Reviewer #1 (Public review):

The study by Korona and colleagues presents a rigorous experimental strategy for generating and maintaining a nearly complete set of monosomic yeast lines, thereby establishing a new standard for studying monosomes. Their careful approach in generating and handling monosome yeast lines, coupled with their use of high-throughput DNA sequencing and RNA sequencing, addresses concerns related to genomic instability and is commendable. However, I would like to express my concerns regarding the second part of the study, particularly the calculation of epistasis and the conclusion that vast positive epistatic effects have been observed. I believe that the conclusion of positive epistasis for fitness might be premature due to potential errors in estimating the expected fitness.

The method used to calculate fitness expectation (1 + sum(di), where di = rDRi - 1) may be inappropriate. The logarithm transformation mentioned by the authors is designed to transform the exponential growth curve into a linear relation for estimating doubling rate, and thus the fitness expectation should be calculated as the product of rDRi values. As an illustration, if gene A exhibits a 20% reduction in fitness when halved (A/-) and gene B exhibits a 30% reduction (B/-), the expected fitness of A/- B/- should be 56%, rather than the 50% estimated in the study. In other words, the formula used by the authors could underestimate the fitness expectation.

This issue is evident in Figure 2b, where negative values were obtained due to the use of an incorrect formula for estimating fitness expectations. It is worth noting that Figure 2a shows rDR values around one, indicating that no further logarithmic transformation was applied.

While widespread positive epistasis in yeast has been reported by other studies (e.g., doi: 10.1038/ng.524, but not to the extent reported in this study), the conclusion of the current study might not be sufficiently supported. I recommend that the authors revisit their calculation methods to provide a more convincing conclusion on the presence of positive epistasis for fitness in their dataset. Overall, I appreciate the authors' efforts in this study but believe that addressing these concerns is essential for strengthening the validity of their findings.

Comments on revised version:

The authors have adequately addressed all my previous concerns during revision.

Reviewer #2 (Public review):

Summary:

The authors set out to study whether the cooling agent binding site in TRPM8, which is located between the S1-S4 and the TRP domain, is conserved within the TRPM family of ion channels. They specifically chose the TRPM4 channel as the model system, which is directly activated by intracellular Ca2+. Using electrophysiology, the authors characterized and compared the Ca2+ sensitivity and the voltage-dependence of TRPM4 channels in the absence and presence of synthetic cooling agonist icilin. They also analyzed the mutational effects of residues (A867G and R901H; equivalent mutations in TRPM8 were shown involved in icilin sensitivity) on Ca2+ sensitivity and voltage-dependence of TRPM4 in the absence and presence of Ca2+. Based on the results as well as structure/sequence alignment, the authors concluded that icilin likely binds to the same pocket in TRPM4 and suggested that this cooling agonist binding pocket is conserved in TRPM channels.

Strengths:

The authors gave a very thorough introduction of the TRPM channels. They have nicely characterized the Ca2+ sensitivity and the voltage-dependence of TRPM4 channels and demonstrated icilin potentiates the Ca2+ sensitivity and diminishes the outward rectification of TRPM4. These results indicate icilin modulates TRPM4 activation by Ca2+.

The authors have incorporated additional data analysis and control experiments in the revised manuscript to strengthen their findings. They have well addressed the concerns raised by reviewers in the responses.

Weaknesses:

The study is conducted based on an assumption that TRPM4 activation is controlled by Ca2+ binding to a single site in the S1-S4 pocket in each subunit, and the second Ca2+ site in the cytoplasmic MHRs is simplified.

Despite the technical reasons presented by the authors in the rebuttal, the conclusion of this study can be strengthened if more cooling compounds- the most well-studied natural cooling agonist menthol, and/or other cooling agonists such as WS-12 and/or C3-are tested for their effects on TRPM4 and several other TRPM channels.

Reviewer #1 (Public review):

In this manuscript, Yang et al report a novel regulatory role of SIRT4 in the progression of kidney fibrosis. The authors showed that in the fibrotic kidney, SIRT4 exhibited an increased nuclear localization. Deletion of Sirt4 in renal tubule epithelium attenuated the extent of kidney fibrosis following injury, while overexpression of SIRT4 aggravates kidney fibrosis. Employing a battery of in vitro and in vivo experiments, the authors demonstrated that SIRT4 interacts with U2AF2 in the nucleus upon TGF-β1 stimulation or kidney injury and deacetylates U2AF2 at K413, resulting in elevated CCN2 expression through alternative splicing of Ccn2 gene to promote kidney fibrosis. The authors further showed that the translocation of SIRT4 is through the BAX/BAK pore complex and is dependent on the ERK1/2-mediated phosphorylation of SIRT4 at S36, and consequently the binding of SIRT4 to importin α1. This fundamental work substantially advances our understanding of the progression of kidney fibrosis and uncovers a novel SIRT4-U2AF2-CCN2 axis as a potential therapeutic target for kidney fibrosis.

Comment on revised version:

In the new version of the manuscript, the authors have addressed most of my concerns . Overall, the authors have done an extensive, well-performed study. The results are convincing, and the conclusions are mostly well supported by the data. The message is interesting to a wider community working on kidney fibrosis, protein acetylation and SIRT4 biology. This work substantially advances our understanding of the mechanism of kidney fibrosis and uncovers a novel SIRT4-U2AF2-CCN2 axis as a potential therapeutic target for kidney fibrosis.

Reviewer #1 (Public review):

Summary:

The authors want to determine the role of the sperm hook of the house mouse sperm in movement through the uterus. They use transgenic lines with fluorescent labels to sperm proteins, and they cross these males to C57BL/6 females in pathogen-free conditions. They use 2-photon microscopy on ex vivo uteri within 3 hours of mating and the appearance of a copulation plug. There are a total of 10 post-mating uteri that were imaged with 3 different males. They provide 10 supplementary movies that form that basis for some of the quantitative analysis in the main body figures. Their data suggest that the role of the sperm hook is to facilitate movement along the uterine wall.

Strengths:

Ex vivo live imaging of fluorescently labeled sperm with 2-photon microscopy is a powerful tool for studying the behavior of sperm.

Weaknesses:

The paper is descriptive and the data are correlations.

The authors cannot directly test their proposed function of the sperm hook in sliding and preventing backward slipping.

Reviewer #1 (Public Review):

Summary:

This is a well-written and detailed manuscript showing important results on the molecular profile of 4 different cohorts of female patients with lung cancer.

Strengths:

The authors used several different methods to identify potential novel targets for therapeutic interventions.

Weaknesses:

Statistical test results need to be provided in comparisons between cohorts. This was addressed by the authors in the revisions.

Reviewer #1 (Public review):

Summary:

Arman Angaji and his team delved into the intricate world of tumor growth and evolution, utilizing a blend of computer simulations and real patient data from liver cancer.

Strengths:

Their analysis of how mutations and clones are distributed within tumors revealed an interesting finding: tumors don't just spread from their edges as previously believed. Instead, they expand both from within and the edges simultaneously, suggesting a unique growth mode. This mode naturally indicates that external forces may play a role in cancer cells dispersion within the tumor. Moreover, their research hints at an intriguing phenomenon - the high death rate of progenitor cells and extremely slow pace in growth in the initial phase of tumor expansion. Understanding this dynamic could significantly impact our comprehension of cancer development.

Weaknesses:

It's important to note, however, that this study relies on specific computer models, metrics derived from inferred clones, and a limited number of patient data. While the insights gained are promising, further investigation is essential to validate these findings. Nonetheless, this work opens up exciting avenues for comprehending the evolution of cancers.

Comments on revised submission:

The authors have effectively addressed my concerns. This revision is excellent.

Reviewer #1 (Public Review):

Summary:

This manuscript provides a solid advance to the scavenger receptor field by reporting the crystal structures of the domains of SCARF1 that bind modified LDL such as oxidized LDL and acylated LDL. The crystal packing reveals a new interface for homodimerization of SCARF1. The authors characterize SCARF1 binding to modified LDL using flow cytometry, ELISA, and fluorescent microscopy. They identify a positively-charged surface on the structure that they predict will bind the LDLs, and they support this hypothesis with several mutant constructs in binding experiments.

Strengths:

The authors have crystallized domains of an understudied scavenger receptor and used the structure to identify a putative binding site for modified LDL particles. An especially strong set of experiments are binding studies with chimeras of SCARF1 and SCARF2, where they show gain-of-function results (binding of modified LDLs) by SCARF2, a related protein that does not normally bind modified LDLs. The paper is a straightforward set of experiments that identify the likely binding site of modified LDL on SCARF1

Weaknesses:

In the current revision, the authors addressed my technical concerns.<br /> Two remaining considerations that may limit the broader impact of this paper are 1) that it does not explain the structural basis for specificity of the binding of SCARF1 to various lipoproteins (i.e. why SCARF1 binds oxLDL and AcLDL but not LDL or HDL) and 2) a lack of a biological assay to interpret the functional consequences of the SCARF1 mutants. These may be addressed in future work.

Reviewer #1 (Public review):

The authors have tried to identify the plausible Na+ entry pathway in an important SLC6 member GAT1, using computational approaches to assess residence times of the ions as they enter the vestibule of GAT1. The authors identify a patch of negative residues in TM6a and implicate them for being important to attract the Na+ ions during their movement towards the binding sites Na1 and Na2. Besides this they also suggest that sodium binding at site 1 is flexible and at times can occupy the primary binding site when the substrate is not available. Na2 site as other literature also suggests is demonstrated to be vital for the stability of the outward-open state.

Studies of ion permeation are challenging given that the states are challenging to trap through structural studies and computational methods are vital for understanding these steps. The authors suggest that two negatively charged residues are vital to attract Na+ ions to the vestibule. Using a combination of simulations and PCA analysis the authors identify the importance of Na+ binding at site 2 that stabilises the outward-open state and the flexibility observed in Na1 site for ion binding which happens alongside substrate in the GABA bound state. The study reconfirms earlier observations in the SLC6 family that Na2 site is critical for conformational transitions and Na1 site is substrate dependent in amino acid transporters.<br /> One of the challenges in such studies is to conclusively establish the presence of additional Na+ sites or regions of ion-binding with experimental structures as they are nearly impossible to trap. Such studies using simulations therefore become the only resort to understand such phenomena.

The work is likely to further provide insights into the transport mechanism of GAT1 and lends credence to some structural studies where the sodium at site1 is displaced but the ion remains proximal to the bound substrate.

Reviewer #1 (Public review):

In their paper, Kang et al. investigate rigidity sensing in amoeboid cells, showing that, despite their lack of proper focal adhesions, amoeboid migration of single cells is impacted by substrate rigidity. In fact, many different amoeboid cell types can durotax, meaning that they preferentially move towards the stiffer side of a rigidity gradient.

The authors observed that NMIIA is required for durotaxis and, buiding on this observation, they generated a model to explain how durotaxis could be achieved in the absence of strong adhesions. According to the model, substrate stiffness alters the diffusion rate of NMAII, with softer substrates allowing for faster diffusion. This allows for NMAII accumulation at the back, which, in turn, results in durotaxis.

The authors responded to all my comments and I have nothing to add. The evidence provided for durotaxis of non adherent (or low-adhering) cells is strong. I am particularly impressed by the fact that amoeboid cells can durotax even when not confined. I wish to congratulate the authors for the excellent work, which will fuel discussion in the field of cell adhesion and migration.

Reviewer #1 (Public review):

Summary:

In the manuscript "FABP4-mediated lipid accumulation and lipolysis in tumor-associated macrophages promote breast cancer metastasis", Yorek, et al. provide a novel mechanism explaining how unsaturated fatty acids induce macrophages to accumulate lipid droplets, which when contained in tumor-associated macrophages (TAMs) are associated with increased metastasis in breast cancer. The authors conclude that unsaturated fatty acids are transported into macrophages by the chaperone FABP4 where they induce C/EBPalpha expression and transcriptional activity resulting in upregulation of enzymes involved in triacylglycerol and lipid droplet biosynthesis. The resulting accumulation of lipid droplets in macrophages creates a store of fatty acids that can subsequently be released through FABP4-dependent lipolysis and thereby stimulate the migration of nearby breast cancer cells. While generally well-written and developed, there are a few concerns about the rigor of experimental evidence that supports some conclusions, including the existence of a FABP4-C/EBPalpha pathway. Overall, the mechanism identified is a valuable contribution to our understanding of how tumor-associated macrophages may influenced by available metabolites to promote the aggressiveness of certain cancers. FABP4 has the potential to be used as a novel biomarker of macrophage-induced cancer aggressiveness and/or a therapeutic target to prevent metastasis.

Strengths:

(1) The study is logically organized and provides extensive evidence in support of the overall model proposed.

(2) Multiple complementary techniques are used to identify and quantify lipid droplets.

(3) Primary macrophages and macrophage cell lines are used and provide consistent data.

(4) Knock-down and knock-out cells are used to assess the contributions of FABP4 and C/EBPalpha to gene expression.

(5) Public gene expression data (GEO, TCGA) is used effectively throughout.

Weaknesses:

(1) After Figure 1, a single saturated (palmitic acid; PA) and a single unsaturated (linoleic acid; LA) fatty acid are used for the remaining studies, bringing into question whether effects are in fact the result of a difference in saturation vs. other potential differences.

(2) While primary macrophages are used in several mechanistic studies, tumor-associated macrophages (TAMs) are not used. Rather, correlative evidence is provided to connect mechanistic studies in macrophage cell lines and primary macrophages to TAMs.

(3) C/EBPalpha and FABP4 clearly regulate LA-induced changes in gene expression. However, whether these two key proteins act in parallel or as a pathway is not resolved by presented data.

(4) It is very interesting that FABP4 regulates both lipid droplet formation and lipolysis, yet is unclear if the regulation of lipolysis is direct or if the accumulation of lipid droplets - likely plus some other signal(s) - induces upregulation of lipolysis genes.

(5) In several places increased expression of genes coding for enzymes with known functions in lipid biology is conflated with an increase in the lipid biology process the enzymes mediate. Additional evidence would be needed to show these processes are in fact increased in a manner dependent on increased enzyme expression.

Reviewer #1 (Public review):

Summary:

The authors show that the Gαs-stimulated activity of human membrane adenylyl cyclases (mAC) can be enhanced or inhibited by certain unsaturated fatty acids (FA) in an isoform-specific fashion. Thus, with IC50s in the 10-20 micromolar range, oleic acid affects 3-fold stimulation of membrane-preparations of mAC isoform 3 (mAC3) but it does not act on mAC5. Enhanced Gαs-stimulated activities of isoforms 2, 7, and 9, while mAC1 was slightly attenuated, but isoforms 4, 5, 6, and 8 were unaffected. Certain other unsaturated octadecanoic FAs act similarly. FA effects were not observed in AC catalytic domain constructs in which TM domains are not present. Oleic acid also enhances the AC activity of isoproterenol-stimulated HEK293 cells stably transfected with mAC3, although with lower efficacy but much higher potency. Gαs-stimulated mAC1 and 4 cyclase activity were significantly attenuated in the 20-40 micromolar by arachidonic acid, with similar effects in transfected HEK cells, again with higher potency but lower efficacy. While activity mAC5 was not affected by unsaturated FAs, neutral anandamide attenuated Gαs-stimulation of mAC5 and 6 by about 50%. In HEK cells, inhibition by anandamide is low in potency and efficacy. To demonstrate isoform specificity, the authors were able to show that membrane preparations of a domain-swapped AC bearing the catalytic domains of mAC3 and the TM regions of mAC5 are unaffected by oleic acid but inhibited by anandamide. To verify in vivo activity, in mouse brain cortical membranes 20 μM oleic acid enhanced Gαs-stimulated cAMP formation 1.5-fold with an EC50 in the low micromolar range.

Strengths:

(1) A convincing demonstration that certain unsaturated FAs are capable of regulating membrane adenylyl cyclases in an isoform-specific manner, and the demonstration that these act at the AC transmembrane domains.

(2) Confirmation of activity in HEK293 cell models and towards endogenous AC activity in mouse cortical membranes.

(3) Opens up a new direction of research to investigate the physiological significance of FA regulation of mACs and investigate their mechanisms as tonic or regulated enhancers or inhibitors of catalytic activity.

(4) Suggests a novel scheme for the classification of mAC isoforms.

Weaknesses:

(1) Important methodological details regarding the treatment of mAC membrane preps with fatty acids are missing.

(2) It is not evident that fatty acid regulators can be considered as "signaling molecules" since it is not clear (at least to this reviewer) how concentrations of free fatty acids in plasma or endocytic membranes are hormonally or otherwise regulated.

Reviewer #1 (Public review):

Summary:

The paper demonstrated through a comprehensive multi-omics study of the oviduct that the transcriptomic and proteomic landscape of the oviduct at 4 different preimplantation periods was dynamic during natural fertilization, pseudopregnancy, and superovulation using three independent cell/tissue isolation and analytical techniques. This work is very important for understanding oviductal biology and physiology. In addition, the authors have made all the results available in a web search format, which will maximize the public's access and foster and accelerate research in the field.

Strengths:

(1) The manuscript addresses an important and interesting question in the field of reproduction: how does the oviduct at different regions adapt to the sperm and embryos for facilitating fertilization and preimplantation embryo development and transport?

(2) Authors used cutting-edge techniques: Integrated multi-modal datasets followed by in vivo confirmation and machine learning prediction.

(3) RNA-seq, scRNA-seq, and proteomic results are immediately available to the scientific community in a web search format.

(4) Substantiated results indicate the source of inflammatory responses was the secretory cell population in the IU region when compared to other cell types; sperm modulate inflammatory responses in the oviduct; the oviduct displays immuno-dynamism.

Weaknesses:

(1) The rationale for using the superovulation model is not clear. The oviductal response to sperm and embryos can be studied by comparing mating with normal and vasectomized mice and comparing pregnancy vs pseudopregnancy (induced by mating with vasectomized males). Superovulation causes supraphysiological hormone levels and other confounding conditions.

(2) This study involves a very complex dataset with three different models at four time points. If possible, it would be very informative to generate a graphic abstract/summary of their major findings in oviductal responses in different models and time points

(3) The resolution of Figures 3A-3C in the submitted file was not high enough to assess the authors' conclusion.

(4) The authors need to double-check influential transcription factors identified by machine learning. Apparently, some of them (such as Anxa2, Ift88, Ccdc40) are not transcription factors at all.

Reviewer #1 (Public review):

Summary:

This work seeks to provide genetic evidence for a role for beta-adrenergic receptors that regulate heart rate and blood flow on cavernous malformation development using a zebrafish model, and to extend information regarding beta-adrenergic drug blockade in cavernous malformation development, with the idea that these drugs may be useful therapeutically.

Strengths:

The work shows that genetic loss of a specific beta-adrenergic receptor in zebrafish, adrb1, prevents embryonic venous malformations and CCM in adult zebrafish brains. Two drugs, propranolol and metoprolol, also blunt CCM in the adult fish brain. These findings are predicted to potentially impact the treatment of human CCM, and they increase understanding of the factors leading to CCM.

Weaknesses:

There are minor weaknesses that detract slightly from enthusiasm, including poor annotation of the Figure panels and lack of a baseline control for the study of Klf2 expression (Figure 4).

Reviewer #1 (Public review):

Summary:

Ma et al. show that melanoma cells induce an EMT-like state in nearby keratinocytes and that when this state is induced experimentally by Twist-overexpression the resulting alteration in keratinocytes is inhibitory for melanoma invasion. These conclusions are based on experiments in vivo with zebrafish and, in vitro, with human cells. The work is carefully done and provides new insights into the interactions between melanoma cells and their environment.

Strengths:

The use of both zebrafish and human cells adds confidence that findings are relevant to human melanomas while also further demonstrating the utility of the zebrafish system for discovering important new features of melanoma biology that could ultimately have clinical impacts. The work also combines a nice suite of approaches including different models for induced melanomagenesis in zebrafish, single-cell RNA-sequencing, and more. Some of the final observations are intriguing as well, especially the possibility of EMT-induced melanocyte-keratinocyte interactions via Jam3 expression; it will be interesting to see if this is indeed a mechanism for restraining melanoma invasion. The paper is clearly written and the inferences are appropriate for the results obtained. Overall the work makes a solid contribution to our understanding of important, but too often neglected, roles of the tumor microenvironment in promoting or inhibiting tumor progression and outcome.

