eLife Assessment

This valuable study presents findings linking prophage carriage to lifestyle regulation in the marine bacterium Shewanella fidelis, with potential implications for niche occupation within a host (Ciona robusta) and mediation of host immune responses. The study leverages a unique animal model system that offers distinct advantages in identifying select phenotypes to present overall solid evidence that supports findings relating to the impact of a prophage on host-microbe interaction. Understanding the role of integrated lysogenic phages in bacterial fitness, both within a host and in the environment, is a significant concept in bacterial eco-physiology, potentially contributing to the success of certain strains.

eLife Assessment

This work provides valuable insights by introducing a post-translational extrusion mechanism that could reshape how we understand the coupling between DnaA activity and DNA-replication initiation. While solid evidence is presented for some of the key results, other claims rest on indirect proxies and could be improved.

eLife Assessment

This paper reports the development of proteins and small molecules that drive bridge LMO2, an oncogenic transcription factor in T-ALL, to E3 ligases (Cereblon and VHL), and demonstrates their effectiveness in degrading FMO2, causing growth arrest and inducing apoptosis in T cell lines in vitro. The findings are valuable because they provide evidence that intrinsically disordered proteins can be targeted for degradation by PROTAC-type chemicals. The paper also provides a route for rational PROTAC design based on intracellular antibody paratopes. Overall, the paper is supported by solid evidence and will be of interest to chemical biologists and cancer pharmacologists.

eLife Assessment

This well-designed, valuable study uses isotope tracing to analyse how iron limitation alters TCA cycle metabolism in Mycobacterium tuberculosis, revealing potential antibiotic targets for non-replicating bacteria in the host. The findings provide insights into metabolic remodelling under iron-limited conditions. Whilst some of the evidence is solid, the data around the GABA shunt is incomplete, requiring genetic validation, as was done for the glyoxylate shunt. Questions remain about the underlying mechanisms and their specific role in M. tuberculosis pathogenesis.

eLife Assessment

This important paper reports the discovery of calcarins, a protein family that seems to be involved in calcification in the calcareous sponge Sycon ciliatum, significantly enhancing our understanding of the molecular and cellular mechanisms underlying spicule formation in sponges and the evolution of carbonate biomineralization. The conclusions are supported by compelling evidence based on an integrated analysis that combines transcriptomics, genomics, proteomics, and precise in situ hybridization. These findings will be of broad interest to cell biologists, biochemists, and evolutionary biologists.

eLife Assessment

This revised study provides fundamental insights into the differences in migratory primordial germ cells based on their anterior or posterior location. Through convincing methodology and analysis of single-cell RNA sequencing of an exceptionally large number of migratory primordial germ cells and surrounding somatic cells, the novel findings and datasets generated from this study provide many hypotheses of interest to germ cell biologists.

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. It also demonstrates that the asymptomatic reservoir is unevenly distributed across host age groups. The data presented are convincing and the work shows how genetic studies could be used to monitor changes in disease transmission.

eLife Assessment

This study presents fundamental new findings introducing a new approach for the reprogramming of brain glial cells to corticospinal neurons. The data is highly compelling, with multiple lines of evidence demonstrating the success of this new assay. These exciting findings set the stage for future studies of the potential of these reprogrammed cells to form functional connections in vivo and their utility in clinical conditions where corticospinal neurons are compromised.

eLife Assessment

The authors use a range of techniques to examine the role of Aurora Kinase A (AurA) in trained immunity. The study is hypothesis driven, it uses solid experimental approaches, and the data are presented in a logical manner. The findings are valuable to the trained immunity field because they provide an in-depth look at a common inducer of trained immunity, beta-glucan.

eLife Assessment

This manuscript reports a large series of experiments to investigate specific aspects of plant adaptation, leveraging genetic and genomic resources of Arabidopsis thaliana. The study provides convincing evidence for local adaptation in this highly selfing plant. This is an important dataset contributing to the developing understanding of non-linear selection in plants and beyond.

eLife Assessment

This valuable study provides a 3D standardised anatomical atlas of the brain of an orb-weaving spider. The authors describe the brain's shape and its inner compartments - the neuropils - and add information on the distribution of a number of neuroactive substances such as transmitters and neuropeptides. Through the use of histological and microscopy methods, the authors provide a more complete view of an arachnid brain than previous studies and also present convincing evidence about the organisation and homology of brain regions. The work will serve as a reference for future studies on spider brains and will enable comparisons of brain regions with insects so that the evolution of these structures can be inferred across arthropods.

eLife Assessment

This manuscript presents an in-depth analysis of gene expression across multiple brown algal species with differing life histories, providing convincing evidence for the conservation of life cycle-specific gene expression. While largely descriptive, the study is an important step forward in understanding the core cellular processes that differ between life cycle phases, and its findings will be of broad interest to developmental and evolutionary biologists.

eLife Assessment

This study presents useful findings on how the transient absence of visual input (i.e., darkness) affects tactile neural encoding in the somatosensory cortex. The evidence supporting the authors' claims is incomplete, as key conclusions rely on subtle differences in surface roughness discriminability between sensory conditions, whose physiological underpinnings remain unclear. Potential methodological confounds are also not fully addressed. With additional analyses and methodological clarifications, this work could substantially inform neuroscientists studying cross-modal interactions.

eLife Assessment

This important study addresses how wing morphology and kinematics change across hoverflies of different body sizes. The authors provide convincing evidence that there is no significant correlation between body size and wing kinematics across 28 species and instead argue that non-trivial changes in wing size and shape evolved to support flight across the size range. Overall, this paper illustrates the power and beauty of an integrative approach to animal biomechanics and will be of broad interest to biologists, physicists and engineers.

eLife Assessment

This valuable observational study was conducted in Dar es Salaam, Tanzania, to investigate potential associations between genetic variation in Mycobacterium tuberculosis and human host vs. disease severity. The authors conclude that human genetic ancestry did not contribute to tuberculosis severity and the evidence supporting this is generally convincing. The findings have significance for the understanding of the influence of host/bacillary genetics on tuberculosis disease.

eLife Assessment

This important study shows that the activity of hypothalamic hypocretin/orexin neurons (HONs) correlates with body movement over multiple behaviors. Compelling evidence, supported by sophisticated, cutting-edge tools and data analyses, highlights a link that appears to be unique to HONs. This work should be of interest to scientists studying peptidergic neurons, movement, energy regulation, and brain-body coordination.

