eLife Assessment
This important study significantly advances our understanding of the skeleton of cartilaginous fishes by using a range of state of the art and complementary approaches to compare the skeleton amongst three cartilagenous fishes (catshark, little skate and ratfish). The evidence presented is compelling and likely to impact several fields of study.
eLife Assessment
This study presents significant and novel insights into the roles of zinc in mammalian meiosis/fertilization events. These findings are useful to our understanding of these processes. The evidence presented is solid, with experiments being well-designed, carefully described, and interpreted with appropriate rigor. The main limitation of lack of mechanistic insight needs to be acknowledged.
If we’re not careful, learning algorithms will generalize based on the majority culture, leading to a high error rate for minority groups. Attempting to avoid this by making the model more complex runs into a different problem: overfitting to the training data, that is, picking up patterns that arise due to random noise rather than true differences. One way to avoid this is to explicitly model the differences between groups, although there are both technical and ethical challenges associated with this.
Challenging to address high error rate for minority groups
machine learning might perform worse for some groups than others is sample size disparity. If we construct our training set by sampling uniformly from the training data, then by definition we’ll have fewer data points about minorities. Of course, machine learning works better when there’s more data, so it will work less well for members of minority groups, assuming that members of the majority and minority groups are systematically different in terms of the prediction task.
minorities under-represented in data used for training leads to performance issues
Absent specific intervention, machine learning will extract stereotypes, including incorrect and harmful ones, in the same way that it extracts knowledge.
ML emphasizes societal stereotypes.
it’s important to understand when observed disparities can be considered to be discrimination.
disparities -> discrimination
younger defendants are statistically more likely to re-offend, judges are loath to take this into account in deciding sentence lengths, viewing younger defendants as less morally culpable.
Important example of using experience and intuition over data
But there are serious risks in learning from examples. Learning is not a process of simply committing examples to memory. Instead, it involves generalizing from examples: honing in on those details that are characteristic of (say) cats in general, not just the specific cats that happen to appear in the examples. This is the process of induction: drawing general rules from specific examples—rules that effectively account for past cases, but also apply to future, as yet unseen cases, too. The hope is that we’ll figure out how future cases are likely to be similar to past cases, even if they are not exactly the same.
flaws in only relying on examples.
We cannot hand code a program that exhaustively enumerates all the relevant factors that allow us to recognize objects from every possible perspective or in all their potential visual configurations.
The need for "learning" over "branching"
In many head-to-head comparisons on fixed tasks, data-driven decisions are more accurate than those based on intuition or expertise.
Data-driven decisions triumph over intuition or experience. However, intuition and experience plays an important role in addressing or resolving unusual (outlier) situations.
eLife Assessment
This study presents valuable findings on the ability of a state-of-the-art method – temporally delayed linear modelling (TDLM) – to detect the replay of sequences in human memory. The investigation provides convincing evidence that TDLM has limitations in its sensitivity to detect replay when being applied to extended (minutes-long) rest periods, though a more thorough treatment of the relationship to prior positive findings would make the demonstration even stronger. The work will be of particular interest to researchers investigating memory reactivation in humans, especially using iEEG, MEG, and EEG.
eLife Assessment
In this important manuscript, Cassell and colleagues set out on a mechanistic and pharmacological exploration of an engineered chimeric small conductance calcium-activated potassium channel 2 (SK2). They show compelling evidence that the SK2 channel possesses a unique extracellular structure that modulates the conductivity of the selectivity filter, and that this structure is the target for the SK2 inhibitor apamin. The interpretations are sound and the writing is clear, and the manuscript was strengthened during review by providing more detailed information for the electrophysiological experiments and the structural analyses attempted, in addition to relating dilation of the filter to mechanisms of inactivation in other potassium channels. This high-quality study will be of interest to membrane protein structural biologists, ion channel biophysicists, and chemical biologists, and will be valuable for future drug development targeting SK channels.
eLife Assessment
This important study fills a gap in our knowledge of the evolution of GPCRs in holozoans, as well as the phylogeny of associated signaling pathway components such as G proteins, GRKs, and RIC8 proteins. The evidence supporting the conclusions is compelling, with the analysis of extensive new genomic data from choanoflagellates and other non-animal holozoans. Overall, the study is thorough and well-executed. It will be a resource for researchers interested in both the comparative genomics of multicellularity and GPCR biology more broadly, especially given the importance of GPCRs as highly druggable targets
eLife Assessment
This important study convincingly shows that Vibrio bacteria act as predators of ecologically significant algae that contribute to harmful blooms in the lab, as well as in their natural habitat. While the data strongly suggest that starvation may induce predation, further work is needed to fully establish this link. Similarly, the evidence for a social component in the predation process remains incomplete. This study will be very impactful to those interested in the diversity of microbial predator-prey interactions and controlling toxic algal bloom, but the paper could be strengthened by more clearly showing the degree of replication, by better defining the terms used to describe the observed behaviour, and by providing better support for starvation and collective behaviour.
eLife Assessment
How secretion is regulated during cell division and how membrane trafficking factors cooperate with the cytoskeleton during cell division remain poorly understood. In this work the authors find protein-protein interactions and localization dependencies between the polymeric septin cytoskeleton and the exocyst complex, using fission yeast as a model organism and using alphafold 3 based structural predictions. The work provides a valuable body of new information that will be of great interest to the cell biology community. The evidence is solid and provides the authors and the community a framework to test if the identified interfaces reflect bona fide interaction sites in vivo and in vitro in future.
eLife Assessment
In flies defective for axonal transport of mitochondria, the authors report the upregulation of one subunit, the beta subunit, of the heterotrimeric eIF2 complex via mass spectroscopy proteomics. Neuronal overexpression of eIF2β phenocopied aspects of neuronal dysfunction observed when axonal transport of mitochondria was compromised. Conversely, lowering eIF2β expression suppressed aspects of neuronal dysfunction. While these are intriguing and useful observations, technical weaknesses limit the interpretation. On balance, the evidence supporting the current claims is suggestive but incomplete, especially concerning the characterization of the eIF2 heterotrimer and the data regarding translational regulation.
eLife Assessment
This work presents important findings suggesting that a combination of transcranial stimulation approaches applied for a short period could improve memory performance. Solid methods and evidence, in line with current standards for non-invasive stimulation and recording, are included to broadly support the main findings. The results potentially have implications for non-invasive enhancement of cognitive functions.
eLife Assessment
This study presents a valuable finding that KDM5 inhibitors may enable a wide therapeutic window as compared to STING agonists or Type I Interferons. The evidence supporting the claims of the authors is convincing. The work will be of broad interest to scientists working in the field of breast cancer research.
eLife Assessment
The study showcases a significant and important enhancement of the MAGIC transgenesis method, by extending it genome-wide to all chromosomes. The authors convincingly demonstrate that the MAGIC mosaic clones can be generated for genes from all, including the 4th chromosome. With this toolkit extension, the method is now most likely set to strongly rival the classical FRT/Flp recombination system for gene manipulation in flies.
eLife Assessment
This study provides valuable insights into human valve development by integrating snRNA-seq and spatial transcriptomics to characterize cell populations and regulatory programs in the embryonic and fetal outflow tract. The methods, data, and analyses are solid overall, but with some weaknesses that can be strengthened. The findings will be of interest to those who work in the field of heart development and congenital heart disease.
eLife Assessment
This manuscript presents useful insights into the molecular basis underlying the positive cooperativity between the co-transported substrates (galactoside sugar and sodium ion) in the melibiose transporter MelB. Building on years of previous studies, this work improves on the resolution of previously published structures and reports the presence of a water molecule in the sugar binding site that would appear to be key for its recognition, introduces further structures bound to different substrates, and utilizes HDX-MS to further understand the positive cooperativity between sugar and the co-transported sodium cation. Although the experimental work is solid, the presentation of the data lacks clarity, and in particular, the HDX-MS data interpretation requires further explanation in both methodology and discussion, as well as a clearer description of the new insight that is obtained in relation to previous studies. The work will be of interest to biologists and biochemists working on cation-coupled symporters, which mediate the transport of a wide range of solutes across cell membranes.
eLife Assessment
This manuscript reports important findings that have theoretical or practical implications beyond a single subfield. However, despite the combination of numerous analytical tools established and applied in the study, the work has substantial experimental limitations leading to incomplete evidence, indicating that the conclusions may be an over-interpretation of the findings.
eLife Assessment
This fundamental study provides new insights into the plasticity mechanisms underlying the formation of spatial maps in the hippocampus. Supported by a large and comprehensive dataset, the evidence is convincing. This study will be of interest to neuroscientists focusing on spatial navigation, learning, and memory.
eLife Assessment
This manuscript describes a useful study describing an interesting infection phenotype that differs between adult male and female zebrafish. The authors argue that male-biased expression of Cyp17a2 is implicated in mediating infection levels through STING and USP8 activity regulation. Thus, this study highlights an unexpected factor involved in antiviral immunity that could open new avenues of investigation for infection, metabolism, and other contexts. Although the manuscript presents some evidence supporting its main claims, the evidence for the main argument made in the study on sex dimorphism remains incomplete at this stage.
eLife Assessment
The study by Reed et al. provides fundamental findings and convincing evidence defining the topological changes that occur during tumorigenesis. The findings enhance the understanding of stable long-range connections among genes that reprogram cancer-related functions. Nevertheless, performing additional experiments is recommended.
eLife Assessment
This study demonstrates that conditional knockout of afadin disrupts retinal laminar organization and reduces the number of photoreceptors, while preserving certain aspects of retinal ganglion cell structure and light responsiveness. The work is valuable and well-supported by revised figures and comprehensive data on retinal cell types, lamination patterns, and visual functio. The findings are solid and intriguing, and the study provides insights into the relationship between retinal lamination and neural circuit function.
eLife Assessment
This valuable study employs a formalized computational model of learning to assess memory deficits in Alzheimer's Disease with the goal of developing an early diagnosis tool. Using an established mouse model of the disease, the authors studied multiple behavioral tasks and ages with the goal of showing similarities in behavioral deficits across tasks. Using the model, the authors indicate specific deficits in memory (overgeneralization and over differentiation) in mice with the transgene for the disease. The evidence presented is solid, yet certain concerns remain regarding the interpretation of the results of the modeling.
eLife Assessment
This manuscript describes an AI-automated microscopy-based approach to characterize both bacterial and host cell responses associated with Shigella infection of epithelial cells. The methodology is compelling and should be helpful for investigators studying a variety of intracellular pathogens. The authors have acquired important findings regarding host and bacterial responses in the context of infection, which should be followed up with further mechanistic-based studies.
