Reviewer #1 (Public review):

In this manuscript, Ferhat and colleagues describe their study aimed at developing a blood brain barrier (BBB) penetrant agent that could induce hypothermia and provide neuroprotection from the sequelae of status epilepticus (SE) in mice. Hypothermia is used clinically in an attempt to reduce neurological sequelae of injury and disease. Hypothermia can be effective, but physical means used to reduce core body temperature is associated with untoward effects. Pharmacological means to induce hypothermia could be as effective with fewer untoward complications. Intracerebroventricularly applied neurotensin can cause hypothermia; however, neurotensin applied peripherally is degraded and does not cross the BBB. Here the authors develop and characterize a neurotensin conjugate that can reach the brain, induce hypothermia, and reduce seizures, cognitive changes, and inflammatory changes associated with status epilepticus.

Strengths:

(1) In general, the study is well reasoned, well designed, and seemingly well executed.<br /> (2) Strong dose-response assessment of multiple neurotensin conjugates in mice.<br /> (3) Solid assessment of binding affinity, in vitro stability ion blood, and brain uptake of the conjugate.<br /> (4) Appropriate inclusion of controls for SE and for drug injections.<br /> (5) Multifaceted assessment of neurodegeneration, inflammation, and mossy fiber sprouting in the different groups.<br /> (6) Inclusion of behavioral assessments.<br /> (7) Evaluate NSTR1 receptor distribution in multiple ways.<br /> (8) Demonstrate that this conjugate can induce hypothermia and have positive effects on the sequelae of SE. Could have great impact on the application of pharmacologically-induced hypothermia as a neuroprotective measure in patients.

Weaknesses:

(1) The authors make the claim, repeatedly, that the hypothermia caused by the neurotensin conjugate is responsible for the effects they see; however, what they really show is that the conjugate causes hypothermia AND has favorable effects on the sequelae of SE. They have now discussed this limitation in the manuscript.

Reviewer #2 (Public review):

Summary:

The authors generated analogs consisting of modified neurotensin (NT) peptides capable of binding to low density lipoprotein (LDL) and NT receptors. Their lead analog was further evaluated for additional validation as a novel therapeutic. The putative mechanism of action for NT in its antiseizure activity is hypothermia, and as therapeutic hypothermia has been demonstrated in epilepsy, NT analogs may confer antiseizure activity and avoid the negative effects of induced hypothermia.

Strengths:

The authors demonstrate an innovative approach, i.e. using LDLR as a means of transport into the brain, that may extend to other compounds. They systematically validate their approach and its potential through binding, brain penetration, in vivo antiseizure efficacy, and neuroprotection studies.

Weaknesses:

Tolerability studies are warranted, given the mechanism of action and the potential narrow therapeutic index. In vivo studies were used to assess efficacy of the peptide conjugate analogs in the mouse KA model. However, it would be beneficial to have shown tolerability in naïve animals to better understand the therapeutic potential of this approach.

Mice may be particularly sensitive to hypothermia. It would be beneficial to show similar effects in a rat model.

Reviewer #1 (Public review):

Summary

Das and Menon describe an analysis of a large open-source iEEG dataset (UPENN-RAM). From encoding and recall phases of memory tasks, they analyzed power and phase-transfer entropy as a measure of directed information flow in regions across a hypothesized tripartite network system. The anterior insula (AI) was found to have heightened high gamma power during encoding and retrieval, which corresponded to suppression of high gamma power in medial prefrontal cortex (mPFC) and posterior cingulate cortex (PCC) during encoding but not recall. In contrast, directed information flow from (but not to) AI to mPFC and PCC is high during both time periods when PTE is analyzed with broadband but not narrowband activity. They claim that these findings significantly advance an understanding of how network communication facilitates cognitive operations during memory tasks, and that the AI of the salience network (SN) is responsible for influencing both the frontoparietal network (FPN) and default-mode network (DMN) during memory encoding and retrieval.

I find this question interesting and important, and agree with the authors that iEEG presents a unique opportunity to investigate the temporal dynamics within network nodes. Their findings convey intriguing information about the structure and order of communication between network regions during on-task cognition in general (though, perhaps not specific to memory - see Weaknesses), with the AI of the SN ostensibly playing an important role in possibly influencing the DMN and FPN.

Strengths

- The authors present results from an impressively sized iEEG sample. For reader context, this type of invasive human data is difficult and time-consuming to collect and many similar studies in high-level journals include 5-20 participants, typically not all of whom have electrodes in all regions of interest. It is excellent that they have been able to leverage open-source data in this way.<br /> - Preprocessing of iEEG data also seems sensible and appropriate based on field standards.<br /> - The authors tackle the replication issues inherent in much of the literature by replicating findings across task contexts, demonstrating that the principles of network communication evidenced by their results generalize in multiple task memory contexts. Again, the number of iEEG patients who have multiple tasks' worth of data is impressive.<br /> - Though the revised manuscript presents a broader and more novel investigation of the tripartite network's role in memory encoding and retrieval (as opposed to cognitive control of memory) the authors now thoroughly review the literature motivating this investigation of open-source data.

Weaknesses

- As the authors discuss, it is currently unclear if the directed information flow from AI to DMN and FPN nodes truly arises from memory-associated processes as opposed to more general attentional and cognitive demands, especially given that information flow does not relate meaningfully to task performance (whether memory retrieval is successful or not). I also note this is a concern because - though the authors have now demonstrated that information flow is increased compared to an off-task baseline - influences of AI on DMN or FPN were not increased relative to baseline epochs during the task in the original preprint version, again suggesting these effects may not be specific to the memory component of the analyzed tasks. The authors have thoughtfully noted in the Discussion several ways that experimental design can be improved in future studies to address this limitation.

Because phase-transfer entropy is referenced as a "causal" analysis in this investigation (PTE), I believe it is important to highlight for readers recent discussions surrounding the description of "causal mechanisms" in neuroscience (see "Confusion about causation" section from Ross and Bassett, 2024, Nature Neuroscience). A large proportion of neuroscientists (myself included) use "causal" only to refer to a mechanism whose modulation or removal (with direct manipulation, such as by lesion or stimulation) is known to change or control a given outcome (such as a successful behavior). As Ross and Bassett highlight, it is debatable whether such mechanistic causality is captured by Granger "causality" (a.k.a. Granger prediction) or the parametric PTE, and imprecise use of "causation" may be confusing. The authors have defined in the revised Introduction what their definition of "causality" is within the context of this investigation.

Reviewer #2 (Public review):

Based on reviewer feedback, Das and Menon have made several modifications to their manuscript, including a revised Introduction with a reframed motivation (now more oriented around the role of tripartite network in memory operations), new control analyses (as requested by Reviewers, including an updated and more appropriate baseline period and a control region, the IFG), an assessment of narrowband phase synchronization (as requested), as well as updates for clarity throughout the Methods section.

While I believe the authors have been responsive to reviewer feedback, and these modifications do enhance the manuscript, I have a few suggestions for how these new analyses could be made more statistically robust and better contextualized against the main findings of the manuscript. I continue to have some reservations about a tendency for their data to be overinterpreted, and for conclusions to be drawn more strongly than the data actually warrant.

(1) Clarifying the new control analyses. The authors have been responsive to our feedback and implemented several new analyses. The use of a pre-task baseline period and a control brain region (IFG) definitively help to contextualize their results, and the findings shown in the revision do suggest that (1) relative to a pre-task baseline, directed interactions from the AI are stronger and (2) relative to a nearby region, the IFG, the AI exhibits greater outward-directed influence.

However, it is difficult to draw strong quantitative conclusions from the analyses as presented, because they do not directly statistically contrast the effect in question (directed interactions with the FPN and DMN) between two conditions (e.g. during baseline vs. during memory encoding/retrieval). As I understand it, in their main figures the authors ask, "Is there statistically greater influence from the AI to the DMN/FPN in one direction versus another?" And in the AI they show greater "outward" PTE than "inward" PTE from other networks during encoding/retrieval. The balance of directed information favors an outward influence from the AI to DMN/FPN.

But in their new analyses, they simply show that the degree of "outward" PTE is greater during task relative to baseline in (almost) all tasks. I believe a more appropriately matched analysis would be to quantify the inward/outward balance during task states, quantify the inward/outward balance during rest states, and then directly statistically compare the two. It could be that the relative balance of directed information flow is non-significantly changed between task and rest states, which would be important to know.

Likewise, a similar principle applies to their IFG analysis. They show that the IFG tends to have an "inward" balance of influence from the DMN/FPN (the opposite of the AIs effect), but this does not directly answer whether the AI occupies a statistically unique position in terms of the magnitude of its influence on other regions. More appropriate, as I suggest above, would be to quantify the relative balance inward/outward influence, both for the IFG and the AI, and then directly compare those two quantities. (Given the inversion of the direction of effect, this is likely to be a significant result, but I think it deserves a careful approach regardless.)

(2) Consider additional control regions. The authors justify their choice of IFG as a control region very well. In my original comments, I perhaps should have been more clear that the most compelling control analyses here would be to subject every region of the brain outside these networks (with good coverage) to the same analysis, quantify the degree of inward/outward balance, and then see how the magnitude of the AI effect stacks up against all possible other options. If the assertion is that the AI plays a uniquely important role in these memory processes, showing how its influence stacks up against all possible "competitors" would be a very compelling demonstration of their argument.

(3) Reporting of successful vs. unsuccessful memory results. I apologize if I was not clear in my original comment (2.7, pg. 13 of the response document) regarding successful vs. unsuccessful memory. The fact that no significant difference was found in PTE between successful/unsuccessful memory is a very important finding that adds valuable context to the rest of the manuscript. I believe it deserves a figure, at least in the Supplement, so that readers can visualize the extent of the effect in successful/unsuccessful trials. This is especially important now that the manuscript has been reframed to focus more directly on claims regarding episodic memory processing; if that is indeed the focus, and their central analysis does not show a significant effect conditionalized on the success of memory encoding/retrieval, it is important that readers can see these data directly.

(4) Claims regarding causal relationships in the brain. I understand that the authors have defined "causal" in a specific way in the context of their manuscript; I do believe that as a matter of clear and transparent scientific communication, the authors nonetheless bear a responsibility to appreciate how this word may be erroneously interpreted/overinterpreted and I would urge further review of the manuscript to tone down claims of causality. Reflective of this, I was very surprised that even as both reviewers remarked on the need to use the word "causal" with extreme caution, the authors added it to the title in their revised manuscript.

Reviewer #1 (Public Review):

Summary:

This work focuses on the structure and regulation of the Anaphase-Promoting Complex/Cyclosome (APC/C), a large multi-subunit ubiquitin ligase that controls the onset of chromosome segregation in mitosis. Previous high-resolution structural studies have uncovered numerous structural features and regulatory mechanisms of the human APC/C, but it has remained unclear if these mechanisms are conserved in other model eukaryotes. To address this gap in our understanding, the authors employed cryo-electron microscopy to generate structural models of APC/C from the budding yeast S. cerevisiae, a key model organism in cell cycle analysis. In their comparison of the human and yeast complexes, the authors uncover many conserved structural features that are documented here in detail, revealing widespread similarities in the fundamental structural features of the enzyme. Interestingly, the authors also find evidence that two of the key mechanisms of human APC/C regulation are not conserved in the yeast enzyme. Specifically:

(1) The ubiquitin ligase activity of the APC/C depends on its association with a co-activator subunit such as CDH1 or CDC20, which serves both as a substrate-binding adaptor and as an activator of interactions with the E2 co-enzyme. Previous studies of the human APC/C revealed that co-activator binding induces a conformational change that enables E2 binding. In contrast, the current work shows that this E2-binding conformation already exists in the absence of a co-activator in the yeast enzyme, suggesting that the enhancement of E2 binding in yeast depends on other, as yet undiscovered, mechanisms.

(2) APC/C phosphorylation on multiple subunits is known to enhance APC/C activation by the CDC20 co-activator in mitosis. Previous studies showed that phosphorylation acts by promoting the displacement of an autoinhibitory loop that occupies part of the CDC20-binding site. In the yeast enzyme, however, there is no autoinhibitory loop in the CDC20-binding site, and there is no apparent effect of APC/C phosphorylation on co-activator binding sites. Thus, phosphorylation activates the yeast CDC20-APC/C by unknown mechanisms.

Strengths:

The strength of this paper is that it provides a comprehensive analysis of yeast APC/C structure and how it compares to previously determined human structures. The article systematically unwraps the key features of the structure in a subunit-by-subunit fashion, carefully revealing the key features that are the same or different in the two species. These descriptions are based on a thorough overview of past work in the field; indeed, this article serves as a concise review of the key features, conserved or otherwise, of APC/C structure and regulation.

Weaknesses:

No significant weaknesses were identified.

Reviewer #2 (Public Review):

Summary:

This paper from the Barford lab describes medium/high-resolution cryo-EM structures of three versions of the S. cerevisiae anaphase-promoting complex/cyclosome (APC/C):

(1) the recombinant apo complex purified from insect cells,

(2) the apo complex phosphorylated in vitro by cyclin-dependent kinase, and

(3) an active APC/C-Cdh1-substrate ternary complex.

The focus of the paper is on comparing similarities and differences between S. cerevisiae and human APC/C structures, mechanisms of activation by coactivator, and regulation by phosphorylation. The authors find that the overall structures of S. cerevisiae and human APC/C are remarkably similar, including the binding sites and orientation for the substrate-recruiting coactivator, Cdh1. In addition, the mechanism of Cdh1 inhibition by phosphorylation appears conserved across kingdoms. However, key differences were also observed that reveal divergence in APC/C mechanisms that are important for researchers in this field to know. Specifically, the mechanism of APC/C-Cdc20 activation by mitotic phosphorylation appears to be different, due to the absence of the key Apc1 autoinhibition loop in the S. cerevisiae complex. In addition, the conformational activation of human APC/C by coactivator binding was not observed in the S. cerevisiae complex, implying that stimulation of E2 binding must occur via a different mechanism in this species.

Strengths:

Consistent with the numerous prior cryo-EM structures of human APC/C from the Barford lab, the technical quality of the structure models is a major strength of this work. In addition, the detailed comparison of similarities and differences between the two species will be a very valuable resource for the scientific community. The manuscript is written very well and allows readers lacking expertise in cryo-EM to understand the important aspects of the conservation of APC/C structure and mechanism across kingdoms.

Weaknesses:

The lack of experimentation in this work to test some of the putative differences in APC/C mechanism (e.g. stimulation of E2 binding by coactivator and stimulation of activity by mitotic phosphorylation) could be considered a weakness. Nonetheless, the authors do a nice job explaining how the structure interpretations imply these differences likely exist, and this work sets the stage nicely for future studies to understand these differences at a mechanistic level. There is enough value in having the S. cerevisiae structure models and the comparison to the human structures, without any additional experimentation.

The validation of APC/C phosphorylation in the unphosphorylated and hyperphosphorylated states is not very robust. Given the lack of significant effects of phosphorylation on APC/C structure observed here (compared to the human complex), this becomes important. A list of phosphorylation sites identified by mass spec before and after in vitro phosphorylation is provided but lacks quantitative information. This list indicates that a significant number of phosphorylation sites are detected in the purified APC/C prior to reaction with purified kinases. Many more sites are detected after in vitro kinase reaction, but it isn't clear how extensively any of the sites are modified. There is reason for caution then, in accepting the conclusions that structures of unphosphorylated and hyperphosphorylated APC/C from S. cerevisiae are nearly identical.

Reviewer #3 (Public Review):

Vazquez-Fernandez et al. present a comprehensive and detailed analysis of the S. cerevisiae APC/C complex, providing new insights into its structure and function. The authors determined the medium-resolution structures of three recombinant S. cerevisiae APC/C complexes, including unphosphorylated apo-APC/C (4.9 Å), the ternary APC/CCDH1-substrate complex (APC/CCDH1:Hsl1 , 4.0 Å), and phosphorylated apo-APC/C (4.4 Å). Prior structures of human, E. cuniculi, S. cerevisiae, and S. pombe APC/C subunits, as well as AlphaFold2 predictions were used to guide model building. Although the determined structures are not sufficient to fully explain the molecular mechanism of APC/C activation and regulation in S. cerevisiae, they provide valuable insights into the similarities and differences with the human complex, shedding light on the conserved and divergent features of APC/C function.

The manuscript synthesizes the structural analysis of the APC/C complex in S. cerevisiae, with literature into a cohesive and clear picture of the complex's structure and function. It is well-written and clear, making the complex biology of the APC/C complex accessible to a wide range of readers. The complex forms a triangular shape, with a central cavity surrounded by two modules: the TPR lobe and the platform module. The TPR lobe consists of three TPR proteins (APC3, APC6, and APC8), which stack on top of each other to form a quasi-symmetric structure. The platform module is composed of the large APC1 subunit, together with APC4 and APC5. The authors also analyzed the structure of several smaller subunits that are involved in regulating the activity of the APC/C complex and showed their structural similarities to and discrepancies from their human counterparts. These subunits, including CDC26/APC12, SWM1/APC13, APC9, and MND2/APC15, form extended, irregular structures that simultaneously contact multiple large globular APC/C subunits.

While the authors report the similarity between the overall structure of S. cerevisiae and human APC/C complexes, they also found two unexpected differences. First, in the S. cerevisiae apo-complex, the E2 binding site on APC11RING is accessible, whereas, in humans, it requires CDH1 binding. Second, a structural element similar to the human APC1 auto-inhibitory segment is missing in S. cerevisiae. In humans, the phosphorylation-dependent displacement of this segment allows CDC20 binding to APC/C. In S. cerevisiae, the binding requires phosphorylation however the structures reported here are suggestive that this could involve a different (presently unknown) mechanism. These structural insights highlight the importance of understanding the species-specific features of APC/C function.

Strengths:

The manuscript does a great job of revealing new structures.

Opportunity for increasing impact: It would have been nice if some functional differences were demonstrated, for example regarding the mechanism of CDC20 binding, and the comparison between apo-APC/C and ternary APC/CCDH1:Hsl1 does not explain the molecular activation mechanism of S. cerevisiae APC/C. Nonetheless, the authors nicely integrate their data with well-established literature on the similarities and differences between yeast and human systems.

Reviewer #1 (Public Review):

The study identifies the epigenetic reader SntB as a crucial transcriptional regulator of growth, development, and secondary metabolite synthesis in Aspergillus flavus, although the precise molecular mechanisms remain elusive. Using homologous recombination, researchers constructed sntB gene deletion (ΔsntB), complementary (Com-sntB), and HA tag-fused sntB (sntB-HA) strains. Results indicated that deletion of the sntB gene impaired mycelial growth, conidial production, sclerotia formation, aflatoxin synthesis, and host colonization compared to the wild type (WT). The defects in the ΔsntB strain were reversible in the Com-sntB strain.

Further experiments involving ChIP-seq and RNA-seq analyses of sntB-HA and WT, as well as ΔsntB and WT strains, highlighted SntB's significant role in the oxidative stress response. Analysis of the catalase-encoding catC gene, which was upregulated in the ΔsntB strain, and a secretory lipase gene, which was downregulated, underpinned the functional disruptions observed. Under oxidative stress induced by menadione sodium bisulfite (MSB), the deletion of sntB reduced catC expression significantly. Additionally, deleting the catC gene curtailed mycelial growth, conidial production, and sclerotia formation, but elevated reactive oxygen species (ROS) levels and aflatoxin production. The ΔcatC strain also showed reduced susceptibility to MSB and decreased aflatoxin production compared to the WT.

This study outlines a pathway by which SntB regulates fungal morphogenesis, mycotoxin synthesis, and virulence through a sequence of H3K36me3 modification to peroxisomes and lipid hydrolysis, impacting fungal virulence and mycotoxin biosynthesis.

The authors have achieved the majority of their aims at the beginning of the study, finding target genes, which led to catC mediated regulation of development, growth and aflatoxin metabolism. Overall most parts of the study are solid and clear.

Comments on revision:

The authors have thoroughly addressed all the concerns I raised. The current manuscript is robust and effectively presents evidence supporting its claims. The overall quality of the manuscript has significantly improved.

Reviewer #2 (Public Review):

The authors fully addressed my concerns and made appropriate changes in the manuscript. The quality of the manuscript is now significantly improved.

Reviewer #1 (Public review):

Summary:

The study used root tips from semi-hydroponic tea seedlings. The strategy followed sequential steps to draw partial conclusions.

Initially, protoplasts obtained from root tips were processed for scRNA-seq using the 10x Genomics platform. The sequencing data underwent pre-filtering at cell and gene levels, leading to 10,435 cells. These cells were then classified into eight clusters using t-SNE algorithms. The present study scrutinised cell typification through protein sequence similarity analysis of homologs of cell type marker genes. The analysis was conducted to ensure accuracy using validated genes from previous scRNA-seq studies and the model plant Arabidopsis thaliana. The cluster cell annotation was confirmed using in situ RT-PCR analyses. This methodology provided a comprehensive insight into the cellular differentiation of the sample under study. The identified clusters, spanning 1 to 8, have been accurately classified as xylem, epidermal, stem cell niche, cortex/endodermal, root cap, cambium, phloem, and pericycle cells.

Then, the authors performed a pseudo-time analysis to validate the cell cluster annotation by examining the differentiation pathways of the root cells. Lastly, they created a differentiation heatmap from the xylem and epidermal cells and identified the biological functions associated with the highly expressed genes.

Upon thoroughly analysing the scRNA-seq data, the researchers delved into the cell heterogeneity of nitrate and ammonium uptake, transport, and nitrogen assimilation into amino acids. The scRNA-seq data was validated by in situ RT-PCR. It allows the localisation of glutamate and alanine biosynthetic enzymes along the cell clusters and confirms that both constituent the primary amino acid metabolism in the root. Such investigation was deemed necessary due to the paramount importance of these processes in theanine biosynthesis since this molecule is synthesised from glutamate and alanine-derived ethylamine.

Afterwards, the authors analysed the cell-specific expression patterns of the theanine biosynthesis genes, combining the same molecular tools. They concluded that theanine biosynthesis is more enriched in cluster 8 "pericycle cells" than glutamate biosynthesis (Lines 271-272). However, the statement made in Line 250 states that the highest expression levels of genes responsible for glutamate biosynthesis were observed in Clusters 1, 3, 4, 6 and 8, leading to an unclear conclusion.<br /> The regulation of theanine biosynthesis by the MYB transcription factor family is well-established. In particular, CsMYB6, a transcription factor expressed specifically in roots, has been found to promote theanine biosynthesis by binding to the promoter of the TSI gene responsible for theanine synthesis. However, their findings indicate that CsMYB6 expression is present in Cluster 3 (SCN), Cluster 6 (cambium cells), and Cluster 1 (xylem cells) but not in Cluster 8 (pericycle cells), which is known for its high expression of CsTSI. Similarly, their scRNA-seq data indicated that CsMYB40 and CsHHO3, which activate and repress CsAlaDC expression, respectively, did not show high expression in Cluster 1 (the cell cluster with high CsAlaDC expression). Based on these findings, the authors speculated that transcription factors and target genes are not necessarily always highly expressed in the same cells.

Lastly, the authors have discovered a novel transcription factor belonging to the Lateral Organ Boundaries Domain (LBD) family known as CsLBD37 that can co-regulate the synthesis of theanine and the development of lateral roots. The authors observed that CsLBD37 is located within the nucleus and can repress the CsAlaDC promoter's activity. To investigate this mechanism further, the authors conducted experiments to determine whether CsLBD37 can inhibit CsAlaDC expression in vivo. They achieved this by creating transiently CsLBD37-silenced or over-expression tea seedlings through antisense oligonucleotide interference and generation of transgenic hairy roots. Based on their findings, the authors theorise that CsLBD37 regulates CsAlaDC expression to modulate the synthesis of ethylamine and theanine in tea roots. Apologies for the inadvertent mistake concerning glutamate and glutamine.

Strength:

The manuscript showcases significant dedication and hard work, resulting in valuable insights that are fundamental for generating knowledge. The authors skillfully integrated various tools available for this type of study and meticulously presented and illustrated every step involved in the survey. The overall quality of the work is exceptional, and it would be a valuable addition to any academic or professional setting.

Weaknesses:

The authors have effectively addressed the feedback and revised the manuscript, presenting their debatable conclusions as speculative. Consequently, I find the manuscript's current form free of any apparent weaknesses.

Reviewer #2 (Public review):

Summary:

In their manuscript, Lin et al. present a comprehensive single-cell analysis of tea plant roots. They measured the transcriptomes of 10,435 cells from tea plant root tips, leading to the identification and annotation of 8 distinct cell clusters using marker genes. Through this dataset, they delved into the cell-type-specific expression profiles of genes crucial for the biosynthesis, transport, and storage of theanine, revealing potential multicellular compartmentalization in theanine biosynthesis pathways. Furthermore, their findings highlight CsLBD37 as a novel transcription factor with dual regulatory roles in both theanine biosynthesis and lateral root development.

Strengths:

This manuscript provides the first single-cell dataset analysis of roots of the tea plants. It also enables detailed analysis of the specific expression patterns of the gene involved in theanine biosynthesis. Some of these gene expression patterns in roots were further validated through in-situ RT-PCR. Additionally, a novel TF gene CsLBD37's role in regulating theanine biosynthesis was identified through their analysis.

Weaknesses:

The revised manuscript has addressed the concerns raised during the initial review.

Reviewer #3 (Public review):

Summary:

Lin et al., performed a scRNA-seq-based study of tea roots, as an example, to elucidate the biosynthesis and regulatory processes for theanine, a root-specific secondary metabolite, and established the first map of tea roots comprised of 8 cell clusters. Their findings contribute to deepening our understanding of the regulation of the synthesis of important flavor substances in tea plant roots. They have presented some innovative ideas.

Comment on revised version:

The reviewer has addressed all my concerns and I have no further comments.

Reviewer #1 (Public review):

Summary:

This manuscript addresses two main issues: (i) do MAPKs play an important role in SAC regulation in single cell organism such as S pombe? (ii) what is the nature of their involvement and what are their molecular targets?<br /> The authors have extensively used the cold-sensitive β-tubulin mutant to activate or inactivate SAC employing an arrest-release protocol. Localization of Cdc13 (cyclin B) to the SPBs is used as a readout for the SAC activation or inactivation. The roles of two major MAPK pathways i.e. stress activated pathway (SAP) and cell integrity pathway (CIP), have been explored in this context (with CIP more extensively than SAP). Sty1Δ or pmk1Δ mutants were used to inactivate the SAP or CIP pathways and wis1DD or pek1DD expression was utilized to constitutively activate these pathways, respectively. Lowering of Slp1Cdc20 abundance (by phosphorylation of Slp1-Thr 480) is revealed as the main function of MAPK to augment the robustness of spindle assembly checkpoint.

Strengths:

The experiments are generally well-conducted, and the results support the interpretations in various sections. The experimental data clearly support some of the key conclusions:<br /> (i) while inactivation of SAP and CIP compromises SAC-imposed arrest, their constitutive activation delays the release from the SAC-imposed arrest (ii) CIP signaling, but not SAP signaling, attenuates Slp1Cdc20 levels (iii) Pmk1 and Cdc20 physical interact and Pmk1-docking sequences in Slp1 (PDSS) is identifies and confirmed by mutational/substitution experiments (iv) Thr480 (and also S76) is identified as the residue phosphorylated by Pmk1. S28 and T31 are identified as Cdk1 phosphorylation sites. These are confirmed by mutational and other related analyses (v) Functional aspects of the phosphorylation sites have been elucidated to some extent: (a) Phosphorylation of Slp1-T480 by Pmk1 reduces its abundance thereby augmenting the SAC-induced arrest (b) S28, T31 (also S59) are phosphorylated by Cdk1 (v) K472 and K479 residues are involved in ubiquitylation of Slp1

Weaknesses:

(i) Cdc13 localization to SPBs has been used as a readout for SAC activation/inactivation throughout the manuscript. However, the only image showing such localization (Figure 1C) is of poor quality where the Cdc13 localization to SPBs barely visible. This should be replaced by a better image.

(ii) The overlapping error-bars in Cdc13-localization data in some figures (for instance Figure 3E and 4H) makes the effect of various mutations on SAC activation/inactivation rather marginal. In some of these cases, Western-blotting data support the author's conclusions better.

(iii) This specific point is not really a weakness but rather a loose end:<br /> One of the conclusions of this study is that MAPK (PMK1) contributes to the robustness of SAC-induced arrest by lowering the abundance of Slp1Cdc20. The authors have used pmk1Δ or constitutively activating the MAPK pathways (Pek1DD) and documenting their effect on SAC activation/inactivation dynamics. It is not clear if SAC activation also leads to activation of MAPK pathways for them to contribute to the SAC robustness. To tie this loose end, the author could have checked if MAPK pathway is also activated under the conditions when SAC is activated. Unless this is shown, one must assume that the authors are attributing the effect they observe to the basal activity of MAPKs.

(iv) This is also a loose end:<br /> The authors show that activation of stress pathways (by addition of KCL instance) causes phosphorylation-dependent Slp1Cdc20 downregulation (Figure 6) under SAC-activating conditions. Does activation of the stress pathway cause phosphorylation-dependent Slp1Cdc20 downregulation under non-SAC-activation conditions or does it occur only under SAC-activating conditions?

(v) Although the authors have gone to some length to identify S28, T31 (also S59) as phosphorylation sites for Cdk1, their functional significance in the context of MAPK involvement is not yet clear. Perhaps it is outside the scope of this study to dig deeper into this aspect more than the authors have.

(vi) In its current state, the Discussion section is quite disjointed. The first section "Involvement of MAPKs in cell cycle regulation" should be in the Introduction section (very briefly, if at all). It certainly does not belong to the Discussion section. In any case, the Discussion section should be more organized with better flow of arguments/interpretations.

Reviewer #2 (Public review):

Summary:

This study by Sun et al. presents a role for the S. pombe MAP kinase Pmk1 in the activation of the Spindle Assembly Checkpoint (SAC) via controlling the protein levels of APC/C activator Cdc20 (Slp1 in S. pombe). The data presented in the manuscript is thorough and convincing. The authors have shown that Pmk1 binds and phosphorylates Slp1, promoting its ubiquitination and subsequent degradation. Since Cdc20 is an activator of APC/C, which promotes anaphase entry, constitutive Pmk1 activation leads to an increased percentage of metaphase-arrested cells. The authors have used genetic and environmental stress conditions to modulate MAP kinase signalling and demonstrate their effect on APC/C activation. This work provides evidence for the role of MAP kinases in cell cycle regulation in S. pombe and opens avenues for exploration of similar regulation in other eukaryotes.

Strengths:

The authors have done a very comprehensive experimental analysis to support their hypothesis. The data is well represented, and including a model in every figure summarizes the data well.

Weaknesses:

As mentioned in the comments, the manuscript does not establish that MAP kinase activity leads to genome stability when cells are subjected to genotoxic stressors. That would establish the importance of this pathway for checkpoint activation.

Reviewer #1 (Public review):

Summary:

The manuscript characterizes a functional peptidergic system in the echinoderm Apostichopus japonicus that is related to the widely conserved family of calcitonin/diuretic hormone 31 (CT/DH31) peptides in bilaterian animals. In vitro analysis of receptor-ligand interactions, using multiple receptor activation assays, identifies three cognate receptors for two CT-like peptides in the sea cucumber, which stimulate cAMP, calcium, and ERK signaling. Only one of these receptors is closely related to the family of calcitonin and calcitonin-like receptors (CTR/CLR) in bilaterian animals, whereas two other receptors cluster with invertebrate pigment dispersing factor receptors (PDFRs). In addition, this study sheds light on the transcript expression and in vivo functions of CT-like peptides in A. japonicus, by quantitative real-time PCR, in situ hybridization, pharmacological experiments on body wall muscle and intestine preparations, and peptide injection and RNAi knockdown experiments. This reveals a conserved function of CT-like peptides as muscle relaxants and hints at a potential role as growth regulators in A. japonicus.

Strengths:

This work combines both in vitro and in vivo functional assays to identify a CT-like peptidergic system in an economically relevant echinoderm species, the sea cucumber A. japonicus. A major strength of the study is that it identifies three G protein-coupled receptors for AjCT-like peptides, one related to the CTR/CLR family and two related to the PDFR family. A similar finding was previously reported for the CT-related peptide DH31 in Drosophila melanogaster that activates both CT-type and PDF-type receptors. Here, the authors expand this observation to a deuterostomian animal, which suggests that receptor promiscuity is a more general feature of the CT/DH31 peptide family and that CT/DH31-like peptides may activate both CT-type and PDF-type receptors in other animals as well.

Besides the identification of receptor-ligand pairs, the downstream signaling pathways of AjCT receptors have been characterized, highlighting broad effects on cAMP, calcium, and ERK signaling. Functional characterization of the CT-related peptide system in heterologous cells is complemented with ex vivo and in vivo experiments. First, peptide injection and RNAi knockdown experiments establish transcriptional regulation of all three identified receptors in response to changing AjCT peptide levels. Second, ex vivo experiments reveal a conserved role for the two CT-like peptides as muscle relaxants, which have differential effects on body wall muscle and intestine preparations. Finally, peptide injection studies suggest a putative role for one of the two CT-like peptides (AjCT2) in growth regulation.

Weaknesses:

Analysis of transcript expression is limited to the CT-peptide encoding gene, while no gene expression analysis was attempted for the three identified receptors. Differences in the activation of downstream signaling pathways between the three receptors are also questionable due to unclarities in the statistical analysis and variation in the control and experimental data in heterologous assays. Together, this makes it difficult to propose a mechanism underlying differences in the functions of the two CT-like peptides in muscle control and growth regulation.

The authors also suggest a putative orexigenic role for the CT-like peptidergic system in feeding behavior. This effect is not well supported by the experimental data provided, as no detailed analysis of feeding behavior was carried out (only indirect measurements were performed that could be influenced by other peptidergic effects, such as on muscle relaxation) and no statistically significant differences were reported in these assays.

Overall, details regarding statistical analyses are not (clearly) specified in the manuscript, and there are several instances where statements are not supported by literature evidence.

Reviewer #2 (Public review):

Summary:

The authors show that A. japonicus calcitonins (AjCT1 and AjCT2) activate not only the calcitonin/calcitonin-like receptor but also activate the two PDF receptors, ex vivo. They also explore secondary messenger pathways that are recruited following receptor activation. They determine the source of CT1 and CT2 using qPCR and in situ hybridization and finally test the effects of these peptides on tissue contractions, feeding, and growth. This study provides solid evidence that CT1 and CT2 act as ligands for calcitonin receptors; however, evidence supporting cross-talk between CT peptides and PDF receptors is only based on ex vivo experiments.

Strengths:

This is the first study to report the pharmacological characterization of CT receptors in an echinoderm. Multiple lines of evidence in cell culture (receptor internalization and secondary messenger pathways) support this conclusion.

Weaknesses:

The authors claim that A. japonicus CTs activate "PDF" receptors and suggest that this cross-talk is evolutionarily ancient since a similar phenomenon also exists in the fly Drosophila melanogaster. These conclusions are not fully supported for several reasons. The authors perform phylogenetic analysis to show that the two "PDF" receptors form an independent clade. This clade is sister to the clade comprising CT receptors. This phylogenetic analysis suffers from several issues. Firstly, the phylogenies lack bootstrap support. Secondly, the resolution of the phylogeny is poor because representative members from diverse phyla have not been included. For instance, insect or other protostomian PDF receptors have not been included so how can the authors distinguish between "PDF" receptors or another group of CT receptors? Thirdly, no in vivo evidence has been presented to support that CT can activate "PDF" receptors in vivo.

The source of CT which mediates the effects on longitudinal muscles and intestine is unclear. Is it autocrine or paracrine signaling by CT from the same tissue or is it long-range hormonal signaling?

Pharmacology experiments showing the effects of CT1 and CT2 on ACh-induced contractions were performed. Sample traces have been provided but no traces with ACh alone have been included. How long do ACh-induced contractions persist? These controls are necessary to differentiate between the eventual decay of ACh effects and relaxation induced by CT1 and CT2. The traces also do not reflect the results portrayed in dose-response curves. For instance, in Figure 6B, maximum relaxation is reported for 10-6M. Yet, the trace hardly shows any difference before and after the addition of 10-6M peptide. The maximum effect in the trace appears to be after the addition of 10-8M peptide.

I am unsure how differences in wet mass indicate feeding and growth differences since no justification has been provided. Couldn't wet mass also be influenced by differences in osmotic balance, a key function of calcitonin-like peptides in protostomian invertebrates? The statistical comparisons have not been included in Figure 7B.

While the authors succeeded in knocking down CT, the physiological effects of reduced CT signaling were not examined.

Reviewer #1 (Public review):

Summary:

In this study, the authors use ChEC-seq, an MNase-based method to map yeast RNA pol II. Part of the reasoning for this study is that earlier biochemical work suggested pol II initiation and termination should involve slow steps at the UAS/promoter and termination regions that are not well visualized by formaldehyde-based ChIP methods. Here the authors find that pol II ChIP and ChEC give complementary patterns. Pol II ChIP signals are strongest in the coding region (where ChIP signal correlates well with transcription (rho = 0.62)). In contrast, pol II ChEC signals are strongest at promoters (rho = 0.52) and terminator regions. Weaker upstream ChEC signals are also observed at the STM class genes where biochemical studies have suggested a form of Pol (and maybe other general factors) is recruited to UAS sites. ChEC of TFIIA and TFIIE give promoter-specific ChEC signals as expected. Extending this work to elongation factors Ctk1 and Spt5 unexpectedly give strong signals near the PIC location and little signals over the coding region. This, and mapping CTD S2 and S5 phosphorylation by ChEC suggests to me that, for some reason, ChEC isn't optimal for detecting components of the elongation complex over coding regions.

Examples are also presented where perturbations of transcription can be measured by ChEC. Modeling studies are shown where adjustment of kinetic parameters agree well with ChEC data and that these models can be used to estimate which steps in transcription are affected by various perturbations. No tests were performed to see if the predictions could be validated by other means. Finally, the role of nuclear pore binding by Gcn4 is explored, although the results do not seem convincing. Overall, the authors show that pol II ChEC is a valuable and complementary method for investigating transcription mechanisms and slow steps at the initiation and termination regions.

Reviewer #2 (Public review):

Summary:

The study by VanBelzen et. al. compares chromatin immunoprecipitation (ChIP-seq) and chromatin endogenous cleavage sequencing (ChEC-seq2) to examine RNA polymerase II (RNAPII) binding patterns in yeast. While ChIP-seq shows RNAPII enrichment mainly over transcribed regions, ChEC-seq2 highlights RNAPII binding at promoters and upstream activating sequences (UASs), suggesting it captures distinct RNAPII populations that the authors speculate are linked more tightly to active transcription. The authors develop a stochastic model for RNAPII kinetics using ChEC-seq2 data, revealing insights into transcription regulation and the role of the nuclear pore complex in stabilizing promoter-associated RNAPII. The study suggests that ChEC-seq2 identifies regulatory events that ChIP-seq may overlook.

Strengths:

(1) This is a carefully crafted study that adds significantly to existing literature in this area. Transgenic MNase fusions with endogenous Rpb1 and Rpb3 subunits were carefully performed, and complemented by fusions with several additional proteins that help the authors to dissect the transcription cycle. Both the S. cerevisiae lines and the sequencing data are likely to be of significant use to the community.

(2) The validation of ChEC-seq2 and its comparison with ChIP-seq is highly valuable technical information for the community.

(3) The kinetic modeling appears to be thoughtfully done.

Weaknesses:

(1) The term "nascent transcription" is all too often used interchangeably for NET-seq, PRO-seq, 4sU-seq, and other assays that often provide different types of information. The authors should make it clear their use of the term refers to SLAM-seq data.

(2) The authors do not perform any comparison to run-on (PRO-seq) data. My impression is that the distribution of PRO-seq signal in S. cerevisiae agrees better with the distribution the authors observe by ChIP-seq. PRO-seq only captures RNAPII that is engaged and actively transcribing. If PRO-seq does indeed provide a similar profile as ChIP-seq, wouldn't this indicate that the high frequency of association between RNAPII and either the promoter or UAS reflects RNAPII that has not yet started transcription elongation? Perhaps this could help sort out what types of activities are occurring at the UAS (which does not appear to require a full PIC) or at the promoter (which does)?

Reviewer #1 (Public Review):

Summary:

In a previous study, the authors developed a human iPS cell line which expresses Cre under the control of the Lmx1a promoter in order to track, select for, and differentiate human dopamine neurons. In the manuscript under review, the authors are using methods which they have modified to generate astrocytes from the same cell line. The authors are interested in examining astrocytes which are derived from regionalized, floor plate progenitors.

