eLife assessment

This manuscript presented convincing single-cell transcriptomic data of hematopoietic cells and immunocytes in zebrafish kidney marrow and showed that these cells have distinctive responses to viral infection. The findings in this study suggest that zebrafish kidney is a secondary lymphatic organ and hematopoietic stem cells in zebrafish may exhibit trained immunity. This represents a valuable discovery of the unique features of the fish immune system.

eLife assessment

This useful work provides insight into agonist binding to nicotinic acetylcholine receptors, which is the stimulus for channel activation that regulates muscle contraction at the neuromuscular junction. The authors use in silico methods to explore the transient conformational change from a low to high affinity agonist-bound conformation as occurs during channel opening, but for which structural information is lacking owing to its transient nature. The evidence supporting the main conclusion that ligands flip ~180 degrees in the binding site as it transitions from a low to high affinity bound conformation is incomplete because little support is available for the starting low affinity docked conformations, and the rather approximate methods for computing binding free energies differ significantly from experimental measures for two of the four tested ligands. Nonetheless, this work presents an intriguing possibility for the nature of a transient conformational change at the agonist binding site correlated with channel opening. If the ligand flip observed in these simulations can be reproduced or verified by other studies, then this work would stand as a significant advance in our knowledge of nicotinic receptor gating.

eLife assessment

This manuscript presents important findings that inform the genetic underpinnings of the model plant Arabidopsis' resistance to turnip mosaic virus (TuMV). The strength of the evidence in the manuscript is exceptional, with very large sample sizes, careful controls, multiple follow-up experiments, and broadening to the evolutionary context. The evidence provides robust support for each of the manuscript's conclusions and could pave the way for functional studies.

eLife assessment

This is an important study on the role of phenotypic aging in cancer risk. It presents results that show that Phenotypic Age Acceleration (PhenoAgeAccel) can predict cancer incidence of different types and could be used with genetic risk to facilitate the identification of cancer-susceptible individuals. This article presents solid results that would be of broad interest to the research community and clinicians.

eLife assessment

This manuscript shows that manipulating the expression of the histone acetyltransferase Gcn5 affects blood cell homeostasis in the Drosophila larval hematopoietic organ. The data suggest a link between autophagy and the mTOR pathway, as could be expected from the literature. The authors use several genetic manipulations as well as some chemical modulators to generate solid evidence supporting most of their conclusions, but some of the analyses are inadequate and would benefit from improvement.

eLife assessment

This important work describes the first high-resolution structure of HGSNAT, a lysosomal membrane protein required for the degradation of heparan sulfate (HS). Through careful structural analysis, this work proposes potential reasons why certain mutations in HGSNAT lead to lysosomal storage disorders and outlines the enzyme's catalytic mechanism. The experimental evidence presented provides incomplete support for the proposed molecular mechanism of the HS acetylation reaction and the impact of disease-causing mutations.

eLife assessment

This research advance article describes a valuable image analysis method to identify individual cells (neurons) within a ‎population of fluorescently labeled cells in the nematode C. elegans. The findings are solid and the method succeeds to identify cells with high precision. The method will be valuable to the C. elegans research community.

eLife assessment

This valuable study addresses the question of whether pupil size can serve as a sensitive physiological marker of information anticipation in human infants. The authors present solid experimental findings indicating that pupil size differs depending on the expected information content of a visual signal and that this effect might rapidly generalize to new visual information. The results could be further strengthened by additional eye movement processing and statistical analyses to rule out confounding effects of saccades and other artifacts as well as a stronger and more consistent rationale for excluding data.

eLife assessment

By leveraging optical coherence tomography this study provides important insight into the deformation of human fingertip ridges when contacting raised features such as edges and contours. The study provides solid evidence that such features tend to cause deformation and relative movement of what the authors term ridge flanks rather than bending of the ridges themselves. Clarification about the anatomical structures under study is needed to fully interpret the claims and the resulting implications for both skin mechanics as well as the neural coding of touch.

eLife assessment

This is an important study that leverages a human-chimpanzee tetraploid iPSC model to test whether cis-regulatory divergence between species tends to be cell type-specific. The evidence supporting the study's primary conclusions together provide convincing evidence for enrichment of species differences in gene regulation in cell type-specific genes and regulatory elements, motivating future work with larger sample sizes of cell lines. This work will be of broad interest in evolutionary and functional genomics.

eLife assessment

This work represents an important contribution to computational neuroscience by providing a parsimonious model for spiking-phase precession/procession in the hippocampus. The proposed model, which relies on firing-rate adaptation, is able to capture many distinct experimental observations about phase precession/procession, such as forward and backward sweeps, as well as constant cycling of sweeps across different arms of a T-maze. The convincing evidence presented in support of this work relies on classical analytical and computational techniques about continuous attractor networks.

eLife assessment

This important work reports on the transcriptomic analysis of leukocytes in the brain of adult zebrafish. A specific novel finding is the identification of dendritic cells distinct from microglia or macrophages; regional distribution of these subsets is described using transgenic lines and immunhistochemistry. The dependence of these subsets of specific transcription factors or receptors is addressed with mutants. This is a thorough and compelling analysis, of interest for scientists using the zebrafish models for neurology, immunology, and infectiology, as well as for those interested in the evolution of the brain and immune system.

eLife assessment

This fundamental work substantially advances our understanding of the molecular basis of long-term memory formation. The study identifies PKCδ as a major molecular player in long-term memory formation and describes its translocation to mitochondria to promote pyruvate metabolism, specifically after spaced training. The evidence supporting the conclusions is compelling and the work will be of broad interest to neuroscience and medicine.

eLife assessment

Shore et al. report important findings on the impact of a gain-of-function mutation (Y777H) in the Kcnt1 gene on ion currents and firing behavior in both excitatory and inhibitory neurons in the mouse cortex. The KCNT1 gene encodes a subunit of the Na+-activated K+ (KNa) channel, and the authors substantiate their claims with solid evidence from electrophysiological patch-clamp recordings of dissociated cortical neurons. Nevertheless, the majority of reviewers recommended additional studies to reinforce key findings, proposing the replication of experiments using a more physiologically intact preparation, such as an ex vivo slice.