Weaknesses:

No critical weaknesses were noted.

Reviewer #1 (Public review):

In this study, Hama et al. explored the molecular regulatory mechanisms underlying the formation of the ULK1 complex. By employing the AlphaFold structural prediction tool, they showed notable differences in the complex formation mechanisms between ULK1 in mammalian cells and Atg1 in yeast cells. Their findings revealed that in mammalian cells, ULK1, ATG13, and FIP200 form a complex with a stoichiometry of 1:1:2. These predicted interaction regions were validated through both in vivo and in vitro assays, enhancing our understanding of the molecular mechanisms governing ULK1 complex formation in mammalian cells. Importantly, they identified a direct interaction between ULK1 and FIP200, which is crucial for autophagy. However, some aspects of this manuscript require further clarification, validation, and correction by the authors.

Reviewer #1 (Public review):

Summary:

In this manuscript, the authors have tried to dissect the functions of Proteasome activator 28γ (PA28γ) which is known to activate proteasomal function in an ATP-independent manner. Although there are multiple works that have highlighted the role of this protein in tumours, this study specifically tried to develop a correlation with Complement C1q binding protein (C1QBp) that is associated with immune response and energy homeostasis.

Strengths:

The observations of the authors hint that beyond PA28y's association with the proteasome, it might also stabilize certain proteins such as C1QBP which influences energy metabolism.

Weaknesses:

The strength of the work also becomes its main drawback. That is, how PA28y stabilizes C1QBP or how C1QBP elicits its pro-tumourigenic role under PA28y OE.<br /> In most of the experiments, the authors have been dependent on the parallel changes in the expression of both the proteins to justify their stabilizing interaction. However, this approach is indirect at best and does not confirm the direct stabilizing effect of this interaction. IP experiments do not indicate direct interaction and have some quality issues. The upregulation of C1QBP might be indirect at best. It is quite possible that PA28y might be degrading some secondary protein/complex that is responsible for C1QBP expression. Since the core idea of the work is PA28y direct interaction with C1QBP stabilizing it, the same should be demonstrated in a more convincing manner.

In all of the assays, C1QBP has been detected as doublet. However, the expression pattern of the two bands varies depending on the experiment. In some cases, the upper band is intensely stained and in some the lower bands. Do C1QBP isoforms exist and are they differentially regulated depending on experiment conditions/tissue types?

Problems with the background of the work: Line 76. This statement is far-fetched. There are presently a number of works of literature that have dealt with the metabolic programming of OSCC including identification of specific metabolites. Moreover, beyond the estimation of OCR, the authors have not conducted any experiments related to metabolism. In the Introduction, the significance of this study and how it will extend our understanding of OSCC needs to be elaborated.

Reviewer #1 (Public review):

Summary:

The authors investigate the role of HSPA2 during mouse preimplantation development. Knocking down HSPA2 in zygotes, the authors describe lower chances of developing into blastocysts, which show a reduced number of inner cell mass cells. They find that HSPA2 mRNA and protein levels show some heterogeneity among blastomeres at the 4-cell stage and propose that HSPA2 could contribute to skewing their relative contribution to embryonic lineages. To test this, the authors try to reduce HSPA2 expression in one of the 2-cell stage blastomere and propose that it biases their contribution to towards extra-embryonic lineages. To explain this, the authors propose that HSPA2 would interact with CARM1, which controls chromatin accessibility around genes regulating differentiation into embryonic lineage.

Strengths:

(1) The study offers simple and straightforward experiments with large sample sizes.

(2) Unlike most studies in the field, this research often relies on both mRNA and protein levels to analyse gene expression and differentiation.

Weaknesses:

(1) Image and statistical analyses are not well described.

(2) The functionality of the overexpression construct is not validated.

(3) Tracking of KD cells in embryos injected at the 2-cell stage with GFP is unclear.

(4) A key rationale of the study relies on measuring small differences in the levels of mRNA and proteins using semi-quantitative methods to compare blastomeres. As such, it is not possible to know whether those subtle differences are biologically meaningful. For example, the lowest HSPA2 level of the embryo with the highest level is much higher than the top cell from the embryo with the lowest level. What does this level mean then? Does this mean that some blastomeres grafted from strong embryos would systematically outcompete all other blastomeres from weaker embryos? That would be very surprising. I think the authors should be more careful and consider the lack of quantitative power of their approach before reaching firm conclusions. Although to be fair, the authors only follow a long trend of studies with the same intrinsic flaw of this approach.

(5) Some of the analyses on immunostaining do not take into account that this technique only allows for semi-quantitative measurements and comparisons.<br /> a) Some of the microscopy images are shown with an incorrect look-up table.<br /> b) Some of the schematics are incorrect and misleading.

Reviewer #1 (Public review):

Summary:

This is a comprehensive study that clearly and deeply investigates the function of GATA6 in human early cardiac development.

Strengths:

This study combines hESC engineering, differentiation, detailed gene expression, genome occupancy, and pathway modulation to elucidate the role of GATA6 in early cardiac differentiation. The work is carefully executed and the results support the conclusions. The use of publicly available data is well integrated throughout the manuscript. The RIME experiments are excellent.

Weaknesses:

Much has been known about GATA6 in mesendoderm development, and this is acknowledged by the authors.

Reviewer #1 (Public Review):

In the current manuscript, the authors use theoretical and analytical tools to examine the possibility of neural projections to engage ensembles of synaptic clusters in active dendrites. The analysis is divided into multiple models that differ in the connectivity parameters, speed of interactions, and identity of the signal (electric vs. second messenger). They first show that random connectivity almost ensures the representation of presynaptic ensembles. As expected, this convergence is much more likely for small group sizes and slow processes, such as calcium dynamics. Conversely, fast signals (spikes and postsynaptic potentials) and large groups are much less likely to recruit spatially clustered inputs. Dendritic nonlinearity in the postsynaptic cells was found to play a highly important role in distinguishing these clustered activation patterns, both when activated simultaneously and in sequence. The authors tackled the difficult issue of noise, showing a beneficiary effect when noise 'happens' to fill in gaps in a sequential pattern but degraded performance at higher background activity levels. Last, the authors simulated selectivity to chemical and electrical signals. While they find that longer sequences are less perturbed by noise, in more realistic activation conditions, the signals are not well resolved in the soma.

While I think the premise of the manuscript is worth exploring, I have a number of reservations regarding the results.

(1) In the analysis, the authors made a simplifying assumption that the chemical and electrical processes are independent. However, this is not the case; excitatory inputs to spines often trigger depolarization combined with pronounced calcium influx; this mixed signaling could have dramatic implications on the analysis, particularly if the dendrites are nonlinear (see below)

(2) Sequence detection in active dendrites is often simplified to investigating activation in a part of or the entirety of individual branches. However, the authors did not do that for most of their analysis. Instead, they treat the entire dendritic tree as one long branch and count how many inputs form clusters. I fail to see why simplification is required and suspect it can lead to wrong results. For example, two inputs that are mapped to different dendrites in the 'original' morphology but then happen to fall next to each other when the branches are staggered to form the long dendrites would be counted as neighbors.

(3) The simulations were poorly executed. Figures 5 and 6 show examples but no summary statistics. The authors emphasize the importance of nonlinear dendritic interactions, but they do not include them in their analysis of the ectopic signals! I find it to be wholly expected that the effects of dendritic ensembles are not pronounced when the dendrites are linear.

To provide a comprehensive analysis of dendritic integration, the authors could simulate more realistic synaptic conductances and voltage-gated channels. They would find much more complicated interactions between inputs on a single site, a sliding temporal and spatial window of nonlinear integration that depends on dendritic morphology, active and passive parameters, and synaptic properties. At different activation levels, the rules of synaptic integration shift to cooperativity between different dendrites and cellular compartments, further complicated by nonlinear interactions between somatic spikes and dendritic events.

While it is tempting to extend back-of-the-napkin calculations of how many inputs can recruit nonlinear integration in active dendrites, the biological implementation is very different from this hypothetical. It is important to consider these questions, but I am not convinced that this manuscript adequately addressed the questions it set out to probe, nor does it provide information that was unknown beforehand.

Not only was I surprised, but the witnesses in the story were as well. This surprise could be related to the truth being revealed or the curiosity about who is responsible.

The passage shows the cruelness of an animal and also illustrates the behavior of animals being skilled at imitation. Though it did it unconsciously, it’s also harmful.

Showing Dupin's prowess in deduction and his unpredictable personality through a random dialogue. Even before the case officially begins, let the reader understand his character

I am not quite sure about the meaning of this sentence, is it means that normal people over interpreting the coincidences as the motivation of murderer?

I think the detective is smart. When he find the sash is difficult to be opened and needed to be fasten inside, he doesn’t quit the possibility that murderer could escape from the window but try to find if the window can fasten by itself.

When it comes to the crime, we will assume that it is committed by human, so the unusual sound could be interpreted as the terrified scream of the women or the shout of the murder; however, it couldn’t be recognized as any kinds of language, implying that the murderer might not be a human.

This may surprise you because it suggests that being clever doesn’t mean someone can analyze things well, which goes against the common belief that cleverness and analytical skill go hand in hand.

Reviewer #1 (Public review):

Summary

In this manuscript, Day et al. present a high-throughput version of expansion microscopy to increase the throughput of this well-established super-resolution imaging technique. Through technical innovations in liquid handling with custom-fabricated tools and modifications to how the expandable hydrogels are polymerized, the authors show robust ~4-fold expansion of cultured cells in 96-well plates. They go on to show that HiExM can be used for applications such as drug screens by testing the effect of doxorubicin on human cardiomyocytes. Interestingly, the effects of this drug on changing DNA organization were only detectable by ExM, demonstrating the utility of HiExM for such studies.

Overall, this is a very well-written manuscript presenting an important technical advance that overcomes a major limitation of ExM - throughput. As a method, HiExM appears extremely useful and the data generally support the conclusions.

Strengths

Hi-ExM overcomes a major limitation of ExM by increasing the throughput and reducing the need for manual handling of gels. The authors do an excellent job of explaining each variation introduced to HiExM to make this work and thoroughly characterize the impressive expansion isotropy. The dox experiments are generally well-controlled and the comparison to an alternative stressor (H2O2) significantly strengthens the conclusions.

Weaknesses

(1) It is still unclear to me whether or not cells that do not expand remain in the well given the response to point 1. The authors say the cells are digested and washed away but then say that there is a remaining signal from the unexpanded DNA in some cases. I believe this is still a concern that potential users of the protocol should be aware of.

(2) Regarding the response to point 9, I think this information should be included in the manuscript, possibly in the methods. It is important for others to have a sense of how long imaging may take if they were to adopt this method.

Joint Public Review:

TRPML1 functions as a lysosomal ion channel whose variants are associated with lysosomal storage disorder mucolipidosis type IV. Understanding the structure and function of sites involved in the allosteric control TRPML1 may provide new molecular moieties to target with prototypic drugs.

Gan et al provide the first high resolution cryo-EM structure of a mutant (Y404W) TRPML1 channel in the open state without any activating ligands. This new structure demonstrates how a mutation at a site some distance away from the pore can influence channel gating. The authors provide compelling electrophysiology evidence which supports the proposed Y404W gain of function effect.

The authors propose an allosteric mechanism whereby the engineered W404 sidechain provides extra van der Waals contacts within a pocket surrounded by helices of the voltage sensor-like domain (VSLD) and causes S4 bending which in turn opens the pore through the S4-S5 linker. Conversely, the authors functionally demonstrate that an alanine mutation at this site causes a loss of function. Although the authors do not provide a structure of the Y404A mutant, they propose that the alanine substitution disrupts the sidechain packing and likely destabilizes the open conformation.

TRPML1 channels are regulated by PIP2 species in the cell. In the lysosomal membrane, PI(3,5)P2 activates the channel, whereas in the plasma membrane PI(4,5)P2 inhibits it. Towards understanding its lipid regulation, the authors solve a cryo-EM structure of TRPML1 bound to PI(4,5)P2 in the closed state and provide functional evidence that PI(4,5)P2 occupancy inhibits TRPML1 currents.

Within this same structure, the authors observe a density which may be attributed to sphingomyelin (or possibly phosphocholine). Using electrophysiology on WT and Y404W channels, the authors report an antagonist effect of sphingomyelin on TRPML1 currents.

Taken together, the study provides convincing evidence for a gating (opening/closing) mechanism of the TRPML1 pore which can be allosterically regulated by altered side-chain packing and by lipid interactions within the VSLD.

Reviewer #1 (Public Review):

Summary:

This manuscript by Meissner and colleagues described a novel take on a classic social cognition paradigm developed for marmosets. The classic pull task is a powerful paradigm that has been used for many years across numerous species, but its analog approach has several key limitations. As such, it has not been feasible to adopt the task for neuroscience experiments. Here the authors capture the spirit of the classic task but provide several fundamental innovations that modernize the paradigm - technically and conceptually. By developing the paradigm for marmosets, the authors leverage the many advantages of this primate model for studies of social brain functions and their particular amenability to freely-moving naturalistic approaches.

Strengths:

The current manuscript describes one of the most exciting paradigms in primate social cognition to be developed in many years. By allowing for freely-moving marmosets to engage in high numbers of trials, while precisely quantifying their visual behavior (e.g. gaze) and recording neural activity this paradigm has the potential to usher in a new wave of research on the cognitive and neural mechanisms underlying primate social cognition and decision-making. This paradigm is an elegant illustration of how naturalistic questions can be adapted to more rigorous experimental paradigms. Overall, I thought the manuscript was well written and provided sufficient details for others to adopt this paradigm.

Reviewer #1 (Public review):

Summary:

Understanding large-scale neural activity remains a formidable challenge in neuroscience. While several methods have been proposed to discover the assemblies from such large-scale recordings, most of previous studies do not explicit modeling the temporal dynamics. This study is an attempt to uncover the temporal dynamics of assemblies using a tool that have been establish in other domains.

The authors previously introduced the compositional Restricted Boltzmann Machine (cRBM) to identify neuron assemblies in zebrafish brain activity. Building upon this, they now employ the Recurrent Temporal Restricted Boltzmann Machine (RTRBM) to elucidate the temporal dynamics within these assemblies. By introducing recurrent connections between hidden units, RTRBM could retrieve neural assemblies and their temporal dynamics from simulated and zebrafish brain data.

Strengths:

The RTRBM has been previously used in other domains. Training the model has been already established. This study is an application of such model to neuroscience. Overall, the paper is well-structured and the methodology is robust, the analysis is solid to support the authors claim.

Weaknesses:

The overall degree of advance is very limited. The performance improvement by RTRBM compared to their cRBM is marginal, and insights into assembly dynamics are limited.

(1) The biological insights from this method are constrained. Though the aim is to unravel neural ensemble dynamics, the paper lacks in-depth discussion on how this method enhances our understanding of zebrafish neural dynamics. For example, the dynamics of assemblies can be analyzed using various tools such as dimensionality reduction methods once we have identified them using cRBM. What information can we gain by knowing the effective recurrent connection between them? It would be more convincing to show this in real data.

(2) Including predicted and measured neural activity traces could aid readers in evaluating model efficacy. The current version only contains comparison of the statistics, such as mean and covariance.

Reviewer #1 (Public Review):

Summary:

This study provides valuable insights into the therapeutic effects of two parathyroid hormone (PTH) analogs on bone regeneration and osseointegration. The research is methodologically sound, employing a robust animal model and a comprehensive array of analytical techniques, including micro-CT, histological/histomorphometric analyses, and serum biochemical analysis.

Strengths:

The use of a large animal model, which closely mimics postmenopausal osteoporosis in humans, enhances the study's relevance to clinical applications. The study is well-structured, with clear objectives, detailed methods, and a logical flow from introduction to conclusion. The findings are significant, demonstrating the potential of rhPTH(1-34) and dimeric R25CPTH(1-34) in enhancing bone regeneration, particularly in the context of osteoporosis.

Weaknesses:

There are no major weaknesses.

Reviewer #1 (Public review):

Summary:

This paper presents a mechanistic study of rDNA origin regulation in yeast by SIR2. Each of the ~180 tandemly repeated rDNA gene copies contains a potential replication origin. Early-efficient initiation of these origins is suppressed by Sir2, reducing competition with origins distributed throughout the genome for rate-limiting initiation factors. Previous studies by these authors showed that SIR2 deletion advances replication timing of rDNA origins by a complex mechanism of transcriptional de-repression of a local PolII promoter causing licensed origin proteins (MCMcomplexes) to re-localize (slide along the DNA) to a different (and altered) chromatin environment. In this study, they identify a chromatin remodeler, FUN30, that suppresses the sir2∆ effect, and remarkably, results in a contraction of the rDNA to about one-quarter it's normal length/number of repeats, implicating replication defects of the rDNA. Through examination of replication timing, MCM occupancy and nucleosome occupancy on the chromatin in sir2, fun30, and double mutants, they propose a model where nucleosome position relative to the licensed origin (MCM complexes) intrinsically determines origin timing/efficiency. While their interpretations of the data are largely reasonable and can be interpreted to support their model, a key weakness is the connection between Mcm ChEC signal disappearance and origin firing. While the cyclical chromatin association-dissociation of MCM proteins with potential origin sequences may be generally interpreted as licensing followed by firing, dissociation may also result from passive replication and as shown here, displacement by transcription and/or chromatin remodeling. Moreover, linking its disappearance from chromatin in the ChEC method with such precise resolution needs to be validated against an independent method to determine the initiation site(s). Differences in rDNA copy number and relative transcription levels also are not directly accounted for, obscuring a clearer interpretation of the results. Nevertheless, this paper makes a valuable advance with the finding of Fun30 involvement, which substantially reduces rDNA repeat number in sir2∆ background. The model they develop is compelling and I am inclined to agree, but I think the evidence on this specific point is purely correlative and a better method is needed to address the initiation site question. The authors deserve credit for their efforts to elucidate our obscure understanding of the intricacies of chromatin regulation. At a minimum, I suggest their conclusions on these points of concern should be softened and caveats discussed. Statistical analysis is lacking for some claims.

Strengths are the identification of FUN30 as suppressor, examination of specific mutants of FUN30 to distinguish likely functional involvement. Use of multiple methods to analyze replication and protein occupancies on chromatin. Development of a coherent model.

Weaknesses are failure to address copy number as a variable; insufficient validation of ChEC method relationship to exact initiation locus; lack of statistical analysis in some cases.

Review of revised version and response letter:

In the response, the authors make some improvements by better quantifying 2D gels, adding some missing statistical analyses, analyzing the effect of fun30 on rDNA replication in strains with reduced rDNA copy number, and using ChIP-seq of MCMs to support the ChEC-seq data. However, these additions do not address the main issue that is at the heart of their model: where initiation precisely occurs and whether the location is altered in the mutant(s). Thus, mechanistic insight is limited.

Under the section "Addressing Alternative Explanations", the authors claim that processes like transcription and passive replication cannot affect the displaced complex specifically. Why? They are not on same DNA (as mentioned in the Fig 1 legend).

The model in Fig 7 implies that initiation sites are different in WT versus the mutants and this determines their timing/efficiency. But they also suggest that the same site might be used with different efficiencies in this response. I agree that both are possibilities and are not resolved.

Supporting their model requires better resolution to determine the actual replication initiation site. While this may be challenging, it should be feasible with methods to map nascent strands like DNAscent, or Okazaki fragment mapping.

The 2D gel analysis of strains with reduced rDNA copy numbers adequately addresses the copy number variable with regard to the replication effect.

Overall, the paper is improved by providing additional data and improved analysis. The paper nicely characterizes the effect of Fun30. The model is reasonable but remains lacking in precise details of mechanism.

Topic: Defining Distance Education Date: 1980 Course/Subject: Distance Education Studies

Notes Main Idea The paper analyzes existing definitions of distance education and identifies six essential components that should be included in a comprehensive definition. The analysis covers different educational philosophies and institutional contexts for distance education.

