eLife assessment

This important work by Veneditto and colleagues developed a new modeling approach, called a mixture-of-agent hidden Markov model (MoA-HMM), in which choice behaviors are modeled as transitions between discrete states defined by different weighting of several reinforcement learning and decision strategies. The authors apply this approach to their previous data collected from rats performing the two-step task, and show that this method provides better fits to the data than previous methods, and predicts fluctuations in neural and other behavioral data. The reviewers found this study to be overall convincing, and the method is of general interest to the field.

eLife assessment

This fundamental work demonstrates the importance of considering overlapping modes of functional organization (i.e. gradients) in the hippocampus, showing associations between with aging, dopaminergic receptor distribution and episodic memory. The evidence supporting the conclusions is solid, although some clarifications about testing procedures and a discussion of the limitations of the dopaminergic receptor mapping techniques employed should be provided along with analysis code. The work will be of broad interest to basic and clinical neuroscientists.

eLife assessment

This study offers valuable insight into the remarkable resistance of tardigrades to ionizing radiation by showing that radiation treatment induces a suite of DNA repair proteins and by identifying a strongly induced tardigrade-specific DNA-binding protein that can reduce the number of double-strand breaks in human U2OS cells. The evidence of upregulation of repair proteins is convincing, and the case for a role of the newly identified protein in repair can be strengthened as genetic tools for tardigrades become better developed. The results will interest the fields of DNA repair and radiobiology as well as tardigrade biologists.

eLife assessment

The manuscript presents a machine-learning method to predict protein hotspot residues. The validation is incomplete, along with the misinterpretation of the results with other current methods like FTMap.

eLife assessment

This is an important study characterizing the unique expression of mouse Schlemm's canal endothelial cells (SECs), which function in the aqueous humor outflow pathway of the eye. The work convincingly identifies novel biomarkers for SECs and molecular markers for inner wall and outer wall SECs, followed by targeted RNA and protein expression validation in mouse eyes. Gene networks and pathways were analyzed for their potential contribution to glaucoma pathogenesis.

eLife assessment

This study reports single-cell RNA sequencing results of lung adenocarcinoma, comparing 4 treatment-naive and 5 post-neoadjuvant chemotherpy tumor samples. Of interest is the delineation of two macrophage subtypes : Anti-mac cells (CD45+CD11b+CD86+) and Pro-mac cells (CD45+CD11b+ARG+), with the proportion of Pro-mac/pro-tumorigenic cells significantly increasing in LUAD tissues after neoadjuvant chemotherapy. In terms of significance, the findings might be useful but only if robust statistical comparisons (currently missing) can be provided. As it stands, the level of supportive evidence is inadequate.

eLife assessment

The paper uses published data and a proposed cell-based model to understand how growth and death mechanisms lead to the observed data. This work provides an important insight into the early stages of tumour development. From the work provided here, the results are solid, showing a thorough analysis. However, the work has not fully specified the model, which can lead to some questions around the model's suitability.

eLife assessment

This useful study reports on the impact of antibiotic pressure on the genomic stability of the mc2155 strain of Mycobacterium smegmatis, a model for Mycobacterium tuberculosis. The study concludes that exposure to antibiotics did not lead to the emergence of new adaptive mutations in laboratory settings, contradicting the prevailing theory of antibiotic resistance development through drug-induced microevolution. While the genomic analysis provided detailed insights into the stability of M. smegmatis following exposure to standard TB treatment antibiotics, the evidence presented for antibiotic pressure not contributing to the occurrence of new adaptive mutations is still incomplete.

eLife assessment

This paper presents a valuable optimization algorithm for determining the spatio-temporal organization of chromatin. The algorithm identifies the polymer model that best fits population averaged Hi-C data and makes predictions about the spatio-temoral organization of specific genomic loci such as the oncogenic Myc locus. While the algorithm will be of value to biologists and physicists working in the field of genome organization, the provided methodological details and evidence are incomplete to fully substantiate the conclusions. In particular, the following would be beneficial: analysis of single-cell data, the inclusion of loci beyond Myc, testing the dependence of results on the chosen parameters, providing more details on CTCF occupancy at loop anchors, and better substantiating the claim about predictions of single-cell heterogeneity.

eLife assessment

This valuable study presents a series of results aimed at uncovering the involvement of the endosomal sorting protein SNX4 in neurotransmitter release. While the evidence supporting the conclusions is solid, the molecular mechanisms remain unclear, and the study would significantly benefit from additional experiments to strengthen its findings. This paper will be of interest to cell biologists and neurobiologists.

eLife assessment

This valuable study assesses through simulations how several known features of local cortical circuits - interneuron subtypes, their specific targeting of dendritic compartments, and certain brain rhythms - together affect the integration of synaptic inputs by a pyramidal cell into a spiking output signal. Employing several carefully considered simulation setups they convincingly demonstrate that beta rhythms are best suited to modulate and control dendritic Ca-spikes while gamma rhythms affect their coupling to somatic spiking, or how basal inputs are directly integrated into somatic spikes. However, the baseline setup may be idealized for the generation of the events in question and it would be beneficial if the similarity to the in-vivo activity regime was demonstrated further. The results will be relevant for neuroscientists studying local circuits or developing more abstract theories at the systems level.

eLife assessment

This valuable paper presents convincing evidence that changing the constraint of how long to stop at an intermediate target significantly influences the degree of coarticulation of two sequential reaching movements, as well as their response to mechanical perturbations. Using an optimal-control framework, the authors offer a normative explanation of how both co-articulated and separated sequential movement can be understood as an optimal solution to the task requirements.

eLife assessment

This study provides important evidence that links acetylcholine responses in the sensory cortex to motor actions during perceptual tasks, rather than to rewards. The evidence for the association between acetylcholine responses and motor actions is solid, but does not demonstrate the causal link implied by the title and abstract. The manuscript would benefit from a more detailed description of results and methodologies. This study is of broad interest to the neuroscience field.

