Evaluation Summary: 

Given the well-known importance of the SYNGAP1 mutations in the pathophysiology of neurodevelopmental disorders and the key regulatory roles of SynGAP1 for excitatory synaptic functions, this study provides timely and comprehensive sets of data supporting the in vivo functions of individual SynGAP1 splice variants, including the alpha-1/2 variants, and suggests the therapeutic potential of increasing specific SynGAP1-alpha variants. 

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Evaluation Summary:

The authors present a method for measuring the oligomerisation state of tagged membrane proteins by PALM co-localisation that is new, interesting and potentially very useful for identifying oligomerization states of unknown proteins in native cells. While the authors develop a basic theory and apply the method to a set of candidate proteins with solid results, their implementation could be refined and improved, which would help to better delineate the full scope and the limitations of their method. An open-source software tool would help other researchers to adopt this analysis. The work is relevant for cell biologists, especially those studying membrane proteins.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 agreed to share their name with the authors.)

Evaluation Summary:

This manuscript reports the cryoEM structure of somatostatin receptor 2 (SSTR2) bound to its agonist SST-14 and a heterotrimeric G protein. In addition to presenting the structure itself, the authors include discussion and analysis of ligand recognition and subtype specificity, guided by AlphaFold2 modeling of other somatostatin receptor subtypes. Additional functional data to test the importance of proposed receptor-ligand contacts will be critical to understanding which of the features directly contribute to subtype specificity. Because somatostatin signaling is important in endocrine biology, including in diseases such as acromegaly and some cancers, the work should in principle be of interest to a broad audience.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Evaluation Summary:

This is a tour de force for mutagenesis and analysis of an ion channel protein, using a straightforward method the authors have developed for the comprehensive functional analysis of a deep mutational library. The approach introduced here will not only be of broad interest to the ion channel community, but it will also serve as a roadmap for performing similar studies on other proteins. The authors demonstrate the usefulness of this method by defining the functional domains of Kir2.1, thereby rediscovering known disease causing mutants, and highlighting a number of mutations with similar phenotypes that may also result in disease phenotypes.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #2 and Reviewer #3 agreed to share their name with the authors.)

Evaluation Summary:

This is an interesting quantitative study of the anatomical connections of a region of prefrontal cortex that has often been overlooked - the Ventrolateral Prefrontal Cortex. The idea that this is a special region that is different to both the rest of ventrolateral prefrontal cortex and probably the rest of orbitofrontal cortex is important because it helps us understand some otherwise puzzling results. The quantitative analysis of connections is an unusual strength of the study as is the comparison of tracer data in macaques, fMRI connectivity data in macaques, and human fMRI connectivity data.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 agreed to share their name with the authors.)

Evaluation Summary:

Neurons use activity-responsive gene programs to shape cell specific identity and respond appropriately to environmental stimuli. By combining elegant protein degradation and cell-specific knockout approaches with transcriptional profiling and chromatin structure analysis, this manuscript delineates the contributions of cohesin (a key protein responsible for genome structure and organization), in activity-dependent gene expression programs and stimulus-dependent chromatin reorganization. These results demonstrate that cohesin is required for full expression of key genes required for the maturation and activation of cortical excitatory neurons, and reveal a tight correlation between cohesin effects and the genomic distance of higher order chromatin loops.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Evaluation Summary:

The research detailed in this manuscript investigates whether young chicks represent the absence of objects. This work is important to multiple fields of inquiry such as ethology and neuroscience, and is the first time this ability has been studied spontaneously in such a population, as opposed to after many trials of experience. The data effectively support most of the conclusions, though a few elements need clarification, especially in regards to possible sex-dependent representations of absence.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 and Reviewer #2 agreed to share their names with the authors.)

Evaluation Summary:

This manuscript will be of broad interest to readers interested in understanding characteristics of variants in ongoing epidemics that lead to faster (or slower) growth rates, and will be of particular interest to those wishing to understand the factors leading to selection of SARS-CoV-2 variants. The transmission advantage of a novel strain of a pathogen depends not only on its relative transmissibility, but also on its generation time relative to other strains; the relation between transmissibility, transmission advantage and generation time changes across different phases of the epidemic, enabling statistical inferences to be made about both the transmissibility advantage and generation time of an emerging variant. The method is supported by simulation studies and applied to the Alpha and Delta SARS-CoV-2 variants to show that selection was likely driven by changes in transmissibility rather than changes in the generation time.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Evaluation Summary:

Three experts in the field reviewed this manuscript from slightly different perspectives. All three reviewers are generally positive about this interesting, well-presented paper and think that it leads to several advances in the field. However, the reviewers also think changes can be made that would considerably strengthen the current version and its impact. Specific modifications have been requested to improve analysis of the screening data, to discuss hits besides the mevalonate pathway that increase Streptococcus pneumoniae cell length and shape, to clarify some issues about how mevalonate depletion changes pneumococcal cell shape and peptidoglycan synthesis, and to provide more context for clomiphene potentiation of amoxicillin killing of Streptococcus pneumoniae in comparison to previously published results in Staphylococcus aureus.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #2 agreed to share their name with the authors.)

Evaluation Summary:

This is an interesting study that reveals a completely new mechanism by which inhaled fine particles may promote lung tumor development. The authors provide direct evidence that protein corona on those foreign objects can elicit such adverse effects. Their findings highlight the importance of the corona-endowed, 'new' bioactivity of nanomaterials in vivo - and even in a particular tissue-lungs.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #2 agreed to share their name with the authors.)

Evaluation Summary: 

The manuscript reports that when lowland plants were transplanted into alpine turfs under lowland climatic conditions, they rapidly increase soil microbial decomposition of carbon stocks due to root exudates feeding the microbes. The authors conclude that when lowland plants migrate to alpine sites and these warm up, they may also cause a pulse of carbon loss from soil. An alternative explanation of their findings might be that when alpine plants are transplanted into alpine turfs under lowland climatic conditions, these are unable to increase soil microbial decomposition as much as lowland plants because the latter are better adapted to their climatic home environment.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 and Reviewer #4 agreed to share their names with the authors.)

Evaluation Summary:

This paper employs sophisticated modeling of human behavior in well-controlled tasks to study how limitations of working memory constrain decision-making. Because both are key cognitive processes, that have so far largely been studied in isolation, the paper should be of broad interest to neuroscientists and psychologists. The observed working memory limitations support and extend previous findings, but some of the most interesting claims need additional support.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 agreed to share their name with the authors.)

Evaluation Summary: 

Soyman and colleagues investigate intensity coding for the "pain of others" in the human insula with intracranial human recordings. Additional data of a related fMRI study is analyzed and discussed in the context of the intracranial data. The paper addresses an important research question of broad interest, with extremely unusual data which is investigated in considerable detail. 

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #2 agreed to share their name with the authors.)

