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 #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 #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 #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 #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 #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 #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 #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 #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 #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):

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 #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):

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.

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 #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 #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 #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 #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 #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 #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 #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 #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 #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 #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 #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 #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 #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 #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 #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 #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 #2 (Public Review):

Summary:

Yang et al. present an article investigating the spatiotemporal atlas of NFATc1+ and PDGFR-α+ cells within the dental and periodontal mesenchyme. The study explores their capacity for progeny cell generation and their relationships - both inclusive and hierarchical - under homeostatic conditions. Utilizing the Cre/loxP-Dre/Rox system to construct tool mice, combined with tissue transparency and continuous tissue slicing for 3D reconstruction, the researchers effectively mapped the distribution of NFATc1+ and PDGFR-α+ cells. Additionally, in conjunction with DTA mice, the study provides preliminary validation of the impact of PDGFR-α+ cells on dental pulp and periodontal tissues. Primarily, this study offers an in-situ distribution atlas for NFATc1+ and PDGFR-α+ cells but provides limited information regarding their origin, fate differentiation, and functionality.

Strengths:

(1) Tissue transparency techniques and continuous tissue slicing for 3D reconstruction, combined with transgenic mice, provide high-quality images and rich, reliable data.<br /> (2) The Cre/loxP and Dre/Rox systems used by the researchers are powerful and innovative.<br /> (3) The IR1 lineage tracing model is significantly important for investigating cellular differentiation pathways.<br /> (4) This study provides effective spatial distribution information of NFATc1+/PDGFR-α+ cell populations in the dental and periodontal tissues of adult mice.

Weaknesses:

(1) In the functional experiment section, the investigation into the role of NFATc1+/PDGFR-α+ cell populations is somewhat lacking.

(2) The author mentions that 3D reconstruction of consecutive tissue slices can provide more detailed information on cell distribution, so what is the significance of using tissue-clearing techniques in this article?

(3) After reading the entire article, it is confusing whether the purpose of the article is to explore the distribution and function of NFATc1+/PDGFR-α+ cells in teeth and periodontal tissues, or to compare the differences between tissue clearing techniques and 3D reconstruction of continuous histological slices using NFATc1+/PDGFR-α+ cells?

(4) The researchers did not provide a clear definition of the cell types of NFATc1+/PDGFR-α+ cells in teeth and periodontal tissues.

(5) In studies related to long bones, the author defines the NFATc1+/PDGFR-α+ cell population as SSCs, which as a stem cell group should play an important role in tooth development or injury repair. However, the distribution patterns and functions of the NFATc1+/PDGFR-α+ cell population in these two conditions have not been discussed in this study.

Reviewer #2 (Public review):

Summary:

The authors propose a methodology to perform causal (temporal) discovery. The approach appears to be robust and is tested in the different scenarios: one related with live-cell imaging data, and another one using synthetic (mathematically defined) time series data. They compare the performance of their findings against another well-know method by using metrics like F-score, precision and recall,

Strengths:

Performance, robustness, the text is clear and concise, The authors provide the code to review.

Weaknesses:

One concern could be the applicability of the method in other areas like climate, economy. For those areas, public data are available and might be interesting to test how the method performs with this kind of data.

Reviewer #2 (Public review):

Summary:

In this manuscript, the authors provide evidence that posttranslational modification of synuclein by N-acetylation increases clustering of synaptic vesicles in vitro. When using liposomes the authors found that while clustering is enhanced by the presence of either lysophosphatidylcholine (LPC) or phosphatidylcholine in the membrane, N-acetylation enhanced clustering only in the presence of LPC. Enhancement of binding was also observed when LPC micelles were used, which was corroborated by increased intra/intermolecular cross-linking of N-acetylated synuclein in the presence of LPC.

Strengths:

It is known for many years that synuclein binds to synaptic vesicles but the physiological role of this interaction is still debated. The strength of this manuscript is clearly in the structural characterization of the interaction of synuclein and lipids (involving NMR-spectroscopy) showing that the N-terminal 100 residues of synuclein are involved in LPC-interaction, and the demonstration that N-acetylation enhances the interaction between synuclein and LPC.

Weaknesses:

Lysophosphatides form detergent-like micelles that destabilize membranes, with their steady-state concentrations in native membranes generally being a lot lower than in the experiments reported here. Since no difference in binding between the N-acetylated and unmodified form was observed when the acidic phospholipid phosphatidylserine was included. It remains unclear to which extent binding to LPC is physiologically relevant, particularly in the light of recent reports from other laboratories showing that synuclein may interact with liquid-liquid phases of synapsin I, or associate with the unfolded regions of VAMP that both were reported to cause vesicle clustering.

Reviewer #2 (Public review):

Summary:

The manuscript by David et al. describes a novel image segmentation method, implementing Local Moran's method, which determines whether the value of a datapoint or a pixel is randomly distributed among all values, in differentiating pixel clusters from the background noise. The study includes several proof-of-concept analyses to validate the power of the new approach, revealing that implementation of Local Moran's method in image segmentation is superior to threshold-based segmentation methods commonly used in analyzing confocal images in neuroanatomical studies.

Strengths:

Several proof-of-concept experiments are performed to confirm the sensitivity and validity of the proposed method. Using composed images with varying levels of background noise and analyzing them in parallel with the Local Moran's or a Threshold-Based Method (TBM), the study is able to compare these approaches directly and reveal their relative power in isolating clustered pixels.

Similarly, dual immuno-electron microscopy was used to test the biological relevance of a colocalization that was revealed by Local Moran's segmentation approach on dual-fluorescent labeled tissue using immuno-markers of the axon terminal and a membrane-protein (Figure 5). The EM revealed that the two markers were present in terminals and their post-synaptic partners, respectively. This is a strong approach to verify the validity of the new approach for determining object-based colocalization in fluorescent microscopy.

The methods section is clear in explaining the rationale and the steps of the new method (however, see the weaknesses section). Figures are appropriate and effective in illustrating the methods and the results of the study. The writing is clear; the references are appropriate and useful.

Weaknesses:

While the steps of the mathematical calculations to implement Local Moran's principles for analyzing high-resolution images are clearly written, the manuscript currently does not provide a computation tool that could facilitate easy implementation of the method by other researchers. Without a user-friendly tool, such as an ImageJ plugin or a code, the use of the method developed by David et al by other investigators may remain limited.

This weakness is eliminated in the revision, which now provides the approach as a Matlab tool.

Reviewer #2 (Public Review):

Summary:

Alison G. Barber et al. reports the function of Msi2 in mouse models of non-small cell lung cancer. The expression of Msi2 in normal lung was evaluated using a knockin reporter allele. Msi2 expressing cells were found to be around 30-40% in normal lung epithelium without a strong bias in subsets of lung cells. Knocking out Msi2 in a KrasG12D and P53 KO model reduced lung cancer initiation. Knocking down Msi2 in established lung cancer cells reduced in vitro sphere formation and in vivo xenograft. Finally, the authors identified several genes whose expression was downregulated by Msi2 knockdown. Knocking down four of these genes, including Ptgds, Arl2bp, hRnf157, and Syt11, each with a single shRNA, reduced lung sphere formation in vitro, suggesting their involvement in lung cancer.

Strengths:

This manuscript represents an interesting advance on the role of Msi2 in lung cancer. While some of the data (for example the knockdown effect of Msi2 in established lung cancer cells) corroborated previous findings, the study of Msi2 expression in normal lung and the characterization of the KO phenotype in lung cancer initiation are new and interesting.

Weaknesses:

Two areas can be further strengthened. Several conclusions are not fully supported by the existing data. The stable/dynamic nature of Msi2 expressing cells in lung would benefit from more detailed investigations for proper data interpretation.

(1) It will be interesting to determine whether Msi2+ cells are a relatively stable subset or rather the Msi2+ cells in lung is a dynamic concept that is transient or interconvertible. This is relevant to the interpretation of what Msi2 positivity really means.

(2) Does Kras mutation and/or p53 loss upregulate Msi2? This point and the point above are related to whether Msi2+ cells are truly more susceptible to tumorigenesis, as the authors suggested.

(3) The KO of Msi2 reducing tumor number and burden in the lung cancer initiation model is interesting. However, there are two alternative interpretations. First, it is possible that the Msi2 KO mice (without Kras activation and p53 loss) has reduced total lung cell numbers or altered percentage of stem cells. There is currently only one sentence citing data not shown on line 125, commenting that there is no difference in BASC and AT2 cell populations. It will be helpful that such data are shown and the effect of KO on overall lung mass or cellularity is clarified. Second, the phenotype may also be due to a difference in the efficiencies of cre on Kras and p53 in the Msi2 WT and KO mice.

(4) All shRNA experiments (for both Msi2 KD and the KD of candidate genes) utilized a single shRNA. This approach cannot exclude off-target effects of the shRNA.

(5) The technical details of the PDX experiment (Figure 4F) are not fully explained.

Reviewer #3 (Public Review):

Summary:<br /> Adamic and colleagues present fMRI data from ADE patients and a healthy control group acquired during two interoceptive tasks (attention and perturbation) from the same session. They report convergent activity within the granular and dysgranular insular cortex during both tasks, with a patient group-specific lateralisation effect. Furthermore, insular functional connectivity was found to be linked to disease severity.

Strengths:<br /> The study is well-designed and - despite some limitations noted by the authors - provides much-needed insight into the functional pathways of interoceptive processing in health and disease. The manuscript is clear, concise, and well-written.

Weaknesses:<br /> None remain after the authors' revision.

Reviewer #2 (Public review):

Summary:

This paper presents an interesting and useful analysis of grid cell heterogeneity, showing that the experimentally observed heterogeneity of spacing and orientation within a grid cell module can allow more accurate decoding of location from a single module.

Strengths:

I found the statistical analysis of the grid cell variability to be very systematic and convincing. I also found the evidence for enhanced decoding of location based on between-cell variability within a module to be convincing and important, supporting their conclusions.

Weaknesses:

(1) Even though theoreticians might have gotten the mistaken impression that grid cells are highly regular, this might be due to an overemphasis on regularity in a subset of papers. Most experimentalists working with grid cells know that many if not most grid cells show high variability of firing fields within a single neuron, though this analysis focuses on between neurons. In response to this comment, the reviewers should tone down and modify their statements about what are the current assumptions of the field (and if possible provide a short supplemental section with direct quotes from various papers that have made these assumptions).

(2) The authors state that "no characterization of the degree and robustness of variability in grid properties within individual modules has been performed." It is always dangerous to speak in absolute terms about what has been done in scientific studies. It is true that few studies have had the number of grid cells necessary to make comparisons within and between modules, but many studies have clearly shown the distribution of spacing in neuronal data (e.g. Hafting et al., 2005; Barry et al., 2007; Stensola et al., 2012; Hardcastle et al., 2015) so the variability has been visible in the data presentations. Also, most researchers in the field are well aware that highly consistent grid cells are much rarer than messy grid cells that have unevenly spaced firing fields. This doesn't hurt the importance of the paper, but they need to tone down their statements about the lack of previous awareness of variability (specific locations are noted in the specific comments).

(3) The methods section needs to have a separate subheading entitled: How grid cells were assigned to modules" that clearly describes how the grid cells were assigned to a module (i.e. was this done by Gardner et al., or done as part of this paper's post-processing?

Reviewer #2 (Public review):

Summary:

While bacteria have the ability to induce genes in response to specific stresses, they also use the General Stress Response (GSR) to deal with growth conditions that presumably include a larger range of stresses (for instance, stationary phase growth). The activation of GSR-specific sigma factors is frequently at the heart of the induction of a GSR. Given the range of stresses that can lead to GSR induction, the regulatory inputs are frequently complex. In B. subtilis, the stressosome, a multi-protein complex, contains a set of proteins that, upon appropriate stresses, initiate partner switching cascades that free the sigma B sigma factor from an anti-sigma. The focus here is on the mode of activation of RsbU, a serine/threonine phosphatase of the PPM family, leading to sigB activation. RbsT, a component of the degradosome interacts with RsbU upon stress, activating the phosphatase activity. Once active, RsbU dephosphorylates its target (RsbV, an anti-antisigma), which in turn binds the anti-sigma. The conclusion is that flexible linker domains upstream of the phosphatase domain are the target for activation, via binding of proteins to the N-terminal domain, resulting in a crossed-linker dimeric structure. The authors then use the information on RsbU to suggest that parallel approaches are used to activate PPM phosphatases for the GSR response in other bacteria. (Biology vs. Mechanism, evolution?)

Strengths and Weaknesses:

Many of these have to do with clarifying what was done and why. This includes the presentation and content of the figures.

One issue relates to the background and context. A bit more information on the stresses that release RsbT would be useful here. The authors might also consider a figure showing the major conclusions and parallels for SpoIIE activation and possibly other partner switches that are discussed, introducing the switch change more clearly to set the stage for the work here (and the generalization). There are a lot of players to keep track of.

Reviewer #2 (Public Review):

Summary:

Mutations in SUFU are implicated in SHH medulloblastoma (MB). SUFU modulates Shh signaling in a context-dependent manner, making its role in MB pathology complex and not fully understood. This study reports that elevated FGF5 levels are associated with a specific subtype of SHH MB, particularly in pediatric cases. The authors demonstrate that Sufu deletion in a mouse model leads to abnormal proliferation of granule cell precursors (GCPs) at the secondary fissure (region B), correlating with increased Fgf5 expression. Notably, pharmacological inhibition of FGFR restores normal cerebellar development in Sufu mutant mice.

Strengths:

The identification of increased FGF5 in subsets of MB is novel and a key strength of the paper.

Weaknesses:

The study appears incomplete despite the potential significance of these findings. The current paper does not fully establish the causal relationship between Fgf5 and abnormal cerebellar development, nor does it clarify its connection to SUFU-related MB. Some conclusions seem overstated, and the central question of whether FGFR inhibition can prevent tumor formation remains untested.

Reviewer #2 (Public review):

The regulation of protein function heavily relies on the dynamic changes in the shape and structure of proteins and their complexes. These changes are widespread and crucial. However, examining such alterations presents significant challenges, particularly when dealing with large protein complexes in conditions that mimic the natural cellular environment. Therefore, much emphasis has been put on developing novel methods to study protein structure, interactions, and dynamics. Crosslinking mass spectrometry (CSMS) has established itself as such a prominent tool in recent years. However, doing this in a quantitative manner to compare structural changes between conditions has proven to be challenging due to several technical difficulties during sample preparation. Luo and Ranish introduce a novel set of isobaric labeling reagents, called Qlinkers, to allow for a more straightforward and reliable way to detect structural changes between conditions by quantitative CSMS (qCSMS).

The authors do an excellent job describing the design choices of the isobaric crosslinkers and how they have been optimized to allow for efficient intra- and inter-protein crosslinking to provide relevant structural information. Next, they do a series of experiments to provide compelling evidence that the Qlinker strategy is well suited to detect structural changes between conditions by qCSMS. First, they confirm the quantitative power of the novel-developed isobaric crosslinkers by a controlled mixing experiment. Then they show that they can indeed recover known structural changes in a set of purified proteins (complexes) - starting with single subunit proteins up to a very large 0.5 MDa multi-subunit protein complex - the polII complex.

The authors give a very measured and fair assessment of this novel isobaric crosslinker and its potential power to contribute to the study of protein structure changes. They show that indeed their novel strategy picks up expected structural changes, changes in surface exposure of certain protein domains, changes within a single protein subunit but also changes in protein-protein interactions. However, they also point out that not all expected dynamic changes are captured and that there is still considerable room for improvement (many not limited to this crosslinker specifically but many crosslinkers used for CSMS).

Taken together the study presents a novel set of isobaric crosslinkers that indeed open up the opportunity to provide better qCSMS data, which will enable researchers to study dynamic changes in the shape and structure of proteins and their complexes. However, in its current form, the study some aspects of the study should be expanded upon in order for the research community to assess the true power of these isobaric crosslinkers. Specifically:

Although the authors do mention some of the current weaknesses of their isobaric crosslinkers and qCSMS in general, more detail would be extremely helpful. Throughout the article a few key numbers (or even discussions) that would allow one to better evaluate the sensitivity (and the applicability) of the method are missing. This includes:

(1) Throughout all the performed experiments it would be helpful to provide information on how many peptides are identified per experiment and how many have actually a crosslinker attached to it.

(2) Of all the potential lysines that can be modified - how many are actually modified? Do the authors have an estimate for that? It would be interesting to evaluate in a denatured sample the modification efficiency of the isobaric crosslinker (as an upper limit as here all lysines should be accessible) and then also in a native sample. For example, in the MBP experiment, the authors report the change of one mono-linked peptide in samples containing maltose relative to the one not containing maltose. The authors then give a great description of why this fits to known structural changes. What is missing here is a bit of what changes were expected overall and which ones the authors would have expected to pick up with their method and why have they not been picked up. For example, were they picked up as modified by the crosslinker but not differential? I think this is important to discuss appropriately throughout the manuscript to help the reader evaluate/estimate the potential sensitivity of the method. There are passages where the authors do an excellent job doing that - for example when they mention the missed site that they expected to see in the initial the polII experiments (lines 191 to 207). This kind of "power analysis" should be heavily discussed throughout the manuscript so that the reader is better informed of what sensitivity can be expected from applying this method.

(3) It would be very helpful to provide information on how much better (or not) the Qlinker approach works relative to label-free qCLMS. One is missing the reference to a potential qCLMS gold standard (data set) or if such a dataset is not readily available, maybe one of the experiments could be performed by label-free qCLMS. For example, one of the differential biosensor experiments would have been well suited.

Reviewer #2 (Public review):

Summary:

Excessive sucrose is a possible initial factor for the development of metabolic dysfunction-associated fatty liver disease (MAFLD). To investigate the possibility that intervention with JNK inhibitor could lead to the treatment of metabolic dysfunction caused by excessive sucrose intake, the authors performed multi-organ transcriptomics analysis (liver, visceral fat (vWAT), skeletal muscle, and brain) in a rat model of MAFLD induced by sucrose overtake (+ a selective JNK2 and JNK3 inhibitor (JNK-IN-5A) treatment). Their data suggested that changes in gene expression in the vWAT as well as in the liver contribute to the pathogenesis of their MAFLD model and revealed that the JNK inhibitor has a cross-organ therapeutic effect on it.