eLife assessment

This valuable study examines the role of a host in conditions that shift pathogenicity of opportunistic microbes. The use of single-cell microbial transcriptomics and metabolomics to demonstrate the host's effects on pathogen dynamics is interesting and convincing. However, the connection to host antimicrobial peptides driving these effects is incomplete and would benefit from additional evidence and improved explanation in the text. This paper has the potential to be of broad interest to those working in host-microbe (microbiome and pathogen) interactions.

eLife assessment

This valuable study explores the sequence characteristics and conservation of high-occupancy target loci, which are genomic regions bound by a multitude of transcription factors, at promoters and enhancers throughout the human genome. The computational analyses presented in this study are solid, although the evidence for some claims is inadequate. This study would be a helpful resource for researchers performing ChIP-seq based analyses of transcription factor binding.

eLife assessment

This important study addresses the challenge of antimicrobial resistance by targeting plasmid proteins that interfere with plasmid transfer as a novel strategy to limit the spread of antibiotic resistance genes. While the evidence presented is solid, the work would benefit from a clear integration of the approaches used and more thorough analyses to fully assess the effectiveness of this strategy. This study will interest those working on plasmid transfer and antimicrobial resistance.

eLife assessment

This important study presents new knowledge of the spermatogonial stem cell (SSC) niche in trans women after gender-affirming hormone therapy (GAHT). While the evidence supporting the claims is convincing, weaknesses identified by both reviewers should be addressed. The work will be of interest to researchers and clinicians working in the field of sexual medicine and andrology.

eLife assessment

This important work reports that genome-wide patterns of relaxed purifying selection on genes involved in male fertility may represent a response to the reduced sperm competition in the gorillas' mating system. However, the evidence supporting the conclusion is incomplete and needs to be strengthened. This work will be of interest to researchers working on evolution and reproductive biology.

eLife assessment

Using a set of animal models, this valuable paper shows tumor suppressive function of the non-core regions of RAG1/2 recombinases. The conclusions are supported by solid evidence.

eLife assessment

This valuable study reports on a series of artificial selection experiments for microbiomes that confer drought tolerance to rice plants. A major strength is the solid experimental design with multiple soils, which will likely guide others in designing their experiments, but the study has also shortcomings in that the rescuing effect is not benchmarked against healthy well-watered plants, the sterilized controls do not add much information, and the dispersal between inocula confounds the interpretation of the results. In addition, while the type of work presented here is a first step towards the eventual goal of plant microbiome engineering, that goal is still mainly an ambition. The abstract would benefit from this being made clear, and the presentation would overall benefit from more extensive consideration of recent developments in the field.

eLife assessment

This article is a valuable addition to the growing literature on the developmental patterning of insect wings. Using CRISPR mutagenesis and localization of mRNA, the authors present solid evidence that the transcription factor Mirror is necessary for specifying the morphological identity of the most posterior regions of butterfly wings. The manuscript would benefit from more careful use of terminology and appropriate citation of related Drosophila literature, and there are also some concerns about whether the phenotype represents transformation or loss which might be clarified through a closer look at ultrastructure. With a clearer presentation of terminology, this paper would be of general interest to developmental and evolutionary biologists.

eLife assessment

This valuable paper describes the stiffness of meiotic chromosomes in both oocytes and spermatocytes. The authors identify differences in stiffness between meiosis I and II chromosomes, as well as an age-dependent increase in stiffness in meiosis I (and meiosis II) chromosomes, results that are highly significant for the field of chromosome biology. The mechanisms underlying age-dependent changes in chromosome stiffness remain unclear, and the evidence to suggest that changes in stiffness are independent of cohesin, which is known to deteriorate with age, is incomplete.

eLife assessment

This useful paper explores a mathematical model of subsecond time perception, testing potential neural mechanisms behind the linear psychophysical law, Weber's law, and dopaminergic modulation of subjective durations. The model employed readout units to decode an interval. Nevertheless, the work is incomplete and presented as data-driven, but there is no analysis of empirical data.

eLife assessment

This study presents a useful strategy in which the authors devised a simple method to attenuate Candida albicans and deliver a live whole-cell vaccine in a mouse model of systemic candidiasis. The reviewers are not convinced about the completeness of the study: the strength of the evidence is incomplete and could be augmented with additional experiments to more fully characterize vaccine efficacy and host immune responses.

eLife assessment

This valuable study addresses the interpretation of patterns of synonymous and nonsynonymous diversity in microbial genomes. The authors present solid theoretical and computational evidence that adaptive mutations that revert the amino acids to an earlier state can significantly impact the observed ratios of synonymous and nonsynonymous mutations in human commensal bacteria. This paper will be of interest to microbiologists with a background in evolution.

eLife assessment

This important work identifies a p. aeruginosa strain and enzyme that can degrade 1-naphthylamine, a harmful industrial pollutant. Data resulting from in vivo and structural approaches are compelling, but additional mutagenesis would further test and establish the broad substrate specificity of NpaA1. With this additional data, this paper would be of high interest to biologists and enzymologists studying biodegradation of industrial pollutants.

eLife assessment

This valuable study offers new insight into the role of centrosome protein ninein in skeletal development through an analysis of the skeletal phenotype of ninein-deficient mice. While there is solid evidence supporting the conclusion that the absence of ninein leads to transient skeletal abnormalities and a lasting reduction in osteoclastogenesis, the evidence to substantiate the claim that enhanced ossification is attributed to reduced osteoclast formation/activity is insufficient. This work will be of interest to scientists in bone biology and skeletal development field.

eLife assessment

Using anchored phylogenomic analyses, this valuable study sheds new light on the evolutionary history of the plant diet of Belidae weevil beetles and their geographic distribution. Using convincing methodological approaches, the authors suggest a continuous association of certain belid lineages with Araucaria hosts, since the Mesozoic era. While the biogeographical analysis has weaknesses due to uncertainties in vicariance explanations, the study overall offers contributions to understanding the evolutionary dynamics of Belidae and provides novel insights into ancient community ecology.

