Reviewer #1 (Public Review):

This study examined whether mitochondrial acyl-CoA thioesterase-2 (ACOT2) regulates mitochondrial matrix acyl-CoA levels. Acot2 deletion in murine skeletal muscle (SM) resulted in acyl-CoA build-up. When energy demand and pyruvate availability were elevated, a lack of ACOT2 activity promoted glucose oxidation. This preference for glucose over fatty acid oxidation was recapitulated in C2C12 myotubes with acute depletion of Acot2. In mice fed a high-fat diet, ACOT2 enabled the accretion of acyl-CoAs and ceramide derivatives in glycolytic SM, and this was associated with worse glucose homeostasis compared to when ACOT2 was absent. The authors suggest that ACOT2 supports CoASH availability to facilitate β-oxidation in glycolytic SM when lipid supply is modest. However, when lipid supply is high, ACOT2 enables acyl-CoA and lipid accumulation, CoASH sequestration, and poor glucose homeostasis. Thus, ACOT2 regulates matrix acyl-CoA concentration in glycolytic muscle, and its impact depends on lipid supply.

Based on the data provided in this study, the authors propose that ACOT2 regulates mitochondrial matrix acyl-CoA levels in white skeletal muscle to facilitate fatty acid oxidation β-oxidation. However, I do not believe the data supports this concept, since ACOT2 deletion actually increased fatty acid oxidation in the mitochondrial JO2 studies. In addition, there are some problems with the experimental data that the authors need to address. This includes the experimental conditions used to assess JO2 in the mitochondria, and not using Cre control mice.

Reviewer #1 (Public Review):

The authors focused on genetic variability in relation to insulin resistance. The used genetically different lines of mice and exposed them to the same diet. They found that genetic predisposition impacts the overall outcome of metabolic disturbances.

Reviewer #2 (Public Review):

The authors use a high-throughput sequencing-based enrichment assay to measure how individual amino acids substitutions in the Rep proteins of AAV change the production of AAV. The key experiment involved the creation of all possible single codon mutations of the AAV2 rep gene in a barcoded format, transfection of the library into HEK293T cells for production of AAV, and sequencing to see which rep variants were enriched in the viral particles produced from the library. As the library rep variants were flanked by inverted terminal repeats for packaging into viral particles, the authors could use high-throughput sequencing of the barcodes to determine how much each rep variant supported the production of AAV. The rep gene libraries were cleverly made through a cloning process that ensured each mutant was attached to an exactly known 20nt barcode included in each mutagenic oligo (and subsequently moved to the end of the library genes by another cloning step). This allowed the authors to confidently observe nearly all rep variants in their experiments, resulting in a comprehensive map between Rep protein variants and AAV production. The overall map should act as a useful guide for AAV engineering. Not only did certain variants improve AAV production by ~2-fold and show generality across AAV capsid serotypes, the map might be used to predict greater effects through combinations of mutations, especially if augmented by natural evolutionary datasets and statistical learning.

In interpreting the results of this study, the reader should bear in mind that what has been measured and validated in high throughput is the production of intact genome-containing AAVs. The authors also successfully show transduction for selected high production variants. This is important as the efficiency by which an AAV preparations transduce cells is most relevant property for gene therapy.

Overall, this is a well-executed and well-analyzed study. The results support the conclusions and claims of the work. I see this work as a useful resource for engineering recombinant AAVs to increase their production, which should have broad impact as the use of AAVs in gene therapy grows.

Reviewer #2 (Public Review):

Summary:

In this manuscript Nie et al investigate the effect of PARG KO and PARG inhibition (PARGi) on pADPR, DNA damage, cell viability and synthetic lethal interactions in HEK293A and Hela cells. Surprisingly, the authors report that PARG KO cells are sensitive to PARGi and show higher pADPR levels than PARG KO cells, which is abrogated upon deletion or inhibition of PARP1/PARP2. The authors explain the sensitivity of PARG KO to PARGi through incomplete PARG depletion and demonstrate complete loss of PARG activity when incomplete PARG KO cells are transfected with additional gRNAs in the presence of PARPi. Furthermore, the authors show that the sensitivity of PARG KO cells to PARGi is not caused by NAD depletion but by S-phase accumulation of pADPR on chromatin coming from unligated Okazaki fragments, which are recognized and bound by PARP1. Consistently, PARG KO or PARG inhibition show synthetic lethality with Pol beta, which is required for Okazaki fragment maturation. PARG expression levels in ovarian cancer cell lines correlate negatively with their sensitivity to PARGi.

Strengths:

The authors show that PARG is essential for removing ADP-ribosylation in S-phase.

Weaknesses:

1) This begs the question as to the relevant substrates of PARG in S-phase, which could be addressed, for example, by analysing PARylated proteins associated with replication forks in PARG-depleted cells (EdU pulldown and Af1521 enrichment followed by mass spectrometry).<br /> 2) The results showing the generation of a full PARG KO should be moved to the beginning of the Results section, right after the first Results chapter (PARG depletion leads to drastic sensitivity to PARGi), otherwise the reader is left to wonder how PARG KO cells can be sensitive to PARGi when there should be presumably no PARG present.<br /> 3) Please indicate in the first figure which isoforms were targeted with gRNAs, given that there are 5 PARG isoforms. You should also highlight that the PARG antibody only recognizes the largest isoform, which is clearly absent in your PARG KO, but other isoforms may still be produced, depending on where the cleavage sites were located.<br /> 4) FACS data need to be quantified. Scatter plots can be moved to Supplementary while quantification histograms with statistical analysis should be placed in the main figures.<br /> 5) All colony formation assays should be quantified and sensitivity plots should be shown next to example plates.<br /> 6) Please indicate how many times each experiment was performed independently and include statistical analysis.

Reviewer #1 (Public Review):

Hu et al. performed sc-RNA-seq analyses of kidney cells with or without virus infection, vaccines, and vaccines+virus infections from pooled adult zebrafish. They compared within these experimental groups as well as kidney vs spleen. Their analyses identified expected populations but also revealed new hematopoietic stem/progenitor cell (HSPC), even in the spleen. Their analyses show that HSPCs in the kidney can respond to virus infection differentially and can be trained to recognize the same infection and argue that zebrafish kidney can serve as a secondary immune organ. The findings are important and interesting. The manuscript is well written and a pleasure to read. However, there are several issues with their figure presentation and figure qualities, as well as the lack of clarity in some of figure legends. Some of the data presentation can be improved for better clarity. It is also important to outline what is conserved and what is unique for fish.

Major concerns:

1. The visualization for several figure panels is very poor. Please provide high resolution images and larger font sizes for gene list or Y and X axis labels. This includes Figure 1B, Figure 1-figure supplement 2, Figure 2B-2C, 3A-3D, 4F, 5B, 6G, Figure 6-figure supplement 1B, Figure 6-figure supplement 2. Figure 7B, 8C-8E, Figure 8-figure supplement 1., 10F, 10G-10J, Figure 10-figure supplement 1.<br /> 2. What are the figures at the end of the manuscript without any figure legends?<br /> 3. It would be better to use a Table to organize the gene signatures that define each unique population of immune cells such as T, B, NK, etc.<br /> 4. What are the similarities for HSPC and immune cell populations between fish and man based on this research? It is better to form a table to compare and discuss.<br /> 5. It is highly likely that sex and age could be the biological variation for how HSPC responds to virus infections and vaccination. The author should clearly state the fish sex and age from their samples and discuss their results taking into consideration of these variations.<br /> 6. The authors claim that the spleen and kidney share HSPCs. However, their data did not demonstrate this result clearly in Figure 4A. Perhaps they should use different color to make the overlay becoming more obvious? Or include a table to show which HSPCs are shared between the kidney and spleen? Are they sure if these are just HSPCs seeding the spleen to differentiate into B cells or other immune cells?

Reviewer #1 (Public Review):

Summary:<br /> This useful work provides insight into agonist binding to muscle nicotinic receptors. The authors want to understand the fundamental steps in ligand binding to muscle nicotinic receptors using computational methods. The study builds on a large basis of empirical studies of the various states involved in receptor activation. However, the evidence supporting the conclusions is incomplete, because little support is available for the starting structures that are derived from ligand docking. This work is a useful starting point for more detailed work on ligand binding to this important class of receptors.

Strengths:<br /> The strengths include the number of ligands tried, and the relation to the mature analysis of the receptor function.

Weaknesses:<br /> The weaknesses are the brevity of the simulations, the concomitant lack of scope of the simulations, the lack of depth in the analysis, and the incomplete relation to other relevant work.

Reviewer #3 (Public Review):

Summary:

In the manuscript "Ebola Virus Sequesters IRF3 in Viral Inclusion bodies to Evade Host Antiviral Immunity " by Lin Zhu et al, the authors elucidated an evasion mechanism by which EBOV evades host innate immunity.

Strengths:

Using data from immunofluorescence analysis, TEM and Western Blot, the authors conclude that Ebola virus VP35 protein evades host antiviral immunity by interacting with STING to sequester IRF3 into IBs and inhibit type-I interferon production.

Weaknesses:

Similar mechanisms have already been found in other viruses, such as SFTSV, RSV and so on. In addition, the presented results are also relatively rough, and the mechanism explained is not deep enough, so this story is not innovative

Reviewer #1 (Public Review):

Bian et al showed that biomarker-informed PhenoAgeAccel was consistently related to an increased risk of site-specific cancer and overall cancer within and across genetic risk groups. The results showed that PhenoAgeAccel and genetic liability of a bunch of cancers serve as productive tools to facilitate the identification of cancer-susceptible individuals under an additive model. People with a high genetic risk for cancer may benefit from PhenoAgeAccel-informed interventions.

As the authors pointed out, the large sample size, the prospective design UK Biobank study, and the effective application of PhenoAgeAccel in predicting the risk of overall cancer are the major strengths of the study. Meanwhile, the CPRS seems to be a solid and comprehensive score based on incidence-weighted site-specific polygenic risk scores across 20 well-powered GWAS for cancers.

It wouldn't be very surprising to identify the association between PhenoAgeAccel and cancer risk, since the PhenoAgeAccel was constructed as a predictor for mortality which attributed a lot to cancer. Although cancer is an essential mediator for the association, sensitivity analyses using cancer-free mortality may provide an additional angle. It would be interesting to see, to what extent, PhenoAgeAccel could be reversed by environmental or lifestyle factors. G by E for PhenoAgeAccel might be worth a try.

Reviewer #1 (Public Review):

The objective of this study was to investigate the influence of the C. trachomatis effector Cdu1 on the ubiquitination of proteins in infected host cells and its correlation with the previously identified role of Cdu1 in facilitating Golgi distribution around the Chlamydia inclusion.

To achieve this, the authors created a cdu1-null mutant in C. trachomatis and employed proteomics to analyze ubiquitinated proteins in cells infected with Cdu1-producing and Cdu1-deficient chlamydiae, comparing them to mock-infected cells. The results revealed that, among the proteins specifically ubiquitinated after infection with Cdu1-deficient chlamydiae, three were other C. trachomatis effectors (InaC, IpaM, and CTL0480), members of a large family of Chlamydia effectors (Incs) that insert in the inclusion membrane.

Subsequently, the authors focused on understanding how Cdu1 shields InaC, IpaM, and CTL0480 from ubiquitination and the implications of this protection for the protein levels and functions of these Incs during infection. Data is presented showing that Cdu1 can bind to InaC, IpaM, and CTL0480, and protects these Incs and itself from ubiquitination and proteasomal degradation. This protective role of Cdu1 is dependent on its acetylation, but not on its deubiquitinating activity. Host cells infected by the cdu1 null mutant displayed defects resembling those observed in cells infected by inaC, ipaM, or ctl0480 null mutants.

Additionally, it was previously established that CTL0480 inhibits a chlamydial egress pathway involving the extrusion of the inclusion. This study now revealed that InaC and IpaM also play a role in promoting the extrusion of C. trachomatis inclusion, and the cdu1 null mutant exhibited a defect in this process. This leads to the title's conclusion that Cdu1 regulates chlamydial exit from host cells by safeguarding specific C. trachomatis effectors from degradation.

In summary, this work is excellent and impressive, both technically and conceptually, providing mechanistic insights into the action of Cdu1. The data provides convincing support for the proposed model, illustrating how the acetylation activity of Cdu1 protects itself and three Incs (InaC, IpaM, and CTL0480) from degradation. While the study indicates that the observed phenotypes in cells infected by the cdu1 null mutant are linked to reduced levels of InaC, IpaM, and CTL0480, these Incs are still detectable in cells infected by the cdu1 null mutant. Even if very unlikely, this leaves room for the possibility that Cdu1 directly promotes assembly of F-actin and Golgi repositioning around the inclusion, MYPT1 recruitment to the inclusion, and extrusion of the inclusion. Nevertheless, the major significance of this work lies in the integration of proteomics and chlamydial genetics to unveil a unique mechanism in which one effector controls the levels of other effectors, emphasizing the intricate relationships among bacterial effectors injected into host cells.

Reviewer #1 (Public Review):

This article by Navratna et al. reports the first structure of human HGSNAT in an acetyl-CoA-bound state. Through careful structural analysis, the authors propose potential reasons why certain human mutations lead to lysosomal storage disorders and outline a catalytic mechanism. The structural data are of good quality, and the manuscript is clearly written. This study represents an important step toward understanding the mechanism of HGSNAT and is valuable to the field. I have the following suggestions:

1. The authors should characterize whether the purified protein is active. Otherwise, how does one know if the detergent used maintains the protein in a biologically relevant state? The authors should at least attempt to do so. If these prove to be challenging, at the very least, the authors should try a cell-based assay to demonstrate that the GFP tag does not interfere with the function.

2. In Figure 5, the authors present a detailed schematic of the catalytic cycle, which I find to be too speculative. There is no evidence to suggest that this enzyme undergoes isomerization, similar to a transporter, between open-to-lumen and open-to-cytosol states. Could it not simply involve some movements of side chains to complete the acetyl transfer?

Reviewer #1 (Public Review):

In this paper, the authors developed an image analysis pipeline to automatically identify individual ‎‎neurons within a population of fluorescently tagged neurons. This application is optimized to deal with ‎‎multi-cell analysis and builds on a previous software version, developed by the same team, to resolve ‎‎individual neurons from whole-brain imaging stacks. Using advanced statistical approaches and ‎‎several heuristics tailored for C. elegans anatomy, the method successfully identifies individual ‎‎neurons with a fairly high accuracy. Thus, while specific to C. elegans, this method can ‎become ‎instrumental for a variety of research directions such as in-vivo single-cell gene expression ‎analysis ‎and calcium-based neural activity studies.‎

Reviewer #1 (Public Review):

In this study, the authors examined the putative functions of hypothalamic groups identifiable through Foxb1 expression, namely the parvofox Foxb1 of the LHA and the PMd Foxb1, emphasizing innate defensive responses. First, they reported that chemogenetic activation of Foxb1hypothalamic cell groups led to tachypnea. The authors tend to attribute this effect to the activation of hM3Dq expressed in the parvofox Foxb1 but did not rule out the participation of the PMd Foxb1 cell group, which may as well have expressed hM3Dq, particularly considering the large volume (200 nl) of the viral construct injected. Notably, the activation of the Foxb1hypothalamic cell groups in this experiment did not alter the gross locomotor activity, such as time spent immobile state. Thus, this contrasts with the authors' finding on the optogenetic activation of the Foxb1hypothalamic fibers projecting to the dorsolateral PAG. In the second experiment, the authors applied optogenetic ChR2-mediated excitation of the Foxb1+ cell bodies' axonal endings in the dlPAG, leading to freezing and, in a few cases, bradycardia. The effective site to evoke freezing was the rostral PAGdl, and fibers positioned either ventral or caudal to this target had no response. Considering the pattern of Foxb1hypothalamic cell groups projection to the PAG, the fibers projecting to the rostral PAGdl are likely to arise from the PMd Foxb1 cell group and not from the parvofox Foxb1 of the LHA. Here, it is important to consider that activation of PMd CCK cell group, which consists of around 90% of the PMd cells, evokes escape, not freezing. According to the present findings, a specific population of PMd Foxb1 cells may be involved in producing freezing. In addition, only a few of the animals with correct fiber placement presented sudden onset of bradycardia in response to the photostimulation. Considering the authors' findings, the Foxb1+ hypothalamic groups are likely to mediate behavioral responses related to innate defensive responses, where the parvofox Foxb1 of the LHA would be involved in promoting tachypnea and the PMd Foxb1group in mediating freezing and bradycardia. These findings are exciting, and, at this point, they need to be tested in a scenario of actual exposure to a natural predator.

Reviewer #1 (Public Review):

This study investigates the underlying mechanisms of information-seeking in infancy. Eight-month-old Dutch infants were tested in a screen-based eye-tracking task in which one of two geometrical shape cues (differing in their shape and motion) either announced the location of an upcoming reward cartoon (informative) or not (non-informative). The authors measured the infants' pupil size before the cartoon appeared. Infants showed smaller pupil sizes when presented with the informative cue as compared to the noninformative cue. The decrease in pupil size in the informative condition emerged over the course of trials whereas infants' pupil size remained unchanged in the noninformative condition. The authors interpret their findings as supportive evidence of statistical learning and generalization processes organizing infants' information-seeking.

It was a pleasure to read the paper and I think the study makes a valuable contribution to our understanding of information-seeking in infancy. The manuscript is very well written and the study is cleverly designed. My following comments are based on my reading of the manuscript and the supplemental materials. It should be noted that evaluating the details of the statistical procedure the authors used lies outside my expertise. The same applies to some decisions of the authors related to pre-processing and filtering the pupil data. I very much appreciate that the authors shared all their raw data and analysis scripts openly accessible on the Open Science Framework. The study was unfortunately not preregistered, making it difficult to trace when in the study process certain decisions or assumptions were made.

My two main concerns relate to the conceptualization and definition of information-seeking and the proposed speed of the mechanisms explaining infants' behavior. I outline my general comments below before listing some more concrete issues.

1) While reading the manuscript, I was sometimes confused about what the authors refer to when talking about information-seeking - both in terms of the broader conceptualization of the phenomenon as well as when referring to their own study. What information are infants seeking? The informative value of the cue shape in terms of their motion (because it carries information about the location of a rewarding animation)? Or is the target (the rewarding video) the information being sought? From how the study is set up, I assume the authors refer mainly to the first aspect, but I think the manuscript would benefit from some clearer distinctions and definitions of terms.

More specifically, I think it could help if the authors would specify the different aspects involved in information-seeking in the introduction (e.g., seeking information "directly", seeking cues guiding them towards information, etc.). Secondly, it would help if they would sharpen their (already in some parts existing) definitions for their study and then keep consistent with their definitions throughout the methods, results, and discussion. Is the cue the information being sought or the "behavior" (motion) of the cue? Or is the target animation the information being sought and guided via the cueing?

2) Speed of the generalization process:<br /> From my understanding of the study design, the shape of the geometrical shape gains informative value over time (serving as an informative cue) and the *motion* of the shape is the actual informative or non-informative visual cue in that it either reliably highlights the actual target region (or all regions). In the generalization trials, only the shape was manipulated while the motion aspect remained consistent with the previous trials. Based on infants' behavior across learning and generalization trials, the authors make an argument about two distinct processes taking place: a slower allowing to learn where to find info and a faster generalization process. Apologies if I missed something, but given that the motion remains consistent, it's maybe not surprising that the generalization trials are "faster"? Maybe the generalization process would have been slower if not only the shape had changed but if also a novel informative motion had been introduced. Also, it would be helpful if the authors could clarify what they mean by the statistical learning process being more "data-hungry" (line 274).

3) I would find it very helpful if the authors would discuss statistical learning and information-seeking processes from other possible mechanisms such as reward learning mechanisms. For example, the authors use a "rewarding" (not informative) stimulus as the target-wouldn't it be possible that the results can be also explained by reinforcement learning processes? Relatedly, in line 396 they write that they used TD learning to predict whether "information will be delivered" and contrast this with the approach being used to predict whether a reward will be delivered. But in their study reward was being delivered, too (in the form of the target), in addition to the informative motion of the cue.

Reviewer #1 (Public Review):

Summary:<br /> This manuscript uses optical coherence tomography (OCT) to visualize tissue microstructures about 1-2 mm under the finger pad skin surface. Their geometric features are tracked and used to generate tissue strains upon skin surface indentation by a series of transparent stimuli both normal and tangential to the surface. Then movements of the stratum corneum and the upper portion of the viable epidermis are evaluated. Based upon this data, across a number of participants and ridges, around 300 in total, the findings report upon particular movements of these tissue microstructures in various loading states. A better understanding of the mechanics of the skin microstructures is important to understand how surface forces propagate toward the locations of mechanoreceptive end organs, which lie near the edge of the epidermis and dermis, from which tactile responses of at least two peripheral afferents originate. Indeed, the microstructures of the skin are likely to be important in shaping how neural afferents respond and enhance their sensitivity, receptive field characteristics, etc.

Strengths:<br /> The use of OCT in the context of analyzing the movements of skin microstructures is novel. Also novel and powerful is the use of distinct loading cases, e.g., normal, tangential, and stimulus features, e.g., edges, and curves. I am unaware of other empirical visualization studies of this sort. They are state-of-the-art in this field. Moreover, in addition to the empirical imaging observations, strain vectors in the tissues are calculated over time.

Weaknesses:<br /> The interpretation of the results and their framing relative to the overall hypotheses/questions and prior works could be articulated more clearly. In particular, the major findings of the manuscript are in newly describing a central concept regarding "ridge flanks," but such structures are neither anatomically nor mechanistically defined in a clear fashion. For example, "... it appears that the primary components of ridge deformation and, potentially, neural responses are deformations of the ridge flanks and their relative movement, rather than overall bending of the ridges themselves." From an anatomical perspective, I think what the authors mean by "ridge flanks" is a differential in strain from one lateral side of a papillary ridge to the other. But is it unclear what about the continuous layers of tissue would cause such behaviors. Perhaps a sweat duct or some other structure (not visible to OCT) would subdivide the "flanks" of a papillary ridge somehow? If not due to particular anatomy, then is the importance of the "ridge flank" due to a mechanistic phenomenon of some sort? Given that the findings of the manuscript center upon the introduction of this new concept, I think a greater effort should be made to define what exactly are the "ridge flanks." It is clear from the results, especially the sliding case, that there is something important that the manuscript is getting at with this concept.

The OCT used herein cannot visualize deep and fully into what the manuscript refers to as a "ridge" (note others have previously broken apart this concept apart into "papillary", "intermediate" and "limiting" ridges) near locations of the mechanoreceptive end organs lie at the epidermal-dermal border. Therefore, the OCT must make inferences about the movements of these deeper tissues, but cannot see them directly, and it is the movements of these deeper tissues that are likely driving the intricacies of neural firing. Note the word "ridge" is used often in the manuscript's abstract, introduction, and discussion but the definition in Fig. 1 and elsewhere differs in important ways from prior works of Cauna (expert in anatomy). Therefore, the manuscript should clarify if "ridge" refers to the papillary ridge (visible at the exterior of the skin), intermediate ridge (defined by Cauna as what the authors refer to as the primary ridge), and limiting ridge (defined by Cauna as what the authors refer to as the secondary ridge). What the authors really mean (I think) is some combination of the papillary and intermediate ridge structures, but not the full intermediate ridge. The manuscript acknowledges this in the "Limitations and future work" section, stating that these ridges cannot be resolved. This is important because the manuscript is oriented toward tracking this structure. It sets up the narrative and hypotheses to evaluate the prior works of Cauna, Gerling, Swensson, and others who all directly addressed the movement of this anatomical feature which is key to understanding ultimately how stresses at these locations might move the peripheral end organs (i.e., Merkel cells, Meissner corpuscles).

Reviewer #1 (Public Review):

This study aims to identify gene expression differences exclusively caused by cis-regulatory genetic changes by utilizing hybrid cell lines derived from human and chimpanzee. While previous attempts have focused on specific tissues, this study expands the comparison to six different tissues to investigate tissue specificity and derive insights into the evolution of gene expression.

One notable strength of this work lies in the use of composite cell lines, enabling a comparison of gene expression between human and chimpanzee within the same nucleus and shared trans factors environment. However, a potential weakness of the methodology is the use of bulk RNA-seq in diverse tissues, which limits the ability to determine cell-type-specific gene expression and chromatin accessibility regions. Their approach, using hybrid lines, naturally accounts for cell type heterogeneity avoiding the risk of false positives introduced by the otherwise confounding differences in cell type abundances between species, albeit the challenge of false negatives remains an issue. The authors now dully acknowledge this limitation in the manuscript.

Another concern is the use of two replicates derived from the same pair of individuals. While the authors produced cell lines from two pairs of individuals in a previous study (Agloglia et al., 2021). The reason for this experimental design is cost limitations. The authors now acknowledge that the use of replicates could enhance the ability to detect "more" species-specific changes in expression and chromatin accessibility. I would emphasize that replicates would increase robustness to the present findings, given that they are derived from a single pair of individuals.

Furthermore, the study offers the opportunity to relate inter-species differences to trends in molecular evolution. The authors discovered that expression variance and haploinsufficiency score do not fully account for the enrichment of divergence in cell-type-specific genes. The reviewer suggested exploring this further by incorporating external datasets that bin genes based on interindividual transcriptomics variation as a measure of extant transcriptomics constraint (e.g., GTEx reanalysis by Garcia-Perez et al., 2023 - PMID: 36777183). The authors considered this question to be out of the scope of the paper, yet in my opinion this would enhance one of the main findings of this study.

Additionally, stratifying sequence conservation on ASCA regions, which exhibit similar enrichment of cell-type-specific features, using the Zoonomia data mentioned also in the text (Andrews et al., 2023 -- PMID: 37104580) could provide valuable insights. While the author did not find Zoonomia Phastcons values available, they used PhastCons derived from a 470-way alignment of mammals. I commend the authors for their diligent efforts, which undoubtedly bolster their findings that an enrichment in ASCA is evident across all levels of sequence conservation. However, this recent analysis indicates the presence of a potential relationship between sequence conservation and ASCA. It may be advantageous to consider evaluating more quantile subdivisions of maxZ values and pPhastCons values, with the inclusion of these results in the supplementary materials. This approach would be preferable, even if the precise reasons behind the observed discrepancy are not fully elucidated.

Another potential strength of this study is the identification of specific cases of paired allele-specific expression (ASE) and allele-specific chromatin accessibility (ASCA) with biological significance. Prioritizing specific variants remains a challenge, and the authors apply a machine learning approach to identify potential causative variants that disrupt binding sites in two examples (FABP7 and GAD1 in motor neurons). However, additional work is needed to convincingly demonstrate the functionality of these selected variants. Strengthening this section with additional validation of ASE, ASCA, and the specific putative causal variants identified would enhance the overall robustness of the paper. The authors have opted to defer these validations to future studies.