eLife assessment

This important study presents the first comprehensive catalog of the large neurons that compute optic flow in any insect. The morphological reconstructions from volume electron microscopy of the large arbors of these neurons, the Lobula Plate Tangential Neurons, were followed by the examination of their spatial arrangement to estimate their individual receptive fields and predict their optimal motion sensitivity. This compelling, rigorous data set, which includes the synaptic connectivity of the neurons under study with major target neurons in the fly brain, establishes a foundation for future studies on visual processing on the basis of a known connectome plus genetic driver lines to manipulate its constituent neurons. It will be of interest beyond insect vision to those studying sensory processing and neural circuit function.

eLife assessment

This important study provides convincing evidence of artifactual calcium micro-waves during calcium imaging of populations of neurons in the hippocampus using methods that are common in the field. The evidence that this artifact occurs in the data is convincing; however, the evidence for the particular conditions under which the calcium waves occur is incomplete. The work raises awareness of these artifacts so that any research labs planning to do calcium imaging in the hippocampus can avoid them by using alternative strategies that the authors propose.

eLife assessment

This study presents a valuable confirmation of the roles of Dact1 and Dact2, two factors involved in Wnt signaling, during zebrafish gastrulation and craniofacial development. The limitation of the study is that its examination of genetic interactions with other Wnt factors does not conclusively distinguish primary from secondary effects for each factor. Addressing this weakness is essential for supporting claims on interactions between dact1/2 and any Wnt factors examined. The findings of a new potential target of dact1/2-mediated Wnt signaling are potentially of value; however, experimental evidence supporting the veracity of this finding is incomplete due to an apparent lack of reproducibility.

eLife assessment

Urofacial syndrome is a rare early-onset lower urinary tract disorder characterized by variants in HPSE2, the gene encoding heparanase-2. This valuable study demonstrates that AAV9-based gene therapy for urofacial syndrome is feasible and safe, at least over the time frame evaluated, with restoration of HPSE2 expression leading to re-establishment of evoked contraction and relaxation of bladder and outflow tract tissue, respectively, in organ bath studies. The evidence supporting these findings is solid, although the analysis would benefit from evaluation of additional replicates for several endpoints, quantitative assessment of HPSE2 expression, inclusion of in vivo analyses such as void spot assays or cystometry, more rigorous assessment of viral integration, and single-cell analysis of the urinary tract in mutants versus controls, all of which make the analysis of the data currently incomplete.

eLife assessment

P-glycoprotein is a major ABC-transporter that exports drugs used in chemotherpay and effects the pharmacokinetics of other drugs. Here the authors have determined cryo-EM structures of drug complexes in previously unforeseen outward-facing conformations. These convincing findings are mechanistically important and reveal potential regions to be exploited by rational-based drug design.

eLife assessment

This is an important follow-up study to a previous paper in which the authors reconstituted CO2 metabolism (autotrophy) in Escherichia coli. Here, the authors define a set of just three mutations that promote autotrophy, highlighting the malleability of E. coli metabolism. The authors make a convincing case that mutations in pgi are loss-of-function mutations that prevent metabolic efflux from the reductive pentose phosphate autocatalytic cycle, and their data suggest possible roles of mutations in two other genes - crp and rpoB. This research will be particularly interesting to synthetic biologists, systems biologists, and metabolic engineers aiming to develop synthetic autotrophic microorganisms.

eLife assessment

Efforts to increase the representation of women in academia have focussed on efforts to recruit more women and to reduce the attrition of women. This study - which is based on analyses of data on more than 250,000 tenured and tenure-track faculty from the period 2011-2020, and the predictions of counterfactual models - shows that hiring more women has a bigger impact than reducing attrition. The study is an important contribution to work on gender representation in academia, and while the evidence in support of the findings is solid, the description of the methods used is in need of improvement.

eLife assessment

This study defines a fundamental aspect of protein kinase signalling in the protist parasite Toxoplasma gondii that is required for acute and chronic infections. The authors provide compelling evidence for the role of SPARK/SPARKEL kinases in regulating cAMP/cGMP signalling, although evidence linking the loss of these kinases to changes in the phosphoproteome is incomplete. Overall, this study will be of great interest to those who study Toxoplasma and related apicomplexan parasites.

eLife assessment

This study presents a valuable finding on how lentiviral infection has driven the diversification of the HIV/SIV entry receptor CD4. Using a combination of molecular evolution approaches coupled with functional testing of extant and ancestral reconstructions of great ape CD4, the authors provide solid evidence to support the idea that endemic simian immunodeficiency virus infection in gorillas have selected for gorilla CD4 alleles that are more resistant to SIV infection. However, this conclusion would be supported more strongly with additional functional testing of other great ape CD4 relative to human and ancestral sequences. Additionally, given the difficulty in definitively proving drivers of selection, the current title of the study is considered an overstatement relative to the data presented.

eLife assessment

This study presents evidence that suggests that the coalescence of sister chromatids induced by global double-strand DNA breaks (DSBs) during late mitosis is mediated by cohesin SMC3. These findings are valuable for studying the mechanism of eukaryotic cells to repair DNA during late mitosis. Although the discrete DSB induction system in budding yeast is sound, the strength of evidence is incomplete and could be buttressed to better support the major claims and to represent a clear advance with respect to the authors' previous contributions to this field.

eLife assessment

This manuscript offers valuable information on the effect of two small molecule combinations (2C), CHIR99021 and A-485, during the reprogramming of mature cardiomyocytes into regenerative cardiac cells. This manuscript is incomplete, as the mechanistic insights derived from transcriptomic and genomic datasets are without experimental validation. This manuscript also needs additional experimental support to confirm the regenerative potential of 2C and improvements in the data analysis and presentation. Overall, this interesting work provides insights into the development of therapeutic targets for cardiac regeneration in infarcted hearts.

eLife assessment

The study elucidates a detailed molecular mechanism of the initial stages of transport in a medically relevant GABA neurotransmitter transporter GAT1 and thus generates useful new insights for this protein family. In particular, it presents convincing evidence for the presence of a "staging binding site" that locally concentrates Na+ ions to increase transport activity, whilst solid evidence for how Na+ binding affects the larger scale dynamics.

eLife assessment

This study provides fundamental new knowledge into the role of reversible cysteine oxidation and reduction in protein kinase regulation. The data provide convincing evidence that intra-molecular disulfide bonds serve a repressive regulatory role in the Brain Selective Kinases (BRSK) 1 & 2; part of the as yet understudied 'dark kinome'. The findings will be of broad interest to biochemists, structural biologists, and those interested in the rationale design and development of next-generation kinase inhibitors.

