7,013 Matching Annotations
  1. Oct 2022
    1. eLife assessment

      Harkin and colleagues explore functional properties of dorsal raphe serotonin neurons using the approach called a generalized integrate-and-fire [aGIF] model, which incorporates a relatively small number of salient biophysical properties of a specific neuron type, and whose parameters are optimized based on voltage dynamics obtained experimentally. The authors make an interesting finding that after-hyperpolarization and A-type potassium currents, in combination with heterogeneous feedforward inhibition from local GABA neurons, give rise to a derivative-like input-output relationship in serotonin neurons.

    1. eLife assessment

      This manuscript is of interest to readers in the field of bone biology. It identifies a novel role for the vacuolar ATPase accessory protein ATP6AP2 within the osteoblast lineage and shows that loss of ATP6AP2 in the mature osteoblast results in disorganized bone formation. A similar, but milder, bone disorganization phenotype is also observed when this gene is knocked out in osteocytes. The authors show that this bone phenotype is partially rescued via restoration of MMP14 action.

    1. eLife assessment

      This paper reports on the development of an impressive microfluidic platform for the study of motility, and motility transitions, exhibited by single algal cells in circular confinement. Building on previous work that showed a three-state motility repertoire for certain green algae, the present work uses extremely long time series and a variety of physical perturbations to show how those dynamics can be altered by environmental conditions. The work will be of interest to a wide range of scientists studying motility and nonequilibrium dynamics, but its impact would be improved by a more insightful analysis of the voluminous data, with connections to physical principles.

    1. eLife assessment

      This paper asks whether a risk score integrating the impact of common genetic variants across the genome (polygenic risk score) on Type II Diabetes is also to any degree predictive of diabetes in pregnancy (Gestational diabetes or GDM).The study population comprises women of South Asian ancestry, who are particularly susceptible to GDM. Strong evidence is presented in favour of the hypothesis of the hypothesis in two sizeable cohorts, one from Canada and the other from the UK. The paper will be useful to those studying women's health in pregnancy, and in particular GDM, which is associated with a number of adverse pregnancy outcomes.

    1. eLife assessment

      We admired the study by Krehenwinkel and colleagues for its novelty, depth, and ecological breadth, but have questions regarding the laboratory, bioinformatic and statistical methodologies that require clarification. It is likely to make a substantial impact in the field of plant-based arthropod metabarcoding, revealing ecological insights that can be derived from existing bio-banked material. The work, which creatively exploits herbarium material to track arthropod communities, will be interesting to a general audience in addition to ecologists, foresters, phytopathologists, and industry.

    1. eLife assessment

      This manuscript will be of interest to cardiovascular clinicians, medical geneticists, pharmaceutical companies, and the general cardiovascular disease research community. The study adds evidence for the causal role of triglyceride to several atherosclerotic cardiovascular diseases. Their use of Mendelian Randomization method is appropriate and provides convincing support to their findings, which may provide insights on the mechanism of TG biology and drug repurposing of TG-lowering agents.

    1. eLife assessment

      This fundamental study demonstrates that the two isoforms of the ARPC5 subunit (ARPC5 and ARPC5L) of the Arp2/3 complex have specific functions in regulating cytoplasmic and nuclear actin filament assembly in response to DNA replication stress and T cell receptor signaling in T lymphocytes. The data presented in the manuscript are convincing and of good technical quality, and the study provides interesting new insights into specific cellular roles of different Arp2/3 isoforms in T lymphocytes.

    1. eLife assessment

      This work examines the evolutionary origins of acid-sensing ion channels (ASICs), a class of pH-sensing receptors expressed throughout the brain and body. By combining analysis of sequences, functional measurements, and measures of tissue distribution, the authors provide solid evidence that ASICs existed far earlier than previously believed. The present data indicate that ASICs emerged after the split between bilaterians (organisms with two-fold symmetry) and Cnidaria (jellyfish, anemones, corals, etc.), approximately 680 million years ago. This evolutionary and functional analysis of ASIC channels across bilaterian lineages provides relevant information about the evolution of nervous and sensory systems.

    1. eLife assessment

      This work, which will be of interest to all who study plant-microbe interactions as well as plant cell biology, addresses a fundamental question in symbiosis, placing a classic nodulation defective mutant (rpg) into a plausible protein complex and establishing a hierarchy of "infectosome" assembly. Evidence includes convincing genetics and subcellular localization of components during establishment and maintenance of infection. The study also includes compelling new FLIM-based imaging techniques to distinguish signals from closely associated domains in plant cells.

    1. eLife assessment

      This is an important paper that is of interest to researchers interested in the psychological and neurochemical mechanisms of pain and pain relief. It shows that the perception of pain relief is modulated by controllability, surprise and novelty seeking. Moreover, these modulations are influenced by dopaminergic but not by opioidergic manipulations. These findings are supported by solid evidence.

    1. eLife assessment

      The parabrachial nuclei are groups of neurons in the brainstem (one on each side) that integrate information about the state of the body to guide appropriate homeostatic responses. The manuscript by Pauli and Chen et al. is a compelling and much-needed study that characterizes the cell types that make up these nuclei and genetic tools to study them. The result is a highly valuable resource to the academic community.

    1. eLife assessment

      This paper, of relevance to a broad range of plant biologists and colleagues in the circandian field, reports important results that demonstrate circadian coordination of characteristic floral development in sunflower. The current manuscript includes convincing observations and possible hypotheses, but the ecological relevance of the temporally-controlled flower development is incompletely shown.

    1. eLife Assessment:

      This paper by Möller and colleagues investigates and compares spontaneous turn-taking behavior by pairs of macaque monkeys and human participants in a social coordination game. The study uses a novel format for interaction - the "transparent game" in which subjects play together on a clear glass screen, so that decisions take on properties of continuousness. The results suggest differences between species in their tendencies toward cooperative, mutually beneficial behaviors, with humans exhibiting more prosocial tendencies. Interestingly, training with humans could encourage the monkeys to become less selfish and adopt a turn-taking strategy. The behavior analyses are rigorous and convincingly support the conclusions, and the study is likely to be of interest to researchers in the field of social neuroscience and decision-making, as well as to a more general audience who studies cognition, psychology, economics, especially game theory, and animal behavior.

      (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.)

    1. Evaluation Summary:<br /> <br /> This manuscript employs in vitro studies and elegant mouse models to detail how specific pyruvate kinase isoforms impact pancreatic beta-cell ATP/ADP levels, ATP-sensitive K+ channel (KATP channel) activity, calcium handling, and insulin secretion. This is an important study that challenges the current paradigms of KATP-channel regulation, the major signaling mechanism through which pancreatic beta cells couple blood glucose levels to insulin release. Future studies will be necessary to determine whether similar mechanisms are used in human pancreatic beta cells.

      (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.)

    1. Evaluation Summary:

      The authors leverage genotyping data from the islands of Cabo Verde to study its admixture history and to gain insights into the onset of the Trans-Atlantic Slave Trade. They find that patterns of ancestry between the islands are not the same, suggesting diversity in the founding populations of these islands. These results provide a nice example of how ancestry patterns vary across admixed populations due in part to their unique local history and social practices of that 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. Reviewer #1 and Reviewer #2 agreed to share their names with the authors.)

    1. eLife Assessment:

      The authors aim to predict bacterial enzymes responsible for drug biotransformation, and the work showcases the potential of this approach as a hypothesis generator for characterizing and validating novel bacterial enzymes in vitro. The authors describe the relevance of an accurate input (in terms of reaction completeness, including cofactors and reaction products) as paramount for the quality of the prediction. The conclusions, however, require additional experimental and non-experimental validations.

      (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.)

    1. eLife Assessment:

      This manuscript uses a genetically-encoded calcium indicator to assess neural activity across a population of axons connecting the fly's brain to its ventral nerve cord while the tethered fly behaves on a floating ball. Changes in fluorescence signal correlate better with states such as walking, resting, and grooming than with particular limb movements or joint angles, suggesting that specific descending neurons represent the larger behavioral subdivisions. The preparation and large-scale analysis represent a significant step forward in determining how the brain compresses sensory and state information to convey commands to the ventral nervous system for behavior execution by motor circuits.

      (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.)

    1. eLife Assessment:

      This paper should be of high interest to scientists within the field of developmental neuroscience. The authors characterize the earliest spontaneous waves of the retina - a topic that is poorly understood. The ability to monitor waves over the entire retina at high resolution is a strength of the work. Weaknesses include reliance on pharmacology and some missing details in the analysis.

      (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.)

    1. eLife Assessment:

      A comprehensive single-cell transcriptomic study was performed in this study to gain insight into the development of endothelial cells and other co-developing mural cells derived from human induced pluripotent stem cells (hiPSCs) in 3D environment. This study gave us important information about signature genes, trajectories, and cell-cell interactions at various stages of vessel formation. Accordingly, the results of this study could potentially be of valuable interest to scientists working in the fields of stem cells, regenerative medicine, and tissue engineering.

      (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.)

    1. eLife Assessment:

      This is a rigorous evaluation of whether the compression of time cells in the hippocampus follows the Weber-Fechner Law, using a hierarchical Bayesian model that simultaneously accounts for the firing pattern at the trial, cell, and population levels. The two key results are that the time field width increases linearly with delay, even after taking into account the across trial response variability, and that the time cell population is distributed evenly on a logarithmic time scale. Overall, the paper is well written, the experiment and data analysis are technically sound, and the conclusions are mostly well supported.

      (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.)

    1. eLife Assessment:

      This manuscript sheds light on the biology of embryonal rhabdomyosarcoma, a common pediatric muscle tumor, by exploiting an established zebrafish model. Specifically, new knowledge is revealed of how the p53 tumor suppressor contributes to progression and extent of disease. This paper will be of interest not only to pediatric oncologists but also the broader cancer research community given the frequency of TP53 mutations as secondary lesions in human cancer.

      (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.)

    1. eLife Assessment:

      The authors perform a Transposon-Sequencing screen to determine bacterial factors (including receptors) important for infection by two phages in the model bacterium Corynebacterium glutamicum. Using their established high-density transposon library, they identify genes required for infection with the phages Cog and CL31. They also identified a spontaneous phage-resistant mutant that led to the discovery of a gene involved in mycolic acid synthesis. Overall, the work is of broad interest to scientists in the field of cell wall biogenesis, phage infection, and bacterial cell 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, Reviewer #2 and Reviewer #3 agreed to share their name with the authors.)

    1. eLife Assessment:

      In this manuscript, the authors perform an extensive systematic analysis of membrane contacts sites to uncover novel proteins required for tethering organelles and modulation of membrane contacts. The authors identify over 100 new potential contact site proteins and effectors including proteins associated with the recently discovered plasma membrane-LD (pClip) and Golgi-peroxisome (GoPo) contact sites. Further, the authors identify and characterize novel lipid transport proteins associated with the pClip as well as Lec1, an ER-Lipid droplet contact site associated protein which contains a novel putative lipid binding domain and may facilitate ergosterol transport between the plasma membrane and lipid droplets.

      (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.)

    1. eLife Assessment:

      This manuscript presents a biophysical study of the nature of the mechanosensitivity of voltage-gated sodium channels. The identification of a voltage-independent mechanosensitive step is well founded, the proposal that this step is the intracellular gate is plausible speculation. It is expected to be of interest to scientists studying the physical basis of mechanosensitivity in electrophysiology.

      (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.)

    1. eLife Assessment:

      This manuscript presents the cryo-EM structure of the Yta7 chromatin remodeler, which provides new mechanistic insight into how this AAA+ protein unfolds histone H3 in yeast for DNA replication. The study details the putative role of the C-terminal bromodomains, as well as an N-terminal bromo-interaction motif, in engaging nucleosomes for subsequent capture of the H3 tail for ATP-driven translocation by the upper AAA1 ring. The accompanying functional work helps establish the proposed nucleosome recognition mechanism, providing a structural framework that may be generally used by AAA+ nucleosome remodelers. The work will be of interest to colleagues in chromatin biology as well as all who study the very large family of AAA-ATPases.

      (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.)