eLife Assessment

This manuscript describes a novel approach for assessing cognitive function in freely moving mice in their home-cage, without human involvement. The authors provide convincing evidence in support of the tasks they developed to capture a variety of complex behaviors and demonstrate the utility of a machine learning approach to expedite the acquisition of task demands. This work is important given its potential utility for other investigators interested in studying mouse cognition.

eLife Assessment

This important study explores the power of computational methods to predict lifespan-extending small molecules, demonstrating that while these methods significantly increase hit rates, experimental validation remains essential. The study uses all-trans retinoic acid in Caenorhabditis elegans as a model, providing genetic and transcriptomic insights into its longevity effects. The data are compelling in describing a robust, computationally informed screening process for discovering compounds that extend lifespan in this species.

eLife Assessment

The authors of this important study investigate how telomere length regulates hTERT expression via non-telomeric binding of the telomere-associated protein TRF2. They conclusively show that TRF2 binding to long telomeres results in a reduction in its binding to the hTERT promoter, while short telomeres restore TRF2 binding in the hTERT promoter, recruiting repressor complexes like PRC2, and suppressing hTERT expression. There is convincing support for the claims and the findings should be of broad interest for cell biologists and those working in fields where telomeres alter function, such as cancer and aging.

eLife Assessment

This study provides valuable insights into the anti-senescence effects of enalapril, identifying pSmad1/5/9 signaling and associated antioxidant pathways as key mediators of its physiological benefits in aged mice. The authors present solid experimental evidence across both in vitro and in vivo systems, demonstrating improved organ function and reduced senescence markers following treatment. Overall, the work supports the repurposing potential of enalapril in aging research and expands understanding of its molecular targets.

eLife Assessment

This valuable study provides solid evidence that MgdE, a conserved mycobacterial nucleomodulin, downregulates inflammatory gene transcription by interacting with the histone methyltransferase COMPASS complex and altering histone H3 lysine methylation. There are areas where the evidence could be strengthened, for example, GFP immunoblotting and examining MgdE localization during infection. To enhance impact, the authors could consider Mycobacterium tuberculosis infection experiments and/or reworking the manuscript to emphasize general relevance to microbiologists and cell biologists.

eLife Assessment

This study addresses an important question in sensory neuroscience: how the olfactory system distinguishes decreases in stimulus intensity from decreases in neural responses due to adaptation. Based on a combination of electrophysiological and behavioral analyses, solid evidence establishes that neural coding changes differently between intensity reductions and adaptation, with intensity changes altering which neurons are activated while adaptation preserves the active ensemble but reduces response magnitude. Intriguingly, behavioral responses tend to increase as the neural responses decrease, suggesting that core features of the odor response persist through adaptation. While the experimental results are convincing overall, the conclusions will be strengthened by future work recording behavior and neural dynamics in the same animals.

eLife Assessment

The manuscript is an important study which aims to demonstrate the conserved and crucial role of IgM in both systemic and mucosal antiviral immunity in teleost, challenging the established differential roles of IgT and IgM. The strength of the evidence is solid and supported by a combination of in vivo studies, viral infection models, and complementary in vitro assays. In the current version, authors validate the MoAb against IgM

eLife Assessment

This study presents important findings on the insecticidal mechanism of betulin, a plant-derived metabolite, in controlling the aphid Myzus persicae and it provides a demonstration that betulin targets the GABA receptor in aphids, with strong supporting evidence from transcriptomic, biochemical, electrophysiological, and genetic approaches. In particular, the identification of a specific conserved residue (THR228) critical for betulin binding advances our understanding of insect neuropharmacology and offers translational potential for pest management strategies. The evidence supporting the primary claims is solid, with well-integrated methodologies and appropriate controls; however, some interpretative and methodological limitations remain, including the option to further explore off-target effects, as well as the broader evolutionary and ecological context. Addressing these points would strengthen the broader implications of the study.

eLife Assessment

This valuable study provides evidence supporting a critical role of the axonemal protein ANKRD5 in male infertility. The data generally supports the conclusions and is considered solid, although there are concerns about the cryo-ET analysis. This work will be of interest to biomedical researchers studying ciliogenesis and fertility.

eLife Assessment

The formation of the Z-ring at the time of bacterial cell division interests researchers working towards understanding cell division across all domains of life. The manuscript by Jasnin et al reports the cryoET structure of toroid assembly formation of FtsZ filaments driven by ZapD as the cross linker. The findings are important and have the potential to open a new dimension in the field, and the evidence to support these exciting claims is solid.

eLife Assessment

This important study provides evidence for dynamic coupling between translation initiation and elongation that can help maintain low ribosome density and translational homeostasis. The authors combine single-molecule imaging with a new approach to analyze mRNA translation kinetics using Bayesian modeling. This work is overall solid, but certain key aspects and model assumptions could be strengthened.

eLife Assessment

This important work elucidates the biological processes and detailed mechanisms by which testosterone influences seminal plasma metabolites in mice. The evidence supporting the upregulation of metabolic enzymes and the role of ACLY is solid, highlighting the potential contributions of fatty acids to sperm motility.

eLife Assessment

This important study provides new insights into the lesser-known effects of the sodium-potassium pump on how nerve cells process signals, particularly in highly active cells like those of weakly electric fish. The computational methods used to establish the claims in this work are compelling and can be used as a starting point for further studies.

eLife Assessment

This study offers a valuable contribution to the understanding of how inorganic nutrient transporters, particularly SUL1, influence yeast lifespan through signaling pathways rather than transport functions. The findings suggest a novel link between SUL1 deletion and extended replicative lifespan, supported by transcriptomic and stress-response data. However, the strength of the evidence remains incomplete, with key experiments-such as sulfate supplementation tests, functional autophagy validation, and transport assays-either missing or insufficiently described. As a result, while the manuscript presents promising insights, additional work is needed to robustly support its conclusions.

eLife Assessment

This study presents useful findings that explore the prognostic and immunotherapeutic relevance of specific immune-related genes (CALR, IL1R1, IFNB1, and IFNG) in the bladder cancer tumor microenvironment. While the analysis highlights potentially meaningful associations with survival and treatment response, the strength of evidence is incomplete, as some claims lack sufficient experimental or mechanistic validation. Further refinement and validation of the predictive models would enhance the impact and generalizability of the conclusions.