eLife Assessment
This study presents a computational-experimental workflow for optimizing RNA aptamers targeting SARS-CoV-2 RBD. While the integrated approach combining docking, molecular dynamics, and experimental validation shows some promise, the useful findings are limited by the extremely weak binding affinities (>100 µM KD) and restriction to a single target system. The evidence is incomplete, with experimental design issues in the antibody competition assays and a lack of specificity testing undermining confidence in the conclusions.
eLife Assessment
This study is a valuable contribution to the evidence base. However, the evidence provided is incomplete as the study results only partially support the study conclusions. Addressing the methodological and reporting issues raised by the peer reviewers and properly aligning the claim made for providing a tool for early warning with the study analysis/results would improve the study quality and usefulness of its findings.
eLife Assessment
This landmark manuscript comprehensively examines the roles of nine structural proteins in herpes simplex virus 1 (HSV-1) assembly and nuclear egress. By integrating cryo-light microscopy and soft X-ray tomography, the study presents an innovative approach to investigating viral assembly within cells. The research is thoroughly executed, yielding exceptional data that explain previously unknown functions expected to bear widespread influence. This work is of broad interest to virologists, cellular biologists, and structural biologists, offering a robust, contextually rich methodology for studying large protein complex assembly within the cellular environment, serving as an excellent starting point for high-resolution techniques.
eLife Assessment
The ratio of nuclei to cell volume is a well-controlled parameter in eukaryotic cells. This study now reports important findings that expand our understanding of the regulatory relationship between cell size and number of nuclei. The evidence supporting the conclusions is convincing obtained by applying appropriate and validated methodology in line with current state-of-the-art. The paper will be of broad interest for cell biologists and fungal biotechnologists seeking to understand mechanisms determining cell size and number of nuclei and why this knowledge might also be of importance for the production of enzymes and thus production strains not only of Aspergillus oryzae but also other industrially used fungi.
eLife Assessment
This study presents a valuable finding regarding the role of Arp2/3 and the actin nucleators N-WASP and WAVE complexes in myoblast fusion. The data presented is convincing, and the work will be of interest to biologists studying skeletal muscle stem cell biology in the context of skeletal muscle regeneration.
eLife Assessment
This computational modeling study builds on multiple previous lines of experimental and theoretical research to investigate how a single neuron can solve a nonlinear pattern classification task. The revised manuscript presents convincing evidence that the location of synapses on dendritic branches, as well as synaptic plasticity of excitatory and inhibitory synapses, influences the ability of a neuron to discriminate combinations of sensory stimuli. The ideas in this work are very interesting, presenting an important direction in the computational neuroscience field about how to harness the computational power of "active dendrites" for solving learning tasks.
eLife Assessment
This important computational study investigates homeostatic plasticity mechanisms that neurons may employ to achieve and maintain stable target activity patterns. The work extends previous analyses of calcium-dependent homeostatic mechanisms based on ion channel density by considering activity-dependent shifts in channel activation and inactivation properties that operate on faster and potentially variable timescales. The model simulations convincingly demonstrate the potential functional importance of these mechanisms.
eLife Assessment
This study presents a valuable investigation into cell-specific microstructural development in the neonatal rat brain using diffusion-weighted magnetic resonance spectroscopy. The evidence supporting the core claims is solid, with innovative in vivo data acquisition and modeling, noting residual caveats with regard to the limitations of diffusion-weighted magnetic resonance spectroscopy for strict validation of cell-type-specific metabolite compartmentation. In addition, the study provides community resources that will benefit researchers in this field. The work will be of interest to researchers studying brain development and biophysical imaging methods.
eLife Assessment
This valuable work explores how synaptic activity encodes information during memory tasks. All reviewers agree that the work is of very high quality and that the methodological approach is praiseworthy. Although the experimental data support the possibility that phospholipase diacylglycerol signaling and synaptotagmin 7 (Syt7) dynamically regulate the vesicle pool required for presynaptic release, a concern remains that the central finding of paired-pulse depression at very short intervals could be due to a mechanism that does not depend on exocytosis, such as Ca²⁺ channel inactivation, rather than vesicle pool depletion. Overall, this is a solid study although the results still warrant consideration of alternative interpretations.
eLife Assessment
This study tested the specific hypothesis that age-related changes to hearing involve a partial loss of synapse connections between sensory cells in the ear and the nerve fibers that carry information about sounds to the brain, and that this interferes with the ability to discriminate rapid temporal fluctuations in sounds. Physiological, behavioral, and histological analyses provide a powerful combination to test this hypothesis in gerbils. Contrary to previous suggestions, it was found that chemically-induced isolated synaptopathy (at similar levels as observed in aged gerbils) did not result in worse performance on a behavioral task measuring sensitivity to temporal fine-structure, nor did it produce degradations in auditory-nerve fiber encoding of fine structure. Aged gerbils showed degraded behavior and stronger than normal envelope responses, but temporal fine-structure coding was not affected; interpreted by the authors as suggesting central processing contributions to aging effects on discrimination. These findings are important for advancing our knowledge of the mechanistic bases for age-related changes to hearing, and the evidence provided is solid with the results largely supporting the claims made and minor limitations related to possible confounds discussed in reasonable depth.
eLife Assessment
This valuable study introduces a non-perturbative pulse-labeling strategy for yeast nuclear pore complexes (NPCs), employing a nanobody-based approach in order to selectively capture Nup84-containing complexes for imaging and biochemical analysis. The data convincingly demonstrate that a short induction period (20 minutes to 1 hour) yields a strong and sustained signal, enabling affinity purification that faithfully recapitulates the endogenous Nup84 interactome. This tool offers a powerful framework for investigating NPC dynamics and associated interactomes through both imaging and biochemical assays.
eLife Assessment
The authors examined the frequency of alternative splicing across prokaryotes and eukaryotes and found that the rate of alternative splicing varies with taxonomic groups and genome coding content. This solid work, based on nearly 1,500 high-quality genome assemblies, relies on a novel genome-scale metric that enables cross-species comparisons and that quantifies the extent to which coding sequences generate multiple mRNA transcripts via alternative splicing. This timely study provides an important basis for improving our general understanding of genome architecture and the evolution of life forms.
eLife Assessment
This important study examines the evolution of virulence and antibiotic resistance in Staphylococcus aureus under multiple selection pressures. The evidence presented is convincing, with rigorous data that characterizes the outcomes of the evolution experiments. However, the manuscript's primary weakness is in its presentation, as claims about the causal relationship between genotypes and phenotypes are based on correlational evidence. The manuscript needs to be revised to address these limitations, clarify the implications of the experimental design, and adjust the overall narrative to better reflect the nature of the findings.
eLife Assessment
This study reports on the development and characterization of chickens with genetic deficiencies in type I or type III interferon receptors, which is an important contribution to the field of avian immunology. The data reflecting the development of the new interferon-receptor-deficient chickens is compelling. However, the characterization of IFN biology and infection responses in these knockout chickens is somewhat incomplete and could be improved by addressing the noted weaknesses.
eLife Assessment
Non-essential amino acids such as glutamine have been known to be required for T cell general activation through sustaining basic biosynthetic processes, including nucleotide biosynthesis, ATP generation, and protein synthesis. In this important study, the authors found that extracellular asparagine (Asn) is required not only for T cells to generally refuel metabolic reprogramming, but to produce helper T cell lineage-specific cytokine, for instance, IL17. In particular, the importance of Asn in IL17 production was convincingly demonstrated in the mouse experimental autoimmune encephalomyelitei (EAE) model, mimicking human multiple sclerosis disease.
eLife Assessment
This study illustrates a valuable application of BID-seq to bacterial RNA, allowing transcriptome-wide mapping of pseudouridine modifications across various bacterial species. The evidence presented includes a mix of solid and incomplete data and analyses, and would benefit from more rigorous approaches. The work will interest a specialized audience involved in RNA biology.
eLife Assessment
This study presents valuable data suggesting that ATP-induced modulation of alveolar macrophage (AM) functions is associated with NLRP3 inflammasome activation and enhanced phagocytic capacity. While the in vivo and in vitro data reveal an interesting phenotype, the evidence provided is incomplete and does not fully support the paper's conclusions. Additional investigations would be of value in complementing the data and strengthening the interpretation of the results. This study should be of interest to immunologists and the mucosal immunity community.
eLife Assessment
This convincing study, which is based on a survey of researchers, finds that women are less likely than men to submit articles to elite journals. It also finds that there is no relation between gender and reported desk rejection. The study is an important contribution to work on gender bias in the scientific literature.
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 convincing 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
This fundamental work advances our understanding of how SP5 and SP8 promote neuromesodermal competent progenitors in murine embryos. Generally the evidence is compelling, with strong developmental genetics, transcriptomic, and genomic transcription binding surveys contributing to the strength of the data. Some of the language could be softened to avoid overinterpretation of the data, and figures and diagrams could be improved.
eLife Assessment
This work presents important information on rhythmicity of overlapping target and distractor processing and how this affects behaviour. The methods are, in general, clearly laid out and defensible, with several supplementary analyses leading to a solid base of evidence for their claims.
eLife Assessment
This fundamental work significantly advances our understanding of gravity sensing and orientation behavior in the ctenophore, an animal of major importance in understanding the evolution of nervous systems. Through comprehensive reconstruction with volumetric electron microscopy, and time-lapse imaging of cilia motion, the authors provide compelling evidence that the aboral nerve net coordinates the activity of balancer cilia. The resemblance to the ciliomotor circuit in marine annelids provides a fascinating example of how neural circuits may convergently evolve to solve common sensorimotor challenges.
eLife Assessment
This valuable work presents a novel computational framework for modeling macroscopic traveling waves in the mouse cortex by integrating open-source connectomic and transcriptomic data into a spiking network model. This approach allows the computational model to assign excitatory/inhibitory connections based on neurotransmitter profiles and extends simulations to the 3D domain. The authors present results that demonstrate how spatiotemporal dynamics such as slow oscillations (0.5-4 Hz) emerge and self-organize at the whole-brain scale. This study provides convincing initial insights into the structural basis of traveling waves at the whole-brain scale in the mouse.
eLife Assessment
This important study utilizes behavioral data and computational modeling to show that spatial properties of visual attention affect human planning. The methodology and statistical analyses are solid, though the way attention is conceptualized and modeled could be refined. The findings of this study will interest cognitive scientists studying attention, perception, and decision-making.
eLife Assessment
In this manuscript, the authors investigate the migration of human cortical interneurons under hypoxic conditions using forebrain assembloids and developing human brain tissue, and probe the underlying mechanisms. The study provides the first direct evidence that hypoxia delays interneuron migration and identifies adrenomedullin (ADM) as a potential therapeutic intervention. The findings are important, and the conclusions are convincingly supported by experimental evidence.