Strengths:

(1) It has been previously reported that inhibition of JNK signalling can contribute to the prevention of hepatic steatosis (HS) and related metabolic syndrome in other models, but the role of JNK signalling in the metabolic disruption caused by excessive intake of sucrose, a possible initial factor for the development of MAFLD, has not been well understood, and the authors have addressed this point.

(2) This study is also important because pharmacological therapy for MAFLD has not yet been established.

(3) By obtaining transcriptomic data in multiple organs and comprehensively analyzing the data using gene co-expression network (GCN) analysis and genome-scale metabolic models (GEM), the authors showed the multi-organ interaction in not only in the pathology of MAFLD caused by excessive sucrose intake but also in the treatment effects by JNK-IN-5A.

(4) Since JNK signalling has diverse physiological functions in many organs, the authors effectively assessed possible side effects with a view to the clinical application of JNK-IN-5A.

Weaknesses:

(1) The metabolic process activities were evaluated using RNA-seq results in Figure 7, but direct data such as metabolite measurements are lacking.

(2) There is a lack of consistency in the data between JNK-IN-5A_D1 and _D2, and there is no sufficient data-based explanation for why the effects observed in D1 were inconsistent in the D2 samples.

(3) Although it is valuable that the authors were able to suggest the possibility of JNK inhibitor as a therapeutic strategy for MAFLD, the evaluation of the therapeutic effect was limited to the evaluation of plasma TG, LDH, and gene expression changes. As there was no evaluation of liver tissue images, it is unclear what changes were brought about in the liver by the excessive sucrose intake and the treatment with JNK-IN-5A.

Reviewer #2 (Public review):

Summary:<br /> The authors goal is to develop a more accurate system that reports TDP-43 activity as a splicing regulator. Prior to this, most methods employed western blotting or QPCR-based assays to determine whether targets of TDP-43 were up or down-regulated. The problem with that is the sensitivity. This approach uses an ectopic delivered construct containing splicing elements from CFTR and UNC13A (two known splicing targets) fused to a GFP reporter. Not only does it report TDP-43 function well, but it operates at extremely sensitive TDP-43 levels, requiring only picomolar TDP-43 knockdown for detection. This reporter should supersede the use of current TDP-43 activity assays, it's cost-effective, rapid and reliable.

Strengths:<br /> In general, the experiments are convincing and well designed. The rigor, number of samples and statistics, and gradient of TDP-43 knockdown were all viewed as strengths. In addition, the use of multiple assays to confirm the splicing changes were viewed as complimentary (ie PCR and GFP-fluorescence) adding additional rigor. The final major strength I'll add is the very clever approach to tether TDP-43 to the loss of function cassette such that when TDP-43 is inactive it would autoregulate and induce wild-type TDP-43. This has many implications for the use of other genes, not just TDP-43, but also other protective factors that may need to be re-established upon TDP-43 loss of function.

Weaknesses:<br /> Admittedly, one needs to initially characterize the sensor and the use of cell lines is an obvious advantage, but it begs the question of whether this will work in neurons. Additional future experiments in primary neurons will be needed. The bulk analysis of GFP-positive cells is a bit crude. As mentioned in the manuscript, flow sorting would be an easy and obvious approach to get more accurate homogenous data. This is especially relevant since the GFP signal is quite heterogeneous in the image panels, for example, Figure 1C, meaning the siRNA is not fully penetrant. Therefore, stating that 1% TDP-43 knockdown achieves the desired sensor regulation might be misleading. Flow sorting would provide a much more accurate quantification of how subtle changes in TDP-43 protein levels track with GFP fluorescence.

Some panels in the manuscript would benefit from additional clarity to make the data easier to visualize. For example, Figure 2D and 2G could be presented in a more clear manner, possibly split into additional graphs since there are too many outputs. Sup Figure 2A image panels would benefit from being labeled, its difficult to tell what antibodies or fluorophores were used. Same with Figure 4B.

Figure 3 is an important addition to this manuscript and in general is convincing showing that TDP-43 loss of function mutants can alter the sensor. However, there is still wild-type endogenous TDP-43 in these cells, and it's unclear whether the 5FL mutant is acting as a dominant negative to deplete the total TDP-43 pool, which is what the data would suggest. This could have been clarified. Additional treatment with stressors that inactivate TDP-43 could be tested in future studies.

Overall, the authors definitely achieved their goals by developing a very sensitive readout for TDP-43 function. The results are convincing, rigorous, and support their main conclusions. There are some minor weaknesses listed above, chief of which is the use of flow sorting to improve the data analysis. But regardless, this study will have an immediate impact for those who need a rapid, reliable, and sensitive assessment of TDP-43 activity, and it will be particularly impactful once this reporter can be used in isolated primary cells (ie neurons) and in vivo in animal models. Since TDP-43 loss of function is thought to be a dominant pathological mechanism in ALS/FTD and likely many other disorders, having these types of sensors is a major boost to the field and will change our ability to see sub-threshold changes in TDP-43 function that might otherwise not be possible with current approaches.

Reviewer #2 (Public review):

Summary

This work investigates how multiple DNA elements combine to regulate gene expression. The authors use an episomal reporter assay which measures the transcriptional output of the reporter under the regulation of an enhancer-enhancer-promoter triple. The authors test all combinations of 8 promoters and 59 enhancers in this assay. There are two main findings: (1) enhancer pairs generally combine additively on reporter output (2) the extent to which enhancers increase reporter output over the promoter (individually and as enhancer-enhancer pairs) is inversely related to the intrinsic strength of the promoter. Both of these findings are interesting and are well supported by the data.

This study extends previous results on enhancer-promoter combinations to enhancer-enhancer-promoter triples. For example the near equivalence of Fig. 5b and Fig. S7b is intriguing. This experimental design also provides the ability to investigate the notion of selectivity (also commonly referred to as compatibility) between enhancer-enhancer pairs and promoters.

The authors note many limitations, including the selection of the elements and the size and spacing of the tested elements. Some of the enhancer-enhancer-promoter triples they test were also investigated by a different experimental design in Brosh et al 2023. Brosh et al observed non-additivity between these elements while this study did not. Ultimately we do not know which mechanisms produce the non-additivity that has been observed in native loci and which experimental designs would preserve such mechanisms.

Overall this is a nice experimental design and a great dataset for probing how enhancers and promoters combine to regulate gene expression. I have no major concerns, but I will try to clarify some methodological points I found confusing.

Methodology<br /> The following two comments are meant to help the reader understand the methodology/terminology used in this paper and how it relates to other similar studies.

The interpretation that "promoters scale enhancer signals in a non-linear manner" is potentially confusing. I believe that the authors use "non-linear" to refer to the slopes (represented by the letter 'b' in Fig. 5b) being not equal to 1. Given how the boost index is defined, this implies the relationship

Activity of EEP = (Activity of CCP) * (Average Linear Boost)^b

One potential source of confusion is that the Average Linear Boost term itself depends on the set of promoters that are assayed. Averaging across (many) promoters may alleviate this concern, in which case Average Linear Boost may be considered some form of intrinsic enhancer strength. If so, there is a correspondence between this terminology and the terminology presented in Bergman et al 2022. If b not equal to 1 refers to a non-linear scaling, then the reader may think that b=1 refers to a linear scaling. But if b=1, and the Average Linear Boost term is interpreted as intrinsic enhancer strength, then the equation above implies that the activity of EEP is equal to an intrinsic promoter strength times an intrinsic enhancer strength. This is essentially the relationship that is considered in Bergman et al 2022 and which is referred to in that paper as 'multiplicative'. The purpose of this comment is not to argue for what is the relationship that best explains the data, it is just to clarify the terminology.

Enhancer-promoter selectivity: As a follow-up to a previous study (Martinez-Ara et al, Molecular Cell 2022) the authors mention that the data in this study also shows that enhancers show selectivity for certain promoters. I found the methodology hard to follow, so this section of the review is meant to guide the reader in understanding how the authors define 'selectivity'. The authors consider an enhancer to be not selective if its 'boost index' is the same across a set of promoters. 'Boost index' is defined to be the ratio of the reporter output with the enhancer and promoter divided by the reporter output with just the promoter. Conceptually, I think that considering the boost index is a reasonable way to quantify selectivity. The authors use a frequentist approach to classify each enhancer as selective or not selective. The null hypothesis is that the boost index of the enhancer is equal across a set of promoters. This can be visualized in Fig. 2C where the null hypothesis is that the mean of each vertical distribution is equal. Note that in Figure S4b of this paper (and in Figure 4B of their 2022 paper) the within-group variance is not plotted. Statistical significance is assessed using a Welch F-test.

Reviewer #3 (Public Review):

This is an interesting manuscript that builds off of this group's previous work focused on the interface between Hsf1, heat shock protein (HSP) mRNA production, and 3D genome topology. Here the group subjects the yeast Saccharomyces cerevisiae to either heat stress (HS) or ethanol stress (ES) and examines Hsf1 and Pol II chromatin binding, Histone occupancy, Hsf1 condensates, HSP gene coalescence (by 3C and live cell imaging), and HSP mRNA expression (by RT-qPCR and live cell imaging). The manuscript is well written, and the experiments seem well done, and generally rigorous, with orthogonal approaches performed to support conclusions. The main findings are that both HS and ES result in Hsf1/Pol II-dependent intergenic interactions, along with formation of Hsf1 condensates. Yet, while HS results in rapid and strong induction of HSP gene expression and Hsf1 condensate resolution, ES result in slow and weak induction of HSP gene expression without Hsf1 condensate resolution. Thus, the conclusion is somewhat phenomenological - that the same transcription factor can drive distinct transcription, topologic, and phase-separation behavior in response to different types of stress.

Reviewer #2 (Public review):

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

Overall, the findings are interesting, and in general, the experiments are very well executed.

Comments on revised version:

The authors have generally addressed all of my concerns (and the other reviewer's) and adapted the manuscript where necessary. The revised version has significantly improved the manuscript. From my perspective there are no further concerns.

Reviewer #3 (Public review):

Summary:

The authors found two endosomal fusion modes by live cell imaging of endosomes in yolk sac lateral endoderm cells of 8.5-day-old embryonic mice and described the fusion modes by mathematical models and simulations. They also showed that actin polymerization is involved in the regulation of one of the fusion modes.

Strengths:

The strength of this study is that the authors' claims are well supported by beautiful live cell images and theoretical models. By using specialized cells, yolk sac visceral endoderm cells, the live images of endosomal fusion, localization of actin-related molecules, and validation data from multiple inhibitor experiments are clear.

Weaknesses:

Although it would be out of scope of this study, there is no experimental verification of whether the mechanism of endosome fusion claimed by the authors occurs in general cells, so the article is limited to showing a phenomenon specific to yolk sac lateral endoderm cells. The methods used were very basic and solid. Most of the image analysis was performed manually, but the results were statistically tested.

Summary:

Seiichi Koike et al. studied two fusion models, explosive fusion, and bridge fusion, utilizing yolk sac visceral endoderm cells. They elucidated these two fusion models in vivo by employing mathematical modeling and incorporating fluctuations derived from actin dynamics as a key regulator for rapid homotypic fusion between late endosomes.

Strengths:

This study uncovered the role of actin dynamics in regulating the transition of fusion models in homotypic fusion between late endosomes and introduced a method for observing the fusion of single vesicles with two different targets.

Weaknesses:

The physiological significance of different fusion models is lacking.

Reviewer #2 (Public review):

Summary:

In this study, Geurts et al. investigated the effects of the catecholamine reuptake inhibitor methylphenidate (MPH) on value-based decision-making using a combination of aversive and appetitive Pavlovian to Instrumental Transfer (PIT) in a human cohort. Using an elegant behavioural design they showed a valence- and action-specific effects of Pavlovian cues on instrumental responses. Initial analyses show no effect of MPH on these processes. However the authors performed a more in-depth analysis and demonstrated that MPH actually modulates PIT in action-specific manner depending of individual working memory capacities. The authors interpret that as an effect on cognitive control of Pavlovian biasing of actions and decision-making more than an invigoration of motivational biases.

Strengths:

A major strength of this study is its experimental design. The elegant combination of appetitive and aversive Pavlovian learning with approach/avoidance instrumental actions allows to precisely investigate the different modulation of value-based decision making depending on the context and environmental stimuli. Important MPH is only administered after Pavlovian and instrumental learning, restricting the effect on PIT performance only. Finally, the use of a placebo-controlled crossover design allows within-comparisons between PIT effect under placebo and MPH and the investigation of the relationships between working memory abilities, PIT and MPH effects.

Weaknesses:

As authors stated in their discussion, this study is purely correlational and their conclusions could be strengthened by the addition of interesting (but time- and resource-consuming) neuroimaging work.<br /> The originality of this work compared to their previous published work using the same cohort could also be clarified at different stages of the article, as I initially wondered what was really novel. This point is much clearer in the discussion section.<br /> A point which, in my opinion, really requires clarification is when the working memory performance presented in Figure 2B has been determined. Was it under placebo (as I would guess) or under MPH? If it is the former, it would be also interesting to look at how MPH modulates working memory based on initial abilities.<br /> A final point is that it could be interesting to also discuss these results, not only regarding dopamine signalling, but also including potential effect of MPH on noradrenaline in frontal regions, considering the known role of this system in modulating behavioural flexibility.

Reviewer #2 (Public Review):

Summary:

The Mutational Hazard Hypothesis (MHH) is a very influential hypothesis in explaining the origins of genomic and other complexity that seem to entail the fixation of costly elements. Despite its influence, very few tests of the hypothesis have been offered, and most of these come with important caveats. This lack of empirical tests largely reflects the challenges of estimating crucial parameters.

The authors test the central contention of the MHH, namely that genome size follows effective population size (Ne). They martial a lot of genomic and comparative data, test the viability of their surrogates for Ne and genome size, and use correct methods (phylogenetically corrected correlation) to test the hypothesis. Strikingly, they not only find that Ne is not THE major determinant of genome size, as is argued by MHH, but that there is not even a marginally significant effect. This is remarkable, making this an important paper.

Strengths:

The hypothesis tested is of great importance.

The negative finding is of great importance for reevaluating the predictive power of the tested hypothesis.

The test is straightforward and clear.

The analysis is a technical tour-de-force, convincingly circumventing a number of challenges of mounting a true test of the hypothesis.

Weaknesses:

I note no particular strengths, but I believe the paper could be further strengthened in three major ways.

(1) The authors should note that the hypothesis that they are testing is larger than the MHH. The MHH hypothesis says that<br /> (i) low-Ne species have more junk in their genomes and<br /> (ii) this is because junk tends to be costly because of increased mutation rate to nulls, relative to competing non/less-junky alleles.

The current results reject not just the compound (i+ii) MHH hypothesis, but in fact any hypothesis that relies on i. This is notably a (much) more important rejection. Indeed, whereas MHH relies on particular constructions of increased mutation rates of varying plausibility, the more general hypothesis i includes any imaginable or proposed cost to the extra sequence (replication costs, background transcription, costs of transposition, ectopic expression of neighboring genes, recombination between homologous elements, misaligning during meiosis, reduced organismal function from nuclear expansion, the list goes on and on). For those who find the MHH dubious on its merits, focusing this paper on the MHH reduces its impact - the larger hypothesis that the small costs of extra sequence dictate the fates of different organisms' genomes is, in my opinion, a much more important and plausible hypothesis, and thus the current rejection is more important than the authors let on.

(2) In addition to the authors' careful logical and mathematical description of their work, they should take more time to show the intuition that arises from their data. In particular, just by looking at Figure 1b one can see what is wrong with the non-phylogenetically-corrected correlations that MHH's supporters use. That figure shows that mammals, many of which have small Ne, have large genomes regardless of their Ne, which suggests that the coincidence of large genomes and frequently small Ne in this lineage is just that, a coincidence, not a causal relationship. Similarly, insects by and large have large Ne, regardless of their genome size. Insects, many of which have large genomes, have large Ne regardless of their genome size, again suggesting that the coincidence of this lineage of generally large Ne and smaller genomes is not causal. Given that these two lineages are abundant on earth in addition to being overrepresented among available genomes (and were even more overrepresented when the foundational MHH papers collected available genomes), it begins to emerge how one can easily end up with a spurious non-phylogenetically corrected correlation: grab a few insects, grab a few mammals, and you get a correlation. Notably, the same holds for lineages not included here but that are highly represented in our databases (and all the more so 20 years ago): yeasts related to S. cerevisiae (generally small genomes and large median Ne despite variation) and angiosperms (generally large genomes (compared to most eukaryotes) and small median Ne despite variation). Pointing these clear points out will help non-specialists to understand why the current analysis is not merely a they-said-them-said case, but offers an explanation for why the current authors' conclusions differ from the MHH's supporters and moreover explain what is wrong with the MHH's supporters' arguments.

(3) A third way in which the paper is more important than the authors let on is in the striking degree of the failure of MHH here. MHH does not merely claim that Ne is one contributor to genome size among many; it claims that Ne is THE major contributor, which is a much, much stronger claim. That no evidence exists in the current data for even the small claim is a remarkable failure of the actual MHH hypothesis: the possibility is quite remote that Ne is THE major contributor but that one cannot even find a marginally significant correlation in a huge correlation analysis deriving from a lot of challenging bioinformatic work. Thus this is an extremely strong rejection of the MHH. The MHH is extremely influential and yet very challenging to test clearly. Frankly, the authors would be doing the field a disservice if they did not more strongly state the degree of importance of this finding.