Evaluation Summary:

In this study Byazrova and colleagues provide an assessment of antibody and B cell responses in a small cohort of naïve and previously infected individuals after Sputnik V immunisation. This research will be of interest to those in the fields of vaccinology and immunology, providing some insight into B cell responses following Sputnik V vaccination.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Evaluation Summary:

Morozova et al. describe potential mechanisms contributing to the flexibility of burst patterns and dynamic responses to perturbations within an isolated reciprocally inhibitory circuit derived from the stomatogastric ganglion of the crab. The authors use the dynamic clamp approach to study the interactions between pharmacologically isolated, intrinsically silent gastric mill neurons, an approach pioneered by Andrew Sharp in the 1990s. The authors demonstrate that the mechanisms of switching between components of the reciprocally organized half-center network are not fixed and may shift to favor a release or escape mechanism depending on factors such as the synaptic threshold, Ih conductance, and synaptic conductance. This is a fundamentally important study because reciprocally organized networks are ubiquitous and found virtually in every organism. It is assumed that this half-center-type network organization governs rhythmic activity with a wide range of functions.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewers #1, #2 and #3 agreed to share their names with the authors.)

Evaluation Summary:

The authors report that hyperglicemia suppresses HIF1a activity in models of diabetic nephropathy, which in turn leads to cell death by increasing mitochondrial ROS. The notion that HIF1a regulates mitochondrial respiration and thus mitochondrial ROS production is well documented in numerous systems. However, this model has not been tested in the context of diabetic nephropathy so far. The study is thus novel, informative and with interesting translational implications.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 agreed to share their name with the authors.)

Evaluation Summary:

This is an interesting study of the relation between vividness of visual imagery and the pupillary light response that can result from it. It provides evidence for the absence of imagery in individuals that self-report as aphantasic. The results will likely be of interest to researchers in a range of disciplines such as psychology, neuroscience and philosophy. There were some shared concerns related to demand characteristics and eye movements, and the authors might be able to address these concerns with more data analysis and/or control experiments.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 and Reviewer #2 agreed to share their names with the authors.”)

Evaluation Summary: 

In this paper the authors dissect the across-the-genome consequences of sexual recombination in Trypanosoma cruzi. It summarises an extensive piece of work, which includes a 5-year in vitro growing of parasites and relatively rigorous genome analyses. It will be of interest to microbiologists working on microbes with cryptic or parasexual modes of genetic exchange.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 and Reviewer #2 agreed to share their names with the authors.)

Evaluation Summary:

Challa and Ryu et al. systematically evaluated various combinations of ADP-ribose-binding modules to make sensors detecting poly(ADP-ribose). They developed and tested two indicator designs optimized for analyses in cell culture (dimerization-dependent GFP-based) or intact tissues (split Nano luciferase-based). Overall, with further experimental controls and quantification, this timely set of cell biology probes will be useful to study the biological functions of ADP-ribosylation in cultured cells and whole organisms.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 agreed to share their name with the authors.)

Evaluation Summary: 

This paper will be of interest to scientists studying metabolism and those interested in the evolution of genomic imprinting. The authors show how parent-of-origin effects in crosses between inbred strains of mice can arise from epistasis between imprinted and unimprinted loci. They consider scenarios for the interactions of imprinted and unimprinted genes in adipocytes. 

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 agreed to share their name with the authors.)

Evaluation Summary: 

The authors of this paper model the D61G mutation in the gene PTPN11 that encodes the protein-tyrosine phosphatase SHP2 in zebrafish, creating a model consistent with the human Noonan syndrome (NS), which is predisposed to a juvenile myelomonocytic leukemia (JMML) and myeloproliferative neoplasm (MPN)-like syndrome. The study nicely provides a new model that can be used as the basis of future studies in the field. Because the mutant variably displays phenotypes along a spectrum from NS to MPN, different researchers can choose to focus on this as they see fit. 

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Evaluation Summary: 

In this work, the authors study the previously reported positive association between the presence of the gut bacterium Paracoccus aminovorans and Vibrio cholerae during infection. They describe and image dual species-biofilm formed in vitro as well as enhanced V. cholerae gut colonization in the presence of P. aminovorans in a neonatal mouse model. Collectively, the authors conclude that P. aminovorans enhances biofilm formation by Vc, which could explain the increased susceptibility of P. aminovorans-containing humans in cholera endemic areas. 

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Evaluation Summary:

This study investigates and characterizes the representations of actions in naturalistic movie stimuli. The combination of the analytical techniques and stimulus domain make the paper likely to be of broad interest to scientists interested in action representation amidst complex sequences. This paper will potentially broaden our understanding of visual action representation and the extraction of such information in natural settings, but clarification of the analyses and aspects of the data are required to strengthen the claims.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 and Reviewer #2 agreed to share their names with the authors.)

Evaluation Summary:

This study is of interest to researchers who study cell migration and or muscle development. It builds upon prior analysis of Double Anal fin (Da) mutants by using detailed bioinformatic and time-lapse analysis to explain dorsal somite extension and find evidence that dorsal muscle morphogenesis is actively guided, rather than being passively shaped by physical constraints alone. This work illustrates the dynamic behaviors of dorsal somitic cells, which form elaborate protrusions, delaminate from their parent somite, and bridge the gap between opposing epaxial myotomes. Looking downstream of Da, they show that Wnt signaling is central to dorsal extension of the epaxial myotome in medaka and propose that similar functions may shape the dorsal musculature across vertebrates.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Evaluation Summary:

Manipulations of sex hormones in animals in ecologically relevant environments usually involve long-term manipulations using chronic implants or injections of esterified steroids with longer half-lives than the endogenous hormones. This has been done in line with the prevailing idea of the long-lasting effects of steroids mediated by the transcritpional actions of their liganded receptors. The specific novelty of this study lies in the transiency of hormone availability (testosterone's half-life is about 2 hours). This might suggest that the observed effects depend on a mode of action different from the mode of action during chronic sex hormone exposure. It should also be noted that any study in natural settings is significantly more difficult to perform than in the lab. However, as all brain/hormonal functions evolved in natural environments, these studies are absolutely crucial to understand the function of the respective systems.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Evaluation Summary:

A member of a large class of metalloproteases with representatives in mammals as well as bacteria, its status as a multipass membrane protein has made illuminating the molecular basis of SpoIVFB inhibition challenging. In this study, Olenic and colleagues combine genetics, cross-linking, and co-evolutionary analysis to develop a structural model of interaction between SpoIVFB and its inhibitors SpoIVFA and BofA. Given the conservation and importance of this family of metalloproteases, this work should have broad impact, influencing our understanding of the regulation of this class of proteins across the tree of life.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 and Reviewer #3 agreed to share their names with the authors.)