eLife assessment

This paper provides useful information about how the ionome of Arabidopsis thaliana adapts to very high CO2-levels, backed up by solid evidence and carefully designed studies. The work will be of interest to anyone studying natural genetic variation as well as the response of plants to altered CO2 levels in the atmosphere.

eLife assessment

This important work identifies a previously uncharacterized capacity for songbird to recover vocal targets even without sensory experience. The evidence supporting this claim is convincing, with technically difficult and innovative experiments exploring goal-directed vocal plasticity in deafened birds. This work has broad relevance to the fields of vocal and motor learning.

eLife assessment

This study provides evidence that the quality of research in female-dominated fields of research is systematically undervalued by the research community. The authors' findings are based on analyses of data from a research assessment exercise in New Zealand and data on funding success rates in Australia, Canada, the European Union and the United Kingdom. This work is an important contribution to the discourse on gender biases in academia, underlining the pervasive influence of gender on whole fields of research, as well as on individual researchers. The evidence supporting the conclusions is solid, but the work would benefit from further explorations into the nuances of specific fields of fields of research.

eLife assessment

In this study, the authors developed a cell-based screening assay for the identification of small molecule inhibitors of nonsense-mediated decay (NMD). They used it to validate a novel small molecule SMG1 kinase inhibitor that inhibits NMD in cultured cells leading to the expression of neoantigens from NMD-targeted genes, and in vivo slows tumor growth of cells with a significant number of out-of-frame indel mutations. The conclusions are supported by convincing evidence, and the significance of this work consists in the development of a novel and very promising NMD inhibitor drug that acts as an inhibitor of the SMG1 NMD kinase and is suitable for use in animals. This is an important advance for the field, as previous NMD inhibitors were not specific, lacked efficacy, or were very toxic and hence not suitable for animal application.

eLife assessment

In this study, the authors present convincing evidence to demonstrate theta cycle skipping by individual neurons of the lateral septum, which they then relate to population coding of future trajectories encapsulated by theta cycles. This valuable finding furthers our understanding of how the septum conveys navigational information downstream.

eLife assessment

This study presents valuable findings on the potential role of a peptide typically associated with feeding in the control of a pituitary hormone, FSH, which is a critical regulator of reproductive physiology. The evidence supporting the main claims of the authors is thought-provoking but incomplete. In particular, the authors demonstrate that the peptide is sufficient to regulate FSH, but they have not established its necessity. The work will be of interest to reproductive biologists, especially those with an interest in the endocrine control of fertility.

eLife assessment

This important study provides a comprehensive analysis of ITP and its role as an anti-diuretic and metabolic hormone in Drosophila. The evidence supporting the conclusion is solid in general with combined genetic, comparative genomic approaches, classical physiological techniques, and biochemical assays. However, the evidence of direct binding between ITPa and Gyc76C and their physiological functions is incomplete. This work represents a contribution to the field of neuropeptides and neurohormones in insects and other animals.

eLife assessment

This important study investigates the structural organization of a series of diblock elastin-like polypeptide condensates. The methodology is highly compelling, as it combines multiscale simulations and fluorescence lifetime imaging microscopy experiments. The results increase our understanding of model biomolecular condensates.

eLife assessment:

This work describes an easily implemented method for measuring solid food intake in Drosophila, which is necessary for studying the consumption of experimentally challenging diets, such as high-fat foods, as well as their nutritional impacts on the organism. It is a valuable technical contribution with solid evidence supporting the conclusions, filling a significant gap in the field.

eLife assessment

This study reports some useful information on the mechanisms by which a high-fat diet induces arrhythmias in the model organism Drosophila. Specifically, the authors propose that adipokinetic hormone (Akh) secretion is increased with this diet, and through binding of Akh to its receptor on cardiac neurons, arrhythmia is induced. The presented data, however, incompletely support the conclusions, with a number of concerns identified, such as the need for editorial clarifications, issues with experimental design (including additional control experiments), and over or misinterpretation of some of the experimental data. Nonetheless, some of the data will be helpful to those who wish to extend the research to a more complex model system, such as the mouse.

eLife assessment

This fundamental study for the first time defines genetically the role of the Clock gene in basal metazoa, using the cnidarian Nematostella vectensis. With convincing evidence, the study provides insight into the early evolution of circadian clocks. Clock in this species is necessary for daily rhythms under constant conditions, but not under a rhythmic light/dark cycle, suggesting that the major role of the circadian oscillator in this species could be a stabilizing function under non-rhythmic environmental conditions.

eLife assessment

This important study investigates the intracellular localization patterns of G proteins involved in GPCR signaling, presenting convincing evidence for their preference for plasma and lysosomal membranes over endosomal, endoplasmic reticulum, and Golgi membranes. This discovery has significant implications for understanding GPCR action and signaling from intracellular locations. This research will interest cell biologists studying protein trafficking and pharmacologists exploring localized signaling phenomena.

eLife assessment

This study addresses the effects of estrogen on the kisspeptin1 subset of neurons in the arcuate nucleus of the hypothalamus of female mice after ovaries were surgically removed. The authors repeat some of their prior work and provide new and interesting findings about the effects of estrogen on currents mediated by calcium and potassium channels, suggest a neurotransmitter "switch", and suggest Trpc5 regulates Kisspeptin 1 neuron excitability. While useful in its significance, there are concerns that the evidence for some conclusions is incomplete. This study will be of interest to endocrinologists and reproductive biologists.

eLife assessment

Unlocking the potential of molecular genetic tools (optogenetics, chemogenetics, sensors, etc.) for the study of systems neuroscience in nonhuman primates requires the development of effective regulatory elements for cell-type specific expression to facilitate circuit dissection. This study provides a valuable building block, by carefully characterizing the laminar expression profile of two viral vectors, one designed for general GABA+ergic neurons and the second for parvalbumin+ cell-type selective expression in the marmoset primary visual cortex. The authors provide solid evidence for the first enhancer S5E2 and incomplete evidence for the second one, h56D. This study contributes to our understanding of these tools but is limited by the understandably small number of animals used.