eLife Assessment

This study describes a genetic screen to identify deubiquitinases (DUBs) that counteract the activity of small-molecule degraders (PROTACs). The presented data are valuable, identifying OTUD6A and UCHL5 as DUBs that impact the efficacy and potency of PROTACs. While the conclusions are broadly supported and the methods employed are solid, the mechanistic depth and validation are incomplete. Overall, these findings merit further evaluation by the targeted protein degradation community when developing and optimizing PROTACs.

eLife Assessment

In this important contribution, Yan and colleagues describe a powerful and compelling strategy to generate concatamers of the BK channel and their fusion constructs with the auxiliary gamma subunits, which allows exploring contributions of individual subunits of the tetrameric channel to its gating and the study of heteromeric channel complexes of defined composition. Distinct examples are presented, which illustrate great diversity in the stoichiometric control of BK channel gating, depending on the site and nature of molecular perturbations. The molecular approaches could be extended to other membrane proteins whose N and C termini face opposite sides of the membrane.

eLife Assessment

This manuscript reports a high-quality genome assembly of the European cuttlefish, Sepia officinalis, a representative species of the Cephalopod lineage. The data are based on current best practices for sequencing and genome assembly, including PacBio HiFi long reads and Hi-C chromatin conformation capture; the analysis is currently in parts incomplete, as further analyses are required to confirm the correct chromosome number. This genome will be a useful resource for the community of researchers interested in cuttlefish biology and comparative genomics in general.

eLife Assessment

This important study systematically investigates the effects of calnexin, an endoplasmic reticulum chaperone, on the drug response of approximately 230 disease-causing variants of the cystic fibrosis transmembrane conductance regulator (CFTR) protein. Through deep mutational scanning, interactome profiling, and functional assays, the findings provide convincing evidence that calnexin significantly influences both CFTR expression and the efficacy of corrector drugs in a variant-specific manner. These insights advance our understanding of how cellular quality control machinery shapes the pharmacological responsiveness of CFTR variants, which are broadly relevant for researchers in protein folding and genetic disease therapeutics.

eLife Assessment

This valuable study presents computational analyses of over 5,000 predicted extant and ancestral nitrogenase structures. The data analyses are convincing, it offers unique insights into the relationship between structural evolution and environmental and biological phenotypes. The data generated in this study provide a vast resource that can serve as a starting point for studies of reconstructed and extant nitrogenases.

eLife Assessment

The macromolecular organization of photosynthetic complexes within the thylakoids of higher plant chloroplasts has been a topic of significant debate. Using in situ cryo-electron tomography, this study reveals the native thylakoid architecture of spinach thylakoid membranes with single-molecule precision. The experimental methods are unique and compelling, providing important information for understanding the structural features that impact photosynthetic regulation in vascular plants and addressing several long-standing questions about the organization and regulation of photosynthesis.

Editors Assessment:

This paper presents Chevreul, a new open-source R Bioconductor (meta-)package for processing and integration of scRNA-seq data from cDNA end-counting, full-length short-read or long-read protocols. Alongside a R Shiny app for easy visualization, formatting, and analysis for exploratory analyses of scRNA-seq data processed in the SingleCellExperiment Bioconductor or Seurat formats. The name of the tool is inspired by the colour theorist Michel-Eugène Chevreul and the optical illusion of the same name. To demonstrate the use of Chevreul, the authors provide a sample analysis, which helps to demonstrate how users can visualize a wide range of parameters, enabling transparent and reproducible scRNA-seq analyses. Peer review also pushing the author to provide extensive guidance materials to assist with use. Being implemented in R, the R package and integrated Shiny application are freely available under an open-source MIT license in Bioconductor and their GitHub page here: https://github.com/cobriniklab/chevreul

This evaluation refers to version 1 of the preprint

eLife Assessment

This manuscript provides valuable evidence comparing the performance of mathematical models and opinions from experts engaged in outbreak response in forecasting the spatial spread of an Ebola epidemic. The evidence supporting the conclusions is convincing. It will be of interest to disease modellers, infectious disease epidemiologists, policy-makers, and those who need to inform policy-makers during an outbreak.

eLife Assessment

This important work substantially advances our understanding of the interaction among gut microbiota, lipid metabolism, and the host in type 2 diabetes. The evidence supporting the claims of the authors is convincing. The work will be of interest to medical biologists working on microbiota and diabetes.

eLife Assessment

This is a valuable study that explores the role of the conserved transcription factor POU4-2 in the maintenance, regeneration, and function of planarian mechanosensory neurons. The authors provide solid evidence provided by gene expression and functional studies to demonstrate that POU4-2 is required for the maintenance and regeneration of functional mechanosensory neurons in planarians. Furthermore, the authors identify conserved genes associated with human auditory and rheosensory neurons as potential targets of this transcription factor.

eLife Assessment

This study offers useful findings demonstrating the cartilage-protective effects of osteoactivin in inflammatory experimental models. The study provides compelling evidence that osteoactivin may serve as a promising therapeutic target for inflammatory joint diseases.

eLife Assessment

This valuable study investigates the role of HIF1a signaling in epicardial activation and neonatal heart regeneration in mice. Through a combination of genetic and pharmacological approaches, the authors show that stabilization of HIF1a enhances epicardial activation and extends the regenerative capacity of the heart beyond the typical neonatal window following myocardial infarction (MI). However, several aspects of the study remain incomplete and would benefit from further clarification and additional experimental support to solidify the conclusions.

eLife Assessment

This study introduces a useful method to estimate the probability that a malaria case is imported and to identify the geographic origin of parasites by using a Bayesian approach that integrates epidemiological, travel, and genetic data. The authors provide convincing evidence that the approach can reliably identify the main sources of malaria imports. This work will be of great interest to the area of genomic epidemiology and public health strategies aiming to eliminate malaria.

eLife Assessment

This study presents an important finding that ant nest structure and digging behavior depend on ant age demographics for a ground-dwelling ant species (Camponotus fellah). By asking whether ants employ age-polyethism in excavation, the authors address a long-standing question about how individuals in collectives determine the overall state of the task they must perform, and their results may prove to be a key consideration for interpreting results from other studies in the field of social insect behavior. The experimental evidence that the age of the ants and the group composition affect the digging of tunnels is solid, although some aspects of the modeling and certain analyses may benefit from further clarification regarding their added value to the core findings.