Evaluation Summary:

This study covers a series of experiments designed to characterize conditioned pain processing using a novel animal model in which mechanical nociception (von Frey test) is assessed following exposure to contextual cues that have been paired with visceral pain (intraperitoneal acid injection). These experiments address an important topic from a translational perspective, both because learning is an important but understudied contributor to the human pain experience and because there is evidence for sex differences in human pain expression. The results reveal that such cues exert complex, dose- and sex-dependent effects on pain processing that will be of broad interest to researchers across fields of associative learning, neuroscience, and pain research.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1, Reviewer #2 and Reviewer #3 agreed to share their names with the authors.)

Evaluation Summary:

This study will be of interest for the fields of T cell immunology and computational biology. It represents a careful descriptive study of the T cell repertoires of young and old mice, quantifying the relationships between naive, regulatory, effector and memory subsets. It represents a first step and would benefit from additional analyses and interpretations.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #3 agreed to share their name with the authors.)

Evaluation Summary:

The authors investigate the mechanisms underlying the regulation of microtubule dynamics and length regulation in cells. Understanding how microtubule-binding proteins synergize to affect microtubule behavior is important, and resolving the seemingly contradictory effects of Kif18a on microtubules in mitotic cells vs. in vitro microtubule assays is a worthy endeavor. A major conclusion is that on dynamic microtubules, combining EB3, MCAK, and Kif18b increases microtubule catastrophe compared to other single or double protein combinations. This is in principle a new and interesting finding, but additional evidence would help to more strongly support this conclusion.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 agreed to share their name with the authors.)

Evaluation Summary:

The manuscript by Zhang et al. describes the combined use of a new surgical procedure and therapeutic hypothermia to deliver local therapy to the optic nerve in large mammals. In addition, the work describes a novel computer program that can optimize surgical approaches to access the optic nerve endonasally by using anatomical parameters obtained by tomography scan. The study represents a significant step forward in the use of therapeutic hypothermia in the treatment of ocular conditions and is of interest to neurobiologists studying therapeutic interventions for acute trauma to the optic nerves or to other regions of the central nervous system.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 agreed to share their name with the authors.)

Evaluation Summary:

This study carefully quantifies microtubule dynamics during anaphase in the fission yeast S. pombe. The high quality data revealed two new observations: that microtubule rescue occurs preferentially at the edge of the midzone and that microtubule growth speed decreases when the nuclear membrane wraps around the spindle midzone in late anaphase. This sheds new light on the interplay between the nuclear membrane and the midspindle in closed mitosis, and the study will be of interest to cell biologists studying spindle dynamics and mitosis.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Evaluation Summary:

This paper extends our understanding of blood flow regulation in the ischemic kidney and adds to a growing body of literature on the role played by pericyte contraction in the aftermath of ischemia/reperfusion (much of it based on the CNS microvasculature), and the potential of capillary pericytes as therapeutic targets in mitigating ischemia/reperfusion injury. This is an important study which should be of interest to a wide variety of investigators in vascular and renal biology.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 and Reviewer #3 agreed to share their names with the authors.)

Evaluation Summary:

The authors evaluate a novel crowd-sourcing method to interpret minimum inhibitory concentrations of Mycobacterium tuberculosis, the causative agent of tuberculosis. To provide valuable test results without the need for available expert mycobacteriologists, the authors demonstrate that when presented appropriately, 11-17 interpretations by lay interpreters can provide reproducible results for most tuberculosis drugs. This analysis demonstrates that among those samples that can be reliably interpreted by automated detection software, lay interpretation provides a potential alternative means to provide a timely confirmatory read. The work will be of interest to bacteriologists and those with an interest in antimicrobial resistance.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Evaluation Summary:

The study addressed interactions between two key striatal transmitters, dopamine and acetylcholine during an appetitive behavioral task. Helping to reconcile conflicting evidence in the literature, the data show that changes in both transmitters are correlated and that decreases in acetylcholine with reward and reward cues is only partially a consequence of elevated dopamine release acting at D2 dopamine receptors on striatal cholinergic interneurons. The behavioral significance of this correlation remains to be fully clarified. This manuscript will be of interest to those interested in the neural correlates of appetitive behavior and dopamine and striatal function.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 agreed to share their name with the authors.)

Evaluation Summary:

This paper addresses a fundamental cell biological question - the de-novo development of an apical membrane during the integration of an initially unpolarized cell, the enterocyst, into an an existing epithelium, the Drosophila midgut. The data will be of interest to a wide range of researchers including those in the fields of cell, development, stem cell and cancer biology.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #3 agreed to share their name with the authors.)

Evaluation Summary:

This study reports new post-translational modifications (PTMs) to β-myosin heavy chain, using tissue samples from normal and failing human hearts. Atomistic simulations of myosin molecular dynamics suggest that these PTMs lead to meaningful alterations in structure, solvent exposure, and dynamics of certain regions of the protein. These data and simulations provide a foundation for further work to determine the precise functional significance of β-myosin heavy chain PTMs. The work will be of interest to cell biologists and cardiologists.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #3 agreed to share their name with the authors.)

Evaluation Summary:

This article is dealing with the unmet need to generate a machine-learning approach for the early and accurate estimation of the risk among COVID-19 admission. The presented data generate confidence on the validity since they have been developed in a vast number of patients and they are validated in cohorts from different geographical regions.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 and Reviewer #3 agreed to share their name with the authors.)

Evaluation Summary:

This elegantly performed systems-genetics paper on the predicted human skeletal muscle secretome highlights the importance of sex and sex hormones in regulating myokine expression and predicted cross-tissue effects. Male and female mice lacking estrogen receptor α (Esr1) were used to understand how estrogen signalling affects myokine genes expression. The methods used and data presented in this manuscript can serve as an important resource for other researchers in the field.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #3 agreed to share their name with the authors.)

Evaluation Summary:

This paper will be of interest to a broad audience of cell biologists and biochemists who study the cytoskeleton. It reports the development and rigorous characterization of a fully functional, fluorescently labeled version of profilin that can be used to visualize profilin's dynamic interactions in live cells. Owing to profilin's dual functions in regulating actin and microtubule assembly, this technological development will be a useful tool for a wide range of studies aimed at understanding the role of the cytoskeleton in driving fundamental cellular processes.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 agreed to share their name with the authors.)

Evaluation Summary:

The authors provide compelling evidence to show that injury induces activation of glycolysis during zebrafish adult tail fin regeneration. This early activation is crucial for osteoblast dedifferentiation and proliferation, which are required for blastema formation and tail fin regeneration. However, additional data are required to support the claim of a "metabolic switch" from oxidative phosphorylation to glycolysis. This study will be of interest to a broad audience in the fields of regeneration and metabolic regulation of developmental processes.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #2 agreed to share their name with the authors.)