eLife assessment

This study presents an important contribution to cardiac arrhythmia research by demonstrating long noncoding RNA Dachshund homolog 1 (lncDACH1) tunes sodium channel functional expression and affects cardiac action potential conduction and rhythms. The evidence supporting the major claims are solid. The work will be of broad interest to cell biologists and cardiac electrophysiologists.

eLife assessment

This study provides an important cell atlas of the gill of the mussel Gigantidas platifrons using a single nucleus RNA-seq dataset, a resource for the community of scientists studying deep sea physiology and metabolism and intracellular host-symbiont relationships. The evidence supporting the conclusions is convincing with high-quality single-nucleus RNA-sequencing and transplant experiments. This work will be of broad relevance for scientists interested in host-symbiont relationships across ecosystems.

eLife assessment

In this important study, the authors describe a novel function for RAPSYN in bcr-abl fusion associated leukemia, presenting convincing evidence that RAPSYN stabilizes the oncogenic BCR-ABL fusion protein. Compared to an earlier version of the manuscript, the authors have added data using primary samples that strengthen the conclusions.

eLife assessment

The authors provide important insights into the pathogenesis of erectile dysfunction (ED) in patients with diabetes. The authors present compelling evidence, using single-cell transcriptomic analysis in both mouse and human cavernous tissues, to support their claims regarding the key roles of pericytes in diabetic ED. The identification of LBH as a potential pericyte-specific marker in both mouse and human tissues further strengthens their findings. This well-written manuscript offers novel and significant contributions to the field, identifying potential therapeutic targets for further investigation.

eLife assessment

The studies described here are useful; they are broadly applicable to all antibody discovery subfields but do not add significant improvement to techniques already published. The findings are incomplete with respect to the methodology since details that are crucial in order to repeat the experiment are lacking (such as a timestamp) and they do not take into account multiple recent papers that have tested similar strategies. These studies will be of interest to a specialized audience working on making antibodies to infectious agents.

eLife assessment

The authors present valuable findings on trends in hind limb morphology through the evolution of titanosaurian sauropod dinosaurs, the land animals that reached the most remarkable gigantic sizes. The solid results include the use of 3D geometric morphometrics to examine the femur, tibia, and fibula to provide new information on the evolution of this clade and on evolutionary trends between morphology and allometry. Further justification of the ontogenetic stages of the sampled individuals would help strengthen the manuscript's conclusions, and the inclusion of additional large-body mass taxa could provide expanded insights into the proposed trends.

eLife assessment

This fundamental work significantly advances our understanding of how FOG1 nuclear localization is regulated during erythropoiesis and megakaryopoiesis, including the role of EPO and MPL/TPO signaling in this process. The authors provide compelling evidence using both K562 and CD34+ cells that heat shock cognate B (HSCB) can promote the proteasomal degradation of TACC3 to regulate the nuclear localization of FOG1, and that this function is independent of its role in iron-sulfur cluster (ISC) biogenesis. Together these data will be of interest to the fields of hematopoiesis and cell biology.

eLife assessment

This useful work shows that the experimental application of serotonin to locust antennal lobes induces an increased feeding-related response to some odorants (even in food-satiated animals). To explain how the odorant-specific effects are seen despite similar consequences of 5-HT modulation on all projection neuronal types, the authors propose a simple quantitative model built around projection with different downstream connections. While they are consistent with the authors' conclusions, the current panel of experiments is incomplete and additional future work will be required to fully support the conclusions the authors currently draw from their observations.

eLife assessment

This important study builds on a previous publication (with partially overlapping authors), demonstrating that T. brucei has a continuous endomembrane system, which probably facilitates high rates of endocytosis. Using a range of cutting-edge approaches, the authors present compelling evidence that an actomyosin system, with the myosin TbMyo1 as the molecular motor, is localized close to the endosomal system in the bloodstream form (BSF) of Trypanosoma brucei. It shows convincingly that actin plays a role in the organization and integrity of the endosomal system, and that the trypanosome Myo1is an active motor that interacts with actin and transiently associates with endosomes, but a role of Myo1 in endomembrane function in vivo was not directly demonstrated. This work should be of interest to cell biologists and microbiologists working on the cytoskeleton, and unicellular eukaryotes.

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

This study focuses on nuclear pore complex dysfunction in a mouse model of Alzheimer's disease related Aβ pathology. If future revisions can adequately respond to the reviewer comments, the findings may eventually be useful in supporting the idea that nuclear cytoplasmic transport defects occur prior to plaque deposition in this disease model and may be caused by Alzheimer's disease pathology. However, even after revision, the work suffers from overinterpretation of some of the data and remains incomplete in several respects.

eLife assessment

This valuable study reports a chemogenetic screen for resistance and sensitivity towards three compounds that inhibit cell cycle progression: camptothecin, colchicine, and palbociclib. Following up on the palbociclib results, the authors provide solid evidence that knockdown of the PRC2.1 complex, likely through increasing D-type cyclin expression, confers resistance to palbociclib. The generality of the results would be improved by demonstrating the effect of PRC2.1 on cyclin expression and cell cycle progression in more than one cell line.

eLife assessment

The authors explore ER stress signalling mediated by ATF6 using a genome-wide gene depletion screen. They find that the ER chaperone Calreticulin binds and directly represses ATF6; this proposed function for Calreticulin is intriguing and constitutes an important finding. The evidence presented is based on CHO genetic evidence and biochemical results and is convincing.

eLife assessment

This important study investigates the relationship between transcription factor condensate formation, transcription, and 3D gene clustering of the MET regulon in the model organism S. cerevisiae. The authors provide solid experimental evidence that transcription factor condensates enhance transcription of MET-regulated genes, but the evidence that nuclear condensates per se drive MET gene clustering is incomplete and would benefit from further experimental analyses. This paper will be of interest to molecular biologists working on chromatin and transcription, although its impact would be strengthened by revising the literature citations and including additional experimental work.

