary expression systems (e.g., Gal4 > reporter 1 and LexA > reporter 2), or isolated separately from different fly lines. If the latter, differences in genetic background, staging, or batch effects could influence transcriptional comparisons. This should be explicitly clarified in the Methods, and any associated limitations discussed in the manuscript.

The authors have made important findings that contribute to our understanding of axon growth and regrowth. As written, some major claims are only partially supported, but these issues can be addressed through reframing and clarification. In particular, the manuscript would benefit from (1) a more cautious interpretation of the mevalonate pathway's role, potentially considering Pmvk non-canonical functions, and (2) addressing methodological ambiguities in the transcriptomic analysis.

Reviewer #1 (Public review):

Summary:

Here, the authors have addressed the recruitment and firing patterns of motor units (MUs) from the long and lateral heads of triceps in the mouse. They used their newly developed Myomatrix arrays to record from these muscles during treadmill locomotion at different speeds, and they used template-based spike sorting (Kilosort) to extract units. Between MUs from the two heads, the authors observe differences in their firing rates, recruitment probability, phase of activation within the locomotor cycle and interspike interval patterning. Examining different walking speeds, the authors find increases in both recruitment probability and firing rates as speed increases. The authors also observed differences in the relation between recruitment and the angle of elbow extension between motor units from each head. These differences indicate meaningful variation between motor units within and across motor pools, and may reflect the somewhat distinct joint actions of the two heads of triceps.

Strengths:

The extraction of MU spike timing for many individual units is an exciting new method that has great promise for exposing the fine detail in muscle activation and its control by the motor system. In particular, the methods developed by the authors for this purpose seem to be the only way to reliably resolve single MUs in the mouse, as the methods used previously in humans and in monkeys (e.g. Marshall et al. Nature Neuroscience, 2022) do not seem readily adaptable for use in rodents.

The paper provides a number of interesting observations. There are signs of interesting differences in MU activation profiles for individual muscles here, consistent with those shown by Marshall et al. It is also nice to see fine scale differences in the activation of different muscle heads, which could relate to their partially distinct functions. The mouse offers greater opportunities for understanding the control of these distinct functions, compared to the other organisms in which functional differences between heads have previously been described.

The Discussion is very thorough, providing a very nice recounting of a great deal of relevant previous results.

Weaknesses:

The findings are limited to one pair of muscle heads. While the findings are important in their own right, the lack of confirmation from analysis of other muscles acting at other joints leaves the generalization of these findings unclear.

While differences between muscle heads with somewhat distinct functions are interesting and relevant to joint control, differences between MUs for individual muscles, like those in Marshall et al., are more striking because they cannot be attributed potentially to differences in each head's function. The present manuscript does show some signs of differences for MUs within individual heads (e.g. Figure 2C), but the manuscript falls short of providing a statistical basis for the existence of distinct subpopulations.

Reviewer #1 (Public review):

Summary:

Mazer & Yovel 2025 dissect the inverse problem of how echolocators in groups manage to navigate their surroundings despite intense jamming using computational simulations.

The authors show that despite the 'noisy' sensory environments that echolocating groups present, agents can still access some amount of echo-related information and use it to navigate their local environment. It is known that echolocating bats have strong small and large-scale spatial memory that plays an important role for individuals. The results from this paper also point to the potential importance of an even lower-level, short-term role of memory in the form of echo 'integration' across multiple calls, despite the unpredictability of echo detection in groups. The paper generates a useful basis to think about the mechanisms in echolocating groups for experimental investigations too.

Strengths:

The paper builds on biologically well-motivated and parametrised 2D acoustics and sensory simulation setup to investigate the various key parameters of interest

The 'null-model' of echolocators not being able to tell apart objects & conspecifics while echolocating still shows agents successfully emerge from groups - even though the probability of emergence drops severely in comparison to cognitively more 'capable' agents. This is nonetheless an important result showing the direction-of-arrival of a sound itself is the 'minimum' set of ingredients needed for echolocators navigating their environment.

The results generate an important basis in unraveling how agents may navigate in sensorially noisy environments with a lot of irrelevant and very few relevant cues.

The 2D simulation framework is simple and computationally tractable enough to perform multiple runs to investigate many variables - while also remaining true to the aim of the investigation.

Reviewer #1 (Public review):

The key discovery of the manuscript is that the authors found that genetically wild type females descended from Khdc3 mutants shows abnormal gene expression relating to hepatic metabolism, which persist over multiple generations and pass through both female and male lineages. They also find dysregulation of hepatically-metabolized molecules in the blood of these wild type mice with Khdc3 mutant ancestry. These data provide solid evidence further support that phenotype can be transmitted to multiple generations without altering DNA sequence, supporting the involvement of epigenetic mechanisms. The authors further performed exploratory studies on the small RNA profiles in the oocytes of Khdc3-null females, and their wild type descendants, suggesting that altered small RNA expression could be a contributor of the observed phenotype transmission, although this has not been functionally validated.

Comments on revisions:

My previous comments are addressed.

Reviewer #1 (Public review):

Summary:

This paper describes a number of alterations in pulmonary surfactant recovered from bottlenosed dolphins. Although the sample consists of only seven diseased and two control animals, due to the difficulty in obtaining these animals, this is considered adequate. However, conclusions must be considered in view of this small sample size. The authors employ a number of sophisticated techniques to show differences in the composition and in the structure of bilayers formed by these two surfactant samples

Strengths:

The availability of these samples makes this study quite original. The authors apply mass spectroscopy to observe an increase of an acidic phospholipid and in the level of plasmalogens in the diseased (i.e. pneumonia) aquatic animals. They suggest these increases contribute to hampered function in vivo. They show alterations in lipid bilayers formed from lipid extracts of these surfactants by electron microscopy, by Atomic Force Microscopy and by small and wide-angle X-ray scattering -SAXS/WAXS. They have previously shown that adding small amounts of cardiolin to the clinical surfactant BLES results in altered bilayer structure, consistent with the current study.