Evaluation Summary:

The manuscript introduces a new enhancement to the dynamic clamp technique, CapClamp that, analogous to the artificial conductances of standard Dynamic Clamp, allows the experimenter to adjust the somatic time constant by setting a new membrane artificial capacitance independent of any change in input resistance. The technique is shown to have application for studying temporal integration, energetic costs of spiking and bifurcations. The technique is rigorously tested in model and physiological application and is robust when sampling frequency of the feedback (clamp) loop is fast compared to the fastest electrical event in a neuron (usually action potentials), and for vertebrate neurons it should be 20KHz or faster and yet faster for fast spiking neurons.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 and Reviewer #3 agreed to share their names with the authors.)

Evaluation Summary:

This manuscript is of significant interest to readers in the field of neural control of breathing and for researches interested in the generation of biological rhythms in general. The study assembles a sophisticated computational modelling approach to test long-standing theories and emerging views in neural control of breathing and more specifically on biophysical mechanisms of burstlet generation in the respiratory network (the preBötzinger complex network). This work is an important contribution to a better understanding of the respiratory rhythm generation, will help validate (or not) running hypotheses and will guide future experiments.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #2 and Reviewer #3 agreed to share their names with the authors.)

Evaluation Summary:

Berra and colleagues revisit several mechanistic questions mainly centered on the accessory helix of mouse complexin (mCpx) and its contribution to the 'fusion clamp' property of mCpx whereby mCpx-SNARE interactions prevent full assembly and subsequent membrane fusion. This clamping function is believed to help generate a metastable pool of release-ready vesicles at the synapse, and it has been studied in a wide variety of systems including mouse, fly, worm, squid, fish, and diverse in vitro biochemical preps over the past ~ 20 years. The authors derive several conclusions from their efforts, but most relevant is a reiteration of a previous proposal that the accessory helix region of mCpx stabilizes a pre-fusion clamped state via interactions with SNAREs.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Evaluation Summary: 

The authors have produced a rich dataset that illuminates how root-associated bacteria differ among diverse maize lines, under low and high nitrogen treatment. The authors make use of this dataset to describe interesting patterns related to the genetic architecture of factors associated with maize rhizosphere microbiome assembly, although it is not clear yet whether the microbiome is an agent of natural selection in this case, or whether other selective forces shape maize roots in a manner that in turn affect smicrobiome recruitment. In addition to interesting insights reported in the present manuscript, these data are likely to be used for and/or compared to, in many future studies. 

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 agreed to share their name with the authors.)

Evaluation Summary: 

In this study, the authors attempted to further examine the existence of a potential direct projection from the anterior cingulate cortex to the hippocampus which has important functional implication but is currently supported by only one major publication in the literature. They used distinct anterograde et retrograde viral tracing strategies and analyzed the data available in the Allen atlas but found no evidence in support of the existence of this connection. 

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 and Reviewer #2 agreed to share their names with the authors.)

Evaluation Summary:

This work convincingly provides important novel mechanisms on how microglial states are shaped during retinal development, an important question that should be of interest for a broad readership.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Evaluation Summary: 

Han et al. report the discovery of an amino acid transporter that is required locally at axon terminals of fly photoreceptors neurons for the uptake of histidine, the precursor of the neurotransmitter histamine. This function is required for transmitter synthesis locally and neurotransmission. The work exemplifies a specialized model for local monoamine transmitter synthesis at synapses in the nervous system, the generality of which for other monoamine systems remains to be tested. 

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #2 agreed to share their name with the authors.)

Evaluation Summary: 

The authors successfully demonstrated the immunogenic effects of a new dendritic cell-based vaccine on AML with NPM1 mutation. Using a transgenic mouse model that carries human NPM1 mutation and an elegant bone marrow chimera approach, they showed that the tumor growth is reduced by the vaccine. Furthermore, they provided evidence for increased CD8+ T cell presence and activity at the tumor site and increased anti-NPMc antibody levels in the serum. These findings are timely and novel and the new methods presented here would be of interest to a broad audience from immunology, inflammation and cancer fields. 

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Evaluation Summary:

The SNX-BAR family of sorting nexins are a diverse group of dimeric proteins that form tubules from endosomal membranes where they also select protein cargoes for incorporation into these transport carriers. The authors of this manuscript describe a new SNX-BAR complex in budding yeast, named the VINE complex, that uniquely harbors a guanine nucleotide exchange factor (GEF) domain for Rab5-related small GTP-binding proteins. The author's data implicate VINE in endosomal membrane remodeling events and the sorting of a vacuolar hydrolase receptor. The paper would be strengthened by some additional quantifications and by taking advantage of new modeling opportunities.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 and Reviewer #2 agreed to share their name with the authors.)

Evaluation Summary:

This study describes a novel "maturation phase transient reprogramming" (MPTR) method to restore the epigenome of cells to a more youthful state. The authors demonstrate the effectiveness of the method to reverse several age-related changes including remodeling of the transcriptome. The method appears to peform favorably compared to other transient reprogramming protocols, and the study will be of interest to developmental biologists as well as researchers that study ageing.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Evaluation Summary:

Oxygen consumption in mitochondria by the respiratory chain leads to a major source of reactive oxygen species, and mitochondrial glutathione is an important line of defence against free radical production. The ABC transporter Atm3 exports oxidized glutathione from the mitochondria to help maintain a suitable reducing environment. Here, the authors have determined structure of Atm3 in multiple conformations by single-particle cryo EM and have revealed new insights into local changes coupled to substrate export of oxidised glutathione and ABC exporters in general. The work will be of interest to the mitochondrial biology and transporter communities.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 and Reviewer #2 agreed to share their name with the authors.)

Evaluation Summary:

Pan et al investigated associations of self-reported egg consumption with plasma metabolic markers and these plasma metabolic markers with the risk of cardiovascular diseases. In general there was some impact on metabolic markers which could protect against CVD. The paper will interest scientists in the field of nutritional epidemiology.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Evaluation Summary:

The paper unequivocally proves that the key function of proline during bone formation is being incorporated into proline-enriched proteins rather than contributing to other metabolic processes.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Evaluation Summary:

Urbanization has broad impacts for macroecology but its consequences for wildlife microbial ecology remain unclear. Dillard et al. hypothesize that humans living in an urban setting may transfer their microbes to wildlife with potential adverse effects. They analyze 16S rRNA gene sequencing data from humans, crested anoles, and coyotes, leading to the discovery of multiple bacteria that fit the pattern of urbanization and inter-species transfer.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1, Reviewer #2 and Reviewer #3 agreed to share their name with the authors.)