eLife Assessment

The medicinal leech preparation is an amenable system in which to understand the neural basis of locomotion. Here a previously identified non-spiking neuron was studied in leech and found to alter the mean firing frequency of a crawl-related motoneuron, which fires during the contraction phase of crawling. The findings are valuable and the experiments were diligently done and generally solid; The results lay a foundation for additional studies in this system.

eLife Assessment

The paper presents a new behavioral assay for Drosophila aggression and demonstrates that social experience influences fighting strategies, with group-housed males favoring high-intensity but low-frequency tussling over aggressive lunging observed in isolated males. This paper is important for researchers studying the impact of social isolation on aggression, while the description of tussling behavior and the interpretation of the link between tussling and mating success are incomplete.

eLife Assessment

This important study examines the role of endothelin signaling in nerve regeneration, providing convincing evidence that it functions as a default brake on axon regrowth. Inhibiting endothelin signaling with Bosentan promotes regeneration and counteracts the decline in regenerative potential caused by aging. Since Bosentan is an FDA-approved drug, these findings could have therapeutic value in clinical settings where peripheral nerve regeneration is not adequate or seriously impaired, as is often the case in older individuals.

eLife Assessment

This study presents a valuable finding about how receptor-ligand binding pathways with multi-site phosphorylation can show non-monotonic responses to increasing ligand affinity and to kinase activity. The authors provide convincing evidence through a simple ordinary differential equation model of such signaling networks with the key new ingredient of ligand-induced receptor degradation. The work will be of interest to physicists and biologists working on signal transduction and biological information processing.

eLife Assessment

This important work provides mechanistic insights into the development of cardiac arrhythmia and establishes a new experimental use case for optogenetics in studying cardiac electrophysiology. The agreement between computational models and experimental observations provides a convincing level of evidence that wave train-induced pacemaker activity can originate in continuously depolarized tissue, with the limitation that there may be differences between depolarization arising from constant optogenetic stimulation, as opposed to pathophysiological tissue depolarization. Future experiments in vivo and in other tissue preparations would extend the generality of these findings.

eLife Assessment

This manuscript presents a valuable methodological approach for investigating context-dependent activity of cis-regulatory elements within defined genomic loci. The authors combine a locus-specific massively parallel reporter assay, enabling unbiased and high-coverage profiling of enhancer activity across large genomic regions, with a degenerate reporter assay to identify nucleotides critical for enhancer function. The data supporting the conclusions are solid, highlighted by the successful identification and characterization of both previously known and new regulatory elements across multiple developmental stages, cell types, and species; however, concerns regarding assay sensitivity, statistical rigor in distinguishing active regions, and limitations inherent to the design of the reporter assays remain to be addressed. With strengthened quantitative analysis, statistical validation, and additional functional experiments to directly establish regulatory element-gene relationships, this study will be of broad interest to researchers investigating gene regulation mechanisms in development and disease.

eLife Assessment

This important study offers substantial technical advancements for neural circuit tracing in larval zebrafish, a model for systems and developmental neurobiology. The enhanced rabies virus-based retrograde transneuronal tracing improves efficiency and provides a method for combined structural and functional brain mapping. The supporting evidence is solid, and there is strong confidence in the technique's utility for neurobiologists working with zebrafish.

eLife Assessment

This manuscript presents solid experimental data using Fmr1 knockout mice to explore the fundamental role of Fmr1 in sleep regulation. The study supports the hypothesis that scheduled feeding can improve circadian rhythm and behavior in a mouse model of Fragile X syndrome. These findings may offer new insights into neurodevelopmental disorders and their potential treatment strategies.

eLife Assessment

This important work advances our understanding of DNA methylation and its consequences for susceptibility to DNA damage. This work presents evidence that DNA methylation can accentuate the genomic damage propagated by DNA damaging agents as well as potentially being an independent source of such damage. The experimental results reported are sound but the evidence presented to support the conclusions drawn is incomplete and other interpretations are possible. The work will be of broad interest to biochemists, cell and genome biologists.

eLife Assessment

The findings are valuable, given that they highlight the flexible and future-oriented nature of working memory. However, the evidence for the claims about context/color generalization, behavioural relevance of context decoding, dimensionality reduction, neural geometry, the XOR representation, and the specific contribution of working memory is incomplete. The work could be reframed in terms of prospective remapping.

eLife Assessment

This study provides potentially important findings on the understanding of circannual timing in mammals, for which iodothyronine deiodinases (DIOs) have been suggested to be of critical importance, yet functional genetic evidence has been missing. The authors aim to implicate dio3, the major inactivator of the biologically active thyroid hormone T3, in circannual timing in Djungarian hamsters, using a combination of correlative and gene knock-out experiments. Currently, several questions have been raised concerning either the methodological description and/or the design of the experiments, and so the experimental evidence is considered incomplete.

eLife Assessment

Avoidance of UV and blue light by the nematode C. elegans is mediated by the unusual transmembrane protein LITE-1, a non-canonical photoreceptor. In this valuable work, the authors provide convincing evidence that LITE-1 function is also required for avoidance of very high concentrations of the food-associated cue diacetyl, suggesting that it may also function as a diacetyl chemoreceptor. While the evidence for this idea is incomplete, these intriguing findings suggest an unexpected complexity in the function of this unusual photoreceptor.

eLife Assessment

This study examines how the neuronal cytoskeleton contributes to the formation of the axonal membrane-associated periodic skeleton (MPS) in embryonic dorsal root ganglia (DRG) neurons, using STED imaging. Conclusions are supported by convincing methods, data, and analyses. This useful work confirms previous data and improves our understanding of the roles of microtubules and actin dynamics in the chronological recruitment of MPS components.

eLife Assessment

These findings are among some of the first to identify a behavioral and neurobiological substrate that disentangles nonassociative from associative fear responses following stress, providing a fundamental push forward in the field. The evidence supporting this is convincing and uses a variety of conceptual and technological approaches. This investigation will be of interest to neuroscientists and behaviourists broadly, as well as clinicians for its relevance to post-traumatic stress disorder.