Weaknesses:

It seems surprising to me that the small changes in cardiolipin can alter surfactant function i.e., reducing surface tension to near zero. As it happens, no surfactant function tests monitoring the reduction in surface tension were conducted. This would add a great deal to the paper. Further, the paper would benefit greatly from the inclusion of a table listing the lipid composition of surfactant recovered from diseased and normal animals and comparing this to the composition of BLES, a clinical surfactant. Finally, there is a possibility that the minor lipid identified by mass spec is the lysosomal marker, bis-(monoacylglcerol)phosphate rather than the metachronal marker, cardiolipin.

Reviewer #1 (Public review):

Summary:

This manuscript presents an ambitious attempt to examine whether episodic memory traces ("engrams") of forgotten associations persist in the human brain and whether these traces continue to influence behavior implicitly. Using 7T fMRI, the authors track 96 one-shot face-object associations across learning, 30-minute retrieval, and 24-hour retrieval, complemented by a recognition test. Participants classify each memory as sure, unsure, or guess, enabling an operational dissociation between consciously accessible and inaccessible memories.

Strengths:

The study addresses a timely and theoretically important question arising from rodent engram research, i.e., whether forgotten human memories leave detectable neural signatures. The use of high-resolution 7T fMRI, representational similarity analysis (RSA), and gPPI connectivity analyses aims at a detailed systems-level perspective. The results suggest that correct guess responses (i.e., when participants believe they are guessing) are accompanied by hippocampal activity and connectivity patterns that correlate with behavioral performance, potentially pointing to residual memory traces. The study also presents evidence for divergent consolidation trajectories: consciously accessible memories become more neocortically distributed after sleep, whereas inaccessible memories exhibit strengthened hippocampal signatures.

Weaknesses:

Despite the methodological rigor, some interpretational issues merit caution. First, the reliance on participants' subjective "guess" reports to categorize trials as forgotten is problematic. Guess responses at the 30-minute retrieval were at chance level, whereas guess responses during recognition were above chance; interpreting both as "implicit episodic memory" may conflate different mechanisms (episodic retrieval, familiarity, associative priming).

Second, several analyses raise concerns about circularity or insufficient independence, for example, when contrasting correct vs. incorrect guess trials to locate "engram" activity and then correlating that activity with guessing accuracy. Similarly, the behavioral analyses are fragmented (multiple t-tests across conditions) rather than using a factorial model that accounts for dependencies among confidence levels and timepoints.

Third, the choice to include only "sure" and "guess" responses discards a substantial portion of trials ("unsure"), reducing power and complicating interpretation, especially given that unsure responses show above-chance performance.

Finally, the study's two-scanner-sequence design (small-FOV vs. whole-brain) is challenging as it complicates comparisons across analyses, especially when some critical results (e.g., hippocampal reinstatement patterns) do not consistently replicate across sequences.

Conclusion:

Overall, the manuscript provides preliminary evidence that neural traces of forgotten episodic memories might persist in humans and could guide behavior in the absence of conscious awareness. While interpretational caution is warranted, especially regarding the nature of "guess"-based retrieval and the independence of neural contrasts, the study makes a valuable contribution to debates on engram persistence, systems consolidation, and the role of consciousness in episodic memory.

Reviewer #1 (Public review):

Summary:

This study extends the short-term synaptic plasticity (STP)-based theory of activity-silent working memory (WM) by introducing a physiological mechanism for chunking that relies on synaptic augmentation (SA) and specialized chunking clusters. The model consists of a recurrent neural network comprising excitatory clusters representing individual items and a global inhibitory pool. The self-connections within each cluster dynamically evolve through the combined effects of STP and SA. When a chunking cue, such as a brief pause in a stimulus sequence, is presented, the chunking cluster transiently suppresses the activity of the item clusters, enabling the grouped items to be maintained as a coherent unit and subsequently reactivated in sequence. This mechanism allows the network to enhance its effective memory capacity without exceeding the number of simultaneously active clusters, which defines the basic capacity. They further derive a new upper limit of WM capacity, the new magic number. When the basic capacity is four, the upper bound for complete recall becomes eight, and the optimal hierarchical structure corresponds to a binary tree of two-item pairs forming four chunks that combine into two meta-chunks. Reanalysis of linguistic data and single-neuron recordings from human epilepsy patients (identifying boundary neurons) provides qualitative support for the model's predictions.

Strengths:

This study makes an important contribution to theoretical and computational neuroscience by proposing a physiologically grounded mechanism for chunking based on STP and SA. By embedding these processes in a recurrent neural network, the authors provide a unified account of how chunks can be formed, maintained, and sequentially retrieved through local circuit dynamics, rather than through top-down cognitive strategies. The work is conceptually original, analytically rigorous, and clearly presented, deriving a simple yet powerful capacity law that extends the classical magic number framework from four to eight items under hierarchical chunking. The modeling results are further supported by preliminary empirical evidence from linguistic data and single-neuron recordings in the human medial temporal lobe, lending credibility to the proposed mechanism. Overall, this is a well-designed and well-written study that offers novel insights into the neural basis of working-memory capacity and establishes a solid bridge between theoretical modeling and experimental findings.

Weaknesses:

This study is conceptually strong and provides an elegant theoretical framework, but several aspects limit its biological and empirical grounding.

First, the control mechanism that triggers and suppresses chunking clusters remains only schematically defined. The model assumes that chunking events are initiated by pauses, prosodic cues, or internal control signals, but does not specify the underlying neural circuits (e.g., prefrontal-basal ganglia loops) that could mediate this gating in the brain. Clarifying where, when, and how the chunking clusters are turned on and off will be critical for establishing biological plausibility.

Second, the network representation is simplified: item clusters are treated as non-overlapping and homogeneous, whereas real cortical circuits exhibit overlapping representations, distinct excitatory/inhibitory populations, and multiscale local and long-range connectivity. It remains unclear how robust the proposed dynamics and derived capacity limit would be under such biologically realistic conditions.

Third, the model heavily relies on SA operating over a timescale of several seconds, yet in vivo, the time constants and prevalence of SA can vary widely across cortical regions and neuromodulatory states. The stability of the predicted "new magic number" under realistic noise levels and modulatory influences, therefore, needs to be systematically evaluated.