Reviewer #2 (Public review):

Summary:

Fei, Lu, Shi, et al. present a thorough evaluation of the immune cell landscape in pre-eclamptic human placentas by single-cell multi-omics methodologies compared to normal control placentas. Based on their findings of elevated frequencies of inflammatory macrophages and memory-like Th17 cells, they employ adoptive cell transfer mouse models to interrogate the coordination and function of these cell types in pre-eclampsia immunopathology. They demonstrate the putative role of the IGF1-IGF1R axis as the key pathway by which inflammatory macrophages in the placenta skew CD4+ T cells towards an inflammatory IL-17A-secreting phenotype that may drive tissue damage, vascular dysfunction, and elevated blood pressure in pre-eclampsia, leaving researchers with potential translational opportunities to pursue this pathway in this indication.

They present a major advance to the field in their profiling of human placental immune cells from pre-eclampsia patients where most extant single-cell atlases focus on term versus preterm placenta, or largely examine trophoblast biology with a much rarer subset of immune cells. While the authors present vast amounts of data at both the protein and RNA transcript level, we, the reviewers, feel this manuscript is still in need of much more clarity in its main messaging, and more discretion in including only key data that supports this main message most effectively.

Strengths:

(1) This study combines human and mouse analyses and allows for some amount of mechanistic insight into the role of pro-inflammatory and anti-inflammatory macrophages in the pathogenesis of pre-eclampsia (PE), and their interaction with Th17 cells.

(2) Importantly, they do this using matched cohorts across normal pregnancy and common PE comorbidities like gestation diabetes (GDM).

(3) The authors have developed clear translational opportunities from these "big data" studies by moving to pursue potential IGF1-based interventions.

Weaknesses:

(1) Clearly the authors generated vast amounts of multi-omic data using CyTOF and single-cell RNA-seq (scRNA-seq), but their central message becomes muddled very quickly. The reader has to do a lot of work to follow the authors' multiple lines of inquiry rather than smoothly following along with their unified rationale. The title description tells fairly little about the substance of the study. The manuscript is very challenging to follow. The paper would benefit from substantial reorganizations and editing for grammatical and spelling errors. For example, RUPP is introduced in Figure 4 but in the text not defined or even talked about what it is until Figure 6. (The figure comparing pro- and anti-inflammatory macrophages does not add much to the manuscript as this is an expected finding).

(2) The methods lack critical detail about how human placenta samples were processed. The maternal-fetal interface is a highly heterogeneous tissue environment and care must be taken to ensure proper focus on maternal or fetal cells of origin. Lacking this detail in the present manuscript, there are many unanswered questions about the nature of the immune cells analyzed. It is impossible to figure out which part of the placental unit is analyzed for the human or mouse data. Is this the decidua, the placental villi, or the fetal membranes? This is of key importance to the central findings of the manuscript as the immune makeup of these compartments is very different. Or is this analyzed as the entirety of the placenta, which would be a mix of these compartments and significantly less exciting?

(3) Similarly, methods lack any detail about the analysis of the CyTOF and scRNAseq data, much more detail needs to be added here. How were these clustered, what was the QC for scRNAseq data, etc? The two small paragraphs lack any detail.

(4) There is also insufficient detail presented about the quantities or proportions of various cell populations. For example, gdT cells represent very small proportions of the CyTOF plots shown in Figures 1B, 1C, & 1E, yet in Figures 2I, 2K, & 2K there are many gdT cells shown in subcluster analysis without a description of how many cells are actually represented, and where they came from. How were biological replicates normalized for fair statistical comparison between groups?

(5) The figures themselves are very tricky to follow. The clusters are numbered rather than identified by what the authors think they are, the numbers are so small, that they are challenging to read. The paper would be significantly improved if the clusters were clearly labeled and identified. All the heatmaps and the abundance of clusters should be in separate supplementary figures.

(6) The authors should take additional care when constructing figures that their biological replicates (and all replicates) are accurately represented. Figure 2H-2K shows N=10 data points for the normal pregnant (NP) samples when clearly their Table 1 and test denote they only studied N=9 normal subjects.

(7) There is little to no evaluation of regulatory T cells (Tregs) which are well known to undergird maternal tolerance of the fetus, and which are well known to have overlapping developmental trajectory with RORgt+ Th17 cells. We recommend the authors evaluate whether the loss of Treg function, quantity, or quality leaves CD4+ effector T cells more unrestrained in their effect on PE phenotypes. References should include, accordingly: PMCID: PMC6448013 / DOI: 10.3389/fimmu.2019.00478; PMC4700932 / DOI: 10.1126/science.aaa9420.

(8) In discussing gMDSCs in Figure 3, the authors have missed key opportunities to evaluate bona fide Neutrophils. We recommend they conduct FACS or CyTOF staining including CD66b if they have additional tissues or cells available. Please refer to this helpful review article that highlights key points of distinguishing human MDSC from neutrophils: https://doi.org/10.1038/s41577-024-01062-0. This will both help the evaluation of potentially regulatory myeloid cells that may suppress effector T cells as well as aid in understanding at the end of the study if IL-17 produced by CD4+ Th17 cells might recruit neutrophils to the placenta and cause ROS immunopathology and fetal resorption.

(9) Depletion of macrophages using several different methodologies (PLX3397, or clodronate liposomes) should be accompanied by supplementary data showing the efficiency of depletion, especially within tissue compartments of interest (uterine horns, placenta). The clodronate piece is not at all discussed in the main text. Both should be addressed in much more detail.

(10) There are many heatmaps and tSNE / UMAP plots with unhelpful labels and no statistical tests applied. Many of these plots (e.g. Figure 7) could be moved to supplemental figures or pared down and combined with existing main figures to help the authors streamline and unify their message.

(11) There are claims that this study fills a gap that "only one report has provided an overall analysis of immune cells in the human placental villi in the presence and absence of spontaneous labor at term by scRNA-seq (Miller 2022)" (lines 362-364), yet this study itself does not exhaustively study all immune cell subsets...that's a monumental task, even with the two multi-omic methods used in this paper. There are several other datasets that have performed similar analyses and should be referenced.

(12) Inappropriate statistical tests are used in many of the analyses. Figures 1-2 use the Shapiro-Wilk test, which is a test of "goodness of fit", to compare unpaired groups. A Kruskal-Wallis or other nonparametric t-test is much more appropriate. In other instances, there is no mention of statistical tests (Figures 6-7) at all. Appropriate tests should be added throughout.

Reviewer #2 (Public review):

Summary:<br /> Biomechanical forces, such as blood flow, are crucial for organ formation, including heart development. This study by Shuo Chen et al. aims to understand how cardiac cells respond to these forces. They used zebrafish as a model organism due to its unique strengths, such as the ability to survive without heartbeats, and conducted transcriptomic analysis on hearts with impaired contractility. They thereby identified id2b as a gene regulated by blood flow and is crucial for proper heart development, in particular, for the regulation of myocardial contractility and valve formation. Using both in situ hybridization and transgenic fish they showed that id2b is specifically expressed in the endocardium, and its expression is affected by both pharmacological and genetic perturbations of contraction. They further generated a null mutant of id2b to show that loss of id2b results in heart malformation and early lethality in zebrafish. Atrioventricular (AV) and excitation-contraction coupling were also impaired in id2b mutants. Mechanistically, they demonstrate that Id2b interacts with the transcription factor Tcf3b to restrict its activity. When id2b is deleted, the repressor activity of Tcf3b is enhanced, leading to suppression of the expression of nrg1 (neuregulin 1), a key factor for heart development. Importantly, injecting tcf3b morpholino into id2b-/- embryos partially restores the reduced heart rate. Moreover, treatment of zebrafish embryos with the Erbb2 inhibitor AG1478 results in decreased heart rate, in line with a model in which Id2b modulates heart development via the Nrg1/Erbb2 axis. The research identifies id2b as a biomechanical signaling-sensitive gene in endocardial cells that mediates communication between the endocardium and myocardium, which is essential for heart morphogenesis and function.

Strengths:<br /> The study provides novel insights into the molecular mechanisms by which biomechanical forces influence heart development and highlights the importance of id2b in this process.

Weaknesses:<br /> The claims are in general well supported by experimental evidence, but the following aspects may benefit from further investigation:

(1) In Figure 1C, the heatmap demonstrates the up-regulated and down-regulated genes upon tricane-induced cardiac arrest. Aside from the down-regulation of id2b expression, it was also evident that id2a expression was up-regulated. As a predicted paralog of id2b, it would be interesting to see whether the up-regulation of id2a in response to tricane treatment was a compensatory response to the down-regulation of id2b expression.

(2) The study mentioned that id2b is tightly regulated by the flow-sensitive primary cilia-klf2 signaling axis; however aside from showing the reduced expression of id2b in klf2a and klf2b mutants, there was no further evidence to solidify the functional link between id2b and klf2. It would therefore be ideal, in the present study, to demonstrate how Klf2, which is a transcriptional regulator, transduces biomechanical stimuli to Id2b.

(3) The authors showed the physical interaction between ectopically expressed FLAG-Id2b and HA-Tcf3b in HEK293T cells. Although the constructs being expressed are of zebrafish origin, it would be nice to show in vivo that the two proteins interact.

Reviewer #2 (Public Review):

Summary:<br /> The study wanted to functionally identify individual DANs that mediate larval olfactory<br /> learning. Then search for DAN-specific driver strains that mark single dopaminergic neurons, which subsequently can be used to target genetic manipulations of those neurons. 56 GAL4 drivers identifying dopaminergic neurons were found (Table 1) and three of them drive the expression of GFP to a single dopaminergic neuron in the third-instar larval brain hemisphere. The DAN driver R76F02-AD;R55C10-DBD appears to drive the expression to a dopaminergic neuron innervating the lower peduncle (LP), which would be DAN-c1.<br /> Split-GFP reconstitution across synaptic partners (GRASP) technique was used to investigate the "direct" synaptic connections from DANs to the mushroom body. Potential synaptic contact between DAN-c1 and MB neurons (at the lower peduncle) were detected.<br /> Then single odor associative learning was performed and thermogenetic tools were used (Shi-ts1 and TrpA1). When trained at 34{degree sign}C, the complete inactivation of dopamine release from DAN-c1 with Shibirets1 impaired aversive learning (Figure 2h), while Shibirets1 did not affect learning when trained at room temperature (22{degree sign}C). When paired with a gustatory stimulus (QUI or SUC), activation of DAN-c1 during training impairs both aversive and appetitive learning (Figure 2k).<br /> They examined the expression pattern of D2R in fly brains and were found in dopaminergic neurons and the mushroom body (Figure 3). To inspect whether the pattern of GFP signals indeed reflected the expression of D2R, three D2R enhancer driver strains (R72C04, R72C08, and R72D03-GAL4) were crossed with the GFP-tagged D2R strain.<br /> D2R knockdown (UAS-RNAi) in dopaminergic neurons driven by TH-GAL4 impaired larval aversive learning. Using a microRNA strain (UAS-D2R-miR), a similar deficit was observed. Crossing the GFP-tagged D2R strain with a DAN-c1-mCherry strain demonstrated the expression of D2R in DAN-c1 (Figure 4a). Knockdown of D2R in DAN-c1 impaired aversive learning with the odorant pentyl acetate, while appetitive learning was unaffected (Figure 4e). Sensory and motor functions appear not affected by D2R suppression.<br /> To exclude possible chronic effects of D2R knockdown during development, optogenetics was applied at distinct stages of the learning protocol. ChR2 was expressed in DAN-c1, and blue light was applied at distinct stages of the learning protocol. Optogenetic activation of DAN-c1 during training impaired aversive learning, not appetitive learning (Figure 5b-d).<br /> Knockdown of D2Rs in MB neurons by D2R-miR impaired both appetitive and aversive learning (Figure 6a). Activation of MBNs during training impairs both larval aversive and appetitive learning.<br /> Finally, based on the data the authors propose a model where the effective learning requires a balanced level of activity between D1R and D2R (Figure 7).

Strengths:<br /> The work is well written, clear, and concise. They use well documented strategies to examine GAL4 drivers with expression in a single DAN, behavioral performance in larvae with distinct genetic tools including those to do thermo and optogenetics in behaving flies. Altogether, the study was able to expand our understanding of the role of D2R in DAN-c1 and MB neurons in the larva brain.

Weaknesses:<br /> Is not completely clear how the system DAN-c1, MB neurons and Behavioral performance work. We can be quite sure that DAN-c1;Shits1 were reducing dopamine release and impairing aversive memory (Figure 2h). Similarly, DAN-c1;ChR2 were increasing dopamine release and also impaired aversive memory (Figure 5b). However, is not clear what is happening with DAN-c1;TrpA1 (Figure 2K). In this case the thermos-induction appears to impair the behavioral performance of all three conditions (QUI, DW and SUC) and the behavior is quite distinct from the increase and decrease of dopamine tone (Figure 2h and 5b).

The study successfully examined the role of D2R in DAN-c1 and MB neurons in olfactory conditioning. The conclusions are well supported by the data, with the exception of the claim that dopamine release from DAN-c1 is sufficient for aversive learning in the absence of unconditional stimulus (Figure 2K). Alternatively, the authors need to provide a better explanation of this point.<br /> The study provides insight into the role of D2R in associative learning expanding our understanding and might be a reference similar to previous key findings (Qi and Lee, 2014, https://doi.org/10.3390/biology3040831).

Reviewer #2 (Public Review):

Summary:

Ning and colleagues present studies supporting a role for breast carcinoma amplified sequence 2 (Bcas2) in positively regulating primitive wave hematopoiesis through amplification of beta-catenin-dependent (canonical) Wnt signaling. The authors present compelling evidence that zebrafish bcas2 is expressed at the right time and place to be involved in primitive hematopoiesis, that there are primitive hematopoietic defects in hetero- and homozygous mutant and knockdown embryos, that Bcas2 mechanistically positively regulates canonical Wnt signaling, and that Bcas2 is required for nuclear retention of B-cat through physical interaction involving armadillo repeats 9-12 of B-cat and the coiled-coil domains of Bcas2. Overall, the data and writing are clean, clear, and compelling. This study is a first-rate analysis of a strong phenotype with highly supportive mechanistic data. The findings shed light on the controversial question of whether, when, and how canonical Wnt signaling may be involved in hematopoietic development. We detail some minor concerns and questions below, which if answered, we believe would strengthen the overall story and resolve some puzzling features of the phenotype. Notwithstanding these minor concerns, we believe this is an exceptionally well-executed and interesting manuscript.

Strengths:

(1) The study features clear and compelling phenotypes and results.

(2) The manuscript narrative exposition and writing are clear and compelling.

(3) The authors have attended to important technical nuances sometimes overlooked, for example, focusing on different pools of cytosolic or nuclear b-catenin.

(4) The study sheds light on a controversial subject: regulation of hematopoietic development by canonical Wnt signaling and presents clear evidence of a role.

(5) The authors present evidence of phylogenetic conservation of the pathway.

Weaknesses:

(1) The authors present compelling data that Bcas2 regulates nuclear retention of B-cat through physical association involving binding between the Bcas2 CC domains and B-cat arm repeats 9-12. Transcriptional activation of Wnt target genes by B-cat requires physical association between B-cat and Tcf/Lef family DNA binding factors involving key interactions in Arm repeats 2-9 (Graham et al., Cell 2000). Mutually exclusive binding by B-cat regulatory factors, such as ICAT that prevent Tcf-binding is a documented mechanism (e.g. Graham et al., Mol Cell 2002). It would appear - based on the arm repeat usage by Bcas2 (repeats 9-12)-that Bcas2 and Tcf binding might not be mutually exclusive, which would support their model that Bcas2 physical association with B-cat to retain it in the nucleus would be compatible with co-activation of genes by allowing association with Tcf. It might be nice to attempt a three-way co-IP of these factors showing that B-cat can still bind Tcf in the presence of Bcas2, or at least speculate on the plausibility of the three-way interaction.

(2) A major way that canonical Wnt signaling regulates hematopoietic development is through regulation of the LPM hematopoietic competence territories by activating expression of cdx1a, cdx4, and their downstream targets hoxb5a and hoxa9a (Davidson et al., Nature 2003; Davidson et al., Dev Biol 2006; Pilon et al., Dev Biol 2006; Wang et al., PNAS 2008). Could the authors assess (in situ) the expression of cdx1a, cdx4, hoxb5a, and hoxa9a in the bcas2 mutants?

(3) The authors show compellingly that even heterozygous loss of bcas2 has strong Wnt-inhibitory effects. If Bcas2 is required for canonical Wnt signaling and bcas2 is expressed ubiquitously from the 1-cell stage through at least the beginning of gastrulation, why do bcas2 KO embryos not have morphological axis specification defects consistent with loss of early Wnt signaling, like loss of head (early), or brain anteriorization (later)? Could the authors provide some comments on this puzzle? Or if they do see any canonical Wnt signaling patterning defects in het- or homozygous embryos, could they describe and/or present them?

Reviewer #3 (Public Review):

Summary:

Well-illustrated new material is documented for Acanthomeridion, a formerly incompletely known Cambrian arthropod. The formerly known facial sutures are proposed be associated with ventral plates that the authors homologise with the free cheeks of trilobites (although also testing alternative homologies). An update of a published phylogenetic dataset permits reconsideration of whether dorsal ecdysial sutures have a single or multiple origins in trilobites and their relatives.

Strengths:

Documentation of an ontogenetic series makes a sound case that the proposed diagnostic characters of a second species of Acanthomeridion are variation within a single species. New microtomographic data shed light on appendage morphology that was not formerly known. The new data on ventral plates and their association with the ecdysial sutures are valuable in underpinning homologies with trilobites.

Reviewer #2 (Public Review):

In this manuscript, Yang et al. present a modeling framework to understand the pattern of response biases and variance observed in delayed-response orientation estimation tasks. They combine a series of modeling approaches to show that coupled sensory-memory networks are in a better position than single-area models to support experimentally observed delay-dependent response bias and variance in cardinal compared to oblique orientations. These errors can emerge from a population-code approach that implements efficient coding and Bayesian inference principles and is coupled to a memory module that introduces random maintenance errors. A biological implementation of such operation is found when coupling two neural network modules, a sensory module with connectivity inhomogeneities that reflect environment priors, and a memory module with strong homogeneous connectivity that sustains continuous ring attractor function. Comparison with single-network solutions that combine both connectivity inhomogeneities and memory attractors shows that two-area models can more easily reproduce the patterns of errors observed experimentally.

