Reviewer #1 (Public review):

This study examines how two types of RNA polymerases organize themselves within the nucleus of C. elegans cells, building directly on the same group's prior publication and largely functioning as a companion to that earlier work. While the observation that the two polymerases occupy distinct but neighboring locations at the same genomic region adds nuance to our understanding of gene cluster regulation, the manuscript would benefit from more clearly delineating which findings are new versus continuations of previously published work. Protein localization, gene expression effects, and genomic mapping data appear to overlap substantially with the earlier paper.

The condensate claims would also benefit from additional experimental support. Demonstrating fusion events and concentration-dependent assembly are now standard expectations in the field. Additionally, one measurement reported appears inconsistent with a condensate model, warranting further discussion.

Some findings would benefit from more interpretive context. Why does polymerase clustering fluctuate with the cell cycle? What are the functional implications of ATTF-6 being required for one polymerase's foci but not the others?

The elevated-temperature experiments are intriguing but difficult to interpret, as the temperature used is well-established as a broad stress trigger in this organism. Acknowledging this and considering additional controls would help clarify whether the observed effects are specific to foci behavior.

Finally, the manuscript would be strengthened by adding quantification to some figures and revising the model diagram to better reflect what the current data support.

Reviewer #1 (Public review):

Summary:

This study reports a novel and potentially impactful role for NINJ2 in maintaining lysosomal integrity and regulating cellular susceptibility to ferroptosis. The authors demonstrate that NINJ2 localizes to lysosomes and interacts with LAMP1, a key lysosomal membrane glycoprotein involved in sensing lysosomal stress. Loss of NINJ2 increases lysosomal membrane permeabilization (LMP), resulting in selective leakage of lysosomal contents, including labile iron, into the cytosol. The authors further show that NINJ2 deficiency reduces the expression of ferritin storage proteins, thereby sensitizing cells to ferroptosis induced by RSL3 and erastin. Collectively, the work proposes a mechanistic link between NINJ2-mediated control of LMP, iron homeostasis, and ferroptotic vulnerability, with potential relevance to cancer biology.

Strengths:

This study identifies a novel role for NINJ2 in regulating lysosomal integrity and ferroptosis and establishes a mechanistic link between lysosomal membrane permeabilization, iron homeostasis, and ferroptotic sensitivity, with potential translational relevance in cancer.

Weaknesses:

The results overall support the authors' conclusions and provide a plausible mechanistic framework; however, additional quantification of Western blot data and further discussion of mechanistic questions would strengthen the study.

The findings are likely to have a broad impact by linking lysosomal integrity to ferroptosis and iron homeostasis, both of which are relevant to cancer biology and therapeutic targeting.

Reviewer #1 (Public review):

Summary:

This study aims to test whether human mate choice is influenced by HLA similarity while accounting for genome-wide relatedness, using the Himba as an evolutionarily relevant small-scale society population, unique among most HLA-mate choice studies. By comparing self-chosen ("love") and arranged marriages and using NGS-based 8-locus HLA class I and II sequences and genome-wide SNP data, the authors ask whether partners who freely choose each other are more HLA-dissimilar than those paired through social arrangements or random pairs. They further extend their work by examining functional differences in peptide-binding divergence among pairs and predicted pathogen recognition in potential offspring.

Strengths:

This study has many strengths. The most obvious is their ability to test for HLA-based mate choice in the Himba, a non-European, non-admixed, small-scale society population, the type of population that has been missing, in my opinion, from the majority of HLA mate choice studies. While Hedrick and Black (1997) used a similarly evolutionarily relevant remote tribe of native South Americans, they only considered 2 class I loci (HLA-A and HLA-B) at the first typing field (serological allele group) and did not have data for genome-wide relatedness. The Himba are also unique among previously studied populations because they have both socially arranged and self-chosen partnerships, so the authors could test if freely-chosen partners had lower MHC-similarity than assigned or randomly chosen partners.

Another key strength of the study was the relatively large sample size (HLA allele calls from 366 individuals, 102 unrelated) and 219 individuals with HLA data, whole genome SNP data, and involved in a partnership.

The study was also unique among HLA-mate choice studies for comparing peptide binding region protein divergence (calculated as the Grantham distance between amino acid sequences) among partner types and randomly generated pairs. This was also the first time I have seen a study use peptide binding prediction analysis of relevant human pathogens for potential offspring among partners to test if there would be a pathogen-relevant fitness benefit of partner selection.

Weaknesses:

My main concerns relate to the reliance on imputed HLA haplotypes and on IBD-based metrics in a region of the genome where both approaches are known to be problematic.

First, several key results depend on HLA haplotypes inferred through imputation rather than directly observed sequence data. The authors trained HIBAG imputation models on Himba SNP data across the full 5 Mb HLA region using paired HLA allele calls from target capture sequencing (L251-253). However, the underlying SNP data were generated by mapping reads to a 1000 Genomes Yoruba reference, meaning that both SNP discovery and subsequent imputation depend on the haplotypes represented in that reference panel. As a result, the imputation framework is likely biased toward common haplotypes shared between the Himba and Yoruba populations, while rare or Himba-specific HLA alleles are less likely to be imputed accurately or at all. This limitation has been noted previously for HLA imputation, particularly for novel or low-frequency variants and for populations that are poorly represented in reference panels. While the authors compare (first-field) imputed alleles to sequenced alleles to assess imputation accuracy, this validation step itself may be biased toward the same common haplotypes that are easiest to impute. This becomes especially problematic if IBD is inferred using imputed haplotypes, because haplotype sharing would then primarily reflect common, reference-supported haplotypes, while true population-specific variation would be effectively invisible. In this scenario, downstream estimates of IBD sharing may be inflated for common haplotypes and deflated for rare ones, potentially biasing conclusions about haplotype sharing, selection, and mate choice at the HLA region.

Second, the interpretation of excess identity-by-descent (IBD) sharing in the HLA region is difficult given the well-documented genomic properties of this locus. The classical HLA region is highly gene-dense, structurally complex, and characterized by extreme heterogeneity in recombination rates, with pronounced hot- and cold-spots (Miretti et al. 2005; de Bakker et al. 2006, reviewed in Radwan et al. 2020). Elevated IBD in such regions can arise from low recombination, background selection, or demographic processes such as bottlenecks, all of which can mimic signals of recent positive selection. While the authors suggest fluctuating or directional selection, extensive haplotype sharing is also consistent with long-term balancing selection at the MHC (Albrechtsen et al. 2010) or recent demographic history in this population.

Beyond these main issues, there are several additional concerns that affect interpretation. Sample sizes and partnership counts are sometimes unclear; some figures would benefit from clearer scaling (Figure 1) and annotation (Figures S6 and S7), and key methodological choices (e.g., treatment of DRB copy number variation, no recombination correction in IBD calling) require further explanation. Finally, some conclusions, particularly those invoking optimality or specific selective mechanisms, are not directly tested by the analyses presented and would benefit from more cautious framing.

Reviewer #1 (Public review):

Summary:

Hsiung et al. investigated whether the effects of autophagy gene knockdown on the lifespan of long-lived C. elegans mutants depend on experimental conditions. The authors first compiled published data on autophagy-dependent lifespan regulation in daf-2 and wild-type backgrounds, highlighting that prior results are notably inconsistent and likely context-dependent. They then systematically tested the lifespan effects of RNAi knockdown of six autophagy genes (atg-2, atg-4.1, atg-9, atg-13, atg-18, and bec-1) in wild-type (N2), daf-2 (reduced insulin/IGF-1 signalling), and glp-1 (germlineless) animals, while varying temperature, daf-2 allele, FUDR concentration, and bacterial infection status.

The key findings are as follows. In wild-type animals, lifespan suppression by most autophagy gene knockdowns was more pronounced at 20{degree sign}C than at 25{degree sign}C, where little or no effect was observed. In daf-2 mutants, stronger lifespan suppression was seen in the weaker daf-2(e1368) allele at 20{degree sign}C, but not in the stronger daf-2(e1370) allele, and effects were largely absent at 25{degree sign}C. In glp-1 mutants, four of six gene knockdowns suppressed lifespan to a greater extent than in N2, though again in a temperature-dependent manner. FUDR at a high concentration (800 µM) abolished the life-shortening effects of most knockdowns and, in the case of atg-9 and atg-13, led to lifespan extension. Kanamycin treatment to eliminate bacterial proliferation did not fully account for the lifespan effects, suggesting that increased susceptibility to infection is not the primary mechanism. The authors also tested the programmed aging hypothesis that autophagy promotes lifespan reduction through biomass repurposing, but found no changes in vitellogenin levels upon knockdown of any of the six genes.

Altogether, among all genes tested, atg-18 knockdown produced the strongest and most consistent lifespan suppression across nearly all conditions, including both daf-2 and glp-1 backgrounds. The authors probed whether atg-18 acts through the FOXO transcription factor DAF-16 by examining dauer formation and ftn-1 expression, but found no evidence for this, suggesting a DAF-16-independent mechanism.

Strengths:

The primary strength of this work lies in its systematic and comprehensive approach to dissecting how experimental variables influence the outcome of autophagy-lifespan epistasis tests. The compilation of prior data alongside the authors' own multi-condition dataset is a genuinely useful resource for the field. The study raises a timely and important point about condition selection bias, which is relevant not only to autophagy research but to C. elegans aging studies more broadly. The finding that atg-18 behaves distinctly from other autophagy genes across all conditions is noteworthy and opens avenues for future mechanistic work.

Weaknesses:

Despite its breadth, the study has several weaknesses that limit the strength of some conclusions.

(1) Variability in control lifespan data. The N2 lifespan values under ostensibly identical conditions (e.g., GFP RNAi at 20{degree sign}C) differ substantially across experiments (compare Tables S2, S5, S6, S7, and S9). Since N2 serves as the baseline for calculating whether the effect is greater in long-lived mutants via Cox proportional hazard (CPH) analysis, this variability in controls directly affects the reliability of those comparisons.

(2) Limited biological replication. Most experiments were performed with only two biological replicates. In several cases, the two replicates yield contradictory outcomes: one showing significant lifespan suppression and the other showing no effect or even extension. The authors combine these into cumulative datasets for analysis, which, while not incorrect in principle, may obscure genuine irreproducibility. Given that the central message of the paper concerns variability and condition dependence, additional replication would have substantially strengthened confidence in the reported results.

(3) Low sample sizes in individual trials. A number of lifespan assays were conducted with only 40-50 worms per replicate, and in some cases, as few as 30. Such sample sizes are below the standard commonly used in the C. elegans aging field and are likely to contribute to the variability observed.

(4) RNAi efficacy measured only in N2 at 20{degree sign}C. The authors demonstrated that atg-2 and atg-4.1 RNAi did not significantly reduce target mRNA levels, which may explain their weaker lifespan effects. However, these same RNAi treatments significantly affected lifespan in several other conditions (e.g., daf-2(e1368) at 20{degree sign}C, glp-1 at 20{degree sign}C and 25{degree sign}C, and N2 with 15 µM FUDR). Measuring RNAi efficacy across different genetic backgrounds and conditions would be needed to properly interpret these variable results.

(5) Incomplete mechanistic exploration. The investigation of why atg-18 knockdown has uniquely strong effects was limited to DAF-16. Given published evidence that atg-18 may regulate HLH-30/TFEB, a master transcriptional regulator of autophagy and lysosomal biogenesis, testing whether atg-18 specifically affects HLH-30 nuclear localisation or activity could have provided valuable mechanistic insight and would distinguish atg-18 from the other genes tested.

Reviewer #1 (Public review):

Summary:

The current study by Xing et al. establishes the methodology (machine vision and gaze pose estimation) and behavioral apparatus for examining social interactions between pairs of marmoset monkeys. Their results enable unrestrained social interactions under more rigorous conditions with detailed quantification of position and gaze. It has been difficult to study social interactions using artificial stimuli, as opposed to genuine interactions between unrestrained animals. This study makes an important contribution for studying social neuroscience within a laboratory setting that will be valuable to the field.

Strengths:

Marmosets are an ideal species for studying primate social interactions due to their prosocial behavior and the ease of group housing within laboratory environments. They also predominantly orient their gaze through head-movements during social monitoring. Recent advances in machine vision pose estimation set the stage for estimating 3D gaze position in marmosets but requires additional innovation beyond DeepLabCut or equivalent methods. A six point facial frame is designed to accurately fit marmoset head gaze. A key assumption in the study is that head-gaze is a reliable indicator of the marmoset's gaze direction, which will also depend on the eye position. Overall, this assumption has been well supported by recent studies in head-free marmosets. Thus the current work introduces an important methodology for leveraging machine vision to track head-gaze and demonstrates its utility for use with interacting marmoset dyads as a first step in that study.

Comments on revisions:

I thank the authors for their careful revisions of the manuscript. It has addressed all of my comments.

One final suggestion would be to add a scale bar in Supplemental Figure 2A so the size of the video/image stimuli is clear (in cm of monitor size) and also to report a range for how far away was the marmoset in viewing these stimuli (in cm). This will enable calculation of the rough accuracy in visual degrees.

Reviewer #1 (Public review):

The authors show experimentally that, in 2D, bacteria swim up a chemotactic gradient much more effectively when they are in the presence of lateral walls. Systematic experiments identify an optimum for chemotaxis for a channel width of ~8µm, a value close to the average radius of the circle trajectories of the unconfined bacteria in 2D. These chiral circles impose that the bacteria swim preferentially along the right-side wall, which indeed yields chemotaxis in the presence of a chemotactic gradient. These observations are backed by numerical simulations and a geometrical analysis.

Reviewer #2 (Public review):

Summary:

Dr Lenz and colleagues report on their in vitro studies comparing gene transcription and epigenetic modifications in Plasmodium falciparum NF54 parasites selected or not selected for adhesion of the infected erythrocytes (IEs) to the placental IE adhesion receptor chondroitin sulfate A (CSA).

The authors report that selection led to preferential transcription of var2csa, the gene that encodes the VAR2CSA-type PfEMP1 well-established as the PfEMP1 mediating IE adhesion to CSA. They confirm that transcriptional activation of var2csa is associated with distinct depletion of H3K9me3 marks and that transcriptional activation is linked to repositioning of var2csa. Finally, they provide preliminary evidence potentially implicating 5mC in transcriptional regulation of var2csa.

Strengths:

The study confirms previously reported features of gene transcription and epigenetic modifications in Plasmodium falciparum.

Weaknesses:

No major new finding is reported.

Comments on revisions:

I suggest replacing the term "pregnancy-associated malaria (PAM)" with the more current and more precise term "placental malaria (PM)" throughout the manuscript.

L. 59-60: "... shielding of the parasite antigens expressed on pRBC surfaces by leukocytes...". It is unclear to me what this means - I suggest a rephrasing for improved clarity.

L. 144-6: Please provide a reference for the primary antibody reagent used.

Reviewer #3 (Public review):

Summary:

This work investigates whether human imprecision in numeric perception is a fixed structural constraint or an endogenous property that adapts to environmental statistics and task objectives. By measuring behavioral variability across different uniform prior distributions in both estimation and discrimination tasks, the authors show that perceptual imprecision increases sublinearly with prior width. They demonstrate that the specific exponents of this scaling (1/2 for estimation and 3/4 for discrimination) can be derived from an efficient-coding model, wherein decision-makers optimally balance task-specific expected rewards against the metabolic costs of neural coding. The revised manuscript expands this framework to accommodate logarithmic representations and validates the core model against an independent dataset of risky choices.

Strengths:

The authors have effectively addressed my previous concerns with rigorous additions:

(1) The mathematical formulation has been revised into a discrete signal accumulation framework, making the objective function and resource trade-offs much more transparent and mathematically tractable.

(2) The incorporation of the logarithmic representation resolves prior ambiguities regarding structural constraints.

(3) The new split-half analysis effectively addresses the temporal dynamics of adaptation. The stability of the sublinear scaling across the experiment provides solid evidence that human subjects utilize rapid, top-down modulation to adjust their encoding strategy when explicitly informed about the environment.

(4) Validating the derived scaling exponents on an independent risky-choice dataset robustly supports the generalizability of the theoretical framework beyond a single cognitive domain.

Comments on revisions:

The authors have addressed my remaining theoretical concern regarding the model's predictions for mean estimation bias. I have no further comments.

Reviewer #1 (Public review):

Summary:

The integration of single-cell datasets across species is a powerful approach to understanding how cell types and patterns of gene expression have evolved. Current methods to perform such integrations require multiple steps: clustering, the integration itself, and downstream differential expression analysis. In this study, the authors describe a new approach, called ANTIPODE, that combines these steps by integrating deep learning with interpretable decoding and linear modeling. This method builds on previous deep learning approaches to dataset integration, namely SCVI and scANVI, that employ a variational autoencoder to model single-cell RNA-sequencing datasets. However, gene expression estimates from these previous methods are challenging to interpret due to non-linear decoding from the modeled latent space. ANTIPODE seeks to address this issue by using a single-layer decoder coupled to a linear model to estimate patterns of differential expression, e.g. differential expression by coexpression module, across cell types, etc.

The authors apply their framework to a large single-cell RNA-seq dataset (~1.8M cells) containing cells from the central nervous systems of humans, macaques, and mice spanning in utero developmental time points. They identify a consensus set of cell clusters across each species. They find that ANTIPODE performs at least as well as SCVI in terms of species integration and batch correction. The authors demonstrate several use cases of this integrated approach by analyzing differential expression that correlates with gene structure, the evolution of expression differences in neuropeptide systems, and the anatomical and phylogenetic variation in neurodevelopmental timing.

Strengths:

ANTIPODE is a welcome addition to techniques that integrate large single-cell RNA-seq datasets across multiple species. The approach's simultaneous inference of cell clusters, integration manifolds, and differential expression should streamline analysis pipelines whose elements are often disjointed and sometimes work at cross purposes.

Weaknesses:

The authors note several limitations to their method that will be targets for future development. First, clustering "resolution" is inferred from the data and cannot be tuned as with other approaches. Second, because of the linear decoding, ANTIPODE does not accommodate combining datasets obtained from different modalities (e.g. single-cell with single-nucleus RNA-seq). Third, as currently implemented, ANTIPODE does not explicitly model phylogenetic relationships. However, the authors describe an extension that could enable this, enhancing the power of multiple species integrations. A weakness with the current manuscript is the organization and readability of the figures. The supplemental figures in particular need to be restructured and reformatted to increase their interpretability.

Reviewer #1 (Public review):

This manuscript by Niño-González and collaborators shows that PIF4 undergoes alternative splicing in response to elevated temperature, generating distinct isoforms that may contribute to early seedling responses of Arabidopsis thaliana to heat stress (37 {degree sign}C). This work provides an intriguing perspective on how PIF activity may be modulated under stress conditions.

The authors report rapid heat-induced changes in seedling morphology, with cotyledon angle and hypocotyl length altered as early as 3 hours after transfer to 37 {degree sign}C. These responses correlate with a transient increase in PIF4 transcript levels, followed by a return to control values at later time points. Notably, heat induces preferential production of an exon 5-skipping isoform of PIF4. The resulting short protein variant (PIF4-S) lacks part of the bHLH domain and is therefore unlikely to be transcriptionally active.

To explore functional consequences, the authors expressed the exon 5 inclusion (functional) isoform, PIF4-L, in the pif4-101 mutant background. Some heat-induced phenotypes, such as protochlorophyllide accumulation and subsequent photobleaching, were reduced or absent in these lines. Interestingly, pif4-101 mutants themselves largely resemble WT plants for most heat-responsive traits, with the exception of hypocotyl length. PIF4-L expression specifically attenuates the cotyledon angle response to heat, without strongly affecting hypocotyl elongation.

An important point is that PIF4 itself is not essential for the observed heat responses, as pif4 mutants respond largely like wild-type plants. This implies that the phenotypes described are likely controlled by multiple PIFs acting redundantly. In this context, the generation of the PIF4-S isoform may represent one of several mechanisms by which heat stress reduces overall functional PIF levels, rather than a PIF4-specific regulatory switch.

Other caveats should be considered when interpreting the work. The functional relevance of the PIF4-S isoform under heat stress is not tested, as heat responses of these transgenic lines were not examined. Transcriptome analysis of heat-stressed WT, pif4-101 mutant, and PIF4-L-expressing plants revealed an enrichment of PIF-regulated genes, supporting a possible role for this family of transcription factors in the heat stress response. Notably, the heat responsiveness of the mutant and of the transgenic lines differs only marginally from that of WT plants. In addition, the study relies primarily on total transcript-level analyses, without quantitative assessment of individual PIF isoforms or direct measurement of PIF protein abundance. Given that other PIFs are also expressed and may be subject to alternative RNA processing, it needs to be determined whether PIF4-S alone could exert a dominant effect, counteracting all the other functional PIFs by itself, under heat stress. Hence, the proposed model is a plausible but still incomplete framework that requires further experimental validation and analysis.

Altogether, the results presented in this manuscript could also be interpreted as follows: multiple PIFs contribute to the observed phenotypes in response to heat, with overlapping (redundant) functions. Heat stress may reduce functional PIF levels through different mechanisms, one of which is the regulation of alternative splicing, as shown here for PIF4, leading to the production of non-functional proteins or protein variants that could act as negative competitors (such as PIF4-S). Restoring PIF levels to values of control conditions could therefore reverse heat-induced phenotypes, as observed in the PIF4-L expression lines.

Main concerns:

(1) The existence of a shorter isoform of PIF4 and PIF6 is relevant, and PIF4 could indeed play a role in the context of heat stress, as it does in thermomorphogenesis. In this sense, the interplay between PIF4-S and PIF4-L might be linked to plant morphological responses to heat; however, the present work requires further investigation to determine whether this is indeed the case. It is important to note that pif4 mutants behave similarly to WT plants, indicating that PIF4 is not necessary for the observed responses. These phenotypes are therefore most likely related to several PIFs rather than to one specific family member. The results obtained with the transgenic lines expressing PIF4-L or PIF4-S support this interpretation, as increasing a functional PIF (PIF4-L) reduces some phenotypes, while expressing a dominant-negative version mimics heat-induced phenotypes under control conditions. Thus, it is reasonable to interpret that under heat stress, functional PIF levels are reduced through multiple mechanisms, alternative splicing and PIF4-S generation being one of them in the case of PIF4, but likely with additional effects on other family members. This clearly requires further study.

(2) RT-qPCR quantification of total PIF4 transcripts, as well as the long and short isoforms under the tested conditions, is necessary. While we agree with the authors that PIF4-S could act as a dominant-negative factor, demonstrating this requires comparison of phenotypes under heat versus control conditions using the PIF4-S transgenic lines. Importantly, for the authors' hypothesis to be valid, PIF4-S must be able to outcompete other PIFs; therefore, accurate quantification of its expression levels across conditions is crucial. Combining the results shown in Figures 2A and Figure 2G suggests that the levels of the functional PIF4-L isoform are unchanged or even reduced after 3 h of heat treatment, as the increase in total PIF4 does not fully compensate for the diversion toward PIF4-S. Additionally, it would be equally relevant to quantify the expression of other PIFs (or at least those shown in Suppl. Fig. 6) to determine whether PIF4-S could exert such a strong effect even when expressed at relatively low levels. By "proper quantification", we refer specifically to functional protein-coding variants, as in the PIF4-L case. Supplemental Figure 6 shows that PIF3 and PIF5 appear unaffected by heat, while PIF1 expression is increased. However, JBrowse data for dark-grown seedlings indicate that PIF1 is subject to alternative transcription initiation, alternative splicing, and alternative polyadenylation at its 3′ end. A similar situation occurs for PIF3, at least at the 5′ end of the transcriptional unit. Therefore, alternative RNA processing mechanisms may play a key role in modulating functional PIF protein levels in response to heat. Without considering diverted isoforms of other PIFs, the interpretation becomes problematic, as PIF1 is upregulated by heat, and PIF4-S would therefore need to overcome its activity as well. This is particularly relevant given that the cotyledon angle phenotype at 37 {degree sign}C appears even stronger than in the pif1pif3pif5 triple mutant, if such a comparison is feasible.

(3) In addition, PP2A is a well-established housekeeping gene for normalization across different light regimes, as its expression is not affected by light. However, we are not convinced this holds true under heat stress conditions (see Li et al., Plant Cell 2019 Jul 29;31(10):2353-2369. doi:10.1105/tpc.19.00519).

(4) Furthermore, the mechanistic conclusions would be strengthened by directly assessing PIF protein levels, for example, by western blot analysis, to determine whether changes in transcript isoform abundance translate into corresponding changes in protein accumulation under heat stress.

(5) Importantly, the authors' interpretation that "PIF4-L.1 expresses the long isoform at levels similar to those of WT plants (Supplemental Figure 9A), ruling out the possibility that the suppression of heat-induced phenotypes (cotyledon opening and Pchlide accumulation) is due to elevated PIF4 expression levels" is not correct. The RT-qPCR assay quantifies all isoforms containing exon 6, which include both long and short variants with respect to exon 5 inclusion. Since WT plants at 37 {degree sign}C express both isoforms (L/S ≈ 60/40), the PIF4-L lines actually express 2-4-fold higher levels of the functional PIF4 isoform, based on the values shown in the figures.

(6) Figure 3B should include a statistical analysis, as it appears that PIF4-L expression does not significantly reduce photobleaching. Cotyledon angle is not affected by either the pif4 mutation or PIF4-L expression under 22 {degree sign}C conditions (Figure 3C). However, after 24 h at 37 {degree sign}C, there is a clear effect, with cotyledon angles closer to those observed in WT plants at 22 {degree sign}C. Regarding hypocotyl length, although statistical testing was not performed, it is evident that pif4-101 affects this parameter, while PIF4-L expression in this background does not substantially alter the mutant response.

Other comments:

(1) We do not believe that Figure 3E is an optimal way to demonstrate attenuation of transcriptional changes by PIF4-L expression in pif4 mutants. A heat map representation would likely be more direct and informative.<br /> The authors should consider expressing another functional PIF in the pif4 mutant background to determine whether the observed effects are specific to PIF4, as proposed, or whether they reflect a general PIF function.

(2) It would also be informative to examine the response under Light + 37 {degree sign}C conditions. Since PIF4 mRNA accumulation is induced by light, the authors should test whether plants incubated in light show a similar response to heat or whether it is attenuated. Potential cross-regulation between light and heat responses would be worth exploring.

(3) As the authors acknowledge in the introduction, most of our knowledge regarding PIFs in temperature signalling has focused on thermomorphogenesis. Therefore, we believe it is important to place these new findings (exon 5 skipping) within that framework, as they could help explain observations made under better-characterized conditions. In addition, would be interesting to see the phenotypes of the pifq mutant under heat stress. Even though this mutant line displays a heat-stress-like phenotype under control conditions, it may still respond to heat treatment. If so, this would indicate that PIFs are not fully determinative of this response.

(4) The authors should clearly state the genetic background of the PIF4-S expression lines, which appear to be in the pif4-101 background but are not explicitly described as such in the manuscript.

Reviewer #1 (Public review):

The authors aim to interrogate the sets of intramolecular interactions that cause kinesin-1 hetero-tetramer autoinhibition and the mechanism by which cargo interactions via the light chain tetratricopeptide repeat domains can initiate motor activation. The molecular mechanisms of kinesin regulation remain a key question with respect to intracellular transport and this study adds important perspectives to our understanding. It has implications for the accuracy and efficiency of motor transport by different motor families, for example the direction of cargos in one or other direction on microtubules.

The authors focus on the response of inactivated kinesin-1 to peptides found in cargos and the cascade of conformational changes that are induced. They also test the effects of the known activator of kinesin-1 - MAP7 - in the context of their model. The study benefits from multiple complementary, albeit relatively low-resolution, methods - structural prediction using AlphaFold3, 2D and 3D analysis of (mainly negative stain) TEM images of several engineered kinesin constructs, biophysical characterisation of the complexes, peptide design, hydrogen/deuterium-exchange mass spectrometry and simple cell-based imaging. Each set of experiments is carefully designed and the intrinsic limitations of each method are offset by other approaches, such that the assembled data convincingly supports the authors' regulatory model of kinesin activation.

This study benefits from prior work by the authors on this system and the tools and constructs they previously accrued, as well as from other recent contributions to the field. This work will be of broad interest to cell and structural biologists, especially those seeking to tackle small and flexible macromolecular complexes, as well as biophysicists and those interested in protein engineering.

Reviewer #1 (Public review):

Barré et al. investigated the role of Shp1 and Shp2 in megakaryocytes (MKs) and platelets by conditional knock-out of Shp1, Shp2, or both under the control of the Gp1ba promoter. Deletion of Shp1 and Shp2 in MKs and platelets was almost complete. The Shp1/Shp2 double knock-out mice displayed macrothrombocytopenia and increased bleeding, whereas the single knock-outs did not show significant defects. Platelet function was aberrant in DKOs, but not in single knock-outs, and so was ligand-induced signaling, particularly Syk phosphorylation.

Megakaryocyte maturation was impaired in Shp1/Shp2 DKO mice. Ligand-induced signaling was impaired in Shp2 knock-out and DKO. Ex vivo formation of platelets and in vivo maturation of MKs were impaired in DKO mice. Pharmacological inhibitors of Shp1 and Shp2 had largely similar effects as observed in the single knock-outs. The authors conclude that Shp1 and Shp2 have synergistic functions in the MK/platelet lineage, and that Shp2 may be a potential therapeutic target in myeloproliferative neoplasms.

Strengths:

The data clearly show effects of the Shp1/Shp2 double knock-out on MKs and platelets.