Reviewer #1 (Public review):

Summary:

This study addresses the encoding of forelimb movement parameters using a reach-to-grasp task in mice. The authors use a modified version of the water-reaching paradigm developed by Galinanes and Huber. Two-photon calcium imaging was then performed with GCaMP6f to measure activity across both the contralateral caudal forelimb area (CFA) and the forelimb portion of primary somatosensory cortex (fS1) as mice perform the reaching behavior. Established methods were used to extract the activity of imaged neurons in layer 2/3, including methods for deconvolving the calcium indicator's response function from fluorescence time series. Video-based limb tracking was performed to track the positions of several sites on the forelimb during reaching and extract numerous low-level (joint angle) and high-level (reach direction) parameters. The authors find substantial encoding of parameters for both the proximal and distal parts of the limb across both CFA and fS1, with individual neurons showing heterogeneous parameter encoding. Limb movement can be decoded similarly well from both CFA and fS1, though CFA activity enables decoding of reach direction earlier and for a more extended duration than fS1 activity. Collectively, these results indicate involvement of a broadly distributed sensorimotor region in mouse cortex in determining low-level features of limb movement during reach-to-grasp.

Strengths:

The technical approach is of very high quality. In particular, the decoding methods are well designed and rigorous. The use of partial correlations to distinguish correlation between cortical activity and either proximal or distal limb parameters or either low- or high-level movement parameters was very nice. The limb tracking was also of extremely high quality, and critical here to revealing the richness of distal limb movement during task performance.

The task itself also reflects an important extension of the original work by Galinanes and Huber. The demonstration of a clear, trackable grasp component in a paradigm where mice will perform hundreds of trials per day expands the experimental opportunities for the field. This is an exciting development.

The findings here are important and the support for them is solid. The work represents an important step forward toward understanding the cortical origins of limb control signals. One can imagine numerous extensions of this work to address basic questions that have not been reachable in other model systems.

Collectively, these strengths made this manuscript a pleasure to read and review.

Reviewer #1 (Public review):

Wang et al. studied an old, still unresolved problem: Why are reaching movements often biased? Using data from a set of new experiments and from earlier studies, they identified how the bias in reach direction varies with movement direction and movement extent, and how this depends on factors such as the hand used, the presence of visual feedback, the size and location of the workspace, the visibility of the start position and implicit sensorimotor adaptation. They then examined whether a target bias, a proprioceptive bias, a bias in the transformation from visual to proprioceptive coordinates and/or biomechanical factors could explain the observed patterns of biases. The authors conclude that biases are best explained by a combination of transformation and target biases.

A strength of this study is that it used a wide range of experimental conditions with also a high resolution of movement directions and large numbers of participants, which produced a much more complete picture of the factors determining movement biases than previous studies did. The study used an original, powerful and elegant method to distinguish between the various possible origins of motor bias, based on the number of peaks in the motor bias plotted as a function of movement direction. The biomechanical explanation of motor biases could not be tested in this way, but this explanation was excluded in a different way using data on implicit sensorimotor adaptation. This was also an elegant method as it allowed the authors to test biomechanical explanations without the need to commit to a certain biomechanical cost function.

Overall, the authors have done a good job mapping out reaching biases in a wide range of conditions, revealing new patterns in one of the most basic tasks, and the evidence for the proposed origins is convincing. The study will likely have substantial impact on the field, as the approach taken is easily applicable to other experimental conditions. As such, the study can spark future research on the origin of reaching biases.

Comments on revisions:

The authors have addressed my concerns convincingly. The inclusion of the data on movement extent, and the comparison with the data and explanation of Gordon et al. (1994), has strengthened the paper, as it shows that the proposed model can also explain biases in movement extent. I also appreciate the addition of the mathematical analysis, although I suspect that this analysis can be developed further to yield more detailed insights into the conditions under which the 1-, 2- and 4-peaked patterns arise, but that is a more suitable question for follow-up work.

Reviewer #1 (Public review):

In this study, the authors explore the implications of two types of rhythmic inhibition - "gamma" (30-80 Hz) and "beta"(13-30Hz) - for synaptic integration. They study this in a multi-compartmental model L5 pyramidal neuron with Poisson excitation and rhythmic inhibition (16 Hz and 64 Hz), applied either to the perisomatic or apical tuft regions in the neuron. They find that 64 Hz inhibition applied to the cell body is effective in phasic modulation of AP generation, while 16 Hz inhibition applied to the apical tufts is effective in phasic modulation of dendritic spikes (in addition to APs). Switching the location of the two kinds of rhythmic inhibition reduces the overall excitability, but is not effective in phasic modulation of either dendritic spikes and weakly so for somatic APs.

Strengths:

The effect of the timescale of rhythmic inhibition on synaptic integration is an interesting question, since a) rhythmic spiking is most strongly evident in inhibitory population, b) rhythmic spiking is modulated by behavioral states and the sensory environment. The methods are clear and data are well-presented. The study systematically explores the effect of two frequencies of rhythmic inhibition in a biophysically detailed model. The study considers not only idealized rhythmic inhibition but also the bursty kind that is observed in in-vivo conditions. Both distributed and clustered excitatory synaptic organization are simulated, which covers the two extremes of the spatial organization of excitatory inputs in-vivo.

Reviewer #1 (Public review):

Summary:

The authors investigate the determinants of population-level cell size variability, quantified via the coefficient of variation, in budding yeast populations. Using a combination of computational modeling and experimental readouts, they conclude that mother-daughter division asymmetry is the dominant factor shaping the coefficient of variation of cell size. In particular, through parameter sensitivity analysis of the Chandler-Brown model and empirical perturbations, the authors show that size-control mutations have limited effects on CV, whereas modulating mother-daughter asymmetry, by changing the growth environment, produces substantially larger shifts.

Strengths:

(1) The study addresses a fundamental question in biophysics, i.e., what are the mechanisms that produce and maintain population size heterogeneity?

(2) It provides a conceptual reconciliation for previous observations that size-control mutants often alter mean size but not CV.

(3) The modeling framework is clearly explained and compared to the data.

(4) The parameter sensitivity analysis is thoughtfully performed and provides transparent intuition about which parameters influence variability.

(5) The writing is clear, and the figures are well-organized.

Weaknesses:

(1) The work focuses on the Chandler-Brown model, so it is not clear to what extent the conclusions depend on it. A sensitivity or robustness check using an alternative model would strengthen generality.

