9,040 Matching Annotations
  1. Jan 2025
    1. eLife Assessment

      This valuable study proposes that protein secreted by colon cancer cells induces cells with Paneth-like properties that favor colon cancer metastasis. The evidence supporting the conclusions is strong but would benefit from more direct experiments to test the functional role of Paneth-like cells and to monitor metastasis from colon tumors. The work will be of interest to researchers studying colon cancer metastasis.

    1. eLife Assessment

      The ingenious design in this study achieved the observation of 3D cell spheroids from an additional lateral view and gained more comprehensive information than the traditional one angle of imaging. This extended the methods to investigate cell behaviors in the growth or migration of tumor organoids in a time-lapse manner and these extensions should be important to the field. The authors provide compelling evidence that the methods work as described.

    1. eLife Assessment

      This useful work reveals differential activity to food and shock outcomes in central amygdala GABAergic neurons. Evidence supports claims of unconditioned stimulus activity that changes with learning. Compelling evidence that the circular shift method rigorously identifies functional neuron types is also presented. However, the evidence regarding claims related to valence or salience signaling in these neurons is incomplete. This work will be of interest to neuroscientists studying sensory processing and learning in the amygdala.

    1. eLife Assessment

      This is a valuable report of a spatially-extended model to study the complex interactions between immune cells, fibroblasts, and cancer cells, providing insights into how fibroblast activation can influence tumor progression. The model opens up new possibilities for studying fibroblast-driven effects in diverse settings, which is crucial for understanding potential tumor microenvironment manipulations that could enhance immunotherapy efficacy. While the results presented are convincing and follow logically from the model's assumptions, some of these assumptions, as acknowledged by the authors, may oversimplify certain aspects in light of complex experimental findings, system geometry, and general principles of active matter research. Nonetheless, the authors provide justification for their work as a meaningful step towards more comprehensive modeling approaches.

    1. eLife Assessment

      In this manuscript, the authors describe the creation of a transgenic mouse expressing a reporter for Integrated Stress Response (ISR) activation in a CRE-dependent manner. Reliable tools for detecting ISR activation in situ are lacking, so this manuscript describes a potentially valuable tool that builds on and overcomes some of the limitations of a similar viral vector described by the authors in a previous publication. Solid evidence suggests that distinct populations of cells (ChAT) in the nervous system are marked by some level of ISR activation, and that the mouse could be most helpful as a screen for cell types in which the ISR is particularly active, although it would be difficult to draw conclusions from the reporter alone. Additional validations of the reporter activity in situ will further strengthen the manuscript.

    1. eLife Assessment

      This is an important study that reports the mechanism by which Ankle2 (LEM4 in humans) interacts with and recruits PP2A and the ER protein Vap33 to promote BAF dephosphorylation and mediate nuclear membrane reformation, using Drosophila as their model. Using Ankle2 mutants, they find that the ER protein Vap33 is key for the normal interphase localisation of Ankle2/LEM4 and also impacts on the function of Ankle2/LEM4 during mitosis. The conclusions on the subcellular localization of Ankle2 are drawn from overexpression of constructs. Overall, the authors use a variety of complementary techniques and provide convincing evidence to support the claims and advance our knowledge in the field of mitosis and nuclear envelope biology.

    1. eLife Assessment

      This study proposes a new model that could solve some long-standing puzzles about inversion polymorphisms in Drosophila melanogaster by invoking sexually antagonism and negative frequency-dependent selection. While the idea developed here is a valuable contribution to the field, the experiment only addresses one element of the hypothesis, so that the empirical evidence in support of the model remains incomplete.

    1. eLife Assessment

      This valuable work provides novel insights into the substrate binding mechanism of a tripartite ATP-independent periplasmic (TRAP) transporter, which may be helpful for the development of specific inhibitors. The structural analysis is convincing, but additional work will be required to establish the transport mechanism as well as well as binding sites for all ligands. This study will be of interest to the membrane transport and bacterial biochemistry communities.

    1. eLife assessment

      The article has important scientific merit in the field of cardiovascular research and other fields where the design and rigor of scientific experiments is key for translation of preclinical research to clinical studies. This study holds convincing evidence that sheds light on the lack of progress in this area over the past decade, despite a substantial body of existing research. Although there is a need to re-evaluate the statistical test used, the descriptive paper outcomes serves as a strong call to action for the wider scientific community.