Strengths:

The model provides an integration of two modeling approaches to the computational bases of behavioral biases: one based on Bayesian and efficient coding principles, and one based on attractor dynamics. These two perspectives are not usually integrated consistently in existing studies, which this manuscript beautifully achieves. This is a conceptual advancement, especially because it brings together the perceptual and memory components of common laboratory tasks.

The proposed two-area model provides a biologically plausible implementation of efficient coding and Bayesian inference principles, which interact seamlessly with a memory buffer to produce a complex pattern of delay-dependent response errors. No previous model had achieved this.

Weaknesses:

The correspondence between the various computational models is not clearly shown. It is not easy to see clearly this correspondence because network function is illustrated with different representations for different models. In particular, the Bayesian model of Figure 2 is illustrated with population responses for different stimuli and delays, while the attractor models of Figure 3 and 4 are illustrated with neuronal tuning curves but not population activity.

The proposed model has stronger feedback than feedforward connections between the sensory and memory modules (J_f = 0.1 and J_b = 0.25). This is not the common assumption when thinking about hierarchical processing in the brain. The manuscript argues that error patterns remain similar as long as the product of J_f and J_b is constant, so it is unclear why the authors preferred this network example as opposed to one with J_b = 0.1 and J_f = 0.25.

Reviewer #2 (Public review):

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

This study convincingly demonstrates that many unstable misfolded glycoproteins undergo accelerated degradation without UGGTs. Also, this study provides evidence of a "tug of war" model involving UGGTs (pulling glycoproteins to being refolded) and EDEMs (pulling glycoproteins to ERAD).

The study explores the physiological role of UGGT, particularly examining the impact of ATF6α in UGGT knockout cells' stress response. The authors further investigate the physiological consequences of accelerated ATF6α degradation, convincingly demonstrating that cells are sensitive to ER stress in the absence of UGGTs and unable to mount an adequate ER stress response.

These findings offer significant new insights into the ERAD field, highlighting UGGT1 as a crucial component in maintaining ER protein homeostasis. This represents a major advancement in our understanding of the field.

Reviewer #2 (Public review):

Summary:

Together with the known anatomical connectivity, molecular atlasses paves the way toward functional maps of the nervous system of C. elegans. Along with the analysis of previous scRNA sequencing and reporter strains, new expression patterns are generated for hermaphrodite and males based on CRISPR-knocked-in GFP reporter strains and the use of the color-coded Neuropal strain to accurately identify neurons. Beyond a map of the known neurotransmitters (GABA, Acetylcholine, Glutamate, dopamine, serotonin, tyramine, octopamine), the atlas also identifies neurons likely using betaine and suggests sets of neurons employing new unknown monoaminergic transmission, or using exclusively peptidergic neurotransmission.

Strengths:

The use of CRISPR reporter alleles and of the Neuropal strain to assign neurotransmitter usage to each neuron is much more rigourous than previous analysis and reveal intriguing differences between scRNA seq, fosmid reporter and CRISPR knock-in approaches. The differences between approaches are discussed.

Weaknesses:

All have been addressed.

Reviewer #2 (Public Review):

Summary:

This interesting manuscript describes a study investigating the role of MC4R (melanocortin 4 receptor) signalling on kisspeptin (Kiss1) neurons. The initial question is a good one. Infertility in human MC4R mutations has typically been ascribed to the consequent obesity and impaired metabolic regulation. Whether MC4R directly regulates the hypothalamic-pituitary-gonadal (HPG) axis has not been thoroughly examined. Here, the researchers assembled an elegant combination of loss and gain of function in vivo experiments, specifically targeting MC4R expression in Kiss1 neurons. This is an excellent experimental design and one that should provide compelling evidence for whether there is a direct role for melanocortin signalling in arcuate Kiss1 neurons to support normal reproductive function. There were definite effects on reproductive function (irregular estrous cycle, reduced magnitude of LH surge induced by exogenous estradiol). Still, the magnitude of these responses and the overall effect on fertility were relatively minor, as mice lacking MC4R in Kiss1 neurons remained fertile despite these irregularities. The second part of the manuscript describes a series of electrophysiological studies evaluating the pharmacological effects of melanocortin signalling in Kiss1 neurons in ex-vivo brain slides. These studies characterised interesting differential actions of melanocortins in two different Kiss1 neuronal populations. The study provides some novel insights into how direct actions of melanocortin signalling via the MC4R in Kiss1 neurons contribute to the metabolic regulation of the reproductive system. Importantly, however, it is clear that other mechanisms are also at play.

Strengths:

The loss and gain of function experiments provide a conceptually simple but hugely informative experimental design, which is the key strength of the current paper - especially the knock-in study that showed improved reproductive function even in the presence of ongoing obesity. This is a very convincing result that documents that reproductive deficits in MC4R knockout animals (and humans with deleterious MC4R gene variants) can be ascribed to impaired signalling in the hypothalamic Kiss1 neurons and not necessarily simply caused as a consequence of obesity. Validation experiments for these studies are needed, given their great prominence in the manuscript, because these are critical to interpretation.

Weaknesses:

(1) Given the fact that mice lacking MC4R in Kiss1 neurons remained fertile despite some reproductive irregularities, the overall tone and some of the conclusions of the manuscript (e.g., from the abstract: "... Mc4r expressed in Kiss1 neurons is required for fertility in females") were overstated. Perhaps this can be described as a contributing pathway, but other mechanisms must also be involved in conveying metabolic information to the reproductive system.

(2) The mechanistic studies evaluating melanocortin signalling in Kiss1 neurons were all completed in ovariectomised animals (with and without exogenous hormones) that do not experience cyclical hormone changes. Such cyclical changes are fundamental to how these neurons function in vivo and may dynamically alter the way they respond to neuropeptides. Therefore, eliminating this variable makes interpretation difficult.

(3) Use of the POMC-Cre to target ontogenetic inputs to Kiss1 neurons might have targeted a wider population of cells than intended.

Reviewer #2 (Public Review):

Summary:

In this work, the authors present a new Python software package, Avian Vocalization Network (AVN) aimed at facilitating the analysis of birdsong, especially the song of the zebra finch, the most common songbird model in neuroscience. The package handles some of the most common (and some more advanced) song analyses, including segmentation, syllable classification, featurization of song, calculation of tutor-pupil similarity, and age prediction, with a view toward making the entire process friendlier to experimentalists working in the field.

For many years, Sound Analysis Pro has served as a standard in the songbird field, the first package to extensively automate songbird analysis and facilitate the computation of acoustic features that have helped define the field. More recently, the increasing popularity of Python as a language, along with the emergence of new machine learning methods, has resulted in a number of new software tools, including the vocalpy ecosystem for audio processing, TweetyNet (for segmentation), t-SNE and UMAP (for visualization), and autoencoder-based approaches for embedding.

Strengths:

The AVN package overlaps several of these earlier efforts, albeit with a focus on more traditional featurization that many experimentalists may find more interpretable than deep learning-based approaches. Among the strengths of the paper are its clarity in explaining the several analyses it facilitates, along with high-quality experiments across multiple public datasets collected from different research groups. As a software package, it is open source, installable via the pip Python package manager, and features high-quality documentation, as well as tutorials. For experimentalists who wish to replicate any of the analyses from the paper, the package is likely to be a useful time saver.

Weaknesses:

I think the potential limitations of the work are predominantly on the software end, with one or two quibbles about the methods.

First, the software: it's important to note that the package is trying to do many things, of which it is likely to do several well and few comprehensively. Rather than a package that presents a number of new analyses or a new analysis framework, it is more a codification of recipes, some of which are reimplementations of existing work (SAP features), some of which are essentially wrappers around other work (interfacing with WhisperSeg segmentations), and some of which are new (similarity scoring). All of this has value, but in my estimation, it has less value as part of a standalone package and potentially much more as part of an ecosystem like vocalpy that is undergoing continuous development and has long-term support. While the code is well-documented, including web-based documentation for both the core package and the GUI, the latter is available only on Windows, which might limit the scope of adoption.

That is to say, whether AVN is adopted by the field in the medium term will have much more to do with the quality of its maintenance and responsiveness to users than any particular feature, but I believe that many of the analysis recipes that the authors have carefully worked out may find their way into other code and workflows.

Second, two notes about new analysis approaches:

(1) The authors propose a new means of measuring tutor-pupil similarity based on first learning a latent space of syllables via a self-supervised learning (SSL) scheme and then using the earth mover's distance (EMD) to calculate transport costs between the distributions of tutors' and pupils' syllables. While to my knowledge this exact method has not previously been proposed in birdsong, I suspect it is unlikely to differ substantially from the approach of autoencoding followed by MMD used in the Goffinet et al. paper. That is, SSL, like the autoencoder, is a latent space learning approach, and EMD, like MMD, is an integral probability metric that measures discrepancies between two distributions. (Indeed, the two are very closely related: https://stats.stackexchange.com/questions/400180/earth-movers-distance-and-maximum-mean-discrepency.) Without further experiments, it is hard to tell whether these two approaches differ meaningfully. Likewise, while the authors have trained on a large corpus of syllables to define their latent space in a way that generalizes to new birds, it is unclear why such an approach would not work with other latent space learning methods.

(2) The authors propose a new method for maturity scoring by training a model (a generalized additive model) to predict the age of the bird based on a selected subset of acoustic features. This is distinct from the "predicted age" approach of Brudner, Pearson, and Mooney, which predicts based on a latent representation rather than specific features, and the GAM nicely segregates the contribution of each. As such, this approach may be preferred by many users who appreciate its interpretability.

In summary, my view is that this is a nice paper detailing a well-executed piece of software whose future impact will be determined by the degree of support and maintenance it receives from others over the near and medium term.

Reviewer #2 (Public Review):

This manuscript proposes a model of replay that focuses on the relation between an item and its context, without considering the value of the item. The model simulates awake learning, awake replay, and sleep replay, and demonstrates parallels between memory phenomenon driven by encoding strength, replay of sequence learning, and activation of nearest neighbor to infer causality. There is some discussion of the importance of suppression/inhibition to reduce activation of only dominant memories to be replayed, potentially boosting memories that are weakly encoded. Very nice replications of several key replay findings including the effect of reward and remote replay, demonstrating the equally salient cue of context for offline memory consolidation.

I have no suggestions for the main body of the study, including methods and simulations, as the work is comprehensive, transparent, and well-described. However, I would like to understand how the CMRreplay model fits with the current understanding of the importance of excitation vs inhibition, remembering vs forgetting, activation vs deactivation, strengthening vs elimination of synapses, and even NREM vs REM as Schapiro has modeled. There seems to be a strong association with the efforts of the model to instantiate a memory as well as how that reinstantiation changes across time. But that is not all this is to consolidation. The specific roles of different brain states and how they might change replay is also an important consideration.

Do the authors suggest that these replay systems are more universal to offline processes beyond episodic memory? What about procedural memories and working memory?

Though this is not a biophysical model per se, can the authors speak to the neuromodulatory milieus that give rise to the different types of replay?

Reviewer #2 (Public review):

Summary:

In this manuscript, the authors have tried to repurpose cipargamin (CIP), a known drug against plasmodium and toxoplasma against babesia. They proved the efficacy of CIP on babesia in the nanomolar range. In silico analyses revealed the drug resistance mechanism through a single amino acid mutation at amino acid position 921 on the ATP4 gene of babesia. Overall, the conclusions drawn by the authors are well justified by their data. I believe this study opens up a novel therapeutic strategy against babesiosis.

Strengths:

The authors have carried out a comprehensive study. All the experiments performed were carried out methodically and logically.

Weaknesses:

The introduction section needs to be more informative. The authors are investigating the binding of CIP to the ATP4 gene, but they did not give any information about the gene or how the ATP4 inhibitors work in general.

The resolution of the figures is not good and the font size is too small to read properly.

I also have several minor concerns which have been addressed in the "Recommendations for the authors" section.

Reviewer #2 (Public review):

Summary:

Bohorquez et al. investigate the molecular determinants of intracellular gradient formation in the B. subtilis Min system. To this end, they generate B. subtilis strains that express MinD mutants that are locked in the monomeric or dimeric states, and also MinD mutants with amphipathic helices of varying membrane affinity. They then assess the mutants' ability to bind to the membrane and form gradients using fluorescence microscopy in different genetic backgrounds. They find that, unlike in the E. coli Min system, the monomeric form of MinD is already capable of membrane binding. They also show that MinJ is not required for MinD membrane binding and only interacts with the dimeric form of MinD. Using kinetic Monte Carlo simulations, the authors then test different models for gradient formation, and find that a MinD gradient along the cell axis is only formed when the polarly localized protein MinJ stimulates dimerization of MinD, and when the diffusion rate of monomeric and dimeric MinD differs. They also show that differences in the membrane affinity of MinD monomers and dimers are not required for gradient formation.

Strengths:

The paper offers a comprehensive collection of the subcellular localization and gradient formation of various MinD mutants in different genetic backgrounds. In particular, the comparison of the localization of these mutants in a delta MinC and MinJ background offers valuable additional insights. For example, they find that only dimeric MinD can interact with MinJ. They also provide evidence that MinD locked in a dimer state may co-polymerize with MinC, resulting in a speckled appearance.

The authors introduce and verify a useful measure of membrane affinity in vivo.

The modulation of the membrane affinity by using distinct amphipathic helices highlights the robustness of the B. subtilis MinD system, which can form gradients even when the membrane affinity of MinD is increased or decreased.

Weaknesses:

The main claim of the paper, that differences in the membrane affinity between MinD monomers and dimers are not required for gradient formation, does not seem to be supported by the data. The only measure of membrane affinity presented is extracted from the transverse fluorescence intensity profile of cells expressing the mGFP-tagged MinD mutants. The authors measure the valley-to-peak ratio of the profile, which is lower than 1 for proteins binding to the membrane and higher than 1 for cytosolic proteins. To verify this measure of membrane affinity, they use a membrane dye and a soluble GFP, which results in values of ~0.75 and ~1.25, respectively. They then show that all MinD mutants have a value - roughly in the range of 0.8-0.9 - and they use this to claim that there are no differences in membrane affinity between monomeric and dimeric versions.

While this way to measure membrane affinity is useful to distinguish between binders and non-binders, it is unclear how sensitive this assay is, and whether it can resolve more subtle differences in membrane affinity, beyond the classification into binders and non-binders. A dimer with two amphipathic helices should have a higher membrane affinity than a monomer with only one such copy. Thus, the data does not seem to support the claim that "the different monomeric mutants have the same membrane affinity as the wildtype MinD". The data only supports the claim that B. subtilis MinD monomers already have a measurable membrane affinity, which is indeed a difference from the E. coli Min system.

While their data does show that a stark difference between monomer and dimer membrane affinity may not be required for gradient formation in the B. subtilis case, it is also not prevented if the monomer is unable to bind to the membrane. They show this by replacing the native MinD amphipathic helix with the weak amphipathic helix NS4AB-AH. According to their membrane affinity assay, NS4AB-AH does not bind to the membrane as a monomer (Figure 4D), but when this helix is fused to MinD, MinD is still capable of forming a gradient (albeit a weaker one). Since the authors make a direct comparison to the E. coli MinDE systems, they could have used the E. coli MinD MTS instead or in addition to the NS4AB-AH amphipathic helix. The reviewer suspects that a fusion of the E. coli MinD MTS to B. subtilis MinD may also support gradient formation.

The paper contains insufficient data to support the many claims about cell filamentation and minicell formation. In many cases, statements like "did not result in cell filamentation" or "restored cell division" are only supported by a single fluorescence image instead of a quantitative analysis of cell length distribution and minicell frequency, as the one reported for a subset of the data in Figure 5.

The paper would also benefit from a quantitative measure of gradient formation of the distinct MinD mutants, instead of relying on individual fluorescent intensity profiles.

The authors compare their experimental results with the oscillating E. coli MinDE system and use it to define some of the rules of their Monte Carlo simulation. However, the description of the E. coli Min system is sometimes misleading or based on outdated findings.

The Monte Carlo simulation of the gradient formation in B. subtilis could benefit from a more comprehensive approach:

(1) While most of the initial rules underlying the simulation are well justified, the authors do not implement or test two key conditions:<br /> (a) Cooperative membrane binding, which is a key component of mathematical models for the oscillating E. coli Min system. This cooperative membrane binding has recently been attributed to MinD or MinCD oligomerization on the membrane and has been experimentally observed in various instances; in fact, the authors themselves show data supporting the formation of MinCD copolymers.

(2) Local stimulation of the ATPase activity of MinD which triggers the dimer-to-monomer transition; E. coli MinD ATP hydrolysis is stimulated by the membrane and by MinE, so B. subtilis MinD may also be stimulated by the membrane and/or other components like MinJ. Instead, the authors claim that (a) would only increase differences in diffusion between the monomer and different oligomeric species, and that a 2-fold increase in dimerization on the membrane could not induce gradient formation in their simulation, in the absence of MinJ stimulating gradient formation. However, a 2-fold increase in dimerization is likely way too low to explain any cooperative membrane binding observed for the E. coli Min system. Regarding (b), they also claim that implementing stimulation of ATP hydrolysis on the membrane (dimer-to-monomer transition) would not change the outcome, but no simulation result for this condition is actually shown.

(3) To generate any gradient formation, the authors claim that they would need to implement stimulation of dimer formation by MinJ, but they themselves acknowledge the lack of any experimental evidence for this assertion. They then test all other conditions (e.g., differences in membrane affinity, diffusion, etc.) in addition to the requirement that MinJ stimulates dimer formation. It is unclear whether the authors tested all other conditions independently of the "MinJ induces dimerization" condition, and whether either of those alone or in combination could also lead to gradient formation. This would be an important test to establish the validity of their claims.