(2) CV is the sole descriptor used to quantify heterogeneity; while this is an efficient descriptor, it must be handled with care when used on experimental data, as it may vary due to differences in the chosen observables (e.g., if size is identified via cell volume, length, area, number of proteins, etc.) instead of real differences in the distribution.

(3) The experimental validation using varied nutrient conditions is interesting; however, the statistical significance of the found correlations should be provided/discussed.

Reviewer #1 (Public review):

Summary:

The Drosophila wing disc is an epithelial tissue which study has provided many insights into the genetic regulation of organ patterning and growth. One fundamental aspect of wing development is the positioning of the wing primordia, which occurs at the confluence of two developmental boundaries, the anterior-posterior and the dorsal-ventral. The dorsal-ventral boundary is determined by the domain of expression of the gene apterous, which is set early in the development of the wing disc. For this reason, the regulation of apterous expression is a fundamental aspect of wing formation.

In this manuscript the authors used state of the art genomic engineering and a bottom-up approach to analyze the contribution of a 463 base pair fragment of apterous regulatory DNA. They find compelling evidence about the inner structure of this regulatory DNA and the upstream transcription factors that likely bind to this DNA to regulate apterous early expression in the Drosophila wing disc.

Strengths:

This manuscript has several strengths concerning both the experimental techniques used to address a problem of gene regulation and the relevance of the subject. To identify the mode of operation of the 463 bp enhancer, the authors use a balanced combination of different experimental approaches. First, they use bioinformatic analysis (sequence conservation and identification of transcription factors binding sites) to identify individual modules within the 463 bp enhancer. Second, they identify the functional modules through genetic analysis by generating Drosophila strains with individual deletions. Each deletion is characterized by looking at the resulting adult phenotype and also by monitoring apterous expression in the mutant wing discs. They then use a clever method to interfere in a more dynamic manner with the function of the enhancer, by directing the expression of catalytically inactive Cas9 to specific regions of this DNA. Finally, they recur to a more classical genetic approach to uncover the relevance of candidate transcription factors, some of them previously know and other suggested by the bioinformatic analysis of the 463 bp sequence. This workflow is clearly reflected in the manuscript, and constitute a great example of how to proceed experimentally in the analysis of regulatory DNA.

Weaknesses:

The previously pointed weakness (vg expression, P compartment specific effects, early vs late analysis of ap expression in mutants) have been throughly and satisfactorily addressed by the authors.

Reviewer #1 (Public review):

Summary:

I read the paper by Parrotta et al with great interest. The authors are asking an interesting and important question regarding pain perception, which is derived from predictive processing accounts of brain function. They ask: If the brain indeed integrates information coming from within the body (interoceptive information) to comprise predictions about the expected incoming input and how to respond to it, could we provide false interoceptive information to modulate its predictions, and subsequently alter the perception of such input? To test this question, they use pain as the input and the sounds of heartbeats (falsified or accurate) as the interoceptive signal.

Strengths:

I found the question well-established, interesting and important, with important implications and contributions for several fields, including neuroscience of prediction-perception and pain research. The study is clearly written, the methods are generally adequate, and the results indeed support the claim that false cardiac feedback modulates both pain perception and anticipatory cardiac frequency. Importantly, the authors include a control experiment using exteroceptive auditory feedback to test whether effects are specific to heartbeat-like cues. This addition substantially strengthens interpretability.

Weaknesses:

In my view, the authors' central interpretation, namely that the effects arise because the manipulation targets interoceptive rather than exteroceptive or high-level threat-related cues, cannot be fully supported by the current design. The evidence does not rule out the possibility that participants interpret increased heartbeat sounds as a generic danger/threat cue rather than as (manipulated) interoceptive input. I also disagree with several other claims, though they are less critical, for example, that the use of specific comparisons without pre-registering them, the use of sensitivity analysis to justify sample size, and the intentional use of only 6 trials per participant.

Conclusion:

To conclude, the authors have shown in their findings that predictions about an upcoming aversive (pain) stimulus - and its subsequent subjective perception - can be altered not only by external expectations, or manipulating the pain cue, as was done in studies so far, but also by manipulating a cue that has fundamental importance to human physiological status, namely heartbeats. Whether this is a manipulation of actual interoception as sensed by the brain is, in my view, left to be proven.

Even if the authors drop this claim, the paper has important implications in several fields of science, ranging from neuroscience prediction-perception research, to pain research, and may have implications for clinical disorders, as the authors propose. Furthermore, it may lead - either the authors or someone else - to further test this interesting question of manipulation of interoception in a different or more controlled manner.

I salute the authors for coming up with this interesting question and encourage them to continue and explore ways to study it and related follow-up questions.

Reviewer #1 (Public review):

Summary:

This study was designed to manipulate and analyze the effects of chemosensory cues on visuomotor control. They approach this by analyzing how eye-body coordination and brain-wide activity are altered with specific chemosensation in larval zebrafish. After analyzing the dynamics of coupled saccade-tail coordination sequences - directionally linked and typically coupled to body turns - the authors investigated the effects of sensory cues shown to be either aversive or appetitive on freely swimming zebrafish on the eye-body coordination. Aversive chemicals lead to an increase in saccade-tail sequences in both number and dynamics, seemingly facilitating behaviors like escape. Brain-wide imaging led the authors to neurons in the telencephalic pallium as a target to study eye-body coordination. Pallium neuron activity correlated with both aversive chemicals and coupled saccade-tail movements.

Recommendations for improvement are minimal. So much of the data is ultimately tabular, and the figures are an impenetrable wall of datapoints. 1c is an excellent example: three concentrations are presented, but it's rare for the three averages to trend appropriately. The key point, which is that aversive odors are repulsive and attractive odors (sometimes) attractive just gets lost in showing the three concentrations individually; it also makes direct comparisons impossible. There are similar challenges abound in the violin plots in 4e-4h, the error bars on the "fits" in 4i-4m, and so on. We recommend selecting an illustrative subset of data to present to permit interpretation and putting the rest in a supplemental table. (Presenting) less is more (effective).