eLife assessment

The authors use a powerful combination of phylogenetics, structure prediction, biochemistry, and mutagenesis to provide an understanding of the mechanism that provides target specificity of Drosophila HP1 homolog Rhino vs. HP1, with Rhino specifically binding to piRNA loci. The authors show that a single amino acid substitution in the chromodomain of Rhino allows binding of the zinc finger protein Kipferl, which directs the complex to a subset of heterochromatic regions that other HP1 homologs do not. The evidence supporting the conclusions is compelling, providing an impressive level of mechanistic understanding of how the specificity of the piRNA genome defense system is defined. Also, the study highlights how a single amino acid change can change the functionality of a protein, providing fundamental insight into protein evolution.

eLife assessment

Using genomic data from ancient and modern samples, this important study investigates the genomic history of cattle in Iberia, focusing on the admixture between domestic cattle and their wild ancestors, aurochs. The authors present solid evidence for interbreeding between domestic cattle and wild aurochs since the Neolithic period, although the extent, sex bias, and directionality of genetic flow over time remain highly unclear. The authors also show that the aurochs ancestry in cattle stabilized at ~20% since ~4000 years ago and continues into modern breeds, including the Lidia breed that is bred for aggressiveness and used in bullfighting. The work will be of interest to evolutionary biologists and quantitative geneticists who seek to understand the genomic history and genetic basis of trait variation of domesticated animals.

eLife assessment

This useful study, which is of potential interest to a broad readership as it systematically addresses off-target effects of a commonly used chemotherapy drug on bone and bone marrow cells, presents evidence that reducing systemic inflammation induced by doxorubicin limits to some extent bone loss. Unfortunately, the work does not inform sufficiently on the mechanisms of doxorubicin action on bone, although the demonstration of the effect of systemic inflammation on bone loss is convincing. While this finding is not new, additional genetic and pharmacologic experiments and a deeper analysis of the bone phenotype would improve our understanding of what the mechanisms involved in doxorubicin-induced bone loss are, and may substantiate the clinical relevance of targeting inflammation in order to limit the negative impact of chemotherapies on bone quality.

eLife assessment

This study follows the career trajectories of the winners of an early-career funding award in the United States, and finds that researchers with greater mobility, men, and those hired at well-funded institutions experience greater subsequent funding success. Using data on K99/R00 awards from the National Institutes of Health's grants management database, the authors provide compelling evidence documenting the inequalities that shape faculty funding opportunities and career pathways, and show that these inequalities disproportionately impact women and faculty working at particular institutions, including historically black colleges and universities. Overall, the article is an important addition to the literature examining inequality in biomedical research in the United States.

eLife assessment

This study examines the human voltage-gated chloride channel CLC-2. A combination of cryo-EM, electrophysiology, and computational analysis provides compelling support for a "ball and chain" mechanism of inactivation. This and other findings regarding the gating and inhibition mechanisms of the channel are of fundamental interest to ion channel physiologists.

eLife assessment

The paper addresses the mechanism of initiation of DNA replication in human cells by analyzing published data on the location of origins of DNA replication and the location of binding sites in the genome for ORC and MCM2-7 complexes. There are some useful analyses of existing data but there are concerns regarding the conclusion that there might be alternative mechanisms for determining the location of origins of DNA replication in human cells compared to the well known mechanism known from many eukaryotic systems, including yeast, Xenopus, C. elegans and Drosophila. The lack of overlap between binding sites for ORC1 and ORC2, which are known to form a complex in human cells, is a particular concern and points to the evidence for the accurate localization of their binding sites in the genome being incomplete.

eLife assessment

By developing a novel method for detecting genetic variants associated with germline mutation spectrum variation, this important study identifies a new "mutator" locus in a population of inbred mouse strains, although the causal gene(s) and allele(s) within this locus remain uncertain. The authors further demonstrate that this new mutator locus interacts epistatically with a previously identified mutator allele on C>A mutation rate, showcasing the complexity of the genetic basis underlying variation in mutation rate and spectrum. Evidence for major findings in this paper is convincing, and the new method has the potential to be applicable to a variety of experimental systems and natural populations.

eLife assessment:

This valuable manuscript by Go et al. provides an interesting account documenting the role of resident CD56(br) NK cells in driving interaction with DCs that attract CD8+ T cells to the pancreas cancer tumor microenvironment (TME). The work convincingly illustrates how irradiation combined with CCR5i and PD1 blockade leads to a reduction in pancreatic cancer growth that correlates with a reduction in Tregs and enhancement of NK and CD8 T cells in the TME. The correlation of NKC1 signature with survival in pancreatic cancer patients is indeed of broader interest regarding potential relevance to other types of cancer.

eLife assessment

This study discloses important physiological function for TMEM63 in regulating postnatal growth in mice. The data supporting the impaired body growth and skeletal phenotype as well as disrupted growth hormone/insulin-like growth factor-I (GH/IGF-I) signaling in TMEM63 knockout mice are compelling. However, to establish that alteration of hepatic GH/IGF-I signaling is the cause for observed growth and skeletal phenotype in TMEM63 knockout mice would need additional work.

eLife assessment

The authors' findings have theoretical or practical deep implications, which makes them important. The methods, data, and analyzes support the authors' arguments with only minor weaknesses, and overall they are solid. In vitro culture experiments could provide evidence to strengthen the evidence for the functional significance of Th1-mediated cytokines in the observed B cell responses.

eLife assessment

This important study advances the understanding of physiological mechanisms in deep-sea Planctomycetes bacteria, revealing unique characteristics such as the only known Phycisphaerae using a budding mode of division, extensive involvement in nitrate assimilation, and release phage particles without cell death. The study uses convincing evidence based on experiments using growth assays, phylogenetics, transcriptomics, and gene expression data. The work will be of interest to bacteriologists and microbiologists in general.

eLife assessment

This study presents a computational model to explore how neurostimulation could impact hippocampal theta oscillations. The computational model combines a detailed physiologically realistic hippocampus model and an abstract theta oscillator. The study could provide valuable predictions on pathological changes in this network. The modelling is based on convincing approaches that could be improved with experimental validation in future experiments.

eLife assessment

This paper reports the development of SCA-seq, a new method derived from PORE-C for simultaneously measuring chromatin accessibility, genome 3D and CpG DNA methylation. Most of the conclusions are supported by convincing data. SCA-seq has the potential to become a useful tool to the scientific communities to interrogate genome structure-function relationships.