Reviewer #2 (Public Review):

Summary:

In this study, Ju Q et al performed both in vitro and in vivo experiments to test the effect of TAK1 on cancer metastasis. They demonstrated that TAK1 is capable of directly phosphorylating PLCE1 and this modification represses its enzyme activity, leading to suppression of PIP2 hydrolysis and subsequently signal transduction in the PKC/GSK-3β/β-Catenin axis.

Strengths:

The quality of data is good, and the presentation is well organized in a logical way.

Weaknesses:

The study missed some key link in connecting the effect of TAK1 on cancer metastasis via phosphorylating PLCE1.

Reviewer #2 (Public review):

Summary:

The findings highlight the importance of targeting the ELF3-MED23 protein-protein interaction (PPI) as a potential therapeutic strategy for HER2-overexpressing cancers, notably gastric cancers, as an alternative to trastuzumab. The evidence, including the strong potency of compound 10 in inhibiting ELF3-MED23 PPI, its capacity to lower HER2 levels, induce apoptosis, and impede proliferation both in laboratory settings and animal models, indicates that compound 10 holds promise as a novel therapeutic option, even for cases resistant to trastuzumab treatment.

Strengths:

The experiments conducted are robust and diverse enough to address the hypothesis posed.

Reviewer #2 (Public review):

Summary:

This manuscript combines live yeast cell imaging and other genomic approaches to study how transcription factor (TF) condensates might help organize and enhance the transcription of the target genes in the methionine starvation response pathway. The authors show that the TFs in this response can form phase separated condensates through their intrinsically disordered regions (IDRs), and mediate the spatial clustering of the related endogenous genes as well as reporter inserted near the endogenous target loci.

Strengths:

This work uses rigorous experimental approaches, including imaging of endogenously labeled TFs, determining expression and clustering of endogenous target genes and reporter integrated near the endogenous target loci. The importance of TFs is shown by rapid degradation. Single cell data are combined with genomic sequencing-based assays. Control loci engineered in the same way are usually included. Some of these controls are very helpful in showing the pathway-specific effect of the TF condensates in enhancing transcription.

Weaknesses:

The main weakness of this work is that the role of IDR and phase separation in mediating the target gene clustering is unclear. TF IDRs may have many functions including mediating phase separation and binding to other transcriptional molecules (not limited to proteins). The authors did not get clear results on gene clustering upon IDR deletion. IDR deletion may affect binding of other molecules (not the general transcription machinery) that are specifically important for target gene transcription. If the self-association of the IDR is the main driving force of the clustering and target gene transcription enhancement, replacing this IDR with totally unrelated IDRs that have been shown to mediate phase separation in non-transcription systems would preserve the gene clustering and transcription enhancement effects. However, this type of replacement experiment is challenging for endogenous locus.

Reviewer #2 (Public Review):

Summary:

The authors of this manuscript aim to develop a novel animal model to accurately simulate the retinal ischemic process in retinal artery occlusion (RAO). A unilateral pterygopalatine ophthalmic artery occlusion (UPOAO) mouse model was established using silicone wire embolization combined with carotid artery ligation. This manuscript provided data to show the changes of major classes of retinal neural cells and visual dysfunction following various durations of ischemia (30 minutes and 60 minutes) and reperfusion (3 days and 7 days) after UPOAO. Additionally, transcriptomics was utilized to investigate the transcriptional changes and elucidate changes in the pathophysiological process in the UPOAO model post-ischemia and reperfusion. Furthermore, the authors compared transcriptomic differences between the UPOAO model and other retinal ischemic-reperfusion models, including HIOP and UCCAO, and revealed unique pathological processes.

Strengths:

The UPOAO model represents a novel approach for studying retinal artery occlusion. The study is very comprehensive.

Weaknesses:

Originally, some statements were incorrect and confusing. However, the authors have made clarifications in the revised manuscript to avoid confusion.

Reviewer #2 (Public Review):

Summary:

The manuscript expands the current bulk sequencing data deconvolution toolkit to include ATAC-seq. The EPIC-ATAC tool successfully predicts accurate proportions of immune cells in bulk tumour samples and EPIC-ATAC seems to perform well in benchmarking analyses. The authors achieve their aim of developing a new bulk ATAC-seq deconvolution tool.

Strengths:

The manuscript describes simple and understandable experiments to demonstrate the accuracy of EPIC-ATAC. They have also been incredibly thorough with their reference dataset collections and have been robust in their benchmarking endeavours and measured EPIC-ATAC against multiple datasets and tools. This tool will be valuable to the community it serves.

Reviewer #2 (Public Review):

Summary:

The study combines computational modeling of choice behavior with an economic, effort-based decision-making task to assess how willingness to exert physical effort for a reward varies as a function of individual differences in apathy and anhedonia, or depression, as well as chronotype. They find an overall reduction in effort selection that scales with apathy, anhedonia and depression. They also find that later chronotypes are less likely to choose effort than earlier chronotypes and, interestingly, an interaction whereby later chronotypes are especially unwilling to exert effort in the morning versus the evening.

Strengths:

This study uses state-of-the-art tools for model fitting and validation and regression methods which rule out multicollinearity among symptom measures and Bayesian methods which estimate effects and uncertainty about those estimates. The replication of results across two different kinds of samples is another strength. Finally, the study provides new information about the effects not only of chronotype but also chronotype by timepoint interactions which are previously unknown in the subfield of effort-based decision-making.

Weaknesses:

The study has few weaknesses. The biggest drawback is that it does not provide evidence for the idea that a match between chronotype and delay matters is especially relevant for people with depression or continuous measures like anhedonia and apathy. It is unclear whether disorders further interact with chronotype and time of day to determine a bias against effort. On the other hand, the study does provide evidence that future studies should consider such interactions when examining questions about effort expenditure in psychiatric disorders.

Reviewer #2 (Public review):

Summary:

This series of experiments studied the involvement of PVN OT neurons and their projection to the mPFC in pup-care and attack behavior in virgin male and female Mandarin voles. Using Fos visualization, optogenetics, fiber photometry and IP injection of OT the results converge on OT regulating caregiving and attacks on pups. Some sex differences were found in the effects of the manipulations.

Strengths:

Major strengths are the modern multi-method approach and including both sexes of Mandarin vole in every experiment.

Weaknesses:

The few weaknesses include 1) Some experiments' groups have small sample sizes (4-5 animals) which may render some results difficult for others to replicate when different extraneous variables are likely to be present, and 2) the authors discuss PVN OT cell stimulation findings seen in other rodents so the work seems less conceptually novel. Overall, the findings add to the knowledge about OT regulation of pup-directed behavior in male and female rodents, especially the PVN-mPFC OT

Reviewer #2 (Public review):

Summary:

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

Strengths:

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

Weaknesses:

Due to a technical error, this study failed to counterbalance the conditions of the first trial in both the iBEAT and iBREATH tests. Although the authors addressed this issue as much as possible by employing alternative analyses, it should be noted that this error may have critically influenced the results and, thus, the conclusions.

Reviewer #2 (Public review):

Summary:

In this study Amason et al employ spatial transcriptomics and intervention studies to probe the spatial and temporal dynamics of chemokines and their receptors, and their influence on cellular dynamics in C. violaceum granulomas. As a result of their spatial transcriptomic analysis, the authors narrow in on the contribution of neutrophil-and monocyte-recruiting pathways to host response. This results in the observation that monocyte recruitment is critical for granuloma formation and infection control, while neutrophil recruitment via CXCR2 may be dispensable.

Strengths:

Since C. violaceum is a self-limiting granulomatous infection, it makes an excellent case study for 'successful' granulomatous inflammation. This stands in contrast to chronic, unproductive granulomas that can occur during M. tuberculosis infection, sarcoidosis, and other granulomatous conditions, infectious or otherwise. Given the short duration of C. violaceum infection, this study specifically highlights the importance of innate immune responses in granulomas.

Another strength of this study is the temporal analysis. This proves to be important when considering the spatial distribution and timing of cellular recruitment. For example, the authors observe that the intensity and distribution of neutrophil and monocyte recruiting chemokines vary substantially across infection time and correlate well with their previous study of cellular dynamics in C. violaceum granulomas.

The intervention studies done in the last part of the paper bolster the relevance of the authors' focus on chemokines. The authors provide important negative data demonstrating the null effect of CXCR1/2 inhibition on neutrophil recruitment during C. violaceum infection. That said, the authors' difficulty with solubilizing reparixin in PBS is an important technical consideration given the negative result. On the other hand, monocyte recruitment via CCR2 proves to be indispensable for granuloma formation and infection control.

Weaknesses:

There are several shortcomings that limit the impact of this study. The first is that the cohort size is very limited. While the transcriptomic data is rich, the authors analyze just one tissue from one animal per timepoint. This assumes that the selected individual will have a representative lesion and prevents any analysis of inter-individual variability. Granulomas in other infectious diseases, such as schistosomiasis and tuberculosis, are very heterogeneous. The authors do assert that in C. violaceum infection granulomas are very consistent in their composition and kinetics, alleviating, in part, this concern.

Another caveat to these data is the limited or incompletely informative data analysis. This dataset has been previously published with more extensive and broad characterization. Here, the authors use Visium in a more targeted manner to interrogate certain chemokines and cytokines. While this is a great biological avenue, key findings rely on qualitative inspection of gene expression overlaid on to images or data that has been qualitatively binned or thresholded. Upon revision the authors did supplement their analyses with important information, such as the top expressed genes in each Visium cluster and the dynamic range of RNA counts retrieved across clusters.

Furthermore, the authors are underutilizing the spatial information provided by Visium with no spatial analysis conducted to quantify the patterning of expression patterns or spatial correlation between factors. The authors acknowledge the challenge of conducting this analysis given the variable size and geometry of the granulomas. In future studies, this can be overcome through size- or distance-based normalization or spatial clustering approaches that evaluate local neighborhood composition across different scales.

Impact:

The author's analysis helps highlight the chemokine profiles of protective, yet host protective granulomas. As that authors comment on in their discussion, these findings have important similarities and differences with other notable granulomatous conditions, such as tuberculosis. Beyond the relevance to C. violaceum infection, these data can help inform studies of other types of granulomas and hone candidate strategies for host-directed therapy strategies.

Reviewer #3 (Public review):

Summary:

This study presents a solid framework for the metabolic modeling of microbial species and resources in the rhizosphere environment. It is an ambitious effort to tackle the huge complexity of the rhizosphere and reveal the plant-microbiota interactions therein. Considering previously published data by Berihu et al., going through a series of steps, the framework then finds associations between an apple tree disease state and both microbes and metabolites. The framework is well explained and motivated. I think that further work should be done to validate the method, both using synthetic data, with a known ground truth and following up on key findings experimentally.

Strengths:

- The manuscript is well written with a good balance between detail and readability. The framework steps are well motivated and explained.

- The authors faithfully acknowledge the limitations of their approach and do not try to "over-sell" their conclusions.

- The presented framework has potential for significant discovery if the hypotheses generated are followed up with experimental validation.

Weaknesses:

- It would be better for the framework to be validated on synthetic data.

Justification of claims and conclusions:

The claims and conclusions are sufficiently well justified since the limitations of this approach are acknowledged by the authors.

Reviewer #2 (Public review):

Summary:

The current study is presented to assess the shift in metabolism (Glycolysis and Oxidative phosphorylation) of differently primed human Alveolar macrophages and Monocyte derived macrophages in response to TLR4 activating signals (such as LPS and dead Mtb bacteria). They conducted this macrophage characterization in response to type II interferon and IL-4 priming signals, followed by different stimuli of irradiated Mycobacterium tuberculosis and LPS.

Strengths:

(1) The study employs thorough measurement of metabolic shift in metabolism by assessing extracellular acidification rate (ECAR) and oxygen consumption rate (OCR) of differentially polarized primary human macrophages using the Seahorse XFe24 Analyzer.<br /> (2) The effect of differential metabolic shift on the expression of different surface markers for macrophage activation is evaluated through immunofluorescence flow cytometry and cytokine measurement via ELISA.

Weaknesses:

(1) Prior studies with human macrophages have shown a glycolytic shift with similar signals, including live Mycobacterium tuberculosis infection.<br /> (2) Results are often described with detailed methodology for each experiment, and data are replotted and presented in duplicates for cross-analyses which can be confusing.<br /> (3) The data presented shows a distinct functional profile of airway macrophages (AMs) compared to monocyte (blood)-derived macrophages (MDMs) in response to the same priming signals. However, the study does not attempt to explore the underlying mechanisms for this difference.

Appraisal:

(1) The authors have achieved their aim of preliminarily characterizing the glycolysis-dependent cytokine profile and activation marker expression of IFN-g and IL-4 primed primary human macrophages.<br /> (2) The results of the study support its conclusion of glycolysis-dependent phenotypical differences in cytokine secretion and activation marker expression of AMs and MDMs.<br /> (3) However, the study is descriptive in nature, and the results validate IFN-g-mediated glycolytic reprogramming in primary human macrophages without providing mechanistic insights.

Impact:

The study provides evidence of metabolic reprogramming in human primary macrophages and their dependence on glycolysis for downstream secretion of cytokines and expression of activation markers.

Additional comments:

The results of this study are generated from a very large experiment with different treatments and phenotypic characterization. The data is plotted and analyzed in different figures to aid the reader.

Reviewer #2 (Public review):

Summary:

The biologically realistic model of the locomotor circuits developed by this group continues to define the state of the art for understanding spinal genesis of locomotion. Here the authors have achieved a new level of analysis of this model to generate surprising and potentially transformative new insights. They show that these circuits can operate in three very distinct states and that, in the intact spinal cord, these states come into successive operation as the speed of locomotion increases. Equally important, they show that in spinal injury, the model is "stuck" in the low-speed "state machine" behavior.

Strengths:

There are many strengths for the simulations results presented here. The model itself has been closely tuned to match a huge range of experimental data and this has a high degree of plausibility. The novel insight presented here, with the three different states, constitutes a truly major advance in the understanding of neural genesis of locomotion in spinal circuits. The authors systematically consider how the states of the model relate to presently available data from animal studies. Equally important, they provide a number of intriguing and testable predictions. It is likely that these insights are the most important achieved in the past 10 years. It is highly likely proposed multi-state behavior will have a transformative effect on this field.

Weaknesses:

I have no major weaknesses. A moderate concern is that the authors should consider some basic sensitivity analyses to determine if the 3-state behavior is especially sensitive to any of the major circuit parameters-e.g., connection strengths in the oscillators.

Reviewer #2 (Public Review):

This manuscript describes the impact of deleting or enhancing the expression of the neuronal-specific kinase DLK in glutamatergic hippocampal neurons using clever genetic strategies, which demonstrates that DLK deletion had minimal effects while overexpression resulted in neurodegeneration in vivo. To determine the molecular mechanisms underlying this effect, ribotag mice were used to determine changes in active translation which identified Jun and STMN4 as DLK-dependent genes that may contribute to this effect. Finally, experiments in cultured neurons were conducted to better understand the in vivo effects. These experiments demonstrated that DLK overexpression resulted in morphological and synaptic abnormalities.

Strengths:

This study provides interesting new insights into the role of DLK in the normal function of hippocampal neurons. Specifically, the study identifies:

(1) CA1 vs CA3 hippocampal neurons have differing sensitivity to increased DLK signaling.

(2) DLK-dependent signaling in these neurons is similar to but distinct from the downstream factors identified in other cell types, highlighted by the identification of STMN4 as a downstream signal.

(3) DLK overexpression in hippocampal neurons results in signaling that is similar to that induced by neuronal injury.

The study also provides confirmatory evidence that supports previously published work through orthogonal methods, which adds additional confidence to our understanding of DLK signaling in neurons. Taken together, this is a useful addition to our understanding of DLK function.

Weaknesses:

There are a few weaknesses that limit the impact of this manuscript, most of which are pointed out by the authors in the discussion. Namely:

(1) It is difficult to distinguish whether the changes in the translatome identified by the authors are DLK-dependent transcriptional changes, DLK-dependent post-transcriptional changes or secondary gene expression changes that occur as a result of the neurodegeneration that occurs in vivo. Additional expression analysis at earlier time points could be one method to address this concern.

(2) Related to the above, it is difficult to conclusively determine from the current data whether the changes in synaptic proteins observed in vivo are a secondary result of neuronal degeneration or a primary impact on synapse formation. The in vitro studies suggest this has the potential to be a primary effect, though the difference in experimental paradigm makes it impossible to determine whether the same mechanisms are present in vitro and in vivo.

(3) The phenotype of DLK cKO mice is very subtle (consistent with previous reports) and while the outcome of increased DLK levels is interesting, the relevance to physiological DLK signaling is less clear. What does seem possible is that increased DLK may phenocopy other neuronal injuries but there are no real comparisons to directly address this in the manuscript. It would be helpful for the authors to provide this analysis as well as a table with all of the translational changes along with fold changes.

(4) For the in vivo experiments, it is unclear whether multiple sections from each animal were quantified for each condition. More information here would be helpful and it is important that any quantification takes multiple sections from each animal into account to account for natural variability.

Reviewer #2 (Public Review):

Summary:

This manuscript focuses on the apparent involvement of a proposed copper-responsive regulator in the chemotactic response of Pseudomonas putida to Cu(II), a chemorepellent. Broadly, this area is of interest because it could provide insight into how soil microbes mitigate metal stress. Additionally, copper has some historical agricultural use as an antimicrobial, thus can accumulate in soil. The manuscript bases its conclusions on an in vitro screen to identify interacting partners of CheA, an essential kinase in the P. putida chemotaxis-signaling pathway. Much of the subsequent analysis focuses on a regulator of the CsoR/RcnR family (PP_2969).

Weaknesses:

The data presented in this work does not support the model (Figure 8). In particular, PP_2969 is linked to Ni/Co resistance, not Cu resistance. Further, it is not clear how the putative new interactions with CheA would be integrated into diverse responses to various chemoattract/repellents. These two comments are justified below.