Reviewer #1 (Public review):

Summary:

Witte et al. examined whether canonical behavioral functions attributed to the cerebellum decline with age. To test this, they recruited younger, old, and older-old adults in a comprehensive battery of tasks previously identified as cerebellar-dependent in the literature. Remarkably, they found that cerebellar function is largely preserved across the lifespan-and in some cases even enhanced. Structural imaging confirmed that their older adult cohort was representative in terms of both cerebellar gray- and white-matter volume. Overall, this is an important study with strong theoretical implications and convincing evidence supporting the motor reserve hypothesis, demonstrating that cerebellar-dependent measures remain largely intact with aging.

Strengths:

(1) Relatively large sample size.

(2) Most comprehensive behavioral battery to date assessing cerebellar-dependent behavior.

(3) Structural MRI confirmation of age-related decline in cerebellar gray and white matter, ensuring representativeness of the sample.

Weaknesses:

(1) Although the authors note this was outside the study's scope, the absence of a voxel-based morphometry (VBM) analysis limits anatomical and functional specificity. Such an analysis would clarify which functions are cerebellar-dependent rather than solely inferring this from prior neuropsychological literature.

(2) As acknowledged in the Discussion, task classification (cerebellar-dependent vs. general measures) remains somewhat ambiguous. Some "general" measures may still rely on cerebellar processes based on the paper's own criteria - for example, tasks in which individuals with cerebellar degeneration show impairments.

(3) Cerebellar-dependent and general measures may inherently differ in measurement noise, potentially biasing results toward detecting effects in general measures but not in cerebellar-dependent ones.

Reviewer #1 (Public review):

Summary

Wang et al. address the challenge of tracking goal-relevant visual signals amidst distractions, a fundamental aspect of adaptive visual information processing. By employing functional magnetic resonance spectroscopy (fMRS) during a visual tracking task, they quantify changes in both inhibitory (GABA) and excitatory (glutamate) neurotransmitter concentrations in the parietal and visual cortices. The results reveal that increases in GABA and glutamate in the parietal cortex are closely tied to the number of targets, and individual differences in GABAergic and glutamatergic responses within the parietal cortex predict tracking performance and distractor suppression. These findings underscore a neural mechanism in which GABAergic inhibition in the parietal cortex actively suppresses goal-irrelevant distractors, thereby facilitating goal-directed visual tracking and highlighting the dynamic role of these key metabolites in cognitive control during visual processing. I found the study to be well-written and thoughtful from an experimental standpoint, although it would benefit from some targeted revisions.

Strengths

(1) The study employs robust and validated fMRS methodology, allowing for real-time monitoring of metabolite changes during goal-directed tasks.

(2) Simultaneous measurement of both GABA and Glx in parietal and visual cortices yields nuanced insights into the neurochemical correlates of visual attention.

(3) The link between neurochemical changes and behavioral performance is clearly established, providing strong evidence for GABAergic involvement in distractor suppression.

(4) Experimental protocols align with current standards for MEGA-PRESS, bolstering the technical reliability of the findings.

Weaknesses

(1) Certain aspects of terminology, methodological reporting, and confound management are inconsistently described throughout the manuscript.

(2) Important confounding factors are not systematically reported or controlled.

(3) Opportunities for additional analysis (e.g., behavioral dynamics, use of alternate fitting methods, more comprehensive quality metrics) have not been fully explored.

(4) Open access data and/or codes for the analysis are not shared in the main manuscript

Reviewer #1 (Public review):

This is a highly original and impactful study that significantly advances our understanding of transcriptional regulation, in particular RNAPII pausing, during early heart development. The Chen lab has a long history of producing influential studies in cardiac morphogenesis, and this manuscript represents another thorough and mechanistically insightful contribution. The authors have thoroughly addressed this Reviewer's concerns and incorporated all of my suggestions in the revised manuscript. In addition, their responses to the other reviewer's comments are also very clear. As it is, this work is of great interest to the readership of Elife, as well as to the general scientific community.

The authors reveal a fundamentally new role for Rtf1-a component of the PAF1 complex-in governing promoter-proximal RNAPII pausing in the context of myocardial lineage specification. While transcriptional pausing has been implicated in stress responses and inducible gene programs, its developmental relevance has remained poorly defined. This study fills that gap with rigorous in vivo evidence demonstrating that Rtf1-dependent pausing is indispensable for activating the cardiac gene program from the lateral plate mesoderm.

Importantly, the study also provides compelling therapeutic implications. Showing that CDK9 inhibition-using either flavopiridol or targeted knockdown-can restore promoter-proximal pausing and rescue cardiomyocyte formation in Rtf1-deficient embryos suggests that modulation of pause-release kinetics may represent a new avenue for correcting transcriptionally driven congenital heart defects. Given that many CDK inhibitors are clinically approved or in active development, this connection significantly elevates the translational impact of the findings.

In sum, this study is rigorous, innovative, and transformative in its implications for developmental biology and cardiac medicine. I strongly support its publication.

Reviewer #1 (Public review):

Summary:

Here, the authors are proposing a role for miR-196, a microRNA that has been shown to bind and enhance degradation of mRNA targets in the regulation of cell processes, has a novel role in allowing the emergence of CD19+ cells in cells in which Ebf1, a critical B-cell transcription factor, has been genetically removed.

Strengths:

That over-expression of mR-195 can allow the emergence of CD19+ cells missing Ebf1 is somewhat novel.

Their data does perhaps support to a degree the emergence of a transcriptional network that may bypass the absence of Ebf1, including the FOXO1 transcription factor, but this data is not strong or definitive.

Weaknesses:

It is unclear whether this observation is in fact physiological. When the authors analyse a knockout model of miR-195, there is not much of a change in the B-cell phenotype. Their findings may therefore be an artefact of an overexpression system.

The authors have provided insufficient data to allow a thorough appraisal of the step-wise molecular changes that could account for their observed phenotype.

On review of the resubmitted manuscript, while I note the authors have attempted to address several of my comments, unfortunately, their resubmission is not sufficient to address several of the comments I had previously made.

In particular, in the resubmitted data that includes western blots for PAX5 and ERG in their EBF1-/- model, Supp Fig S3, the bands they show infer that that PAX5 and ERG expression can still be significantly detected in their EBF1-/- early B-cell model. This should not be the case, as no expression of PAX5 or ERG should be seen, as has been shown in prior literature.