    1. eLife Assessment:

      This paper demonstrates an integrated labeling and block face fluorescence imaging method that enables the rapid evaluation of biological specimens as large as an E18 mouse embryo with single cell resolution. Such capabilities will likely be of great interest to developmental biologists and pathologists. While the approach can be considered a major step forward, additional experimental support is necessary to gauge how quantitative the method is.

      (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.)

    1. Evaluation Summary:

      By the use of liver specific gene knock-out approaches Tang et al have clearly documented an important role for an endoplasmic reticulum sorting receptor, SURF4, in the efficient secretion of PCSK9, a protein in circulation that binds to and enhances the intracellular uptake and degradation of the low density lipoprotein receptor. As a consequence of liver specific knock-outs, adult mice survive well with an exceptionally lower level of circulating cholesterol, triglycerides and various lipoproteins. These compelling results reinforce the prospect for the development of therapeutic approaches in cholesterol and LDL reduction by targeting the intracellular association of PCSK9 and the SURF4 receptor. The work is elegant and complete with the only concern that some of the work and results overlap work published previously by some of these authors.

      (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.)

  2. Sep 2022
    1. Evaluation Summary:

      In this manuscript entitled "Dietary palmitic acid induces innate immune memory via ceramide production that enhances severity of acute septic shock and clearance of infection" Seufert and colleagues have investigated how saturated fatty acids increase susceptibility of the host in a murine model of LPS-mediated septic shock. Pretreatment of macrophages with palmitic acid (PA) was found to reprogram macrophages towards hyper-inflammatory phenotype, which was dependent on ceremide. Importantly, depletion of macrophages intracellular ceremide with oleic acid reversed their hyper-inflammatory phenotype. Interestingly, while PA was harmful in the LPS-acute septic shock model, it was beneficial in clearance of C. albicans in Rag-deficient mice lacking both B and T cells. While this is an exciting study, the presented data don't fully support the central hypothesis and the link with trained immunity is currently weak.

      (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.)

    1. eLife Assessment:

      In this manuscript the authors describe targeted, imaging-based RNAi screens to identify novel modulators of nuclear size and shape — two traits that are diagnostic and prognostic for many human diseases including cancers. The work provides novel insights into how and what dictates nuclear morphology, further decoupling key different components of lamins, chromatin, and the nuclear envelope, but there are some notable concerns regarding the scoring approach applied in the screen and hit validation. The authors also provide new evidence that lamin A may directly bind to (modified) histone H3 and how histone H3 disease mutations impact nuclear shape; this aspect of the manuscript would benefit from a more thorough analysis.

      (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.)

    1. eLife Assessment:

      Replogle et al. present their design of a compact and functionally validated dual sgRNA libary and dCas9-effector protein that will enable new forms of CRISPRi-based screening in mammalian cells. Quantitative comparisons to previously published standards demonstrate strengths and weaknesses, which, along with the protocols and design strategies outlined, should enable end users to rapidly adopt their approach.

      (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.)

    1. eLife Assessment:

      This paper presents a new mathematical model describing biologically plausible feedback that glial cells might use to properly modify the conduction velocity in axons and promote optimal timing of neural impulses through changes in myelination. This problem is of great importance in the field of neuronal plasticity. The mathematical model is solid and predicts that individual oligodendrocytes are able to modify their myelination pattern in response to correlated action potentials. This work provides an important step forward by providing the theory for myelin-mediated neuronal plasticity. The study will benefit from adapting physiological parameters for oligodendrocytes that are guided by experimental 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.)

    1. eLife Assessment:

      This study presents a large sample of participants ranging from 6-18 years investigating the association between white matter measures and reading using a sophisticated analysis. The results show a clear association between intra-axonal volume and single-word reading abilities. In sum, this valuable study complements other large-scale studies by applying sophisticated fixel-based 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. Reviewer #1 agreed to share their name with the authors.)

    1. eLife Assessment:

      This is a very valuable study that describes the bone phenotype and mechanism of the action of the obesity gene Ksr2. That there is a site-selective bone phenotype is interesting as is the identification of KSR2 as an actionable target.

      (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.)

    1. eLife Assessment:

      The authors use their expertise in live-cell imaging and mathematical modeling to explore the relationship between chromatin structure, gene positioning and transcriptional co-regulation, using two publicly available datasets encompassing chromatin tracing and transcriptional activity. The resulting analysis reveals a weak association between transcription and proximity, but needs more statistical validation to strengthen the validity of the conclusions. With some clarifications and revisions, several findings, such as coupling of spatiotemporal positioning with activity, in-depth analysis of existing imaging/ChIP-seq datasets, could make this work impactful to both specialists and non-specialists.

      (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.)

    1. eLife Assessment:

      Juette and coworkers employed single-molecule fluorescence, cryogenic-electron microscopy structures, and in vivo measurements to investigate the mechanism whereby two natural products with potential as cancer therapeutics, didemnin B and ternatin-4, act. The compounds are shown to inhibit tRNA accommodation within the ribosomal A site during translation elongation by interfering with movement of eukaryotic elongation factor 1 alpha after its activation by the GTPase activation site of the ribosome, with the degree and nature of this restriction differing subtly between the two compounds, leading to more marked differences in their effects on global translation and cell growth. The compelling results of this interdisciplinary work solidify prior conclusions, particularly on didemnin B, and illuminate the similarities and differences on how these two drugs interfere with the normal functioning of the elongating ribosome in vitro and inhibit protein synthesis and cell growth in vivo. Some revisions of figures and text are required to clarify the results and the authors' 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 #1, Reviewer #2 and Reviewer #3 agreed to share their names with the authors.)

    1. eLife Assessment:

      This manuscript describes a highly novel barcoding strategy for forward genetic lineage tracing of tumor cells in vitro and in the in vivo environment. The technique, coined WILDseq, can be used to track cells present in vitro which are enriched or depleted in the in vivo environment. Treatment further contributes to clonal expansion and retraction and emergence of populations with sensitivity to alternate agents. The studies are rigorously conducted and are highly impactful.

      (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.)

    1. eLife Assessment:

      The authors sought to enhance antibody binding to target antigens via reversible catenation, as an alternative to affinity maturation, beginning by computationally establishing parameters under which this type of binding enhancement via avidity effects would occur, and then following up with proof-of-principle experiments. While computational predictions and experiments are in excellent agreement, some controls that would further strengthen data interpretation are lacking. If generally applicable, the approach would accelerate efforts to develop antibodies with enhanced binding potency relative to their progenitors, applicable to any area of research employing antibodies.

      (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.)

    1. eLife Assessment:

      This study is a useful extension of previous work on the relationship between body size and cancer risk and the mechanisms by which large-bodied mammals reduce their cancer risk. Through solid analyses of the genomes and several aspects of the cell biology of sloths, armadillos and their relatives, the study explores whether the evolution of large body size in their relatives (some extinct) was correlated with genomic changes such as the duplication of tumor suppressor genes, experimentally demonstrating that cells of Xenarthrans (sloths, armadillos, anteaters) are exceptionally sensitive to DNA damage. The study concerns a topic of great interest and contributes to our understanding of how cancer risk has evolved in mammals.

      (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.)

    1. eLife Assessment:

      This manuscript will be of interest to microbial ecologists and biogeochemists working on soil carbon cycling and responses to climate warming. This study uses an elegant experiment to show that standing variation, both phylogenetic and phenotypic, enables microbial community adaptation to higher temperatures. The authors' conclusions are supported by the data, and this work lays a foundation for future experimental and modeling 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. The reviewers remained anonymous to the authors.)

    1. Evaluation Summary:

      This is an interesting discovery of a role for NINL in antiviral defense through modulation of interferon signaling. They found that there is diversifying selection of this factor as well as viral antagonism. This discovery paves the way to a better understanding of how viruses and hosts co-evolve.

      (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.)

    1. Evaluation Summary:

      The manuscript by Kane et al. described transcriptional profiles of various subsets of activated iNKT cells using longitudinal scRNA-Seq analysis. The finding that IL-10 producing iNKT cells have a cMAF-associated gene signature similar to Tr1 cells is novel. Overall, the data is well presented, however, functional consequences of some findings require 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.)

    1. Evaluation Summary:

      This is one of the most thorough assessments to date of suppression gene drives against mosquitoes. The models specifically consider the spatial dynamics of gene drives and whether a form of group selection may prevent the drive from eradicating the population, with mosquito ecology parameters. This manuscript will be of interest to those working in the technical development of gene drives, those predicting how such genetically modified insects would spread in the wild, and those evaluating the technology from regulatory and funding standpoints.

      (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.)

    1. Evaluation Summary:

      In this study, the authors identified that NFATc1 acts as a key regulator of articular chondrocyte differentiation during early mouse development. Using multiple pulse-chase experiments the authors found that NFATc1 expressing cells generated most of the articular chondrocytes, but not growth plate chondrocytes. Interestingly, NFATc1 expression in chondrocytes diminished as mice aged, suggesting that NFATc1 expressing progenitors are no longer expressing NFATc1 after articular cartilage development. This is an important study since it provides valuable evidence to reveal the regulatory mechanism of articular chondrocyte differentiation. The data presented in this manuscript, in general, support their 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. The reviewers remained anonymous to the authors.)

    1. Evaluation Summary:

      The authors suggest that PINK1-dependent endothelial mitophagy is pro-inflammatory by increasing the release of mitochondrial formyl peptides, one of the mitochondrial DAMPs. This study is important to identify the origin of serum formyl peptides during inflammation and to propose a new role of mitophagy in inflammation, which may be context and/or tissue specific.

      (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.)

    1. Evaluation Summary:

      This study will be of interest to a broad audience of microbiologists by providing one of the few examples of a clear phenotype for a toxin-antitoxin system. The conclusion that an oxygen-regulated toxin-antitoxin system is required for an important step in biofilm development in the model organism Caulobacter crescentus is well supported by the data and experiments are well designed and controlled. Some possible limitations in interpretations from incompletely controlled phenotype reporters should be resolved by simple 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. The reviewers remained anonymous to the authors.)

    1. Evaluation Summary:

      This manuscript describes the mesenchymal cells expressed Axin1 as a key regulator for Wnt and BMP signaling pathway which is essential for lower limb development. Fibular hemimelia (FH) is a rare genetic disorder with unknown mechanisms. Their data clearly demonstrated that inhibition of β-catenin and BMP signaling genetically and pharmacologically could largely reverse fibular hemimelia phenotype in mice. In general, the manuscript is clear, well written, and concise, the study is well-structured and various techniques have been used to validate the data. It presents as a thorough study highlighting the importance of Axin1/ β-catenin/BMP signaling in FH development, and, furthermore, the interpretation of the results and the following conclusions are convincing.

      (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.)

    1. Evaluation Summary:

      This paper reports the structure of the M protein of SARS-CoV-2, as determined by cryoEM. The structure is well-determined and reveals a homodimer with overall similar structure as ORF3a, another virally encoded protein. The surface charge distribution is skewed towards positive at the C-terminal domain, which suggests roles in interactions with viral N and S proteins, and possibly viral RNA. The work is of relevance to virologists, especially those studying SARS-CoV-2.

      (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.)

    1. Evaluation Summary:

      This is a valuable manuscript that addresses an important question and provides interesting mechanistic insights into the roles of specific regions of the IR and IGF1R in their activation. While many of the data convincingly support the conclusions, in some areas the data are incomplete so we are left with an unfinished picture of the mechanisms of activation of the IR and IGF1R, and why they differ.

      (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.)

    1. Evaluation Summary:

      This manuscript reports useful data on how human papillomavirus 8E6 protein regulates DSB repair pathways in human cells. The data support the claim that 8E6 promotes alternative end-joining through binding and destabilizing the p300 acetyltransferase, but the study remains relatively descriptive and incomplete as it is not yet clear which alternative end-joining pathway is involved lacking a test of a direct involvement of DNA polymerases theta (POLθ).

      (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.)