eLife assessment

This important study reports on the dynamics of PKA investigated at the single-cell level in vitro and in epithelia in vivo. Using different fluorescent biosensors and optogenetic actuators, the authors dissect the signaling pathway responsible for PKA waves, finding that PKA activation is a consequence of PGE2 release, which in turn is triggered by calcium pulses, requiring high ERK activity. The evidence supporting the claims is solid. At this stage the work is still partly descriptive in nature, and additional measurements would increase the strength of mechanistic insights and physiological relevance.

eLife assessment

This study has important implications for theoretical proposals concerning how language lateralization affects the lateralization of other cognitive functions. The methods are solid, with an appropriate selection of cognitive control tasks that share homotopic regions of the brain with language, comparing participants with typical and atypical organization of language. The participants included in the study were mainly bilinguals, a population previously reported to have a more bilateral organization of cognitive control regions than monolinguals, limiting the generalizability of the results to the general population. Despite this limitation, the results will be of interest to researchers working of brain plasticity and development, in addition to those interested in language and cognitive control.

eLife assessment

This paper presents important findings into the response of epithelial monolayers to the combined effects of surface curvature and hydraulic stress, offering insights into how these cues contribute to epithelial cell extrusion. Most of the evidence is convincing, relying mainly on a combination of imaging-based techniques. This paper is of interest to a broad and growing community of biologists, biophysicists, and engineers interested in cell-geometry interactions.

eLife assessment

The authors use a combination of structural and MD simulation approaches to characterize phospholipid interactions with the pentameric ligand-gated ion channel, GLIC. The general agreement between structures and simulations increases confidence in the description of the lipid interaction poses and provides a solid basis for the prediction of a state-dependent interaction site where lipids could dynamically modulate channel gating. The results will be very useful to understand the nature of phospholipid interactions with pentameric ligand-gated ion channels, although the functional or structural significance of these lipid interactions remains to be verified.

eLife assessment

In this study, neurons were recorded and combined across the parahippocampal area while rats performed a memory-guided spatial navigation task. Sophisticated analytical tools were used to provide convincing evidence that neuronal populations in these areas show behavior-related changes that might indicate the encoding of errors by the system. The valuable results suggest that rate remapping is a likely mechanism to support changes in representations that support memory-guided behavior in these regions, most interestingly in neurons that code head direction.

eLife assessment

This is a potentially important study that deals with the toxic effects of an intermediary in lipid degradation [trans-2-hexadecenal (t-2-hex)] in yeast through modification of mitochondrial protein import via the TOM complex. However, in the current version, the claims are incompletely supported by the data. Lacking is evidence that Tom40 is a direct target of the lipid derivative or causally implicated in the described consequences. Were such evidence forthcoming, the paper would be interesting to a broad audience of molecular and cell biologists.

eLife assessment

This important study reports on the causal role of the inferior frontal gyrus (IFG) in behavioral control. Transcranial ultrasonic stimulation is used to stimulate the IFG in a stop-signal task. The results are compelling while the analyses remain incomplete and some claims are unsubstantiated.

eLife assessment

This is an important biophysical study combining native mass spectrometry with mutant cycles to estimate the thermodynamic components of lipid A binding to the ABC transporter MsbA. Solid evidence supports the binding energies for lipid-protein interactions to MsbA using this approach, which could be later applied to other membrane proteins in general.

eLife assessment

This manuscript characterized signaling pathways for growth control and aflatoxin production in the important plant pathogen Aspergillus flavus. Associating tor and tapA with the control of aflatoxin production would be important. However, the copy number of the tor and tapA genes needs to be more clearly established, and without such work, the evidence remains incomplete.

eLife assessment

This study presents valuable insights into the evolution of the gasdermin family, making a strong case that a GSDMA-like gasdermin that was activated by caspase-1 cleavage was already present in early land vertebrates. Convincing biochemical evidence is provided that extant avian, reptile, and amphibian GSDMA proteins can still be activated by caspase-1 and upon cleavage induce pyroptosis-like cell death - at least in human cell lines. The caspase-1 cleavage site is only lost in mammals, which use the more recently evolved GSDMD as a caspase-1 cleavable pyroptosis inducer. The work will be of considerable interest to scientists working on the evolution of cell death pathways, or on cell death regulation in non-mammalian vertebrates.

eLife assessment

This important research uses an elegant combination of protein-protein biochemistry, genetics, and microscopy to demonstrate that the novel bacterial protein FipA is required for polar flagella synthesis and binds to FlhF in multiple bacterial species. This manuscript is convincing, providing evidence for the early stages of flagellar synthesis at a cell pole; however, the protein biochemistry is incomplete and would benefit from additional rigorous experiments. This paper could be of significant interest to microbiologists studying bacterial motility, appendages, and cellular biology.

eLife assessment

This important study characterizes various cell populations and describes a developmental trajectory using snRNAseq data, highlighting the cell state transitions including periosteal stem cells during bone repair. However, there was a general consensus that the evidence provided is currently incomplete, necessitating the additional data and a more thorough verification of the conclusions. Despite this, the work provides a helpful resource that will be of broad interest to the bone community.

eLife assessment

This valuable study investigates the implementation of an efference copy mechanism in the visual flight control system of Drosophila, a topic of broad interest to sensorimotor neuroscientists. Although the behavioral data and computational analysis are solid, the lack of physiological data, as well as the absence of flight saccades in the model, provide incomplete support for the paper's conclusions.

eLife assessment

The work by O'Reilly and Delis is important to extend the synergy ideas using methods from signal processing and information theory to cluster muscles and task parameters, thereby advancing our understanding of the modular architecture of motor control. The method is innovative, and the findings are compelling from theoretical and practical perspectives. The work will be of broad interest to motor control and neural engineering researchers.

eLife assessment

This study presents valuable new structures of a carbamylation-mimetic K125E mutant of the Cx26 gap junction channel uncovering the cytoplasmic loop structure and information about the closed state of the channel. The cryo-EM maps are in high quality and serve as strong foundations for dissecting the gating mechanism by CO2. However, incomplete functional studies fall short of supporting the proposed mechanism of gap junction channel modulation through carbamylation.