Weaknesses:

There appears to be a discrepancy between the results with the Shp2 single knock-out and the Shp2 inhibitor: the Shp2 knock-out does not affect MKs and platelets, except Erk1/2 signaling, whereas the Shp2 inhibitors appear to affect MK function.

This work is interesting and may have potential from a therapeutic point of view.

Reviewer #1 (Public review):

Summary:

Jackman et al report the analysis of a cis-regulatory region upstream of the dlx2b gene in zebrafish, that is hypothesised to control gene expression in the developing tooth. To demonstrate this, the authors performed solid promoter bashing analysis to assess the gene expression driven by the regulatory region, and validated the expression against a GFP-reporter knock-in. They narrowed down the tooth-specific enhancer activity to the MTE, which was sufficient to drive gene expression. Interestingly, they have identified a vertebrate conserved region which contained four predicted transcription factor binding sites, which when mutated individually, did not alter the reported gene expression. However, in combination, the expression was disrupted. The authors propose a putative upstream regulator cebpa binding one of the predicted TFBS, using in situ hybridisation to show overlapping gene expression domains.

Strengths:

The experiments presented in this paper were rigorously executed and the authors' effort to systematically dissect the different elements of the enhancer are commendable. The discussion and limitations of the study were very well-balanced.

First, the results represent important findings first for the enhancer biology field to sustain evidence of the role of redundant TFBSs. Too often, only TFBS mutations that are sufficient and necessary to drive gene expression patterns are reported, but work providing evidence that some TFBS are necessary but not sufficient by themselves to drive expression is rarer. TFBS redundancy is a crucial concept in enhancer biology but also a difficult concept to prove that hinders the accurate prediction of enhancer function. In an era where increasingly more powerful machine learning models are developed to predict enhancer function, this work is a reminder of the complexity of enhancer biology and provides ground truths for experimental validation.

Second, the results present valuable findings for the field of tooth development. While the authors have comprehensively described work performed in this space, there are still not many tooth-specific enhancers identified and accurately described. The work also presents further avenues for studying upstream regulators.

Weaknesses:

It seems to me that one of the greatest outcomes of this work is demonstrating the collective action of mutated TFBSs where individual mutations are not affecting gene expression. These findings fall into the realm of enhancer redundancy but this concept was not thoroughly discussed in the introduction of the paper.

The claimed results are generally well-supported by the experiments performed, and hypothesis and speculations have been clearly stated. However, some speculative statements remain that should be addressed, for example in the abstract line 33 "These findings suggest that loss of MTE function permits alternative cis-regulatory elements to gain control of the promoter". There is no data indicating what these cis-regulatory elements could be, hence this sentence might be better suited in the discussion.

The manuscript could be strengthened by further exploration of the wider region upstream of dlx2b to support the recruitment of other TFBSs: Were there any other vertebrate-conserved regulatory regions just outside of the MTE? Were there any other family members of the predicted TFs expressed in the tooth? Transcription factor binding sites identity remains a prediction; it could be expanded to other TFs within the same family.

[Editors' note: this version has been assessed by the Reviewing Editor without further input from the original reviewers. The authors have addressed the comments raised in the previous round of review.]

Reviewer #1 (Public review):

Summary:

The manuscript by Ma et al. provides robust and novel evidence that the noctuid moth Spodoptera frugiperda (Fall Armyworm) possesses a complex compass mechanism for seasonal migration that integrates visual horizon cues with Earth's magnetic field (likely its horizontal component). This is an important and timely study: apart from the Bogong moth, no other nocturnal Lepidoptera has yet been shown to rely on such a dual-compass system. The research therefore expands our understanding of magnetic orientation in insects with both theoretical (evolution and sensory biology) and applied (agricultural pest management, a new model of magnetoreception) significance.

The study uses state-of-the-art methods and presents convincing behavioural evidence for a multimodal compass. It also establishes the Fall Armyworm as a tractable new insect model for exploring the sensory mechanisms of magnetoreception, given the experimental challenges of working with migratory birds. Overall, the experiments are well designed, the analyses are appropriate, and the conclusions are generally well supported by the data.

Strengths:

• Novelty and significance: First strong demonstration of a magnetic-visual compass in a globally relevant migratory moth species, extending previous findings from the Bogong moth and opening new research avenues in comparative magnetoreception.<br /> • Methodological robustness: Use of validated and sophisticated behavioural paradigms and magnetic manipulations consistent with best practices in the field. The use of 5 min bins to study a dynamic nature of magnetic compass which is anchored to a visual cue but updated with latency of several minutes is an important finding and a new methodological aspect in insect orientation studies.<br /> • Clarity of experimental logic: The cue-conflict and visual cue manipulations are conceptually sound and capable of addressing clear mechanistic questions.<br /> • Ecological and applied relevance: Results have implications for understanding migration in an invasive agricultural pest with expanding global range.<br /> • Potential model system: Provides a new, experimentally accessible species for dissecting the sensory and neural bases of magnetic orientation.

Weaknesses:

Overall, this is a strong study, and the authors have completed an excellent major revision.

Reviewer #1 (Public review):

Summary:

The researchers aimed to identify which neurotransmitter pathways are required for animals to withstand chronic oxidative stress. This work thus has important implications for disease processes that are caused/linked to oxidative stress. This work identified specific neurotransmitters and receptors that coordinate stress resilience, both prior to and during stress exposure. Further, the authors identified specific transcriptional programs coordinated by neurotransmission that may provide stress resistance.

Strengths:

The manuscript is very clearly written with a well-formulated rationale. Standard C. elegans genetic analysis and rescue experiments were performed to identify key regulators of the chronic oxidative stress response. These findings were enhanced by transcriptional profiling that identified differentially expressed genes that likely affect survival when animals are exposed to stress.

Weaknesses:

Where the gar-3 promoter drives expression was not discussed in the context of the rescue experiments in Fig 7.

Comments on revisions:

This issue has now been appropriately addressed in the revision.

Reviewer #1 (Public review):

This study makes a fundamental contribution to our understanding of interocular suppression, particularly continuous flash suppression (CFS). Using neuroimaging data from two macaque monkeys, the study provides compelling evidence that CFS suppresses orientation responses in neurons within V1. These findings enrich the CFS literature by demonstrating that neural activity under CFS may prevent high-level visual and cognitive processing.

Comments on revisions:

The authors have addressed all my previous comments.

Reviewer #1 (Public review):

This study by Li and colleagues examines how defensive responses to visual threats during foraging are modulated by both reward level and social hierarchy. Using a naturalistic paradigm, the authors test how the availability of water or sucrose, with sucrose being more rewarding than water, shapes escape behavior in mice exposed to looming stimuli of different intensities, which are used to probe perceived threat level and defensive responses. In parallel, the study compares dominant and subordinate animals to assess how social rank biases the trade off between reward seeking and threat avoidance. By combining detailed behavioral analyses with computational modeling, the work addresses how reward level and social context jointly influence escape decisions in an ethologically relevant setting.

Across the different experimental conditions, perceived threat level is the main determinant of behavior. The authors show that looming stimuli associated with higher threat (contrast) consistently elicit faster and more robust escape responses than lower threat stimuli. This effect is particularly evident during early exposures, when animals are highly vigilant and have not yet habituated to the looming stimulus (learned that it is not dangerous). Later they described that as animals gain experience and habituate, behavior becomes more flexible, and reward level begins to exert a graded modulation of the escape response. Importantly, the authors show that under high threat conditions increasing reward value leads to more frequent and faster escape rather than greater reward pursuit. This finding is particularly relevant, as it suggests that highly valued rewards can heighten vigilance and thereby enhance responsiveness to threat, highlighting that reward does not simply compete with defensive behavior but can also reshape it depending on the perceived level of danger, in contrast to low threat conditions, where threat can be more easily outweighed by reward. Thus, an important conceptual contribution of the study is the introduction of vigilance as a useful framework to interpret these effects. Vigilance is treated as a behavioral state reflecting heightened attention to potential danger. In line with what is known from natural foraging, mice initially maintain high vigilance when confronted with an innate threat. This perspective helps clarify a finding that might otherwise appear counterintuitive. One might expect higher rewards to motivate animals to tolerate risk, explore more, and habituate faster in any scenario. Instead, the data suggest that highly rewarding outcomes can elevate vigilance, making animals more responsive to threat and leading to faster or more frequent escape under high threat conditions. In this sense, reward does not simply compete with threat but can also amplify sensitivity to it, depending on the internal state of the animal.

The social results are particularly interesting in this context as well. Dominant mice consistently prioritize avoidance over reward, showing stronger escape responses and slower habituation than subordinates. This behavior is well captured by the vigilance framework proposed by the authors: dominant animals appear to maintain higher vigilance, which biases decisions toward threat avoidance. The authors further suggest that stable social relationships sustain high vigilance and slow habituation, framing this as an evolutionarily conserved strategy that may enhance survival. This interpretation provides a valuable perspective on how social structure shapes defensive behavior beyond immediate physical interactions. At the same time, there are important limitations to this interpretation. All experiments were conducted in male mice, and it is possible that the relationship between social hierarchy, vigilance, and defensive behavior would differ substantially in females. In addition, the idea that stable social relationships maintain elevated vigilance does not straightforwardly align with broader views of social stability as protective for mental health and as a buffer against anxiety and stress. These points do not undermine the findings but suggest that the social effects described here should be interpreted with caution and within the specific context of the task and sex studied.

Another important limitation is that the neural mechanisms underlying these effects remain speculative. The manuscript includes an extensive discussion of candidate circuits, particularly involving the superior colliculus and downstream structures, but this section is necessarily based on prior literature rather than on data presented in the study. Given the complexity of the circuits involved in integrating internal state, reward, social context, and vigilance, the current work should be viewed as providing a strong behavioral and conceptual framework rather than direct insight into underlying neural mechanisms.

Methodologically, the behavioral paradigm is well suited for studying escape decisions in socially housed animals, and the machine learning based classification of defensive responses is a clear strength. The computational model provides a useful formalization of how threat level, reward level, and vigilance interact and may be valuable for other laboratories studying escape, approach avoidance, or conflict situations, particularly as a way to classify behavioral outcomes after pose estimation. More generally, the work will be of interest to the neuroethology community for its detailed characterization of escape behavior under naturalistic conditions.

Given the ethological nature of the study and the high inter individual variability reported by the authors, clarity and precision in the methods are especially important for reproducibility. While the revised manuscript addresses many earlier concerns, some aspects remain slightly difficult to follow. For example, the main text states that animals were not water deprived to avoid differences in internal state, whereas parts of the methods describe conditions in which animals were water deprived, suggesting that internal state manipulation may differ across experiments. Clearer separation and explanation of these conditions would further strengthen confidence in the work.

Overall, this study provides a rich and thoughtful analysis of how reward level and social hierarchy modulate defensive behavior through changes in vigilance. It offers a useful conceptual advance for thinking about escape behavior in naturalistic settings and lays a solid foundation for future work aimed at linking these behavioral states to underlying neural circuits.

Reviewer #1 (Public review):

In this manuscript, the authors report that GPR55 activation in presynaptic terminals of Purkinje cells decrease GABA release at the PC-DCN synapse. The authors use an impressive array of techniques (including highly challenging presynaptic recordings) to show that GPR55 activation reduces the readily releasable pool of vesicle without affecting presynaptic AP waveform and presynaptic Ca2+ influx. This is an interesting study, which is seemingly well-executed and proposes a novel mechanism for the control of neurotransmitter release. However, the authors' main conclusions are heavily, if not solely, based on pharmacological agents that most often than not demonstrate affinity at multiple targets. Below are points that the authors should consider in a revised version.

Major points:

(1) There is no clear evidence that GPR55 is specifically expressed in presynaptic terminals at the PC-DCN synapse. The authors cited Ryberg 2007 and Wu 2013 in the introduction, mentioning that GPR55 is potentially expressed in PCs. Ryberg (2007) offers no such evidence, and the expression in PC suggested by Wu (2013) does not necessarily correlate with presynaptic expression. The authors should perform additional experiments to demonstrate presynaptic expression of GPR55 at PC-DCN synapse.

(2) The authors' conclusions rest heavily on pharmacological experiments, with compounds that are sometimes not selective for single targets. Genetic deletion of GPR55 would be a more appropriate control. The authors should also expand their experiments with occlusion experiments, showing if the effects of LPI are absent after AM251 or O-1602 treatment. In addition, the authors may want to consider AM281 as a CB1R antagonist without reported effects at GPR55.

(3) It is not clear how long the different drugs were applied, and at what time the recording were performed during or following drug application. It appears that GPR55 agonists can have transient effects (Sylantyev, 2013; Rosenberg, 2023), possibly due to receptor internalization. The timeline of drug application should be reported, where IPSC amplitude is shown as a function of time and drug application windows are illustrated.

(4) A previous investigation on the role of GPR55 in the control of neurotransmitter release is not cited nor discussed Sylantyev et al., (2013, PNAS, Cannabinoid- and lysophosphatidylinositol-sensitive receptor GPR55 boosts neurotransmitter release at central synapses). Similarities and differences should be discussed.

Minor point:

(1) What is the source of LPI? What isoform was used? The multiple isoforms of LPI have different affinities for GPR55.

Comments on revisions:

In this revised version, the authors have addressed my major concerns. Notably, they used CRISPR/Cas9 genetic knockdown of GPR55 to independently validate their original findings. The main conclusions are now well supported and represent an important contribution to the field.

Reviewer #1 (Public review):

Summary:

The "number sense" refers to an imprecise and noisy representation of number. Many researchers propose that the number sense confers a fixed (exogenous) subjective representation of number that adheres to scalar variability, whereby the variance of the representation of number is linear in the number.

This manuscript investigates whether the representation of number is fixed, as usually assumed in the literature, or whether it is endogenous. The two dimensions on which the authors investigate this endogeneity are the subject's prior beliefs about stimuli values and the task objective. Using two experimental tasks, the authors collect data that are shown to violate scalar variability and are instead consistent with a model of optimal encoding and decoding, where the encoding phase depends endogenously on prior and task objectives. I believe the paper asks a critically important question. The literature in cognitive science, psychology, and increasingly in economics, has provided growing empirical evidence of decision-making consistent with efficient coding. However, the precise model mechanics can differ substantially across studies. This point was made forcefully in a paper by Ma and Woodford (2020, Behavioral & Brain Sciences), who argue that different researchers make different assumptions about the objective function and resource constraints across efficient coding models, leading to a proliferation of different models with ad-hoc assumptions. Thus, the possibility that optimal coding depends endogenously on the prior and the objective of the task, opens the door to a more parsimonious framework in which assumptions of the model can be constrained by environmental features. Along these lines, one of the authors' conclusions is that the degree of variability in subjective responses increases sublinearly in the width of the prior. And importantly, the degree of this sublinearity differs across the two tasks, in a manner that is consistent with a unified efficient coding model.

Comments on revisions:

The authors have done an excellent job addressing my main concerns from the previous round. The new analyses that address the alternative model of "no cognitive noise and only motor noise" are compelling and provide quantitative evidence that bolsters the paper's overall contribution. The authors also went above and beyond by reanalyzing the Frydman and Jin (2022) dataset to provide new and very interesting analyses that provide an additional out of sample test of the model proposed in the current paper.

Reviewer #1 (Public review):

Summary:

The authors aimed to assess the variability in expression of surface protein multigene families between amastigote and trypomastigote Trypanosoma cruzi, as well as between individuals within each population. The analysis presented shows higher expression of multigene family transcripts in trypomastigotes compared to amastigotes and that there is variation in which copies are expressed between individual parasites. Notably, they find no clear subpopulations expressing previously characterised trans-sialidase groups and that no patterns of coexpressed TcS genes were evident within individual cells or subpopulations. They also note that TcS encoded in the core genome are more often expressed, compared to TcS genes encoded in other genome compartments.

Strengths:

Additionally, the authors successfully process methanol fixed parasites with the 10x Genomics platform. This approach is valuable for other studies where using live parasites for these methods is logistically challenging.

In this second submission the authors show the kallisto mapping approach used is as robust as possible, and that this approach outperforms STAR mapping.

Weaknesses:

The authors describe a single experiment, which lacks repeats, controls or complementation with other approaches and the investigation is limited to the trans-sialidase transcripts.

Comments on revised version:

Thank you to the authors for taking the time to thoroughly address the peer review. The main concerns have now been addressed, and the manuscript edited to make points of confusion clearer.

Reviewer #1 (Public review):

Summary:

In this manuscript, Rupasinghe and co-authors introduce a new statistical model for spiking neurons. Building on earlier work, they propose to model spikes as arising from a Poisson process whereby the firing rate is the product of stimulus drive and a stimulus-independent gain signal. The critical innovation of this work is that the gain signal is modeled in continuous time. Earlier explorations of this statistical construction treated the gain-signal as constant within a trial. This innovation is elegant and important. It makes the model richer, more plausible, and more broadly applicable. The authors show that the model parameters are recoverable from realistic amounts of data and then apply the framework to previously studied datasets. They show that the new model outperforms earlier models and alternative candidates in capturing spiking data across four visual areas of the macaque monkey. Analysis of the model parameters replicates some earlier findings and uncovers several new insights. The model and fitting methods can be broadly applied to partition different types of signals and noise from spiking data and are likely to be widely adopted in the systems neuroscience community.

Strengths:

(1) Through clever use of advanced statistical techniques, the authors manage to infer critical information from single-trial single-cell data.

(2) The question of which aspect of a spike train is signal and which is noise is omnipresent in neuroscience. By improving our ability to characterize the distinct factors that shape spiking activity, this work makes a fundamental contribution to the literature.

Weaknesses:

Overall, I find the work impressive and important. I have a couple of questions and suggestions.

(1) The work is entirely focused on single-cell data. While this is a great starting point, expanding the approach to spiking activity in neural populations is an important future goal.

(2) Line 49-53: These statements seem incorrect to me. The modulated Poisson model, as introduced in Goris et al (2014), is a process model that can perfectly be used to generate spike trains (within a trial, spiking emerges from a Poisson process, which can be homogeneous or inhomogeneous). Moreover, the model contains a parameter that represents the duration of the counting window (delta t). The dependency of over-dispersion on the size of the time bins for real neurons is shown in Figure 1b (inset plot) of that paper (and shown to resemble the model prediction). This time-dependency was further explored by the same authors in Goris et al (2018 - Journal of Vision) and also in Hénaff et al (2020 - Nature Communications ). I suggest that the authors rephrase this argument (here and at some later points in the paper). They could just say that the Goris model makes the simplistic and implausible assumption that, within a given trial, gain does not fluctuate. This is clearly an important limitation and the key difference with the continuous model introduced here.

(3) Line 54-55: I think the first part of the claim is a bit misleading. There is nothing in the Goris model that would inherently limit it to homogeneous Poisson processes, as seems to be implied by this description. The model is built on the assumption that spike generation within a trial arises from a Poisson process. This may very well be an inhomogeneous Poisson process (i.e., a stimulus-dependent time-varying firing rate). Homogeneous and inhomogeneous Poisson processes both give rise to Poisson distributed spike counts (and thus a mixture of Poisson distributions across trials in the Goris model). I suggest the authors clarify this description a bit. Note that the two model variants illustrated in Figure 1b and c were also explored in Hénaff et al (2020 - Nature Communications).

(4) The extension to the continuous case is very elegant!

(5) I find the result shown in Appendix 3 critically important. The recoverability of the model for realistic amounts of data is foundational for the rest of the paper. I would consider including this analysis in the main results section. Not all readers may check Appendix 3, but they should know about this result.

(6) Figure 3: I am wondering whether the inferred gain is capturing some response fluctuations that originate from the cell's phase-selectivity. Could the authors compute the trial-averaged inferred gain (ideally, aligned to stimulus-phase at the start of the trial if this experimental parameter varied across repeats)? If they have successfully partitioned the response variance, the trial-averaged gain should have no systematic temporal structure. If it has a sinusoidal modulation, it may partially capture stimulus-drive. This could be an interesting test to run on all model fits to further validate that the partitioning into a signal and noise component succeeded as intended.

(7) One common observation that is currently not explored is the quenching of neuronal response variability following stimulus onset (Churchland et al 2010 - Nature Neuroscience), which was suggested to reflect a quenching of gain variability in Goris et al (2024 - Nature Reviews Neuroscience). Building on the previous suggestion, the authors could compute the temporal evolution of cross-trial gain variability from the inferred gain traces. Do they recognize a reduction in gain variability following stimulus onset? If so, it would be worthwhile to show this.

(8) Line 543-565: I want to make sure I understand the Baseline Poisson model and Poisson-GP correctly. For the baseline model, I had imagined that the authors would simply use the stimulus-conditioned PSTH as an estimate of the time-dependent firing rate, coupled with an inhomogeneous Poisson process assumption. But they additionally assume a Gamma prior on the firing rate to compensate for the sparseness of the data (sometimes only 5 repeats per condition). The Poisson-GP includes exactly the same model components, but now the time-dependent firing rate is modeled by a Gaussian process. Doing this massively improves the goodness-of-fit (Fig 4A). Do I understand this correctly?

Reviewer #1 (Public review):

Summary:

Maigler et al. set out to test the hypothesis that individual differences in taste preferences are (in part) due to individual differences in central taste processing. The first tested rats' preferences for a variety of taste stimuli on multiple days. They then recorded responses of neurons in the taste cortex to the same tastes on two consecutive days.

Strengths:

The authors collected high-resolution behavioral data from the same animals across multiple days, allowing for a detailed characterization of individual variation in taste preferences. They then performed recordings from the same set of animals in response to the same stimuli, allowing them to draw parallels between behavioral and neural responses. They convincingly show that preference ranks for a variety of basic tastes change over time and that the correlation between neural responses and preferences is not stable, correlating more strongly with more recent measures of preference.

Weaknesses:

Behavioral analysis: Data presentation does not show how preferences change over the course of testing. In particular, it is unclear whether there are any systematic changes in preferences over the course of testing that could explain the observed changes in correlation with neural responses, such as changes due to learning (e.g., flavor nutrient conditioning, relief of neophobia), changes in deprivation state, or habituation to/proficiency with the BAT setup. A secondary point is whether any changes in preference are attributed to internal individual versus external contextual factors. Both types of variation (i.e., across individuals and across time within an individual) are mentioned in the introduction, but it is not clear what the authors believe about the nature or neural representation of these sources of variation.

With respect to neural data analysis, no individual animal/day data are shown, making it difficult to assess the extent to which differences in correlation match individual differences in preferences and/or changes in preference with time within individuals. The correlation analysis is also lacking control for the fact that there is a certain degree of "chance" associated with behavioral and neural measures having matching ranks.

Finally, the conclusion that correlations between final day preferences and neural responses obtained from the second recording session are the result of experience needs more justification; it is unclear to what extent changes in correlation may be attributed to overall changes in responsiveness of the neural population.

Reviewer #1 (Public review):

Summary:

The authors provide extensive immunoreactivity and expression data to map monoaminergic neurotransmitter production sites in Pristionchus pacificus. This nematode is relatively distantly related to the popular model nematode Caenorhabditis elegans, for which such information is already available. They find that dopamine, tyramine, and octopamine are present in the same neurons in both species, but differences are observed for serotonin. This forms the basis for a comparison of serotonergic neurons across 22 nematode species. In addition, they evaluate monoaminergic effects on egg-laying, head movement during reversals, and nictation behavior, to find that monoaminergic control over the latter differs between C. elegans and P. pacificus. This shows that some anatomical flexibility supports similar outcomes, whereas in other cases it is the basis of evolved regulatory differences.

Strengths:

The comparative efforts are laudable and valuable, including a thorough revisiting of old data and corrections of what is judged as a historic misannotation. The expected continued value of this work is also appreciated, because nematodes have similar anatomies and behaviors, cellular-resolution data of different species permits the study of functional evolution of neurotransmitter usage in homologous neurons.

Despite the strong experimental approach, there are some points that require addressing:

(1) Not all the concepts of the introduction ('feeding behaviors', to a lesser extent also 'evolution of neurotransmitter usage in homologous neurons') are followed up upon in the results or discussion sections.

(2) The choice of nematodes ('only' 13 species) may affect what is perceived as ancestral. Also, identifying their cells based on comparisons with Ce or Ppa identifications only is understandable but mildly risky: there are many cells in the head, and mistakes would go unnoticed until detailed analysis in each species can provide conclusive evidence.

(3) It is not reported whether the nictation-defective mutants have general locomotion defects; therefore, whether the reported problem is specific to this host-finding behavior or not.

(4) The section on RIP neurons makes sense for Ppa, but not for Ce (dauers in fact have weakened IL2-to-RIP connections), and should be revised. The nictation data also do not support the breadth of the conclusions, which should either be toned down or rephrased as hypothetical.

(5) The discussion mostly reiterates the results, leaving little room for the author's interpretations and opinions. I would suggest reworking in favor of conceptual discussion.

Reviewer #1 (Public review):

Summary:

This manuscript examines whether retrieval practice protects memory-based inference from acute stress and proposes rapid neural reactivation of a bridging memory element as the underlying mechanism. Using a two-day associative inference paradigm combined with EEG decoding, the authors report that stress impairs inference accuracy and speed, while retrieval practice eliminates these deficits and restores neural signatures associated with bridge-element reactivation. The study addresses an important and timely question by integrating research on retrieval-based learning, stress effects on memory, and neural dynamics of inference. While the work provides promising multi-level evidence linking behavioral and neural findings, limitations in experimental design, causal interpretation, and decoding specificity weaken the strength of the mechanistic claims and suggest that further work is needed to disentangle strengthened associative memory from inference-specific protection effects

Strengths:

(1) Strong theoretical integration<br /> The study integrates three influential frameworks: memory integration through associative inference, stress-induced retrieval impairment, and the testing effect. The authors present a clear theoretical narrative linking these domains and derive testable hypotheses that retrieval practice protects inference by strengthening neural reactivation of a bridge element. The conceptual framing is well-grounded in prior literature and addresses an important gap regarding neural dynamics during inference.

(2) Multi-level evidence<br /> The study provides converging behavioral and neural evidence. The authors demonstrate that stress reduces inference accuracy and speed, while retrieval practice eliminates these deficits. EEG decoding further suggests that bridge element reactivation predicts successful inference. The combination of behavioral performance and neural decoding strengthens the overall argument.

(3) Transparent experimental implementation<br /> The procedures are described in substantial detail, including stimulus construction, stress manipulation, and decoding pipelines. Data and code availability are also strengths, facilitating reproducibility.

Weaknesses:

(1) Insufficient evidence that retrieval practice specifically protects inference rather than strengthening associative memories

A central claim of the manuscript is that retrieval practice specifically protects inference ability rather than simply strengthening underlying associative memories. However, the current data do not convincingly distinguish between these possibilities. Although the authors limited analyses to trials in which AB and BC pairs were correctly retrieved in the subsequent memory test, this procedure does not fully rule out the possibility that improved inference performance reflects stronger base associative memories rather than enhanced integrative processes.

Importantly, the direct memory retrieval test used a two-alternative forced-choice (2AFC) format, which inherently allows a substantial proportion of correct responses to arise from guessing. Consequently, trials classified as "successfully retrieved" may still include weak associative memory traces, making it difficult to conclude that failures in inference reflect deficits in integration rather than incomplete associative learning.

The authors further argue that retrieval practice does not improve inference in the absence of stress, suggesting independence between inference and associative memory strength. However, this null effect does not sufficiently rule out mediation through strengthened premise memory. A factorial design and/or mediation analysis would be necessary to determine whether inference resilience emerges independently of premise memory strength.

(2) Apparent below-chance inference performance raises interpretational concerns

One surprising aspect of the results is that inference performance across experiments and groups appears to fall below the theoretical chance level (0.33) in Figure 4A. This is particularly unexpected because analyses were restricted to trials in which participants correctly retrieved both AB and BC associations.

If performance is indeed below chance, this raises concerns regarding whether participants fully understood the task instructions or whether other methodological factors influenced performance. Additionally, below-chance performance complicates the interpretation of subsequent behavioral and neural analyses. It is possible that this reflects my misunderstanding of the figure; therefore, clarification from the authors regarding how inference accuracy is calculated and presented would be helpful.

(3) Between-experiment implementation of retrieval practice weakens causal inference

The retrieval practice manipulation was implemented as a separate experiment rather than as part of a factorial design. Experiment 2 was conducted after results from Experiment 1 were known, and the authors acknowledge this post hoc decision. This design introduces several potential confounds, including cohort differences between experiments, possible differences in participant motivation or task familiarity, and reduced ability to rigorously test interaction effects.

Although the authors combined data across experiments to test interactions between stress and retrieval practice, such post hoc aggregation cannot fully substitute for a factorial design. A within-experiment 2 × 2 design (Stress × Retrieval Practice) would provide substantially stronger causal evidence and reduce confounding influences.

(4) Lack of an appropriate comparison condition for retrieval practice limits the interpretation of the mechanism

Although acknowledged briefly in the discussion, the absence of an appropriate comparison condition for retrieval practice represents a critical limitation. Without a matched re-exposure or restudy control condition, it remains unclear whether observed benefits are attributable specifically to retrieval practice or to additional exposure to AB and BC associations.

Furthermore, it is unclear whether retrieval practice operates at the trial level or the participant level. Retrieval practice could enhance memory representations for specific practiced items, making those trials more resistant to stress, or it could induce a more global change in cognitive strategy or stress resilience across participants. One way to address this issue would be to analyze inference performance separately for trials that were successfully retrieved during the retrieval practice phase versus those that were not.