    1. Evaluation Summary:

      This is an interesting and timely paper that presents thermodynamic and structural (NMR) analyses of six KOW domains from the NusG superfamily of transcription factors. The authors identify a second fold-switching member of the NusG superfamily, VcRfaH, and investigate the physical basis of this fold-switching transition. The authors also compare the thermodynamic and structural properties of six fold-switching and single-folding KOW domains from different organisms, and show that fold-switching domains are less thermodynamically stable than their single-folding counterparts. This work will be of great interest for scientists in the fields of protein folding (theory and experiment), structural biophysics, and advanced protein NMR spectroscopy.

      (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.)

    1. Evaluation Summary:

      This is a useful quantification of the links of vascular disease on the development of subsequent mental health issues. It uses a robust dataset to quantify this association. Further work to focus the analyses, ensure claims are supported by the data, and consider alternative explanations is needed.

      (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.)

    1. Evaluation Summary:

      This manuscript has the potential to be of interest to a broad range of behavioral scientists. It provides insights into how biases can affect value-based behavior in invertebrates, similar to what has been reported in humans. However, there are a number of potential confounders that need to be addressed before drawing robust conclusions from the data reported.

      (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 #4 agreed to share their name with the authors.)

    1. Evaluation Summary:

      This is a valuable paper that uses solid computational modeling approaches to link plasticity in the hippocampal circuit with behavioral learning. The work focuses on reinforcement learning, a theoretical framework for how animals can optimize learning by extracting the statistical structure of the sensory environments. While a vast range of experimental data regarding the physiological properties of neurons in the hippocampus exists, reinforcement learning often lacks such physiological details. The manuscript begins to fill this gap, by developing a spiking computational model of the hippocampus that can implement reinforcement learning and capture some features of hippocampal physiology.

      (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.)

    1. Evaluation Summary:

      In this elegant study, Leyhr et al. identify the first potent nkx3.2 jaw joint enhancer, which they show to be deeply conserved across gnathostomes and likely to be absent from jawless fishes. The data support the hypothesis that this enhancer arose with the origin of hinged jaws during vertebrate evolution and is required for some aspects of early joint development in zebrafish. The work has important implications both for our basic understanding of enhancer function and evolution as well as potential genetic causes of craniofacial defects in humans.

      (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.)

    1. Evaluation Summary:

      This paper will be of interest to readers who perform extracellular recordings with high-density electrodes. It provides a proof of principle that high-density recordings allow assessing the interactions of pairs of neurons within local cortical networks in nonhuman primates.

      (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.)

    1. Evaluation Summary:

      The authors identify a new FOXP2-CPED1 gene fusion in prostate cancer that leads to the increased expression of FOXP2 and subsequent transformation of non-cancer cells. Increased FOXP2 was shown to promote prostate cancer in part through the increased expression and activation of the receptor tyrosine kinase MET, a known driver of prostate cancer. Notably, the authors created new genetically engineered mouse models of FOXP2 and FOXP2-CPED1 overexpression in prostate luminal epithelial cells which was sufficient to cause prostatic intraepithelial neoplasia in these mice with lesions that confirmed increased MET signaling. Oncogenes are typically interesting drug targets or interact with possible drug targets, and the manuscript could thus have a significant societal impact on better understanding drivers of the disease.

      (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.)

    1. Evaluation Summary:

      The authors combined atomistic simulations and continuum mechanics models to probe how structural features of the M2 channel impact the local membrane properties and stability of the channel in membranes of different curvatures. The insights gained in this work can potentially lead to novel strategies that screen for drug molecules that stabilize fission-incompetent conformations of the M2 channel. The multi-scale computational approach will find utility to many problems in membrane reshaping.

      (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.)

    1. Evaluation Summary:

      This manuscript is a timely contribution to the CRISPR/Cas field: the mode of function of the type III-E Cas7-11 CRISPR-Cas system. This is an RNA-guided RNA targeting system only characterized last year. In contrast to Cas13 systems, Cas7-11 does not possess collateral damaging activity, hence does not show cytotoxicity when introduced into human cells. These are highly desirable traits in practical applications. High resolution mechanistic studies would be essential for driving the further development of Cas7-11 based biotechnology applications.

      (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.)

    1. Evaluation Summary:

      This important study shows that methods currently used to predict which animals species might be at risk of infection by SARS-CoV-2, by looking at features of the host cell receptor the virus binds to, are fundamentally flawed, with exceptionally strong support for this conclusion. Much work on the potential host range of SARS-CoV-2 has focused on measuring the susceptibility of different species' ACE2 receptors to sarbecovirus entry and extending predictions to other unmeasured species based on ACE2 sequence features. Mollentze and colleagues show that ACE2 sequences are not more than a proxy for generic species relationships. In other words, species phylogeny alone can provide equivalent predictive power, allowing for predictions of mammalian susceptibility to sarbecovirus infection for the many species for which ACE2 sequences are not known yet.

      (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.)

    1. Evaluation Summary:

      By integrating a range of computational techniques, the authors generated a structural model for the AT3 domain, which is predicted to adopt a new fold. The key features of the structural model are consistent with the activity of the enzyme as an acyltransferase, with a transmembrane channel that can accommodate an acyl-CoA donor, and an outer cavity formed with a second domain that can accommodate a nascent LPS molecule as substrate. Overall, the study will help stimulate specific experimental analyses that can further evaluate and improve the model for better mechanistic understanding of this class of enzymes. The work will be of interest to structural biologists, and all studying acyltransferase enzymes.

      (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.)

    1. Evaluation Summary:

      The authors dissect the phenotypes of bone-marrow derived myeloid cells in a murine model of pulmonary vasculitis with relevance to human disease, revealing the association of novel phenotypic subsets associated with lung injury, yet the role of these subsets in regulating or contributing to tissue injury is less clearly determined.

      (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 reviewer remained anonymous to the authors.)

    1. Evaluation Summary:

      The work presented by Masson et al. highlights experimental approaches using spatial indentation and contrast-enhanced 3-D x-ray imaging to topographically map cartilage thickness in mouse knee joints. This methods described have the potential to impact the field of musculoskeletal biomechanics, especially for researchers using mouse models to study cartilage wear and disease, given the high resolution and sensitivity of the described approaches.

      (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.)

    1. Evaluation Summary:

      This work describes mouse ovary morphogenesis from E14.5 to birth using recently developed methods combining CUBIC and iDISCO and optimized 3D imaging using light sheet microscopy. The manuscript is of interest to all developmental biologists as it will serve as a reference to whole embryo morphogenesis, in particular vertebrate ovary morphogenetic 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.)

    1. Evaluation Summary:

      Grande and colleagues provide new insights into how different regions of the entorhinal cortex functionally interact with specific cortical brain areas and how, in turn, subregions of the entorhinal cortex interact with the hippocampus during 'scene' and 'object' processing. This paper is relevant to cognitive neuroscientists with an interest in the entorhinal cortex - hippocampal pathways and 'scene' and 'object' representation in the medial temporal lobe. The study is well-motivated, well-designed and appropriately analysed to address the research questions. Most conclusions of the paper are well supported by 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 #1 and Reviewer #2 agreed to share their name with the authors.)

    1. Evaluation Summary:

      The authors use an elegant experimental design to study genetic variation in the ubiquitin-proteasome degradation system in yeast. They identify a large number of QTLs for naturally occurring variation, and they elucidate the causal variants and likely functional mechanisms of several of these. The paper illustrates an innovative new approach to high-throughput QTL mapping for specific molecular processes and it will be of interest to colleagues aiming to harness natural variation for understanding a range of biological 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.)

    1. Evaluation Summary:

      This manuscript described the effects of two different CoronaVac vaccination schedules in a Chilean adult population. They find that a 0 and 28-day two-dose schedule produced superior levels of neutralizing antibodies and antibodies with a great breadth of interaction across variants compared to a 0 and 14-day two-dose schedule. They find no differences in T cell responses or total antibody levels between the two groups. These findings demonstrate that a short two-week two-dose interval should provide sufficient immunity to reduce the likelihood of serious outcomes during a COVID infection.

      (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.)

    1. Evaluation Summary:

      This study bridges the gap between connectomic data from the fly hemibrain and driver lines needed for functional experiments through a new freely available computational tool, NeuronBridge. It demonstrates that this software provides users with the ability to identify the same neurons within different driver lines, and the opportunity to match expression of neurons in a driver line with those in a connectomic database. Overall, this manuscript does a commendable job of describing an important resource for the community, which will hopefully be built upon via collaborative science of many groups as the field develops.

      (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.)

    1. Evaluation Summary:

      This manuscript addresses a long-standing question regarding the highly variable cellular composition and functions as well as immune environments along the epididymis. Using multiple mouse models (bacterial infection and parabiosis between WT and Ccr2 KO) in conjunction with powerful scRNA-seq analyses, the authors provided solid evidence supporting the notion that resident immune cells are strategically positioned along the epididymal duct, potentially providing different immunological environments required for sperm maturations and elimination of pathogens ascending the urogenital tract.

      (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.)

    1. Evaluation Summary:

      The manuscript by Noel et al reports parallel neurophysiological responses from the three brain areas MST, 7a and dlPFC of monkeys during a novel behavioural paradigm developed by the same group previously. The continual nature of this paradigm with a closed action-perception loop makes the animal behaviour more naturalistic compared to classical paradigms with artificial breaks between sensory stimulation and action. Findings of neurophysiology under such a paradigm are novel and of broad interest to cognitive and systems neuroscientists. The data presented in the paper support the claim of distributed neural coding in which task-specific sub-networks may form.

      (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.)

    1. Evaluation Summary:

      This is an important and delicately designed study that uses integrated tools to reveal underlying mechanisms of repair of the endometrium at menstruation. It combines single cell sequencing analysis and lineage tracing technologies to strongly prove that repair-specific cells originate from the fibroblast cell clusters and PDGFRα+ endometrial fibroblasts undergo MET and can become incorporated into the luminal epithelium of the post repair tissue.

      (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.)

    1. Evaluation Summary:

      The manuscript is well organized and clearly written. The discussion provides the required information to easily understand the relevance of each finding. the authors demonstrated using an osteocyte cell model that connexin43 is localized to mitochondria and that this is enhanced in response to oxidative stress. Several lines of evidence were presented showing that mitochondrial connexin43 forms functional hemichannels and that connexin43 is required for optimal mitochondrial respiration and ATP generation. These aspects were major strengths of the study.

      (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.)

    1. Evaluation Summary:

      This work provides substantial new insights into how semantic association strength influences the function and relationships across brain regions along a topographical structure of cerebral cortex. A principal gradient with the separation of default mode network from sensory-motor systems represents a hallmark of the retrieval of strong conceptual links. This study will be of interest to cognitive neuroscientists, especially those who are interested in semantic cognition.

      (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.)

    1. Evaluation Summary:

      This paper uses a new statistical approach called within family Mendelian randomization and asserts that claims of childhood BMI affecting a range of psychiatric traits are unfounded and were mainly caused by confounders that this new approach is able to better identify and control for. They do find a role for maternal BMI on a child's risk for developing depression. The main issue raised is that they do not convincingly show if they do not replicate the old association of childhood BMI with a range of psychiatric traits due to their technique simply having lower power to detect the signal or due to a true lack of this effect.

      (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.)

    1. Evaluation Summary:

      The authors investigate how HIV-1 infection affects the immune response in the context of SARS-CoV-2 infection by characterising the circulating B cell response. They conclude that people with HIV-1 infection, who become infected by SARS-CoV-2, produce B cell responses via an extra-follicular pathway to a greater degree than people who do not have HIV-1 infection. These findings imply that in HIV-1 infected individuals, long-term B cell and antibody responses against SARS-CoV-2 might not be as robust and durable compared to those in people without HIV-1 infection. The manuscript will be of interest to infectious disease specialists, virologists, and immunologists.

      (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.)

    1. Evaluation Summary:

      This paper is of interest to skeletal biologists studying skeletal development and tissue regeneration. The study applies a well-established and elegant axolotl limb regeneration model and transgenic reporter strains to reveal the potential role of osteoclast-mediated resorption in limb regeneration.

      (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.)