eLife Assessment
This study presents a valuable and rigorous molecular resource, offering subtype-specific insight into the composition of ribosome-associated protein complexes in the developing cerebral cortex. The evidence is compelling in terms of data quality and is strongly supported by the results, given the rigorous technical execution. However, the findings remain primarily descriptive, as the study lacks functional validation to support mechanistic conclusions.
eLife Assessment
This valuable model-based study seeks to mimic bat echolocation behavior and flight under conditions of high interference, such as when large numbers of bats leave their roost together. Although some of the assumptions made in the model may be questioned, the simulations convincingly suggest that the problem of acoustic jamming in these situations may be less severe than previously thought. This finding will be of broad interest to scientists working in the fields of bat biology and collective behaviour.
eLife Assessment
In this fundamental manuscript, Richter et al. present a thorough anatomical characterization of the Drosophila melanogaster larval pharyngeal sensory system, which is involved in taste-guided behaviors. This study fills a major gap in the larval sensory map, providing a compelling neuroanatomical foundation for future investigations into sensory circuits and behavior. The data presented here are of exceptional quality and will be of interest to the Drosophila neurobiology community.
eLife Assessment
This important work provides convincing evidence of the cognitive and neural mechanisms that give rise to feelings of shame and guilt, as well as their transformation into compensatory behavior. The authors combine well-designed manipulations of responsibility and harm with computational cognitive modeling and neuroimaging to provide a comprehensive account of how emotions are experienced and acted upon.
eLife Assessment
This is a useful analysis of STORM data that characterizes the clustering of active zones in retinogeniculate terminals across ages and in the absence of retinal waves. The design makes it possible to relate fixed time point structural data to a known outcome of activity-dependent remodeling. However, the evidence is incomplete, weakening the claims the authors make regarding how activity influences the clustering of these synapses. This basic criticism has not improved with revisions.
eLife Assessment
This manuscript uses modeling approaches to provide mechanistic insight into the structural and dynamic properties of enhancer-promoter interactions in Drosophila. Given the interest in this field, this is a timely approach, and the results give useful insights by providing predictions about the processivity of cohesin loop extrusion in Drosophila and concluding that the compartmental interaction strength is poised near criticality in the coil-globule phase space. The evidence provided to support some of the conclusions is, however, incomplete and would be strengthened by better considering some of the caveats in the data used to constrain the models, such as the use of "homie" genetic elements in the dynamic data. There is insufficient evidence provided for the dynamics being criticality-driven, and in addition, consideration of alternative models would further strengthen the conclusions of the manuscript.
eLife Assessment
This paper explores the role of extracellular vesicles in providing extracellular matrix signals for migration of vascular smooth muscle cells. The evidence, based on cell culture experiments and supporting imaging of human samples, is mostly convincing. The paper will be valuable for researchers investigating cell migration during vessel repair and atherogenesis.
eLife Assessment
Decron and colleagues combine common psychiatric treatments with a probabilistic reward learning task and trial-by-trial ratings of affect, confidence, and engagement. Using computational cognitive modeling, they show that, while both treatments serve to counter negative biases in affect and confidence, cognitive distancing and antidepressant medication have dissociable effects on subjective evaluations and reward-based choice behavior. This work provides convincing evidence regarding an important line of investigation into the dynamic integration of affect, cognition, and learning.
eLife Assessment
This important study describes the development and validation of an Automated Reproducible Mechano-stimulator (ARM), a tool for standardizing and automating tactile behavior experiments. The data supporting the use of the ARM system are compelling, and demonstrate that by removing experimenter effects on animals, it reduces variability in various parameters of stimulus application. Moreover, the authors demonstrate that any noise emitted from the ARM does not induce an increased stress state. Once commercially available, the ARM system has the potential to increase experimental reproducibility between laboratories in the somatosentation and pain fields.
eLife Assessment
This paper discusses the cognitive implications of potential intentional burial, wall engraving creation, and fire as light source use behaviors by relatively small-brained Homo naledi hominins. The discussion presented in the paper is valuable theoretically in its healthy questioning of prior assumptions concerning the socio-biological constraints of hominin meaning-making behavior. The discussion also contributes practically given that these behaviors have been ascribed to Homo naledi in two associated papers. Still, the strength of evidence in this contribution relies on the validity of the conclusions from the two associated papers, which remain actively questioned. The ultimate assessment of this work will vary among individual readers depending on how they view this debate, but if the conclusions from the associated papers hold up, the conclusions in the current paper can be considered solid.
eLife Assessment
This manuscript introduces a useful protein-stability-based fitness model for simulating protein evolution and unifying non-neutral models of molecular evolution with phylogenetic models. The model is applied to five viral proteins that are of structural and functional importance. While the general modelling approach is solid, and effectively preserves folding stability, the evidence for the model's predictive power remains limited, since it shows little improvement over neutral models in predicting protein evolution. The work should be of interest to researchers developing theoretical models of molecular evolution.
eLife Assessment
This work characterizes the function and localization of SLC4A1 variants associated with distal renal tubular acidosis in human patients. Cell culture and limited animal studies provide partial but incomplete support to the authors' claim that the variants disrupt normal protein degradative flux by alkalinizing the intracellular pH. The study is valuable in providing preliminary evidence for future exploration of the link between intracellular pH regulation by SLC4A1 and kidney cell function in vivo.
eLife Assessment
This study presents the important finding that lysosomal damage triggers inflammatory signaling through ubiquitination and the TAB-TAK1-IKK-NF-kB axis. The data obtained from the unbiased transcriptomic and proteomic analyses are convincing and provide invaluable information to the field. Although further experiments will be required to clarify how TAB2/3 are recruited after various types of lysosome damage, this work will be of interest to researchers in the fields of organelle biology and inflammation.
eLife Assessment
This important work describes the adaptation and evaluation of two red-shifted anion channelrhodopsins (RubyACRs) for optogenetic inhibition in Drosophila. The study provides convincing evidence for the effectiveness of RubyACRs in fly neurons, including electrophysiology, calcium imaging, and behavioral analysis. With minor revisions to address potential toxicity and compatibility with 2-photon imaging, this paper and the publicly available fly lines it describes will be resources that are of value to the neuroscience community.
eLife Assessment
This manuscript is useful as it demonstrates that Rv2577, a Fe³⁺/Zn²⁺-dependent metallophosphatase, is secreted by Mycobacterium bovis BCG and localizes to the nucleus of mammalian cells, altering transcriptional and inflammatory responses. However, the study is incomplete as it lacks activity validation in macrophage cells and with virulent Mycobacterium tuberculosis strains. It is necessary to confirm Rv2577 secretion from a virulent strain and to clarify the direct or indirect role of MmpE in modulating host pathways, together with mechanistic insight into how MmpE influences lysosomal biogenesis and trafficking.
eLife Assessment
This important study applies a novel signal decomposition method to disentangle distinct signals contributing to the decision-making process, and provides convincing evidence for the operation of separate sensory encoding, attentional orienting, and ramping evidence accumulation signals. These findings are consistent with previous work, except for the absence of a motor component, which may relate to limitations of the analysis approach.
eLife Assessment
This important report describes the changing antiviral activity of IFIT1 across mammals and in response to distinct viruses, likely as a result of past arms races. One of the main strengths of the manuscript is the breadth of mammalian IFIT1 orthologs and viruses that were tested, as well as the thoroughness of the positive selection analysis. Overall the evidence is convincing, and the discussion conveys well the limitations due to physical interactions with other IFITs that are not accounted for.
eLife Assessment
In this valuable contribution, the authors present a novel and versatile probabilistic tool for classifying tracking behaviors and understanding parameters for different types of single-particle motion. The software package will be broadly applicable to single-particle tracking studies. The methodology has been convincingly tested by computational comparisons and experimental data, although the mathematical foundation for the hypothesis testing method can be further strengthened.
eLife Assessment
The paper reports valuable findings about the mechanism of regulation of the heat shock response in plants that acts as a brake to prevent hyperactivation of the stress response, which have theoretical or practical implications for a subfield. The study presented by the authors provides solid methods, data, and analysis that broadly support the claims. This report presents helpful information regarding new spliced HSFs forms in Arabidopsis that highlights key information in the understanding of heat stress and plant growth.
eLife Assessment
This manuscript reports the development and characterization of iGABASnFR2, a genetically encoded GABA sensor that demonstrates substantially improved performance compared to its predecessor, iGABASnFR1. The work is comprehensive and methodologically rigorous, combining high-throughput mutagenesis, functional screening, structural analysis, biophysical characterization, and in vivo validation. The significance of the findings is fundamental, and the supporting evidence is compelling. iGABASnFR2 represents a notable advance in GABA sensor engineering, enabling enhanced imaging of GABA transmission both in brain slices and in vivo, and constitutes a timely, technically robust addition to the molecular toolkit for neuroscience research.
eLife Assessment
This useful study characterises motor and somatosensory cortex neural activity during naturalistic eating and drinking tongue movement in nonhuman primates. The data, which include both electrophysiology and nerve block manipulations, will be of value to neuroscientists and neural engineers interested in tongue use. Although the current analyses provide a solid description of single neuron activity in these areas, both the population level analyses and the characterisation of activity changes following nerve block could be improved.
eLife Assessment
This paper performs a valuable critical reassessment of anatomical and functional data, proposing a reclassification of the mouse visual cortex in which almost all the higher visual areas are consolidated into a single area V2. However, the evidence supporting this unification is incomplete, as the key experimental observations that the model attempts to reproduce do not accurately reflect the literature. This study will likely be of interest to neuroscientists focused on the mouse visual cortex and the evolution of cortical organization.
eLife Assessment:
This study addresses valuable questions about the neural mechanisms underlying statistical learning of room acoustics, combining robust behavioral measures with non-invasive brain stimulation. The behavioral findings are strong and extend previous work in psychoacoustics, but the TMS results are modest, with methodological limitations and over-interpretation that weaken the mechanistic conclusions. The strength of evidence is therefore incomplete, and a more cautious interpretation of the stimulation findings, alongside strengthened analyses, would improve the manuscript.
eLife Assessment
This important study evaluates a model for multisensory correlation detection, focusing on the detection of correlated transients in visual and auditory stimuli. Overall, the experimental design is sound and the evidence is compelling. The synergy between the experimental and theoretical aspects of the article is strong, and the work will be of interest to both neuroscientists and psychologists working in the domain of sensory processing and perception
eLife Assessment
This study is a fundamental advance in the field of developmental biology and transcriptional regulation that demonstrates the use of hPSC-derived organoids to generate reproducible organoids to study the mechanisms that drive neural tube closure. The work is exceptional in its development of tools to use CRISPR interference to screen for genes that regulate morphogenesis in human PSC organoids. The additional characterization of the role of specific transcription factors in neural tube formation is solid. The work provides both technical advances and new knowledge on human development through embryo models.