Evaluation Summary:

The gut of honeybees is colonized with stable community of bacterial symbionts. The molecular mechanisms involved in this stable associations are poorly understood. Here Schmidt et. al. focused on the identification of bacterial factors required for the colonization of the bee gut symbiont Frischella perrara. They identified a major regulator involved in controlling the expression of multiple colonization factors in F. perrara which include factors that are either required for the induction of a distinct scab phenotype upon gut colonization, or are involved in promoting colonization through adhesin or the production of secondary metabolites. The work is of potential interest for researchers in the field of host-microbe interactions and symbiosis, and for the study of bee health. The valuable integration of different techniques used in this study and rigor of the experiments lead to solid data and justified conclusions.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1, Reviewer #2 and Reviewer #3 agreed to share their name with the authors.)

Evaluation Summary:

This paper reports the surprising observation that the general transcription factor TFIIH, but not transcription, is required for chromosome condensation in frog egg extracts. TFIIH may act by facilitating condensin localization and function. This opens up a lot of interesting new questions and lines of research that promise to add significantly to the field of chromosome biology. It will now be interesting to directly test the mechanism of action, and to examine whether this role of TFIIH extends to somatic cells and other animals.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #2 and Reviewer #3 agreed to share their name with the authors.)

Evaluation Summary:

The authors report that upon exposure of yeast cells to paraquat-induced superoxide production, specific mitochondrial DNA genes encoding electron transport chain proteins are deleted to minimize the generation of endogenous superoxide. Reversible loss of mitochondrial DNA as an adaptive response to paraquat stress is an interesting idea. The data presented appear to support the proposed model, but could be further strengthened as alternative interpretations of the described observations are possible.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 agreed to share their name with the authors.)

Evaluation Summary:

This paper presents a novel computational model of metacognition that parameterizes links between sensory evidence and confidence. The proposed model relies on perceptual decision-making to formalize different sources of noise and bias that impact confidence, with the aim of developing metacognitive metrics that are independent of perceptual sensitivity - a continued endeavor in the field. Despite the clear merits of this approach, more evidence is needed to validate the proposed architecture, which is particularly modular, and may therefore impair the generalizability of the proposed mechanisms.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #2 agreed to share their name with the authors.)

Evaluation Summary: 

The manuscript presents a potentially interesting new method to study alternative splicing at the single-cell level in the mouse. With further testing and benchmarking, this method would be of interest to researchers working with single-cell data and/or interested in alternative splicing. 

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Evaluation Summary:

This paper is of interest to scientists and clinicians within the field of muco-obstructive diseases in the airways, such as cystic fibrosis (CF) and chronic obstructive pulmonary disease (COPD). It identifies the sodium-bicarbonate cotransporter SLC4A4 as a key component of the mechanism by which normal airways prevent the formation of sticky mucus and defend theirselves against bacterial and viral infections.

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Evaluation Summary:

Lövestam et al. report 76 cryo-EM structures of in vitro assembled recombinant tau filaments, including 27 previously unobserved ones. Together with the recent paper from Scheres and Goedert research groups, the structure-based knowledge of amyloid assembly will be boosted several fold. Most importantly, a few in vitro conditions were found to replicate the amyloid structures from both Alzheimer's disease and chronic traumatic encephalopathy. Those findings will open up new avenues to quickly screen compounds that inhibit filament formation under in vitro conditions, as well as the (self-)assembly process of amyloid fibrils.

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Evaluation Summary: 

Zhou et al. provide a robust study on isotopic and metabolic changes of a soil community across a gradient of different land-use types in Sumatra, Indonesia. By mixing community-based analyses of stable isotopes and size-based metabolic measures, they are able to elucidate, for the first time, important links among plants and the soil food web in tropical ecosystems. This study is of importance to tropical biologists, ecosystem ecologists and biodiversity conservationists aiming to understand the impacts of humans on tropical forests. 

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Evaluation Summary: 

This is an excellent, innovative and high quality study that reveals an essential role for isoprenoids within the Plasmodium apicoplast, and demonstrates a likely polyprenol synthase that is required for apicoplast biogenesis. This is an important finding for understanding apicoplast and isoprenoid biology in general, and is significant because synthesis of isoprenoids appears to be the only essential role for the apicoplast in asexual intraerythrocytic stages. 

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Evaluation Summary: 

Key steps in the evolution of more complex life involve evolutionary transitions in individuality-the origin of new biological entities (i.e., multicellular organisms). This paper presents a novel criterion for measuring when this transition has occurred, via the presence of trade-off breaking adaptations. This work has considerable merit and will be of particular interest for diverse researchers studying transitions in individuality. Some of the author's overarching claims require further clarification.

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Evaluation Summary:

This study is a meta-analysis of previously reported studies on G protein-coupled receptor (GPCR) coupling to G proteins. Three separate data sets that describe the coupling of members of the superfamily of non-sensory GPCRs (~200 genes) to the large family of G protein alpha subunits (~20 genes). The authors try to arrive at a consensus for receptor-G protein coupling from the three data sets, as well as identify and highlight differences or incongruencies. Compiling these vast data sets into a unified format will be extremely useful for investigators to understand receptor and effector relationships. The meta-analysis will help to deconvolute the complex physiology and pharmacology underlying hormone or drug actions acting on receptor superfamilies.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Evaluation Summary:

The authors present an interesting approach of COVID-19 pathogenesis with emphasis on the role of innate lymphoid cells as a major correlate of the severity of COVID-19 and of the levels of inflammatory markers. The main strength of the manuscript is the novelty of approach, and the fact that the authors are the first to find this potentially interesting correlation, which brings up a number of both translational and mechanistic possibilities of significance. The limitation, of course, is the difficulty in showing a cause-and-effect relationship between the reduction in of innate lymphoid cells and the severity of COVID-19 inflammation. 

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 and Reviewer #2 agreed to share their names with the authors.)

Evaluation Summary:

This paper is the first to characterize overdispersion of COVID-19 spread in schools using crowdsourcing . It has the potential to serve as a useful platform for assessing preventative measures in schools but needs more clarity regarding the sensitivity of the approach to the completeness of input data, as evidence by different model conclusions when sparse data from the US is used as an input as opposed to the more detailed Canadian data.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 agreed to share their name with the authors.)

Evaluation Summary:

A challenge to understanding the physiology and therapeutic potential of G protein-coupled receptors (GPCRs) is to understand the range of their couplings to different G proteins. Avet et al developed of a novel set of biosensors to assess the coupling specificity of 100 therapeutically relevant G protein-coupled receptors (GPCRs) to various G protein isoforms and arrestins. The novel screen and results obtained with reference ligands will have broad use for researchers studying GPCRs, potentially impacting discovery of new physiological pathways, understanding adverse effects of currently marketed therapeutics, and discovery of novel, safer therapeutics.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 agreed to share their name with the authors.)