    1. eLife Assessment

      This valuable work presents an interesting strategy to interfere with the HBV infectious cycle as it identifies two previously unexplored HBc-Ag binding pockets. The experimental data is compelling and opens the door to generating and testing novel anti-HBV therapies.

    1. eLife Assessment

      In this manuscript, the authors describe a new AlphaFold2 pipeline called PabFold that can represent a useful tool for identifying linear antibody epitopes (B-cell epitopes) for different antigens. This information can be used in the selection of different reagents in competitive ELISA assays which can save time and reduce costs. Because several questions about the work remain, the study is currently incomplete.

    1. eLife Assessment

      The objective of this important study is to assess the study design and rigor, enhance the quality of clinical research studies, and emphasize crucial design elements in basic science research. It specifically tackles the ongoing problem of experimental design deficiencies that obstruct the effective translation of research findings into clinical applications. This paper is particularly convincing as it highlights the lack of progress in addressing these issues over the past decade, despite a substantial body of existing research. It serves as a strong call to action for the broader scientific community to improve research practices.

    1. eLife Assessment

      This is a valuable study that generates an inventory of accessible genomic regions bound by a transcription factor ZFHX3 within the suprachiasmatic nucleus in the hypothalamus and details the impact of its depletion on daily rhythms in behaviour and gene expression patterns. Analysis using circadian phase-estimation algorithms makes the argument that gene regulatory networks are at play and changes in gene expression of a few clock genes cannot account for the observed animal behaviour. While the transcriptome analysis is solid, the data do not currently support the mechanism of activity of the TF in rhythmic gene expression.

    1. eLife Assessment

      This study answers an essential question about how migratory primordial germ cells mobilize based on their anterior or posterior location. Convincing data support the model that interactions of migrating mouse PGCs with their niches influences their proliferation, cytoskeletal regulation, epigenetic state and pluripotent state. Rigorous methodology and analysis of single-cell RNA sequencing of migratory primordial germ cells and surrounding somatic cells result in datasets which will be valuable to developmental biologists.

    1. eLife Assessment

      This useful manuscript provides a newly curated database (termed AACDB) of antibody-antigens structural information, alongside annotations that are either taken and from the PDB, or added de-novo. Sequences, structures, and annotations can be easily downloaded from the AACDB website, speeding up the development of structure-based algorithms and analysis pipelines to characterize antibody-antigen interactions. The methodology presented for this data curation is solid, although some key annotations are missing which would greatly improve the database.

    1. eLife Assessment

      Mackie and colleagues present a valuable comparison of lateralized gustation in two well-studied nematodes. The evidence they present that ASEL/R lateralization exists and is achieved by different means in P. pacificus compared to C. elegans is solid, but would be strengthened by the inclusion of calcium imaging data for C. elegans and additional verification of P. pacificus AFD neuron identity. This work will be of interest to evolutionary biologists, ecologists, and sensory neurobiologists interested in how small nervous systems make sense of the environment, and how evolution can take multiple paths to asymmetry within a neuron class.

    1. eLife Assessment

      This valuable paper describes the regulatory pathway of rRNA synthesis by Meioc-Piwil1 in germ cell differentiation in zebrafish. Using the molecular genetic and cytological approaches, the authors provide convincing evidence that Meioc antagonizes Piwil1, which downregulates the 45S pre-rRNA synthesis by heterochromatin formation for spermatocyte differentiation. The key results are solid and of use to researchers in the field of germ cell/meiosis as well as RNA biosynthesis and chromatin.

    1. ­eLife Assessment

      The authors examine the role of Numb, a Notch inhibitor, in intestinal stem cell self-renewal in Drosophila during homeostasis and regeneration. This is an important study providing evidence of a Numb-mediated, back-up mechanism for intestinal stem cell maintenance. The strength of evidence is convincing as the authors present a carefully constructed series of experiments, robust genetics, large sample sizes, and appropriate statistical analyses.

    1. eLife Assessment

      This is a useful study that seeks to address the role of the TET family of DNA demethylation enzymes in pancreatic beta cell senescence in the context of type 2 diabetes (T2DM). Although the concepts are novel and of interest, the study presents incomplete evidence to fully support its main conclusions.