(5) Interpretation of EEG decoding as bridge-element reactivation may be overstated

The neural decoding results form the mechanistic foundation of the manuscript; however, the interpretation that decoding reflects reactivation of specific bridging memories may be overstated. The classifier distinguishes between face and building categories, and because the bridging element belongs to one of these categories, successful decoding may reflect category-level semantic activation rather than reinstatement of item-specific episodic representations.

Alternative explanations include category-level retrieval, strategic task differences, or even attentional biases. Because only two categories were used, the decoding analysis lacks the specificity necessary to distinguish between category-level and item-level reactivation. As such, conclusions regarding the reinstatement of specific bridging memories should be tempered or supported with additional analyses.

Reviewer #1 (Public review):

Summary:

The authors report a novel binding partner of the TolC channel protein that forms complexes with the two principal classes of transporter-based tripartite assemblies (both ABC- and RND-transporter based) and appears to modulate their function, while also anchoring TolC into the outer membrane, compensating for the lack of direct lipidation seen in other members of the OMF family.

The newly identified protein, YbjP, is comprehensively characterized from both phylogenetic and structural perspectives. Two independent cryo-EM structures (MacAB-TolC-YbjP and AcrABZ-TolC-YbjP) provide strong structural evidence for its role and are generated using peptidiscs, mimicking the membrane environment. These findings are further supported by pull-down experiments (including state-of-the-art in vivo photo crosslinking) and functional assays for a well-rounded characterisation of the protein, and a significant amount of modelling and phylogenetic analysis. This work sheds light on the function of the members of the DUF3828-containing protein family, which appear to anchor TolC to the outer membrane and influence the expression of the TnaB and YojI transporters.

Strengths:

The strengths of the manuscript are numerous, and it presents a well-rounded package of structural biology complemented by functional and computational studies.

The full assemblies of both MacAB-TolC-YbjP and AcrABZ-TolC-YbjP are reconstituted and resolved to near-atomic resolution using cryo-EM for unambiguous assignment of binding interfaces, which are then validated using a number of techniques, including ITC, in vitro and in vivo binding assays and cross-linking.

The evolutionary analysis is particularly notable, and provides genuine insight into the DUF3828-containing proteins, the function of which remains enigmatic till now. Similarly, the involvement of YbjP in trafficking of TolC and the analysis of the impact of YbjP deletion of the full E. coli proteome is commendable.

Overall, this is a very solid piece of work, competently executed and presented, which significantly advances the field.

Weaknesses:

None obvious, however the presentation and especially main-text illustrative material seems to focus disproportionately on MacAB-TolC-YbjP complex, and the AcrABZ-TolC-YbjP is relegated to supplementary data which is somewhat confusing. There is no high-resolution side view of the AcrABZ-TolC-YbjP side-by-side to MacAB-TolC-YbjP which may be helpful to spot parallels and differences in the organisation of the two systems.

Supplementary Figure 2 may also be better presented in the main text, as it shows specific displacements of residues upon binding of the YbjP relative to the apo-complexes, although this can be left at the authors' discretion.

Reviewer #1 (Public review):

Summary:

The authors introduce EMUsort, an open-source algorithm for the automatic decomposition of high-resolution intramuscular EMG recordings. The method builds upon the Kilosort4 framework and incorporates modifications designed to better handle the spatial and temporal characteristics of intramuscular signals. The performance of EMUsort is evaluated on openly available datasets and compared against KS4 and MUEdit, demonstrating improved motor unit accuracy.

Strengths:

(1) The manuscript is clearly written, technically detailed, and well structured.

(2) The open-source software is thoroughly documented, both within the manuscript and in the accompanying repository README, facilitating adoption by the community.

(3) The availability of both code and datasets is a major strength, enabling reproducibility and independent validation.

(4) The authors provide quantitative comparisons with existing decomposition algorithms, which is essential for contextualizing the proposed method.

(5) The methodological details are sufficiently described to allow replication and further development by other researchers.

Weaknesses:

While the manuscript is strong overall, I have several suggestions that could further strengthen its impact and clarity.

(1) Benchmarking and community integration

A recent work has proposed standardized datasets and benchmarking pipelines for high-density surface EMG decomposition ("MUniverse: A Simulation and Benchmarking Suite for Motor Unit Decomposition", Mamidanna*, Klotz*, Halatsis* et al, NeurIPS 2025). A similar effort for intramuscular EMG would be highly valuable to the field. The authors may consider discussing how their dataset and algorithm could be integrated into broader benchmarking initiatives (e.g., platforms such as MUniverse), enabling systematic comparisons across multiple datasets and decomposition methods.

(2) Comparison with additional decomposition algorithms

Since the manuscript compares EMUsort with MUEdit, it would be appropriate to also include a comparison with Swarm-Contrastive Decomposition (SCD), which has been proposed for both surface and intramuscular EMG signals. Including this comparison, or explicitly discussing why it was not feasible, would strengthen the positioning of EMUsort relative to the current state of the art.

(3) Manual editing and post-processing

In practical EMG decomposition workflows, manual inspection and editing of motor units are often required after automatic decomposition. It would be useful for readers to know whether EMUsort provides (or is compatible with) a graphical interface or workflow for manual refinement, or how the authors envision this step being handled.

(4) Ablation analysis of algorithmic modifications

EMUsort is described as an extension of Kilosort4. An ablation analysis examining the impact of the main modifications introduced relative to KS4 would help clarify which changes contribute most to the observed performance improvements and under which conditions.

(5) Failure modes and limitations

A more explicit discussion of when EMUsort is likely to fail or degrade in performance would be valuable. For example, sensitivity to the number of channels, recording duration, signal quality, or motor unit density could be discussed to guide users.

(6) Generalisability to surface EMG

Given the shared methodological foundations between surface and intramuscular EMG decomposition, it would be helpful to know whether EMUsort has been tested on high-density surface EMG datasets or whether the authors expect limitations when applied outside the intramuscular domain.

(7) Applicability to human intramuscular recordings

The authors could clarify whether EMUsort has been tested on human intramuscular EMG, and discuss any expected differences in performance due to anatomical or physiological factors.

(8) Parameter sensitivity

Clustering-based methods can be sensitive to parameter choices. Reporting a parameter sensitivity analysis, or at least discussing the robustness of EMUsort to parameter variations, would increase confidence in the method's reliability and ease of use.

(9) Differences between template matching and BSS methods

Since the manuscript proposes a new template matching algorithm, but it compares its performance with a BSS one (MUedit), BSS algorithms should be described in the introduction. The differences between the methodologies should be highlighted, and the pros and cons of each described.

Conclusion:

The authors largely achieve their stated aims, and the results mostly support the main conclusions. EMUsort represents a meaningful contribution to the EMG decomposition literature, particularly for researchers working with high-resolution intramuscular recordings. With additional clarification regarding benchmarking, algorithmic ablations, and limitations, the manuscript would be further strengthened and likely to have a substantial impact on the field.

Reviewer #1 (Public review):

Summary:

Freas and Wystrach present a computational model of steering in insects. In this model, the central complex provides an error signal indicating the animal should turn left or right; this error signal biases the function of an oscillator composed of two mutually inhibiting self-exciting units. The output of these units generates a "steering signal" that is used both to set the direction and speed of the ant. Additionally, a separate module induces pauses, and an inverse relation between forward speed and turning speed is externally imposed. Statistics of the trajectories generated by the model are compared to the measured behaviors of ants.

Strengths:

While the model is very simple compared to state-of-the-art models, that simplicity makes it a potentially useful guide to researchers studying insect navigation. Some predictions that emerge from the model appear to be experimentally testable, although a more complete description of the model and its parameters, as well as an analysis of how this model's predictions differ from previous models' predictions, would be required to design these experiments.

Weaknesses:

I found it difficult to identify evidence in the paper supporting central elements of the abstract. Hopefully, these difficulties can be resolved with a clearer presentation and the addition of supporting detail, especially in the methods.

(1) The model is not clearly described

In the Materials and Methods, there is no description of the model, just "The computational model is presented in Figure 1." (This is probably a typo and may refer to Figure 2A-C), and a link to Matlab source code. It is inappropriate to ask readers or reviewers to examine source code in lieu of providing a method, but I attempted to do so anyway. To my eye, the source code does not match the model presented in 2A-C. For instance, in 2C, "Steering signal" inhibits "Freeze", but I couldn't find this in the source. "Freeze" is shown to inhibit "steering signal," but as "steering signal" is a signed quantity, it's not clear what this means. Literally, since "ang_speed_raw = L-R," it would seem to indicate the "freeze" would bias towards right turns. In the code, "freeze" appears to be implemented through the boolean variable "speed_inhibition_time." The logic controlled by this variable doesn't appear to inhibit the "steering signal" but instead (depending on control parameters) either reduces the movement speed and amplifies the turning rate, or it turns the angular speed output into a temporal integral of the control signal.

There are a number of parameters in the source code that aren't described at all in the paper, including the internal oscillator parameters.

Together, these limitations make it difficult to understand what is being simulated, what parts of the model are tied to biology, and where the model improves on or departs from previous work.

It is absolutely essential that authors fully describe the computational model, that they explain the meaning of all parameters of the model, and that they explain how the particular values of these parameters were chosen.

(2) The biological inspiration is unclear

A central claim of the paper is that the model is "biologically grounded." But some elements, for instance, using a signed quantity to represent left-right steering drive, are not biologically possible; at best, these are shorthand for biologically possible implementations, e.g., opposing groups of left-right driving neurons.

The mechanism that produces fixations and saccades - the "freeze" module - is not tied to any particular anatomy of the insect brain. Initiation of a freeze occurs at a specific time coded into the model by the authors; it is not generated by an internal model signal. Release of a freeze is by drawing a random variable; there is no neural mechanism proposed to generate this signal.

In some versions of the model, instead of directly controlling the signal, during fixations, the angular drive signal is integrated into a variable "cumul_drive." No neural substrate is proposed for this integrator. In the code, if cumul_drive passes a threshold, the angular heading of the ant changes (saccades), but only if this threshold is passed before the Poisson process ends the fixation. No neural substrate is proposed for any of this logic.

The model steps forward in time by a fixed increment - the actual duration (in seconds) of this time step is not specified. From Figure 4F, G, it appears a simulation time step is meant to be about 10ms. This would imply an oscillator frequency of about 2 Hz (Fig 2B), that the heading oscillates at a similar frequency (2G), and that a forward crawling ant stops moving every 500 ms (2I). Are these plausible? Can they be compared to an experiment?

Model parameters, including the ones that control the frequency of the oscillator, are non-dimensionalized. It is not possible to evaluate whether these parameters are biologically plausible or match experimental results.

(3) Claims that behaviors emerge from the model may be overstated

The abstract claims that steering correction and fixations/saccades emerge naturally from the same model. But it appears to me that fixations/saccades are externally imposed by the specification of specific times for a "freeze." Faster angular rotation during saccades than during course correction is imposed and does not emerge naturally from neural simulations.

(4) Citations to previous literature are difficult to follow, and modeling results are presented as though they are experimental data

I would ask the authors to be much clearer in their description and citation of previous work. It should be clear whether the cited work was experimental or computational. To the extent possible, the actual measurement should be described succinctly. Instead of grouping references together to support a sentence with multiple claims, references should be cited for each claim. Studies of computational models should not be presented as proving a biological result.

For example:

a) Lines 141-146:<br /> "Previous studies have established many key components of insect navigation, including .... the intrinsic oscillatory dynamics in the lateral accessory lobes (LALs) that support continuous zigzagging locomotion (Clément et al., 2023; Kanzaki, 2005; Namiki and Kanzaki, 2016; Steinbeck et al., 2020)."

The first reference is to one author's previous modeling work - it hypothesizes that oscillations in the LAL support zigzagging but includes no data that would "establish" the fact. Kanzaki et al. 2005 describes numerical modeling and simulation with a physical robot. Namiki and Kanzaki, 2016 is a review article that links the LAL to zigzagging behavior. It describes the LAL as a winner-take-all bistable network but does not describe or hypothesize that the LAL has intrinsic oscillatory dynamics. Steinbeck et al. 2020 is a more comprehensive review; it reinforces that the LAL is a winner-take-all bistable network that drives left-right steering, including during zig-zagging behavior. But in my reading, I could not find a statement that the LAL has intrinsic oscillatory dynamics (the closest is Steinbeck et al. saying the activity pattern switches regularly, as does the behavior; this doesn't imply that the LAL is intrinsically oscillatory.)

b) Lines 701-703:<br /> "In plume-tracking moths, CX output has been shown to modulate LAL flip-flop neurons driving zigzagging (Adden et al., 2022)."

This reads as though an experimental measurement was made, but in fact, this is modeling work.

c) Lines 703-706:<br /> "In ants, strong goal signals in the CX - whether elicited by the path integrator or visual familiarity (Wehner et al., 2016; Wystrach et al., 2020b, 2015) do not only sharpen directional accuracy but also increase oscillation frequency (Clément et al., 2023)."

Here again, modeling results are presented as though they were experimental data.

Reviewer #1 (Public review):

Summary:

D. Fuller et al. set out to study the molecular partners that cooperate with ATG2A, a lipid transfer protein essential for phagophore elongation, during the process of autophagy. Through a series of experiments combining microscopy and biochemistry, the authors identify ARFGAP1 and Rab1A as components of early autophagic membranes, which accumulate at the periphery of aberrant pre-autophagosomal structures induced by loss of ATG2. While ARFGAP1 has no apparent function in autophagy, the authors show that RAB1A is implicated in autophagy, although the precise mechanisms are not explored in the manuscript.

Strengths:

The work presented by Fuller et al. provides new insights into the composition of early autophagic membranes. The authors provide a series of MS experiments identifying proteins in close proximity to ATG2A, which is a valuable dataset for the field. Furthermore, they show for the first time the interaction between ATG2A and RAB1A both in fed and starved conditions, which extends the characterisation of the pre-autophagosomal structures observed in ATG2 DKO cells.

Weaknesses / Specific comments:

(1) The authors claim that Rab1A/B knockdown phenocopies the LC3-II accumulation observed in ATG2 DKO cells. While LC3-II accumulation is consistent with this interpretation, depletion of many autophagy-related proteins can give rise to a similar phenotype, even when they function at distinct stages of the autophagic cascade. Therefore, LC3-II accumulation alone is insufficient to support phenocopying in my vew. Immunofluorescence analyses demonstrating comparable cellular phenotypes-such as membrane accumulation of pre-autophagosomal structures-following Rab1 knockdown should be provided. Moreover, p62 does not accumulate upon Rab1 depletion, suggesting that loss of Rab1 does not fully phenocopy ATG2 deficiency. Consequently, it remains unclear whether Rab1A depletion truly phenocopies ATG2A depletion with respect to autophagy progression or the accumulation of pre-autophagosomal structures.

(2) Interpretation of the significance of the data

(2.1) The significance statement asserts that "this study elucidates the role of early secretory membranes in autophagosome biogenesis." While the data convincingly demonstrate an association between the RAB1A GTPase and ATG2A, the study does not provide mechanistic insight into how this interaction functionally contributes to autophagy. As presented, the findings support a correlative relationship rather than a defined role in autophagosome biogenesis.

(2.2) The title states that ATG2A "engages" Rab1A- and ARFGAP1-positive membranes during autophagosome formation. However, both Rab1A and ARFGAP1 are shown to localize to pre-autophagosomal structures independently of ATG2A. In the absence of evidence demonstrating a functional or causal dependency, the term "engages" appears overstated. A more descriptive term, such as "associates," would more accurately reflect the data.

(2.3) In the Discussion, the authors state that previous studies have reported increased LC3-II levels following knockdown of Rab1 proteins (refs. 38 and 49). However, it is unclear where this observation is documented in the cited references.

(3) Some concerns remain in specific figures, as outlined below:<br /> • Quantification is missing in Fig S2D.<br /> • The authors claim: "siRNA against ARFGAP1 had very little effect" but the quantification and blots show actually no effect.<br /> • Conclusions drawn from KD experiments in Fig. S2 should be interpreted with caution, as knockdown efficiency is very low, particularly for ARFGAP1/3 in the triple knockdown.<br /> • In New Fig. 4, the representative blot is not representative of the results showed in the quantification as previously noted.

Reviewer #1 (Public review):

Summary:

Participants learned a graph-based representation, but, contrary to the hypotheses, failed to show neural replay shortly after. This prompted a critical inquiry into temporally delayed linear modeling (TDLM)--the algorithm used to find replay. First, it was found that TDLM detects replay only at implausible numbers of replay events per second. Second, it detects replay-to-cognition correlations only at implausible densities. Third, there are concerning baseline shifts in sequenceness across participants. Fourth, spurious sequences arise in control conditions without a ground truth signal. Fifth, the revised manuscript adapts a previously published synthetic simulation to show that previous validations/support of TDLM may have overestimated TDLM sensitivity because synthetic assumptions can produce unrealistically high pattern separability and reduced baseline confounds.

Strengths:

- This work is meticulous and meets a high standard of transparency and open science, with preregistration, code and data sharing, external resources such as a GUI with the task and material for the public.

- The writing is clear, balanced, and matter-of-fact.

- By injecting visually evoked empirical data into the simulation, many surface-level problems are avoided, such as biological plausibility and questions of signal-to-noise ratio.

- The investigation of sequenceness-to-cognition correlations is an especially useful add-on because much of the previous work uses this to make key claims about replay as a mechanism.

- In the revised version, the authors foreshadow ways to improve sequenceness detection by introducing a sign-flipping analysis.

Weaknesses:

Many of the weaknesses are not so much flaws in the analyses, but shortcomings when it comes to interpretation and a lack of making these findings as useful as they could be. Furthermore, as I will explain below, some weaknesses have been partially improved in the last round of revisions.

- I found the bigger picture analysis to be lacking, though improved in the latest version. Let us take stock: in other work during active cognition, including at least one study from the Authors, TDLM shows significant sequenceness. But the evidence provided here suggests that even very strong localizer patterns injected into the data cannot be detected as replay except at implausible speeds. How can both of these things be true? Assuming these analyses are cogent, do these findings not imply something more destructive about all studies that found positive results with TDLM? In the revisions, the manuscript concentrates a bit more on criteria that influence detection of sequences, though it is still not entirely clear what consequences there are for previous work.

- All things considered, TDLM seems like a fairly vanilla and low assumption algorithm for finding event sequences. Although the authors have improved their discussion of "boundary conditions" or factors for why TDLM might fail, it remains not fully clear to what extent the core problem is TDLM on an algorithmic/mathematical level (intrinsic factor), vs data quality, power, window size (extrinsic factors).

- The new sign-flip analysis underscores the authors' goal of being solution-oriented, though it is important to emphasize that a comprehensive way forward is not yet provided. This is fine, but the manuscript could be improved further through a concrete alternative or a revised version of the original approach.

Reviewer #1 (Public Review):

Summary:

Zeng et al. have investigated the impact of inhibiting lactate dehydrogenase (LDH) on glycolysis and the tricarboxylic acid cycle. LDH is the terminal enzyme of aerobic glycolysis or fermentation that converts pyruvate and NADH to lactate and NAD+ and is essential for the fermentation pathway as it recycles NAD+ needed by upstream glyceraldehyde-3-phosphate dehydrogenase. As the authors point out in the introduction, multiple published reports have shown that inhibition of LDH in cancer cells typically leads to a switch from fermentative ATP production to respiratory ATP production (i.e., glucose uptake and lactate secretion are decreased, and oxygen consumption is increased). The presumed logic of this metabolic rearrangement is that when glycolytic ATP production is inhibited due to LDH inhibition, the cell switches to producing more ATP using respiration. This observation is similar to the well-established Crabtree and Pasteur effects, where cells switch between fermentation and respiration due to the availability of glucose and oxygen. Unexpectedly, the authors observed that inhibition of LDH led to inhibition of respiration and not activation as previously observed. The authors perform rigorous measurements of glycolysis and TCA cycle activity, demonstrating that under their experimental conditions, respiration is indeed inhibited. Given the large body of work reporting the opposite result, it is difficult to reconcile the reasons for the discrepancy. In this reviewer's opinion, a reason for the discrepancy may be that the authors performed their measurements 6 hours after inhibiting LDH. Six hours is a very long time for assessing the direct impact of a perturbation on metabolic pathway activity, which is regulated on a timescale of seconds to minutes. The observed effects are likely the result of a combination of many downstream responses that happen within 6 hours of inhibiting LDH that causes a large decrease in ATP production, inhibition of cell proliferation, and likely a range of stress responses, including gene expression changes.

Strengths:

The regulation of metabolic pathways is incompletely understood, and more research is needed, such as the one conducted here. The authors performed an impressive set of measurements of metabolite levels in response to inhibition of LDH using a combination of rigorous approaches.

Weaknesses:

Glycolysis, TCA cycle, and respiration are regulated on a timescale of seconds to minutes. The main weakness of this study is the long drug treatment time of 6 hours, which was chosen for all the experiments. In this reviewer's opinion, if the goal was to investigate the direct impact of LDH inhibition on glycolysis and the TCA cycle, most of the experiments should have been performed immediately after or within minutes of LDH inhibition. After 6 hours of inhibiting LDH and ATP production, cells undergo a whole range of responses, and most of the observed effects are likely indirect due to the many downstream effects of LDH and ATP production inhibition, such as decreased cell proliferation, decreased energy demand, activation of stress response pathways, etc.

Comments on revisions:

Based on the response to comments that the authors have submitted, I do not think I need to make any changes to my review, as the time course experiment that could have explained the difference between reported results and extensive prior literature has not been performed.

Reviewer #1 (Public review):

Summary:

In this manuscript, Chengjian Zhao et al. focused on the interactions between vascular, biliary, and neural networks in the liver microenvironment, addressing the critical bottleneck that the lack of high-resolution 3D visualization has hindered understanding of these interactions in liver disease.

Strengths:

This study developed a high-resolution multiplex 3D imaging method that integrates multicolor metallic compound nanoparticle (MCNP) perfusion with optimized CUBIC tissue clearing. This method enables the simultaneous 3D visualization of spatial networks of the portal vein, hepatic artery, bile ducts, and central vein in the mouse liver. The authors reported a perivascular structure termed the Periportal Lamellar Complex (PLC), which is identified along the portal vein axis. This study clarifies that the PLC comprises CD34⁺Sca-1⁺ dual-positive endothelial cells with a distinct gene expression profile, and reveals its colocalization with terminal bile duct branches and sympathetic nerve fibers under physiological conditions.

Comments on revisions:

The authors very nicely addressed all concerns from this reviewer. There are no further concerns and comments.

Reviewer #1 (Public review):

Summary:

This study by Xu et al. investigates how clathrin-independent endocytosis in cancer cells influences T cell activation. Using a combination of biochemical approaches and imaging, the authors identify ICAM1, the ligand for the T cell integrin LFA-1, as a novel cargo of EndoA3-mediated endocytosis.

The authors then explore the functional consequences of EndoA3 depletion in cancer cells on T cell function using cytokine measurements, surface marker analyses, cytotoxicity assays and imaging. Loss of EndoA3 results in reduced T cell cytokine production, while expression of activation and exhaustion markers such as TIM-3, PD-1, and CD137 remains largely unchanged. EndoA3 knockout is associated with reduced ICAM1 surface levels and increased ALCAM levels in cancer cells. Imaging experiments further reveal directional transport of ICAM1 toward the immunological synapse, seemingly slightly reduced ICAM1 levels at the synapse upon EndoA3 depletion and an enlarged contact area between T cells and cancer cells.

Based on these observations, the authors propose a model in which EndoA3-mediated endocytosis and retrograde trafficking of ICAM1 (and ALCAM) supplies the immunological synapse with ligands for adhesion molecules. In the absence of EndoA3, T cells are suggested to compensate for suboptimal ICAM1 availability by enlarging the synaptic contact area, altering synapse architecture, leading to reduced cytokine secretion but modestly enhanced cytotoxicity.

Overall, the study provides convincing evidence for a modulatory role of EndoA3-mediated endocytosis in regulating T cell-cancer cell interactions. However, the choice of cellular model systems, the limited number of biological replicates and insufficiently supported mechanistic interpretations weaken the manuscript and weaken the strength of its conclusions.

Strengths:

The authors employ a rigorous and innovative experimental strategy that convincingly identifies ICAM1 as a novel cargo of EndoA3-mediated endocytosis with convincing visualization of directional ICAM1 transport toward the immunological synapse. In addition, the study provides a comprehensive characterization of how EndoA3 depletion in cancer cells affects T cell cytokine production, activation, proliferation and cytotoxic function, representing a valuable contribution to our understanding of how membrane trafficking pathways in target cells can modulate immune responses.

Comments on revised version:

Thank you very much for submitting your revised manuscript. I appreciated your efforts to answer all of the reviewers questions. While in my opinion the manuscript truly improved I think there are still lingering questions, in particular regarding the following points:

(1) Limited biological replication:

The LB33-MEL system remains problematic, as also noted by other reviewers. While it clearly represents an improvement over highly derived model systems such as Jurkat or Raji cells, it nevertheless effectively restricts the study to a single biological replicate. In this context, it may be more appropriate to compare the chosen approach to more state-of-the-art systems, such as expression of HLA-A*02:01, peptide loading (e.g. NY-ESO), and introduction of the matching TCR into donor-derived primary T cells. Such an approach would allow the use of multiple T cell donors and would substantially strengthen the generalizability of the conclusions.

(2) Expression levels of ICAM1:

Based on available database information (e.g. UniProt) and published literature (PMID: 9371813), ICAM1 appears to be expressed at relatively low levels in both HeLa and LB33-MEL cells. While the effects on T cells are initially discussed in terms of broader changes in EndoA3-mediated recycling of multiple surface proteins, including ICAM1 and ALCAM (and potentially others), the focus of the manuscript increasingly shifts toward ICAM1 as the primary driver of the observed phenotypes. Given the comparatively low endogenous expression of ICAM1 in the chosen model systems, it is unclear whether this emphasis is fully justified. In addition, if ICAM1 polarization toward the immunological synapse was assessed using ICAM1 overexpression, whereas other phenotypes (such as enlarged contact area) were analyzed under endogenous expression conditions, this further complicates the interpretation. As a first step toward clarifying these issues, it would be helpful to include representative flow cytometry histograms showing surface expression levels of ICAM1 and ALCAM, rather than only normalized quantifications.

(3) Cell-cell contact dynamics:

The manuscript suggests that altered contact dynamics may underlie the observed increase in cytotoxicity upon EndoA3 depletion. However, these claims are not directly tested. Such effects could be addressed with relatively straightforward experiments, for example by directly measuring T cell-cancer contact duration in co-culture assays.

Reviewer #1 (Public review):

Summary:

The authors investigate how infestation of rice plants by the small brown planthopper (Laodelphax striatellus), an important pest in rice cultivation, alters host plant carbohydrate metabolism and how these changes affect insect physiology and fitness. They show that planthopper infestation leads to a density-dependent increase in glucose levels in rice plants, which the authors suggest results from a redistribution of carbohydrates from roots to shoots. Elevated glucose levels in plants are reflected by increased glucose contents in the insects themselves, an effect that is particularly pronounced in gravid females and associated with enhanced fecundity.

In addition, the authors demonstrate that increased glucose availability enhances tolerance of the small brown planthopper to the neonicotinoid insecticide imidacloprid. These findings suggest that insect-mediated changes in plant carbohydrate allocation may benefit insect fitness in multiple ways, including increased reproductive output and enhanced tolerance to insecticides, both of which are relevant for understanding insect population dynamics in agroecosystems.

Beyond these physiological observations, the authors aim to elucidate the underlying molecular mechanisms. They propose that glucose functions not only as a nutritional resource but also as a signaling molecule. Specifically, they show that increased glucose availability is associated with activation of the Target Of Rapamycin (TOR) pathway, a conserved nutrient-sensing signaling pathway regulating growth and metabolism across eukaryotes. Activation of TOR signaling is linked to increased juvenile hormone levels, which in turn stimulate vitellogenesis and likely contribute to increased fecundity. Furthermore, elevated juvenile hormone levels are associated with increased expression of glutathione S-transferases, suggesting a mechanism contributing to enhanced detoxification capacity. Independent of this pathway, increased glucose availability also leads to higher expression of glutamate-cysteine ligase, the rate-limiting enzyme in glutathione synthesis. Together, these mechanisms provide a non-exclusive explanation for the observed increase in imidacloprid tolerance and form the basis of the authors' proposed mechanistic framework linking glucose availability to reproduction and detoxification.

Strengths:

A major strength of the manuscript is its substantial mechanistic depth and the extensive use of complementary experimental approaches that converge on a coherent mechanistic interpretation. The authors combine plant manipulations, dietary supplementation, injection assays, RNAi-mediated gene silencing, pharmacological inhibition, and rescue experiments to systematically test the role of glucose as a signaling molecule linking plant-derived nutrition to insect reproduction and insecticide tolerance. Results obtained from independent experimental strategies are highly consistent, and the different datasets collectively support the central conclusions of the study.

The role of glucose is supported by multiple lines of evidence demonstrating that increased glucose availability, whether induced by prior planthopper feeding, dietary supplementation, or direct injection, consistently results in elevated glucose levels in insects, increased oviposition, and enhanced expression of vitellogenesis-related genes (LsVg and LsVgR). The specificity of this effect is further strengthened by experiments using alternative carbohydrates that release glucose upon enzymatic cleavage, as well as inhibitor and rescue experiments, supporting the interpretation that glucose acts beyond a purely nutritional role.