Additionally, the authors support the selected ASE-ASCA pairs by examining external datasets of adult brain comparative genomics (Ma et al., 2022) and organoids (Kanton et al., 2019). While these resources are valuable for comparing observed species biases, the analysis is not systematic, even for the two selected genes. For example, it would be beneficial to investigate if FABP7 exhibits species bias in any cell type in Kanton et al.'s organoids or if GAD1 is species-biased in adult primate brains from Ma et al. Comparing these datasets with the present study, along with the Agoglia et al. reference, would provide a more comprehensive perspective. In the revised version of the manuscript the authors have evaluated the expression of GAD1 in Ma et al, and FABP7 in Sousa et al 2017. For instance, GAD1 show cell type specific species biases in the later. The authors opted for not showing this in the manuscript, However, it remains unclear why certain datasets were favored over others, or why FABP7 should not be evaluated in Kanton et al.

The use of the term "human-derived" in ASE and ASCA has now been avoided.

Finally, throughout the paper, the authors refer to "hybrid cell lines." It has been suggested to use the term "composite cell lines" instead to address potential societal concerns associated with the term "hybrid," which some may associate with reproductive relationships (Pavlovic et al., 2022 -- PMID: 35082442). The authors have presented an eloquent and persuasive explanation that I found to be highly informative.

Joint Public Review:

In this manuscript, the authors introduced an explicit ion model using the coarse-grained modelling approach to model the interactions between nucleosomes and evaluate their effects on chromatin organization. The strength of this method lies in the explicit representation of counterions, especially divalent ions, which are notoriously difficult to model. To achieve their aims and validate the accuracy of the model, the authors conducted coarse-grained molecular dynamics simulations and compared predicted values to the experimental values of the binding energies of protein-DNA complexes and the free energy profile of nucleosomal DNA unwinding and inter-nucleosome binding. Additionally, the authors employed umbrella sampling simulations to further validate their model, reproducing experimentally measured sedimentation coefficients of chromatin under varying salt concentrations of monovalent and divalent ions.

The significance of this study lies in the authors' coarse-grained model which can efficiently capture the conformational sampling of molecules while maintaining a low computational cost. The model reproduces the scale and, in some cases, the shape of the experimental free energy profile for specific molecule interactions, particularly inter-nucleosome interactions. Additionally, the authors' method resolves certain experimental discrepancies related to determining the strength of inter-nucleosomal interactions. Furthermore, the results from this study support the crucial role of intrinsic physicochemical interactions in governing chromatin organization within the nucleus.

The authors have successfully addressed the majority of my key concerns. I appreciate the clarification regarding the parameterization from Pablo's lab and the addition of comparisons of energy profiles as a function of inter-nucleosome distances.

However, the statement "The agreement is evident" may not sufficiently capture the essence of Figure S4, as there is a shortage of substantial agreement. The authors rightly acknowledge it but should delineate the nature of the observed discrepancies.

Reviewer #1 (Public Review):

Continuous attractor networks endowed with some sort of adaptation in the dynamics, whether that be through synaptic depression or firing rate adaptation, are fast becoming the leading candidate models to explain many aspects of hippocampal place cell dynamics, from hippocampal replay during immobility to theta sequences during run. Here, the authors show that a continuous attractor network endowed with spike frequency adaptation and subject to feedforward external inputs is able to account for several previously unaccounted aspects of theta sequences, including (1) sequences that move both forwards and backwards, (2) sequences that alternate between two arms of a T-maze, (3) speed modulation of place cell firing frequency, and (4) the persistence of phase information across hippocampal inactivations.

I think the main result of the paper (findings (1) and (2)) are likely to be of interest to the hippocampal community, as well as to the wider community interested in mechanisms of neural sequences. In addition, the manuscript is generally well written and the analytics are impressive. However, several issues should be addressed, which I outline below.

Major comments:

In real data, population firing rate is strongly modulated by theta (i.e., cells collectively prefer a certain phase of theta - see review paper Buzsaki, 2002) and largely oscillates at theta frequency during run. With respect to this cyclical firing rate, theta sweeps resemble "Nike" check marks, with the sweep backwards preceding the sweep forwards within each cycle before the activity is quenched at the end of the cycle. I am concerned that (1) the summed population firing rate of the model does not oscillate at theta frequency, and (2) as the authors state, the oscillatory tracking state must begin with a forward sweep. With regards to (1), can the authors show theta phase spike preference plots for the population to see if they match data? With regards to (2), can the authors show what happens if the bump is made to sweep backwards first, as it appears to do within each cycle?

I could not find the width of the external input mentioned anywhere in the text or in the table of parameters. The implication is that it is unclear to me whether, during the oscillatory tracking state, the external input is large compared to the size of the bump, so that the bump lives within a window circumscribed by the external input and so bounces off the interior walls of the input during the oscillatory tracking phase, or whether the bump is continuously pulled back and forth by the external input, in which case it could be comparable to the size of the bump. My guess based on Fig 2c is that it is the latter. Please clarify and comment.

I would argue that the "constant cycling" of theta sweeps down the arms of a T-maze was roughly predicted by Romani & Tsodyks, 2015, Figure 7. While their cycling spans several theta cycles, it nonetheless alternates by a similar mechanism, in that adaptation (in this case synaptic depression) prevents the subsequent sweep of activity from taking the same arm as the previous sweep. I believe the authors should cite this model in this context and consider the fact that both synaptic depression and spike frequency adaptation are both possible mechanisms for this phenomenon. But I certainly give the authors credit for showing how this constant cycling can occur across individual theta cycles.

The authors make an unsubstantiated claim in the paragraph beginning with line 413 that the Tsodyks and Romani (2015) model could not account for forwards and backwards sweeps. Both the firing rate adaptation and synaptic depression are symmetry breaking models that should in theory be able to push sweeps of activity in both directions, so it is far from obvious to me that both forward and backward sweeps are not possible in the Tsodyks and Romani model. The authors should either prove that this is the case (with theory or simulation) or excise this statement from the manuscript.

The section on the speed dependence of theta (starting with line 327) was very hard to understand. Can the authors show a more graphical explanation of the phenomenon? Perhaps a version of Fig 2f for slow and fast speeds, and point out that cells in the latter case fire with higher frequency than in the former?

I had a hard time understanding how the Zugaro et al., (2005) hippocampal inactivation experiment was accounted for by the model. My intuition is that while the bump position is determined partially by the location of the external input, it is also determined by the immediate history of the bump dynamics as computed via the local dynamics within the hippocampus (recurrent dynamics and spike rate adaptation). So that if the hippocampus is inactivated for an arbitrary length of time, there is nothing to keep track of where the bump should be when the activity comes back on line. Can the authors please explain more how the model accounts for this?

Can the authors comment on why the sweep lengths oscillate in the bottom panel of Fig 5b during starting at time 0.5 seconds before crossing the choice point of the T-maze? Is this oscillation in sweep length another prediction of the model? If so, it should definitely be remarked upon and included in the discussion section.

Perhaps I missed this, but I'm curious whether the authors have considered what factors might modulate the adaptation strength. In particular, might rat speed modulate adaptation strength? If so, would have interesting predictions for theta sequences at low vs high speeds.

I think the paper has a number of predictions that would be especially interesting to experimentalists but are sort of scattered throughout the manuscript. It would be beneficial to have them listed more prominently in a separate section in the discussion. This should include (1) a prediction that the bump height in the forward direction should be higher than in the backward direction, (2) predictions about bimodal and unimodal cells starting with line 366, (3) prediction of another possible kind of theta cycling, this time in the form of sweep length (see comment above), etc.

Reviewer #1 (Public Review):

The study isolated extracellular vesicles (EV) from healthy controls (HCs) and Parkinson patients (PwP), using plasma from the venous blood of non-fasting people. Such EVs were characterized and validated by the presence of markers, their size, and their morphology. The main aim of the manuscript is to correlate the presence of synaptic proteins, namely SNAP-25, GAP-43, and SYNAPTOTAGMIN-1, normalized with HSP70, with the clinical progression of PwP. Changes in synaptic proteins have been documented in the CSF of Alzheimer's and Parkinson's patients. The demographics of participants are adequately presented. One important limiting, as well as puzzling aspect, is the fact that authors did not find differences between groups at the beginning of the study nor after one year, after age and sex adjustment.

Reviewer #1 (Public Review):

Summary:<br /> The authors used several zebrafish reporter lines to demonstrate the presence, regional distribution, and transcriptional profile of the immune cells in adult zebrafish brains. They identified DC-like cells distinct from microglia or other macrophages, resembling murine cDC1s. Analysis of different mutants further revealed that this DC population was dependent on Irf8, Batf3, and Csf1rb, but did not rely on Csf1ra.

Strengths:<br /> It is an elegantly designed study providing compelling evidence for further heterogeneity among brain mononuclear phagocytes in zebrafish, consisting of microglia, macrophages, and DC-like cells. This will provide a better understanding of the immune landscape in the zebrafish brain and will help to better distinguish the different cell types from microglia, and to assign specific functions.

Weaknesses:<br /> While scRNA-seq data clearly revealed different subsets of microglia, macrophages, and DCs in the brain, it remains somewhat challenging to distinguish DC-like cells from P2ry12- macrophages by immunohistochemistry or flow cytometry.

Reviewer #1 (Public Review):

Summary:<br /> This is a detailed description of the role of PKCδ in Drosophila learning and memory. The work is based on a previous study (Placais et al. 2017) that has already shown that for the establishment of long-term memory, the repetitive activity of MP1 dopaminergic neurons via the dopamine receptor DAMB is essential to increase mitochondrial energy flux in the mushroom body.

In this paper, the role of PKCδ is now introduced. PKCδ is a molecular link between the dopaminergic system and the mitochondrial pyruvate metabolism of mushroom body Kenyon cells. For this purpose, the authors establish a genetically encoded FRET-based fluorescent reporter of PKCδ-specific activity, δCKAR.

Strengths:<br /> This is a thorough study of the long-term memory of Drosophila. The work is based on the extensive, high-quality experience of the senior authors. This is particularly evident in the convincing use of behavioral assays and imaging techniques to differentiate and explore various memory phases in Drosophila. The study also establishes a new reporter to measure the activity of PKCδ - the focus of this study - in behaving animals. The authors also elucidate how recurrent spaced training sessions initiate a molecular gating mechanism, linking a dopaminergic punishment signal with the regulation of mitochondrial pyruvate metabolism. This advancement will enable a more precise molecular distinction of various memory phases and a deeper comprehension of their formation in the future.

Weaknesses:<br /> Apart from a few minor technical issues, such as the not entirely convincing visualisation of the localisation of a PKCδ reporter in the mitochondria, there are no major weaknesses. Likewise, the scientific classification of the results seems appropriate, although a somewhat more extensive discussion in relation to Drosophila would have been desirable.

Reviewer #1 (Public Review):

Summary:<br /> This manuscript reports the effects of a heterozygous mutation in the KCNT1 potassium channels on the properties of ion currents and the firing behavior of excitatory and inhibitory neurons in the cortex of mice expressing KCNT1-Y777H. In humans, this mutation as well as multiple other heterozygotic mutations produce very severe early-onset seizures and produce a major disruption of all intellectual function. In contrast, in mice, this heterozygous mutation appears to have no behavioral phenotype or any increased propensity to seizures. A relevant phenotype is, however, evident in mice with the homozygous mutation, and the authors have previously published the results of similar experiments with the homozygotes. As perhaps expected, the neuronal effects of the heterozygous mutation presented in this manuscript are generally similar but markedly smaller than the previously published findings on homozygotes. There are, however, some interesting differences, particularly on PV+ interneurons, which appear to be more excitable than wild type in the heterozygotes but more excitable in the heterozygotes. This raises the interesting question (which could be more explicitly discussed by the authors) as to whether the reported changes represent homeostatic events that suppress the seizure phenotype in the mouse heterozygotes or simply changes in excitability that do not reach the threshold for behavioral outcomes.

Strengths and Weaknesses:<br /> 1) The authors find that the heterozygous mutation in PV+ interneurons increases their excitability, a result that is opposite from their previous observation in neurons with the corresponding homozygous mutation. They propose that this results from the selective upregulation of a persistent sodium current INaP in the PV+ interneurons. While the observations are very interesting, there are three issues concerning this interpretation that should be addressed:<br /> A) The protocol for measuring the INaP current could potentially lead to results that could be (mis)interpreted in different ways in different cells. First, neither K currents nor Ca currents are blocked in these experiments. Instead, TTX is applied to the cells relatively rapidly (within 1 second) and the ramp protocol is applied immediately thereafter. It is stated that, at this time, Na currents and INaP are fully blocked but that any effects on Na-activated K currents are minimal. In theory, this would allow the pre- to post-difference current to represent a relatively uncontaminated INaP. This would, however, only work if activation of KNa currents following Na entry is very slow, taking many seconds. A good deal of literature has suggested that the kinetics of activation of KNa currents by Na influx vary substantially between cell types, such that single action potentials and single excitatory synaptic events rapidly evoke KNa currents in some cell types. This is, of course, much faster than the time of TTX application. Most importantly, the kinetics of KNa activation may be different in different neuronal types, which would lead to errors that could produce different estimates of INaP in PV+ interneurons vs other cell types.<br /> B) As the authors recognize, INaP current provides a major source of cytoplasmic sodium ions for the activation. An expected outcome of increased INaP is, therefore, further activation of KNa currents, rather than a compensatory increase in an inward current that counteracts the increase in KNa currents, as is suggested in the discussion.<br /> C) Numerical simulations, in general, provide a very useful way to evaluate the significance of experimental findings. Nevertheless, while the in-silico modeling suggests that increases in INaP can increase firing rate in models of PV+ neurons, there is as yet insufficient information on the relative locations of the INaP channels and the kinetics of sodium transfer to KNa channels to evaluate the validity of this specific model.

2) The greatest effect of TTX application would be expected to be the elimination of large transient inward sodium currents. Why are no such currents visible in the control (pre-TTX) or the difference currents (Fig. 2)? Is it possible I missed something in the methods?

3) As expected, the changes in many of the measured parameters are smaller in the present study with heterozygotes than those previously reported for the homozygous mutation. Some of the statements on the significance of some of the present findings need to be stated more clearly. For example, in the results section describing Fig. 2, it is stated that "In glutamatergic and NFS GABAergic YH-HET neurons, the overall KNa current was increased ...as measured by a significant effect of genotype ...." Later in the same paragraph it is stated that the increases in KNa current are not significant. Apparently, different tests lead to different conclusions. Both for the purpose of understanding the pathophysiological effects of changes in KNa current and for making further numerical simulations, more explicit clarifying statements should be made.

4) The effects of the KCNT1 channel blocker VU170 on potassium currents are somewhat larger and different from those of TTX, suggesting that additional sources of sodium may contribute to activating KCNT1, as suggested by the authors. Because VU170 is, however, a novel pharmacological agent, it may be appropriate to make more careful statements on this. While the original published description of this compound reported no effect on a variety of other channels, there are many that were not tested, including Na and cation channels that are known to activate KCNT1, raising the possibility of off-target effects.

5) The experiments were carried out at room temperature. Is it possible that different effects on firing patterns in heterozygotes and homozygotes would be observed at more physiological temperatures?

Reviewer #1 (Public Review):

Summary: This paper reported interesting aberrant calcium microwaves in the hippocampus when synapsin promoter driven GCaMPs were expressed for a long period of time. These aberrant hippocampal Ca2+ micro-waves depend on the viral titre of the GECI. The microwave of Ca2+ was not observed when GECI was expressed only in a sparse set of neurons.

Strengths: These findings are important to the wide neuroscience community, especially considering a great number of investigators are using similar approaches. Results look convincing and are consistent across several laboratories.

Weaknesses: One important question is needed to further clarify the mechanisms of aberrant Ca2+ microwaves as described below.

Synapsin promoter labels both excitatory pyramidal neurons and inhibitory neurons. To avoid aberrant Ca2+ microwave, a combination of Flex virus and CaMKII-Cre or Thy-1-GCaMP6s and 6f mice were tested. However, all these approaches limit the number of infected pyramidal neurons. While the comprehensive display of these results is appreciated, a crucial question remains unanswered. To distinguish whether the microwave of Ca2+ is caused selectively via the abnormality of interneurons, or just a matter of pyramidal neuron density, testing Flex-GCaMP6 in interneuron specific mouse lines such as PV-Cre and SOM-Cre will be critical.

Reviewer #1 (Public Review):

Summary:<br /> This study delves into the roles of dact1 and dact2 during zebrafish embryonic axis formation and craniofacial morphogenesis. The researchers seek to unravel the mechanisms by which dact1/2 influences Wnt signaling modulation throughout embryonic development and patterning. They propose distinct spatiotemporal roles for Dact1 and Dact2 proteins in zebrafish embryonic development, highlighting their involvement in modulating noncanonical Wnt signaling during convergent extension events. Their findings demonstrate that dact1 and dact2 exhibit distinct spatiotemporal expression domains during development and that dact1/2 mutation leads to convergent extension defects. Furthermore, the study attempts to establish a link between convergent extension defects resulting from dact1/2 mutation and subsequent craniofacial abnormalities during development. To investigate the connection between dact1 and dact2, compound mutants were employed since single mutants did not exhibit craniofacial phenotypes. Additionally, the research encompasses comprehensive transcriptomics and pathway analyses of differentially expressed genes in dact1/2 mutants. This analysis reveals the overexpression of a calcium-dependent cysteine protease, calpain 8. The study suggests a connection between the upregulation of calpain 8 and the observed craniofacial dysmorphology in dact1/2 mutants, implying a potential link between the altered expression of calpain 8 and the craniofacial abnormalities observed in these mutants.

Strengths:<br /> The study beautifully recapitulates previous findings on the role of dact1/2 in modulating convergent extension during zebrafish embryogenesis.

A combination of multiple approaches, including in vivo time-lapse imaging, has been employed to elucidate the etiology of the rod-like neurocranial phenotype in dact1/2 double mutant.<br /> This study utilizes and discusses several 'traditional' mutant lines and newly created ones, analyzing them through single-cell transcriptomics.

Weaknesses:<br /> 1. Enhancing Reproducibility and Robustness:<br /> To enhance the reproducibility and robustness of the findings, it would be valuable for the authors to provide specific numbers of animals used in each experiment.<br /> Explicitly stating the penetrance of the rod-like neurocranial shape in dact1/2-/- animals would provide a clearer understanding of the consistency of this phenotype.

2. Strengthening Single-Cell Data Interpretation:<br /> To further validate the single-cell data and strengthen the interpretation of the gene expression patterns, I recommend the following:<br /> -Provide a more thorough explanation of the rationale for comparing dact1/2 double mutants with gpc4 mutants.<br /> -Employ genotyping techniques after embryo collection to ensure the accuracy of animal selection based on phenotype and address the potential for contamination of wild-type "delayed" animals.<br /> -Supplement the single-cell data with secondary validation using RNA in situ or immunohistochemistry techniques.

3. Directly Investigating Non-Cell-Autonomous Effects:<br /> To directly assess the proposed non-cell-autonomous role of dact1/2, I suggest conducting transplantation experiments to examine the ability of ectodermal/neural crest cells from dact1/2 double mutants to form wild-type-like neurocranium.

4. Further Elucidating Calpain 8's Role:<br /> To strengthen the evidence supporting the critical role of Calpain 8, I recommend conducting overexpression experiments using a sensitized background to enhance the statistical significance of the findings.

Reviewer #1 (Public Review):

In this work Wu, J., et al., highlight the importance of a previously overlooked region on kinases: the αC-β4 loop. Using PKA as a model system, the authors extensively describe the conserved regulatory elements within a kinase and how the αC-β4 loop region integrates with these important regulatory elements. Previous biochemical work on a mutation within the αC-β4 loop region, F100A showed that this region is important for the synergistic high affinity binding of ATP and the pseudo substrate inhibitor PKI. In the current manuscript, the authors assess the importance of the αC-β4 loop region using computational methods such as Local Spatial Pattern Alignment (LSP) and MD simulations. LSP analysis of the F100A mutant showed decreased values for degree centrality and betweenness centrality for several key regulatory elements within the kinase which suggests a loss in stability/connectivity in the mutant protein as compared to the WT. Additionally, based on MD simulation data, the side chain of K105, another residue within the αC-β4 loop region had altered dynamics in the F100A mutant as compared to the WT protein. While these changes in the αC-β4 loop region seem to be consistent with the previous biochemical data, the manuscript can be strengthened with additional experiments.

Comments on the revised version:

Additional experiments (both computational and experimental) assessing the role of the αC-β4 loop region (especially residues such as K105) are needed to bolster their hypothesis. My initial assessment therefore remains unchanged. While this manuscript falls short of expectations when it comes to experimental findings, it is an excellent review on the structural elements of kinases and how the newly identified αC-β4 loop region integrates with these important regions. Perhaps the experimental section (LSP analysis and MD simulation data) could be removed and this manuscript could be converted into a Review Article?

Reviewer #1 (Public Review):

Summary:

The authors try to use a gene therapy approach to cure urofacial symptoms in an HSPE2 mutant mouse model.

Strengths:

The authors have convincingly shown the expression of AAV9/HSPE2 in pelvic ganglion and liver tissues. They have also shown the defects in urethra relaxation and bladder muscle contraction in response to EFS in mutant mice, which were reversed in treated mice.

Weaknesses:

Some important and interesting data are missing. For example, whether the gene therapy can extend the life span of these mutants? The overall in vivo voiding function is missing. AAV9/HSPE2 expression in the bladder wall is not shown.

Reviewer #1 (Public Review):

Summary<br /> Here the authors have tethered a Pgp substrate to strategically place cysteine residues in the protein. Notably, the cysteine-linked substate (ANC-DNPT)- stimulate ATP hydrolyse and so are able to undergo IF to OF transitions. The authors then determined cryo-EM structures of these complexes and MD simulations of bound states. By capturing unforeseen OF conformations with substate they propose that TM1 undergoes local conformational changes that are sufficient to translocate substrates, rather than large bundle movements.

Strengths: This paper provides the first substrate (ANC-DNPT)- bound conformations of PgP and a new mechanistic model of how substrates are translocated.

Weaknesses: Although the cross-links stimulate ATP hydrolysis, it is unclear if the TM1 conformations are exactly the same under physiological conditions, since they have been covalently-trapped to the substrate.

Joint Public Review:

The authors previously showed that expressing formate dehydrogenase, rubisco, carbonic anhydrase, and phosphoribulokinase in Escherichia coli, followed by experimental evolution, led to the generation of strains that can metabolise CO2. Using two rounds of experimental evolution, the authors identify mutations in three genes - pgi, rpoB, and crp - that allow cells to metabolise CO2 in their engineered strain background. The authors make a strong case that mutations in pgi are loss-of-function mutations that prevent metabolic efflux from the reductive pentose phosphate autocatalytic cycle. The authors also use proteomic analysis to probe the role of the mutations in crp and rpoB. While they do not reach strong conclusions about how these mutations promote autotrophic growth, they provide some clues, leading to valuable speculation.

Comments on revised version:

The authors have thoroughly addressed the reviewers' comments. The major addition to the paper is the proteomic analysis of single and double mutants of crp and rpoB. These new data provide clues as to the role of the crp and rpoB mutations in promoting autotrophic growth, which the authors discuss. The authors acknowledge that it will require additional experiments to determine whether the speculated mechanisms are correct. Nonetheless, the new data provide valuable new insight into the role of the crp and rpoB mutations. The authors have also expanded their description of the crp and rpoB mutations, making it clearer that the effects of these mutations are likely to be distinct, albeit with potential for overlap in function.

Reviewer #1 (Public Review):

Summary and strengths<br /> This is an interesting paper that concludes that hiring more women will do more to improve the gender balance of (US) academia than improving the attrition rates of women (which are usually higher than men's). Other groups have reported similar findings but this study uses a larger than usual dataset that spans many fields and institutions, so it is a good contribution to the field.

Weaknesses<br /> The paper uses a mixture of mathematical models (basically Leslie matrices, though that term isn't mentioned here) parameterised using statistical models fitted to data. However, the description of the methods needs to be improved significantly. The author should consider citing Matrix Population Models by Caswell (Second Edition; 2006; OUP) as a general introduction to these methods, and consider citing some or all of the following as examples of similar studies performed with these models:<br /> Shaw and Stanton. 2012. Proc Roy Soc B 279:3736-3741<br /> Brower and James. 2020. PLOS One 15:e0226392<br /> James and Brower. 2022. Royal Society Open Science 9:220785<br /> Lawrence and Chen. 2015. [http://128.97.186.17/index.php/pwp/article/view/PWP-CCPR-2015-008]<br /> Danell and Hjerm. 2013. Scientometrics 94:999-1006

The analysis also runs the risk of conflating the fraction of women in a field with gender diversity! In female-dominated fields (e.g. Nursing, Education) increasing the proportion of women in the field will lead to reduced gender diversity. This does not seem to be accounted for in the analysis. It would also be helpful to state the number of men and women in each of the 111 fields in the study.

Reviewer #1 (Public Review):

Summary:<br /> Herneisen et al characterise the Toxoplasma PDK1 orthologue SPARK and an associated protein SPARKEL in controlling important fate decisions in Toxoplasma. Over recent years this group and others have characterised the role of cAMP and cGMP signalling in negatively and positively regulating egress, motility, and invasion, respectively. This manuscript furthers this work by showing that SPARK and SPARKEL likely act upstream, or at least control the levels of the cAMP and cGMP-dependent kinases PKA and PKG, respectively, thus controlling the transition of intracellular replicating parasites into extracellular motile forms (and back again).

The authors use quantitative (phospho)proteomic techniques to elegantly demonstrate the upstream role of SPARK in controlling cAMP and cGMP pathways. They use sophisticated analysis techniques (at least for parasitology) to show the functional association between cGMP and cAMP signalling pathways. They therefore begin to unify our understanding of the complicated signalling pathways used by Toxoplasma to control key regulatory processes that control the activation and suppression of motility. The authors then use molecular and cellular assays on a range of generated transgenic lines to back up their observations made by quantitative proteomics that are clear in their design and approach.

The authors then extend their work by showing that SPARK/SPARKEL also control PKAc3 function. PKAc3 has previously been shown to negatively regulate differentiation into bradyzoite forms and this work backs up and extends this finding to show that SPARK also controls this. The authors conclude that SPARK could act as a central node of regulation of the asexual stage, keeping parasites in their lytic cell growth and preventing differentiation. Whether this is true is beyond the scope of this paper and will have to be determined at a later date.

Strengths:<br /> This is an exceptional body of work. It is elegantly performed, with state-of-the-art proteomic methodologies carefully being applied to Toxoplasma. Observations from the proteomic datasets are masterfully backed up with validation using quantitative molecular and cellular biology assays.

The paper is carefully and concisely written and is not overreaching in its conclusions. This work and its analysis set a new benchmark for the use of proteomics and molecular genetics in apicomplexan parasites.

Weaknesses:<br /> This reviewer did not identify any weaknesses.