PP_2969

(1) The authors present a sequence alignment (Figure S5) that is the sole basis for their initial assignment of this ORF as a CsoR protein. There is a conservation of the primary coordinating ligands (highlighted with asterisks) known to be involved in Cu(I) binding to CsoR (ref 31). There are some key differences, though, in residues immediately adjacent to the conserved Cys (the preceding Ala, which is Tyr in the other sequences). The effect of these changes may be significant in a physiological context.

(2) The gene immediately downstream of PP_2969 is homologous to E. coli RcnA, a demonstrated Ni/Co efflux protein, suggesting that P2969 may be Ni or Co responsive. Indeed PP_2970 has previously been reported as Ni/Co responsive (J. Bact 2009 doi:10.1128/JB.00465-09). The host cytosol plays a critical role in determining metal response, in addition to the protein, which can explain the divergence from the metal response expected from the alignment.

(3) The previous JBact study also explains the lack of an effect (Figure 5b) of deleting PP_2969 on copper-efflux gene expression (copA-I, copA-II, and copB-II) as these are regulated by CueR not PP_2969 consistent with the previous report. Deletion of CsoR/RcnR family regulator will result in constitutive expression of the relevant efflux/detoxification gene, at a level generally equivalent to the de-repression observed in the presence of the signal.

(4) Further, CsoR proteins are Cu(I) responsive so measuring Cu(II) binding affinity is not physiologically relevant (Figures 5a and S5b). The affinities of demonstrated CsoR proteins are 10-18 M and these values are determined by competition assay. The MTS assay and resulting affinities are not physiologically relevant.

(5) The DNA-binding assays are carried out at protein concentrations well above physiological ranges (Figures 5c and d, and S5c, d). The weak binding will in part result from using DNA sequences upstream of the copA genes and not from from PP_2970.

CheA interactions

(1) There is no consideration given to the likely physiological relevance of the new interacting partners for CheA.

(2) How much CheA is present in the cell (copies) and how many copies of other proteins are present? How would specific responses involving individual interacting partners be possible with such a heterogenous pool of putative CheA-complexes in a cell? For PP_2969, the affinity reported (Figure 5A) may lay at the upper end of the CsoR concentration range (for example, CueR in Salmonella is present at ~40 nM).

(3) The two-hybrid system experiment uses a long growth time (60 h) before analysis. Even low LacZ activity levels will generate a blue colour, depending upon growth medium (see doi: 10.1016/0076-6879(91)04011-c). It is also not clear how Miller units can be accurately or precisely determined from a solid plate assay (the reference cited describes a protocol for liquid culture).

Reviewer #2 (Public review):

The authors of this paper have done much pioneering work to decipher and understand LRRK2 structure and function, to uncover the mechanism by which LRRK2 binds to microtubules, and to study the roles that this may play in biology. Their previous data demonstrated that LRRK2 in the active conformation (pathogenic mutation or Type I inhibitor complex) bound to microtubule filaments in an ordered helical arrangement. This they showed induced a "roadblock" in the microtubule impacting vesicular trafficking. The authors have postulated that this is a potentially serious flaw with Type 1 inhibitors and that companies should consider generating Type 2 inhibitors in which the LRRK2 is trapped in the inactive conformation. Indeed the authors have published much data that LRRK2 complexed to Type 2 inhibitors does not seem to associate with microtubules and cause roadblocks in parallel experiments to those undertaken with type 1 inhibitors published above.

In the current study, the authors have undertaken an in vitro reconstitution of microtubule-bound filaments of LRRK2 in the inactive conformation, which surprisingly revealed that inactive LRRK2 can also interact with microtubules in its auto-inhibited state. The authors' data shows that while the same interphases are seen with both the active LRRK2 and inactive microtubule bound forms of LRRK2, they identified a new interphase that involves the WD40-ARM-ANK- domains that reportedly contributes to the ability of the inactive form of LRRK2 to bind to microtubule filaments. The structures of the inactive LRRK2 complexed to microtubules are of medium resolution and do not allow visualisation of side chains.

This study is extremely well-written and the figures are incredibly clear and well-presented. The finding that LRRK2 in the inactive autoinhibited form can be associated with microtubules is an important observation that merits further investigation. This new observation makes an important contribution to the literature and builds upon the pioneering research that this team of researchers has contributed to the LRRK2 fields. However, in my opinion, there is still significant work that could be considered to further investigate this question and understand the physiological significance of this observation.

Reviewer #2 (Public Review):

Summary:

Cong et al. investigated the regulatory effects of ABHD6 on AMPARs. The authors performed adequate electrophysiology recordings to show the exact pattern of this regulation and covered major critical points.

Strengths:

The authors have performed high-quality ephys recordings and examined all potential regulatory aspects of ABHD6 on AMPARs. This is important to understand the AMPAR functions.

Weaknesses:

(1) The authors discussed CNIH-2 extensively from line 92-110 in the introduction, however, they did not perform related experiments. I suggest they move this part to the discussion where they also discussed the roles of CNIH.<br /> (2) The authors need to report the "n" for all the experiments they have presented in this manuscript. How many cells were recorded in each condition? How many batches? This information has to be in all of the figure legends, but it is missing except Fig. 4.<br /> (3) One question is what the physiological meanings of this regulatory effect are. The authors may consider adding some discussions.<br /> (4) About statistics. The authors need to add more details and make sure their statistics sound. For example, they also need to check the equality of variances. In their Table EVs, where the P values are reported, the authors need to report which statistics they have used, one-way ANOVA, K-W test, or others, and the exact post-hoc test type for each comparison. For one-way ANOVA, report the F values simultaneously with the P values in all figure legends.<br /> (5) Fig. 3J, the authors need to correct the label of the Y axis. It is shifted.

Reviewer #2 (Public review):

Summary:

This is an outstanding piece of work on the potential of FLO as a viable analgesic biologic for the treatment of postsurgical pain. The authors purified the HC-HA/PTX3 from FLO and demonstrated its potential as an effective non-opioid therapy for postsurgical pain. They further unraveled the mechanisms of action of the compound at cellular and molecular levels.

Strengths:

Prominent strengths include the incorporation of behavioral assessment, electrophysiological and imaging recordings, the use of knockout and knockdown animals, and the use of antagonist agents to verify biological effects. The integrated use of these techniques, combined with the hypothesis-driven approach and logical reasoning, provides compelling evidence and novel insight into the mechanisms of the significant findings of this work.

Weaknesses:

I did not find any significant weaknesses even with a critical mindset. The only minor suggestion is that the Results section may focus on the results from this study and minimize the discussions of background information.

Reviewer #2 (Public review):

Summary:

Saijilafu et al. demonstrate that MLCK/MLCP proteins promote axonal regeneration in both the central nervous system (CNS) and peripheral nervous system (PNS) using primary cultures of adult DRG neurons, hippocampal and cortical neurons, as well as in vivo experiments involving sciatic nerve injury, spinal cord injury, and optic nerve crush. The authors show that axon regrowth is possible across different contexts through genetic and pharmacological manipulation of these proteins. Additionally, they propose that MLCK/MLCP may regulate F-actin reorganization in the growth cone, which is significant as it suggests a novel strategy for promoting axonal regeneration.

Strengths:

This manuscript presents a comprehensive array of experimental models, addressing the biological question in a broad manner. Particularly noteworthy is the use of multiple in vivo models, which significantly strengthens the overall validity of the study.

Weaknesses:

The following aspects apply:

(1) The manuscript initially references prior research by the authors suggesting that NMII inhibition enhances axonal growth and that MLCK activates NMII. However, the study introduces a contradiction by demonstrating that MLCK inhibition (via ML-7 or siMLCK) inhibits axonal growth. This inconsistency is not adequately addressed or discussed in the manuscript.

(2) While the study proposes that MLCK/MLCP regulates F-actin redistribution in the growth cone, the mechanism is not explored in depth. The only figure showing how pharmacological manipulation affects the growth cone suggests that not only F-actin but also the microtubule cytoskeleton might be affected, indicating that the mechanism may not be specific. A deeper exploration of this relationship in DRG neurons, in addition to cortical neurons, as shown in the study, would be beneficial.

(3) In the sciatic nerve injury experiments, it would be crucial to include additional controls that clearly demonstrate that siMYPT1 treatment increases MLCP in the L4-L5 ganglia. Additionally, although the manuscript mentions quantifying axons expressing EGFP, the Materials and Methods section only discusses siMYPT1 electroporation, which could lead to confusion.

(4) In some panels, it is difficult to differentiate the somas from the background (Figures 3, 4, 7). In conditions where images with shorter axonal lengths are represented, it is unclear whether this is due to fewer cells or reduced axonal growth (Figures 2, 4, 6).

Reviewer #2 (Public Review):

Summary:

In this study, the authors investigate the potential role of other cleavage products of amyloid precursor protein (APP) in neurodegeneration. They combine in vitro and in vivo experiments, revealing that β-CTF, a product cleaved by BACE1, promotes synaptic loss independently of Aβ. Furthermore, they suggest that β-CTF may interact with Rab5, leading to endosomal dysfunction and contributing to the loss of synaptic proteins.

Weaknesses:

Most experiments were conducted in vitro using overexpressed β-CTF. Additionally, the study does not elucidate the mechanisms by which β-CTF disrupts endosomal function and induces synaptic degeneration.

Reviewer #2 (Public review):

I previously reviewed this important and timely manuscript at a previous journal where, after two rounds of review, I recommended publication. Because eLife practices an open reviewing format, I will recapitulate some of my previous comments here, for the scientific record.

In that previous review, I revealed my identity to help reassure the authors that I was doing my best to remain unbiased because I work in this area and some of the authors' results directly impact my prior research. I was genuinely excited to see the earlier preprint version of this paper when it first appeared. I get a lot of joy out of trying to - collectively, as a field - really understand the nature of our data, and I continue to commend the authors here for pushing at the sources of aperiodic activity!

In their manuscript, Schmidt and colleagues provide a very compelling, convincing, thorough, and measured set of analyses. Previously I recommended that the push even further, and they added the current Figure 5 analysis of event-related changes in the ECG during working memory. In my opinion this result practically warrants a separate paper its own!

The literature analysis is very clever, and expanded upon from any other prior version I've seen.

In my previous review, the broadest, most high-level comment I wanted to make was that authors are correct. We (in my lab) have tried to be measured in our approach to talking about aperiodic analyses - including adopting measuring ECG when possible now - because there are so many sources of aperiodic activity: neural, ECG, respiration, skin conductance, muscle activity, electrode impedances, room noise, electronics noise, etc. The authors discuss this all very clearly, and I commend them on that. We, as a field, should move more toward a model where we can account for all of those sources of noise together. (This was less of an action item, and more of an inclusion of a comment for the record.)

I also very much appreciate the authors' excellent commentary regarding the physiological effects that pharmacological challenges such as propofol and ketamine also have on non-neural (autonomic) functions such as ECG. Previously I also asked them to discuss the possibility that, while their manuscript focuses on aperiodic activity, it is possible that the wealth of literature regarding age-related changes in "oscillatory" activity might be driven partly by age-related changes in neural (or non-neural, ECG-related) changes in aperiodic activity. They have included a nice discussion on this, and I'm excited about the possibilities for cognitive neuroscience as we move more in this direction.

Finally, I previously asked for recommendations on how to proceed. The authors convinced me that we should care about how the ECG might impact our field potential measures, but how do I, as a relative novice, proceed. They now include three strong recommendations at the end of their manuscript that I find to be very helpful.

As was obvious from previous review, I consider this to be an important and impactful cautionary report, that is incredibly well supported by multiple thorough analyses. The authors have done an excellent job responding to all my previous comments and concerns and, in my estimation, those of the previous reviewers as well.

Reviewer #2 (Public Review):

Summary:

Li et al. investigated the potential anti-ageing role of 17α-Estradiol on the hypothalamus of aged rats. To achieve this, they employed a very sophisticated method for single-cell genomic analysis that allowed them to analyze effects on various groups of neurons and non-neuronal cells. They were able to sub-categorize neurons according to their capacity to produce specific neurotransmitters, receptors, or hormones. They found that 17α-Estradiol treatment led to an improvement in several factors related to metabolism and synaptic transmission by bringing the expression levels of many of the genes of these pathways closer or to the same levels as those of young rats, reversing the ageing effect. Interestingly, among all neuronal groups, the proportion of Oxytocin-expressing neurons seems to be the one most significantly changing after treatment with 17α-Estradiol, suggesting an important role of these neurons in mediating its anti-ageing effects. This was also supported by an increase in circulating levels of oxytocin. It was also found that gene expression of corticotropin-releasing hormone neurons was significantly impacted by 17α-Estradiol even though it was not different between aged and young rats, suggesting that these neurons could be responsible for side effects related to this treatment. This article revealed some potential targets that should be further investigated in future studies regarding the role of 17α-Estradiol treatment in aged males.

Strengths:

(1) Single-nucleus mRNA sequencing is a very powerful method for gene expression analysis and clustering. The supervised clustering of neurons was very helpful in revealing otherwise invisible differences between neuronal groups and helped identify specific neuronal populations as targets.

(2) There is a variety of functions used that allow the differential analysis of a very complex type of data. This led to a better comparison between the different groups on many levels.

(3) There were some physiological parameters measured such as circulating hormone levels that helped the interpretation of the effects of the changes in hypothalamic gene expression.

Weaknesses:

(1) One main control group is missing from the study, the young males treated with 17α-Estradiol.

(2) Even though the technical approach is a sophisticated one, analyzing the whole rat hypothalamus instead of specific nuclei or subregions makes the study weaker.

(3) Although the authors claim to have several findings, the data fail to support these claims.

(4) The study is about improving ageing but no physiological data from the study demonstrated such a claim with the exception of the testes histology which was not properly analyzed and was not even significantly different between the groups.

(5) Overall, the study remains descriptive with no physiological data to demonstrate that any of the effects on hypothalamic gene expression are related to metabolic, synaptic, or other functions.

Reviewer #2 (Public Review):

The tubulin subunits that make up microtubules can be posttranslationally modified and these PTMs are proposed to regulate microtubule dynamics and the proteins that can interact with microtubules in many contexts. However, most studies investigating the roles of tubulin PTMs have been conducted in vitro either with purified components or in cultured cells. Lu et al. use CRISPR/Cas9 genome editing to mutate tubulin genes in C. elegans, testing the role of specific tubulin residues on neuronal development. This study is a real tour de force, tackling multiple proposed tubulin modifications and following the resulting phenotypes with respect to neurite outgrowth in vivo. There is a ton of data that experts in the field will likely reference for years to come as this is one of the most comprehensive in vivo analyses of tubulin PTMs in vivo.

This paper will be very important to the field, however would be strengthened if: 1) the authors demonstrated that the mutations they introduced had the intended consequences on microtubule PTMs, 2) the authors explored how the various tubulin mutations directly affect microtubules, and 3) the findings are made generally more accessible to non C. elegans neurobiologists.

(1) The authors introduce several mutations to perturb tubulin PTMs, However, it is unclear to what extent the engineered mutations affect tubulin in the intended way i.e. are the authors sure that the PTMs they want to perturb are actually present in C. elegans. Many of the antibodies used did not appear to be specific and antibody staining was not always impacted in the mutant cases as expected. For example, is there any evidence that S172 is phosphorylated in C. elegans, e.g. from available phosphor-proteomic data? Given the significant amount of staining left in the S172A mutant, the antibody seems non-specific in this context and therefore not a reliable readout of whether MTs are actually phosphorylated at this residue. As another example, there is no evidence presented that K252 is acetylated in C. elegans. At the very least, the authors should consider demonstrating the conservation of these residues and the surrounding residues with other organisms where studies have demonstrated PTMs exist.

(2) Given that the authors have the mutants in hand, it would be incredibly valuable to assess the impact of these mutations on microtubules directly in all cases. MT phenotypes are inferred from neurite outgrowth phenotypes in several cases, the authors should look directly at microtubules and/or microtubule dynamics via EBP-2 when possible OR show evidence that the only way to derive the neurite phenotypes shown is through the inferred microtubule phenotypes. For example, the effect of the acetylation or detyrosination mutants on MTs was not assessed.

(3) There is a ton of data here that will be important for experts working in this field to dig into, however, for the more general cell biologist, some of the data are quite inaccessible. More cartoons and better labeling will be helpful as will consistent comparisons to control worms in each experiment.

(4) In addition, I am left unconvinced of the negative data demonstrating that MBK does not phosphorylate tubulin. First, the data described in lines 207-211 does not appear to be presented anywhere. Second, RNAi is notoriously finicky in neurons, thus necessitating tissue-specific degradation using either the ZF/ZIF-1 or AID/TIR1 systems which both work extremely well in C. elegans. Third, there appears to be increasing S172 phosphorylation in Figure 3 Supplement 2 with added MBK-2, but there is no anti-tubulin blot to show equal loading, so this experiment is hard to interpret.

Reviewer #2 (Public Review):

Summary:

The authors show that a spiking network model with clustered neurons produces intrinsic spike sequences when driven with a 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 critiques of the paper relate to the form of the input to the network.

First, because the input is the same across trials (i.e. all traversals are the same duration/velocity), there is no ability to distinguish a representation of space from a representation of time elapsed since the beginning of the trial. The authors should test what happens e.g. with traversals in which the animal travels at different speeds, and in which the animal's speed is not constant across the entire track, and then confirm that the resulting tuning curves are a better representation of position or duration.

Second, 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. The authors should verify that their results do not depend on this idealization. Specifically, I would suggest the authors also test the spatial coding properties of their network in 2-dimensional environments, and with different kinds of input that have a range of degrees 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.

Finally, I was left wondering how the cells' spatial tuning relates to their cluster membership, and how the capacity of the network (number of different environments/locations that can be represented) relates to the number of clusters. It seems that if clusters of cells tend to code for nearby locations in the environment (as predicted by the results of Figure 5), then the number of encodable locations would be limited (by the number of clusters). Further, there should be a strong tendency for cells in the same cluster to encode overlapping locations in different environments, which is not seen in experimental data.