The authors further establish a mechanistic link between glucose availability, TOR signaling, juvenile hormone regulation, and vitellogenesis. Activation of TOR signaling by glucose, demonstrated at the level of protein phosphorylation, together with RNAi knockdown and pharmacological inhibition, allows causal placement of TOR upstream of juvenile hormone signaling. Consistent reductions in juvenile hormone titers, vitellogenesis-related gene expression, and oviposition following TOR inhibition, as well as rescue of reproductive output by juvenile hormone analog treatment, provide strong functional support for a glucose-TOR-juvenile hormone axis regulating fecundity. The absence of additive effects following combined knockdown of TOR and juvenile hormone synthesis components further supports the interpretation that these factors act within the same signaling cascade.

Similarly, the authors provide a detailed mechanistic analysis of glucose-mediated effects on imidacloprid tolerance. Functional assays demonstrate that glutathione S-transferases contribute to detoxification in this species and that increased glucose availability enhances GST activity, glutathione synthesis, and overall glutathione levels. Transcriptomic analyses and targeted RNAi experiments further identify specific GSTs contributing to insecticide tolerance and indicate that glucose enhances detoxification through both TOR-dependent and TOR-independent mechanisms. The combined knockdown experiments, which produce additive effects on mortality, provide particularly strong support for the involvement of multiple interacting glucose-dependent pathways.

Weaknesses:

While I am impressed by the mechanistic depth of the study and the clarity with which the authors dissect the underlying physiological pathways, I am less convinced by the current conceptual framing of the phenomenon as a sophisticated adaptive strategy "co-opted" by the small brown planthopper. The data convincingly demonstrate that glucose availability activates conserved nutrient-sensing and endocrine pathways, including TOR signaling and juvenile hormone regulation, which in turn affect reproduction and detoxification capacity. However, these pathways are deeply conserved and likely operate in many insects in response to nutritional status. As such, the results may reflect a general physiological response to elevated carbohydrate availability rather than a species-specific, evolved strategy. Relatedly, herbivory-induced changes in plant carbohydrate allocation appear to be relatively common across plant-insect systems, and it would be helpful to discuss how specific (or general) the observed phenomenon is likely to be.

In particular, I encourage the authors to more clearly distinguish between (i) a conserved nutrient-responsive signaling cascade and (ii) an adaptive mechanism that evolved specifically under selection imposed by insecticide exposure. The presented data strongly support the former interpretation, whereas evidence for the latter is less clear. The increased tolerance to imidacloprid appears to arise as a consequence of enhanced metabolic and detoxification capacity under elevated glucose conditions, rather than as a trait shaped directly by insecticide-driven selection. Framing this phenomenon as an adaptation to insecticide stress may therefore overextend the conclusions that can be drawn from the data. A more cautious discussion acknowledging that glucose-mediated activation of conserved metabolic and endocrine pathways may incidentally enhance insecticide tolerance, without necessarily having evolved under insecticide selection, would strengthen the conceptual clarity of the manuscript.

Reviewer #1 (Public review):

Summary:

In their manuscript, Richter and colleagues comprehensively investigate the cell wall recycling pathway in the model alphaproteobacterium Caulobacter crescentus using biochemical, imaging, and genetic approaches. They clearly demonstrate that this organism encodes a functional peptidoglycan recycling pathway and demonstrate the activities of many enzymes and transporters within this pathway. They leverage imaging and growth assays to demonstrate that mutants in peptidoglycan recycling have varying degrees of beta-lactam sensitivity as well as morphological and cell division defects. They propose that, rather than impacting the levels or activity of the major beta-lactamase, BlaA, defects in PG recycling lead to beta-lactam sensitivity by limiting the availability of new cell wall precursors. The findings will be of interest to those in the field of bacterial cell wall biochemistry, antibiotics and antibiotic resistance, and bacterial morphogenesis.

Strengths:

Overall the manuscript is laid out logically, and the data are comprehensive, quantitative, and rigorous. The mutants and their phenotypes will be a valuable resource for Caulobacter researchers, and the findings may be relevant to cell wall recycling in other organisms.

Weaknesses:

No major weaknesses are noted.

Comments on revisions:

The authors addressed all of our concerns with the initial submission.

Reviewer #3 (Public review):

Summary:

The authors propose a new version of idTracker.ai for animal tracking. Specifically, they apply contrastive learning to embed cropped images of animals into a feature space where clusters correspond to individual animal identities. By doing this, they address the requirement for so-called global fragments - segments of the video, in which all entities are visible/detected at the same time. In general, the new method reduces the long tracking times from the previous versions, while also increasing the average accuracy of assigning the identity labels.

Comments on revisions:

I have no additional comments, the authors have responded to all the points I raised previously.

Reviewer #1 (Public review):

Summary:

This paper by Karimian et al proposes an oscillator model tuned implementing binding by (gamma) synchrony principles in a visual task. The authors set out to show how well these principles explain human behavior in a figure-ground segregation tasks. The model is inspired by electrophysiological findings in non-human primates suggesting that gamma oscillations in early visual cortex implement feature-binding through a synchronization of feature-selective neurons. The psychophysics experiment involves the identification of a figure consisting of gabor annuli, presented on a background of gabor annuli. The participants' task is to identify the orientation of the figure. The task difficulty is varied based on the contrast and density of the gabor annuli that make up the figure. The same figures are used as inputs to the oscillator model. The authors report that both the discrimination accuracy in the psychophysics experiment and the synchrony of the oscillators in the proposed model follow a similar "Arnold Tongue" relationship when depicted as a function of the texture-defining features of the figure. This finding is interpreted as evidence for gamma synchrony being the underlying mechanism of the figure-ground segregation.

Strengths:

The design of the proposed model is well-informed by electrophysiological findings, and the idea of using computational modeling to bridge between intracranial recordings in non-human primates and behavioral results in human participants is interesting. Previous work has criticized the gamma synchrony theories based on the observation that synchronization in the gamma-band is highly localized and the frequency of the oscillation depends on the visual features of the stimulus. I appreciate how the authors demonstrate that frequency-dependence and local synchronization can be features of gamma synchrony, and not contradictory to the theory. As such, I feel that this work has the potential to contribute meaningfully to the debate on whether binding by gamma synchrony is a biophysically realistic model of feature-binding in visual cortex.

I also acknowledge the additional simulations the authors present in this version of the manuscript, showing that the model is able to segregate figure from ground.

Weaknesses:

The authors have addressed my previous concerns regarding the quantification of effect sizes. I also appreciate the authors argument that the results support the idea of feature-binding through synchronization in the gamma-band, as the model's parameters were informed by electrophysiological recordings from non-human primates. Personally, I would have been curious to see if the intrinsic frequencies of the model are indeed in the gamma-band, I don't believe the authors include a figure on that. Weaknesses are still the absence of electrophysiological recordings to support the frequency-specificity of the claims, e.g. in the form of EEG/MEG recordings, but I understand that these may be difficult to obtain, as gamma oscillations are relatively weak in response to static gratings. As the authors emphasize in this updated version, they present one possible mechanism of feature binding that is not contrasted to alternative mechanisms such as binding by increased firing rates. Understandably, implementing a second model would be out of scope.

The presented simulations and behavioural results support the authors aim of presenting an oscillator model informed by gamma synchronization in V1 that supports figure-ground segregation.

Likely impact:

This work makes several predictions about the degree of synchronization for different visual properties of the figure, that could be tested with electrophysiological methods. I therefore believe that the paper has the potential to motivate interesting follow-up studies to understand how visual cortex solves the binding problem.

Comment on revised version:

In this reviewed version of the manuscript, the authors present several follow-up simulations and clarifications that address previously outlined weaknesses.

Reviewer #2 (Public review):

Summary:

The manuscript by Hathaway et al. describes a set of elegant behavioral experiments designed to understand which aspects of cue-reward contingencies drive risky choice behavior. The authors developed several clever variants of the well established rodent gambling task (also developed by this group) to understand how audiovisual cues alter learning, choice behavior, and risk. Computational and sophisticated statistical approaches were used to provide evidence that: 1) audiovisual cues drive risky choice if they are paired with rewards and decrease risk if only paired with loss, 2) pairing cues with rewards reduces learning from punishment, and 3) differences in risk taking seem to be present early on in training.

Strengths:

The paper is well written, the experiments well designed, and the results are highly interesting particularly for understanding how cues can motivate and invigorate normal and abnormal behavior.

Comments on revisions:

The authors have done an exceptional job at addressing my initial concerns and questions regarding the evidence to support their claims. I have no additional suggestions or concerns.

Reviewer #1 (Public review):

Summary:

During vertebrate gastrulation, mesendoderm cells are initially specified by morphogens (e.g. Nodal) and segregate into endoderm and mesoderm in part based on Nodal concentrations. Using zebrafish genetics, live imaging, and single-cell multi-omics, the manuscript by Cheng et al presents evidence to support a claim that anterior endoderm progenitors derive primarily from prechordal plate progenitors, with transcriptional regulators goosecoid (gsc) and ripply1 playing key roles in this cell fate determination. Such a finding would represent a significant advance in our understanding of how anterior endoderm is specified in vertebrate embryos.

Strengths:

Live imaging based tracking of PP and endo reporters (Fig 2) are well executed and convincing, though a larger number of individual cell tracks will be needed. In the first round of review, only a single cell track (n=1) was quantified. Now, more tracks have been collected but these data are still not clearly reported in a way that warrants their evaluation.

Weaknesses:

(1) While the authors have made an effort to include a gsc:CRE lineage tracing component to their study, the experimental data now presented (Figure S4E and reviewer figures) could be much stronger and more thorough. In the new panel, authors show a single microscopy image containing both red and green fluorescent cells. The green signal, which seems to mark the PP, is presumably derived from Tg(gsc:EGFP). The red mCherry signal is presumably derived from the combined effects of a Tg(gsc:CRE) and Tg(sox17-lox-STOP-lox-mCherry), i.e., labeling the progeny of gsc+ progenitors which expressed CRE and underwent recombination to create a productive endoderm-specific Tg(sox17:mCherry) reporter. The result appears to be promising and in line with the authors' predictions. However, this result should be strengthened by performing the experiment in stable transgenic lines (not just freshly injected F0 embryos) and should be properly quantified. The authors state in the legend that "the experiment was performed on at least 3 independent replicates", but offer no further detail, explanations, or quantifications. This issue is reminiscent of concerns from the previous round of review, where live tracking data derived from examining just a single (n=1) cell were presented. These standards might be adequate for generating preliminary insights, but fall far below what we would have previously expected from an Elife publication.

(2) I found the authors' rebuttal to my concerns about URD-trajectory derived insights and gsc/sox17 expression timing confusing. The authors claim that they get different results regarding gsc expression prevalence in the hypothetical PP/endoderm progenitor cluster when comparing scRNAseq data from embryos vs explants. Then they seem to use this difference to justify the use of the explants over the embryos - presumably because the explants enriched for the behavior that they wanted to see? They conclude that "directly using embryonic data to dissect the mechanism of fate separation between PP and anterior endoderm might not yield highly accurate results." I strongly disagree with this. I would argue that the whole-embryo dataset is likely doing a better job of cleanly separating these trajectories from each other.

(3) My concern about the use of n=1 cell for live tracking has been partially but not fully addressed. The authors should plot data point from each individual cell in the revised Figure 2D, instead of just saying "multiple cells" they should report the total number of cells that are actually included now (n=?), and should provide representative movies for a few additional examples.

At present the authors' data, as presented, still only partially support their aims and conclusions.

Reviewer #1 (Public review):

Summary:

The authors aimed to elucidate the recruitment order and assembly of the Cdv proteins during Sulfolobus acidocaldarius archaeal cell division using a bottom-up reconstitution approach. They employed liposome-binding assays, EM, and fluorescence microscopy with in vitro reconstitution in dumbbell-shaped liposomes to explore how CdvA, CdvB, and the homologues of ESCRT-III proteins (CdvB, CdvB1, and CdvB2) interact to form membrane remodeling complexes.<br /> The study sought to reconstitute the Cdv machinery by first analyzing their assembly as two sub-complexes: CdvA:CdvB and CdvB1:CdvB2ΔC. The authors report that CdvA binds lipid membranes only in the presence of CdvB and localizes preferentially to membrane necks. Similarly, the findings on CdvB1:CdvB2ΔC indicate that truncation of CdvB2 facilitates filament formation and enhances curvature sensitivity in interaction with CdvB1. Finally, the authors reconstitute a quaternary CdvA:CdvB:CdvB1:CdvB2 complex and demonstrate its enrichment at membrane necks. The mechanistic details of how these complexes drive membrane remodeling, particularly through subcomplex removal by the proteasome and/or CdvC, remain insufficiently addressed, and the study therefore mainly provides an experimental framework for future mechanistic investigation.

Strengths:

The study of machinery assembly and its involvement in membrane remodeling, particularly using bottom-up reconstituted in vitro systems, presents significant challenges. This is particularly true for systems like the ESCRT-III complex, which localizes uniquely at the lumen of membrane necks prior to scission. The use of dumbbell-shaped liposomes in this study provides a promising experimental model to investigate ESCRT-III and ESCRT-III-like protein activity at membrane necks.<br /> The authors present intriguing evidence regarding the sequential recruitment of ESCRT-III proteins in crenarchaea-a close relative of eukaryotes.

Weaknesses:

The findings of this study suggest that the hierarchical recruitment characteristic of eukaryotic systems may predate eukaryogenesis, which represents a significant and exciting contribution. However, the broader implications of these findings for membrane remodeling mechanisms remain largely unexplored. Nevertheless, this study provides a valuable experimental framework to address these questions in the future.

Reviewer #1 (Public review):

In this manuscript, the authors aim to define how rapid eye movement sleep supports memory consolidation by identifying the brain circuits that are selectively engaged during this sleep state. They focus on a pathway linking a hypothalamic region involved in sleep regulation to the medial septum and onward to a hippocampal subregion that is critical for social memory. By combining recordings of neural activity with sleep-state-specific circuit manipulations, the study seeks to explain how information is routed during sleep to support distinct types of memory.

A major strength of the work is the use of state-of-the-art circuit-based approaches to link sleep dynamics to defined long-range connections and behavioral outcomes. The authors show that neurons in the lateral supramammillary region projecting to the medial septum are selectively active during rapid eye movement sleep, and that silencing this pathway during this sleep state disrupts consolidation of both social and contextual fear memories. Further dissection of downstream circuitry reveals that inhibition of the medial septum-to-hippocampal CA2 pathway during rapid eye movement sleep selectively impairs social memory. These results provide support for functional specialization within parallel pathways and suggest that this circuit acts as a hub for routing memory-related information during sleep.

While the evidence supporting a role for this circuit in sleep-dependent memory consolidation is compelling, several important mechanistic details remain unresolved. The chemical signaling used by the neurons connecting the hypothalamus to the medial septum is not clearly defined, leaving open whether these cells release excitatory signals, inhibitory signals, or a combination of both. In addition, the medial septum contains multiple neuronal populations with distinct downstream targets, and the specific cell types receiving input from this pathway are not clearly identified. Similarly, the nature of the signals delivered from the medial septum to the hippocampus remains unclear, making it difficult to link circuit anatomy to the observed behavioral specificity. Finally, because different circuit segments are manipulated independently, the causal relationship between upstream and downstream pathways remains suggestive rather than definitive and should be discussed explicitly as a limitation or addressed experimentally.

Overall, the authors largely achieve their aims by identifying a rapid eye movement sleep-specialized circuit that contributes to memory consolidation in a modality-specific manner. The findings are likely to have a meaningful impact on the field by advancing understanding of how sleep organizes memory through parallel neural pathways and by providing a useful framework for future studies of sleep-dependent brain state regulation. With additional clarification of circuit mechanisms or a clearer discussion of current limitations, the study would offer even greater value to the neuroscience community.

Reviewer #3 (Public review):

Summary:

Kroeg et al. introduced a novel method for generating 3D cortical layer-like organization in hiPSC-derived models, achieving remarkably consistent topography within compact dimensions. Their approach involves seeding frontal cortex-patterned iPSC-derived neural progenitor cells into 384-well plates, which triggers the spontaneous assembly of adherent cortical organoids comprising diverse neuronal subtypes, astrocytes, and oligodendrocyte-lineage cells.

Strengths:

Compared with existing brain organoid models, these adherent cortical organoids exhibit enhanced reproducibility and improved cell viability during prolonged culture, thereby providing versatile opportunities for high-throughput drug discovery, neurotoxicological screening, and investigation of brain disorder pathophysiology. Overall, this study addresses an important and timely need for advancing current brain organoid systems.

Weaknesses:

Highlighting the consistency of differentiation across different cell lines and standardizing functional outputs are crucial to emphasize the broad future potential of this new organoid system for large-scale pharmacological screening. The authors provided a substantial amount of new data during the revision process to support the reproducibility of neuronal activity. The next step would be to leverage this platform for functional screening of chemical and genetic perturbations to identify new drug candidates.

Comments on revisions:

Most of my previous concerns were adequately addressed through the revision.

Reviewer #2 (Public review):

Summary:

Xu et al. used fMRI to examine the neural correlates associated with retrieving temporal information from an external compared to internal perspective ('mental time watching' vs. 'mental time travel'). Participants first learned a fictional religious ritual composed of 15 sequential events of varying durations. They were then scanned while they either (1) judged whether a target event happened in the same part of the day as a reference event (external condition); or (2) imagined themselves carrying out the reference event and judged whether the target event occurred in the past or will occur in the future (internal condition). Behavioural data suggested that the perspective manipulation was successful: RT was positively correlated with sequential distance in the external perspective task, while a negative correlation was observed between RT and sequential distance for the internal perspective task. Neurally, the two tasks activated different regions, with the external task associated with greater activity in the supplementary motor area and supramarginal gyrus, and the internal condition with greater activity in default mode network regions. Of particular interest, only a cluster in the posterior parietal cortex demonstrated a significant interaction between perspective and sequential distance, with increased activity in this region for longer sequential distances in the external task but increased activity for shorter sequential distances in the internal task. Only a main effect of sequential distance was observed in the hippocampus head, with activity being positively correlated with sequential distance in both tasks. No regions exhibited a significant interaction between perspective and duration, although there was a main effect of duration in the hippocampus body with greater activity for longer durations, which appeared to be driven by the internal perspective condition. On the basis of these findings, the authors suggest that the hippocampus may represent event sequences allocentrically, whereas the posterior parietal cortex may process event sequences egocentrically.

Strengths:

The topic of egocentric vs. allocentric processing has been relatively under-investigated with respect to time, having traditionally been studied in the domain of space. As such, the current study is timely and has the potential to be important for our understanding of how time is represented in the brain in the service of memory. The study is well thought out and the behavioural paradigm is, in my opinion, a creative approach to tackling the authors' research question. A particular strength is the implementation of an imagination phase for the participants while learning the fictional religious ritual. This moves the paradigm beyond semantic/schema learning and is probably the best approach besides asking the participants to arduously enact and learn the different events with their exact timings in person. Importantly, the behavioural data point towards successful manipulation of internal vs. external perspective in participants, which is critical for the interpretation of the fMRI data. The use of syllable length as a sanity check for RT analyses as well as neuroimaging analyses is also much appreciated.

Suggestions:

The authors have satisfactorily addressed my last remaining suggestion.

Reviewer #1 (Public review):

The authors use Flow cytometry and scRNA seq to identify and characterize the defect in gdT17 cell development from HEB f/f, Vav-icre (HEB cKO) and Id3 germline-deficient mice. HEB cKO mice showed defects in the gdT17 program at an early stage, and failed to properly upregulate expression of Id3 along with other genes downstream of TCR signaling. Id3KO mice showed a later defect in maturation. The results together indicate HEB and Id3 act sequentially during gdT17 development. The authors further showed that HEB and TCR signaling synergize to upregulate Id3 expression in the Scid-adh DN3-like T cell line. Analysis of previously published Chip-seq data revealed binding of HEB (and Egr2) at overlapping regulatory regions near Id3 in DN3 cells.The study provides insight into mechanisms by which HEB and Id3 act to mediate gdT17 specification and maturation. The work is well performed and clearly presented.

Comments on revisions:

The authors have answered all of my questions. I am strongly supportive of the revised work.

Reviewer #2 (Public review):

Summary:

The premise of the manuscript by Matteucci et al. is interesting and elaborates a mechanism via which TNFa regulates monocyte activation and metabolism to promote murine survival during Plasmodium infection. The authors show that TNF signaling (via an unknown mechanism) induces nitrite synthesis, which (via yet an unknown mechanism), and stabilizes the transcription factor HIF1a. Furthermore, that HIF1a (via an unknown mechanism) increases GLUT1 expression and increases glycolysis in monocytes. The authors demonstrate that this metabolic rewiring towards increased glycolysis in a subset of monocytes is necessary for monocyte activation including cytokine secretion, and parasite control.

Strengths:

The authors provide elegant in vivo experiments to characterize metabolic consequences of Plasmodium infection, and isolate cell populations whose metabolic state is regulated downstream of TNFa. Furthermore, the authors tie together several interesting observations to propose an interesting model regarding

Weaknesses:

The main conclusion of this work - that "Reprogramming of host energy metabolism mediated by the TNF-iNOS-HIF1a axis plays a key role in host resistance to Plasmodium infection" is unsubstantiated. The authors show that TNFa induces GLUT1 in monocytes, but never show a direct role for GLUT1 or glucose uptake in monocytes in host resistance to infection (nor the hypoglycemia phenotype they describe).

Comments on revisions:

The demonstration that the established TNF-iNOS-HIF-1α-glycolysis axis operates in vivo during P. chabaudi infection is valuable and relevant. However, it constitutes contextual validation and must be carefully described as such. This distinction, i.e., "what has already been shown vs. what is new" is not consistently reflected in the framing of the manuscript raising overstatement concerns. This is particularly evident in the abstract and other conclusive statements, where mechanistic novelty is implied, even when the underlying pathways/mechanisms are already known. To improve the manuscript, all sentences that refer to already established findings should be accurately described as such.

For example, the abstract states: "Here, we show that TNF signaling hampers physical activity, food intake, and energy expenditure while enhancing glucose uptake by the liver and spleen as well as controlling parasitemia in P. chabaudi-infected mice." In this sentence, the effects of TNF signaling on physical activity, food intake, energy expenditure, glucose metabolism and control of parasitemia are unequivocally established and therefore do not, in themselves, constitute new findings. Feeding behavior, not cell-intrinsic metabolism, may drive glycemic differences

The authors propose that TNF signaling leads to GLUT1 upregulation (in inflammatory monocytes, MO-DCs, and within the liver and spleen) during Plasmodium infection, and that this results in increased glucose uptake contributing to systemic hypoglycemia. While this is an intriguing hypothesis, we urge the authors to consider an alternative explanation that, at present, is not adequately ruled out. Given that glycemia serves as a central functional readout in the manuscript, this distinction is essential to clarify.

The observed regulation of glycemia is likely not a direct consequence of increased glucose uptake by immune cells or by tissues but may instead reflect broader differences in disease severity across genotypes. The iNOS KO, TNFR KO, and HIF-19775ΔαLyz2 mice likely experience a dampened inflammatory response, which would blunt infection-induced anorexia and help preserve overall metabolic homeostasis. This alternate interpretation is supported by the authors' metabolic cage data showing increased physical activity in TNFR KO mice and the elevated food intake shown in Figure 2B.

Since anorexia and energy expenditure are tightly coupled to the inflammatory milieu, it is plausible that these behavioral and systemic differences-not monocyte nor tissue GLUT1 expression per se-are the primary contributors to the observed glycemic patterns. To support their current interpretation, the authors should perform a pair-feeding experiment in which (at least) TNFR KO mice are restricted to the same food intake as infected WT controls. This would help disentangle whether differences in glycemia truly reflect immune-driven metabolic rewiring or are secondary to differences in caloric intake.

The contribution of monocyte-specific glucose metabolism to host resistance remains unresolved.

We appreciate the authors' effort to address the mechanistic role of glycolysis in host resistance using in vivo 2-deoxyglucose (2DG) treatment. However, I would like to point out that while this experiment is informative, it does not fully resolve the specific concern raised regarding the cell-intrinsic role of TNF-induced glycolysis in monocytes. 2DG acts systemically, inhibiting glycolysis across a wide range of cell types-including hepatocytes, endothelial cells, lymphocytes, and myeloid populations. Therefore, the observed increase in parasitemia following 2DG treatment may reflect the broad importance of glycolysis for host defense, or alternatively, may result from elevated circulating glucose levels induced by 2DG (PMID: 35841892), which could enhance parasite growth by increasing nutrient availability. Therefore, this experiment does not allow for a specific conclusion about the requirement for TNF-driven metabolic reprogramming in monocytes.

Reviewer #1 (Public review):

Summary:

The manuscript of Heydasch et al. addresses the spatiotemporal regulation of Rho GTPase signaling in living cells and its coupling to the mechanical state of the cell. They focus on a GAP of RhoA, the Rho specific GAP Deleted in Liver Cancer 1 (DLC1). They first show that removing DLC1 either by a CRISPR KO or by downregulation using siRNA leads to an increased contractility and globally elevated RhoA activity, as revealed by a FRET biosensor. This result was expected, since DLC1 is deactivating RhoA its absence should lead to increasing amounts of active RhoA. To go beyond global and steady levels of RhoA activity, the authors developed an acute optogenetic system to study transient RhoA activity dynamics in different genetic and subcellular contexts. In WT cells, they found that pulses of activation lead to an increased RhoA activity at focal adhesions (FA) compared to plasma membrane (PM), which suggests that FAs contain less RhoA GAPs, more RhoA, or that FAs involve positive feedbacks implying others GEFs for example. In DLC1 KO cells, they found that the RhoA response upon pulses of optogenetic activation was increased (higher peak) both at FA and PM, which could be expected since less GAP should increase the amount of active RhoA. But surprisingly, they observed also a higher rate of RhoA deactivation in DLC1 KO cells, which is counterintuitive: less GAP should result in a slower rate of deactivation. Less GAP should also lead to a lower rate of observed RhoA activation (smaller koff) and delayed peak. Using a modeling approach and control experiments (to monitor the optogenetic intrinsic dynamics), the authors propose that there is a negative feedback in WT cell between activated RhoA and the activity of its GAPs (other than DLC1). More active RhoA decreases GAP activity such that active RhoA relaxation to its basal state is relatively slow. This negative feedback would be absent in DCL1-deficient cells, explaining the relatively faster relaxation. This hypothesis is convincing given the data and the model, and it shows that there are compensatory mechanisms at play when DLC1 is knocked down. Further on, the authors study the dynamics of DLC1 on FAs depending on the mechanical state and nicely show a causal decrease of DLC1 enrichment at FA upon FA reinforcement, hereby probing a positive feedback where RhoA activation is further amplified as the force exerted at FA is increasing. Altogether, this work highlight the extremely fine regulation in space and time of RhoGTPases that is only revealed through acute perturbations, while at the cell scale and long time scale, complex compensatory mechanisms are at play rendering knock-down or overexpression experiments not always straightforward to interpret (in the present case, knock-down of a deactivator lead to an increase of deactivation rate through the induced absence of other activity dependent-deactivators).

Strengths:

- Experiments are precise and well done.

- Technically, the work brings original and interesting data. The use of transient optogenetic activation within focal adhesions together with a biosensor of activity is new and elegant.

- The link between DLC1 and global contractility/RhoA activity is clear and convincing.

- The surprising higher rate of RhoA deactivation in DLC1 KO cells is convincing, as well as the differences in the dynamics of RhoA between focal adhesions and plasma membrane.

- The model is very helpful to support the hypothesis of the negative feedback loop.

- The correlation between DLC1 enrichment and focal adhesion dynamics is very clear.

Weaknesses:

- The negative and positive feedback loops could have been dug more deeply molecularly (in particular discover what are the compensatory mechanisms at play), but this could be the purpose of future work.

Comments on revised version:

I thank the authors for the great improvement of their work and their detailed answers to my comments. The modeling work is great and really brings novelty to the story. It also helps a lot to have the data for the optoLARG recruitment. I suggest authors move to the Version of Record.

Reviewer #1 (Public review):

Summary:

The authors were seeking to identify a molecular mechanism whereby the small molecule RY785 selectively inhibits Kv2.1 channels. Specifically, the authors sought to explain some of the functional differences that RY785 exhibits in experimental electrophysiology experiments as compared to other Kv inhibitors, namely the charged and non-specific inhibitor tetraethylammonium (TEA). The authors used a recently published cryo-EM Kv2.1 channel structure in the open activated state and performed a series of multi-microsecond-long all-atom molecular dynamics simulations to study Kv2.1 channel conduction under the applied membrane voltage with and without RY785 or TEA present. They observed that while TEA directly blocks K+ permeation by occluding ion permeation pathway, RY785 binds to multiple non-polar residues near the hydrophobic gate of the channel driving it to a semi-closed non-conductive state. They confirmed this mechanism using an additional set of simulations and used it to explain experimental electrophysiology data,

Strengths:

The total length of simulation time is impressive, totaling many tens of microseconds. The authors develop their own forcefield parameters for the RY785 molecule based on extensive QM based parameterization. The computed permeation rate of K+ ions through the channel observed under applied voltage conditions is in reasonable agreement with experimental estimates of the single channel conductance. The authors have performed extensive simulations with the apo channel as well as both TEA and RY785. The simulations with TEA reasonably demonstrate that TEA directly blocks K+ permeation by binding in the center of the Kv2.1 channel cavity, preventing K+ ions from reaching the SCav site. The authors conclude that RY785 likely stabilizes a partially closed conformation of the Kv2.1 channel and thereby inhibits K+ current. This conclusion is plausible given that RY785 makes stable contacts with multiple hydrophobic residues in the S6 helix, which they can also validate using a recently published closed-state Kv2.1 channel cryo-EM structure. This further provides a possible mechanism for the experimental observations that RY785 speeds up the deactivation kinetics of Kv2 channels from a previous experimental electrophysiology study.