Reviewer #1 (Public review):

Summary:

Rahmani et al. utilize the TurboID method to characterize global proteome changes in the worm's nervous system induced by a salt-based associative learning paradigm. Altogether, they uncover 706 proteins tagged by the TurboID method in worms that underwent the memory-inducing protocol. Next, the authors conduct a gene enrichment analysis that implicates specific molecular pathways in salt-associative learning, such as MAP kinase and cAMP-mediated pathways, as well as specific neuronal classes including pharyngeal neurons, and specific sensory neurons, interneurons, and motor neurons. The authors then screen a representative group of hits from the proteome analysis. They find that mutants of candidate genes from the MAP kinase pathway, namely dlk-1 and uev-3, do not affect performance in the learning paradigm. Instead, multiple acetylcholine signaling mutants, as well as a protein-kinase-A mutant, significantly affected performance in the associative memory assay (e.g., acc-1, acc-3, lgc-46, and kin-2). Finally, the authors demonstrate that protein-kinase-A mutants, as well as acetylcholine signaling mutants, do not exhibit a phenotype in a related but distinct conditioning paradigm-aversive salt conditioning-suggesting their effect is specific to appetitive salt conditioning.

Overall, the authors addressed the concerns raised in the previous review round, including the statistics of the chemotaxis experiments and the systems-level analysis of the neuron class expression patterns of their hits. I also appreciate the further attempt to equalize the sample size of the chemotaxis experiments and the transparent reporting of the sample size and statistics in the figure captions and Table S9. The new results from the panneuronal overexpression of the kin-2 gain-of-function allele also contribute to the manuscript. Together, these make the paper more compelling.

Reviewer #1 (Public review):

Summary:

In this manuscript, Bisht et al. investigate the role of PPE2, a Mycobacterium tuberculosis (Mtb) secreted virulence factor, in adipose tissue physiology during tuberculosis (TB) infection. Previous work by this group established the significance of PPE proteins in Mtb virulence and their role in modulating the innate immune response. Here, the authors present compelling evidence that PPE2 regulates host cell adipogenesis and lipolysis, thereby establishing a link to the development of insulin resistance during TB infection. These fundamental findings demonstrate, for the first time, that a bacterial virulence factor is directly involved in the profound body fat loss, or "wasting," which is a long-established clinical symptom of active TB.

Key Strengths:

The confidence in the major findings of this study is significantly strengthened by the authors' comprehensive approach. They judiciously employ multiple experimental systems, including:

(1) Purified PPE2 protein.

(2) A non-pathogenic Mycobacterium strain engineered to express PPE2.

(3) A pathogenic clinical Mtb strain (CDC1551) utilizing a targeted PPE2 deletion mutant.

(4) While the presence of Mtb in adipose tissues in human and animal models is well-documented, this study is groundbreaking in demonstrating that an Mtb virulence-associated factor actively modulates host fatty acid metabolism within the adipose tissue.

Key Weakness:

Although the manuscript provides solid evidence associating the presence of PPE2 with transcriptional changes in host fatty acid machinery within the adipose tissue, the underlying mechanistic details remain elusive. A focused, deep mechanistic follow-up study will be essential to fully appreciate the complex biological implications of the findings reported here.

Reviewer #1 (Public review):

Summary:

Syed et al. investigate the circuit underpinnings for leg grooming in the fruit fly. They identify two populations of local interneurons in the right front leg neuromere of ventral nerve cord, i.e. 62 13A neurons and 64 13B neurons. Hierarchical clustering analysis identifies each 10 morphological classes for both populations. Connectome analysis reveals their circuit interactions: these GABAergic interneurons provide synaptic inhibition either between the two subpopulations, i.e. 13B onto 13A, or among each other, i.e. 13As onto other 13As, and/or onto leg motoneurons, i.e. 13As and 13Bs onto leg motoneurons. Interestingly, 13A interneurons fall into two categories with one providing inhibition onto a broad group of motoneurons, being called "generalists", while others project to few motoneurons only, being called "specialists". Optogenetic activation and silencing of both subsets strongly effects leg grooming. As well activating or silencing subpopulations, i.e. 3 to 6 elements of the 13A and 13B groups has marked effects on leg grooming, including frequency and joint positions and even interrupting leg grooming. The authors present a computational model with the four circuit motifs found, i.e. feed-forward inhibition, disinhibition, reciprocal inhibition and redundant inhibition. This model can reproduce relevant aspects of the grooming behavior.

Strengths:

The authors succeeded in providing evidence for neural circuits interacting by means of synaptic inhibition to play an important role in the generation of a fast rhythmic insect motor behavior, i.e. grooming of the body using legs. Two populations of local interneurons in the fruit fly VNC comprise four inhibitory circuit motifs of neural action and interaction: feed-forward inhibition, disinhibition, reciprocal inhibition and redundant inhibition. Connectome analysis identifies the similarities and differences between individual members of the two interneuron populations. Modulating the activity of small subsets of these interneuron populations markedly affects generation of grooming behavior thereby exemplifying their relevance. The authors carefully discuss strengths and limitations of their approaches and place their findings into the broader context of motor control.

Weaknesses:

Effects of modulating activity in the interneuron populations by means of optogenetics were conducted in the so-called "closed-loop" condition. This does not allow to differentiate between direct and secondary effects of the experimental modification in neural activity, as feedforward and feedback effects cannot be disentangled. To do so open loop experiments, e.g. in deafferented conditions, would be needed. Given that many members of the two populations of interneurons do not show one, but two or more circuit motifs, it remains to be disentangled which role the individual circuit motif plays in the generation of the motor behavior in intact animals.

Comments on revisions:

The authors have carefully revised the manuscript. I have no further suggestions or criticisms.

Reviewer #1 (Public review):

Summary:

The authors assess the impact of E-cigarette smoke exposure on mouse lungs using single-cell RNA sequencing. Air was used as control and several flavors (fruit, menthol, tobacco) were tested. Differentially expressed genes (DEGs) were identified for each group and compared against the air control. Changes in gene expression in either myeloid or lymphoid cells were identified for each flavor and the results varied by sex. The scRNAseq dataset will be of interest to the lung immunity and e-cig research communities, and some of the observed effects could be important. Unfortunately, the revision did not address the reviewers' main concerns about low replicate numbers and lack of validations. The study remains preliminary and no solid conclusions could be drawn about the effects of E-cig exposure as a whole or any flavor-specific phenotypes.