The fundamental weakness of this paper is that the authors are making arguments about regional identity but their work is limited to experiments in vitro. Some of the claims that the authors make should be tested in vivo - ie, in sections, at least. Are floor plate markers or other ventral markers ever expressed in astrocytes or glial progenitors in the mammalian fetus? When do astrocytes emerge in the floor plate? All of the data here are based on an overly simplified in vitro platform.

Lmx1a expression is not limited to the ventral midbrain; it is also expressed in other parts of the developing, ventral CNS and in the roof plate and dorsal CNS (Millonig et al, Nature 2000). Indeed, many of the phenotypes of the Lmx1a mutant mouse (dreher) have little to do with the ventral midbrain. The authors are making an assumption that regional identity is fixed when they begin their astrocyte differentiation protocol - not necessarily true. After astrocytic differentiation is initiated, the authors have done little to demonstrate that floor plate identity is maintained even in selected cells; in fact, the transcriptomic data suggests that the cells are released from a floor plate fate. The authors seem to realize this but do not make any attempt to prove their thesis. If regional identity is not maintained, the authors need a better experiment.

If regional identity is not maintained, so what? Don't we already know that this can happen? The authors acknowledge that this is known in the discussion.

The authors have done transcriptomics studies to follow the changes in these cells but they have not told us very much that is meaningful. It would be useful to validate some of the new astrocytic markers that they have identified - Pax and Irx genes (Welle et al., Glia 2021) come quickly to mind. What about genes related to Shh and Wnt signaling that are prevalent in the floor plate? In particular, a lot of work has been done examining the role of Shh on the properties and lineage of astrocytes (Farmer et al., Science 2016; Hill et al., eLife 2019; Gingrich et al., Neural Dev 2022; Xie et al., Cell Rep 2022). There are a lot of stones which remain unturned, here, and the authors could actually tell us much more without doing an immense amount of work. These suggestions and criticisms are described in far greater detail in the confidential comments to the authors.

Work Cited:

Chizhikov et al., Mamm Genome 2006. https://pubmed.ncbi.nlm.nih.gov/17019651/

Chizhikov et al., Development 2004. https://journals.biologists.com/dev/article/131/11/2693/42269/Control-of-roof-plate-formation-by-Lmx1a-in-the

Chizhikov et al., PNAS 2010. https://pubmed.ncbi.nlm.nih.gov/20498066/

Emsley and Macklis. Neuron Glia Biol 2007. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1820889/

Farmer et al., Science 2016. https://pubmed.ncbi.nlm.nih.gov/26912893/

Gross et al., Development 2016. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4958331/

Hill et al., eLife 2019. https://pubmed.ncbi.nlm.nih.gov/31194676/

Gingrich et al., Neural Dev 2022. https://pubmed.ncbi.nlm.nih.gov/35027088/

Iskusnykh et al., eLife 2023. https://elifesciences.org/articles/84095

Millonig et al, Nature 2000. https://pubmed.ncbi.nlm.nih.gov/10693804/

Welle et al. Glia 2021. https://pubmed.ncbi.nlm.nih.gov/36342840/

Xie et al., Cell Rep 2022. https://pubmed.ncbi.nlm.nih.gov/35196485/

Reviewer #2 (Public Review):

In the current manuscript Li et al., study the preservation of the regional identity during the process of astrocyte generation from pluripotent stem cells. More precisely, this work investigates if neural progenitor cells patterned for the ventral midbrain give rise to astrocytes with conserved regional specification, which could reflect the astrocytic heterogeneity in the brain. To this end, the authors utilized a previously generated reporter iPSC line in which the expression of introduced blue fluorescence protein (BFP) is subjacent to the activation of LMXA1, a ventral midbrain floor plate marker. The study reports that following a defined patterning protocol based on SHH and FGF8, over 90% of d19 cells, corresponding to a neural progenitor stage, acquired the midbrain floor plate identity. However, during the subsequent astrogenic induction and glial progenitor expansion, this identity is gradually lost, supposedly due to the growth advantage of cells deriving from the residual LMX1A- neural progenitors. Contrariwise, if the LMX1A+ progenitors were purified, regional identity would be maintained throughout the astrocytic generation and incur an early astrogenic switch and maturation of derived astrocytes. By using single-cell RNA sequencing, the authors further identified distinct transcriptomic signatures on the astrocytic progeny of LMX1A- and LMX1A- progenitors.

Strengths and weaknesses:

(1) The main model utilized was engineered from the KOLF2 human iPSC line into an elegant LMX1A-reporter line based on the expression of BFP. This results in an attractive model for studies tracing the fate of LMX1A cells. However, consideration should be given to the fact that the parental line, exhibits a splice disruption in the COL3A1 gene encoding type III collagen (Pantazis 2022, doi:10.1016/j.stem.2022.11.004 ), which has been identified as being enriched in certain ventral astrocytic populations (Bradley 2019, doi:10.1242/dev.170910).

(2) The authors argue that the depletion of BFP seen in the unsorted population immediately after the onset of astrogenic induction is due to the growth advantage of the derivatives of the residual LMX1A- population. However, no objective data supporting this idea is provided, and one could also hypothesize that the residual LMX1A- cells could affect the overall LMX1A expression in the culture through negative paracrine regulation. Therefore, cell cycle or proliferation studies of these cells are needed to prove the authors' assumption. Furthermore, on line 124 it is stated that: "Interestingly, the sorted BFP+ cells exhibited similar population growth rate to that of unsorted cultures...". In the face of the suggested growth disadvantage of those cells, this statement needs clarification.

(3) Regarding the fidelity of the model system, it is not clear to me how the TagBFP expression was detected in the BFP+ population supposedly in d87 and d136 pooled astrocytes (Fig S6C) while no LMX1A expression was observed in the same cells (Fig S6F).

(4) The generated single-cell RNASeq dataset is extremely valuable. However, given the number of conditions included in this study (i.e. early vs late astrocytes, BFP+ vs BFP-, sorted vs unsorted, plus non-patterned and neuronal samples) the resulting analysis lacks detail. For instance, from a developmental perspective and to better grasp the functional significance of astrocytic heterogeneity, it would be interesting to map the identified clusters to early vs late populations and to the BFP status. Moreover, although comprehensive, Figure S7 is complex to understand given that citations rather than the reference populations are depicted.

(5) Do the authors have any consideration regarding the morphology of the astrocytes obtained in this study? None of the late astrocyte images depict a prototypical stellate morphology, which is reported in many other studies involving the generation of iPSC-derived astrocytes and which is associated with the maturity status of the cell.

Reviewer #1 (Public review):

Summary:

García-Vázquez et al. identify GTSE1 as a novel target of the cyclin D1-CDK4/6 kinases. The authors show that GTSE1 is phosphorylated at four distinct serine residues and that this phosphorylation stabilizes GTSE1 protein levels to promote proliferation.

Strengths:

The authors support their findings with several previously published results, including databases. In addition, the authors perform a wide range of experiments to support their findings.

Weaknesses:

I feel that important controls and considerations in the context of the cell cycle are missing. Cyclin D1 overexpression, Palbociclib treatment and apparently also AMBRA1 depletion can lead to major changes in cell cycle distribution, which could strongly influence many of the observed effects on the cell cycle protein GTSE1. It is therefore important that the authors assess such changes and normalize their results accordingly.

Reviewer #2 (Public review):

Summary:

The manuscript by García-Vázquez et al identifies the G2 and S phases expressed protein 1(GTSE1) as a substrate of the CycD-CDK4/6 complex. CycD-CDK4/6 is a key regulator of the G1/S cell cycle restriction point, which commits cells to enter a new cell cycle. This kinase is also an important therapeutic cancer target by approved drugs including Palbocyclib. Identification of substrates of CycD-CDK4/6 can therefore provide insights into cell cycle regulation and the mechanism of action of cancer therapeutics. A previous study identified GTSE1 as a target of CycB-Cdk1 but this appears to be the first study to address the phosphorylation of the protein by Cdk4/6.

The authors identified GTSE1 by mining an existing proteomic dataset that is elevated in AMBRA1 knockout cells. The AMBRA1 complex normally targets D cyclins for degradation. From this list, they then identified proteins that contain a CDK4/6 consensus phosphorylation site and were responsive to treatment with Palbocyclib.

The authors show CycD-CDK4/6 overexpression induces a shift in GTSE1 on phostag gels that can be reversed by Palbocyclib. In vitro kinase assays also showed phosphorylation by CDK4. The phosphorylation sites were then identified by mutagenizing the predicted sites and phostag got to see which eliminated the shift.

The authors go on to show that phosphorylation of GTSE1 affects the steady state level of the protein. Moreover, they show that expression and phosphorylation of GTSE1 confer a growth advantage on tumor cells and correlate with poor prognosis in patients.

Strengths:

The biochemical and mutagenesis evidence presented convincingly show that the GTSE1 protein is indeed a target of the CycD-CDK4 kinase. The follow-up experiments begin to show that the phosphorylation state of the protein affects function and has an impact on patient outcomes.

Weaknesses:

It is not clear at which stage in the cell cycle GTSE1 is being phosphorylated and how this is affecting the cell cycle. Considering that the protein is also phosphorylated during mitosis by CycB-Cdk1, it is unclear which phosphorylation events may be regulating the protein.

Reviewer #3 (Public review):

Summary:

This paper identifies GTSE1 as a potential substrate of cyclin D1-CDK4/6 and shows that GTSE1 correlates with cancer prognosis, probably through an effect on cell proliferation. The main problem is that the phosphorylation analysis relies on the over-expression of cyclin D1. It is unclear if the endogenous cyclin D1 is responsible for any phosphorylation of GTSE1 in vivo, and what, if anything, this moderate amount of GTSE1 phosphorylation does to drive proliferation.

Strengths:

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

Weaknesses:

The main weakness is that it is unclear if the endogenous cyclin D1 is responsible for phosphorylating GTSE1 in the G1 phase. For example, in Figure 2G there doesn't seem to be a higher band in the phos-tag gel in the early time points for the parental cells. This experiment could be redone with the addition of palbociclib to the parental to see if there is a reduction in GTSE1 phosphorylation and an increase in the amount in the G1 phase as predicted by the authors' model.

The experiments involving palbociclib do not disentangle cell cycle effects. Adding Cdk4 inhibitors will progressively arrest more and more cells in the G1 phase and so there will be a reduction not just in Cdk4 activity but also in Cdk2 and Cdk1 activity. More experiments, like the serum starvation/release in Figure 2G, with synchronized populations of cells would be needed to disentangle the cell cycle effects of palbociclib treatment.

It is unclear if GTSE1 drives the G1/S transition. Presumably, this is part of the authors' model and should be tested.

The proliferation assays need to be more quantitative. Figure 4B should be plotted on a log scale so that the slope can be used to infer the proliferation rate of an exponentially increasing population of cells. Figure 4c should be done with more replicates and error analysis since the effects shown in the lower right-hand panel are modest.

Reviewer #1 (Public review):

Summary:

In their paper, Hosack and Arce-McShane investigate how the 3D movement direction of the tongue is represented in the orofacial part of the sensory-motor cortex and how this representation changes with the loss of oral sensation. They examine the firing patterns of neurons in the orofacial parts of the primary motor cortex (MIo) and somatosensory cortex (SIo) in non-human primates (NHPs) during drinking and feeding tasks. While recording neural activity, they also tracked the kinematics of tongue movement using biplanar video-radiography of markers implanted in the tongue. Their findings indicate that most units in both MIo and SIo are directionally tuned during the drinking task. However, during the feeding task, directional turning was more frequent in MIo units and less prominent in SIo units. Additionally, in some recording sessions, they blocked sensory feedback using bilateral nerve block injections, which resulted in fewer directionally tuned units and changes in the overall distribution of the preferred direction of the units.

Strengths:

The most significant strength of this paper lies in its unique combination of experimental tools. The author utilized a video-radiography method to capture 3D kinematics of the tongue movement during two behavioral tasks while simultaneously recording activity from two brain areas. Moreover, they employed a nerve-blocking procedure to halt sensory feedback. This specific dataset and experimental setup hold great potential for future research on the understudied orofacial segment of the sensory-motor area.

Weaknesses:

Aside from the last part of the result section, the majority of the analyses in this paper are focused on single units. I understand the need to characterize the number of single units that directly code for external variables like movement direction, especially for less-studied areas like the orofacial part of the sensory-motor cortex. However, as a field, our decade-long experience in the arm region of sensory-motor cortices suggests that many of the idiosyncratic behaviors of single units can be better understood when the neural activity is studied at the level of the state space of the population. By doing so, for the arm region, we were able to explain why units have "mixed selectivity" for external variables, why the tuning of units changes in the planning and execution phase of the movement, why activity in the planning phase does not lead to undesired muscle activity, etc. See (Gallego et al. 2017; Vyas et al. 2020; Churchland and Shenoy 2024) for a review. Therefore, I believe investigating the dynamics of the population activity in orofacial regions can similarly help the reader go beyond the peculiarities of single units and in a broader view, inform us if the same principles found in the arm region can be generalized to other segments of sensory-motor cortex.

Further, for the nerve-blocking experiments, the authors demonstrate that the lack of sensory feedback severely alters how the movement is executed at the level of behavior and neural activity. However, I had a hard time interpreting these results since any change in neural activity after blocking the orofacial nerves could be due to either the lack of the sensory signal or, as the authors suggest, due to the NHPs executing a different movement to compensate for the lack of sensory information or the combination of both of these factors. Hence, it would be helpful to know if the authors have any hint in the data that can tease apart these factors. For example, analyzing a subset of nerve-blocked trials that have similar kinematics to the control.

Reviewer #2 (Public review):

Summary:

This manuscript by Hosack and Arce-McShane examines the directional tuning of neurons in macaque primary motor (MIo) and somatosensory (SIo) cortex. The neural basis of tongue control is far less studied than, for example, forelimb movements, partly because the tongue's kinematics and kinetics are difficult to measure. A major technical advantage of this study is using biplanar video-radiography, processed with modern motion tracking analysis software, to track the movement of the tongue inside the oral cavity. Compared to prior work, the behaviors are more naturalistic behaviors (feeding and licking water from one of three spouts), although the animals were still head-fixed.

The study's main findings are that:

• A majority of neurons in MIo and a (somewhat smaller) percentage of SIo modulated their firing rates during tongue movements, with different modulations depending on the direction of movement (i.e., exhibited directional tuning). Examining the statistics of tuning across neurons, there was anisotropy (e.g., more neurons preferring anterior movement) and a lateral bias in which tongue direction neurons preferred that was consistent with the innervation patterns of tongue control muscles (although with some inconsistency between monkeys).

• Consistent with this encoding, tongue position could be decoded with moderate accuracy even from small ensembles of ~28 neurons.

• There were differences observed in the proportion and extent of directional tuning between the feeding and licking behaviors, with stronger tuning overall during licking. This potentially suggests behavioral context-dependent encoding.

• The authors then went one step further and used a bilateral nerve block to the sensory inputs (trigeminal nerve) from the tongue. This impaired the precision of tongue movements and resulted in an apparent reduction and change in neural tuning in Mio and SIo.

Strengths:

The data are difficult to obtain and appear to have been rigorously measured, and provide a valuable contribution to this under-explored subfield of sensorimotor neuroscience. The analyses adopt well-established methods, especially from the arm motor control literature, and represent a natural starting point for characterizing tongue 3D direction tuning.

Weaknesses:

There are alternative explanations for some of the interpretations, but those interpretations are described in a way that clearly distinguishes results from interpretations, and readers can make their own assessments. Some of these limitations are described in more detail below.

One weakness of the current study is that there is substantial variability in results between monkeys, and that only one session of data per monkey/condition is analyzed (8 sessions total). This raises the concern that the results could be idiosyncratic. The Methods mention that other datasets were collected, but not analyzed because the imaging pre-processing is very labor-intensive. While I recognize that time is precious, I do think in this case the manuscript would be substantially strengthened by showing that the results are similar on other sessions.

This study focuses on describing directional tuning using the preferred direction (PD) / cosine tuning model popularized by Georgopoulous and colleagues for understanding neural control of arm reaching in the 1980s. This is a reasonable starting point and a decent first-order description of neural tuning. However, the arm motor control field has moved far past that viewpoint, and in some ways, an over-fixation on static representational encoding models and PDs held that field back for many years. The manuscript benefits from drawing the readers' attention (perhaps in their Discussion) that PDs are a very simple starting point for characterizing how cortical activity relates to kinematics, but that there is likely much richer population-level dynamical structure and that a more mechanistic, control-focused analytical framework may be fruitful. A good review of this evolution in the arm field can be found in Vyas S, Golub MD, Sussillo D, Shenoy K. 2020. Computation Through Neural Population Dynamics. Annual Review of Neuroscience. 43(1):249-75

Can the authors explain (or at least speculate) why there was such a large difference in behavioral effect due to nerve block between the two monkeys (Figure 7)?

Do the analyses showing a decrease in tuning after nerve block take into account the changes (and sometimes reduction in variability) of the kinematics between these conditions? In other words, if you subsampled trials to have similar distributions of kinematics between Control and Block conditions, does the effect hold true? The extreme scenario to illustrate my concern is that if Block conditions resulted in all identical movements (which of course they don't), the tuning analysis would find no tuned neurons. The lack of change in decoding accuracy is another yellow flag that there may be a methodological explanation for the decreased tuning result.

The manuscript states that "Our results suggest that the somatosensory cortex may be less involved than the motor areas during feeding, possibly because it is a more ingrained and stereotyped behavior as opposed to tongue protrusion or drinking tasks". Could an alternative explanation be more statistical/technical in nature: that during feeding, there will be more variability in exactly what somatosensation afferent signals are being received from trial to trial (because slight differences in kinematics can have large differences in exactly where the tongue is and the where/when/how of what parts of it are touching other parts of the oral cavity)? This variability could "smear out" the apparent tuning using these types of trial-averaged analyses. Given how important proprioception and somatosensation are for not biting the tongue or choking, the speculation that somatosensory cortical activity is suppressed during feedback is very counter-intuitive to this reviewer.

Reviewer #3 (Public review):

Summary:

In this study, the authors aim to uncover how 3D tongue direction is represented in the Motor (M1o) and Somatosensory (S1o) cortex. In non-human primates implanted with chronic electrode arrays, they use X-ray-based imaging to track the kinematics of the tongue and jaw as the animal is either chewing food or licking from a spout. They then correlate the tongue kinematics with the recorded neural activity. Using linear regressions, they characterize the tuning properties and distributions of the recorded population during feeding and licking. Then, they recharacterize the tuning properties after bilateral lidocaine injections in the two sensory branches of the trigeminal nerve. They report that their nerve block causes a reorganization of the tuning properties. Overall, this paper concludes that M1o and S1o both contain representations of the tongue direction, but their numbers, their tuning properties, and susceptibility to perturbed sensory input are different.

Strengths:

The major strengths of this paper are in the state-of-the-art experimental methods employed to collect the electrophysiological and kinematic data.

Weaknesses:

However, this paper has a number of weaknesses in the analysis of this data.

It is unclear how reliable the neural responses are to the stimuli. The trial-by-trial variability of the neural firing rates is not reported. Thus, it is unclear if the methods used for establishing that a neuron is modulated and tuned to a direction are susceptible to spurious correlations. The authors do not use shuffling or bootstrapping tests to determine the robustness of their fits or determining the 'preferred direction' of the neurons. This weakness colors the rest of the paper.

The authors compare the tuning properties during feeding to those during licking but only focus on the tongue-tip. However, the two behaviors are different also in their engagement of the jaw muscles. Thus many of the differences observed between the two 'tasks' might have very little to do with an alternation in the properties of the neural code - and more to do with the differences in the movements involved. Many of the neurons are likely correlated with both Jaw movements and tongue movements - this complicates the interpretations and raises the possibility that the differences in tuning properties across tasks are trivial.

The population analyses for decoding are rudimentary and provide very coarse estimates (left, center, or right), it is also unclear what the major takeaways from the population decoding analyses are. The reduced classification accuracy could very well be a consequence of linear models being unable to account for the complexity of feeding movements, while the licking movements are 'simpler' and thus are better accounted for.

The nature of the nerve block and what sensory pathways are being affected is unclear - the trigeminal nerve contains many different sensory afferents - is there a characterization of how effectively the nerve impulses are being blocked? Have the authors confirmed or characterized the strength of their inactivation or block, I was unable to find any electrophysiological evidence characterizing the perturbation.

Overall, while this paper provides a descriptive account of the observed neural correlations and their alteration by perturbation, a synthesis of the observed changes and some insight into neural processing of tongue kinematics would strengthen this paper.

Reviewer #1 (Public review):

Summary:

This study by Wang et al. identifies a new type of deacetylase, CobQ, in Aeromonas hydrophila. Notably, the identification of this deacetylase reveals a lack of homology with eukaryotic counterparts, thus underscoring its unique evolutionary trajectory within the bacterial domain.

Strengths:

The manuscript convincingly illustrates CobQ's deacetylase activity through robust in vitro experiments, establishing its distinctiveness from known prokaryotic deacetylases. Additionally, the authors elucidate CobQ's potential cooperation with other deacetylases in vivo to regulate bacterial cellular processes. Furthermore, the study highlights CobQ's significance in the regulation of acetylation within prokaryotic cells.

Weaknesses:

The problem I raised has been well resolved. I have no further questions.

Reviewer #2 (Public review):

In recent years, lots of researchers tried to explore the existence of new acetyltransferase and deacetylase by using specific antibody enrichment technologies and high resolution mass spectrometry. Here is an example for this effort. Yuqian Wang et al. studied a novel Zn2+- and NAD+-independent KDAC protein, AhCobQ, in Aeromonas hydrophila. They studied the biological function of AhCobQ by using biochemistry method and MS identification technology to confirm it. These results extended our understanding of the regulatory mechanism of bacterial lysine acetylation modifications. However, I find this conclusion is a little speculative, and unfortunately, it also doesn't totally support the conclusion as the authors provided.

Reviewer #3 (Public review):

Summary:

This study reports on a novel NAD+ and Zn2+-independent protein lysine deacetylase (KDAC) in Aeromonas hydrophila, termed as AhCobQ (AHA_1389). This protein is annotated as a CobQ/CobB/MinD/ParA family protein and does not show similarity with known NAD+-dependent or Zn2+-dependent KDACs. The authors showed that AhCobQ has NAD+ and Zn2+-independent deacetylase activity with acetylated BSA by western blot and MS analyses. They also provided evidence that the 195-245 aa region of AhCobQ is responsible for the deacetylase activity, which is conserved in some marine prokaryotes and has no similarity with eukaryotic proteins. They identified target proteins of AhCobQ deacetylase by proteomic analysis and verified the deacetylase activity using site-specific Kac proteins. Finally, they showed that AhCobQ activates isocitrate dehydrogenase by deacetylation at K388.

Strengths:

The finding of a new type of KDAC has a valuable impact on the field of protein acetylation. The characters (NAD+ and Zn2+-independent deacetylase activity in an unknown domain) shown in this study are very unexpected.

Weaknesses:

(1) The characters (NAD+ and Zn2+-independent deacetylase activity in an unknown domain) shown in this study are very unexpected. To convince readers, MSMS data must be necessary to accurately detect (de)acetylation at the target site in the deacetylase activity assay. The authors showed the MSMS data in assays with acetylated BSA, but other assays only rely on western blot.

(2) They prepared site-specific Kac proteins and used them in deacetylase activity assays. Incorporation of acetyllysine at the target site should be confirmed by MSMS and shown as supplementary data.

(3) The authors imply that the 195-245 aa region of AhCobQ may represent a new domain responsible for deacetylase activity. The feature of the region would be of interest but is not sufficiently described in Figure 5. The amino acid sequence alignments with representative proteins with conserved residues would be informative. It would be also informative if the modeled structure predicted by AlphaFold is shown and the structural similarity with known deacetylases is discussed.

Reviewer #1 (Public review):<br /> <br /> Summary:

Balasubramanian et al. characterized the cell types comprising mouse Schlemm's canal (SC) using bulk and single cell RNA sequencing (scRNA-seq). The results identify expression patterns the delineate the SC inner and outer wall cells and two inner wall 'states'. Further analysis demonstrates expression patterns of glaucoma associated genes and receptor ligand pairs between SEC's and neighboring trabecular meshwork.

Strengths:

While mouse SC has been profiled in previous scRNA-seq studies (van Zyl et al 2020, Thomson et al 2021), these data provide higher resolution of SC cell types, particularly endothelial cell (SEC) populations. SC is an important regulator of anterior chamber outflow and has important consequences for glaucoma.

Comments on the latest version:

The authors have addressed my primary concerns with the first version of the manuscript. This study represents a valuable resource in the molecular characterization of mouse Schlemm's canal cell types.

Reviewer #2 (Public review):

Summary:

This revised article has characterized the mouse Schlemm's canal expression profile using a comprehensive approach based on sorted SEC, LEC, and BEC total RNA-Seq, scRNA-Seq, and snRNA-Seq to enrich the selection of SECs. The revised study has successfully profiled genome-wide gene expression using sorted SECs, demonstrating that SECs have a closer similarity to LECs than BECs. The combined scRNA- and snRNA-Seq data with deep coverage of gene expression led to the successful identification of many novel biomarkers for inner wall SECs, outer wall SECs, collector channel ECs, and pericytes. In addition, the study also identified two novel states of inner wall SECs separated by new markers. The study provides significant novel information about the biology and expression profile of SECs in the inner and outer walls. It is of great significance to have this novel, convincing, and comprehensive study led by leading researchers published in this journal. The revision has improved the clarity and significance of the study with more details.

Strengths:

This is a comprehensive study using various data to support the expression characterization of mouse SECs. First, the study profiled genome-wide expression using sorted SECs, LECs, and BECs from the same tissue/organ to identify the similarities and differences among the three types of cells. Second, snRNA-Seq was applied to enrich the number of SECs from mouse ocular tissues significantly. Increased sampling of SECs and other cells led to more comprehensive coverage and characterization of cells, including pericytes. Third, the combined scRNA- and snRNA-Seq data analyses increase the power to further characterize the subtle differences within SECs, leading to identifying the expression markers of Inner and Outer wall SECs, collector channel ECs, and distal region cells. Fourth, the identified unique markers were validated for RNA and protein expression in mouse ocular tissues. Fifth, the study explored how the IOP- and glaucoma-associated genes are expressed in the ScRNA- and snRNA-Seq data, providing potential connections of these GWAS genes with IOP and glaucoma. Sixth, the initial pathway and network analyses generated exciting hypotheses that could be tested in other independent studies.

Weaknesses:

The authors have addressed most of the previous comments by adding more details about the protocol and additional discussions. Several comments requiring additional experimental data have been addressed as future directions, such as protein validation, RNA expression validation in human samples, and GWAS-identified IOP genes.

Comments on the latest version:

The authors have addressed previous comments responsively. The authors have suggested several experiments to be completed in the future since these could be time-consuming with human samples. The revised article is with better clarity and clearer significance. No additional comments.

Reviewer #1 (Public review):

Summary:

This paper reports the first results on the effects of a novel waveform for weak transcranial magnetic stimulation, which is refered to as "perturbation" (kTMP). The waveform is sinusoidal at kHz frequency with subthreshold intensities of 2V/m, instead of the suprathreshold pulses used in conventional TMS (~100V/m). The effect reported here concerns motor-evoked potentials (MEPs) elicited on the hand with single-pulse TMS. These MEPs are considered a marker of "corotico-spinal excitability". The manuscripts report that kTMP at 3.5kHz enhances MEPs with a medium effect size, with independent replication of this finding on 3 separate cohorts of subjects (N=16, 15, 16). This result is important for the field of non-invasive brain stimulation. The evidence in support of this claim is compelling. Despite the replications, this remains an exploratory study that will require replication with adequately powered planned comparisons.

Strengths:

• This is a novel modality for non-invasive brain stimulation.<br /> • Knowing the history in this field, this is likely to lead to a large number of follow-up studies in basic and clinical research.<br /> • The modality causes practically no sensation, which makes it perfectly suitable for control conditions. Indeed, the study itself used a persuasive double-blinding procedure.<br /> • The replication of the main result in two subsequent experiments is very compelling.<br /> • The effect size of Cohen's d=0.5 is very promising.<br /> • It is nice the E-fields were measured on a phantom, in addition to modeling.

Weakness:

• Statistical analysis combining Experiments 1, 2, 3 after inspecting the data is inappropriate.<br /> • Post-hoc definition of outliers that were removed is unfortunate.<br /> • While sensation has been documented, blinding was not directly assessed.<br /> • Despite the replications, this remains an exploratory study as it lacks power analysis and planned comparisons.

Other comments from an earlier review were adequately addressed.

Reviewer #2 (Public review):

Summary:

kTMP is a novel method of stimulating the brain using electromagnetic fields. It has potential benefits over existing technology because it is a safe and easy technology. It explores a range of brain frequencies that has not been explored in depth before (2-5kHz) and thus offers new opportunities.

Strengths:

This work relied on standard methods and was carefully and conservatively performed.

Weaknesses:

There were few weaknesses. The sham condition was prepared as well as could be done, but sham is always challenging in a treatment with sound and sensation, and with knowledgeable operators. New technology, also, is very exciting to subjects and it is difficult to achieve a natural experiment. These difficulties are related to the technology, however, and not to the execution of these experiments..

Reviewer #1 (Public review):

Summary:

This work by Leclercq and colleagues performed metabolomics on biospecimens collected from 96 patients diagnosed with severe alcohol use disorder (AUD). The authors discovery strong alterations in circulating glycerophospholipids, bile acids, and some gut microbe-derived metabolites in AUD patients compared to controls. An exciting part of this work is that metabolomics was also done in post-mortem samples of the frontal cortex and cerebrospinal fluid of heavy alcohol users, and some of the same metabolites were seen to be altered in the central nervous system. This important study will form the basis for hypothesis generation around diet-microbe-host interactions in alcohol use disorder. The work is done in a highly rigorous manner, and the rigorously collected human samples is an evident strength of this work. Overall, this work will provide many new insights, and it is poised to have a high impact on the field.

Strengths:

(1) The rigorously collected patient-derived samples<br /> (2) There is high rigorous in the metabolomics investigation<br /> (3) Statistical analyses are well-described and strong.<br /> (4) The careful control of taking blood samples at the same time to avoid alterations in meal- and circadian-related fluctuations in metabolites is a clear strength.

Weaknesses:

None remaining

Reviewer #2 (Public review):

The authors carried out the current studies with the justification that the biochemical mechanisms that lead to alcohol addiction are incompletely understood. The topic and question addressed here are impactful and indeed deserve further research. To this end, a metabolomics approach toward investigating the metabolic effects of alcohol use disorder and the effect of alcohol withdrawal in AUD subjects is valuable. However, this work is primarily descriptive in nature, and these data alone do not meet the stated goal of investigating biochemical mechanisms of alcohol addiction. The current work's most significant limitation is the cross-sectional study design, though inadequate description and citation of the underlying methodological approaches also hampers interest.

Most of the data are cross-sectional in study design, i.e., alcohol use disorder vs controls. However, it is well established that there is a high degree of interpersonal variation with metabolism, and further, there is somewhat high intra-personal variation in metabolism over time. This means that the relatively small cohort of subjects is unlikely to just reflect the broader condition of interest (AUD/withdrawal). The authors report a comparison of a later time-point after alcohol withdrawal (T2) vs the AUD condition. Nonetheless, without replicate time points from the control subjects it is difficult to assess how much of these changes are due to withdrawal vs the intra-personal variation described above. Overall, insufficient experimental context exists to interpret these findings into a biological understanding. For example, while several metabolites are linked with AUD and associated with microbiome or host metabolism based on existing literature, it is unclear from the current study what function these changes have concerning AUD, if any. The authors also argue that alcohol withdrawal shifts the AUD plasma metabolic fingerprint towards healthy controls (line 153). However, this is hard to assess based on the provided plots since the direction of change of the orange data subset considers AUD T2 vs. T1. In contrast, AUD T2 vs. Control would represent the claimed shift. To substantiate these claims, the authors would better support their argument by showing this comparison in all experimental groups (including control subjects) in their multi-dimensional model (e.g., PCA). The authors attempt to extend the significance of their findings by assessing post-mortem brain tissues from AUD subjects; however, the finding that many of the metabolites changed in T2/T1 are also found in AUD brain tissues is interesting but does not strongly support the authors' claims that these metabolites are markers of AUD (line 173). Concerning the plasma cohort itself, it is unclear how the authors assessed for compliance with alcohol withdrawal or whether the subjects' blood-alcohol levels were independently verified.

The second area of concern is the lack of description of the analytical methodology, the lack of metabolite identification validation evidence, and related statistical questions. The authors cite reference #59 regarding the general methodology. However, this reference from their group is a tutorial/review/protocol focused resource paper and it needs to be clarified how specific critical steps were actually applied to the current plasma study samples, given the range of descriptions provided in the citations. The authors report a variety of interesting metabolites, including their primary fragment intensities, which is appreciated (Supp Table 3), but no MS2 matching scores are provided for level 2 or 3 hits. Further, level 1 hits under their definition are validated by an in-house standard, but not supporting data are provided other than this categorization. Finally, a common risk in such descriptive studies is finding spurious associations, especially considering the many factors as described in the current work. These include AUD, depression, anxiety, craving, withdrawal, etc. The authors describe the use of BH correction for multiple-hypothesis testing. Still, this approach only accounts for the many possible metabolite association tests within each comparison (such as metabolites vs. depression) and does not account for the multi-variate comparisons to the many behavior/clinical factors described above. The authors should employ one of several common strategies, such as linear mixed effects models for these types of multi-variate assessments.

Revised Review after Resubmission:

I thank the authors for their responses and revisions to the figures and data and their clarifications of their results and study goals. However, based on this updated information, it is now more apparent that the paper falls into the common trap of descriptive studies where insufficient experimental design was considered to test the association in question robustly. Further, follow-up initiatives are lacking to test the findings by other experimental means. Despite the authors' responses, the paper still fails to convert or interpret the metabolomics findings into any new biological understanding or meaningfully testable hypotheses, and the results remain descriptive in nature with significant caveats.

The authors clarify that their study's "goal was not to investigate the biochemical mechanisms of AUD but how metabolomics could contribute to the psychological alterations of AUD." However, the 2nd sentence of the abstract remains as follows: "The biochemical mechanisms that lead to this disorder are not yet fully understood, and in this respect, metabolomics represents a promising approach to decipher metabolic events related to AUD."This leads the reader to conclude that the purpose of the current study is to use metabolomics to address this gap, despite their later clarification. In the revised response, the authors walk back their claims of these goals, yet the manuscript text and data is largely unchanged in the revision. The serious caveats pointed out by several reviewers concerning the study as reported significantly reduces the utility of the described findings for the broader scientific community, and the authors largely downplay these limitations without addressing the underlying issues.

The authors also clarified in their response that the study's key purpose of the study is to assess "correlations between the blood metabolome and psychological symptoms developed in AUD patients." This goal is dubious as the vast majority of metabolites are not psychoactive, and it is implausible that the metabolome would affect mental state or vice versa. More biological frameworks and citations are needed for this paradigm. The soundness of the goal is further questioned by the study's simplistic design and the authors' admission that "In this discovery-based approach, the aim was to discover potential candidates linked with psychological symptoms for subsequent work to evaluate causality." Yet, the authors side-step the point about the risk of finding spurious associations and decline to control this risk using widely-accepted approaches such as multi-variate correction, instead continuing to use only BH correction for multiple hypothesis testing. The reviewers previously pointed out that BH correction only accounts for the many possible metabolite association tests within each comparison (such as metabolites vs depression). However, it does not account for the multi-variate comparisons to the many behavior/clinical factors. This issue is ignored in the response because the study's goal is hypothesis generating. Instead, the authors focused their responses on the issue of causality which was not the central point of the criticism.

Further, the authors employ mainly systemic plasma analyses unlikely to reflect brain biochemistry. The authors deny that the purpose of including the post-mortem brain tissue data was to demonstrate that "metabolites significantly correlated with the psychological symptoms - and present in the central nervous system (frontal cortex or CSF) - are "markers of AUD," yet if this is not the goal, the structure of the experiment, and the value of these data, is unclear. Another reviewer pointed out that it is difficult to control cross-sectional post-mortem tissue due to a lack of suitable controls, and the authors again side-step the question by citing the lack of suitable controls and the impossibility of "healthy controls" in post-mortem samples. This is true, but this lack of technical feasibility and the confounding factor of CVD/lipid metabolism does not justify the weak experimental design in this respect. Therefore, it remains unclear what can be understood from these data, given the limitations.

Finally, the authors acknowledge the limitation in their revision that they did not assess a second-time point in the control cohort of samples which could have been used to tease apart intra-personal variation from AUD-associated changes during alcohol-abstinence. Unfortunately, this is not a small caveat to simply acknowledge in the discussion section; it severely limits the interpretation and utility of the reported data more broadly, and the authors do not address this underlying problem.

Reviewer #3 (Public review):

Summary:

The authors have compared different groups of AUD patients at different levels and have examined metabolomics.

Strengths:

A well-written and comprehensive study.

Reviewer #1 (Public review):

Summary:

The authors study age-related changes in the excitability and firing properties of sympathetic neurons, which they ascribe to age-related changes in the expression of KCNQ (Kv7, "M-type") K+ currents in rodent sympathetic neurons, whose regulation by GPCRs has been most thoroughly studied for over 40 years.

Strengths:

The strengths include the rigor of the current-clamp and voltage-clamp experiments and the lovely, crisp presentation of the data, The separation of neurons into tonic, phasic and adapting classes is also interesting, and informative. The ability to successfully isolate and dissociate peripheral ganglia from such older animals is also quite rare and commendable! There is much useful detail here.

Weaknesses:

Whereas the description of the data are very nice, and useful, the manuscript does not provide much in the way of mechanistic insights. As such, the effect is more of an epi-phenomenon of unclear insight, and the authors cannot ascribe changes in signaling mechanisms, such as that of M1 mAChRs to the phenomena that is supported by data.

Comments on latest version:

I do not have any additional issues to be addressed by the authors.

Reviewer #2 (Public review):

Summary:

This research provides compelling and detailed evidence showing that aging influences intrinsic membrane properties of peripheral sympathetic motor neurons, which become hyperexcitable. The authors found that sympathetic motor neurons from old mice exhibit increased firing rates (spontaneous and evoked), more depolarized membrane resting potential, and increased rheobase. Furthermore, the study investigates cellular mechanisms underlying age-associated hyperexcitability and shows solid evidence supporting that a decreased activity of KCNQ2/3 channels during aging is a major contributor to the increased excitability of sympathetic old neurons. The conclusions of this paper are supported by the data.

Strengths:

Detailed and rigorous analysis of electrical responses of peripheral sympathetic motor neurons using electrophysiology (perforated patch and whole-cell recordings). The study identifies a decreased KCNQ2/3 current as a cellular mechanism behind age-induced hyperexcitability in sympathetic motor neurons.

Weaknesses:

The revised version of the manuscript has addressed all my concerns.

Reviewer #3 (Public review):

This revised study described changes in membrane excitability and Na+ and K+ current amplitudes of sympathetic motor neurons in culture. The findings indicate that neurons isolated from aged animals show increased membrane excitability manifested as increased firing rates in response to electrical stimulation and changes in related membrane properties including depolarized resting membrane potential, increased rheobase, and spontaneous firing. By contrast, neuron cultures from young mice show little to no spontaneous firing and relatively low firing rates in response to current injection. These changes in excitability correlate with reductions in the magnitude of KCNQ currents in neurons cultured from aged mice compared to neurons from cultured from young mice. The authors conclude that aging promotes hyperexcitability of sympathetic motor neurons through changes in KCNQ channels.

Joint Public Review:

This study describes a group of CRH-releasing neurons, located in the paraventricular nucleus of the hypothalamus, which, in mice, affects both the state of sevoflurane anesthesia and a grooming behavior observed after it. PVHCRH neurons showed elevated calcium activity during the post-anesthesia period. Optogenetic activation of these PVHCRH neurons during sevoflurane anesthesia shifts the EEG from burst-suppression to a seemingly activated state (an apparent arousal effect), although without a behavioral correlate. Chemogenetic activation of the PVHCRH neurons delays sevoflurane-induced loss of righting reflex (another apparent arousal effect). On the other hand, chemogenetic inhibition of PVHCRH neurons delays recovery of righting reflex and decreases sevoflurane-induced stress (an apparent decrease in the arousal effect). The authors conclude that PVHCRH neurons "integrate" sevoflurane-induced anesthesia and stress. The authors also claim that their findings show that sevoflurane itself produces a post-anesthesia stress response that is independent of any surgical trauma, such as an incision. In its revised form, the article does not achieve its intended goal and will not have impact on the clinical practice of anesthesiology nor on anesthesiology research.