Reviewer #1 (Public Review):

Summary:<br /> The authors previously demonstrated that species-specific variation in primate CD4 impacts its ability to serve as a functional receptor for diverse SIVs. Here, Warren and Barbachano-Guerrero et al. perform population genetics analyses and functional characterization of great ape CD4 with a particular focus on gorillas, which are natural hosts of SIVgor. They first used ancestral reconstruction to derive the ancestral hominin and hominid CD4. Using pseudotyped viruses representing a panel of envelopes from SIVcpz and HIV strains, they find that these ancestral reconstructions of CD4 are more similar to human CD4 in terms of being a broadly susceptible entry receptor (in the context of mediating entry into Cf2Th cells stably expressing human CCR5). In contrast, extant gorilla and chimpanzee CD4 are functional entry receptors for a narrower range of HIV and SIVcpz isolates. Based on these differences, authors next surveyed gorilla sequences and identified several CD4 haplotypes, specifically in the region encoding the CD4 D1 domain, which directly contacts the viral glycoprotein and thus may impact the interaction. Consistent with this possibility, the authors demonstrated that gorilla CD4 haplotypes are, on average, less capable of supporting entry than human CD4, and that some are largely unable to function as SIV entry receptors. Interestingly, individual residues found at key positions in the gorilla CD4 D1 when tested in the context of human CD4 reduce entry of some virions pseudotyped with diverse SIVcpz envelopes, suggesting that individual amino acids can in part explain the observed differences across gorilla CD4 haplotypes. Finally, the authors perform statistical tests to infer that CD4 from great apes with endemic SIV (i.e., chimpanzees and gorillas) but not non-reservoirs (i.e., orangutans, bonobos) or recent spillover hosts (i.e., humans), have been subject to selection as a result of pressure from endemic SIV.

The conclusions of this paper are mostly well supported by data.

Strengths:<br /> The functional assays are appropriate to test the stated hypothesis, and the authors use a broad diversity of envelopes from HIV and SIVcpz strains. The authors also partially characterize one potential mechanism of gorilla CD4 resistance - receptor glycosylation at the derived N15 found in 5/6 gorilla haplotypes.

Ancestral reconstruction provides a particularly interesting aspect of the study, allowing authors to infer the ancestral state of hominid CD4 relative to modern CD4 from gorillas and chimpanzees. This, coupled with evidence supporting SIV-driven selection of gorilla CD4 diversity and the characterization of functional diversity of extant haplotypes provides several interesting findings.

Weaknesses:<br /> The major inference of the work is that SIV infection of gorillas drove the observed diversity in gorilla CD4. This is supported by the majority of SNPs being localized to the CD4 D1, which directly interacts with the envelope, and the demonstrated functional consequences of that diversity for viral entry. However, SIVgor (to the best of my knowledge) only infects Western lowland gorillas (Gorilla gorilla gorilla), and one Gorilla gorilla diehli and three Gorilla beringei graueri individuals were included in the haplotype and allele frequency analyses. The presence of these haplotypes or the presence of similar allele frequencies in Eastern lowland and mountain gorillas would impact this conclusion. It would be helpful for the authors to clarify this point.

The authors appear to use a somewhat atypical approach to assess intra-population selection to compensate for relatively small numbers of NHP sequences (Fig. 6). However, they do not cite precedence for the robustness of the approach or the practice of grouping sequences from multiple species for the endemic vs other comparison. They also state in the methods that some genes encoded in the locus were removed from the analysis "because they have previously been shown to directly interact with a viral protein." This seems to undercut the analysis and prevents alternative explanations for the observed diversity in CD4 (e.g., passenger mutations from selection at a neighboring locus).

Data in Figure 5 is graphed as % infected cells instead of virus titer (TDU/mL). It's unclear why this is the case, and prevents a comparison to data in Figure 2 and Figure 4.

The lack of pseudotyping with SIVgor envelope is a surprising omission from this study, that would help to contextualize the findings. Similarly, building gorilla CD4 haplotype SNPs onto the hominin ancestor (as opposed to extant human CD4) may provide additional insights that are meaningful toward understanding the evolutionary trajectory of gorilla CD4.

Reviewer #1 (Public Review):

Wang et al investigated the evolution, expression, and function of the X-linked miR-506 miRNA family. They showed that the miR-506 family underwent rapid evolution. They provided evidence that miR-506 appeared to have originated from the MER91C DNA transposons. Human MER91C transposon produced mature miRNAs when expressed in cultured cells. A series of mouse mutants lacking individual clusters, a combination of clusters, and the entire X-linked cluster (all 22 miRNAs) were generated and characterized. The mutant mice lacking four or more miRNA clusters showed reduced reproductive fitness (litter size reduction). They further showed that the sperm from these mutants were less competitive in polyandrous mating tests. RNA-seq revealed the impact of deletion of miR-506 on the testicular transcriptome. Bioinformatic analysis analyzed the relationship among miR-506 binding, transcriptomic changes, and target sequence conservation. The miR-506-deficient mice did not have apparent effect on sperm production, motility, and morphology. Lack of severe phenotypes is typical for miRNA mutants in other species as well. However, the miR-506-deficient males did exhibit reduced litter size, such an effect would have been quite significant in an evolutionary time scale. The number of mouse mutants and sequencing analysis represent a tour de force. This study is a comprehensive investigation of the X-linked miR-506 miRNA family. It provides important insights into the evolution and function of the miR-506 family.

The conclusions of this preprint are mostly supported by the data except being noted below. Some descriptions need to be revised for accuracy.

L219-L285: The conclusion that X-linked miR-506 family miRNAs are expanded via LINE1 retrotransposition is not supported by the data. LINE1s and SINEs are very abundant, accounting for nearly 30% of the genome. In addition, the LINE1 content of the mammalian X chromosome is twice that of the autosomes. One can easily find flanking LINE1/SINE repeat. Therefore, the analyses in Fig. 2G, Fig. 2H and Fig. S3 are not informative. In order to claim LINE1-mediated retrotransposition, it is necessary to show the hallmarks of LINE1 retrotransposition, which are only possible for new insertions. The X chromosome is known to be enriched for testis-specific multi-copy genes that are expressed in round spermatids (PMID: 18454149). The conclusion on the LINE1-mediated expansion of miR-506 family on the X chromosome is not supported by the data and does not add additional insights. I think that the LINE1 related figure panels and description (L219-L285) need to be deleted. In discussion (L557-558), "...and subsequently underwent sequence divergence via LINE1-mediated retrotransposition during evolution" should also be deleted. This section (L219-L285) needs to deal only with the origin of miR-506 from MER91C DNA transposons, which is both convincing and informative.

Fig. 3A: can you speculate/discuss why the miR-506 expression in sperm is higher than in round spermatids?

Reviewer #1 (Public Review):

Summary:<br /> The cohesin complex maintains sister chromatid cohesion from S phase to anaphase. Beyond that, DSBs trigger cohesin recruitment and post-replication cohesion at both damage sites and globally, which was originally reported in 2004. In their recent study, Ayra-Plasencia et al reported in telophase, DSBs are repaired via HR with re-coalesced sister chromatids (Ayra-Plasencia & Machín, 2019). In this study, they show that HR occurs in a Smc3-dependent way in late mitosis.

Strengths:<br /> The authors take great advantage of the yeast system, they check the DSB processing and repair of a single DSB generated by HO endonuclease, which cuts the MAT locus in chromosome III. In combination with cell synchronization, they detect the HR repair during G2/M or late mitosis. and the cohesin subunit SMC3 is critical for this repair. Beyond that, full-length Scc1 protein can be recovered upon DSBs.

Weaknesses:<br /> These new results basically support their proposal although with a very limited molecular mechanistic progression, especially compared with their recent work.

Reviewer #1 (Public Review):

Summary:

This manuscript reports that a combination of two small molecules, 2C (CHIR99027 and A-485) enabled to induce the dedifferentiation of hESC-derived cardiomyocytes (CMs) into regenerative cardiac cells (RCC). These RCCs had disassembled sarcomeric structures and elevated expression of embryonic cardiogenic genes such as ISL1, which exhibited proliferative potential and were able to differentiate into cardiomyocytes, endothelial cells, and smooth muscle cells. Lineage tracing further suggested that RCCs originated from TNNT2+ cells, not pre-existing ISL1+ cells. Furthermore, 2C treatment increased the numbers of RCC cells in neonatal rat and adult mouse hearts and improved cardiac function post-MI in adult mice. Mechanistically, bulk RNA-seq analysis revealed that 2C led to elevated expression of embryonic cardiogenic genes while down-regulation of CM-specific genes. Single-cell RNA-seq data showed that 2C promoted cardiomyocyte transition into an intermediate state that is marked with ACTA2 and COL1A1, which subsequently transformed into RCCs. Finally, ChIP-seq analysis demonstrated that CHIR99027 enhanced H3K9Ac and H3K27Ac modifications in embryonic cardiac genes, while A-485 inhibited these modifications in cardiac-specific genes. These combined alterations effectively induced the dedifferentiation of cardiomyocytes into RCCs.

Strengths:

Overall, this work is quite comprehensive and is logically and rigorously designed. The phenotypic and functional data on 2C are strong.

Weaknesses:

The mechanistic insights of 2C are primarily derived from transcriptomic and genomic datasets without experimental verification.

Reviewer #1 (Public Review):

Summary:<br /> The manuscript authored by Stockner and colleagues delves into the molecular simulations of Na+ binding pathway and the ionic interactions at the two known sodium binding sites site 1 and site 2. They further identify a patch of two acidic residues in TM6 that seemingly populate the Na+ ions prior to entry into the vestibule. These results highlight the importance of studying the ion-entry pathways through computational approaches and the authors also validate some of their findings through experimental work. They observe that sodium site 1 binding is stabilized by the presence of the substrate in the s1 site and this is particularly vital as the GABA carboxylate is involved in coordinating the Na+ ion unlike other monoamine transporters and binding of sodium to the Na2 site stabilizes the conformation of the GAT1 by reducing flexibility among the helical bundles involved in alternating access.

Strengths:<br /> The study displays results that are generally consistent with available information from experiments on SLC6 transporters particularly GAT1 and puts forth the importance of this added patch of residues in the extracellular vestibule that could be of importance to the ion permeation in SLC6 transporters. This is a nicely performed study and could be improved if the authors could comment on and fix the following queries.

Weaknesses:<br /> 1. How conserved are the residue pair of D281-E283 in other SLC6 transporters. The authors commented on the presence of these residues in SERT but it would be nice to know how widespread these residues are in other SLC6 transporters like NET, GlyT, and DAT.

2. Further, one would like to see the effect of individual mutations D281A and E283A on transport, surface expression, and EC50 of Na+ to gauge the effect on transport.

3. A clear figure of the S1 site where Na+ tends to stay prior to Na1 site interactions needs to be provided with a clear figure. Further, it is not entirely clear how access to S1 is altered if the transporter is in an outward-occluded conformation if F294 is blocking solvent access. Please comment.

4. The p-value of the EC50 differences between GAT1WT and GAT1double mutant need to be mentioned. The difference in sodium dependence EC50 seems less than twofold and it would be useful to mention how critical the role of the recruitment site is. Since the transport is not affected the site could play a transient role in attracting ions.

5. It would be very nice to know how K+ ions are attracted by this recruitment site. This could further act as a control simulation to test the preference for Na+ ions among SLC6 members.

6. Some of the important figures are not very clear. For instance, there should be a zoomed-in view of the recruitment site. The current one in Fig. 1b and 1c could be made clearer. Similarly as mentioned earlier the Na residence at the S1 site away from the Na1 and Na2 sites needs to be shown with greater clarity by putting side chain information in Fig. 6d.

7. The structural features that comprise the two principle components PC1 and PC2 should be described in greater detail.

Reviewer #1 (Public Review):

Summary:<br /> Bendzunas, Byrne et al. explore two highly topical areas of protein kinase regulation in this manuscript. Firstly, the idea that Cys modification could regulate kinase activity. The senior authors have published some standout papers exploring this idea of late, and the current work adds to the picture of how active site Cys might have been favoured in evolution to serve critical regulatory functions. Second, BRSK1/2 are understudied kinases listed as part of the "dark kinome" so any knowledge of their underlying regulation is of critical importance to advancing the field.

Strengths:<br /> In this study, the author pinpoints highly-conserved, but BRSK-specific, Cys residues as key players in kinase regulation. There is a delicate balance between equating what happens in vitro with recombinant proteins relative to what the functional consequence of Cys mutation might be in cells or organisms, but the authors are very clear with the caveats relating to these connections in their descriptions and discussion. Accordingly, by extension, they present a very sound biochemical case for how Cys modification might influence kinase activity in cellular environs.

Weaknesses:<br /> I have very few critiques for this study, and my major points are barely major.

Major points<br /> 1. My sense is that the influence of Cys mutation on dimerization is going to be one of the first queries readers consider as they read the work. It would be, in my opinion, useful to bring forward the dimer section in the manuscript.

2. Relatedly, the effect of Cys mutation on the dimerization properties of preparations of recombinant protein is not very clear as it stands. Some SEC traces would be helpful; these could be included in the supplement.

3. Is there any knowledge of Cys mutants in disease for BRSK1/2?

4. In bar charts, I'd recommend plotting data points. Plus it is crucial to report in the legend what error measure is shown, the number of replicates, and the statistical method used in any tests.

5. In Figure 5b, the GAPDH loading control doesn't look quite right.

6. In Figure 7 there is no indication of what mode of detection was used for these gels.

9. Recombinant proteins - more detail should be included on how they were prepared. Was there a reducing agent present during purification? Where did they elute off SEC... consistent with a monomer of higher order species?

Joint Public Review:

This article is a direct follow-up to the paper published last year in eLife by the same group. In the previous article, the authors discovered a zinc finger protein, Kipferl, capable of guiding the HP1 protein Rhino towards certain genomic regions enriched in GRGGN motifs and packaged in heterochromatin marked by H3K9me3. Unlike other HP1 proteins, Rhino recruitment activates the transcription of heterochromatic regions, which are then converted into piRNA source loci. The molecular mechanism by which Kipferl interacts specifically with Rhino (via its chromodomain) and not with other HP1 proteins remained enigmatic.

In this latest article, the authors go a step further by elucidating the molecular mechanisms important for the specific interaction of Rhino and not other HP1 proteins with Kipferl. A phylogenetic study carried out between the HP1 proteins of 5 Drosophila species led them to study the importance of an AA Glycine at position 31 located in the Rhino chromodomain, an AA different from the AA (aspartic acid) found at the same position in the other HP1 proteins. The authors then demonstrate, through a series of structure predictions, biochemical, and genetic experiments, that this specific AA in the Rhino-specific chromodomain explains the difference in the chromatin binding pattern between Rhino and the other Drosophila HP1 proteins. Importantly, the G31D conversion of the Rhino protein prevents interaction between Rhino and Kipferl, phenocopying a Kipfer mutant.

Strengths:

The authors' effective use of phylogenetic analyses and protein structure predictions to identify a substitution in the chromodomain that allows Rhino's specific interaction with Kipferl is very elegant. Both genetic and biochemical approaches are applied to rigorously probe the proposed explanation. They used a point mutation in the endogenous locus that replaces the Rhino-specific residue with the aspartic acid residue present in all other HP1 family members. This novel allele largely phenocopies the defects in hatch rate, chromatin organization, and piRNA production associated with kipferl mutants, and does not support Kipferl localization to clusters. The data are of high quality, the presentation is clear and concise, and the conclusions are generally well-supported.

Weaknesses:

The reviewers identified potential ways to further strengthen the manuscript.

1) The one significant omission is RNAseq on the rhino point mutant, which would allow direct comparison to cluster, transposon, and repeat expression in kipferl mutants.

2) The manuscript would benefit from adding more evolutionary comparisons. The following or similar analyses would help put the finding into a broader evolutionary perspective: i) Is Kipferl's surface interacting with Rhino also conserved in Kipferl orthologs? In other words, are the Rhino-interacting amino acids of Kipferl under any pressure to be conserved? ii) The remarkable conservation of Rhino's G31 is at odds with the arms race that is proposed to be happening between the fly's piRNA pathway proteins and transposons. Does this mean that Rhino's chromodomain is "untouchable" for such positive selection?

Reviewer #1 (Public Review):

My main concern is the use of the 700K SNP dataset. This set of SNPs suffers from a heavy ascertainment bias, which can be seen in the PCA in the supplementary material where all the aurochs cluster in the center within the variation of cattle. Given the coverage of some of the samples, multiple individuals would have less than 10K SNP covered. The majority of these are unlikely to be informative here given that they would just represent fixed positions between taurine and indicine or SNPs mostly variable in milk cattle breeds. The authors would get a much better resolution (i.e. many more SNPs to work with their very low genome coverage data) using the 1000 bull genome project VCF data set: https://www.ebi.ac.uk/ena/browser/view/PRJEB42783 which based on whole genome resequencing data from many cattle. This will certainly help with improving the resolution of qpAdm and f4 analysis, which have huge confidence intervals in most cases. Right now some individuals have huge confidence intervals ranging from 0 to 80% auroch ancestry...

I agree with the authors that qpAdm is likely to give quite a noisy estimate of ancestry here (likely explain part of the issue I mentioned above). Although qpAdm is good for model testing here for ancestry proportion the authors instead could use an explicit f4 ratio - this would allow them to specify a model which would make the result easier to interpret.

The interpretation of the different levels of allele sharing on X vs autosome being the result of sex-bias admixture is not very convincing. Could these differences simply be due to a low recombination rate on the X chromosome and/or lower effective population size, which would lead to less efficient purifying selection?

The authors suggest that 2 pop model rejection in some domestic population might be due to indicine ancestry, this seems relatively straightforward to test.

The first sentence of the paper is a bit long-winded, also dogs were domesticated before the emergence of farming societies.

It would be good to be specific about the number of genomes and coverage info in the last paragraph of the intro.

Reviewer #1 (Public Review):

Summary:<br /> Doxorubincin has long been known to cause bone loss by increasing osteoclast and suppressing osteoblast activities. The study by Wang et al. reports a comprehensive investigation into the off-target effects of doxorubicin on bone tissues and potential mechanisms. They used a tumor-free model with wild-type mice and found that even a single dose of doxorubicin has a major influence by increasing leukopenia, DAMPs, and inflammasomes in macrophages and neutrophils, and inflammation-related cell death (pyroptosis and NETosis). The gene knockout study shows that AIM2 and NLRP3 are the major contributors to bone loss. Overall, the study confirmed previous findings regarding the impact of doxorubicin on tissue inflammation and expanded the research further into bone tissue. The presented data are consistent; however, a major question remains regarding whether doxorubicin drives inflammation and its related events. Most in vitro studies showed that the effect of doxorubincin cannot be demonstrated without LPS priming. This observation raises the question of whether doxorubincin itself could activate the inflammasome and the related events. In vivo study, on the other hand, suggested that it doesn't require LPS. The inconsistency here was not explained further. Moreover, a tumor-free mouse model was used for the study; however, immune responses in tumor-bearing models would likely be distinct from tumor-free ones. The justification for using tumor-free models is not well-established.

Strengths:<br /> The paper includes a comprehensive study that shows the effects of doxorubincin on cytokine levels in serum, the release of DAMPs and NETosis, and leukopenia using both in vivo and in vitro models. Bone marrow cells, macrophages, and neutrophils were isolated from the bone marrow, and the levels of cytokines in serum were also determined.

They employed multiple knockout models with a deficiency in Aim 2, Nlirp3, and double deficiencies to dissect the functional involvement of these two inflammasomes.

The experiments in general are well designed. The paper is also logically written, and the figures were clearly labeled.

Weaknesses:<br /> Most of the data presented are correlative, and there is not much effort to dissect the underlying molecular mechanism.

It is not entirely clear why a tumor-free model is chosen to study immune responses, as immune responses can differ significantly with or without tumor-bearing.

Immune responses in isolated macrophages, neutrophils, and bone marrow cells require priming with LPS, while such responses are not observed in vivo. There is no explanation for these differences.

The band intensities on Western blots in Fig. 4 and Fig. 5 are not quantified, and the numbers of repeats are also not provided.

Many abbreviations are used throughout the text, and some of the full names are not provided.

Fig. 5B needs a label on the X axis.

Reviewer #1 (Public Review):

Summary and strengths:

This is an interesting, timely and informative article. The authors used publicly available data (made available by a funding agency) to examine some of the academic characteristics of the individuals recipients of the National Institutes of Health (NIH) k99/R00 award program during the entire history of this funding mechanism (17 years, total ~ 4 billion US dollars (annual investment of ~230 million USD)). The analysis focuses on the pedigree and the NIH funding portfolio of the institutions hosting the k99 awardees as postdoctoral researchers and the institutions hiring these individuals. The authors also analyze the data by gender, by whether the R00 portion of the awards eventually gets activated and based on whether the awardees stayed/were hired as faculty at their k99 (postdoctoral) host institution or moved elsewhere. The authors further sought to examine the rates of funding for those in systematically marginalized groups by analyzing the patterns of receiving k99 awards and hiring k99 awardees at historically black colleges and universities.

The goals and analysis are reasonable and the limitations of the data are described adequately. It is worth noting that some of the observed funding and hiring traits are in line with the Matthew effect in science (Merton, 1968: https://www.science.org/doi/10.1126/science.159.3810.56) and in science funding (Bol et al., 2018: https://www.pnas.org/doi/10.1073/pnas.1719557115). Overall, the article is a valuable addition to the research culture literature examining the academic funding and hiring traits in the United States. The findings can provide further insights for the leadership at funding and hiring institutions and science policy makers for individual and large-scale improvements that can benefit the scientific community.

Weaknesses:

The authors have addressed my recommendations in the previous review round in a satisfactory way.

Reviewer #1 (Public Review):

This manuscript deftly combines cryo-EM and electrophysiology to investigate gating mechanisms of human CLC-2. Although another structure of CLC-2 was recently reported, this is the first structure to report density for the absolutely critical gating glutamate, and - an even more exciting result - the first structure to identify the N-terminal gating peptide that is the heart of this manuscript. There has been previous controversy over such a gating peptide in CLC-2, but the combined structural/functional approach appears to establish a role for this peptide in gating, and sets up future experiments to understand why its effects might change under different physiological scenarios. The experiments reported here are thoughtful and well-controlled and the data presentation is excellent. For the electrophysiology experiments, the use of inhibitor AK-42 (developed by the current senior author's lab) to establish a zero current level is a welcome advance and should become standard for electrophysiological studies of CLC-2.

Reviewer #1 (Public Review):

In the best genetically and biochemically understood model of eukaryotic DNA replication, the budding yeast, Saccharomyces cerevisiae, the genomic locations at which DNA replication initiates are determined by a specific sequence motif. These motifs, or ARS elements, are bound by the origin recognition complex (ORC). ORC is required for loading of the initially inactive MCM helicase during origin licensing in G1. In human cells, ORC does not have a specific sequence binding domain and origin specification is not specified by a defined motif. There have thus been great efforts over many years to try to understand the determinants of DNA replication initiation in human cells using a variety of approaches, which have gradually become more refined over time.

In this manuscript Tian et al. combine data from multiple previous studies using a range of techniques for identifying sites of replication initiation to identify conserved features of replication origins and to examine the relationship between origins and sites of ORC binding in the human genome. The authors identify a) conserved features of replication origins e.g. association with GC-rich sequences, open chromatin, promoters and CTCF binding sites. These associations have already been described in multiple earlier studies. They also examine the relationship of their determined origins and ORC binding sites and conclude that there is no relationship between sites of ORC binding and DNA replication initiation. While the conclusions concerning genomic features of origins are not novel, if true, a clear lack of colocalization of ORC and origins would be a striking finding. However, the majority of the datasets used do not report replication origins, but rather broad zones in which replication origins fire. Rather than refining the localisation of origins, the approach of combining diverse methods that monitor different objects related to DNA replication leads to a base dataset that is highly flawed and cannot support the conclusions that are drawn, as explained in more detail below.

Methods to determine sites at which DNA replication is initiated can be divided into two groups based on the genomic resolution at which they operate. Techniques such as bubble-seq, ok-seq can localise zones of replication initiation in the range ~50kb. Such zones may contain many replication origins. Conversely, techniques such as SNS-seq and ini-seq can localise replication origins down to less than 1kb. Indeed, the application of these different approaches has led to a degree of controversy in the field about whether human replication does indeed initiate at discrete sites (origins), or whether it initiates randomly in large zones with no recurrent sites being used. However, more recent work has shown that elements of both models are correct i.e. there are recurrent and efficient sites of replication initiation in the human genome, but these tend to be clustered and correspond to the demonstrated initiation zones (Guilbaud et al., 2022).

These different scales and methodologies are important when considering the approach of Tian et al. The premise that combining all available data from five techniques will increase accuracy and confidence in identifying the most important origins is flawed for two principal reasons. First, as noted above, of the different techniques combined in this manuscript, only SNS-seq can actually identify origins rather than initiation zones. It is the former that matters when comparing sites of ORC binding with replication origin sites, if a conclusion is to be drawn that the two do not co-localise.

Second, the authors give equal weight to all datasets. Certainly, in the case of SNS-seq, this is not appropriate. The technique has evolved over the years and some earlier versions have significantly different technical designs that may impact the reliability and/or resolution of the results e.g. in Foulk et al. (Foulk et al., 2015), lambda exonuclease was added to single stranded DNA from a total genomic preparation rather than purified nascent strands), which may lead to significantly different digestion patterns (ie underdigestion). Curiously, the authors do not make the best use of the largest SNS-seq dataset (Akerman et al., 2020) by ignoring these authors separation of core and stochastic origins. By blending all data together any separation of signal and noise is lost. Further, I am surprised that the authors have chosen not to use data and analysis from a recent study that provides subsets of the most highly used and efficient origins in the human genome, at high resolution (Guilbaud et al., 2022).

References

Akerman I, Kasaai B, Bazarova A, Sang PB, Peiffer I, Artufel M, Derelle R, Smith G, Rodriguez-Martinez M, Romano M, Kinet S, Tino P, Theillet C, Taylor N, Ballester B, Méchali M (2020) A predictable conserved DNA base composition signature defines human core DNA replication origins. Nat Commun, 11: 4826

Foulk MS, Urban JM, Casella C, Gerbi SA (2015) Characterizing and controlling intrinsic biases of lambda exonuclease in nascent strand sequencing reveals phasing between nucleosomes and G-quadruplex motifs around a subset of human replication origins. Genome Res, 25: 725-735

Guilbaud G, Murat P, Wilkes HS, Lerner LK, Sale JE, Krude T (2022) Determination of human DNA replication origin position and efficiency reveals principles of initiation zone organisation. Nucleic Acids Res, 50: 7436-7450

Update in response to authors' comments on the original review:

While the authors have clarified their approach to some aspects of their analysis, I believe they and I are just going to have to disagree about the methodology and conclusions of this work. I do not find the authors responses sufficiently compelling to change my mind about the significance of the study or veracity of the conclusions. In my opinion, the method for identification of strong origins is not robust and of insufficient resolution. In addition, the resolution and the overlap of the MCM Chip-seq datasets is poor. While the conclusion of the paper would indeed be striking and surprising if true, I am not at all persuaded that it is based on the presented data.