    1. eLife Assessment

      Building on earlier evidence that Topoisomerase 2 depletion can extend yeast lifespan, the authors present convincing data demonstrating that reduced Top2 levels confer significant longevity benefits in C. elegans and mice. They show that these benefits encompass not only extended survival but also improved healthspan and mitigation of aging phenotypes, supported by robust transcriptomic, epigenetic, and histological analyses. While the exact mechanistic underpinnings-such as the potential connection to classical aging pathways and the selective down-regulation of genes with active promoters-remain to be fully elucidated, the breadth of these important findings strongly indicates a conserved role for Top2 in aging regulation.

    1. eLife Assessment

      This study offers a valuable treatment of how the population of excitatory and inhibitory neurons integrates principles of energy efficiency in their coding strategies. The convincing analysis provides a comprehensive characterisation of the model, highlighting the structured connectivity between excitatory and inhibitory neurons. The role of the many free parameters are discussed and studied in depth.

    1. eLife Assessment

      This is a useful study depicting the ultrastructural features of layer 1 of the human temporal cortex, the authors assess various synaptic parameters, astrocytic coverage, and mitochondrial morphology. High-quality data were collected using a solid methodology, however, the analysis of the functional vesicle pools is incomplete, technical issues remaining related to the identification of astrocytic processes and the measurement of vesicle diameters, and reliance solely on electron microscopy limits the scope of the work to structural observation. The work will be of interest to neuroscientists and computational researchers investigating cortical and network function.

    1. eLife Assessment

      This valuable study uses high-field fMRI to test the hypothesized involvement of subcortical structures, particularly the striatum, in updating working memory. The study overcomes limitations of prior work by applying high-field imaging with a more precise definition of regions of interest in the brain. Thus, the empirical observations are of use to specialists interested in working memory gating or the reference back task specifically. The evidence is generally solid, but strong conclusions on dopaminergic contributions must await additional work using molecular imaging or related techniques.

    1. eLife Assessment

      This important study successfully applies an innovative chemogenetic tool to investigate cerebellar function to advance our understanding of the contributions of Purkinje cell populations to postural control in larval zebrafish. The evidence supporting the conclusions is convincing and supported by rigorous statistical analysis. The study highlights the power of combining genetically targeted perturbations with quantitative high-throughput behavioral analysis and original microscopy tools.

    1. eLife Assessment

      This important study provides convincing evidence that developing neurons in the neocortex regulate glial cell development. The data demonstrates that the transcription factor FOXG1 negatively regulates gliogenesis by controlling the expression of a member of the FGF ligand family and by suppressing the receptor for this ligand in developing neurons. This study leads to a new understanding of the cascade of events regulating the timing of glial development in the neocortex.

    1. eLife Assessment

      The work by Han and collaborators describes valuable findings on the role of Akkermansia muciniphila during ETEC infection. If confirmed, these findings will add to a growing list of beneficial properties of this organism. The strength of the evidence used to justify the conclusions in the manuscript is solid, as the analyses broadly support the claims with only minor weaknesses.

    1. 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 fine-structure. Further, altered neural coding of rapid fluctuations produced no perceptual deficits in either these gerbils or in aged gerbils. These findings are important for understanding age-related changes to hearing; however, the evidence provided is incomplete due to problems in interpretation and the discussion of possible confounds and/or limitations of these data that currently limits mechanistic insight.

    1. eLife Assessment

      This valuable study shows that a very slow (infraslow) oscillation occurs in voltage recordings from the dentate gyrus of the adult mouse. The authors suggest that it is related to sleep stage and serotonin acting at one type of serotonin receptor in the dentate gyrus. The ideas are potentially significant because they suggest that this oscillation affects memory through serotonin receptors in the dentate gyrus. Solid evidence is provided to broadly support the main claims, although analytical weaknesses remain that could be improved by clarification of methods, analyses, and data shown in the figures.

    1. eLife Assessment

      This important study introduces a new cortical circuit model for predictive processing. Simulations effectively illustrate that, with appropriate synaptic plasticity, a canonical layer 2/3 cortical circuit - comprising two classes of interneurons providing subtractive and divisive inhibition - can generate uncertainty-modulated prediction errors by pyramidal neurons. The model is compelling; although it relies on many assumptions and has not yet been compared directly to data, the model does align with empirical observations and yields a range of testable predictions. The study is expected to be of great interest to those involved in cortical and predictive processing research.