    1. Evaluation Summary:

      This important paper uses molecular simulations to explain how actomyosin networks transition from small clusters to the cortex or ring-shaped actin networks. The authors provide compelling evidence that variation in filament turnover rate and myosin concentration triggers a phase transition of these networks. The predictions of this model are consistent with observations made in T cells, where actin ring formation can be induced following their activation by antibodies.

      (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.)

    1. Evaluation Summary:

      Knowledge of the protein composition of defined sub-cellular compartments is of key importance for the characterization of protein machines that mediate defined cellular functionalities. The current paper presents a novel mouse line that will serve as a helpful tool in this context - a Cre-inducible APEX2 reporter mouse line for acute ex-vivo proximity biotinylation. The paper documents the successful use of the novel reporter line to assess circuit-specific proteomes and phosphoproteomes in the corticostriatal system during development. The corresponding data largely align with the published record, but potentially new biological insights deduced from bioinformatic analyses of proteomic data were not followed up by experimental validation. In sum, the new APEX2 reporter mouse line will be of substantial interest to researchers in many fields of mammalian biology. The extent of 'new biology' provided is rather limited, but will be of interest to readers in neurodevelopment.

      (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.)

    1. Evaluation Summary:

      This paper will be of interest to researchers studying control of respiration and also those developing functional magnetic resonance imaging methodology. The work provides insight into the relationship between brain activity (measured directly) and non-invasive functional magnetic resonance imaging measures. The authors find that the respiration signal is associated with the gamma band in the cingulate cortex, and both the gamma signal and respiration signal correlate with distributed neuronal networks across the brain. This contributes to our knowledge of the contribution of respiration on neuro and neuro-vascular signals during resting conditions.

      (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.)

    1. Evaluation Summary:

      The authors developed a set of synthetic proteins, Designed Ankyrin Repeat Proteins (DARPins), that bind gephyrin, the main scaffold protein at inhibitory postsynaptic sites, and characterize them extensively to study gephyrin cluster morphology and biochemistry. In several aspects, DARPins outperform traditional antibodies. This study is clear, well organized and well written, demonstrating that DARPins can be important tools synaptic, cellular and circuit neuroscience 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. Reviewer #1 agreed to share their name with the authors.)

    1. Evaluation Summary:

      These studies establish a role for the D2 pseudophosphatase domain of the PTPRK receptor-like phosphotyrosine phosphatase in recruiting Afadin, a cell-cell junction protein that is reported to be a PTPRK substrate, for dephosphorylation by the active D1 phosphatase domain. These findings suggest that the D2 pseudophosphatase domains of RPTPKs might have a general function as platforms to recruit specific phosphotyrosine substrates.

      (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.)

    1. Evaluation Summary:

      The present manuscript examines cortical representations of basic visual attributes following a manipulation shown to enhance plasticity in the adult brain: binocular dark exposure for several days, followed by light re-introduction. The work has fundamental therapeutic and conceptual implications, and will be of potential interest to a broad readership of vision scientists, neuroscientists, clinicians and modelers. The paper is well-written and based on sophisticated experiments. The evidence provided convincingly supports the authors' contention that dark exposure does not have a negative impact on visual representations in V1. The study uses a generally appropriate study design. However, it would benefit from the addition of some key experimental details, and additional analyses and statistical tests to explore alternative interpretations of results.

      (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.)

    1. Evaluation Summary:

      Protein-RNA interactions are involved in many diseases and targeting them with drugs can be valuable. Because protein-RNA complexes are considered difficult to target both computationally and experimentally, an integrated computational-experimental approach to solve this limitation is introduced. The approach is demonstrated by targeting the mRNA-binding protein YB-1, which works remarkably well. Inhibitors in the micromolar range are detected, including a previously approved drug. The main strength here is the proof of concept that protein-RNA interactions are targetable. However, additional data are required to support the central claims of the paper.

      (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.)

    1. Evaluation Summary:

      Bacteria living in stressful and fluctuating environments need to respond to changing conditions. Many species, including Mycobacterium tuberculosis, the causative agent of tuberculosis, use cAMP as a secondary messenger to sense and respond to specific stimuli. What distinguishes M. tuberculosis, is that its genome encodes for at least 15 adenylate cyclases, enzymes that synthesize cAMP from ATP. The authors characterized one specific adenylate cyclase, Rv3645, and demonstrate that it is the most significant contributor to cAMP levels and mediates fatty acid metabolism and antibiotic resistance. This manuscript will be of broad interest to readers in the field of tuberculosis drug discovery and bacterial metabolism.

      (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.)

    1. Evaluation Summary:

      This work presents a series of enhancements to the PhIP-seq method of autoantibody discovery, with the goal of improving scaling to larger cohorts and increasing disease specificity. The strength of the paper is the validation of the high throughput format, although results from screening patient samples confirm or only modestly extend previous 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.)

    1. Evaluation Summary:

      KdpFABC is a bacterial potassium uptake transporter made up of a channel-like subunit (KdpA) and a P-type ATPase (KdpB). When potassium levels are low (< 2 mM), the transporter actively and selectively uptakes potassium, but must be switched off again to prevent excessive K+ accumulation. Although structures of KdpFABC have been determined before, the structural basis for inhibition by phosphorylation is unknown. Here, the authors have determined the structure of KdpABC in an arrested (off-state) that is in a distinct conformation from previously determined P-type ATPase structures. More detailed structural comparisons are needed to more convincingly show this, however, and the protein required to inhibit KdpABC by phosphorylation remains unknown. This paper will be of interest to researchers in the microbiology 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 agreed to share their name with the authors.)

    1. Evaluation Summary:

      The manuscript reports a new tissue clearing procedure that is faster (clearing within 48 hours), uses less hazardous chemicals, and importantly appears to result in less tissue volume change compared to other methods. The simple protocol adds further to the toolbox of tissue clearing methods and is one that is likely to be even more popular than many current methods, although the scope of tissue on which it can be used and rigorous comparisons to existing protocols have not been fully investigated.

      (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.)

    1. Evaluation Summary:

      In their study, Gicking et al. study the physical properties of artificial complexes composed of the dynein-dynactin-BicD2 (DDB) complex linked to one of three classes of kinesins (1, 2, or 3) via a DNA scaffold. They find that all three kinesins can move to the plus-end of microtubules when coupled to the DDB complex. This is surprising because motors in the kinesin-2 and kinesin-3 families have been shown to have a higher load sensitivity. However, the authors show that the faster reattachment kinetics of these motors compensate for their faster detachment rates under load. This work is relevant to both the biophysics field for advancing knowledge in fundamental science, and in the neuroscience field since disruption of neuronal transport leads to a variety of neurodegenerative diseases.

      (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.)

    1. Evaluation Summary:

      This paper addresses the toxicity of fluorescent calcium indicators, comparing two series of indicators (GCaMPs and GCaMP-Xs) in mouse neurons. The paper documents GCaMP toxicity during development and following prolonged strong expression, and establishes that GCaMP-X indicators are less toxic. The paper will be of interest primarily to neuroscientists who use fluorescence calcium indicators to monitor calcium dynamics during neuronal 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 #2 agreed to share their name with the authors.)

    1. Evaluation Summary:

      There is a debate whether ROS (reactive oxygen species) generated through redox signaling could be a friend or foe. There are several paradoxical studies (both animal and human) wherein exercise health benefits were reported to be accompanied by increases in ROS generation. Utilizing the in-vitro studies as well as mice model work, this manuscript illustrates the different regulatory mechanisms of exercise and antioxidant intervention on redox balance and blood glucose level in diabetes. The manuscript does address some advancements in the area of research specialization.

      (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.)

    1. Evaluation Summary:

      This is an important study that investigates whether older adults have selective impairments in allocentric navigation (using distal cues to navigate). Using a combination of ecologically inspired real-world navigation, virtual reality, eye tracking, and body-tracking, the study reports, for the first time, that older adults show no difference from younger adults when using geometry to navigate a Y maze. Instead, their deficits appear to relate to perceptual difficulties with processing individual landmarks. This large sample study therefore provides somewhat compelling evidence of age-related difficulties in processing landmarks visually rather than a selective deficit in allocentric navigation.

      (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.)

    1. Evaluation Summary:

      A new and interesting operant conditioning paradigm is established for the Drosophila larva. A novel role for serotonergic pathways in the VNC in operant learning points to new circuits and mechanisms for learning and memory. Impressive technology opens doors for new and exciting studies on learned behavior in the small and tractable circuits of the larva.

      (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.)

    1. Evaluation Summary:

      This well-written report provides new insights for neuroscientists studying sleep architecture and stress sensitivity. A particularly important conclusion is that differences in sleep architecture before chronic social defeat stress may serve as a predictive biomarker of stress resilience. Overall the work is very strong, but there are some conceptual and methodological issues that need to be addressed.

      (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.)

    1. Evaluation Summary:

      This paper will be of interest to the neuroscience community studying brain oscillations. It presents a new method to detect sharp-wave ripples in the hippocampus with deep learning techniques, instead of the more traditional signal processing approach. The overall detection performance improves and this technique may help identify and characterize previously undetected physiological events.

      (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.)

    1. Evaluation Summary:

      Analysis of molecular data from genome sequencing provides crucial information on the diversity of biological and evolutionary processes that shape genetic diversity. However, the models of genetic evolution used to make these inferences sometimes oversimplify important aspects of species biology. This study shows that accounting for high variance in reproductive success in models can better explain the genetic diversity of an extremely fecund marine species, the Atlantic cod. The manuscript is scientifically sound and provides careful statistical analyses of alternative evolutionary models. It concludes that pervasive selection, rather than demographic changes or sweepstakes reproduction, is one of the main drivers of genetic diversity in Atlantic cod.

      (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.)

    1. Evaluation Summary:

      The experiments presented in this extensive study by Ronzano et al. are a tour-de-force investigating the spatial organization of premotor interneurons in the mouse spinal cord to re-examine the fundamental question of whether there is spatial segregation of interneurons with monosynaptic connections to motoneurons innervating functionally antagonistic (flexor and extensor) pairs of limb muscles. The authors' premotor circuit mapping experiments, involving four different collaborating laboratories applying an extensive set of complementary rabies virus-based trans-synaptic circuit tracing techniques, convincingly demonstrate complete spatial overlap among flexor and extensor premotor interneurons, contradicting previous mapping results that suggest spatial segregation. The present results revise our understanding of the spatial organization of spinal premotor circuits with fundamental implications for understanding spinal motor circuit 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.)

    1. Evaluation Summary:

      The manuscript describes an interesting phenomenon of long-range transport in self-organized canal structures formed in colonies of the pathogenic bacterium Pseudomonas aeruginosa. The authors measured and analyzed the fluid flows in these open channels, revealing that it is capable of supporting high-speed transport of outer membrane vesicles and bacterial cells over centimeters. This study sheds new light on the potential amplitude of cargo exchange among bacterial communities over long distances.

      (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.)

    1. Evaluation Summary:

      This manuscript by Deng et al., is a valuable evaluation of zbtb14 and its role in normal myelopoiesis. The authors provided convincing data supporting the role played by zbtb14 in monocyte and macrophage development and its regulation involving the modulation of PU.1 expression. The finding that a mutation in ZBTB14 exists in AML patients also implies how important this gene product is in normal human myelopoiesis.

      (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.)

    1. Evaluation Summary:

      Drs Zhao and Sharpe have highlighted the role of a relatively understudied cell type, the telocyte, in periodontitis, using a mouse model. Periodontitis is a widely occurring inflammatory disease of the gums, that will eventually progress to bone resorption and teeth that are embedded less favorably and will eventually fall out. This disease is linked to many other illnesses, such as rheumatoid arthritis, cardiac disease and even Alzheimer's disease, so more in depth knowledge is needed on cell types that play a role in the progression of the disease.

      (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.)

    1. Evaluation Summary:

      Sefton et al. analyze how fibroblast-derived HGF integrates muscle and nerve development during morphogenesis of the mammalian diaphragm. The new findings are based on in-depth analyses of the development of the diaphragm muscle, and the role of Met and HGF in the process. The work is relevant for the understanding of muscle development, and congenital disease (hernia).