Strengths:

The manuscript uses targeted manipulation of the PVHCRH neurons with state-of-the-art methods and is technically sound. Also, the number of experiments is substantial.

Weaknesses:

The most significant weaknesses remain: a) overinterpretation of the significance of their findings b) the failure to use another anesthetic as a control, c) a failure to compellingly link their post-sevoflurane measures in mice to anything measured in humans, and d) limitations in the novelty of the findings. These weaknesses are related to the primary concerns described below:

Concerns about the primary conclusion that PVHCRH neurons integrate the anesthetic effects and post-anesthesia stress response of sevoflurane GA:

It is important to compare the effects of sevoflurane with at least one other inhaled ether anesthetic as one step towards elevating the impact of this paper to the level required for a journal such as eLife. Isoflurane, desflurane, and enflurane are ether anesthetics that are very similar to each other, as well as being similar to sevoflurane. For example, one study cited by the authors (Marana et al. 2013) concludes that there is weak evidence for differences in stress-related hormones between sevoflurane and desflurane, with lower levels of cortisol and ACTH observed during the desflurane intraoperative period. It is important to determine whether desflurane activates PVHCRH neurons in the post-anesthesia period, and whether this is accompanied by excess grooming in the mice because this will distinguish whether the effects of sevoflurane generalize to other inhaled anesthestics, or, alternatively, relate to unique idiosyncratic properties of this gas that may not be a part of its anesthetic properties.

Concerns about the clinical relevance of the experiments:

In anesthesiology practice, perioperative stress observed in patients is more commonly related to the trauma of the surgical intervention, with inadequate levels of antinociception or unconsciousness intraoperatively and/or poor post-operative pain control. The authors seem to be suggesting that the sevoflurane itself is causing stress because their mice receive sevoflurane but no invasive procedures, but there is no evidence of sevoflurane inducing stress in human patients. It is important to know whether sevoflurane effectively produces behavioral stress in the recovery room in patients that could be related to the putative stress response (excess grooming) observed in mice. For example, in surgeries or procedures which required only a brief period of unconsciousness that could be achieved by administering sevoflurane alone (comparable to the 30 min administered to the mice), is there clinical evidence of post-operative stress? It is also important to describe a rationale for using a 30 min sevoflurane exposure. What proportion of human surgeries using sevoflurane use exposure times that are comparable to this?

It is the experience of one of the reviewers that human patients who receive sevoflurane as the primary anesthetic do not wake up more stressed than if they had had one of the other GABAergic anesthetics. If there were signs of stress upon emergence (increased heart rate, blood pressure, thrashing movements) from general anesthesia, this would be treated immediately. The most likely cause of post-operative stress behaviors in humans is probably inadequate anti-nociception during the procedure, which translates into inadequate post-op analgesia and likely delirium. It is the case that children receiving sevoflurane do have a higher likelihood of post-operative delirium. Perhaps the authors' studies address a mechanism for delirium associated with sevoflurane, but this is barely mentioned. Delirium seems likely to be the closest clinical phenomenon to what was studied. As noted by the Besnier et al (2017) article cited by the authors, surgery can elevate postoperative glucocorticoid stress hormones, but it generally correlates with the intensity of the surgical procedure. Besnier et al also note the elevation of glucocorticoids is generally considered to be adaptive. Thus, reducing glucocorticoids during surgery with sevoflurane may hamper recovery, especially as it relates to tissue damage, which was not measured or considered here. This paper only considers glucocorticoid release as a negative factor, which causes "immunosuppression", "proteolysis", and "delays postoperative recovery and...leads to increased morbidity".

It is also the case that there are explicit published findings showing that mild and moderate surgical procedures in children receiving sevoflurane (which might be the closest human proxy to the brief 30 minute sevoflurane exposure used here) do not have elevated cortisol (Taylor et al, J Clin Endocrinol Metab, 2013). This again raises the question of whether the enhanced grooming or elevated corticosterone observed in the mice here has any relevance to humans.

Concerns about the novelty of the findings:

The key finding here is that CRH neurons mediate measures of arousal, and arousal modulates sevoflurane anesthesia induction and recovery. However, CRH is associated with arousal in numerous studies. In fact, the authors' own work, published in eLife in 2021, showed that stimulating the hypothalamic CRH cells lead to arousal and their inhibition promoted hypersomnia. In both papers the authors use fos expression in CRH cells during a specific event to implicate the cells, then manipulate them and measure EEG responses. In the previous work, the cells were active during wakefulness; here- they were active in the awake state the follows anesthesia (Figure 1). Thus, the findings in the current work are incremental and not particularly impactful. Claims like "Here, a core hypothalamic ensemble, corticotropin-releasing hormone neurons in the paraventricular nucleus of the hypothalamus, is discovered" are overstated. PVHCRH cell populations were discovered in the 1980s. Suggesting that it is novel to identify that hypothalamic CRH cells regulate post-anesthesia stress is unfounded as well: this PVH population has been shown over four decades to regulate a plethora of different responses to stress. Anesthesia stress is no different. Their role in arousal is not being discovered in this paper. Even their role in grooming is not discovered in this paper.

The activation of CRH cells in PVH has already been shown to result in grooming by Jaideep Bains (a paper cited by the authors). Thus, the involvement of these cells in this behavior is not surprising. The authors perform elaborate manipulations of CRH cells and numerous analyses of grooming and related behaviors. For example, they compare grooming and paw licking after anesthesia with those after other stressors such as forced swim, spraying mice with water, physical attack and restraint. The authors have identified a behavioral phenomenon in a rodent model that does not have a clear correlation with a behavior state observed in humans during the use of sevoflurane as part of an anesthetic regimen. The grooming behaviors are not a model of the emergence delirium or the cognitive dysfunction observed commonly in patients receiving sevoflurane for general anesthesia. Emergence delirium is commonly seen in children after sevoflurane is used as part of general anesthesia and cognitive dysfunction is commonly observed in adults-particularly the elderly -- following general anesthesia.

Reviewer #1 (Public review):

Summary:

Li Zhang et al. characterized two new Gram-negative endolysins identified through an AMP-targeted search in bacterial proteomes. These endolysins exhibit broad lytic activity against both Gram-negative and Gram-positive bacteria and retain significant antimicrobial activity even after prolonged exposure to high temperatures (100{degree sign}C for 1 hour). This stability is attributed to a temperature-reversible transition from a dimer to a monomer. The authors suggest several potential applications, such as complementing heat sterilization processes or being used in animal feed premixes that undergo high-temperature pelleting, which I agree with.

Strengths:

The claims are well-supported by relevant and complementary assays, as well as extensive bioinformatic analyses.

Weaknesses:

My last comments are minor and nearly all aim to improve the use of English language in the manuscript. However, a section describing the statistical analysis is still lacking. I believe that the presented manuscript can benefit from language editing, but I leave this decision with the editor.

Reviewer #2 (Public review):

Summary:

The study explores a new strategy of lysin-derived antimicrobial peptide-primed screening to find peptidoglycan hydrolases from bacterial proteomes. Using this strategy authors identified five peptidoglycan hydrolases from A. baumannii. They further tested their antimicrobial activities on various Gram positive and Gram-negative pathogens.

Strengths:

Overall, the study is good and adds new members to the peptidoglycan hydrolases family. The authors also show that these lysins have bactericidal activities against both Gram-positive and Gram-negative bacteria. The crystal structure data is good, reveals different thermostablility to the peptidoglycan hydrolases. Structural data also reveals that PhAb10 and PHAb11 form thermostable dimer and data is corroborated by generating variant protein defective in supporting intermolecular bond pairs. The mice bacterial infection shows promise for the use of these hydrolases as antimicrobial agents.

Weaknesses:

While the authors have employed various mechanisms to justify their findings, some aspects are still unclear. Only CFU has been used to test bactericidal activity. This should also be corroborated by live/dead assay. Moreover, SEM or TEM analysis would reveal the effect of these peptidoglycan hydrolases on Gram-negative /Gram-positive cell envelopes. The authors claim that these hydrolases are similar to T4 lysozyme, but they have not correlated their findings with already published findings on T4 lysozyme. T4 lysozyme has C-terminal amphipathic helix with antimicrobial properties. Moreover, heat, denatured lysozyme also shows enhanced bactericidal activity due to the formation of hydrophobic dimeric forms, which are inserted in the membrane. Authors also observe that heat denatured PHAb10 and PHAb11 have bactericidal activity but no enzymatic activity. These findings should be corroborated by studying the effect of these holoenzymes/ truncated peptides on bacterial cell membranes. Also, a quantitative peptidoglycan cleavage assay should be performed in addition to halo assay. Including these details would make the work more comprehensive.

Revised version: The authors have addressed most of the questions in the revised version of the paper.

Reviewer #1 (Public review):

Summary:

The work seeks to investigate the efficacy of linalool as a natural alternative for combating Saprolegnia parasitica infections, which would provide great benefit to aquaculture. This paper shows the effect of linalool in vitro using a variety of techniques including changes in S. parasitica membrane integrity following linalool exposure and alterations in cell metabolism and ribosome function. Additionally, this work goes on to show that prophylactic and concurrent treatment of linalool at the time of S. parasitica infection can improve survival and tissue damage in vivo in their grass carp infection model. The conclusions of the paper are partially supported by the data, cleaning up, clarifying, and elaborating on some aspects of this work is necessary.

(1) Adding microscopy of the untreated group to compare Figure 2A with would further strengthen the findings here.

(2) Quantification of immune infiltration and histological scoring of kidney, liver, and spleen in the various treatment groups would increase the impact of Figure 4.

(3) The data in Figure 6 I is not sufficiently convincing as being significant.

(4) Comparisons of the global transcriptomic analysis of the untreated group to the PC, LP, and LT groups would strengthen the author's claims about the immunological and transcriptomic changes caused by linalool and provide a true baseline.

Reviewer #2 (Public review):

Summary:

In this study, the authors aimed to delineate the antimicrobial activity of linalool and tried to investigate the mode of action of linalool against S. parasitica infection. One of the main focuses of this work was to identify the in vitro and in vivo mechanisms associated with the protective role of linalool against S. parasitica infection.

Strengths:

(1) The authors have used a variety of techniques to prove their hypothesis.

(2) An adequate number of replicates were used in their studies.

(3) Their findings showed a protective role of linalool against oomycetes and makes it an attractive future antibiotic in the aquaculture industry.

Weaknesses:

There are several weaknesses in this manuscript.

(1) The authors have taken for granted that the readers already know the experiments/assays used in the manuscript. There was not enough explanation for the figures as well as figure legends.

(2) The authors missed adding the serial numbers to the references.

(3) The introduction section does not provide adequate rationale for their work, rather it is focused more on the assays done.

(4) Full forms are missing in many places (both in the text and figure legends), also the resolution of the figures is not good. In some figures, the font size is too small.

(5) There is much mislabeling of the figure panels in the main text. A detailed explanation of why and how they did the experiments and how the results were interpreted is missing.

(6) There is not enough experimental data to support their hypothesis on the mechanism of action of linalool. Most of the data comes from pathway analysis, and experimental validation is missing.

Overall, the conclusions drawn by the authors are partially justified by the data. Importantly, this paper has discovered the novelty of the compound linalool as a potent antimicrobial agent and might open up future possibilities to use this compound in the aquaculture industry.

Reviewer #1 (Public review):

Summary:

Here, the authors attempt to show that CCL5 is increased after stroke, possibly due to decreased miR-324, and that this is a modifiable system to decrease stroke damage. By bidirectionally manipulating CCL5 levels through direct injection of CCL5; a CCL5 blocking antibody; miR324; miR324 antagomir; or CCR5-blocking Maraviroc, they broadly show improvement with lower CCL5 levels. This includes infarct size, behavioral analysis, and immunohistochemical analysis of astrocytes, microglia, and neurons. They further try to mechanistically tie miR324 and CCL5 in astrocytes specifically to stroke-induced changes using a neuronal/astrocytic coculture system. They argue that decreasing CCL5 leads to increased ERK and CREB phosphorylation as a potential neuroprotective mechanism. CCL5 is one potential ligand for CCR5, and recent work identified CCR5 as a targetable mechanism by clinically-approved drug Maraviroc to enhance stroke recovery. Particularly given the high level of interest in CCR5 in stroke recovery, the focus on CCL5 - one of CCR5's potential ligands - and its miR regulation is an exciting expansion of this area of stroke biology.

Strengths:

The authors' findings that decreasing CCL5 acutely after stroke shows behavioral improvement appear robust. This broadly replicates work from other groups, although the finding that miR324 manipulation can phenocopy direct CCL5 manipulation is novel and intriguing. However, many of their other claims are difficult to evaluate based on a combination of missing methodological information, inappropriate statistical testing, and a flawed culture system.

Weaknesses:

Broadly speaking, the manuscript takes a zoomed-out view of what is fundamentally highly localized biology.

(1) miRNA-based regulation, by definition, has to include miR and mRNA in the same cell type; as the authors note, CCL5 is expressed in many cells. It is therefore impossible to propose any interaction on the basis of the tissue-level changes described; any evidence of in vivo cell-type specificity would dramatically improve the claims.

(2) The authors treat an extensive area of ipsilesional cortex uniformly as "IP". Astrocytic and microglial responses to localized injuries such as stroke are highly location-dependent and undoubtedly change dramatically within this area. The presented data cannot be interpreted without confirmation that these were taken at identical distances from the injury, and what that distance was. These do not appear to be adjacent to the injury, where the responses would presumably be the most informative. Similarly, it is difficult to interpret the neuronal Sholl and spine data without more information on where within the large IP region these neurons were found.

The authors attempt to narrow in on cell-type specificity via culture. However, astrocytes are notoriously prone to a dramatic change in culture and require careful methods (immunopanning; see eg doi: 10.1016/j.neuron.2011.07.022) to maintain much resemblance to their in vivo counterpart. It is difficult to conclude much about the role of astrocytes in the CCL5 pathway based on the use of this shaking-based culture system, particularly in the absence of cell-type specific validation in vivo.

There is missing methodological information, including infarct size measurements, TUNEL staining, and statistical testing. The TTC figures look very odd, like a collection of overlapping stars have been placed on the images rather than the natural relatively smooth infarct edges one would expect. It is unclear if the infarct volume measurements accounted for edema, as is standard; there is no description of the protocol used for quantification. It is also unclear if the infarct volume measurement comparisons were also done with t-tests vs ANOVA, as the statistical test used is not listed in the figure legends. In numerous cases where statistical testing is listed, repeated t-tests between subgroups are used vs the more appropriate ANOVA (assuming normality; nonparametric testing as appropriate), making it difficult to have confidence in the results.

Reviewer #2 (Public review):

The authors presented evidence from various in vivo and in vitro experiments demonstrating the mutual interaction between CCL5 and astrocytic miR-342-5p in the ipsilateral core of cerebral ischemia. However, miR-342-5p was downregulated only late after MCAO (D3-7). Additionally, this downregulation was observed not only in the ipsilateral core but also in the ipsilateral penumbra and contralateral sides. Therefore, it is not convincing that the upregulation of CCL5 in the ipsilateral core at later time points (D3 and D7) is attributable to the decreased expression of miR-342-5p. In particular, infarct injury was already evident within a short time period (say 24 h) following MCAO.

(1) The temporal and spatial expression patterns of miR-324-5p do not match those of CCL-5, especially at D1 and D3 (see Figure 1C, 1D). Despite the inverse relationship between miR-324-5p and CCL-5 expression at D7 after MCAO, what was the purpose of administering miR-324-5p agomir (or antagomir) at D1 post-MCAO? If the connection cannot be clearly established, the conclusion reached at the end will be difficult to accept.

(2) Would administering miR-342-5p or anti-CCL5 at later time points (e.g., after D3) reduce infarct size or improve functional recovery? If this is not the case, the effect of CCL5 on neuronal cell damage (infarct size formation) must occur within a very short time after MCAO. Additionally, if the increased CCL5 expression is due to the downregulation of miR-342-5p, its impact would likely be less significant.

(3) While the study offers valuable insights into the roles of CCL5 and its connection with the regulation of miR-342-5p (though this connection is somewhat weak), it is recommended that the authors explore potential translational applications of these findings.

Overall, given the experimental designs and results, it is difficult to support the conclusions drawn in the manuscript.

Reviewer #1 (Public review):

Summary:

The authors of this study use an optimization algorithm approach, based on the established Nelder-Mead method, to infer polymer models that best match input bulk Hi-C contact data. The procedure infers the best parameters of a generic polymer model that combines loop-extrusion (LE) dynamics and compartmentalisation of chromatin types driven by weak biochemical affinities. Using this and DNA FISH, the authors investigate the chromatin structure of the MYC locus in leukaemia cells, showing that loop extrusion alone cannot explain local pathogenic chromatin rearrangements. Finally, they study the locus single-cell heterogeneity and time dynamics.

In the revised manuscript the authors have adequately addressed my questions and comments. The exception concerns point #5 of my original review:

(5) Besides cumulative probability distributions, I asked the authors to show the TAD2-TAD4 (model vs. exp) distances in Fig. 3c as relative frequency histograms. This allows readers to more accurately evaluate whether model and experimental distributions have same shape and variance.

Reviewer #1 (Public Review):

The individual roles of both cosolvents and intrinsically disordered proteins (IDPs) in desiccation have been well established, but few studies have tried to elucidate how these two factors may contribute synergistically. The authors quantify the synergy for the model and true IDPs involved with desiccation and find that only the true IDPs have strong desiccation tolerance and synergy with cosolvents. Using these as model systems, they quantify the local (secondary structure vis-a-vi CD spectroscopy) and global dimensions (vis-a-vi the Rg of SAXS experiments) and find no obvious changes with the co-solvents. Instead, they focus on the gelation of one of the IDPs and, using theory and experiments, suggest that the co-solvents may enable desiccation tolerance, an interesting hypothesis to guide future in vivo desiccation studies. A few minor points that remained unclear to this reviewer and that were noted previously have been reasonably addressed in this revision.

Strengths:

This paper is quite extensive and has significant strengths worth highlighting. Notably, the number and type of methods employed to study IDPs are quite unusual, employing CD spectroscopy, SAXS measurements, and DSC. The use of the TFE is an exciting integration of the physical chemistry of cosolvents into the desiccation field is a nice approach and a clever way of addressing the gap of the lack of conformational changes depending on the cosolvents. Furthermore, I think this is a major point and strength of the paper; the underlying synergy of cosolvents and IDPs may lie in the thermodynamics of the dehydration process.

Figure S6A is very useful. I encourage readers who are confused about the DSC analysis, interpretation, and calculation to refer to it.

Weaknesses:

All minor weaknesses were addressed in this revision.

Reviewer #2 (Public Review):

Summary:

The paper aims to investigate the synergies between desiccation chaperones and small molecule cosolutes, and describe its mechanistic basis. The paper reports that IDP chaperones have stronger synergies with the cosolutes they coexist with, and in one case suggests that this is related to oligomerization propensity of the IDP.

Strengths:

The authors have done a good job improving the paper. The study uses a lot of orthogonal methods and the experiments are technically well done. They are addressing a new question that has not really been addressed previously.

Weaknesses:

The conclusions are still based on a few examples and only partial correlations. However, this is now acknowledged by the authors and the conclusions are presented with appropriate caveats.

Reviewer #1 (Public review):

Summary:

The manuscript by Sztangierska et al explores how the Hsp70 chaperone together with its JDP-NEF cofactors and Hsp104 disentangle aggregated proteins. Specifically, the study provides mechanistic findings that explain what role the NEF class Hsp110 has in protein disaggregation. The results explain several previous observations related to Hsp110 in protein disaggregation. Importantly, the study provides compelling evidence that Hsp110 acts early in the disaggregation process.

Strengths:

(1) This is a very well performed study with multiple in vitro experiments that provide convincing support for the claims.

(2) An important finding is that the study places Hsp110 function early in the disaggregation process.

(3) The study has an important value in that it picks up on a number of observations in the field that have not been explored or directly tested by experiment. The presented results settle questions and controversy regarding Hsp110 function in disaggregation.

Weaknesses:

(1) While the key finding of this manuscript is that it places Hsp110 early in the disaggregation process, the other findings are advancing the field less.

Reviewer #2 (Public review):

Sztangierska et al. have investigated the impact of the nucleotide exchange (NEF) factor Hsp110 on the Hsp70-dependent dissolution of amorphous aggregates in the presence of representative members of two classes of J-domain protein.<br /> The authors find that the nucleotide exchange factor of the Hsp110 family, sse1, stimulates the disaggregation activity of yeast Hsp70, ssa1, in particular in the presence of the J-domain protein sis1. Linking chaperone-substrate interactions as determined by biolayer interferometry (BLI) to activity assays, they show that sse1 facilitates the loading of more ssa1 onto the aggregate substrate and propose that this is due to active remodelling of the protein aggregate which exposes more chaperone binding sites and thus facilitates reactivation. This study highlights two important facets of Hsp70 biology: different Hsp70 functions rely on the functional cooperation of specific co-chaperone combinations and the stoichiometry of the different players of the Hsp70 system is an important parameter in tuning Hsp70 chaperone activity.

Strengths:

The manuscript presents a systematic analysis of the functional cooperation of sse1 with a class B J-domain protein sis1 in the disaggregation of two different model aggregate substrates, allowing the authors to draw more general conclusions about Hsp70 disaggregation activity.

The authors can pinpoint the role of sse1 to the initial remodeling of aggregates, rather than the later stages of refolding, highlighting the functional specificity of Hsp70 co-chaperones.

They demonstrate the competitive nature of binding to ssa1 between sse1 and sis1 which can explain the poisoning of Hsp70 chaperone activities observed at high NEF concentrations.

Weaknesses:

While structural requirements have been identified that allow sse1, in cooperation with sis1, to facilitates the loading of Hsp70 on the amorphous aggregate substrate, how this is achieved on a mechanistic level remains an open question.

Reviewer #3 (Public review):

Summary:

The authors studied the function of Hsp110 co-chaperones (e.g. yeast Sse1) in Hsp70-dependent protein disaggregation reactions. The study builds on former work by the authors (Wyszkowski et al., 2021, PNAS), analyzing the binding of Hsp70 and J-domain protein (JDP) cochaperones to protein aggregates using bio-layer interferometry (BLI). It was shown before by other groups that Hsp110 enhances Hsp70 disaggregation activity. The mechanism of Hsp110-stimulated disaggregation activity, however, remained poorly defined. Here, the authors show that yeast Hsp110 increases Hsp70 recruitment to the surface of protein aggregates. The effect is largely dependent on J-domain protein (JDP) identity and particularly pronounced for class B JDPs (e.g. yeast Sis1), which are also more effective in disaggregation reactions. The authors also confirm former results, showing inhibition by increased Hsp110 levels and provide novel evidence that the inhibitory effect is caused by competition between Hsp110 and JDPs for Hsp70 binding.

Strengths:

The work represents a very thoroughly executed study, which provides novel insights into the mechanism of Hsp70-mediated protein disaggregation. Key findings established for yeast chaperones are also documented for human counterparts. The observation that Hsp110 might displace JDPs from Hsp70 during the disaggregation reaction is very appealing. It will now become important to validate this initial finding and dissect how it propels the disaggregation reaction.

Weaknesses:

How exactly the interplay between JDPs and Hsp110 orchestrates protein disaggregation remains largely speculative and further analysis is required for a deeper mechanistic understanding.

Reviewer #1 (Public review):

Summary:

Matsui et al. present an experimental pipeline for visualizing molecular machinery of synapses in the brain, which includes numerous techniques, starting with generating labeled antibodies and recombinant mice, continuing with HPF and FIB milling and finishing with tilt series collection and 3D image processing. This pipeline represents a breakthrough in preparation of brain tissue for high resolution imaging and can be used in future tomographic research to reconstruct molecular details of synaptic complexes as well as pre- and post-synaptic assemblies. This methodology can also be adapted for a broader range of tissue preparations and signifies the next step towards better structural understanding of how molecular machineries operate in natural conditions.

Strengths:

The manuscript is very well written, contains a detailed description of methodology, provides nice illustrations and will be an outstanding guide for future research.

Weaknesses:

None noted.

Reviewer #2 (Public review):

Summary

The authors present a method that allows for the identification and localization of molecular machinery at chemical synapses in unstained, unfixed native brain tissue slices. They believe that this approach will provide a 3D structural basis for understanding different mechanisms of synaptic transmission, plasticity, and development. To achieve this, the group used genetically engineered mouse lines and generated thin brain slices that underwent high-pressure freezing (HPF) and focused ion beam (FIB) milling. Utilizing cryo-electron tomography (cryo-ET) and integrating it with cryo-fluorescence microscopy, they achieved micrometer resolution in identifying the glutamatergic synapses along with nanometer resolution to locate AMPA receptors GluA2-subunits using Fab-AuNP conjugates. The findings are summarized with detailed examples of successfully prepared substrates for cryo-ET, specific morphological identification and localization, and the detailed structural organization of excitatory synapses, including synaptic vesicle clusters close to the postsynaptic density and in the cleft.

Strengths

The study advances previous work that used cultured neurons or synaptosomes. Combining cryo-electron tomography (cryo-ET) with fluorescence-guided targeting and labeling with Fab-AuNP conjugates enabled the study of synapses and molecular structures in their native environment without chemical fixation or staining. This preserves their near-native state, offering high specificity and resolution. The methods developed are mostly generalizable, allowing adaptation for identifying and localizing other key molecules at glutamatergic synapses and potentially useful for studying a variety of synapses and cellular structures beyond the scope of this research.

Weaknesses

The preparation and imaging techniques are complex and require highly specialized equipment and expertise, potentially limiting their accessibility and widespread adoption.

Additionally, the methods might need further modifications/tweaks to study other types of synapses or molecular structures effectively.

The reliance on genetically engineered mouse lines and monoclonal, high-affinity antibodies/Fab fragments to specifically label receptors/proteins would limit the wider employment of these methods.

Reviewer #1 (Public review):

Summary:

This paper by Yang et al. established an in vitro triple co-culture BBB model and demonstrated its advantages compared with the mono or double co-culture BBB model. Further, the authors used their established in vitro BBB model and combined it with other methodologies to investigate the specific signaling mechanisms that co-culture with astrocytes but also neurons enhancing the integrity of endothelial cells.

Strengths:

The results persuasively demonstrated that the established triple co-culture BBB model well mimicked several important characteristics of BBB compared with the mono-culture BBB model, including better barrier function and in vivo/in vitro correlation. The use of human-derived immortalized cells made the model construction process faster and more efficient and had a better in vivo correlation without the complications of species differences. This model is expected to be a useful high-throughput evaluation tool for CNS drug development.

Moreover, the authors used a variety of experiments to prove that the triple co-culture model also reflected the interactions between NVU cells, including promoting endothelial cell proliferation and the formation of intercellular junctions. Interestingly, the authors found that neurons also released GDNF to promote barrier properties of brain endothelial cells, as most current research has focused on the promoting effect of astrocytes-derived GDNF on BBB. Meanwhile, the author also validated the functions of GDNF for BBB integrity in vivo by silencing GDNF in mouse brains. Overall, the experiments and data presented support the claim that neurons, alongside astrocytes, contribute to the promoting effects of the barrier function of endothelial cells through GDNF secretion.

Weaknesses:

While the authors explained that the use of human-derived immortalized cells has been justified as more reproducible and efficient in constructing the model, the TEER value of the triple co-culture model remains lower than that of the physiological statement. Future research may need to explore additional methods to further enhance the barrier function of the model.

Reviewer #2 (Public review):

Summary:

Yang and colleagues developed a new in vitro blood-brain barrier model that is relatively simple yet outperforms previous models. By incorporating a neuroblastoma cell line, they demonstrated increased electrical resistance and decreased permeability to small molecules

Strengths:

The authors initially elucidated the soluble mediator responsible for enhancing endothelial functionality, namely GDNF. Subsequently, they elucidated the mechanisms by which GDNF upregulates the expression of VE-cadherin and Claudin-5. They further validated these findings in vivo, and demonstrated predictive value for molecular permeability as well. The study is meticulously conducted and easily comprehensible. The conclusions are firmly supported by the data, and the objectives are successfully achieved. This research is poised to advance future investigations in BBB permeability, leakage, dysfunction, disease modeling, and drug delivery, particularly in high-throughput experiments. I anticipate an enthusiastic reception from the community interested in this area. While other studies have produced similar results with tri-cultures (PMID: 25630899), this study notably enhances electrical resistance compared to previous attempts.

Weaknesses:

The power of this system lies in its simplicity, which is enough to study BBB permeability. However, it also lacks some other important cell-cell interactions such as those involving pericytes. Nonetheless, this is still a valuable tool for high throughput screening.

As with many other similar systems, it has lower TEER values compared to the in vivo counterpart, this is an issue that researchers in the field will have to address in future studies

Reviewer #1 (Public review):

Herzog and colleagues investigated the interactions between working memory (WM) task condition (updating, maintenance) and BMI (body-mass-index), while considering selected dopaminergic genes (COMT, Taq1A, C957T, DARPP-32). Emerging evidence suggest that there might be a specific negative association with BMI in the updating but not maintenance condition, with potential bearings to reversal reward learning in obesity. The inclusion of multiple dopaminergic genes is a strength in the present study, considering the complexity of the interactions between tonic and phasic dopamine across the brain that may distinctly associate with the component processes of WM. Here, the finding was that BMI was negatively associated with WM performance regardless of the condition (updating, maintenance), but in models including moderation by either Taq1A or DARPP-32 (but not by COMT and C957T) an interaction by task condition was observed. Furthermore, a two-way interaction effect between BMI and genotype was observed exclusively in the updating condition. These findings are in line with the accounts by which striatal dopamine as reflected by Taq1A and DARPP-32 play an important role in working memory updating, while cortical dopamine as reflected by COMT is mainly associated with maintenance. The authors conclude that the genetic moderation reflects a compound effect of having high BMI and an advantageous allele in Taq1A or DARPP-32 to working memory updating specifically.

These data increment the accumulating evidence that the dopamine system plays an important role in obesity. The result that Taq1A and DARPP-32 moderated the interaction between WM condition and BMI required intricate post hoc analysis to understand the bearings to updating. The authors found that Taq1A or DARPP-32 genotype moderated the negative association between BMI and WM exclusively in update condition (significant two-way interaction effect), suggesting that the BMI-WM associations in other conditions were similar across genotypes. Importantly, visual inspection of the relationship between WM and BMI (Fig 4 & 5) suggests more prevalent positive effects of the putatively advantageous Taq1A-A1 and DARPP-32-AA genotypes to the overall negative relationship between WM and BMI in updating, but not in the other conditions. Given that an overall negative relationship was statistically supported across all conditions (model 1), a plausible interpretation would be that updating condition stands out in terms of a positive moderation by putative advantageous genotypes, rather than compound negative consequences of BMI and genotype in updating. Statistical testing stratified by Taq1A genotype confirmed that the interaction with task condition was driven by the carriers of the advantageous genotype, whereas stratification by DARPP-32 genotype revealed a significant task-condition interaction in both A/A- and G-carriers. Taken together, the present results highlight inter-subject variability in the associations between obesity, dopamine, and working memory, which can sometimes be captured using blood-based dopamine markers. This finding indicates that not all individuals with obesity show the same patterns of dopamine-related alterations and underscores the necessity to address inter-individual variability in future research and treatment efforts.

Reviewer #2 (Public review):

Summary:

The authors investigated if obesity is associated with elevated working memory deficits. Prior theorizing would suggest that individuals with a higher BMI would be worse at working memory updating, potentially due to impaired dopaminergic signaling in the striatum. However, the authors find that higher BMI was associated with worse working memory performance, irrespective of having to ignore or update new information. To further explore the putative dopaminergic mechanisms, participants are stratified according to genetic polymorphisms in COMT, Taq1A, DARPP and C957T and the ratio of the amino acids phenylalanine and tyrosine, all implicated in dopamine-signaling. They find that carrying specific alleles of Taq1A and DARPP, but not of COMT and C957T, mitigated the otherwise negative relationship between BMI and working memory for updating, but not for maintenance.

The authors put forward several possible mechanistic explanations of these observations, including imbalances in the striatal go/no-go dopamine pathways. However, only future, more direct measures of dopamine signaling can provide a confirmation of these hypotheses.

Strengths:

Differentiating between working memory maintenance (ignoring) and updating is a powerful way to get a deeper insight into specific working memory deficits in individuals with obesity. This way of assessing working memory could potentially be applied to various populations at risk for cognitive or working memory deficits.

By pooling data from three studies, the authors reached a relatively large sample of 320 participants, which enables the assessment of more subtle effects on working memory, including the differentiation between updating and ignoring.

Working memory gating has long implicated striatal dopamine signaling. This paper shows that a specific combination of a high BMI and specific dopamine-related genotypes can selectively moderate working memory updating. More insight into how these risk factors interact can ultimately lead to more tailor-made treatments.

Weaknesses:

The introduction mentions that specific alleles can alter dopamine signaling in various ways. However, the authors are less clear on how they expect these alterations to subsequently affect working memory updating and maintenance in the current study. While I understand that the complexity of these mechanisms might make it challenging to form specific predictions, it would be helpful if the authors acknowledged this uncertainty and clarified that their analyses are exploratory in nature, and they will therefore refrain from any directional hypotheses regarding the genotypes.

The majority of participants seems to fall within the normal BMI-range, whereas the interaction between BMI and genetic variations or amino acid ratio particularly surfaces at higher BMI. As genetic variations are usually associated with small effect sizes, the effective sample size, although large for a behavioral analysis only, might have been too small to detect meaningful effects of particular alleles of COMT and C957T.

The relationships between genetic variations, BMI and specific disturbances in dopamine signaling are complex, as compensating mechanisms might be at play to mitigate any detrimental effects. Future studies that apply more direct measures or manipulations of dopaminergic processes could therefore aid in mechanistically explaining the results.

Reviewer #1 (Public Review):

In the current study, Papandreou et al. developed an iPSC-based midbrain dopaminergic neuronal cell model of Beta-Propeller Protein-Associated Neurodegeneration (BPAN), which is caused by mutations in the WDR45 gene and is known to impair autophagy. They also noted defective autophagy and abnormal BPAN-related gene expression signatures. Further, they performed a drug screening and identified five cardiac glycosides. Treatment with these drugs effectively in improved autophagy defects and restored gene expression. Seeing the autophagy defects and impaired expression of BPAN-related genes adds strength to this study. Importantly, this work shows the value of iPSC-based modeling in studying disease and finding therapeutic strategies for genetic disorders, including BPAN.

Reviewer #2 (Public Review):

Summary:

In this manuscript, the authors aim to demonstrate that cardiac glycosides restore autophagy flux in an iPSC-derived mDA neuronal model of WDR45 deficiency. They established a patient-derived induced pluripotent stem cell (iPSC)-based midbrain dopaminergic (mDA) neuronal model and performed a medium-throughput drug screen using high-content imaging-based IF analysis. Several compounds were identified that ameliorate disease-specific phenotypes in vitro.

Strengths:

This manuscript engaged in an important topic and yielded some interesting data.

Reviewer #2 (Public review):

Prior work by the Sehgal group has shown that a small group of neurons in the fly brain (anterior posterior (ap) α'β' mushroom body neurons (MBNs)) promote sleep and sleep-dependent appetitive memory specifically under fed conditions (Chouhan et al., (2021) Nature). Here, Li, Chouhan et al. combine cell-specific transcriptomics with measurements of sleep and memory to identify molecular processes underlying this phenomenon. They define transcriptional changes in ap α'β' MBNs and suggest a role for two genes downregulated following memory induction (Polr1F and Regnase-1) in regulating sleep and memory.

The transcriptional analyses in this manuscript are impressive. The authors have now included additional experiments that define acute and developmental roles for Polr1F and Regnase-1 respectively in regulating sleep. They have also provided additional data to strengthen their conclusion that Polr1F knockdown in α'β' mushroom body neurons enhances sleep.

The resubmitted work represents a convincing investigation of two novel sleep-regulatory proteins that may also play important roles in memory formation.

The authors have comprehensively addressed my comments, which I very much appreciate. I congratulate them on this excellent work.

Reviewer #3 (Public review):

Previous work (Chouhan et al., 2022) from the Sehgal group investigated the relationship between sleep and long-term memory formation by dissecting the role of mushroom body intrinsic neurons, extrinsic neurons, and output neurons during sleep-dependent and sleep-independent memory consolidation. In this manuscript, Li et al., profiled transcriptome in the anterior-posterior (ap) α'/β' neurons and identified genes that are differentially expressed after training in fed condition, which supports sleep-dependent memory formation. By knocking down candidate genes systematically, the authors identified Polr1F and Regnase-1 as two important hits that play potential roles in sleep and memory formation. What is the function of sleep and how to create a memory are two long-standing questions in science. The present study used a new approach to identify novel components that may link sleep and memory consolidation in a specific type of neuron. Importantly, these components implicated that RNA processing may play a role in these processes.

While I am enthusiastic about the innovative approach employed to identify RNA processing genes involved in sleep regulation and memory consolidation, I feel that the data presented in the manuscript is insufficient to support the claim that these two genes establish a definitive link between sleep and memory consolidation. First, the developmental role of Regnase-1 in reducing sleep remains unclear because knocking down Regnase-1 using the GeneSwitch system produced neither acute nor chronic sleep loss phenotype. In the revised manuscript, the author used the Gal80ts to restrict the knockdown of Regnase-1 in adult animals and concluded that Regnase-1 RNAi appears to affect sleep through development. Conducting overexpression experiments of Regnase-1 would lend some credibility to the phenotypes, however, this is not pursued in the revised manuscript. Second, while constitutive Regnase-1 knockdown produced robust phenotypes for both sleep-dependent and sleep-independent memory, it also led to a severe short-term memory phenotype. This raises the possibility that flies with constitutive Regnase-1 knockdown are poor learners, thereby having little memory to consolidate. The defect in learning could be simply caused by chronic sleep loss before training. Thus, this set of results does not substantiate a strong link between sleep and long-term memory consolidation. Lastly, the discussion on the sequential function of training, sleep, and RNA processing on memory consolidation appears speculative based on the present data.

Reviewer #4 (Public review):

Summary:

Li and Chouhan et al. follow up on a previous publication describing the role of anterior-posterior (ap) and medial (m) ɑ′/β′ Kenyon cells in mediating sleep-dependent and sleep-independent memory consolidation, respectively, based on feeding state in Drosophila melanogaster. The authors sequenced bulk RNA of ap ɑ′/β′ Kenyon cells 1h after flies were either trained-fed, trained-starved or untrained-fed and find a small number of genes (59) differentially expressed (3 upregulated, 56 downregulated) between trained-fed and trained-starved conditions. Many of these genes encode proteins involved in the regulation of gene expression. The authors then screened these differentially expressed genes for sleep phenotypes by expressing RNAi hairpins constitutively in ap ɑ′/β′ Kenyon cells and measuring sleep patterns. Two hits were selected for further analysis: Polr1F, which promoted sleep, and Regnase-1, which reduced sleep. The pan-neuronal expression of Polr1F and Regnase-1 RNAi constructs was then temporally restricted to adult flies using the GeneSwitch system. Polr1F sleep phenotypes were still observed, while Regnase-1 sleep phenotypes were not, indicating developmental defects. Appetitive memory was then assessed in flies with constitutive knockdown of Polr1F and Regnase-1 in ap ɑ′/β′ Kenyon cells. Polr1F knockdown did not affect sleep-dependent or sleep-independent memory, while Regnase-1 knockdown disrupted sleep-dependent memory, sleep-independent memory, as well as learning. Polr1F knockdown increased pre-ribosomal RNA transcripts in the brain, as measured by qPCR, in line with its predicted role as part of the RNA polymerase I complex. A puromycin incorporation assay to fluorescently label newly synthesized proteins also indicated higher levels of bulk translation upon Polr1F knockdown. Regnase-1 knockdown did not lead to observable changes in measurements of bulk translation.

Strengths:

The proposed involvement of RNA processing genes in regulating sleep and memory processes is interesting, and relatively unexplored. The methods are satisfactory.