Reviewer #2 (Public review):

This work started with transcriptomic profiling of ductal cells to identify the upregulation of calcineurin in the zebrafish after beta-cell ablation. By suppressing calcineurin with its chemical inhibitor cyclosporin A and expressing a constitutively active form of calcineurin ubiquitously or specifically in ductal cells, the authors found that inhibited calcineurin activity promoted beta-cell regeneration transiently while ectopic calcineurin activity hindered beta-cell regeneration in the pancreatic tail. They also showed similar effects in the basal state but only when it was within a particular permissive window of Notch activity. To further investigate the roles of calcineurin in the ductal cells, the authors demonstrated that calcineurin inhibition additionally induced the proliferation of the ductal cells in the regenerative context or under a limited level of Notch activity. Interestingly, the enhanced proliferation was followed by a depletion of ductal cells, suggesting that calcineurin inhibition would exhaust the ductal cells. Based on the data, the authors proposed a very attractive and intriguing model of the role of calcineurin in maintaining the balance of the progenitor proliferation and the endocrine differentiation. However, the conclusions of this paper are only partially supported by the data as some evidence of the lineage between ductal cells and beta cells remains suggestive.

Reviewer #2 (Public Review):

In the manuscript Liu et al. observed that glucose and noncaloric monosaccharides can prompt an excessive formation of blood vessels, particularly intersegmental vessels (ISVs). They propose that these branched vessels arise from the ectopic activation of quiescent endothelial cells (ECs) into tip cells. Moreover, through single-cell transcriptome sequencing analysis of embryonic endothelial cells exposed to glucose, they noted an increased proportion of arterial and capillary endothelial cells, proliferative endothelial cells, along with a series upregulated genes in categories of blood vessel morphogenesis, development, and pro-angiogenesis. The authors provide evidence suggesting that caloric and noncaloric monosaccharides (NMS) induce excessive angiogenesis via the Foxo1a-Marcksl1a pathway.

Reviewer #2 (Public Review):

Summary:

In this important study, Baniulyte and Wade describe how the translation of an 8-codon uORF denoted toiL upstream of the topAI-yjhQP operon is responsive to different ribosome-targeting antibiotics, consequently controlling translation of the TopAI toxin as well as Rho-dependent termination with the gene.

Strengths:

I appreciate that the authors used multiple different approaches such as a genetic screen to identify factors such as 23S rRNA mutations that affect topA1 expression and ribosome profiling to examine the consequences of various antibiotics on toiL-mediated regulation. The results are convincing and clearly described.

Weaknesses:

I have relatively minor suggestions for improving the manuscript. These mainly relate to the figures.

Reviewer #2 (Public Review):

Summary:

Bonnifet et al. sought to characterize the expression pattern of L1 ORF1p expression across the entire mouse brain, in young and aged animals, and to corroborate their characterization with Western blotting for L1 ORF1p and L1 RNA expression data from human samples. They also queried L1 ORF1p interacting partners in the mouse brain by IP-MS.

Strengths:

A major strength of the study is the use of two approaches: a deep-learning detection method to distinguish neuronal vs. non-neuronal cells and ORF1p+ cells vs. ORF1p- cells across large-scale images encompassing multiple brain regions mapped by comparison to the Allen Brain Atlas, and confocal imaging to give higher resolution on specific brain regions. These results are also corroborated by Western blotting on six mouse brain regions. Extension of their analysis to post-mortem human samples, to the extent possible, is another strength of the paper. The identification of novel ORF1p interactors in the brain is also a strength in that it provides a novel dataset for future studies.

Weaknesses:

The main weakness of the study is that cell type specificity of ORF1p expression was not examined beyond neuron (NeuN+) vs non-neuron (NeuN-). Indeed, a recent study (Bodea et al. 2024, Nature Neuroscience) found that ORF1p expression is characteristic of parvalbumin-positive interneurons, and it would be very interesting to query whether other neuronal subtypes in different brain regions are distinguished by ORF1p expression. The data suggesting that ORF1p expression is increased in aged mouse brains is intriguing, although it seems to be based upon modestly (up to 27%, dependent on brain region) higher intensity of ORF1p staining rather than a higher proportion of ORF1+ neurons. Indeed, the proportion of NeuN+/Orf1p+ cells actually decreased in aged animals. It is difficult to interpret the significance and validity of the increase in intensity, as Hoechst staining of DNA, rather than immunostaining for a protein known to be stably expressed in young and aged neurons, was used as a control for staining intensity. The main weakness of the IP-MS portion of the study is that none of the interactors were individually validated or subjected to follow-up analyses. The list of interactors was compared to previously published datasets, but not to ORF1p interactors in any other mouse tissue.

The authors achieved the goals of broadly characterizing ORF1p expression across different regions of the mouse brain, and identifying putative ORF1p interactors in the mouse brain. However, findings from both parts of the study are somewhat superficial in depth.

This provides a useful dataset to the field, which likely will be used to justify and support numerous future studies into L1 activity in the aging mammalian brain and in neurodegenerative disease. Similarly, the list of ORF1p interacting proteins in the brain will likely be taken up and studied in greater depth.

Reviewer #2 (Public review):

Summary:

The manuscript reports the computational study of the dynamics of PROTAC-induced degradation complexes. The research investigates how different linkers within PROTACs affect the formation and stability of ternary complexes between the target protein BRD4BD1 and Cereblon E3 ligase, and the degradation machinery. Using computational modeling, docking, and molecular dynamics simulations, the study demonstrates that although all PROTACs form ternary complexes, the linkers significantly influence the dynamics and efficacy of protein degradation. The findings highlight that the flexibility and positioning of Lys residues are crucial for successful ubiquitination. The results also discussed the correlated motions between the PROTAC linker and the complex.

Strengths:

The field of PROTAC discovery and design, characterized by its limited research, distinguishes itself from traditional binary ligand-protein interactions by forming a ternary complex involving two proteins. The current understanding of how the structure of PROTAC influences its degradation efficacy remains insufficient. This study investigated the atomic-level dynamics of the degradation complex, offering potentially valuable insights for future research into PROTAC degradability.

Reviewer #2 (Public review):

Summary:

The inferior colliculus (IC) has been explored for its possible functions in behavioral tasks and has been suggested to play more important roles rather than simple sensory transmission. The authors revealed the climbing effect of neurons in IC during decision-making tasks, and tried to explore the reward effect in this condition.

Strengths:

Complex cognitive behaviors can be regarded as simple ideals of generating output based on information input, which depends on all kinds of input from sensory systems. The auditory system has hierarchic structures no less complex than those areas in charge of complex functions. Meanwhile, IC receives projections from higher areas, such as auditory cortex, which implies IC is involved in complex behaviors. Experiments in behavioral monkeys are always time-consuming works with hardship, and this will offer more approximate knowledge of how the human brain works.

Weaknesses:

These findings are more about correlation but not causality of IC function in behaviors. And I have a few major concerns.

Comparing neurons' spike activities in different tests, a 'climbing effect' was found in the oddball paradigm. The effect is clearly related to training and learning process, but it still requires more exploration to rule out a few explanations. First, repeated white noise bursts with fixed inter-stimulus-interval of 0.6 seconds was presented, so that monkeys might remember the sounds by rhymes, which is some sort of learned auditory response. It is interesting to know monkeys' responses and neurons' activities if the inter-stimuli-interval is variable. Second, the task only asked monkeys to press one button and the reward ratio (the ratio of correct response trials) was around 78% (based on the number from Line 302). so that, in the sessions with reward, monkeys had highly expected reward chances, does this expectation cause the climbing effect?

"Reward effect" on IC neurons' responses were showed in Fig. 4. Is this auditory response caused by physical reward action or not? In reward sessions, IC neurons have obvious response related to the onset of water reward. The electromagnetic valve is often used in water-rewarding system and will give out a loud click sound every time when the reward is triggered. IC neurons' responses may be simply caused by the click sound if the electromagnetic valve is used. It is important to find a way to rule out this simple possibility.

Reviewer #2 (Public review):

Summary:

RNAs can function across cell borders and animal generations as sources of epigenetic information for development and immunity. The specific mechanistic pathways how RNA travels between cells and progeny remains an open question. Here, Shugarts, et al. use molecular genetics, imaging, and genomics methods to dissect specific RNA transport and regulatory pathways in the C. elegans model system. Larvae ingesting double stranded RNA is noted to not cause continuous gene silencing throughout adulthood. Damage of neuronal cells expressing double stranded target RNA is observed to repress target gene expression in the germline. Exogenous supply of short or long double stranded RNA required different genes for entry into progeny. It was observed that the SID-1 double-stranded RNA transporter showed different expression over animal development. Removal of the sid-1 gene caused upregulation of two genes, the newly described sid-1-dependent gene sdg-1 and sdg-2. Both genes were observed to also be negatively regulated by other small RNA regulatory pathways. Strikingly, loss then gain of sid-1 through breeding still caused variability of sdg-1 expression for many, many generations. SDG-2 protein co-localizes with a Z-granule marker, an intracellular site for heritable RNA silencing machinery. Collectively, sdg-1 presents a model to study how extracellular RNAs can buffer gene expression in germ cells and other tissues.

Strengths:

(1) Very clever molecular genetic methods and genomic analyses, paired with thorough genetics, were employed to discover insights into RNA transport, sdg-1 and sdg-2 as sid-1-dependent genes, and sdg-1's molecular phenotype.

(2) The manuscript is well cited, and figures reasonably designed.

(3) The discovery of the sdg genes being responsive to the extracellular RNA cell import machinery provides a model to study how exogenous somatic RNA is used to regulate gene expression in progeny. The discovery of genes within retrotransposons stimulates tantalizing models how regulatory loops may actually permit the genetic survival of harmful elements.

Weaknesses:

(1) As presented, the manuscript is incredibly broad, making it challenging to read and consider the data presented. This concern is exemplified in the model figure, that requires two diagrams to summarize the claims made by the manuscript.

(2) The large scope of the manuscript denies space to further probe some of the ideas proposed. The first part of the manuscript, particularly Figures 1 and 2, presents data that can be caused by multiple mechanisms, some of which the authors describe in the results but do not test further. Thus, portions of the results text come across as claims that are not supported by the data presented.

(3) The manuscript focuses on the genetics of SDGs but not the proteins themselves. Few descriptions of the SDGs functions are provided nor is it clarified why only SDG-1 was pursued in imaging and genetic experiments. Additionally, the SDG-1 imaging experiments could use additional localization controls.

Reviewer #2 (Public review):

Summary:

Held et al. investigated the distinct activities of Insulin-Producing Cells (IPCs) by electrophysiological recordings and calcium imaging. In the brain of the fruit fly Drosophila melanogaster, there are approximately 14 IPCs that are analogous to mammalian pancreatic beta cells and provide a good model system for monitoring their activities in vivo. The authors performed single-nucleus RNA sequencing analysis to examine what types of neuromodulatory inputs are received by IPCs. A variety of neuromodulatory receptors are expressed heterogeneously in IPCs, which would explain the distinct activities of IPCs in response to the activations of neuromodulatory neurons. The authors also conducted the connectome analysis and G-protein prediction analysis to strengthen their hypothesis that the heterogeneity of IPCs may underlie the flexible insulin release in response to various environmental conditions.

Strengths:

The authors succeeded patch-clamp recordings and calcium imaging of individual IPCs in living animals at a single-cell resolution, which allows them to show the heterogeneity of IPCs precisely. They measured IPC activities in response to 9 types of neurons in patch-clamp recordings and 5 types of neurons in calcium imaging, comparing the similarities and differences in activities between two methods. These results support the idea that the neuromodulatory system affects individual IPC activities differently in a receptor-dependent manner.

Weaknesses:

One concern is how much extent the heterogeneity of IPC activities in a short time scale is relevant to the net output, a release of insulin-like peptides in response to metabolic demands in a relatively longer time scale. The authors can test their hypothesis by manipulating the heterogeneous expressions of receptor genes in IPCs and examining IPC activities on a longer time scale. Moreover, while the authors focus on IPC activities, they did not show the activation of the neuromodulatory inputs and the net output of insulin levels in the data. The readers might want to know which neurons are indeed activated to send signals to IPCs and how IPC activities result in the secretion of insulin peptides.

Reviewer #2 (Public Review):

As discussed in the original review, this manuscript is an important contribution to a mechanistic understanding of LRRK2 kinase. Kinetic parameters for the GTPase activity of the ROC domain have been determined in the absence/presence of kinase activity. A feedback mechanism from the kinase domain to GTP/GDP hydrolysis by the ROC domain is convincingly demonstrated through these kinetic analyses. However, a regulatory mechanism directly linking the T1343 phospho-site and a monomer/dimer equilibrium is not fully supported. The T1343A mutant has reduced catalytic activity and can form similar levels of dimer as WT. The revised manuscript does point out that other regulatory mechanisms can also play a role in kinase activity and GTP/GDP hydrolysis (Discussion section). The environmental context in cells cannot be captured from the kinetic assays performed in this manuscript, and the introduction contains some citations regarding these regulatory factors. This is not a criticism, the detailed kinetics here are rigorous, but it is simply a limitation of the approach.

Reviewer #2 (Public Review):

Summary:

Kreeger et.al provided mechanistic evidence for flexible coincidence detection of auditory nerve synaptic inputs by octopus cells in the mouse cochlear nucleus. The octopus cells are specialized neurons that can fire repetitively at very high rates (> 800 Hz in vivo), yield responses dominated by the onset of sound for simple stimuli, and integrate auditory nerve inputs over a wide frequency span. Previously, it was thought that octopus cells received little inhibitory input, and their integration of auditory input depended principally on temporally precise coincidence detection of excitatory auditory nerve inputs, coupled with a low input resistance established by high levels of expression of certain potassium channels and hyperpolarization-activated channels.

In this study, the authors used a combination of numerous genetic mouse models to characterize synaptic inputs and enable optogenetic stimulation of subsets of afferents, fluorescent microscopy, detailed reconstructions of the location of inhibitory synapses on the soma and dendrites of octopus cells, and computational modeling, to explore the importance of inhibitory inputs to the cells. They determined through assessment of excitatory and inhibitory synaptic densities that spiral ganglion neuron synapses are densest on the soma and proximal dendrite, while glycenergic inhibitory synaptic density is greater on the dendrites compared to the soma of octopus cells. Using different genetic lines, the authors further elucidated that the majority of excitatory synapses on the octopus cells are from type 1a spiral ganglion neurons, which have low response thresholds and high rates of spontaneous activity. In the second half of the paper, the authors employed electrophysiology to uncover the physiological response of octopus cells to excitatory and inhibitory inputs. Using a combination of pharmacological blockers in vitro cellular and computational modeling, the authors conclude that glycine in fact evokes IPSPs in octopus cells; these IPSPs are largely shunted by the high membrane conductance of the cells under normal conditions and thus were not clearly evident in prior studies. Pharmacological experiments point towards a specific glycine receptor subunit composition. Lastly, Kreeger et. al demonstrated with in vitro recordings and computational modeling that octopus cell inhibition modulates the amplitude and timing of dendritic spiral ganglion inputs to octopus cells, allowing for flexible coincidence detection.

Strengths:

The work combines a number of approaches and complementary observations to characterize the spatial patterns of excitatory and inhibitory synaptic input, and the type of auditory nerve input to the octopus cells. The combination of multiple mouse lines enables a better understanding of and helps to define, the pattern of synaptic convergence onto these cells. The electrophysiology provides excellent functional evidence for the presence of the inhibitory inputs, and the modeling helps to interpret the likely functional role of inhibition. The work is technically well done and adds an interesting dimension related to the processing of sound by these neurons. The paper is overall well written, the experimental tests are well-motivated and easy to follow. The discussion is reasonable and touches on both the potential implications of the work as well as some caveats.

Weaknesses:

While the conclusions presented by the authors are solid, a prominent question remains regarding the source of the glycinergic input onto octopus cells. In the discussion, the authors claim that there is no evidence for D-stellate, L-stellate, and tuberculoventral cell (all local inhibitory neurons of the ventral and dorsal cochlear nucleus) connections to octopus cells, and cite the relevant literature. An experimental approach will be necessary to properly rule out (or rule in) these cell types and others that may arise from other auditory brainstem nuclei. Understanding which cells provide the inhibitory input will be an essential step in clarifying its roles in the processing of sound by octopus cells.

The authors showed that type 1a SGNs are the most abundant inputs to octopus cells via microscopy. However, in Figure 3 they compare optical stimulation of all classes of ANFs, then compare this against stimulation of type 1b/c ANFs. While a difference in the paired-pulse ratio (and therefore, likely release probability) can be inferred by the difference between Foxg1-ChR2 and Ntng1-ChR2, it would have been preferable to have specific data with selective stimulation of type 1a neurons.

Reviewer #2 (Public Review):

Summary:

The authors have analyzed ethnogeographic differences in the comorbidity factors, such as a diabetes and heart disease, for the incidences of stroke and whether it leads to mortality.

Strengths:

The idea is interesting and data are compelling. The results are technically solid when presented, but in many cases statistical analyses are yet to be carried out to support statements of statistical significance.

The authors identify specific genetic loci that increase the risk of a stroke and how they differ by region.

Weaknesses:

The presentation is not focused. It is important to include p-values for all comparisons and focus the presentation on the main effects from the dataset analysis.

Reviewer #2 (Public Review):

This is a genome-wide association study of COVID-19 in individuals of admixed American ancestry (AMR) recruited from Brazil, Colombia, Ecuador, Mexico, Paraguay and Spain. After quality control and admixture analysis, a total of 3,512 individuals were interrogated for 10,671,028 genetic variants (genotyped + imputed). The genetic association results for these cohorts were meta-analyzed with the results from The Host Genetics Initiative (HGI), involving 3,077 cases and 66,686 controls. The authors found two novel genetic loci associated with COVID-19 at 2q24.2 (rs13003835) and 11q14.1 (rs77599934), and other two independent signals at 3p21.31 (rs35731912) and 6p21.1 (rs2477820) already reported as associated with COVID-19 in previous GWASs. Additional meta-analysis with other HGI studies also suggested risk variants near CREBBP, ZBTB7A and CASC20 genes.