eLife Assessment
This useful manuscript reports mechanisms behind the increase in fecundity in response to sub-lethal doses of pesticides in the crop pest, the brown plant hopper. The authors hypothesize that the pesticide works by inducing the JH titer, which through the JH signaling pathway induces egg development, for which the evidence was judged to be solid.
eLife assessment
This is a useful study that applies deep transfer learning to assign patient-level disease attributes to single cells of T2D and non-diabetic patients, including obese patients. This analysis identified a single cluster of T2D-associated β-cells; and two subpopulations of obese- β-cells derived from either non-diabetic or T2D donors. The findings were validated at the protein level using immunohistochemistry on islets derived from non-diabetic and T2D organ donors, contributing solid experimental evidence for the computational analyses.
eLife Assessment
This is an important study that takes a key step towards understanding developmental disorders linked to mutations in the O-GlcNAc transferase enzyme by generating a mouse model harboring the C921Y mutation. The study thoroughly examines behavioral and anatomical differences in these mice and finds behavioral hyperactivity and learning/memory deficits, as well as phenotypic differences in skull and brain formation. However, the experimental evidence is incomplete owing to discrepancy in OGT protein/RNA levels in the C921Y mutant mice in this paper and the previous paper ("Neurodevelopmental defects in a mouse model of O-GlcNAc transferase intellectual disability "). This line of research will benefit from investigation of the differences in associated glycoproteins and mechanistic insights. This study will be of interest to those studying neurodevelopment, learning and behavior, or associated brain mechanisms.
eLife Assessment
This useful study uses fiber photometry, implantable lenses, and optogenetics to show that a subset of subthalamic nucleus neurons is active during movement, and that active but not passive avoidance depends in part on STN projections to substantia nigra. The strength of the evidence for these claims is solid, whereas evidence supporting the claims that STN is involved in cautious responding or the speed of avoidance is incomplete. This paper will be of interest to basic and applied behavioural neuroscientists working on avoidance if suitably streamlined to support the strongest claims.
eLife Assessment
This study demonstrates the potential role of 17α-estradiol in modulating neuronal gene expression in the aged hypothalamus of male rats, identifying key pathways and neuron subtypes affected by the drug. While the findings are useful and provide a foundation for future research, the strength of supporting evidence is incomplete due to the lack of female comparison, a young male control group, unclear link to 17α-estradiol lifespan extension in rats, and insufficient analysis of glial cells and cellular stress in CRH neurons.
eLife Assessment
This is a well-done study that provides compelling data from a diverse set of approaches from single cell transcriptome data and network analysis from genetically diverse mouse cells to identify novel driver genes underlying human GWAS associations. The authors present solid evidence that network analysis of scRNA-seq data from genetically diverse mouse bone-marrow derived stromal cells can be informative for identifying human BMD GWAS driver genes. Their approach should be broadly useful and applicable to other GWAS studies.
eLife Assessment
This manuscript introduces a potentially valuable large-scale fMRI dataset pairing vision and language, and employs rigorous decoding analyses to investigate how the brain represents visual, linguistic, and imagined content. The current manuscript blurs the line between a resource paper and a theoretical contribution, and the evidence for truly modality-agnostic representations remains incomplete at this stage. Clarifying the conceptual aims and strengthening both the dataset technicality and the quantitative analyses would improve the manuscript's significance for the fields of cognitive neuroscience and multimodal AI.
eLife Assessment
This study provides new important insights concerning pathogen variant-specific reproduction parameters from molecular sequencing and case finding. The methods for inferring which variants will likely emerge in subsequent epidemic cycles are solid. This article is of broad interest to infectious disease epidemiology researchers and mathematical modellers of the COVID-19 pandemic.
eLife Assessment
This study provides an important extension of credibility-based learning research with a well-controlled paradigm by showing how feedback reliability can distort reward-learning biases in a disinformation-like bandit task. The strength of evidence is convincing for the core effects reported (greater learning from credible feedback; robust computational accounts, parameter recovery) but incomplete for the specific claims about heightened positivity bias at low credibility, which depend on a single dataset, metric choices (absolute vs relative), and potential perseveration or cueing confounds. Limitations concerning external validity and task-induced cognitive load, and the use of relatively simple Bayesian comparators, suggest that incorporating richer active-inference/HGF benchmarks and designs that dissociate positivity bias from choice history would further strengthen this paper.
eLife Assessment
This valuable study combined careful computational modeling, a large patient sample, and replication in an independent general population sample to provide a computational account of a difference in risk-taking between people who have attempted suicide and those who have not. It is proposed that this difference reflects a general change in the approach to risky (high-reward) options and a lower emotional response to certain rewards. Evidence for the specificity of the effect to suicide, however, is incomplete, which would require additional analyses.
eLife Assessment
This study presents a valuable finding on the molecular mechanisms that govern GABAergic inhibitory synapse function. The authors propose that Endophilin A1 serves as a novel regulator of GABAergic synapses by acting as a component of the inhibitory postsynaptic density. The findings are convincing and likely to interest a broad audience of scientists focusing on inhibitory synaptic transmission, the excitation-inhibition balance, and its disruption in disorders such as epilepsy.
Editors Assessment:
This paper presents present the genome sequencing of the house sparrow (Passer domesticus) carrying out genome assembly and annotation using in silico approaches with tools that could be a valuable resource for understanding passerine evolution, biology, ethnology, geography, and demography. The final genome assembly was generated using short read sequencing and a computational workflow that included Shovill, SPAdes, MaSuRCA, and BUSCO benchmarking. Producing a 922 MB reference genome with 24,152 genes. The first draft was significantly smaller than this but peer review provided suggestions on how to improve the assembly quality. And after a few attempts and assembly with a reasonable size and BUSCO score was achieved. This openly available data potentially serving as a valuable resource for checking adaptation, divergence, and speciation of birds.
This evaluation refers to version 2 of the preprint
eLife Assessment
This paper presents an important theoretical exploration of how a flexible protein domain with multiple DNA binding sites may simultaneously provide stability to the DNA-bound state and enables exploration of the DNA strand. The authors propose a mechanism ("octopusing") for protein doing a random walk while bound to DNA which simultaneously enables exploration of the DNA strand and enhances the stability of the bound state. This study presents compelling evidence that their findings has implications for the way intrinsically disordered regions (IDR) of transcription factors proteins (TF) can enhance their ability to efficiently find their binding site on the DNA from which they exert control over the transcription of their target gene. The paper concludes with a comparison of model predictions with experimental data which gives further support to the proposed model.
eLife Assessment
This is an important study that examines the impact of Streptococcus pneumoniae genetics on its in vitro growth kinetics, aiming to identify potential targets for vaccines and therapeutics. The study identified significant variations in growth characteristics among capsular serotypes and lineages, linked to phylogeny and high heritability, but genome-wide association studies did not reveal specific genomic loci associated with growth features independent of the genetic background. The evidence supporting these findings is convincing.
eLife Assessment
This important study describes newly identified light-gated ion channel homologs (channelrhodopsins, ChRs) in several protist species, with a primary focus on the biophysical characterization of ChRs of ancyromonads. The authors employed a powerful combination of bioinformatics, manual and automated patch-clamp electrophysiology, absorption spectroscopy, and flash photolysis. Additionally, they evaluated the applicability of the newly discovered anion-conducting ChRs in cortical neurons of mouse brain slices and in living C. elegans worms. The evidence supporting most of the claims is compelling, and this work will be of interest to the microbial rhodopsin community and neuro- and cardioscientists utilizing optogenetics in their research.
eLife Assessment:
In this revised version, the authors provide a thorough investigation of the interaction of megakaryocytes (MK) with their associated extracellular matrix (ECM) during maturation; they provide compelling evidence that the existence of a dense cage-like pericellular structure containing laminin γ1 and α4 and collagen IV is key to fixing the perisinusoidal localization of MK and preventing their premature intravasation. Adhesion of MK to this ECM cage is dependent on integrin beta1 and beta3 expressed by MK. This strong conclusion is based on the use of state-of-the art techniques such f primary murine bone marrow MK cultures, mice lacking ECM receptors, namely integrin beta1 and beta3 null mice, as well as high-resolution 2D and 3D imaging. The study provides valuable insight into the role of cell-matrix interactions in MK maturation and provides an interesting model with practical implications for the fields of hemostasis and thrombosis.
eLife Assessment
This study provides new and interesting findings that SCoR2 acts as a denitrosylase to control cardioprotective metabolic reprogramming and prevent injury following ischemia/reperfusion. The compelling evidence is supported by a novel multi-omics approach, but questions remain regarding the stability and human relevance of BDH1 as well as the sufficiency of SCoR2. Overall, the work will be of interest to cardiovascular researchers and provides useful information to the field, though some mechanistic aspects require further clarification.
eLife Assessment
This paper is important in demonstrating a requirement for sulfation in organizing apical extracellular matrix (aECM) during tubulogenesis in Drosophila melanogaster. The authors identify and characterize the organization of some of the first known components of the non-chitinous aECM in the Drosophila salivary gland tube, and these findings are supported by convincing data. This study would be of interest to developmental and cell biologists.
[Editors' note: this paper was reviewed by Review Commons.]
eLife Assessment
This valuable study concerns a highly interesting and biologically relevant topic, the regulation of the PIN auxin transporter, which is of broad interest to the plant biology community. The authors propose NPY1 to act downstream of PID in auxin-mediated development by modulating PIN phosphorylation, which, if experimentally solidified, would expand our understanding of PIN regulation. While the genetic evidence is solid, the mechanistic role of NPY1 and the functional relevance of phosphorylated PIN residues are still uncertain. There are also concerns regarding experimental rigor and methodological transparency.
eLife Assessment
This useful paper examined the mechanism of planar cell polarity (PCP) using Drosophila pupal wing, investigating how 'cellular level', 'molecular level' and 'tissue level' mechanisms intersect to establish PCP. This represents a progress for the field, and the conclusions are mostly backed up by solid data. Whereas the manuscript is sound overall, the reviewers found remaining concerns, which can mostly be addressed by textual clarification of the concepts used in the manuscript.