Reviewer #1 (Public Review):

The mutation rate and spectrum have been found to differ between populations as well as across individuals within the same population. Hypothesizing that some of the observed variation has a genetic basis, the authors of this paper have made important contributions in the past few years in identifying genetic variants that modify mutation rate or spectrum in natural populations. This paper makes one significant step further by developing a new method for mapping genetic variants associated with the mutation spectrum, which reveals new biological insights.

Using traditional quantitative trait locus (QTL) mapping in the BXD mouse recombinant inbred lines (RILs), the authors of this paper previously identified a genetic locus associated with C>A mutation rate. However, this approach has limited power, as it suffers from multiple testing burden as well as noise in the "observed mutation spectrum phenotype" due to rarity and randomness of mutation events. To overcome these limitations, the authors developed a new method that they named "aggregate mutation spectrum distance" (AMSD), which in short measures the difference in the aggregate mutation spectrum between two groups of individuals with distinct genotypes at a specific genomic locus. With this new approach, they recover the previously reported candidate mutator locus (near Mutyh gene) and identify a new candidate locus that modifies the C>A mutation rate on only the mutator allele genetic background at the Mutyh locus. Using more rigorous statistical testing, the authors show convincingly synergistic epistatic effects between the mutator alleles at the two loci.

Overall, the analyses presented are well done and provide convincing evidence for the major findings, including the new candidate mutator locus and its epistatic interaction with the Mutyh locus. The new AMSD method introduced is innovative and outperforms traditional QTL mapping under most conditions, as demonstrated by extensive simulations. I identify no major issues with this paper and think it is very well written.

One of the major advantages of the AMSD method over QTL mapping is alleviation of the multiple testing burden, as one comparison tests for any changes in the mutation spectrum, including simultaneous, small changes in the relative abundance of multiple mutation types. The flip side of this advantage of AMSD is that, when a significant association is detected, it is not immediately clear which mutation type is driving the signal. To narrow the signal to specific candidate mutation type(s), additional analyses are needed, such as testing for differential proportions of each mutation type between individuals with or without the candidate mutator allele. However, such analysis may be less powerful when the mutator allele leads to small changes in the relative abundance of multiple mutation types. This will be an area of improvement for future studies.

Reviewer #1 (Public Review):

This is an interesting study by Pinos and colleagues that examines the effect of beta carotene on atherosclerosis regression. The authors have previously shown that beta carotene reduces atherosclerosis progress and hepatic lipid metabolism, and now they seek to extend these findings by feeding mice a diet with excess beta carotene in a model of atherosclerosis regression (LDLR antisense oligo plus Western diet followed by LDLR sense oligo and chow diet). They show some metrics of lesion regression are increased upon beta carotene feeding (collagen content) while others remain equal to normal chow diet (macrophage content and lesion size). These effects are lost when beta carotene oxidase (BCO) is deleted. The study adds to the existing literature that beta carotene protects from atherosclerosis in general, and adds new information regarding regulatory T-cells. However, the study does not present significant evidence about how beta-carotene is affecting T-cells in atherosclerosis. For the most part, the conclusions are supported by the data presented, and the work is completed in multiple models, supporting its robustness. However there are a few areas that require additional information or evidence to support their conclusions and/or to align with the previously published work.

Specific additional areas of focus for the authors:<br /> The premise of the story is that b-carotene is converted into retinoic acid, which acts as a ligand of the ROR transcription factor in T-regs. The authors measure hepatic markers of retinoic acid signaling (retinyl esters, Cyp26a1 expression) but none of these are measured in the lesion, which calls into question the conclusion that Tregs in the lesion are responsible for the regression observed with b-carotene supplementation.

There does not appear to be a strong effect of Tregs on the b-carotene induced pro-regression phenotype presented in Figure 5. The only major CD25+ cell dependent b-carotene effect is on collagen content, which matches with the findings in Figure 1 +2. This mechanistically might be very interesting and novel, yet the authors do not investigate this further or add any additional detail regarding this observation. This would greatly strengthen the study and the novelty of the findings overall as it relates to b-carotene and atherosclerosis.

The title indicates that beta-carotene induces Treg 'expansion' in the lesion, but this is not measured in the study.

Revised manuscript:<br /> In the revised manuscript, the authors provide quantification of an RA-responsive gene in the plaque as evidence that RA signalling is indeed elevated upon b-carotene supplementation. It is not reduced upon blocking CD25 (Tregs) which implies that other cells in addition to Tregs are impacted by b-carotene supplementation that favourably remodels the plaque. The authors properly account for this by tempering their conclusions and recognize that Tregs are only partially responsible for the plaque phenotype upon b-carotene supplementation.

The authors chose not to further investigate why b-carotene impacted collagen production, instead including a discussion point. In this reviewer's opinion, it is a missed opportunity but hopefully something that can be investigated further by others.

Reviewer #1 (Public Review):

Summary:

The authors demonstrate that the immunosuppressive environment in pancreatic ductal adenocarcinoma (PDAC) can be mitigated by a combination of ionizing radiation (IR), CCR5 inhibition, and PD1 blockade. This combination therapy increases tissue-resident natural killer (trNK) cells that facilitate CD8 T cell activity, resulting in a reduction of E-cadherin positive tumor cells. They identify a specific "hypofunctional" NK cell population in both mouse and human PDAC that supports CD8 T cell involvement. A trNK signature is found to be associated with better survival outcomes in PDAC and other solid tumors.

Strengths:

Overall, I think this is an interesting study that combines testing of therapeutic concepts in mice with bioinformatics analysis of single-cell transcriptome data in primary tumors and exploration of clinical outcomes using signature genes in TCGA data. The key finding is that immunoregulatory properties of tumor-infiltrating/resident CD56-bright NK cells (assumed to be non-cytotoxic) are beneficial for outcome through cross-talk with DC and recruitment of CD8 T cells. The latter is specifically induced by irradiation combined with CCR5i and PD1 blockade.

"These results collectively support the notion that IR/CCR5i/αPD1 combination treatment alters immune infiltration by reducing Tregs and increasing NK and CD8 T cells, thereby resulting in greater local tumor control." I agree with this conclusion.

Weaknesses:

There are a few points to discuss and that the authors may want to address.

1) "Notably, CCR5i significantly reduced Treg infiltration but had no effect on the infiltration of other immune cells, indicating the active recruitment of CCR5+ Tregs in PDAC (Figure 2B)."<br /> CCR5i treatment seems to inhibit infiltration of CD8 T cells and NK cells to a greater extent, in relative terms, compared to Treg, albeit it is not statistically significant. If this visual inspection of the graph does not reflect reality, additional experiments may be needed to verify the selective targeting of Tregs or confirm the fact that also CD8 T cells and NK cells are affected by single agent CCR5i. The reduced recruitment of Treg, NK cells, and CD8T cells was completely reversed when combined with irradiation. In the data shown in Figure 3E it seems as if CCR5i induced infiltration of Tregs along with other immune cells. However, this said, I agree with the conclusion of the authors that this combined treatment leads to an altered immune composition and ratio between Tregs and effector cells (CD8T cells and NK cells). Could this altered composition be displayed more clearly?

2) The definition of active and hypofunctional NK cells based on solely NKG2D expression alone seems like an oversimplification. I realize it is not trivial to test tumor-infiltrating NK cells from these tumors functionally but perhaps scRNAseq of the tumors would allow for characterization of cytotoxicity scores using KEGG or GO analysis or reversed gene set enrichment in responders/non-responders. It seems as if the abstract refers to this phenotype incorrectly since the "hyporesponsive" subset is described as NKG2C-negative.

3) "The NK_C1 cluster correlates best with the hypofunction NK phenotype observed in mice as similarly displayed reduced activation (reduced NKG7, NKp80, GZMA, and PRF1) with additional expression of tissue residency markers CD103, CD49a and, surprisingly, the adaptive activating receptor NKG2C (KLRC2) (Figure 5B, C)."

There is no doubt that NK_C1 represents tumor-infiltrating NK cells with a CD56bright gene signature with a strong tissue resident score. However, the transcriptional expression of KLRC2 on these is not surprising! It is well established that KLRC2 transcripts (but not protein) are highly expressed on conventional CD56bright NK cells. There are several published sources where the authors can find such data for confirmation. Thus, this is not to be confused with adaptive NK cells having an entirely different transcriptional signature and expressing high levels of NKG2C at the cell surface. I strongly recommend re-interpreting the results based on the fact that KLRC2 is expressed at high levels in conventional CD56bright NK cells. If not, it would be important to verify that these tissue-resident NK cells express NKG2C and not NKG2A at the cell surface.

4) NCAM1 transcript alone is not sufficient to deconvolute CD56bright NK cells in TCGA data (Figure 7A). As a single marker, it likely reflects NK cell infiltration without providing further evidence on the contribution of the bright/dim components. Therefore, the use of the bright Tr NK signature described in Table 1 is very important (Figure 7B). Table 1 is not provided. Nor Supplementary Table 1. There is only one supplementary figure in the ppt attached.

Reviewer #2 (Public Review):

Summary:

The study demonstrates that deletion of a small cytoplasmic membrane protein, Tmem263, caused severe impairment of longitudinal bone growth and that the impaired bone growth was caused by suppression of expression and/or protein levels of growth hormone receptor in the liver.

Strengths:

The experimental design of the study is sound and the results are in general of supportive of the conclusions.

Weaknesses:

The study lacks mechanistic investigation into how the deletion of a gene corresponding to a small cytoplasmic membrane protein would lead to substantial reduction in the gene expression of growth hormone receptor, which takes place in the nuclei. Accordingly, the manuscript is of largely descriptive nature.

Reviewer #1 (Public Review):

Summary<br /> Developing vaccination capable of inducing persistent antibody responses capable of broadly neutralizing HIV strains is of high importance. However, our ability to design vaccines to achieve this is limited by our relative lack of understanding of the role of T-follicular helper (Tfh) subtypes in the responses. In this report Verma et al investigate the effects of different prime and boost vaccination strategies to induce skewed Tfh responses and its relationship to antibody levels. They initially find that live-attenuated measles vaccine, known to be effective at inducing prolonged antibody responses has a significant minority of germinal center Tfh (GC-Tfh) with a Th1 phenotype (GC-Tfh1) and then explore whether a prime and boost vaccination strategy designed to induce GC-Tfh1 is effective in the context of anti-HIV vaccination. They demonstrate that a vaccine formulation referred to as MPLA induces higher GC-Tfh1 and link this to increased antibody production.

Strengths:<br /> While there is a lot of literature on Tfh subtypes in blood, how this related to the germinal centers is not always clear. The strength of this paper is that they use a relevant model to allow some longitudinal insight into the detailed events of the germinal center Tfh (GC-Tfh) compartment across time and how this related to antibody production.

Weaknesses:<br /> The authors focus strongly on the proportion of GC-Tfh1 of GC-Tfh. There seems to be an assumption that since the MPLA vaccine has a higher number of GC-Tfh1 that this explains the higher levels of antibodies. This is not an entirely unreasonable assumption but the mechanistic link between the two is never tested.

Reviewer #1 (Public Review):

The authors isolated a novel marine Planctomycetes bacterium with unique characteristics using a budding mode of division from the deep-sea cold seep sediment and named it Poriferisphaera heterotrophicis ZRK32. This work demonstrated that strain ZRK32 preferred nutrient-rich medium, moreover, the addition of nitrate or ammonia promoted the growth of strain ZRK32 and further caused the release of bacteriophage without killing the host. These results are interesting, well presented and documented in the revised manuscript.

Reviewer #1 (Public Review):

In this article, Vardakalis et al. propose a novel model of hippocampal oscillations whereby an external input (emulating the medial septum) can drive theta rhythms. This model displays phase-amplitude coupling of gamma oscillations, as well as theta resetting, which are known features of physiological theta that have been missing in previous models. The end goal proposed by the authors is to have a framework to explore the mechanisms of neurostimulation, which have shown promising applications in pathological conditions, but for which the underlying dynamics remain largely unknown. To reach this objective, the authors implement an existing biophysical model of the hippocampus that is able to generate gamma oscillations, and receives inputs from a set of Kuramoto oscillators to emulate theta drive originating from the medial septum.

Overall, the hypotheses and results are clearly presented and supported by high quality figures. The study is presented in a didactic way, making it easy for a broad audience to understand the significance of the results. The study does present some weaknesses that could easily be addressed by the authors. First, there are some anatomical inaccuracies: line 129 and fig1C, the authors omit medial septum projections to area CA1 (in addition to the entorhinal cortex). Moreover, in addition to CA1, CA3 also provides monosynaptic feedback projections to the medial septum CA3. Finally, an indirect projection from CA1/3 excitatory neurons to the lateral septum, which in turn sends inhibitory projections to the medial septum could be included or mentioned by the authors. This could be of particular relevance to support claims related to effects of neurostimulations, whereby minutious implementation of anatomical data could be key. If not updating their model, the authors could add this point to their limitation section, where they already do a good job of mentioning some limitations of using the EC as a sole oscillatory input to CA1. The authors test conditions of low theta inputs, which they liken to pathological states (line 112). It is not clear what pathology the authors are referring to, especially since a large amount of 'oscillopathies' in the septohippocampal system are associated with decreased gamma/PAC, but not theta oscillations (e.g. Alzheimer's disease conditions). While relevant for the clinical field, there is overall a missed opportunity to explain many experimental accounts with this novel model. Although to this day, clinical use of DBS is mostly restricted to electrical (and thus cell-type agnostic) stimulation, recent studies focusing on mechanisms of neurostimulations have manipulated specific subtypes in the medial septum and observed effects on hippocampal oscillations (e.g. see Muller & Remy, 2017 for review). Focusing stimulations in CA1 is of course relevant for clinical studies but testing mechanistic hypotheses by focusing stimulation on specific cell types could be highly informative. For instance, could the author reproduce recent optogenetic studies (e.g. Bender et al. 2015 for stimulation of fornix fibers; Etter et al., 2019 & Zutshi et al. 2018 for stimulation of septal inhibitory neurons)? Cell specific manipulations should at least be discussed by the authors.

Beyond these weaknesses, this study has a strong utility for researchers wanting to explore hypotheses in the field of neurostimulations. In particular, I see value in such models for exploring more intricate, phase specific effects of continuous, as well as close loop stimulations which are on the rise in systems neuroscience.

Reviewer #1 (Public Review):

In recent years, Auxin treatment is frequently used for inducing targeted protein degradation in Drosophila and various other organisms. This approach provides the way to acutely alter the levels of specific proteins. In this manuscript, the authors carefully examine the impact of Auxin treatment and provide strong evidence that Auxin treatment elicits alterations in feeding activity, survival rates, lipid metabolism, and gene expression patterns. Researchers need to be aware of these effects to design experiment/controls and interpret their data.

Strengths:<br /> Regarding widespread usage of Auxin mediated gene manipulation method, it is important to address whether the application of Auxin itself causes any physiological changes. Authors provide evidence of several Auxin effects on lipid metabolism, feeding behavior and gene expression changes. Experiments are suitably designed with appropriate sample size, data analysis methods.

Weaknesses:<br /> Data shown here are limited for certain method of treatment. No time course, dose dependency information is provided, and cell-type-specific responses are unknown. Therefore, this work basically provides the cautionary note for the field for researchers who use this method suggesting the importance that they should thoroughly check the gene expression pattern for their specific tissue of interest under their normal standard or altered food conditions.

Joint Public Review:

In this work, Xie et al. developed SCA-seq, which is a multiOME mapping method that can obtain chromatin accessibility, methylation, and 3D genome information at the same time. SCA-seq first uses M.CviPI DNA methyltransferase to treat chromatin, then perform proximity ligation followed by long-read sequencing. This method is highly relevant to a few previously reported long read sequencing technologies. Specifically, NanoNome, SMAC-seq, and Fiber-seq have been reported to use m6A or GpC methyltransferase accessibility to map open chromatin, or open chromatin together with CpG methylation; Pore-C and MC-3C have been reported to use long read sequencing to map multiplex chromatin interactions, or together with CpG methylation. Therefore, as a combination of NanoNome/SMAC-seq/Fiber-seq and Pore-C/MC-3C, SCA-seq is one step forward. The authors tested SCA-seq in 293T cells and performed benchmark analyses testing the performance of SCA-seq in generating each data module (open chromatin and 3D genome). The QC metrics appear to be good and I am convinced that this is a valuable addition to the toolsets of multi-OMIC long-read sequencing mapping.

Reviewer #1 (Public Review):

This research article by Watabe T and colleagues characterizes PKA waves triggered by prostaglandin E2 (PGE2). What the author discovered is that waves of PKA occur both in vitro, in MDCK epithelial monolayers, and in vivo, in the ear epidermis in mice. The PKA waves are the consequence PGE2 discharge, that in turn is triggered by Calcium bursts. Calcium level and ERK activity intensity control that mechanism by acting at different levels.<br /> This article is a technological tour de force using different biosensors and optogenetic actuators. However, what makes this article interesting is the ability of combining these tools together to dissect a complex signaling pathway at the single-cell level and with highly dynamic processes. For this reason, this paper represents the essence of modern cell biology and paves the way for the cell biology of the future.

However, we think that the paper in this stage is still partly descriptive in its nature, and more measurements are needed to increase the strength of the mechanistic insights. Here below the points that we believe that need some improvement.

1)Even though the phenomenon of PGE2 signal propagation is elegantly demonstrated and well described, the whole paper is mostly of descriptive nature - the PGE2 signal is propagated via intercellular communication and requires Ca transients as well as MAPK activity, however function of these RSPAs in dense epithelium is not taken into consideration.<br /> What is the function of these RSPAs in cellular crowding? - Does it promote cell survival or initiate apoptosis? Does it feed into epithelial reorganization during cellular crowding? Still something else? The authors discuss possible roles of this phenomenon in cell competition context, but show no experimental or statistical efforts to answer this question. I believe some additional analysis or simple experiment would help to shed some light on the functional aspect of RSPAs and increase the importance of all the elegant demonstrations and precise experimental setups that the manuscript is rich of. Monolayer experiments using some perturbations that challenge the steady state of epithelial homeostasis - drug treatments/ serum deprivation/ osmotic stress/ combined with live cell imaging and statistical methods that take into account local cell density might provide important answers to these questions. The authors could consider following some of these ideas to improve the overall value of the manuscript.

2) In the line 82-84 the authors claim: "We found that the pattern of cAMP concentration change is very similar to the activity change of PKA, indicating that a Gs protein-coupled receptor (GsPCR) mediates RSPA". In our opinion, this conclusion is not well-supported by the results. The authors should at least show that some measurement of the two patterns show correlation. Are the patterns of cAMP of the same size as the pattern of PKA? Do they have the same size depending on cell density? Do they occur at the same frequency as the PKA patterns, depending on the cell density? Do they have an all or nothing activation as PKA or their activation is shading with the distance from the source?

3) In general, the absolute radius of the waves is not a good measurement for single-cell biology studies, especially when comparing different densities or in vivo vs in vitro experiments. We suggest the authors to add the measurement of the number of the cells involved in the waves (or the radius expressed in number of cells).

4) In 6D, the authors should also show the single-cell trajectories to understand better the correlation between PKA and ERK peaks. Is the huger variability in ERK activity ratio dues to different peak time or different ERK activity levels in different cells? The authors should show both the variability in the time and intensity.

5) In lines 130-132, the authors write, "This observation indicates that the amount of PGE2 secretion is predetermined and that there is a threshold of the cytoplasmic calcium concentration for the triggered PGE2 secretion". How could the author exclude that the amount of PGE2 is not regulated in its intensity as well? For sure, there is a threshold effect regarding calcium, but this doesn't mean that PGE2 secretion can be further regulated, e.g. by further increasing calcium concentration or by other mechanisms.

6) The manuscript shows that not all calcium transients are followed by RSPAs. Does the local cell density/crowding increase the probability of overlap between calcium transients and RSPAs?

The revision of the Watabe T paper provides additional data and analyses in response to the reviewers' comments. On our side, we are satisfied by these improvements.<br /> In the answer to our first question, the authors claim that they did multiple experiments to understand the function of RSPA in MDCK cell, all providing negative results. The authors could consider publishing the negative results as well, as they can be useful for the community.

In sum, we are convinced of the value of this article, and we thank the authors for the work that has been done.

Reviewer #1 (Public Review):

Summary:<br /> Here, Boor et al focus on the regulation of daf-7 transcription in the ASJ chemosensory neurons, which has previously shown to be sensitive to a variety of external and internal signals. Interestingly, they find that soluble (but not volatile) signals released by food activate daf-7 expression in ASJ, but that this is counteracted by signals from the ASIC channels del-3 and del-7, previously shown to detect the ingestion of food in the pharynx. Importantly, the authors find that ASJ-derived daf-7 can promote exploration, suggesting a feedback loop that influences locomotor states to promote feeding behavior. They also implicate signals known to regulate exploratory behavior (the neuropeptide receptor PDFR-1 and the neuromodulator serotonin) in the regulation of daf-7 expression in ASJ. Additionally, they identify a novel role for a pathway previously implicated in C. elegans sensory behavior, HEN-1/SCD-2, in the regulation of daf-7 in ASJ, suggesting that the SCD-2 homolog ALK may have a conserved role in feeding and metabolism.

Strengths:<br /> The studies reported here, particularly the quantitation of gene expression and the careful behavioral analysis, are rigorously done and interpreted appropriately. The results suggest that, with respect to food, DAF-7 expression encodes a state of "unmet need" - the availability of nearby food to animals that are not currently eating. This is an interesting finding that reinforces and extends our understanding of the neurobiological significance of this important signaling pathway. The identification of a role for ASJ-derived daf-7 in motor behavior is a valuable advance, as is the finding that SCD-2 acts in the AIA interneurons to influence daf-7 expression in ASJ.

Weaknesses:<br /> A limitation of the work is that some mechanistic relationships between the identified signaling pathways remains unclear, but this provides interesting opportunities for future work. There are some minor concerns about the statistical analysis in the paper, but these are unlikely to affect the authors' interpretation of their results.

Reviewer #1 (Public Review):

The authors' aim was to test to what extent atypical organization of language is associated with a mirrored brain organization of other cognitive functions. In particular, they focused on the inferior frontal gyri (IFG) by studying the inhibitory control network. This allowed them to directly test support for the Causal hypothesis of hemispheric specialization, arguing for fast sequences of cognitive processes being better performed by a single hemisphere, versus the Statistical hypothesis of lateralization, postulating an independent lateralization of each cognitive function.

Previous studies on this topic did not focus on functions involving homotopic language regions. This limitation is bypassed in this study by assessing inhibition with a Stop-Signal Task which also engages the IFG in the contralateral site to the verb generation task. By studying a combination of structural and functional information, in addition to the activation contrasts, the authors are able to test whether atypical organization is accompanied by stronger interhemispheric connectivity. Although relying mainly on correlations and lacking important methodological information that may be critical to understand the reported effects, the results are quite straightforward. However the bilingual/monolingual status and gender of the participants is not reported which might affect the relationship between language and inhibitory control.

The conclusions of the paper are supported by the data. With their design, the authors observed that, as a group, individuals with atypical organization show a mirror organization of the whole inhibitory network to the contralateral site, supporting the Causal hypothesis at the group level. However, individual data support the Statistical hypothesis, since the segregation between language and inhibition was not observed in all individuals and a variety of configurations in bilateral and bilateral organisation of language and inhibition were also observed.

The results of this study have important implications for our understanding of the independence of different cognitive functions, which is crucial when addressing brain damage and rehabilitation. This aspect also indirectly speaks to researchers interested in evolution and in bilingualism and its relation to cognitive control. These aspects are not discussed but incorporating them would broaden the interest of the paper beyond the current implications mentioned.

Joint Public Review

In this study, Mitra and coworkers extend their previous analyses of the functional role of Orai in the excitability of central dopaminergic neurons in Drosophila. The authors show that a dominant-negative mutant of Orai (OraiE180A) significantly alters the gene expression profile of flight-promoting dopaminergic neurons (fpDANs), including that of Set2, E(z), and Trl, thereby shifting the level of epigenetic signatures that modulate gene expression. The Orai-Trl-Set2 pathway modulates the expression of voltage gated calcium channels, which, in turn, are involved in dopamine release. The study is generally well-done, is in-depth, and comprehensive. The finding that SOCE regulates a wide range of neuronal genes necessary for neuronal excitability and effector signaling by controlling chromatin remodeling genes is a noteworthy discovery.

The authors have adequately answered the previous concerns.

Joint Public Review:

Summary:

The existence of hox gene complexes conserved in animals with bilateral symmetry and in which the genes are arranged along the chromosome in the same order as the structures they specify along the anteroposterior axis of organisms is one of the most spectacular discoveries of recent developmental biology. In brief, homeotic mutations leads to the transformation of a given body segment of the fly into the copy of the next adjacent segment. For the sake of understanding the main observation of this work, it is important to know that in loss-of-function (LOF) alleles, a given segment develops like a copy of the segment immediately anterior to it, and in gain-of-function mutations (GOF), the affected segment develop like a copy of the immediately posterior segment. Over the last 30 years the molecular lesions associated with GOF alleles led to a model where the sequential activation of the hox genes along the chromosome result from the sequential opening of chromosomal domains. Most of these GOF alleles turned out to be deletions of boundary elements (BE) that define the extend of the segment-specific regulatory domains. The fruit fly Drosophila is a highly specialized insect with a very rapid mode of segmentation. Furthermore, the hox clusters in this lineage have split. Given these specificities it is legitimate to question whether the regulatory landscape of the BX-C we know of in D.melanogaster is the result of very high specialization in this lineage, or whether it reflects a more ancestral organization. In this article, the authors address this question by analyzing the continuous hox cluster in butterflies. They focus on the integenic region between the Antennapedia and the Ubx gene, where the split occurred in D.melanogaster. Hi-C and ATAC-seq data suggest the existence of a boundary element between 2 Topologically-Associated-Domain (TAD) which is also characterized by the presence of CTCF binding sites. Butterflies have 2 pairs of wings originating form T2 (forewing) specified by Antp and T3 specified by Ubx (hindwing). Remarkably, CRISPR mutational perturbation of this boundary leads to the hatching of butterflies with homeotic clones of cells with hindwings identities in the forewing (a posteriorly oriented homeotic transformation). In agreement with this phenotype, the authors observe ectopic expression of Ubx in these clones of cells. In other words, CRISPR mutagenesis of this BE region identified by molecular tool give rise to homeotic transformations directed towards more posterior segment as the boundary mutations that had been 1st identified on the basis of their posterior oriented homeotic transformation in Drosophila. None of the mutant clones they observed affect the hindwing, indicating that their scheme did not affect the nearby Ubx transcription unit. This is a reassuring and important 1st evidence that some of the regulatory paradigm that have been proposed in fruit flies are also at work in the common ancestor to Drosophilae and Lepideptora.