eLife assessment

This important study identifies candidate mitochondrial metabolite carriers in stramenopile protists that may allow these divergent eukaryotes to maintain a compartmentalized glycolytic pathway. This study fills a gap in our understanding of glycolysis evolution and opens avenues for drug design to combat stramenopile parasites. The evidence, based on phylogenetic analysis, thermostability shift assays, and in vitro reconstitution of transport reactions, is convincing, albeit lacking direct in vivo confirmation of the physiological function of these candidates.

eLife assessment

This fundamental study provides insight into the fascinating process of self- and non-self-recognition in the protist Tetrahymena thermophila, a species with seven distinct mating types. Using an elegant combination of phenotypic assays, protein studies, and imaging, the authors present convincing evidence that a large multifunctional protein complex at the cell surface mediates both self- and non-self mating-type recognition. This study extends our understanding of how more than two mating types/sexes may be specified in a species, and it will be relevant for anyone interested in sexual systems and cell-cell communication.

eLife assessment

This valuable study demonstrates the requirement of a DEAD-box helicase DDX6 for the cotranslational mRNA decay pathway in human cells. The authors performed a set of solid experiments, combining DDX6 KO cells with reporter assay and global analysis of mRNA stability/translation efficiency. Although some conclusions drawn by the authors need a more careful examination of alternative possibilities, this study will be of broad interest to RNA biologists working on translational control and mRNA stability.

eLife assessment

In this valuable paper, the authors use an existing theoretical framework relying on information theory and maximum entropy inference in order to quantify how much information single cells can carry, taking into account their internal state. They reanalyze experimental data in this light. Despite some limitations of the data, the study convincingly highlights the difference between single-cell and population channel capacities. This result should be of interest to the quantitative biology community, as it contributes to explaining why channel capacities are apparently low in cells.

eLife assessment

This study provides useful insights into the subcellular localization, interaction with integrins, and functional importance of the cell surface receptor Piezo1 in migrating human T-cells. Whether Piezo1 is critically sensing mechano-physical cues during T-cell migration is however not well supported by direct experimental evidence. The data collected is solid otherwise.

eLife assessment

This important study uses the novel light sheet imaging technique to investigate how different TLR4 agonists regulate Myddosome formation. The data showing that LPS and A-beta can control the kinetic and size of Myddosome assembly are compelling. This work would further benefit from establishing the linkage between these results and downstream signal efficiency. With this aspect strengthened, this paper would be of great interest to the innate immunity field.

eLife assessment

Following small molecule screens, this study provides convincing evidence that 7,8 dihydroxyflavone (DHF) is a competitive inhibitor of pyridoxal phosphatase. These results are important since they offer an alternative mechanism for the effects of 7,8 dihdroxyflavone in cognitive improvement in several mouse models. This paper is also significant due to the interest in the phosphatases and neurodegeneration fields.

eLife assessment

Therapeutic treatments for congenital and acquired craniofacial (CF) bone abnormalities are not well developed. This study provides convincing evidence for an innovative regenerative treatment for pediatric craniofacial bone loss using Jagged1-PEG-MAL hydrogel with pediatric human bone cells. The report is a valuable advance in this field.

eLife assessment

TRPV4 is a unique cation channel that has been demonstrated to play a role in a variety of sensory processes. The authors provide useful new data to indicate that TRPV4 activation occurs in eccrine gland cells. They then show that temperature-dependent perspiration is TRPV4-dependent in mouse skin. This provides new insight, but the data are incomplete in that more orthogonal assays could be used to more comprehensively support the conclusions.

eLife assessment

This so-far most comprehensive, spatially resolved in 2D, dynamical, multicellular model of murine muscle regeneration after injury is is an attempt to combine many contributors to muscle regeneration into one coherent calibrated framework. It has the potential to be a very valuable tool in the areas of tissue morphogenesis, regenerative therapies, quantitative modeling and simulation. However, the presentation of the experimental validation is incomplete.

eLife assessment

This study offers useful insights into the structural architecture of the mammalian egg-sperm fusion synapse, shedding light on the role of specific proteins in fertilization. The strength of the findings lies in the potential identification of a pentameric complex involved in gamete fusion by utilizing a new multimer structure prediction tool, AlphaFold Multimer. The absence of experimental validation weakens the strength of evidence supporting these claims and leaves this work incomplete.

eLife assessment

This study presents a valuable model for the emergence of planar cell polarity from the interplay of local interactions and global gradient. The framework of this model is solid, although the appreciation of its result should in places be more quantitative. A quality of this model is its simplicity and its convenience for experimental testing.

eLife assessment

This useful study introduces the development of Salmonella infection model in zebrafish embryos as an important model to study the interaction between macrophages and Salmonella during in vivo infection. Overall, the data presented are convincing and provide an inventory of genes mediating macrophage cell-cell adhesion and interactions that are useful for dissecting tissue macrophage responses and heterogeneity during intracellular bacterial infection. This is important to characterize the infection outcome and the dynamics of the immune response. The work will be of interest to microbiologists.

eLife assessment

This paper makes a valuable contribution to approaches to studying the stimulus selectivity of sensory neurons. The imaging data that forms the core of the paper is compelling, but the evidence for some of the conclusions reached is limited. A central issue is a reliance on linear measures of stimulus selectivity, which may miss key aspects of retinal coding.

eLife assessment

This valuable study addresses both commonly accepted and alternative hypotheses for the mechanism by which an intercrop supports pest control in push-pull agriculture, a promising and broadly recognized approach for sustainable intensification. The findings address a widely recognized gap in data on the mechanism underlying push-pull systems and thus can be important for work on pest control in agroecology as well as plant-herbivore interactions more generally. The support of claims is solid, combining observations of several different mechanistic aspects in an uncommonly broad range of relevant environments with clear reasoning regarding experimental design, but also using some non-standard approaches that are not as well explained, complicating comparisons to the current state of the art.

eLife assessment

This paper is of interest to a broad audience of cell biologists, and researchers who work in cell death and the role of NETosis in the pathogenesis of chronic diseases. This study presents valuable new insights to support NETosis plays an important role in the development of aristolochic acid nephropathy (AAN). A series of compelling experiments using in vivo and in vitro model supported that AAN induced NET formation via IL-19-IL20-beta receptor can induce inflammation and cell death. This new knowledge of the interaction between kidney cells and neutrophils could have clinical implications in the treatment of AAN.

eLife assessment

In this manuscript the authors describe the expression and regulatory function of a self-cleaving ribozyme in the Cpeb3 gene. This is an important study because although many self-cleaving ribozymes have been identified in the genome, the functions of these RNA enzymes even for molecular control of their target genes is mostly unknown. The manuscript provides solid data for the molecular function of the ribosome in gene regulation and its role in hippocampal learning. The study will be of interest to neurobiologists who study gene regulatory mechanisms in learning.