eLife assessment

Wounds are commonly infected, which can lead to delayed or poor wound healing, thereby significantly impacting morbidity and overall quality of life for patients. This manuscript uses single cell RNA sequencing to try to understand the impact of infection on various cell types during wound healing in a mouse model. The methodology is solid and the results provide a valuable 'atlas' of the cellular changes associated with infected and uninfected wounds which will be of interest to the field.

eLife assessment

The current manuscript re-examines an established claim in the literature that human PANX-1 is regulated by Src kinase phosphorylation at two tyrosine residues, Y199 and Y309. This issue is important for our understanding of Pannexin channel regulation. The authors present an extensive series of experiments that fail to detect PANX-1 phosphorylation at these sites. Although the authors' approach is more rigorous than the previous studies, this work relies primarily on negative results that are not unambiguously definitive; the work nonetheless provides a compelling reason for the field to reexamine conclusions drawn in earlier studies.

eLife assessment

The authors present an important study of a multi-cellular platform involving co-culturing of various hiPSC-derived hepatocyte like cells, cholangiocytes, stellate cells and macrophages to mimic the liver microenvironment. The aggregates are then treated with fatty acids and examined through transcriptomic and functional assays. The techniques and methodologically are sound, and the evidence supporting the conclusion is convincing, although more clinically relevant data demonstrating the effect of some potential pharmacological agents on the platform would serve to strengthen the study.

eLife assessment

The work by Lewis and co-workers presents important findings on the role of myosin structure/energetics on the molecular mechanisms of hibernation by comparing muscle samples from small and large hibernating mammals. The solid methodological approaches have revealed insights into the mechanisms of non-shivering thermogenesis and energy expenditure.

eLife assessment

This valuable study reports a potential connection between the seminal microbiome and sperm quality/male fertility. The data are generally convincing, but the statistical methods employed need further justification. This study will be of interest to clinicians and biomedical researchers who work on microbiome and male fertility.

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 rational design and development of next-generation kinase inhibitors.

eLife assessment

In this interesting study, Drożdżyk and colleagues analyze the ability of placental CALHM orthologs to form stable complexes, identifying that CALHM2 and CALHM4 form heterooligomeric channels. The authors then determine cryo-EM structures of heterooligomeric CALHM2 and CALHM4 that reveal a distinct arrangement in which the two orthologs can interact, but preferentially segregate in the channel. This is an important study; the data provide compelling support for the interpretations and overall, the work is clearly described.

eLife assessment

In this valuable manuscript, Yeo et al. describe new methods for assessing the intracellular itinerary of Botulinum neurotoxin A (BoNT/A), a potent toxin used in clinical and cosmetic applications. The current manuscript challenges previously held views on how the catalytic portion of the toxin makes its way from the endocytic compartment to the cytosol, to meet its substrates. The approach taken is deemed innovative and the experiments are carefully performed, presenting solid evidence for some of the drawn conclusion; however, the conclusions one may draw from the experimental results are somewhat limited, as it is possible that the scope of their findings could be restricted to the specific neuron model and molecular tools that were used. This paper could be of interest to both cell biologists and physicians.

eLife assessment

This valuable paper describes innovative force measurements of the bending modulus of gliding cyanobacteria, along with measurements of the critical buckling length of the cells, which in combination lead to insight into how these cells produce the force necessary to move. Quantitative analysis convincingly shows that the propulsive force and resistive friction coefficient are strongly coupled, which supports propulsion based on adhesion forces rather than slime extrusion.

eLife assessment

This study investigates associations between retrotransposon element expression and methylation with age and inflammation, using multiple public datasets. The study is valuable because a systematic analysis of retrotransposon element expression during human aging ishas beenlacking. However, the data provided are incomplete due to the sole reliance on microarray expression data for the core analysis of the paper.

eLife assessment

This valuable paper characterizes a murine model for congenital cystic airway abnormalities (CPAM). In contrast to previous assumptions that only epithelial cells are involved in the formation of pulmonary cysts, the authors provide compelling new evidence that defective BMP signaling in lung mesenchymal cells can disrupt airway development. Knowing that proper BMP signaling in mesenchymal cells is required for normal cyst-free lungs could potentially pave the way to understanding and preventing CPAM in infants at risk for this common disorder, which can be fatal if untreated. The relevance of the murine model could be enhanced by further molecular and histological comparison with human cysts.

eLife assessment

This important study presents a novel pipeline for the large-scale genomic prediction of members of the non-ribosomal peptide group of pyoverdines based on a dataset from nearly 2000 Pseudomonas genomes. The advance presented in this study is largely based on solid evidence, although some main claims are only incompletely supported. This study on bacterial siderophores has broad theoretical and practical implications beyond a singular subfield.

eLife assessment

In this manuscript the authors present high-speed atomic force microscopy (HSAFM) to analyze real-time structural changes in actin filaments induced by cofilin binding. This important study enhances our understanding of actin dynamics which plays a crucial role in a broad spectrum of cellular activities. However, some technical questions remain, making the data interpretation incomplete.

eLife assessment

This manuscript reports important in vitro biochemical and in planta experiments to study the receptor activation mechanism of plant membrane receptor kinase complexes with non-catalytic intracellular kinase domains. Several lines of evidence convincingly show that one such putative pseudokinase, the immune receptor EFR achieves an active conformation following phosphorylation by a co-receptor kinase, and then in turn activates the co-receptor kinase allosterically to enable it to phosphorylate down-stream signaling components. This manuscript will be of interest to scientists focusing on cell signalling and allosteric regulation.

eLife assessment

This study provides an important finding that the local abundance of metabolites impacts the biology of the tumor microenvironment by utilizing kidney tumors from patients and adjacent normal tissues. The evidence supporting the claims of the authors is convincing. The work will of interest to the research community working on metabolism and kidney cancer especially.

eLife assessment

This study provides valuable evidence indicating that SynGap1 regulates the synaptic drive and membrane excitability of parvalbumin- and somatostatin-positive interneurons in the auditory cortex. Since haplo-insufficiency of SynGap1 has been linked to intellectual disabilities without a well-defined underlying cause, the central question of this study is timely. However, the support for the authors' conclusions is incomplete in general and some parts of the experimental evidence are inadequate. Specifically, the manuscript requires further work to properly evaluate the impact on synaptic currents, intrinsic excitability parameters, and morphological features.