Given the large size of the Ubx transcription unit and its associated regulatory regions it is not surprising that the authors have identified ncRNA that are conserved in 4 species of Nymphalinae butterflies, some of which also present in D.melanogaster. Attempts to target the promoters by CRISPR give rise to clones of cells in both forewings and hindwings, suggesting the generation of regulatory mutations associated with both LOF and GOF transformations. The presence of clones with dual homeosis suggest the targeting of Ubx activator and repression CRMs. Unfortunately, these experiments do not allow us to make further conclusions on the role of these ncRNA or in the identification of specific regulatory elements. To the opinion of this referee, some recent papers addressing the role that these ncRNA may play into boundary function should be taken with caution, and evidences that ncRNA(s) regulate boundaries in the BX-C in a WT context are still lacking.

Strengths: the convincing GOF phenotype resulting from the targeting of the Antp-Ubx_BE

Weaknesses: the lack of comparisons with the equivalent phenotypes obtained in D.melanogaster with for example the Fub mutation

Reviewer #1 (Public Review):

In this manuscript, Butkovic et al. perform a genome-wide association (GWA) study on Arabidopsis thaliana inoculated with the natural pathogen turnip mosaic virus (TuMV) in laboratory conditions, with the aim to identify genetic associations with virus infection-related parameters. For this purpose, they use a large panel of A. thaliana inbred lines and two strains of TuMV, one naïve and one pre-adapted through experimental evolution. A strong association is found between a region in chromosome 2 (1.5 Mb) and the risk of systemic necrosis upon viral infection, although the causative gene remains to be pinpointed.

This project is a remarkable tour de force, but the conclusions that can be reached from the results obtained are unfortunately underwhelming. Some aspects of the work could be clarified, and presentation modified, to help the reader.

Reviewer #1 (Public Review):

Gametocytes are erythrocytic sexual stages of the malaria-causing parasite Plasmodium, and are essential for parasite transmission and reproduction in the mosquito vector. In this study, Murata et al investigated the mechanisms of gene regulation in female gametocytes in the rodent malaria model parasite Plasmodium berghei. According to current views, gene regulation in Plasmodium parasites is dominated by the family of AP2 transcription factors (TFs), such as the AP2-G TF, which drives sexual commitment. The same authors previously identified one AP2 TF, called AP2-FG, as an essential TF mediating differentiation of female gametocytes. Here, they identified a novel protein, called PFG (for partner of AP2-FG, also described as Fd2 in a recently published study), which cooperates with AP2-FG to regulate a subset of female gametocyte genes.

PFG was identified among AP2-G targets, but possesses no known DNA binding or other characterized domain. The authors show that PFG-knockout P. berghei parasites can form male and female gametocytes yet cannot transmit to mosquitoes, due to a defect in female gametocyte development. Using RNA-seq, they show that many female-specific genes are down-regulated in PFG(-)parasites. Chromatin immunoprecipitation combined with DNA sequencing (ChIP-seq) revealed that PFG colocalizes with AP2-FG on a ten-base motif that is enriched upstream of female-specific genes. Importantly, the ChIP-seq profile of PFG is unchanged in the absence of AP2-FG, suggesting that PFG binds to DNA independently of AP2-FG. Mutation of the ten-base motif in one target gene using CRISPR-Cas9 demonstrates that this motif is required for PFG localization at the gene locus. The data also show that binding of AP2-FG is affected in the absence of PFG, with disruption of AP2-FG interaction with the ten-base motif, but conservation of AP2-FG binding to distinct five-base motifs. Using a recombinant AP2 domain from AP2-FG, the authors demonstrate that the AP2 domain of AP2-FG binds to the five-base motifs. Using CRISPR they show that disruption of the five-base motifs in the genome abrogates AP2-FG binding, and using a reporter expression system they confirm that these motifs act as a cis-activating promoter element.

Through the analysis of target genes based on the presence of the ten- versus five-base motifs, the authors propose a model where AP2-FG can function in two forms, associated or not with PFG, and acting on the ten- or five-base motifs, respectively, to regulate distinct gene subsets during development of female gametocyte development.

The paper is well written, with a clear narrative, and the work is very well performed, relying on robust molecular approaches. Generally the conclusions and the model proposed by the authors are well supported by the data. Nevertheless, the study as it stands raises a number of questions. While the data convincingly show that PFG and AP2-FG cooperate to regulate the expression of a subset of female-specific genes, the paper does not show whether the two proteins actually interact with each other to form a complex. Also, how PFG binds to DNA and whether the protein has transactivating activity remains elusive, as the protein apparently possesses no known DNA-binding or activating domain. These points could be discussed in more detail in the manuscript and/or be the subject of follow up studies.

In summary, this work reveals the essential role of a Plasmodium protein with no known DNA binding or regulatory domain, illustrating that unknown facets remain to be uncovered in this fascinating pathogen.

Joint Public Review:

Xie et al. propose that the asymmetric segregation of the NuRD complex is regulated in a V-ATPase-dependent manner, and plays a crucial role in determining the differential expression of the apoptosis activator egl-1 and thus critical for the life/death fate decision.

While the model is very intriguing, the reviewers raised concerns regarding the rigor of the method. One issue is with statistics (either insufficient information or inadequate use of statistics), and second is the concern that the asymmetry observed may be caused by one cell dying (resulting in protein degradation, RNA degradation etc). We recommend that the authors address these issues.

Major #1:

There are still many misleading statements/conclusions that are not rigorously tested or that are logically flawed. These issues must be thoroughly addressed for this manuscript to be solid.

1. Asymmetry detected by scRNA seq vs. imaging may not represent the same phenomenon, thus should not be discussed as two supporting pieces of evidence for the authors' model, and importantly each method has its own flaw. First, for scRNA seq, when cells become already egl-1 positive, those cells may be already dying, and thus NuRD complex's transcripts' asymmetry may not have any significance. The data presented in FigS1D, E show that there are lots of genes (6487 out of 8624) that are decreased in dying cells. Thus, it is not convincing to claim that NuRD asymmetry is regulated by differential RNA amount.

2. Regarding NuRD protein's asymmetry, there are still multiple issues. Most likely explanation of their asymmetry is purely daughter size asymmetry. Because one cell is much bigger than the other (3 times larger), NuRD components, which are not chromatin associated, would be inherited to the bigger cell 3 times more than the smaller daughter. Then, upon nuclear envelope reformation, NuRD components will enter the nucleus, and there will be 3 times more NuRD components in the bigger daughter cell. It is possible that this is actually the underling mechanism to regulate gene expression differentially, but this possibility is not properly acknowledged. Currently, the authors use chromatin associated protein (Mys-1) as 'symmetric control', but this is not necessarily a fair comparison. For NuRD asymmetry to be meaningful, an example of protein is needed that is non-chromatin associated in mitosis, distributed to daughter cells proportional to daughter cell size, and re-enter nucleus after nuclear envelope formation to show symmetric distribution. And if daughter size asymmetry is the cause of NuRD asymmetry, other lineages that do not undergo apoptosis but exhibit daughter size asymmetry would also show NuRD asymmetry. The authors should comment on this (if such examples exist, it is fine in that in those cell types, NuRD asymmetry may be used for differential gene expression, not necessarily to induce cell death, but such comparison provides the explanation for NuRD asymmetry, and puts the authors finding in a better context).

3. For the analysis of protein asymmetry between two daughters in Fig S4C, the method of calibration is unclear, making it difficult to interpret the results.

4. As for pHluorin experiments, the authors were asked to test the changes in fluorescence observed are due to changes in pH or changes in the amount of pHluorin protein. They need to add a ratio-metric method in this manuscript. A brief mention to Page 12 line 12 is insufficient to clarify this issue.

Major #2:

Some issues surrounding statistics must be resolved.

1. Fig. 1FG, 2D, 3BDEG, 5BD and 6B used either one-sample t-test or unpaired two-tailed parametric t-test for statistical comparison. These t-tests require a verification of each sample fitting to a normal distribution. The authors need to describe a statistical test used to verify a normal distribution of each sample.

2. Fig. 2D, 3D, and 3G have very small sample size (N=3-4, N=6, N=3, respectively), it is possible that a normal distribution cannot be verified. How can the authors justify the use of one-sample t-test and unpaired parametric t-test ?

3. Statistical comparison in Fig. 2D and Fig. 6B should be re-assessed. For Fig. 2D, the authors need to compare the intensity ratio of HDA-1/LIN53 between sister cells dying within 35 min and those over 400 min. For Fig. 6B, they need to compare the intensity ratio of VHA-17 between DMSO- and BafA1- treated cells at the same time point after anaphase.

Sourcing? Look this up.<br /> https://www.a5-size.com/history/

Reviewer #1 (Public Review):

Huang C-K. and colleagues in this work address the understudied role of environmental conditions and external forces in cell extrusion as a fundamental part of epithelial homeostasis. They suggest that hydrostatic stress plays a significant role in counteracting cell extrusion forces through the indirect regulation of the focal adhesion kinase (FAK) - protein kinase B (AKT) survival pathway. The team nicely exploits their expertise in fabricating cell culture substrates to control hydrostatic stress on a common epithelial cell model from the kidney (i.e., MDCK). This was done by creating waving surfaces with different lengths from 50µm to 200 µm, thus creating a heterogenous distribution of monolayer forces towards the substrate. Finally, using a specific inhibitor for FAK, they suggest that the survivor pathway FAK-AKT is involved in the observed phenomenon.

In conclusion, the presented data underline the importance of considering external forces and tissue geometry in regulating epithelial homeostasis and the selective transport of water and solutes. These results may have a significant impact on understanding the basic mechanisms of epithelial physiology and pathology, such as in the kidney, intestine, or retina.

Comments on the revised version:

Overall, most of my comments were reasonably addressed. Nevertheless, one comment was not convincingly addressed ("Recommendation 5" - reviewer #1).

The authors did not show that the FAK inhibitor directly induced the reduction of AKT phosphorylation but used this experiment to conclude that FAK - AKT survivor pathway is involved in the observed phenomenon (Fig. 4). The authors mentioned that additional immunoblotting experiments are currently underway. This is a minor control for the manuscript message, but I feel it is necessary. The connection between the levels of FAK and p-AKT shown in Fig. 4E is purely correlative and can be caused by ECM adhesion-independent reasons.

Alternatively, the authors could reduce the stress on the FAK - AKT survivor pathway's involvement and conclude only on the involvement of FAK.

Reviewer #1 (Public Review):

The authors use a combination of structural and MD simulation approaches to characterize phospholipid interactions with the pentameric ligand-gated ion channel, GLIC. By analyzing the MD simulation data using clusters of closed and open states derived previously, the authors also seek to compare lipid interactions between putative functional states. The ultimate goal of this work is to understand how lipids shape the structure and function of this channel.

The strengths of this article include the following:

1) The MD simulation data provide extensive sampling of lipid interactions in GLIC, and these interactions were characterized in putative closed and open states of the channel. The extensive sampling permits confident delineation of 5-6 phospholipid interaction sites per subunit. The agreement in phospholipid binding poses between structures and the all-atom MD simulations supports the utility of MD simulations to examine lipid interactions.

2) The study presents phospholipid binding sites/poses that agree with functionally important lipid binding sites in other pLGICs, supporting the notion that these sites are conserved. For example, the authors identify interactions of POPC at an outer leaflet intersubunit site that is specific for the open state. This result is quite interesting as phospholipids or drugs that positively modulate other pLGICs are known to occupy this site. Also, the effect of mutating W217 in the inner leaflet intersubunit site suggests that this residue, which is highly conserved in pLGICs, is an important determinant of the strength of phospholipid interactions at this site. This residue has been shown to interact with phospholipids in other pLGICs and forms the binding site of potentiating neurosteroids in the GABA(A) receptor.

Comments on the revised version:

We appreciate the authors' thorough response and revisions.

Specifically, the authors address the issue of interaction times by providing measures of the diffusion coefficients and mean displacements of the lipids. These show that there is sufficient movement of lipids within the first shell to indicate that certain residues are forming binding interactions with lipids while others are not. Longer simulation times would be necessary to determine the strength of these interactions and how they may differ between different conformations.

Reviewer #1 (Public Review):

In this study, single neurons were recorded, using tetrodes, from the parahippocampal cortex of 5 rats navigating a double-Y maze (in which each arm of a Y-maze forks again). The goal was located at any one of the 4 branch terminations, and rats were given partial information in the form of a light cue that indicated whether the reward was on the right or left side of the maze. The second decision point was un-cued and the rat had no way of knowing which of the two branches was correct, so this phase of the task was more akin to foraging. Following the outbound journey, with or without reward, the rat had to return (inbound journey) to the maze start, to begin again.

Neuronal activity was assessed for correlations with multiple navigation-relevant variables including location, head direction, speed, reward side, and goal location. The main finding is that a high proportion of neurons showed an increase in firing rate when the animal made a wrong turn at the first branch point (the one in which the correct decision was signalled). This increase, which the authors call rate remapping, persisted throughout the inbound journey as well. It was also found that head direction neurons (assessed by recording in an open field arena) in the same location in the room were more likely to show the rate change. The overall conclusion is that "during goal-directed navigation, parahippocampal neurons encode error information reflective of an animal's behavioral performance" or are "nodes in the transmission of behaviorally relevant variables during goal-directed navigation."

Overall I think this is a well-conducted study investigating an important class of neural representation: namely, the substrate for spatial orientation and navigation. The analyses are very sophisticated - possibly a little too much so, as the basic findings are relatively straightforward and the analyses take quite a bit of work to understand. A difficulty with the study is that it was exploratory (observational) rather than hypothesis-driven. Thus, the findings reveal correlations in the data but do not allow us to infer causal relationships. That said, the observation of increased firing in a subset of neurons following an erroneous choice is potentially interesting. However, the effect seems small. What were the actual firing rate values in Hz, and what was the effect size?

I also feel we are lacking information about the underlying behavior that accompanies these firing rate effects. The authors say "one possibility is that the head-direction signal in the parahippocampal region reflects a behavioral state related to navigational choice or the lack of commitment to a particular navigational route" which is a good thought and raises the possibility that on error trials, rats are more uncertain and turn their heads more (vicarious trial and error) and thus sample the preferred firing direction more thoroughly. Another possibility is that they run more slowly, which is associated with a higher firing rate in these cells. I think we therefore need a better understanding of how behaviour differed between error trials in terms of running speed, directional sampling, etc. A few good, convincing raw-data plots showing a remapping neuron on an error trial and a correct trial on the same arm would also be helpful (the spike plots were too tiny to get a good sense of this: fewer, larger ones would be more helpful). It would be useful to know at what point the elevated response returned to baseline, how - was it when the next trial began, and was the drop gradual (suggesting perhaps a more neurohumoral response) or sudden?

Comments on the revised submission:

The authors have clarified a number of points arising from my original review but some remain.

On the issue of hypotheses: I was really referring, and apologies that I was unclear on this, to the hypothesis about the neural responses predicted in this experiment. The authors aimed to "examine whether spatial representations flexibly adapt to behaviorally relevant factors" but this is not really a hypothesis as such, in the true mechanistic sense so much as "let's see what we can find" which is not an invalid reason to do this type of study. However, no manipulations were made that test causal relationships arising from the study. It thus remains observational. It does however raise testable hypotheses which is valuable. The strongest in my mind is that the rise in firing rates is a catecholamine response to frustration, a conclusion supported by the slow temporal dynamics of the changes.

On the issue of running speed: it needs to be ruled out that this might have been the cause of the altered firing rates since running speeds were different. More generally, the lack of other concurrent behavioral data means we cannot rule out other possible behavioral bases to this effect that are unrelated to error but are related to the motor correlates of the error.

Reviewer #1 (Public Review):

The authors set out to determine the causal influence of the rIFG on stop-signal inhibition by using the innovative method of focused ultrasound to modulate this area during a stop-signal task. They report that tFUS during the stop signal only (and not the go) affected the probability of making a stop (only for long SSD) and reduced reaction time. tFUS also looked to affect some ERP components thus lending 'causal' evidence for the role of rIFG in stopping behavior and N200/P300 dynamics. The background and premise seem solid, the experimental design looks appropriate with good controls however, I do not think the authors' conclusions are supported. The methods are difficult to understand, and lack citations (background for performing these analyses/pre-processing) - some are listed but not in the reference list - but also leave out important methodology and detail. Despite the fact that there are many statistical tests in the results there are none for their main conclusions that the P300 latency indexes stop-signal inhibition - this is only descriptive. Individuals with expertise in the field of stop signal inhibition are encouraged to read this pre-print to gauge the veracity of the authors' conclusions and the appropriateness of their methodology.

Reviewer #1 (Public Review):

Summary:<br /> In their revised manuscript, the authors analyze the evolution of the gasdermin family and observe that the GSDMA proteins from birds, reptiles and amphibians does not form a clade with the mammalian GSDMAs. Moreover, the non-mammalian GSDMA proteins share a conserved caspase-1 cleavage motif at the predicted activation site. The authors provide several series of experiments showing that the non-mammalian GSDMA proteins can indeed be activated by caspase-1 and that this activation leads to cell death (in human cells). They also investigate the role of the caspase-1 recognition tetrapeptide for cleavage by caspase-1 and for the pathogen-derived protease SpeB.

Strengths:<br /> The evolutionary analysis performed in this manuscript appears to use a broader data basis than what has been used in other published work. An interesting result of this analysis is the suggestion that GSDMA is evolutionary older than the main mammalian pyroptotic GSDMD, and that birds, reptiles and amphibians lack GSDMD but use GSDMA for the same purpose. The consequence that bird GSDMA should be activated by an inflammatory caspase (=caspase1) is convincingly supported by the experiments provided in the manuscript.

Weaknesses:<br /> While the cleavability of bird/reptile GSDMA by caspase-1 is well-supported by several experiments, the role of this cleavage for pyroptotic cell killing is addressed more superficially. The experiments performed to this end all use human cells; it is likely - but not guaranteed - that the human model recapitulaes the physiological role of non-mammalian GSDMA proteins. While the data provided in this paper help to understand GSDMA evolution and the activation mechanism of bird/reptile GSDMA, it does not address the still elusive activation mechanism for mammalian GSDMA

As a consequence, the significance of this finding is mostly limited to birds and reptiles.

Reviewer #1 (Public Review):

Their absolute quantification PCR results with the sumo reference gene led the authors to conclude that A. flavus has two copies of tor and tapA in its genome. However, the the genomic location of the additional copies of tor and tapA are unknown.

I have concerns about the conclusion for the following reasons:

First, the authors should provide more convincing data showing that tor and tapA genes are indeed duplicated genes in A. flavus. The authors appeared to use the A. flavus PTS strain as a parental strain for constructing the tor and tapA mutants. If so, the A. flavus CA14 strain (Hua et al., 2007) should be the parental wild-type strain for the A. flavus PTS strain. I did a BLAST search in NCBI for the torA (AFLA_044350) and tapA (AFLA_092770) genes using the most recent CA14 genome assembly sequence (GCA_014784225.2) and only found one allele for each gene: torA on chromosome 7 and tapA on chromosome 3. I could not find any other parts with similar sequences. Even in another popular A. flavus wild-type strain, NRRL3357, both torA and tapA exist as a single allele. Based on the published genome assembly data for A. flavus, there is no evidence to support the idea that tor and tapA exist as copies of each other. Therefore, the authors could perform a Southern blot analysis to further verify their claim. If torA and tapA indeed exist as duplicate copies in different chromosomal locations, Southern blot data could provide supporting results.

If the tor and tapA genes indeed exist as dual copies, do the duplicate genes have identical DNA and protein sequences? If they have different DNA or protein sequences, they should be named differently as paralogs, such as torA and torB or tapA and tapB.

Second, the authors should consider the possibility of aneuploidy for their constructed mutants. When an essential gene is targeted for deletion, aneuploidy often occurs even in a fungal strain without the "ku" mutation, which results in seemingly dual copies of the gene. As the authors appear to use the A. flavus PTS strain having the "ku" mutation, the parental strain has increased genome instability, which may result in enhanced chromosomal rearrangements. So, it will be necessary to Illumina-sequence their tor and tapA mutants to make sure that they are not aneuploidy.

Furthermore, the genetic nomenclature +/- and -/- should be reserved for heterozygous and homozygous mutants in a diploid strain. As A. flavus is not a diploid strain, this type of description could cause confusion for the readers.

Reviewer #1 (Public Review):

Summary:<br /> The preprint by Laganowsky and co-workers describes the use of mutant cycles to dissect the thermodynamic profile of specific lipid recognition by the ABC transporter MsbA. The authors use native mass spectrometry with a variable temperature source to monitor lipid binding to the native protein dimer solubilized in detergent. Analysis of the peak intensities (that is, relative abundance) of 1-3 bound lipids as a function of solution temperature and lipid concentration yields temperature-dependent Kds. The authors use these to then generate van't Hoff plots, from which they calculate the enthalpy and entropy contributions to binding of one, two, and in some cases, three lipids to MsbA. The authors have previously demonstrated that MS can indeed extract thermodynamic contributions to lipid binding. The authors then employ mutant cycles, in which basic residues involved in headgroup binding are mutated to alanine. By comparing the thermodynamic signatures of single and double (and in one instance triple) mutants, they aim to identify cooperativity between the different positions. They furthermore use inward and outward locking conditions which should control access to the different binding sites determined previously. The main conclusion is that lipid binding to MsbA is driven mainly by energetically favorable entropy increase upon binding, which stems from the release of ordered water molecules that normally coordinate the basic residues, which helps to overcome the enthalpic barrier of lipid binding. The authors also report an increase in lipid binding at higher temperatures which they attribute to a non-uniform heat capacity of the protein. Although they find that most residue pairs display some degree of cooperativity, particularly between the inner and outer lipid binding sites, they do not provide a structural interpretation of these results.

Strengths:<br /> The use of double mutant cycles and mass spectrometry to dissect lipid binding is novel and interesting. For example, the observation that mutating a basic residue in the inner and one in the outer binding site abolishes lipid binding to a greater extent than the individual mutations is highly informative even without having to break it down into thermodynamic terms. The method and data reported here opens new avenues for the structure/activity relationship of MsbA. The "mutant cycle" approach is in principle widely applicable to other membrane proteins with complex lipid interactions.

Weaknesses:<br /> The use of double mutant cycles to dissect binding energies is well-established, and has, as the authors point out, been employed in combination with mass spectrometry to study protein-protein interactions. Its application to extract thermodynamic parameters is robust in cases where a single binding event is monitored, e.g. the formation of a complex with well-defined stoichiometry, where dissociation constants can be determined with high confidence. It is, however, complicated significantly by the fact that for MsbA-lipid interactions, we are not looking at a single binding event, but a stochastic distribution of lipids across different sites. Even if the protein is locked in a specific conformation, the observation of a single lipid adduct does not guarantee that the one lipid is always bound to a specific site. The authors discuss this issue in the manuscript. As they point out, one can assume that the most high-affinity sites will be populated first. Hence, the Kd values determined by MS likely describe (mostly) lipid binding to these sites, although this does not seem to hold universally true, as seen for example for the two (in principle equivalent) binding sites in the vanadate-locked protein. In addition, mutation of a binding site (which the authors show reduces lipid binding) may instead allow the lipid to bind to a lower-affinity site elsewhere. In summary, the Kds are an approximation.<br /> (Minor comment: The protein concentrations used for MS titration experiments should be stated in the methods.)

The authors conclude that solvation entropy is a major factor driving lipid binding (Figure 6). If the increase in entropy upon lipid binding comes from the release of ordered water molecules around the basic residues, we should see a smaller increase in entropy for proteins where several basic residues have been changed to alanine, which is not the case. The authors explain this by stating that other entropic factors likely are at play. Judging from their data, that is certainly correct, but why then focus on solvation entropy in the discussion if its contribution to the total entropy change cannot be determined?

Joint Public Review:

Bacteria exhibit species-specific numbers and localization patterns of flagella. How specificity in number and pattern is achieved in Gamma-proteobacteria needs to be better understood but often depends on a soluble GTPase called FlhF. Here, the authors take an unbiased protein-pulldown approach with FlhF, resulting in identifying the protein FipA in V. parahaemolyticus. They convincingly demonstrate that FipA interacts genetically and biochemically with previously known spatial regulators HubP and FlhF. FipA is a membrane protein with a cytoplasmic DUF2802; it co-localizes to the flagellated pole with HubP and FlhF. The DUF2802 mediates the interaction between FipA and FlhF, and this interaction is required for FipA function. Altogether, the authors show that FipA likely facilitates the recruitment of FlhF to the membrane at the cell pole together with the known recruitment factor HupB. This finding is crucial in understanding the mechanism of polar localization. The authors show that FipA co-occurs with FlhF in the genomes of bacteria with polarly-localized flagella and study the role of FipA in three of these organisms: V. parahaemolyticus, S. purtefaciens, and P. putida. In each case, they show that FipA contributes to FlhF polar localization, flagellar assembly, flagellar patterning, and motility, though the details differ among the species. By comparing the role of FipA in polar flagellum assembly in three different species, they discover that, while FipA is required in all three systems, evolution has brought different nuances that open avenues for further discoveries.<br /> <br /> Strengths:

The discovery of a novel factor for polar flagellum development. The solid nature and flow of the experimental work.

The authors perform a comprehensive analysis of FipA, including phenotyping of mutants, protein localization, localization dependence, and domains of FipA necessary for each. Moreover, they perform a time-series analysis indicating that FipA localizes to the cell pole likely before, or at least coincident with, flagellar assembly. They also show that the role of FipA appears to differ between organisms in detail, but the overarching idea that it is a flagellar assembly/localization factor remains convincing.

The work is well-executed, relying on bacterial genetics, cell biology, and protein interaction studies. The analysis is deep, beginning with discovering a new and conserved factor, then the molecular dissection of the protein, and finally, probing localization and interaction determinants. Finally, the authors show that these determinants are important for function; they perform these studies in parallel in three model systems.

Weaknesses:

The comparative analysis in the different organisms was on balance, a weakness. Mixing the data for the organisms together made the text difficult to read and took away key points from the results. The individual details crowded out the model in its current form. Indeed, because some of the phenotypes and localization dependencies differ between model systems, the comparison is challenging to the reader. The authors could more clearly state what these differences mean, why they arise, and (in the discussion) how they might relate to the organism's lifestyle. 

More experiments would be needed to fully analyze the effects of interacting proteins on individual protein stability; this absence slightly detracted from the conclusions.

Reviewer #1 (Public Review):

This study delineates an important set of uninjured and injured periosteal snRNAseq data that provides an overview of periosteal cell responses to fracture healing. The authors also took additional steps to validate some of the findings using immunohistochemistry and transplantation assays. This study will provide a valuable publicly accessible dataset to reexamine the expression of the reported periosteal stem and progenitor cell markers.

Strengths:<br /> 1. This is the first single-nuclei atlas of periosteal cells that are obtained without enzymatic cell dissociation or targeted cell purification by FACS. This integrated snRNAseq dataset will provide additional opportunities for the community to revisit the expression of many periosteal cell markers that have been reported to date.

2. The authors delved further into the dataset using cutting-edge algorithms, including CytoTrace, SCENIC, Monocle, STRING, and CellChat, to define the potential roles of identified cell populations in the context of fracture healing. These additional computation analyses generate many new hypotheses regarding periosteal cell reactions.