      (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.)

    1. Evaluation Summary:

      This Methods paper seeks procedures evaluating the balance between muscle cell quiescence and activation. These could well permit investigations of long-standing questions in key areas of muscle function. The latter include the regulation of adult stem cell pool size and functional heterogeneities in this, as well as regulators of muscle quiescence.

      (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.)

    1. Evaluation Summary:

      The Cretaceous dinosaur Spinosaurus has recently drawn significant attention as it was hypothesized to be the first aquatic dinosaur, using tail-powered swimming in surface waters and at depth. In a reappraisal of the "aquatic hypothesis", new lines of evidence – including the CT-based skeletal restoration of Spinosaurus and biomechanical tests – support the alternative "semi-aquatic hypothesis". This article will be of interest to vertebrate paleontologists and functional morphologists, as well as wider academic and non-academic audiences.

      (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.)

    1. Evaluation Summary:

      There is currently a lack of available fine-grained infant-dedicated cortical parcellation maps. The present study fills an important gap in the research of infant brain development by generating an age-dependent functional brain parcellation from birth to 24 months, leveraging on the 1064 high-resolution longitudinal resting-state fMRI scans from 197 infants. These age-specific parcellation maps have the potential to facilitate scientific discoveries, comparisons, and validations in brain functional development. Moreover, the proposed method of establishing functional correspondences across individuals using functional gradient densities can also be applied to study brain changes across lifespan.

      (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.)

    1. Evaluation Summary:

      This paper will be of interest to neurophysiologists and system neuroscientists interested in memory and more specifically in hippocampo-cortical interactions. Using a combination of imaging and electrophysiological techniques, the study characterizes neocortical activity patterns around awake hippocampal ripples. Unlike sleep ripples, cortical activity seems to be dominated by inhibition around ripples but differences between intrinsic activity and synaptic transmission highlight complex interactions in the underlying neuronal circuits and dynamics.

      (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.)

    1. Evaluation Summary:

      This manuscript presents an interesting and informative study on two regulatory elements found near atrial fibrillation-associated regions and their effect on Tbx5 expression and arrhythmia susceptibility in a mouse model. The multilevel approaches and analyses are rigorous, and the conclusions are justified by the data. Tbx5 expression may be of relevance for human atrial fibrillation and disease risk in patients, and the work is of potential interest to scientists in the fields of gene dosage, gene regulation, genetic susceptibility, genetic variants and cardiovascular 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 #2 agreed to share their name with the authors.)

    1. Evaluation Summary:

      This important work provides compelling evidence for the biological plausibility of the Successor Representation (SR) algorithm. The SR is a leading computational hypothesis to explore whether neural representations are consistent with the hypothesis that the neural networks in specific brain area perform predictive computations. Establishing a biologically plausible learning rule for SR representations to form is of high importance in the field of neuroscience. This is also important for comparing the predictive ability of neural circuits with other predictive frameworks designed in machine learning.

      (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.)

    1. Evaluation Summary:

      In this manuscript, of interest to those studying insect reproductive biology and specifically mosquitoes, the authors show that females of the yellow fever mosquito retain eggs when fresh water is not readily available. The authors then use RNA expression analyses to identify genes potentially involved in the trait. This leads the authors to focus on two genes that seem to be recent duplicates. The authors generate genetic knockouts and use these to show that these two alleles affect the trait in question. The study includes interesting and technically impressive experiments, but the framing in the context of previous work could be improved.

      (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.)

    1. Evaluation Summary:

      This manuscript from Singh and colleagues investigates neural connections between the central amygdala and the zona incerta, two subcortical brain regions previously implicated in pain, and further describes the role of the zona incerta to preclinical pain-related behavior in mice. This study employed anatomical tracing, electrophysiology, optogenetics, chemogenetics, and behavioral assays in various pain modalities to link the zona incerta to pain modulation by providing new evidence for a direct inhibitory connection from the central amygdala to the zona incerta that could explain neuropathic pain hypersensitivity. While rigorous, well written, and well executed, the study in its current form lacked evidence to directly support the PKCδ neurons in the central amygdala projecting to the zona incerta as being explicitly involved in this process.

      (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.)

    1. Evaluation Summary:

      This paper introduces a light microscopy pipeline for imaging and fast reconstruction of the synaptic connections of individual neuronal types in the fruit fly and for correlated investigation of circuit structure, function and behavior in the same animal. Because of its speed and accessibility, this approach enables mapping of selected neuronal circuits of multiple animals across different conditions and behavioral states, thus filling an important gap in brain 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. The reviewers remained anonymous to the authors.)

    1. Evaluation Summary:

      This valuable paper proposes an innovative iterative masking approach that enables models such as the MSA Transformer to generate new protein sequence designs, which are validated using a wide-ranging set of computational experiments. A key strength of the MSA Transformer is the ability to learn and generalize across protein families, enabling impressive performance across a range of downstream tasks. However, to date, these models have not been used to generate new protein sequence designs. The approach proposed in this paper is quite novel, and a number of metrics are used to examine the resulting performance of the MSA Transformer at generating new protein sequences from specific families.

      (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.)

    1. Evaluation Summary:

      Almeida and Macklin provide one of the first studies to closely examine early oligodendrocyte behaviors at high resolution. These studies use live imaging in zebrafish to provide valuable new insights about the earliest onset of myelination in the central nervous system and add to a body of work showing how oligodendrocytes initiate and maintain myelin sheaths.

      (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.)

    1. Evaluation Summary:

      Engineering NLR proteins to improve disease resistance in crop plants is a major goal of the field. This study applies knowledge from structural and evolutionary studies of the rice NLR protein Pik-1 and cognate effector protein AVR-Pik to engineering of new disease resistance genes. The authors nicely demonstrate that it is indeed possible to engineer resistance proteins with broad recognition specificity for the rice blast fungus. The work is of interest to colleagues in synthetic biology, protein engineering and plant-pathogen interactions.

      (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.)

    1. Evaluation Summary:

      The manuscript by Li and coworkers characterizes sorted human non-hematopoietic bone marrow cells by scRNA-seq and predicts their lineage relationships and possible interactions with mature and immature hematopoietic cells. Transcriptionally-different stromal cell subsets are identified, and their lineage relationships, cell-cell interactions and possible specialized functions are inferred or predicted from in-silico studies, paving the way for future functional and validation studies. This resource significantly adds to the current understanding human non-hematopoietic bone marrow stromal cells and their hematopoietic regulatory 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. Reviewer #1 and Reviewer #2 agreed to share their name with the authors.)

    1. Evaluation Summary:

      A meta-analysis of over 14,000 fMRI studies revealed a principle rostral-caudal gradient in the lateral prefrontal cortex. This gradient reflected an internal/external axis, which helps to organize the LPFC's involvement in widespread processes from affect, to memory, to control, and action. This is an important contribution to the literature, particularly as a meta-analytic approach has not been applied to this axis of organization and can complement the limitations of single studies. The evidence for the conclusions could be strengthened by ruling out bias in the analysis and drawing a clearer relationship to functional networks.

      (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.)

    1. Evaluation Summary:

      This paper makes a comprehensive survey of the relationship between mtDNAcn and the personality dimensions, as well as how and whether they mediate the relationships between personality dimensions and mortability as well as other behavioural measures that may lead to mortality. More work needs to be performed to truly understand the relationship between personality dimensions and mortality, as well as the physiological traits (like mtDNAcn) that may be mediating it.

      (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.)

    1. Evaluation Summary:

      Liu et al. describes an unsupervised method that clusters colorectal cancer samples based on perturbations to gene interactions. They show that this method strongly suggests 6 distinct clusters of samples and identifies phenotypes associated with the clusters, including survival, drug response, immune phenotype, response to immune checkpoint inhibitors and perturbed pathways. This is an interesting and significant manuscript, which has been well conducted.

      (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.)

    1. Evaluation Summary:

      Fan and colleagues disclose the development of covalent TEAD inhibitors and they report on the therapeutic potential of this class of agents in the treatment of TEAD-YAP-driven cancers (e.g., malignant pleural mesothelioma, MPM). Optimized derivatives of a previously reported covalent TEAD inhibitor are described and characterized, using diverse profiling approaches that range from biochemical and cell-based assays to X-ray co-crystallographic analysis and in vivo efficacy in a relevant mouse xenograft model. The manuscript represents an impressive and deep characterization of this small molecule class. The authors' claims and conclusions are very well supported and justified by the data, although differentiation from a very closely related compound termed K-975 is not entirely clear as currently presented.

      (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.)

    1. Evaluation Summary:

      This study provides a thorough functional analysis of three mutations in the BRCA2 gene that do not seem to necessarily cause breast cancer. The authors use functional assays in cancer cells and with recombinant proteins to determine that two BRCA2 variants, S1221P and T1980I, are indeed pathogenic, while the T13461 variant is fully functional and benign. The strength of the study is the rigorous assessment of these mutations in a variety of established assays for BRCA2. The work is likely to have a broad impact in the breast cancer 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 #2 agreed to share their name with the authors.)

    1. Evaluation Summary:

      The paper by Smith and colleagues provides a framework for understanding a seemingly paradoxical observation in human genetics: two phenotypes may be closely correlated to each other, and the patterns of genetic variation that influence both phenotypes may be widely shared at the genome-wide level, but there are often specific genetic variants that show discordant patterns. Though the observations in this paper are derived from analysis of metabolic phenotypes, this may have broader relevance to interpreting the results from disease-related genetic association studies, and shed light on the processes that connect different 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 #1 and Reviewer #2 agreed to share their names with the authors.)

    1. Evaluation Summary:

      This study will be interesting to a broad audience of neuroscientists, as it reveals for the first time that mutations in klc4, which are known to cause a form of early onset hereditary spastic paraplegia in human, affect specific aspects of neuronal development and nervous system functions. High resolution movies of developing sensory neurons in vivo and behavioral assays support the key findings that klc4 plays an essential role in the control of neuronal morphogenesis and behavior. The data presented in the manuscript are overall of a descriptive nature but provide a foundation for future mechanistic studies aimed at addressing the specific functions of KLC4.

      (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.)

    1. Evaluation Summary:

      Whether airway basal cells exhibit extensive cell state heterogeneity and whether this is relevant for their function has been unclear. This study provides important evidence that such heterogeneity exists and may dictate airway basal cell function in a spatially restricted manner.

      (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.)

    1. Evaluation Summary:

      The authors made paired recordings from synaptically-connected excitatory and inhibitory neurons in slices of human neocortex and used posthoc molecular methods to identify major classes of the recorded interneurons. The principal finding is that, as found previously in rodent cortex, short-term plasticity of the synaptic connections from excitatory to inhibitory neurons depends on the molecular identity of the inhibitory neurons. This is important, as it suggests that many rodent studies carried out over the past decades are physiologically relevant to humans.

      (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.)

    1. Evaluation Summary:

      The authors explore how the actin network in the fat body impacts nutrient uptake in multiple ways. Overall, this is an interesting study that sheds light on adipocyte cytoskeletal dynamics and it's impact on nutrient trafficking and fat body storage. The work can be further strengthened by additional validation of tools and 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. The reviewers remained anonymous to the authors.)

    1. Evaluation Summary:

      PTPN22 is a protein tyrosine phosphatase which negatively regulates antigen receptor signaling. It has been proposed that several genetic variants of PTPN22 might be loss of function (LOF) variants, leading to hyper-responsive T cell proliferative and effector responses. The authors investigate how the PTPN22 R620W variant, associated with multiple autoimmune diseases, might contribute to breech of peripheral T cell tolerance. This work greatly advances and clarifies ongoing confusion of whether PTPN22 SNP(620W) is a LOF mutant.

      (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.)

    1. Evaluation Summary:

      This manuscript offers a valuable transcriptomic data set of known types of adult zebrafish photoreceptors (rod and cones). The study further identifies a large set of differentially expressed transcription factors, many of which still have an unidentified function in photoreceptors. Using CRISPR F0 screening, the study shows that the two tbx2 zebrafish paralogues are involved in photoreceptors specification beyond what is currently known. The study uses a solid methodology and the results will be valuable for researchers interested in photoreceptor biology. At present, however, the manuscript has a misleading title and focus: the analysis of adult photoreceptors can hardly offer a scenario of the transcription factors involved in the specification of photoreceptors.