eLife assessment

This study presents an important new technology for transdifferentiation of fibroblasts into muscle cells. The data and methods used for analysis were compelling. This study will have broad interest to cellular reprogramming biologists in particular as well as the general public.

eLife assessment

This study reports a novel substrate and a mediator of oncogenesis downstream of mTORC1, a fundamental advance in our understanding of the mechanistic basis of mTORC1-regulated cap-dependent translation and protein synthesis. Using an array of biochemical, proteomic and functional assays, the authors provide compelling evidence for a novel mTORC1/S6K1-IBTK-eIF4A1 signaling axis that promotes cancer pathogenic translation. This work is of broad interest and significance, given the importance of aberrant protein synthesis in cancer.

eLife assessment

This important work presents a consolidated overview of the NeuroML2 open community standard. It provides convincing evidence for its central role within a broader comprehensive software ecosystem for the development of neuronal models that are open, shareable, reproducible, and interoperable. A major strength of the presented work is the persistence of the development over more than two decades to establish, maintain, and adapt this standard to meet the evolving needs of the field. This work is of broad interest to the sub-cellular, cellular, computational, and systems neuroscience communities undertaking studies involving theory, modeling, and simulation.

eLife assessment

This manuscript reports important findings regarding the development, anatomical placement and synaptic connectivity of a subtype of V1 spinal inhibitory interneurons. Using a combination of techniques, the authors show convincingly how V1 interneurons in the spinal cord, specifically those expressing the transcription factor Foxp2, differ in their birthdates, synaptic connectivity to motor neurons and their postnatal location. The study is an important addition to the literature on spinal cord interneurons and opens avenues for their functional assessment.

eLife assessment

This important work advances our understanding of how memories interact to facilitate or interfere with one another, also informing our understanding of how humans build knowledge. The study provides convincing evidence that semantic relatedness proactively benefits memory using clean experimental design, rigorous statistics, large N samples, and well-characterized stimuli. The study also demonstrates the boundaries of these proactive benefits, showing that when studied items have weaker semantic relationships, proactive interference may be observed. This research will be of interest to memory researchers as well as cognitive psychologists, neuroscientists, and educators more broadly.

eLife assessment

This study presents a valuable finding on how the sensorimotor control system deals with redundancy within our body, based on a novel bimanual task. The evidence supporting the authors' claims is convincing, as demonstrated over four different experiment. The work will be of interest to researchers from the motor control community and related fields, and further investigation into the interpretation of the findings could increase the generalisation of the study to a broader audience.

eLife assessment

This useful study identifies a population of CD81-positive fibroblasts showing senescence signatures that can activate neutrophils through the C3/C3aR1 axis, hence contributing to the inflammatory response in periodontitis. Solid evidence, combining in vitro and in vivo analyses and mouse and human data, supports these findings. The work could be of interest to researchers working in the senescence and oral medicine fields

eLife assessment

This valuable study presents a machine learning model to recommend effective antimicrobial drugs from patients' samples analysed with mass spectrometry. While the proposed approach of training a single model across different bacterial species and drugs seems promising, the comparison with baselines and related work is incomplete. With the evaluation part strengthened, this paper would be of interest to computational biologists, microbiologist, and clinicians.

eLife assessment

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

eLife assessment

This study presents a valuable finding on the heterogeneity of tumour metabolism using fluorescence lifetime imaging, measured across 4 cell lines, 4 tumour types of in vivo mouse models, and 21 patient samples. The indication is that the level of heterogeneity of cellular metabolism increases with model complexity and demonstrates high heterogeneity at a clinical level. The evidence supporting the claims of the authors is solid, although the inclusion of a larger number of patient samples would have strengthened the study. The work will be of interest to medical biologists developing methods for quantifying metabolic heterogeneity.

eLife assessment

This is an important study describing a neuromuscular junction co-culture system using human cells that the authors use to study the synaptic consequences of ALS mutations. The data supporting the system are solid and show the value of using myotubes and motor neurons from the same donor. The study will be of interest to researchers who model neuromuscular junction disorders, however, the authors could more comprehensively compare and contrast their system with previous literature describing other similar models. There are also technical weaknesses that limit the interpretation of specific findings.

eLife assessment

The authors examined whether the frequency of alternative splicing across entire genomes correlates with measures of complexities across prokaryotes and eukaryotes. Although the question is very interesting and important for our general understanding of the evolution of life forms, the work is inadequate: the methods, data, and analyses do not support the primary claims. The measure of alternative splicing frequency used by the authors is problematic; the method is inappropriate; the observed correlations may also be explained by known population genetics principles; and parts of the manuscript are difficult to understand.

eLife assessment

This valuable study is of relevance for those interested in the mechanism required for infections of humans by Klebsiella pneumoniae. The authors apply TraDIS (high-density TnSeq) to K. pneumoniae with the goal of identifying genes required for survival under various infection-relevant conditions and the gene sets identified, together with the raw sequence data, will be resources for the Klebsiella research community. The evidence to support the lists of essential and conditionally-essential genes is convincing. The study provides strong evidence that some genes are conditionally essential in urine because of iron limitation, but there is less mechanistic insight for genes that are conditionally essential in serum.

eLife assessment

This paper addresses an important topic (normative trajectory modelling), seeking to provide a method aiming to accurately reflect the individual deviation of longitudinal/temporal change compared to the normal temporal change characterized based on a pre-trained population normative model. The evidence provided for the new methods is, however, inadequate. There is a lack of simulation studies to formally evaluate the performance of the proposed method in making accurate estimations and inferences about the longitudinal changes, the novelty of the method is not sufficiently described, and the example provided is unsatisfactory.