    1. eLife Assessment

      This valuable study reports the induction of supernumerary inner hair cells in the mouse cochlea upon reducing the expression level of a tight-junction protein (claudin-9) at developmental stages. Although these ectopic hair cells are functional and persists through adulthood, the evidence supporting some of the claims is incomplete, particularly regarding the underlying mechanisms of cell differentiation and the potential of the approach for hair-cell regeneration. The work will be of interest to scientists working in the development and regeneration of hair cells in the inner ear.

    1. eLife Assessment

      What makes one member of the species behave differently from another? This is a core problem in behavioral neuroscience. This valuable study seeks an answer for the specific case of the fruit fly expressing preferences for one odor over another. By a combination of behavioral measurements, neurophysiology, and network modeling, the authors find solid evidence for at least one locus of individuality in the peripheral olfactory system.

    1. eLife Assessment

      The study evaluates the feasibility, safety, and tolerability of neoadjuvant radiotherapy followed by a CDK4/6 inhibitor (dalpiciclib) and hormonal therapy in treatment-naive patients with unilateral early-stage HR+/HER2- breast cancer. The findings are convincing, with a strong scientific rationale supported by integrated correlative studies. The trial is considered to be important as the outcomes could inform the design of larger, future studies. The strength of the conclusions should be tempered as the study included only a small cohort of patients (n=12) and was not adequately powered to definitively assess the efficacy or safety of this combinatorial treatment approach.

    1. eLife Assessment

      This valuable study uses zebrafish as a model to reveal a role for the cell cycle protein kinase CDK2 as a negative regulator of type I interferon signaling. The evidence supporting the authors' claims is convincing, including both in vivo and in vitro investigative approaches that corroborate a role for CDK2 in regulating TBK1 degradation. In this latest version, the authors included data addressing concerns raised by the reviewers at the first peer review round that strengthens the conclusions. This work will interest cell biologists, immunologists, and virologists.

    1. eLife Assessment

      In this important work, Lodhiya et al. provide evidence that excessive ATP underlies the killing of the model organism Mycobacterium smegmatis by two mechanistically-distinct antibiotics. The data are generally solid as the authors deploy multiple, orthogonal readouts and methods for manipulating reactive oxygen species and ATP. The work will be of interest to those studying antibiotic mechanisms of action.

    1. eLife Assessment

      This fundamental work extends our understanding of the role of TGFβ2 as a modulator of mechanosensing in the eye and identifies the TRPV4 ion channel as a common regulator of Trabecular Meshwork (TM) contractility and pathological OHT. The data and evidence are convincing, with some minor limitations. This work will clearly be of interest to researchers investigating the role of mechanosensors in the TM and may underpin future research into treatments that aim to lower intra ocular pressure. This work will additionally be of interest to the growing field of researchers investigating the regulation of force sensing via ion channels and their roles in health and disease, in particular the ion channel TRPV4.

    1. eLife Assessment

      The findings are important and intriguing, with theoretical or practical implications beyond a single subfield. The computational methods employed are clever and sophisticated and the strength of evidence is convincing. However, all three reviewers also highlight a lack of focus and clarity, as well as missing information about model comparison, fit statistics and group comparison of parameters from different models.

    1. eLife Assessment

      This valuable study tests a methodology for the discovery of new honey bee-repellent odorants via machine learning. The conclusions of the study are supported by solid evidence, with predicted compounds validated in the lab and the field. This work will be of interest to researchers in ecology, pest control and olfactory neuroscience.

    1. eLife Assessment

      This is a fundamental body of work reporting anatomical, molecular, and functional mapping of the central complex in Drosophila. The tools generated and the findings, which include characterization of neuromodulators used by different cells, will undoubtedly serve as a foundation for future studies of this brain region. Overall, the data are compelling and likely to have a major impact.

    1. eLife Assessment

      This important study investigates how hummingbird hawkmoths integrate stimuli from across their visual field to guide flight behavior. Cue conflict experiments provide solid evidence for an integration hierarchy within the visual field: hawkmoths prioritize the avoidance of dorsal visual stimuli, potentially to avoid crashing into foliage, while they use ventrolateral optic flow to guide flight control. With a more systematic quantification of specific parameter combinations, this paper would be of broad interest to enthusiasts of visual neuroscience and ethology.

    1. eLife Assessment

      This important Research Advance presents convincing evidence on the neuroprotective effects of reserpine in a well-established model of retinitis pigmentosa (P23H-1). This study builds on previous work establishing reserpine as a neuroprotectant in models of Leber congenital amaurosis. Here authors show reserpine's disease gene-independent influence on photoreceptor survival and emphasizes the importance of considering biological sex in understanding inherited retinal degeneration and the impact of drug treatments on mutant retinas. The work will be of interest to vision researchers as well as a broad audience in translational research.