Strengths:

The study is the first to use scRNAseq to systematically analyze the impact of e-cigarettes on the lung. The dataset will be of broad interest.

Weaknesses:

This study had only N=1 biological replicates for the single-cell sequencing data per sex per group and some sex-dependent effects were observed. This could have been remedied by validating key observations from the study using traditional methods such as flow cytometry and qPCR, but the limited number of validation experiments did not support the conclusions of the scRNAseq analysis. An important control group (PG:VG) had extremely low cell numbers and therefore could not be used to derive meaningful conclusions. Statistical analysis is lacking in almost all figures. Overall, this is a preliminary study with some potentially interesting observations.

(1) The only new validation experiment for this revision is the immunofluorescent staining of neutrophils in Figure 4. The images are very low resolution and low quality and it is not clear which cells are neutrophils. S100A8 (calprotectin) is highly abundant in neutrophils but not strictly neutrophil-specific. It's hard to distinguish positive cells from autofluorescence in both ly6g and S100a8 channels. No statistical analysis is presented for the quantified data from this experiment.

(2) The relevance of Fig. 3A and B are unclear since these numbers only reflect the number of cells captured in the scRNAseq experiment and the biological meaning of this data is not explained. Flow cytometry quantification is presented as cell counts but percentage of cells from the CD45+ gate should be shown. No statistical analysis is shown, and flow cytometry results do not support the conclusions of scRNAseq data.

Reviewer #1 (Public review):

IBEX Knowledge Database

Here, Yanid Z. and colleagues present the IBEX knowledge base. A community tool developed to centralize knowledge and help its adoption by more users. Authors have done a fantastic job, and there is careful consideration of the many aspects of the data management and FAIR principles. The manuscript needs no further work, as it is very well written and have detailed descriptions for data contribution as well as describing the KB itself. Overall, it is a great initiative, especially the aim to inform about negative data and non-recommended reagents, which will positively affect the user community and scientific reproducibility.

This initiative will serve as a groundwork to include technical details of other multiple immunofluoresecence methods (such as immunoSABER, 4i, etc). Including other methods would help the knowledge base itself and related methods to evolve and assist their communities in the future.

Significant care has been taken to allow the report of negative data. While there might be limitations as to how this information is included, transparency and community usage will ensure the knowledge base offers a fair representation.

There are two ways to contribute to the knowledge base. While authors have contributed significantly to its creation, it will be the role of the maintainers to assist potential users and contributors. It is specially appreciated that a path to contribute is possible with no coding skills. I am keen to see how the KB evolves and it helps disseminate the use of this and other great techniques.

6:22 "what I think a lot of people don't understand is, when you take all of these different datasets, and you start to overlay them on top of each other, pattern recognition, calculator brain being one of the things that I'm gifted with, is you get to the conclusions that one must draw when you start layering all the different datasets on top of each other like lasagna, is, this place is going to shit, and it's going to shit pretty quickly. There's a lot of information being thrown out as far as 2027 is concerned with the timeline."

general intelligence versus special intelligence. maximum abstraction. global view. wholistic view. element fire @ alchemy. intuiting @ carl jung. role model @ Martin Gerlach 2018. communist @ hans eysenck.

Reviewer #1 (Public review):

Summary:

A central function of glial cells is the ensheathment of axons. Wrapping of larger-diameter axons involves myelin-forming glial classes (such as oligodendrocytes), whereas smaller axons are covered by non-myelin forming glial processes (such as olfactory ensheathing glia). While we have some insights into the underlying molecular mechanisms orchestrating myelination, our understanding of the signaling pathways at work in non-myelinating glia remains limited. As non-myelinating glial ensheathment of axons is highly conserved in both vertebrates and invertebrates, the nervous system of Drosophila melanogaster, and in particular the larval peripheral nerves, have emerged as powerful model to elucidate the regulation of axon ensheathment by a class of glia called wrapping glia. This study seeks to specifically address the question, as to which molecular mechanisms contribute to the regulation of the extent of glial ensheathment focusing on the interaction of wrapping glia with axons.

Strengths and Weaknesses:

For this purpose, the study combines state-of-the-art genetic approaches with high-resolution imaging, including classic electron microscopy. The genetic methods involve RNAi mediated knockdown, acute Crispr-Cas9 knock-outs and genetic epistasis approaches to manipulate gene function with the help of cell-type specific drivers. The successful use of acute Crispr-Cas9 mediated knockout tools (which required the generation of new genetic reagents for this study) will be of general interest to the Drosophila community.

The authors set out to identify new molecular determinants mediating the extent of axon wrapping in the peripheral nerves of third instar wandering Drosophila larvae. They could show that over-expressing a constitutive-active version of the Fibroblast growth factor receptor Heartless (Htl) causes an increase of wrapping glial branching, leading to the formation of swellings in nerves close to the cell body (named bulges). To identify new determinants involved in axon wrapping acting downstream of Htl, the authors next conducted an impressive large-scale genetic interaction screen (which has become rare, but remains a very powerful approach), and identified Uninflatable (Uif) in this way. Uif is a large single-pass transmembrane protein which contains a whole series of extracellular domains, including Epidermal growth factor-like domains. Linking this protein to glial branch formation is novel, as it has so far been mostly studied in the context of tracheal maturation and growth. Intriguingly, a knock-down or knock-out of uif reduces branch complexity and also suppresses htl over-expression defects. Importantly, uif over-expression causes the formation of excessive membrane stacks. Together these observations are in in line with the notion that htl may act upstream of uif.

Further epistasis experiments using this model implicated also the Notch signaling pathway as a crucial regulator of glial wrapping: reduction in Notch signaling reduces wrapping, whereas over-activation of the pathway increases axonal wrapping (but does not cause the formation of bulges). Importantly, defects caused by over-expression of uif can be suppressed by activated Notch signaling. Knock-down experiments in neurons suggest further that neither Delta nor Serrate act as neuronal ligands to activate Notch signaling in wrapping glia, whereas knock-down of Contactin, a GPI anchored Immunoglobulin domain containing protein led to reduced axon wrapping by glia, and thus could act as an activating ligand in this context.