[Editors' note: this paper was reviewed by Review Commons.]
eLife Assessment
This important study investigates how signals from the nervous system can influence the response to different food sources. To demonstrate the role of specific neuronal and intestinal regulators in sensing food quality and modulating digestion, the authors present evidence through a combination of genetic screening, RNA-seq analysis, and functional studies. These findings shed light on an adaptive strategy to integrate food perception with physiological responses, with a mix of solid and convincing evidence supporting the work.
eLife Assessment
In this valuable manuscript, Rao and colleagues investigate the UFD-1/NPL-4 complex, which is involved in extracting misfolded proteins in the plasma membrane and the accumulation of pathogenic bacteria in the intestine. Using convincing methods, the authors find that knockdown of the ufd-1 and npl-4 genes leads to shortened lifespan of the nematode C. elegans and reduced accumulation of the bacterial pathogen P. aeruginosa in the intestine.
eLife Assessment
The identification of RBMX2 as a novel regulator linking mycobacterial infection to Epithelial-Mesenchymal Transition and cancer progression are fundamental findings that advance our understanding of a major research question about the link between infectious and non-infectious diseases, microbiology and oncology. It does so by introducing RBMX2 as a novel host factor, a potential therapeutic target and biomarker for both TB and lung cancer. The evidence provided is convincing because it is appropriate and the validated multi-omics methodologies used are in line with the current state of the art. This study will be of interest to scientists working in the fields of drug discovery, microbiology and oncology.
eLife Assessment
The article presents important findings describing the role of IL27 in maintaining HSCs at steady state, and in emergency haematopoiesis in response to T. goodii by limiting the inflammatory monocyte outcomes. The evidence provided are solid and support that IL27 acts at the level of HSCs and not downstream. This study will be of interest to immunologists and hematologists, as well as infectious disease researchers.
eLife Assessment
This important study describes the effect of beta-glucan innate training of macrophages and its effect on uptake of tumour cells and on the production of inflammatory cytokines. The data are convincing and show decreased phagocytic activity of apoptotic tumour cells accompanied by lower levels of secreted IL-1β, and in vivo findings are also provided in the revision. This finding has potential impact on designing potential macrophage-targeted cancer immuno-therapeutic approaches.
eLife Assessment
The manuscript provides important findings on how striatal projection neurons regulate spontaneous locomotion speed in the context of implicit motivation and distinct contextual valence. The manuscript presented convincing supporting evidence for the findings. This work will be of broad interest to neuroscientists in the fields of basal ganglia, movement control, and cognition.
eLife Assessment
In this manuscript, Park et al. developed a multiplexed CRISPR construct to genetically ablate the GABA transporter GAT3 in the mouse visual cortex, with effects on population-level neuronal activity. This work is important, as it sheds light on how GAT3 controls the processing of visual information. The findings are compelling, leveraging state-of-the-art gene CRISPR/Cas9, in vivo two-photon laser scanning microscopy, and advanced statistical modeling.
eLife Assessment
This important study presents a cross-species and cross-disciplinary analysis of cortical folding. The authors use a combination of physical gel models, computational simulations, and morphometric analysis, extending prior work in human brain development to macaques and ferrets. The findings support the hypothesis that mechanical forces driven by differential growth can account for major aspects of gyrification. The evidence presented, though limited in certain species-specific and parametric details, is overall strong and convincingly supports the central claims; the findings will be of broad interest in developmental neuroscience.
eLife Assessment
This valuable study introduces a novel experimental and modeling framework to quantify passive joint torques in Drosophila, revealing that passive forces are insufficient to support body weight, contrary to prior assumptions based on larger insects. The approach is technically impressive, combining genetic silencing, kinematic tracking, and biomechanical modeling. However, the strength of evidence is incomplete, limited by concerns about the specificity of the genetic tools, simplifications in the mechanical model, and limited functional interpretation.
eLife Assessment
This important study characterises the morphogenesis of cortical folding in the ferret and human cerebral cortex using complementary physical and computational modelling. Notably, these approaches are applied to charting, in the ferret model, known abnormalities of cortical folding in humans. The study finds that variation in cortical thickness and expansion account for deviations in morphology, and supports these findings using cutting-edge approaches from both physical gel models and numerical simulations. The strength of evidence is convincing, and although it could benefit from more quantitative assessment, the study will be of broad interest to the field of developmental neuroscience.
eLife Assessment
This is an important study reporting a new phenotype for a gene cluster that has previously been associated with the responses of the Gram-negative opportunistic pathogen Pseudomonas aeruginosa to flow fluid. Expression of the froABCD gene cluster is induced by HOCl in vitro and by activated immune cells, which produce these types of reactive chlorine species. Overall, the evidence presented by the authors is solid; however, the mechanism of fro-induction by HOCl remains unclear, and the evidence in support of the authors' claims is descriptive, which needs to be improved. This study is of interest to infection biologists interested in mechanisms of bacterial pathogenicity.
eLife Assessment
This study provides valuable insights into the host's variable susceptibility to Mycobacterium tuberculosis, using a novel collection of wild-derived inbred mouse lines from diverse geographic locations, along with immunological and single-cell transcriptomic analyses. While the data are convincing, a deeper mechanistic investigation into neutrophil subset functions would have further enhanced the study. This work will interest microbiologists and immunologists in the tuberculosis field.
eLife Assessment
In this important study, the authors develop a microfluidic "Vessel-on-Chip" model to study Neisseria meningitidis interactions in an in vitro vascular system. Compelling evidence demonstrates that endothelial cell-lined channels can be colonized by N. meningitidis, triggering neutrophil recruitment with advantages over complex surgical xenograft models. This system offers potential for follow-on studies of N. meningitidis pathogenesis, though it lacks the cellular complexity of true vasculature including smooth muscle cells and pericytes.
[Editors' note: this paper was reviewed by Review Commons.]
eLife Assessment
Yabaji et al. reports a fundamental study highlighting the mechanistic connection for susceptibility to TB infection via the sst1 locus, this was shown to involve increased IFN and Myc production causing the down-regulation of anti-oxidant defence genes and chronic lipidation. Ultimately, lipid peroxidation may underlie infectivity and macrophage dysfunction. Overall, the data presented are compelling, supported by a well designed multi-omics approach and the findings will be of broad interest to researchers investigating the molecular mechanisms of TB infection.
[Editors' note: this paper was reviewed by Review Commons.]
eLife Assessment
This useful study shows that stimuli of a certain size elicit theta oscillations in V1 neurons both in spikes and local field potentials, and monkeys performing a dot detection task on these stimuli show theta rhythmicity in their response times. This replicates previous findings showing rhythmic theta activity in V4 and behaviour when stimuli are presented in the receptive field along with a surrounding flanker stimulus. However, there is incomplete evidence that rhythmicity in neural activity is related to the rhythmicity in behavior, and the mechanisms underlying these oscillations remain unclear.
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 proposed in the revised manuscript is still not fully supported by the data presented.
eLife Assessment
This valuable study revisits the effects of substitution model selection on phylogenetics by comparing reversible and non-reversible DNA substitution models. The authors provide solid evidence that 1) it can be beneficial to include non-time-reversible models in addition to general time-reversible models when inferring phylogenetic trees out of simulated viral genome sequence data sets, and that 2) non time-reversible models may fit the real data better than the reversible substitution models commonly used in phylogenetics, a finding consistent with previous work.
eLife Assessment
This useful paper presents evidence from several experimental approaches that suggest that changes in membrane potential directly affect ERK signaling to regulate cell division. This result is relevant because it supports an ion channel-independent pathway by which changes in membrane voltage can affect cell growth. The reviewers point out that while some experimental results and interpretations are compelling, the strength of evidence is still incomplete and changes to the manuscript are needed to rule out other possible interpretations of the data.
eLife Assessment
This is a fundamental study providing molecular insight into how cross-talk between histone modifications regulates the histone H3K36 methyltransferase SETD2. The manuscript contains excellent quality data, and the conclusions are convincing and justified. This work will be of interest to many biochemists working in the field of chromatin biology and epigenetics.
eLife Assessment
This study identifies novel approaches to improving transgene expression in the injured mammalian myocardium through a combination of a tissue regeneration enhancer element and engineered AAVs - specifically, a liver-detargeting capsid, AAV.cc84, and an in vivo library screen-selected AAV-IR41. The evidence is convincing, and the AAV vectors are of fundamental value to the field of cardiac gene therapy. Future research exploring how to combine the features of AAV.cc84 and AAV-IR41 could yield an even more promising vector for therapeutic use.
eLife Assessment
This important study provides a conceptual advance in our understanding of how membrane geometry modulates the balance between specific and non-specific molecular interactions, reversing multiphase morphologies in postsynaptic protein assemblies. Using a mesoscale simulation framework grounded in experimental binding affinities, the authors successfully recapitulate key experimental observations in both solution and membrane-associated systems, providing novel mechanistic insight into how spatial constraints regulate postsynaptic condensate organization. The conclusions are supported by solid strength of evidence and the findings are of broad significance for both computational and experimental biologists
eLife Assessment
Kin selection and inclusive fitness have generated significant controversy. This paper reconsiders the general form of Hamilton's rule in which benefits and costs are defined as regression coefficients, with higher-order coefficients being added to accommodate non-linear interactions. The paper is a landmark contribution to the field with compelling, systematic analysis, giving clarity to long-standing debates.
eLife Assessment
The ratio of nuclei to cell volume is a well-controlled parameter in eukaryotic cells. This study now reports important findings that expand our understanding of the regulatory relationship between cell size and number of nuclei. The evidence supporting the conclusions is convincing obtained by applying appropriate and validated methodology in line with current state-of-the-art. The paper will be of broad interest for cell biologists and fungal biotechnologists seeking to understand mechanisms determining cell size and number of nuclei and why this knowledge might also be of importance for the production of enzymes and thus production strains not only of Aspergillus oryzae but also other industrially used fungi.
eLife Assessment
This important study reports that an oncogenic population in an epithelium can either be repressed or spread, depending on the tissues. This is explained based on the differential interfacial tension hypothesis, and supported by pharmacological perturbations and numerical simulations using the vertex model. The study conveys a key message, but, as it stands, the strength of evidence is incomplete, and a more detailed analysis of the mechanistic origin of the different tensions and better comparison between experiments and simulations would strongly strengthen the message.
eLife Assessment
In this important study, the authors use computational modeling to explore how fast learning can be reconciled with the accumulation of stable memories in the olfactory bulb, where adult neurogenesis is prominent. Their model demonstrates that changes in excitability, plasticity, and susceptibility to apoptosis during the maturation of adult-born granule cells can help resolve the flexibility-stability dilemma. These compelling results provide a coherent picture of a neurogenesis-dependent learning process that is consistent with diverse experimental observations and may serve as a foundation for further experimental and computational studies.