      (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.)

    1. Evaluation Summary:

      The authors show that how high-dimensional neural signals can be reduced to low-dimensional models with variables that can be directly linked to behavior. The reduced model can account for long timescales of persistent activity that arise from transisions between metastable model states. The authors further show that the rate of these transitions is modulated by water temperature according to the classic Arrhenius law.

      (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.)

    1. Evaluation Summary:

      The capacity to flexibly modify our actions in order to seek goals relies upon specific brain regions and neurochemicals. Cerpa et al identify norepinephrine (but not dopamine) within the ventrolateral orbitofrontal cortex (OFC) as key to updating identity-specific action-outcome associations when environmental conditions change. These conclusions are relatively well supported by the data and will be of interest to behavioural neuroscientists studying the function of OFC or noradrenaline signalling, as well as researchers studying associative learning.

      (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.)

    1. Evaluation Summary:

      This is an important paper that uses state of the art technology to address the underlying neurobiology of neuropathic pain, a topic of considerable translational relevance. The study describes changes in gene expression at a single cell resolution in somatosensory neurons following peripheral nerve injury. Bioinformatics analyses were employed to segregate neurons in sub-classes and to derive predictions on potential functions of regulated genes. While the work has considerable strengths, such as the single cell approach, there are also some weaknesses, including the fact that new gene candidates did not undergo functional analysis.

      (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.)

    1. Evaluation Summary:

      This paper is of potential interest to a broad audience across myeloma study and single cell technology, as it implies a major adjustment to our current understanding of pathogenesis and treatment of myeloma. Overall the data quality is good, although reasonable alternative explanations of the data can be identified.

      (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.)

    1. Evaluation Summary:

      This paper is of interest to people studying how differentially spliced genes regulate biological processes, and in particular, those interested in the intersection of cell death and immunity. This work offers new insight into how an alternatively spliced protein with a well-known function in cell death regulates the basal expression of genes involved in immunity and sensitizes cells to apoptotic cell death. Overall, the major conclusions are supported by the data but more investigation is needed to support the mechanism by which BAX splicing is inducing the phenotypes observed.

      (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.)

    1. Evaluation Summary:

      Mutations in MINAR2 causes deafness in human and mice. Loss of function of Minar2 in mice causes a reduction of stereocilia and subsequent hair cell degeneration but the underlying mechanism is unclear. This zebrafish study demonstrated that the Minar2 protein interacts with cholesterol and is localized to the stereocilia of hair cells. The loss of Minar2 reduces cholesterol enrichment in the stereocilia with concomitant accumulation in lysosomes. Thus, this study provides the mechanistic insight of Minar2 and the first glimpse at the importance of cholesterol homeostasis in hair cell 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 #2 agreed to share their name with the authors.)

    1. Evaluation Summary:

      Iago De Castro et al, constitute an exciting study conveying to readers that neutrophil-to-lymphocyte ratio dynamics predict pancreatic cancer pathologic response to neoadjuvant therapy. Specifically, the authors aim to determine the effect of gemcitabine/paclitaxel and anti-Ly6G treatment on stromal T cells and CAF populations. They conclude that neutrophil-to-lymphocyte ratios are associated with survival following this treatment and use animal models to show metastatic effects allied to it. The authors attempt to convey that microenvironmental neutrophils could play a causal role in pancreatic cancer chemoresistance. It was agreed that while the discoveries are very interesting, the public could benefit from the authors improving: the relevance to the human condition, providing a stronger link to fibroblastic cell functional transitions, broadening the discussion regarding previous/related published studies, and strengthening the anti-Ly6G specificity proof within the provided 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.)

    1. Evaluation Summary:

      This work presents a new model that leverages imaging and non-imaging data for the prediction of the survival of patients with early-stage NSCLC. The new model sought to demonstrate the roles of imaging and non-imaging features in determining high-risk nodes within the graph neural network, and the results have the potential of broad interest to clinicians within the field of cancer and have a high value towards clinical application.

      (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 reviewer remained anonymous to the authors.)

    1. Evaluation Summary:

      This manuscript presents the first molecular dynamics (MD) simulations of full-length membrane-bound Thyroid Stimulating Hormone Receptor (TSHR). The authors find that its linker region (LR) is disordered, contrasting previous models. While this is largely a solid study that would interest researchers working in computational modeling, thyroid hormone metabolism, and signaling, the rationale for the arbitrarily chosen starting model and unclear mechanistic relevance need to be clarified further.

      (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.)

    1. Evaluation Summary:

      This paper is of broad interest to clinicians focused on improving sepsis outcomes. The method developed by the authors can identify 10 common pathogens with species-specificity in 4 hours, thus significantly reducing the turnaround time compared to conventional diagnostic methods. Using their method to identify sepsis-causing pathogens early to guide antibiotic treatment, the authors demonstrate high clinical sensitivity and specificity, and some clinical benefit in a real-world scenario.

      (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.)

    1. Evaluation Summary:

      Chen et al. demonstrate a pro-survival role of the NRF2/DKK1 axis in mesenchymal stem cells. Furthermore, the authors provide evidence that targeting this pathway can enhance survival in response to liver failure in vivo. These data highlight a novel signaling pathway to enhance efficacy of MSCs in promoting regeneration.

      (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.)

    1. Evaluation Summary:

      Carboxysomes enable the efficient fixation of carbon dioxide in specific bacteria. Phase separation has been invoked as a mechanism that drives the formation of carboxysomes. The current work focuses on the biophysical principles of how one of two essential specific protein components enable spatial regulation over carboxysomes. This important work highlights the connection between oligomerization via specific molecular interactions and phase separation. The work is of interest to the areas of biochemistry and carbon dioxide fixation as well as phase separation.

      (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.)

    1. Evaluation Summary:

      Drosophila ovarian follicle cells have been utilized as a model system to study organogenesis and epithelial tumorigenesis. The analysis of single-cell transcriptomes of follicle cells now shows that transcriptionally distinct cell populations emerge shortly after induction of loss of polarity. Strengths of the work include the use of advanced single cell omics and imaging analyses to identify cell types and factors playing a role the disruption of polarity and the implications of this work for epithelial cancers. The authors' claims are generally well supported by the data and analyses. Weaknesses include the lack of high magnification images and need to clarify motivation for the study and highlight the biology rather than technical advances in the results section. Overall, this work is viewed as an important contribution to cell biologists who work on the epithelial morphogenesis or tumorigenesis.

      (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.)

    1. Evaluation Summary:

      This manuscript addresses G protein-coupled receptor signaling and proposes an additional site on Beta-arrestin2 (arrestin 3) as being responsible, in significant part, for the downregulation and likely onward signalling from endosomes of a range of GPCRs. The cell biology appears to be thoroughly carried out and data presented in a statistically appropriate manner. With some textual changes and minor experimental clarification of the route taken and molecules involved, this work will be of broad 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.)

    1. Evaluation Summary:

      The authors use high spatial resolution MEG in humans to link two important components (time - transient bursts, space - waves) of neural sensorimotor dynamics by investigating how transient beta bursts propagate in the brain. The authors find two directions of propagating waves during beta bursts. The work links two fundamental aspects of neural dynamics which may yield new insights into the origins of sensorimotor behavior, with wide appeal to neuroscientists and clinicians. The reviewers considered the methodological work largely sound, although concerns were raised by the reviewers to what extent the travelling waves correspond to underlying neural activity or reflect the generative nature of field potentials.

      (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.)

    1. Evaluation Summary:

      This paper will be of interest to researchers studying meniscus homeostasis and knee osteoarthritis. It uncovers distinct subtypes of cell populations in inner and outer part of human meniscus using single-cell RNA sequencing. In particular, this work further identifies how alterations in meniscal cell populations may contribute to inflammation and osteoarthritis and thus serves as a resource paper for 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 #2 agreed to share their name with the authors.)

    1. Evaluation Summary:

      This manuscript reports the development of a proteo-genomic screening methodology to identify protein-protein interactions between secreted proteins and their cell surface receptors. The authors use a CRISPRa-based approach to overexpress membrane proteins in cells and then use magnetic cell sorting to identify receptors that bind candidate ligands. This approach leads to the identification of several novel interaction pairs that are validated biochemically, including receptor tyrosine phosphatase ligands and other interactions with implications for immune system function. The work is of interest to a wide variety of fields including biochemistry and signaling.

      (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.)

    1. Evaluation Summary:

      The authors provide a summary of single and double mutants in five self-cleaving ribozymes using next-generation sequencing. They dissect their data in terms of epistasis effects, which provides a new angle to understanding ribozyme function. In principle, this allows conclusions to be drawn on bases involved in pairs and in catalysis that have the potential to be of use to the field, although there is also a series of technical weaknesses that should be addressed.

      (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.)

    1. Evaluation Summary:

      Identification of transcriptional phenotypes driven by TBI across meningeal immune cell subsets and the effect of aging on these responses is an important and not well-defined area in the field. Multiple complementary and high-end approaches are taken to demonstrate the long-lasting effects that TBI drives in the brain and support the main findings of the manuscript. This manuscript will be of interest to readers in the field(s) of neuroimmunology, aging, and traumatic brain injury.

      (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.)

    1. Evaluation Summary:

      Menjivar et al. identify a previously unrecognized role of myeloid cell Arginase1 (Arg1) activity in shaping the anti-tumor immune response in pancreatic ductal adenocarcinoma (PDAC). The proposed therapeutic combination is a new approach for pancreatic cancer, with an enhanced response to immune therapy upon arginase inhibition.

      (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.)

    1. Evaluation Summary:

      The authors investigate what type and degree of information (either absolute, relative, or a weighted combination of both) is used by bumblebees when retrieving the value of an item. There is recent evidence in humans and birds that suggests that these organisms use a combination of absolute memories and remembering of subjective ranking in these tasks. The authors conclude that bumblebees indeed use remembered ranking, but that they seem not to be able to retain (or at least utilise) absolute property information for very long. The absence of relevant work in invertebrates would make this study a potentially valuable addition to the scientific literature.

      (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.)

    1. Evaluation Summary:

      Li et al. use biochemical binding analysis to explore the role of Rabphilin 3A in dense-core vesicle exocytosis in neuroendocrine PC12 cells and in an in vitro SNARE assembly assay. They propose that the Rph3A binding to SNAP25 pre-structures the protein to efficiently assemble with Syntaxin and VAMP2, and thus, promoting the vesicle docking and priming process. This work will be of interest to scientists studying the molecular basis of synaptic vesicle release.

      (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.)

    1. Evaluation Summary:

      Iron acquisition is an essential problem for microbial growth and survival. Host defense mechanisms generally reduce iron availability and microbes often find themselves in iron poor environments. This study provides new insights into how the fungal pathogen Candida albicans obtains iron during infection.

      (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.)

    1. Evaluation Summary:

      This manuscript will be of interest to readers in the field of microbiology, particularly those interested in bacterial interactions, secretion systems, and stress responses. It identifies the molecules and mechanisms that explain a competitive interaction between two soil-dwelling bacterial species. The data support most of the conclusions of the manuscript, but some controls are lacking and some of the interpretations are not fully justified by the experiments shown.

      (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.)

    1. Evaluation Summary:

      This manuscript reports the CryoEM structure of OmcZ cytochrome nanowires of Geobacter sulfurreducens, the third cytochrome nanowire of Geobacter to be structurally resolved. OmcZ differs structurally from these previously determined nanowire structures, showing a different heme chain configuration. Based on these and other differences the authors speculate about the evolutionary origin of these nanowires and the mechanism of long-range electron transport. This manuscript is an important contribution to the field of electron transfer and will be of interest to everyone working in electron transfer and filament formation and interested in their evolution.

      (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.)