3. The authors also sought to validate some of the computational findings using immunohistochemistry and transplantation assays to support the conclusion.

Weaknesses:<br /> 1. The current snRNAseq datasets contain only a small number of nuclei (1,189 nuclei at day 0, 6,213 nuclei on day 0-7 combined). It is unclear if the number is sufficient to discern subtle biological processes such as stem cell differentiation.

2. The authors' designation of Sca1+CD34+ cells as SSPCs is not sufficiently supported by experimental evidence. It will be essential to demonstrate stem/progenitor properties of Sca1+CD34+ cells using independent biological approaches such as CFU-F assays. In addition, the putative lineage trajectory of SSPCs toward IIFCs, osteoblasts, and chondrocytes remains highly speculative without concrete supporting data.

3. The designation of POSTN+ clusters as injury-induced fibrogenic cells (IIFCs) is not fully supported by the presented data. The authors' snRNAseq datasets (Figure 1d) demonstrate that there are many POSTN+ cells prior to injury, indicating that POSTN+ cells are not specifically induced in response to injury. It has been widely recognized that POSTN is expressed in the periosteum without fracture. This raises a possibility that the main responder of fracture healing is POSTN+ cells, not SSPCs as they postulate. The authors cannot exclude the possibility that Sca1+CD34+ cells are mere bystanders and do not participate in fracture healing.

4. Detailed spatial organization of Sca1+CD34+ cells and POSTN+ cells in the uninjured periosteum with respect to the cambium layer and the fibrous layer is not demonstrated.

5. Interpretation of transplantation experiments in Figure 5 is not straightforward, as the authors did not demonstrate the purity of Prx1Cre-GFP+SCA1+ cells and Prx1Cre-GFP+CD146- cells to pSSPCs and IIFCs, respectively. It is possible that these populations contain much broader cell types beyond SSPCs or IIFCs.

Reviewer #1 (Public Review):

In this manuscript Rubin and Aso provide important new tools for the study of learning and memory in Drosophila. In flies, olfactory learning and memory occurs at the Mushroom Body (MB) and is communicated to the rest of the brain through Mushroom Body Output Neurons (MBONs). Previously, typical MBONs were thoroughly studied. Here, atypical MBONs that have dendritic input both within the MB lobes and in adjacent brain regions are studied. The authors describe new cell-type-specific GAL4 drivers for the majority of atypical MBONs (and other MBONs) and using an optogenetic activation screen they examined their ability to drive behaviors and learning.

The experiments in this manuscript were carefully performed and the results are clear. The tools provided in this manuscript are of great importance to the field.

Reviewer #1 (Public Review):

Summary:<br /> The manuscript "Drosophila Visuomotor Integration: An Integrative Model and Behavioral Evidence of Visual Efference Copy" provides an integrative model of the visuomotor control in Drosophila melanogaster. This model presents an experimentally derived model based on visually evoked wingbeat pattern recordings of three strategically selected visual stimulus types with well-established behavioral response characteristics. By testing variations of these models, the authors demonstrate that the virtual model behavior can recapitulate the recorded wing beat behavioral results and those recorded by others for these specific stimuli when presented individually. Yet, the novelty of this study and their model is that it allows predictions for natural visual scenes in which multiple visual stimuli occur simultaneously and may have opposite or enhancing effects on behavior. Testing three models that would allow interactions of these visual modalities, the authors show that using a visual efference copy signal allows visual streams to interact, replicating behavior recorded when multiple stimuli are presented simultaneously. Importantly, they validated the prediction of this model in real flies using magnetically tethered flies, e.g., presenting moving bars with varying backgrounds. In conclusion, the presented manuscript presents a commendable effort in developing and demonstrating the validity of a mixture model that allows predictions of the behavior of Drosophila in natural visual environments.

Strengths:<br /> Overall, the manuscript is well-structured and clear in its presentation, and the modeling and experimental research are methodically conducted and illustrated in visually appealing and easy-to-understand figures and their captions.

The manuscript employs a thorough, logical approach, combining computational modeling with experimental behavioral validation using magnetically tethered flies. This iterative integration of simulation and empirical behavioral evidence enhances the credibility of the findings.

The associated code base is well documented and readily produces all figures in the document.

Suggestions:<br /> However, while the experiments provide evidence for the use of a visual efference copy, the manuscript would be even more impressive if it presented specific predictions for the neural implementation or even neurophysiological data to support this model. Or, at the very least, a thorough discussion. Nonetheless, these models and validating behavioral experiments make this a valuable contribution to the field; it is well executed and addresses a significant gap in the modeling of fly behavior and holistic understanding of visuomotor behaviors.

Here are a few points that should be addressed:<br /> 1. The biomechanics block (Figure 2) should be elaborated on, to explain its relevance to behavior and relation to the underlying neural mechanisms.<br /> 2. It is unclear how the three integrative models with different strategies were chosen or what relevance they have to neural implementation. This should be explained and/or addressed.<br /> 3. There should be a discussion of how the visual efference could be represented in the biological model and an evaluation of the plausibility and alternatives.

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Reviewer #1 (Public Review):

The proposed study provides an innovative framework for the identification of muscle synergies taking into account their task relevance. State-of-the-art techniques for extracting muscle interactions use unsupervised machine-learning algorithms applied to the envelopes of the electromyographic signals without taking into account the information related to the task being performed. In this work, the authors suggest to include the task parameters in extracting muscle synergies using a network information framework previously proposed. This allows the identification of muscle interactions that are relevant, irrelevant, or redundant to the parameters of the task executed.

The proposed framework is a powerful tool to understand and identify muscle interactions for specific task parameters and it may be used to improve man-machine interfaces for the control of prostheses and robotic exoskeletons.

With respect to the network information framework recently published, this work added an important part to estimate the relevance of specific muscle interactions to the parameters of the task executed.

It is not clear how the well-known phenomenon of cross-talk during the recording of electromyographic muscle activity may affect the performance of the proposed technique and how it may bias the overall outcomes of the framework.

Reviewer #1 (Public Review):

Gap junction channels establish gated intercellular conduits that allow the diffusion of solutes between two cells. Hexameric connexin26 (Cx26) hemichannels are closed under basal conditions and open in response to CO2. In contrast, when forming a dodecameric gap-junction, channels are open under basal conditions and close with increased CO2 levels. Previous experiments have implicated Cx26 residue K125 in the gating mechanism by CO2, which is thought to become carbamylated by CO2. Carbamylation is a labile post-translational modification that confers negative charge to the K125 side chain. How the introduction of a negative charge at K125 causes a change in gating is unclear, but it has been proposed that carbamylated K125 forms a salt bridge with the side chain at R104, causing a conformational change in the channel. It is also unclear how overall gating is controlled by changes in CO2, since there is significant variability between structures of gap-junction channels and the cytoplasmic domain is generally poorly resolved. Structures of WT Cx26 gap-junction channels determined in the presence of various concentrations of CO2 have suggested that the cytoplasmatic N-terminus changes conformation depending on the concentration of the gas, occluding the pore when CO2 levels are high.

In the present manuscript, Deborah H. Brotherton and collaborators use an intercellular dye-transfer assay to show that Cx26 gap-junction channels containing the K125E mutation, which mimics carbamylation caused by CO2, is constitutively closed even at CO2 concentrations where WT channels are open. Several cryo-EM structures of WT and mutant Cx26 gap junction channels were determined at various conditions and using classification procedures that extracted more than one structural class from some of the datasets. Together, the features on each of the different structures are generally consistent with previously obtained structures at different CO2 concentrations and support the mechanism that is proposed in the manuscript. The most populated class for K125E channels determined at high CO2 shows a pore that is constricted by the N-terminus, and a cytoplasmic region that was better resolved than in WT channels, suggesting increased stability. The K125E structure closely resembles one of the two major classes obtained for WT channels at high CO2. These findings support the hypothesis that the K125E mutation biases channels towards the closed state, while WT channels are in an equilibrium between open and closed states even in the presence of high CO2. Consistently, a structure of K125E obtained in the absence of CO2 appeared to also represent a closed state but at lower resolution, suggesting that CO2 has other effects on the channel beyond carbamylation of K125 that also contribute to stabilizing the closed state. Structures determined for K125R channels, which are constitutively open because arginine cannot be carbamylated, and would be predicted to represent open states, yielded apparently inconclusive results.

A non-protein density was found to be trapped inside the pore in all structures obtained using both DDM and LMNG detergents, suggesting that the density represents a lipid rather than a detergent molecule. It is thought that the lipid could contribute to the process of gating, but this remains speculative. The cytoplasmic region in the tentatively closed structural class of the WT channel obtained using LMNG was better resolved. An additional portion of the cytoplasmic face could be resolved by focusing classification on a single subunit, which had a conformation that resembled the AlphaFold prediction. However, this single-subunit conformation was incompatible with a C6-symmetric arrangement. Together, the results suggest that the identified states of the channel represent open states and closed states resulting from interaction with CO2. Therefore, the observed conformational changes illuminate a possible structural mechanism for channel gating in response to CO2.

Some of the discussion involving comparisons with structures of other gap junction channels are relatively hard to follow as currently written, especially for a general readership. Also, no additional functional experiments are carried out to test any of the hypotheses arising from the data. However, structures were determined in multiple conditions, with results that were consistent with the main hypothesis of the manuscript. No discussion is provided, even if speculative, to explain the difference in behavior between hemichannels and gap junction channels. Also, no attempt was made to measure the dimensions of the pore, which is relevant because of the importance of identifying if the structures indeed represent open or closed states of the channel.

Reviewer #1 (Public Review):

Summary:<br /> This study identifies a family of solute transports in the enteric protist, Blastocystis, that may mediate the transport of glycolytic intermediates across the mitochondrial membrane. The study builds on previous observations suggesting that Blastocystis (and other Stramenopiles) are unusual in having a compartmentalized glycolytic pathway with enzymes involved in upper and lower glycolysis being located in the cytosol and mitochondria, respectively. In this study, the authors identified two putative Stamenopile metabolite transporters that are related to plant di/tricarboxylic acid transporters that might mediate the transport of glycolytic intermediates across the mitochondrial membrane. These GIC-transporters were localized to the Blastocystis mitochondrion using specific rabbit antibodies and shown to bind several glycolytic intermediates (including GAP, DHAP, and PEP) based on thermostability shift assays. Direct evidence for transport activity was obtained by reconstituting native proteins in proteoliposomes and measuring the uptake of 14C-malate or 35S-sulphate against unlabelled substrates. This assay showed that GIC-2 transported DHAP, GAP, and PEP. However, significant transport activity was not observed for bGIC-2. Overall, the study provides strong, but not conclusive evidence that bGIC-1 is involved in transporting glycolytic intermediates across the inner membrane of the mitochondria, while the function of GIC-2 remains unclear, despite exhibiting the same metabolite binding properties as bGIC-2 in thermostability assays.

Strengths:<br /> Overall, the findings are of interest in the context of understanding the diversity of core metabolic pathways in evolutionarily diverse eukaryotes, as well as the process by which cytosolic glycolysis evolved in most eukaryotes. The experiments are carefully performed and clearly described.

Weaknesses:<br /> The main weakness of the study is the lack of direct evidence that either bGIC-1 and/or bGIC2 are active in vivo. While it is appreciated that the genetic tools for disrupting GIC genes in Blastocystis are limited/lacking, are there opportunities to ectopically express or delete these genes in other Stamenopiles, such as Phaeodactylum triconuteum, to demonstrate function in vivo?

The authors demonstrate that both bGIC-1 and bGIC-2 are targeted to the mitochondrion, based on immunofluorescence studies. However, the precise localization and topology of these carriers in the inner or outer membrane are not defined. The conclusions of the study would be strengthened if the authors could show that one/both transporters are present in the inner membrane using protease protection experiments following differential solubilization of the outer and inner mitochondrial membranes.

It is not clear why hetero-exchange reactions were not performed for bGIC-1 (only for bGIC-2).

The summary slide depicted in Fig 7 is somewhat simplified and inaccurate. First, the authors show that TPI is located in the mitochondria in this study, while in the summary figure, TPI is shown to be present in both the cytosol and mitochondrial matrix. A cytosolic localization for TPI provides a functional rationale for having a triose-P carrier in the inner membrane - however, this is not supported by the data shown here. Second, if bGIC1/2 uses PEP as a counter ion to import GA3P and DHAP into the mitochondrion, as proposed in Fig 7, the lower glycolytic pathway would be effectively truncated at PEP, removing substrate for pyruvate kinase and formation of pyruvate/ATP. Third, the authors suggest that DHAP may have other functions in the mitochondria although these are not shown in the figure.

Reviewer #1 (Public Review):

Summary:<br /> In this study, Yan et al. investigate the molecular bases underlying mating type recognition in Tetrahymena thermophila. This model protist possesses a total of 7 mating types/sexes and mating occurs only between individuals expressing different mating types. The authors aimed to characterize the function of mating type proteins (MTA and MTB) in the process of self- and non-self recognition, using a combination of elegant phenotypic assays, protein studies, and imaging. They showed that the presence of MTA and MTB in the same cell is required for the expression of concavalin-A receptors and for tip transformation - two processes that are characteristic of the costimulation phase that precedes cell fusion. Using protein studies, the authors identify a set of additional proteins of varied functions that interact with MTA and MTB and are likely responsible for the downstream signaling processes required for mating. This is a description of a fascinating self- and non-self-recognition system and, as the authors point out, it is a rare example of a system with numerous mating types/sexes. This work opens the door for the further understanding of the molecular bases and evolution of these complex recognition systems within and outside protists.

The results shown in this study point to the unequivocal requirement of MTA and MTB proteins for mating. Nevertheless, some of the conclusions regarding the mode of functioning of these proteins are not fully supported and require additional investigation.

Strengths:<br /> 1. The authors have established a set of very useful knock-out and reporter lines for MT proteins and extensively used them in sophisticated and well-designed phenotypic assays that allowed them to test the role of these proteins in vivo.

2. Despite their apparent low abundance, the authors took advantage of a varied set of protein isolation and characterization techniques to pinpoint the localization of MT proteins to the cell membrane, and their interaction with multiple other proteins that could be downstream effectors. This opens the door for the future characterization of these proteins and further elucidation of the mating type recognition cascade.

Weaknesses:<br /> The manuscript is structured and written in a very clear and easy-to-follow manner. However, several conclusions and discussion points fall short of highlighting possible models and mechanisms through which MT proteins control mating type recognition:

1. The authors dismiss the possibility of a "simple receptor-ligand system", even though the data does not exclude this possibility. The model presented in Figure 2 S1, and on which the authors based their hypothesis, assumes the independence of MTA and MTB proteins in the generation of the intracellular cascade. However, the results presented in Figure 2 show that both proteins are required to be active in the same cell. Coupled with the fact that MTA and MTB proteins interact, this is compatible with a model where MTA would be a ligand and MTB a receptor (or vice-versa), and could thus form a receptor-ligand complex that could potentially be activated by a non-cognate MTA-MTB receptor-ligand complex, leading to an intracellular cascade mediated by the identified MRC proteins. As it stands, it is not clear what is the proposed working model, and it would be very beneficial for the reader for this to be clarified by having the point of view of the authors on this or other types of models.

2. The presence of MTA/MTB proteins is required for costimulation (Figure 2), and supplementation with non-cognate extracellular fragments of these proteins (MTAxc, or MTBxc) is a positive stimulator of pairing. However, alone, these fragments do not have the ability to induce costimulation (Figure 5). Based on the results in Figures 5 and 6 the authors suggest that MT proteins mediate both self and non-self recognition. Why do MTAxc and MTBxc not induce costimulation alone? Are any other components required? How to reconcile this with the results of Figure 2? A more in-depth interpretation of these results would be very helpful, since these questions remain unanswered, making it difficult for the reader to extract a clear hypothesis on how MT proteins mediate self- and non-self-recognition.

Reviewer #1 (Public Review):

Summary:<br /> Fita-Torró et al. study the toxic effects of the intermediary lipid degradation product trans-2-hexadecenal (t-2-hex) on yeast mitochondria and suggest a mechanism by which Hfd1 safeguards Tom40 from lipidation by t-2-hex and its consequences, such as mitochondrial protein import inhibition, cellular proteostasis deregulation, and stress-responses.<br /> The authors aimed to dissect a mechanism for t-2-hex' apoptotic consequences in yeast and they suggest it is via lipidation of Tom40 but really under the tested conditions everything seems lipidated. Thus, it is unclear whether Tom40 is the crucial causal target. They also do not provide much biochemical experiments to investigate this phenomenon further functionally. Tom40 is one possible and perhaps, given the cellular consequences, a reasonable candidate but not validated beyond in vitro lipidation by exogenous t-2-hex.

Strengths:<br /> The effects of lipids and their metabolic intermediates on protein function are understudied thus the authors' research contributing to elucidating direct effects of a single lipid is appreciated. It is particularly unknown by which mechanism t-2-hex causes cell death in yeast. The authors elegantly use modulation of the levels of enzyme Hfd1 that endogenously catabolizes t-2-hex as an approach to studying t-2-hex stress. Understanding the cause and consequences of this stress is relevant for understanding fundamental regulation mechanisms, and also to human health since the human homolog of Hfd1, ALDH3A2, is mutated in Sjögren-Larsson Syndrome. The application of a variety of global transcriptomic, functional genomic, and chemoproteomic approaches to study t-2-hex stress targets in the yeast model is laudable.

Weaknesses:<br /> - The extent of the contribution of Tom40 lipidation to the general t-2-hex stress phenotype is unclear. Is Tom40 lipidation alone enough to cause the phenotype? An alteration of the cysteine residue in question could help answer this key question.<br /> - It is unclear whether the exogenously applied amounts of t-2-hex (concentrations chosen between 25-200 uM) are physiologically relevant in yeast cells. For comparison, Chipuk et al. (2012) used at most 1 uM on mitochondria of human cells, while Jarugumilli et al. (2018) considered 25 uM a 'lower dose' on human cells. Since the authors saw responses below 10 uM (Fig. 3B) and at the lowest selected concentration of 25 uM (Fig. 8), why were no lower, likely more specific, concentrations applied for the global transcriptomic and chemoproteomic experiments? Key experiments have to be repeated with the lower concentrations.<br /> - The amount of t-2-hex applied is especially important to consider in light of over 1300 proteins lipidated to an extent equal to or greater than Tom40 (Supp. Table 6). This chemoproteomic experiment (Fig. 8B, Supp. Table 6) is also weakened by the inclusion of only 2 replicates, thus precluding assessment of statistical significance. The selection of targets in Fig. 8B as "among the best hits" is neither immediately comprehensible nor further explained and represents at best cherry-picking. Further evidence based on statistical significance or validation by other means should be provided.<br /> - The authors unfortunately also underuse the possible contribution of mass spectrometry technology to in addition determine the extent and localization of lipidation on a global scale (especially relevant since Cohen et al. (2020) suggest site-specific mechanisms).<br /> - The general novelty of studying t-2-hex stress is lowered in light of existing literature in humans (see e. g. Chipuk et al., 2012; Cohen et al., 2020; Jarugumilli et al., 2018), and in yeast by the same authors (Manzanares-Estreder et al., 2017) and as the authors comment themselves, a significant part of the manuscript may represent rather a confirmation of the already described consequences of t-2-hex stress

Reviewer #1 (Public Review):

Weber et al. investigated the role of human DDX6 in messenger RNA decay using CRISPR/Cas9 mediated knockout (KO) HEK293T cells. The authors showed that stretches of rare codons or codons known to cause ribosome stalling in reporter mRNAs leads to a DDX6 specific loss of mRNA decay. The authors moved on to show that there is a physical interaction between DDX6 and the ribosome. Using co-immunoprecipitation (co-IP) experiments, the authors determined that the FDF-binding surface of DDX6 is necessary for binding to the ribosome, the same domain which is necessary for binding several decapping factors such as EDC3, LSM14A, and PatL. However, they determine the interaction between DDX6, and the ribosome is independent of the DDX6 interaction with the NOT1 subunit of the CCR4-NOT complex. Interestingly, the authors were able to determine that all known functional domains, including the ATPase activity of DDX6, are required for its effect on mRNA decay. Using ribosome profiling and RNA-sequencing, the authors were able to identify a group of 260 mRNAs that exhibit increased translational efficiency (TE) in DDX6 Knockout cells, suggesting that DDX6 translationally represses certain mRNAs. The authors determined this group of mRNAs has decreased GC content, which has been previously noted to coincide with low codon optimality, the authors thus conclude DDX6 may translationally repress transcripts of low codon optimality. Furthermore, the authors identify 35 transcripts that are both upregulated in DDX6 KO cells and exhibit locally increased ribosome footprints (RBFs), suggestive of a ribosome stalling sequence. Lastly, the authors showed that both endogenous and tethering of DDX6 to reporter mRNAs with and without these translational stalling sequences leads to a relative increase in ribosome association to a transcript. Overall, this work confirms that the role of DDX6 in mRNA decay shares several conserved features with the yeast homolog Dhh1. Dhh1 is known to bind slow-moving ribosomes and lead to the differential decay of non-optimal mRNA transcripts (Radhakrishnan et al. 2016). The novelty of this work lies primarily in the identification of the physical interaction between DDX6 and the ribosome and the breakdown of which domains of DDX6 are necessary for this interaction. This work provides major insight into the role of the human DDX6 in the process of mRNA decay and emphasizes the evolutionary conservation of this process across Eukaryotes.<br /> Strengths: Weber et al. take our knowledge of dhh1, the yeast homolog of the human DDX6, and determine several features that are conserved across eukaryotes. The authors take our understanding of DDX6 a step further by identifying the specific domains involved in the interaction between DDX6 and the ribosome. As well as, differentiating those interactions from other factors known to interact with DDX6, such as NOT1. All of this is necessary and important to understand how mRNA decay plays a role in post-transcriptional gene regulation in humans.<br /> Weaknesses: The authors fail to truly define codon optimality, rare codons, and stalling sequences in their work, all of which are distinct terminologies. They use reporters with rare codon usage but do not mention what metrics they use to determine this, such as cAI, codon usage bias, or tAI. The distinction between the type of codon sequences that DDX6 affects is very important to differentiate and should be done here as certain stretches of codons are known to lead to different quality control RNA decay pathways that are not reliant on canonical mRNA decay factors. Likewise, the authors sort their Ribo-seq data to determine genes that might exhibit a DDX6 specific mRNA decay effect but fail to go into great depth about common features shared among these genes other than GO term analysis, GC content, and coding sequence (CDS) length. The authors then sort out 35 genes that are both upregulated at the mRNA level and have increased local ribosome footprint along the ORF. They are then able to show that 6 out of 9 of those genes had a DDX6-dependent mRNA decay effect. There was no comment or effort as to why 2 out of those 6 genes tested did not show as strong of a DDX6-dependent decay effect relative to the other targets tested. Thus, the efforts to identify mRNA features at a global level that exhibited DDX6-dependent mRNA decay effects are lacking in this analysis.<br /> Overall, the work done by Weber et al. is sound, with the proper controls. The authors expand significantly on the knowledge of what we know about DDX6 in the process of mRNA decay in humans, confirming the evolutionary conservation of the role of this factor across eukaryotes. The analysis of the RNA-seq and Ribo-seq data could be more in-depth, however, the authors were able to show with certainty that some transcripts containing known repetitive sequences or polybasic sequences exhibited a DDX6-mRNA decay effect.

Reviewer #2 (Public Review):

In this paper the authors present an existing information theoretic framework to assess the ability of single cells to encode external signals sensed through membrane receptors. The main point is to distinguish actual noise in the signaling pathway from cell-cell variability, which could be due to differences in their phenotypic state, and to formalize this difference using information theory. After correcting for this cellular variability, the authors find that cells may encode more information than one would estimate from ignoring it, which is expected. The authors show this using simple models of different complexities, and also by analyzing an imaging dataset of the IGF/FoxO pathway.

I am only partially satisfied by the authors response. To me, the main question that was unanswered, while being at the core of the claim of the paper, was the magnitude of within-cell variability across repetitions of the stimulus.

This can only be done on the IGF/FoxO system because, as the authors acknowledge, the EGF/EGFR system does not have any data to support any claim about single-cell information that's not heavily informed by models, which assume by construction that this variability is small, naturally leading the desired conclusion.

The authors now measure within-cell, across-repetition variability (delta_0) for IGF/FoxO, but:<br /> - they compare it to cell-to-cell variability, finding that it's smaller. That's good and that supports the main claim of the paper that single cells are more precise than a mean cell. However they don't show it in the paper, but only in the response.<br /> - they also don't compare it to within-cell, within-stimulation variability across time. But this latter variability is what they (wrongly) used to estimate information, and still do in this revision. However I think this is approximated by the blue "simulation" violin plot in Reviewer Figure 2. The true variability is clearly larger than previously assumed. So it's strange that they conclude that "our estimates of cell-to-cell variability signaling fidelity are stable and reliable."<br /> - they don't use this delta_0 variability to revise their estimate of the information accordingly.<br /> - since variability is small compared to the differences between distinct stimulations, of which there are only 4, all information quantities they get are around 2 bits, which is not approaching the information capacity but merely a statement that the number of tested doses is small.

I strongly recommend that the authors actually report the figure they provided as Reviewer Figure 2 in the manuscript. In addition, they should not claim that the within-cell variability (captured by the variability across distinct presentations of the stimulus) is well captured by their initial estimate (based on the variance within a single presentation of the stimulus).

Joint Public Review:

This work by Liu CSC et al. is an extension of the author's previous work on the role of Piezo1 mechano-sensor in human T cell activation. In this study, the authors address whether Piezo1 plays a role in T-cell chemotactic migration.

The authors used CD4+ T cells or Jurkat T cells to test the effects of siRNA-mediated depletion of Piezo1 on chemotactic migration. They establish that Piezo1 is implicated in chemotactic migration, although the effects of depletion are relatively moderate.

They show that Piezo1 is redistributed to the leading edge of T-cells.

They identify that relocation of Piezo1 to the leading edge follows an increase in membrane tension.

In Piezo-1 depleted cells, they observe a moderate reduction of LFA-1 polarity. With the use of specific inhibitors, they propose Piezo1 activation to be downstream of focal adhesion formation and upstream of calpain-mediated LFA-1, integrin alpha L beta 2, or CD11a/CD18 recruitment at the leading edge.

Strengths:

Together with their 2018 paper, this study presents Pieszo1 as a regulator of T-cell activation, implicating it as a player in the coordination of the chemotactic immune response.

Weaknesses:<br /> Most of the effects observed are relatively modest. The authors did not challenge the cells with various physico-mechanical conditions to see when Piezo-1 might become really important. For instance, there are no experiments that expose T cells to varying counter-acting forces to see how piezo1 might affect migration.

Technical weaknesses:

The authors state that "these high tension edges are usually further emphasized at later time points", but after ten minutes the median tension and tension (Figure 2C and Supplementary Figure 2C respectively) reduce down to the pretreatment time point. It would be clearer if the author stated within which timeframe the tension edges are "further emphasized".