eLife Assessment

The authors show that innate defensive behavior in mice is shaped by threat intensity, reward value, and social hierarchy, highlighting how value and social context influence instinctive decisions. The authors provide useful behavioural findings supported by strong data, yet the evidence is incomplete due to ambiguities about methodology and the computational model that remains largely descriptive.

eLife Assessment

This is a methodologically rich manuscript that is important for elucidating the neural mechanisms of expectation in perception. The analyses are convincing in extending analogous findings in attention and working memory. With further clarification, the findings will be of broad interest to vision researchers.

eLife Assessment

This valuable study presents a theoretical framework for building continuous attractor networks that integrate with a wide range of topologies, which are of increasing relevance to neuroscientists. While the work offers solid evidence for most claims, the evidence supporting biological plausibility and key claims - such as the existence of a continuum of stable states and robustness across geometries - is currently incomplete and would benefit from further analysis or discussion. The study will be of interest to computational and systems neuroscientists working on neural dynamics and network models of cognition.

eLife Assessment

This study provides valuable insights into humans' ability to generalize knowledge of learned graph structures to new experiences that share the same structure but are built from different stimuli. However, the evidence for the authors' claims is incomplete, with the main claims of structural generalization and compositionality only partially supported by MEG and behavioral data. This study will be of interest to cognitive neuroscientists studying structure learning and generalization.

eLife Assessment

This study introduces a valuable simulation-based inference (SBI) framework to identify degenerate compensatory mechanisms that stabilize network activity despite neuronal hyperexcitability, a feature common to many brain disorders. By estimating posterior distributions of network parameters, the authors highlight factors such as threshold potential and interneuron-to-principal cell connectivity as key compensators for increased intrinsic excitability and interneuron loss. While the approach is promising and could become a key tool for probing network degeneracy, the study is currently incomplete. To fully realize its potential, the framework requires improved scalability and more rigorous cross-validation.

eLife Assessment

This valuable short paper is an ingenious use of clinical patient data to address an issue in imaging neuroscience. The authors clarify the role of face-selectivity in human fusiform gyrus by measuring both BOLD fMRI and depth electrode recordings in the same individuals; furthermore, by comparing responses in different brain regions in the two patients, they suggested that the suppression of blood oxygenation is associated with a decrease in local neural activity. The methods are solid and provide a rare dataset of potentially general importance.

eLife Assessment

In their study, Diana et al. introduce a novel method for spike inference from calcium imaging data using a Monte Carlo-based approach, emphasizing the quantification of uncertainties in spike time estimates through a Bayesian framework. This method employs particle Gibbs sampling for estimating model parameter probabilities, offering accuracy comparable to existing methods with the added benefit of directly assessing uncertainties. The presentation of the underlying methods and its characterization is convincing and it presents a valuable advancement for neuroscientists interested in new approaches for parameter estimation from calcium imaging data.

eLife Assessment

These useful findings assigned a novel functional implication of histone acylation, crotonylation. Mechanistic insights have been provided in great detail regarding the role of the YEATS2-GCDH axis in modulating epithelial-to-mesenchymal transition (EMT) in head and neck cancer, and overall the strength of evidence is solid.

eLife Assessment

In this work, the authors intend to assess the existence of a redox potential across germline stem cells and neighboring somatic stem cells in the Drosophila testis. Some aspects of the manuscript are solid, like the clear effect of SOD KD on cyst cell differentiation state. Other conclusions of the work, such as the non-autonomous effect of this KD in germ cells are not sufficiently supported by the data. The work is potentially useful if the critiques of the reviewers are fully addressed; the strength of the evidence of the manuscript as it stands is incomplete.

eLife Assessment

This study provides valuable insights into the influence of sex on bile acid metabolism and the risk of hepatocellular carcinoma (HCC). The data to support that there are inter-relationships between sex, bile acids, and HCC in mice are convincing, although this is a largely descriptive study. Future studies are needed to understand the interaction of sex hormones, bile acids, and chronic liver diseases and cancer at a mechanistic level. Also, there is not enough evidence to determine the clinical significance of the findings given the differences in bile acid composition between mice and men.

eLife Assessment

This study presents data on sex differences in gene expression across organs of four mice taxa. The authors have generated a unique and convincing dataset that fills a gap left by previous studies. They claim that sex-biased expression in the soma can overlap between genetic males and females, and that the relevant patterns both turn over quickly over short evolutionary times and do so faster in somatic than gonadal tissues. These conclusions could largely have been predicted by extrapolating from previous findings in the field, but nevertheless demonstrating them directly is a fundamental advance.

[Editorial note: The work was originally assessed by colleagues who are active in the field of evolution of sex differences or in areas adjacent to this field (see initial assessment at https://doi.org/10.7554/eLife.99602.2). The appeals process involved consultation with experts working in other areas of evolutionary biology. The above assessment synthesises the opinions of both sets of reviewers.]

eLife Assessment

This study investigated the role of insulin receptor (IR) and insulin-like growth factor 1 receptor (IGF1R) in the renal glomerular podocytes by characterizing the mice with dual deletion of both receptors in vivo as well as the cultured murine podocytes with induced deletion of both receptors in vitro. The solid data presented in this paper demonstrated the critical requirement of both IR and IGF1R signaling in normal podocyte physiology in mice, albeit a more detailed characterization of the mouse model is desired. Interestingly, long-range sequencing revealed significant retention of introns in mRNAs, due to an altered spliceosome level resulted from the loss of IR and IGF1 signaling in cultured podocytes. This new finding suggests an essential role of IR and IGF1R signaling in regulating RNA metabolism in podocyte, which provides useful information for the understanding of physiology and metabolism of podocytes. However, the underlying molecular mechanism for such a regulation is still unclear and awaits further studies.