eLife assessment

This important, clearly written, and timely manuscript links the timing of ART with the kinetics of total and intact proviral HIV DNA. The conclusions are interesting and somewhat novel, and the importance of the work is high because the focus is on African women and clade C virus, both of which are understudied in the HIV reservoir field. The strength of the evidence is convincing though some definitions could be more precise and in some places the data could be reported slightly more clearly. Overall, this work will be of very high interest to scientists and clinicians in the HIV cure/persistence fields.

eLife assessment

This study presents an important method and resource in cell lines and in mice for mass spectrometry-based identification of interactors of the proteasome, a multi-protein complex with a central role in protein turnover in almost all tissues and cell types. The method presented, including the experimental workflow and analysis pipeline, as well as the several lines of validation provided throughout, is convincing. Given the growing interest in protein aggregation and targeted protein degradation modalities, this work will be of interest to a broad spectrum of basic cell biologists and translational researchers.

eLife assessment

This important study suggests that capsaicin nanoparticle administration in rats activates the transcription factor Nrf2 by directly binding to its repressor KEAP1, leading to cytoprotective gene induction, and preventing alcohol-induced gastric damage, an avenue to treat alcoholism-related gastric disorders. The evidence is currently incomplete as there is no experimental proof that capsaicin exerts its cytoprotective effects via Nrf2, and not via any of its multiple known pharmacological effects. In particular, Nrf2-deficient mice should be used to show that Nrf2 is causal to the cytoprotective effect, and better controls should be provided for the direct KEAP2-capsaicin interaction, given the high concentrations used.

eLife assessment

This study presents useful findings about daily rhythm changes of the Drosophila melanogaster adult gut metabolome, which is shown to be dependent on the fly microbiota, diet, and genotype. The phenomena observed are supported by solid experimental evidence, however, there are limitations regarding the analysis and a deeper interpretation of results would improve the manuscript. An absence of mechanistic functional investigation limits the power of the proposed conclusions. The experiments are currently incomplete as the effect of food intake timing was not directly addressed by measuring the quantity and timing of food consumption. The authors should strongly consider including the model organism used in the study in the title of the manuscript to reflect the work. This study will be of interest to physiologists of circadian biology and nutrition.

eLife assessment

This is a valuable paper that uses super-resolution microscopy to show the nanoclustering of the Nipah virus fusion protein on cell and viral membranes. Some of the conclusions regarding the clustering of viral fusion proteins is supported by solid biochemical and super-resolution imaging data while other conclusions such as significance for viral fusion mechanisms is not fully supported by the data provided.

eLife assessment

This study presents important new insights linking obesity to kidney disease using a Drosophila model. A series of compelling experiments demonstrated that a high-fat diet induces the excretion of a leptin-like JAK-STAT ligand from the fat body, driving the adipose-nephrocyte axis through activated JAK-STAT signaling and subsequently causing a functional defect in nephrocytes. While the combination of genetic tools and pharmacological intervention provides solid data and confirms the mechanistic link, the phenotypic analysis is restricted to tracer endocytosis and would benefit from immunofluorescence studies and higher animal numbers.

eLife assessment

This manuscript finds evidence for a latent capability in several members of the TMEM16 and OSCA/TMEM family of ion channels for lipid scramblase activity. The authors demonstrate that the introduction of lysine mutations in evolutionarily conserved areas of TM4 can confer constitutive ion conduction and scramblase activity. Although the significance and scope of the work are important, the strength of the evidence is incomplete and could be improved.

eLife assessment

This study presents a useful characterization of 3D chromosome conformation changes in activated T lymphocytes, linking risk variants for autoimmune disease to putative target genes. The study employs solid methods and approaches and demonstrates the utility of using chromatin conformation to understand gene regulatory processes. However, the same data modality (chromatin conformation) was previously generated by another group in the same model system, and a more in-depth comparison of results would have improved the utility of this study.

eLife assessment

This valuable study contributes to the understanding of phase separation in Dishevelled (DVL) proteins, by investigating the endogenous complexes of DVL2 using ultracentrifugation and contrasting them with DVL1 and DVL3 behavior and the functional validation of the DVL2 intrinsically disordered regions mediating the protein condensate. The study is, however, incomplete due to the lack of several controls and its focus on overexpression and mutants lacking key domains.

eLife assessment

This is a valuable manuscript describing the competitive binding between the RING2 and phosphorylated Ubl domains within Parkin involved in the regulation of Parkin activity. The evidence supporting this conclusion is incomplete, as it primarily relies on a single biochemical assay and does not utilize more stringent, quantitative biophysical approaches to probe this competitive binding. This work will be of interest to the research communities focused on the molecular basis of ubiquitin ligase regulation, PINK-PARKIN-regulated mitophagy, and mitochondrial quality control.

eLife assessment

This useful study reports an unexpected phenotype of atrophy of the male reproductive system and infertility upon combined knockout in adult mice of the genes encoding the two kinases CDK8 and CDK19. While the morphological evidence and single-cell transcriptomic data are solid, the proposed mechanism remains unconvincing as there is little evidence for causality, and some controls are missing. This work will be of interest to reproductive biologists, developmental biologists, and andrologists.

eLife assessment

This manuscript presents an important analysis of the role that the nucleosome acidic patch plays in SWR1-catalyzed histone exchange. This manuscript contains convincing data which significantly expands our understanding of the complex process of H2A.Z deposition by SWR1 and therefore would be of interest to a broad readership.

eLife assessment

The authors present an important theoretical framework that describes the interplay between liquid-liquid phase separation and protein aggregation within a mean-field model. This work will be of high interest to the biophysics and molecular biology communities, as it will understand and analyse assembly within biomolecular condensates in cells or in-vitro. Major strengths of this convincing work are the consideration of aggregates with various dimensionality and the possibility for protein gelation. A relative weakness is the lack of intuitive interpretation of some of the results and the work could be more accessible to non-experts.

eLife assessment

This important study describes how PhoP regulates cyclic-AMP production in the human pathogen Mycobacterium tuberculosis. The authors provide convincing evidence that PhoP acts as a repressor of the cyclic-AMP-specific phosphodiesterase, Rv0805, which can degrade cyclic-AMP. The revised manuscript has addressed all outstanding comments and the work will be of interest to bacteriologists.