Weaknesses:

The authors, however, did not directly observe this semi-closed channel conformation and in fact acknowledge that more direct simulation evidence would require extensive enhanced-sampling simulations beyond the scope of this study. They have not estimated the effect of RY785 binding on the protein-based hydrophobic pore constriction, which may further substantiate their proposed mechanism. And while the authors quantified K+ permeation, they have not made any estimates of the ligand binding affinities or rates, which could have been potentially compared to experiment and used to validate their models.

However, despite those relatively minor weaknesses, the conclusions of the study are convincing, and overall this is a solid study helping us to understand two distinct molecular mechanisms of the voltage-gated potassium channel Kv2.1 inhibition by TEA and RY785, respectively.

Reviewer #2 (Public review):

Summary:

The work set out to better understand the phenomenon of antibiotic persistence in mycobacteria. Three new observations are made using the pathogenic Mycobacterium abscessus as an experimental system: phenotypic tolerance involves suppression of ROS, protein synthesis inhibitors can be lethal for this bacterium, and levofloxacin lethality is unaffected by deletion of catalase, suggesting that this quinolone does not kill via ROS.

Strengths:

The ROS experiments are supported in three ways: measurement of ROS by a fluorescent probe, deletion of catalase increases lethality of selected antibiotics, and a hypoxia model suppresses antibiotic lethality. A variety of antibiotics are examined, and transposon mutagenesis identifies several genes involved in phenotypic tolerance, including one that encodes catalase. The methods are adequate for making these statements.

Overall impact:

Showing that ROS accumulation is suppressed during phenotypic tolerance, while expected, adds to the examples of the protective effects of low ROS levels. Moreover, the work, along with a few others, extends the idea of antibiotic involvement with ROS to mycobacteria. These observations help solidify the field. The work raises an important unanswered question: why are rifampicin and many protein synthesis inhibitors bacteriostatic with E. coli but bactericidal with pathogenic mycobacteria?

Comments on revisions:

I call attention to word choice, because it can indicate how familiar the authors are with the field. An issue that caught my attention was the use of the words persistence and tolerance, because they are not uniformly used in the generally accepted way (see Balaban 2019 Nat Rev Micro). In this consensus statement persistence refers specifically to a subpopulation and as such has survival kinetics that are distinct from those seen with tolerance, a phenomenon that refers to the entire population. I notice that the Balaban paper is not in the reference list. My suggestion is to take a look at the Balaban paper and then examine every use of the words tolerance and persistence in the manuscript to be sure that they fit the Balaban definition.

Reviewer #1 (Public review):

Summary:

The authors created a metric to score the toxicity of specific amino acid homorepeats that accounts for differences in physicochemical properties. This "neutrality" score reflects how often a particular homorepeat appears in nature across the proteomes of different species. This can be used to understand known proteins and their characteristics, as well as inform on the upcoming field of protein design.

Strengths:

This study represents a very careful and thorough study of the amino acid homorepeats and does a remarkable job of accounting for the effects of the fluorescent protein tags.

Weaknesses:

The initial characterization of the neutrality score is missing a control of a known toxic homorepeat to help validate this method of characterizing amino acid homorepeats.

The authors did achieve their aim of developing a metric by which to score the toxicity and properties of amino acid homorepeats. This can be used in the future with other common amino acid motifs that are not homorepeats and can help scientists refine computer models for rational protein design.

Reviewer #1 (Public review):

Summary:

This manuscript describes a putative clinical association between ARID5B genetic variants and a novel neurodevelopmental syndrome characterized by global developmental delay, intellectual disability, and occasional neuroinflammatory episodes. While the identification of 29 individuals with overlapping phenotypes and the use of a CRISPR-Cas9 mouse model suggest a potential gene-disease link, the study suffers from significant methodological gaps in variant prioritization and a lack of robust mechanistic evidence to support its primary claims. Specifically, the "neuroinflammation" component is over-emphasized despite appearing in only a minor subset of the cohort, and the molecular pathogenesis remains insufficiently explored beyond initial protein localization assays.

Strengths:

(1) The study proposes a new clinical syndrome associated with the ARID5B gene, distinguishing it from established Coffin-Siris syndromes related to other ARID family members.

(2) The recruitment of a relatively large cohort of 29 individuals from diverse geographical and ethnic backgrounds strengthens the initial phenotypic description.

(3) The combination of human clinical data, in vitro localization assays, and an in vivo mouse model provides a multi-level framework for investigating the gene's function.

(4) The identification of variants in the exceptionally long final exon of ARID5B that escape nonsense-mediated mRNA decay (NMD) offers an interesting perspective on the molecular pathology of this gene.

Weaknesses:

(1) The description of the genomic methodology appears limited. A more detailed explanation of the filtration and selection process for variant prioritization is essential. The authors should provide a comprehensive summary of evidence (e.g., CADD scores, allele frequencies in gnomAD, and segregation analysis) to justify the selection of the reported variants, even if they do not strictly meet all ACMG/AMP criteria.

(2) The cohort includes several inherited variants and missense mutations that require more robust evidence of pathogenicity. For example, the presence of the variant in population databases (gnomAD) suggests the need for careful re-evaluation of its causality. A more rigorous assessment using diverse computational metrics, such as PhyloP scores and conservation analysis, is necessary to confirm the pathogenicity of the missense variants.

It is recommended that the authors re-evaluate the cohort to ensure that only variants with strong evidence of causality are included to maintain a clear genotype-phenotype correlation.

(3) The proposed molecular mechanism would benefit from further empirical support. The claim of NMD escape is currently supported by only a small number of cases, and a much more detailed explanation is also required for the experimental data provided.

Although the mouse model exhibits developmental abnormalities, it does not recapitulate the other systemic features reported in humans. In addition, given that "brain development" is a central theme, the manuscript lacks detailed neuroanatomical data, histopathology, or other molecular biological (e.g., RNA-seq) evidence from brain specimens to substantiate these claims at a molecular level.

(4) The emphasis on "neuroinflammation" in the title may be disproportionate to its observed frequency. Central nervous system inflammation was identified in only a small subset of the cohort (2 of 29 individuals).

Without additional experimental validation, such as immunological challenges in the Arid5b mouse model, it is premature to characterize this as a hallmark feature. Additionally, the inconsistent response to immunotherapy suggests that the autoimmune component requires further investigation.

(5) Supplementary tables require reorganization to improve clarity. The current structures make it difficult for readers to effectively analyze the data, and a more standardized format is recommended.

(6) As the manuscript proposes a novel disease entity, a more comprehensive clinical discussion is warranted. The authors should provide a more systematic description of the core clinical features and, crucially, address the genotype-phenotype correlation. Specifically, a more detailed analysis is required to determine whether the clinical severity or the presence of specific features varies according to the location of the variant or the type of mutation. Such insights are essential for clinicians to differentiate this syndrome from other ARID-related disorders.

Reviewer #1 (Public review):

Summary:

This is an excellent and strong paper. The authors not only show the mechanisms of action of destabilizing mutations in VHL, but notably, they also go on to computationally design and experimentally test an inhibitor that restores wild-type pVHL function, offering starting points for a new class of kidney cancer drugs. The approach that the authors take here can be used to target destabilizing mutations in repressor proteins, common in diseases, including cancer.

Strengths:

This paper is the culmination of an extraordinary amount of work, over years, including method development and testing by a broad range of tools and experiments. It is thorough and comprehensive. It is also well-written and easy to follow.

Reviewer #1 (Public review):

The current study is a follow-up to a previously published article in eLife in 2021, demonstrating that the transcription factor MYRF-1 interacts with the transmembrane protein PAN-1, which is required for the stability and targeting of MYRF-1 to the plasma membrane. There, MYRF-1 undergoes self-catalytic cleavage of its intracellular domain and translocates to the nucleus. Here, the authors analyze the activation of MYRF-1 during the larval development of C. elegans. They nicely show that MYRF-1 cleavage and nuclear translocation oscillate with larval stage transitions. They further identify two regions in MYRF-1 and PAN-1 that negatively regulate MYRF-1 cleavage and activation, and show that relief of this negative regulation causes premature lin-4 activation and overrides nutrient-responsive developmental checkpoints. The experiments are elegant and accurately support the conclusions raised. There are only minor comments and suggestions to improve the manuscript.

Reviewer #1 (Public review):

Summary:

This manuscript by Feng et al. uses mouse models to study the embryonic origins of HSPCs. Using multiple types of genetic lineage tracing, the authors aimed to identify whether BM-resident endothelial cells retain hematopoietic capacity in adult organisms. Through an important mix of various labeling methodologies (and various controls), they reach the conclusion that BM endothelial cells contribute up to 3-4% of hematopoietic cells in young mice.

Strengths:

The major strength of the paper lies in the combination of various labeling strategies, including multiple Cdh5-CreER transgenic lines, different CreER lines (col1a2), and different reporters (ZsGreen, mTmG), including a barcoding-type reporter (PolyLox). This makes it highly unlikely that the results are driven by a rare artifact due to one random Cre line, or one leaky reporter. The transplantation control (where the authors show no labeling of transplanted LSKs from the Cdh5 model) is also very supportive of their conclusions.

Weaknesses:

While the updated manuscript now provides strong evidence for Cdh5-CreER+ cells as a source of myeloid-biased hematopoiesis, the true identity of these "adult EHT stem cells", their differentiation hierarchy, the kinetics, the EHT mechanism, and the physiological relevance of this process remain unaddressed.

DOI: 10.7554/eLife.106720

Resource: None

Curator: @evieth

SciCrunch record: RRID:ZFIN_ZDB-ALT-120508-1

What is this?

DOI: 10.7554/eLife.106720

Resource: None

Curator: @evieth

SciCrunch record: RRID:ZFIN_ZDB-ALT-160809-1

What is this?

DOI: 10.7554/eLife.106720

Resource: (ZFIN Cat# ZDB-ALT-070316-1,RRID:ZFIN_ZDB-ALT-070316-1)

Curator: @evieth

SciCrunch record: RRID:ZFIN_ZDB-ALT-070316-1

What is this?

DOI: 10.1242/dev.204359

Resource: None

Curator: @scibot

SciCrunch record: RRID:ZFIN_ZDB-ALT-070529-1

What is this?

DOI: 10.1242/dev.204359

Resource: None

Curator: @evieth

SciCrunch record: RRID:ZFIN_ZDB-ALT-111104-1

What is this?

DOI: 10.1242/dev.204359

Resource: None

Curator: @evieth

SciCrunch record: RRID:ZFIN_ZDB-ALT-090625-1

What is this?

Reviewer #1 (Public review):

Summary:

The goal of this paper was to determine whether the T cell receptor (TCR) repertoire differs between a male or female human. To address this, this group sequenced TCRs from double-positive and single-positive thymocytes in male and female humans of various ages. Such an analysis on sorted thymocyte subsets has not been performed in the past. The only comparable dataset is a pediatric thymocyte dataset where total thymocytes were sorted.

They report on participant ages and sexes, but not on ethnicity, race, nor provide information about HLA typing of individuals. The experiments are heroic, yet do represent a relatively small sampling of diverse humans. They observed no differences in TCRbeta or TCRalpha usage, combinational diversity, or differences in the length of the CDR3 region, or amino acid usage in the CD3aa region between males or females. Though they observed some TCRbeta CD3aa sequence motifs that differed between males and females, these findings could not be replicated using an external dataset and therefore were not generalizable to the human population.

They also compared TCRbeta sequences against those identified in the past databases using computational approaches to recognize cancer-, bacterial-, viral-, or autoimmune-antigens. They found little overlap of their sequences with these annotated sequences (depending on the individual, ranged from 0.82-3.58% of sequences). Within the sequences that were in overlap, they found that certain sequences against autoimmune or bacterial antigens were significantly over-represented in female versus male CD8 SP cells. Since no other comparable dataset is available, they could not conclude whether this is a generalizable finding in the human population.

Strengths:

It is a novel dataset that attempts to understand sex differences in the T cell repertoire in humans. Overall, the methodologies are sound and are the current state-of-the-art. There was an attempt to replicate their findings in cases where an appropriate dataset was available. I agree that there are no gross differences in TCR diversity between males and females. This is an important negative result.

Weaknesses:

Overall, the sample size is small given that it is an outbred population. This reviewer recognizes the difficulty in obtaining samples for this experiment (which were from deceased donors), and this limitation was appropriately discussed. Their analysis was limited by the current availability of other TCR sequences. These weaknesses were appropriately discussed and considered.

Reviewer #1 (Public review):

Summary:

This paper tackles an important question: What drives the predictability of pre-stimulus brain activity? The authors challenge the claim that "pre-onset" encoding effects in naturalistic language data have to reflect the brain predicting the upcoming word. They lay out an alternative explanation: because language has statistical structure and dependencies, the "pre-onset" effect might arise from these dependencies, instead of active prediction. The authors analyze two MEG datasets with naturalistic data.

Strengths:

The paper proposes a very interesting alternative hypothesis for claims in prior work (e.g., Goldstein et al., 2022). In contrast to claims in prior work, the current paper convincingly demonstrates that prior results can be explained by inherent stimulus dependencies in natural language, as opposed to the brain actively predicting future linguistic content.

Two independent datasets are analyzed. The analyses with the most and least predictive words is clever, and is nicely complementing the more naturalistic analyses. The work emphasizes how claims about linguistic prediction cannot be trivially drawn using encoding models in naturalistic designs.

Reviewer #1 (Public review):

Summary:

The authors investigated the population structure of the invasive weed Lantana camara from 36 localities in India using 19,008 genome-wide SNPs obtained through ddRAD sequencing.

Strengths:

The manuscript is well-written, the analyses are sound, and the figures are of great quality.

Weaknesses:

The narrative almost completely ignores the fact that this plant is popular in horticultural trade and the different color morphs that form genetic populations are most likely the result of artificial selection by humans for certain colors for trade, and not the result of natural selfing. Although it may be possible that the genetic clustering of color morphs is maintained in the wild through selfing, there is no evidence in this study to support that. The high levels of homozygosity are more likely explained as a result of artificial selection in horticulture and relatively recent introductions in India. Therefore, the claim of the title that "the population structure.. is shaped by its mating system" is in part moot, because any population structure is in large part shaped by the mating system of the organism, but further misleading because it is much more likely artificial selection that caused the patterns observed.

Update after manuscript was revised by authors:

The authors added a selfing experiment, showing that the wild plants are selfing and not outcrossing, which limits the genetic exchange. This supports their claims, but a link with the horticultural industry is still lacking in the study, and conclusions should still be viewed in the regional context of India rather than globally.

Reviewer #1 (Public review):

Summary:

In this paper, Chen et al. identified a role for the circadian photoreceptor CRYPTOCHROME (CRY) in promoting wakefulness under short photoperiods. This research is potentially important as hypersomnolence is often seen in patients suffering from SAD during winter times. The mechanisms underlying these sleep effects are poorly known.

Strengths:

The authors clearly demonstrated that mutations in cry lead to elevated sleep under 4:20 Light-Dark (LD) cycles. Furthermore, using RNAi, they identified GABAergic neurons as a primary site of CRY action to promote wakefulness under short photoperiods. They then provide genetic and pharmacological evidence demonstrating that CRY acts on GABAergic transmission to modulate sleep under such conditions.

Weaknesses:

The authors then went on to identify the neuronal location of this CRY action on sleep. This is where this reviewer is much more circumspect about the data provided. The authors hypothesize that the l-LNvs which are known to be arousal promoting may be involved in the phenotypes they are observing. To investigate this, they undertook several imaging and genetic experiments.

While the authors have made improvements in this resubmitted manuscript, there are still multiple concerns about the paper. I think the authors provide enough evidence suggesting that CRY plays a role in sleep under short photoperiod. The data also supports that CRY acts in GABAergic neurons. However, there are still major issues with the quality of the confocal images presented throughout the paper. In many cases it appears that the images are oversaturated with poor resolution, making it hard to understand what is going on. In addition, none of the drivers used in this study are specific to the neurons the authors aim to manipulate. Therefore, the identity of the GABAergic neurons involved in this CRY dependent sleep mechanism remains unclear. Similarly, whether l-LNvs are the target of this GABA mediated sleep regulation under short photoperiod is not fully demonstrated. The data presented suggests that but does not prove it.

Major concerns:

(1) While the authors provided sleep parameters like consolidation or waking activity for some experiments. These measurements are still not shown for several experiments (for example Figures 2E, 3, 4, 5, and 6). These data are essential, these metrics must be reported for all sleep experiments.

(2) Line 144 "We fed flies with agonists of GABA-A (THIP) and GABA-B receptor (SKF-97541) (Ki and Lim, 2019; Matsuda et al., 1996; Mezler et al., 2001). Both drugs enhance sleep in WT," The proper citation is needed here, Dissel et al., 2015 PMID:25913403. Both THIP and SKF-97541 were used in that paper.

(3) Figure 2C and 2F: it appears that the control data is the same in both panels. That is not acceptable.

(4) Figure 4A: With the quality of the images, it is impossible to assess whether GABA levels are increased at the l-LNvs soma.

(5) Fig 4 S1A shows colabeling of l-LNvs and Gad1-Gal4 expressing neurons. They are almost 100% overlapping signals. This would indicate that the l-LNvs are GABAergic themselves, or that there is a problem with this experiment.

(6) Fig 4 S1B: Again, I can see colabelling of the GFP and PDF staining, suggesting that Gad1-Gal4 expresses in l-LNvs.

(7) Line 184: "Consistently, knocking down Rdl in the l-LNvs rescues the long sleep phenotype of cry mutants (Figure 4-figure supplement 1D)." This statement is incorrect as the driver used for this experiment, 78G01-GAL4 is not specific to the l-LNvs, so it is possible that the phenotypes observed are not coming from these neurons.

(8) Figure 4G-K: None of these manipulations are specific to the l-LNvs. The authors describe 10H10-GAL4 and 78G01-GAL4 as l-LNvs specific tools, but this is not the case. Why not use the SS00681 Split-GAL4 line described in Liang et al., 2017 PMID: 28552314? It is possible that some of the effects reported in this manuscript are not caused by manipulating the l-LNvs.

(9) Similarly for the manipulation of s-LNvs, the authors cannot rule out effect that are coming from other cells as R6-GAL4 is not specific to s-LNvs.

(10) The staining presented in Fig 5 S1 is not very convincing. Difficult to see whether Gad1-GAL4 only expresses in the s-LNvs.

Reviewer #1 (Public review):

Summary:

The authors developed a new autofocusing method, LUNA (Locking Under Nanoscale Accuracy), to address severe focus drift-a major challenge in time-lapse microscopy. Using this method, they tackle a fundamental question in bacterial cold shock response: whether cells halt growth and division following an abrupt temperature downshift. Overall, the experimental design, modeling, and data analysis are solid and well executed. However, several points require clarification or further support to fully substantiate the authors' conclusions.

Strengths:

(1) The LUNA method outperforms existing autofocusing systems with nanoscale precision over a large focusing range. The focusing time is reasonable for the presented experiments, and the authors note potential improvements by using faster motors and optimized control algorithms, suggesting broad applicability. The theoretical simulations and experimental validation provide solid support for the robustness of the method.

(2) Using LUNA, the authors address a long-standing question in bacterial physiology: whether cells arrest growth and division after an abrupt cold shock. Single-cell analyses monitoring the entire course of cold adaptation and steady-state growth reveal features that are obscured in bulk-culture studies: cells continue to grow at reduced rates with smaller cell sizes, resulting in an apparently unchanged population-level OD. The experiments are well designed and analyses are generally solid and largely support the authors' conclusions.

(3) The authors also propose a model describing how population-level OD measurements depend on cell dry mass density, volume, and concentration. This provides a valuable conceptual contribution to the interpretation of OD-based growth measurements, which remain a gold-standard method in microbiology.

Weaknesses:

(1) It is unclear whether the author's model explaining the population-level OD during acclimation is broadly applicable. Most analyses focus on a shift from 37˚C to 14˚C, where the model agrees well with experimental data. However, in the 37˚C to 12˚C experiment, OD600 decreases after cold shock (Fig. 5e), and the computed OD does not match the experimental measurements (Fig. S16a). Although the authors attribute this discrepancy to a "complicated interplay," no further explanation is provided, which limits confidence in the model's general applicability.

(2) The manuscript proposes that cell-cycle progression becomes synchronized across the population after cold shock, but the supporting evidence is not fully convincing. If synchronization refers primarily to the uniform reduction in growth rate following cold shock, this could plausibly arise from global translation inhibition affecting all cells. However, the additional claim that "cells encountering a relatively late CSR will accelerate division to maintain synchronization" is not strongly supported by the presented data.

(3) Several technical terms used in the method development section are not clearly defined and may be unfamiliar to a broad readership, which makes it difficult to fully understand the methodology and evaluate its performance. Examples include depth of focus, focusing precision, focusing time, focusing frequency, and drift threshold value. In addition, the reported average focusing time per location (~0.6 s) lacks sufficient context, limiting the reader's ability to assess its significance relative to existing autofocusing methods.

Reviewer #1 (Public review):

Summary

The manuscript by Peden-Asarch et al. introduces MPS, a new open-source software package for processing miniscope data. The authors aim to provide a fast, end-to-end analysis pipeline tailored to miniscope users with minimal experience in coding or version control. The work addresses an important practical barrier in the field by focusing on usability and accessibility.

Strengths

The authors identify a clear and well-motivated need within the miniscope community. Existing pipelines for miniscope data analysis are often complex, difficult to install, and challenging to maintain. In addition, users frequently encounter technical limitations such as out-of-memory errors, reflecting the substantial computational demands of these workflows-resources that are not always available in many laboratories. MPS is presented as an attempt to alleviate these issues by offering a more streamlined, accessible, and robust processing framework.

Weaknesses

The authors state that "MPS is the first implementation of Constrained Non-negative Matrix Factorization (CNMF) with Nonnegative Double Singular Value Decomposition (NNDSVD) initialization." However, NNDSVD initialization is the default method in scikit-learn's NMF implementation and is also used in CaIMAN. I recommend rephrasing this claim in the abstract to more accurately reflect MPS's novelty, which appears to lie in the specific combination of constrained NMF with NNDSVD initialization, rather than being the first use of NNDSVD initialization itself.

At present, there are practical issues that limit the usability of the software. The link to the macOS installer on the documentation website is not functional. Furthermore, installation on a MacBook Pro was unsuccessful, producing the following error:<br /> "rsync(95755): error: ... Permission denied ... unexpected end of file."

For the purposes of this review, resolving this issue would significantly improve the evaluation of the software and its accessibility to users.

More broadly, the authors propose self-contained installers as a solution to the "package-management burden" commonly associated with scientific software. While this approach is appealing and potentially useful for novice users, current best practices in software development increasingly rely on continuous integration and continuous deployment (CI/CD) pipelines to ensure reproducibility, testing, and long-term maintenance. In this context, it has become standard for Python packages to be distributed via PyPI or Conda. Without dismissing the value of standalone installers, the overall quality and sustainability of MPS would be greatly enhanced by also supporting conventional environment-based installations.

Reviewer #2 (Public review):

Summary:

In this work, the authors investigate the role of fluid flow in shaping the colony size of a freshwater cyanobacterium Microcystis. To do so, they have created a novel assay by combining a rheometer with a bright field microscope. This allows them to exert precise shear forces on cyanobacterial cultures and field samples, and then quantify the effect of these shear forces on the colony size distribution. Shear force can affect the colony size in two ways: reducing size by fragmentation and increasing size by aggregation. They find limited aggregation at low shear rates, but high shear forces can create erosion-type fragmentation: colonies do not break in large pieces, but many small colonies are sheared off the large colonies. Overall, bacterial colonies from field samples seem to be more inert to shear than laboratory cultures, which the authors explain in terms of enhanced intercellular adhesion mediated by secreted polysaccharides.

Strengths:

-This study is timely, as cyanobacterial blooms are an increasing problem in freshwater lakes. They are expected to increase in frequency and severeness because of rising temperatures, and it is worthwhile learning how these blooms are formed. More generally, how physical aspects such as flow and shear influence colony formation is often overlooked, at least in part because of experimental challenges. Therefore, the method developed by the authors is useful and innovative, and I expect applications beyond the presented system here.

-A strong feature of this paper is the highly quantitative approach, combining theory with experiments, and the combination of laboratory experiments and field samples.

Weaknesses:

This study has no major weaknesses. Although the initial part of the introduction seems to imply that fluid flow is the predominant factor in shaping cyanobacterial colony (de)formation, the ensuing discussion is sufficiently nuanced for the reader to understand that the multicellular lifestyle of cyanobacterium Microcystis is shaped by multiple effects, that include bacterial behavior (e.g. which and how much EPS is produced), environmental variables that control cellular aggregation or adhesion and, indeed, fluid flow.

Joint Public Review:

Summary:

The authors state the study's goal clearly: "The goal of our study was to understand to what extent animal individuality is influenced by situational changes in the environment, i.e., how much of an animal's individuality remains after one or more environmental features change." They use visually guided behavioral features to examine the extent of correlation over time and in a variety of contexts. They develop new behavioral instrumentation and software to measure behavior in Buridan's paradigm (and variations thereof), the Y-maze, and a flight simulator. Using these assays, they examine the correlations between conditions for a panel of locomotion parameters. They propose that inter-assay correlations will determine the persistence of locomotion individuality.

Comments from the editors on the latest version:

In the latest communication, the authors were asked to (i) justify their selection of metrics (i.e. why these specific five behavioural metrics were chosen from the many recorded), (ii) discuss the variation in ICCs, and (iii) in light of this variation and the reliance on a few selected behavioural parameters, tone down the general claim so as not to overstate that individuality persists across all behaviours.

We note that the justification for choosing the five metrics and the discussion of ICC variation are purely qualitative, and, despite the edits, the manuscript continues to frame individual behaviours as broadly stable.

Reviewer #1 (Public review):

Summary:

The authors present a compelling case for the necessity of age-specific templates in functional hyperalignment. Given that the brain undergoes substantial developmental, structural, and functional changes across the lifespan, a 'one-size-fits-all' canonical template is often insufficient. This study effectively demonstrates that incorporating age-congruent features significantly enhances the performance and sensitivity of hyperalignment models. By validating these findings across two independent datasets (Cam-CAN and DLBS), the paper provides robust evidence that accounting for age-related functional organization is a critical prerequisite for accurate functional alignment in lifespan research.

Strengths:

(1) The authors used three metrics to evaluate performance. Across all metrics, they found that age-congruent templates outperformed age-incongruent templates, suggesting that age-specific templates can improve alignment.

(2) These findings highlight the superiority of age-congruent templates for hyperalignment. This work underscores the importance of age-matching in cross-subject functional mapping and represents a vital step forward for the methodology.

Weaknesses:

(1) Participant Demographics and Group Separation:

The study defines the 'older' cohort as 65-90 years and the 'younger' cohort as 18-45 years. While this 20-year gap (ages 46-64) effectively maximizes the contrast between groups, the results in Figure 4a suggest that the predicted individualized connectomes follow a continuous distribution. Given this continuity, could the authors provide the average median trends for Figures 2a and 2b to illustrate how the model behaves across the missing age range?

(2) Request for Implementation:

I have been unable to locate the source code associated with this publication. Could the authors please provide a link to the repository or clarify if the implementation is available for reproduction?

(3) Analysis of Prediction Performance and Distribution:

While Figures 3b and 5b clearly demonstrate that the congruent template improves correlation, Figure 4a shows a distinct shift in the scatter distribution. Could the authors provide a detailed explanation of the prediction performance metrics used? Specifically, I would like to understand how the underlying method accounts for the distribution differences observed when applying the congruent template.

Reviewer #1 (Public review):

Summary:

The manuscript examines the factors that restrict the induction of IL-17-producing T cells during Mycobacterium tuberculosis (Mtb) infection. The authors show that neither the infectious route nor the duration of infection is responsible. But they do show that mice that lack the Th1-defining transcription factor, a finding consistent with prior reports in the field of immunology. They also show that 2 highly attenuated Mtb mutants in ESX-1 and PDIM, two well-known Mtb virulence factors, do induce IL-17-producing T cells. In contrast, Mtb mutants in mmpl4 are also similarly attenuated, but do not induce IL-17-producing T cells, suggesting that this property is not simply a result of attenuation but due to specific properties of ESX-1 and PDIM-deficient mutants.

Strengths:

(1) It is interesting that mice infected with ESX-1 and PDIM mutants have increased induction of Th17 cells.

(2) The data are solid and convincing throughout.

Weaknesses:

There are two main criticisms:

(1) It is not clear how much the factors uncovered here are true beyond B6 mice. B6 mice, compared to humans, are known to be very Th1-skewed, and Tbet is a strong inhibitor of Th17-specific T cells. Many people make IL-17-producing T cells in response to Mtb infection.