[Editors' note: this paper was reviewed by Review Commons.]

eLife Assessment

In their important manuscript, Gangadharan, Kober and Rice focus on how Stu2/XMAP215-family microtubule polymerases use their TOG domains to catalytically promote microtubule growth, testing whether their mechanism follows an enzyme-like kinetic model similar to that of actin polymerases. The authors integrate measurements including microtubule polymerization rates and TOG-tubulin binding kinetics to convincingly show that Stu2 follows an enzyme-like model where tight tubulin binding enables efficient polymerization, revealing a shared mechanism with actin polymerases despite their evolutionary divergence. This work will be of general interest to the cell biology and biophysics communities.

eLife Assessment

This valuable study provides new insights into the movement of ions through the bacterial pump KdpFABC, which regulates intracellular potassium concentration, by solving a 2.1 Å cryo-EM structure of the nanodisc-embedded active wild-type protein, and carrying out mutagenesis and activity assays. Although the structural data and analysis are solid, additional information about other structural classes identified in the EM data, as well as a discussion of relevant work done by others, would further strengthen these findings. The description of the activity assays is currently incomplete because more information is required to rigorously assess these experiments. This work will be of interest to the membrane transporter and channel communities and to microbiologists interested in osmoregulation and potassium homeostasis.

As I take up this office a statement must be properly made. There is not new current information to present but I hope to encourage a better future. Four years ago we were worried about a war, both parties were in social conflict. The Union divided over the legality and morality of slavery and war came. Slaves who mainly lived in the south knew this rising conflict was in relation to them. Neither party had expected the war to be this long, brutal and that it would continue even after the resolution of slavery in Congress. How could both sides be under the same God, the same religion and still have both of their prayers left unanswered.

Slavery is now an offence to god and he wishes it to be removed. He shall pray for justice to be brought upon corrupt slave owners and the freed slaves they have hurt through emotional and physical toil; He shall pray for the end of this war. What was said three thousand years ago, must still be said. "the judgments of the Lord are true and righteous altogether.”

With malice toward none; with charity for all; with firmness in the right, as God gives us to see the right, let us strive on to finish the work we are in. To bind up the nation’s wounds; to care for him who shall have borne the battle, and for his widow, and his orphan — to do all which may achieve and cherish, a just and a lasting peace, among ourselves, and with all nations.

eLife Assessment

This study presents an important computational framework, FLiSimBA (Fluorescence Lifetime Simulation for Biological Applications), for modeling experimental limitations in Fluorescence Lifetime Imaging Microscopy (FLIM). FLiSimBA is readily available in MATLAB and Python, enables users to simulate effects of noise and varying sensor expression levels, and provides practical guidance for both lifetime imaging experiments and biosensor development. The analyses are robust, and the evidence supporting the tool's utility in distinguishing between multiple lifetime signals is compelling, indicating strong potential for multiplexed dynamic imaging. However, users should also consider that the tool's effectiveness depends on the suitability of a two-component discrete exponential model.

eLife Assessment

This study presents important findings on increased ground beetle diversity in strip cropping compared with crop monocultures. Solid methods are used to analyze data from multiple sites with heterogeneous systems of mixed crops, allowing broad conclusions, albeit at the expense of lacking taxonomic specificity. The work will be of interest to all those applying plant diversity treatments to improve the diversity of associated animals in agricultural fields.

eLife Assessment

This study shows, for the first time, the structure and snapshots of the dynamics of the full-length soluble Angiotensin-I converting enzyme dimer. The combination of structural and computational analyses provides compelling evidence that reveals the conformational dynamics of the complex and key regions mediating the conformational change. This fundamental work illustrates how conformational heterogeneity can be used to gain insights into protein function.

eLife Assessment

This important study provides a potential framework for understanding the regulatory mechanisms of DON toxin biosynthesis in F. graminearum and identifies potential molecular targets for Fusarium head blight control. While FgDML1 remains under-explored with an unclear role in the biology of filamentous fungi, the supporting evidence in this study is incomplete. Providing details on methods and adding controls will strengthen the work.

eLife Assessment

This work presents potentially important findings suggesting that a combination of transcranial stimulation approaches applied for a short period could improve memory performance. However, the evidence supporting the conclusions is currently incomplete. In particular, the claims relating to the specific neural mechanisms and anatomical sites of action underlying effects were viewed as overstated in the current version. The results potentially have implications for non-invasive enhancement of cognitive functions.

eLife Assessment

In this valuable study, the authors show the physiological response and molecular pathway mediating the effect of quinofumelin, a developed fungicide with an unknown mechanism. The authors present convincing data suggesting the involvement of the uridine/uracil biosynthesis pathway, by combining in vivo microbiology characterization as well as in vitro biochemical binding results.

eLife Assessment

This important study reveals how Drosophila may be used to investigate the role of missense variants in the PLCG1 phospholipase gene in human diseases. The experimental evidence is compelling and brings together rigorous analysis of clinical and model organism phenotypes with a structural analysis of the PLCG1 protein.

eLife Assessment

This useful study characterizes the evolution of medial prefrontal cortex activity during the learning of an odor-based choice task. While the evidence for an increase in task-informative cells with learning, the emergence of population sequences, and the presence of replay events is intriguing, it remains incomplete; notably, the study does not adequately consider the extensive literature on the role of olfactory and hippocampal networks in similar odor-guided tasks. Furthermore, the experimental design appears insufficient to support strong conclusions regarding pre-existing representations or the functional relevance of neural sequences. The study will be of interest to neuroscientists investigating learning and decision-making processes.

eLife Assessment

This important study presents JABS, an open-source platform that integrates hardware and user-friendly software for standardized mouse behavioral phenotyping. The work has practical implications for improving reproducibility and accessibility in behavioral neuroscience, especially for linking behavior to genetics across diverse mouse strains. The strength of evidence is convincing, with validation of key platform components, although incomplete methodological details and limited documentation, particularly around pose estimation and classifier generalizability, currently limit its interpretability and broader adoption.

eLife Assessment

This carefully conducted study aims to understand how the early visual experience of premature infants induces lasting deficits, including compromised motion processing. The authors address this important question in a ferret animal model, exposing the developing visual system prematurely to patterned visual input by opening one or both eyes at a time when both retinal waves and light traveling through closed lids can drive sensory responses. Convincing evidence is presented, suggesting that eye opening at this time impacts temporal frequency tuning and elevates spontaneous firing rates. These findings will have great relevance for neuroscientists studying visual system development, particularly in the context of premature birth.

eLife Assessment

This important study uses long-term behavioural observations to understand the factors that influence female-on-female aggression in gorilla social groups. The evidence supporting the claims is convincing, as it includes novel methods of assessing aggression and considers other potential factors. The work will be of interest to broad biologists working on the social interactions of animals.