eLife assessment

This valuable work presents the latest version of CTFFIND, which is the most popular software for determination of the contrast transfer function (CTF) in cryo-electron microscopy. CTFFIND5 estimates and considers acquisition geometry and sample thickness, which leads to improved CTF determination. The paper describes convincing evidence that CTFFIND5 finds better CTF parameters than previous methods, in particular for tilted samples (e.g. for cryo-electron tomography) or where thickness is an issue (e.g. cellular samples, or electron microscopy at low voltages).

eLife assessment

This work is of fundamental significance and has a compelling level of evidence for a new population that protects against obesity-induced hypothalamic inflammation. This topic will attract attention from a broad base of readers, from hypothalamic neuroscientists to immunologists with an interest in metabolism.

eLife assessment

This fundamental study advances our understanding of the cell specific treatment of cone photoreceptor degeneration by Txnip. The evidence supporting the conclusions is compelling with rigorous genetic manipulation of Txnip mutations. The work will be of broad interest to vision researchers, cell biologists and biochemists.

eLife assessment

In this important study, Castello-Serrano and colleagues describe, model and quantify the role of transmembrane domains in protein sorting in the secretory pathway, first at the ER and subsequently at the Golgi. Convincing data support the role of a cytoplasmic motif in ER exit, while further experiments are necessary to support a direct connection between the phase partitioning capability of the transmembrane regions and the sorting potential of domains at the Golgi/TGN.

eLife assessment

This manuscript presents useful findings on several phage from deep sea isolates of Lentisphaerae strains WC36 and zth2 that further our understanding of deep sea microbial life. The manuscript's primary claim is that phage isolates augment polysaccharide use in Pseudomonas bacteria via auxiliary metabolic genes (AMGs). However, the strength of the evidence is incomplete and does not support the primary claims. Namely, there are not data presented to rule out phage contamination in the polysaccharide stock solution, AMGs are potentially misidentified, and there is missing evidence of successful infection.

eLife assessment

In this small-scale study, Fawaz et al. report a significant prevalence of somatic mutations such as Clonal Hematopoiesis of Indeterminate Potential (CHIP) and mosaic loss of Y chromosome (mLOY), but lack of their association with a history of myocardial infarction (MI). The study utilized sensitive techniques, including targeted high-throughput sequencing and digital PCR. The valuable findings by the authors present a contrast to earlier reports, yet they align somewhat with some studies that have demonstrated little or no link between clonal hematopoiesis and atherothrombotic events. Although the study offers convincing results, its limited sample size and brief follow-up period preclude drawing definitive conclusions.

eLife assessment

This study provides valuable information on a novel gene that regulates meiotic progression in both male and female meiosis, but the evidence supporting the conclusions of the authors on the role of BEND2 in oogenesis and reproductive aging is incomplete. This study will be of interest to developmental and reproductive biologists.

eLife assessment

This small-sized clinical trial comparing nebulized dornase-alfa to the best available care in patients hospitalized with COVID-19 pneumonia is valuable, but in its present form the paper is incomplete.

eLife assessment

The manuscript presents potentially valuable findings of bone remodeling by chronic unpredictable mild stress (CUMS). This is an interesting topic on mental stress on bone health and osteoporosis, and the authors offer solid evidence of decreased bone mass by micro-CT. However, to strengthen the work, the validation should be conducted in vivo, and the mechanism behind this should be investigated further.

eLife assessment

In this work, the authors make a valuable contribution based on convincing evidence that children 6-to-7-years-old improve in 2 years of development towards utilising more optimal value-based decision-making strategies while performing a reinforcement learning task. They found that delayed feedback learning was associated with volume in the hippocampus while immediate feedback learning was not. Striatal volume was associated with both forms of learning, in contrast to prior research funding in adults. Brain-behaviour correlations were stable across the 2-year period, despite the hippocampus increasing in volume and striatal volume remaining stable.

eLife assessment

This study presents important novel findings on how heterosynaptic plasticity can transform a weak associative memory into a stronger one, or produce a memory when stimuli were not paired. This work expands our views on the role of temporal- and input-specific plasticity in shaping learning and memory processes. The evidence, based on state-of-the-art in vivo manipulations, activity recordings, and behavioral analysis, is convincing. Findings will be of broad interest to neuroscience community, and especially those studying synaptic plasticity and associative memory.

eLife assessment

This valuable study investigates how a predicted - but not presented - stimulus within a sequence is represented in the brain using time-resolved EEG decoding. The results demonstrate that when the predicted stimulus is omitted, it is still represented at the expected space and time, although at present they provide only incomplete support given some alternative explanations. The findings will have implications for researchers across domains who are interested in learning and perception.

eLife assessment

This study establishes a two distinct feature-encoding visual projection neurons in Drosophila as a model for the development of synaptic specificity. The comprehensive description of connectivity development in this system is valuable to a more general understanding of principles that underlie neural circuit development. The high-quality supporting evidence is convincing.

eLife assessment

This study provides valuable insights into our understanding of the development of the enteric nervous system. The authors use genetically engineered mice to study the behavior of stem cells in organizing the enteric nervous system and the secreted signals that regulate these cells. The study rests on a degree of incomplete evidence since the characterization of some of the mouse resources is not complete in the current version.

eLife assessment

This important work explores the modulation of pain by intense stress. The authors employed a series of cutting-edge techniques and provided convincing evidence suggesting that the dorsal lateral septum-> lateral hypothalamus-> rostral ventromedial medulla circuit is responsible for mediating stress-induced analgesia. This work will be of interest to neuroscientists interested in the neural circuits of behavior, and scientists interested in stress or pain.

eLife assessment

This study presents valuable findings as it shows that sleep rhythm formation and memory capabilities depend on a balanced and rich diet in fly larvae. The evidence supporting the claims of the authors is convincing with rigorous behavioral assays and state-of-the-art genetic manipulations. The work will be of interest to researchers working on sleep and memory.