Weaknesses:

The main weakness of the paper is in the overinterpretation of their results, particularly relating to the proposed link between sleep and memory consolidation, as stated in the title. Constitutive Polr1F knockdown in ap ɑ′/β′ Kenyon cells had no effect on appetitive long-term memory, while constitutive Regnase-1 knockdown affected both learning and memory. Since the effects of constitutive Regnase-1 knockdown on sleep could be attributed to developmental defects, it is quite plausible that these same developmental defects are what drive the observed learning and memory phenotypes. In this case, an alternative explanation of the authors' findings is that constitutive Regnase-1 knockdown disrupts the entire functioning of ap ɑ′/β′ Kenyon cells, and as a consequence behaviors involving these neurons (i.e. learning, memory and sleep) are disrupted. It will be important to provide further evidence of the function of RNA processing genes in memory in order to substantiate the memory link proposed by the authors.

Reviewer #1 (Public review):

This is a very nice study of Belidae weevils using anchored phylogenomics that presents a new backbone for the family and explores, despite a limited taxon sampling, several evolutionary aspects of the group. I find that the methodology is appropriate, and all analytical steps are well presented. The paper is well written and presents interesting aspects of Belidae systematics and evolution. The major weakness of the study being the very limited taxon sampling that has deep implications for the discussion of ancestral estimations.

Reviewer #2 (Public review):

Summary:

The authors used a combination of anchored hybrid enrichment and Sanger sequencing to construct a phylogenomic data set for the weevil family Belidae. Using evidence from fossils and previous studies they are able to estimate a phylogenetic tree with a range of dates for each node - a timetree. They use this to reconstruct the history of the belids' geographic distributions and associations with their hostplants. They infer that the belids' association with conifers pre-dates the rise of the angiosperms. They offer an interpretation of belid history in terms of the breakup of Gondwanaland, but acknowledge that they cannot rule out alternative interpretations that invoke dispersal.

Strengths:

The strength of any molecular-phylogenetic study hinges on four things: the extent of the sampling of taxa; the extent of the sampling of loci (DNA sequences) per genome; the quality of the analysis; and - most subjectively - the importance and interest of the evolutionary questions the study allows the authors to address. The first two of these, sampling of taxa and loci, impose a tradeoff: with finite resources, do you add more taxa or more loci? The authors follow a reasonable compromise here, obtaining a solid anchored-enrichment phylogenomic data set (423 genes, >97 kpb) for 33 taxa, but also doing additional analyses that included 13 additional taxa from which only Sanger sequencing data from 4 genes was available. The taxon sampling was pretty solid, including all 7 tribes and a majority of genera in the group. The analyses also seemed to be solid - exemplary, even, given the data available.

This leaves the subjective question of how interesting the results are. The very scale of the task that faces systematists in general, and beetle systematists in particular, presents a daunting challenge to the reader's attention: there are so many taxa, and even a sophisticated reader may never have heard of any of them. Thus it's often the case that such studies are ignored by virtually everyone outside a tiny cadre of fellow specialists. The authors of the present study make an unusually strong case for the broader interest and importance of their investigation and of its focal taxon, the belid weevils.

The belids are of special interest because - in a world churning with change and upheaval, geologically and evolutionarily - relatively little seems to have been going on with them, at least with some of them, for the last hundred million years or so. The authors make a good case that the Araucaria-feeding belid lineages found in present-day Australasia and South America have been feeding on Araucaria continuously since the days when it was a dominant tree taxon nearly worldwide, before it was largely replaced by angiosperms. Thus these lineages plausibly offer a modern glimpse of an ancient ecological community.

Comments on current version:

The MS was already in pretty good shape last time around, and the authors have made most of the minor revisions and copy-edits suggested by the reviewers. There may be a few remaining points of disagreement with the reviewers, but these seem to be minor matters of opinion and nothing that ought to delay publication.

Reviewer #1 (Public Review):

Summary:

The study investigated how root cap cell corpse removal affects the ability of microbes to colonize Arabidopsis thaliana plants. The findings demonstrate how programmed cell death and its control in root cap cells affect the establishment of symbiotic relationships between plants and fungi. Key details on molecular mechanisms and transcription factors involved are also given. The study suggests reevaluating microbiome assembly from the root tip, thus challenging traditional ideas about this process. While the work presents a key foundation, more research along the root axis is recommended to gain a better understanding of the spatial and temporal aspects of microbiome recruitment.

Comments on revised version:

The authors have positively addressed all the critical points I raised in the previous review.

Reviewer #2 (Public Review):

Summary:

The authors identify the root cap as an important key region for establishing microbial symbioses with roots. By highlighting for the first time the crucial importance of tight regulation of a specific form of programmed cell death of root cap cells and the clearance of their cell corpses, they start unraveling the molecular mechanisms and its regulation at the root cap (e.g. by identifying an important transcription factor) for the establishment of symbioses with fungi (and potentially also bacterial microbiomes).

Strengths:

It is often believed that the recruitment of plant microbiomes occurs from bulk soil to rhizosphere to endosphere. These authors demonstrate that we have to re-think microbiome assembly as a process starting and regulated at the root tip and proceeding along the root axis.

Comments on revised version:

The authors have addressed all critical points in their revision.

Reviewer #1 (Public review):

In this manuscript, the role of orexin receptors in dopamine transmission is studied. It extends previous findings suggesting an interplay of these two systems in regulating behaviour by first characterising the expression of orexin receptors in the midbrain and then disrupting orexin transmission in dopaminergic neurons by deleting its predominant receptor, OX1R (Ox1R fl/fl, Dat-Cre tg/wt mice). Electrophysiological and calcium imaging data suggest that orexin A acutely and directly stimulates SN and VTA dopaminergic neurons, but does not seem to induce c-Fos expression. Behavioural effects of depleting OX1R from dopaminergic neurons includes enhanced novelty-induced locomotion and exploration, relative to littermate controls (Ox1R fl/fl, Dat-Cre wt/wt). However, no difference between groups is observed in tests that measure reward processing, anxiety, and energy homeostasis. To test whether depletion of OX1R alters overall orexin-triggered activation across the brain, PET imaging is used in OX1R∆DAT knockout and control mice. This analysis reveals that several regions show a higher neuronal activation after orexin injection in OX1R∆DAT mice, but the authors focus their follow up study on the dorsal bed nucleus of the stria terminalis (BNST) and lateral paragigantocellular nucleus (LPGi). Dopaminergic inputs and expression of dopamine receptors type-1 and -2 (DRD1 & DRD2) is assessed and compared to control demonstrating moderate decrease of DRD1 and DRD2 expression in BNST of OX1R∆DAT mice and unaltered expression of DRD2, with absence of DRD1 expression in LPGi of both groups. Overall, this study is valuable for the information it provides on orexin receptor expression and function on behaviour and for the new tools it generated for the specific study of this receptor in dopaminergic circuits.

Strengths:

The use of a transgenic line that lacks OX1R in dopamine-transporter expressing neurons is a strong approach to dissect the direct role of orexin in modulating dopamine signalling in the brain. The battery of behavioural assays to study this line provides a valuable source of information for researchers interested in the role of orexin in animal physiology.

Weaknesses:

This study falls short in providing evidence for an anatomical substrate of the altered behaviour observed in mice lacking orexin receptor subtype 1 in dopaminergic neurons. How orexin transmission in dopaminergic neurons regulates the expression of postsynaptic dopamine receptors (as observed in BNST of OX1R∆DAT mice) is an intriguing question poorly discussed. Whether disruption of orexin activity alters dopamine release in target areas is an important point not addressed.

Reviewer #2 (Public review):

Summary:

This manuscript examines expression of orexin receptors in midbrain - with a focus on dopamine neurons - and uses several fairly sophisticated manipulation techniques to explore the role of this peptide neurotransmitter in reward-related behaviors. Specifically, in situ hybridization is used to show that dopamine neurons predominantly express orexin receptor 1 subtype and then go on to delete this receptor in dopamine transporter-expressing using a transgenic strategy. Ex vivo calcium imaging of midbrain neurons is used to show that, in the absence of this receptor, orexin is no longer able to excite dopamine neurons of the substantia nigra.

The authors proceed to use this same model to study the effect of orexin receptor 1 deletion on a series of behavioral tests, namely, novelty-induced locomotion and exploration, anxiety-related behavior, preference for sweet solutions, cocaine-induced conditioned place preference, and energy metabolism. Of these, the most consistent effects are seen in the tests of novelty-induced locomotion and exploration in which the mice with orexin 1 receptor deletion are observed to show greater levels of exploration, relative to wild-type, when placed in a novel environment, an effect that is augmented after icv administration of orexin.

In the final part of the paper, the authors use PET imaging to compare brain-wide activity patterns in the mutant mice compared to wildtype. They find differences in several areas both under control conditions (i.e., after injection of saline) as well as after injection of orexin. They focus in on changes in dorsal bed nucleus of stria terminalis (dBNST) and the lateral paragigantocellular nucleus (LPGi) and perform analysis of the dopaminergic projections to these areas. They provide anatomical evidence that these regions are innervated by dopamine fibers from midbrain, are activated by orexin in control, but not mutant mice, and that dopamine receptors are present. Thus, they argue these anatomical data support the hypothesis that behavioral effects of orexin receptor 1 deletion in dopamine neurons are due to changes in dopamine signaling in these areas.

Strengths:

Understanding how orexin interacts with the dopamine system is an important question and this paper contains several novel findings along these lines. Specifically:

(1) Distribution of orexin receptor subtypes in VTA and SN is explored thoroughly.<br /> (2) Use of the genetic model that knocks out a specific orexin receptor subtype from dopamine-transporter-expressing neurons is a useful model and helps to narrow down the behavioral significance of this interaction.<br /> (3) PET studies showing how central administration of orexin evokes dopamine release across the brain is intriguing, especially that two key areas are pursued - BNST and LPGi - where the dopamine projection is not as well described/understood.

Weaknesses:

The role of the orexin-dopamine interaction is not explored in enough detail. The manuscript presents several related findings, but the combination of anatomy and manipulation studies do not quite tell a cogent story. Ideally, one would like to see the authors focus on a specific behavioral parameter and show that one of their final target areas (dBNST or LPGi) was responsible or at least correlated with this behavioral readout.

In many places in the Results, insufficient explanation and statistical reporting is provided. Throughout the Results - especially in the section on behavior although not restricted to this part - statements are made without statistical tests presented to back up the claims, e.g., "Compared to controls, Ox1RΔDAT 143 mice did not show significant changes in spontaneous locomotor activity in home cages" (L143) and "In a hole-board test, female Ox1RΔDAT mice showed increased nose pokes into the holes in early (1st and 2nd) sessions compared to control mice" (L151). In other places, ANOVAs are mentioned but full results including main effects and interactions are not described in detail, e.g., in F3-S3, only a single p-value is presented and it is difficult to know if this is the interaction term or a post hoc test (L205). These and all other statements need statistics included in the text as support. Addition of these statistical details was also requested by the editor.

In the presentation of reward processing this is particularly important as no statistical tests are shown to demonstrate that controls show a cocaine-induced preference or a sucrose preference. Here, one option would be to perform one-sample t-tests showing that the data were different to zero (no preference). As it is, the claim that "Both of the control and Ox1RΔDAT groups showed a preference for cocaine injection" is not yet statistically supported.

Reviewer #1 (Public review):

Summary:

The authors investigated the anatomical features of the synaptic boutons in layer 1 of the human temporal neocortex. They examined the size of each synapse, the macular or perforated appearance, the size of the synaptic active zone, the number and volume of the mitochondria, and the number of synaptic and dense core vesicles, also differentiating between the readily releasable, the recycling, and the resting pool of synaptic vesicles. The coverage of the synapse by astrocytic processes was also assessed, and all the above parameters were compared to other layers of the human temporal neocortex. The authors conclude that the subcellular morphology of the layer 1 synapses are suitable for the functions of the neocortical layer, i.e. the synaptic integration within the cortical column. The low glial coverage of the synapses might allow increased glutamate spillover from the synapses, enhancing synpatic crosstalk within this cortical layer.

Strengths:

The strengths of this paper are the abundant and very precious data about the fine structure of the human neocortical layer 1. Quantitative electron microscopy data (especially that derived from the human brain) are very valuable since this is a highly time- and energy-consuming work. The techniques used to obtain the data, as well as the analyses and the statistics performed by the authors are all solid, strengthen this manuscript, and mainly support the conclusions drawn in the discussion.

Weaknesses:

There are several weaknesses in this work. First, the authors should check and review extensively for improvements to the use of English. Second, several additional analyses performed on the existing data could substantially elevate the value of the data presented. Much more information could be gained from the existing data about the functions of the investigated layer, of the cortical column, and about the information processing of the human neocortex. Third, several methodological concerns weaken the conclusions drawn from the results.

Reviewer #2 (Public review):

Summary:

The study of Rollenhagen et al. examines the ultrastructural features of Layer 1 of the human temporal cortex. The tissue was derived from drug-resistant epileptic patients undergoing surgery, and was selected as far as possible from the epilepsy focus, and as such considered to be non-epileptic. The analyses included 4 patients with different ages, sex, medication, and onset of epilepsy. The manuscript is a follow-on study with 3 previous publications from the same authors on different layers of the temporal cortex:

Layer 4 - Yakoubi et al 2019 eLife<br /> Layer 5 - Yakoubi et al 2019 Cerebral Cortex<br /> Layer 6 - Schmuhl-Giesen et al 2022 Cerebral Cortex.

They find, that the L1 synaptic boutons mainly have a single active zone, a very large pool of synaptic vesicles, and are mostly devoid of astrocytic coverage.

Strengths:

The manuscript is well-written and easy to read. The Results section gives a detailed set of figures showing many morphological parameters of synaptic boutons and glial elements. The authors provide comparative data of all the layers examined by them so far in the Discussion. Given that anatomical data in the human brain are still very limited, the current manuscript has substantial relevance.

The work appears to be generally well done, the EM and EM tomography images are of very good quality. The analysis is clear and precise.

Weaknesses:

One of the main findings of this paper is that "low degree of astrocytic coverage of L1 SBs suggests that glutamate spillover and as a consequence synaptic cross-talk may occur at the majority of synaptic complexes in L1". However, the authors only quantified the volume ratio of astrocytes in all 6 layers, which is not necessarily the same as the glial coverage of synapses. In order to strengthen this statement, the authors could provide 3D data (that they have from the aligned serial sections) detailing the percentage of synapses that have glial processes in close proximity to the synaptic cleft, that would prevent spillover.

A specific statement is missing on whether only glutamatergic boutons were analysed in this MS, or GABAergic boutons were also included. There is a statement, that they can be distinguished from glutamatergic ones, but it would be useful to state it clearly in the Abstract, Results, and Methods section what sort of boutons were analysed. Also, what is the percentage of those boutons from the total bouton population in L1?

Synaptic vesicle diameter (that has been established to be ~40nm independent of species) can properly be measured with EM tomography only, as it provides the possibility to find the largest diameter of every given vesicle. Measuring it in 50 nm thick sections results in underestimation (just like here the values are ~25 nm) as the measured diameter will be smaller than the true diameter if the vesicle is not cut in the middle, (which is the least probable scenario). The authors have the EM tomography data set for measuring the vesicle diameter properly.

It is a bit misleading to call vesicle populations at certain arbitrary distances from the presynaptic active zone as readily releasable pool, recycling pool, and resting pool, as these are functional categories, and cannot directly be translated to vesicles at certain distances. Indeed, it is debated whether the morphologically docked vesicles are the ones, that are readily releasable, as further molecular steps, such as proper priming are also a prerequisite for release.

Tissue shrinkage due to aldehyde fixation is a well-documented phenomenon that needs compensation when dealing with density values. The authors cite Korogod et al 2015 - which actually draws attention to the problem comparing aldehyde fixed and non-fixed tissue, still the data is non-compensated in the manuscript. Since all the previous publications from this lab are based on aldehyde fixed non-compensated data, and for this sake, this dataset should be kept as it is for comparative purposes, it would be important to provide a scaling factor applicable to be able to compare these data to other publications.

Reviewer #3 (Public review):

Summary:

Rollenhagen et al. offer a detailed description of layer 1 of the human neocortex. They use electron microscopy to assess the morphological parameters of presynaptic terminals, active zones, vesicle density/distribution, mitochondrial morphology, and astrocytic coverage. The data is collected from tissue from four patients undergoing epilepsy surgery. As the epileptic focus was localized in all patients to the hippocampus, the tissue examined in this manuscript is considered non-epileptic (access) tissue.

Strengths:

The quality of the electron microscopic images is very high, and the data is analyzed carefully. Data from human tissue is always precious and the authors here provide a detailed analysis using adequate approaches, and the data is clearly presented.

Weaknesses:

The study provides only morphological details, these can be useful in the future when combined with functional assessments or computational approaches. The authors emphasize the importance of their findings on astrocytic coverage and suggest important implications for glutamate spillover. However, the percentage of synapses that form tripartite synapses has not been quantified, the authors' functional claims are based solely on volumetric fraction measurements.

The distinction between excitatory and inhibitory synapses is not clear, they should be analyzed separately.

The text connects functional and morphological characteristics in a very direct way. For example, connecting plasticity to any measurement the authors present would be rather difficult without any additional functional experiments. References to various vesicle pools based on the location of the vesicles are also more complex than suggested in the manuscript. The text should better reflect the limitations of the conclusions that can be drawn from the authors' data.

Reviewer #1 (Public review):

Assessment:

This important work advances our understanding of navigation and path integration in mammals by using a clever behavioral paradigm. The paper provides compelling evidence that mice are able to create and use a cognitive map to find "short cuts" in an environment, using only the location of rewards relative to the point of entry to the environment and path integration, and need not rely on visual landmarks.

Summary:

The authors have designed a novel experimental apparatus called the 'Hidden Food Maze (HFM)' and a beautiful suite of behavioral experiments using this apparatus to investigate the interplay between allothetic and idiothetic cues in navigation. The results presented provide a clear demonstration of the central claim of the paper, namely that mice only need a fixed start location and path integration to develop a cognitive map. The experiments and analyses conducted to test the main claim of the paper -- that the animals have formed a cognitive map -- are conclusive. While I think the results are quite interesting and sound, one issue that needs to be addressed is the framing how landmarks are used (or not), as discussed below, although I believe this will be a straight forward issue for the authors to address.

Strengths:

The 90 degree rotationally symmetric design and use of 4 distal landmarks and 4 quadrants with their corresponding rotationally equivalent locations (REL) lends itself to teasing apart the influence of path integration and landmark-based navigation in a clever way. The authors use a really complete set of experiments and associated controls to show that mice can use a start location and path integration to develop a cognitive map and generate shortcut routes to new locations.

Weaknesses:

There were no major weaknesses identified that were not addressed during revisions.

Reviewer #3 (Public review):

Summary:

How is it that animals find learned food locations in their daily life? Do they use landmarks to home in on these learned locations or do they learn a path based on self-motion (turn left, take ten steps forward, turn right, etc.). This study carefully examines this question in a well designed behavioral apparatus. A key finding is that to support the observed behavior in the hidden food arena, mice appear to not use the distal cues that are present in the environment for performing this task. Removal of such cues did not change the learning rate, for example. In a clever analysis of whether the resulting cognitive map based on self-motion cues could allow a mouse to take a shortcut, it was found that indeed they are. The work nicely shows the evolution of the rodent's learning of the task, and the role of active sensing in the targeted reduction of uncertainty of food location proximal to its expected location.

Strengths:

A convincing demonstration that mice can synthesize a cognitive map for the finding of a static reward using body frame-based cues. Showing that uncertainty of final target location is resolved by an active sensing process of probing holes proximal to the expected location. Showing that changing the position of entry into the arena rotates the anticipated location of the reward in a manner consistent with failure to use distal cues.

Weaknesses:

The task is low stakes, and thus the failure to use distal cues at most costs the animal a delay in finding the food; this delay is likely unimportant to the animal, and the pre-training procedure is likely to make it clear to the animal's that distal cues are unreliable even if desirable to use. Thus, it is unclear whether this result would generalize to a situation where the animal may be under some time pressure, urgency due to food (or water) restriction, or due to predatory threat, or situations where distal cues are reliable. In such cases, the use of distal cues to make locating the reward robust to changing start locations may be more likely to be observed.

Reviewer #1 (Public review):

Summary:

This study focuses on characterizing a previously identified gene, encoding the secreted protein Ppe1, that may play a role in rice infection by the blast fungus Magnaporthe oryzae. Magnaporthe oryzae is a hemibiotrophic fungus that infects living host cells before causing disease. Infection begins with the development of a specialized infection cell, the appressorium, on the host leaf surface. The appressorium generates enormous internal turgor that acts on a thin penetration peg at the appressorial base, forcing it through the leaf cuticle. Once through this barrier, the peg elaborates into bulbous invasive hyphae that colonizes the first infected cell before moving to neighboring cells via plasmodesmata. During this initial biotrophic growth stage, invasive hyphae invaginate the host plasma membrane, which surrounds growing hyphae as the extra-invasive hyphae membrane (EIHM). To avoid detection, the fungus secretes apoplastic effectors into the EIHM matrix via the conventional ER-Golgi secretion pathway. The fungus also forms a plant-derived structure called the biotrophic interfacial complex (BIC) that receives cytoplasmic effectors through an unconventional secretion route before they are delivered into the host cell. Together, these secreted effector proteins act to evade or suppress host innate immune responses. Here the authors contribute to our understanding of M. oryzae infection biology by showing how Ppe1, which localizes to both the appressorial penetration peg and to the appressorial-like transpressoria associated with invasive hyphal movements into adjacent cells, maximizes host cell penetration and disease development and is thus a novel contributor to rice blast disease.

Strengths:

A major goal of M. oryzae research is to understand how the fungus causes disease, either by determining the physiological underpinnings of the fungal infection cycle or by identifying effectors and their host targets. Such new knowledge may point the way to novel mitigation strategies. Here, the authors make an interesting discovery that bridges both fungal physiology and effector biology research by showing how a secreted protein Ppe1, initially considered an effector with potential host targets, associates with its own penetration peg (and transpressoria) to facilitate host invasion. In a previous study, the authors had identified a small family of small secreted proteins that may function as effectors. Here they suggest Ppe1 (and, later in the manuscript, Ppe2/3/5) localizes outside the penetration peg when appressoria develops on surfaces that permit penetration, but not on artificial hard surfaces that prevent peg penetration. Deleting the PPE1 gene reduced (although did not abolish) penetration, and a fraction of those that penetrated developed invasive hyphae that were reduced in growth compared to WT. Using fluorescent markers, the authors show that Ppe1 forms a ring underneath appressoria, likely where the peg emerges, which remained after invasive hyphae had developed. The ring structure is smaller than the width of the appressorium and also lies within the septin ring known to form during peg development. This so-called penetration ring also formed at the transpressorial penetration point as invasive hyphae moved to adjacent cells. This structure is novel, and required for optimum penetration during infection. Furthermore, Ppe1, which carries a functional signal peptide, may form on the periphery of the peg, together suggesting it is secreted and associated with the peg to facilitate penetration. Staining with aniline blue also suggests Ppe1 is outside the peg. Together, the strength of the work lies in identifying a novel appressorial penetration ring structure required for full virulence.

Weaknesses:

The main weakness of the paper is that, although Ppe1 is associated with the peg and optimizes penetration, the function of Ppe1 is not known. The work starts off considering Ppe1 a secreted effector, then a facilitator of penetration by associating with the peg, but what role it plays here is only often speculated about. For example, the authors consider at various times that it may have a structural role, a signaling role orchestrating invasive hyphae development, or a tethering role between the peg and the invaginated host plasma membrane (called throughout the host cytoplasmic membrane, a novel term that is not explained). However, more effort should be expended to determine which of these alternative roles is the most likely. Otherwise, as it stands, the paper describes an interesting phenomenon (the appressorial ring) but provides no understanding of its function.

The inability to nail down the function of Ppe1 likely stems from two underlying assumptions with weak support. Firstly, the authors assume that Ppe1 is secreted and associated with the peg to form a penetration ring between the plant cell wall and cytoplasm membrane. However, the authors do not demonstrate it is secreted (for instance by blocking Ppe1 secretion and its association with the peg using brefeldin A). Also, they do not sufficiently show that Ppe1 localizes on the periphery of the peg. This is because confocal microscopy is not powerful enough to see the peg. The association they are seeing (for example in Figure 4) shows localization to the bottom of the appressorium and around the primary hyphae, but the peg cannot be seen. Here, the authors will need to use SEM, perhaps in conjunction with gold labeling of Ppe1, to show it is associating with the peg and, indeed, is external to the peg (rather than internal, as a structural role in peg rigidity might predict). It would also be interesting to repeat the microscopy in Figure 4C but at much earlier time points, just as the peg is penetrating but before invasive hyphae have developed - Where is Ppe1 then? Finally, the authors speculate, but do not show, that Ppe1 anchors penetration pegs on the plant cytoplasm membrane. Doing so may require FM4-64 staining, as used in Figure 2 of Kankanala et al, 2007 (DOI: 10.1105/tpc.106.046300), to show connections between Ppe1 and host membranes. Note that the authors also do not show that the penetration ring is a platform for effector delivery, as speculated in the Discussion.

Secondly, the authors assume Ppe1 is required for host infection due to its association with the peg. However, its role in infection is minor. The majority of appressoria produced by the mutant strain penetrate host cells and elaborate invasive hyphae, and lesion sizes are only marginally reduced compared to WT (in fact, the lesion density of the 70-15 WT strain itself seems reduced compared to what would be expected from this strain). The authors did not analyze the lesions for spores to confirm that the mutant strains were non-pathogenic (non-pathogenic mutants sometimes form small pinprick-like lesions that do not sporulate). Thus, the pathogenicity phenotype of the knockout mutant is weak, which could contribute to the inability to accurately define the molecular and cellular function of Ppe1.

In summary, it is important that the role of Ppe1 in infection be determined.

Reviewer #2 (Public review):

The article focuses on the study of Magnaporthe oryzae, the fungal pathogen responsible for rice blast disease, which poses a significant threat to global food security. The research delves into the infection mechanisms of the pathogen, particularly the role of penetration pegs and the formation of a penetration ring in the invasion process. The study highlights the persistent localization of Ppe1 and its homologs to the penetration ring, suggesting its function as a structural feature that facilitates the transition of penetration pegs into invasive hyphae. The article provides a thorough examination of the infection process of M. oryzae, from the attachment of conidia to the development of appressoria and the formation of invasive hyphae. The discovery of the penetration ring as a structural element that aids in the invasion process is a significant contribution to the understanding of plant-pathogen interactions. The experimental methods are well-documented, allowing for reproducibility and validation of the results.

Reviewer #1 (Public Review):

The paper itself has a reasonable aim, to compare the inputs to the hippocampus from cortical regions across mammals. But for some reason, the conclusions that are reached are very limited. We know for example that the main laboratory rodents investigated, rats and mice, are nocturnal, live in underground tunnels, and have a very wide field of view with no fovea. In contrast, primates have a highly developed cortical system for vision and a fovea, and so have very different capabilities to rodents, as they have an ability to identify people or objects at a distance, and to remember where they have been seen. Despite this major difference in the visual cortical processing in these different mammals, somehow important points are missed in this paper about how the cortical processing is organised in these different mammals, and how this is reflected in the anatomy.

Reviewer #2 (Public Review):

Summary:

The manuscript emphasizes a phylogenetic conservation of the hippocampal region and primary sensory cortical regions in mammalian species. The authors then propose that the evident species-specific differences in behavior and memory-related functions may be due to differences in type and amount of cortico-hippocampal connectivity.

Strengths:

The authors are well-established researchers with a long history of excellent results and publications. The question (co-influence of cortical and hippocampal connections) is potentially interesting.

Weaknesses:

The treatment is very broad and macro scale, ignoring the likelihood that hippocampal-cortical connectivity and behavioral outcomes result from multiple differences at a more micro-scale. The designated "mammalian" sample is also broad. Thus, it can appear incomplete as a sample, and incompletely discussed.

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:

(1) Modeling and implementation of estimation task

The biggest concern I have with the paper is about the experimental implementation and theoretical account of the estimation task. The salient features of the experimental data (Figure 1C) are that the standard deviations of subjects' estimated quantities are hump-shaped in the true stimulus x and that the standard deviation, conditional on the true stimulus x, is increasing in prior width. The authors attribute these features to a Bayesian encoding and decoding model in which the internal representation of the quantity is noisy, and the degree of noise depends on the prior - as in models of efficient coding (Wei and Stocker 2015 Nature Neuro; Bhui and Gershman 2018 Psych Review; Hahn and Wei 2024 Nature Neuro).

The concern I have is about the final "step" in the model, where the authors assume there is an additional layer of motor noise in selecting the response. The authors posit that the subject's selection of the response is drawn from a Gaussian with a mean set to the optimally decoded estimate x*(r), and variance set to a free parameter sigma_0^2. However, the authors also assume that the Gaussian distribution is "truncated to the prior range." This truncation is a nontrivial assumption, and I believe that on its own, it can explain many features of the data.

To see this, assume that there is no noise in the internal representation of x, there is only motor noise. This corresponds to a special case of the authors' model in which υ is set to 0. The model then reduces to a simple account in which responses are drawn from a Gaussian distribution centered at the true value of x, but with asymmetric noise due to the truncation. I simulated such a model with sigma_0=7. The resulting standard deviations of responses for each value of x (based on 1000 draws for each value of x), across the three different priors, reproduce the salient patterns of the standard deviation in Figure 1C: i) within each condition, the standard deviation is hump-shaped and peaks at x=60 and ii) conditional on x, standard deviation increases in prior width. The takeaway is that this simple model with only truncated motor noise - and without any noisy or efficient coding of internal representations - provides an alternative channel through which the prior affects behavior.

Of course, this does not imply that subjects' coding is not described by the efficient encoding and decoding model posited by the authors. However, it does suggest an important alternative mechanism for the authors' theoretical results in the estimation task. Moreover, some of the quantitative conclusions about the differences in behavior with the discrimination task would be greatly affected by the assumption of truncated motor noise.

Turning to the experiment, a basic question is whether such a truncation was actually implemented in the design. That is, was the range of the slider bar set to the range of the prior? (The methods section states that the size on the screen of the slider was proportional to the prior width, but it was unclear whether the bounds of the slider bar changed with the prior). If the slider bar range did depend on the prior, then it becomes difficult to interpret the data. If not, then perhaps one can perform analyses to understand how much the motor noise is responsible for the dependence of the standard deviation on both x and the prior width. Indeed, the authors emphasize that their model is best fit at α=0.48, which would seem to imply that the best fitting value of υ is strictly positive. However, it would be important to clarify whether the estimation procedure allowed for υ=0, or whether this noise parameter was constrained to be positive (i.e., clarify whether the estimation assumed noisy and efficient coding of internal representations).

(2) Differences across tasks

A main takeaway from the paper is that optimal coding depends on the expected reward function in each task. This is the explanation for why the degree of sublinearity between standard deviation and prior width changes across the estimation and discrimination task. But besides the two different reward functions, there are also other differences across the two tasks. For example, the estimation task involves a single array of dots, whereas the discrimination task involves a pair of sequences of Arabic numerals. Related to the discussion above, in the estimation task the response scale is continuous whereas in the discrimination task, responses are binary. Is it possible that these other differences in the task could contribute to the observed different degrees of sublinearity? It is likely beyond the scope of the paper to incorporate these differences into the model, but such differences across the two tasks should be discussed as potential drivers of differences in observed behavior.

If it becomes too difficult to interpret the data from the estimation task due to the slider bar varying with the prior range, then which of the paper's conclusions would still follow when restricting the analysis to the discrimination task?

(3) Placement literature

One closely related experiment to the discrimination task in the current paper can be found in Frydman and Jin (2022 Quarterly Journal of Economics). Those authors also experimentally vary the width of a uniform prior in a discrimination task using Arabic numerals, in order to test principles of efficient coding. Consistent with the current findings, Frydman and Jin find that subjects exhibit greater precision when making judgments about numbers drawn from a narrower distribution. However, what the current manuscript does is it goes beyond Frydman and Jin by modeling and experimentally varying task objectives to understand and test the effects on optimal coding. This contribution should be highlighted and contrasted against the earlier experimental work of Frydman and Jin to better articulate the novelty of the current manuscript.

Reviewer #2 (Public review):

Summary:

This paper provides an ingenious experimental test of an efficient coding objective based on optimization as a task success. The key idea is that different tasks (estimation vs discrimination) will, under the proposed model, lead to a different scaling between the encoding precision and the width of the prior distribution. Empirical evidence in two tasks involving number perception supports this idea.

Strengths:

- The paper provides an elegant test of a prediction made by a certain class of efficient coding models previously investigated theoretically by the authors.

The results in experiments and modeling suggest that competing efficient coding models, optimizing mutual information alone, may be incomplete by missing the role of the task.

Weaknesses:

- The claims would be more strongly validated if data were present at more than two widths in the discrimination experiment.

- A very strong prediction of the model -- which determines encoding entirely from prior and task -- is that Fisher Information is uniform throughout the range, strongly at odds with the traditional assumption of imprecision increasing with the numerosity (Weber/Fechner law). This prediction should be checked against the data collected. It may not be trivial to determine this in the Estimation experiment, but should be feasible in the Discrimination experiment in the Wide condition: Is there really no difference in discriminability at numbers close to 10 vs numbers close to 90? Figure 2 collapses over those, so it's not evident whether such a difference holds or not. I'd have loved to look into this in reviewing, but the authors have not yet made their data publicly available - I strongly encourage them to do so.

Importantly, the inverse u-shaped pattern in Figure 1 is itself compatible with a Weber's-law-based encoding, as shown by simulation in Figure 5d in Hahn&Wei [1]. This suggests a potential competing variant account, in apparent qualitative agreement with the findings reported: the encoding is compatible with Fisher's law, and only a single scalar, the magnitude of sensory noise, is optimized for the task for the loss function (3). As this account would be substantially more in line with traditional accounts of numerosity perception - while still exhibiting task-dependence of encoding as proposed by the authors - it would be worth investigating if it can be ruled out based on the data gathered for this paper.

References:

[1] Hahn & Wei, A unifying theory explains seemingly contradictory biases in perceptual estimation, Nature Neuroscience 2024

Reviewer #3 (Public review):

Summary:

This work demonstrates that people's imprecision in numeric perception varies with the stimulus context and task goal. By measuring imprecision across different widths of uniform prior distributions in estimation and discrimination tasks, the authors find that imprecision changes sublinearly with prior width, challenging previous range normalization models. They further show that these changes align with the efficient encoding model, where decision-makers balance expected rewards and encoding costs optimally.

Strengths:

The experimental design is straightforward, controlling the mean of the number distribution while varying the prior width. By assessing estimation errors and discrimination accuracy, the authors effectively highlight how imprecision adjusts across conditions.

The model's predictions align well with the data, with the exponential terms (1/2 and 3/4) of imprecision changes matching the empirical results impressively.

Weaknesses:

Some details in the model section are unclear. Specifically, I'm puzzled by the Wiener process assumption where r∣x∼N(m(x)T,s^2T). Does this imply that both the representation of number x and the noise are nearly zero at the beginning, increasing as observation time progresses? This seems counterintuitive, and a clearer explanation would be helpful.

The authors explore range normalization models with Gaussian representation, but another common approach is the logarithmic representation (Barretto-García et al., 2023; Khaw et al., 2021). Could the logarithmic representation similarly lead to sublinearity in noise and distribution width?

Additionally, Heng et al. (2020) found that subjects did not alter their encoding strategy across different task goals, which seems inconsistent with the fully adaptive representation proposed here. I didn't find the analysis of participants' temporal dynamics of adaptation. The behavioral results in the manuscript seem to imply that the subjects adopted different coding schemes in a very short period of time. Yet in previous studies of adaptation, experimental results seem to be more supportive of a partial adaptive behavior (Bujold et al., 2021; Heng et al., 2020), which might balance experimental and real-world prior distributions. Analyzing temporal dynamics might provide more insight. Noting that the authors informed subjects about the shape of the prior distribution before the experiment, do the results in this manuscript suggest a top-down rapid modulation of number representation?

Barretto-García, M., De Hollander, G., Grueschow, M., Polanía, R., Woodford, M., & Ruff, C. C. (2023). Individual risk attitudes arise from noise in neurocognitive magnitude representations. Nature Human Behaviour, 7(9), 1551-1567. https://doi.org/10.1038/s41562-023-01643-4

Bujold, P. M., Ferrari-Toniolo, S., & Schultz, W. (2021). Adaptation of utility functions to reward distribution in rhesus monkeys. Cognition, 214, 104764. https://doi.org/10.1016/j.cognition.2021.104764

Heng, J. A., Woodford, M., & Polania, R. (2020). Efficient sampling and noisy decisions. eLife, 9, e54962. https://doi.org/10.7554/eLife.54962

Khaw, M. W., Li, Z., & Woodford, M. (2021). Cognitive Imprecision and Small-Stakes Risk Aversion. The Review of Economic Studies, 88(4), 1979-2013. https://doi.org/10.1093/restud/rdaa044

Reviewer #1 (Public review):

Summary:

In this work, the authors recorded the dynamics of the 5-HT with fiber photometry from CA1 in one hemisphere and LFP from CA1 in the other hemisphere. They observed an ultra-slow oscillation in the 5-HT signal during both wakefulness and NREM sleep. The authors have studied different phases of the ultra-slow oscillation to examine the potential difference in the occurrence of some behavioral state-related physiological phenomena (hippocampal ripples, EMG, and inter-area coherence).

Strengths:

The relation between the falling/rising phase of the ultra-slow oscillation and the ripples is sufficiently shown. There are some minor concerns about the observed relations that should be addressed with some further analysis.

Systematic observations have started to establish a strong relation between the dynamics of neural activity across the brain and measures of behavioral arousal. Such relations span a wide range of temporal scales that are heavily inter-related. Ultra-slow time scales are specifically understudied due to technical limitations and neuromodulatory systems are the strongest mechanistic candidates for controlling/modulating the neural dynamics at these time scales. The hypothesis of the relation between a specific time scale and one certain neuromodulator (5-HT in this manuscript) could have a significant impact on the understanding of the hierarchy in the temporal scales of neural activity.

Weaknesses:

One major caveat of the study is that different neuromodulators are strongly correlated across all time scales and related to this, the authors need to discuss this point further and provide more evidence from the literature (if any) that suggests similar ultra-slow oscillations are weaker or lack from similar signals recorded for other neuromodulators such as Ach and NA.

A major question that has been left out from the study and discussion is how the same level of serotonin before and after the peak could be differentially related to the opposite observed phenomenon. What are the possible parallel mechanisms for distinguishing between the rising and falling phases? Any neurophysiological evidence for sensing the direction of change in serotonin concentration (or any other neuromodulator), and is there any physiological functionality for such mechanisms?

Reviewer #2 (Public review):

Summary:

In their study, Cooper et al. investigated the spontaneous fluctuations in extracellular 5-HT release in the CA1 region of the hippocampus using GRAB5-HT3.0. Their findings revealed the presence of ultra-low frequency (less than 0.05 Hz) oscillations in 5-HT levels during both NREM sleep and wakefulness. The phase of these 5-HT oscillations was found to be related to the timing of hippocampal ripples, microarousals, electromyogram (EMG) activity, and hippocampal-cortical coherence. In particular, ripples were observed to occur with greater frequency during the descending phase of 5-HT oscillations, and stronger ripples were noted to occur in proximity to the 5-HT peak during NREM. Microarousal and EMG peaks occurred with greater frequency during the ascending phase of 5-HT oscillations. Additionally, the strongest coherence between the hippocampus and cortex was observed during the ascending phase of 5-HT oscillations. These patterns were observed in both NREM sleep and the awake state, with a greater prevalence in NREM. The authors posit that 5-HT oscillations may temporally segregate internal processing (e.g., memory consolidation) and responsiveness to external stimuli in the brain.

Strengths:

The findings of this research are novel and intriguing. Slow brain oscillations lasting tens of seconds have been suggested to exist, but to my knowledge they have never been analyzed in such a clear way. Furthermore, although it is likely that ultra-slow neuromodulator oscillations exist, this is the first report of such oscillations, and the greatest strength of this study is that it has clarified this phenomenon both statistically and phenomenologically.

Weaknesses:

As with any paper, this one has some limitations. While there is no particular need to pursue them, I will describe ten of them below, including future directions:

(1) Contralateral recordings: 5-HT levels and electrophysiological recordings were obtained from opposite hemispheres due to technical limitations. Ipsilateral simultaneous recordings may show more direct relationships.

(2) Sample size: The number of mice used in the experiments is relatively small (n=6). Validation with a larger sample size would be desirable.