Figures 3 and 4 - The author states the number of cells quantified from the images, but it is not clear whether the data is actually from 3 biological replicates.

Some of the data has no representative images or videos included. There is no video in the supplementary for Figures 1 A and B. There are no representative images of transwell migration assay in Figures 1 D and E.

Joint Public Review:

Iske et al. provide experimental data that NAD+ lessens disease severity in bacterial sepsis without impacting on the host pathogen load. They show that in macrophages, NAD+ prevents Il1b secretion potentially mediated by Caspase11.

While the in vivo and in vitro data is interesting and hints towards a crucial role of NAD+ to promote metabolic adaptation in sepsis, the manuscript has shortcomings and would profit from several changes and additional experiments that support the claims.

Conceptually, the definition of sepsis is outdated. Sepsis is not SIRS, as in sepsis-2. Sepsis-3 defines sepsis as infection-associated organ dysfunction. This concept needs to be taken into account for the introduction and when describing the potential effects of NAD+ in sepsis. Also, LPS application cannot be considered an appropriate sepsis model, since it only recapitulates the consequence of TLR-4 activation. It is a model of endotoxemia. Also, the LPS data does not allow to draw conclusions about bacterial clearance (L135).

The authors state that protective effects by NAD were independent of the host pathogen load. This clearly indicates that NAD confers protection via enhancing a disease tolerance mechanism, potentially via reducing immunopathology. This aspect is not considered by the authors. The authors should incorporate the concept of disease tolerance in their work, cite the relevant literature on the topic and discuss it their findings in light of the published evidence for metabolic alteration sand adaptations in sepsis.

For the in vitro data, the manuscript would benefit from additional experiments using in vitro infection models.

The figure legend should not repeat the methods and materials section. The nomenclature for mouse protein and genes needs to be thoroughly revised.

L350. The authors write that they dissect the capacity of NAD+ to dampen auto- and alloimmunity. In this work, no data that supports this statement is shown and experiments with autoantigens or alloantigens are not performed. If this refers to another previous publication by the same group, it needs to be put into this context and appropriately cited.

L163 The authors describe pyroptosis but in the figure legend call it apoptosis (Fig.2D). Specific markers for each cell death should be measured and determined which cell death mechanisms is involved.

Animal data comes from an infection model and LPS application. The RNAseq data is obtained from cells primed with Pam3CSK4 and subsequently subjected to LPS. It is unclear how the cell culture model reflects the animal model. As such the link between IFN signaling and the bacterial infection/LPS model are not convincing and need to be further elaborated.

Further experiments with primary cells from Il10 k.o. and Caspase11 k.o. animals should be provided that support the findings in macrophages.

Joint Public Review:

Summary:

In this manuscript, the authors set out to understand how different TLR4 agonists trigger Myddosome assembly and seek to examine how the potent LPS agonist induces a heightened TLR4 response. A strength of the study is that the authors employ a novel light sheet imaging modality coupled to nanopipette delivery of TLR4 ligands. The authors use this technological innovation to resolve the dynamics of Myddosome formation within the whole cell volume of macrophage cell lines expressing MyD88-YFP. The main finding is that the kinetics of Myddosome formation is slower for the weaker agonist Abeta than LPS. However, Abeta amyloids resulted in the formation of larger MyD88-YFP puncta that persisted for longer. The authors suggest the slower kinetics of formation and larger puncta size reflect how Abeta amyloids are a less efficient TLR4 agonist. Many Toll-like receptors are now known to recognize endogenous produced danger signals and microbially derived molecules. This work is the first to compare the signaling kinetics of endogenous versus microbially derived TLR agonists.

Strengths:

A key strength of this work is the technological achievement of imaging Myddosomes within the entire cell volume and using a nanopipette to administer ligands directly to single cells. The authors also combine this light sheet microscopy with STORM imaging to gain a super-resolved view of the assembly of Myddosomes. These findings suggest that Myddosomes formed in response to Abeta have a more irregular morphology. We conclude that these technological achievements are significant in improving our understanding of the dynamics of TLR4 signaling in response to diverse agonists. Given the limited literature on the molecular dynamics of innate immune signal transduction, this study is an important addition to the field.

Weaknesses:

One limitation of the paper is that a suitable explanation for how larger Myddosomes would contribute to an attenuated downstream signaling response. Do the larger clusters of nucleated MyD88 polymers reflect inefficiency in assembling fully formed Myddosomes that contain IRAK4/2? Could the MyD88-GFP puncta be stained with antibodies against IRAK4 (or IRAK2) to determine the frequency and probably of the two ligands to stimulate signal transduction beyond MyD88 assembly?

A second weakness is the discussion. The authors should explore other explanations for the observed differences in Myddosome formation between TLR4 agonists. For example, could the observed delay in Myddosome assembly in response to Abeta be due to different binding affinity or kinetics to TLR4? Can this be ruled out?

Reviewer #1 (Public Review):

Summary:<br /> Zink et al set out to identify selective inhibitors of the pyridoxal phosphatase (PDXP). Previous studies had demonstrated improvements in cognition upon removal of PDXP, and here the authors reveal that this correlates with an increase in pyridoxal phosphate (PLP; PDXP substrate and an active coenzyme form of vitamin B6) with age. Since several pathologies are associated with decreased vitamin B6, the authors propose that PDXP is an attractive therapeutic target in the prevention/treatment of cognitive decline. Following high throughput and secondary small molecule screens, they identify two selective inhibitors. They follow up on 7, 8 dihydroxyflavone (DHF). Following structure-activity relationship and selectivity studies, the authors then solve a co-crystal structure of 7,8 DHF bound to the active site of PDXP, supporting a competitive mode of PDXP inhibition. Finally, they find that treating hippocampal neurons with 7,8 DHF increases PLP levels in a WT but not PDXP KO context. The authors note that 7,8 DHF has been used in numerous rodent neuropathology models to improve outcomes. 7, 8 DHF activity was previously attributed to activation of the receptor tyrosine kinase TrkB, although this appears to be controversial. The present study raises the possibility that it instead/also acts through modulation of PLP levels via PDXP, and is an important area for future work.

Strengths:<br /> The strengths of the work are in the comprehensive, thorough, and unbiased nature of the analyses revealing the potential for therapeutic intervention in a number of pathologies.

Weaknesses:<br /> Potential weaknesses include the poor solubility of 7,8 DHF that might limit its bioavailability given its relatively low potency (IC50= 0.8 uM), which was not improved by SAR. However, the compound has an extended residence time and the co-crystal structure could aid the design of more potent molecules and would be of interest to those in the pharmaceutical industry. The images related to crystal structure could be improved.

Reviewer #1 (Public Review):

Summary:

In this manuscript, the authors introduced a compelling study that explored an innovative regenerative treatment for pediatric craniofacial bone loss, with a particular focus on investigating the impacts of JAGGED1 (JAG1) signaling.

Strengths:

Building on their prior research involving the effect of JAG1 on murine cranial neural crest cells, the authors demonstrated successful bone regeneration in an in vivo murine bone loss model with a critically-sized cranial defect, where they delivered JAG1 with pediatric human bone-derived osteoblast-like cells in the hydrogel. Additionally, their findings unveiled a crucial mechanism wherein JAG1 induces pediatric osteoblast commitment and bone regeneration through the phosphorylation of p70 S6K. This discovery offers a promising avenue for potential treatment, involving targeted delivery of JAG1 and activation of downstream p70 s6K, for pediatric craniofacial bone loss. Overall, the experimental design is appropriate, and the results are clearly presented.

Weaknesses:

Several methodology details need to be clearly included and gender differences should be evaluated and discussed.

Reviewer #1 (Public Review):

Summary:

Makiko Kashio et al aimed to uncover a potential role of exocrine gland-expressing TRPV4 in perspiration. Pharmacological and genetic tools were employed to verify a TRPV4-dependent cytosolic Ca2+ increase, which may contribute to sweat in mice.

Strengths:

(1) The authors identified a functional expression of TRPV4 in sweat glands.<br /> (2) The lower expression of TRPV4 in anhidrotic skin from patients with AIGA suggested a potential role of TRPV4 in perspiration.

Weaknesses:

(1) Measurement of secreted amylase could be seen as direct evidence of sweating, however, how to determine the causal relationship between climbing behavior and sweating? Friction force may also be reduced when there is too much fingertip moisture.

(2) For the human skin immunostaining, did the author use the same TRPV4 antibody as used in the mouse staining? Did they validate the specificity of the antibody for the human TRPV4 channel?

(3) In lines 116-117, the authors tried to determine "the functional interaction of TRPV4 and ANO1 is involved in temperature-dependent sweating", however, they only used the TRPV4 ko mice and did not show any evidence supporting the relationship between TRPV4 and ANO1.

(4) Figure 3-4 is quite confusing. At 25˚C, no sweating difference was observed between TRPV4 and wt mice (Fig 3A-3D), suggesting both Ach-induced sweating and basal sweating are TRPV4-independent at 25˚C, however, the climbing test was done at 26-27 ˚C and the data showed a climbing deficit in TRPV4 ko mice. How to interpret the data is unclear.

(5) Was there any gender differences associated with sweating in mice? In Figure 3, the mouse number for behavior tests should be at least 5.

(8) 8- to 21-week-old mice were used in the immunostaining, the time span is too long.

(6) The authors used homozygous TRPV4 ko mice for all experiments. What are control mice? Are they littermates of the TRPV4 ko mice?

Reviewer #1 (Public Review):

Summary:

This work extends previous agent-based models of murine muscle regeneration by the authors (especially Westman et al., 2021) and by others (especially Khuu et al, 2023) by incorporating additional agent rules (altogether now based on over 100 published studies), threshold parameters and interactions with fields of cytokines and growth factors as well as capillaries (dynamically changing through damage and angiogenesis) and lymphatic vessels. The estimation of 52 unknown parameters against three time courses of tissue-scale observables (muscle cross-sectional area recovery, satellite stem cell count and fibroblast cell count) employs the CaliPro algorithm (Joslyn et al., 2021) and sensitivity analysis. The model is validated against additional time courses of tissue-scale observables and qualitative perturbation data, which match for almost all conditions. This model is here used to predict (also non-monotonic) responses of (combinations of) cytokine perturbations but it moreover represents a valuable resource for further analysis of emergent behavior across multiple spatial scales in a physiologically relevant system.

Strengths:

This work (almost didactically) demonstrates how to develop, calibrate, validate and analyze a comprehensive, spatially resolved, dynamical, multicellular model. Testable model predictions of (also non-monotonic) emergent behaviors are derived and discussed. The computational model is based on a widely-used simulation platform and shared openly such that it can be further analyzed and refined by the community.

Weaknesses:

While the parameter estimation approach is sophisticated, this work does not address issues of structural and practical non-identifiability (Wieland et al., 2021, DOI:10.1016/j.coisb.2021.03.005) of parameter values, given just tissue-scale summary statistics, and does not address how model predictions might change if alternative parameter combinations were used. Here, the calibrated model represents one point estimate (column "Value" in Suppl. Table 1) but there is specific uncertainty of each individual parameter value and such uncertainties need to be propagated (which is computationally expensive) to the model predictions for treatment scenarios.<br /> Suggested treatments (e.g. lines 484-486) are modeled as parameter changes of the endogenous cytokines (corresponding to genetic mutations!) whereas the administration of modified cytokines with changed parameter values would require a duplication of model components and interactions in the model such that cells interact with the superposition of endogenous and administered cytokine fields. Specifically, as the authors also aim at 'injections of exogenously delivered cytokines' (lines 578, 579) and propose altering decay rates or diffusion coefficients (Fig. 7), there needs to be a duplication of variables in the model to account for the coexistence of cytokine sub-types. One set of equations would have unaltered (endogenous) and another one have altered (exogenous or drugged) parameter values. Cells would interact with both of them.

This work shows interesting emergent behavior from nonlinear cytokine interactions but the analysis does not provide insights into the underlying causes, e.g. which of the feedback loops dominates early versus late during a time course.

Reviewer #1 (Public Review):

Summary:

Taking advantage of the Alphafold-multimer program, which predicts the tertiary structure of the macromolecular complex, the authors analyzed the interaction of essential factors involved in sperm-egg fusion. In particular, the authors predicted that the presence of a large complex of the novel factor TMEM81 with IZUMO1, SPACA6, JUNO, and CD9.

Strengths:

The authors postulated that the type I transmembrane sperm protein TMEM81 may be involved in gamete fusion, as predicted by the Alphafold-multimer.

Weaknesses:

All data except Figure 1 are mere predictive models, and their physiological importance is extremely unreliable. In addition, the data lacks experimental validation compared to another group's preprint (https://www.biorxiv.org/content/10.1101/2023.07.27.550750v1).

Reviewer #1 (Public Review):

The manuscript by Singh et al proposes a new theoretical model for the phenomenon of planar cell polarity (PCP). The new model is simulating the emergence of the subcellular polarity of the Fat-Ds pathway, based on the interactions of the protocadherins Fat and Ds at the boundary between cells and in response to external gradients. Several mathematical models for PCP have been previously developed focusing on different aspects of PCP, including non-autonomy domineering (Amonlirdviman et al.), the effect of stochasticity on polarity (Burak et al.), gradient sensing (Mani et al), formation of molecular bridges (Fisher et al.) to name a few. The current modeling approach suggests a new model, based on a relatively simple set of equations for membrane Fat and Ds and their interactions, both in 1D (line of cells) and in 2D (hexagonal array). The equations are relatively simple on one hand, allowing performing tractable computational analysis as well as analytical approximations, while on the other hand allowing tracking membrane protein levels, which is what is measured experimentally. It has been previously shown that achieving polarity requires local feedback that amplify complexes in one orientation at the expense of complexes in the opposite orientation (e.g. Mani et al.). Interestingly, the current manuscript shows that a simple assumption, that Fat-DS complexes are stabilized when bound is sufficient to induce PCP when concentrations are high enough. The authors use the model to show how it captures several experimental observations, as well as to analyze the sensitivity to noise, the response to gradients, and the response to local perturbations (mutant clones). The manuscript is clear and the analysis is mostly coherent and sensible (although some parts need to be clarified, see below). The main issue I have with the manuscript is that it mostly describes how it captures different features that were mostly explained in previous models. I do think the authors should do more with their model to explain features that were not explained by other models, and/or generate non-trivial predictions that can be tested experimentally.

Reviewer #1 (Public Review):

In this manuscript, the authors seek to investigate the spatiotemporal dynamics of macrophage polarization during Salmonella infection. They undertake intravital microscopy of Salmonella Typhimurium infection in the hindbrain ventricle of zebrafish larvae and couple this with transcriptomic analysis of macrophages from infected tissues. They find that macrophages and neutrophils are rapidly recruited to the site of infection within hours after inoculation. Macrophage abundance is significantly increased in the persistent infection stage at 4 days post-inoculation (dpi), compared to in the early stage, hours post-inoculation. The authors observe that Salmonella bacilli selectively co-localize with aggregates of macrophages, but not neutrophils, during persistent infection. Furthermore, they show that in early infection stage, a markedly higher fraction of macrophages at the site of infection expressed tnfa and exhibits stronger transcriptional signature of pro-inflammatory, M1-like phenotype, compared to macrophages in persistent infection stage. Additionally, the authors find that genes involved in cell-cell adhesion are down-regulated in persistent stage macrophages and these cells have reduced motility. This study's approach, further developing and employing a zebrafish S. Typhimuirum infection model and intravital microscopy of whole living animals, presents an exciting strategy to investigate macrophage responses and their roles during vacuolar intracellular bacterial infection in vivo, complementary to the more commonly utilized murine infection models. The study's findings are useful and largely observational. The data presented have the potential but additional analyses and experiments are needed to clarify and support the conclusions.

Reviewer #1 (Public Review):

This paper combines a number of cutting-edge approaches to explore the role of a specific mouse retinal ganglion cell type in visual function. The approaches used include calcium imaging to measure responses of RGC populations to a collection of visual stimuli and CNNs to predict the stimuli that maximally activate a given ganglion cell type. The predictions about feature selectivity are tested and used to generate a hypothesized role in visual function for the RGC type identified as interesting. The paper is impressive; my comments are all related to how the work is presented.

Is the MEI approach needed to identify these cells?<br /> To briefly summarize the approach, the paper fits a CNN to the measured responses to a range of stimuli, extracts the stimulus (over time, space, and color) that is predicted to produce a maximal response for each RGC type, and then uses these MEIs to investigate coding. This reveals that G28 shows strong selectivity for its own MEI over those of other RGC types. The feature of the G28 responses that differentiate it appears to be its spatially-coextensive chromatic opponency. This distinguishing feature, however, should be relatively easy to discover using more standard approaches.<br /> The concern here is that the paper could be read as indicating that standard approaches to characterizing feature selectivity do not work and that the MEI/CNN approach is superior. There may be reasons why the latter is true that I missed or were not spelled out clearly. I do think the MEI/CNN approach as used in the paper provides a very nice way to compare feature selectivity across RGC types - and that it seems very well suited in this context. But it is less clear that it is needed for the initial identification of the distinguished response features of the different RGC types.<br /> What would be helpful for me, and I suspect for many readers, is a more nuanced and detailed description of where the challenges arise in standard feature identification approaches and where the MEI/CNN approaches help overcome those challenges.

Interpretation of MEI temporal structure<br /> Some aspects of the extracted MEIs look quite close to those that would be expected from more standard measurements of spatial and temporal filtering. Others - most notably some of the temporal filters - do not. In many of the cells, the temporal filters oscillate much more than linear filters estimated from the same cells. In some instances, this temporal structure appears to vary considerably across cells of the same type (Fig. S2). These issues - both the unusual temporal properties of the MEIs and the heterogeneity across RGCs of the same type - need to be discussed in more detail.<br /> Related to this point, it would be nice to understand how much of the difference in responses to MEIs in Figure 4d is from differences in space, time, or chromatic properties. Can you mix and match MEI components to get an estimate of that? This is particularly relevant since G28 responds quite well to the G24 MEI.

Explanation of RDM analysis<br /> I really struggled with the analysis in Figure 5b-c. After reading the text several times, this is what I think is happening. Starting with a given RGC type (#20 in Figure 5b), you take the response of each cell in that group to the MEI of each RGC type, and plot those responses in a space where the axes correspond to responses of each RGC of this type. Then you measure euclidean distance between the responses to a pair of MEIs and collect those distances in the RDM matrix. Whether correct or not, this took some time to arrive at and meant filling in some missing pieces in the text. That section should be expanded considerably.

Centering of MEIs<br /> How important is the lack of precise centering of the MEIs when you present them? It would be helpful to have some idea about that - either from direct experiments or using a model.

Reviewer #2 (Public Review):

This MS reveals that plants that have long been said to push are not, in fact, doing so, but are trapping and killing pests, thereby reducing pest outbreaks. The volatiles data of Desmodium are stable and useful. And the method of showing volatiles data is great.

Reviewer #1 (Public Review):

The author tried to figure out whether neutrophil extracellular traps are involved in aristolochic acid nephropathy. Overall, this study provided some novel findings to support the conclusion. But the generation of knockin mice, IL-19 function in vivo, and the underlying mechanism by which PSTPIP2 influences NF-KB-IL-19 need to be further clarified.

Reviewer #1 (Public Review):

In this manuscript the authors describe the expression and regulatory function of a self-cleaving ribozyme in the Cpeb3 gene. Cpeb3 knockout is associated with altered memory formation, and there are tempting correlations from the mid-2000s between a human CPEB3 SNP at the ribozyme cleavage site and memory performance, suggesting that regulation of Cpeb3 protein expression could impact memory. Here the authors test the impact of inhibiting Cpeb3 ribozyme self-excision with the hypothesis that this will promote splicing and Cpeb3 protein expression. They study the temporal regulation of ribozyme cleavage and find that it is in sync with transcription. Then they use their in vitro cleavage assay to identify an ASO that blocks cleavage. The validation of the effects of the ASO on ribozyme cleavage, and Cpeb3 mRNA expression and processing in membrane depolarized neurons and in the hippocampus in vivo are rigorous and establish the molecular function of the ribozyme. The authors also show an increase in CPEB3 protein expression and increased expression (and polyadenylation) of known translational targets of CPEB3 in cultures and in vivo with the latter only in the presence of elevated neural activity, consistent with an effect on protein synthesis. The final part of the study assesses the regulation and function of CPEB3 in the context of learning and memory.

The significance of this study lies in the molecular analysis of the ribozyme function. This ribozyme is well established and the gene in which it lies has important links to synaptic plasticity. Gene regulation is known to be important in the context of learning and memory and this is a new mechanism that the authors show has the potential to influence this process.

Reviewer #1 (Public Review):

The evolution of dioecy in angiosperms has significant implications for plant reproductive efficiency, adaptation, evolutionary potential, and resilience to environmental changes. Dioecy allows for the specialization and division of labor between male and female plants, where each sex can focus on specific aspects of reproduction and allocate resources accordingly. This division of labor creates an opportunity for sexual selection to act and can drive the evolution of sexual dimorphism.

In the present study, the authors investigate sex-biased gene expression patterns in juvenile and mature dioecious flowers to gain insights into the molecular basis of sexual dimorphism. They find that a large proportion of the plant transcriptome is differentially regulated between males and females with the number of sex-biased genes in floral buds being approximately 15 times higher than in mature flowers. The functional analysis of sex-biased genes reveals that chemical defense pathways against herbivores are up-regulated in the female buds along with genes involved in the acquisition of resources such as carbon for fruit and seed production, whereas male buds are enriched in genes related to signaling, inflorescence development and senescence of male flowers. Furthermore, the authors implement sophisticated maximum likelihood methods to understand the forces driving the evolution of sex-biased genes. They highlight the influence of positive and relaxed purifying selection on the evolution of male-biased genes, which show significantly higher rates of non-synonymous to synonymous substitutions than female or unbiased genes. This is the first report (to my knowledge) highlighting the occurrence of this pattern in plants. Overall, this study provides important insights into the genetic basis of sexual dimorphism and the evolution of reproductive genes in Cucurbitaceae.

Reviewer #1 (Public Review):

Summary: Translating discoveries from model organisms to humans is often challenging, especially in neuropsychiatric diseases, due to the vast gaps in the circuit complexities and cognitive capabilities. Kajtor et al. propose to bridge this gap in the fly models of Parkinson's disease (PD) by developing a new behavioral assay where flies respond to a moving shadow by modifying their locomotor activities. The authors believe the flies' response to the shadow approximates their escape response to an approaching predator. To validate this argument, they tested several PD-relevant transgenic fly lines and showed that some of them indeed have altered responses in their assay.

Strengths: This single-fly-based assay is easy and inexpensive to set up, scalable, and provides sensitive, quantitative estimates to probe flies' optomotor acuity. The behavioral data is detailed, and the analysis parameters are well-explained.

Weaknesses: While the abstract promises to give us an assay to accelerate fly-to-human translation, the authors need to provide evidence to show that this is indeed the case. They have used PD lines extensively characterized by other groups, often with cheaper and easier-to-setup assays like negative geotaxis, and do not offer any new insights into them. The conceptual leap from a low-level behavioral phenotype, e.g. changes in walking speed, to recapitulating human PD progression is enormous, and the paper does not make any attempt to bridge it. It needs to be clarified how this assay provides a new understanding of the fly PD models, as the authors do not explore the cellular/circuit basis of the phenotypes. Similarly, they have assumed that the behavior they are looking at is an escape-from-predator response modulated by the central complex- is there any evidence to support these assumptions? Because of their rather superficial approach, the paper does not go beyond providing us with a collection of interesting but preliminary observations.

Reviewer #1 (Public Review):

Summary:<br /> The focus of this manuscript was to investigate the role of Cldn9 in the development of the mammalian cochlea. The main rationale of the study is the fact that cochlear hair cells do not regenerate, so when damaged they are lost forever, causing irreparable hearing loss. The authors have attempted to address this problem by inducing the ectopic production of additional hair cells and testing whether they acquire the morphological and functional characteristics of native hair cells. They show that downregulation of Cldn9 using a well-established genetic manipulation of transgenic mice led to the production of extra numerary inner hair cells, which were able to survive for several months. By performing a large battery of experiments, the authors were able to determine that the native and ectopic inner hair cells have comparable morphological and physiological characteristics. There are several conclusions highlighted by the authors in different parts of the manuscript, including the key role of Cldn9 in coordinating embryonic and postnatal development, the differentiation of supporting cells into inner hair cells, and the possible use of Cldn9 to induce inner hair cell differentiation following deafness induced by hair cell loss.

Strengths:<br /> Several of the conclusions in this study are well supported by the experimental work.

Weaknesses:<br /> Some aspects of the data and its interpretation needs better explanation and requires further investigation.

1) The Results section is the most difficult part to read and understand. It contains a very limited, and in some places confusing and repetitive, description of the data. Statistical analysis is missing for some of the key data (e.g., ABRs), and in some places the text contradicts the data presented in the figures (e.g., Figure 8). I am sure a careful revision of the text would clarify some of these issues.

2) One puzzling finding that is not addressed in the manuscript is the lack of functional benefit from these additional inner hair cells. In fact, it appears to be detrimental based on the increased ABR thresholds. Maybe it would be useful to analyze the wave 1 characteristics.

3) It is not clear what direct evidence there is, apart from some immunostaining, indicating that the ectopic inner hair cells derive from the supporting cells. This part would benefit from a more careful consideration and maybe an attempt at a more direct experimental approach.

4) One point that should be made clear throughout the manuscript is that the ectopic inner hair cells are generated in a cochlea that is undergoing normal maturation. Thus, there is no guarantee that modulating the expression levels of Cldn9 in a deaf mouse lacking hair cells would produce the same result as that shown in this study. My guess is that it probably won't, but I am sure this could be tested (maybe in the future) using the excellent experimental approach applied in this study.

Reviewer #1 (Public Review):

MacDonald et al., investigated the consequence of double knockout of substance P and CGRPα on pain behaviors using a newly created mouse model. The investigators used two methods to confirm knockout of these neuropeptides: traditional immunolabeling and a neat in vitro assay where sensory neurons from either wildtype or double knock are co-cultured with substance P "sniffer cells", HEK cells stably expressing NKR1 (a substance P receptor), GCaMP6s and Gα15. It should be noted that functional assays confirming CGRPα knockout were not performed. Subsequently, the authors assayed double knockout mice (DKO) and wildtype (WT) mice in numerous behavioral assays using different pain models, including acute pain and itch stimuli, intraplanar injection of Complete Freund's Adjuvant, prostaglandin E2, capsaicin, AITC, oxaliplatin, as well as the spared nerve injury model. Surprisingly, the authors found that pain behaviors did not differ between DKO and WT mice in any of the behavioral assays or pain paradigms. Importantly, female and male mice were included in all analyses. These data are important and significant, as both substance P and CGRPα have been implicated in pain signaling, though the magnitude of the effect of a single knockout of either gene has been variable and/or small between studies.