Evaluation Summary:

Protein kinase A phosphorylation of phospholamban (PLN) is part of the "fight or flight" response, which ultimately increases the force of cardiac contraction. Mutations in PLN have been linked to familial dilated cardiomyopathy (DCM). Crystal structures of wild-type and mutant PLN in complex with the PKA catalytic domain provide insights into both the nature of the complex, and potential mechanisms by which DCM mutations may cause disease. This paper is of interest to scientists interested in the mechanism of substrate recruitment by protein kinases, and particularly those who have an interest in understanding the mechanism of mutations associated with dilated cardiomyopathy.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #3 agreed to share their name with the authors.)

Evaluation Summary:

This manuscript describes a model of Ewing sarcoma , which represents an improvement upon previous zebrafish sarcoma models and the data suggest that the methods employed yield tumours that resemble human disease. This new model may be used to better understand sarcoma progression so that new therapeutic targets may be realised.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Evaluation Summary:

Wang et al. adapt a new statistical framework for a multi-site multi-year data set to investigate the effects of environmental variables on the temporal stability of plant communities and biomass productivity in Chinese grassland communities. This new framework may well turn out to be one that the larger ecological and ecosystem academic communities, interested in temporal changes of ecological processes across large spatial scales, have been looking for.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Evaluation Summary:

The authors demonstrate a molecular mechanism responsible for the rewiring of stroma cells that makes them supportive of acute myeloid leukaemia (AML) cells. Understanding metabolic interactions between leukaemia cells and the bone marrow microenvironment may provide new targets for leukaemia treatments. It has already been shown that the inhibition of gap junctions reduces AML growth in vivo, and here the authors provide evidence for a potential mechanism explaining that finding. The work will be very interesting for those working in the fields of hematopoiesis, leukemia (especially AML), cancer metabolism and cancer microenvironment.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #3 agreed to share their name with the authors.)

Evaluation Summary:

This manuscript describes pioneering work providing detailed description of iPS-derived muscle fiber differentiation in culture. It demonstrates that muscle fibers show self-organising capacities in vitro and form bundles with identified attachment points; this self-organisation generates internal tension within myofibers. Overall, this study suggests that tension drives sarcomerogenesis in multi fibrillar vertebrate muscles and will be of interest to researchers in the muscle field and also biophysicists interested in collective cell behaviour.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Evaluation Summary:

This manuscript is of interest to readers in the field of microbiology and antimicrobial resistance. It reports that genetically identical antibiotic-sensitive bacteria can escape killing upon exposure to an otherwise lethal concentration of antibiotics because they have a low ATP level. The authors further attempt to demonstrate that variation in the level of expression of some genes in energy-generating metabolic pathways allows for a wide range of ATP levels among the cells in a population, thus generating a subpopulation with low ATP levels that can survive antibiotic exposure.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Evaluation Summary:

This paper uses single-cell genomics to examine the heterogeneity of virus-specific CD4 T cells over time in both acute and chronic viral infection. Further, the authors build a comprehensive atlas of the transcriptional evolution of virus-specific CD4 T cell responses that could be used as a reference tool to interpret other datasets. This work characterizes how the antiviral CD4 T cell transcriptional landscape changes with time and will be of broad interest to those that study acute and chronic CD4 T cell responses.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 agreed to share their name with the authors.)

Evaluation Summary:

How biological patterns such as concentration gradient scale with the size of the cell or organism is a long-standing question in developmental and cell biology. In this study, Datta et al show theoretically that directed membrane transport of biomolecules and their release at the cell pole results in a cytoplasmic gradient that scales with cell size if two requirements are met: the cell grows while maintaining its spheroid proportions, (i.e. not by elongation), and the binding of the cytoplasmic fraction of the biomolecule to the membrane should be close to irreversible. A strength of this manuscript is that it invokes a realistic cellular mechanism that could be achieved through several biochemical implementations and can inspire experimental studies. Stronger biological examples and a deeper search in the literature or change in some of the simulation parameters would improve the study, and give the "impetus for experiments" the authors wish to provide.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Evaluation Summary:

The manuscript provides strong support for the concept that oligodendrocyte alterations contribute to neurological disorders that were previous thought to be primarily cell autonomous to neurons. The work is very well done, the results presented are clear and convincing, and the discussion is reasonable and interesting. The study will have considerable impact on the assessment of various neurodegenerative disorders with TDP-43 alterations.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #3 agreed to share their name with the authors.)

Evaluation Summary:

The manuscript describes the presence and genetic control of endocardial cell protrusions in zebrafish hearts that resemble endocardial sprouts recently described in the mouse heart, and which appear necessary for the process of trabeculation, whereby chamber cardiomyocytes undergo staged morphogenesis to form a spongy inner layer. This manuscript is of broad interest to readers who study cardiogenesis and developmental biology. This first formal dissection of endocardial protrusions in zebrafish hearts describes how they anchor to cardiomyocytes, and how they participate in signaling pathways involved in trabeculation. The work combines elegant zebrafish reporters and high-quality imaging, as well as mutant lines and pathway inhibitors to provide key findings of how mutual regulation between the myocardium and the endocardium contribute to understanding of mechanisms underlying organ development.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 agreed to share their name with the authors.)

Evaluation Summary:

This manuscript explores how microbial foraging strategies contribute to species coexistence in aquatic environments, and will be of interest to microbial ecologists and theoretical ecologists. Using mathematical modeling, the authors demonstrate that differences in particle detachment rates across bacterial species can promote coexistence. Additional explanation and documentation of methods, along with a discussion of the generality of the results, would strengthen the manuscript and ensure reproducibility.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 agreed to share their name with the authors.)

Evaluation Summary:<br /> <br /> This manuscript will be of interest to those studying gene transcription and its regulation by co-activator complexes in metazoans. The identification of the large TRAPP subunit shared between two conserved histone modification complexes as a negative regulator of the interferon type I pathway in colorectal cancer cell line provides novel insights into the functions of this TRAPP subunit, which was previously known only for this positive effects on gene transcription.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 agreed to share their name with the authors.)

Evaluation Summary:

This manuscript will be of interest to readers in the field of microRNA (miRNA) biology, particularly those interested in miRNA targeting. The authors interrogated non-canonical miRNA target recognition to a depth vastly exceeding any study to date. The results revealed unexpected, sequence-specific diversity in miRNA-targeting modes, providing new insights relevant for improved target prediction.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #2 and Reviewer #3 agreed to share their name with the authors.)

Evaluation Summary:

This manuscript focuses on a missense mutation of Nucleoporin107 (Nup107) gene, which encodes a nuclear pore complex protein. Phenotypic analyses demonstrate similar phenotypes compared to syndromes identified in human XX-ovarian-dysgenesis patients. Further RNA-seq analyses revealed potential targets of Nup107, through which the authors identified the doublesex (dsx) gene as a critical target with functional readouts. Both Nup107 and Dsx act in the somatic gonadal cells to regulate germ cell function, and have connections with the BMP signaling pathway. This study provides a great example to use Drosophila as a model organism to study the molecular and cellular mechanisms of a known human disease and should be of general interest.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #3 agreed to share their name with the authors.)