(3) Lack of causality: The observed associations show correlations, not direct causal relationships, between 5-HT oscillations and neural activity patterns.

(4) Limited behavioral states: The study focuses primarily on sleep and quiet wakefulness. Investigation of 5-HT oscillations during a wider range of behavioral states (e.g., exploratory behavior, learning tasks) may provide a more complete understanding.

(5) Generalizability to other brain regions: The study focuses on the CA1 region of the hippocampus. It's unclear whether similar 5-HT oscillation patterns exist in other brain regions.

(6) Long-term effects not assessed: Long-term effects of ultra-low 5-HT oscillations (e.g., on memory consolidation or learning) were not assessed.

(7) Possible species differences: It's uncertain whether the findings in mice apply to other mammals, including humans.

(8) Technical limitations: The temporal resolution and sensitivity of the GRAB5-HT3.0 sensor may not capture faster 5-HT dynamics.

(9) Interactions with other neuromodulators: The study does not explore interactions with other neuromodulators (e.g., norepinephrine, acetylcholine) or their potential ultraslow oscillations.

(10) Limited exploration of functional significance: While the study suggests a potential role for 5-HT oscillations in memory consolidation and arousal, direct tests of these functional implications are not included.

Reviewer #3 (Public review):

Summary:

The activity of serotonin (5-HT) releasing neurons as well as 5-HT levels in brain structures targeted by serotonergic axons are known to fluctuate substantially across the animal's sleep/wake cycle, with high 5-HT levels during wakefulness (WAKE), intermediate levels during non-REM sleep (NREM) and very low levels during REM sleep. Recent studies have shown that during NREM, the activity of 5-HT neurons in raphe nuclei oscillates at very low frequencies (0.01 - 0.05 Hz) and this ultraslow oscillation is negatively coupled to broadband EEG power. However, how exactly this 5-HT oscillation affects neural activity in downstream structures is unclear.

The present study addresses this gap by replicating the observation of the ultraslow oscillation in the 5-HT system, and further observing that hippocampal sharp wave-ripples (SWRs), biomarkers of offline memory processing, occur preferentially in barrages on the falling phase of the 5-HT oscillation during both wakefulness and NREM sleep. In contrast, the raising phase of the 5-HT oscillation is associated with microarousals during NREM and increased muscular activity during WAKE. Finally, the raising 5-HT phase was also found to be associated with increased synchrony between the hippocampus and neocortex. Overall, the study constitutes a valuable contribution to the field by reporting a close association between raising 5-HT and arousal, as well as between falling 5-HT and offline memory processes.

Strengths:

The study makes compelling use of the state-of-the-art methodology to address its aims: the genetically encoded 5-HT sensor used in the study is ideal for capturing the ultraslow 5-HT dynamics and the novel detection method for SWRs outperforms current state-of-the-art algorithms and will be useful to many scientists in the field. Explicit validation of both of these methods is a particular strength of this study.

The analytical methods used in the article are appropriate and are convincingly applied, the use of a general linear mixed model for statistical analysis is a particularly welcome choice as it guards against pseudoreplication while preserving statistical power.

Overall, the manuscript makes a strong case for distinct sub-states across WAKE and NREM, associated with different phases of the 5-HT oscillation.

Weaknesses:

All of the evidence presented in the study is correlational. While the study mostly avoids claims of causality, it would still benefit from establishing whether the 5-HT oscillation has a direct role in the modulation of SWR rate via e.g. optogenetic activation/inactivation of 5-HT axons. As it stands, the possibility that 5-HT levels and SWRs are modulated by the same upstream mechanism cannot be excluded.

Reviewer #1 (Public review):

Summary:

In the manuscript by Hoisington et al., the authors utilized a novel conditional neuronal prosap2-interacting protein 1 (Prosapip1) knockout mouse to delineate the effects of both neuronal and dorsal hippocampal (dHP)-specific knockout of Prosapip1 impacts biochemical and electrophysiological neuroadaptations within the dHP that may mediate behaviors associated with this brain region.

Strengths:

(1) Methodological Strengths

a. The generation and use of a conditional neuronal knockout of Prosapip1 is a strength. These mice will be useful for anyone interested in studying or comparing and contrasting the effects of loss of Prosapip1 in different brain regions or in non-neuronal tissues.

b. The use of biochemical, electrophysiological, and behavioral approaches are a strength. By providing data across multiple domains, a picture begins to emerge about the mechanistic role for Prosapip1. While questions still remain, the use of the 3 domains is a strength.

c. The use of both global, constitutive neuronal loss of Prosapip1 and postnatal dHP-specific knockout of Prosapip1 help support and validate the behavioral conclusions.

(2) Strengths of the results

a. It is interesting that loss of Prosapip1 leads to specific alterations in the expression of GluN2B and PSD95 but not GluA1 or GluN2A in a post-homogenization fraction that the author's term a "synaptic" fraction. Therefore, these results suggest protein-specific modulation of glutamatergic receptors within a "synaptic" fraction.

b. The electrophysiological data demonstrate an NMDAR-dependent alteration in measures of hippocampal synaptic plasticity, including long-term potentiation (LTP) and NMDAR input/output. These data correspond with the biochemical data demonstrating a biochemical effect on GluN2B localization. Therefore, the conclusion that loss of Prosapip1 influences NMDAR function is well supported.

c. The behavioral data suggest deficits in memory in particular novel object recognition and spatial memory, in the Prosapip1 knockout mice. These data are strongly bolstered by both the pan-neuronal knockout and the dHP Cre transduction.

Weaknesses:

(1) Methodological Weaknesses

a. The synapsin-Cre mice may more broadly express Cre-recombinase than just in neuronal tissues. Specifically, according to Jackson Laboratories, there is a concern with these mice expressing Cre-recombinase germline. As the human protein atlas suggests that Prosapip1 protein is expressed extraneuronally, validation of neuron or at least brain-specific knockout would be helpful in interpreting the data. Having said that, the data demonstrating that the brain region-specific knockout has similar behavioral impacts helps alleviate this concern somewhat; however, there are no biochemical or electrophysiological readouts from these animals, and therefore an alternative mechanism in this adult knockout cannot be excluded.

b. The use of the word synaptic and the crude fractionation make some of the data difficult to interpret/contextualize. It is unclear how a single centrifugation that eliminates the staining of a nuclear protein can be considered a "synaptic" fraction. This is highlighted by the presence of GAPDH in this fraction which is a cytosolically-enriched protein. While GAPDH may be associated with some membranes it is not a synaptic protein. There is no quantification of GAPDH against total protein to validate that it is not enriched in this fraction over control. Moreover, it should not be used as a loading control in the synaptic fraction. There are multiple different ways to enrich membranes, extrasynaptic fractions, and PSDs and a better discussion on the caveats of the biochemical fractionation is a minimum to help contextualize the changes in PSD95 and GluN2B.

c. Also, the word synaptosomal on page 7 is not correct. One issue is this is more than synaptosomes and another issue is synaptosomes are exclusively presynaptic terminals. The correct term to use is synaptoneurosome, which includes both pre and postsynaptic components. Moreover, as stated above, this may contain these components but is most likely not a pure or even enriched fraction.

d. The age at which the mice underwent injection of the Cre virus was not mentioned.

(2) Weaknesses of results

a. There were no measures of GluN1 or GluA2 in the biochemical assays. As GluN1 is the obligate subunit, how it is impacted by the loss of Prosapip1 may help contextualize the fact that GluN2B, but not GluN2A, is altered. Moreover, as GluA2 has different calcium permeance, alterations in it may be informative.

b. While there was no difference in GluA1 expression in the "synaptic" fraction, it does not mean that AMPAR function is not impacted by the loss of Prosapip1. This is particularly important as Prosapip1 may interact with kinases or phosphatases or their targeting proteins. Therefore, measuring AMPAR function electrophysiologically or synaptic protein phosphorylation would be informative.

c. There is a lack of mechanistic data on what specifically and how GluN2B and PSD95 expression is altered. This is due to some of the challenges with interpreting the biochemical fractionation and a lack of results regarding changes in protein posttranslational modifications.

d. The loss of social novelty measures in both the global and dHP-specific Prosapip1 knockout mice were not very robust. As they were consistently lost in both approaches and as there were other consistent memory deficits, this does not impact the conclusions, but may be important to temper discussion to match these smaller deficits within this domain.

e. Alterations in presynaptic paired-pulse ratio measures are intriguing and may point to a role for Prosapip1 in synapse development, as discussed in the manuscript. It would be interesting to delineate if these PPR changes also occur in the adult knockout to help detail the specific Prosapip1-induced neuroadaptations that link to the alterations in novelty-induced behaviors.

Reviewer #2 (Public review):

Summary:

The authors provide valuable findings characterizing a Prosapip1 conditional knockout mouse and the effects of knockout on hippocampal excitatory transmission, NMDAR transmission, and several learning behaviors. Furthermore, the authors selectively and conditionally knockout Prosapip1 in the dorsal hippocampus and show that it is required for the same spatial learning and memory assessed in the conditional knockout mice. The study uncovers how Prosapip1 is involved PSD organization and is a functional and critical player in dorsal Hippocampal LTP via its interaction with GluN2B subunits.

Strengths:

The study is well-controlled and detailed, and the data in the paper match the conclusions.

Weaknesses:

Some statistical information is lacking.

Reviewer #1 (Public review):

The authors investigate the function and neural circuitry of reentrant signals in the visual cortex. Recurrent signaling is thought to be necessary to common types of perceptual experience that are defined by long-range relationships or prior expectations. Contour illusions - where perceptual objects are implied by stimuli characteristics - are a good example of this. The perception of these illusions is thought to emerge as recurrent signals from higher cortical areas feedback onto the early visual cortex, to tell the early visual cortex that it should be seeing object contours where none are actually present.

The authors test the involvement of reentrant cortical activity in this kind of perception using a drug challenge. Reentrance in the visual cortex is thought to rely on NMDAR-mediated glutamate signalling. The authors accordingly employ an NMDA antagonist to stop this mechanism, looking for the effect of this manipulation on visually evoked activity recorded in EEG.

The motivating hypothesis for the paper is that NMDA antagonism should stop recurrent activity and that this should degrade perceptual activity supporting the perception of a contour illusion, but not other types of visual experience. Results in fact show the opposite. Rather than degrading cortical activity evoked by the illusion, memantine makes it more likely that machine learning classification of EEG will correctly infer the presence of the illusion.

On the face of it, this is confusing, and the paper currently does not entirely resolve this confusion. But there are relatively easy ways to improve this. The authors would be well served by entertaining more possible outcomes in the introduction - there's good reason to expect a positive effect of memantine on perceptual brain activity, and I provide details on this below. The authors also need to further emphasize that the directional expectations that motivated E1 were, of course, adapted after the results from this experiment emerged. The authors presumably at least entertained the notion that E2 would reproduce E1 - meaning that E2 was motivated by a priori expectations that were ultimately met by the data.

I broadly find the paper interesting, graceful, and creative. The hypotheses are clear and compelling, the techniques for both manipulation of brain state and observation of that impact are cutting edge and well suited, and the paper draws clear and convincing conclusions that are made necessary by the results. The work sits at the very interesting crux of systems neuroscience, neuroimaging, and pharmacology. I believe the paper can be improved in revision, but my suggestions are largely concerning presentation and nuance of interpretation.

(1) I miss some treatment of the lack of behavioural correlate. What does it mean that metamine benefits EEG classification accuracy without improving performance? One possibility here is that there is an improvement in response latency, rather than perceptual sensitivity. Is there any hint of that in the RT results? In some sort of combined measure of RT and accuracy?

(2) An explanation is missing, about why memantine impacts the decoding of illusion but not collinearity. At a systems level, how would this work? How would NMDAR antagonism selectively impact long-range connectivity, but not lateral connectivity? Is this supported by our understanding of laminar connectivity and neurochemistry in the visual cortex?

(3) The motivating idea for the paper is that the NMDAR antagonist might disrupt the modulation of the AMPA-mediated glu signal. This is in line with the motivating logic for Self et al., 2012, where NMDAR and AMPAR efficacy in macacque V1 was manipulated via microinfusion. But this logic seems to conflict with a broader understanding of NMDA antagonism. NMDA antagonism appears to generally have the net effect of increasing glu (and ACh) in the cortex through a selective effect on inhibitory GABA-ergic cells (eg. Olney, Newcomer, & Farber, 1999). Memantine, in particular, has a specific impact on extrasynaptic NMDARs (that is in contrast to ketamine; Milnerwood et al, 2010, Neuron), and this type of receptor is prominent in GABA cells (eg. Yao et al., 2022, JoN). The effect of NMDA antagonists on GABAergic cells generally appears to be much stronger than the effect on glutamergic cells (at least in the hippocampus; eg. Grunze et al., 1996).

This all means that it's reasonable to expect that memantine might have a benefit to visually evoked activity. This idea is raised in the GD of the paper, based on a separate literature from that I mentioned above. But all of this could be better spelled out earlier in the paper, so that the result observed in the paper can be interpreted by the reader in this broader context.

To my mind, the challenging task is for the authors to explain why memantine causes an increase in EEG decoding, where microinfusion of an NMDA antagonist into V1 reduced the neural signal Self et al., 2012. This might be as simple as the change in drug... memantine's specific efficacy on extrasynaptic NMDA receptors might not be shared with whatever NMDA antagonist was used in Self et al. 2012. Ketamine and memantine are already known to differ in this way.

(4) The paper's proposal is that the effect of memantine is mediated by an impact on the efficacy of reentrant signaling in visual cortex. But perhaps the best-known impact of NMDAR manipulation is on LTP, in the hippocampus particularly but also broadly. Perception and identification of the kanisza illusion may be sensitive to learning (eg. Maertens & Pollmann, 2005; Gellatly, 1982; Rubin, Nakayama, Shapley, 1997); what argues against an account of the results from an effect on perceptual learning? Generally, the paper proposes a very specific mechanism through which the drug influences perception. This is motivated by results from Self et al 2012 where an NMDA antagonist was infused into V1. But oral memantine will, of course, have a whole-brain effect, and some of these effects are well characterized and - on the surface - appear as potential sources of change in illusion perception. The paper needs some treatment of the known ancillary effects of diffuse NMDAR antagonism to convince the reader that the account provided is better than the other possibilities.

(5) The cross-decoding approach to data analysis concerns me a little. The approach adopted here is to train models on a localizer task, in this case, a task where participants matched a kanisza figure to a target template (E1) or discriminated one of the three relevant stimuli features (E2). The resulting model was subsequently employed to classify the stimuli seen during separate tasks - an AB task in E1, and a feature discrimination task in E2. This scheme makes the localizer task very important. If models built from this task have any bias, this will taint classifier accuracy in the analysis of experimental data. My concern is that the emergence of the kanisza illusion in the localizer task was probably quite salient, respective to changes in stimuli rotation or collinearity. If the model was better at detecting the illusion to begin with, the data pattern - where drug manipulation impacts classification in this condition but not other conditions - may simply reflect model insensitivity to non-illusion features.

I am also vaguely worried by manipulations implemented in the main task that do not emerge in the localizer - the use of RSVP in E1 and manipulation of the base rate and staircasing in E2. This all starts to introduce the possibility that localizer and experimental data just don't correspond, that this generates low classification accuracy in the experimental results and ineffective classification in some conditions (ie. when stimuli are masked; would collinearity decoding in the unmasked condition potentially differ if classification accuracy were not at a floor? See Figure 3c upper, Figure 5c lower).

What is the motivation for the use of localizer validation at all? The same hypotheses can be tested using within-experiment cross-validation, rather than validation from a model built on localizer data. The argument may be that this kind of modelling will necessarily employ a smaller dataset, but, while true, this effect can be minimized at the expense of computational cost - many-fold cross-validation will mean that the vast majority of data contributes to model building in each instance.

It would be compelling if results were to reproduce when classification was validated in this kind of way. This kind of analysis would fit very well into the supplementary material.

Reviewer #2 (Public review):

Summary:

In this paper, the authors investigate the role of NMDA-receptors in recurrent processing. In doing so, the authors present data from two studies, where they attempt to decode different stimulus features, namely contrast, collinearity, and illusory contours. The latter of which the authors claim relies uniquely on recurrent processing. Therefore, to test whether NMDA receptors are particularly involved in recurrent processing they administer a NMDA-antagonist to see whether the decoding of illusory contours is specifically perturbed, and leaves the decoding of other features intact. They further aim to disentangle the role of NMDA-receptors by manipulating visibility and task relevance of the decoded features

In the first experiment, the authors decode two targets, the first was always presented clearly, the second's visibility was manipulated by presenting it after a short lag rather than a long lag (inducing attentional blink), as well as masking the target on half the trials. First, they find for target 1 clear evidence for the NMDA-receptor increasing (rather than decreasing) decoding performance of illusory contours. They move on to analyse target 2 to explore the manipulations of lag and masking. Here they find that masking reduced decoding of all three stimulus features, but only the lag reduced decoding of illusory contours. Importantly, the NMDA-antagonist improved decoding only in the unmasked, long lag condition, in the cluster analyses. However, the interaction with the lag condition was not significant, and the effect on decoding was primarily present in the later decoding time window, and not significant when exploring the peak of the decoding time window.

The second experiment was highly similar, but got rid of the lag manipulation, and replaced it with a manipulation of task relevance. Notably, masking did not abolish the decoding of illusory contours completely, in contrast to the first experiment. More importantly, they find that the NMDA-receptor now clearly increases decoding of illusory contours, particularly when the illusory contours are not masked. No effect of task relevance is found.

Taken together the authors state that evidence is found for NMDA-receptors role in recurrent processing.

Strengths:

This is an interesting study using state-of-the-art methods in combination with drug manipulation to study recurrent processing. Their analysis methods are state-of-the-art, and the question that they are trying to address is topical and interesting to a wide research audience, encompassing both researchers interested in visual perception and consciousness, as well as those interested in perturbed vision as found in psychiatric disorders.

Weaknesses:

The experimental design is somewhat complicated, which can make it difficult to match the authors' claims to the actual evidence that is provided. I have some reservations about the paper which are born out of a few issues.<br /> (1) The title, abstract, and introduction hide their counterintuitive finding of increased decoding, presumably as it was unexpected.<br /> (2) Their analysis choices are sometimes unclear, making it difficult to assess whether the analyses are sensible.<br /> (3) The appropriate tests for the interactions that the authors claim they found are often lacking.

To start off, I think the reader is being a bit tricked when reading the paper. Perhaps my priors are too strong, but I assumed, just like the authors, that NMDA-receptors would disrupt recurrent processing, in line with previous work. However, due to the continuous use of the ambiguous word 'affected' rather than the more clear increased or perturbed recurrent processing, the reader is left guessing what is actually found. That's until they read the results and discussion finding that decoding is actually improved. This seems like a really big deal, and I strongly urge the authors to reword their title, abstract, and introduction to make clear they hypothesized a disruption in decoding in the illusion condition, but found the opposite, namely an increase in decoding. I want to encourage the authors that this is still a fascinating finding.

Apologies if I have missed it, but it is not clear to me whether participants were given the drug or placebo during the localiser task. If they are given the drug this makes me question the logic of their analysis approach. How can one study the presence of a process, if their very means of detecting that process (the localiser) was disrupted in the first place? If participants were not given a drug during the localiser task, please make that clear. I'll proceed with the rest of my comments assuming the latter is the case. But if the former, please note that I am not sure how to interpret their findings in this paper.

The main purpose of the paper is to study recurrent processing. The extent to which this study achieves this aim is completely dependent to what extent we can interpret decoding of illusory contours as uniquely capturing recurrent processing. While I am sure illusory contours rely on recurrent processing, it does not follow that decoding of illusory contours capture recurrent processing alone. Indeed, if the drug selectively manipulates recurrent processing, it's not obvious to me why the authors find the interaction with masking in experiment 2. Recurrent processing seems to still be happening in the masked condition, but is not affected by the NMDA-receptor here, so where does that leave us in interpreting the role of NMDA-receptors in recurrent processing? If the authors can not strengthen the claim that the effects are completely driven by affecting recurrent processing, I suggest that the paper will shift its focus to making claims about the encoding of illusory contours, rather than making primary claims about recurrent processing.

An additional claim is being made with regards to the effects of the drug manipulation. The authors state that this effect is only present when the stimulus is 1) consciously accessed, and 2) attended. The evidence for claim 1 is not supported by experiment 1, as the masking manipulation did not interact in the cluster-analyses, and the analyses focussing on the peak of the timing window do not show a significant effect either. There is evidence for this claim coming from experiment 2 as masking interacts with the drug condition. Evidence for the second claim (about task relevance) is not presented, as there is no interaction with the task condition. A classical error seems to be made here, where interactions are not properly tested. Instead, the presence of a significant effect in one condition but not the other is taken as sufficient evidence for an interaction, which is not appropriate. I therefore urge the authors to dampen the claim about the importance of attending to the decoded features. Alternatively, I suggest the authors run their interactions of interest on the time-courses and conduct the appropriate cluster-based analyses.

How were the length of the peak-timing windows established in Figure 1E? My understanding is that this forms the training-time window for the further decoding analyses, so it is important to justify why they have different lengths, and how they are determined. The same goes for the peak AUC time windows for the interaction analyses. A number of claims in the paper rely on the interactions found in these post-hoc analyses, so the 223- to 323 time window needs justification.

Reviewer #3 (Public review):

Summary:

In this study, Stein and colleagues use a clever masking/attentional blink paradigm using Kanisza stimuli, coupled with EEG decoding and the NMDA antagonist memantine, to isolate putative neural markers of feedforward, lateral, and feedback processing.

In two elegant experiments, they show that memantine selective influences EEG decoding of only illusory Kanisza surfaces (but not contour continuation or raw contrast), only when unmasked, only when attention is available (not when "blinked"), and only when task-relevant.

This neatly implicates NMDA receptors in the feedback mechanisms that are believed to be involved in inferring illusory Kanisza surfaces, and builds a difficult bridge between the large body of human perceptual experiments and pharmacological and neurophysiological work in animals.

Strengths:

Three key strengths of the paper are<br /> (1) The elegant and thorough experimental design, which includes internal replication of some key findings.<br /> (2) The clear pattern of results across the full set of experiments.<br /> (3) The clear writing and presentation of results.

The paper effectively reports a 4-way interaction, with memantine only influencing decoding of surfaces (1) that are unmasked (2), with attention available (3) and task-relevant (4). Nevertheless, the results are very clear, with a clear separation between null effects on other conditions and quite a strong (and thus highly selective) effect on this one intersection of conditions. This makes the pattern of findings very convincing.

Weaknesses:

Overall this is an impressive and important paper. However, to my mind, there are two minor weaknesses.

First, despite its clear pattern of neural effects, there is no corresponding perceptual effect. Although the manipulation fits neatly within the conceptual framework, and there are many reasons for not finding such an effect (floor and ceiling effects, narrow perceptual tasks, etc), this does leave open the possibility that the observation is entirely epiphenomenal, and that the mechanisms being recorded here are not actually causally involved in perception per se.

Second, although it is clear that there is an effect on decoding in this particular condition, what that means is not entirely clear - particularly since performance improves, rather than decreases. It should be noted here that improvements in decoding performance do not necessarily need to map onto functional improvements, and we should all be careful to remain agnostic about what is driving classifier performance. Here too, the effect of memantine on decoding might be epiphenomenal - unrelated to the information carried in the neural population, but somehow changing the balance of how that is electrically aggregated on the surface of the skull. *Something* is changing, but that might be a neurochemical or electrical side-effect unrelated to actual processing (particularly since no corresponding behavioural impact is observed.)

Reviewer #1 (Public review):

Summary:

This study investigated the role of transcriptional and translational controls of gene expression in dorsal root ganglia and lumbar spinal cord in neuropathic pain in mice. Using ribosome profiling (Ribo-seq) and translating ribosome affinity purification (TRAP), they show changes in transcriptomic and translational gene expression at the peripheral and central levels rapidly after nerve injury. While translational changes in gene expression remained elevated for more than two months in both DRGs and the spinal cord, transcriptomic regulation was absent in the spinal cord long after the onset of neuropathy. Disrupting mRNA translation in dorsal horn neurons using antisense oligonucleotides reduced mechanical withdrawal threshold and facial expression of pain. Using fluorescent noncanonical amino acid tagging (FUNCAT), the authors further show that de novo protein expression primarily occurs in inhibitory neurons in the superficial dorsal horn after nerve injury. Accordingly, a selective increase in translational control of gene expression in spinal inhibitory neurons, or a subset of mainly inhibitory neurons expressing parvalbumin (PV), using transgenic mice, led to a decrease in the excitability of PV neurons and mechanical allodynia. In contrast, decreasing the translational control of spinal PV neurons prevented the alteration of the electrophysiological properties of the PV cells induced by nerve injury.

Strengths:

This is a well-written article that uncovers a previously unappreciated role of gene expression control in PV neurons, which seems to play an important part in the loss of inhibitory control of spinal circuits typically seen after peripheral nerve injury. The conclusions are generally well supported by the data.

Weaknesses:

The study would benefit from further clarifications in the methods section and a deeper analysis of gene expression changes in mRNA expression and ribosomal footprint observed after nerve injury.

Antisense oligonucleotides used to reduce translation by disrupting eIF4E expression were administered i.c.v. It is unknown if the authors controlled for locomotor deficits, which might add confounds in the interpretation of behavioral results. A more local route should have been preferable to avoid targeting brain regions, which could potentially affect behavior.

Only female mice were used for Ribo-Seq, TRAP, FUNCAT, and electrophysiology, but both sexes were used for behavior experiments.

The conditional KO of 4E-BP1 using transgenic animals should be total in the targeted cells. However, only a partial reduction is reported in Figure S2 in GAD2, PV, Vglut2, or Tac1 cells. Again, proper methods for quantification of fluorescence in these experiments are lacking.

The elegant knockdown of eIF4E using AAV-mediated shRNAmir shows a recovery of the electrophysiological intrinsic properties of PV neurons after injury. It is unclear if such manipulation would be sufficient to reverse mechanical allodynia in vivo.

Reviewer #2 (Public review):

Summary:

I reviewed the manuscript titled "Translational Control in the Spinal Cord Regulates Gene Expression and Pain Hypersensitivity in the Chronic Phase of Neuropathic Pain." This manuscript compares transcription and translation in the spinal cord during the acute and chronic phases of neuropathic pain induced by surgical nerve injury. The authors chose to focus their investigation on translation in the chronic phase due to its greater impact on gene expression in the spinal cord compared to transcription.

(1) The study is significant because the molecular mechanisms underlying chronic pain remain elusive. The role of translational regulation in the spinal cord has not been investigated in neuroplasticity and chronic pain mouse models. The manuscript is innovative and technically robust. The authors employed several cutting-edge techniques such as Rio-seq, TRAP-seq, slice electrophysiology, and viral approaches. Despite the technical complexity, the manuscript is well-written. The authors demonstrated that inhibition of eIF4E alleviates pain hypersensitivity, that de novo protein synthesis is more pronounced in inhibitory interneurons, and that manipulating mTOR-eIF4E pathways alters mechanical sensitivity and neuroplasticity.

(2) Strengths: innovation (conceptual and technical levels), data support the conclusions.

Weakness:

Confusion about the sex of the animals. It is unclear whether eIF4E ASO affects translation and which cells. It is not determined that modulating translation in PV+ neurons impacts neuropathic pain behaviors.

Reviewer #3 (Public review):

Summary:

This study provides evidence for translational changes in inhibitory spinal dorsal horn neurons following chronic nerve injury. Gene expression changes have been widely studied in the context of pain induction and provided key insights into the adaptation of the nervous system in the early phases of chronic pain. Whereas this is interesting biologically, most patients will arrive in the clinic beyond the acute phase of their injury, thus limiting the translational relevance of these studies. Recent studies have extended this work to highlight the difference between acute and chronic pain states, potentially explaining the cascading factors leading to chronic pain, and hopefully how to prevent this in vulnerable populations. The present study suggests that translational changes within spinal inhibitory populations could underlie long-term chronic pain, leading to decreased inhibition and heightened pain thresholds.

Strengths:

The approaches used and the broad outcomes of the manuscript are interesting and could be an exciting development in the field. The authors are using approaches more common in molecular biology and extending these into neuroscientific research, getting into the detail of how pathology could impact gene expression differentially across the course of an injury. This could open up new areas of research to selectively target not only defined populations but additionally help alleviate pain symptoms once an injury has already reached the maintenance phase. There is an opportunity to delve into what must be a very large data set and learn more about what genes are differentially translated and how this could affect circuit function.

Weaknesses:

Whereas the authors approach a key question in pain chronicity, the manuscript falls a little short of providing any conclusive data.

The manuscript was in some areas very difficult to follow. Terminology was not always consistent or clear, and the flow of the manuscript could use some attention to highlight key areas. Whereas the overall message is clear in the summary, this would not necessarily be the case when reading the manuscript alone.

The study claims to show that translational control mechanisms in the spinal cord play a role in mediating neuropathic pain hypersensitivity, but the studies presented do not fully support this statement. The authors instead provide some correlation between translation and behavioural reflex excitability (namely vfh and Hargreaves).

It is difficult to fully interpret the work, as there are a number of inconsistencies, namely the range of timings pre- and post-injury, lack of controls for manipulations, the use of shmiRNA versus lineage deletions, and lack of detailed somatosensory testing. It is not completely clear how this work could be translatable as is, without a deeper understanding of how translational control affects circuit function and whether all of this is necessarily bad for the system, or whether this is a positive homeostatic adaptation to the hyperexcitability of the circuit following injury.

A large portion of the work is focussed on showing an inhibitory-selective change in translation following chronic nerve injury. The evidence for this is however lacking. Statistics to show that translational effects are restricted to inhibitory subpopulations are inadequate. The author's choice of transgenic lines is not clear and seems to rely on availability rather than hypothesis.

Reviewer #1 (Public Review):

In the article by Dearlove et al., the authors present evidence in strong support of nucleotide ubiquitylation by DTX3L, suggesting it is a promiscuous E3 ligase with capacity to ubiquitylate ADP ribose and nucleotides. The authors include data to identify the likely site of attachment and the requirements for nucleotide modification.

While this discovery potentially reveals a whole new mechanism by which nucleotide function can be regulated in cells, there are some weaknesses that should be considered. Is there any evidence of nucleotide ubiquitylation occurring cells? It seems possible, but evidence in support of this would strengthen the manuscript. The NMR data could also be strengthened as the binding interface is not reported or mapped onto the structure/model, this seems of considerable interest given that highly related proteins do have the same activity.

The paper is for the most part well well-written and is potentially highly significant

Comments on revised version:

The revised manuscript has addressed many of the concerns raised and clarified a number of points. As a result the manuscript is improved.

The primary concern that remains is the absence of biological function for Ub-ssDNA/RNA and the inability to detect it in cells. Despite this the manuscript will be of interest to those in the ubiquitin field and will likely provoke further studies and the development of tools to better assess the cellular relevance. As a result this manuscript is important.

Minor issue:<br /> Figure 1A - the authors have now included the constructs used but it would be more informative if the authors lined up the various constructs under the relevant domains in the full-length protein.

Reviewer #2 (Public Review):

The manuscript by Dearlove et al. entitled "DTX3L ubiquitin ligase ubiquitinates single-stranded nucleic acids" reports a novel activity of a DELTEX E3 ligase family member, DTX3L, which can conjugate ubiquitin to the 3' hydroxyl of single-stranded oligonucleotides via an ester linkage. The findings that unmodified oligonucleotides can act as substrates for direct ubiquitylation and the identification of DTX3 as the enzyme capable of performing such oligonucleotide modification are novel, intriguing, and impactful because they represent a significant expansion of our view of the ubiquitin biology. The authors perform a detailed and diligent biochemical characterization of this novel activity, and key claims made in the article are well supported by experimental data. However, the studies leave room for some healthy skepticism about the physiological significance of the unique activity of DTX3 and DTX3L described by the authors because DTX3/DTX3L can also robustly attach ubiquitin to the ADP ribose moiety of NAD or ADP-ribosylated substrates. The study could be strengthened by a more direct and quantitative comparison between ubiquitylation of unmodified oligonucleotides by DTX3/DTX3L with the ubiquitylation of ADP-ribose, the activity that DTX3 and DTX3L share with the other members of the DELTEX family.

Comment on revised version:

In my opinion, reviewers' comments are constructively addressed by the authors in the revised manuscript, which further strengthens the revised submission and makes it an important contribution to the field. Specifically, the authors perform a direct quantitative comparison of two distinct ubiquitylation substrates, unmodified oligonucleotides and fluorescently labeled NADH and report that kcat/Km is 5-fold higher for unmodified oligos compared to NADH. This observation suggests that ubiquitylation of unmodified oligos is not a minor artifactual side reaction in vitro and that unmodified oligonucleotides may very well turn out to be the physiological substrates of the enzyme. However, the true identity of the physiological substrates and the functionally relevant modification site(s) remain to be established in further studies.

Reviewer #1 (Public review):

Summary:

Tian et al. describes how TIPE regulates melanoma progression, stemness, and glycolysis. The authors link high TIPE expression to increased melanoma cell proliferation and tumor growth. TIPE causes dimerization of PKM2, as well as translocation of PKM2 to the nucleus, thereby activating HIF-1alpha. TIPE promotes the phosphorylation of S37 on PKM2 in an ERK-dependent manner. TIPE is shown to increase stem-like phenotype markers. The expression of TIPE is positively correlated with the levels of PKM2 Ser37 phosphorylation in murine and clinical tissue samples. Taken together, the authors demonstrate how TIPE impacts melanoma progression, stemness, and glycolysis through dimeric PKM2 and HIF-1alpha crosstalk.

The authors manipulated TIPE expression using both shRNA and overexpression approaches throughout the manuscript. Using these models, they provide strong evidence of the involvement of TIPE in mediating PKM2 Ser37 phosphorylation and dimerization. The authors also used mutants of PKM2 at S37A to block its interaction with TIPE and HIF-1alpha. In addition, an ERK inhibitor (U0126) was used to block the phosphorylation of Ser37 on PKM2. The authors show how dimerization of PKM2 by TIPE causes nuclear import of PKM2 and activation of HIF-1alpha and target genes. Pyridoxine was used to induce PKM2 dimer formation, while TEPP-46 was used to suppress PKM2 dimer formation. TIPE maintains stem cell phenotypes by increasing expression of stem-like markers. Furthermore, the relationship between TIPE and Ser37 PKM2 was demonstrated in murine and clinical tissue samples.

The evaluation of how TIPE causes metabolic reprogramming can be better assessed using isotope tracing experiments and improved bioenergetic analysis.

Reviewer #2 (Public review):

In this article, Tian et al present a convincing analysis of the molecular mechanisms underpinning TIPE-mediated regulation of glycolysis and tumor growth in melanoma. The authors begin by confirming TIPE expression in melanoma cell lines and identify "high" and "low" expressing models for functional analysis. They show that TIPE depletion slows tumour growth in vivo, and using both knockdown and over expression approaches, show that this is associated with changes in glycolysis in vitro. Compelling data using multiple independent approaches is presented to support an interaction between TIPE and the glycolysis regulator PKM2, and over-expression of TIPE promoted nuclear translocation of PKM2 dimers. Mechanistically, the authors also demonstrate that PKM2 is required for TIPE-mediated activation of HIF1a transcriptional activity, as assessed using an HRE-promoter reporter assay, and that TIPE-mediated PKM2 dimerization is p-ERK dependent. Finally, the dependence of TIPE activity on PKM2 dimerization was demonstrated on tumor growth in vivo and in regulation of glycolysis in vitro, and ectopic expression of HIF1a could rescue inhibition of PKM2 dimerization in TIPE overexpressing cells and reduced induction of general cancer stem cell markers, showing a clear role for HIF1a in this pathway.

The detailed mechanistic analysis of TIPE mediated regulation of PKM2 to control aerobic glycolysis and tumor growth is a major strength of the study and provides new insights into the molecular mechanisms that underpin the Warburg effect in melanoma cells. The main conclusions of this paper are well supported by data, however further investigation of a potential oncogenic effect of TIPE in melanoma patients is warranted to support the tumor promoting role of TIPE identified in the experimental models. Analysis of patient samples showed a significant increase in TIPE protein levels in primary melanoma compared to benign skin tumours, and a further increase upon metastatic progression. Moreover, TIPE levels correlate with proliferation (Ki67) and hypoxia gene sets in the TCGA melanoma patient dataset. However, the authors note in the discussion that high TIPE expression associates with better survival outcomes in the TCGA melanoma patients and these data should be included in this paper. Further investigation of how TIPE-mediated regulation of glycolysis contributes to melanoma progression is warranted to confirm the authors claims of a potential oncogenic function. Regardless, the new insights into the molecular mechanisms underpinning TIPE-mediated aerobic glycolysis in melanoma are convincing and will likely generate interest in the cancer metabolism field.

Reviewer #1 (Public review):

Summary:

This manuscript uses PS-coated and IgG-opsonized targets to model the engulfment of apoptotic cells and pathogens. It demonstrates that differential activation of the respiratory burst accounts for variations in cell morphology, adhesion, and migration following phagocytosis of different particles. Specifically, reactive oxygen species produced by phagosomes containing IgG-opsonized targets activate Rho GTPases. This activation triggers Formin- and ERM-dependent compaction of the cortical actin network, leading to rounded cell morphology, reduced membrane ruffling, disassembly of podosomes, and decreased migration. Some of these findings are validated in cells exposed to pathogens or soluble MAMPs.

Strengths:

The manuscript presents well-executed and controlled experiments. It proposes an intriguing model to explain the distinct behaviors of myeloid cells when confronted with different phagocytic cargoes and offers fresh insights into immune surveillance.

Weaknesses:

Certain aspects of the proposed model require further experimental evidence. The significance of the cellular behavioral differences in response to various phagocytic cargoes warrants further exploration within physiological contexts.

Specific comments:

How do reactive oxygen species lead to an increase in Rho activation while simultaneously reducing Rac activity? The underlying molecular mechanisms remain unresolved, although potential regulatory pathways are discussed.

Given that the number of phagocytosed particles affects cell behavior (SF1), it is important to ensure that an equivalent number of particles are phagocytosed when comparing cells treated with PS-beads and IgG-beads (Figure 1a). How was this experimentally controlled, and how many particles are phagocytosed under each condition?

Why were experiments conducted in BMDM, Raw264.7, and PMN cells under different conditions? For Raw264.7 and PMN cells, cell behavior was only compared between those treated with IgG-RBC and untreated cells. What occurs to these cells when they are exposed to PS-beads as opposed to IgG-beads?

How long does it take for cells treated with IgG-beads to recover and regain their mobility and surveillance activity? Does this recovery occur following a reduction in reactive oxygen species production?

A contractile actin cortex usually requires the activity of both Formin and myosin II. It is a bit surprising that inhibitors of ROCK and myosin II, when added to Raw cells engulfing IgG-RBC, did not affect podosome disassembly. Is the cytoskeletal rearrangement observed in Figure 2 also independent of myosin II activity?

Reviewer #2 (Public review):

Summary:

The manuscript by Ferling et al. describes how phagocytosis of IgG but not PS-opsonized targets induces the cells to round up and disassemble their podosomes. The mechanism downstream of the FcR is then dissected. The authors show that RhoA-mediated actin polymerization is involved, as well as actin nucleators of the Formin family, but not ROCK or Myosin II. ERM proteins and ROS production play a role in podosome loss and RhoA activation. Similar observations were made after cells were put in contact with Candida albicans or with soluble LPS.

Strengths:

The manuscript is of very good scientific standards, based on solid cell biology and biochemistry approaches, both in a murine macrophage cell line and in murine primary macrophages. It reaches the criteria for a significant advance in the field.

Reviewer #1 (Public review):

Summary:

The paper examined livestock abortion, as it is an important disease syndrome that affects productivity and livestock economies. If livestock abortion remains unexamined it poses risks to public health.

Several pathogens are associated with livestock abortions but across Africa however the livestock disease surveillance data rarely include information from abortion events, little is known about the aetiology and impacts of livestock abortions, and data are not available to inform prioritisation of disease interventions. Therefore the current study seeks to examine the issue in detail and proposes some solutions.

The study took place in 15 wards in northern Tanzania spanning pastoral, agropastoral and smallholder agro-ecological systems. The key objective is to investigate the causes and impacts of livestock abortion.

The data collection system was set up such that farmers reported abortion cases to the field officers of the Ministry of Livestock and Fisheries livestock<br /> The reports were made to the investigation teams. The team only included abortion of those that the livestock field officers could attend to within 72 hours of the event occurring.