Universal Summarizer

(Summary generated with Kagi's Universal Summarizer.)

Bandcamp has operated as an online music store for over a decade, providing artists and labels with an easy-to-use platform to sell music directly to fans. While receiving little mainstream attention, Bandcamp has paid out $270 million to artists and maintained a simple, artist-focused design. The platform allows free streaming but encourages direct purchases from artists. Chance the Rapper has been a notable champion of Bandcamp, using it for early mixtapes and helping to bring attention to its role in supporting independent musicians. While other services focus on algorithms and playlists, Bandcamp prioritizes direct artist support through low fees and transparent sales data. It has changed little over the years but provides a niche alternative for direct fan-artist connections without the culture-diluting aspects of other streaming services. Bandcamp's low-key approach has helped it avoid issues faced by competitors while continuing to innovate for artists.

eLife assessment

The finding that Fusicoccin (FC-A) promotes locomotor recovery after spinal cord injury is supported by solid data, and the idea of harnessing small molecules that may affect protein-protein interactions to promote axon regeneration is valuable. The evidence showing that 14-3-3 and spastin interact and that 14-3-3 enhances spastin function and stability in cells is also solid.

eLife assessment

This valuable paper examines gene expression differences between male and female individuals over the course of flower development in the dioecious angiosperm Trichosantes pilosa. Male-biased genes evolve faster than female-biased and unbiased genes, which is frequently observed in animals, but this is the first report of such a pattern in plants. In spite of the limited sample size, the evidence is mostly solid and the methods appropriate for a non-model organism. The resources produced will be used by researchers working in the Cucurbitaceae, and the results obtained advance our understanding of the mechanisms of plant sexual reproduction and its evolutionary implications: as such they will broadly appeal to evolutionary biologists and plant biologists.

eLife assessment

The authors present useful findings on the use of a Drosophila behavioral paradigm for assessing different fly genetic models of neurodegeneration. The experimental design and analyses are solid and can be used for quick behavioral assessment in fly models of various neurodegenerative diseases, especially those having an impact on locomotion. The work will be of interest to Drosophila biologists using behavior as a readout for their studies.

eLife assessment

This valuable study reports the induction of supernumerary inner hair cells in the mouse cochlea upon reducing the expression level of a tight-junction protein (claudin-9). However, the evidence supporting the claims is incomplete and the work would be strengthened by adding several control experiments, resolving inconsistencies and imprecisions in the presentation of the results, and providing more mechanistic insight. The work will be of interest to scientists working in the development and regeneration of hair cells in the inner ear.

eLife assessment

This important study used a new double knockout mouse model to investigate the role of two neuropeptides, substance P and CGRPa, in pain signaling. There is convincing evidence that double knockout of these two molecules, both of which have historically been associated with pain, does not affect nociception or acute pain behaviors in males and females. The conclusions would further benefit from additional validation of the approach, consideration of potential outliers and statistical approach in cases with smaller sample sizes, and consideration of the potential for opposing effects across region or peptide. This paper will be of interest to those interested in the neurobiology of pain and/or neuropeptide function.

eLife assessment

Yang et al. investigate whether distinct sources of conflict are represented in a common cognitive space. The study uses an interesting task that mixes different sources of difficulty and reports that the brain appears to represent these sources as a mixture on a continuum in prefrontal areas. While the findings could be valuable to theory in this area, there are concerns with the analysis, design and results, that raise uncertainty regarding the main conclusion of a shared cognitive space. Thus, the evidence reported here ranges from solid to incomplete.

eLife assessment

This work is of fundamental significance to the field of nervous system development as it advances our mechanistic understanding of axon guidance. The rigorous biochemical and genetic approaches are compelling, experiments are well-controlled, and the major claims are supported by convincing data. The study should be of general interest to the developmental neurobiology community.

eLife assessment

These ingenious and thoughtful studies present important findings concerning how people represent and generalise abstract patterns of sensory data. The issue of generalisation is a core topic in neuroscience and psychology, relevant across a wide range of areas, and the findings will be of interest to researchers across areas in perception, learning, and cognitive science. The findings have the potential to provide compelling support for the outlined account, but there appear other possible explanations, too, that may affect the scope of the findings but could be considered in a revision.

eLife assessment

This valuable study links the "taste" of botanicals to their application as medicines used by the ancient Greco-Roman society. The authors used phylogenetic linear mixed models in a Bayesian framework to test the relationships between taste qualities, intensities, complexities, and therapeutic use. The evidence supporting the conclusions is solid, although there is a minor weakness concerning the somewhat inconsistent method of botanical preparation and presentation to the taster panelists; subjective bias and robustness of the participants' responses might have been overlooked. The study may be of broad interest to pharmacologists and scientists working on drug discovery, particularly those interested in natural products.

eLife assessment

This fundamental study provides compelling evidence to explain how chemical variations within a set of kinase inhibitors drive the selection of specific Erk2 conformations. Conformational selection plays a critical role in targeting medically relevant kinases such as Erk2 and the findings reported here open new avenues for designing small molecule inhibitors that block the active site while also steering the population of the enzyme into active or inactive conformations. Since protein dynamics and conformational ensembles are essential for enzyme function, this work will be of broad interest to those working in drug development, signal transduction, and enzymology.

eLife assessment

This valuable study reports on a new tool that allows for light-controlled protein degradation in Escherichia coli. With the improved light-responsive protein tag, endogenous protein levels can be reduced severalfold. The methodology is convincing and will be of interest to the fields of gene expression regulation in bacteria and, more generally to synthetic biologists.

eLife assessment

This work shows for the first time that the balance of mTOR (mTORC1 and mTORC2) in Sertoli cells regulates the rate of sperm epigenetic aging. The manuscript presents valuable findings that have some theoretical and practical implications. The strength of the evidence is however incomplete: they are limited in some places and the aims are not always fully supported by the results.