Evaluation Summary:

This manuscript will be of broad interest for biologists, in particular developmental biologists and ecologists, as it addresses essential questions on the interaction between organisms and their environment. How organisms manage to maintain a stable phenotype (robustness) or how they adjust their phenotype (plasticity) in response to environmental variations is a major issue. In this article, the authors show that the hormone ecdysone is involved in Drosophila in the plasticity of wing size and the robustness of wing pattern.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 agreed to share their name with the authors.)

Evaluation Summary:

This manuscript would be interesting for cell biologists and biophysicists studying nuclear organization and mechanics. The work provides new insights into how pulling forces from the cell cortex influence the dynamics of nuclear rupture during mitosis.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Evaluation Summary:

This is interesting and potentially impactful work uncovering mechanisms of stem cell exhaustion and impaired self-renewal that precede inflammatory phenotypes in Alzheimer's disease. The authors describe a mechanism converging on BMP signaling that may represent an early therapeutic target. The reviewers of this manuscript were excited about the potential impact but had some concerns which, if addressed, will strengthen the conclusions reached in this work.

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Evaluation Summary:

The manuscript dives into how protein structure/function robustness to mutation or polymorphism relates across evolutionary distance. The work indicates that evolutionarily related genes will have different shapes of robustness to variation, and that this will not necessarily track with phylogenetic relationships. The conclusions have potential ramifications for protein engineering, protein structure as well as population genetics and phylogenetics.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Evaluation Summary:

Single-cell RNA sequencing allows us to quantify variability of gene expression patterns within a population, and thus devise patterns with prognostic, diagnostic and predictive potential, called "gene expression signatures". Here, Noureen and collaborators benchmark four methods used for identifying these gene expression signatures, and evaluate their performance at overcoming a number of analytical challenges. They conclude that caution should be exercised when using bulk sample-based methods in single-cell data analyses, and cellular contexts should be taken into consideration. With strengthening of some statistical and methodological aspects to support the validity of the conclusions, this paper will be an informative and potentially valuable addition to the literature.

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Evaluation Summary:

The paper makes the provocative claim that SARS-CoV-2 Nsp14 is the key protein that mediates the effects of viral infection on the host cell transcriptome. The current evidence for this claim is good, but the paper would benefit from a few additional experiments. If confirmed by these experiments, the conclusion is unexpected and important, especially in these COVID times.

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Evaluation summary:

This paper documents a novel aspect of how T cell activation is regulated by the PTPN22 phosphatase, namely reversible oxidation which transiently reduces the activity of PTPN22 to allow the T cell antigen receptor to drive a strong activation signal. This compelling work adds to our understanding of how an immune response is initiated and provides new insights that could be exploited for the development of new drugs to treat immune-mediated diseases.

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Evaluation Summary:

This manuscript describes timely work on the structural dynamics of the SARS-CoV-2 spike protein that will be of importance to a broad range of scientists with interests in the biology of SARS-CoV-2 and COVID-19 and the function of anti-COVID-19 vaccines and antibodies as well as to molecular biophysicists generally interested in single-molecule imaging, protein dynamics, allostery, and molecular mechanisms. The experiments were very well-designed, controlled, and executed, and the data are of very high quality. Nonetheless, although the conclusions seem to be generally supported by the data and consistent with expectations based on previous findings, there are some concerns regarding the modeling and error analysis of some of the data.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #2 agreed to share their name with the authors.)

Evaluation Summary:

Tubulin mutations underlie a number of neurodevelopmental diseases, but their effect on microtubule function remains largely unknown. Using a combination of approaches and model systems, the authors provide evidence that the disease-associated alpha-tubulin mutations V409A and V409I may perturb microtubule polymerization. In addition, the mutations in alpha tubulin directly impact Tumor Overexpressed Gene domain proteins from recruiting tubulins to regulate microtubule dynamics. This study demonstrates a link between regulators of microtubule dynamics and disease pathogenesis. It will be of interest to the cytoskeleton and neurobiology fields.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Evaluation Summary:

This study is aimed to determine whether infection or vaccination affects activation of pre-existing cross-reactive memory B cells. The data are clear and have implications for further development of new-generation of vaccines.

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Evaluation Summary: 

The authors test the hypothesis that components of the TOM complex regulate efficient mitochondrial biogenesis by coordinating the synthesis (via controlling transcription of the corresponding RNAs) of mitochondrial proteins with the rate of mitochondrial protein import. It has previously been established that failure to import mitochondrial proteins results in the accumulation of toxic protein aggregates in the cytosol. The authors conclude that Tom70 fulfills this role and find that Tom70 expression declines as cells age, which contributes to age-associated mitochondrial dysfunction. 

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Evaluation Summary: 

The authors quantified sleep oscillations and their coordination in young people with 22q11.2 Deletion Syndrome and their siblings. This was done to identify potential biomarkers of later neurodevelopmental diagnoses in 22q11.2DS. The core findings demonstrate that sleep rhythms in 22q11.2DS are altered in comparison to the control group, as is their relationship with the behavioural expressions of memory consolidation. 

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Evaluation Summary: 

This manuscript will be of interest to the motor neuroscience, movement disorder, human electrophysiology, and brain computer interface communities. It examines the effectiveness of signals recorded from the subthalamic nucleus (STN) and along sensorimotor regions of the cortex for decoding simple movements in patients with Parkinson's disease. Additionally, a relationship between symptom severity and decoding performance is identified. With the recent advent of implantable closed-loop stimulators for neurological conditions such as Parkinson's disease, this paper addresses current knowledge gaps that may inform both surgical and engineering considerations for optimizing these new types of therapies. 

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Evaluation Summary: 

Liao et al. aim to improve our understanding of the genetic networks that underlie mouse male gonadogenesis and germ cell maturation during the fetal to neonatal transition. This goal was pursued by performing scATACseq on multiple timepoints, followed by definition of cell types and identification of potential transcription factors that could control the progress of differentiation. This is an exciting paper that may have far-reaching implications in the field of reproductive biology and male infertility, but additional validation is needed to confirm the newly identified cell populations. 

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Evaluation Summary:

This manuscript will be of interest people studying mechanosensation (particularly touch and pain sensation) and ion channels. The authors use a combination of electrophysiology and imaging to provide evidence that the force-gated ion channel Piezo2 is negatively regulation by the enzyme Tmem120A/Tacan. The results from the heterologous expression aspects of study are relatively robust and may have potential impact on the field. The physiological relevance of these findings await further investigation.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Evaluation Summary:

This manuscript examines how retinoid acid signaling controls the timing of neural crest production in avian embryos. The authors propose that local production of retinoid acid signaling activates the expression of BMP inhibitors in the dorsal neural tube. Disruption of BMP signaling results in the termination of neural crest migration and the establishment of the definite neural plate.