    1. eLife Assessment

      This valuable study addresses the growing threat of multi-drug-resistant (MDR) pathogens by focusing on the enhanced efficacy of colistin when combined with artesunate and EDTA against colistin-resistant Salmonella strains. The evidence is solid, supported by comprehensive microbiological assays, molecular analyses, and in vivo experiments demonstrating the effectiveness of this synergic combination.

    1. eLife Assessment

      This study provides important insights into how IL-1 cytokines protect cells against SARS-CoV-2 infection. By inducing a non-canonical RhoA/ROCK signaling pathway, IL-1beta inhibits the ability of SARS-CoV-2 infected cells to fuse with uninfected cells and produce syncytia. Convincing evidence underlies the identification of the key signaling components required for this inhibitory phenotype, and suggests that this process may also function to inhibit SARS-CoV-2 infection in vivo.

    1. eLife Assessment

      This fundamental study demonstrates the role of TRPV4 channels in mechano-transduction during carcinoma progression, showing how high cell confluence in DCIS cells activates pathways regulating calcium homeostasis, cell volume reduction, and invasiveness. The authors addressed all prior concerns, with the shRNA knockdown providing compelling evidence for TRPV4's role in metastasis.

    1. eLife Assessment

      In an important fMRI study with an elegant experimental design and rigorous cross-decoding analyses, this work shows a convincing dissociation between two parietal regions in visually processing actions. Specifically, aIPL is found to be sensitive to the causal effects of observed actions, while SPL is sensitive to the patterns of body motion involved in those actions. The work will be of broad interest to cognitive neuroscientists, particularly vision and action researchers.

    1. eLife Assessment

      Wang et al. presented visual (dot) motion and/or the sound of a walking person and found solid evidence that EEG activity tracks the step rhythm, as well as the gait (2-step cycle) rhythm, with some demonstration that the gait rhythm is tracked superadditively (power for A+V condition is higher than the sum of the A-only and V-only condition). The valuable findings will be of wide interest to those examining biological motion perception and oscillatory processes more broadly. Some of the theoretical interpretations concerning entrainment must remain speculative when the authors cannot dissociate evoked responses from entrained oscillatory effects.

    1. eLife Assessment

      This study empirically investigates the neural noise hypothesis of developmental dyslexia using electroencephalography (EEG) during a spoken language task and 7T magnetic resonance spectroscopy (MRS). The convincing findings indicate no evidence of an imbalance between excitatory and inhibitory (E/I) brain activity in adolescents and young adults with dyslexia compared to controls, thereby challenging the neural noise hypothesis. This research is valuable for advancing our understanding of the neural mechanisms underlying dyslexia and offers broader insights into the neural processes involved in reading development.

    1. eLife Assessment

      In this valuable study, the authors studied a novel Zn2+- and NAD+-independent KDAC protein, AhCobQ, in Aeromonas hydrophila, which lacks homology with eukaryotic counterparts, thus underscoring its unique evolutionary trajectory within the bacterial domain. They attempt to demonstrate deacetylase activity, however, whilst the revised manuscript has been improved, significant aspects of the data are still incomplete and require further refinement. The work will be of interest to microbiologists studying metabolism and post-translational modifications.

    1. eLife Assessment

      This work shows that newborn Thbs4-positive astrocytes generated in the adult subventricular zone (SVZ) respond to middle carotid artery occlusion (MCAO) by secreting hyaluronan at the lesion penumbra, and that hyaluronin is a chemoattractant to SVZ astrocytes. These findings are valuable, despite being mostly descriptive, as they point to a relevant function of SVZ newborn astrocytes in the modulation of the glial scar after brain ischemia. The methods, data and analyses are convincing and broadly support the claims made by the authors with only some weaknesses.

    1. eLife Assessment

      This valuable study decoded target-associated information in prefrontal and sensory cortex during the preparatory period of a visual search task, suggesting a memory-driven attentional template. The evidence supporting this claim is convincing, based on multivariate pattern analyses of fMRI data. The results will be of interest to psychologists and cognitive neuroscientists.