Also a field investigation was carried out to collect diagnostic samples from aborted materials. In addition aborting dams and questionnaires were administer to collect data on herd/flock management. Laboratory diagnostic tests were carried out for a range of abortigenic pathogens

Over the period of the study 215 abortion events in cattle (n=71), sheep (n=44) and goats (n=100) were investigated. In all 49 investigated cases varied widely across wards, with three .The Aetiological attribution, achieved for 19.5% of cases through PCR-based diagnostics, was significantly affected by delays in field investigation.

The result also revealed that vaginal swabs from aborting dams provided a practical and sensitive source of diagnostic material for pathogen detection.

Livestock abortion surveillance can generate valuable information on causes of zoonotic disease outbreaks, and livestock reproductive losses and can identify important pathogens that are not easily captured through other forms of livestock disease surveillance. The study demonstrated the feasibility of establishing an effective reporting and investigation system that could be implemented across a range of settings, including remote rural areas,

Strengths:

The paper combines both science and socio economic methodology to achieve the aim of the study.

The methodology was well presented and the sequence was great. The authors explain where and how the data was collected. Figure 2 was used to describe the study area which was excellently done. The section on Investigation of cases was well written. The sample analysis was also well written. The authors devoted a section to summarizing the investigated cases and description of the livestock 221-study population. The logic model has been well presented

Weaknesses:

All the weaknesses identified have been resolved by the the authors

Reviewer #2 (Public review):

The paper provides a comprehensive analysis of the importance of livestock abortion surveillance in Tanzania. The authors aim to highlight the significance of this surveillance system in identifying disease priorities and guiding interventions to mitigate the impact of livestock abortions on both animal and human health.

Summary:

The paper begins by discussing the context of livestock farming in Tanzania and the significant economic and social impact of livestock abortions. The authors then present a detailed overview of the livestock abortion surveillance system in Tanzania, including its objectives, methods, and data collection process. They analyze the data collected from this surveillance system over a specific period to identify the major causes of livestock abortions and assess their public health implications.

Evaluation:

Overall, this paper provides valuable insights into the importance of livestock abortion surveillance as a tool for disease prioritization and intervention planning in Tanzania. The authors effectively demonstrate the utility of this surveillance system in identifying emerging diseases, monitoring disease trends, and informing evidence-based interventions to control and prevent livestock abortions.

Strengths:

(1) Clear Objective: The paper clearly articulates its objective of highlighting the value of livestock abortion surveillance in Tanzania.

(2) Comprehensive Analysis: The authors provide a thorough analysis of the surveillance system, including its methodology, data collection process, and findings as seen in the supplementary files.

(3) Practical Implications: The paper discusses the practical implications of the surveillance system for disease control and public health interventions in Tanzania.

(4) Well-Structured: The paper is well-organized, with clear sections and subheadings that facilitate understanding and navigation.

All suggestions made for improvement of the manuscript have been appropriately effected.

Final Recommendation:

Overall, this paper makes a significant contribution to the literature on livestock abortion surveillance and its implications for disease control in Tanzania.

Reviewer #3 (Public review):

The authors delved into an important aspect of abortifacient diseases of livestock in Tanzania. The thoughts of the authors on the topic and its significance have been clarified. The number of wards in the study area, statistical selection of wards, type of questionnaire ie open or close ended. and statistical analyses of outcomes have been clearly elucidated in the manuscript. The exclusion criteria for two wards out of the fifteen wards mentioned in the text are clearly stated. Observations were from pastoral, agro-pastoral and small holder agro ecological farmers. Sample numbers or questionnaires attributed to the above farming systems correlate findings with management systems. The impacts of the research investigation output are clearly visible as to warrant intervention methods. The identified pathogens from laboratory investigation, particularly with the use of culture and PCR, as well as the zoonotic pathogens encountered are stated in the manuscript and the supplementary files.

In conclusion, based on the intent of the authors and content of this research, and the weight of the research topic, the seeming weaknesses in the critical data analysis observed have been clarified, to demonstrate cause, effect and impact.

The authors have carried out the necessary corrections.

The findings do imply that identification of some of the abortifacient of livestock in Tanzania will necessitate important interventions in the control of the diseases in the study area

Reviewer #1 (Public review):

Summary:

Deletion of the hrp2 and hrp3 loci in P. falciparum poses an immediate public health threat. This manuscript provides a more complete understanding of the dynamic nature with which these deletions are generated. By delving into the likely mechanisms behind their generation, the authors also provide interesting insight into general Plasmodium biology that can inform our broader understanding of the parasite's genomic evolution.

Strengths:

The sub-telomeric regions of P. falciparum (where hrp2 and hrp3 are located) are notoriously difficult to study with short-read sequence data. The authors take an appropriate, targeted approach toward studying the loci of interest, which includes read-depth analysis and local haplotype reconstruction. They additionally use both long-read and short-read data to validate their major findings. There is an extensive set of supplementary plots, which helps clarify several aspects of the data.

Weaknesses:

The revised version of this manuscript has helpfully expanded the details regarding methodology, however, publication of the tool PathWeaver (which is used for local haplotype reconstruction) remains in preparation.

Reviewer #2 (Public review):

This work investigates the mechanisms, patterns and geographical distribution of pfhrp2 and pfhrp3 deletions in Plasmodium falciparum. Rapid diagnostic tests (RDTs) detect P. falciparum histidine-rich protein 2 (PfHRP2) and its paralog PfHRP3 located in subtelomeric regions. However, laboratory and field isolates with deletions of pfhrp2 and pfhrp3 that can escape diagnosis by RDTs are spreading in some regions of Africa. They find that pfhrp2 deletions are less common and likely occurs through chromosomal breakage with subsequent telomeric healing. Pfhrp3 deletions are more common and show three distinct patterns: loss of chromosome 13 from pfhrp3 to the telomere with evidence of telomere healing at breakpoint (Asia; Pattern 13-); duplication of a chromosome 5 segment containing pfhrp1 on chromosome 13 through non-allelic homologous recombination (NAHR) (Asia; Pattern 13-5++); and the most common pattern, duplication of a chromosome 11 segment on chromosome 13 through NAHR (Americas/Africa; Pattern 13-11++). The loss of these genes impact the sensitivity od RDTs, and knowing these patterns and geographic distribution makes it possible to make better decisions for malaria control.

Comments on latest version:

The authors answered all my questions.

Reviewer #3 (Public review):

The study provides a detailed analysis of the chromosomal rearrangements related to the deletions of histidine-rich protein 2 (pfhrp2) and pfhrp3 genes in P. falciparum that have clinical significance since malaria rapid diagnostic tests detect these parasite proteins. A large number of publicly available short sequence reads for whole-genome of the parasite were analyzed and data on coverage and on discordant mapping allowed to identify deletions, duplications and chromosomal rearrangements related to pfhrp3 deletions. Long-read sequences showed support for the presence of a normal chromosome 11 and a hybrid 13-11 chromosome lacking pfhrp3 in some of the pfhrp3-deleted parasites. The findings support that these translocations have repeatedly occurred in natural populations. The authors discuss the implications of these findings and how they support or not previous hypothesis on the emergence of these deletions and the possible selective pressures involved.

The genomic regions where these genes are located are challenging to study since they are highly repetitive and paralogous and the use of long read sequencing allowed to span the duplicated regions, giving support to the identification of the hybrid 13-11 chromosome.

All publicly available whole-genome sequences of the malaria parasite from around the world were analysed which allowed an overview of the worldwide variability, even though this analysis is biased by the availability of sequences, as the authors recognize.

Despite the reduced sample size, the detailed analysis of haplotypes and identification of location of breakpoints gives support to a single origin event for the 13-5++ parasites.

The analysis of haplotype variation across the duplicated chromosome-11 segment identified breakpoints at varied locations that support multiple translocation events in natural populations. The authors suggest these translocations may be occurring at high frequency in meiosis in natural populations but strongly selected against in most circumstances, which remains to be tested.

In this new version, the authors have addressed the points raised previously and adequately discuss the limitations of the study.

Reviewer #3 (Public review):

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

In general the data are convincing. The conditional KO mouse model has some inherent limitations due to incomplete recombination and the existence of 'escaper' cells that express ARID1A and progress through meiosis normally. This reviewer feels that the authors have addressed this point thoroughly and have demonstrated clear and specific phenotypes using the best available animal model. The data demonstrate that the mutant cells fail to progress past pachytene, although it is unclear whether this specifically reflects pachytene arrest, as accumulation in other stages of Prophase is also suggested by the data in Table 1.

The revised manuscript more appropriately describes the relationship between ARID1A and DNA damage response (DDR) signaling. The authors don't see defects in a few DDR markers in ARID1A CKO cells (including a low resolution assessment of ATR), suggesting that ARID1A may not be required for meiotic DDR signaling. However, as previously noted the data do not rule out the possibility that ARID1A is downstream of DDR signaling, and the authors note the possibility of a role for DDR signaling upstream of ARID1A.

A final comment relates to the impacts of ARID1A loss on DMC1 focus formation and the interesting observation of reduced sex chromosome association by DMC1. The authors additionally assess the related recombinase RAD51 and suggest that it is unaffected by ARID1A loss. However, only a single image of RAD51 staining in the cKO is provided (Fig. S11) and there are no associated quantitative data provided. The data are suggestive and conclusions about the impacts of ARID1A loss on RAD51 must be considered as preliminary until more rigorously assessed.

Comments on latest version:

The authors have effectively addressed the minor issues raised in the most recent round of non-public reviews. This reviewer has no additional recommendations.

Reviewer #1 (Public review):

In the revision of their paper, N'Guessan et al have improved the report of their study of expression QTL (eQTL) mapping in yeast using single cells. The authors make use of advances in single cell RNAseq (scRNAseq) in yeast to increase the efficiency with which this type of analysis can be undertaken. Building on prior research led by the senior author that entailed genotyping and fitness profiling of almost 100,000 cells derived from a cross between two yeast strains (BY and RM) they performed scRNAseq on a subset of ~5% (n = 4,489) individual cells. To address the sparsity of genotype data in the expression profiling they used a Hidden Markov Model (HMM) to infer genotypes and then identify the most likely known lineage genotype from the original dataset. To address the relationship between variance in fitness and gene expression the authors partition the variance to investigate the sources of variation. They then perform eQTL mapping and study the relationship between eQTL and fitness QTL identified in the earlier study.

This paper seeks to address the question of how quantitative trait variation and expression variation are related. scRNAseq represents an appealing approach to eQTL mapping as it is possible to simultaneously genotype individual cells and measure expression in the same cell. As eQTL mapping requires large sample sizes to identify statistical relationships, the use of scRNAseq is likely to dramatically increase the statistical power of such studies. However, there are several technical challenges associated with scRNAseq and the authors' study is focused on addressing those challenges. Most of the points raised by my review of the initial version have been addressed. However, one point remains and one additional point should be considered.

(1) Given that the authors overcame many technical and analytical challenges in the course of this research, the study would be greatly strengthened through analysis of at least one, and ideally several, more conditions which would expand the conclusions that could be drawn from the study and demonstrate the power of using scRNAseq to efficiently quantify expression in different environments.

(2) In this version the authors have introduced the use of data imputation using a published algorithm, DISCERN. This has greatly increased the variation explained by their model as presented in figure 3. However, it is possible that the explained variance is now an overestimation as a result of using the imputed expression data. I think that it would be appropriate to present figure 3 using the sparse data presented in the initial version of the paper and the newly presented imputed data so that the reader can draw their own conclusions about the interpretation.

Reviewer #2 (Public review):

The authors now say the main take-home for their work is (1) they have established methods for linkage mapping with scRNA-seq and that these (2) "can help gain insights about the genotype-phenotype map at a broader scale." My opinion in this revision is much the same as it was in the first round: I agree that they have met the first goal, and the second theme has been so well explored by other literature that I'm not convinced the authors' results meet the bar for novelty and impact. To my mind, success for this manuscript would be to support the claim that the scRNA-seq approach helps "reveal hidden components of the yeast genotype-to-phenotype map." I'm not sure the authors have achieved this. I agree that the new Figure 3 is a nice addition-a result that apparently hasn't been reported elsewhere (30% of growth trait variation can't be explained by expression). The caveats are that this is a negative result that needs to be interpreted with caution; and that it would be useful for the authors to clarify whether the ability to do this calculation is a product of the scRNA-seq method per se or whether they could have used any bulk eQTL study for it. Beside this, I regret to say that I still find that the results in the revision recapitulate what the bulk eQTL literature has already found, especially for the authors' focal yeast cross: heritability, expression hotspots, the role of cis and trans-acting variation, etc.

Likewise, when in the first round of review I recommended that the authors repeat their analyses on previous bulk RNA-seq data from Albert et al., my point was to lead the authors to a means to provide rigorous, compelling justification for the scRNA-seq approach. The response to reviewers and the text (starting on line 413) says the comparison in its current form doesn't serve this purpose because Albert et al. studied fewer segregants. Wouldn't down-sampling the current data set allow a fair comparison? Again, to my mind what the current manuscript needs is concrete evidence that the scRNA-seq method per se affords truly better insights relative to what has come before.

I also recommend that the authors take care to improve the main text for readability and professionalism. It would benefit from further structural revision throughout (especially in the figure captions) to allow high-impact conclusions to be highlighted and low-impact material to be eliminated. Figure 4 and the results text sections from line 319 onward could be edited for concision or perhaps moved to supplementary if they obscure the authors' case for the scRNA-seq approach. The text could also benefit from copy editing (e.g. three clauses starting with "while" in the paragraph starting on line 456; "od ratio" on line 415). I appreciate the authors' work on the discussion, including posing big picture questions for the field (lines 426-429), but I don't see how they have anything to do with the current scRNA-seq method.

Reviewer #1 (Public review):

The goal of this work is to understand the clinical observation of a subgroup of diabetics who experience extremely high levels of blood glucose levels after a period of high carbohydrate intake. These symptoms are similar to the onset of Type 1 diabetes but, crucially, have been observed to be fully reversible in some cases.

The authors interpret these observations by analyzing a simple yet insightful mathematical model in which β-cells temporarily stop producing insulin when exposed to high levels of glucose. For a specific model realization of such dynamics (and for specific parameter values) they show that such dynamics lead to two distinct stable states. One is the relatively normal/healthy state in which β-cells respond appropriately to glucose by releasing insulin. In contrast, when enough β-cells "refuse" to produce insulin in a high-glucose environment, there is not enough insulin to reduce glucose levels, and the high-glucose state remains locked in because the high-glucose levels keep β-cells in their inactive state. The presented mathematical analysis shows that in their model the high-glucose state can be entered through an episode of high glucose levels and that subsequently the low-glucose state can be re-entered through prolonged insulin intake.

The strength of this work is twofold. First, the intellectual sharpness of translating clinical observations of ketosis-prone type 2 diabetes (KPD) into the need for β-cell responses on intermediate timescales. Second, the analysis of a specific model clearly establishes that the clinical observations can be reproduced with a model in which β-cells dynamics reversibly enter a non-insulin-producing state in a glucose-dependent fashion.

The likely impact of this work is a shift in attention in the field from a focus on the short and long-term dynamics in glucose regulation and diabetes progression to the intermediate timescales of β-cell dynamics. I expect this to lead to much interest in probing the assumptions behind the model to establish what exactly the process is by which patients enter a 'KPD state'. Furthermore, I expect this work to trigger much research on how KPD relates to "regular" type 2 diabetes and to lead to experimental efforts to find/characterize previously overlooked β-cell phenotypes.

In summary, the authors claim that observed clinical dynamics and possible remission of KPD can be explained through introducing a temporarily inactive β-cell state into a "standard model" of diabetes. The evidence for this claim comes from analyzing a mathematical model and clearly presented. Importantly, the authors point out that this does not mean their model is correct. Other hypotheses are that:

- Instead of switching to an inactive state, individual β-cells could adjust how they respond to high glucose levels. If this response function changes reversibly on intermediate timescales the clinical observations could be explained without a reversible inactive state.

- Kidney function is indirectly impaired through chronic high glucose levels. The apparent rapid glucose increase might then not highlight a new type of β-cell phenotype but would reflect rapid changes in kidney function.

- In principle, the remission could be due to a direct response of β-cells to insulin and not mediated through the lowering of glucose levels.

Crucially, the hypothesized reversibly inactive state of β-cells remains to be directly observed. One of the key contributions of this theoretical work is directing experimental focus towards looking for reversible β-cell phenotypes.

Reviewer #2 (Public review):

In this manuscript, Ridout et al. present an intriguing extension of beta cell mass-focused models for diabetes. Their model incorporates reversible glucose-dependent inactivation of beta cell mass, which can trigger sudden-onset hyperglycemia due to bistability in beta cell mass dynamics. Notably, this hyperglycemia can be reversed with insulin treatment. The model is simple, elegant, and thought-provoking.

Concerning the grounding in experimental phenomenology, it would be beneficial to identify specific experiments to strengthen the model. In particular, what evidence supports reversible beta cell inactivation? This could potentially be tested in mice, for instance, by using an inducible beta cell reporter, treating the animals with high glucose levels, and then measuring the phenotype of the marked cells. Such experiments, if they exist, would make the motivation for the model more compelling. For quantitative experiments, the authors should be more specific about the features of beta cell dysfunction in KPD. Does the dysfunction manifest in fasting glucose, glycemic responses, or both? Is there a "pre-KPD" condition? What is known about the disease's timescale?

The authors should also consider whether their model could apply to other conditions besides KPD. For example, the phenomenology seems similar to the "honeymoon" phase of T1D. Making a strong case for the model in this scenario would be fascinating.

Reviewer #1 (Public review):

Summary:

Barlow and coauthors utilized the high-parameter imaging platform of CODEX to characterize the cellular composition of immune cells in situ from tissues obtained from organ donors with type 1 diabetes, subjects presented with autoantibodies who are at elevated risk, or non-diabetic organ donor controls. The panels used in this important study were based on prior publications using this technology, as well as a priori and domain-specific knowledge of the field by the investigators. Thus, there was some bias in the markers selected for analysis. The authors acknowledge that these types of experiments may be complemented moving forward with the inclusion of unbiased tissue analysis platforms that are emerging that can conduct a more comprehensive analysis of pathological signatures employing emerging technologies for both high-parameter protein imaging and spatial transcriptomics.

Strengths:

In terms of major findings, the authors provide important confirmatory observations regarding a number of autoimmune-associated signatures reported previously. The high parameter staining now increases the resolution for linking these features with specific cellular subsets using machine learning algorithms. These signatures include a robust signature indicative of IFN-driven responses that would be expected to induce a cytotoxic T-cell-mediated immune response within the pancreas. Notable findings include the upregulation of indolamine 2,3-dioxygenase-1 in the islet microvasculature. Furthermore, the authors provide key insights as to the cell:cell interactions within organ donors, again supporting a previously reported interaction between presumably autoreactive T and B cells.

Weaknesses:

These studies also highlight a number of molecular pathways that will require additional validation studies to more completely understand whether they are potentially causal for pathology, or rather, epiphenomenon associated with increased innate inflammation within the pancreas of T1D subjects. Given the limitations noted above, the study does present a rich and integrated dataset for analysis of enriched immune markers that can be segmented and annotated within distinct cellular networks. This enabled the authors to analyze distinct cellular subsets and phenotypes in situ, including within islets that peri-islet infiltration and/or intra-islet insulitis.

Despite the many technical challenges and unique organ donor cohort utilized, the data are still limited in terms of subject numbers - a challenge in a disease characterized by extensive heterogeneity in terms of age of onset and clinical and histopathological presentation. Therefore, these studies cannot adequately account for all of the potential covariates that may drive variability and alterations in the histopathologies observed (such as age of onset, background genetics, and organ donor conditions). In this study, the manuscript and figures could be improved in terms of clarifying how variable the observed signatures were across each individual donor, with the clear notion that non-diabetic donors will present with some similar challenges and variability.

Reviewer #2 (Public review):

Summary:

The authors aimed to characterize the cellular phenotype and spatial relationship of cell types infiltrating the islets of Langerhans in human T1D using CODEX, a multiplexed examination of cellular markers

Strengths:

Major strengths of this study are the use of pancreas tissue from well-characterized tissue donors, and the use of CODEX, a state-of-the-art detection technique of extensive characterization and spatial characterization of cell types and cellular interactions. The authors have achieved their aims with the identification of the heterogeneity of the CD8+ T cell populations in insulitis, the identification of a vasculature phenotype and other markers that may mark insulitis-prone islets, and the characterization of tertiary lymphoid structures in the acinar tissue of the pancreas. These findings are very likely to have a positive impact on our understanding (conceptual advance) of the cellular factors involved in T1D pathogenesis which the field requires to make progress in therapeutics.

Weaknesses:

A major limitation of the study is the cohort size, which the authors directly state. However, this study provides avenues of inquiry for researchers to gain further understanding of the pathological process in human T1D.

Reviewer #3 (Public review):

Summary:

The authors applied an innovative approach (CO-Detection by indEXing - CODEX) together with sophisticated computational analyses to image pancreas tissues from rare organ donors with type 1 diabetes. They aimed to assess key features of inflammation in both islet and extra-islet tissue areas; they reported that the extra-islet space of lobules with extensive islet infiltration differs from the extra-islet space of less infiltrated areas within the same tissue section. The study also identifies four sub-states of inflamed islets characterized by the activation profiles of CD8+T cells enriched in islets relative to the surrounding tissue. Lymphoid structures are identified in the pancreas tissue away from islets, and these were enriched in CD45RA+ T cells - a population also enriched in one of the inflamed islet sub-states. Together, these data help define the coordination between islets and the extra-islet pancreas in the pathogenesis of human T1D.

Strengths:

The analysis of tissue from well-characterized organ donors, provided by the Network for the Pancreatic Organ Donor with Diabetes, adds strength to the validity of the findings.

By using their innovative imaging/computation approaches, key known features of islet autoimmunity were confirmed, providing validation of the methodology.

The detection of IDO+ vasculature in inflamed islets - but not in normal islets or islets that have lost insulin-expression links this expression to the islet inflammation, and it is a novel observation. IDO expression in the vasculature may be induced by inflammation and may be lost as disease progresses, and it may provide a potential therapeutic avenue.

The high-dimensional spatial phenotyping of CD8+T cells in T1D islets confirmed that most T cells were antigen-experienced. Some additional subsets were noted: a small population of T cells expressing CD45RA and CD69, possibly naive or TEMRA cells, and cells expressing Lag-3, Granzyme-B, and ICOS.

While much attention has been devoted to the study of the insulitis lesion in T1D, our current knowledge is quite limited; the description of four sub-clusters characterized by the activation profile of the islet-infiltrating CD8+T cells is novel. Their presence in all T1D donors indicates that the disease process is asynchronous and is not at the same stage across all islets. Although this concept is not novel, this appears to be the most advanced characterization of insulitis stages.

When examining together both the exocrine and islet areas, which is rarely done, authors report that pancreatic lobules affected by insulitis are characterized by distinct tissue markers. Their data support the concept that disease progression may require crosstalk between cells in the islet and extra-islet compartments. Lobules enriched in β-cell-depleted islets were also enriched in nerves, vasculature, and Granzyme-B+/CD3- cells, which may be natural killer cells.

Lastly, authors report that immature tertiary lymphoid structures (TLS) exist both near and away from islets, where CD45RA+ CD8+T cells aggregate, and also observed an inflamed islet-subcluster characterized by an abundance of CD45RA+/CD8+ T cells. These TLS may represent a point of entry for T cells and this study further supports their role in islet autoimmunity.

Weaknesses:

As the authors themselves acknowledge, the major limitation is that the number of donors examined is limited as those satisfying study criteria are rare. Thus, it is not possible to examine disease heterogeneity and the impact of age at diagnosis. Of 8 T1D donors examined, 4 would be considered newly diagnosed (less than 3 months from onset) and 4 had longer disease durations (2, 2, 5, and 6 years). It was unclear if disease duration impacted the results in this small cohort. In the introduction, the authors discuss that most of the pancreata from nPOD donors with T1D lack insulitis. This is correct, yet it is a function of time from diagnosis. Donors with shorter duration will be more likely to have insulitis. A related point is that the proportion of islets with insulitis is low even near diagnosis, Finally, only one donor was examined that while not diagnosed with T1D, was likely in the preclinical disease stage and had autoantibodies and insulitis. This is a critically important disease stage where the methodology developed by the investigators could be applied in future efforts.

While this was not the focus of this investigation, it appears that the approach was very much immune-focused and there could be value in examining islet cells in greater depth using the methodology the authors developed.

Additional comments:

Overall, the authors were able to study pancreas tissues from T1D donors and perform sophisticated imaging and computational analysis that reproduce and importantly extend our understanding of inflammation in T1D. Despite the limitations associated with the small sample size, the results appear robust, and the claims well-supported.

The study expands the conceptual framework of inflammation and islet autoimmunity, especially by the definition of different clusters (stages) of insulitis and by the characterization of immune cells in and outside the islets.

Factually wrong.

Reviewer #1 (Public review):

Many labs world-wide now use the blind source deconvolution technique to identify the firing patterns of multiple motor units simultaneously in human subjects. This technique has had a truly transformative effective on our understanding of the structure of motor output in both normal subjects and, increasingly, in persons with neurological disorders. The key advance presented here is that the software provides real time identification of these firing patterns.

The main strengths are the clarity of the presentation and the great potential that real-time decoding will provide. Figures are especially effective and statistical analyses are excellent.

Reviewer #3 (Public review):

In this manuscript, Rossato and colleagues present a method for real-time decoding of EMG into putative single motor units. Their manuscript details a variety of decision points in their code and data collection pipeline that lead to a final result of recording on the order of ~10 putative motor units per muscle in human males. Overall the manuscript is highly restricted in its potential utility but may be of interest to aficionados. For those outside the field of human or nonhuman primate EMG, these methods will be of limited interest.

Comment on revised version

The revised manuscript has thoroughly and responsively addressed the concerns and suggestions raised in the first review. I think the method will be of use to the field and fits well within the purview of eLife's publications on methods development.

Reviewer #1 (Public review):

This study describes a useful antibody-free method to map G-quadruplexes in vertebrate cells. The analysis of the data is solid but it remains primarily descriptive and does not substantially add to existing publications (such as PMID:34792172 for example). Nevertheless, the datasets generated here might constitute a good starting point for more functional studies.

Comments on revised version:

It is disappointing to see that the authors decided to brush aside most of the comments made by the three referees, even though these comments were largely consistent with each other. As a result, the revised manuscript is not substantially changed or improved. Legitimate concerns regarding the specificity of the Cut&Tag signals were not addressed and therefore remain. The sensitivity of the HBD-seq signals to a combination of RNase A and RNase H does not demonstrate that HBD-seq specifically reports the presence of RNA:DNA hybrids. The new Figure 9 comparing HepG4-seq to existing datasets does not unequivocally demonstrate the superiority of the Hemin-based strategy to map G4s.

Reviewer #2 (Public review):

Summary:

In this study, Liu et al. explore the interplay between G-quadruplexes (G4s) and R-loops. The authors developed novel techniques, HepG4-seq and HBD-seq, to capture and map these nucleic acid structures genome-wide in human HEK293 cells and mouse embryonic stem cells (mESCs). They identified dynamic, cell-type-specific distributions of co-localized G4s and R-loops, which predominantly localize at active promoters and enhancers of transcriptionally active genes. Furthermore, they assessed the role of helicase Dhx9 in regulating these structures and their impact on gene expression and cellular functions.

The manuscript provides a detailed catalogue of the genome-wide distribution of G4s and R-loops. However, the conceptual advance and the physiological relevance of the findings are not obvious. Overall, the impact of the work on the field is limited to the utility of the presented methods and datasets.

Strengths:<br /> (1) The development and optimization of HepG4-seq and HBD-seq offer novel methods to map native G4s and R-loops.<br /> (2) The study provides extensive data on the distribution of G4s and R-loops, highlighting their co-localization in human and mouse cells.<br /> (3) The study consolidates the role of Dhx9 in modulating these structures and explores its impact on mESC self-renewal and differentiation.

Comments on revised version:

In this revised manuscript, Liu et al. address most of the previous concerns raised by this reviewer. Namely, the comparison between the novel methods and existing ones is an important addition.

Reviewer #3 (Public review):

Summary:

The authors developed and optimized the methods for detecting G4s and R-loops independent of BG4 and S9.6 antibody, and mapped genomic native G4s and R-loops by HepG4-seq and HBD-seq, revealing that co-localized G4s and R-loops participate in regulating transcription and affecting the self-renewal and differentiation capabilities of mESCs.

Strengths:

By utilizing the peroxidase activity of G4-hemin complex and combining proximity labeling technology, the authors developed HepG4-seq (high throughput sequencing of hemin-induced proximal labelled G4s) , which can detect the dynamics of G4s in vivo. Meanwhile, the "GST-His6-2xHBD"-mediated CUT&Tag protocol (Wang et al., 2021) was optimized by replacing fusion protein and tag, the optimized HBD-seq avoids the generation of GST fusion protein aggregates and can reflect the genome-wide distribution of R-loops in vivo.

The authors employed HepG4-seq and HBD-seq to establish comprehensive maps of native co-localized G4s and R-loops in human HEK293 cells and mouse embryonic stem cells (mESCs). The data indicate that co-localized G4s and R-loops are dynamically altered in a cell type-dependent manner and are largely localized at active promoters and enhancers of transcriptional active genes.

Combined with Dhx9 ChIP-seq and co-localized G4s and R-loops data in wild-type and dhx9KO mESCs, the authors found that the helicase Dhx9, a major regulator of co-localized G4s and R-loops, affects the self-renewal and differentiation capacities of mESCs.

In conclusion, the authors provide an approach to study the interplay between G4s and R-loops, shedding light on the important roles of co-localized G4s and R-loops in development and disease by regulating the transcription of related genes.

Weaknesses:

As we know, there are at least two structure data of S9.6 antibody very recently, and the questions about the specificity of the S9.6 antibody on RNA:DNA hybrids should be finished. The authors referred (Hartono et al., 2018; Konig et al., 2017; Phillips et al., 2013) need to be updated, and the author's bias against S9.6 antibodies needs also to be changed. In contrast to S9.6 CUT&Tag and other inactive ribonucleotide H1-based methods including MapR (inactive ribonucleotide H1-mediated CUT&Run) (Yan et al., 2019)and GST-2xHBD CUT&Tag (Wang et al., 2021), HBD-seq did not perform satisfactorily and its binding specificity was questionable.

Although HepG4-seq is an effective G4s detection technique, and the authors have also verified its reliability to some extent, given the strong link between ROS homeostasis and G4s formation, hemin's affinity for different types of G4s and their differences in peroxidase activities, whether HepG4-seq reflects the dynamics of G4s in vivo more accurately than existing detection techniques still needs to be more carefully corroborated.

The authors focus on the interaction of non-B DNA structures G4s and R-loops and their roles in development and disease by regulating the transcription of related genes. Compared to the complex regulatory network of G4s and R-loops, the authors provide limited mechanistic insight into the major regulator of co-localized G4s and R-loops, helicase Dhx9. However, the authors propose that "A degron system-mediated simultaneous and/or stepwise degradation system of multiple regulators will help us elucidate the interplaying effects between G4s and R-loops." is attractive. The main innovations of this article are the proposal of new antibody-independent methods for detecting G4s and the optimization of the GST-2xHBD CUT&Tag (Wang et al., 2021) method for detecting R-loops. Unfortunately, however, the reliability and accuracy of these methods are still debatable, and the reference value of the G4s and R-loops datasets based on these methods is relatively limited.

Reviewer #2 (Public review):

Qin, Sanbo and Zhou, Huan-Xiang created a model, SeqDYN, to predict nuclear magnetic resonance (NMR) spin relaxation spectra of intrinsically disordered proteins (IDPs), based primarily on amino acid sequence. To fit NMR data, SeqDYN uses 21 parameters, 20 that correspond to each amino acid, and a sequence correlation length for interactions. The model demonstrates that local sequence features impact the dynamics of the IDP, as SeqDYN performs better than a one residue predictor, despite having similar numbers of parameters. SeqDYN is trained using 45 IDP sequences and is retrained using both leave-one-out cross validation and five-fold cross validation, ensuring the model's robustness. While SeqDYN can provide reasonably accurate predictions in many cases, the authors note that improvements can be made by incorporating secondary structure predictions, especially for alpha-helices that exceed the correlation length of the model. The authors apply SeqDYN to study nine IDPs and a denatured ordered protein, demonstrating its predictive power. The model can be easily accessed via the website mentioned in the text.

The authors have adequately addressed the majority of my previous concerns. However, I still wonder if an attempt to fit the individual protein fitting parameter based on temperature and magnetic field strength would be possible. The authors would have 45 data points on which to fit such a parameter, which would only depend on two variables.

Reviewer #3 (Public review):

The revised manuscript adds some new relevant analyses. It still, however, is unclear which timescales of motions the method refers to and there is confusion about whether the model can predict "slower motions". While the authors answer some of my points, others are left unanswered. That is of course the authors' prerogative, and readers will in any case be able to read the reviewer comments. I am not sure it is productive to add further comments at this point.

Below are my comments from the first round of review:

The manuscript by Qin and Zhou presents an approach to predict dynamical properties of an intrinsically disordered protein (IDP) from sequence alone. In particular, the authors train a simple (but useful) machine learning model to predict (rescaled) NMR R2 values from sequence. Although these R2 rates only probe some aspects of IDR dynamics and the method does not provide insight into the molecular aspects of processes that lead to perturbed dynamics, the method can be useful to guide experiments.

A strength of the work is that the authors train their model on an observable that directly relates to protein dynamics. They also analyse a relatively broad set of proteins which means that one can see actual variation in accuracy across the proteins.

A weakness of the work is that it is not always clear what the measured R2 rates mean. In some cases, these may include both fast and slow motions (intrinsic R2 rates and exchange contributions). This in turn means that it is actually not clear what the authors are predicting. The work would also be strengthened by making the code available (in addition to the webservice), and by making it easier to compare the accuracy on the training and testing data.

Joint Public Review:

The paper sought to determine the number of myosin 10 molecules per cell and localized to filopodia, where they are known to be involved in formation, transport within, and dynamics of these important actin-based protrusions. The authors used a novel method to determine the number of molecules per cell. First, they expressed HALO tagged Myo10 in U20S cells and generated cell lysates of a certain number of cells and detected Myo10 after SDS-PAGE, with fluorescence and a stained free method. They used a purified HALO tagged standard protein to generate a standard curve which allowed for determining Myo10 concentration in cell lysates and thus an estimate of the number of Myo10 molecules per cell. They also examined the fluorescence intensity in fixed cell images to determine the average fluorescence intensity per Myo10 molecule, which allowed the number of Myo10 molecules per region of the cell to be determined. They found a relatively small fraction of Myo10 (6%) localizes to filopodia. There are hundreds of Myo10 in each filopodia, which suggests some filopodia have more Myo10 than actin binding sites. Thus, there may be crowding of Myo10 at the tips, which could impact transport, the morphology at the tips, and dynamics of the protrusions themselves. Overall, the study forms the basis for a novel technique to estimate the number of molecules per cell and their localization to actin-based structures. The implications are broad also for being able to understand the role of myosins in actin protrusions, which is important for cancer metastasis and wound healing.

Comments on latest version (from the Reviewing Editor):

One of the main critiques that still remains is that the results were derived from experiments with overexpressed Myo10 and therefore are hard to extrapolate to physiological conditions. Measurement were also only performed in a single cell line. The authors counter this critique with the argument that their results provide insight into a system in which Myo10 is a limiting factor for controlling filopodia formation. They demonstrate that U20S cells do not express detectable levels of Myo10 and thus introducing Myo10 expression demonstrates how triggering Myo10 expression impacts filopodia. An example is given of how melanoma cells often heavily upregulate Myo10.

Reviewer #1 (Public review):

Summary:

The authors provide an genome annotation resource of 33 insects using a motif-blind prediction methods for tissue-specific cis-regulatory modules. This is a welcome addition that may facilitate further research in new laboratory systems, and the approach seem to be relatively accurate, although it should be combined with other sources of evidence to be practical.

Strengths:

The paper clearly presents the resource, including the testing of candidate enhancers identified from various insects in Drosophila. This cross-species analysis, and the inherent suggestion that training datasets generated in flies can predict a cis-regulatory activity in distant insects, is interesting. While I can not be sure this approach will prevail in the future, for example with approaches that leverage the prediction of TF binding motifs, the SCRMShaw tool is certainly useful and worth of consideration for the large community of genome scientists working on insects.

Weaknesses from the previous version were appropriately corrected in this revision, as the authors improved data availability including with genome annotation resources.

Reviewer #3 (Public review):

Summary:

In this ambitious paper, the authors develop an unparalleled community resource of insect genome regulatory annotations spanning five insect orders. They employ their previously-developed SCRMshaw method for computational cross-species enhancer prediction, drawing on available training datasets of validated enhancer sequence and expression from Drosophila melanogaster, which had been previously shown to perform well across select holometabolous insects (representing 160-345MY divergence). In this work they expand regulatory sequence annotation to 33 insect genomes spanning Holometabola and Hemiptera, which is even more distantly related to the fly model. They perform multiple downstream analyses of sets of predicted enhancers to assess the true-positive rate of predictions; the independent comparisons of real predictions with simulated predictions and with chromatin accessibility data, as well as the functional validation through reporter gene analysis strengthen their conclusions that their annotation pipeline achieves a high true-positive rate and can be used across long divergence times to computationally annotate regulatory genome regions, an ability that has been largely inaccessible for non-model insects and now is possible across the many newly-sequenced insect scaffold-level genomes.

Strengths:

This work fills a large gap in current methods and resources for predicting regulatory regions of the genome, a task that has long lagged behind that of coding region prediction and analysis.

Despite technical constraints in working outside of well-developed model insect systems, the authors creatively draw on existing resources to scaffold a pipeline and independently assess likelihood of prediction validity.

The established database will be a welcome community resource in its current state, and even more so as the authors continue to expand their annotations to more insect genomes as they indicate. Their available analysis pipeline itself will be useful to the community as well for research groups that may want to undertake their own regulatory genome annotation.

Weaknesses:

The work here is limited by the field-wide lack of an independently validated set of tissue specific enhancers that could be used to directly benchmark this pipeline. The prediction of true positive enhancer identification rates and in vivo reporter gene assays offer some insight into the rates of successful prediction, but the output of SCRMshaw regulatory annotation should be regarded as another prediction-generating tool.

Reviewer #1 (Public review):

This study comes to an interesting conclusion: a polyunsaturated fatty acid, Lin-Glycine, increases the conductance of KCNQ1/KCNE1 channels by stabilizing a state of the selectivity filter that allows K+ conduction. The stabilization of a conducting state is well supported by single channel analysis, which shows that normally infrequent opening bursts occur more often in the presence of the PUFA. The linkage to PUFA action through the selectivity filter is supported by disruption of PUFA effects by mutation of residues which change conformation in two KCNQ1 structures from the literature. A definitive functional experiment is conducted by single channel recordings with selectivity filter domain mutation Y315F which ablates the Lin-Glycine effect on Gmax. The computational exploration of two selectivity filter structures proposed to interact distinctly with Lin-Glycine is informative. Both mutation results and simulations converge on the proposed selectivity filter mechanism, although other possibilities for Lin-Glycine binding and action might be possible. Overall, the major claim of the abstract is well-supported: "... that the selectivity filter in KCNQ1 is normally unstable ... and that the PUFA-induced increase in Gmax is caused by a stabilization of the selectivity filter in an open-conductive state."

Reviewer #2 (Public review):

Golluscio et al. address one of the mechanisms of IKs (KCNQ1/KCNE1) channel upregulation by polyunsaturated fatty acids (PUFAs). PUFAs are known to upregulate KCNQ1 and KCNQ1/KCNE1 channels through two mechanisms: one shifts the voltage dependence in a negative direction, and the other increases the maximum conductance (Gmax). While the first mechanism is known to affect the voltage sensor equilibrium through a charge effect, the second mechanism is less understood. Using single-channel recordings and mutagenesis at putative PUFA binding sites, they successfully demonstrate that the selectivity filter is stabilized in a conducting state by PUFA binding, and that this is the mechanism by which PUFAs increase Gmax. Their single-channel recordings are straightforward and clearly show that the selectivity filter tends to become conductive upon PUFA binding. Since PUFAs are potential therapeutic reagents for cardiac arrhythmias such as long QT syndrome, their findings are beneficial for future research and applications of these compounds.