Key Definitions and Theorists Holmberg's Definition

Distance education involves the separation of teacher and learner. Requires planned, structured learning materials and institutional support. French Law (Loi 71.556 du 12 juillet 1971)

Defines distance education as learning where the teacher is not physically present, except for occasional tasks. Moore's Definition

Highlights separation of teaching and learning behaviors. Emphasizes the use of technical media and the importance of two-way communication. Peters’ Definition

Describes distance education as an industrialized form of education. Incorporates principles like division of labor, mass production, and mechanization in the teaching process. Six Essential Components of Distance Education Separation of Teacher and Student

Physical and temporal separation in the teaching and learning process. Role of Educational Organization

Planning, preparing, and providing learning materials and support. Use of Technical Media

Communication between teacher and learner facilitated by print, radio, television, or computers. Provision of Two-Way Communication

Opportunities for dialogue between teacher and learner. Possibility of Occasional Seminars

Allowing for some face-to-face interaction for didactic or social purposes. Participation in an Industrialized Form of Education

Incorporates aspects of industrial processes in the delivery of education, such as standardized materials and automated communication. Analysis and Discussion Educational Contexts and Models

Different definitions cater to various levels and types of education (e.g., correspondence, open learning, external studies). Theoretical frameworks like Peters' focus on the structural separation and mechanization of distance education. Challenges and Misconceptions

Confusion over terminology, such as correspondence study vs. distance education. Misunderstanding of the relationship between traditional and distance education models. Proposed Solution

The term 'distance education' is suggested as the most suitable to encompass various forms and philosophies of education that involve separation of teacher and learner. Implications The need for clarity in defining distance education for consistent policy development and theoretical analysis. Importance of recognizing the distinct nature of distance education as an industrialized form of learning. Questions/Cues What are the key differences between Holmberg’s and Peters’ definitions of distance education? How does Keegan's six-component framework help in distinguishing distance education from other forms of non-traditional education? Why is Peters’ view on industrialization important in understanding distance education? Summary The paper provides a detailed analysis of distance education by examining prominent definitions and proposing a comprehensive framework. Keegan emphasizes the industrialized nature of distance education and the necessity for clear terminology to distinguish it from other educational forms.

Reference Keegan, D. J. (1980). On defining distance education. Distance Education, 1(1), 13-36.

Reviewer #1 (Public review):

This manuscript describes soluble Uric Acid (sUA) as an endogenous inhibitor of CD38, affecting CD38 activity and NAD+ levels both in vitro and in vivo. Importantly, the inhibition constants calculated supports the claim that sUA inhibits CD38 under physiological conditions. These findings are of extreme importance to understand the regulation of an enzyme that has been shown to be the main NAD+/NMN-degrading enzyme in mammals, which impacts several metabolic processes and has major implications to understanding aging diseases. The manuscript is well written, the figures are self explanatory, and in the experiments presented, the data is very solid. The authors discuss the main limitations of the study, especially in regard to the in vivo results. As a whole, I believe that this is a very interesting manuscript that will be appreciated by the scientific community and that opens a lot of new questions in the field of metabolism and aging.

During the revision process, the authors have performed new experiments to respond to relevant questions raised by the reviewers. In other cases, they have made changes in the text to improve the manuscript.

I believe that this manuscript in its current form is a mature and relevant set of findings that deserve attention and future developments.

Reviewer #1 (Public review):

Summary:

In previous work, the authors described necrosis-induced apoptosis (NiA) as a consequence of induced necrosis. Specifically, experimentally induced necrosis in the distal pouch of larval wing imaginal discs triggers NiA in the lateral pouch. In this manuscript, the authors confirmed this observation and found that while necrosis can kill all areas of the disc, NiA is limited to the pouch and to some extent to the notum, but is excluded from the hinge region. Interestingly and unexpectedly, signaling by the Jak/Stat and Wg pathways inhibits NiA. Further characterization of NiA by the authors reveals that NiA also triggers regenerative proliferation which can last up to 64 hours following necrosis induction. This regenerative response to necrosis is significantly stronger compared to discs ablated by apoptosis. Furthermore, the regenerative proliferation induced by necrosis is dependent on the apoptotic pathway because RNAi targeting the RHG genes is sufficient to block proliferation. However, NiA does not promote proliferation through the previously described apoptosis-induced proliferation (AiP) pathway, although cells at the wound edge undergo AiP. Further examination of the caspase levels in NiA cells allowed the authors to group these cells into two clusters: some cells (NiA) undergo apoptosis and are removed, while others referred to as Necrosis-induced Caspase Positive (NiCP) cells survive despite caspase activity. It is the NiCP cells that repair cellular damage including DNA damage and that promote regenerative proliferation. Caspase sensors demonstrate that both groups of cells have initiator caspase activity, while only the NiA cells contain effector caspase activity. Under certain conditions, the authors were also able to visualize effector caspase activity in NiCP cells, but the level was low, likely below the threshold for apoptosis. Finally, the authors found that loss of the initiator caspase Dronc blocks regenerative proliferation, while inhibiting effector caspases by expression of p35 does not, suggesting that Dronc can induce regenerative proliferation following necrosis in a non-apoptotic manner. This last finding is very interesting as it implies that Dronc can induce proliferation in at least two ways in addition to its requirement in AiP.

Strengths:

This is a very interesting manuscript. The authors demonstrate that epithelial tissue that contains a significant number of necrotic cells is able to regenerate. This regenerative response is dependent on the apoptotic pathway which is induced at a distance from the necrotic cells. Although regenerative proliferation following necrosis requires the initiator caspase Dronc, Dronc does not induce a classical AiP response for this type of regenerative response. In future work, it will be very interesting to dissect this regenerative response pathway genetically.

Weaknesses:<br /> No weaknesses were identified.

Reviewer #1 (Public review):

Summary:

This work develops a simple, rapid, low-cost methodology for assembling combinatorially complete microbial consortia using basic laboratory equipment. The motivation behind this work is to make the study of microbial community interactions more accessible to laboratories that lack specialized equipment such as robotic liquid handlers or microfluidic devices. The method was tested on a library of Pseudomonas aeruginosa strains to demonstrate its practicality and effectiveness. It provided a means to explore the complex functional interactions within microbial communities and identify optimal consortia for specific functions, such as biomass production.

Strengths:

The primary strength of this manuscript lies in its accessibility and practicality. The method proposed by the authors allows any laboratory with standard equipment, such as multichannel pipettes and 96-well plates, to readily construct all possible combinations of microbial consortia from a given set of species. This greatly enhances access to full factorial designs, which were previously limited to labs with advanced technology.

Another strength of the manuscript is the measurement and analysis of the biomass of all possible combinations of 8 strains of P. aeruginosa. This analysis provides a concrete example of how the authors' new methodology can be used to identify the best-performing communities and map pairwise and higher-order functional interactions.

Notably, the authors do exceptionally well in providing a thorough description of the methodology, including detailed protocols and an R script for customizing the method to different experimental needs. This enhances the reproducibility and adaptability of the methodology, making it a valuable resource for researchers wishing to adopt this methodology.

Weaknesses:

While the methodology is robust and well-presented, there are some limitations that should be acknowledged more thoroughly. First, the method's scalability is an important factor. The authors indicate that it should be effective for up to 10-12 species, but there is no discussion of what sets this scale: time, amount of labor, consumables, the likelihood of error, sample volume, etc. Second, this methodology is tailored to construct communities where the abundance of each strain is identical in each combination. Therefore, combinations with a different number of strains also differ in the total initial amount of microbial cells. Second, variations in the initial proportions of the same set of strains cannot be readily explored. Third, the manuscript only discusses how to construct the combinations, and not how to assay them afterward (e.g. for community function, interspecific interactions, etc'). While details on how to achieve these goals are clearly outside the scope of this work, the use of biomass as an example function may obfuscate this caveat, which should be stated more explicitly.

Reviewer #1 (Public review):

Summary:

Odor- and taste-sensing are mediated by two different systems, the olfactory and gustatory systems, and have different behavioral roles. In this study, Wei et al. challenge this dichotomy by showing that odors can activate gustatory receptor neurons (GRNs) in Drosophila to promote feeding responses, including the proboscis extension response (PER) that was previously thought to be driven only by taste. While previous studies suggested that odors can promote PER to appetitive tastants, Wei et al. go further to show that odors alone cause PER, this effect is mediated through sweet-sensing GRNs, and sugar receptors are required. The study also shows that odor detection by bitter-sensing GRNs suppresses PER. The authors' conclusions are supported by behavioral assays, calcium imaging, electrophysiological recordings, and genetic manipulations. The observation that both attractive and aversive odors promote PER leaves an open question as to why this effect is adaptive. Overall, the study sheds new light on chemosensation and multimodal integration by showing that odor and taste detection converge at the level of sensory neurons, a finding that is interesting and surprising while also being supported by another recent study (Dweck & Carlson, Sci Advances 2023).

Strengths:

(1) The main finding that odors alone can promote PER by activating sweet-sensing GRNs is interesting and novel.

(2) The study uses video tracking of the proboscis to quantify PER rather than manual scoring, which is typically used in the field. The tracking method is less subjective and provides a higher-resolution readout of the behavior.

(3) The study uses calcium imaging and electrophysiology to show that odors activate GRNs. These represent complementary techniques that measure activity at different parts of the GRN (axons versus dendrites, respectively) and strengthen the evidence for this conclusion.

(4) Genetic manipulations show that odor-evoked PER is primarily driven by sugar GRNs and sugar receptors rather than olfactory neurons. This is a major finding that distinguishes this work from previous studies of odor effects on PER and feeding (e.g., Reisenman & Scott, 2019; Shiraiwa, 2008) that assumed or demonstrated that odors were acting through olfactory neurons.

Weaknesses/Limitations:

1) The authors may want to discuss why PER to odors alone has not been previously reported, especially as they argue that this is a broad effect evoked by many different odors. Previous studies testing the effect of odors on PER only observed odor enhancement of PER to sugar (Oh et al., 2021; Reisenman & Scott, 2019; Shiraiwa, 2008) and some of these studies explicitly show no effect of odor alone or odor with low sugar concentration; regardless, the authors likely would have noticed if PER to odor alone had occurred. Readers of this paper may also be aware of unpublished studies failing to observe an effect of PER on odor alone (including studies performed by this reviewer and unrelated work by other colleagues in the field), which of course the authors are not expected to directly address but may further motivate the authors to provide possible explanations.

(2) Many of the odor effects on behavior or neuronal responses were only observed at very high concentrations. Most effects seemed to require concentrations of at least 10-2 (0.01 v/v), which is at the high end of the concentration range used in olfactory studies (e.g., Hallem et al., 2004), and most experiments in the paper used a far higher concentration of 0.5 v/v. It is unclear whether these are concentrations that would be naturally encountered by flies.

(3) The calcium imaging data showing that sugar GRNs respond to a broad set of odors contrasts with results from Dweck & Carlson (Sci Adv, 2023) who recorded sugar neurons with electrophysiology and observed responses to organic acids, but not other odors. This discrepancy is not discussed.

(4) Related to point #1, it would be useful to see a quantification of the percent of flies or trials showing PER for the key experiments in the paper, as this is the standard metric used in most studies and would help readers compare PER in this study to other studies. This is especially important for cases where the authors are claiming that odor-evoked PER is modulated in the same way as previously shown for sugar (e.g., the effect of starvation in Figure S4).

(5) Given the novelty of the finding that odors activate sugar GRNs, it would be useful to show more examples of GCaMP traces (or overlaid traces for all flies/trials) in Figure 3. Only one example trace is shown, and the boxplots do not give us a sense of the reliability or time course of the response. A related issue is that the GRNs appear to be persistently activated long after the odor is removed, which does not occur with tastes. Why should that occur? Does the time course of GRN activation align with the time course of PER, and do different odors show differences in the latency of GRN activation that correspond with differences in the latency of PER (Figure S1A)?

(6) Several controls are missing, and in some cases, experimental and control groups are not directly compared. In general, Gal4/UAS experiments should include comparisons to both the Gal4/+ and UAS/+ controls, at least in cases where control responses vary substantially, which appears to be the case for this study. These controls are often missing, e.g. the Gal4/+ controls are not shown in Figure 2C-G and the UAS/+ controls are not shown in Figure 2J-L (also, the legend for the latter panels should be revised to clarify what the "control" flies are). For the experiments in Figure S5, the data are not directly compared to any control group. For several other experiments, the control and experimental groups are plotted in separate graphs (e.g., Figure 2C-G), and they would be easier to visually compare if they were together. In addition, for each experiment, the authors should denote which comparisons are statistically significant rather than just reporting an overall p-value in the legend (e.g., Figure 2H-L).

(7) Additional controls would be useful in supporting the conclusions. For the Kir experiments, how do we know that Kir is effective, especially in cases where odor-evoked PER was not impaired (e.g., Orco/Kir)? The authors could perform controls testing odor aversion, for example. For the Gr5a mutant, few details are provided on the nature of the control line used and whether it is in the same genetic background as the mutant. Regardless, it would be important to verify that the Gr5a mutant retains a normal sense of smell and shows normal levels of PER to stimuli other than sugar, ruling out more general deficits. Finally, as the method of using DeepLabCut tracking to quantify PER was newly developed, it is important to show the accuracy and specificity of detecting PER events compared to manual scoring.

(8) The authors' explanation of why both attractive and aversive odors promote PER (lines 249-259) did not seem convincing. The explanation discusses the different roles of smell and taste but does not address the core question of why it would be adaptive for an aversive odor, which flies naturally avoid, to promote feeding behavior.

Reviewer #1 (Public review):

Summary:

Here the authors address how reinforcement-based sensorimotor adaptation changes throughout development. To address this question, they collected many participants in ages that ranged from small children (3 years old) to adulthood (18+ years old). The authors used four experiments to manipulate whether binary and positive reinforcement was provided probabilistically (e.g., 30 or 50%) versus deterministically (e.g.,100%), and continuous (infinite possible locations) versus discrete (binned possible locations) when the probability of reinforcement varied along the span of a large redundant target. The authors found that both movement variability and the extent of adaptation changed with age.

Strengths:

The major strength of the paper is the number of participants collected (n = 385). The authors also answer their primary question, that reinforcement-based sensorimotor adaptation changes throughout development, which was shown by utilizing established experimental designs and computational modelling.

Weaknesses:

Potential concerns involve inconsistent findings with secondary analyses, current assumptions that impact both interpretation and computational modelling, and a lack of clearly stated hypotheses.

(1) Multiple regression and Mediation Analyses.

The challenge with these secondary analyses is that:<br /> (a) The results are inconsistent between Experiments 1 and 2, and the analysis was not performed for Experiments 3 and 4,<br /> (b) The authors used a two-stage procedure of using multiple regression to determine what variables to use for the mediation analysis, and<br /> (c) The authors already have a trial-by-trial model that is arguably more insightful.

Given this, some suggested changes are to:<br /> (a) Perform the mediation analysis with all the possible variables (i.e., not informed by multiple regression) to see if the results are consistent.<br /> (b) Move the regression/mediation analysis to Supplementary, since it is slightly distracting given current inconsistencies and that the trial-by-trial model is arguably more insightful.

(2) Variability for different phases and model assumptions:

A nice feature of the experimental design is the use of success and failure clamps. These clamped phases, along with baseline, are useful because they can provide insights into the partitioning of motor and exploratory noise. Based on the assumptions of the model, the success clamp would only reflect variability due to motor noise (excludes variability due to exploratory noise and any variability due to updates in reach aim). Thus, it is reasonable to expect that the success clamps would have lower variability than the failure clamps (which it obviously does in Figure 6), and presumably baseline (which provides success and failure feedback, thus would contain motor noise and likely some exploratory noise).

However, in Figure 6, one visually observes greater variability during the success clamp (where it is assumed variability only comes from motor noise) compared to baseline (where variability would come from:<br /> (a) Motor noise.<br /> (b) Likely some exploratory noise since there were some failures.<br /> (c) Updates in reach aim.

Given the comment above, can the authors please:<br /> (a) Statistically compare movement variability between the baseline, success clamp, and failure clamp phases.<br /> (b) The authors have examined how their model predicts variability during success clamps and failure clamps, but can they also please show predictions for baseline (similar to that of Cashaback et al., 2019; Supplementary B, which alternatively used a no feedback baseline)?<br /> (c) Can the authors show whether participants updated their aim towards their last successful reach during the success clamp? This would be a particularly insightful analysis of model assumptions.<br /> (d) Different sources of movement variability have been proposed in the literature, as have different related models. One possibility is that the nervous system has knowledge of 'planned (noise)' movement variability that is always present, irrespective of success (van Beers, R. J. (2009). Motor learning is optimally tuned to the properties of motor noise. Neuron, 63(3), 406-417). The authors have used slightly different variations of their model in the past. Roth et al (2023) directly compared several different plausible models with various combinations of motor, planned, and exploratory noise (Roth A, 2023, "Reinforcement-based processes actively regulate motor exploration along redundant solution manifolds." Proceedings of the Royal Society B 290: 20231475: see Supplemental). Their best-fit model seems similar to the one the authors propose here, but the current paper has the added benefit of the success and failure clamps to tease the different potential models apart. In light of the results of a), b), and c), the authors are encouraged to provide a paragraph on how their model relates to the various sources of movement variability and other models proposed in the literature.<br /> (e) line 155. Why would the success clamp be composed of both motor and exploratory noise? Please clarify in the text

(3) Hypotheses:

The introduction did not have any hypotheses of development and reinforcement, despite the discussion above setting up potential hypotheses. Did the authors have any hypotheses related to why they might expect age to change motor noise, exploratory noise, and learning rates? If so, what would the experimental behaviour look like to confirm these hypotheses? Currently, the manuscript reads more as an exploratory study, which is certainly fine if true, it should just be explicitly stated in the introduction. Note: on line 144, this is a prediction, not a hypothesis. Line 225: this idea could be sharpened. I believe the authors are speaking to the idea of having more explicit knowledge of action-target pairings changing behaviour.

Reviewer #1 (Public review):

Summary:

Sidarta-Oliveira et al. present TopOMetry, a novel dimensionality reduction method based on the eigendecomposition of approximated Laplace-Beltrami Operator. Shortly, TopOMetry is an iterative version of the existing spectral methods (e.g., Laplacian Eigenmap or Diffusion map). It approximates the Laplacian operators twice, once in a "phenotypic space" and then once again in the eigenbases space. By doing this the approximated operator will contain more information of the manifold, which allows for more robust and accurate downstream analyses.

Strengths:

(1) The approach was rigorously tested based on synthetic and real single-cell RNA-seq datasets.

(2) The package is well-made and easily scalable to millions of cells.

(3) The comprehensive documentation helps the end-users to run desired analyses.

Weaknesses:

(1) The method is an extension of the current state-of-art methods, not a fundamentally new one.

(2) Considering the target readers, the paper contains a lot of jargon.

Reviewer #1 (Public review):

Summary:

The signaling pathways regulating the immune response to bacteria and fungi have been well characterized in Drosophila. Using the recently identified anti-parasitoid effector Lectin24A as a read-out, this article describes the signaling pathways regulating the humoral response against parasites.

Strengths:

This study reveals a role of JAK-STAT, Toll, and GATA in the fat body in the regulation of Lectin24A. They also observe an enrichment of binding sites for NF-kB, STAT, and GATA factors upstream of ORFs of genes induced upon encapsulation. Based on this observation, they generalize their findings on the involvement of JAK-STAT, Toll, and Gata in the humoral response to encapsulation. Although roles for the Toll and JAK-STAT pathways in capsule formation have previously been identified, the merit of this article is in analyzing the roles of these pathways in the humoral response using a new gene readout that will be a precious tool in the community.

Weaknesses:

The data are mostly convincing, but not always analyzed with sufficient detail; their conclusions should be reinforced by monitoring Lectin24A gene expression by RT-qPCR, by adding additional time points and by using alternative genetic tools. Using read-outs of the Toll and Imd pathways as comparisons is also important. Thus, this paper is interesting and important in advancing our understanding of Drosophila immunity but not yet enough solid to reach definitive conclusions on the proposed claims.

DOI: 10.1038/s41419-024-06886-1

Resource: RRID:Addgene_81070

Curator: @olekpark

SciCrunch record: RRID:Addgene_81070

What is this?

DOI: 10.1186/s13041-024-01134-1

Resource: RRID:Addgene_92284

Curator: @olekpark

SciCrunch record: RRID:Addgene_92284

What is this?

DOI: 10.1038/s44161-024-00431-1

Resource: RRID:Addgene_73178

Curator: @olekpark

SciCrunch record: RRID:Addgene_73178

What is this?