(2) Very few novel insights are mechanistically revealed about how Th17 induction is restricted by Mtb. Tbet induction is known to restrict Th17 development, and this is a T-cell intrinsic mechanism. In contrast, the IL-23 association revealed seems to be extrinsic to T cells and to act on T cells. How, if at all, are these factors related to each other in restricting Th17 induction? Also, the conclusion that it is not a result of attenuation is not completely convincing.

Other points:

(1) The authors show that mice infected with a deficiency in ESX-1 have more IL-17-producing CD4 T cells in response to stimulation with an ESAT-6 peptide pool (Figure 3B). Because ESAT-6 is encoded by ESX-1, why do mice infected with this Mtb mutant have any ESAT-6-specific T cells? Is it an incomplete knockdown?

(2) The manuscript states, "Under the conditions where Th17s are highly induced, mice infected with either ΔESX-1 or PDIM lacking Mtb, the Il17a-/- mice had ~3-5 fold higher CFU than WT mice (Figures 3F-G). These results indicate that the induction of Th17s is not dependent on the attenuation of Mtb in general, but instead Mtb utilizes ESX-1 and PDIM to suppress the induction of a Th17 response that enhances protection against Mtb infection." I don't think the last sentence is necessarily true. I can imagine a scenario in which the induction of the Th17s is, in fact, due to the attenuation, and the Th17 induction still contributes to protection.

(3) ESX-1, PDIM, and mmpl4 mutants all have similarly reduced CFUs in the lung, but what about the LN? The bacterial burden in the LN may be more important for regulating T-bet, IL-23, and Th17 differentiation, since the LN is where T cell priming occurs, than the CFU in the lung. Perhaps ESX-1 and PDIM mutants have reduced CFU in the LN, but mmpl4 does not. This difference in LN burdens may be the primary driver of Th17 priming, as high avidity interactions are thought to be an important driver of T-bet induction.

(4) Do LN cDC1 and high levels of IL-12 p35 in mice infected with the mmpl4 mutant? Likewise, LN cDC2's express low levels of IL-12 p19 (akin to those infected with WT Mtb)? If these observations for ESX-1 and PDIM mutants are mechanistically linked to the increased numbers of Th17 cells, then you would expect mice infected with mmpl4 mutants to be more like those infected with WT Mtb than those infected with ESX-1 and PDIM mutants.

(5) ESX-1 and PDIM are very different virulence factors - a protein secretory pathway and cell wall lipid, respectively? Mechanistically, how would mutants in these pathways give very similar outcomes regarding Th17 cells unless it was simply as an aspect of their attenuation? Perhaps, mmpl4 mutants simply differ in some aspects of their attenuation, such as bacterial burdens in LNs, or their interaction with cDCs?

Reviewer #1 (Public review):

Summary:

In this study, the authors examine the effect of Chlorpyrifos (CPF) exposure on zebrafish social development. They expose larval zebrafish to CPF (0 - 3 dpf), and report social deficits at juvenile stages. They show that the gut microbial metabolite butyrate can rescue these social deficits, proposing that butyrate acts as a histone deacetylase (HDAC) inhibitor, given that inhibition of some HDACs can also rescue social deficits. They also show that CPF changes neuronal gene expression, and butyrate partially rescues these changes. Finally, they demonstrate changes in gut microbiome and metabolome composition, pointing to potential modulation of nitrogen metabolism pathways. They then hypothesise that NO can modulate HDAC activity and attempt to link the NO pathway to social behavior.

Strengths:

The authors demonstrate an interesting link between early Chlorpyrifos (CPF) exposure and later-life social deficits, such as changes in neuronal gene expression, including some autism-related genes, and provide solid evidence that butyrate and epigenetic modulation (histone deacetylase inhibition) may be involved.

They also comprehensively characterise the microbiome and metabolome of CPF-exposed zebrafish, providing a useful resource for further investigation into its gut-brain mechanisms.

They are cautious in framing some of their conclusions as a hypothesis and provide some suggestions for future analyses.

Weaknesses:

The claim that butyrate's effects on CPF-induced social deficits and neuron activity changes are mediated by histone deacetylase inhibition is lacking some additional controls and, hence, is not completely supported.

Details on the social behavior assay performed and other potential morphological or behavioral changes were not provided.

Claims on the mechanism of action of CPF are inconclusive. The causal role of the gut microbiome is not established, especially since gut microbial dysbiosis may also be a downstream consequence of direct effects of CPF on the host, such as changes in host gut gene expression. Evidence for the role of nitrogen metabolism is also incomplete, and the authors have not discussed or ruled out the potential alternative mechanism of reduced butyrate production due to gut microbiome changes.

Reviewer #1 (Public review):

Summary:

In this manuscript, the authors investigate how the anterior claustrum may integrate temporally separated task-relevant signals to guide behavior in a delayed escape paradigm. Because in vivo neural recordings from claustrum during this task are extremely limited - comprising single-trial data with small neuronal samples - the authors adopt a modeling-driven approach. They train recurrent neural networks (RNNs) using only behavioral data (escape latency) to reproduce task performance and then analyze the internal dynamics of the trained networks. Within these networks, they identify a subset of units whose activity exhibits persistent responses and strong correlations with behavior, which the authors label as "claustrum-like." Using dimensionality reduction, decoding, and information-theoretic analyses, they argue that these units dynamically integrate conditioned stimulus (CS) and door-opening signals via nonlinear, trajectory-based population dynamics rather than fixed-point attractor states.

To bridge model predictions and biology, the authors complement the modeling with in vitro slice experiments demonstrating recurrent excitatory connectivity and prolonged activity in the anterior claustrum that depends on glutamatergic transmission. They further compare latent neural trajectories derived from previously published in vivo claustrum recordings to those observed in the RNN, reporting qualitative similarities. Based on these results, the authors propose that the claustrum implements temporal signal integration through recurrent excitatory circuitry and dynamic population trajectories, potentially supporting broader theories of integrative brain function.

Strengths:

This study addresses an important and challenging problem: how to infer population-level computation in a brain structure for which in vivo data are sparse and experimentally constrained. The authors are commendably transparent about these limitations and seek to overcome them through a principled modeling framework. The integration of behavioral modeling, RNN analysis, and slice electrophysiology is ambitious and technically sophisticated.

Several aspects stand out as strengths. First, the behavioral RNN is carefully trained and interrogated using a rich set of modern analytical tools, including cross-temporal decoding, trajectory analysis, and partial information decomposition, providing multiple complementary views of network dynamics. Second, the slice experiments convincingly demonstrate recurrent excitatory connectivity in the anterior claustrum, lending biological plausibility to the model's reliance on recurrent dynamics. Third, the manuscript is clearly written, logically organized, and conceptually engaging, and it offers a coherent mechanistic hypothesis that could guide future large-scale recording experiments.

Importantly, the work has significant heuristic value: rather than merely fitting data, it attempts to generate testable computational ideas about claustral function in a regime where direct empirical access is currently limited.

Weaknesses:

Despite these strengths, the manuscript suffers from a recurring and substantial conceptual issue: systematic over-interpretation of model-data correspondence. While the modeling results are potentially insightful, the extent to which they are presented as recapitulating real claustral neural mechanisms goes beyond what the available data can support.

A fundamental limitation is that the RNN is trained solely on behavioral output, without being constrained by neural data at either single-unit or population levels. As a result, the internal network dynamics are underdetermined and non-unique. Many distinct internal solutions could plausibly generate identical behavior. However, the manuscript frequently treats the specific internal solution discovered in the RNN as if it were a close approximation of the actual claustrum circuit.

This issue is compounded by the sparse nature of the in vivo data used for comparison. The GPFA-based trajectory analyses rely on pseudo-populations and single-trial recordings, yet are interpreted as evidence for robust population-level dynamics. Because neurons were not recorded simultaneously, the inferred trajectories necessarily lack true population covariance and shared trial-to-trial variability, limiting their interpretability as genuine population dynamics. Similarly, conclusions about trajectory-based versus attractor-based computation are drawn almost exclusively from model analyses and then generalized to the biological system.

Overall, while the modeling framework is appropriate as a hypothesis-generating tool, the manuscript repeatedly crosses the line from proposing plausible mechanisms to asserting explanatory or even causal equivalence between the model and the brain. This undermines the otherwise strong contributions of the work.

Below are several specific points that warrant further clarification or revision:

(1) Tone of model-data correspondence

Numerous statements describe the RNN as "closely mimicking," "recapitulating," or being "nearly identical" to claustral neural dynamics, sometimes extending to claims about causal relationships between neural activity and behavior. Given that neural data were not used to train the model, and that only a small subset of trained networks showed the reported dynamics, these statements should be substantially softened throughout the manuscript. The RNN should be framed as providing one possible computational realization consistent with existing data, not as a close instantiation of the biological circuit

(2) Non-uniqueness of RNN solutions

The fact that only a small fraction of trained networks exhibited "claustrum-like" clusters deserves deeper discussion. This observation raises the possibility that the identified solution is fragile or highly specific rather than canonical. The authors should explicitly discuss the non-uniqueness of internal solutions in behavior-trained RNNs, including the range of alternative network dynamics that can reproduce the same behavior. In particular, it should be clarified why the specific network exhibiting "claustrum-like" clusters is informative about claustral computation, rather than representing one arbitrary solution among many.

(3) GPFA trajectory comparisons

The qualitative similarity between RNN trajectories and GPFA-derived trajectories from sparse in vivo data is interesting but insufficient to support claims of robustness or population-level structure. Statements suggesting that these patterns are unlikely to arise from noise or random fluctuations are not justified, given the single-trial, pseudo-population nature of the data. Either additional quantitative controls should be added, or the interpretation should be substantially tempered.

(4) Scope of functional claims

The discussion connecting the findings to broad theories of claustral function, global workspace, or consciousness extends well beyond the data presented. These speculative links should be clearly labeled as such and significantly reduced in strength and prominence.

(5) Comment on Conceptual Interpretation of the Behavioral Paradigm:

The manuscript repeatedly describes the delayed escape task as an "inference-based behavioral paradigm" and states that animals "infer that a value-neutral alternative space is likely to be safer" when the CS is presented in a novel environment. While I appreciate that the US-CS association was established in a different context and that the CS is then presented in a new environment, I am not convinced that the current behavioral evidence uniquely supports an inference interpretation.

First, it is not clear that this task is widely recognized in the literature as a canonical inference task, in the sense of, for example, sensory preconditioning, transitive inference, or model-based inference paradigms. Rather, the observed effect-that CS animals escape faster to a neutral compartment than neutral-CS controls-can be parsimoniously interpreted in terms of generalized threat value, heightened fear/anxiety, or a bias toward avoidance/escape under elevated threat, without requiring an explicit inferential step about the specific safety of the alternative compartment. The fact that no prior training is needed is compatible with flexible generalization, but does not by itself demonstrate inference in a more formal computational sense.

Second, the inference claim becomes central to the manuscript's conceptual framing (e.g., the idea that rsCla supports "inference-based escape"), yet the behavioral analyses presented here and in the cited prior work do not clearly rule out simpler accounts. Clarifying this distinction would help avoid overstating both the inferential nature of the behavior and the specific role of rsCla and the RNN's "claustrum-like" cluster in supporting inference per se, as opposed to more general integration of threat-related signals with an opportunity for escape.

Overall Assessment:

This manuscript presents an interesting and potentially valuable modeling-based framework for thinking about temporal integration in the claustrum, supported by solid slice physiology. However, in its current form, it overstates the degree to which the proposed RNN dynamics reflect actual claustral neural mechanisms. With substantial revision - especially a more cautious interpretation of model-data similarity and a clearer articulation of modeling limitations - the study could make a meaningful contribution as a hypothesis-generating work rather than a definitive mechanistic account.

Reviewer #1 (Public review):

Summary:

The electrocardiogram (ECG) is routinely used to diagnose and assess cardiovascular risk. However, its interpretation can be complicated by sex-based and anatomical variations in heart and torso structure. To quantify these relationships, Dr. Smith and colleagues developed computational tools to automatically reconstruct 3D heart and torso anatomies from UK Biobank data. Their regression analysis identified key sex differences in anatomical parameters and their associations with ECG features, particularly post-myocardial infarction (MI). This work provides valuable quantitative insights into how sex and anatomy influence ECG metrics, potentially improving future ECG interpretation protocols by accounting for these factors.

Strengths:

• The study introduces an automated pipeline to reconstruct heart and torso anatomies from a large cohort (1,476 subjects, including healthy and post-MI individuals). • The 3-stage reconstruction achieved high accuracy (validated via Dice coefficient and error distances). • Extracted anatomical features enabled novel analyses of disease-dependent relationships between sex, anatomy, and ECG metrics. • Open-source code for the pipeline and analyses enhances reproducibility.

Weaknesses:

• The study attributes residual ECG differences to sex/MI status after controlling for anatomical variables. However, regression model errors could distort these estimates. A rigorous evaluation of potential deviations (e.g., variance inflation factors or alternative methods like ridge regression) would strengthen the conclusions.

Reviewer #1 (Public review):

Summary:

The electrocardiogram (ECG) is routinely used to diagnose and assess cardiovascular risk. However, its interpretation can be complicated by sex-based and anatomical variations in heart and torso structure. To quantify these relationships, Dr. Smith and colleagues developed computational tools to automatically reconstruct 3D heart and torso anatomies from UK Biobank data. Their regression analysis identified key sex differences in anatomical parameters and their associations with ECG features, particularly post-myocardial infarction (MI). This work provides valuable quantitative insights into how sex and anatomy influence ECG metrics, potentially improving future ECG interpretation protocols by accounting for these factors.

Strengths:

(1) The study introduces an automated pipeline to reconstruct heart and torso anatomies from a large cohort (1,476 subjects, including healthy and post-MI individuals).

(2) The 3-stage reconstruction achieved high accuracy (validated via Dice coefficient and error distances).

(3) Extracted anatomical features enabled novel analyses of disease-dependent relationships between sex, anatomy, and ECG metrics.

(4) Open-source code for the pipeline and analyses enhances reproducibility.

Weaknesses:

(1) The linear regression approach, while useful, may not fully address collinearity among parameters (e.g., cardiac size, torso volume, heart position). Although left ventricular mass or cavity volume was selected to mitigate collinearity, other parameters (e.g., heart center coordinates) could still introduce bias.

(2) The study attributes residual ECG differences to sex/MI status after controlling for anatomical variables. However, regression model errors could distort these estimates. A rigorous evaluation of potential deviations (e.g., variance inflation factors or alternative methods like ridge regression) would strengthen the conclusions.

(3) The manuscript's highly quantitative presentation may hinder readability. Simplifying technical descriptions and improving figure clarity (e.g., separating superimposed bar plots in Figures 2-4) would aid comprehension.

(4) Given established sex differences in QTc intervals, applying the same analytical framework to explore QTc's dependence on sex and anatomy could have provided additional clinically relevant insights.

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.<br /> - 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 on revisions:

The authors have thoroughly addressed all of my previous comments. Congratulations on an excellent paper!

Reviewer #1 (Public review):

The manuscript "Heterozygote advantage cannot explain MHC diversity, but MHC diversity can explain heterozygote advantage" explores two topics. First, it is claimed that the recently published by Mattias Siljestam and Claus Rueffler conclusion (in the following referred to as [SR] for brevity) that heterozygote advantage explains MHC diversity does not withstand an even very slight change in ecological parameters. Second, a modified model that allows an expansion of MHC gene family shows that homozygotes outperform heterozygotes. This is an important topic and could be of potential interest to the readership of eLife if the conclusions are valid and non-trivial.

The resubmitted manuscript addresses several questions from my previous review. In particular, there is a more detailed description of how the code of Siljestam and Rueffler ([SR]) was used for the simulations and the calculation of the factor 2.7 x 10^43 that is the key to the alleged breakdown of the numerical reasoning presented by in [SR].

Yet I think that important aspects of my critique of the first statement of the manuscript about the flaws of [SR] model remain unanswered. I guess the discussion becomes rather general about the universality and robustness of various types of models to parameter changes. My point is that none of the models is totally universal. The model in [SR] is not phenomenological as none of the parameters or functional forms were derived empirically. Instead, it is a proof of principle demonstration that inevitably grossly simplifies the actual immune response. The choice of constants and functions used in Eqs. (1-5) is dictated by the mathematical convenience and works in a limited range of parameter values. It is shown in [SR] that for 3 pathogens and reasonable "virulence " \nu, the alleles branch. These conclusions are supported by the analytically derived Adaptive Dynamics branching criteria (7), which, contrary to the statement is the cover letter (" It is clear from Fig. 4 of Siljestam and Rueffler that the branching condition is far from sufficient for high MHC diversity.") is perfectly confirmed by the simulation data shown in Fig. 4.

The mathematical simplicity of the [SR] model generates various artifacts, such as the mentioned by the Author reduction of the "condition" by an enormous factor 2.7 x 10^43 and the resulting decrease in the "survival" induced by the addition of a new pathogen. This occurs at the very large value of \nu=20, whose effect is enormous due to the Gaussian form of (1), which, once again, was chosen for the mathematical convenience. In reality, a new pathogen cannot reduce the "survival" by such a factor as it would wipe out any resident population. So to compensate for such an artifact, the additional factor c_max was introduced to buffer such an excess. There is no reason to fix c_max once for an arbitrary number of pathogens, because varying c_max basically reflects the observation that a well-adapted individual must have a reasonable survival probability. At the same time, there are many ways in which the numerical simulation may break down when the survival rates become of the order of 10^(-43) instead of one, so it comes to no surprise that the diversification, predicted by the adaptive dynamics, does not readily occur in the scenario with an addition or removal of the 8th pathogen with a very high virulence \nu=20.

I have doubts that the reported breakdown of the [SR] model with fixed c_max remains observable with less extreme values of m and \nu (say, for \nu=7 and m=3 plus or minus 1 used in Fig. 3 in the manuscript).

So I still find the claim that " the phenomenon that leads to high diversity in the simulations of Siljestam and Rueffler depends on finely tuned parameter values" is not well substantiated.

Reviewer #1 (Public review):

Summary:

This study examined whether infraslow fluctuations in noradrenaline and in heart rate are coupled and how they are affected by sleep transitions. The authors used the fluorescent NA biosensor GRAB-NE2m in the medial prefrontal cortex of mice to record extracellular NA while also recording EEG and EMG during sleep-wake episodes. They also analyzed previously published human data to reproduce relationships they found between sigma power and RR intervals in mice.

Strengths:

This is an impressive study with significant strengths, as it involves a rich set of data that includes not only observations of associations between heart rate and noradrenergic dynamics but also optogenetic manipulation of the locus coeruleus. Human data is presented to show parallels in the association between sigma power during sleep and phasic heart-rate bursts.

Weaknesses:

(1) Language could be clearer and more precise. As detailed below, in both the introduction and the discussion, the way the hypotheses and study objectives are described could use some revision to be more precise and accurate.

1A) In the introduction on p. 4: The overarching question is framed as "could the peripheral autonomous systems be a read-out of the central LC-NE system and thus be a biomarker of memory consolidation and LC dysfunction?" This gives the impression that the LC function would be the main influence on peripheral autonomous systems. There are, of course, many influences on peripheral autonomous systems, so it would be advisable for the authors to be more specific here about what signal(s) in particular would be predicted to be sensitive markers of LC function.

1B) In the discussion on p. 12: "In this study, we leveraged real-time measurements of mPFC NE levels and HR measurements from EMG recordings in mice to investigate the causal link between the two variables with high temporal resolution in freely moving sleeping mice, with similar inspection in humans." To test the causal link between mPFC NA levels and HR measures, the study would manipulate NA levels just in the mPFC and not elsewhere in the brain. However, in this study, the manipulation occurred in the LC, and so there would be broad cortical changes in NA levels. Thus, it could be that LC activity causes HR changes via a non-PFC pathway.

(2) Comparisons with the control condition need further development.

2A) While the authors did include a key YFP control condition, in the main text no direct statistical comparison between the closed-loop optogenetic stimulation (ChR2) condition and the YFP control condition was reported. (It was reported in Supplementary Figure 2c-d.) Instead, in the main text, the authors only reported that the effects of stimulation were significant in the closed-loop condition and not in the control. However, that is not the same as demonstrating that the two conditions significantly differed from each other, and it is the direct test that is important for the conclusions, so it seems important to include this result in the main presentation.

2B) In addition, the authors should address the issue that the pre-stimulation NE was consistently significantly lower in the YFP condition than in the ChR2 condition (see Supplementary Figure 2c), which is a potential confound.

2C) Direct comparison of the strengths of correlations shown in Figure 2h vs. Supplementary Figure 2f should be included. Currently, we see relatively weak correlations in both ChR2 and YFP conditions, and it is not clear if the relationships differ in the control. It seems they are still present in the control condition but weaker, which would contradict the apparently broad claim on p. 7 that "No such effects were present in the control condition" (it is not entirely clear whether this claim refers to all effects discussed in the figure or just a subset - this language should be clarified).

2D) Did the YFP controls vs. ChR2 animals show any differences in the number of NA states that triggered stimulation in the closed-loop system? With ChR2 animals, stimulation changes NA, which could change future triggering. In YFP animals, nothing changes NA (other than natural fluctuations), so the dynamics of stimulation timing could diverge between groups in a way that complicates interpretation. Specifically, if ChR2 stimulation raises NA and prevents future threshold crossings, ChR2 animals may end up receiving fewer subsequent stimulations than YFP animals (or a different temporal clustering). If the number or pattern of stimulation differed in two groups, it would be important to have a yoked control where matched animals get the same stimulation pattern but not triggered by their own NA.

(3) Some more discussion/explanation of the rationale for the closed-loop approach and how it influences how we should interpret the results could be useful. For instance, currently, it is not clear whether LC stimulation needs to be timed after an NA dip to yield the effects seen.

(4) The section on heart rate decelerations is hard to follow. In particular, I was not sure how to interpret Figure 3f-j. For Figure 3f, what does the middle line represent? The laser onset or the max RR value after laser onset? What is the baseline that is used to correct the values to obtain amplitudes? If it is the whole period before the maximal RR value or the laser onset, wouldn't baseline values differ significantly across conditions and so potentially account for differences seen between conditions in the reported HR decelerations? Larger HR decelerations may be seen in conditions with higher HR simply as a regression to the mean phenomenon.

(5) The findings regarding LC suppression could be further clarified.

5A) Page 8: "observed a response in NE decline" - please be more precise. Did NE decline more or less?

5B) It would be helpful to also show the correlation between NE and RR in the control (YFP) condition and whether there were any differences between YFP and Arch conditions (Figure 4e).

5C) This sentence took me multiple readings to understand - it would be helpful to rewrite to make it clearer: "indicating that, while HR generally did not respond strongly to LC suppression, the variability in RR responses was dependent on NE changes to the suppression (Figure 4e)."

5D) The two colors in Figure 4 are similar and hard to distinguish.

5E) The correlations shown in Figure 4j seem to be driven by just two of the cases. Are the effects significant when outliers are removed?

5D) Page 10: Were there any differences in memory performance between the Arch and YFP conditions?

5E) Page 10: "We found a correlation between RR responses to LC suppression and sigma power, suggesting that a stronger HR reduction response is linked to higher spindle power." It should be noted in the text that the correlation was not specific to sigma (it was also seen for theta and beta, Figure 4i).

(6) It is not clear which of the sigma power and RR interval findings do/do not exactly line up between the mice and humans. It could be helpful to have a table comparing them. For instance, was the finding in humans that pre-HRB sigma power was positively associated with slowing in heart rate after the HRB also seen in mice? Was there evidence in mice (as seen in the human sample) that sleep-dependent memory improvement was associated with pre-HRB sigma power?

(7) Page 18: It is not clear if the sex of mice was balanced across controls and optogenetics groups.

Reviewer #1 (Public review):

Summary:

Liao et al. performed a large-scale integrative analysis to explore the function of two cancer genes (BRCA1 and BRCA2) in lung cancer, which is one of the cancers with an extremely high mortality rate. The detailed genetic analysis demonstrated new roles of BRCA1/2 in causing the tumor microenvironment in lung cancer. In particular, the discovery of different mechanisms of BRCA1 and BRCA2 provides an essential foundation for developing drugs that target BRCA1 or BRCA2 in lung cancer therapy.

Strengths:

(1) This study leveraged large-scale genomic and transcriptomic datasets to investigate the prognostic implications of BRCA1/2 mutations in LUAD patients (~2,000 samples). The datasets range from genomics to single-cell RNA-seq to scTCR-seq.

(2) In particular, the scTCR-seq offers a powerful approach for understanding T cell diversity, clonal expansion, and antigen-specific immune responses. Leveraging these data, this study found that BRCA1 mutations were associated with CD8+ Trm expansion, whereas BRCA2 mutations were linked to tumor CD4+ Trm expansion and peripheral T/NK cell cytotoxicity.

(3) This study also performed a comprehensive analysis of genomic variation, gene expression, and clinical data from the TCGA program, which provides an independent validation of the findings from LUAD patients newly collected in this study.

(4) This study provides an exemplary integration analysis using both computational biology and wet bench experiments. The experimental testing in the A549 cell line further supports the robustness of the computational analysis.

(5) The findings of this study offer a comprehensive view of the molecular mechanisms underlying BRCA1 and BRCA2 mutations in LUAD. BRCA1 and BRCA2 are two well-known cancer-related genes in multiple cancers. However, their role in shaping the tumor microenvironment, particularly in lung cancer, is largely unknown.

(6) By focusing on PD-L1-negative LUAD patients, this study demonstrated the molecular mechanisms underlying resistance to immune therapy. These new insights highlight new opportunities for personalized therapeutic strategies to BRCA-driven tumors. For example, they found histone deacetylase (HDAC) inhibitors consistently downregulated 4-R genes in A549 cells.

(7) The deposition of raw single-cell sequencing (including scRNA-seq and scTCR-seq) data will provide an essential data resource for further discovery in this field.

Weaknesses:

(1) The finding of histone deacetylase (HDAC) inhibitors suggests the potential roles of epigenetic regulation in lung cancer. It would be interesting to explore epigenetic changes in LUAD patients in the future.

(2) For some methods, more detailed information is needed.

(3) There are grammar issues in the text that need to be fixed.

(2) Some text in the figures is not labeled well.

Reviewer #1 (Public review):

Summary:

Small molecule therapeutics for snakebite have received a lot of attention for their potential to close the gap between bite and treatment, where antivenom is not immediately available.

Strengths:

There has been a lot of focus on Africa, Asia, and India, but very little work related to neotropical regions. The authors seek to begin filling this gap in the preclinical literature. The authors use well-developed methods for preclinical assessment.

Weaknesses:

A clearer and more focused discussion of the limitations of the overall present work would be desirable (e.g. protection vs. rescue, why marimastat over prinomastat for in vivo assays when both have been through clinical trials for other indications; real-world feasibility of nafamostat, which has a half-life of 1-2 minutes compared to camostat, which has a half-life of hours). All of this could be be improved in a revision.

Reviewer #1 (Public review):

Summary:

This study addresses a fundamental question in cognitive neuroscience regarding how the brain transitions from a reactive state of following external instructions to a proactive state of self-directed agency. The authors utilize an ambitious multimodal design by combining the spatial precision of fMRI with the temporal resolution of EEG across two independent datasets from the University of Florida and UC Davis. By applying multivariate pattern analysis, the work demonstrates that while both instructed and willed attention engage the Dorsal Attention Network, willed choices uniquely recruit a frontoparietal decision network including the dACC and anterior insula. Furthermore, the study shows that pre cue alpha oscillations can predict subsequent spontaneous choices. This provides a neural link between pre-existing brain states and intentional action, representing a significant technical effort to characterize the neural scaffolding of internal goal generation.

Strengths:

The primary strengths of this work include the integration of fMRI and EEG which allows the authors to bridge the gap between slow metabolic signals and fast oscillatory brain states. The use of two independent cohorts is a commendable effort to ensure the reproducibility of the willed attention effect, which is often a concern in small sample neuroimaging studies. Additionally, the move beyond univariate activation toward information based mapping demonstrates that the identified networks actually contain specific information about the direction of attention.

Weaknesses:

However, several critical weaknesses must be addressed to support the fundamental claims made in the manuscript. There are significant behavioral differences in performance between the two sites, specifically regarding the UC Davis cohort exhibiting slower reaction times and lower accuracy compared to the UF group. These discrepancies suggest potential differences in subject populations or experimental environments that are not currently accounted for in the neural models. The fMRI analysis lacks temporal precision because the use of beta series regression collapses the complex BOLD response into a single estimate per trial. This loss of temporal information obscures the evolution of the decision process and makes it difficult to distinguish whether the identified patterns represent a truly spontaneous choice or a slow building pre planned strategy.

Furthermore, the EEG decoding approach utilized the entire topography of electrodes rather than a biologically motivated posterior region of interest. Given that alpha mediated spatial attention is traditionally localized to parieto occipital sensors, using the full electrode set risks the inclusion of non neural artifacts such as micro saccades or muscle activity which can contaminate multivariate classifiers. The introduction of the neural efficiency metric also requires further validation as the current ratio is mathematically sensitive to small denominators in the BOLD contrast.

Crucially, the manuscript does not address the physiological implications of recruiting additional frontoparietal networks when behavioral performance remains identical across conditions. The activation of the anterior insula and dACC is frequently associated with increased autonomic arousal and effort. If the willed condition requires more extensive neural scaffolding to reach the same behavioral output as the instructed condition, it raises the question of whether this internal decision process is accompanied by changes in arousal levels. The authors should consider whether the lack of a behavioral tax is due to a compensatory increase in arousal, which could be reflected in the EEG data or pupil diameter if recorded, and potentially also in the amplitude of BOLD activity, which is being masked by the neural efficiency metric. Without an account of how the brain balances this increased computational demand without impacting behavioral performance, the functional significance of the willed attention network remains partially obscured.