eLife Assessment

In this important study, the authors model reinforcement-learning experiments using a recurrent neural network. The work examines if the detailed credit assignment necessary for back-propagation through time can be replaced with random feedback. The authors provide solid evidence that the solution is adequate within relatively simple tasks.

eLife Assessment

This work investigates ZC3H11A as a cause of high myopia through the analysis of human data and experiments with genetic knockout of Zc3h11a in mouse, providing a useful model of myopia. The evidence supporting the conclusion is still incomplete in the revised manuscript as the concerns raised in the previous review were not fully addressed. The article would benefit from a more robust genetic analysis and comprehensive presentation of human phenotypic data to clarify the modes of inheritance in the families, currently limited by loss of patient follow-up and addressing whether there is a reduction in bipolar cell number or decreased marker protein expression through cell counts or quantifiable, less saturated Western blots. The work will be of interest to ophthalmologists and researchers working on myopia

eLife Assessment

This important study provides convincing evidence that the Kinesin protein family member KIF7 regulates the development of the cerebral cortex and its connectivity and the specificity of Sonic Hedgehog signaling by controlling the details of Gli repressor vs activator functions. This study provides new insights into general aspects of cortical development.

eLife Assessment

This study presents useful findings on the application of HPV cfDNA as a marker for monitoring treatment response and prognosis in patients with recurrent or metastatic cervical cancer. The evidence supporting the claims of the authors is solid, although inclusion of a larger number of patient samples would have strengthened the study. The work will be of interest to medics and biologists working on cervical cancer.

eLife Assessment

This valuable study introduces a modern and accessible PyTorch reimplementation of the widely used SpliceAI model for splice site prediction. The authors provide solid evidence that their OpenSpliceAI implementation matches the performance of the original while improving usability and enabling flexible retraining across species. These advances are likely to be of broad interest to the computational genomics community.

eLife Assessment

The manuscript by Hawes et al. provides important findings on how striatal projection neurons regulate spontaneous locomotion speed in the context of implicit motivation and distinct contextual valence. The supporting evidence for the findings is convincing. This work will be of broad interest to neuroscientists in the fields of basal ganglia, movement control, and cognition.

eLife Assessment

This important study is the first characterization of the phenotype caused by a lack of Eml3 expression in mice. Mutant animals present a disrupted pial basement membrane, leading to focal extrusions from the cerebral cortex, called ectopias. The methodology is convincing and the conclusions are solid, although further investigations on the mechanisms and inclusion of the experiments performed, but not presented, will improve the manuscript. This work would be of interest to neural development biologists and human geneticists working on brain disorders.

eLife Assessment

This paper presents the important finding that BNIP3/NIX, a mitophagy receptor, and its binding to ATG18 are required for mitophagy during muscle cell reorganization in Drosophila. Although the involvement of the BNIP3-ATG18/WIPI axis in mitophagy induction has been reported in mammalian cell culture systems, this study provides the first compelling evidence for this pathway in vivo in animals. The physiological significance of this BNIP3-dependent mitophagy will require further investigation.

eLife Assessment

Understanding how neural circuits mediate decision-making is a core problem in neuroscience. In this interesting and important work, the authors use detailed behavioral analysis and rigorous quantitative modeling to convincingly support the idea that the nematode C. elegans uses an "accept-reject" behavioral strategy, based on learned features of its environment, to make decisions upon encountering food patches. The work expands our understanding of the behavioral repertoire of this species, providing a foundation for future mechanistic studies in this powerful model system.

eLife Assessment

This is a well-written study that presents a solid genetic screen to identify regulators of adipose morphology and remodeling in zebrafish. The authors generated a rigorous screening platform based on live, whole animal imaging and statistical methods that revealed both novel and known genes critical for adipose regulation. This work is valuable because it provides several candidate genes relevant to metabolic health and a quantitative screening pipeline that will be beneficial for future studies. A limitation of the study is that it precludes a definitive distinction between developmental and remodeling effects.

eLife Assessment

This paper makes a valuable contribution to our understanding of the tradeoffs in eye design - specifically between improvements in optics and in photoreceptor performance. The authors successfully build a formal theory that enables comparisons across a wide range of species and eye types. One notable example is that how space should be allocated to optics and photoreceptors depends on eye type - with particularly notable differences between compound and simple eyes. The framework introduced to compare different design properties is convincing and provides a nice example of how to study tradeoffs in seemingly disparate design properties.

eLife Assessment

This work is a important resource for hypothesis testing of candidate upstream transcriptional regulatory factors that control the spatiotemporal expression of selector genes and their targets for GABAergic vs glutamatergic neuron fate in the anterior brainstem. Extensive high-quality datasets were generated and state of the art computational methods were convincingly implemented to identify candidate regulatory elements. The work will be of interest to biologists working to understand neuronal gene regulatory networks.

eLife Assessment

This valuable study reports the physiological function of a putative transmembrane UDP-N-acetylglucosamine transporter called SLC35G3 in spermatogenesis. The conclusion that SLC35G3 is a new and essential factor for male fertility in mice and probably in humans is supported by convincing data. This study will be of interest to reproductive biologists and physicians working on male infertility.

eLife Assessment

Qiu et al. present multiple dimeric structures of GPR3, which reveal the binding mode of the inverse agonist AF64394. The findings provide important insights into the regulation of GPCR3 and potentially other related orphan GPCRs. The authors present convincing evidence of their claims through thoughtful analysis of their cryo-EM structures, mutagenesis, and cell-based assays. This work will be of interest to GPCR investigators, especially those studying the signaling of orphan receptors.

eLife Assessment

This study provides valuable insights into the crosstalk between ATG2A with components of the early secretory pathway, namely RAB1A and ARFGAP1. The evidence supporting the claims is convincing. However, the manuscript would benefit from a more in-depth exploration of the details of the role of RAB1A in autophagy and the functional implications of its interaction with ATG2A. In addition, the molecular details of the role of ARFGAP1 in this complex need further clarification

eLife Assessment

This important study is of relevance for the fields of predictive processing, perception and learning, with a well-designed paradigm allowing the authors to avoid several common confounds in investigating predictions, such as adaptation. Using a state-of-the-art multivariate EEG approach, the authors test the opposing process theory and find evidence in support of it - i.e., the persuasive within trial effects. However, the interactions across block are not well motivated and much less persuasive, such that the support for the conclusions is only incomplete at present.