eLife Assessment
This important work sets out to identify the neural substrates of associative fear responses in adult zebrafish. Through a compelling and innovative paradigm and analysis, the authors suggest brain regions associated with individual differences in fear memory. While several findings are well supported, aspects of the interpretation and presentation are partially incomplete, and the manuscript would benefit from adjusting key claims or including additional experiments. Nonetheless, this study showcases the strength of zebrafish for systems-level neuroscience and will be of broad interest to the neuroscience community.
eLife Assessment
This valuable study focuses on defining how the HSP70 chaperone system utilizes J-domain proteins to regulate the heat shock response-associated transcription factor HSF1. Using a combination of orthogonal techniques in yeast, this manuscript provides compelling evidence that the J-domain protein Apj1 facilitates attenuation of HSF1 transcriptional activity through a mechanism involving its dissociation from heat shock gene promoter regions. This work generates new insight into the mechanism of HSF1 transcriptional regulation and is a significant contribution of broad interest to cell biologists interested in proteostasis, chaperone networks, and stress-responsive signaling.
eLife Assessment
This important study provides compelling evidence that fever-like temperatures enhance the export of Plasmodium falciparum transmembrane proteins, including the cytoadherence protein PfEMP1 and the nutrient channel PSAC, to the red blood cell surface, thereby increasing cytoadhesion. Using rigorous and well-controlled experiments, the authors convincingly demonstrate that this effect results from accelerated protein trafficking rather than changes in protein production or parasite development. These findings significantly advance our understanding of parasite virulence mechanisms and offer insights into how febrile episodes may exacerbate malaria severity.
eLife Assessment
This study provides important insights into how the EBH domain of microtubule end-binding protein 1 (EB1) interacts with SxIP peptides derived from the MACF plus-end tracking protein. The revised manuscript includes convincing ITC and NMR experiments that clarify the role of flanking residues and address the influence of dimerization and cooperativity on binding. While some mechanistic aspects remain difficult to resolve experimentally, the data and analysis now more clearly justify the proposed "dock-and-lock" model and its interpretive value. This work will be of interest to structural biologists and biophysicists studying microtubule-associated protein interactions.
eLife Assessment
This useful study develops an individual-based model to investigate the evolution of division of labor in vertebrates, comparing the contributions of group augmentation and kin selection. The model incorporates several biologically relevant features, including age-dependent task switching and separate manipulation of relatedness and group-size benefits. However, the evidence remains inadequate to support the authors' central claim that group augmentation is the primary driver of vertebrate division of labor. Key modelling assumptions-such as floater dominance advantages, the absence of task synergy, and the narrow parameter space explored-restrict the potential for kin selection to produce division of labor, thereby limiting the generality of the conclusions.
eLife Assessment
This study introduces a novel and potentially valuable metric-phenological lag-to quantify the gap between observed and expected phenological shifts under climate warming. While the dataset is extensive and the framework is clearly defined, key assumptions (e.g., base temperature, linear forcing response) are not empirically tested, and the analysis underexplores key spatial and climatic gradients. The strength of evidence is mostly solid but would benefit from further validation and deeper analysis.
eLife Assessment
This paper presents a valuable software package, named "Virtual Brain Inference" (VBI), that enables faster and more efficient inference of parameters in dynamical system models of whole-brain activity, grounded in artificial network networks for Bayesian statistical inference. The authors have provided convincing evidence, across several case studies, for the utility and validity of the methods using simulated data from several commonly used models, but more thorough benchmarking could be used to demonstrate the practical utility of the toolkit. This work will be of interest to computational neuroscientists interested in modelling large-scale brain dynamics.
eLife Assessment
This important study identifies and partially characterises two proteins optimised for coordinated peptidoglycan degradation during two spore morphogenesis programs in the bacterium Myxococcus xanthus. The evidence supporting the conclusions is solid, although the description of the data is somewhat overstated. After some editing, the paper will be of interest to those studying peptidoglycan synthesis and reorganisation, which is a central aspect of microbial cell biology.
eLife Assessment
In this manuscript, Chen et al. used cryo-ET and in vitro reconstituted system to demonstrate that the autoinhibited form of LRRK2 can also assemble into filaments on the microtubule surface, with a new interface involving the N-terminal repeats that were disordered in the previous active-LRRK2 filament structure. The structure obtained in this study is the highest resolution of LRRK2 filaments done by subtomogram averaging, representing a major technical advance compared to the previous paper from the same group. This is an important study, especially considering the pharmacological implications of the effect of inhibitors of the protein. The strengths of the data are convincing, but the study would be considerably strengthened if the authors explored the physiological significance of the new interfaces and the incomplete decoration of microtubules described here.
eLife Assessment
This is an important study that demonstrates that blood pressure variability impairs myogenic tone and diminishes baroreceptor reflex. The study also provides evidence that blood pressure variability blunts functional hyperemia and contributes to cognitive decline. The evidence is compelling whereby the authors use appropriate and validated methodology in line with or more rigorous than the current state-of-the-art.
eLife Assessment
This study offers a valuable contribution to our understanding of the role of layer 6b cortical neurons in sleep-wake regulation, providing new insight into how this understudied neural population may regulate cortical arousal via orexin signaling. The evidence supporting these findings is solid, although somewhat constrained by limitations in the specificity of the genetic targeting strategy. Nonetheless, the work introduces new avenues for uncovering how the classical wake-promoting peptide, orexin, exerts its effects on the cortex.
eLife Assessment
In this valuable study, the authors use a cutting-edge method to perform voltage imaging of CA1 pyramidal cells in head-fixed mice running on a track while local field potentials (LFPs) were recorded in the contralateral hemisphere. The authors provide solid evidence of synchronous ensembles of CA1 pyramidal neurons that are associated with contralaterally recorded theta rhythms but not with contralaterally recorded sharp wave-ripples during exploration of a novel environment. The paper will be of interest to scientists who are interested in hippocampal neuronal coding of novel environments, particularly those with experimental questions that can benefit from this cutting-edge imaging technique.
eLife Assessment
This paper reports a valuable discovery that specific-mode electroacupuncture (EA) transiently opens the blood-brain barrier (BBB) in rats. The evidence is solid but lacks functional validation of BBB permeability changes. The work will be of interest to medical scientists working in the field of electroacupuncture and drug delivery.
eLife Assessment
This study presents valuable computational findings on the neural basis of learning new motor memories without interfering with previously learned behaviours using recurrent neural networks. The evidence supporting the claims of the authors is solid, but it would benefit from stronger and clearer links with experimental findings. This work will be of interest to computational and experimental neuroscientists working in motor learning.
eLife Assessment
This important study introduces the Life Identification Number (LIN) coding system as a powerful and versatile approach for classifying Neisseria gonorrhoeae lineages. The authors show that LIN codes capture both previously defined lineages and their relationships in a way that aligns with the species' phylogenetic structure. The compelling evidence presented, together with its integration into the PubMLST platform, underscores its strong potential to enhance epidemiological surveillance and advance our understanding of gonococcal population biology.
eLife Assessment
This study provides valuable insights into microtubule remodeling during liver-stage Plasmodium berghei development, demonstrating that deletion of the alpha-tubulin C-terminal tail impairs parasite growth in mosquitoes and abolishes infection in HeLa cells. The work is technically ambitious, employing advanced microscopy, genetic mutants, and pharmacological approaches. However, key claims are only partially supported due to incomplete evidence linking tubulin modifications to microtubule dynamics and uncertain antibody-based PTM detection.
eLife Assessment
This important work shows that fine particulate matter exposure to the lungs led to nociceptor-dependent neutrophilic inflammation. Likely macrophage-neuronal crosstalk, via release of artemin from macrophages and activation of Gfra3 on the JNC neuron, potentiated the response. The data convincingly strengthens links between pollutants, immune and neural interactions.
eLife Assessment
CCL2 is a chemokine with immune cell chemoattractant properties, and it appears to play a role in several chronic inflammatory diseases. The RNA-binding protein HuR controls the stability and translation of CCL2 mRNA. This paper presents convincing evidence that a relatively common genetic variant tied to several disease phenotypes affects the interaction between the mRNA of CCL2 and the RNA-binding protein HuR. While the experiments cannot definitively distinguish between effects on RNA transcription and stability, CCL2 is thought to be relevant for leukocyte migration in various conditions, including chronic inflammation and cancer, and the study presents important findings that may be relevant to a broad audience.
eLife Assessment
In this important study, the authors engineered and characterised novel genetically encoded calcium indicators (GECIs) and an analytical tool (CaFire) capable of reporting and quantifying various sub-synaptic events, including miniature synaptic events, with a speed and sensitivity approaching that of intracellular electrophysiological recordings. While the evidence supporting the improvements in the speed and accuracy of these tools is convincing, including additional information about key imaging parameters, the Bar8f experiments, and CaFire would strengthen the study. This work will be of interest to neurobiologists studying synaptic calcium dynamics in various model systems.
eLife Assessment
This important study describes a non-canonical role for IκBα in regulating mouse embryonic stem cell pluripotency and differentiation, independent of the classical NF-κB pathway. The conclusions are convincingly supported through orthogonal approaches and separation of function mutants. The findings add new insight into pluripotency regulation in mouse cells.
eLife Assessment
This paper reports a useful low-cost platform for studying mosquito behaviors such as flight activity, sugar feeding, and host-seeking responses over the course of several weeks, and demonstrates key applications of this platform. While the authors provide a biological proof of principle, the evidence that supports the validation of the tracking algorithm is incomplete; it lacks biological replicates, independent confirmation of the tracking algorithm, and data on mosquito survival.
eLife Assessment
This valuable work shows that subcortically-generated behaviors, like grooming, can have widespread representations in cortical activity. While the evidence is solid, additional analyses are necessary to strengthen the claims associated with outsized cortical representations of grooming onsets, as well as to address atypical grooming events. This work will be of interest to neuroscientists interested in how subcortically-generated behaviors are represented across the cortex.
eLife Assessment
This valuable study applies transcranial direct current stimulation (tCDS) to the prefrontal cortex of non-human primates during two states: (1) propofol-induced unconsciousness; and (2) wakeful performance of a fixation task. The analysis offers incomplete evidence to indicate that the effect of tDCS on brain dynamics, as recorded with functional magnetic resonance imaging, is contingent on the state of consciousness during which the stimulation is applied. The findings will be of interest to researchers interested in brain stimulation and consciousness.
eLife Assessment
This interesting study presents important information on how human cytomegalovirus (HCMV) infection disrupts the activity of the TEAD1 transcription factor, leading to widespread chromatin alterations. The strength of evidence in revised manuscript is convincing, and includes additional functional data teasing out how TEAD1-driven chromatin changes might influence HCMV replication. This work will be of interest to the virology, chromosome biology and transcriptional co-regulation fields.
eLife Assessment
This paper is important in demonstrating a requirement for sulfation in organizing apical ECM (aECM) during tubulogenesis in Drosophila melanogaster. The authors identify and characterize the organization of some of the first known components of the non-chitinous aECM in the Drosophila salivary gland tube, and these findings are supported by convincing data. This study would be of interest to developmental and cell biologists.