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Evaluation Summary:

This paper aims to address the current gap in the efficient analysis of large-scale multiparameter flow cytometry and other datasets. The authors offer a software toolkit with an efficient algorithm for comparing numerous samples at once. The study is well presented and is relevant to single cell analysis research.

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Evaluation Summary:

This manuscript addresses the cellular and dendritic physiology of cholinergic interneurons in the striatum. The authors use a creative integration of electrophysiology and optical methods to investigate this distinctive cell type, which is critically important at the intersection of motivated behavior and disease. They uncover a mechanism through which two separate active conductances - the hyperpolarization-activated h-current (HCN) and the persistent sodium current (NaP) - act in concert to selectively boost synaptic input from the thalamus onto proximal dendrites of cholinergic interneurons.

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Evaluation Summary:

This work will be of interest to researchers seeking new ways to target malaria parasites. The work provides insight into the energy requirements of parasites during the first day of their two-day life cycle, a period during which they are significantly resistant to a wide variety of antimalarial drugs, and identifies an essential enzyme that could be targeted in early-stage parasites. The study shows this protein is necessary for normal development and growth of parasites in red blood cells.

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Evaluation Summary:

This study uses long-read sequencing to investigate the origin of spontaneous petite mutants in S. cerevisiae. The results illustrate how the S. cerevisiae mitochondrial genome is prone to recombination events that lead to the formation of complex concatemers of fragments of the mitochondrial DNA that contain a high density of replication origins and, as a result, may outcompete the full mitochondrial genome. Apart from confirming existing hypotheses about the nature of petite mutants and revealing the structural diversity of rho-mitochondrial DNA, the results also allow drawing parallels to the origins of mitochondrial mutations in other organisms.

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Evaluation Summary:

The authors demonstrate that patients carrying a gain-of-function S218L mutation in CACNA1A exhibit a gene-dosage-dependent increase in the susceptibility to cortical spreading depression (CSD), seizure activity and brain edema formation following TBI compared with wild-type (WT) mice or mice carrying the milder R192Q mutation. This paper will be of considerable interest to familial hemiplegic migraine (FHM) sufferers who experience traumatic brain injury (and their physicians), as well researchers with an interest in the spectrum and phenotypic consequences of mutations in the voltage-gated, P/Q-type Ca2+ channel, CACNA1A.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Evaluation Summary:

The phenomena of inter brain synchrony is fascinating and has been observed in a variety of situations across different mammalian species. It has also been proposed to play a critical role in certain social behaviors. Here, the authors report that brain activity across two interacting bats display not only similarities but also important differences.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Evaluation Summary:

The authors investigated Atmospheric Particulate Matter (PM) , a mimetic of current air pollution and how it affects myelination in the central nervous system (CNS) using an animal model of demyelination. They showed that the PM caused changes in myelination that associated with microglial activation and markers of inflammation. In vitro modeling indicates PM can activate microglial via the TLR4/NFkB signaling pathway.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Evaluation Summary:

The authors make a compelling case for a special type of potassium channel (Kv3.3) in the control of the presynaptic AP spike waveforms. Importantly, mice that lack Kv3.3 showed auditory response deficits, including increases in pre-synaptic AP halfwidth, AP latency, AP jitter and spontaneous activity. The in vivo recordings are impressive. The study contains an extensive data set and makes a compelling argument for the uniquely important role for Kv3.3 in synaptic transmission. Overall, the findings will significantly advance our understanding of the calyx of Held and the neural circuit of sound processing, as well as the functions of Kv3 channels.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 and Reviewer #2 agreed to share their name with the authors.)

Evaluation Summary:

The authors describe the hei-tag, which, when added to a genome editing enzyme, results in increased editing rates in fish embryos and mammalian cell culture. The hei-tag tool could provide a valuable alternative that can potentially boost genome editing efficiency in different species and systems. The wider applicability of this approach still requires further investigation, since the improvement of editing efficiency is so far supported by experimental data on only a few targets. It would also be important to learn how the authors' design decisions affect activity, especially when benchmarked against current state-of-art genome editing tools.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Evaluation Summary:

The work provides new insight into the potential role of 5hmc DNA in specific transcriptional processes. This implies that 5hmC containing DNA has specific epigenetic features beyond being a simple intermediate in interconversion between repressive 5mC and active C DNA. This work has the merit to focus the attention on a rare DNA modification, helping defining its functions, starting from in vitro evidence and extending these findings in cellular context. There are some weaknesses in the presentation of the data, the controls and the statistical analyses.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Evaluation Summary:

Recently liquid-liquid phase separation (LLPS) has emerged as a mechanism by which membraneless compartments are formed inside the cells to compartmentalize biomolecules. In this paper, the authors show that the P protein from a plant-infecting negative sense RNA virus undergoes LLPS to promote virus replication. The host casein kinase 1 phosphorylates P protein and inhibits phase separation and viral replication. This paper will be of interest to virologists and researchers who study LLPS.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #3 agreed to share their name with the authors.)

Evaluation Summary:

This manuscript will be of interest to oncologists, cardiologists, cardio-oncologists, and primary care providers who treat patients with breast cancer and adds to the growing body of literature that identifies the increased risk for cardiotoxicity associated with breast cancer treatment and does so at the general population level. The results of this study are interesting and supported by the data provided, however they must be interpreted with caution as the database utilized includes intended treatment regimens (chemotherapy, radiotherapy) rather than the confirmed treatments patients received.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #3 agreed to share their name with the authors.)

Evaluation Summary:

FBXW7 is a CRL controlling the abundance of numerous transcription factors through targeted degradation. The authors use isogenic cancer and normal cell lines that differ only in the functional status of FBXW7 to examine the genome-wide effects of FBXW7. The authors demonstrate that null and missense mutations have similar large-scale effects on gene expression and chromatin modification status of many loci at intergenic and intronic regions, but that there are substantial differences in affected loci between the mutant backgrounds. This study represents the first such systematic evaluation of the impact of FBXW7 functional variation on global gene expression.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Evaluation Summary:

This paper is of general interest to a broad audience of scientists working in regenerative medicine, tissue engineering, disease modelling, and stem cell fields. It reveals organ fibroblast heterogeneity and shows that the organ-specific identity is preserved in vitro and during ectopic transplantation in vivo. The right choice of fibroblasts might therefore be critical in the fields mentioned above.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Evaluation Summary:

This paper will be of broad interest to microbiologists interested in gene expression noise and/or metabolic interactions in microbial communities. It provides a novel hypothesis that complements existing theoretical frameworks. The hypothesis is well supported by data from a mathematical model, and it its predictions could be tested experimentally in future work.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)