eLife Assessment

This valuable manuscript addresses the longstanding question of how the brain maintains serial order in working memory, proposing a biologically grounded model based on synaptic augmentation mechanisms that operates on longer time scales than facilitation. The authors show that augmentation provides a mechanism by which this order can be maintained in memory thanks to a temporal gradient of synaptic efficacies. Although the evidence remains incomplete at present, it can be made stronger by demonstrating robustness to network heterogeneity, spiking, and threshold values for encoding the working memory.

eLife Assessment

This important paper takes a novel approach to the problem of automatically reconstructing long-range axonal projections from stacks of images. The key innovation is to separate the identification of sections of an axon from the statistical rules used to constrain global structure. The authors provide compelling evidence that their method is a significant improvement over existing measures in circumstances where the labelling of axons and dendrites is relatively dense.

eLife Assessment

This important work substantially advances our understanding of the interaction among gut microbiota, lipid metabolism, and the host in type 2 diabetes. The evidence supporting the claims of the authors is solid, although additional experiments for the control FMT are not yet satisfactory. The work will be of interest to medical biologists working on microbiota and diabetes.

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. The experimental data is solid, as in their revisions the authors successfully addressed questions related to changes in thalamocortical presynaptic excitability, the contradiction between spontaneous and mini EPSCs data, and the anatomical analysis of excitatory synapses.

eLife Assessment

This paper describes the structure and connectivity of brain neurons that send descending connections to motor neurons and muscle in the fruit fly nerve cord, using a synapse-resolution connectome. This important work provides a wealth of hypotheses and predictions for future experimentation and modelling. Using state-of-the-art methods, the authors provide solid evidence for their conclusions.

eLife Assessment

In this useful study, ectopic expression and knockdown strategies were used to assess the effects of increasing and decreasing Cyclic di-AMP on the developmental cycle in Chlamydia. The authors convincingly demonstrate that overexpression of the dacA-ybbR operon results in increased production of c-di-AMP and early expression of the transitionary gene hctA and late gene omcB. Whilst the authors have attempted to revise the submission, the model currently proposed is not fully supported by the data presented.

eLife Assessment

This important study presents a new framework (ASBAR) that combines open-source toolboxes for pose estimation and behavior recognition to automate the process of categorizing behaviors in wild apes from video data. The authors present compelling evidence that this pipeline can categorize simple wild ape behaviors from out-of-context video at a similar level of accuracy as previous models, while simultaneously vastly reducing the size of the model. The study's results should be of particular interest to primatologists and other behavioral biologists working with natural populations.

eLife Assessment

The authors present a useful agent-based model to study the tensile force generated by myosin mini-filaments in actin systems (bundles and networks); by numerically solving a mechanical model of myosin-II filaments, the authors provide insights into how the geometry of the molecular components and their elastic responses determine the force production. This work is of interest to biophysicists (in particular theoreticians) investigating force generation of motor molecules from a biomechanical engineering and physics perspective. The authors convincingly show that cooperative effects between multiple myosin filaments can enhance the total force generated, but not the efficiency of force generation (force per myosin) if passive cross-linkers are present. This work would benefit from a more extensive discussion of the physiological relevance of the results in view of the existing experimental literature, and how the principles that govern the behavior could be different for different motor proteins.

eLife Assessment

This useful study examines excitation/inhibition (E/I) balance in the CA3-CA1 circuit of the hippocampus. Experimental and computational modeling results are presented, but these results provide incomplete evidence to support the paper's main claims due to shortcomings in the experimental and modeling approaches, as well as concerns about the neurobiological relevance of the results.

eLife Assessment

This valuable study provides evidence that the integration of the nuclear envelope into the endoplasmic reticulum provides a mechanism for mechanical integration across this continuous membrane system. If robustly demonstrated, this work would open up new avenues for studying organelle membrane tension homeostasis. While the evidence is largely convincing and carefully quantified, a key limitation is the absence of data demonstrating that microinjection of cytoskeleton-depolymerizing drugs locally disrupts the target network.

eLife Assessment

This important study presents a meta-analysis confirming a statistically significant association between slow oscillation-spindle coupling and memory formation, although the reported effects are limited (~0.5% of variance). The evidence is overall convincing, but the statistical methods may be difficult to follow for readers unfamiliar with advanced techniques. This work will be of particular interest to neuroscientists studying the neural mechanisms of sleep and memory.

eLife Assessment

This well-designed study combining psychophysical and fMRI data presents a valuable finding regarding how adaptation alters spatial frequency processing in the cortex. The evidence supporting the claims of the authors is solid, although inclusion of more participants and better quality of the fMRI data would have strengthened the study. The study will be of interest to cognitive and perceptual neuroscientists working on human and non-human primates.

eLife Assessment

This work presents potentially important findings suggesting that a combination of transcranial stimulation approaches applied for a short period could improve memory performance. However, the evidence supporting the conclusions is currently incomplete. In particular, the claims relating to the specific neural mechanisms and anatomical sites of action underlying effects were viewed as overstated in the current version. The results potentially have implications for non-invasive enhancement of cognitive functions.

eLife Assessment

This useful study employs optogenetics, genetically-encoded dopamine and serotonin sensors, and patch-clamp electrophysiology to investigate modulations of neurotransmitter release between striatal dopamine and serotonin neurons - a topic of interest to neuroscientists studying the basal ganglia. The results suggest that the dopamine and serotonin systems operate largely in parallel, with the activation of serotonin neurons resulting in a small, transient dopamine release. The authors suggest that this interaction occurs via glutamate release in the ventral tegmental area, findings that are closely related to previous work. Some conclusions are incomplete requiring larger samples-sizes and controls.

eLife Assessment

This valuable paper introduces the Dyadic Interaction Platform, an experimental setup that enables researchers to study real-time social interactions between two participants in a controlled environment while maintaining direct face-to-face visibility. The evidence supporting the platform's effectiveness is convincing, with demonstrations of distinct experimental paradigms showing how transparency and continuous access to partners' actions can influence strategic coordination, decision-making, and learning. The work will be of broad interest to researchers studying social cognition across humans and non-human primates, providing a versatile tool that bridges the gap between naturalistic social interactions and controlled laboratory experiments.