Based on these results the authors put forward a model proposing that Uif normally suppresses Notch signaling, and that activation of Notch by Contactin leads to suppression of Htl, to trigger the ensheathment of axons. While these are intriguing propositions, future experiments will need to conclusively address whether and how Uif could "stabilize" a specific membrane domain capable to interact with specific axons.

Moreover, to obtain evidence for Uif suppression by Notch to inhibit "precocious" axon wrapping and for a "gradual increase" of Notch signaling that silences uif and htl, (1) reporters for N and Htl signaling in larvae, (2) monitoring of different stages at a time point when branch extension begins, and (3) a reagent enabling the visualization of Uif expression could be important next tools/approaches. Considering the qualitatively different phenotypes of reduced branching, compared to excessive membrane stacks close to cell bodies, it would perhaps be worthwhile to explore more deeply how membrane formation in wrapping glia is orchestrated at the subcellular level by Uif.

However, the points raised above remain at present technically difficult to address because of the lack of appropriate genetic reagents. Also more detailed electron microscopy analyses of early developmental stages and comparisons of effects on cell bodies compared to branches will be very labor-intensive, and indeed may represent a new study.

In summary, in light of the importance of correct ensheathment of axons by glia for neuronal function, the proposed model for the interactions between Htl, Uif and N to control the correct extent of neuron and glial contacts will be of general interest to the glial biology community.

Comments on revisions:

The authors have addressed all my comments. However, the sgRNAs in the Star method table are still all for cleavage just before the transmembrane domain, while the Supplemental figure suggests different locations.

Reviewer #2 (Public review):

Summary:

This paper aims to elucidate the gene regulatory network governing the development of cone photoreceptors, the light-sensing neurons responsible for high acuity and color vision in humans. The authors provide a comprehensive analysis through stage-matched comparisons of gene expression and chromatin accessibility using scRNA-seq and scATAC-seq from the cone-dominant 13-lined ground squirrel (13LGS) retina and the rod-dominant mouse retina. The abundance of cones in the 13LGS retina arises from a dominant trajectory from late retinal progenitor cells (RPCs) to photoreceptor precursors and then to cones, whereas only a small proportion of rods are generated from these precursors.

Strengths:

The paper presents intriguing insights into the gene regulatory network involved in 13LGS cone development. In particular, the authors highlight the expression of cone-promoting transcription factors such as Onecut2, Pou2f1, and Zic3 in late-stage neurogenic progenitors, which may be driven by 13LGS-specific cis-regulatory elements. The authors also characterize candidate cone-promoting genes Zic3 and Mef2C, which have been previously understudied. Overall, I found that the across-species analysis presented by this study is a useful resource for the field.

Comments on Revision:

The authors have addressed my questions, and the revised text now presents their findings more clearly.

Reviewer #2 (Public review):

Summary:

Sugimoto et al. explore the relationship between glucose dynamics-specifically value, variability, and autocorrelation-and coronary plaque vulnerability in patients with varying glucose tolerance levels. The study identifies three independent predictive factors for %NC and emphasizes the use of continuous glucose monitoring (CGM)-derived indices for coronary artery disease (CAD) risk assessment. By employing robust statistical methods and validating findings across datasets from Japan, America, and China, the authors highlight the limitations of conventional markers while proposing CGM as a novel approach for risk prediction.The study has the potential to reshape CAD risk assessment by emphasizing CGM-derived indices, aligning well with personalized medicine trends.

Further, the revised version includes expanded biological interpretation, improved statistical justification, and a new web-based calculator for clinical translation. Together, these updates make the study an important contribution to precision risk assessment in diabetes and cardiovascular research.

Strengths:

The introduction of autocorrelation as a predictive factor for plaque vulnerability adds a novel dimension to glucose dynamic analysis.

Inclusion of datasets from diverse regions enhances generalizability.

The use of a well-characterized cohort with controlled cholesterol and blood pressure levels strengthens the findings.

The focus on CGM-derived indices aligns with personalized medicine trends, showcasing potential for CAD risk stratification.

The benchmarking of CGM-derived measures against established CAD risk models (e.g., Framingham Risk Score) enhances interpretability and significance.

The addition of a web-based computational tool makes the proposed indices accessible for potential clinical and research use.

Weaknesses:

The biological mechanism linking glucose autocorrelation to plaque vulnerability, although plausibly associated with insulin clearance pathways, remains largely theoretical.

The primary cohort size is still modest, and while supported by power analysis and external datasets, broader prospective validation will be important.

Strict participant selection criteria as employed by the study may reduce applicability to broader populations.

CGM-derived indices like AC_Var and ADRR may be too complex for routine clinical use without simplified models or guidelines.

Comments on revised version:

The authors have thoroughly addressed previous concerns and produced a much stronger manuscript. The study now provides a coherent, validated, and well-reasoned argument for including autocorrelation as a third major dimension of glucose dynamics. It offers both conceptual novelty and translational potential and will likely stimulate further research on temporal glucose metrics in metabolic and cardiovascular risk assessment.

Reviewer #1 (Public review):

Summary:

Authors explore how sex-peptide (SP) affects post-mating behaviours in adult females, such as receptivity and egg laying. This study identifies different neurons in the adult brain and the VNC that become activated by SP, largely by using an intersectional gene expression approach (split-GAL4) to narrow down the specific neurons involved. They confirm that SP binds to the well-known Sex Peptide Receptor (SPR), initiating a cascade of physiological and behavioural changes related to receptivity and egg laying.

Comments on revised version:

The authors have substantially strengthened the manuscript in response to our main concerns.

In particular, they now explicitly test multiple established PMR nodes (including SAG/SPSN as well as pC1, OviDN/OviEN/OviIN and vpoDN), which helps separate direct SP targets from downstream PMR circuitry and supports their interpretation that some of these known nodes can affect receptivity without necessarily inducing oviposition. They also addressed key technical/clarity points: the requested head/trunk expression controls are provided (Suppl Fig S1), and the VT003280 annotation is corrected (now FD6 rather than "SAG driver"). Overall, these additions make the central conclusion, that distinct CNS neuron subsets ("SPRINz") are sufficient to elicit PMR components, more convincing, and the added comparisons with genital tract expressing lines further argue against a simple "periphery only" explanation.