Strengths:

These findings rely on state-of-the-art methods in the field of Statistical Genomics and help to address the issue of low number of GWASs in non-European populations, ultimately contributing to reduce health inequalities across the globe.

Weaknesses:

There is no replication cohort, as acknowledged by the authors (page 29, line 587) and no experimental validation to assess the biological effect of putative causal variants/genes. Thus, the study provides good evidence of association, rather than causation, between the genetic variants and COVID-19.

Comments on latest version:

The issues identified in the first round of review were well addressed by the authors in the revised version of the manuscript.

Reviewer #2 (Public review):

Summary:

The study by Rößling et al. addresses the link between the biochemical constitution of the cell wall, in particular the methylesterification state of pectin with signalling induced by the extracellular RALF peptide. The work suggests that only in the presence of demethylesterifies pectin, RALF is able to trigger activation of its receptor FERONIA (FER).<br /> Remarkably, the application of RALF peptides leads to rather dramatic FER-dependent changes in wall integrity and plasma membrane invaginations not observed before. Interestingly, RALF can be out-titrated from the wall by short pectin fragments. In addition, the study provides further evidence for multiple FER-dependent pathways by showing the presence of LRX proteins is not required for the pectin/RALF mediated signalling.

Strengths:

This work provides fundamental insight into a complex emerging pathway, or perhaps several pathways, linking pectin sensing, pectin structure and RALF/FER signalling. The study provides convincing evidence that pectin methylesterase activity is required for RALF sensing, indicating that the physical interaction of RALFs with the cell wall is important for signalling. Beyond that, the study documents very clearly how profoundly RALF signalling can affect cell wall integrity and membrane topology.

Weaknesses:

Not a weakness per se, as it cannot be avoided, but drawing conclusions from genetic material with altered pectin always suffers from the possibility of secondary effects as this cell wall component is under heavy surveillance and able to respond plastically to different cues. However, the authors take that into account and have performed adequate controls to minimize that possibility.

Reviewer #2 (Public review):

The reviewed manuscript "Hypersensitivity of the vimentin cytoskeleton to net-charge states and Coulomb repulsion" presents exciting results on the mechanisms governing the assembly and disassembly of the vimentin cytoskeleton. They show, using live-cell imaging, that changes in the intracellular ionic strength induce rapid and dramatic changes to the integrity of the vimentin cytoskeleton. Interestingly, mutants of vimentin with net positive or negative charges display notably different responses to hypotonic stress (and thus changes to the intracellular ionic strength). Even more interesting, the ionic strength-driven mechanism seems to generalize to the several other intermediate filaments explored here. These results are of high interest to the broader cytoskeleton field. A major caveat is that essentially every experiment in the paper is n=1, showing example images of a single cell. The experiments were not repeated, and the results were not quantified. Purported differences between experimental variables/conditions lack statistical significance. Generalization of the ionic strength-based mechanism is hindered by the fact that only one cell type was tested for each cytoskeletal protein. Another caveat is that the fluorescently tagged vimentin used thoroughly in this work is exogenous and overexpressed; it is unclear if the observed effects would also occur at endogenous concentrations of vimentin. As it is currently presented, it is my opinion that all four main figures in this work - although interesting and quite likely correct - should be interpreted as preliminary data by readers.

Reviewer #3 (Public review):

Summary:

The authors provide compelling evidence for the causal role of the subthalamic nucleus (STN) in perceptual decision-making. By recording from a large number of STN neurons and using microstimulation, they demonstrate the STN's involvement in setting decision bounds, scaling evidence accumulation, and modulating non-decision time.

Strengths:

The study tested three hypotheses about the STN's function and identified distinct STN subpopulations whose activity patterns support predictions from previous computational models. The experiments are well-designed, the analyses are rigorous, and the results significantly advance our understanding of the STN's multi-faceted role in decision formation.

Weaknesses:

While the study provides valuable insights into the STN's role in decision-making, there are a few areas that could be improved. First, the interpretation of the neural subpopulations' activity patterns in relation to the computational models should be clarified, as the observed patterns may not directly correspond to the specific signals predicted by the models. Second, a neural population model could be employed to better understand how the STN population jointly contributes to decision-making dynamics.

Reviewer #2 (Public Review):

Cryo_EM structures of the Kv1.2 channel in the open, inactivated, toxin complex and in Na+ are reported. The structures of the open and inactivated channels are merely confirmatory of previous reports. The structures of the dendrotoxin bound Kv1.2 and the channel in Na+ are new findings that will of interest to the general channel community.

Review of the resubmission:

I thank the authors for making the changes in their manuscript as suggested in the previous review. The changes in the figures and the additions to the text do improve the manuscript. The new findings from a further analysis of the toxin channel complex are welcome information on the mode of the binding of dendrotoxin.

Reviewing #2 (Public Review):

This paper reports the role of the Isoform II of RUNX2 in activating PRDX2 expression to suppress ferroptosis in oral squamous cell carcinoma (OSCC).<br /> The following major issues should be addressed.

A major postulate of this study is the specific role of RUNX2 isoform II compared to isoform I.

Figure 1F shows association between patient survival and Iso II expression, but nothing is shown for Iso I, this should be added, in addition the number of patients at risk in each category should be shown.<br /> The authors test Iso I and Iso II overexpression in CAL27 or SCC-9 model cell lines. In Fig. 2A in CAL27, the overexpression of Iso II is much stronger than Iso I so it seems premature to draw any conclusions. More importantly, however, no Iso I silencing is shown in either of the cell lines nor the xenografted tumours. This is absolutely essential for the authors hypothesis and should be tested using shRNA in cells and xenografted tumours.

A major conclusion of this study is that Iso II expression suppresses ferroptosis. To support this idea, the authors use the inhibitor Ferrostatin-1 (Fer-1). While Fer-1 typically does not lead to a 100% rescue, here the effect is only marginal and as shown in Figures 3F and G only marginally better than Z-VAD or Necrostatin 1. These data do not support the idea that the major cause of cell death is ferroptosis. Instead, Iso II silencing leads to cell death through different pathways. The authors should acknowledge this and rephrase the conclusion of the paper accordingly.<br /> Moreover, the authors consistently confound cell proliferation with cell death.

In Fig. 4A the authors investigate GPX1 expression, whereas GPX4 is often the key ferroprosis regulator, this has to be tested. This is important as the authors also test the effect of the GPX4 inhibitor RSL3, however, the authors do not determine IC50 values of the different cell lines with or without Iso II overexpression or silencing or compared to other RSL3 sensitive or resistant cells. Without this information, no conclusions can be drawn.

In summary, while the authors show that RUNX2 Iso II expression enhances cell survival, the idea that cell death is principally via ferroptosis is not fully established by the data. The authors should modify their conclusions accordingly.

Reviewer #2 (Public review):

Summary:

Mark and colleagues test the hypothesis that entorhinal cortical representations may contain abstract structural information that facilitates generalization across structurally similar contexts. To do so, they use a method called "subspace generalization" designed to measure abstraction of representations across different settings. The authors validate the method using hippocampal place cells and entorhinal grid cells recorded in a spatial task, then perform simulations that support that it might be useful in aggregated responses such as those measured with fMRI. Then the method is applied to fMRI data that required participants to learn relationships between images in one of two structural motifs (hexagonal grids versus community structure). They show that the BOLD signal within an entorhinal ROI shows increased measures of subspace generalization across different tasks with the same hexagonal structure (as compared to tasks with different structures) but that there was no evidence for the complementary result (ie. increased generalization across tasks that share community structure, as compared to those with different structures). Taken together, this manuscript describes and validates a method for identifying fMRI representations that generalize across conditions and applies it to reveal entorhinal representations that emerge across specific shared structural conditions.

Strengths:

I found this paper interesting both in terms of its methods and its motivating questions. The question asked is novel and the methods employed are new - and I believe this is the first time that they have been applied to fMRI data. I also found the iterative validation of the methodology to be interesting and important - showing persuasively that the method could detect a target representation - even in the face of a random combination of tuning and with the addition of noise, both being major hurdles to investigating representations using fMRI.

Weaknesses:

In part because of the thorough validation procedures, the paper came across to me as a bit of a hybrid between a methods paper and an empirical one. However, I have some concerns, both on the methods development/validation side, and on the empirical application side, which I believe limit what one can take away from the studies performed.

Regarding the methods side, while I can appreciate that the authors show how the subspace generalization method "could" identify representations of theoretical interest, I felt like there was a noticeable lack of characterization of the specificity of the method. Based on the main equation in the results section of the paper, it seems like the primary measure used here would be sensitive to overall firing rates/voxel activations, variance within specific neurons/voxels, and overall levels of correlation among neurons/voxels. While I believe that reasonable pre-processing strategies could deal with the first two potential issues, the third seems a bit more problematic - as obligate correlations among neurons/voxels surely exist in the brain and persist across context boundaries that are not achieving any sort of generalization (for example neurons that receive common input, or voxels that share spatial noise). The comparative approach (ie. computing difference in the measure across different comparison conditions) helps to mitigate this concern to some degree - but not completely - since if one of the conditions pushes activity into strongly spatially correlated dimensions, as would be expected if univariate activations were responsive to the conditions, then you'd expect generalization (driven by shared univariate activation of many voxels) to be specific to that set of conditions. A second issue in terms of the method is that there is no comparison to simpler available methods. For example, given the aims of the paper, and the introduction of the method, I would have expected the authors to take the Neuron-by-Neuron correlation matrices for two conditions of interest, and examine how similar they are to one another, for example by correlating their lower triangle elements. Presumably, this method would pick up on most of the same things - although it would notably avoid interpreting high overall correlations as "generalization" - and perhaps paint a clearer picture of exactly what aspects of correlation structure are shared. Would this method pick up on the same things shown here? Is there a reason to use one method over the other?

Regarding the fMRI empirical results, I have several concerns, some of which relate to concerns with the method itself described above. First, the spatial correlation patterns in fMRI data tend to be broad and will differ across conditions depending on variability in univariate responses (ie. if a condition contains some trials that evoke large univariate activations and others that evoke small univariate activations in the region). Are the eigenvectors that are shared across conditions capturing spatial patterns in voxel activations? Or, related to another concern with the method, are they capturing changing correlations across the entire set of voxels going into the analysis? As you might expect if the dynamic range of activations in the region is larger in one condition than the other? My second concern is, beyond the specificity of the results, they provide only modest evidence for the key claims in the paper. The authors show a statistically significant result in the Entorhinal Cortex in one out of two conditions that they hypothesized they would see it. However, the effect is not particularly large. There is currently no examination of what the actual eigenvectors that transfer are doing/look like/are representing, nor how the degree of subspace generalization in EC may relate to individual differences in behavior, making it hard to assess the functional role of the relationship. So, at the end of the day, while the methods developed are interesting and potentially useful, I found the contributions to our understanding of EC representations to be somewhat limited.

Reviewer #2 (Public review):

Summary:

Wolbachia are maternally transmitted bacteria that can manipulate host reproduction in various ways. Some Wolbachia induce male killing (MK), where the sons of infected mothers are killed during development. Several MK-associated genes have been identified in Homona magnanima, including Hm-oscar and wmk-1-4, but the mechanistic links between these Wolbachia genes and MK in the native host are still unclear.

In this manuscript, Arai et al. show that Hm-oscar is the gene responsible for Wolbachia-induced MK in Homona magnanima. They provide evidence that Hm-Oscar functions through interactions with the sex determination system. They also found that Hm-Oscar disrupts sex determination in male embryos by inducing female-type dsx splicing and impairing dosage compensation. Additionally, Hm-Oscar suppresses the function of Masc. The manuscript is well-written and presents intriguing findings. The results support their conclusions regarding the diversity and commonality of MK mechanisms, contributing to our understanding of the mechanisms and evolutionary aspects of Wolbachia-induced MK.

Strengths/weaknesses:

(1) The authors found that transient overexpression of Hm-oscar, but not wmk-1-4, in Wolbachia-free H. magnanima embryos induces female-biased sex ratios. These results are striking and mirror the phenotype of the wHm-t infected line (WT12). However, Table 1 lists the "male ratio," while the text presents the "female ratio" with standard deviation. For consistency, the calculation term should be uniform, and the "ratio" should be listed for each replicate.

(2) The error bars in Figure 3 are quite large, and the figure lacks statistical significance labels. The authors should perform statistical analysis to demonstrate that Hm-oscar-overexpressed male embryos have higher levels of Z-linked gene expression.

(3) The authors demonstrated that Hm-Oscar suppresses the masculinizing functions of lepidopteran Masc in BmN-4 cells derived from the female ovaries of Bombyx mori. They should clarify why this cell line was chosen and its biological relevance. Additionally, they should explain the rationale for evaluating the expression levels of the male-specific BmIMP variant and whether it is equivalent to dsx.

(4) Although the authors show that Hm-oscar is involved in Wolbachia-induced MK in Homona magnanima and interacts with the sex determination system in lepidopteran insects, the precise molecular mechanism of Hm-oscar-induced MK remains unclear. Further studies are needed to elucidate how Hm-oscar regulates Homona magnanima genes to induce MK, though this may be beyond the scope of the current manuscript.

Reviewer #2 (Public Review):

I have carefully reviewed the manuscript titled "Pronounced expression of extracellular matrix proteoglycans regulated by Ant pathway underlies the parallel evolution of lip hypertrophy in East African cichlids." I commend the authors for their work on elucidating the mechanism underlying lip thickening that has evolved in parallel across three lakes in Africa.

The use of histological comparison, proteomics, and transcriptomics methods to investigate this phenomenon is commendable and adds depth to the study. The findings indicate that the overexpression of proteoglycans is the cause of lip thickening and provides valuable insights into the evolutionary process.

I found the writing style to be clear and the explanations provided are easy to understand. Overall, I did not identify any significant issues with the manuscript.

Reviewer #2 (Public review):

Summary:<br /> The manuscript by Lima et al examines the role of Prmt1 and SFPQ in craniofacial development. Specifically, the authors test the idea that Prmt1 directly methylates specific proteins that results in intron retention in matrix proteins. The protein SFPQ is methylated by Prmt1 and functions downstream to mediate Prmt1 activity. The genes with retained introns activate the NMD pathway to reduce the RNA levels. This paper describes an interesting mechanism for the regulation of RNA levels during development.

Strengths:<br /> The phenotypes support what the authors claim that Prmt1 is involved in craniofacial development and splicing. The use of state-of-the-art sequencing to determine the specific genes that have intron retention and changes in gene expression is a strength.

Weaknesses:<br /> Some of the data seems to contradict the conclusions. And it is unclear how direct the relationships are between Prmt1 and SFPQ.

Reviewer #3 (Public review):

Hall et al. benchmarked different variant calling methods on Nanopore reads of bacterial samples and compared the performance of Nanopore to short reads produced with Illumina sequencing. To establish a common ground for comparison, the authors first generated a variant truthset for each sample and then projected this set to the reference sequence of the sample to obtain a mutated reference. Subsequently, Hall et al. called SNPs and small indels using commonly used deep learning and conventional variant callers and compared the precision and accuracy from reads produced with simplex and duplex Nanopore sequencing to Illumina data. The authors did not investigate large structural variation, which is a major limitation of the current manuscript. It will be very interesting to see a follow-up study covering this much more challenging type of variation.

In their comprehensive comparison of SNPs and small indels, the authors observed superior performance of deep learning over conventional variant callers when Nanopore reads were basecalled with the most accurate (but also computationally very expensive) model, even exceeding Illumina in some cases. Not surprisingly, Nanopore underperformed compared to Illumina when basecalled with the fastest (but computationally much less demanding) method with the lowest accuracy. The authors then investigated the surprisingly higher performance of Nanopore data in some cases and identified lower recall with Illumina short read data, particularly from repetitive regions and regions with high variant density, as the driver. Combining the most accurate Nanopore basecalling method with a deep learning variant caller resulted in low error rates in homopolymer regions, similar to Illumina data. This is remarkable, as homopolymer regions are (or, were) traditionally challenging for Nanopore sequencing.

Lastly, Hall et al. provided useful information on the required Nanopore read depth, which is surprisingly low, and the computational resources for variant calling with deep learning callers. With that, the authors established a new state-of-the-art for Nanopore-only variant calling on bacterial sequencing data. Most likely these findings will be transferred to other organisms as well or at least provide a proof-of-concept that can be built upon.

As the authors mention multiple times throughout the manuscript, Nanopore can provide sequencing data in nearly real-time and in remote regions, therefore opening up a ton of new possibilities, for example for infectious disease surveillance. In these scenarios, computational resources can be very limited. The highest-performing variant calling method, as established in this study, requires the computationally very expensive sup and/or duplex nanopore basecalling, while the least computationally demanding basecalling method underperforms. To comprehensively guide users through the computational resources required for basecalling and variant calling, the authors provide runtime benchmarks assuming GPU access.

Reviewer #2 (Public Review):

Summary:

Fan et al. investigated the relationship between early acute myocardial infarction (eAMI) and disturbances in the gut microbiome using metabolomics and metagenomics analyses. They studied 30 eAMI patients and 26 healthy controls, finding elevated levels of long-chain fatty acids (LCFA) in the plasma of eAMI patients.

Strengths:

The research attributed a substantial portion of LCFA variance in eAMI to changes in the gut microbiome, as indicated by omics analyses. Computational profiling of gut bacteria suggested structural variations linked to LCFA variance. The authors also conducted molecular docking simulations and platelet assays, revealing that eAMI-associated LCFAs may enhance platelet aggregation.

Weaknesses:

The results should be validated using different assays, and animal models should be considered to explore the mechanisms of action.