Reviewer #3 (Public review):

Summary:

This manuscript reveals an important mechanism of KCNQ1/IKs channel gating such that the open state of the pore is unstable and undergoes intermittent closed and open conformations. PUFA enhances the maximum open probability of IKs by binding to a crevice adjacent to the pore and stabilize the open conformation. This mechanism is supported by convincing single channel recordings that show empty and open channel traces and the ratio of such traces is affected by PUFA. In addition, mutations of the pore residues alter PUFA effects, convincingly supporting that PUFA alters the interactions among these pore residues.

Strengths:

The data are of high quality and the description is clear.

Reviewer #1 (Public review):

Summary:

The authors demonstrate impairments induced by a high cholesterol diet on GLP-1R dependent glucoregulation in vivo as well as an improvement after reduction in cholesterol synthesis with simvastatin in pancreatic islets. They also map sites of cholesterol high occupancy and residence time on active versus inactive GLP-1Rs using coarse-grained molecular dynamics (cgMD) simulations and screened for key residues selected from these sites and performed detailed analyses of the effects of mutating one of these residues, Val229, to alanine on GLP-1R interactions with cholesterol, plasma membrane behaviour, clustering, trafficking and signalling in pancreatic beta cells and primary islets, and describe an improved insulin secretion profile for the V229A mutant receptor.

These are extensive and very impressive studies indeed. I am impressed with the tireless effort exerted to understand the details of molecular mechanisms involved in the effects of cholesterol for GLP-1 activation of its receptor. In general the study is convincing, the manuscript well written and the data well presented. Some of the changes are small and insignificant which makes one wonder how important the observations are. For instance in figure 2 E (which is difficult to interpret anyway because the data are presented in percent, conveniently hiding the absolute results) does not show a significant result of the cyclodextrin except for insignificant increases in basal secretion. That is not identical to impairment of GLP-1 receptor signaling!

To me the most important experiment of them all is the simvastatin experiment, but the results rest on very few numbers and there is a large variation. Apparently, in a previous study using more extensive reduction in cholesterol the opposite response was detected casting doubt on the significance of the current observation. I agree with the authors that the use of cyclodextrin may have been associated with other changes in plasma membrane structure than cholesterol depletion at the GLP-1 receptor. The entire discussion regarding he importance of cholesterol would benefit tremendously from studies of GLP-1 induced insulin secretion in people with different cholesterol levels before and after treatment with cholesterol-lowering agents. I suspect that such a study would not reveal major differences.

Reviewer #2 (Public review):

Summary:

In this manuscript the authors provided a proof of concept that they can identify and mutate a cholesterol-binding site of a high-interest class B receptor, the GLP-1R, and functionally characterize the impact of this mutation on receptor behavior in the membrane and downstream signaling with the intent that similar methods can be useful to optimize small molecules that as ligands or allosteric modulators of GLP-1R can improve the therapeutic tools targeting this signaling system.

Strengths:

The majority of results on receptor behavior are elucidated in INS-1 cells expressing the wt or mutant GLP-1R, with one experiment translating the findings to primary mouse beta-cells. I think this paper lays a very strong foundation to characterize this mutation and does a good job discussing how complex cholesterol-receptor interactions can be (ie lower cholesterol binding to V229A GLP-1R, yet increased segregation to lipid rafts). Table 1 and Figure 9 are very beneficial to summarize the findings. The lower interaction with cholesterol and lower membrane diffusion in V229A GLP-1R resembles the reduced diffusion of wt GLP-1R with simv-induced cholesterol reductions, although by presumably decreasing the cholesterol available to interact with wt GLP-1R. This could be interesting to see if lowering cholesterol alters other behaviors of wt GLP-1R that look similar to V229A GLP-1R. I further wonder if the authors expect that increased cholesterol content of islets (with loading of MβCD saturated with cholesterol or high-cholesterol diets) would elevate baseline GLP-1R membrane diffusion, and if a more broad relationship can be drawn between GLP-1R membrane movement and downstream signaling.

Weaknesses:

I think there are no obvious weaknesses in this manuscript and overall, I believe the authors achieved their aims and have demonstrated the importance of cholesterol interactions on GLP-1R functioning in beta-cells. I think this paper will be of interest to many physiologists who may not be familiar with many of the techniques used in this paper and the authors largely do a good job explaining the goals of using each method in the results section. The intent of some methods, for example the Laurdan probe studies, are better expanded in the discussion. I found it unclear what exactly was being measured to assess 'receptor activity' in Fig 7E and F.

Certainly many follow-up experiments are possible from these initial findings and of primary interest is how this mutation affects insulin homeostasis in vivo under different physiological conditions. One of the biggest pathologies in insulin homeostasis in obesity/t2d is an elevation of baseline insulin release (as modeled in Fig 1E) that renders the fold-change in glucose stimulated insulin levels lower and physiologically less effective. No difference in primary mouse islet baseline insulin secretion was seen here but I wonder if this mutation would ameliorate diet-induced baseline hyperinsulinemia.

I would have liked to see the actual islet cholesterol content after 5wks high-cholesterol diet measured to correlate increased cholesterol load with diminished glucose-stimulated inulin. While not necessary for this paper, a comparison of islet cholesterol content after this cholesterol diet vs the more typical 60% HFD used in obesity research would be beneficial for GLP-1 physiology research broadly to take these findings into consideration with model choice.

Another area to further investigate is does this mutation alter ex4 interaction/affinity/time of binding to GLP-1 or are all of the described findings due to changes in behavior and function of the receptor?

Lastly, I wonder if V229A would have the same impact in a different cell type, especially in neurons? How similar are the cholesterol profiles of beta-cells and neurons? How this mutation (and future developed small molecules) may affect satiation, gut motility, and especially nausea, are of high translational interest. The comparison is drawn in the discussion between this mutation and ex4-phe1 to have biased agonism towards Gs over beta-arrestin signaling. Ex4-phe1 lowered pica behavior (a proxy for nausea) in the authors previously co-authored paper on ex4-phe1 (PMID 29686402) and I think drawing a parallel for this mutation or modification of cholesterol binding to potentially mitigate nausea is worth highlighting.

Reviewer #1 (Public review):

Summary:

In this study, the authors investigate a very interesting but often overlooked aspect of abstract vs. concrete processing in language. Specifically, they study if the differences in processing of abstract vs. concrete concepts in the brain is static or dependent on the (visual) context in which the words occur. This study takes a two-step approach to investigate how context might affect the perception of concepts. First, the authors analyze if concrete concepts, expectedly, activate more sensory systems while abstract concepts activate higher-order processing regions. Second, they measure the contextual situatedness vs. displacement of each word with respect to the visual scenes in which it is spoken and then evaluate if this contextual measure correlates with more activation in the sensory vs. higher-order regions respectively.

Strengths:

This study raises a pertinent and understudied question in language neuroscience. It also combines both computational and meta-analytic approaches.

Reviewer #2 (Public review):

Summary:

This study tests a plausible and intriguing hypothesis that one cause of the differences in the neural underpinnings of concrete and abstract words is differences in their grounding in the current sensory context. The authors reasoned that, in this case, an abstract word presented with a relevant visual scene would be processed in a more similar way to a concrete word. Typically, abstract and concrete words are tested in isolation. In contrast, this study takes advantage of naturalistic movie stimuli to assess the neural effects of concreteness in both abstract and concrete words (the speech within the film), when the visual context is more or less tied to the word meaning (measured as the similarity between the word co-occurrence-based vector for the spoken word and the average of this vector across all present objects). This novel approach allows a test of the dynamic nature of abstract and concrete word processing, and as such provides a useful perspective accounting for differences in processing these word types.

The measure of contextual situatedness (how related a spoken word is to the average of the visually presented objects in a scene) is an interesting approach allowing parametric variation within naturalistic stimuli, which is a potential strength of the study. Additionally, the authors use an interesting peak and valley method and provide a rationale for this approach. This provided additional temporal information on the processing of spoken concrete and abstract words.

The authors predicted that sensory areas would be more active for concrete words, affective areas for abstract and language areas would be involved in both. The use of reverse inference to interpret areas such as the inferior frontal gyrus post hoc, as sensory, affective or language related deserves some caution. It is also important to remember that the different areas identified for each comparison do not necessarily have the same roles. As the number of clusters may therefore be a misleading way to assess the relationship of these areas with the sensory terms, the relationship between each area and the different sensory terms is provided in the supplemental to allow more nuanced interpretation. The study could benefit from being better situated in the prior literature on context and concrete vs abstract regional differences. Overall, the authors successfully demonstrate the context-dependent nature of abstract and concrete word processing.

Reviewer #3 (Public review):

Summary:

The primary aim of this manuscript was to investigate how context, defined from visual object information in multimodal movies, impacts the neural representation of concrete and abstract conceptual knowledge. The authors first conduct a series of analyses to identify context independent regional response to concrete and abstract concepts in order to compare these results with the networks observed in prior research using non-naturalistic paradigms. The authors then conduct analyses to investigate whether regional response to abstract and concrete concepts changes when the concepts are either contextually situated or displaced. A concept is considered displaced if the visual information immediately preceding the word is weakly associated with the word whereas a concept is situated if the association is high. The results suggest that, when ignoring context, abstract and concrete concepts engage different brain regions with overlap in core language areas. When context is accounted for, however, similar brain regions are activated for processing concrete and situated abstract concepts and for processing abstract and displaced concrete concepts. The authors suggest that contextual information dynamically changes the brain regions that support the representation of abstract and concrete conceptual knowledge.

Strengths:

There is significant interest in understanding both the acquisition and neural representation of abstract and concrete concepts, and most of the work in this area has used highly constrained, decontextualized experimental stimuli and paradigms to do so. This manuscript addresses this limitation by using multimodal narratives which allows for an investigation of how context-sensitive the regional response to abstract and concrete concepts is. The authors characterize the regional response in a comprehensive way.

Weaknesses:

The edits made to the manuscript in response to the reviewer comments have clarified and strengthened the methodological concerns flagged by all reviewers, giving me greater confidence that the authors are capturing what they aimed to and are making appropriate inferences given the results.

Reviewer #1 (Public review):

Summary:

The study made fundamental findings in investigations of the dynamic functional states during sleep. Twenty-one HMM states were revealed from the fMRI data, surpassing the number of EEG-defined sleep stages, which can define sub-states of N2 and REM. Importantly, these findings were reproducible over two nights, shedding new light on the dynamics of brain function during sleep.

Strengths:

The study provides the most compelling evidence on the sub-states of both REM and N2 sleep. Moreover, they showed these findings on dynamics states and their transitions were reproducible over two nights of sleep. These novel findings offered unique information in the field of sleep neuroimaging.

Comments on revised version:

Nice work! All my concerns have been addressed, and I have no further suggestions.

Reviewer #2 (Public review):

Summary:

Yang and colleagues used a Hidden Markov Model (HMM) on whole-night fMRI to isolate sleep and wake brain states in a data-driven fashion. They identify more brain states (21) than the five sleep/wake stages described in conventional PSG-based sleep staging, show that the identified brain states are stable across nights, and characterize the brain states in terms of which networks they primarily engage.

Strengths:

This work's primary strengths are its dataset of two nights of whole-night concurrent EEG-fMRI (including REM sleep), and its sound methodology.

Weaknesses:

Weaknesses are its small sample size, and limited attempts at relating the identified fMRI brain states back to EEG.

General appraisal:

The paper's conclusions are generally well-supported, but additional analyses could improve the work further.<br /> The authors' main focus lies in identifying fMRI-based brain states, and they succeed at demonstrating both the presence and robustness of these states in terms of cross-night stability. Additional characterization of brain states in terms of which networks these brain states primarily engage adds additional insights.

A missed opportunity remains the absence of more analyses relating the HMM states back to EEG. While the authors show how power in different EEG bands varies with HMM state (Supplementary Figures 10 and 11) it would be much more informative to show the complete EEG spectra for each of the 21 HMM states, organized by PSG-based sleep/wake state. This would enable answering how EEG spectra of, say, different N2-related HMM states compare. Similarly, it is presently unclear whether anything noticeable happens within the EEG timecourse at the moment of an HMM class switch (particularly when the PSG stage remains stable). Such analyses might have shown that fMRI-based brain states map onto familiar EEG substates, or reveal novel EEG changes that have so far gone unnoticed. Furthermore, if band-specific analyses are to be performed, care should be taken to specify bands in accordance with the dominant sleep EEG features (e.g., slow oscillation and sigma/spindle bands are currently missing).

Reviewer #1 (Public Review):

Summary:

The authors aimed to develop and validate an automated, deep learning-based system for scoring the Rey-Osterrieth Complex Figure Test (ROCF), a widely used tool in neuropsychology for assessing memory deficits. Their goal was to overcome the limitations of manual scoring, such as subjectivity and time consumption, by creating a model that provides automatic, accurate, objective, and efficient assessments of memory deterioration in individuals with various neurological and psychiatric conditions.

Strengths:

Comprehensive Data Collection: The authors collected over 20,000 hand-drawn ROCF images from a wide demographic and geographic range, ensuring a robust and diverse dataset. This extensive data collection is critical for training a generalizable and effective deep learning model.

Advanced Deep Learning Approach: Utilizing a multi-head convolutional neural network to automate ROCF scoring represents a sophisticated application of current AI technologies. This approach allows for detailed analysis of individual figure elements, potentially increasing the accuracy and reliability of assessments.

Validation and Performance Assessment: The model's performance was rigorously evaluated against crowdsourced human intelligence and professional clinician scores, demonstrating its ability to outperform both groups. The inclusion of an independent prospective validation study further strengthens the credibility of the results.

Robustness Analysis Efficacy: The model underwent a thorough robustness analysis, testing its adaptability to variations in rotation, perspective, brightness, and contrast. Such meticulous examination ensures the model's consistent performance across different clinical imaging scenarios, significantly bolstering its utility for real-world applications.

Appraisal and discussion:

By leveraging a comprehensive dataset and employing advanced deep learning techniques, they demonstrated the model's ability to outperform both crowdsourced raters and professional clinicians in scoring the ROCF. This achievement represents a significant step forward in automating neuropsychological assessments, potentially revolutionizing how memory deficits are evaluated in clinical settings. Furthermore, the application of deep learning to clinical neuropsychology opens avenues for future research, including the potential automation of other neuropsychological tests and the integration of AI tools into clinical practice. The success of this project may encourage further exploration into how AI can be leveraged to improve diagnostic accuracy and efficiency in healthcare.

However, the critique regarding the lack of detailed analysis across different patient demographics, the inadequacy of network explainability, and concerns about the selection of median crowdsourced scores as ground truth raises questions about the completeness of their objectives. These aspects suggest that while the aims were achieved to a considerable extent, there are areas of improvement that could make the results more robust and the conclusions stronger.

Comments on revised version:

I appreciate the opportunity to review this revised submission. Having considered the other reviews, I believe this study presents an important advance in using AI methods for clinical applications, which is both innovative and has implications beyond a single subfield.

The authors have developed a system using fundamental AI that appears sufficient for clinical use in scoring the Rey-Osterrieth Complex Figure (ROCF) test. In human neuropsychology, tests that generate scores like this are a key part of assessing patients. The evidence supporting the validity of the AI scoring system is compelling. This represents a valuable step towards evaluating more complex neurobehavioral functions.

However, one area where the study could be strengthened is in the explainability of the AI methods used. To ensure the scores are fully transparent and consistent for clinical use, it will be important for future work to test the robustness of the approach, potentially by comparing multiple methods. Examining other latent variables that can explain patients' cognitive functioning would also be informative.

In summary, I believe this study provides an important proof-of-concept with compelling evidence, while also highlighting key areas for further development as this technology moves towards real-world clinical applications.

Reviewer #2 (Public Review):

The authors aimed to develop and validate a machine-learning driven neural network capable of automatic scoring of the Rey-Osterrieth Complex Figure. They aimed to further assess the robustness of the model to various parameters such as tilt and perspective shift in real drawings. The authors leveraged the use of a huge sample of lay workers in scoring figures and also a large sample of trained clinicians to score a subsample of figures. Overall, the authors found their model to have exceptional accuracy and perform similarly to crowdsourced workers and clinicians with, in some cases, less degree of error/score dispersion than clinicians.

Reviewer #3 (Public Review):

This study presented a valuable inventory of scoring a neuropsychological test, ROCFT, with constructing an artificial intelligence model.

Comments on latest version:

The authors made the system with fundamental AI that is sufficient for clinical use for humans. In human neuropsychology, the test that generates the score is fundamental and relatively easy. Neuropsychologists apply patients to many tests; therefore, the present system is one of them, where we cannot tell the total neurofunction of a patient. The evidence for scoring is thought to be compelling quality, enough for clinical use now and we progress to evaluate other more complicated human neuropsychological functions. For example, persons with dementia change their performance easily when they feel other emotions (worry, boredom, etc. ) and notice other stimulation (announcements in the hospital, a walking nurse by chance, etc.). The score of ROCF is definitely changing, compelling the effort of AI scoring. We should grasp this behavior of humans with diverse tests totally. Therefore, scoring AI with compelling quality is a fundamental step for the next, evaluation against the changeable and ambiguous neurobehavior of humans.

Reviewer #1 (Public review):

Summary:

This study investigated how traumatic brain injury affects oscillatory and single-unit hippocampal activity in awake-behaving rats.

Strengths:

The use of high-density laminar electrodes enabled precise localization of recording sites. To ensure an unbiased, rigorous approach, single-unit analysis was performed by a reviewer who was blind to experimental conditions. A proof of concept study was undertaken to characterize the pathology that resulted from the specific TBI model used in the main study. There was an effort to link abnormalities in hippocampal activity to memory disruption by running a cohort of rats on the Morris Water Maze task.

Weaknesses:

The paper is written as if the experiment was exploratory and not hypothesis-driven despite the fact that there is a wealth of experimental evidence about this TBI model that could have informed very specific predictions to test a hypothesis that is only hinted at in the discussion. The number of rats used for the spatial working memory experiment is not reported. Some of the statistics are not completely reported. It is also unclear what the rationale was for recording single units in a novel and familiar environment. Furthermore, this analysis comparing single-unit activity between familiar and novel environments is quite rudimentary. There are much more rigorous analyses to answer the question of how hippocampal single-unit firing patterns differ across changes in environments. There are details lacking about the number of units recorded per session and per rat, all of which are usually reported in studies that record single units. Spatial working memory assessment is delegated to a single panel of a supplementary figure. More importantly, there is no effort to dissociate between spatial working memory deficits and other motor, motivational, or sensory deficits that could have been driving the lower "memory score" in the experimental group.

Reviewer #2 (Public review):

Summary:

The authors investigate changes in theta-gamma phase amplitude coupling, and action potential entrainment to theta following traumatic brain injury (TBI). Both phenomena are widely hypothesized to be important for cognition, and the authors report deficits in both after TBI. The manuscript is well-written, the figures are well-constructed, and the author's use of high-level analysis methods for TBI EEG data collected from awake, behaving animals is welcome.

Major Comments:

- The animal n's are small (4 sham and 5 injured). In Figure 3, for instance, one wonders if panels D and E might have shown significant differences if more animals had been recorded.

- The text focuses on deficits in the theta and gamma bands, but the reduction in power appears to be broadband (see Figure 1F, especially Pyramidal cell layer panel). Therefore, the overall decrease in broadband (in the injured population) must be normalized between sham and injured animals before a selective comparison between sham and injured animals can be conducted. That is the only way that selective narrow bands i.e., theta and low gamma can be compared between the two cohorts. A brief discussion of the significance of a broadband decrease would be appreciated.

Reviewer #3 (Public review):

Summary:

In this study, the authors studied the effects of traumatic brain injury created by LFPI procedure on the CA1 at the network level. The major findings in this study seem to be that the TBI reduces theta and gamma powers in CA1, reduces phase-amplitude coupling in between theta and gamma bands as well as disrupts the gamma entrainment of interneurons. I think the authors have made some important discoveries that could help advance the understanding of TBI effects at the physiological level, however, more investigations into deciphering the relationship of the behavioral and brain states to the observed effects would help clarify the interpretations for the readers.

Strengths:

The authors in this study were able to combine behavioral verification of the TBI model with the laminar electrophysiological recordings of the CA1 region to bring forward network-level anomalies such as the temporal coordination of network-level oscillations as well as in the firing of the interneurons. Indeed, it seems that the findings may serve future studies to functionally better understand and/or refine the therapies for the TBI.

Weaknesses:

Discoveries made in the paper and their broad interpretations can be helped with further characterization and comparison among the brain and behavioral states both during immobility and movement. The impact of brain injury in several parts of the brain can alter brain-wide LFP and/or behavior. The altered behavior and/or LFP patterns might then lead to reduced spiking and unreliable LFP oscillations in the hippocampus. Hence, claims made in the abstract such as "These results reveal deficits in information encoding and retrieval schemes essential to cognition that likely underlie TBI-associated learning and memory impairments, and elucidate potential targets for future neuromodulation therapies" do not have enough evidence to test whether the disruptions were information encoding and retrieval related or due to sensory-motor and/or behavioral deficits that could also occur during TBI.

Movement velocity is already known to be correlated to the entrainment of spikes with the theta rhythm and also in some cases with the gamma oscillations. So, it is important to disentangle the differences in behavioral variables and the observed effects. As an example, the author's claims of disrupted temporal coding (as shown in the graphical abstract) might have suffered from these confounds. The observed results of reduced entrainment might, on one hand, be due to the decreased LFP power (induced by injury in different brain areas) resulting in altered behavior and/or the unreliable oscillations of the LFP bands such as theta and gamma, rather than memory encoding and retrieval related disruption of spikes synchrony to the rhythms, while on the other hand, they may simply be due to reduced excitability in the neurons particularly in the behavioral and brain state in which the effects were observed, rather than disrupted temporal code. Hence, further investigations into dissociating these factors could help readers mechanistically understand the interesting results observed by the authors.

Joint Public Review

Summary:

The authors sought to elucidate the mechanism by which infections increase sleep in Drosophila. Their work is important because it further supports the idea that the blood-brain barrier is involved in brain-body communication, and because it advances the field of sleep research. Using knock-down and knock-out of cytokines and cytokine receptors specifically in the endocrine cells of the gut (cytokines) as well as in the glia forming the blood-brain barrier (BBB) (cytokines receptors), the authors show that cytokines, upd2 and upd3, secreted by entero-endocrine cells in response to infections increase sleep through the Dome receptor in the BBB. They also show that gut-derived Allatostatin (Alst) A promotes wakefulness by inhibiting Alst A signaling that is mediated by Alst receptors expressed in BBB glia. Their results suggest there may be additional mechanisms that promote elevated sleep during gut inflammation.<br /> The authors suggest that upd3 is more critical than upd2, which is not sufficiently addressed or explained. In addition, the study uses the gut's response to reactive oxygen molecules as a proxy for infection, which is not sufficiently justified. Finally, further verification of some fundamental tools used in this paper would further solidify these findings making them more convincing.

Strengths:

(1) The work addresses an important topic and proposes an intriguing mechanism that involves several interconnected tissues. The authors place their research in the appropriate context and reference related work, such as literature about sickness-induced sleep, ROS, the effect of nutritional deprivation on sleep, sleep deprivation and sleep rebound, upregulated receptor expression as a compensatory mechanism in response to low levels of a ligand, and information about Alst A.

(2) The work is, in general, supported by well-performed experiments that use a variety of different tools, including multiple RNAi lines, CRISPR, and mutants, to dissect both signal-sending and receiving sides of the signaling pathway.

(3) The authors provide compelling evidence that shows that endocrine cells from the gut are the source of the upd cytokines that increase daytime sleep, that the glial cells of the BBB are the targets of these upds, and that upd action causes the downregulation of Alst receptors in the BBB via the Jak/Stat pathways.

Weaknesses:

(1) There is a limited characterization of cell types in the midgut which are classically associated with upd cytokine production.

(2) Some of the main tools used in this manuscript to manipulate the gut while not influencing the brain (e.g., Voilà and Voilà + R57C10-GAL80), are not directly shown to not affect gene expression in the brain. This is critical for a manuscript delving into intra-organ communication, as even limited expression in the brain may lead to wrong conclusions.

(3) The model of gut inflammation used by the authors is based on the increase in reactive oxygen species (ROS) obtained by feeding flies food containing 1% H2O2. The use of this model is supported by the authors rather weakly in two papers (refs. 26 and 27 ): The paper by Jiang et al. (ref. 26) shows that the infection by Pseudomonas entomophila induces cytokine responses upd2 and 3, which are also induced by the Jnk pathway. In addition, no mention of ROS could be found in Buchon et al. (ref 27); this is a review that refers to results showing that ROS are produced by the NADPH oxidase DUOX as part of the immune response to pathogens in the gut. Thus, there is no strong support for the use of this model.

(4) Likewise, there is no support for the use of ROS in the food instead a direct infection by pathogenic bacteria. Furthermore, it is known that ROS damages the gut epithelium, which in turn induces the expression of the cytokines studied. Thus the effects observed may not reflect the response to infection. In addition, Majcin Dorcikova et al. (2023). Circadian clock disruption promotes the degeneration of dopaminergic neurons in male Drosophila. Nat Commun. 2023 14(1):5908. doi: 10.1038/s41467-023-41540-y report that the feeding of adult flies with H2O2 results in neurodegeneration if associated with circadian clock defects. Thus, it would be important to discuss or present controls that show that the feeding of H2O2 does not cause neuronal damage.

(5) The novelty of the work is difficult to evaluate because of the numerous publications on sleep in Drosophila. Thus, it would be very helpful to read from the authors how this work is different and novel from other closely related works such as: Li et al. (2023) Gut AstA mediates sleep deprivation-induced energy wasting in Drosophila. Cell Discov. 23;9(1):49. doi: 10.1038/s41421-023-00541-3.

Reviewer #1 (Public review):

Summary:

This study represents valuable insight into the potential contribution of ciliation deficits and cholinergic neuron survival in an etiologically appropriate Parkinson's disease mouse model. The evidence presented is convincing, employing a validated methodology to assess measures across multiple brain regions and time points, with adequate observation numbers. Similarities between some of the data here and human patients further validate the model, and the study provides numerous avenues to aid future advances.

Strengths:

Overall, this study presents a thorough analysis of ciliary defects and cell loss in cholinergic neurons throughout the brain in the LRRK2 G2019S knockin mouse model of Parkinson's disease. The authors aimed to characterize ciliary defects in areas not only implicated in PD but also in cholinergic neuron function. Additionally, they repeated measures across age and sex, presenting a body of work that is more readily translatable to human disease states. The strengths of the paper included the breadth of brain regions tested and additional mechanistic contributions of LRRK2 that may correlate to their observed phenotypes. The study conveys to the reader the ciliary phenotype observed in all the cholinergic neurons assessed throughout the brains of knock-in LRRK2 mutant mice. Importantly, the pattern of changes is, in some instances, strikingly similar to PD, which strengthens the case for construct and face validation of the G2019S knock-in mouse model. Future investigations of the physiological and behavioural correlates/consequences of these changes will inform ongoing and, as yet untried, therapeutic intervention attempts.

Weaknesses:

At times, the claims are only partially substantiated by how the data are presented (e.g., inappropriate statistics within an age (t-tests, not ANOVA) and a lack of comparison between ages (despite referring to the progress of a phenotype). More appropriate statistical analyses and revisions to the data presentation are required to substantiate basic and more 'progressive' conclusions. Further, distributing the central claim over 10 figures dilutes the impact, many of which could be compressed into a couple of single figures (e.g., cell counts in all regions and ciliation). Also, a summary graphic showing the brain regions affected by ciliation alterations and cell loss at young, middle, and old age in the GS mice would be hugely beneficial. This peer would like to see more discussion of how the observed changes would impact circuit-level function and more speculation of the underlying mechanisms leading to the deficits. Minor changes to the abstract and introduction (to include more detail in the rationale and supporting evidence) are recommended, as summaries of existing literature are vague and could flow better between one statement and the next.

Reviewer #2 (Public review):

Summary:

LRRK2 has previously been shown to affect cilia formation and stability both in vitro and in vivo, in striatal cholinergic interneurons, in both transgenic mice and in human post-mortem brain samples from subjects carrying one of the LRRK2 pathogenic mutations: G2019S. In the current study, Brahmia and colleagues have conducted a comprehensive assessment of G2019S knock-in mice to address some gaps in the field, specifically: extending analysis to additional cholinergic neurons across 3 time points and determining the functional consequences of the ciliation deficits. They find that primary cilia are lost in all cholinergic neurons, with basal forebrain cholinergic neurons displaying an early onset (in 4-5-month-old mice) compared with other regions. They also show early dystrophic changes in cholinergic axons derived from basal forebrain and brainstem cholinergic neurons and age-dependent cholinergic cell loss in select forebrain and brainstem nuclei.

Strengths:

This is a comprehensive and careful analysis of ciliary deficits and their downstream consequences, which we assume are deficits in innervation and cell loss.

Weaknesses:

This study is observational and does not address the underlying mechanisms. The data on pRab12, although downstream of LRRK2, does not clearly address this and, instead, raises more questions than answers: e.g., is there really differentiation from Rab10 and its phosphorylation or is it primarily due to the limitations of pRab10 antibodies with regards to the lack of suitability of this antibody in mouse brain sections (could immunoblots on brain punches have been performed to overcome this?). Are Rab10, Rab12, and LRRK2 expressed at different levels in the vulnerable cell types? Plenty of recent high-quality single-cell/single nuclear RNA-seq data could have been used to address such a fundamental question. LRRK2 small molecule inhibitors are available and progressing in the clinic. They could/should have been used to demonstrate the LRRK2 dependence, reversibility, and timing of therapeutic intervention. The authors suggest that the mouse data mirror (and potentially explain) the cholinergic loss in PD patient brains, but this is not measured in the current work (the authors do acknowledge this limitation and suggest that this is an important further study). There are some recent human data (Khan et al 2024 PMID: 38293195, BioRxiv, which the authors cite) showing loss of primary cilia and cholinergic neurons in sporadic PD (no evidence of aberrant LRRK2 activity) and, interestingly, this is not further exacerbated in G2019S carriers, which may suggest a more complex underlying mechanism.

Reviewer #3 (Public review):

Summary:

The authors described cilia deficits, phospho-Rab12 accumulation, dystrophic axons in cholinergic neurons, and loss of the cholinergic neurons in the mouse brains of G2019S-LRRK2 knock-in mice, a preclinical animal model for Parkinson's disease. They showed that the above changes associated with cholinergic neurons are age-dependent and region-specific. The observation is interesting considering the neuron-type-specific effect of the LRRK2-G2019S in mice.

Strengths:

The observations are important and show neuron type-specific effects of the PD mutation of LRRK2 relevant to PD pathologies.

Weaknesses:

The authors may over-interpret the data, and the study may lack mechanistic investigation.

Reviewer #1 (Public review):

The manuscript by Griesius et al. addresses the dendritic integration of synaptic input in cortical GABAergic interneurons (INs). Dendritic properties, passive and active, of principal cells have been extensively characterized, but much less is known about the dendrites of INs. The limited information is particularly relevant in view of the high morphological and physiological diversity of IN types. The few studies that investigated IN dendrites focused on parvalbumin-expressing INs. In fact, in a previous study, the authors examined dendritic properties of PV INs, and found supralinear dendritic integration in basal, but not in apical dendrites (Cornford et al., 2019 eLife).

In the present study, complementary to the prior work, the authors investigate whether dendrite-targeting IN types, NDNF-expressing neurogliaform cells, and somatostatin(SOM)-expressing O-LM neurons, display similar active integrative properties by combining clustered glutamate-uncaging and pharmacological manipulations with electrophysiological recording and calcium imaging from genetically identified IN types in mouse acute hippocampal slices.

The main findings are that NDNF IN dendrites show strong supralinear summation of spatially- and temporally-clustered EPSPs, which is changed into sublinear behavior by bath application of NMDA receptor antagonists, but not by Na+-channel blockers. L-type calcium channel blockers abolished the supralinear behavior associated calcium transients but had no or only weak effect on EPSP summation. SOM IN dendrites showed similar, albeit weaker NMDA-dependent supralinear summation, but no supralinear calcium transients were detected in these INs. In summary, the study demonstrates that different IN types are endowed with active dendritic integrative mechanisms, but show qualitative and quantitative divergence in these mechanisms.

While the research is conceptionally not novel, it constitutes an important incremental gain in our understanding of the functional diversity of GABAergic INs. In view of the central roles of IN types in network dynamics and information processing in the cortex, results and conclusions are of interest to the broader neuroscience community.

The experiments are well designed, and closely follow the approach from the previous publication in parts, enabling direct comparison of the results obtained from the different IN types. The data is convincing and the conclusions are well-supported, and the manuscript is very well-written.

I see only a few open questions and some inconsistencies in the presentation of the data in the figures (see details below).

Reviewer #2 (Public review):

Summary:

Griesius et al. investigate the dendritic integration properties of two types of inhibitory interneurons in the hippocampus: those that express NDNF+ and those that express somatostatin. They found that both neurons showed supralinear synaptic integration in the dendrites, blocked by NMDA receptor blockers but not by blockers of Na+ channels. These experiments are critically overdue and very important because knowing how inhibitory neurons are engaged by excitatory synaptic input has important implications for all theories involving these inhibitory neurons.

Strengths:

(1) Determined the dendritic integration properties of two fundamental types of inhibitory interneurons.

(2) Convincing demonstration that supra-threshold integration in both cell types depends on NMDA receptors but not on Na+ channels.

Weaknesses:

It is unknown whether highly clustered synaptic input, as used in this study (and several previous studies), occurs physiologically.

Reviewer #3 (Public review):

Summary:

The authors study the temporal summation of caged EPSPs in dendrite-targeting hippocampal CA1 interneurons. There are some descriptive data presented, indicating non-linear summation, which seems to be larger in dendrites of NDNF expressing neurogliaform cells versus OLM cells. However, the underlying mechanisms are largely unclear.

Strengths:

Focal 2-photon uncaging of glutamate is a nice and detailed method to study temporal summation of small potentials in dendritic segments.

Weaknesses:

(1) NMDA-receptor signaling in NDNF-IN. The authors nicely show that temporal summation in dendrites of NDNF-INs is to a certain extent non-linear. However, this non-linearity varies massively from cell to cell (or dendrite to dendrite) from 0% up to 400% (Figure S2). The reason for this variability is totally unclear. Pharmacology with AP5 hints towards a contribution of NMDA receptors. However, the authors claim that the non-linearity is not dependent on EPSP amplitude (Figure S2), which should be the case if NMDA-receptors are involved. Unfortunately, there are no voltage-clamp data of NMDA currents similar to the previous study. This would help to see whether NMDA-receptor contribution varies from synapse to synapse to generate the observed variability? Furthermore, the NMDA- and AMPA-currents would help to compare NDNF with the previously characterized PV cells and would help to contribute to our understanding of interneuron function.

(2) Sublinear summation in NDNF-INs. In the presence of AP5, the temporal summation of caged EPSPs is sublinear. That is potentially interesting. The authors claim that this might be dependent on the diameter of dendrites. Many voltage-gated channels can mediate such things as well. To conclude the contribution of dendritic diameter, it would be helpful to at least plot the extent of sublinearity in single NDNF dendrites versus the dendritic diameter. Otherwise, this statement should be deleted.

(3) Nonlinear EPSP summation in OLM-IN. The authors do similar experiments in dendrite-targeting OLM-INs and show that the non-linear summation is smaller than in NDNF cells. The reason for this remains unclear. The authors claim that this is due to the larger dendritic diameter in OLM cells. However, there is no analysis. The minimum would be to correlate non-linearity with dendritic diameter in OLM-cells. Very likely there is an important role of synapse density and glutamate receptor density, which was shown to be very low in proximal dendrites of OLM cells and strongly increase with distance (Guirado et al. 2014, Cerebral Cortex 24:3014-24, Gramuntell et al. 2021, Front Aging Neurosci 13:782737). Therefore, the authors should perform a set of experiments in more distal dendrites of OLM cells with diameters similar to the diameters of the NDNF cells. Even better would be if the authors would quantify synapse density by counting spines and show how this density compares with non-linearity in the analyzed NDNF and OLM dendrites.

(4) NMDA in OLM. Similar to the NDNF cells, the authors claim the involvement of NMDA receptors in OLM cells. Again there seems to be no dependence on EPSP amplitude, which is not understandable at this point (Figure S3). Even more remarkable is the fact that the authors claim that there is no dendritic calcium increase after activation of NMDA receptors. Similar to NDNF-cell analysis there are no NMDA currents in OLMs. Unfortunately, even no calcium imaging experiments were shown. Why? Are there calcium-impermeable NNDA receptors in OLM cells? To understand this phenomenon the minimum is to show some physiological signature of NMDA-receptors, for example, voltage-clamp currents. Furthermore, it would be helpful to systematically vary stimulus intensity to see some calcium signals with larger stimulation. In case there is still no calcium signal, it would be helpful to measure reversal potentials with different ion compositions to characterize the potentially 'Ca2+ impermeable' voltage-dependent NMDA receptors in OLM cells.

Reviewer #1 (Public review):

Summary:

This study provides convincing evidence on the infraslow oscillation of DG cells during NREM sleep, and how serotonergic innervation modulates hippocampal activity pattern during sleep and memory.

Strengths and Weaknesses:

The authors used state-of-the-art techniques to carry out these experiments. Given that the functional role of infraslow rhythm still remains to be studied, this study provides convincing evidence of the role of DG cells in regulating infraslow rhythm, sleep microarchitecture, and memory.

I have a few minor comments.

(1) Decreased infraslow rhythm during NREMs in the 5ht1a KO mice is striking. It would be helpful to know whether sleep-wake states, MAs, and transitions to REMs are changed.

(2) It would be interesting to discuss whether the magnitude in changes of infraslow rhythm strength is correlated with memory performance (Figure 6).

(3) The authors should cite the Oikonomou Neuron paper that describes slow oscillatory activity of DRN SERT neurons during NREM sleep.

(4) The authors should clarify how they define the phasic pattern of the photometry signal.

Reviewer #2 (Public review):

Summary:

The authors investigated DG neuronal activity at the population and single-cell level across sleep/wake periods. They found an infraslow oscillation (0.01-0.03 Hz) in both granule cells (GC) and mossy cells (MC) during NREM sleep.

The important findings are:

(1) The antiparallel temporal dynamics of DG neuron activities and serotonin neuron activities/extracellular serotonin levels during NREM sleep, and

(2) The GC Htr1a-mediated GC infraslow oscillation.

Strengths:

(1) The combination of polysomnography, Ca-fiber photometry, two-photon microscopy, and gene depletion is technically sound. The coincidence of microarousals and dips in DG population activity is convincing. The dip in activity in upregulated cells is responsible for the dip at the population level.

(2) DG GCs express excitatory Htr4 and Htr7 in addition to inhibitory Htr1a, but deletion of Htr1a is sufficient to disrupt DG GC infraslow oscillation, supporting the importance of Htr1a in DG activity during NREM sleep.

Weaknesses:

(1) The current data set and analysis are insufficient to interpret the observation correctly.

a. In Figure 1A, during NREM, the peaks and troughs of GC population activities seem to gradually decrease over time. Please address this point.

b. In Figure 1F, about 30% of Ca dips coincided with MA (EMG increase) and 60% of Ca dips did not coincide with EMG increase. If this is true, the readers can find 8 Ca dips which are not associated with MAs from Figure 1E. If MAs were clustered, please describe this properly.

c. In Figure 1F, the legend stated the percentage during NREM. If the authors want to include the percentage of wake and REM, please show the traces with Ca dips during wake and REM. This concern applies to all pie charts provided by the authors.

d. In Figure 1C, please provide line plots connecting the same session. This request applies to all related figures.

e. In Figure 2C, the significant increase during REM and the same level during NREM are not convincing. In Figure 2A, the several EMG increasing bouts do not appear to be MA, but rather wakefulness, because the duration of the EMG increase is greater than 15 seconds. Therefore, it is possible that the wake bouts were mixed with NREM bouts, leading to the decrease of Ca activity during NREM. In fact, In Figure 2E, the 4th MA bout seems to be the wake bout because the EMG increase lasts more than 15 seconds.

f. Figure 5D REM data are interesting because the DRN activity is stably silenced during REM. The varied correlation means the varied DG activity during REM. The authors need to address it.

g. In Figure 6, the authors should show the impact of DG Htr1a knockdown on sleep/wake structure including the frequency of MAs. I agree with the impact of Htr1a on DG ISO, but possible changes in sleep bout may induce the DG ISO disturbance.

(2) It is acceptable that DG Htr1a KO induces the reduced freezing in the CFC test (Figure 6E, F), but it is too much of a stretch that the disruption of DG ISO causes impaired fear memory. There should be a correlation.