Reviewer #1 (Public review):

Summary:

The authors investigated the relationship between physical activity (PA) and both structural (MRI) and cognitive brain health in the LIFE-Adult Study, with total baseline recruitment of 2576. Hippocampal volume, an MRI-derived BrainAGE marker, and scores from the Trail Making Test were used as outcomes, with the majority of participants measured at baseline and subsets also measured in a follow-up session. The key findings were a lack of direct association between PA and outcomes, but longitudinal evidence for a higher BrainAge at baseline leading to lower physical capacity at follow-up. This supports a reverse-causation hypothesis in contrast to the prevailing understanding of the positive effects of physical activity on brain health.

Strengths:

The Life-Adult study is a rich and carefully acquired dataset, with multiple follow-up time points. The statistical analyses were conducted carefully with appropriate control for confounds and multiple testing. The study design enables an important assessment for reverse causality. The authors are scrupulous in their consideration of a number of factors that could potentially bias their results, performing an age-stratified analysis, and emphasising discrepancies in PA measurements (specifically, age-reporting bias) across the dataset and other limitations.

Weaknesses:

This is an observational study with inconsistent measures of physical activity. Previous studies have used physical activity interventions, and might be more strongly weighted when considering evidence for these effects (specific confounders involved in interventions notwithstanding).

The model identifying potential reverse causality is relatively limited - it seems possible/likely that brainAge could reflect more general health status, which would expand the potential range of factors underlying this observation.

The important quantitative actigraphy subset is small (n=227), as are the longitudinal subsets. Along with the discrepancy of physical activity/capacity at baseline and follow-up, and other complexities of the dataset, it is difficult to make firm conclusions. The authors point out that the actigraphy subset was quite inactive.

Original post by u/shapeless_nodule at https://reddit.com/r/typewriters/comments/1rp5mh6/brother_deluxe_220_jp1_typewriter_request_for/

Hi All, In a fit overconfidence a couple of years ago, I bought a brother Deluxe 220 typewriter which worked fine other than being sticky. I duly tore it down, cleaned it up, oiled it, put it back together and... watched as nothing happened because somehow all of the springs had fallen out and were now sitting on my workbench. I then put it on a shelf and forgot about it, until starting a clearout last week. I would be deeply indebted to you if anyone who has this typewriter (or one of its sister models, as I understand it most of the JP-1 models are the same) take either some photos or a good video of exactly where all of the springs inside it connect to?

Reply: <br /> This is fairly steep ask, particularly when, for a few dollars, you can get the location of all the springs in the repair manual:<br /> - https://www.lulu.com/shop/ted-munk/the-brother-jp-1-typewriter-repair-bible/paperback/product-186kzqem.html?q=brother&page=1&pageSize=4 - https://twdb.sellfy.store/brother-typewriters/

Reviewer #1 (Public review):

Summary:

This manuscript by Zhao et. al investigates the canonical hedgehog pathway in testis development of Nile tilapia. They used complementary approaches with genetically modified tilapia and transfected TSL cells (a clonal stem Leydig cell line) previously derived from 3-mo old tilapia. The approach is innovative and provides a means to investigate DHH and each downstream component from the ptch receptors to the gli and sf1 transcription factors. They concluded that Dhh binds Ptch2 to stimulate Gli1 to promote an increase in Sf1 expression leading to the onset of 11-ketotesterone synthesis heralding the differentiation of Leydig cells in the developing male tilapia.'

Strengths of the methods and results:

- The use of Nile tilapia is important as it is an important aquaculture species, it shares the genetic pathway for sex determination of mammalian species, and molecular differentiation pathways are highly conserved<br /> - The approach is rigorous and incorporates a novel TSL, clonal stem Leydig cell model that they developed that is relatively faithful in following endogenous developmental steps and can produce the appropriate steroid.<br /> - Tilapia are relatively amenable to CRISPR/Cas9 targeting and, with their accelerated developmental time frame, provide an excellent model system to interrogate specific signaling pathways.<br /> - The stepwise analysis from dhh-gli-sf1 is thoughtful and well done.

Weaknesses of the methods and results:

- Line 162: need to establish and verify the PKH26-labeled TSL cells were unaffected by the dhh-/- environment. No data to support the claim that they were unaffected.<br /> - The rescued phenotype caused by the addition of ptch2-/- to the dhh-/- model is a compelling. To further define potential ptch1 contributions, it would be helpful to examine the expression level of ptch1 in the context of the ptch2-/- and ptch2-/-;dhh-/- mutant animals. Any compensatory increase in ptch1 in either case, without obvious phenotype changes, would support the dominant role for ptch2.<br /> - Activity of individual gli factors need additional reconciliation. The expression profiles for both alternative gli factors should be quantified in each knockout cell line to establish redundancy and/or compensation.<br /> - Figure 5E: An important control is missing that includes evaluation of HEK293 cells transfected with pcDNA3.1-OnGli1 without the addition of pGL3-sf1.

Achieved Aims:

The authors set out to test the hypothesis that the canonical Dhh signaling pathway for Leydig cell differentiation and steroidogenic activity is mediated via ptch2 and gli1 regulation of sf1. The results are strong, there are additional steps needed to verify that redundancy/compensation is not contributing to the outcomes.

This work is important in better understanding of nuanced commonalities and differences in developmental pathways across species. Specific to Leydig cell differentiation and steroidogenesis, their work with tilapia supports conservation of the canonical Dhh pathway; however, there appear to be some differences in downstream mediators compared to mouse. Specifically, they conclude that ptch2/gli1 stimulates sf1 and steroidogenesis in tilapia where gli1 is dispensable in mouse. Instead, Gli3 has recently been shown to play an important role to stimulate Sf1 and support the hedgehog pathway.

Reviewer #1 (Public review):

Summary:

This paper aims to characterize the relationship between affinity and fitness in the process of affinity maturation. To this end, the authors develop a model of germinal center reaction and a tailored statistical approach, building on recent advances in simulation-based inference. The potential impact of this work is hindered by the poor organization of the manuscript. In crucial sections, the writing style and notations are unclear and difficult to follow.

Strengths:

The model provides a framework for linking affinity measurements and sequence evolution and does so while accounting for the stochasticity inherent to the germinal center reaction. The model's sophistication comes at the cost of numerous parameters and leads to intractable likelihood, which are the primary challenges addressed by the authors. The approach to inference is innovative and relies on training a neural network on extensive simulations of trajectories from the model.

Weaknesses:

The text is challenging to follow. The descriptions of the model and the inference procedure are fragmented and repetitive. In the introduction and the methods section, the same information is often provided multiple times, at different levels of detail. This organization sometimes requires the reader to move back and forth between subsections (there are multiple non-specific references to "above" and "below" in the text).

The choice of some parameter values in simulations appears arbitrary and would benefit from more extensive justification. It remains unclear how the "significant uncertainty" associated with these parameters affects the results of inference. In addition, the performance of the inference scheme on simulated data is difficult to evaluate, as the reported distributions of loss function values are not very informative.

Finally, the discussion of the similarities and differences with an alternative approach to this inference problem, presented in Dewitt et al. (2025), is incomplete.

Reviewer #1 (Public review):

Summary:

This paper aims to characterize the relationship between affinity and fitness in the process of affinity maturation. To this end, the authors develop a model of germinal center reaction and a tailored statistical approach, building on recent advances in simulation-based inference.

The model provides a framework for linking affinity measurements and sequence evolution and does so while accounting for the stochasticity inherent to the germinal center reaction. The model's sophistication comes at the cost of numerous parameters and leads to intractable likelihood, which are the primary challenges addressed by the authors. The approach to inference is innovative and relies on training a neural network on extensive simulations of trajectories from the model.

The revised methods section is easier to follow and better explains the approach. Inference results on simulated data are compelling and the real-data findings are compared with alternative approaches, clarifying the relationship to previous work.

Reviewer #1 (Public review):

In this study, Brickwedde et al. leveraged a cross-modal task where visual cues indicated whether upcoming targets required visual or auditory discrimination. Visual and auditory targets were paired with auditory and visual distractors, respectively. The authors found that during the cue-to-target interval, posterior alpha activity increased along with auditory and visual frequency-tagged activity when subjects were anticipating auditory targets. The authors conclude that their results imply that alpha modulation does not solely regulate 'gain control' in early visual areas (also referred to as alpha inhibition hypothesis), but rather orchestrates signal transmission to later stages of the processing stream.

Comments on the first revision:

I thank the authors for their clarifications. The manuscript is much improved now, in my opinion. The new power spectral density plots and revised Figure 1 are much appreciated. However, there is one remaining point that I am unclear about. In the rebuttal, the authors state the following: "To directly address the question of whether the auditory signal was distracting, we conducted a follow-up MEG experiment. In this study, we observed a significant reduction in visual accuracy during the second block when the distractor was present (see Fig. 7B and Suppl. Fig. 1B), providing clear evidence of a distractor cost under conditions where performance was not saturated."

I am very confused by this statement, because both Fig. 7B and Suppl. Fig. 1B show that the visual- (i.e., visual target presented alone) has a lower accuracy and longer reaction time than visual+ (i.e., visual target presented with distractor). In fact, Suppl. Fig. 1B legend states the following: "accuracy: auditory- - auditory+: M = 7.2 %; SD = 7.5; p = .001; t(25) = 4.9; visual- - visual+: M = -7.6%; SD = 10.80; p < .01; t(25) = -3.59; Reaction time: auditory- - auditory +: M = -20.64 ms; SD = 57.6; n.s.: p = .08; t(25) = -1.83; visual- - visual+: M = 60.1 ms ; SD = 58.52; p < .001; t(25) = 5.23)."

These statements appear to directly contradict each other. I appreciate that the difficulty of auditory and visual trials in block 2 of MEG experiments are matched, but this does not address the question of whether the distractor was actually distracting (and thus needed to be inhibited by occipital alpha). Please clarify.

Comments on the latest version:

I am satisfied with the author's response and do not have any additional comments.

Reviewer #1 (Public Review):

Summary:

In their paper, Zhan et al. have used Pf genetic data from simulated data and Ghanaian field samples to elucidate a relationship between multiplicity of infection (MOI) (the number of distinct parasite clones in a single host infection) and force of infection (FOI). Specifically, they use sequencing data from the var genes of Pf along with Bayesian modeling to estimate MOI individual infections and use these values along with methods from queueing theory that rely on various assumptions to estimate FOI. They compare these estimates to known FOIs in a simulated scenario and describe the relationship between these estimated FOI values and another commonly used metric of transmission EIR (entomological inoculation rate).

This approach does fill an important gap in malaria epidemiology, namely estimating the force of infection, which is currently complicated by several factors including superinfection, unknown duration of infection, and highly genetically diverse parasite populations. The authors use a new approach borrowing from other fields of statistics and modeling and make extensive efforts to evaluate their approach under a range of realistic sampling scenarios. However, the write-up would greatly benefit from added clarity both in the description of methods and in the presentation of the results. Without these clarifications, rigorously evaluating whether the author's proposed method of estimating FOI is sound remains difficult. Additionally, there are several limitations that call into question the stated generalizability of this method that should at minimum be further discussed by authors and in some cases require a more thorough evaluation.

Major comments:

(1) Description and evaluation of FOI estimation procedure.

a. The methods section describing the two-moment approximation and accompanying appendix is lacking several important details. Equations on lines 891 and 892 are only a small part of the equations in Choi et al. and do not adequately describe the procedure notably several quantities in those equations are never defined some of them are important to understand the method (e.g. A, S as the main random variables for inter-arrival times and service times, aR and bR which are the known time average quantities, and these also rely on the squared coefficient of variation of the random variable which is also never introduced in the paper). Without going back to the Choi paper to understand these quantities, and to understand the assumptions of this method it was not possible to follow how this works in the paper. At a minimum, all variables used in the equations should be clearly defined.

b. Additionally, the description in the main text of how the queueing procedure can be used to describe malaria infections would benefit from a diagram currently as written it's very difficult to follow.

c. Just observing the box plots of mean and 95% CI on a plot with the FOI estimate (Figures 1, 2, and 10-14) is not sufficient to adequately assess the performance of this estimator. First, it is not clear whether the authors are displaying the bootstrapped 95%CIs or whether they are just showing the distribution of the mean FOI taken over multiple simulations, and then it seems that they are also estimating mean FOI per host on an annual basis. Showing a distribution of those per-host estimates would also be helpful. Second, a more quantitative assessment of the ability of the estimator to recover the truth across simulations (e.g. proportion of simulations where the truth is captured in the 95% CI or something like this) is important in many cases it seems that the estimator is always underestimating the true FOI and may not even contain the true value in the FOI distribution (e.g. Figure 10, Figure 1 under the mid-IRS panel). But it's not possible to conclude one way or the other based on this visualization. This is a major issue since it calls into question whether there is in fact data to support that these methods give good and consistent FOI estimates.

d. Furthermore the authors state in the methods that the choice of mean and variance (and thus second moment) parameters for inter-arrival times are varied widely, however, it's not clear what those ranges are there needs to be a clear table or figure caption showing what combinations of values were tested and which results are produced from them, this is an essential component of the method and it's impossible to fully evaluate its performance without this information. This relates to the issue of selecting the mean and variance values that maximize the likelihood of observing a given distribution of MOI estimates, this is very unclear since no likelihoods have been written down in the methods section of the main text, which likelihood are the authors referring to, is this the probability distribution of the steady state queue length distribution? At other places the authors refer to these quantities as Maximum Likelihood estimators, how do they know they have found the MLE? There are no derivations in the manuscript to support this. The authors should specify the likelihood and include in an appendix an explanation of why their estimation procedure is in fact maximizing this likelihood, preferably with evidence of the shape of the likelihood, and how fine the grid of values they tested is for their mean and variance since this could influence the overall quality of the estimation procedure.

(2) Limitation of FOI estimation procedure.

a. The authors discuss the importance of the duration of infection to this problem. While I agree that empirically estimating this is not possible, there are other options besides assuming that all 1-5-year-olds have the same duration of infection distribution as naïve adults co-infected with syphilis. E.g. it would be useful to test a wide range of assumed infection duration and assess their impact on the estimation procedure. Furthermore, if the authors are going to stick to the described method for duration of infection, the potentially limited generalizability of this method needs to be further highlighted in both the introduction, and the discussion. In particular, for an estimated mean FOI of about 5 per host per year in the pre-IRS season as estimated in Ghana (Figure 3) it seems that this would not translate to 4-year-old being immune naïve, and certainly this would not necessarily generalize well to a school-aged child population or an adult population.

b. The evaluation of the capacity parameter c seems to be quite important and is set at 30, however, the authors only describe trying values of 25 and 30, and claim that this does not impact FOI inference, however it is not clear that this is the case. What happens if the carrying capacity is increased substantially? Alternatively, this would be more convincing if the authors provided a mathematical explanation of why the carrying capacity increase will not influence the FOI inference, but absent that, this should be mentioned and discussed as a limitation.

Reviewer #2 (Public review):

Summary:

The authors combine a clever use of historical clinical data on infection duration in immunologically naive individuals and queuing theory to infer the force of infection (FOI) from measured multiplicity of infection (MOI) in a sparsely sampled setting. They conduct extensive simulations using agent based modeling to recapitulate realistic population dynamics and successfully apply their method to recover FOI from measured MOI. They then go on to apply their method to real world data from Ghana before and after an indoor residual spraying campaign.

Strengths:

- The use of historical clinical data is very clever in this context

- The simulations are very sophisticated with respect to trying to capture realistic population dynamics

- The mathematical approach is simple and elegant, and thus easy to understand

Weaknesses:

- The assumptions of the approach are quite strong, and the authors have made clear that applicability is constrained to individuals with immune profiles that are similar to malaria naive patients with neurosyphilis. While the historical clinical data is a unique resource and likely directionally correct, it remains somewhat dubious to use the exact estimated values as inputs to other models without extensive sensitivity analysis.

Comments on revisions:

The authors have adequately responded to all comments.

Reviewer #1 (Public review):

This manuscript adds to the recent, exciting developments in our understanding of the MmpL/S transporters from mycobacteria. This work provides solid support for the trimeric/hexameric arrangement of subunits in the complex, and reveals a possible pathway for substrate translocation.

Overall, I think this manuscript is a solid body of work that adds to several recent studies from this team and others on the structure and mechanism of the MmpL/S transporter family, particularly MmpL4/S4. The combination of AF, disulfide engineering, and experimental structure is good, though it is a bit puzzling that the experimental structure based on disulfide stabilization of the AF prediction does not recapitulate key elements (MmpS periplasmic domain docking to MmpL, and altered CCD configuration).

I have no major concerns about this manuscript.

Reviewer #1 (Public review):

Summary:

In "Drift in Individual Behavioral Phenotype as a Strategy for Unpredictable Worlds," Maloney et al. (2026) investigate changes in individual responses over time, referred to as behavioral drift within the lifespan of an animal. Drift, as defined in the paper, complements stable behavioral variation (animal individuality/personality within a lifetime) over shorter timeframes, which the authors associate with an underlying bet-hedging strategy. The third timeframe of behavioral variability that the authors discuss occurs within seasons (across several generations of some insects), termed "adaptive tracking." This division of "adaptive" behavioral variability over different timeframes is intuitively logical and adds valuable depth to the theoretical framework concerning the ecological role of individual behavioral differences in animals.

Strengths:

While the theoretical foundations of the study are compelling, the connection between the experimental data (Fig. 1) and the modeling work (Fig. 2-4) is convincing.

Weaknesses:

In the experimental data (Fig. 1), the authors describe the changes in behavioral preferences over time. While generally plausible, I had identified three significant issues with the experiments that were addressed in the revision:

(1) All of the subsequent theoretical/simulation data is based on changing environments, yet all the experiments are conducted in unchanging environments. While this may suffice to demonstrate the phenomenon of behavioral instability (drift) over time, it does not fully link to the theory-driven work in changing environments. A full experimental investigation of this would be beyond the scope of the current work.

(2) The temporal aspect of behavioral instability has been addressed in Figure 1F.

(3) The temporal dimension leads directly into the third issue: distinguishing between drift and learning (e.g., line 56). This issue has been further discussed in the revised manuscript.

Reviewer #1 (Public review):

This manuscript characterizes the effects of isoflurane on visual processing in layer 2/3 of the mouse primary visual cortex (V1). General anesthesia, including isoflurane, has been reported to modulate various neural processes, such as size tuning, direction selectivity, and spatial selectivity in V1. Using two-photon calcium imaging, the authors monitored neural responses to visual stimuli under isoflurane anaesthesia and found that spatial frequency preferences are also affected across cell types, with the magnitude and direction of these effects varying between cell types.

The authors performed careful and rigorous comparisons of neuronal responses between the two conditions using well-chosen nonparametric statistics. At the same time, because two-photon calcium imaging can be combined with cell-type-specific labeling, the authors labelled inhibitory neurons with tdTomato, allowing them to distinguish GCaMP activities in excitatory and specific inhibitory cell classes. We also appreciated that the manuscript provides not only summary statistics but also example GCaMP traces (Figure 1), which makes it easy for readers to understand the quality of the raw data.

We believe that the manuscript could be improved by emphasizing the following three points.

(1) The analyses are limited to the neurons that responded to visual stimuli in both the anesthetized and awake states. According to Table S1, the proportion of visually responsive neurons that met such criteria is only 27.4% for the excitatory neurons. This raises the potential concerns that the reported effects of isoflurane may not fully reflect population-level changes in visual coding. We suggest that the authors repeat the same analyses, including average tuning curves and decoding analyses, for all recorded neurons in each condition.

(2) The manuscript would benefit from tuning curves of spatial frequency preference for individual neurons, as this would help readers assess whether the reported statistics are appropriate (Figures 2A-D). In addition, more in-depth single-neuron analyses would help distinguish between the two proposed hypotheses in Figure 5 that may not be evident from average responses alone. This is because, with the current analysis, it is not clear how the shape of the tuning curves will affect the estimation of spatial frequency preference. To address this potential concern and strengthen the interpretation of the results, we suggest:<br /> a) repeating the analysis at the level of individual neuronal responses, instead of average responses, and<br /> b) using simulated data to examine how changes in tuning-curve width could affect estimated spatial frequency preference.

For example, using the neuronal responses in the awake condition, one could broaden the tuning curves and recompute the preferred spatial frequency, then compare the resulting distribution with that observed under anesthesia.

(3) We believe the manuscript's overall framing is a little broader than what is directly supported by the data. In particular:

(a) the statement "reduced sensory perception during anesthesia is linked to a degradation in spatial resolution at the cellular level" in the Abstract is an unclear and unsupported claim. We suggest removing this sentence and more directly summarizing the findings.

(b) given the discrepancy between the effects of urethane and isoflurane as laid out in the discussion, the current title "Anesthesia Lowers Spatial Frequency Preference in the Primary Visual Cortex" appears overstated and should be revised to explicitly reflect the specific anesthetic tested: "Isoflurane Anesthesia Lowers Spatial Frequency Preference in the Primary Visual Cortex".

Reviewer #1 (Public review):

Summary:

The manuscript entitled "Evaluation of Antibiotic and Peptide Vaccine Strategies for Mirror Bacterial Infections" addresses a topic that is well established in the literature. The authors investigate the activity of enantiomeric (D-form) antibiotics against bacteria and the immunogenicity of D-form peptides, proposing that D-enantiomers are ineffective both as antibacterial agents and as vaccine candidates. While the subject matter is relevant, the concepts explored are already well known, and the manuscript offers limited novelty.

The authors demonstrate that D-enantiomeric antibiotics lack antibacterial activity compared to their naturally occurring L-forms and that D-form peptides fail to elicit detectable immune responses. These observations are consistent with existing knowledge regarding molecular chirality in biological systems. However, the manuscript relies on a limited experimental dataset while extrapolating the findings broadly, which weakens the strength of the conclusions.

Strengths:

The manuscript introduces the topic of Mirror Bacterial Infections, likely to occur if no regulations or restrictions are placed immediately.

The manuscript addresses a relevant topic and has potential value, particularly in framing discussions around chirality and pathogen interactions. With a more cautious interpretation of the results, the manuscript could better justify its conceptual framework and strengthen its contribution to the field.

Weaknesses:

(1) Several sections of the manuscript are overly descriptive and would benefit from deeper comparative analysis and critical synthesis. In multiple instances, the discussion relies on hypothetical scenarios supported primarily by selective citations rather than robust experimental evidence. The introduction of the term "mirror microbiology" or "mirror bacteria" appears largely conceptual and is used to unify what are essentially two separate lines of investigation, enantioselective antibiotic activity and peptide chirality in immune recognition, without sufficient mechanistic integration.

(2) To the best of this reviewer's understanding, the manuscript does not present substantial novelty. The pronounced differences in biological activity between L- and D-forms of small molecules and peptides are well documented, including their implications for antimicrobial efficacy and immune recognition. While the manuscript is written in clear and accessible language suitable for both specialists and interdisciplinary readers, novelty remains limited.

The manuscript reiterates well-established principles of stereochemistry and biological recognition. Given the extensive existing literature demonstrating that enantiomeric antibiotics are typically inactive due to stereospecific target interactions, the failure of D-form antibiotics is expected and does not constitute a novel finding.

(3) Critical experimental details are lacking, particularly regarding the peptide design. It is unclear whether the peptides were synthesized entirely in the D-configuration or whether only select amino acids were substituted. This distinction is essential for interpreting immunogenicity results and for comparison with prior studies.

(4) The authors conclude that D-form peptides are poorly recognized by the immune system. However, the data presented indicate that neither the L- nor the D-form peptides tested elicited a measurable immune response. Without demonstrating immunogenicity of the corresponding L-form peptides, the conclusion that immune non-recognition is specific to the D-form is not sufficiently supported.

Reviewer #1 (Public review):

Summary:

The authors provide in vivo and in vitro evidence for an interaction between AIRE and AID. This has implications for the dynamics of the germinal center response and autoimmunity related to the APSI disease.

The manuscript describes an unexpected function of AIRE, which is more well known for its function to regulate negative selection of T cells in the thymus. Here, the gene has also been shown to be expressed by B cells (Immunity 2015: 26070482). They describe that AIRE interacts with AID, and in its absence, B cells acquire more hypermutations and also produce auto-antibodies against IL-17. These autoantibodies have been described previously.

Strengths:

The study is interesting and provides some additional information about how AIRE regulates immune cell function. Several biochemical and in vivo experiments show the interaction and the function of AIREs in the regulation of AID activity in the GC response.

Weaknesses:

Some of the hypothetical consequences of this regulation are not investigated. This includes responses to model antigens and dynamics of the germinal center related to kinetics.

Major Comments:

(1) AID regulates both switch and somatic hypermutation. Switch is easier to achieve, so which of these processes does AIRE influence the most? Also, the switch is thought to occur before the B cell enters the GC. Looking at the histology, is AIRE also expressed at the early proliferative stage that has been described by Ann Haberman?

(2) In experiments determining anti-CD40-dependent upregulation of AIRE, naïve resting B cells were used from mice. A proportion of the B-cells got activated. Are these MZB or FOB cells as MZBs are more easily activated?

(3) In the BM chimeric experiments in Figure 3. Do the AIRE+ and AIRE - populations distribute equally among B cell subpopulations?

(4) Furthermore, in the NP-KLH experiments, one would expect that B cells with increased affinity would leave the GC earlier and become plasma cells. Thus, the kinetics of the AIRE+ vs AIRE- B cells within the GC would be different? Also, would they maybe take over at some point, as the increased affinity would favor help from Tfh cells that are known to be limited?

(5) Given the previous studies on AIRE's function in regulating transcription (PMID: 34518235), how does this interaction fit into this picture?

(6) In the uracil experiments, the readout for AID to induce double-stranded breaks could be tested.

(7) The candida experiments are a nice connection to the situation in patients. However, why is it mostly auto-antibodies against IL-17? How about other immune responses, as well as T cell-independent type I and II responses?

Reviewer #1 (Public review):

Summary:

Knowing that small pupil-size variations accompany brightness variations (even when these are illusory), the authors asked whether pupil constrictions would accompany the synesthetic perception of a brighter color (compared with a darker one), induced by the presentation of a black-white character. This grapheme-colour synesthesia is only experienced by a few participants, sixteen of whom were enrolled in this study. The results reliably showed that a relative pupil constriction would "betray" the perception of a brighter color in these participants, while no such effect would be observed in control participants who were asked to report a color in association with each grapheme, even though they did not perceive any.

Strengths:

The main strength of the study lies in its combination of psychophysics (brightness ratings) and pupillometry, which allowed for showing clear-cut results.

Weaknesses:

Some relatively minor weaknesses concern the ancillary analyses, which tackle secondary questions and are not entirely convincing.

(1) The linear mixed model approach is a powerful way to identify important variables, but it does not clarify whether the key factors are between-subject or between-trial variations. Some variables are inherently defined at a subject level (e.g., PA scores), others are not. I would strongly recommend an alternative visualisation of the results to examine inter-individual variability.

(2) It is not clear why taking the first derivative of pupil size in Figure 5 would isolate the effect of arousal, eliminating those of luminance and contrast changes (in fact, one could argue for the opposite, since arousal effects are generally constant for extended periods of time while contrast effects are typically more local and transient).

(3) It is a pity that responses to physical brightness modulations were only measured in the synesthete group, not in controls, as this would have allowed for ruling out differences in pupil reactivity across the two populations.

(4) Another concern is with the visualisation of the pupil traces in Figure 3 (main results); these were heavily pre-processed (per-participant demeaned), losing any feature besides the effect of interest and generating the unrealistic expectation that perception of dark/bright colors generate a net dilation/constriction of the pupil - whereas perception-related modulations of pupil size are always relative and generally small compared to the numerous other effects registered in pupil size. It would be far better to see the actual profiles, preserving the unfolding of dilations and constrictions over time, especially since these are further analysed in Figures 4 and 5.

Impact:

Despite these weaknesses, and especially if they are adequately addressed in the review, this work is likely to improve our understanding of synesthesia, providing a new tool to quantify the subjective sensations; an interesting potential extension would be using pupillometry for tracking changes over time of the synesthetic experiences, opening up the possibility to evaluate the importance of learning for this peculiar experience.

Reviewer #1 (Public review):

Summary:

In this work, Huang et al. revealed the complex regulatory functions and transcription network of 172 unknown transcriptional factors (TFs) in Pseudomonas aeruginosa PAO1. They have built a global TF-DNA binding landscape and elucidated binding preferences and functional roles of these TFs. More specifically, the authors established a hierarchical regulatory network and identified ternary regulatory motifs, and co-association modules. Since P. aeruginosa is a well known pathogen, the authors thus identified key TFs associated with virulence pathways (e.g., quorum sensing [QS], motility, biofilm formation), which could be potential drug targets for future development. The authors also explored the TF conservation and functional evolution through pan-genome and phylogenetic analyses. For the easy searching by other researchers, the authors developed a publicly accessible database (PATF_Net) integrating ChIP-seq and HT-SELEX data.

Strengths:

(1) The authors performed ChIP-seq analysis of 172 TFs (nearly half of the 373 predicted TFs in P. aeruginosa) and identified 81,009 significant binding peaks, representing one of the largest TF-DNA interaction studies in the field. Also, The integration of HT-SELEX, pan-genome, and phylogenetic analyses provided multi-dimensional insights into TF conservation and function.