DOI: 10.1038/s41598-024-70853-1

Resource: RRID:Addgene_26646

Curator: @olekpark

SciCrunch record: RRID:Addgene_26646

What is this?

DOI: 10.1038/s41467-024-51273-1

Resource: Addgene_19506

Curator: @olekpark

SciCrunch record: RRID:Addgene_19506

What is this?

DOI: 10.1038/s41420-024-02158-1

Resource: RRID:Addgene_89308

Curator: @olekpark

SciCrunch record: RRID:Addgene_89308

What is this?

DOI: 10.1038/s44320-024-00058-1

Resource: RRID:Addgene_128263

Curator: @olekpark

SciCrunch record: RRID:Addgene_128263

What is this?

Tiku, N., Schaul, K., & Chen, S. Y. (2023, Nov 12). AI-generated images show a world of stereotypes. The Washington Post Retrieved from https://ezproxy.lib.uwm.edu/login?url=https://www.proquest.com/newspapers/ai-generated-images-show-world-stereotypes/docview/2888705247/se-2

Melissa H. "These new tools let you see for yourself how biased AI image models are," https://www.technologyreview.com/2023/03/22/1070167/these-news-tool-let-you-see-for-yourself-how-biased-ai-image-models-are, found by using Google.

Reviewer #1 (Public review):

Summary:

Tian et al. investigated the effects of emotional signals in biological motion on pupil responses. In this study, subjects were presented with point-light biological motion stimuli with happy, neutral, and sad emotions. Their pupil responses were recorded with an eye tracker. Throughout the study, emotion type (i.e., happy/sad/neutral) and BM stimulus type (intact/inverted/non-BM/local) were systematically manipulated. For intact BM stimuli, happy BM induced a larger pupil diameter than neutral BM, and neutral BM also induced a larger pupil diameter than sad BM. Importantly, the diameter difference between happy and sad BM correlated with the autistic trait of individuals. These effects disappeared for the inverted BM and non-BM stimuli. Interestingly, both happy and sad emotions show superiority in pupil diameter.

Strengths:

(1) The experimental conditions and results are very easy to understand.<br /> (2) The writing and data presentation are clear.<br /> (3) The methods are sound. I have no problems with the experimental design and results.

Reviewer #1 (Public Review):

The authors use a previously established reporter comprising a slow- and a fast-folding fluorescent protein fused to a randomly-generated library of penta-peptides at its amino-terminus and a signal sequence for import into the endoplasmic reticulum (ER). They then determine the stability of these constructs in a high throughput FACS-sorting procedure and identify a set of peptides that route the construct to proteasomal degradation. Increasing the copy number of one of these peptides further decreases the stability of the construct. This polypeptide resembles a "degron" for ER proteins, because it also targets other ER proteins with different topological and folding properties for degradation. It only works when placed at the amino-terminus of a protein and utilizes components of the Hrd1 ubiquitin ligase complex, a well-established quality control ubiquitin ligase in the ER membrane. Importantly, the degron also targets ER-proteins in mammalian cells.

The authors convincingly show that fusion of their newly identified degron to the amino terminus of ER-resident proteins with different topology suffices to target them for proteasomal degradation. The data for this are well-founded and contain appropriate controls. While technically sound, the study does only give superficial information on general properties of the degron and its recognition by cellular factors. Further simple experiments would have addressed a number of important points. The authors only provide data about the composition of the identified amino acid sections from the high-throughput approach and the statistical preference for certain amino acids at individual positions. They do not study degron composition experimentally by substituting individual amino acids with other residues and analyzing protein stability. Increasing the numbers of the initially identified degron pentamer increases substrate turnover, but the basis for this remains unclear. Each copy may be actively involved in better recognition, elongation of the degron may facilitate accessibility by recognition factors or multiplying the short amino acid stretch may generate new signatures at the amino-terminus that are more readily recognized by a quality control machinery. Consequently, this study does not allow conclusions to be drawn about general properties of degron composition and/or structure. The degron also functions with cytoplasmic proteins, suggesting that similar characteristics of a polypeptide attract the attention of quality control systems also in other cellular compartments. However, the authors did not pursue this finding further, e.g. by identifying factors for degron recognition in the cytoplasm. It would have been particularly interesting to test whether the degron would initiate degradation when placed at cytoplasmically-exposed amino termini of membrane-bound ER proteins. Information on degron properties is required to better understand principles of substrate recognition by protein quality control pathways and to design constructs for targeting endogenous proteins via proteolysis targeting chimeras (PROTACs).

Reviewer 1 (Public Review):

Multiple sclerosis (MS) is a debilitating autoimmune disease that causes loss of myelin in neurons of the central nervous system. MS is characterized by the presence of inflammatory immune cells in several brain regions as well as the brain barriers (meninges). This study aims to understand the local immune hallmarks in regions of the brain parenchyma that are adjacent to the leptomeninges in a mouse model of MS. The leptomeninges are known to be a foci of inflammation in MS and perhaps "bleed" inflammatory cells and molecules to adjacent brain parenchyma regions. To do so, they use novel technology called spatial transcriptomics so that the spatial relationships between the two regions remain intact. The study identifies canonical inflammatory genes and gene sets such as complement and B cells enriched in the parenchyma in close proximity to the leptomeninges in the mouse model of MS but not control. The manuscript is very well written and easy to follow. The results will become a useful resource to others working in the field and can be followed by time series experiments where the same technology can be applied to the different stages of the disease.

Reviewer #1 (Public Review):

This is a technically sound paper focused on a useful resource around the DRGP phenotypes which the authors have curated, pooled, and provided a user-friendly website. This is aimed to be a crowd-sourced resource for this in the future. The authors should make sure they coordinate as well as possible with the NC datasets and community and broader fly community.

Reviewer #1 (Public Review):

Kainate receptors play various important roles in synaptic transmission. The receptors can be divided into low affinity kainate receptors (GluK1-3) and high affinity kainate receptos (GluK4-5). The receptors can assemble as homomers (GluK1-3) or low-high affinity heteromers (GluK4-5). The functional diversity is further increased by RNA splicing. Previous studies have investigated C-terminal splice variants of GluK1, but GluK1 N-terminal (exon 9) insertions have not been previously characterized. In this study Dhingra et al investigate the functional implications of a GluK1 splice variant that inserts a 15 amino acid segment into the extracellular N-terminal region of the protein using whole-cell and excised outside-out electrophysiology.

The authors convincingly show that the insertion profoundly impacts the function of GluK1-1a - the channels that have the insertion are slower to desensitize. The data also shows that the insertion changes the modulatory effects of Neto proteins, resulting in altered rates of desensitization and recovery from desensitization. To determine the mechanism by which the insertion exerts these functional effects, the authors perform pull-down assays of Neto proteins, and extensive mutagenesis on the insert.<br /> The electrophysiological part of the study is very rigorous and meticulous.

The biggest weakness of the manuscript is the structural work. Due to issues with preferred orientation (a common problem in cryo-EM), the 3D reconstructions are at a low resolution (in the 5-8 Å range) and cannot offer much mechanistic insight into the effects of the insertion. The authors have opted to keep this data unchanged in the revised manuscript.

Despite this, the study is a valuable contribution to the field because it characterizes a GluK1 variant that has not been studied before and highlights the functional diversity that exists within the kainate receptor family.

Reviewer #1 (Public Review):

This manuscript addresses the regulation of the osmosensing protein kinases, WNK1 and WNK3. Prior work by the authors has shown that these enzymes are activated by PEG400 or ethylene glycol and inhibited by chloride ion, and that activation is associated with a conformational transition from dimer to monomer. In X-ray structures of the WNK1/SA inactive dimer, a water-mediated hydrogen bond network was observed between the catalytic loop (CL) and the activation loop (AL), named CWN1. This led to the proposal that bound water may be part of the osmosensing mechanism.

The current study carries this work further, by applying PEG400 to Xtals of dimeric WNK1/SA. This results in a change in kinase conformation and space group, along with 4-9 fewer waters in CWN1 and the complete disappearance of another water cluster (CWN2) located at the dimer interface. Six conserved residues lining the CWN1 pocket in WNK3 are mutated to determine effects on activity and inhibition by chloride ion (measured by AL autophosphorylation) and monomer-dimer interconversion (light scattering).

The results show that two mutants (E314Q/A in WNK3) at a site central to the water cluster result in increased kinase activity (autophosphorylation), and increased SLS, interpreted as aggregation. Three sites (D279A, Y346F, M301A) inhibit kinase activity with varying effects on oligomerization - Y346A and M301A retain monomer-dimer ratios similar to WT while D279N promotes aggregation. K236A and K307A show activity and monomer:dimer ratios similar to WT. Selected mutants (E314Q, D279N, Y346F) and WT appear to retain osmosensitivity with comparable activation by PEG400.

The study concludes that osmolytes may activate the kinase by removing waters from the CWN1 and CWN2 clusters, suggesting that waters might be considered allosteric ligands that promote the inactive structure of WNKs. The differing effects of mutations may be ascribed to disruption of the water networks as well as inhibitory perturbations at the active site.

Comments on latest version:

The revised manuscript incorporated new experiments that satisfactorily addressed my concerns.

Reviewer #1 (Public review):

The authors construct a pair of E. coli populations that differ by a single gene duplication in a selectable fluorescent protein. They then evolve the two populations under differing selective regimes to assess whether the end result of the selective process is a "better" phenotype when starting with duplicated copies. Importantly, their starting duplicated population is structured to avoid the duplication-amplification process often seen in bacterial artificial evolution experiments. They find that while duplication increases robustness and speed of adaptation, it does not result in more highly adapted final states, in contrast to Ohno's hypothesis.

Comments on revised version:

The authors have addressed my prior concerns, and I have no further comments on the manuscript.

Reviewer #3 (Public review):

Summary:

In this manuscript the authors explore the contribution of metabolism to the response of two subpopulations of macrophages to bacterial pathogens commonly encountered in the human lung, as well as the influence of priming signals typically produced at a site of inflammation. The two subpopulations are resident airway macrophages (AM) isolated via bronchoalveolar lavage and monocyte-derived macrophages (MDM) isolated from human blood and differentiated using human serum. The two cell types were primed using IFNγ and Il-4, which are produced at sites of inflammation as part of initiation and resolution of inflammation respectively, followed by stimulation with either heat-killed tuberculosis (Mtb) or LPS to simulate interaction with a bacterial pathogen that is either gram-negative in the case of Mtb or gram-positive in the case of LPS. The authors use human cells for this work, which makes use of widely reported and thoroughly described priming signals, as well as model antigens. This makes the observations on the functional response of these two subpopulations relevant to human health and disease to a greater extent that the mouse models typically used to interrogate these interactions. To examine the relationship between metabolism and functional response, the authors measure rates of oxidative phosphorylation and glycolysis under baseline conditions, primed using IFNγ or IL-4, and primed and stimulated with Mtb or LPS.

Overall, this study reveals how inflammatory and anti-inflammatory cytokine priming contributes to the metabolic reprogramming of AM and MDM populations. Their conclusions regarding the relationship between cytokine secretion and inflammatory molecule expression in response to bacterial stimuli are supported by the data. The involvement of metabolism in innate immune cell function is relevant when devising treatment strategies that target the innate immune response during infection. The data presented in this paper further our understanding of that relationship and advance the field of innate immune cell biology.

Reviewer #1 (Public review):

Summary:

The authors were seeking to define the roles of the Drosophila caspar gene in embryonic development and primordial germ cell (PGC) formation. They demonstrate that PGC number, and the distribution of the germ cell determinant Oskar, change as a result of changes in caspar expression; reduction of caspar reduces PGC number and the domain of Oskar protein expression, while overexpression of caspar does the reverse. They also observe defects in syncytial nuclear divisions in embryos produced from caspar mutant mothers. Previous work from the same group demonstrated that Caspar protein interacts with two partners, TER94 and Vap33. In this paper, they show that maternal knockdown of TER94 results in embryonic lethality and some overlap of phenotypes with reduction of caspar, supporting the idea may work together in their developmental roles. The authors propose models for how Caspar might carry out its developmental functions. The most specific of these is that Caspar and its partners might regulate oskar mRNA stability by recruiting ubiquitin to the translational regulator Smaug.

Strengths:

The work identifies a new factor that is involved in PGC specification and points toward an additional pathway that may be involved in establishing and maintaining an appropriate distribution of Oskar at the posterior pole of the embryo. It also ties together earlier observations about the presence of TER94 in the pole plasm that have not heretofore been linked to a function.

Weaknesses:

(1) A PiggyBac insertion allele casp[c04227] is used throughout the paper and referred to as a loss-of-function allele (casp[lof]). While the authors avoid the terms 'null' or 'amorph' and on one occasion refer to the allele as a 'strong hypomorph', nevertheless terming it a 'loss-of-function' allele is misleading. This is because the phenotype of the allele when homozygous is different from the phenotype produced when heterozygous over a deficiency.

(2) The peptide counts in the mass spectrometry experiment aimed at finding protein partners for Casp are extremely low, except for Casp itself and TER94. Peptide counts of 1-2 seem to me to be of questionable significance.

(3) The pole bud phenotypes from TER94 knockdown and casp mutant shown in Fig 5 appear to be quite different. These differences are unexplained and seem inconsistent with the model proposed that the two proteins work in a common pathway. Whole embryos should also be shown, as the TER94 KD phenotype could result from a more general dysmorphism.

(4) Fig 6 is not quantitative, lacking even a second control staining to check for intensity variation artifacts. Therefore it shows that the distribution of Oskar protein changes in the various genotypes, but not convincingly that the level of Oskar changes as the paper claims.

(5) The error bars are huge in the graphs in Fig 7H, I, and J, and in fact these changes are not statistically significant. Therefore the conclusion that 'Reduction in Casp activity specifically affects Smaug degradation during the MZT' is not supported by the data in this figure.

Reviewer #1 (Public review):

Summary:

The manuscript studies nutrient intake rates for stationary and motile microorganisms to assess the effectiveness of swim vs. stay strategies. This work provides valuable insights on how the different strategies perform in the context of a simplified mathematical model that couples hydrodynamics to nutrient advection and diffusion. The swim and stay strategies are shown to yield similar nutrient flux under a range of conditions.

Strengths:

Strengths of the work include (i) the model prediction in Fig. 3 of nutrient flux applied to a range of microorganisms including an entire clade that are known to use different feeding strategies and (ii) a study of the interaction between cilia and absorption coverage showing the robustness of their predictions provided these regions have sufficient overlap.

Weaknesses:

In the revision, the authors have adequately addressed the weaknesses I raised in the first round of review.

Reviewer #2 (Public review):

Summary:

This computational modeling study addresses the observation that variable observations are interpreted differently depending on how much uncertainty an agent expects from its environment. That is, the same mismatch between a stimulus and an expected stimulus would be less significant, and specifically would represent a smaller prediction error, in an environment with a high degree of variability than in one where observations have historically been similar to each other. The authors show that if two different classes of inhibitory interneurons, the PV and SST cells, (1) encode different aspects of a stimulus distribution and (2) act in different (divisive vs. subtractive) ways, and if (3) synaptic weights evolve in a way that causes the impact of certain inputs to balance the firing rates of the targets of those inputs, then pyramidal neurons in layer 2/3 of canonical cortical circuits can indeed encode uncertainty-modulated prediction errors. To achieve this result, SST neurons learn to represent the mean of a stimulus distribution and PV neurons its variance.

The impact of uncertainty on prediction errors in an understudied topic, and this study provides an intriguing and elegant new framework for how this impact could be achieved and what effects it could produce. The ideas here differ from past proposals about how neuronal firing represents uncertainty. The developed theory is accompanied by several predictions for future experimental testing, including the existence of different forms of coding by different subclasses of PV interneurons, which target different sets of SST interneurons (as well as pyramidal cells). The authors are able to point to some experimental observations that are at least consistent with their computational results. The simulations shown demonstrate that if we accept its assumptions, then the authors' theory works very well: SSTs learn to represent the mean of a stimulus distribution, PVs learn to estimate its variance, firing rates of other model neurons scale as they should, and the level of uncertainty automatically tunes the learning rate, so that variable observations are less impactful in a high uncertainty setting.

Strengths:

The ideas in this work are novel and elegant, and they are instantiated in a progression of simulations that demonstrate the behavior of the circuit. The framework used by the authors is biologically plausible and matches some known biological data. The results attained, as well as the assumptions that go into the theory, provide several predictions for future experimental testing. The authors have taken into account earlier review comments to revise their paper in ways that enhance its clarity.

Weaknesses:

One weakness could be that the proposed theory does rely on a fairly large number of assumptions. However, there is at least some biological support for these. Importantly, the authors do lay out and discuss their key assumptions in the Discussion section, so readers can assess their validity and implications for themselves.

Joint Public Review:

Summary:

This study presents a strategy to efficiently isolate PcrV-specific BCRs from human donors with cystic fibrosis who have/had Pseudomonas aeruginosa (PA) infection. Isolation of mAbs that provide protection against PA may be a key to developing a new strategy to treat PA infection as the PA has intrinsic and acquired resistance to most antibiotic drug classes. Hale et al. developed fluorescently labeled antigen-hook and isolated mAbs with anti-PA activity. Overall, the authors' conclusion is supported by solid data analysis presented in the paper. Four of five recombinantly expressed PcrV-specific mAbs exhibited anti-PA activity in a murine pneumonia challenge model as potent as the V2L2MD mAb (equivalent to gremubamab). However, therapeutic potency for these isolated mAbs is uncertain as the gremubamab has failed in Phase 2 trials. Clarification of this point would greatly benefit this paper.

Strengths:

(1) High efficiency of isolating antigen-specific BCRs using an antigenic hook.

(2) The authors' conclusion is supported by data.

Weaknesses:

Although the authors state that the goal of this study was to generate novel protective mAbs for therapeutic use (P12; Para. 2), it is unclear whether PcrV-specific mAbs isolated in this study have therapeutic potential better than the gremubamab, which has failed in Phase 2 trials. Four of five PcrV-specific mAbs isolated in this study reduced bacterial burdens in mice as potent as, but not superior to, gremubamab-equivalent mAb. Clarification of this concern by revising the text or providing experimental results that show better potential than gremubamab would greatly benefit this paper.

Reviewer #1 (Public review):

Summary:

Animals in natural environments need to identify predator-associated cues and respond with the appropriate behavioral response to survive. In rodents, some chemical cues produced by predators (e.g., cat saliva) are detected by chemosensory neurons in the vomeronasal organ (VNO). The VNO transmits predator-associated information to the accessory olfactory bulb, which in turn projects to the medial amygdala and the bed nucleus of the stria terminalis, two regions implicated in the initiation of antipredator defensive behaviors. A downstream area to these two regions is the ventromedial hypothalamus (VMH), which has been shown to control both active (i.e., flight) and passive (i.e, freezing) antipredator defensive responses via distinct efferent projections to the anterior hypothalamic nucleus or the periaqueductal gray, respectively. However, whether differences in predator-associated sensory information initially processed in the VNO and further conveyed to the VMH can trigger different types of behavioral responses remained unexplored. To address this question, here the authors investigated the behavioral responses of mice exposed to either fresh or old cat saliva, and further compared the underlying neural circuits that are activated by cat saliva with different freshness.

The scientific question of the study is valid, the experiments were well-performed, and the statistical analyses are appropriate. However, there are some concerns that may directly affect the main interpretation of the results.

In this revised version of the manuscript, the authors have made important modifications in the text, inserted new experiments and performed additional data analyses, as recommended. These modifications have significantly improved the quality of the manuscript and addressed all the major concerns detected during the prior submission.

Reviewer #1 (Public review):

This manuscript from Schwintek and coworkers describes a system in which gas flow across a small channel (10^-4-10^-3 m scale) enables the accumulation of reactants and convective flow. The authors go on to show that this can be used to perform PCR as a model of prebiotic replication.

Strengths:

The manuscript nicely extends the authors' prior work in thermophoresis and convection to gas flows. The demonstration of nucleic acid replication is an exciting one, and an enzyme-catalyzed proof-of-concept is a great first step towards a novel geochemical scenario for prebiotic replication reactions and other prebiotic chemistry.

The manuscript nicely combines theory and experiment, which generally agree well with one another, and it convincingly shows that accumulation can be achieved with gas flows and that it can also be utilized in the same system for what one hopes is a precursor to a model prebiotic reaction. This continues efforts from Braun and Mast over the last 10-15 years extending a phenomenon that was appreciated by physicists and perhaps underappreciated in prebiotic chemistry to increasingly chemically relevant systems and, here, a pilot experiment with a simple biochemical system as a prebiotic model.