eLife assessment

The main idea tested in this work is that host galectin-9 inhibits Mycobacterium tuberculosis (Mtb) growth by recognizing the Mtb cell wall component arabinogalactan (AG) and, as a result, disrupting mycobacterial cell wall structure. Moreover, a similar effect is achieved by anti-AG antibodies. While the hypothesis is intriguing and the work has the potential to make a valuable contribution to Mtb therapy, the evidence presented is incomplete and does not explain several critical points including the dose-independent effect of galectin-9 on Mtb growth and how anti-AG antibodies and galectin-9 access the AG layer of intact Mtb.

eLife assessment

This study offers a useful advance by introducing a cord blood DNA methylation score for maternal smoking effects, with the inclusion of diverse cohorts. However, the overall strength of evidence is deemed incomplete, due to concerns regarding low exposure levels, low statistical power, potential overfitting, and the need for clearer descriptions of statistical methods. Building more directly from the existing evidence base, exploring differences between ancestries, and considering additional health outcomes would help to enhance the study.

eLife assessment

This study presents a valuable finding on the impact of metformin-induced shifts in gut microbial community structure and metabolite levels for drug efficacy in a mouse model of liver injury. The current evidence supporting the claims of the authors is incomplete, although inclusion of additional controls and a revision to clarify the reviewer's methodological concerns could strengthen the study. With revision, this paper could be of broad interest to researchers across multiple disciplines, including the microbiome, liver disease, and pharmacology.

eLife assessment

In this important manuscript, the authors used unbiased approaches to identify somatic mutations in publicly available databases that would disrupt clinically approved antibodies targeting HER2. Using a solid combination of both computational and experimental approaches they identify mutations that could restore therapeutic antibody sensitivity in a series of disease-relevant model systems. Additional cell-based and in vivo assays would strengthen the work and increase the translational and potential clinical relevance of the proposed work.

eLife assessment

This important study presents the validation of an oral delta9-tetrahydrocannabinol (THC) consumption mouse model utilizing highly palatable e-capsule gelatin. The results convincingly demonstrate that oral consumption produced THC behavioral and physiological effects, as well as measurable brain levels. The utility of the model for chronic consumption remains to be determined. The authors have clearly acknowledged limitations of their model and areas for future study and development. As the field of cannabinoid research moves toward application of routes of administration that mimic human use, these model systems will be pivotal in assessing the effects of cannabinoid-based drugs.

eLife assessment

Focusing mainly on var genes, the investigators performed comprehensive computational analyses of gene expression in malaria parasites isolated from patients and assessed changes that occur as these parasites adapt to in vitro culture conditions. The study provides an improved computational pipeline for monitoring var gene expression, and importantly, the study documents changes in expression of the core genome and thus provides insights into metabolic adaptations that parasites undergo while transitioning to culture conditions. The findings are important for their technical advances that are more rigorous than the current state-of-the-art. The solid data analyses, broadly support the claims with only minor weaknesses, tell us to be cautious when interpreting results obtained only from cultured parasites.

eLife assessment

This valuable study highlights how the diversity of the malaria parasite population diminishes following the initiation of effective control interventions but quickly rebounds as control wanes. The data presented is solid and the work shows how genetic studies could be used to monitor changes in disease transmission.

eLife assessment

The work by Han and collaborators describes valuable findings on the role of Akkermansia muciniphila during ETEC infection. If confirmed, these findings will add to a growing list of beneficial properties of this organism. However, as it stands, the strength of the evidence used to justify the conclusions in the manuscript is incomplete.

eLife assessment

This valuable study introduces a new simulation model to explain the wide-spread occurrence of genetic inversions in fruit-fly genomes, based on sexually antagonistic alleles and a trade-off between male reproduction and survival. The evidence supporting the conclusions is currently incomplete, but it might be possible to address this with additional simulations and experiments as well as more rigorous analysis of the model and the data. The work will be of interest to population geneticists beyond the fruit-fly system.

eLife assessment

The manuscript presents an analysis of different factors that are required for release of the lipid-linked morphogen Shh from cellular membranes., which will be useful in the field. The evidence is still incomplete as experiments rely on over-expression of Shh in a single cell line and are sometimes of a correlative nature. The study confirms and extends previous findings and will be of interest to developmental biologists who work on Hedgehog signaling.

eLife assessment

This study represents a valuable addition to the understanding of the DNA replication origin selection process in the budding yeast. The authors provide convincing evidence that the number of possible origins of replication is much higher than previously appreciated, although many of the newly identified origins are likely to only direct replication initiation rarely. This work will be of interest to those studying DNA replication and investigating protein-DNA interactions across the genome.

eLife assessment

This investigation of the changes in gene expression and some of the physiological consequences of sublethal exposures to the neonicotinoid insecticide imidacloprid in honeybee larvae is useful, although numerous experiments were not considered based on technical issues. The methodological design leads to concerns and it is therefore not obvious that all conclusions are justified. The study adds to our understanding of how this insecticide impacts development and growth of honeybees, but the evidence supporting the major claims is incomplete.

eLife assessment

This important study furthers our understanding of the antimicrobial properties of siderophores, and their potential use to battle opportunistic pathogens. The evidence supporting the conclusion is solid, based on rigorous biochemical, growth, and virulence assays. The work would benefit from a more in-depth discussion of the consequences and efficacy of 'siderophore therapy' in more complex communities/environments. The work will be of broad interest to colleagues in the fields of evolutionary ecology, microbiology, and medical sciences.

eLife assessment

This important study uses an innovative set of reporter assays to probe the role of the TnpB protein in IS608 transposition. The work provides independent support for the recently reported homing activity of TnpB, where the transposon is restored following excision, and suggests an additional function for TnpB in enhancing the transposase activity of the TnpA transposase. The overall approach is solid, but the authors should consider how the activity of the TnpB protein used, or the levels of ωRNA, impact their model.

eLife assessment

The manuscript offers useful descriptive insights into the potential influence of whole-brain lactate and pH levels on the manifestation of behavioral phenotypes seen in diverse animal models of neuropsychiatric disorders. However, reviewers have raised concerns about the potential loss of specificity in capturing regional and cell-type-specific effects when relying solely on whole-brain analysis methods. While the evidence supporting the conclusions is largely solid, the robustness of these conclusions could be enhanced by the inclusion of additional data and further analysis.