    1. Evaluation Summary:

      This article seeks to address a key question in protein biophysics: are the amino acid positions (and mutations) that influence allostery conserved across homologs of a protein family? Or is allostery implemented by a distinct set of residues that varies amongst homologs? To address this question, the authors follow an innovative approach that combines deep mutational scanning with machine learning. Significant revisions are required to clarify whether the conclusions of the study are well-supported by the data. The work is potentially highly relevant to protein engineers and biophysicists.

      (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.)

    1. Evaluation Summary:

      This paper is of interest to organismal biologists and evolutionary scientists who study cognitive and behavioral sex differences including those with interests in the evolution of complex spatial behaviors. Using intensive field monitoring and experimentally induced navigational challenges, the authors examine two different hypotheses for sex differences in spatial ability in three species of poison frog. A rich and complex story emerges, including from the provision of evidence that is consistent with (but not necessarily yet definitively or exclusively in support of) the hypothesis that androgens may inadvertently affect spatial ability.

      (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.)

    1. Evaluation Summary:

      This manuscript examines the importance of PKA-dependent mTORC1 activation for the weight-loss effects of liraglutide. The work has the potential to provide important insights, but at present is deemed preliminary as it lacks details on the mouse model and control data and needs a more in-depth analysis of the metabolic phenotype.

      (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.)

    1. Evaluation Summary:

      This paper is of broad interest to biologists and climate modelers that study the impact of environmental stress (especially multiple stressors) on marine life. The authors show that exposure to low pH (ocean acidification) decreases the ability of two mussel species to survive freezing stress. The authors measure multiple biochemical parameters to try and identify the mechanisms underlying the change in freeze tolerance, but future work will be needed to resolve the underlying mechanism in 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. The reviewers remained anonymous to the authors.)

    1. Evaluation Summary:

      This paper describes the use of three well-established mathematical models of cervical cancer to estimate the impact of COVID-19 related-delays in screening access on cervical cancer incidence and delays in diagnosis. Consistent with previous work and the known biology of cervical cancers, the findings that short delays have relatively small effects on population-level cervical cancer risk are reassuring overall, but the impact of screening interval and screening test performance suggest that existing disparities related to screening access may be exacerbated. These results should be useful for policy makers in planning responses to future pandemics or other sources of sudden restriction of screening availability.

      (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.)

    1. Evaluation Summary:

      This paper proposes a computational model that combines biologically detailed elements with more simplified components to provide a comprehensive model of synaptic plasticity. It includes the stochastic character of many of the biophysical processes and introduces a new way to readout the plasticity cascade. It is evaluated against impressively many published experimental studies of hippocampal plasticity. The paper should be of interest not only to computational neuroscience but also to the synaptic neuroscience community but will benefit from a clearer description of assumptions and weaknesses, and a clearer separation of the essential elements in this model from the less critical elements.

      (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.)

    1. Evaluation Summary:

      This manuscript, of interest to those studying the evolution of immunity, investigates the evolutionary history of a recently described herbivore-associated molecular pattern (HAMP) receptor, INR, which perceives the caterpillar-derived peptide HAMP, In11. The authors compare INR homologs to identify evolutionarily conserved residues and use chimeric fusion proteins to investigate specificity. The findings presented are valuable and supported by convincing experiments and analysis.

      (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.)

    1. Evaluation Summary:

      This paper will be very interesting to the large class of neuroscientists who study functional roles of glycoprotein hormone receptors in the central nervous system. It provides detailed tissue-selective gene and receptor distributions of the three anterior pituitary hormones, and thus likely facilitates further relevant studies by other scientists.

      (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.)

    1. Evaluation Summary:

      This manuscript compares COVID-19 mortality during the pre-Omicron and Omicron emergence periods in several countries and finds evidence suggesting the Omicron variant was associated with lower mortality than previous dominant variants. This paper will be of interest to infectious disease scientists both for its content and its methods, as it validates that population-level variant frequency can be a good proxy for individual-level variant data to derive insights on variant biology with population 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 #3 agreed to share their name with the authors.)

  3. Aug 2022
    1. Evaluation Summary:

      The findings of the paper are of interest to scientists studying the learning of abstract representations. It provides insights into how feedforward networks evolve during a process of learning to map stimuli onto abstract classes via gradient descent. The results are appealing and the analyses thorough. As well, the paper makes some experimental predictions. It could benefit from a deeper discussion on how the findings may generalize to biologically more realistic networks and tasks.

      (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.)

    1. Evaluation Summary:

      The early differentiation of germ cells, those that will form egg and sperm, is a critical and nearly universal step in animal development. This paper reveals new layers of molecular and cellular regulation that control this process in the fly, and as such be of broad interest to cell and developmental biologists, especially those interested in critical cell fate decisions. The paper contains a wealth of experimental data demonstrating that processes generally thought to be restricted to somatic cells alter the differentiation of germ cells, but provides only limited functional interpretation of the observed 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. The reviewers remained anonymous to the authors.)

    1. Evaluation Summary:

      This manuscript is of broad interest to neuroscientists studying mechanisms regulating synapse formation and maintenance. Following up on the previous work by the authors on trans-synaptic signaling complexes involving neurexins and cerebellins, this study shows that the basic framework of the complexes operates broadly across different synapses in the brain albeit with subtle differences. The experiments are carefully executed, while some key conclusions could be better supported by additional 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. The reviewers remained anonymous to the authors.)

    1. Evaluation Summary:

      The manuscript will be of broad interest to readers in the fields of biochemistry, structural, molecular, and evolutionary biology. It outlines a systematic approach in characterizing nuclear receptor ligands based on the conformational ensemble of the receptor, further exploring the idea that perturbation of the ensemble orchestrates function. The results from the combined use of experiments and simulation are promising, suggesting that the change in the ensemble is responsible for 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 #3 agreed to share their name with the authors.)

    1. Evaluation Summary:

      This paper investigates scenarios in which the environment changes during the course of a decision, and shows that optimal behavior can be highly complex. It will be of broad interest to researchers in psychology, behavioural economics, and neuroscience interested in decision-making in real-world tasks. It also awaits detailed empirical testing.

      (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.)

    1. Evaluation Summary:

      A murine genetic platform reducing fibroblast expression shows normal background indicators of cardiac structure and contractile function. Yet it shows a reduced functional compromise, on ischemic or hypertrophic challenge. This suggests its value for studies of the effect of fibrosis following normal or pathological change.

      (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.)

    1. Evaluation Summary:

      This paper develops evolutionary simulations to identify the type of molecular networks that can give rise to size control. We now know a lot about the functional consequences and underlying molecular biology of different cell size control strategies, but comparatively less about which factors select for particular mechanisms. The authors address this point in an evolutionary framework. They show that the evolution of a specific cell size control mechanism is dependent on the cell cycle structure. The paper will interest researchers in development, evolution, and physics of biological 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. Reviewer #1 and Reviewer #2 agreed to share their name with the authors.)

    1. Evaluation Summary:

      This paper addresses the mechanism of entrapment of DNA in the cohesin SMC complex. Through a series of biochemical studies, the paper convincingly demonstrates that DNA enters cohesin rings through the hinge and SMC3/SCC1 interfaces. How such entrapment is regulated is important for different biological activities including sister chromatid cohesion and the formation of DNA loops. The paper will be of interest to researchers in SMC biology, DNA recombination and 3D genome organization.

      (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.)

    1. Evaluation Summary:

      Adult zebra finch song is highly stereotyped, and it is driven by correspondingly stereotyped neural sequences in premotor cortical nucleus HVC. By imaging HVC activity in juvenile birds isolated from social contact with tutors, the authors discover that stereotyped HVC sequences can exist even without exposure to tutor song. Interestingly, after tutoring, existing sequences in the HVC of isolate birds transitioned from being uncoupled to vocal output to highly coupled to newly copied tutor syllables. Together, these data provide a fascinating glimpse into mechanistic foundations of how nature and nurture work together to a learned motor sequence.

      (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.)

    1. Evaluation Summary:

      The complete metamorphosis of the higher insects is one of the most fascinating and complex processes in nature: The discrepancy in form and function between larvae, pupa, and adult insects is breathtaking, begging the question of how these forms and functions can so seamlessly follow each other. For the highest-order brain centre of the insects, the mushroom body, the authors provide a masterpiece analysis of this process at the cellular level. Given the breadth and depth of the data that the authors present, the current study will serve as a reference for the field of developmental neuroscience for many years to come; this study is eagerly awaited in the field. Perhaps ever more importantly, the insights into the relationship between evolutionary development and individual development at the cellular level might have a profound and lasting conceptual impact on life and natural sciences.

      (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.)

    1. Evaluation Summary:

      This study builds on previous observations of arginine depletion in the pancreatic tumor microenvironment, with the goal of developing and using a cell culture medium (TIFM) that better recapitulates nutrient levels in the TME. With this system, the authors identify arginine biosynthesis as an adaptation of pancreatic cancer cells to arginine starvation. This work reinforces a timely message that builds upon the push for optimizing and reformulating cell culture media, so as to improve fidelity, and better recapitulation of physiological/pathophysiological cellular behavior. The latter is in turn critical for translational and therapeutic applications. The work will be of interest to tumor biologists.

      (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.)

    1. Evaluation Summary:

      The research presented in this manuscript is focused on testing the role of peroxiredoxin (Prdx5) and heterogeneous nuclear ribonucleoprotein K (hnRNPK) in bone biology and osteoporosis. Using cell-base and animal models, as well as various experimental methodologies the authors demonstrated that Prdx5 is upregulated during osteogenesis but suppressed during osteoclastogenesis. This novel function Prdx5 was found to be associated with binding and regulation of hnRNPK which controls the expression of genes involved in osteoclastogenesis, such as osteocalcin (Ocn).

      (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.)

    1. Evaluation Summary:

      This paper provides insight into a potentially new genetically defined subset of prostate tumors driven by concurrent loss of two tumor suppressor genes. This study both validates previous findings and provides new data that is compelling overall. With some additional statistical and biochemical evidence to support the conclusions, the work would be of interest to cancer biologists studying molecular mechanisms of prostate cancer.

      (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.)

    1. Evaluation Summary:

      The authors identify a novel developmental role for the beta-adrenergic system in the regulation of mammalian cardiac regenerative capacity. Using genetic and pharmacological loss-of-function approaches, the authors identify a link between Yap and β-adrenergic receptor blockade. The conditional genetic loss-of-function studies are a particular strength of the manuscript and provide strong support for the Gas/Yap-dependent nature of the cardiomyocyte proliferative response to beta adrenergic blockade. Given the widespread use of beta blockers in the clinical management of heart failure, the findings are potentially very important. However, further evidence is required to substantiate the induction of bona fide cardiomyocyte proliferation and cardiac regeneration and clarify the associated 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 #1 agreed to share their name with the authors.)

    1. Evaluation Summary:

      This work is a bioinformatic analysis of HML-2-like proviruses found in the genomes of Rhesus Macaques, which convincingly argues that an HML-2 provirus underwent an ancient recombination event with a HERV-K (HML-8) related virus. The authors also provide data to suggest that the recombinant retrovirus may have acquired a distinct mechanism for the regulation of expression of spliced and unspliced transcripts. This paper should be of broad interest to virologists as it uses molecular 'fossil-like' evidence contained in the genomes of modern pirates to document the generation of what could be considered a previously undescribed retrovirus species, through recombination.

      (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.)

    1. Evaluation Summary:

      This paper is an extensive analysis of the underlying basis of desiccation resistance in 50 Drosophila species from diverse habitats. The work suggests that the longer methyl-branched alkanes (mbCHC) of the cuticular hydrocarbons are critical for this resistance. The study, which informs on the evolution of desiccation resistance in flies, is well done, although the main hypothesis is currently only partially supported by coating experiments, which presently lack controls and would be greatly strengthened by "replacement" experiments to add mbCHCs to flies without CHCs. The work is of relevance to evolutionary biologists in general.

      (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.)