[Editors' note: this paper was reviewed by Review Commons.]
eLife Assessment
This valuable study combines anatomical tracing and slice physiology to examine how anterior thalamic and retrosplenial inputs converge in the presubiculum, a key region in the navigation circuit. The authors show that near-simultaneous co-activation of retrosplenial and thalamic inputs drives supra-linear presubiculum responses, revealing a potential cellular mechanism for anchoring the brain's head direction system to external visual landmarks. Their thorough experimental approach and analyses provide convincing evidence for the cellular basis of how the brain's internal compass may be anchored to the external world, laying the groundwork for future experimental testing in vivo.
eLife Assessment
This study presents a useful set of experiments to explore how a salivary protein might facilitate planthopper-transmitted rice stripe virus infection by interfering with callose deposition and if fully validated, these findings would significantly advance our understanding of tripartite virus-vector-plant interactions and could be of broad interest to plant science research. The authors provide additional data supporting protein-protein interactions and clarify the transient presence of LssaCA in plants. However, the mechanistic framework remains incomplete, particularly regarding the temporal dynamics of callose function and the sustained effect of LssaCA after virus inoculation. Evidence for the tripartite interaction's functional relevance is still limited, and several critical phenotypic and biochemical details require further substantiation.
eLife Assessment
This paper presents an analysis of demography and selection from whole-genome sequencing of 40 Faroese, with data that are useful beyond the study region. Much of the analysis is solid, but a more fine-scale analysis of demographic history could have led to more interesting findings. In addition, there are concerns about the selection analyses, given the special nature of the studied population and sampling scheme. Finally, lack of data availability limits the broader value of the paper.
eLife Assessment
This valuable study identifies and characterizes probe binding errors in a widely used commercial platform for visualizing gene activity in tissue samples, discovering that at least 21 out of 280 genes in a human breast cancer panel are not accurately detected. The authors provide convincing evidence for their findings validated against multiple independent sequencing technologies and reference datasets. Given the broad adoption of this spatial gene detection platform in biomedical research, this work provides an essential quality control resource that will improve data interpretation across numerous studies.
eLife Assessment
This valuable study reveals the pro-locomotor effects of activating a deep brain region containing diverse range of neurons in both healthy and Parkinson's disease mouse models. While the findings are solid, mechanistic insights remain limited due to the small sample size. This research is relevant to motor control researchers and offers clinical perspectives.
eLife Assessment
Bonnifet et al. present data on the expression and interacting partners of the transposable element L1 in the mammalian brain. The work includes important findings addressing the potential role of L1 in aging and neurodegenerative disease. The reviewers conclude that several aspects of the study are well done and most evidence is solid, with a noted concern related to the RNA-seq analysis.
eLife Assessment
This useful study advances our understanding of how organisms respond to chronic oxidative stress. Using the nematode C. elegans, the authors identified key neuronal signaling molecules and their receptors that are required for stress signaling and survival. The evidence supporting the conclusions is solid, with rigorous genetics, stress response analysis, and transcriptional profiling. This research will be of broad interest to neuroscientists and researchers working in the field of oxidative stress regulation.
eLife Assessment
This important work by Lesser et al provides a first and comprehensive description of Drosophila wing proprioceptors at an EM resolution. By linking peripheral neurons with information on their morphology and connectivity in the central nervous system, the authors provide new hypotheses and tools to study proprioceptive motor control of the wing in the fruit fly. The evidence and techniques supporting this work are solid, and this resource will contribute to connectome-based modeling of fly behavior.
eLife Assessment
This fundamental study identifies specific neural mechanisms through which HIF-1 signaling in ADF serotonergic neurons extends lifespan in C. elegans, revealing that downstream signaling in multiple types of neurons, as well as other neuromodulators like GABA, tyramine, and NLP-17, is required for this effect. The strength of the evidence is largely convincing, as the authors establish the necessity and causality of key neuronal components using multiple genetic tools and functional dissection in a well-validated model organism.
eLife Assessment
This study presents a valuable application of a video-text alignment deep neural network model to improve neural encoding of naturalistic stimuli in fMRI. The authors found that models based on multimodal and dynamic embedding features of audiovisual movies predicted brain responses better than models based on unimodal or static features. The evidence supporting the claims is generally solid, with clear benchmarking against baseline models. The work will be of interest to researchers in cognitive neuroscience and AI-based brain modeling.
eLife Assessment
This important Research Advance builds on the authors' previous work delineating the roles of the rodent perirhinal cortex and the basolateral amygdala in first- and second-order learning. The convincing results show that serial exposure of non-motivationally relevant stimuli influences how those stimuli are encoded within the perirhinal cortex and basolateral amygdala when paired with a shock. This manuscript will be interesting for researchers in cognitive and behavioral neuroscience.
eLife Assessment
This manuscript describes the identification and characterization of 12 specific phosphomimetic mutations in the recombinant full-length human tau protein that trigger tau to form fibrils. This fundamental study will allow in vitro mechanistic investigations. The presented evidence is convincing. This manuscript will be of interest to all scientists in the amyloid formation field.
eLife Assessment
This important work presents a stochastic branching process model of tumour-immune coevolution, incorporating stochastic antigenic mutation accumulation and escape within the cancer cell population. They then used this model to investigate how tumour-immune interactions influence tumour outcome and the summary statistics of sequencing data of bulk and single-cell sequencing of a tumour. The evidence is compelling and the work will be of interest to cancer-immune biology fields.
eLife Assessment
This important study introduces a new class of spectrally tunable, dye-based calcium sensors optimized for imaging in organelles with high calcium concentrations, such as the endoplasmic reticulum and mitochondria. The experimental evidence supporting the applicability of these sensors is convincing, with thorough validation in cultured cells and neurons. The work will be of high interest to researchers studying calcium signaling dynamics in subcellular compartments.
eLife Assessment
This study presents useful findings on the molecular mechanisms driving female-to-male sex reversal in the ricefield eel (Monopterus albus) during aging, which would be of interest to biologists studying sex determination. The manuscript describes an interesting mechanism potentially underlying sex differentiation in M. albus. However, the current data are incomplete and would benefit from more rigorous experimental approaches.
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. The evidence presented to support the conclusions drawn is convincing and alternative interpretations are considered. The work will be of broad interest to biochemists, cell and genome biologists.
eLife Assessment
This study presents DeepTX, a valuable methodological tool that integrates mechanistic stochastic models with single-cell RNA sequencing data to infer transcriptional burst kinetics at genome scale. The approach is broadly applicable and of interest to subfields such as systems biology, bioinformatics, and gene regulation. The evidence supporting the findings is solid, with appropriate validation on synthetic data and thoughtful discussion of limitations related to identifiability and model assumptions.
eLife Assessment
This study reveals that female moths use ultrasonic sounds emitted by dehydrated plants to guide their oviposition decisions. It highlights sound as an additional sensory modality in host searching, adding an important piece to the puzzle of how insects and plants interact. Through convincing experimental approaches, the authors provide insights that advance our understanding of plant-insect interactions.
eLife Assessment
IL-10 balances protective and deleterious immune functions in mice and humans, but if IL-10 also controls avian intestinal homeostasis remains unclear. Generating genetic knockouts, Meunier et al. established that a complete lack of IL-10 strengthened immunity against enteric bacteria in chickens, while also aggravating infection-inflicted inflammatory tissue damage and dysbiosis upon parasite infection, but unlike mouse models, IL-10 deficiency did not provoke spontaneous colitis in chickens. The findings presented are valuable, and the strength of evidence is convincing. The observation may have implications for the livestock industry and additional studies involving genetic knockouts may further unravel conserved and distinct avian IL-10 controls.
eLife Assessment
The authors present a software (TEKRABber) to analyze how expression of transposable elements (TEs) and TE silencing factors KRAB zinc finger (KRAB-ZNF) genes are correlated in experimentally validated datasets. TEKRABber is used to reconstruct regulatory networks of KRAB-ZNFs and TEs during human brain evolution and in Alzheimer's disease. The direction of the work is important, with potentially significant interest from others looking for a tool for correlative gene expression analysis across individual genomes and species. However, the reviews identified biases and shortcomings in the pipeline that could lead to an unacceptable number of false positive and negative signals and thus impact the conclusions, leaving the work in its current form incomplete.
eLife Assessment
This study provides valuable insights into the evolutionary conservation of sex determination mechanisms in ants by identifying a candidate sex-determining region in a parthenogenetic species. The strength of evidence is solid, using well-executed genomic analyses to identify differences in heterozygosity between females and diploid males, though not yet functional validation of the candidate locus.
eLife Assessment
Axon growth is essential to formation of neural connections. This manuscript presents a useful presentation of a new method for assessing the adhesion strength of axons with the use of a laser-induced shock wave. However, the strength of the evidence is incomplete as critical controls for calibration and time course are lacking.
eLife Assessment
Davies et al. present a valuable study proposing that Shot can act as a molecular linker between microtubules and actin during dendrite pruning, suggesting an intriguing role in non-centrosomal microtubule organization. However, the experimental evidence is incomplete and does not robustly support these claims, and the lack of a cohesive model connecting the findings weakens the overall impact. While the data suggest that Shot, actin, and microtubule nucleation contribute to dendritic pruning, their precise interplay remains unresolved.
eLife Assessment
In this useful study, the authors conducted a set of computational and experimental investigations of the mechanism of cholesterol transport in the smoothened (SMO) protein. The computational component integrated multiple state-of-the-art approaches such as adaptive sampling, free energy simulations, and Markov state modeling, providing support for the proposed mechanistic model, which is also consistent with the experimental mutagenesis data. However, substantial revisions are needed for the discussion of the computational results and interpretation of the literature to provide a more balanced and accurate perspective on cholesterol-mediated SMO regulation. In the current form, therefore, the strength of evidence of the study is considered incomplete.
eLife Assessment
This study is valuable for understanding how dysfunctional mitochondria contribute to vascular diseases by investigating the influence of Miro1 on smooth muscle cell proliferation and neointima development. The solid findings collectively indicate that Miro1 regulates mitochondrial cristae architecture and the efficiency of the respiratory chain. Nevertheless, the analysis would benefit from a more thorough assessment of the relationship between Miro1-dependent mitochondrial defects and vascular smooth muscle cell proliferation.