(3) It is necessary to describe the extent of AAV-Cre infection. The authors injected AAV into the dorsal DG (AP -1.9 mm), but the histology shows the ventral DG (Supplementary Figure 4), which reduces the reliability of this study.

Reviewer #3 (Public review):

Summary:

The authors employ a series of well-conceived and well-executed experiments involving photometric imaging of the dentate gyrus and raphe nucleus, as well as cell-type specific genetic manipulations of serotonergic receptors that together serve to directly implicate serotonergic regulation of dentate gyrus (DG) granule (GC) and mossy cell (MC) activity in association with an infra slow oscillation (ISO) of neural activity has been previously linked to general cortical regulation during NREM sleep and microarousals.

Strengths:

There are a number of novel and important results, including the modulation of dentage granule cell activity by the infraslow oscillation during NREM sleep, the selective association of different subpopulations of granule cells to microarousals (MA), the anticorrelation of raphe activity with infraslow dentate activity.

The discussion includes a general survey of ISOs and recent work relating to their expression in other brain areas and other potential neuromodulatory system involvement, as well as possible connections with infraslow oscillations, micro-arousals, and sensory sensitivity.

Weaknesses:

(1) The behavioral results showing contextual memory impairment resulting from 5-HT1a knockdown are fine but are over-interpreted. The term memory consolidation is used several times, as well as references to sleep-dependence. This is not what was tested. The receptor was knocked down, and then 2 weeks later animals were found to have fear conditioning deficits. They can certainly describe this result as indicating a connection between 5-HT1a receptor function and memory performance, but the connection to sleep and consolidation would just be speculation. The fact that 5-HT1a knockdown also impacted DG ISOs does not establish dependency. Some examples of this are:

a. The final conclusion asserts "Together, our study highlights the role of neuromodulation in organizing neuronal activity during sleep and sleep-dependent brain functions, such as memory.". However, the reported memory effects (impairment of fear conditioning) were not shown to be explicitly sleep-dependent.

b. Earlier in the discussion it mentions "Finally, we showed that local genetic ablation of 5-HT1a receptors in GCs impaired the ISO and memory consolidation". The effect shown was on general memory performance - consolidation was not specifically implicated.

(2) The assertion on page 9 that the results demonstrate "that the 5-HT is directly acting in the DG to gate the oscillations" is a bit strong given the magnitude of effect shown in Figure 6D, and the absence of demonstration of negative effect on cortical areas that also show ISO activity and could impact DG activity (see requested cortical sigma power analysis).

(3) Recent work has shown that abnormal DG GC activity can result from the use of the specific Ca indicator being used (GCaMP6s). (Teng, S., Wang, W., Wen, J.J.J. et al. Expression of GCaMP6s in the dentate gyrus induces tonic-clonic seizures. Sci Rep 14, 8104 (2024). https://doi.org/10.1038/s41598-024-58819-9). The authors of that study found that the effect seemed to be specific to GCaMP6s and that GCaMP6f did not lead to abnormal excitability. Note this is of particular concern given similar infraslow variation of cortical excitability in epilepsy (cf Vanhatalo et al. PNAS 2004). While I don't think that the experiments need to be repeated with a different indicator to address this concern, you should be able to use the 2p GCaMP7 experiments that have already been done to provide additional validation by repeating the analyses done for the GCaMP6s photometry experiments. This should be done anyway to allow appropriate comparison of the 2p and photometry results.

(4) While the discussion mentions previous work that has linked ISOs during sleep with regulation of cortical oscillations in the sigma band, oddly no such analysis is performed in the current work even though it is presumably available and would be highly relevant to the interpretation of a number of primary results including the relationship between the ISOs and MAs observed in the DG and similar results reported in other areas, as well as the selective impact of DG 5-HT1a knockdown on DG ISOs. For example, in the initial results describing the cross-correlation of calcium activity and EMG/EEG with MA episodes (paragraph 1, page 4), similar results relating brief arousals to the infraslow fluctuation in sleep spindles (sigma band) have been reported also at .02 Hz associated with variation in sensory arousability (cf. Cardis et al., "Cortico-autonomic local arousals and heightened somatosensory arousability during NREMS of mice in neuropathic pain", eLife 2021). It would be important to know whether the current results show similar cortical sigma band correlations. Also, in the results on ISO attenuation following 5-HT1 knockdown on page 7 (Figure 6), how is cortical EEG affected? Is ISO still seen in EEG but attenuated in DG?

(5) The illustrations of the effect of 5-HT1a knockdown shown in Figure 6 are somewhat misleading. The examples in panels B and C show an effect that is much more dramatic than the overall effect shown in panel D. Panels B and C do not appear to be representative examples. Which of the sample points in panel D are illustrated in panels B and C? It is not appropriate to arbitrarily select two points from different animals for comparison, or worse, to take points from the extremes of the distributions. If the intent is to illustrate what the effect shown in D looks like in the raw data, then you need to select examples that reflect the means shown in panel D. It is also important to show the effect on cortical EEG, particularly in sigma band to see if the effects are restricted to the DG ISOs. It would also be helpful to show that MAs and their correlations as shown in Figure 1 or G as well as broader sleep architecture are not affected.

(6) On page 9 of the results it states that GCs and MCs are upregulated during NREM and their activity is abruptly terminated by MAs through a 5-HT mediated mechanism. I didn't see anything showing the 5-HT dependence of the MA activity correlation. The results indicate a reduction in ISO modulation of GC activity but not the MA-correlated activity. I would like to see the equivalent of Figure 1,2 G panels with the 5-HT1a manipulation.

Reviewer #1 (Public review):

Summary:

This study is an important follow-up to their prior work - Wong et al. (2019), starting with clear questions and hypotheses, followed by a series of thoughtful and organized experiments. The method and results are convincing. Experiment 1 demonstrated the sensory preconditioned fear with few (8) or many (32) sound-light pairings. Experiments 2A and 2B showed the role of PRh NMDA receptors during conditioning for online integration, revealing that this contribution is present only after a few sound-light pairings, not after many sound-light pairings. Experiments 3A and 3B showed the contribution of PRh-BLA communication to online integration, again only after a few but not after many. Contrary to Experiments 3A and 3B, Experiments 4A and 4B showed the contribution of PRh-BLA communication to integration at test only after many but not few sound-light pairings.

Strengths:

Throughout the manuscript, the methods and results are clearly organized and described, and the use of statistics is solid, all contributing to the overall clarity of the research. The discussion section was also well-written, effectively comparing the current research with the prior work and offering insightful interpretations and potential future directions for this line of research. I have only a limited amount of concerns about some results and some details of experiments/statistics.

Weaknesses:

Could you provide further interpretation regarding line 171: the observation that sensory preconditioned fear increased with the number of sound-light pairings? Was this increase due to better sound-light association learning during Stage 1? Additionally, were there any experimental differences between Experiment 1 and the other experiments that might explain why freezing was higher in the P32 group compared to the P8 group? This pattern seemed to be absent in the other experiments. If we consider the hypothesis that the online integration mechanism is more active with fewer pairings and the chaining mechanism at the test is more prominent with many pairings, we wouldn't expect a difference between the P8 and P32 groups. Given the relatively small sample size in Experiment 1, the authors might consider conducting a cross-experiment analysis or something similar to investigate this further.

Reviewer #2 (Public review):

This manuscript builds on the authors' earlier work, most recently Wong et al. 2019, in which they showed the importance of the perirhinal cortex (PRh) during the first-order conditioning stage of sensory preconditioning. Sensory preconditioning requires learning between two neutral stimuli (S2-S1) and subsequent development of a conditioned response to one of the neutral stimuli after pairing of the other stimulus with a motivationally relevant unconditioned stimulus (S1-US). One highly debated question regarding the mechanisms of learning of sensory preconditioning has been whether conditioned responses evoked by the indirectly trained stimulus (S2) occur through a mediated representation at the time of the first-order US training, or whether the conditioned responses develop through a chained evoked representation (S2--> S1 --> US) at the time of test. The authors' prior findings provided strong evidence for PRh being involved in mediated learning during the first-order training. They showed that protein synthesis was required during the first-order S1-US learning to support the conditioned response to the indirectly trained stimulus (S2) at the test.

One question remaining following the previous paper was whether certain conditions may promote a chaining mechanism over mediated learning, as there is some evidence for chained representations at the time of the test. In this paper, the authors directly address this important question and find unambiguous results that the extent of training during the preconditioning stage impacts the involvement of PRh during the first-order conditioning or stage 2. They show that putative blockade of synaptic changes in PRh, using an NMDA antagonist, disrupts responding to the preconditioned cue at test during shorter duration preconditioning training (8 trials), but not during extended training (32 trials). They also show that this is the case for communication between the PRh and BLA during the same stage of training using a contralateral inactivation approach. This confirms their previous findings in 2019 of connectivity between these regions for the short-duration training, while they observe here for the first time that this is not the case for extended training. Finally, they show that with extended training, communication between BLA and the PRh is required at the final test of the preconditioned stimulus, but not for the short duration training.

The results are clear and extremely consistent across experiments within this paper as well as with earlier work. The experiments here are thorough, and well-conceived, and address an important and highly debated question in the field regarding the neural and psychological mechanisms underlying sensory preconditioning. This work is highly impactful for the field as the debate over mediated versus chaining mechanisms has been an important topic for more than 70 years.

Reviewer #3 (Public review):

The authors tested whether the number of stimulus-stimulus pairings alters whether preconditioned fear depends on online integration during the formation of the stimulus-outcome memory or during the probe test/mobilization phase, when the original stimulus, which was never paired with aversive events, elicits fear via chaining of stimulus-stimulus and stimulus-outcome memories. They found that sensory preconditioning was successful with either 8 or 32 stimulus-stimulus pairings. Perirhinal cortex NMDA receptor blockade during stimulus-outcome learning impaired preconditioning following 8 but not 32 pairings during preconditioning. Therefore, perirhinal cortex NMDA activity is required for online integration or mediated learning. Perirhinal-basolateral amygdala had nearly identical effects with the same interpretation: these areas communicate during stimulus-outcome learning, and this online communication is required for later expressing preconditioned fear. Disconnection prior to the probe test, when chaining might occur, had different effects: it impaired the expression of preconditioned fear in rats that received 32, but not 8, pairings during preconditioning. The study has several strengths and provides a thoughtful discussion of future experiments. The study is highly impactful and significant; the authors were successful in describing the behavioral and neurobiological mechanisms of mediated learning versus chaining in sensory preconditioning, which is often debated in the learning field. Therefore this study will have a significant impact on the behavioral neurobiology and learning fields.

Strengths:

Careful, rigorous experimental design and statistics.

The discussion leaves open questions that are very much worth exploring. For example - why did perirhinal-amygdala disconnection prior to the probe have no effect in the 8-pairing group, when bilateral perirhinal inactivation did (in Wong et al, 2019)? The authors propose that perirhinal cortex outputs bypass the amygdala during the probe test, which is an excellent hypothesis to test.

The authors provide evidence that both mediated learning and chaining occur.

Weaknesses:

This is inherent to all neural interference and behavioral experiments: biological/psychological functions do not typically operate binarily. There is no single clear number or parameter at which mediated learning or chaining happens, and both probably happen to some extent. Addressing this is even more difficult given behavioral variability across subjects, implant sites, etc. Thus, this is not so much a weakness particular to this study as much as an existential problem, which the authors were able to work around with careful experimental design and appropriate controls.

Reviewer #1 (Public review):

Summary:

The behavioral strategies underlying decisions based on perceptual evidence are often studied in the lab with stimuli whose elements provide independent pieces of decision-related evidence that can thus be equally weighted to form a decision. In more natural scenarios, in contrast, the information provided by these pieces is often correlated, which impacts how they should be weighted. Tardiff, Kang & Gold set out to study decisions based on correlated evidence and compare the observed behavior of human decision-makers to normative decision strategies. To do so, they presented participants with visual sequences of pairs of localized cues whose location was either uncorrelated, or positively or negatively correlated, and whose mean location across a sequence determined the correct choice. Importantly, they adjusted this mean location such that, when correctly weighted, each pair of cues was equally informative, irrespective of how correlated it was. Thus, if participants follow the normative decision strategy, their choices and reaction times should not be impacted by these correlations. While Tardiff and colleagues found no impact of correlations on choices, they did find them to impact reaction times, suggesting that participants deviated from the normative decision strategy. To assess the degree of this deviation, Tardiff et al. adjusted drift-diffusion models (DDMs) for decision-making to process correlated decision evidence. Fitting these models to the behavior of individual participants revealed that participants considered correlations when weighing evidence, but did so with a slight underestimation of the magnitude of this correlation. This finding made Tardiff et al. conclude that participants followed a close-to-normative decision strategy that adequately took into account correlated evidence.

Strengths:

The authors adjust a previously used experimental design to include correlated evidence in a simple, yet powerful way. The way it does so is easy to understand and intuitive, such that participants don't need extensive training to perform the task. Limited training makes it more likely that the observed behavior is natural and reflective of everyday decision-making. Furthermore, the design allowed the authors to make the amount of decision-related evidence equal across different correlation magnitudes, which makes it easy to assess whether participants correctly take account of these correlations when weighing evidence: if they do, their behavior should not be impacted by the correlation magnitude.

The relative simplicity with which correlated evidence is introduced also allowed the authors to fall back to the well-established DDM for perceptual decisions, which has few parameters, is known to implement the normative decision strategy in certain circumstances, and enjoys a great deal of empirical support. The authors show how correlations ought to impact these parameters, and which changes in parameters one would expect to see if participants mis-estimate these correlations or ignore them altogether (i.e., estimate correlations to be zero). This allowed them to assess the degree to which participants took into account correlations on the full continuum from perfect evidence weighting to complete ignorance. With this, they could show that participants in fact performed rational evidence weighting if one assumed that they slightly underestimated the correlation magnitude.

Weaknesses:

The experiment varies the correlation magnitude across trials such that participants need to estimate this magnitude within individual trials. This has several consequences:

(1) Given that correlation magnitudes are estimated from limited data, the (subjective) estimates might be biased towards their average. This implies that, while the amount of evidence provided by each 'sample' is objectively independent of the correlation magnitude, it might subjectively depend on the correlation magnitude. As a result, the normative strategy might differ across correlation magnitudes, unlike what is suggested in the paper. In fact, it might be the case that the observed correlation magnitude underestimates corresponds to the normative strategy.

(2) The authors link the normative decision strategy to putting a bound on the log-likelihood ratio (logLR), as implemented by the two decision boundaries in DDMs. However, as the authors also highlight in their discussion, the 'particle location' in DDMs ceases to correspond to the logLR as soon as the strength of evidence varies across trials and isn't known by the decision maker before the start of each trial. In fact, in the used experiment, the strength of evidence is modulated in two ways:<br /> (i) by the (uncorrected) distance of the cue location mean from the decision boundary (what the authors call the evidence strength) and<br /> (ii) by the correlation magnitude. Both vary pseudo-randomly across trials, and are unknown to the decision-maker at the start of each trial. As previous work has shown (e.g. Kiani & Shadlen (2009), Drugowitsch et al. (2012)), the normative strategy then requires averaging over different evidence strength magnitudes while forming one's belief. This averaging causes the 'particle location' to deviate from the logLR. This deviation makes it unclear if the DDM used in the paper indeed implements the normative strategy, or is even a good approximation to it.

Given that participants observe 5 evidence samples per second and on average require multiple seconds to form their decisions, it might be that they are able to form a fairly precise estimate of the correlation magnitude within individual trials. However, whether this is indeed the case is not clear from the paper.

Furthermore, the authors capture any underestimation of the correlation magnitude by an adjustment to the DDM bound parameter. They justify this adjustment by asking how this bound parameter needs to be set to achieve correlation-independent psychometric curves (as observed in their experiments) even if participants use a 'wrong' correlation magnitude to process the provided evidence. Curiously, however, the drift rate, which is the second critical DDM parameter, is not adjusted in the same way. If participants use the 'wrong' correlation magnitude, then wouldn't this lead to a mis-weighting of the evidence that would also impact the drift rate? The current model does not account for this, such that the provided estimates of the mis-estimated correlation magnitudes might be biased.

Lastly, the paper makes it hard to assess how much better the participants' choices would be if they used the correct correlation magnitudes rather than underestimates thereof. This is important to know, as it only makes sense to strictly follow the normative strategy if it comes with a significant performance gain.

Reviewer #2 (Public review):

Summary:

This study by Tardiff, Kang & Gold seeks to: i) develop a normative account of how observers should adapt their decision-making across environments with different levels of correlation between successive pairs of observations, and ii) assess whether human decisions in such environments are consistent with this normative model.

The authors first demonstrate that, in the range of environments under consideration here, an observer with full knowledge of the generative statistics should take both the magnitude and sign of the underlying correlation into account when assigning weight in their decisions to new observations: stronger negative correlations should translate into stronger weighting (due to the greater information furnished by an anticorrelated generative source), while stronger positive correlations should translate into weaker weighting (due to the greater redundancy of information provided by a positively correlated generative source). The authors then report an empirical study in which human participants performed a perceptual decision-making task requiring accumulation of information provided by pairs of perceptual samples, under different levels of pairwise correlation. They describe a nuanced pattern of results with effects of correlation being largely restricted to response times and not choice accuracy, which could partly be captured through fits of their normative model (in this implementation, an extension of the well-known drift-diffusion model) to the participants' behaviour while allowing for mis-estimation of the underlying correlations.

Strengths:

As the authors point out in their very well-written paper, appropriate weighting of information gathered in correlated environments has important consequences for real-world decision-making. Yet, while this function has been well studied for 'high-level' (e.g. economic) decisions, how we account for correlations when making simple perceptual decisions on well-controlled behavioural tasks has not been investigated. As such, this study addresses an important and timely question that will be of broad interest to psychologists and neuroscientists. The computational approach to arrive at normative principles for evidence weighting across environments with different levels of correlation is very elegant, makes strong connections with prior work in different decision-making contexts, and should serve as a valuable reference point for future studies in this domain. The empirical study is well designed and executed, and the modelling approach applied to these data showcases a deep understanding of relationships between different parameters of the drift-diffusion model and its application to this setting. Another strength of the study is that it is preregistered.

Weaknesses:

In my view, the major weaknesses of the study center on the narrow focus and subsequent interpretation of the modelling applied to the empirical data. I elaborate on each below:

Modelling interpretation: the authors' preference for fitting and interpreting the observed behavioural effects primarily in terms of raising or lowering the decision bound is not well motivated and will potentially be confusing for readers, for several reasons. First, the entire study is conceived, in the Introduction and first part of the Results at least, as an investigation of appropriate adjustments of evidence weighting in the face of varying correlations. The authors do describe how changes in the scaling of the evidence in the drift-diffusion model are mathematically equivalent to changes in the decision bound - but this comes amidst a lengthy treatment of the interaction between different parameters of the model and aspects of the current task which I must admit to finding challenging to follow, and the motivation behind shifting the focus to bound adjustments remained quite opaque. Second, and more seriously, bound adjustments of the form modelled here do not seem to be a viable candidate for producing behavioural effects of varying correlations on this task. As the authors state toward the end of the Introduction, the decision bound is typically conceived of as being "predefined" - that is, set before a trial begins, at a level that should strike an appropriate balance between producing fast and accurate decisions. There is an abundance of evidence now that bounds can change over the course of a trial - but typically these changes are considered to be consistently applied in response to learned, predictable constraints imposed by a particular task (e.g. response deadlines, varying evidence strengths). In the present case, however, the critical consideration is that the correlation conditions were randomly interleaved across trials and were not signaled to participants in advance of each trial - and as such, what correlation the participant would encounter on an upcoming trial could not be predicted. It is unclear, then, how participants are meant to have implemented the bound adjustments prescribed by the model fits. At best, participants needed to form estimates of the correlation strength/direction (only possible by observing several pairs of samples in sequence) as each trial unfolded, and they might have dynamically adjusted their bounds (e.g. collapsing at a different rate across correlation conditions) in the process. But this is very different from the modelling approach that was taken. In general, then, I view the emphasis on bound adjustment as the candidate mechanism for producing the observed behavioural effects to be unjustified (see also next point).

Modelling focus: Related to the previous point, it is stated that participants' choice and RT patterns across correlation conditions were qualitatively consistent with bound adjustments (p.20), but evidence for this claim is limited. Bound adjustments imply effects on both accuracy and RTs, but the data here show either only effects on RTs, or RT effects mixed with accuracy trends that are in the opposite direction to what would be expected from bound adjustment (i.e. slower RT with a trend toward diminished accuracy in the strong negative correlation condition; Figure 3b). Allowing both drift rate and bound to vary with correlation conditions allowed the model to provide a better account of the data in the strong correlation conditions - but from what I can tell this is not consistent with the authors' preregistered hypotheses, and they rely on a posthoc explanation that is necessarily speculative and cannot presently be tested (that the diminished drift rates for higher negative correlations are due to imperfect mapping between subjective evidence strength and the experimenter-controlled adjustment to objective evidence strengths to account for effects of correlations). In my opinion, there are other candidate explanations for the observed effects that could be tested but lie outside of the relatively narrow focus of the current modelling efforts. Both explanations arise from aspects of the task, which are not mutually exclusive. The first is that an interesting aspect of this task, which contrasts with most common 'univariate' perceptual decision-making tasks, is that participants need to integrate two pieces of information at a time, which may or may not require an additional computational step (e.g. averaging of two spatial locations before adding a single quantum of evidence to the building decision variable). There is abundant evidence that such intermediate computations on the evidence can give rise to certain forms of bias in the way that evidence is accumulated (e.g. 'selective integration' as outlined in Usher et al., 2019, Current Directions in Psychological Science; Luyckx et al., 2020, Cerebral Cortex) which may affect RTs and/or accuracy on the current task. The second candidate explanation is that participants in the current study were only given 200 ms to process and accumulate each pair of evidence samples, which may create a processing bottleneck causing certain pairs or individual samples to be missed (and which, assuming fixed decision bounds, would presumably selectively affect RT and not accuracy). If I were to speculate, I would say that both factors could be exacerbated in the negative correlation conditions, where pairs of samples will on average be more 'conflicting' (i.e. further apart) and, speculatively, more challenging to process in the limited time available here to participants. Such possibilities could be tested through, for example, an interrogation paradigm version of the current task which would allow the impact of individual pairs of evidence samples to be more straightforwardly assessed; and by assessing the impact of varying inter-sample intervals on the behavioural effects reported presently.

Reviewer #1 (Public review):

The manuscript by Chen et al. investigated the interaction between CHI3L1, a chitinase-like protein in the 18 glycosyl hydrolase family, and gut bacteria in the mucosal layers. The authors provided evidence to document the direct interaction between CHI3L1 and peptidoglycan, a major component of bacterial cell wall. Doing so, Chi3l1 produced by gut epithelial cells regulates the balance of gut microbiome and diminishes DSS-induced colitis, potentially through the colonization of protective gram-positive bacteria such as lactobacillus.

The study is the first to systemically document the interactions between Chi3L1 and microbiome. Convincing data were shown to characterize the imbalance of gram-positive bacteria in the newly generated gut epithelial-specific Chi3L1 deficient mice. Comprehensive FMT experiments were performed to demonstrate the contributions of gut microbiome using the mouse colitis model. The manuscript is strengthened by additional mechanistic studies concerning the binding between Chi3l1 and peptidoglycan, and discussions on existing body of literature demonstrating that detrimental roles of Chi3l1 in mouse IBD model, which conflict with the current study.

Reviewer #2 (Public review):

Chen et al. investigated the regulatory mechanism of bacterial colonization in the intestinal mucus layer in mice and its implications to intestinal diseases. They demonstrated that Chi3l1 is a protein produced and secreted by intestinal epithelial cells into the mucus layer upon response to the gut microbiota, which has a turnover effect on facilitating the colonization of gram-positive bacteria in the mucosa. The data also indicate that Chi3l1 interacts with the peptidoglycan of the bacteria cell wall, supporting the colonization of beneficial bacteria strains such as Lactobacillus, and that deficiency in Chi3l1 predisposes mice to colitis. The inclusion of a small but pertinent piece of human data added to solidify their findings in mice.

Overall, the experiments were appropriately designed and executed with precision. The revised manuscript represents a significant improvement over the initial version. The inclusion of new, higher-resolution images provides stronger support for the conclusions drawn. Additionally, statistical analyses of the imaging data, as recommended, have been integrated. The authors have effectively addressed the majority of the reviewers' suggestions and criticisms, making this version well-suited for publication.

Reviewer #1 (Public Review):

Summary:

In this manuscript the authors investigate the contributions of the long noncoding RNA snhg3 in liver metabolism and MAFLD. The authors conclude that liver-specific loss or overexpression of Snhg3 impacts hepatic lipid content and obesity through epigenetic mechanisms. More specifically, the authors invoke that nuclear activity of Snhg3 aggravates hepatic steatosis by altering the balance of activating and repressive chromatin marks at the Pparg gene locus. This regulatory circuit is dependent on a transcriptional regulator SNG1.

Strengths:

The authors developed a tissue specific lncRNA knockout and KI models. This effort is certainly appreciated as few lncRNA knockouts have been generated in the context of metabolism. Furthermore, lncRNA effects can be compensated in a whole organism or show subtle effects in acute versus chronic perturbation, rendering the focus on in vivo function important and highly relevant. In addition, Snhg3 was identified through a screening strategy and as a general rule the authors the authors attempt to follow unbiased approaches to decipher the mechanisms of Snhg3.

Reviewer #2 (Public Review):

Through RNA analysis, Xie et al found LncRNA Snhg3 was one of the most down-regulated Snhgs by high fat diet (HFD) in mouse liver. Consequently, the authors sought to examine the mechanism through which Snhg3 is involved in the progression of metabolic dysfunction-associated fatty liver diseases (MASLD) in HFD-induced obese (DIO) mice. Interestingly, liver-specific Sngh3 knockout reduced, while Sngh3 over-expression potentiated fatty liver in mice on a HFD. Using the RNA pull-down approach, the authors identified SND1 as a potential Sngh3 interacting protein. SND1 is a component of the RNA-induced silencing complex (RISC). The authors found that Sngh3 increased SND1 ubiquitination to enhance SND1 protein stability, which then reduced the level of repressive chromatin H3K27me3 on PPARg promoter. The upregulation of PPARg, a lipogenic transcription factor, thus contributed to hepatic fat accumulation.

The authors propose a signaling cascade that explains how LncRNA sngh3 may promote hepatic steatosis. Multiple molecular approaches have been employed to identify molecular targets of the proposed mechanism, which is a strength of the study.

Reviewer #1 (Public review):

Summary:

This manuscript nicely outlines a conceptual problem with the bFAC model in A-motility, namely, how the energy derived from the inner membrane AglRQS motor transduced through the cell wall into mechanical force on the cell surface to drive motility? To address this, the authors make a significant contribution by identifying and characterizing a lytic transglycosylase (LTG) called AgmT. This work thus provides clues and a future framework work to address mechanical force transmission from the cytoplasm through the cell envelope to the cell surface.

Strengths:

(i) Convincing evidence shows AgmT functions as a LTG and, surprisingly, that mltG from E. coli complements the swarming defect of an agmT mutant.

(ii) Show 13 other LTGs found in M. xanthus are not required for A-motility.

(iii) Authors show agmT mutants develop morphological changes in response to treatment with a beta-lactam antibiotic, mecillinam.

(iv) The use of single molecule tracking to monitor the assembly and dynamics of bFACs in WT and mutant backgrounds.

(v) The authors understand the limitations of their work and do not overinterpret their data.

Weaknesses:

The authors provided more experiments and clearly addressed my prior concerns in their revised manuscript.

Reviewer #2 (Public review):

The manuscript by Carbo et al. reports a novel role for the MltG homolog AgmT in gliding motility in M. xanthus. The authors conclusively show that AgmT is a cell wall lytic enzyme (likely a lytic transglycosylase), its lytic activity is required for gliding motility, and that its activity is required for proper binding of a component of the motility apparatus to the cell wall. The data are generally well-controlled. The marked strength of the manuscript includes the detailed characterization of AgmT as a cell wall lytic enzyme, and the careful dissection of its role in motility. Using multiple lines of evidence, the authors conclusively show that AgmT does not directly associate with the motility complexes, but that instead its absence (or the overexpression of its active site mutant) results in failure of focal adhesion complexes to properly interact with the cell wall.

Reviewer #1 (Public review):

The authors present data on outer membrane vesicle (OMV) production in different mutants, but they state that this is beyond the scope of the current manuscript, which I disagree with. This data could provide valuable physiological context that is otherwise lacking. The preliminary blots suggest that YafK does not alter OMV biogenesis. I recommend repeating these blots with appropriate controls, such as blotting for proteins in the culture media, an IM protein, periplasmic protein and an OM protein to strengthen the reliability of these findings. Including this data in the manuscript, even if it does not directly support the initial hypothesis, would enhance the physiological relevance of the study. Currently, the manuscript relies completely on the experimental setup (labeling-mass spec) previously developed by the authors, which limits the broader scope and interpretability of this study.

Additionally susceptibility of strains to detergents like SDS can be tested to provide a much needed physisological context to the study.

In summary, the authors should consider revising the manuscript to improve clarity, substantiate their claims with more detailed evidence, and include additional experimental results that provide necessary physiological context to their study.

Comments on the revised version:

Regarding my comments from last review on a new figure on OMV analysis, The authors have redirected me to their previous response and have not performed the suggested control blots. I do not get their argument that this is for specialized audience. I do not have any more comments.

Reviewer #1 (Public review):

Summary:

An investigation of the dynamics of a neural network model characterized by sparsely connected clusters of neuronal ensembles. The authors found that such a network could intrinsically generate sequence preplay and place maps, with properties like those observed in the real-world data.

Strengths:

Computational model and data analysis supporting the hippocampal network mechanisms underlying sequence preplay of future experiences and place maps.<br /> The revised version of the manuscript addressed all my comments and as a result is significantly improved.

Weaknesses:

None noted

Reviewer #2 (Public review):

Summary:

The authors show that a spiking network model with clustered connectivity produces intrinsic spike sequences when driven with an ramping input, which are recapitulated in the absence of input. This behavior is only seen for some network parameters (neuron cluster participation and number of clusters in the network), which correspond to those that produce a small world network. By changing the strength of ramping input to each network cluster, the network can show different sequences.

Strengths:

A strength of the paper is the direct comparison between the properties of the model and neural data.

Weaknesses:

My main critique of the paper relates to the form of the input to the network. Specifically, it's unclear how much the results depend on the choice of a one-dimensional environment with ramping input. While this is an elegant idealization that allows the authors to explore the representation and replay properties of their model, it is a strong and highly non-physiological constraint. In order to address this concern, the authors would need to test the spatial tuning of their network in 2-dimensional environments, and with different kinds of input from a population of neurons that have a range of degree of spatial tuning and physiological plausibility. A method for systematically producing input with varying degrees of spatial tuning in both 1D and 2D environments has been previously used in (Fang et al 2023, eLife, see Figures 4 and 5), which could be readily adapted for the current study; and behaviorally plausible trajectories in 2D can be produced using the RatInABox package (George et al 2022, bioRxiv), which can also generate e.g. grid cell-like activity that could be used as physiologically plausible input to the network.

Reviewer #3 (Public review):

This work offers a novel perspective to the question of how hippocampal networks can adaptively generate different spatial maps and replays of the corresponding place cells, without any such maps pre-existing in the network architecture or its inputs. And how can these place cells preplay their sequences even before the environment is experienced? Previous models required pre-existing spatial representations to be artificially introduced, limiting their adaptability to new environments. Others depended on synaptic plasticity rules which made remapping slower that what is seen in recordings. In contrast, this modeling study proposes that quickly-adaptive intrinsic spiking sequences (preplays) and spatially tuned spiking (place cells) can be generated in a network through randomly clustered recurrent connectivity. By simulating spatial exploration through border-cell-like synaptic inputs, the model generates place cells for different "environments" without the need to reconfigure its synaptic connectivity or introduce plasticity. By simulating sleep-like random synaptic inputs, the model generates sequential activations of cells, mimicking preplays. These "preplays" require small-world connectivity, so that cell clusters are activated in sequence. Using a set of electrophysiological recordings from CA1, the authors confirm that the modeled place cells and replays share many features with recorded ones.

Many features of the model are thoroughly examined, and conclusions are overall convincing (within the simple architecture of the model). Even though the modeled connectivity applies more closely to CA3, it remains unclear whether CA3 recapitulates the proposed small world architecture.

In any case, the proposal that a small-world-structured, clustered network can generate flexible place cells and replays without the need for pre-configured maps is novel and of potential interest to a wide computational and experimental community.

Reviewer #1 (Public review):

Summary:

Here, the authors propose that changes in m6A levels may be predictable via a simple model that is based exclusively on mRNA metabolic events. Under this model, m6A mRNAs are "passive" victims of RNA metabolic events with no "active" regulatory events needed to modulate their levels by m6A writers, readers, or erasers; looking at changes in RNA transcription, RNA export, and RNA degradation dynamics is enough to explain how m6A levels change over time.

The relevance of this study is extremely high at this stage of the epi transcriptome field. This compelling paper is in line with more and more recent studies showing how m6A is a constitutive mark reflecting overall RNA redistribution events. At the same time, it reminds every reader to carefully evaluate changes in m6A levels if observed in their experimental setup. It highlights the importance of performing extensive evaluations on how much RNA metabolic events could explain an observed m6A change.

Weaknesses:

It is essential to notice that m6ADyn does not exactly recapitulate the observed m6A changes. First, this can be due to m6ADyn's limitations. The authors do a great job in the Discussion highlighting these limitations. Indeed, they mention how m6ADyn cannot interpret m6A's implications on nuclear degradation or splicing and cannot model more complex scenario predictions (i.e., a scenario in which m6A both impacts export and degradation) or the contribution of single sites within a gene.

Secondly, since predictions do not exactly recapitulate the observed m6A changes, "active" regulatory events may still play a partial role in regulating m6A changes. The authors themselves highlight situations in which data do not support m6ADyn predictions. Active mechanisms to control m6A degradation levels or mRNA export levels could exist and may still play an essential role.

(1) "We next sought to assess whether alternative models could readily predict the positive correlation between m6A and nuclear localization and the negative correlations between<br /> m6A and mRNA stability. We assessed how nuclear decay might impact these associations by introducing nuclear decay as an additional rate, δ. We found that both associations were robust to this additional rate (Supplementary Figure 2a-c)."<br /> Based on the data, I would say that model 2 (m6A-dep + nuclear degradation) is better than model 1. The discussion of these findings in the Discussion could help clarify how to interpret this prediction. Is nuclear degradation playing a significant role, more than expected by previous studies?

(2) The authors classify m6A levels as "low" or "high," and it is unclear how "low" differs from unmethylated mRNAs.

(3) The authors explore whether m6A changes could be linked with differences in mRNA subcellular localization. They tested this hypothesis by looking at mRNA changes during heat stress, a complex scenario to predict with m6ADyn. According to the collected data, heat shock is not associated with dramatic changes in m6A levels. However, the authors observe a redistribution of m6A mRNAs during the treatment and recovery time, with highly methylated mRNAs getting retained in the nucleus being associated with a shorter half-life, and being transcriptional induced by HSF1. Based on this observation, the authors use m6Adyn to predict the contribution of RNA export, RNA degradation, and RNA transcription to the observed m6A changes. However:

(a) Do the authors have a comparison of m6ADyn predictions based on the assumption that RNA export and RNA transcription may change at the same time?

(b) They arbitrarily set the global reduction of export to 10%, but I'm not sure we can completely rule out whether m6A mRNAs have an export rate during heat shock similar to the non-methylated mRNAs. What happens if the authors simulate that the block in export could be preferential for m6A mRNAs only?

(c) The dramatic increase in the nucleus: cytoplasmic ratio of mRNA upon heat stress may not reflect the overall m6A mRNA distribution upon heat stress. It would be interesting to repeat the same experiment in METTL3 KO cells. Of note, m6A mRNA granules have been observed within 30 minutes of heat shock. Thus, some m6A mRNAs may still be preferentially enriched in these granules for storage rather than being directly degraded. Overall, it would be interesting to understand the authors' position relative to previous studies of m6A during heat stress.

(d) Gene Ontology analysis based on the top 1000 PC1 genes shows an enrichment of GOs involved in post-translational protein modification more than GOs involved in cellular response to stress, which is highlighted by the authors and used as justification to study RNA transcriptional events upon heat shock. How do the authors think that GOs involved in post-translational protein modification may contribute to the observed data?

(e) Additionally, the authors first mention that there is no dramatic change in m6A levels upon heat shock, "subtle quantitative differences were apparent," but then mention a "systematic increase in m6A levels observed in heat stress". It is unclear to which systematic increase they are referring to. Are the authors referring to previous studies? It is confusing in the field what exactly is going on after heat stress. For instance, in some papers, a preferential increase of 5'UTR m6A has been proposed rather than a systematic and general increase.

Reviewer #2 (Public review):

Dierks et al. investigate the impact of m6A RNA modifications on the mRNA life cycle, exploring the links between transcription, cytoplasmic RNA degradation, and subcellular RNA localization. Using transcriptome-wide data and mechanistic modelling of RNA metabolism, the authors demonstrate that a simplified model of m6A primarily affecting cytoplasmic RNA stability is sufficient to explain the nuclear-cytoplasmic distribution of methylated RNAs and the dynamic changes in m6A levels upon perturbation. Based on multiple lines of evidence, they propose that passive mechanisms based on the restricted decay of methylated transcripts in the cytoplasm play a primary role in shaping condition-specific m6A patterns and m6A dynamics. The authors support their hypothesis with multiple large-scale datasets and targeted perturbation experiments. Overall, the authors present compelling evidence for their model which has the potential to explain and consolidate previous observations on different m6A functions, including m6A-mediated RNA export.

Reviewer #3 (Public review):

Summary:

This manuscript works with a hypothesis where the overall m6A methylation levels in cells are influenced by mRNA metabolism (sub-cellular localization and decay). The basic assumption is that m6A causes mRNA decay and this happens in the cytoplasm. They go on to experimentally test their model to confirm its predictions. This is confirmed by sub-cellular fractionation experiments which show high m6A levels in the nuclear RNA. Nuclear localized RNAs have higher methylation. Using a heat shock model, they demonstrate that RNAs with increased nuclear localization or transcription, are methylated at higher levels. Their overall argument is that changes in m6A levels are rather determined by passive processes that are influenced by RNA processing/metabolism. However, it should be considered that erasers have their roles under specific environments (early embryos or germline) and are not modelled by the cell culture systems used here.

Strengths:

This is a thought-provoking series of experiments that challenge the idea that active mechanisms of recruitment or erasure are major determinants for m6A distribution and levels.

Reviewer #1 (Public review):

Summary:

The study shows that Zizyphi spinosi semen (ZSS), particularly its non-extracted simple crush powder, has significant therapeutic effects on neurodegenerative diseases. It removes Aβ, tau, and α-synuclein oligomers, restores synaptophysin levels, enhances BDNF expression and neurogenesis, and improves cognitive and motor functions in mouse AD, FTD, DLB, and PD models. Additionally, ZSS powder reduces DNA oxidation and cellular senescence in normal-aged mice, increases synaptophysin, BDNF, and neurogenesis, and enhances cognition to levels comparable to young mice.

Weaknesses:

(1) While the study demonstrates that ZSS has protective effects across a wide range of animal models, including AD, FTD, DLB, PD, and both young and aged mice, it is broad and lacks a detailed investigation into the underlying mechanisms. This is the most significant concern.

(2) The authors highlight that the non-extracted simple crush powder of ZSS shows more substantial effects than its hot water extract and extraction residue. However, the manuscript provides very limited data comparing the effects of these three extracts.

(3) The authors have not provided a rationale for the dosing concentrations used, nor have they tested the effects of the treatment in normal mice to verify its impact under physiological conditions.

(4) Regarding the assessment of cognitive function in mice, the authors only utilized the Morris Water Maze (MWM) test, which includes a five-day spatial learning training phase followed by a probe trial. The authors focused solely on the learning phase. However, it is relevant to note that data from the learning phase primarily reflects the learning ability of the mice, while the probe trial is more indicative of memory. Therefore, it is essential that probe trial data be included for a more comprehensive analysis. A justification should be included to explain why the latency of 1st is about 50s not 60s.

(5) The BDNF immunohistochemical staining in the manuscript appears to be non-specific.

(6) The central pathological regions in PD are the substantia nigra and striatum. Please replace the staining results from the cortex and hippocampus with those from these regions in the PD model.