I think this is exciting work and will be of broad interest to the prebiotic chemistry community.

Weaknesses:

The manuscript states: "The micro scale gas-water evaporation interface consisted of a 1.5 mm wide and 250 µm thick channel that carried an upward pure water flow of 4 nl/s ≈ 10 µm/s perpendicular to an air flow of about 250 ml/min ≈ 10 m/s." This was a bit confusing on first read because Figure 2 appears to show a larger channel - based on the scale bar, it appears to be about 2 mm across on the short axis and 5 mm across on the long axis. From reading the methods, one understands the thickness is associated with the Teflon, but the 1.5 mm dimension is still a bit confusing (and what is the dimension in the long axis?) It is a little hard to tell which portion (perhaps all?) of the image is the channel. This is because discontinuities are present on the left and right sides of the experimental panels (consistent with the image showing material beyond the channel), but not the simulated panels. Based on the authors' description of the apparatus (sapphire/CNC machined Teflon/sapphire) it sounds like the geometry is well-known to them. Clarifying what is going on here (and perhaps supplying the source images for the machined Teflon) would be helpful.

The data shown in Figure 2d nicely shows nonrandom residuals (for experimental values vs. simulated) that are most pronounced at t~12 m and t~40-60m. It seems like this is (1) because some symmetry-breaking occurs that isn't accounted for by the model, and perhaps (2) because of the fact that these data are n=1. I think discussing what's going on with (1) would greatly improve the paper, and performing additional replicates to address (2) would be very informative and enhance the paper. Perhaps the negative and positive residuals would change sign in some, but not all, additional replicates?

The authors will most likely be familiar with the work of Victor Ugaz and colleagues, in which they demonstrated Rayleigh-Bénard-driven PCR in convection cells (10.1126/science.298.5594.793, 10.1002/anie.200700306). Not including some discussion of this work is an unfortunate oversight, and addressing it would significantly improve the manuscript and provide some valuable context to readers. Something of particular interest would be their observation that wide circular cells gave chaotic temperature profiles relative to narrow ones and that these improved PCR amplification (10.1002/anie.201004217). I think contextualizing the results shown here in light of this paper would be helpful. Again, it appears n=1 is shown for Figure 4a-c - the source of the title claim of the paper - and showing some replicates and perhaps discussing them in the context of prior work would enhance the manuscript.

I think some caution is warranted in interpreting the PCR results because a primer-dimer would be of essentially the same length as the product. It appears as though the experiment has worked as described, but it's very difficult to be certain of this given this limitation. Doing the PCR with a significantly longer amplicon would be ideal, or alternately discussing this possible limitation would be helpful to the readers in managing expectations.

DOI: 10.1038/s41598-018-20394-1

Resource: RRID:BDSC_32219

Curator: @maulamb

SciCrunch record: RRID:BDSC_32219

What is this?

Reviewer #1 (Public review):

Summary:

Lejeune et al. demonstrated sex-dependent differences in the susceptibility to MRSA infection. The authors demonstrated the role of the microbiota and sex hormones as potential determinants of susceptibility. Moreover, the authors showed that Th17 cells and neutrophils contribute to sex hormone-dependent protection in female mice.

Strengths:

The role of microbiota was examined in various models (gnotobiotic, co-housing, microbiota transplantation). The identification of responsible immune cells was achieved using several genetic knockouts and cell-specific depletion models. The involvement of sex hormones was clarified using ovariectomy and the FCG model.

Weaknesses:

The mechanisms by which specific microbiota confer female-specific protection remain unclear.

Reviewer #1 (Public review):

Summary:

The authors measured glutamate transients in the DMS of rats as they performed an action selection task. They identified diverse patterns of behavior and glutamate dynamics depending on the pre-existing behavioral phenotype of the rat (sign tracker or goal tracker). Using pathway-specific DREADDs, they showed that these behavioral phenotypes and their corresponding glutamate transients were differentially dependent on input from the prelimbic cortex to the DMS.

Strengths:

Overall there are some very interesting results that make an important contribution to the field. Notably, the results seem to point to differential recruitment of the PL-DMS pathway in goal-tracking vs sign-tracking behaviors.

Weaknesses:

There is a lot of missing information and data that should be reported/presented to allow a complete understanding of the findings and what was done. The writing of the manuscript was mostly quite clear, however, there are some specific leaps in logic that require more elaboration, and the focus at the start and end on cholinergic neurons and Parkinson's disease are, at the moment, confusing and require more justification.

Reviewer #1 (Public review):

The authors found that the loss of cell-ECM adhesion leads to the formation of giant monocular vacuoles in mammary epithelial cells. This process takes place in a macropinocytosis-like process and involves PI3 kinase. They further identified dynamin and septin as essential machinery for this process. Interestingly, this process is reversible and appears to protect cells from cell death.

Strengths: The data are clean and convincing to support the conclusions. The analysis is comprehensive, using multiple approaches such as SIM and TEM. The discussion on lactation is plausible and interesting.

Weaknesses: As the first paper describing this phenomenon, it is adequate. However, the elucidation of the molecular mechanisms is not as exciting as it does not describe anything new. It is hoped that novel mechanisms will be elucidated in the future. Especially the molecules involved in the reversing process could be quite interesting.

Reviewer #2 (Public review):

Summary:

This very interesting study originated from a serendipitous observation that the deletion of the disordered N-terminal tail of human SUMO1 enhances its binding to its interaction partners. This suggested that the N terminus of SUMO1 might be an intrinsic competitive inhibitor of SUMO-interacting motif (SIM) binding to SUMO1. Subsequent experiments support this mechanism, showing that in humans it is specific to SUMO1 and does not extend to SUMO2 or SUMO3 (except, perhaps, when the N terminus of SUMO2 becomes phosphorylated, as the authors intriguingly suggest - and partially demonstrate). The auto-inhibition of SUMO1 via its N-terminal tail apparently explains lower binding of SUMO1 compared to SUMO2 to some SIMs and lower SIM-dependent SUMOylation of some substrates with SUMO1 compared to SUMO2, thus adding an important element to the puzzle of SUMO paralogue preference. In line with this explanation, N-terminally truncated SUMO1 was equally efficient to SUMO2 in the studied cases. The inhibitory role of SUMO1's N terminus appears conserved in other species including S. cerevisiae and C. elegans, both of which contain only one SUMO. The study also elucidates the molecular mechanism by which the disordered N-terminal region of SUMO1 can exert this auto-inhibitory effect. This appears to depend on the transient, very highly dynamic physical interaction between the N terminus and the surroundings of the SIM-binding groove based mostly on electrostatic interactions between acidic residues in the N terminus and basic residues around the groove.

Strengths:

A key strength of this study is the interplay of different techniques, including biochemical experiments, NMR, molecular dynamics simulations, and, at the end, in vivo experiments. The experiments performed with these different techniques inform each other in a productive way and strengthen each others' conclusions. A further strength is the detailed and clear text, which patiently introduces, describes, and discusses the study. Finally, in terms of the message, the study has a clear, mechanistic message of fundamental importance for various aspects of the SUMO field, and also more generally for protein biochemists interested in the functional importance of intrinsically disordered regions. In revision, the authors have further improved the text.

Weaknesses:

In the future, further experimental validation will be required, particularly with regards to the biological importance of the uncovered mechanism. These limitations are satisfactorily pointed out by the authors themselves in the revised manuscript.

Reviewer #1 (Public review):

Summary:

In this study, Abidi and colleagues used Notch pathway neutralizing antibodies to inhibit sebaceous glands in the skin. The authors find that blocking either the Notch1 receptor or the Jag2 ligand caused loss of the glands and increased retention of sebaceous progenitor cells. Moreover, these glands began to reappear 14 days after treatment.

Strengths:

Overall, this study definitively identifies the Notch receptor/ligand combination that maintains these glands in the adult. The manuscript is clearly written and the figures are beautifully made.

In this resubmitted manuscript, the authors have adequately addressed all the previous critiques.

Reviewer #2 (Public review):

Summary:

The preprint by Fawaz et al. presents the findings of a study that aimed to assess the relationship between somatic mutations associated with clonal hematopoiesis (CHIP) and the prevalence of myocardial infarction (MI). The authors conducted targeted DNA sequencing analyses on samples from 149 MI patients and 297 non-MI controls from a separate cohort. Additionally, they investigated the impact of the loss of the Y chromosome (LOY), another somatic mutation frequently observed in clonally expanded blood cells. The results of the study primarily demonstrate no significant associations, as neither CHIP nor LOY were found to be correlated with an increased prevalence of MI. The null findings regarding CHIP are partly in conflict with several larger studies in the literature. However, it must be noted that the authors did find trends to an association between CHIP and a higher incidence of MI during follow-up among those without a history of MI at baseline, which is more consistent with previous research work. The association with incident MI reached statistical significance in men, particularly in those not showing LOY, suggesting potential interactions between different clonally-expanded somatic mutations.

Strengths:

Overall, this is a useful research work on an emerging risk factor for cardiovascular disease (CVD). The use of a targeted sequencing approach is a strength, as it offers higher sensitivity than the whole exome sequencing approaches used in many previous studies. Reporting null findings is definitely relevant in an emerging field such as the role of somatic mutations in cardiovascular disease.

Weaknesses:

The study suffers from important limitations, which cast some doubts onto the authors' conclusions, as detailed below:

(1) The small sample size of the study population is a critical limitation, particularly when reporting null findings that conflict (partly) with positive findings in much larger studies, totaling hundreds of thousands of individuals (e.g. Zekavat et al, Nature CVR 2023, Vlasschaert et al, Circulation 2023; Zhao et al, JAMA Cardio 2024). The authors claim that they have 90% power to detect an effect size of CHIP on MI comparable to that in previous reports (a hazard ratio of 1.7, mainly based on the findings by Jaiswal et al, NEJM 2014,2017). However, this analysis is simply based on the predicted prevalence of CHIP in MI(+) and MI(-) patients, and it does not consider the complex relationship between age CHIP and atherosclerotic disease. More advanced approaches to calculate statistical power may have provided a more accurate estimation. It must also be noted that recent work in much larger populations suggest that the overall effect of CHIP on atherosclerotic CVD is smaller than 1.7, most likely due to the heterogeneity of effects of different mutated genes (e.g. Zekavat et al, Nature CVR 2023, Vlasschaert et al, Circulation 2023; Zhao et al, JAMA Cardio 2024). In addition, several analyses in the current manuscript are conducted separately in MI(+) (n= 149) and MI(-) (N=297) individuals, further limiting statistical power. Power is even lower in the investigation of the effects of LOY and its interaction with CHIP, as only men are included in these analyses. Overall, I believe the study is underpowered from a statistical point of view, so the authors' findings need to be interpreted with caution.

(2) Related to the above, it is widely accepted that the effects of CHIP on CVD are highly heterogeneous, as some mutated genes appear to have a strong impact on atherosclerosis, whereas the effect of others is negligible (e.g. Zekavat et al, Nature CVR 2023, Vlasschaert et al, Circulation 2023, among others). TET2 mutations are frequently considered a "positive control", given the multiple lines of evidence suggesting that these mutations confer a higher risk of atherosclerotic disease. However, no association with MI or related variables was found for TET2 mutations in the current work, which likely reflects the limited statistical power of the study to assess accurately the effects of CHIP mutations on atherosclerotic disease.

(3) One of the most essential features of CHIP is the tight correlation with age. In this study, the effect of age on CHIP (e.g. Supp. Tables S5, S6) is statistically significant, but substantially milder than in previous studies. Given the relatively modest effect size of age on CHIP here, it is not surprising that no association with MI or atherosclerotic disease was found, considering that this association would have a much smaller effect size. It must be considered, however, that the advanced age of the population may have confounded the analysis of these relationships, as acknowledged by the authors.

(4) CHIP represents just one type of clonal hematopoiesis (e.g. see https://doi.org/10.1182/blood.2023022222). In this context, it must be noted that the mutated genes included in the definition of "CHIP" here are markedly different than in most previous studies, particularly when considering specifically the studies that demonstrated an association between CHIP and atherosclerotic CVD. For instance, the definition of CHIP in this manuscript includes genes such as ANKRD26, CALR, CCND2, DDX41... that are not prototypical CHIP genes. This is unlikely to have major impact on the main results, as the vast majority of mutations detected are indeed in bona fide CHIP genes, but it needs to be considered when interpreting the authors' findings. Furthermore, the strategy used here for CHIP variant calling and curation is substantially different than that used in previous studies. This is important, because such differences in the definition of CHIP and the curation of variants are at the basis of most conflicting findings in the literature regarding the effects of this condition. The authors estimate that the effect of these discrepancies on the definition of CHIP is limited, but small differences can have substantial impact in a study with limited sample size.

(5) A major limitation of the current study is the cross-sectional design of most of the analyses. For instance, it is not surprising that no association is found between CHIP and prevalent atherosclerosis burden by ultrasound imaging, considering that many individuals may have developed atherosclerosis years or decades before the expansion of the mutant clones, limiting the possible effect of CHIP on atherosclerosis burden. Similarly, the analysis of the relationship between CHIP and a history of MI may be confounded by the potential effects of MI on the expansion of mutant clones. In this context, it is noteworthy that the only positive results here are found in the analysis of the relationship between CHIP at baseline and incident MI development over follow-up. A larger sample size in these longitudinal analyses would provide deeper insights into the relationship between CHIP and MI.

Reviewer #1 (Public review):

Summary:

Bacteria exhibit species-specific numbers and localization patterns of flagella. How specificity in number and pattern is achieved is poorly understood but often depends on a soluble GTPase called FlhF. Here the authors take an unbiased protein-pulldown approach to identify a protein FipA in V. parahaemolyticus that interacts with FlhF. They show that FipA co-occurs with FlhF in the genomes of bacteria with polarly-localized flagella and study the role of FipA in three different bacteria: 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 to different species-specific extents.

Strengths:

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 prior to, 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.

Weaknesses:

For me the comparative analysis in the different organism was on balance, a weakness. By mixing the data for each of the organisms together, I found it difficult to read, and take away key points from the results. In its current form, the individual details seem to crowd out the model.

Reviewer #1 (Public Review):

Summary:

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

Strengths:

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

Weaknesses:

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

Reviewer #1 (Public review):

Summary:

Lodhiya et al. demonstrate that antibiotics with distinct mechanisms of action, norfloxacin, and streptomycin, cause similar metabolic dysfunction in the model organism Mycobacterium smegmatis. This includes enhanced flux through the TCA cycle and respiration as well as a build-up of reactive oxygen species (ROS) and ATP. Genetic and/or pharmacologic depression of ROS or ATP levels protect M. smegmatis from norfloxacin and streptomycin killing. Because ATP depression is protective, but in some cases does not depress ROS, the authors surmise that excessive ATP is the primary mechanism by which norfloxacin and streptomycin kill M. smegmatis. In general, the experiments are carefully executed; alternative hypotheses are discussed and considered; the data are contextualized within the existing literature. Clarification of the effect of 1) ROS depression on ATP levels and 2) ADP vs. ATP on divalent metal chelation would strengthen the paper, as would discussion of points of difference with the existing literature. The authors might also consider removing Figures 9 and 10A-B as they distract from the main point of the paper and appear to be the beginning of a new story rather than the end of the current one. Finally, statistics need some attention.

Strengths:

The authors tackle a problem that is both biologically interesting and medically impactful, namely, the mechanism of antibiotic-induced cell death.

Experiments are carefully executed, for example, numerous dose- and time-dependency studies; multiple, orthogonal readouts for ROS; and several methods for pharmacological and genetic depletion of ATP.

There has been a lot of excitement and controversy in the field, and the authors do a nice job of situating their work in this larger context.

Inherent limitations to some of their approaches are acknowledged and discussed e.g., normalizing ATP levels to viable counts of bacteria.

Weaknesses:

The authors have shown that treatments that depress ATP do not necessarily repress ROS, and therefore conclude that ATP is the primary cause of norfloxacin and streptomycin lethality for M. smegmatis. Indeed, this is the most impactful claim of the paper. However, GSH and dipyridyl beautifully rescue viability. Do these and other ROS-repressing treatments impact ATP levels? If not, the authors should consider a more nuanced model and revise the title, abstract, and text accordingly.

Does ADP chelate divalent metal ions to the same extent as ATP? If so, it is difficult to understand how conversion of ADP to ATP by ATP synthase would alter metal sequestration without concomitant burst in ADP levels.

Some of the results in the paper diverge from what has been previously reported by some of the referenced literature. These discrepancies should be clarified.

Joint Public Review:

Summary:

This work provides a new general tool for predicting post-ERCP pancreatitis before the procedure depending on pancreatic calcification, female sex, intraductal papillary mucinous neoplasm, a native papilla of Vater, or the use of pancreatic duct procedures. Even though it is difficult for the endoscopist to predict before the procedure which case might have post-ERCP pancreatitis, this new model score can help with the maneuver and when the patient is at high risk of pancreatitis, sometimes can be deadly), so experienced endoscopists can do the procedure from the start. This paper provides a model for stratifying patients before the ERCP procedure into low, moderate, and high risk for pancreatitis. To be validated, this score should be done in many countries and on large numbers of patients. Risk factors can also be identified and added to the score to increase rank.

Strengths:

(1) One of the severe complications of endoscopic retrograde cholangiopancreatography procedure is pancreatitis, so investigators try all the time to find a score that can predict which patients will probably have pancreatitis after the procedure. Most scores depend on the intraprocedural maneuver. Some studies discuss the preprocedural score that can predict pancreatitis before the procure. This study discusses a new preprocedural score for post-ERCP pancreatitis.

(2) Depending on this score that identifies low, moderate, and high-risk patients for post-pancreatitis, so from the start, experienced and well-trained endoscopists can do the procedure or can refer patients to tertiary hospitals or use interventional radiology or endoscopic retrograde cholangiopancreatography.

(3) The number of patients in this study is sufficient to analyze data correctly.

Weaknesses:

(1) It is a single-country, retrospective study.

(2) Many cases were excluded, so the score cannot be applied to those patients.

(3) Many other studies, e.g., https://link.springer.com/article/10.1007/s00464-021-08491-1, https://pubmed.ncbi.nlm.nih.gov/36344369/, that have been published before discussing the same issue, so what is the new with this score?

(4) The discussion section needs reformulation to express the study's aim and results.

(5) Why did the authors select these items in their scoring system and did not add more variables?

Reviewer #1 (Public review):

Summary:

In this manuscript, Muramoto and colleagues have examined a mechanism by which the executioner caspase Drice is activated in a non-lethal context in Drosophila. The authors have comprehensively examined this in the Drosophila olfactory receptor neurons using sophisticated techniques. In particular, they had to engineer a new reporter by which non-lethal caspase activation could be detected. The authors conducted a proximity labeling experiment and identified Fasciclin 3 as a key protein in this context. While the removal of Fascilin 3 did not block non-lethal caspase activation (likely because of redundant mechanisms), its overexpression was sufficient to activate non-lethal caspase activation.

Strengths:

While non-lethal functions of caspases have been reported in several contexts, far less is known about the mechanisms by which caspases are activated in these non-lethal contexts. So, the topic is very timely. The overall detail of this work is impressive and the results for the most part are well-controlled and justified.

Weaknesses:

The behavioral results shown in Figure 6 need more explanation and clarification (more details below). As currently shown, the results of Figure 6 seem uninterpretable. Also, overall presentation of the Figures and description in legends can be improved.

Reviewer #1 (Public review):

Summary:

The authors of this valuable study use linearly polarized UV light rotating at different angular velocities to stimulate photoreceptors in bumblebees and study the response of TL3 neurons to polarized light. Previous work has typically used a single constant rotation velocity of the polarized light, while the authors of this study explore a range of constant rotational velocities spanning from 30deg/s to 1920deg/s. The authors also use linearly polarized UV light rotating at continuously varying velocities following the angular velocity of the head of a flying bumblebee. 

Strengths:

The authors investigate the neuronal responses of TL3 neurons to a variety of rotational velocities. This approach has the potential to reveal the neuronal response to dynamically changing stimuli experienced by the animal as it moves around its environment.