(2) The authors provided informative analytical Framework for presenting the TFs, where a hierarchical network model based on the "hierarchy index (h)" classified TFs into top, middle, and bottom levels. They identified 13 ternary regulatory motifs and co-association clusters, which deepened our understanding of complex regulatory interactions.

(3) The PATF_Net database provides TF-target network visualization and data-sharing capabilities, offering practical utility for researchers especially for the P. aeruginosa field.

Weaknesses:

(1) There is very limited experimental validation for this study. Although 24 virulence-related master regulators (e.g., PA0815 regulating motility, biofilm, and QS) were identified, functional validation (e.g., gene knockout or phenotypic assays) is lacking, leaving some conclusions reliant on bioinformatic predictions. Another approach for validation is checking the mutations of these TFs from clinical strains of P. aeruginosa, where chronically adapted isolates often gain mutations in virulence regulators.

(2) ChIP-seq in bacteria may suffer from low-abundance TF signals and off-target effects. The functional implications of non-promoter binding peaks (e.g., coding regions) were not discussed.

(3) PATF_Net currently supports basic queries but lacks advanced tools (e.g., dynamic network modeling or cross-species comparisons). User experience and accessibility remain under-evaluated. But this could be improved in the future.

Achievement of Aims and Support for Conclusions

(1) The authors successfully mapped global P. aeruginosa TF binding sites, constructed hierarchical networks and co-association modules, and identified virulence-related TFs, fulfilling the primary objectives. The database and pan-genome analysis provide foundational resources for future studies.

(2) The hierarchical model aligns with known virulence mechanisms (e.g., LasR and ExsA at the bottom level directly regulating virulence genes). Co-association findings (e.g., PA2417 and PA2718 co-regulating pqsH) resonate with prior studies, though experimental confirmation of synergy is needed.

Impact on the Field and Utility of Data/Methods

(1) This study fills critical gaps in TF functional annotation in P. aeruginosa, offering new insights into pathogenicity mechanisms (e.g., antibiotic resistance, host adaptation). The hierarchical and co-association frameworks are transferable to other pathogens, advancing comparative studies of bacterial regulatory networks.

(2) PATF_Net enables rapid exploration of TF-target interactions, accelerating candidate regulator discovery.

Comments on revisions:

The authors have done a good job of revising their manuscript. The manuscript is now more concise and logical for readers.

Reviewer #1 (Public review):

This study presents a useful finding about development of task representations in mouse medial prefrontal cortex using 1-photon calcium recordings in an olfactory-guided spatial memory task. A key strength of the study is the use of longitudinal recordings allowing identification of task-related activity that emerges after learning. The study also reports existence of neuronal sequences during learning and their replay at reward locations. The evidence provided is solid, providing quantification of functional classes of cells over the course of learning using the longitudinal calcium recordings in prefrontal cortex, and quantification of prefrontal sequences.

(1) The authors continue to state that task phase selective cells (non-splitter) cells can be considered as "cross-condition generalization" and interpret them as "potential building blocks of schemas". However, cross-condition generalization requires demonstration of cross-condition generalization performance (CCGP) of neural decoders across task conditions, which is not shown here.

(2) The authors note that correlations on short time scales are not similar between sampling and reward phase, acknowledging that these two represent different behavioral states in a cued-memory task, and that the manuscript should more clearly distinguish replay with "pure sequences". However, while the last line in the abstract states that "sub-second neural sequences in the mPFC are more likely involved in behavioral outcomes rather than planning future actions", references are made throughout the manuscript to preplay/replay sequences, including results primarily for non-cued spatial memory tasks, in which there is no cued sampling phase. For example, lines 259-263 state "During odor sampling phase, no such significant replay was observed..." and "... sequence clusters showed small but significant bias to preplay in the sampling phase". If the authors want to distinguish between replay and "pure" sequences, then the terminology "replay" and "preplay" should not be used here.

Further, large parts of the Discussion are devoted to comparison to hippocampal ripple-associated replay. Lines 355-356 in Discussion state that "the suggestion that mPFC sequences may also support planning [Tang et al., 2021] could not be confirmed by our work as sequences in the odor sampling phase were absent". It should be clarified that this is a comparison between what the authors term "pure sequences" in the sampling phase of an odor-cued task, and internally generated sequences during hippocampal ripples in a non-cued spatial memory task, so this is not a like-for-like comparison.

Reviewer #1 (Public review):

Summary:

Jocher, Janssen et al examine the robustness of comparative functional genomics studies in primates that make use of induced pluripotent stem cell-derived cells. Comparative studies in primates, especially amongst the great apes, are generally hindered by the very limited availability of samples, and iPSCs, which can be maintained in the laboratory indefinitely and defined into other cell types, have emerged as promising model systems because they allow the generation of data from tissues and cells that would otherwise would be unobservable.

Undirected differentation of iPSCs into many cell types at once, using a method known as embryoid body differentiation, requires researchers to manually assign all cell types in the dataset so they can be correctly analysed. Typically, this is done using marker genes associated with a specific cell type. These are defined a priori, and have historically tended to be characterised in mice and human and then employed to annotate other species. Jocher, Janssen et al ask if the marker genes and features used to define a given cell type in one species are suitable for use in a second species, and then quantify the degree of usefulness of these markers. They find that genes that are informative and cell type specific in a given species are less valuable for cell type identification in other species, and that this value, or transferability, drops off as the evolutionary distance between species increases.

This paper will help guide future comparative studies of gene expression in primates (and more broadly) as well as add to the growing literature on the broader challenges of selecting powerful and reliable marker genes for use in single cell transcriptomics.

Strengths:

Marker gene selection and cell type annotation is challenging problem in scRNA studies, and successful classification of cells often requires manual expert input. This can be hard to reproduce across studies, as despite general agreement on the identity of many cell types, different methods for identifying marker genes will return different sets of genes. The rise of comparative functional genomics complicates this even further, as a robust marker gene in one species need not always be as useful in a different taxon. The finding that so many marker genes have poor transferability is striking, and by interrogating the assumption of transferability in a thorough and systematic fashion, this paper reminds us of the importance of systematically validating analytical choices. The focus on identifying how transferability varies across different types of marker genes (especially when comparing TFs to lncRNAs), and on exploring different methods to identify marker genes, also suggests additional criteria by which future researchers could select robust marker genes in their own data.

The paper is built on a substantial amount of clearly reported and thoroughly considered data, including EBs and cells from four different primate species - humans, orangutans, and two macaque species. The authors go to great lengths to ensure the EBs are as comparable as possible across species, and take similar care with their computational analyses, always erring on the side of drawing conservative conclusions that are robustly supported by their data over more tenuously supported ones that could be impacted by data processing artefacts such as differences in mappability etc. For example, I like the approach of using liftoff to robustly identify genes in non-human species that can be mapped to and compared across species confidently, rather than relying on the likely incomplete annotation of the non-human primate genomes. The authors also provide an interactive data visualisation website that allows users to explore the dataset in depth, examine expression patterns of their own favourite marker genes and perform the same kinds of analyses on their own data if desired, facilitating consistency between comparative primate studies.

Weaknesses and recommendations:

(1) Embryoid body generation is known to be highly variable from one replicate to the next for both technical and biological reasons, and the authors do their best to account for this, both by their testing of different ways of generating EBs, and by including multiple technical replicates/clones per species. However, there is still some variability that could be worth exploring in more depth. For example, the orangutan seems to have differentiated preferentially towards cardiac mesoderm whereas the other species seemed to prefer ectoderm fates, as shown in Figure 2C. Likewise, Supplementary Figure 2C suggests significant unbalance in the contributions across replicates within a species, which is not surprising given the nature of EBs, while Supplementary Figure 6 suggests that despite including three different clones from a single rhesus macaque, most of the data came from a single clone. The manuscript would be strengthened by a more thorough exploration of the intra-species patterns of variability, especially for the taxa with multiple biological replicates, and how they impact the number of cell types detected across taxa etc.

The same holds for the temporal aspect of the data, which is not really discussed in depth despite being a strength of the design. Instead, days 8 and 16 are analysed jointly, without much attention being paid to the possible differences between them. Are EBs at day 16 more variable between species than at day 8? Is day 8 too soon to do these kinds of analyses? Are markers for earlier developmental progenitors better/more transferable than those for more derived cell types?

(2) Closely tied to the point above, by necessity the authors collapse their data into seven fairly coarse cell types, and then examine the performance of canonical marker genes (as well as those discovered de novo) across the species. But some of the clusters they use are somewhat broad, and so it is worth asking whether the lack of specificity exhibited by some marker genes and driving their conclusions is driven by inter-species heterogeneity within a given cluster.

Comments on revisions:

I think the authors have addressed my previous comments to my satisfaction, and I thank them for the changes they have made, it's good to see that the manuscript is just as sound as it seemed the first time around.

Reviewer #2 (Public review):

Summary:

This study examines the contribution of cerebello-thalamic pathways to motor skill learning and consolidation in an accelerating rotarod task. The authors use chemogenetic silencing to manipulate activity of cerebellar nuclei neurons projecting to two thalamic subregions that target motor cortex and striatum. By silencing these pathways during different phases of task acquisition (during task vs after task), the authors report valuable finding of the involvement of these cerebellar pathways in learning and consolidation.

Strengths:

The experiments are well-executed. The authors perform multiple controls and careful analysis to solidly rule out any gross motor deficits caused by their cerebellar nuclei manipulation. The finding that cerebellar projections to the thalamus are required for learning and execution of the accelerating rotarod task adds to a growing body of literature on the interactions between the cerebellum, motor cortex, and basal ganglia during motor learning. The finding that silencing the cerebellar nuclei after task impairs consolidation of the learned skill is interesting.

Revision comment:

The revised manuscript is improved in clarity and methodological detail. An important addition is the retrograde labeling data showing a degree of anatomical segregation between CN->CL and CN->VAL pathways that strengthens their reported different functional roles. I still think that potential effects on motor execution when cerebellar nuclei are silenced during task performance may complicate interpretations specifically related to learning. However, the evidence supporting a role of the cerebellar nuclei in off-line consolidation is convincing.

Overall, the study outlines a multifaceted role of the cerebellum in motor learning, consolidation, and execution. The demonstration that cerebellar projections to distinct forebrain structures contribute to these processes is significant.

Reviewer #1 (Public review):

Summary:

Fecal virome transfer (FVT) has the potential to take advantage of microbiome associated phages to treat diseases such as NEC. However, FVT is also associated with toxicity due to the presence of eukaryotic viruses in the mixture, which are difficult to filter out. The authors use a chemostat propagation system to reduce the presence of eukaryotic viruses (these become lost over time during culture). They show in pig models of NEC that chemostat propagation reduce the incidence of diarrhea induced by FVTs.

Strengths:

The authors report an innovative yet simple approach that has the potential to be useful for future applications. Most of the experiments are easy to follow and are performed well.

Weaknesses:

The biggest weakness is that the authors show that their technique addresses safety, but they are unable to demonstrate that they retain efficacy in their NEC model. This could be due to technical issues or perhaps the efficacy of FVT reported in the literature is not robust.

During the revision, the authors have acknowledged these limitations and added clarifications where necessary.

Reviewer #1 (Public review):

Summary:

The paper investigates the interplay between fluid flow and biofilm development using Pseudomonas aeruginosa PAO1 in microfluidic channels. By combining experimental observations with mathematical modeling, the study identifies the significant impact of nutrient limitation and hydrodynamic forces on biofilm growth and detachment. The authors demonstrate that nutrient limitation drives the longitudinal distribution of biomass, while flow-induced detachment influences the maximum clogging and temporal dynamics. The study highlights that pressure buildup plays a critical role in biofilm detachment, leading to cyclic episodes of sloughing and regrowth. A stochastic model is used to describe the detachment process, capturing the apparent randomness of sloughing events. The findings offer insights into biofilm behavior during clogging and fouling, potentially relevant to infections, environmental processes, and engineering applications.

Strengths:

This paper demonstrates a strong integration of experimental work and mathematical modeling, providing a comprehensive understanding of biofilm dynamics in a straight microfluidic channel. The simplicity of the microchannel geometry allows for accurate modeling, and the findings have the potential to be applied to more complex geometries. The detailed analysis of nutrient limitation and its impact on biofilm growth offers valuable insights into the conditions that drive biofilm formation. The model effectively describes biofilm development across different stages, capturing both initial growth and cyclic detachment processes. While cyclic pressure buildup has been studied previously, the incorporation of a stochastic model to describe detachment events is a novel and significant contribution, capturing the complexity and randomness of biofilm behavior. Finally, the investigation of pressure buildup and its role in cyclic detachment and regrowth enhances our understanding of the mechanical forces at play, making the findings applicable to a wide range of technological and clinical contexts.

Weaknesses:

The study achieves its primary objective of combining experiments and modeling to elucidate the coupling between flow, biofilm growth, and detachment in a confined microfluidic channel. In the revised manuscript, the authors have clarified several methodological choices and underlying assumptions. The points below are best viewed not as weaknesses, but as aspects that define the scope of the approach.

• Biofilm porosity and permeability. The authors now discuss biofilm porosity and provide a clear rationale for neglecting permeability effects in their system, arguing that flow around dense biofilm structures dominates over flow through the matrix. While this assumption appears reasonable for the conditions explored, permeability effects are not explicitly modeled and could become relevant in less compact or more heterogeneous biofilms.

• Characterization of the EPS matrix. The role of the extracellular matrix is convincingly addressed using polysaccharide‑deficient mutants, which provides a strong and causal link between EPS composition and mechanical stability. At the same time, the absence of complementary biochemical or imaging‑based characterization means that spatial or temporal variations in EPS distribution are not directly resolved, limiting the level of structural details.

• Three‑dimensional interpretation of biofilm development. The authors clarify that three‑dimensional information is primarily obtained from pressure‑based measurements, with two‑dimensional imaging serving as a validation tool. This approach is coherent and supported by scaling arguments and reproducibility across experiments.

Reviewer #1 (Public review):

Summary:

Matsen et al. describe an approach for training an antibody language model that explicitly tries to remove effects of "neutral mutation" from the language model training task, e.g. learning the codon table, which they claim results in biased functional predictions. They do so by modeling empirical sequence-derived likelihoods through a combination of a "mutation" model and a "selection" model; the mutation model is a non-neural Thrifty model previously developed by the authors, and the selection model is a small Transformer that is trained via gradient descent. The sequence likelihoods themselves are obtained from analyzing parent-child relationships in natural SHM datasets. The authors validate their method on several standard benchmark datasets and demonstrate its favorable computational cost. They discuss how deep learning models explicitly designed to capture selection and not mutation, trained on parent-child pairs, could potentially apply to other domains such as viral evolution or protein evolution at large.

Overall, we think the idea behind this manuscript is really clever and shows promising empirical results. Two aspects of the study are conceptually interesting: the first is factorizing the training likelihood objective to learn properties that are not explained by simple neutral mutation rules, and the second is training not on self-supervised sequence statistics but on the differences between sequences along an antibody evolutionary trajectory. If this approach generalizes to other domains of life, it could offer a new paradigm for training sequence-to-fitness models that is less biased by phylogeny or other aspects of the underlying mutation process.

Future versions of the work can consider extending the ideas to additional datasets, species, definitions of fitness, or even different proteins entirely.

Comments on revisions:

We thank the authors for addressing our points and have no remaining questions.

Reviewer #1 (Public review):

Summary:

The paper by ILBAY et al describes a screen in C. elegans for loss-of-function of factors that are presumed to constitutively downregulate heat shock or stress genes regulated by HSF-1. The hypothesis posits an active mechanism of downregulation of these genes under non-stressed conditions. The screen robustly identified ZNF-236, a multi zinc finger containing protein, whose loss upregulates heat-shock and stress-induced prion-like protein genes, but which does not appear to act in cis at the relevant promoters. The authors speculate that ZNF-236 acts indirectly on chromatin or chromatin domains to repress hs genes under non-stressed conditions.

Strengths:

The screen is clever, well-controlled and quite straightforward. I am convinced that ZNF-236 has something to do with keeping heat shock and other stress transcripts low. The mapping of potential binding sites of ZNF-236 is negative, despite the development of a new method to monitor binding sites. I am not sure whether this assay has a detection/sensitivity threshold limit, as it is not widely used. Up to this point, the data are solid, and the logic is easy to follow.

Weaknesses:

While the primary observations are well-documented, the mode of action of ZNF-236 is inadequately explored. Multi Zn finger proteins often bind RNA (TFIII3A is a classic example), and the following paper addresses multivalent functions of Zn finger proteins in RNA stability and processing: Mol Cell 2024 Oct 3;84(19):3826-3842.e8. doi: 10.1016/j.molcel.2024.08.010.). I see no evidence that would point to a role for ZNF-236 in nuclear organization, yet this is the authors' favorite hypothesis. In my opinion, this proposed mechanism is poorly justified, and certainly should not be posited without first testing whether ZNF-236 acts post-transcriptionally, directly down-regulating the relevant mRNAs in some way. It could regulate RNA stability, splicing, export or translation of the relevant RNAs rather than their transcription rates. This can be tested by monitoring whether ZNF-236 alters run-on transcription rates or not. If nascent RNA synthesis rates are not altered, but rather co- and/or post-transcriptional events, and if ZNF-236 is shown to bind RNA (which is likely), the paper could still postulate that the protein plays a role in downregulating stress and heat shock proteins. However, they could rule out that it acts on the promoter by altering RNA Pol II engagement. Another option that should be tested is that ZNF-236 acts by nucleating an H3K9me domain that might shift the affected genes to the nuclear envelope, sequestering them in a zone of low-level transcription. That is also easily tested by tracking the position of an affected gene in the presence and absence of SNF-236. This latter mechanism is also right in line with known modes of action for Zn finger proteins (in mammals, acting through KAP1 and SETDB1). A role for nucleating H3K9me could be easily tested in worms by screening MET-2 or SET-25 knockouts for heat shock or stress mRNA levels. These data sets are already published.

Without testing these two obvious pathways of action (through RNA or through H3K9me deposition), this paper is too preliminary.

Appraisal:

The authors achieved their initial aim with the screen, and the paper is of interest to the field. However, they do not adequately address the likely modes of action. Indeed, I think their results fail to support the conclusion or speculation that ZNF-236 acts on long-range chromatin organization. No solid evidence is presented to support this claim.

Impact:

If the paper were to address and/or rule out likely modes of action, the paper would be of major value to the field of heat shock and stress mRNA control.

Reviewer #1 (Public review):

In this revised manuscript, Qin and colleagues aim to delineate a neural mechanism that is engaged specifically in the sated flies to suppress the intake of sugar solution (the "brake" mechanism for sugar consumption). They identified a three-step neuropeptidergic system that downregulates the sensitivity of sweet-sensing gustatory sensory neurons in sated flies. First, neurons that release a neuropeptide Hugin (which is an insect homolog of vertebrate Neuromedin U (NMU)) are in active state when the concentration of glucose is high. This activation depends on the cell-autonomous function of Hugin-releasing neurons that sense hemolymph glucose levels directly. Next, the Hugin neuropeptides activate Allatostatin A (AstA)-releasing neurons via one of Hugin receptors, PK2-R1. Finally, the released AstA neuropeptide suppresses sugar response in sugar-sensing Gr5a-expressing gustatory sensory neurons through AstA-R1 receptor. Suppression of sugar response in Gr5a-expressing neurons reduces fly's sugar intake motivation. They also found that NMU-expressing neurons in the ventromedial hypothalamus (VMH) of mice (which project to the rostal nucleus of the solitary tract (rNST)) are also activated by high concentrations of glucose independent of synaptic transmission, and that injection of NMU reduces the glucose-induced activity in the downstream of NMU-expressing neurons in rNST. These data suggest that the function of Hugin neuropeptide in the fly is analogous to the function of NMU in the mouse.

The shift of the narrative, which focuses specifically on the hugin-AstA axis as the "brake" on the satiety signal and feeding behavior, clarified the central message of the presented work. The authors have provided multiple lines of compelling evidence generated through rigorous experiments. The parallel study in mice adds a unique comparative perspective that makes the paper interesting to a wide range of readers.

While I deeply appreciate the authors' efforts to substantially restructure the manuscript, I have a few suggestions for further improvements. First, there remains room for discussion whether the "brake" function of the hugin-AstA axis is truly satiety state-dependent. The fact that neural activation (Fig. Supp. 8), peptide injection (Fig. 3A, 4A), receptor knockdown (Fig. 3C,G, 4E), and receptor mutants (Fig. Supp. 10, 12) all robustly modulate PER irrespective of the feeding status suggests that the hugin-AstA axis influences feeding behaviors both in sated and hungry flies. Additionally, their new data (Fig. Supp. 13B, C) now shows that synaptic transmission from hugin-releasing neurons is necessary for completely suppressing feeding even in sated flies. If the hugin-AstA axis engages specifically in sated (high glucose) state, disruption of this neuromodulatory system is expected to have relatively little effect in starved flies (in which the "brake" is already disengaged).

In this context, it is intriguing that the knockdown of PK2-R2 hugin receptor modestly but consistently decreases proboscis extension reflex specifically in starved flies (Fig. 3D, H). The manuscript does not discuss this interesting phenotype at all. Given the heterogeneity of hugin-releasing neurons (Fig. Supp. 7), there remains a possibility that a subset of hugin-releasing neurons and/or downstream neurons can provide a complementary (or even opposing) effect on the feeding behavior.

Given these intriguing yet unresolved issues, it is important to acknowledge that whether this system is "selectively engaged in fed states to dampen sweet sensation (in Discussion)" requires further functional investigations. Consistent effects of manipulation of the hugin-AstA system across multiple experimental approaches underscores the importance of this molecular circuitry axis for controlling feeding behaviors. Moderation of conclusions to accommodate alternative interpretation of data will be beneficial for field to determine the precise mechanism that controls feeding behaviors in future studies.

Reviewer #1 (Public review):

Summary:

The paper uses rigorous methods to determine phase dynamics from human cortical stereotactic EEGs. It finds that the power of the phase is higher at the lowest spatial phase. The application to data illustrates the solidity of the method and their potential for discovery.

Comments on revisions:

The authors have provided responses to the previous recommendations. The paper does not seem to contain further significant improvements. I am thus not inclined to change my judgement.

Reviewer #1 (Public review):

The authors present an approach that uses the transformer architecture to model epistasis in deep mutational scanning datasets. This is an original and very interesting idea. Applying the approach to 10 datasets they quantify the contribution of higher order epistasis, showing it varies quite extensively.

Comments on revisions:

The authors have addressed my concerns.

DOI: 10.1016/j.isci.2026.115231

Resource: None

Curator: @areedewitt04

SciCrunch record: RRID:ZFIN_ZDB-ALT-080917-1

What is this?

Reviewer #1 (Public review):

The manuscript by Luciano et al is a collection of experiments about the yeast histone 3 lysine 4 methyltransferase, Set1, starting with 10 yeast two-hybrid screens (Y2H). Y2H screens were briefly popular 20+ years ago, but the persistently unfavourable false-to-true positive ratios limited their utility, and the conclusion emerged that Y2H is an unreliable approach for gathering protein-protein interaction data. Y2H outcomes are candidate interaction lists at best, strongly contaminated by false positives. Here, the authors employed a company (Hybridomics) to perform the Y2H screens.

The primary data is not presented, and the outcomes are summarized using the Hybridomics in-house quality scoring system in Figure 1A. It is not possible to evaluate these data, and the manuscript presents cartoon summaries that the reader must accept as valuable.

(1) Based on the extensive knowledge about Set1C/COMPASS acquired from genetics and biochemistry by many labs (including the Geli lab), the results presented here from the 10 Y2H screens are notably patchy. Of the 7 subunits of this complex, only one (Spp1) was identified using Set1 as bait. Conversely, as baits, Swd2, Spp1, Shg1, captured Set1, and the Bre2-Sdc1 interaction was reciprocally identified. These interactions were scored at the highest confidence level, which lends some confidence to the screens. However, the missing interactions, even at the third confidence level, indicate that any Y2H conclusions using these data must be qualified with caution. The authors do not appear to be cautious in their lengthy evaluations of these candidate interactions, which are illustrated with cartoons in Figures 2 and 3, with some support from the literature but almost without additional evidence. Snf2 is a particularly interesting candidate, which the authors support with pull-down experiments after mixing the two proteins in vitro (Figure 4). After Y2H, this is the least convincing evidence for a protein-protein interaction, and no further, more reliable evidence is supplied.

(2) Figure 5 continues the cartoon summary of extrapolations from the Y2H screens, again without supporting evidence, except that the authors state, "We have refined the interaction region between Set1, Prp8 and Prp22, showing that Prp8 and Prp22 interact strongly with Set1-F4 (n-SET). Prp22 interacts in addition with Set1-F1 (Figure S2)." However, Figure S2 does not show this evidence and is incoherent.

The figure legends for Figure S2B and C (copied here in bold) do not correspond to the figure.

B - Expression of the F1-F5 fragments in yeast cells. Fusion proteins were detected with an anti-GAL4 monoclonal antibody. TOTO yeast cells (Hybrigenics) were transformed with the different pB66-Set1-F1 to F5 plasmids and subsequently with either P6, pP6-Snf2 762-968, pP6-Prp8 37-250, or pP6-Prp22 379-763 that were identified in the Y2H screens. Transformed cells were incubated 3 days at 30{degree sign}C on SD-LEU-TRP and then restreaked on SD-LEU-TRP-HIS with 3AT. Cell growth was monitored after 2 days at 30{degree sign}C.

C - Solid and dotted arrows indicate that transformed TOTO cells transformed with pB66-Set1-F1 to F5 and the indicated prey (Snf2, Prp8, and Prp22) are growing in the presence of 20 mM and 5 mM of AT, respectively.

Figure S2D is two almost featureless dark grey panels accompanied by the figure legend D) Control experiment showing that TOTO cells transformed with p6 and pB66-Set1-F4 are not gowing (sic) in the presence of 5 mM or 20 mM AT.

Line 343. Interestingly, the two-hybrid screens reveal that Set1 1-754 interacted with Gag capsid-like proteins of Ty1 (Figure S5), raising the possibility that Set1 binding to Ty1 mRNA is linked to the interaction of Set1 1-754 with Gag.

This is another example of the primary mistake repeatedly made by the authors -Y2H interactions are candidate results and not conclusive evidence. To further illustrate this point, the authors highlight the candidate interaction between Nis1 and 3 Set1C subunits.

(3) After multiple speculations based on the Y2H candidates, the authors changed to focus on sumoylation of Set1, which has previously reported to be sumoylated. Evidence identifying two sumoylation sites in Set1, in the N-SET and SET domains, is valuable and adds important progress to the role of sumoylation in the regulation of H3K4 methyltransferase, relevant for all eukaryotes. This illuminating part of the manuscript is only tenuously connected to the preceding Y2H screens and concomitant speculations.

(4) The manuscript then describes a red herring exercise involving Set1 methylation of Nrm1. In an already speculative and difficult manuscript, it is exasperating to read a paragraph about a failed idea. Apart from panel E, Figure 7 is a distraction, and I believe it should not be shared.

(5) However, despite the failure with Nrm1, Line 443 - The H3K4-like domain in Nrm1 raised our attention to other yeast proteins that carry such sequences. This line of thinking is even less connected to the Y2H screens than the sumoylation work.

However, the authors present a reasonable evaluation of the yeast proteome screened for six amino acids similar to the known H3K4 motif ARTKQT (Figure 7e).

(6) However, this evaluation goes nowhere and has no connection with the next section of the manuscript, which is entirely speculation about the regulation of metabolism and stress responses based on the Y2H results and selected evidence from the literature.

(7) The manuscript then describes more failed experiments regarding lysine methylation of Snf2 by Set1C, which unexpectedly reports arginine methylation rather than lysine. The manuscript does not currently meet the standard expected for this type of paper - the composition is somewhat incoherent and there are no previous reports of arginine methylation by SET domain proteins.

The manuscript presents a very experienced grasp of the literature and a sophisticated appreciation of the forefront issues, but a surprising failure to eliminate uninformative failures and peripheral distractions. The overinterpretation of Y2H results is a dominating failure. There are some valuable parts within this manuscript, and hopefully, the authors can reformat to eliminate the defects and appropriately qualify the candidate data.

Reviewer #1 (Public review):

Summary:

This work stratifies depression subgroups based on white matter integrity (Fractional Anisotropy, FA) and evaluates the relationship between white matter (WM) alterations in these subgroups and clinical symptoms. Furthermore, the authors tested these subgroup findings in an independent cohort. This paper provides WM-based depression subtypes that are linked to the clinical symptom profile (anxiety, cognitive, hopelessness, sleep, and psychomotor retardation) and presents the prediction of treatment outcome using these subtypes.

Strengths:

Applying a novel NMF (Non-negative Matrix Factorization) biclustering approach to stratify depression subtypes using white matter integrity. Following the recent functional MRI-based depression subtype stratification, this work provides a structural signature for depression heterogeneity. These subtypes were also tested in an independent cohort, with findings regarding clinical symptom profiles.

Weaknesses:

Although this novel method successfully subgroups depression patients, it is difficult to understand the spatial patterns of WM alteration and which structural connections, such as DMN, SN, ECN, and Limbic, because the findings are distributed across multiple WM bundles in each subgroup. Furthermore, these subtypes fail to predict optimal treatment selection within each group, since all subgroups benefit from different treatments.