The conclusions of the study are largely supported by the data; however, additional experimental controls and analyses would strengthen the authors claims.

1) The authors note that single knockout models of either substance P or CGRPα have produced variable effects on pain behaviors that are study-dependent. Therefore, it would have strengthened the study if the authors included these single knockout strains in a side-by-side analysis (in at least some of the behavioral assays), as has been done in prior studies in the field when using double- or triple-knockout mouse models (for example, see PMID: 33771873). If in the authors hands, single knockouts of either peptide also show no significant differences in pain behaviors, then the finding that double knockouts also do not show significant differences would be less surprising.

2) It is unclear why the authors only show functional validation of substance P knockout using "sniffer" cells, but not CGRPα. Inclusion of this experiment would have added an additional layer of rigor to the study.

3) The authors should be a bit more reserved in the claims made in the manuscript. The main claim of the study is that "CGRPα and substance P are not required for pain transmission." However, the authors also note that neuropeptides can have opposing effects that may produce a net effect of no change. In my view, the data presented show that double knockout of substance P and CGRPα do not affect somatic pain behaviors, but do not preclude a role for either of these molecules in pain signaling more generally. Indeed, the authors also note that these neuropeptides could be involved in nociceptor crosstalk with the immune or vascular systems to promote headache. The authors only assayed pain responses to glabrous skin stimulation. How the DKO mice would behave in orofacial pain assays, migraine assays, visceral pain assays, or bone/joint pain assays, for example, was not tested. I do not suggest the authors include these experiments, only that they address the limitations/weaknesses of their study more thoroughly.

4) A more minor but important point, the authors do not describe the nature of the WT animals used. Are the littermates or a separately maintained colony of WT animals? The WT strain background should be included in the methods section.

Reviewer #1 (Public Review):

People can perform a wide variety of different tasks, and a long-standing question in cognitive neuroscience is how the properties of different tasks are represented in the brain. The authors develop an interesting task that mixes two different sources of difficulty, and find that the brain appears to represent this mixture on a continuum, in the prefrontal areas involved in resolving task difficulty. While these results are interesting and in several ways compelling, they overlap with previous findings and rely on novel statistical analyses that may require further validation.

Strengths<br /> 1. The authors present an interesting and novel task for combining the contributions of stimulus-stimulus and stimulus-response conflict. While this mixture has been measured in the multi-source interference task (MSIT), this task provides a more graded mixture between these two sources of difficulty.

2. The authors do a good job triangulating regions that encoding conflict similarity, looking for the conjunction across several different measures of conflict encoding. These conflict measures use several best-practice approaches towards estimating representational similarity.

3. The authors quantify several salient alternative hypothesis, and systematically distinguish their core results from these alternatives.

4. The question that the authors tackle is important to cognitive control, and they make a solid contribution.

Concerns<br /> 1. The framing of 'infinite possible types of conflict' feels like a strawman. While they might be true across stimuli (which may motivate a feature-based account of control), the authors explore the interpolation between two stimuli. Instead, this work provides confirmatory evidence that task difficulty is represented parametrically (e.g., consistent with literatures like n-back, multiple object tracking, and random dot motion). This parametric encoding is standard in feature-based attention, and it's not clear what the cognitive map framing is contributing.

2. The representations within DLPFC appear to treat 100% Stoop and (to a lesser extent) 100% Simon differently than mixed trials. Within mixed trials, the RDM within this region don't strongly match the predictions of the conflict similarity model. It appears that there may be a more complex relationship encoded in this region.

3. To orthogonalized their variables, the authors need to employ a complex linear mixed effects analysis, with a potential influence of implementation details (e.g., high-level interactions and inflated degrees of freedom).

Reviewer #1 (Public Review):

Summary:<br /> This study is focused on an important aspect of axon guidance at the central nervous system (CNS) midline: how neurons extend axons that either do or do not cross the CNS midline. The authors here address contradictory work in the field relating to how cell surface expression of the slit receptor Robo1 is regulated to generate crossed and non-crossed axon trajectories during Drosophila neural development. They use fly genetics, cell lines, and biochemical assessments to define a complex consisting of the commissureless, Nedd4 and Robo1 proteins necessary for regulating Robo1 protein expression. This work resolves certain remaining questions in the field regarding midline axon guidance, with strengths outweighing weaknesses; however, addressing some of these weaknesses would strengthen this study.

Strengths:<br /> Strengths include:<br /> -The use of well-controlled genetic gain-of-function (overexpression) approaches in vivo in Drosophila to show that phosphorylation sites (there are 2, and this study allows for assessment of the contributions made by each) in the commissureless (Comm) protein are indeed required for Comm function with respect to regulating axon midline guidance via their role in directing Comm-mediated Robo1 ubiquitination and degradation in the lysosome.<br /> -The demonstration that in vitro, and in a sensitized genetic background in vivo, the Nedd4 ubiquitin ligase regulates Robo1 protein cell surface distribution and also midline axon crossing in vivo.<br /> -Important evidence here that serves to resolve many questions raised by previous studies (not from these authors) regarding how Robo1 is regulated by Comm and Nedd4 family ubiquitin ligases. Further, these results are likely to have implications for thinking about the regulation of midline guidance in more complex nervous systems.

Weaknesses:<br /> -The authors in part rely on GOF genetic approaches to infer roles for Comm and Nedd4, and this is understood in light of the lack of phenotypes in certain mutant backgrounds, providing evidence for their capabilities in these GOF paridigms. However, there are a few missed opportunities in some experiments that would allow for conclusions to be drawn regarding endogenous Comm function, some involving relatively simple inclusion of null mutants in the sensitized genetic backgrounds used here.<br /> -A weakness beyond the purview of revision but important to mention is that the authors chose not to complement their GOF experiments with gene editing approaches to generate endogenous PY mutant alleles of Comm that might have been useful in genetic interaction experiments directed toward revealing roles for endogenous Comm in the regulation of Robo1.<br /> -There are very minor concerns regarding protein expression levels in various experiments that should be easy to address.

Reviewer #1 (Public Review):

Summary:<br /> This manuscript reports a series of experiments examining category learning and subsequent generalization of stimulus representations across spatial and nonspatial domains. In Experiment 1, participants were first trained to make category judgments about sequences of stimuli presented either in nonspatial auditory or visual modalities (with feature values drawn from a two-dimensional feature manifold, e.g., pitch vs timbre), or in a spatial modality (with feature values defined by positions in physical space, e.g., Cartesian x and y coordinates). A subsequent test phase assessed category judgments for 'rotated' exemplars of these stimuli: i.e., versions in which the transition vectors are rotated in the same feature space used during training (near transfer) or in a different feature space belonging to the same domain (far transfer). Findings demonstrate clearly that representations developed for the spatial domain allow for representational generalization, whereas this pattern is not observed for the nonspatial domains that are tested. Subsequent experiments demonstrate that if participants are first pre-trained to map nonspatial auditory/visual features to spatial locations, then rotational generalization is facilitated even for these nonspatial domains. It is argued that these findings are consistent with the idea that spatial representations form a generalized substrate for cognition: that space can act as a scaffold for learning abstract nonspatial concepts.

Strengths:<br /> I enjoyed reading this manuscript, which is extremely well-written and well-presented. The writing is clear and concise throughout, and the figures do a great job of highlighting the key concepts. The issue of generalization is a core topic in neuroscience and psychology, relevant across a wide range of areas, and the findings will be of interest to researchers across areas in perception and cognitive science. It's also excellent to see that the hypotheses, methods, and analyses were pre-registered.

The experiments that have been run are ingenious and thoughtful; I particularly liked the use of stimulus structures that allow for disentangling of one-dimensional and two-dimensional response patterns. The studies are also well-powered for detecting the effects of interest. The model-based statistical analyses are thorough and appropriate throughout (and it's good to see model recovery analysis too). The findings themselves are clear-cut: I have little doubt about the robustness and replicability of these data.

Weaknesses:<br /> I have only one significant concern regarding this manuscript, which relates to the interpretation of the findings. The findings are taken to suggest that "space may serve as a 'scaffold', allowing people to visualize and manipulate nonspatial concepts" (p13). However, I think the data may be amenable to an alternative possibility. I wonder if it's possible that, for the visual and auditory stimuli, participants naturally tended to attend to one feature dimension and ignore the other - i.e., there may have been a (potentially idiosyncratic) difference in salience between the feature dimensions that led to participants learning the feature sequence in a one-dimensional way (akin to the 'overshadowing' effect in associative learning: e.g., see Mackintosh, 1976, "Overshadowing and stimulus intensity", Animal Learning and Behaviour). By contrast, we are very used to thinking about space as a multidimensional domain, in particular with regard to two-dimensional vertical and horizontal displacements. As a result, one would naturally expect to see more evidence of two-dimensional representation (allowing for rotational generalization) for spatial than nonspatial domains.

In this view, the impact of spatial pre-training and (particularly) mapping is simply to highlight to participants that the auditory/visual stimuli comprise two separable (and independent) dimensions. Once they understand this, during subsequent training, they can learn about sequences on both dimensions, which will allow for a 2D representation and hence rotational generalization - as observed in Experiments 2 and 3. This account also anticipates that mapping alone (as in Experiment 4) could be sufficient to promote a 2D strategy for auditory and visual domains.

This "attention to dimensions" account has some similarities to the "spatial scaffolding" idea put forward in the article, in arguing that experience of how auditory/visual feature manifolds can be translated into a spatial representation helps people to see those domains in a way that allows for rotational generalization. Where it differs is that it does not propose that space provides a *scaffold* for the development of the nonspatial representations, i.e., that people represent/learn the nonspatial information in a spatial format, and this is what allows them to manipulate nonspatial concepts. Instead, the "attention to dimensions" account anticipates that ANY manipulation that highlights to participants the separable-dimension nature of auditory/visual stimuli could facilitate 2D representation and hence rotational generalization. For example, explicit instruction on how the stimuli are constructed may be sufficient, or pre-training of some form with each dimension separately, before they are combined to form the 2D stimuli.

I'd be interested to hear the authors' thoughts on this account - whether they see it as an alternative to their own interpretation, and whether it can be ruled out on the basis of their existing data.

Reviewer #1 (Public Review):

Summary: The authors explored correlations between taste features of botanical drugs used in ancient times and therapeutic uses, finding some potentially interesting associations between intensity and complexity of flavors and therapeutic potential, plus some more specific associations described in the discussion section. I believe the results could be of potential benefit for the drug discovery community, especially for those scientists working in the field of natural products.

Strengths:

Owing to its eclectic and somehow heterodox nature, I believe the article might be of interest for a general audience. In fact, I have enjoyed reading it and my curiosity was raised by the extensive discussion.

The idea of revisiting a classical vademecum with new scientific perspectives is quite stimulating.

The authors have undertaken a significant amount of work, collecting 700 botanical drugs and exploring their taste and association with known uses via eleven trained panellists.

Weaknesses:

I have some methodological concerns. Robustness in the panelists' perceptions has not been addressed, and not every panellist tasted every drug because of time constrains. The breaks between tasting different samples was not standardized, and depended on the persistence of chemosensory perception, possibly also due to time constraints.

Reviewer #1 (Public Review):

Summary:<br /> The authors set out to determine how chemical variation on kinase inhibitors determines selection of Erk2 conformations and how inhibitor binding affects ERk2 structure and dynamics.

Strengths:<br /> The study is beautifully presented both verbally and visually. The NMR experiments and the HDX experiments complement each other for the study of Erk2 solution dynamics. X-ray crystallography of Erk2 complexes with inhibitors show small but distinct structural changes that support the proposed model for the impact of inhibitor binding.

Reviewer #1 (Public Review):

Specifically controlling the level of proteins in bacteria is an important tool for many aspects of microbiology, from basic research to protein production. While there are several established methods for regulating transcription or translation of proteins with light, optogenetic protein degradation has so far not been established in bacteria. In this paper, the authors present a degradation sequence, which they name "LOVdeg", based on iLID, a modified version of the blue-light-responsive LOV2 domain of Avena sativa phototropin I (AsLOV2). The authors reasoned that by removing the three C-terminal amino acids of iLID, the modified protein ends in "-E-A-A", similar to the "-L-A-A" C-terminus of the widely used SsrA degradation tag. The authors further speculated that, given the light-induced unfolding of the C-terminal domain of iLID and similar proteins, the "-E-A-A" C-terminus would become more accessible and, in turn, the protein would be more efficiently degraded in blue light than in the dark.

Indeed, several tested LOVdeg-tagged proteins show clearly lower cellular levels in blue light than in the dark. Depending on the nature and expression level of the target protein, protein levels are reduced modestly to strongly (2 to 20x lower levels upon illumination). Accordingly, the authors propose to use their system in combination with other light-controlled expression systems and provide data validating this approach. The LOVdeg system allows to modulate protein levels to a similar degree and with comparable kinetics as optogenetic systems controlling transcription or translation of protein, and can be combined with such systems.

The manuscript and the figures are generally very well-composed and follow a clear structure. The schematics nicely explain the underlying principles. Besides the advantages of the LOVdeg approach, including its complementarity to controlled expression of proteins, the revised version of the manuscript also highlights the limitations of the method more clearly, e.g., (i) the need to attach a C-terminal tag of considerable size to the protein of interest, (ii) the limited efficiency (slightly less efficient and slower than EL222, a light-dependent transcriptional control mechanism), and (iii) the incompletely understood prerequisites for its application. Taken together, this manuscripts describes the LOVdeg system as a valuable addition to the tool box for controlling protein levels in prokaryotic cells.

Reviewer #1 (Public Review):

In the manuscript "Mechanistic target of rapamycin (mTOR) pathway in Sertoli cells regulates age-dependent changes in sperm DNA methylation", the authors proposed to test if the balance of mTOR complexes in Sertoli cells may play a significant role in age-dependent changes in the sperm epigenome. The paper could be of interest and has a good scientific aim but there are too many drawbacks that hamper the initial enthusiasm. All sections need extensive revision. The paper is mostly descriptive without a mechanistic-orientated explanation for the observed results.

Specific comments:

1. The abstract is poorly written. There is a lot of unnecessary introduction that does not provide a rationale for the work. It is not possible to understand the experimental approach or the major data just by reading the abstract. It does not clearly represent the work.

2. The introduction is somewhat vague and does not provide a clear rationale for the hypothesis. There should be more focus more on the role of mTOR in Sertoli cells that goes far beyond BTB. That will give more focus on mTOR. Then it is important to focus on BTB and mTOR: what is known? What is the gap and how can it be solved? Several relevant references are missed concerning mTOR and Sertoli cells.

3. The Material and Methods section needs improvement. There is much important information missing. For instance: how many animals were used per group and how was the breeding done? At what age? Statistical analysis should be explained in detail.

4. The results description could be improved. It is vague without highlighting how much difference was detected. The results should be numerically described when possible and the differences should be highlighted. A 10% difference may be significant but not biologically relevant. To correctly evaluate the differences it is important to describe them with some degree of detail.

5. There is no discussion of the data. The authors just summarize their findings without a comprehensive analysis of the literature and how the effects can be mediated. mTOR interacts with different pathways (mTORC1 and mTORC2 are even mediators of distinct pathways). This would be very relevant to discuss. In addition, there are many study limitations not discussed. There is no clear mechanistic explanation of the way by which the mTOR pathway in Sertoli cells regulates age-dependent changes in sperm DNA methylation. The paper seems preliminary.

6. Figure 1 is too simple and does not provide any schematic support for the text.

7. Figure 2 lacks some detail. For instance, how many animals were used for each step?

8. Taking into consideration the roles of mTOR on sperm, particularly mTORC1, it is not clear whether there were any differences in sperm motility.

Reviewer #1 (Public Review):

The molecular interactions that determine infection (and disease) trajectory following human exposure to Mycobacterium tuberculosis (Mtb) are critical to understanding mycobacterial pathogenicity and tuberculosis (TB), a global public health threat that disproportionately impacts a number of high-burden countries and, owing to the emergence of multidrug-resistant Mtb strains, is a major contributor to antimicrobial resistance (AMR). In this submission, Qin and colleagues extend their own previous work which identified a potential role for host galectin-9 in recognizing the major Mtb cell wall component, arabinogalactan (AG). First, the authors present data indicating that galectin-9 inhibits mycobacterial growth during in vitro culture in liquid and on solid media and that the inhibition depends on carbohydrate recognition by galectin-9. Next, the authors identify anti-AG antibodies in sera of TB patients and use this observation to inform isolation of monoclonal anti-AG antibodies (mAbs) via an in vitro screen. Finally, they apply the identified anti-AG mAbs to inhibit Mtb growth in vitro via a mechanism that proteomic and microscopic analyses suggest is dependent on the disruption of the cell wall structure. In summary, the dual observation of (i) the apparent role of naturally arising host anti-AG antibodies to control infection and (ii) the potential utility of anti-AG monoclonal antibodies as novel anti-Mtb therapeutics is compelling; however, as noted in the comments below, the evidence presented to support these insights is inadequate and the authors should address the following:

1. The experiment that utilizes lactose or glucose supplementation to infer the importance of carbohydrate recognition by galectin-9 cannot be interpreted unequivocally owing to the growth-enhancing effect of lactose supplementation on Mtb during liquid culture in vitro.

2. Similar to the comment above, the apparent dose-independent effect of galectin-9 on Mtb growth in vitro is difficult to reconcile with the interpretation that galectin is functioning as claimed.

3. The claimed differences in galectin-9 concentration in sera from tuberculin skin test (TST)-negative or TST-positive non-TB cases versus active TB patients are not immediately apparent from the data presented.

4. Neither fluorescence microscopy nor electron microscopy analyses are supported by high-quality, interpretable images which, in the absence of supporting quantitative data, renders any claims of anti-AG mAb specificity (fluorescence microscopy) or putative mAb-mediated cell wall swelling (electron microscopy) highly speculative.

5. Finally, the absence of any discussion of how anti-AG antibodies (similarly, galectin-9) gain access to the AG layer in the outer membrane of intact Mtb bacilli (which may additionally possess an extracellular capsule/coat) is a critical omission - situating these results in the context of current knowledge about Mtb cellular structure (especially the mycobacterial outer membrane) is essential for plausibility of the inferred galectin-9 and anti-AG mAb activities.

Reviewer #1 (Public Review):

Summary:

The authors report on the development of the first cord blood DNA methylation score to capture the epigenetic effects of maternal smoking. The score was built in a White European cohort and tested in White European and South Asian ancestry cohorts. Additionally, epigenome-wide association studies were conducted to quantify the impact of maternal smoking on newborn health.

Strengths:

The main strengths include the use of multiple cohorts of different ancestries. This is also the first study to build a cord blood predictor of maternal smoking.

Weaknesses:

The manuscript could benefit from a more detailed description of methods, especially those used to derive MRS for maternal smoking, which appears to involve overfitting. In particular, the addition of a flow chart would be very helpful to guide the reader through the data and analyses. The FDR correction in the EWAS corresponds to a fairly liberal p-value threshold.

Reviewer #1 (Public Review):

The major strength of this work is its scope, including detailed mouse phenotyping, inter-disciplinary methods, and numerous complementary experiments. The antibiotic depletion and FMT experiments provide support for a role of the gut microbiota in this mouse model.

A major limitation is the lack of studies narrowing down which microbes are responsible. Sequencing data is shown, but no follow-up studies are done with bacterial isolates or defined communities.

The link to GABA is also somewhat tenuous. While it does match the phenotypic data, there are no targeted experiments in which GABA producing microbial communities/strains are compared to a control community/strain. As such, it seems difficult to know how much of the effects in this model are due to GABA vs. other metabolites.

My major recommendation would be to revise the title, abstract, and discussion to provide more qualification and to consider alternative interpretations.

Some key controls are also missing, which could be addressed by repeat experiments in the mouse model. The antibiotic depletion experiment would be improved by testing the effect of antibiotics in the absence of metformin, to see if the effect is just driven by the model itself as opposed to an interaction between metformin and antibiotics. The FMT experiment lacks a control group and suffers from pseudoreplication: multiple donors from metformin treated and untreated mice could be used to colonize separate groups of recipient mice.

Reviewer #1 (Public Review):

Summary:<br /> Starting from an unbiased search for somatic mutations (from COSMIC) likely disrupting binding of clinically approved antibodies the authors focus on mutations known to disrupt binding between two ERBB2 mutations and Pertuzamab. They use a combined computational and experimental strategy to nominate a position that when mutated could result in restoring the therapeutic activity of the antibody. Using in vitro assays the authors confirm that the engineered antibody binds to the mutant ERBB2 and prevents ERBB3 phosphorylation

Strengths:<br /> 1. In my assessment, the data sufficiently demonstrates that a modified version of Pertuzamab can bind both the wild-type and S310 mutant forms of ERBB2.

2. The engineering strategy employed is rational and effectively combines computational and experimental techniques.

3. Given the clinical activity of HER2-targeting ADCs, antibodies unaffected by ERBB2 mutations would be desired.

Weaknesses:<br /> 1. There is no data showing that the engineered antibody is equally specific as Pertuzamab i.e. that it does not bind to other (non-ERBB2) proteins.

2. There is no data showing that the engineered antibody has the desired pharmacokinetics/pharmacodynamics properties or efficacy in vivo.

3. Computational approaches are only used to design a phage-screen library, but not used to prioritize mutations that are likely to improve binding (e.g. based on predicted impact on the stability of the interaction). A demonstration of how computational pre-screening or lead optimization can improve the time-intensive process would be a welcome advance.

Context:<br /> The conflict of interest statement is inadequate. Most authors of the study (but not the first author) are employees of Biolojic, a company developing multi-specific antibodies, but the statements do not clarify whether the presented antibodies represent Biolojic IP, whether the company sponsored the research, and whether the company is further developing the specific antibodies presented.

Reviewer #1 (Public Review):

The authors put forth the hypothesis that hepatocyte and/or non-parenchymal liver MCT1 may be responsible for physiologic effects (lower body weight gain and less hepatic steatosis) in MCT1 global heterozygote mice. They generate multiple tools to test this hypothesis, which they combine with mouse diets that induce fatty liver, steatohepatitis and fibrosis. Novel findings include that deletion of hepatocyte MCT1 does not change liver lipid content, but increases liver fibrosis. Deletion of hepatic stellate cell (HSC) MCT1 does not substantially affect any liver parameter, but concomitant HSC MCT1 deletion does reverse fibrosis seen with hepatocyte MCT1 knockout or knockdown. In both models, plasma lactate levels do not change, suggesting that liver MCT1 does not substantially affect systemic lactate. In general, the data match conclusions of the manuscript, and the studies are well-conducted and well-described. Further work would be necessary to dissect mechanism of fibrosis with hepatocyte MCT1, and whether this is due to changes in local lactate (as speculated by the authors) or another MCT1 substrate. This would be important to understand this novel potential cross-talk between hepatocytes and HSCs.

A parallel and perhaps more important advance is the generation of new methodology to target HSC in mice, using modified siRNA and by transduction of AAV9-Lrat-Cre. Both methods would reduce the need to cross floxed mice with the Lrat-Cre allele, saving time and resources. These tools were validated to an extent by the authors, but not sufficiently to ensure that there is no cross-reactivity with other liver cell types. For example, AAV9-Lrat-Cre-transduced MCT1 floxed mice show compelling HSC but not hepatocyte Mct1 knockdown, but other liver cell types should be assessed to ensure specificity. This is particularly important as overall liver Mct1 decreased by ~30% in AAV9-Lrat-Cre-transduced mice, which may exceed HSC content of these mice, especially when considering a 60-70% knockdown efficiency. This same issue also affects Chol-MCT1-siRNA, which the authors demonstrate to affect hepatocytes and HSC, but likely affects other cell types not tested. As this is a new and potentially valuable tool, it would be important to assess Mct1 expression across more non-parenchymal cells (i.e. endothelial, cholangiocytes, immune cells) to determine penetration and efficacy.

Reviewer #1 (Public Review):

Summary:<br /> In this paper, the authors investigate the impact of fecal microbiota transfer (FMT) on intestinal recovery from enterotoxigenic E. coli infection following antibiotic treatment. Using a piglet model of intestinal infection, the authors demonstrate that FMT reduces weight loss and diarrhea and enhances the expression of tight junction proteins. Sequencing analysis of the intestinal microbiota following FMT showed significant increases in Akkermansia muciniphila and Bacteroides fragilis. Using additional mouse and organoid models, the authors examine the impact of these microbes on intestinal recovery and modulation of the Wnt signaling pathway. Overall, the data support the notion that FMT following ETEC infection is beneficial, however, additional investigation is required to fully elucidate the mechanisms involved.

Strengths:<br /> Initial experiments used a piglet model of infection to test the value of FMT on recovery from E. coli. The FMT treatment was beneficial and the authors provide solid evidence that the treatment increased the diversity of the microbiota and enhanced the recovery of the intestinal epithelium. Sequencing data highlighted an increase in Akkermansia muciniphila and Bacteroides fragilis after FMT.

The mouse data are consistent with the observations in pigs, and reveal that daily gavage with A. muciniphila or B. fragilis enhances intestinal recovery based on histological analysis, expression of tight junction proteins, and analysis of intestinal barrier function.

The authors demonstrate the benefit of probiotic treatment following infection using a range of model systems.

Weaknesses:<br /> Without sequencing the pre-infection pig microbiota or the FMT input material itself, it's challenging to firmly say that the observed bloom in Akkermansia muciniphila and Bacteroides fragilis stemmed from the FMT.

The lack of details for the murine infection model, such as weight loss and quantification of bacterial loads over time, make it challenging for a reader to fully appreciate how treatment with Akkermansia muciniphila and Bacteroides fragilis is altering the course of infection. Bacterial loads of E. coli were only quantified at one time point, and the mice that received A. muciniphila and B. fragilis had very low levels of E. coli. Therefore, it is not clear if all mice were subjected to the same level of infection in the first place. The reduced translocation of E. coli to the organs and enhanced barrier function may just reflect the low level of infection in these mice. Further, the authors' conclusion that the effect is specific to A. muciniphila or B. fragilis would be more convincing if the experiments included an inert control bacterium, to demonstrate that gavage with any commensal microbe would not elicit a similar effect.

Many of the conclusions in the study are drawn from the microscopy results. However, the methods describing both light microscopy and electron microscopy lack sufficient detail. For example, it is not clear how many sections and fields of view were imaged or how the SEM samples were prepared and dehydrated. The mucus layer does not appear to be well preserved, which would make it challenging to accurately measure the thickness of the mucus layer.

Gene expression data appears to vary across the different models, for example, Wnt3 expression in mice versus organoids. Additional experiments may be required to clarify the mechanisms involved. Considering that both of the bacteria tested elicited similar changes in Wnt signaling, this pathway might be broadly modulated by the microbiota.

The unconventional choice to not include references in the results section makes it challenging for the reader to put the results in context with what is known in the field. Similarly, there is a lack of discussion acknowledging that B. fragilis is a potential pathogen, associated with intestinal inflammation and cancer (Haghi et al. BMC Cancer 19, 879 (2019) ), and how this would impact its utility as a potential probiotic.