The authors make good use of physiology and modeling to validate their hypotheses and findings.  If done right, this line of investigation has the potential to provide a very useful methodology for utilizing more complex stimuli in studies of the visual pathway and central complex than traditionally. 

Weaknesses: 

The attempt of the authors to use more naturalistic stimuli than previous studies is very important, but the stimulus they use, i.e. linearly polarized UV light projected on the whole dorsal rim of the animal's eyes, is very different from the circular pattern of UV light polarization coming through the sky. In particular, as a bumblebee turns under the sky, the light projected on each ommatidium of the dorsal rim area will not smoothly change like the rotating linearly polarized light used in the experiments. The authors need to discuss this and other limitations of their study. 

The authors should also commend the light intensity confound common in polarized light setups as discussed by Reinhard Wolf et al, J. Comp. Physiol. 1980 and in the thesis of Peter Weir, California Institute of Technology, 2013. It is unclear whether the authors performed measurements to quantify the intensity pattern and if they took measures to compensate and make the polarized light intensity uniform. 

The authors show that the neuronal responses of TL3 neurons depend on the recent history of the polarized light stimulus. They use as evidence, the different neuronal firing rates measured when arriving at the same polarization stimulus by following two different preceding stimulus sequences. It would have been worthwhile to investigate to what extent the difference in neuronal response is due to the history alone and to what extent it is due to spike timing stochasticity inherent in the neurons. According to the raster plots in Figure 2F, there is substantial stochasticity in the timing of the action potential firing events.

The authors appear to base their delay calculations and analysis on the response of one single neuron (Figures 2 and 3) even though they have recorded the responses of several TL3 neurons. There is no reason for the authors not to use all neuron recordings in their calculations and analysis.

Another concern is that while the authors make good use of modeling, like any model, the presented models only partially explain the observed phenomena. However, a discussion about the limitations of their model needs to be provided.  Actually, observing the discrepancies between the model's output and the intracellular recordings reveals what the model is missing. That is, careful consideration of the discrepancies would have led the authors to try adding some noise in their model, which would partially resolve the differences observed at the lower rotational speeds (see stars deviating from the fitted line in Figure 2A) and to consider that introducing an asymmetry between the post-stimulus inhibition and excitation time constants could result in a model not deviating as much at the higher rotation velocities during counter-clockwise rotation of the polarized light (see stars deviating from the fitted line in Figure 2A). 

In the end, the authors use the observation that during saccades, the average activity in their model-with-history increases to claim that when the animal does not turn, it uses less neuronal activity and energy. This is not a convincing line of reasoning. To make a claim about energy efficiency, the authors must instead compare their model with alternatives and show that the neuronal activity of their model during straight flight is indeed lower than those alternative models. Note that such a comparison would be meaningful only if the alternative models compared against capture physiology equally well in all other respects. However, the evident deviations of the presented model from the physiology measurements and the short duration of the test stimulus used would make any such claims difficult to substantiate. 

Finally, for most experiments, the models are stimulated with a single short yaw sequence lasting a few seconds to measure responses. Given the dependence of the model on history, using such a small sample, we cannot see how generalizable the observations are. The authors need to show that the same effect is produced using multiple different trajectories.

DOI: 10.1038/s41598-017-18989-1

Resource: RRID:BDSC_10403

Curator: @maulamb

SciCrunch record: RRID:BDSC_10403

What is this?

Reviewer #1 (Public review):

Summary:

The authors use microscopy experiments to track the gliding motion of filaments of the cyanobacteria Fluctiforma draycotensis. They find that filament motion consists of back-and-forth trajectories along a "track", interspersed with reversals of movement direction, with no clear dependence between filament speed and length. It is also observed that longer filaments can buckle and form plectonemes. A computational model is used to rationalize these findings.

Strengths:

Much work in this field focuses on molecular mechanisms of motility; by tracking filament dynamics this work helps to connect molecular mechanisms to environmentally and industrially relevant ecological behavior such as aggregate formation.

The observation that filaments move on tracks is interesting and potentially ecologically significant.

The observation of rotating membrane-bound protein complexes and tubular arrangement of slime around the filament provides important clues to the mechanism of motion.

The observation that long filaments buckle has the potential to shed light on the nature of mechanical forces in the filaments, e.g. through the study of the length dependence of buckling.

Weaknesses:

The manuscript makes the interesting statement that the distribution of speed vs filament length is uniform, which would constrain the possibilities for mechanical coupling between the filaments. However, Figure 1C does not show a uniform distribution but rather an apparent lack of correlation between speed and filament length, while Figure S3 shows a dependence that is clearly increasing with filament length. Also, although it is claimed that the computational model reproduces the key features of the experiments, no data is shown for the dependence of speed on filament length in the computational model. The statement that is made about the model "all or most cells contribute to propulsive force generation, as seen from a uniform distribution of mean speed across different filament lengths", seems to be contradictory, since if each cell contributes to the force one might expect that speed would increase with filament length.

The computational model misses perhaps the most interesting aspect of the experimental results which is the coupling between rotation, slime generation, and motion. While the dependence of synchronization and reversal efficiency on internal model parameters are explored (Figure 2D), these model parameters cannot be connected with biological reality. The model predictions seem somewhat simplistic: that less coupling leads to more erratic reversal and that the number of reversals matches the expected number (which appears to be simply consistent with a filament moving backwards and forwards on a track at constant speed).

Filament buckling is not analysed in quantitative detail, which seems to be a missed opportunity to connect with the computational model, eg by predicting the length dependence of buckling.

Reviewer #1 (Public review):

This is a clever and well-done paper. The authors sought to craft a method, applicable to biobank-scale data but without necessarily using genotyping or sequencing, to detect the presence of de novo mutations and rare variants that stand out from the polygenic background of a given trait. Their method depends essentially on sibling pairs where one sibling is in an extreme tail of the phenotypic distribution and whether the other sibling's regression to the mean shows a systematic deviation from what is expected under a simple polygenic architecture.

Their method is successful in that it builds on a compelling intuition, rests on a rigorous derivation, and seems to show reasonable statistical power in the UK Biobank. (More biobanks of this size will probably become available in the near future.) It is somewhat unsuccessful in that rejection of the null hypothesis does not necessarily point to the favored hypothesis of de novo or rare variants. The authors discuss the alternative possibility of rare environmental events of large effect.

Comments on current version:

The authors have addressed the concerns of the reviewers. I have no further comments.

Reviewer #1 (Public Review):

The authors demonstrate that it is possible to carry out eQTL experiments for the model eukaryote S. cerevisiae, in "one pot" preparations, by using single-cell sequencing technologies to simultaneously genotype and measure expression. This is a very appealing approach for investigators studying genetic variation in single-celled and other microbial systems, and will likely inspire similar approaches in non-microbial systems where comparable cell mixtures of genetically heterogeneous individuals could be achieved.

While eQTL experiments have been done for nearly two decades (the corresponding author's lab are pioneers in this field), this single-cell approach creates the possibility for new insights about cell biology that would be extremely challenging to infer using bulk sequencing approaches. The major motivating application shown here is to discover cell occupancy QTL, i.e. loci where genetic variation contributes to differences in the relative occupancy of different cell cycle stages. The authors dissect and validate one such cell cycle occupancy QTL, involving the gene GPA1, a G-protein subunit that plays a role in regulating the mating response MAPK pathway. They show that variation at GPA1 is associated with proportional differences in the fraction of cells in the G1 stage of the cell cycle. Furthermore, they show that this bias is associated with differences in mating efficiency.

Reviewer #1 (Public review):

Summary:

This important study investigates the neurobiological mechanisms underlying the stable operation and maintenance of functionally appropriate rhythmic motor patterns during changing environmental conditions - temperature in this study in the crab Cancer borealis stomatogastric neural pattern generating network producing the pyloric motor rhythm, which is naturally subjected to temperature perturbations over a substantial range. This study is relevant to the general problem that some rhythmic motor systems adjust to changing environmental conditions and state changes by increasing the cycle frequency in a smooth monotonic fashion while maintaining the relative timing of different network activity pattern phases that determine proper motor coordination. How this is achieved mechanistically in complex dynamic motor networks is not understood, particularly how the frequency and phase adjustments are achieved as conditions change while avoiding operational instabilities on different time scales. The authors specifically studied the contributions of the hyperpolarization-activated inward current (Ih), which is involved in rhythm control, to the adjustments of frequency and phases in the pyloric rhythmic pattern as the temperature was altered from 11 degrees C to 21 degrees C. They present compelling evidence that this current is a critical biophysical feature in the ability of this system to adjust transiently and persistently to temperature perturbations appropriately. After blocking Ih in the pyloric network with cesium, the network was unable to reliably produce its characteristic rapid and smooth increase in the frequency of the triphasic rhythmic motor pattern in response to increasing temperature or its typical steady-state increase in frequency over this Q10 temperature range.

Strengths:

(1) The authors addressed this problem by technically rigorous experiments in the crab Cancer borealis stomatogastric ganglion (STG) in vitro, which readily allows for neuronal activity recording in a behaviorally and architecturally defined rhythmic neural circuit in conjunction with the application of blockers of Ih and synaptic receptors to disrupt circuit interactions. This approach is an effective way to experimentally investigate how complex rhythmic networks, at least in poikilotherms, mechanistically adjust to environmental perturbations such as temperature.

(2) While previous work demonstrated that Ih increases in pyloric neurons as temperature increases, the authors here establish that this increase is necessary for normal responses of STG neural activity to temperature, which consist of a smooth monotonic increase in the frequency of rhythmic activity with increasing temperature.

(3) The data shows that blocking Ih with cesium causes the frequency to transiently decrease ("jags") when the temperature increases and then increases after the temperature stabilizes at a steady state, revealing a non-monotonic frequency response to temperature perturbations.

(4) The authors dissect some of the underlying neuronal and circuit dynamics, presenting evidence that after blocking Ih, the non-monotonic jags in the frequency response are mediated by intrinsic properties of pacemaker neurons, while in the steady state, Ih determined the overall frequency change (i.e., temperature sensitivity) through network interactions.

(5) The authors' results highlight more complex dynamic responses to increasing temperature for the first time, suggesting a longer timescale process than previously recognized that may result from interactions between multiple channels and/or ion channel kinetics.

Weaknesses:

(1) The involvement of Ih in achieving the frequency and phase adjustments as conditions change and allowing smooth transitions to avoid operational instabilities in other complex rhythmic motor networks, for example, in homeotherms, is not established, so the present results may have limited general extrapolations.

Reviewer #1 (Public review):

Summary:

Recruitment of neutrophils to the lungs is known to drive susceptibility to infection with M. tuberculosis. In this study, the authors present data in support of the hypothesis that neutrophil production of the cytokine IL-17 underlies the detrimental effect of neutrophils on disease. They claim that neutrophils harbor a large fraction of Mtb during infection, and are a major source of IL-17. To explore the effects of blocking IL-17 signaling during primary infection, they use IL-17 blocking antibodies, SR221 (an inverse agonist of TH17 differentiation), and celecoxib, which they claim blocks Th17 differentiation, and observe modest improvements in bacterial burdens in both WT and IFN-γ deficient mice using the combination of IL-17 blockade with celecoxib during primary infection. Celecoxib enhances control of infection after BCG vaccination.

Strengths:

The most novel finding in the paper is that treatment with celecoxib significantly enhances control of infection in BCG-vaccinated mice that have been challenged with Mtb. It was already known that NSAID treatments can improve primary infection with Mtb.

Weaknesses:

The major claim of the manuscript - that neutrophils produce IL-17 that is detrimental to the host - is not strongly supported by the data. Data demonstrating neutrophil production of IL-17 lacks rigor. The experiments examining the effects of inhibitors of IL-17 on the outcome of infection are very difficult to interpret. First, treatment with IL-17 inhibitors alone has no impact on bacterial burdens in the lung, either in WT or IFN-γ KO mice. This suggests that IL-17 does not play a detrimental role during infection. Modest effects are observed using the combination of IL-17 blocking drugs and celecoxib, however, the interpretation of these results mechanistically is complicated. Celecoxib is not a specific inhibitor of Th17. Indeed, it affects levels of PGE2, which is known to have numerous impacts on Mtb infection separate from any effect on IL-17 production, as well as other eicosanoids. Finally, the human data simply demonstrates that neutrophils and IL-17 both are higher in patients who experience relapse after treatment for TB, which is expected and does not support their specific hypothesis. The use of genetic ablation of IL-17 production specifically in neutrophils and/or IL-17R in mice would greatly enhance the rigor of this study. The authors do not address the fact that numerous studies have shown that IL-17 has a protective effect in the mouse model of TB in the context of vaccination. Finally, whether and how many times each animal experiment was repeated is unclear.

Reviewer #1 (Public review):

Summary:

In this paper Homan et al used mouse models of Metabolic Dysfunction-Associated Steatotic Liver Disease and different specific target deletions in cells to rule out the role of Complement 3a Receptor 1 in the pathogenesis of disease. They provided limited evidence and only descriptive results that despite C3aR being relevant in different contexts of inflammation, however, these tenets did not hold true.

Weaknesses:

(1) The results are based on readouts showing that C3aR is not involved in the pathogenesis of liver metabolic disease.

(2) The description of the mouse models they used to validate their findings is not clear. Lysm-cre mice - which are claimed to delete C3aR in (?) macrophages are not specific for these cells, and the genetic strategy to delete C3aR in Kupffer cells is not clear.

(3) Taking this into account, it is very challenging to determine the validity of these data, also considering that they are merely descriptive and correlative.

Reviewer #1 (Public review):

Summary:

This study puts forth the model that under IFN-B stimulation, liquid-phase WTAP coordinates with the transcription factor STAT1 to recruit MTC to the promoter region of interferon-stimulated genes (ISGs), mediating the installation of m6A on newly synthesized ISG mRNAs. This model is supported by strong evidence that the phosphorylation state of WTAP, regulated by PPP4, is regulated by IFN-B stimulation, and that this results in interactions between WTAP, the m6A methyltransferase complex, and STAT1, a transcription factor that mediates activation of ISGs. This was demonstrated via a combination of microscopy, immunoprecipitations, m6A sequencing, and ChIP. These experiments converge on a set of experiments that nicely demonstrate that IFN-B stimulation increases the interaction between WTAP, METTL3, and STAT1, that this interaction is lost with the knockdown of WTAP (even in the presence of IFN-B), and that this IFN-B stimulation also induces METTL3-ISG interactions.

Strengths:

The evidence for the IFN-B stimulated interaction between METTL3 and STAT1, mediated by WTAP, is quite strong. Removal of WTAP in this system seems to be sufficient to reduce these interactions and the concomitant m6A methylation of ISGs. The conclusion that the phosphorylation state of WTAP is important in this process is also quite well supported.

Weaknesses:

The evidence that the above mechanism is fundamentally driven by different phase-separated pools of WTAP (regulated by its phosphorylation state) is weaker. These experiments rely relatively heavily on the treatment of cells with 1,6-hexanediol, which has been shown to have some off-target effects on phosphatases and kinases (PMID 33814344). Given that the model invoked in this study depends on the phosphorylation (or lack thereof) of WTAP, this is a particularly relevant concern. Related to this point, it is also interesting (and potentially concerning for the proposed model) that the initial region of WTAP that was predicted to be disordered is in fact not the region that the authors demonstrate is important for the different phase-separated states. Taking all the data together, it is also not clear to me that one has to invoke phase separation in the proposed mechanism.

Reviewer #1 (Public review):

Summary:

The authors aimed to confirm the association between the human leukocyte antigen (HLA)-II region and tuberculosis (TB) susceptibility within admixed African populations. Building upon previous findings from the International Tuberculosis Host Genetics Consortium (ITHGC), this study sought to address the limitations of small sample size and the inclusion of admixed samples by employing the Local Ancestry Allelic Adjusted (LAAA) model, as well as identify TB susceptibility loci in an admixed South African cohort.

Strengths:

The major strengths of this study include the use of six TB case-control datasets collected over 30 years from diverse South African populations and ADMIXTURE for global ancestry inference. The former represents comprehensive dataset used in this study and the later ensures accurate determination of ancestral contributions. In addition, the identified association in the HLA-DPB1 gene shows near-genome-wide significance, enhancing the credibility of the findings.

Weaknesses:

The major weakness of this study includes insufficient significant discoveries and reliance on cross-validation. This study only identified one variant significantly associated with TB status, located in an intergenic region with an unclear link to TB susceptibility. Despite identifying multiple lead SNPs, no other variants reached the genome-wide significance threshold, limiting the overall impact of the findings. The absence of an independent validation cohort, with the study relying solely on cross-validation, is also a major limitation. This approach restricts the ability to independently confirm the findings and evaluate their robustness across different population samples.

Appraisal:

The authors successfully achieved their aims of confirming the association between the HLA-II region and TB susceptibility in admixed African populations. However, the limited number of significant discoveries, reliance on cross-validation, and insufficient discussion of model performance and SNP significance weaken the overall strength of the findings. Despite these limitations, the results support the conclusion that considering local ancestry is crucial in genetic studies of admixed populations.

Impact:

The innovative use of the LAAA model and the comprehensive dataset in this study make substantial contributions to the field of genetic epidemiology.

Reviewer #1 (Public review):

Summary:

The article by Piersma et al. aims to reduce the complex process of NK cell licensing to the action of a single inhibitory receptor for MHC class I. This is achieved using a mouse strain lacking all of the Ly49 receptors expressed by NK cells and inserting the Ly49a gene into the Ncr1 locus, leading to expression on the majority of NK cells.

Strengths:

The mouse model used represents a precise deletion of all NK-expressed genes within the Ly49 cluster. The re-introduction of the Ly49a gene into the Ncr1 locus allows expression by most NK cells. Convincing effects of Ly49a expression on in vitro activation and in vivo killing assay are shown.

Weaknesses:

The choice of Ly49a provides a clear picture of H-2Dd recognition by this Ly49. It would be valuable to perform additional studies investigating Ly49c and Ly49i receptors for H-2b. This is of interest because there are reports indicating that Ly49c may not be a functional receptor in B6 mice due to strong cis interactions.

This work generates an excellent mouse model for the study of NK cell licensing by inhibitory Ly49s that will be useful for the community. It provides a platform whereby the functional activity of a single Ly49 can be assessed.

Reviewer #1 (Public review):

Summary:

This paper describes the covalent interactions of small molecule inhibitors of carbonic anhydrase IX, utilizing a pre-cursor molecule capable of undergoing beta-elimination to form the vinyl sulfone and covalent warhead.

Strengths:

The use of a novel covalent pre-cursor molecule that undergoes beta-elimination to form the vinyl sulfone in situ. Sufficient structure-activity relationships across a number of leaving groups, as well as binding moieties that impact binding and dissociation constants.

Overall, the paper is clearly written and provides sufficient data to support the hypothesis and observations. The findings and outcomes are significant for covalent drug discovery applications and could have long-term impacts on related covalent targeting approaches.

Weaknesses:

No major weaknesses were noted by this reviewer.

Reviewer #1 (Public review):

Summary:

This work presents a computational platform that integrates currently available experimental or precomputed datasets and/or state-of-the-art modeling methods to assemble a proteome structure from a given list of genes (representing a whole proteome of an organism, or some specific subset of interest). The main advancement is that the proteome structure contains not only the tertiary structure information (such as is provided by precomputed AlphaFold predicted proteomes) but also information about the quaternary structure. Adding quaternary structure information on the whole proteomes is a challenging problem (and the manuscript would benefit from a more comprehensive introduction section presenting these challenges). Importantly, this addition of quaternary structure information is likely to significantly improve any downstream modelling or prediction. This is because most proteins form either stable or transient complexes, and a significant proportion of proteins interacts with cellular structures such as the different biological membranes. These interactions provide important context for interpreting residue-level information, such as for example the fitness/functional effects of point mutations.

Strengths:

The main strength of this work is that it approaches the question of protein quaternary structure in a comprehensive way. Namely, in addition to oligomeric state, it also includes membrane and cellular localization. It also demonstrates how to use and combine the available experimental and precomputed modelling to achieve the same for any set of genes.

Weaknesses:

The feasibility of obtaining a similar dataset (of useful/informative size) for a more complex organism is not clear.