Editors Assessment: Antimicrobial resistance (AMR) is a global public health threat, and environmental microbial communities can act as reservoirs for resistance genes. There is a need for genomic surveillance could provide insights into how these reservoirs change and impact public health. With that goal in mind this study tested the ability of nanopore sequencing and adaptive sampling to enrich for AMR genes in a mock community of environmental origin. On average adaptive sampling resulting in a target composition 4x higher than without adaptive sampling, and increased target yield in most replicates. The methods and scripts for this approach were reviewed and curated together, although the scope of this study was limited in terms of communities tested and AMR genes targeted. And the authors improved their analysis by conducting an additional analysis of a diverse microbial community. Demonstrating the method is reusable and its results are promising for developing a flexible, portable, and cost-effective AMR surveillance tool.

*This evaluation refers to version 1 of the preprint *

eLife assessment

This is a compelling study on pro-inflammatory and anti-inflammatory lipids in relation to skeletal muscle injury. It convincingly identifies pro-inflammatory lipids during recovery predisposing to fibrosis, and maresin 1 as an anti-inflammatory lipid reducing fibrosis, improved muscle regeneration, partially restoring contractile function, of fundamental potential clinical application.

eLife assessment

George et al. present a convincing new Python toolbox ("RatInABox") that allows researchers to generate synthetic behavior and neural data specifically focusing on hippocampal functional cell types (place cells, grid cells, boundary vector cells, head direction cells).

This is valuable for theory-driven research where synthetic benchmarks should be used. Beyond just navigation, it can be highly useful for novel tool development that requires jointly modeling behavior and neural data. The authors provide convincing evidence of its utility with well documented and easy to use code and the corresponding manuscript.

eLife assessment

The authors introduce a potentially valuable novel method that provides trial-by-trial probabilistic estimates of learning and decision-making strategies inferred from choice behavior across species. This approach could prove more useful over traditional techniques for arbitrating between strategies and detecting when learning happens, and because it is computationally lightweight. Reviewers identified several concerns that limit the strength of the evidence provided, rendering the findings incomplete.

eLife assessment

This important study combines disparate results from both psychophysics and neural silencing experiments to suggest a new interpretation of how animals and humans represent and interpret recent events in our memory. A key aspect of the model put forward here is the presence of discrete jumps in neural activity within the posterior parietal region of the cortex. The model is distinct from other models, and the authors provide convincing evidence to support it both from existing results as well as from novel experiments.

eLife assessment

This study reports valuable behavioral and computational observations regarding how passive exposure to auditory stimuli can facilitate auditory categorization. The combination of behavioral results in mice with a study of artificial neural network models provides solid evidence for the authors' conclusions. This paper will likely be of broad interest to the general neuroscience community.

eLife assessment

This paper reports valuable results regarding the potential role and time course of the prefrontal cortex in conscious perception. Although the sample size is small, the results are convincing, and strengths include the use of several complementary analysis methods. The behavioral test includes subject report such that the study does not allow for distinguishing between (phenomenal) awareness and conscious access; nevertheless, results do advance our understanding of the contribution of prefrontal cortex to conscious perception.

eLife assessment

This is a valuable study of Eph-Ephrin signaling mechanisms generating pathological changes in amyotropic lateral sclerosis. There are exciting findings bearing on the role of glial cells in this pathology. The study emerges with solid evidence for a novel astrocyte-mediated mechanism for disease propagation. It may help identify potential therapeutic targets.

eLife assessment

This important manuscript investigates the roles of DKK3 in AD synapse integrity. Although previous work has identified the involvement of Wnt and DKK1 in synaptic physiology, this study provides compelling evidence that suppression of DKK3 rescues the changes in excitatory synapse numbers, as well as memory deficits in an established AD model mice. The authors provide both gain and loss of function data that support the main conclusion and advance our understanding of the mechanisms by which Wnt pathway mediates early synaptic dysfunction in AD models.

eLife assessment

This study provides an important starting point for unraveling the molecular basis of the pathological phenotypes of the repeat expansion in the gene associated with open reading frame 72 in human chromosome 9. The coarse-grained simulation method used by the authors goes beyond the state of the art, investigating a compelling number of binding partners. The evidence supporting the claims of the authors is solid, although experimental validation of the results would strengthen the major conclusions of the work. The work will be of broad interest to biophysicists and biochemists.

eLife assessment

In this important study, Guma and colleagues describe the use of structural neuroimaging to assess the cross-species convergence of sex differences in global and regional brain volumes in humans and mice. The goal of the work is to inform to what extent mouse studies of these aforementioned sex differences have relevance to humans. The authors suggest which aspects of brain anatomy (as measured by volume) are conserved or not, across species, which has theoretical and practical implications beyond a single sub-field. The evidence to support the findings is solid, it uses methods and data analysis that are appropriate and validated.

eLife assessment

This important work advances our understanding of how brains flexibly gate actions in different contexts, based on dynamically reconfiguring neural dynamics in motor circuits. The findings, using analyses of many neurons recorded simultaneously during mouse behavior, as well as causal perturbations, are clear and compelling. This work will be of interest to systems neuroscientists and to researchers studying context-dependent computation generally.

eLife assessment

This manuscript reveals important insights into the role of ipsilateral descending pathways in locomotion, especially following unilateral spinal cord injury. The study provides solid evidence that this method improves the injured side's ability to support weight, and as such the findings may lead to new treatments for stroke, spinal cord injuries, or unilateral cerebral injuries. However, the methods and results need to be better detailed, and some of the statistical analysis enhanced.

eLife assessment

This is an important study that investigates BMP signaling mechanisms in the developing chick cerebellum to better understand germinal layer formation, cellular amplification and neuronal differentiation. The data from human tissue is compelling and lends support to the possible links of these processes to medulloblastoma, although these specific statements could be toned down and presented only as part of the discussion. Overall, this is a solid piece of work with beautifully presented findings.

eLife assessment

The manuscript aims to better understand the mechanisms underlying the behavioral responses of C. elegans to hydrogen sulfide, a toxin known to exert remarkable effects on animal physiology in a range of contexts. To this end, the authors provide a series of useful findings regarding the mechanisms by which hydrogen sulfide may be sensed, their relationships to other gas-sensing pathways, and the role of a variety of physiological pathways in responding to hydrogen sulfide exposure. While some of the findings are solid, other aspects of the paper are incomplete, such that some claims are incompletely supported, and an integrated understanding of the authors' observations does not clearly emerge.

eLife assessment

This potentially valuable study provides some evidence that upregulation of sodium-activated potassium channels contributes to neuronal hyperexcitability and seizures following traumatic brain injury. However, the evidence supporting a direct link is incomplete. This work will be of interest to epilepsy and ion channel researchers.