eLife Assessment
This study reports a dynamic association/dissociation between malate dehydrogenase (MDH1) and citrate synthase (CIT1) in Saccharomyces cerevisiae under different metabolic conditions that control TCA pathway flux rate. The research question is timely, the use of the NanoBiT split-luciferase system to monitor protein-protein interactions is innovative, and the significance of the findings is valuable. However, the strength of evidence needed to support the conclusions was found to be incomplete based on a lack of critical control and mechanistic experiments.
eLife Assessment
This useful study analyzed 335 Mycobacterium tuberculosis Complex genomes and found that MTBC has a closed pangenome with few accessory genes. The research provides solid evidence for gene presence-absence patterns which support the appending conclusions however, the main criticism regarding the dominance of genome reduction remains.
eLife Assessment
The authors investigate mechanisms of acquired resistance (AR) to KRAS-G12C inhibitors (sotorasib) in non-small cell lung cancer, proposing that resistance arises from signaling rewiring rather than additional mutations. While the study addresses a valuable clinical question, it is limited by several weaknesses in experimental rigor, data interpretation, and presentation, meaning the strength of evidence is incomplete
eLife Assessment
This important work substantially advances our understanding of how accessory olfactory bulb neurons respond to social odor cues across the estrous cycle, showing that responses vary with the strain and sex of the odor source but display no consistent differences between estrous and non-estrous states. It employs a unique electrophysiology preparation that activates the vomeronasal organ pump via electric stimulation, enabling precise recordings of accessory olfactory bulb cell responses to different chemosignals in anesthetized mice. Overall, the study presents convincing findings on the stability and variability of accessory olfactory bulb response patterns, indicating that while accessory olfactory bulb detects social signals, it does not appear to interpret them based on reproductive state. This work will be of interest to those studying olfaction, social behavior, reproductive cycles, and systems neuroscience more broadly.
eLife Assessment
The study presents a valuable resource of proline hydroxylation proteins for molecular biology studies in oxygen-sensing and cell signaling with the characterization of Repo-man proline hydroxylation site. The evidence supporting the claim of the authors is solid, although further clarification of the overall efficiency of the HILIC analysis, the specificity/sensitivity of immonium ion analysis, as well as quantification of proline hydroxylation identifications will be helpful. The work will be of interest to researchers studying post-translational modification, oxygen sensing, and cell signaling.
eLife Assessment
This valuable study advances our understanding of how bactofilin cytoskeletal proteins associate with cell membranes by identifying and characterizing a conserved membrane-targeting sequence. The evidence is solid, with a well-integrated combination of mutagenesis, biophysical analysis, molecular simulations, and bioinformatics supporting the mechanistic model. The work will be of particular interest to microbiologists and structural biologists studying bacterial cytoskeletons and membrane-protein interactions.
eLife Assessment
This manuscript offers valuable structural and mechanistic insights into the structure and assembly of the Type II internal ribosome entry site (IRES) from encephalomyocarditis virus (EMCV) and the translation initiation complex, revealing a direct interaction between the IRES and the 40S ribosomal subunit. While a solid cryo-EM method was used, enhancing the overall resolution or adding complementary biochemical data would further improve the clarity and impact of this study. This manuscript will attract researchers in cap-independent translation, host-pathogen interactions, and virology.
eLife Assessment
This valuable investigation provides new and solid evidence for a specific cognitive deficit in cerebellar degeneration patients. The authors use three tasks that modulate complexity and violations of cognitive expectations. They show specific slowing of reaction times in the presence of violations but not with task complexity. While some alternative interpretations of the results are possible and are discussed, the work provides a new, invaluable data point in describing the cognitive contribution of cerebellar processing.
eLife Assessment
This study provides fundamental insights into eukaryotic phosphate homeostasis by demonstrating how yeast vacuoles dynamically regulate cytosolic phosphate levels. The conclusions are convincing, supported by an elegant combination of in vitro assays and in vivo measurements. This study will be of interest to cell biologists, particularly for those who are working in the field of phosphate metabolism.
eLife Assessment
This important study suggests that adolescent mice exhibit less accuracy than adult mice in a sound discrimination task when the sound frequencies are very similar. The evidence supporting this observation is solid and suggests that it arises from cognitive control differences between adolescent and adult mice. The adolescent period is largely understudied, despite its contribution to shaping the adult brain, which makes this study interesting for a broad range of neuroscientists.
eLife Assessment
This study presents a valuable finding on the representational structure of task encoding in the prefrontal cortex. The evidence supporting the claims of the authors is solid, representing an impressive data collection effort and best-practice fMRI analyses. However, at least including visual regions as a control and controlling for behavioral differences in the task in representation analyses would have strengthened the study. The work will be of interest to cognitive neuroscientists interested in the neural basis of cognitive control.
eLife Assessment
The study introduces new tools for measuring the intracellular calcium concentration close to transmitter release sites, which may be relevant for synaptic vesicle fusion and replenishment. This approach yields important new information about the spatial and temporal profile of calcium concentrations near the site of entry at the plasma membrane. This experimental work is complemented by a coherent, open-source, computational model that successfully describes changes in calcium domains. The conclusions are solid and well supported by the data.
eLife Assessment
This useful study presents a hierarchical computational model that integrates locomotion, navigation, and learning in Drosophila larvae. The evidence supporting the model is solid, as it qualitatively replicates empirical behavioral data, but the experimental data is incomplete. While some simplifications in neuromechanical representation and sensory-motor integration are limiting factors, the study could be of use to researchers interested in computational modeling of biological movement and adaptive behavior.
eLife Assessment
NeuroSC is an accessible and interactive tool for streamlined observation of neuronal morphology, membrane contact, and synaptic connectivity across developmental stages in the nematode C. elegans. This important tool relies on solid electron microscopy datasets. This resource will be of high interest to C. elegans researchers interested in nervous system wiring and circuit function.
eLife Assessment
This valuable study reports convincing evidence about associations between 35 polygenic indices (PGIs) for social, behavioral, and psychological traits, along with some non-fatal health conditions (e.g., BMI) and all-cause mortality in data from Finnish population-based surveys and a twin cohort linked with administrative registers. PGIs for education, depression, alcohol use, smoking, BMI, and self-rated health showed the strongest associations with all-cause mortality, on the order of ~10% increment in risk per PGI standard deviation. Effect sizes from twin-difference analyses tended to be slightly larger than the effect sizes from population cohorts, opposite the pattern generally observed when testing PGI associations with their target phenotypes and supporting robustness of findings to confounding by population stratification.
eLife Assessment
In this valuable study, the authors developed long-term imaging tools to simultaneously monitor the temporal and spatial dynamics of excitatory and inhibitory synapses and reported that excitatory and inhibitory synapses need to develop synergistically during synaptogenesis to maintain balance. While the analysis and quantification of the imaging data are incomplete, there is convincing evidence that the developed tools are feasible. If these tools can function stably in vivo, their applications will be much broader.
eLife Assessment
This paper presents valuable findings on the processing of sound mixtures in the auditory cortex of ferrets, a species widely used for studies of auditory processing. Using the convenient and relatively high-resolution method of functional ultrasound imaging, the authors provide convincing evidence that background noise invariance emerges across the auditory cortical processing hierarchy. They also draw informative comparisons with previously published fMRI data obtained in humans. This work will be of interest to researchers studying the auditory cortex and the neural mechanisms underlying auditory scene analysis and hearing in noise.
eLife Assessment
This study presents experiments suggesting intriguing mesoscale reorganization of functional connectivity across distributed cortical and subcortical circuits during learning. The approach is technically impressive and the results are potentially of valuable significance. However, in its current form, the strength of evidence is incomplete. More in-depth analyses and the acquisition of data from additional animals in the primary experiment could bolster these findings.
eLife Assessment
This valuable study characterises receptors for calcitonin-related peptides from a deuterostomian animal, the echinoderm Apostichopus japonicus, by a combination of heterologous expression, pharmacological experiments, and the quantification of gene-expression levels. The authors provide solid evidence for a functional calcitonin-related peptide system in the sea cucumber, but further work will be needed to confirm the proposed phylogenetic relationships and physiological functions of PDF receptor system in this species. This work should be of interest to scientists studying the signaling pathways, functions, and evolution of neuropeptides, and could be of relevance to improving the culture conditions of this economically key species.
eLife Assessment
This fundamental study examines infection of the liver and hepatocytes during tuberculosis infection. The authors convincingly demonstrate that aerosol infection of mice and guinea pigs leads to appreciable infection of the liver as well as the lung. A further strength of the study lies in clinical evaluation of the presence of tuberculosis bacteria in human autopsied liver samples from individuals with miliary tuberculosis and the presence of a clear granuloma-like structure, which will prompt further study.
eLife Assessment
This study presents an important finding on the role of GATA4 in aging- and OA-associated cartilage pathology. The conclusions are well supported by compelling in vitro and in vivo evidence. This work will be of broad interest to both cell biologists and orthopedic clinicians.
eLife Assessment
This important study shows that retinal bipolar cell subtype-specific differences in the size of synaptic ribbon-associated vesicle pools contribute to the transient versus sustained kinetics of the responses of retinal ganglion cells. The data are extensive and compelling. This work will be of broad interest to researchers working on synaptic transmission, retinal signal processing, and sensory neurobiology.
eLife Assessment
This important study reports the conservation of sperm-egg envelope binding by demonstrating successful recognition of the micropyle in fish eggs by mouse sperm. The evidence supporting the conclusions drawn is convincing. This study will be of interest to reproductive biologists and clinicians studying the biology of fertilization and fertility.
eLife Assessment
The article presents important findings on the impact of climate change on odonates, integrating phenological and range shifts to broaden our understanding of biodiversity change. The study leverages extensive natural history data, offering a convincing analysis of temporal trends in phenology and range limit and their potential drivers.
eLife Assessment
This study is a valuable contribution to the field of neuronal modeling by way of providing a method for rapidly obtaining neuronal physiology parameters from electrophysiological recordings. The method is solid as the generated models reproduce both ground-truth simulated data and empirical data, and there is now a quantitative comparison with other approaches.
eLife Assessment
This valuable study investigates the implementation of an efference copy mechanism in the visual flight control system of Drosophila, a topic of broad interest to sensorimotor neuroscientists. Although the behavioral data and computational analyses are each individually solid, there is limited quantitative evaluation of how the model predictions compare to the experimental data.
eLife Assessment
This valuable study reports evidence that items maintained in working memory can bias attention in an oscillatory manner, with the attentional capture effect fluctuating at theta frequency. The study provides incomplete evidence that this dynamic attentional bias is associated with oscillatory neural mechanisms, particularly in the alpha and theta bands, as measured by EEG. The study will be relevant for researchers studying attention, working memory, and neural oscillations, particularly those interested in how memory and perception interact over time.