Reviewer #1 (Public review):

"Unraveling the Role of Ctla-4 in Intestinal Immune Homeostasis: Insights from a novel Zebrafish Model of Inflammatory Bowel Disease" suggests the identification of the zebrafish homolog of ctla-4 and generates a 14bp deletion/early stop codon mutation that is viable. This mutant exhibits an IBD-like phenotype, including decreased intestinal length, abnormal intestinal folds, decreased goblet cells, abnormal cell junctions between epithelial cells, increased inflammation, and alterations in microbial diversity. Bulk and single-cell RNA-seq show upregulation of immune and inflammatory response genes in this mutant (especially in neutrophils, B cells, and macrophages) and downregulation of genes involved in adhesion and tight junctions in mutant enterocytes. The work suggests that the makeup of immune cells within the intestine is altered in these mutants, potentially due to changes in lymphocyte proliferation. Introduction of recombinant soluble Ctla-4-Ig to mutant zebrafish rescued body weight, histological phenotypes, and gene expression of several pro-inflammatory genes, suggesting a potential future therapeutic route.

Strengths:

- Generation of a useful new mutant.

- The demonstration of an IBD-like phenotype in this mutant is extremely comprehensive.

- Demonstrated gene expression differences provide mechanistic insight into how this mutation leads to IBD-like symptoms.

- Demonstration of rescue with a soluble protein suggests exciting future therapeutic potential.

- The manuscript is mostly well organized and well written.

Weaknesses:

- Given the sequence similarity between CTLA-4 and its related receptor CD28, and the difference in subcellular localization of this protein vs. human CTLA-4, some confusion remains about which gene is mutated in this manuscript (CD28 or CTLA-4/CD152).

- Some conclusions made from scRNAseq data (e.g. increased apoptosis, changes in immune cell numbers) could potentially result from dissociation artifacts and would be stronger with validation staining.

- The Methods section is woefully incomplete and describes fewer than half of the experiments performed in this manuscript.

Reviewer #1 (Public review):

Summary:

Evading predation is of utmost importance for most animals and camouflage is one of the predominant mechanisms. Wu et al. set out to test the hypothesis of a unique camouflage system in leafhoppers. These animals coat themselves with brochosomes, which are spherical nanostructures that are produced in the Malpighian tubules and are distributed on the cuticle after eclosion. Based on previous findings on the reflectivity properties of brochosomes, the authors provide very good evidence that these nanostructures indeed reduce the reflectivity of the animals thereby reducing predation by jumping spiders. Further, they identify four proteins, which are essential for the proper development and function of brochosomes. In RNAi experiments, the regular brochosome structure is lost, the reflectivity reduced and the respective animals are prone to increased predation. Finally, the authors provide some phylogenetic sequence analyses and speculate about the evolution of these essential genes.

Strengths:

The study is very comprehensive including careful optical measurements, EM and TM analysis of the nanoparticles and their production line in the malphigian tubules, in vivo predation tests, and knock-down experiments to identify essential proteins. Indeed, the results are very convincingly in line with the starting hypothesis such that the study robustly assigns a new biological function to the brochosome coating system.

A key strength of the study is that the biological relevance of the brochosome coating is convincingly shown by an in vivo predation test using a known predator from the same habitat.

Another major step forward is an RNAi screen, which identified four proteins, which are essential for the brochosome structure (BSMs). After respective RNAi knock-downs, the brochosomes show curious malformations that are interesting in terms of the self-assembly of these nanostructures. The optical and in vivo predation tests provide excellent support for the model that the RNAi knock-down leads to a change of brochosomes structure, which reduces reflectivity, which in turn leads to a decrease of the antipredatory effect.

Weaknesses:

The reduction of reflectivity by aberrant brochosomes or after ageing is only around 10%. This may seem little to have an effect in real life. On the other hand, the in vivo predation tests confirm an influence. Hence, this is not a real weakness of the study - just a note to reconsider the wording for describing the degree of reflectivity.<br /> The single gene knockdowns seemed to lead to a very low penetrance of malformed brochosomes (Figure Supplement 3). Judging from the overview slides, less than 1% of brochosomes may have been affected. A quantification of regular versus abnormal particles in both, wildtype and RNAi treatments would have helped to exclude that the shown aberrant brochosomes did not just reflect a putative level of "normal" background defects. Of note, the quadruple knock-down of all BSMs seemed to lead to a high penetrance (Figure 4), which was already reflected in the microtubule production line. While the data shown are convincing, a quantification might strengthen the argument.

While the RNAi effects seemed to be very specific to brochosomes and therefore very likely specific, an off-target control for RNAi was still missing. Finding the same/similar phenotype with a non-overlapping dsRNA fragment in one off-target experiment is usually considered required and sufficient. Further, the details of the targeted sequence will help future workers on the topic.

The main weakness in the current manuscript may be the phylogenetic analysis and the model of how the genes evolved. Several aspects were not clearly or consistently stated such that I felt unsure about what the authors actually think. For instance: Are all the 4 BSMs related to each other or only BSM2 and 3? If so, not only BSM2 and 3 would be called "paralogs" but also the other BSMs. If they were all related, then a phylogenetic tree including all BSMs should be shown to visualize the relatedness (including the putative ancestral gene if that is the model of the authors). Actually, I was not sure about how the authors think about the emergence of the BSMs. Are they real orphan genes (i.e. not present outside the respective clade) or was there an ancestral gene that was duplicated and diverged to form the BSMs? Where in the phylogeny does the first of the BSMs or ancestral proteins emerge (is the gene found in Clastoptera arizonana the most ancestral one?)? Maybe, the evolution of the BSMs would have to be discussed individually for each gene as they show somewhat different patterns of emergence and loss (BSM4 present in all species, the others with different degrees of phylogenetic restriction). Related to these questions I remained unsure about some details in Figure 5. On what kind of analysis is the phylogeny based? Why are some species not colored, although they are located on the same branch as colored ones? What is the measure for homology values - % identity/similarity? The homology labels for Nephotetix cincticeps and N. virescens seem to be flipped: the latter is displayed with 100% identity for all genes with all proteins while the former should actually show this. As a consequence of these uncertainties, I could not fully follow the respective discussion and model for gene evolution.

Conclusion:

The authors successfully tested their hypothesis in a multidisciplinary approach and convincingly assigned a new biological function to the brochosomes system. The results fully support their claims - only the quantification of the penetrance in the RNAi experiments would be helpful to strengthen the point. The author's analysis of the evolution of BSM genes remained a bit vague and I remained unsure about their respective conclusions.

The work is a very interesting study case of the evolutionary emergence of a new system to evade predators. Based on this study, the function of the BSM genes could now be studied in other species to provide insights into putative ancestral functions. Further, studying the self-assembly of such highly regular complex nano-structures will be strongly fostered by the identification of the four key structural genes.

Reviewer #1 (Public review):

In the present work, Chen et al. investigate the role of short heat shock factors (S-HSF), generated through alternative splicing, in the regulation of the heat shock response (HSR). The authors focus on S-HsfA2, an HSFA2 splice variant containing a truncated DNA-binding domain (tDBD) and a known transcriptional-repressor leucin-rich domain (LRD). The authors found a two-fold effect of S-HsfA2 on gene expression. On the one hand, the specific binding of S-HsfA2 to the heat-regulated element (HRE), a novel type of heat shock element (HSE), represses gene expression. This mechanism was also shown for other S-HSFs, including HsfA4c and HsfB1. On the other hand, S-HsfA2 is shown to interact with the canonical HsfA2, as well as with a handful of other HSFs, and this interaction prevents HsfA2 from activating gene expression. The authors also identified potential S-HsfA2 targets and selected one, HSP17.6B, to investigate the role of the truncated HSF in the HSR. They conclude that S-HsfA2-mediated transcriptional repression of HSP17.6B helps avoid hyperactivation of the HSR by counteracting the action of the canonical HsfA2.

The manuscript is well written and the reported findings are, overall, solid. The described results are likely to open new avenues in the plant stress research field, as several new molecular players are identified. Chen et al. use a combination of appropriate approaches to address the scientific questions posed. However, in some cases, the data are inadequately presented or insufficient to fully support the claims made. As such, the manuscript would highly benefit from tackling the following issues:

(1) While the authors report the survival phenotypes of several independent lines, thereby strengthening the conclusions drawn, they do not specify whether the presented percentages are averages of multiple replicates or if they correspond to a single repetition. The number of times the experiment was repeated should be reported. In addition, Figure 7c lacks the quantification of the hsp17.6b-1 mutant phenotype, which is the background of the knock-in lines. This is an essential control for this experiment.

(2) In Figure 1c, the transcript levels of HsfA2 splice variants are not evident, as the authors only show the quantification of the truncated variant. Moreover, similar to the phenotypes discussed above, it is unclear whether the reported values are averages and, if so, what is the error associated with the measurements. This information could explain the differences observed in the rosette phenotypes of the S-HsfA2-KD lines. Similarly, the gene expression quantification presented in Figures 4 and 5, as well as the GUS protein quantification of Figure 3F, also lacks this crucial information.

(3) The quality of the main figures is low, which in some cases prevents proper visualization of the data presented. This is particularly critical for the quantification of the phenotypes shown in Figure 1b and for the fluorescence images in Figures 4f and 5b. Also, Figure 9b lacks essential information describing the components of the performed experiments.

(4) Mutants with low levels of S-HsfA2 yield smaller plants than the corresponding wild type. This appears contradictory, given that the proposed role of this truncated HSF is to counteract the growth repression induced by the canonical HSF. What would be a plausible explanation for this observation? Was this phenomenon observed with any of the other tested S-HSFs?

(5) In some cases, the authors make statements that are not supported by the results:<br /> (i) the claim that only the truncated variant expression is changed in the knock-down lines is not supported by Figure 1c;<br /> (ii) the increase in GUS signal in Figure 3a could also result from local protein production;<br /> (iii) in Figure 6b, the deletion of the HRE abolishes heat responsiveness, rather than merely altering the level of response; and<br /> (iv) the phenotypes in Figure 8b are not clear enough to conclude that HSP17.6B overexpressors exhibit a dwarf but heat-tolerant phenotype.

Reviewer #1 (Public review):

Summary:

This manuscript addresses an important problem of the uncoupling of oxidative phosphorylation due to hypoxia-ischemia injury of the neonatal brain and provides insight into the neuroprotective mechanisms of hypothermia treatment.

Strengths:

The authors used a combination of in vivo imaging of awake P10 mice and experiments on isolated mitochondria to assess various key parameters of the brain metabolism during hypoxia-ischemia with and without hypothermia treatment. This unique approach resulted in a comprehensive data set that provides solid evidence for the derived conclusions.

Weaknesses:

(1) The experiments were performed acutely on the same day when the surgery was performed. There is a possibility that the physiology of mice at the time of imaging was still affected by the previously applied anesthesia. This is particularly of concern since the duration of anesthesia was relatively long. Is it possible that the observed relatively low baseline OEF (~20%) and trends of increased OEF and CBF over several hours after the imaging start were partially due to slow recovery from prolonged anesthesia? The potential effects of long exposure to anesthesia before imaging experiments were not discussed.

(2) The Methods Section does not provide information about drugs administered to reduce the pain. If pain was not managed, mice could be experiencing significant pain during experiments in the awake state after the surgery. Since the imaging sessions were long (my impression based on information from the manuscript is that imaging sessions were ~4 hours long or even longer), the level of pain was also likely to change during the experiments. It was not discussed how significant and potentially evolving pain during imaging sessions could have affected the measurements (e.g., blood flow and CMRO2). If mice received pain management during experiments, then it was not discussed if there are known effects of used drugs on CBF, CMRO2, and lesion size after 24 hr.

(3) Animals were imaged in the awake state, but they were not previously trained for the imaging procedure with head restraint. Did animals receive any drugs to reduce stress? Our experience with well-trained young-adult as well as old mice is that they can typically endure 2 and sometimes up to 3 hours of head-restrained awake imaging with intermittent breaks for receiving the rewards before showing signs of anxiety. We do not have experience with imaging P10 mice in the awake state. Is it possible that P10 mice were significantly stressed during imaging and that their stress level changed during the imaging session? This concern about the potential effects of stress on the various measured parameters was not discussed.

(4) The temperature of the skull was measured during the hypothermia experiment by lowering the water temperature in the water bath above the animal's head. Considering high metabolism and blood flow in the cortex, it could be challenging to predict cortical temperature based on the skull temperature, particularly in the deeper part of the cortex.

(5) The map of estimated CMRO2 (Fig. 4B) looks very heterogeneous across the brain surface. Is it a coincidence that the highest CMRO2 is observed within the central part of the field of view? Is there previous evidence that CMRO2 in these parts of the mouse cortex could vary a few folds over a 1-2 mm distance?

(6) The justification for using P10 mice in the experiments has not been well presented in the manuscript.

(7) It was not discussed how the observations made in this manuscript could be affected by the potential discrepancy between the developmental stages of P10 mice and human babies regarding cellular metabolism and neurovascular coupling

Reviewer #1 (Public review):

In this study, Sarver and colleagues carried out an exhaustive analysis of the functioning of various components (Complex I/II/IV) of the mitochondrial electron transport chain (ETC) using a real-time cell metabolic analysis technique (commonly referred as Seahorse oxygen consumption rate (OCR) assay). The authors aimed to generate an atlas of ETC function in about 3 dozen tissue types isolated from all major mammalian organ systems. They used a recently published improvised method by which ETC function can be quantified in freshly frozen tissues. This method enabled them to collect data from almost all organ systems from the same mouse and use many biological replicates (10 mice/experiment) required for an unbiased and statistically robust analysis. Moreover, they studied the influence of sex (male and female) and aging (young adult and old age) on ETC function in these organ systems. The main findings of this study are (1) cells in the heart and kidneys have very active ETC complexes compared to other organ systems, (2) the sex of the mice has little influence on the ETC function, and (3) aging undermined the mitochondrial function in most tissue, but surprisingly in some tissue aging promoted the activity of ETC complexes (e.g., Quadriceps, plantaris muscle, and Diaphragm).

Comments on revised version:

The revised manuscript has improved significantly, addressing some of my previous concerns in the discussion. There is no doubt the method used to estimate the maximal uncoupled respiration rate in mitochondria across different organ systems and ages is excellent for getting an overview of the mitochondrial state. However, the correlation between the measured maximal respiration rate and the actual mitochondrial ATP production is still not adequately addressed. The authors could performed few straight forward experiments on freshly isolated mitochondria from 1-2 tissue samples of their choice to provide data linking maximal respiration rates with mitochondrial ATP production. Providing evidence that directly links maximal respiration rates with mitochondrial ATP production would help readers understand how mitochondrial function is affected in various tissues.

Reviewer #1 (Public Review):

Summary:

This manuscript by Bomba-Warczak describes a comprehensive evaluation of long-lived proteins in the ovary using a transgenerational diet-derived 15N-labelling in pulse-chased mice. The transgenerational labeling of proteins (and nucleic acids) with 15N allowed the authors to identify regions enriched in long-lived macromolecules at the 6 and 10-month chase time points. The authors also identified the retained proteins in the ovary and oocyte using MS. Key findings include the relative enrichment in long-lived macromolecules in oocytes, pregranulosa cells, CL, stroma, and surprisingly OSE. Gene ontology analysis of these proteins revealed an enrichment for nucleosome, myosin complex, mitochondria, and other matrix-type protein functions. Interestingly, compared to other post-mitotic tissues where such analyses have been previously performed such as the brain and heart, they find a higher fractional abundance of labeled proteins related to the mitochondria and myosin respectively.

Strengths:

A major strength of the study is the combined spatial analyses of LLPs using histological sections with MS analysis to identify retained proteins.

Another major strength is the use of two chase time points allowing assessment of temporal changes in LLPs associated with aging.

The major claims such as an enrichment of LLPs in pregranulosa cells, GCs of primary follicles, CL, stroma, and OSE are soundly supported by the analyses and the caveat that nucleic acids might differentially contribute to this signal is well presented.

The claims that nucleosomes, myosin complex, and mitochondrial proteins are enriched for LLPs are well supported by GO enrichment analysis and well described within the known body of evidence that these proteins are generally long-lived in other tissues.

Weaknesses:

All weaknesses were addressed in the revised manuscript.

Impact of the work:

This work represents the first study addressing the turnover and retention of long-lived protein in the ovary and will be an invaluable resource for the research community, particularly for those studying ovarian aging. This work also raises important unanswered questions worthy of follow-up including interesting findings regarding the timing of turnover of cell types such as the OSE, organelles such as mitochondria, and ECM proteins such as ZP3 and Tubb family proteins. Most striking are the differences between the two timepoints used (6 and 10 months) which lead the authors to infer trajectories and kinetics of replacement of proteins potentially contributing to ovarian longevity or decline. As such I expect the work will contribute to hypothesis generation and stand to have an important impact on the field.

Reviewer #1 (Public review):

Summary:

This is a fine paper that serves the purpose to show that the use of light sheet imaging may be used to provide whole brain imaging of axonal projections. The data provided suggest that at this point the technique provides lower resolution than with other techniques. Nonetheless, the technique does provide useful, if not novel, information about particular brain systems.

Strengths:

The manuscript is well written. In the introduction a clear description of the functional organization of the barrel cortex is provided provides the context for applying the use of specific Cre-driver lines to map the projections of the main cortical projection types using whole brain neuroanatomical tracing techniques. The results provided are also well written, with sufficient detail describing the specifics of how techniques were used to obtain relevant data. Appropriate controls were done, including the identification of whisker fields for viral injections and determination of the laminar pattern of Cre expression. The mapping of the data provides a good way to visualize low resolution patterns of projections.

Weaknesses:

(1) The results provided are, as stated in the discussion, "largely in agreement with previously reported studies of the major projection targets". However it must be stated that the study does not "extend current knowledge through the high sensitivity for detecting sparse axons, the high specificity of labeling of genetically defined classes of neurons and the brain wide analysis for assigning axons to detailed brain regions" which have all been published in numerous other studies. ( the allen connectivity project and related papers, along with others). If anything the labeling of axons obtained with light sheet imaging in this study does not provide as detailed mapping obtained with other techniques. Some detail is provided of how the raw images are processed to resolve labeled axons, but the images shown in the figures do not demonstrate how well individual axons may be resolved, of particular interest would be to see labeling in terminal areas such as other cortical areas, striatum and thalamus. As presented the light sheet imaging appears to be rather low resolution compared to the many studies that have used viral tracing to look at cortical projections from genetically identified cortical neurons.<br /> (2) Amongst the limitations of this study is the inability to resolve axons of passage and terminal fields. This has been done in other studies with viral constructs labeling synaptophysin. This should be mentioned.<br /> (3) Figure 5 is an example of the type of large sets of data that can be generated with whole brain mapping and registration to the Allen CCF that provides information of questionable value. Ordering the 50 plus structures by the density of labeling does not provide much in terms of relative input to different types of areas. There are multiple subregions for different functional types ( ie, different visual areas and different motor subregions are scattered not grouped together. Makes it difficult to understand any organizing principles.<br /> (4) The GENSAT Cre driver lines used must have the specific line name used, not just the gene name as the GENSAT BAC-Cre lines had multiple lines for each gene and often with very different expression patterns. Rbp4_KL100, Tlx3_PL56, Sim1_KJ18, Ntsr1_ GN220.

Reviewer #2 (Public review):

Summary:

The authors developed a bioinformatic pipeline to aid the screening and identification of inhibitory receptors suitable as drug targets. The challenge lies in the large search space and lack of tools for assessing the likelihood of their inhibitory function. To make progress, the authors used a consensus protein membrane topology and sequence motif prediction tool (TOPCOS) combined with both a statistical measure assessing their likelihood function and a machine learning protein structural prediction model (AlphaFold) to greatly cut down the search space. After obtaining a manageable set of 398 high confidence known and putative inhibitory receptors through this pipeline, the authors then mapped these receptors to different functional categories across different cell types based on their expression both in the resting and activated state. Additionally, by using publicly available pan cancer scRNA-seq for tumor-infiltrating T cells data, they showed that these receptors are expressed across various cellular subsets.

Strengths:

The authors presented sound arguments motivating the need to efficiently screen inhibitory receptors and to identify those that are functional. Key components of the algorithm were presented along with solid justification for why they addressed challenges faced by existing approaches. To name a few:

• TOPCON algorithm was elected to optimize the prediction of membrane topology<br /> • A statistical measure was used to remove potential false positives<br /> • AlphaFold is used to filter out putative receptors that are low confidence (and likely intrinsically disordered)

To examine receptors screened through this pipeline through a functional lens, the authors proposed to look at their expression of various immune cell subsets to assign functional categories. This is a reasonable and appropriate first step for interpreting and understanding how potential drug targets are differentially expressed in some disease contexts. They also presented an example showing this pipeline can be used to "rediscover" known targets.