    1. Evaluation Summary:

      This is an important paper that addresses a key mechanism that underlies the canonical computation of direction selectivity in the retina. By using fluorescence imaging of glutamate release from excitatory interneurons combined with a computational model of dendritic integration, the authors make a convincing case that the kinetics of glutamate release contributes to the direction-selectivity of individual neural processes in retinal neurons. This work will appeal to visual neuroscientists as well as cellular physiologists interested in dendritic computations.

      (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.)

    1. Evaluation Summary:

      In this manuscript, of interest to the fields of animal immunity and epigenetics, the authors investigate the crosstalk between PML Nuclear Bodies and HIRA, a member of the H3.3 histone chaperone complex, during inflammatory stress. This study raises interesting perspectives on how availability of HIRA could be regulated by PML Nuclear Bodies for histone deposition onto interferon-stimulated genes, which in turn, could be relevant for immune-response mediated gene regulation.

      (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.)

    1. Evaluation Summary:

      Synaptic plasticity can take place on the presynaptic and/or postsynaptic sites, and these two sites of plasticity are known to involve distinct mechanisms. Using a combined approach of physiology, Drosophila genetics, and behaviour, this study provides evidence that postsynaptic mechanisms underlie plasticity for olfactory learning. This complements the field knowledge that olfactory associative learning largely relies on the presynaptic mechanism in mushroom body neurons. The paper also emphasizes the similarities in learning and memory mechanisms between vertebrates and invertebrates.

      (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.)

    1. Evaluation Summary:

      The paper provides fundamental information through the identification of an E3 ligase and kinase/phosphatase regulatory machinery that regulates the inner nuclear membrane protein SUN2 using a GFP-based assay. The data reveal a model involving extraction of ubiquitylation of SUN2 from the membrane by p97, which is an important contribution to the field. Although the biochemical evidence is solid on the GFP-tagged SUN2 protein, one question is the extent to which this pathway works on endogenous SUN2 and the extent to which this is a quality control mechanism for turnover of unassembled SUN2 or whether it acts on the fully assembled complex.

      (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.)

    1. Evaluation Summary:

      This is a very fundamental study that challenges the paradigm that histones H3 and H4 are imported to the nucleus primarily as heterodimers. Instead this study provides compelling evidence that H3 and H4 are imported by importin 5 as monomers and dimerize on chaperones in the nucleus. The work is of relevance to colleagues studying nuclear import and epigenetic regulation.

      (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.)

    1. Evaluation Summary:

      The authors show that MiR-27a affects osteoclast-mediated bone resorption but not osteoblast-mediated bone formation during skeletal remodeling. Through gene profiling and bioinformatics study authors also identify the specific target of miR-27a in the osteoclast gene. MiR-27a exerts its effects on osteoclast differentiation through modulation of P62. This paper is of interest to scientists within the field of bone biology. The manuscript data analysis and conclusion are clear and directly supporting the previous known findings.

      (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.)

    1. Evaluation Summary:

      This study used 2017-2018 Afrobarometer surveys of more than 45,000 individuals to examine the association between the ownership of mobile phones and proximity to a health clinic in 33 African countries. Findings show that about 40% of people own smartphones and those who live closer to health clinics are more likely to own a mobile phone. This manuscript will be of interest to all people who are involved in the design and implementation of mHealth interventions in Africa.

      (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.)

    1. Evaluation Summary:

      Regulation of NAD and its intermediary metabolites is of critical importance in axon degeneration and in neurodegenerative disease. In mammals, the SARM1 NADase has been shown to be a metabolic sensor activated by an increase in the NMN/NAD+ ratio and SARM1 activation then leads to catastrophic energetic collapse and axon degeneration in disease and injury. This manuscript clarifies the role of NMN in activating the axon degeneration trigger dSARM in Drosophila. The authors analyze the signaling role of NMN, a NAD precursor metabolite involved in injury-induced axon degeneration, by overexpressing NMN-D, a prokaryotic enzyme that consumes NMN, using a stabilized version allowing for prolonged NMN depletion, and find that it is strongly protective in several in vivo injury paradigms in flies. This paper will be of interest to those in the neurodegeneration/axon injury field in general as an extensive set of optimized reagents is presented, confirming the crucial role of for exploring NAD-related axon degenerative pathways, and providing tools for neuroscientists to use Drosophila as a model for neurodegenerative 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 #2 agreed to share their name with the authors.)

    1. Evaluation Summary:

      This work will be of interest to behavioral neuroscientists with a focus on social behavior. The interrogation of the transcriptional signature of pair-bonding, in both short and long-term, is unique and made possible with the use of the monogamous vole. That there is a "degrading" of the transcriptome of pair bonding following separation is evident but there is a gap in understanding how the gene expression changes relate to behavior.

      (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.)

    1. Evaluation Summary:

      This study presents an in-depth analyses of carbon oxidation state and hydration state of proteomes in different taxa and environmental settings, which contributes to our understanding of how microbial communities are shaped by their surroundings. The study has merit, but there also some technical weaknesses.

      (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.)

    1. Evaluation Summary:

      Deposition of hyperphosphorylated misfolded tau is a hallmark of many neurodegenerative diseases, but the exact mechanisms by which misfolded tau spreads to adjacent areas of the brain are not known. In this manuscript, which will be of broad interest to cell biologists and neuroscientists, the authors suggest that tau fibrils that translocate directly through the cell membrane induce aggregation of cytosolic tau. While the results appear stunning, there are alternative explanations to the authors' hypothesis that require 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.)

    1. Evaluation Summary:

      Vignogna et al. used yeast genetics, experimental evolution and biochemistry to investigate human congenital disorders of glycosylation, often caused by mutations in PMM2. They took advantage of the observation that the budding yeast gene SEC53 is almost identical to human PMM2, and used experimental evolution to find interactors of SEC53/PMM2. Mutations in genes corresponding to other human CDG genes, including PGM1, were overrepresented. The mechanisms of how reduced pgm1 activity could compensate for defects of sec53 are not yet clear.

      (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.)

    1. Evaluation Summary:

      The authors of this study characterize human Fip1, an important component of the 3' end processing machinery. They use X-ray crystallography to determine the molecular basis of the interactions between Fip1 and CPSF30 (at a 2:1 stoichiometry) and between Fip1 and CstF77 (at a 2:2 stoichiometry). Together with biochemical assays, they suggest that Fip1 may be central to regulating transitions with CPSF. The work will of relevance to colleagues interested in transcription and RNA processing.

      (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.)

    1. Evaluation Summary:

      This is an in-depth and rigorous analysis of transcriptomic changes in myogenic cells lacking dystrophin. Studies are made in both a mouse model and human subjects. the paper bears on possible roles of such alterations in pathogenesis of Duchenne muscular dystrophy. They draw attention to new therapeutic interventions for this condition.

      (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.)

    1. Evaluation Summary:

      Individual cells may act in response to stimuli or in a self-organized fashion. The relative weight of these two modes determines in the end to which degree cells or rather organs/organisms carry function. This study reports an example of very complex self-organization of actin waves as the coexistence of slowly moving broad waves of high F-actin concentration and rapidly propagating planar F-actin pulses. The paper is interesting for everybody interested in conceptual questions like signalling versus self-organization, in cellular morpho-dynamics and theory of dynamic patterns.

      (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.)

    1. Evaluation Summary:

      This work is of interest to neuroscientists and medical professionals involved in the study of Alzheimer's disease and related neurodegenerative conditions. The findings provide important information about how potential network-based structural and metabolic imaging biomarkers are associated with memory performance during distinct disease stages, in line with previous hypothetical biomarker models. The study is conceptually and methodologically sound, although some aspects of the analysis and reporting of the results could be further clarified.

      (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.)

    1. Evaluation Summary:

      Barber et al present a manuscript discussing predictive factors for chemotherapy efficacy in head and neck squamous cancer (HNSCC). The paper is well written, and its style/formatting are optimal. The baseline signature moderately predicted outcome, and the data after one cycle further improved the algorithm, though this decreases its utility as a pure predictive tool. It is interesting that a subpopulation of monocytes, a subset of white peripheral cells long suspected to correlate with outcomes in HNSCC was one of the key drivers of the algorithm. However the overall impact in the field of this work seems limited by a number of factors, including that the authors focused on immune cell subpopulations and exosomes, which narrows the scope (no cytokines or other biomarkers were included); the signatures were not prospectively validated on an independent cohort; the algorithm was developed around a first-line therapy that is no longer considered to be the standard of care for HNSCC; and, while most of the conclusions are supported by the data, some of the caveats (such as the lack of a validation cohort, key in predictive biomarker development), are not addressed.

      (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.)

    1. Evaluation Summary:

      The study is overall well-planned and the amount of data presented by the authors is impressive. The work nicely incorporates animal-level physiology (echocardiography data), tests for known canonical markers of hypertrophy, and then delves into an unbiased analysis of the transcriptome and proteome of LV tissue in bulk. The techniques and analyses in the study are adequately executed and within the realm of expertise of the Lakatta laboratory. This study is a necessary and crucial first step to extensively phenotype this mouse line and generate hypotheses for further 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. Reviewer #1 agreed to share their name with the authors.)

    1. OAuth, or Open Authorization is a protocol for users to authorize websites to access their information without handing over a password.
    1. Evaluation Summary:

      Park et al.'s work provides insight into the infection processes of the human pathogen Coxiella burnetii with unprecedented detail. Their time course of cellular infection reveals the timing of key events and detects a previously unrecognized membrane structure. This work will shed new insight into the infection process of this pathogen allowing new targets for the treatment of infection with Coxiella.

      (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.)

    1. Evaluation Summary:

      In this paper, the authors show that autobiographical memory recall is related to a specific biophysical property of the parahippocampal cingulum bundle, the so-called MR g-ratio. This paper will be of interest to neuroscientists studying associations between brain structure and cognitive processes. The data support the main conclusions of the paper. However, it is unclear how reliable the results are and whether the findings would generalize to situations beyond the specific one studied.

      (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.)

    1. Evaluation Summary:

      This study seeks to develop the use of a FRET-based sensor for the formation of the folded 'interacting heads motif' structure for cardiac myosin, which is thought by some to represent a super-relaxed state with lower basal ATPase activity. This study offers some evidence that there is a relationship between the super-relaxed state and the 'interacting heads motif' structure, and that a specific dilated cardiomyopathy mutant in this myosin stabilizes the 'interacting heads motif' conformation. This paper will be of interest to muscle and cardiovascular biologists as it provides important insights into the correlation of structural and functional states of motor proteins in the context of cardiac muscle. The data qualitatively support this correlation and suggest a new mode of action of disease-causing mutations that lead to impaired contractile 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 #2 agreed to share their name with the authors.)

    1. Evaluation Summary:

      This study by Krug et al. uses the turquoise killifish, an emerging model for biomedical research, to generate a valuable live-imaging platform. Initially, the authors generate a transparent killifish they named Klara. Specifically, using optimized CRISPR approaches, they simultaneously inactivate three genes that are required for the formation of primary pigment cells in fish (melanophores, iridophores, xanthophores) and next, to monitor cell-cycle arrest and cellular senescence, they generate a cdkn1a-GFP reporter line using HDR-mediated integration. The paper would benefit from a further description of the HDR approach, the genetic models, and improved figures. Together, this platform will be an extremely valuable resource with broad application, including for aging research, physiology, toxicology, and regeneration.

      (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.)

    1. Evaluation Summary:

      This pre-registration study by Kerrén et al. used a proactive interference task in combination with MEG recordings on humans to test predictions of a previous computational model postulating that neural representations of competing memories are associated with varied phases of the hippocampus theta-band rhythm. Their results largely confirmed the hypothesis and suggest that reactivations of target and competitor memories indeed occur at different phases of theta oscillations, which is further related to the intrusion effect in behavior.

      (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.)

    1. Evaluation Summary:

      Using an elegant combination of cutting-edge techniques, the authors show that in the neuromuscular junction of the nematode C. elegans two different classes of voltage-activated calcium channels differentially trigger exocytosis of distinct pools of synaptic vesicles, one docked to the active zone and a second one localized more distant from the active zone. These findings will be of broad interest to neuroscientists interested in the mechanisms of calcium-mediated release of neurotransmitters at chemical synapses.

      (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.)