Weaknesses:

The paper has strength in the pipeline they presented, but the weakness, in my opinion, lies in the lack of direct experimental validation on putative receptors. That said, the authors presented in the revised manuscript, as a proof-of-concept, an analytic approach for using functional categorization of putative inhibitory receptors to select therapeutic targets based on in vitro RNAseq. Such analysis will benefit from further investigation across different cancer types using in vivo expression.

Reviewer #1 (Public review):

Summary:

The manuscript by Jang et al. describes the application of new methods to measure the localization GTP-binding signaling proteins (G proteins) on different membrane structures in a model mammalian cell line (HEK293). G proteins mediate signaling by receptors found at the cell surface (GPCRs), with evidence from the last 15 years suggesting that GPCRs can induce G-protein mediated signaling from different membrane structures within the cell, with variation in signal localization leading to different cellular outcomes. While it has been clearly shown that different GPCRs efficiently traffic to various intracellular compartments, it is less clear whether G proteins traffic in the same manor, and whether GPCR trafficking facilitates "passenger" G protein trafficking. This question was a blind spot in the burgeoning field of GPCR localized signaling in need of careful study, and the results obtained will serve as an important guide post for further work in this field.<br /> The extent to which G proteins localize to different membranes within the cell is the main experimental question tested in this manuscript. This question is pursued by through two distinct methods, both relying on genetic modification of the G-beta subunit with a tag. In one method, G-beta is modified with a small fragment of the fluorescent protein mNG, which combines with the larger mNG fragment to form a fully functional fluorescent protein to facilitate protein trafficking by fluorescent microscopy. This approach was combined with expression of fluorescent proteins directed to various intracellular compartments (different types of endosomes, lysosome, endoplasmic reticulum, golgi, mitochondria) to look for colocalization of G-beta with these markers. These experiments showed compelling evidence that G-beta co-localizes with markers at the plasma membrane and the lysosome, with weak or absent co-localization for other markers. A second method for measuring localization relied on fusing G-beta with a small fragment from a miniature luciferase (HiBit) that combines with a larger luciferase fragment (LgBit) to form an active luciferase enzyme. Localization of G-beta (and luciferase signal) was measured using a method known as bystander BRET, which relies on expression of a fluorescent protein BRET acceptor in different cellular compartments. Results using bystander BRET supported findings from fluorescence microscopy experiments. These methods for tracking G protein localization were also used to probe other questions. The activation of GPCRs from different classes had virtually no impact on the localization of G-beta, suggesting that GPCR activation does not result in shuttling of G proteins through the endosomal pathway with activated receptors.

In the revised version of this manuscript the authors have performed informative and important new experiments in addition to adding new text to address conceptual questions. These new data and discussions are commendable and address most or all of the weaknesses listed in the initial review.

Strengths:

The question probed in this study is quite important and, in my opinion, understudied by the pharmacology community. The results presented here are an important call to be cognizant of the localization of GPCR coupling partners in different cellular compartments. Abundant reports of endosomal GPCR signaling need to consider how the impact of lower G protein abundance on endosomal membranes will affect the signaling responses under study.

*The work presented is carefully executed, with seemingly high levels of technical rigor. These studies benefit from probing the experimental questions at hand using two different methods of measurement (fluorescent microscopy and bystander BRET). The observation that both methods arrive at the same (or a very similar) answer inspires confidence about the validity of these findings.

Weaknesses:

*As noted by the authors, they do not demonstrate that the tagged G-beta is predominantly found within heterotrimeric G protein complexes. In the revised manuscript the authors have added new discussion text on why it is likely that G-beta is mostly found in complexes. This line of reasoning is convincing, although more robust experimental methods for assessing the assembly status of G-beta could be a valuable target for future experimental developments.

Reviewer #3 (Public review):

Summary:

This paper provides presents an automated method to track individual mammalian cells as they progress through the cell cycle using the FUCCI system, and applies the method to look at different tumor cell lines that grow in suspension and determine their cell cycle profile and the effect of drugs that directly affect the cell cycles, on progression through the cell cycle for a 72 hour period.

Strengths:

This is a METHODS paper. The one potentially novel finding is that they can identify cells which are at the G1-S transition by the change in color as one protein starts to go up and the other one goes down, similar to change seen as cells enter G2/M. They have provided detailed data in the resubmission, demonstrating how this can be done in different cell lines and that the resolution of the brief time is about (about 1 hr) when the cells are determined to be in the transition from G1 to S. They further showed how one can explore this period (using EDU labeling in conjunction with FUCCI how one can determine whether cells have entered S-phase. This nicely addressed a weakness identified in the previous review.

Reviewer #1 (Public review):

Summary:

In this revised manuscript, Rincon-Torroella et al. developed ME3BP-7, a microencapsulated formulation of 3BP, as a potential agent to target MCT1 overexpressing PDACs. The authors provided compelling experimental evidence demonstrating the specific and rapid killing of MCT1 overexpressing PDAC cells in vitro, along with the safety and significant anti-tumor efficacy of ME3BP-7 in multiple PDAC orthotopic mouse models. Overall, this study is very novel, with well-designed experiments and a clear, organized presentation of data that supports the conclusions. The authors have effectively addressed the questions raised in the primary review and provided a thorough discussion of the study's significance, limitations, and future directions, which enhances the readers' understanding of the potential clinical impact of this research.

Strengths:

* Developed a novel agent.<br /> * Well-designed experiments and an organized presentation of data that support the conclusions.

Weaknesses:

No significant weaknesses are noticed.

Reviewer #1 (Public Review):

Summary:

The manuscript by Kim et al. describes a role for axonal transport of Wnd (a dual leucine zipper kinase) for its normal degradation by the Hiw ubiquitin ligase pathway. In Hiw mutants, the Wnd protein accumulates dramatically in nerve terminals compared to the cell body of neurons. In the absence of axonal transport, Wnd levels rise and lead to excessive JNK signaling that makes neurons unhappy.

Strengths:

Using GFP-tagged Wnd transgenes and structure-function approaches, the authors show that palmitoylation of the protein at C130 plays a role in this process by promoting golgi trafficking and axonal localization of the protein. In the absence of this transport, Wnd is not degraded by Hiw. The authors also identify a role for Rab11 in the transport of Wnd, and provide some evidence that Rab11 loss-of-function neuronal degenerative phenotypes are due to excessive Wnd signaling. Overall, the paper provides convincing evidence for a preferential site of action for Wnd degradation by the Hiw pathway within axonal and/or synaptic compartments of the neuron. In the absence of Wnd transport and degradation, the JNK pathway becomes hyperactivated. As such, the manuscript provides important new insights into compartmental roles for Hiw-mediated Wnd degradation and JNK signaling control.

Weaknesses:

It is unclear if the requirement for Wnd degradation at axonal terminals is due to restricted localization of HIW there, but it seems other data in the field argues against that model. The mechanistic link between Hiw degradation and compartmentalization is unknown.

Reviewer #1 (Public review):

Summary:

This work used a comprehensive dataset to compare the effects of species diversity and genetic diversity within each trophic level and across three trophic levels. The results showed that species diversity had negative effects on ecosystem functions, while genetic diversity had positive effects. These effects were observed only within each trophic level and not across the three trophic levels studied. Although the effects of biodiversity, especially genetic diversity across multi-trophic levels, have been shown to be important, there are still very few empirical studies on this topic due to the complex relationships and difficulty in obtaining data. This study collected an excellent dataset to address this question, enhancing our understanding of genetic diversity effects in aquatic ecosystems.

Strengths:

The study collected an extensive dataset that includes species diversity of primary producers (riparian trees), primary consumers (macroinvertebrate shredders), and secondary consumers (fish). It also includes the genetic diversity of the dominant species at each trophic level, biomass production, decomposition rates, and environmental data.

The conclusions of this paper are mostly well supported by the data and the writing is logical and easy to follow.

Weaknesses:

While the dataset is impressive, the authors conducted analyses more akin to a "meta-analysis," leaving out important basic information about the raw data in the manuscript. Given the complexity of the relationships between different trophic levels and ecosystem functions, it would be beneficial for the authors to show the results of each SEM (structural equation model).

The main results presented in the manuscript are derived from a "metadata" analysis of effect sizes. However, the methods used to obtain these effect sizes are not sufficiently clarified. By analyzing the effect sizes of species diversity and genetic diversity on these ecosystem functions, the results showed that species diversity had negative effects, while genetic diversity had positive effects on ecosystem functions. The negative effects of species diversity contradict many studies conducted in biodiversity experiments. The authors argue that their study is more relevant because it is based on a natural system, which is closer to reality, but they also acknowledge that natural systems make it harder to detect underlying mechanisms. Providing more results based on the raw data and offering more explanations of the possible mechanisms in the introduction and discussion might help readers understand why and in what context species diversity could have negative effects.

Environmental variation was included in the analyses to test if the environment would modulate the effects of biodiversity on ecosystem functions. However, the main results and conclusions did not sufficiently address this aspect.

Reviewer #1 (Public Review):

Summary:

In this paper the authors provide a thorough demonstration of the role that one particular type of voltage-gated potassium channel, Kv1.8, plays in a low voltage activated conductance found in type I vestibular hair cells. Along the way, they find that this same channel protein appears to function in type II vestibular hair cells as well, contributing to other macroscopic conductances. Overall, Kv1.8 may provide especially low input resistance and short time constants to facilitate encoding of more rapid head movements in animals that have necks. Combination with other channel proteins, in different ratios, may contribute to the diversified excitability of vestibular hair cells.

Strengths:

The experiments are comprehensive and clearly described, both in text and in the figures. Statistical analyses are provided throughout.

Weaknesses:

None.

Reviewer #1 (Public review):

In the revised manuscript Vicario et al. provide new insights on a potential contribution of somatic mutations within the microglia population of the CNS that accelerates microglia activation and disease-associated gene signatures in Alzheimer's disease. Here they especially identified an "enrichment" of pathological SNVs in microglia, but not the peripheral blood, that are associated with clonal proliferative disorders and neurological diseases in a subset of patients with AD. They identified P-SNVs in microglia of AD patients located within the ring domain of CBL, a negative regulator of MAPK signaling. They further provide mechanistic insights how these variants result in MAPK over-activation and subsequently in a pro-inflammatory phenotype in human microglia-like cells in vitro.

Overall, this study provides novel evidence from an AD patient cohort pointing to a potential contribution of microglia-specific somatic mutations to disease onset and/or progression in at least a subset of patients with Alzheimer's disease.

The work within this study is highly relevant and will open new study lines to explore somatic mutations within the microglia compartment and neurodegenerative diseases.

Strengths:

As outlined above, the study identified P-SNVs in microglia of AD patients associated with clonal proliferative disorders, but also give an in depth analysis in re-occurring P-SNVs located within the ring domain of CBL, a negative regulator of MAPK signaling. They further provide mechanistic insights how these variants result in MAPK over-activation and subsequently in a pro-inflammatory phenotype in HEK cells, BV2 cells, MAC cells and human microglia-like cells in vitro. The over-activation of the cells in vitro is convincing.

Great care was taken to identify the limitations of the possible conclusions and to make careful conclusions. For example, they highlight that the pathway proposed to be affected may be an explanation for a subset of AD patients, and emphasize that it is yet unclear whether this accumulation of pathological SNVs is a cause or consequence of disease progression

The study supports an enrichment of P-SNVs in several genes associated clonal proliferative disorders in microglia and nicely separates this from SNVs associated with clonal hematopoiesis in the peripheral blood found in AD patients and controls.

The authors further acknowledged that several age matched control patients were diagnosed with cancer or tumor-associated diseases and carefully dissected the occurring SNVs in these patients are not associated with the P-SNVs identified in the microglial compartment of the AD cohort.

Weaknesses:

The revised study is overall convincing and has improved in the revised version, but some points especially regarding the clear connection of the seen somatic variants in microglia with a potential role in disease progression remain unanswered.

A potential connection between P-SNVs in microglia and disease pathology and symptoms was not further explored by the authors but might be in future work.

Taken this into account, maybe the title is a bit overstated and could be tuned down.

Reviewer #1 (Public review):

Summary:

The work of Muller and colleagues concerns the question where we place our feet when passing uneven terrain, in particular how we trade-off path length against the steepness of each single step. The authors find that paths are chosen that are consistently less steep and deviate from the straight line more than an average random path, suggesting that participants indeed trade off steepness for path length. They show that this might be related to biomechanical properties, specifically the leg length of the walkers. In addition, they show using a neural network model that participants could choose the footholds based on their sensory (visual) information about depth.

Strengths:

The work is a natural continuation of some of the researchers' earlier work that related the immediately following steps to gaze. Methodologically, the work is very impressive and presents a further step forward towards understanding real-world locomotion and its interaction with sampling visual information. While some of the results may seem somewhat trivial in hindsight (as always in this kind of studies), I still think this is a very important approach to understand locomotion in the wild better.

Weaknesses:

The concerns I had regarding the initial version of the manuscript have all been fixed in the current one.

Reviewer #1 (Public review):

This is an important study to characterize cultured neuronal network dynamics, down to the combinations of individual excitatory and inhibitory inputs that result in spiking. The authors effectively combine high-density multi-electrode arrays with patch recordings and a convincing analysis to work out the contributions of multiple simultaneously active input neurons to postsynaptic activity.

In this study the authors develop methods to interrogate cultured neuronal networks to learn about the contributions of multiple simultaneously active input neurons to postsynaptic activity. They then use these methods to ask how excitatory and inhibitory inputs combine to result in postsynaptic neuronal firing in a network context.

The study uses a compelling combination of high-density multi-electrode array recordings with patch recordings. They make effective use of physiology techniques such as shifting the reversal potential of inhibitory inputs, and identifying inhibitory vs. excitatory neurons through their influence on other neurons, to tease apart the key parameters of synaptic connections. The method appears to work on rather low-density cultures so the size of the networks in the current study is in the low tens, and the number of synaptic inputs coming to each neuron is smaller than what would be encountered in vivo.

The authors obtain a number of findings on the conditions in which the dynamics of excitatory and inhibitory inputs permit spiking, and the statistics of connectivity that result in this. This is of considerable interest, and clearly one would like to see how these findings map to larger networks, to non-cortical networks, and ideally to networks in-vivo. The suite of approaches discussed here could potentially serve as a basis for such further development.

One of the challenges in doing such studies in a dish is that the network is simply ticking away without any neural or sensory context to work on, nor any clear idea of what its outputs might mean. Nevertheless, at a single-neuron level one expects that this system might provide a reasonable subset of the kinds of activity an individual cell might have to work on. In their response to earlier comments the authors have made useful comments on features of in-vivo network activity that are seen in culture. This could ideally be incorporated into the discussion.

Reviewer #1 (Public review):

In this manuscript, the authors use a large dataset of neuroscience publications to elucidate the nature of self-citation within the neuroscience literature. The authors initially present descriptive measures of self-citation across time and author characteristics; they then produce an inclusive model to tease apart the potential role of various article and author features in shaping self-citation behavior. This is a valuable area of study, and the authors approach it with a rich dataset and solid methodology.

The revisions made by the authors in this version have greatly improved the validity and clarity of the statistical techniques, and as a result the paper's findings are more convincing.

This paper's primary strengths are: 1) its comprehensive dataset that allows for a snapshot of the dynamics of several related fields; 2) its thorough exploration of how self-citation behavior relates to characteristics of research and researchers.

Its primary weakness is that the study stops short of digging into potential mechanisms in areas where it is potentially feasible to do so - for example, studying international dynamics by identifying and studying researchers who move between countries, or quantifying more or less 'appropriate' self-citations via measures of abstract text similarity.

Yet while these types of questions were not determined to be in scope for this paper, the study is quite effective at laying the important groundwork for further study of mechanisms and motivations, and will be a highly valuable resource for both scientists within the field and those studying it.

Reviewer #1 (Public Review):

In this manuscript, the authors investigate whether enhancers use a common regulatory paradigm to modulate transcriptional bursting in both endogenous and ectopic domains using cis-regulatory mutant reporters of the eve transcriptional locus in early Drosophila embryogenesis.

The authors create a series of cis-regulatory BAC mutants of the eve stripe 1 and 2 enhancers by mutating the binding sites for the transcriptional repressor Giant in the stripe 2 minimal response element (MRE) independently or in combination with deletion of the stripe 1 enhancer sequence. With these enhancer mutations, they are able to generate conditions in which eve is ectopically expressed. Next, the authors investigate if nuclei in these "ectopic" regions have similar transcriptional kinetics to the "endogenous"-expressing eve+ nuclei. They show that bursting parameters are unchanged when comparing endogenous and ectopic gene expression regions. Under a scheme of a 2-state model, the eveS1Δ-EveS2Gt- reporter modulates transcription by increasing the active state switching rate (kon) and the initiation rate (r) while maintaining a constant inactive state switching rate.

Based on these results, the authors support a model whereby kinetic regimes are encoded in the cis-regulatory sequences of a gene instead of imposed by an evolving trans-regulatory environment.

The question asked in this manuscript is important and the eve locus represents an ideal paradigm to address it in a quantitative manner. Most of the results are correctly interpreted and well-presented.

Reviewer #1 (Public Review):

Revised Public Review

This reviewed preprint is essentially three papers combined into one-one paper focused on the role of CIB2/CIB3 in vestibular hair cells, one on the role of CIB2/CIB3 in zebrafish, and one on structural modeling of a CIB2/3 and TMC1/2 complex. The authors try to combine the three parts with the overarching theme of demonstrating that CIB2/3 play a functionally conserved role across species and hair cell types. It is important to note that many of the basic results from the mouse have already been reported by other groups in Liang et al. (2021) and Wang et al. (2023).

That said, their demonstration of the importance of CIB2 and CIB3 in zebrafish hair cell function is novel. The results largely coincide with what is seen in the mouse-they are both important, with stimulus-dependent Ca2+ entry reduced more in cib2 KOs than in cib3 KOs, and the cib2;cib3 showing the greatest impact. Interestingly, cib2 is uniquely localized in and important for specific hair cell types in the neuromast and crista.

The last part of the manuscript also offers significant new findings. Here structural studies (AlphaFold 2 modeling, NMR structure determination, and molecular dynamics simulations) brings us closer to the structure of the mammalian TMCs, alone and in complex with the CIB proteins. Moreover, the structural work supports the assignment of the TMC pore to alpha helices 4-7.

In summary, while this reviewed preprint has some data that replicate data from publications from other labs, it provides a comprehensive look at the CIB family in hair cells, especially in vestibular hair cells.

Reviewer #1 (Public review):

Summary:

This manuscript presents a comprehensive exploration of the role of liver-specific Survival Motor Neuron (SMN) depletion in peripheral and central nervous system tissue pathology through a well-constructed mouse model. This study is pioneering in its approach, focusing on the broader physiological implications of SMN, which has traditionally been associated predominantly with spinal muscular atrophy (SMA).

Strengths:

(1) Novelty and Relevance: The study addresses a significant gap in understanding the role of liver-specific SMN depletion in the context of SMA. This is a novel approach that adds valuable insights into the multi-organ impact of SMN deficiency.

(2) Comprehensive Methodology: The use of a well-characterized mouse model with liver-specific SMN depletion is a strength. The study employs a robust set of techniques, including genetic engineering, histological analysis, and various biochemical assays.

(3) Detailed Analysis: The manuscript provides a thorough analysis of liver pathology and its potential systemic effects, particularly on the pancreas and glucose metabolism.

(4) Clear Presentation: The manuscript is well written. The results are presented clearly with well-designed figures and detailed legends.

Weaknesses:

(1) Limited Time Points: The study primarily focuses on a single time point (P19). This limits the understanding of the temporal progression of liver and pancreatic pathology in the context of SMN depletion. Longitudinal studies would provide a better understanding of disease progression.

(2) Incomplete Recombination: The mosaic pattern of Cre-mediated excision leads to variability in SMN depletion, which complicates the interpretation of some results. Ensuring more consistent recombination across samples would strengthen the conclusions.