    1. eLife Assessment

      MGPfactXMBD is a novel computational method for investigating cell evolutionary trajectory for scRNA-seq samples. It is important, with several potential future applications. The authors benchmarked this method using synthetic and real-world samples and showed superior performance for some of the tasks in cell trajectory analysis compared to other methods with compelling evidence.

    1. eLife Assessment

      This study uses all-optical electrophysiology methods to provide a valuable insight into the organization of cortical networks and their ability to balance the activity of groups of neurons with similar functional tuning. The all-optical approach used in this study is impressive, but the claim that the effects of optical stimulation correspond to a specific homeostatic mechanism are incompletely supported by the statistical analysis of the results. The work will be of interest to neurobiologists and to developers of optical approaches for interrogating brain function.

    1. eLife Assessment

      This important study enhances our understanding of Pseudomonas aeruginosa's transcriptional regulatory network by revealing its hierarchical structure through analysis of transcription factor binding patterns. The conclusions are supported by compelling evidence and will appeal to researchers investigating P. aeruginosa and the regulatory mechanisms underlying its pathogenicity. The paper would be strengthened by clarifying implications of binding and regulatory networks with virulence, and transcription factor divergence across species.

    1. eLife Assessment

      This important study uses machine learning-based network analysis on transcriptomic data from different tissue cell types to identify a small set of conserved (pan-tissue) genes associated with changes in cell mechanics. The new method, which provides a new type of approach for mechanobiology, is accessible, compelling, and well-validated using in silico and experimental approaches. The study provides motivation for researchers to test hypotheses concerning the identified five-gene network, and the method will be strengthened over time with expanded sets of validations, such as testing genes with hitherto unknown roles and different perturbation techniques.

    1. eLife Assessment

      This study addresses a novel and interesting question about how the rise of the Qinghai-Tibet Plateau influenced patterns of bird migration, employing a multi-faceted approach that combines species distribution data with environmental modeling. The findings are valuable for understanding avian migration within a subfield, but the strength of evidence is incomplete due to critical methodological assumptions about historical species-environment correlations, limited tracking data, and insufficient clarity in species selection criteria. Addressing these weaknesses would significantly enhance the reliability and interpretability of the results.

    1. eLife Assessment

      This study presents important findings demonstrating that FZD5 and FZD8, two of the ten Frizzled proteins, undergo Wnt-mediated endocytosis. The E3 ubiquitin ligases RNF43/ZNRF3 regulate their degradation in a Wnt-dependent manner, a mechanism that was not previously recognized. The evidence supporting the claims of the authors is solid. This research will be of interest to biologists specializing in Wnt signaling, cancer, and regenerative medicine.

    1. eLife Assessment

      This important work provides another layer of regulatory mechanism for TGF-beta signaling activity. The evidence supports the involvement of microtubules as a reservoir of Smad2/3 and additional evidence convincingly demonstrates functional involvement of Rudhira in this process. The work will be of board interest to developmental biologists in general and molecular biologists in the field of growth factor signaling.

    1. eLife Assessment

      The authors show that a middle carotid artery occlusion (MCAO) hypoxia lesion leads to hyaluronan-mediated chemoattraction to the lesion penumbra of Thbs-4-expressing astrocytes of the sub-ventricular zone (SVZ). These findings are valuable because they shed light on the function of astrocytes from the adult SVZ in pathological states like brain ischemic injury. The results are convincing, as they rely on a comprehensive analysis of experimental data.

    1. eLife Assessment

      Bowler et al. present a software/hardware system for behavioral control of navigation-based virtual reality experiments, particularly suited for pairing with 2-photon imaging but applicable to a variety of techniques. This system represents a valuable contribution to the field of behavioral and systems neuroscience, as it provides a standardized, easy to implement, and flexible system that could be adopted across multiple laboratories. The authors provide compelling evidence of the functionality of their system by reporting benchmark tests and demonstrating hippocampal activity patterns consistent with standards in the field. This work will be of interest to systems neuroscientists looking to integrate flexible head-fixed behavioral control with neural data acquisition.

    1. eLife Assessment

      Periods in which experience regulates early plasticity in sensory circuits are well established, but the mechanisms that control these critical periods are poorly understood. In this important study, the authors examine early-life critical periods that regulate the Drosophila antennal lobe and show that constant odor exposure markedly reduces the volume, synapse number, and function of a specific glomerulus. The authors offer compelling evidence that these changes are mediated by the invasion of ensheathing glia into the glomerulus where they phagocytose connections via a mechanism involving the engulfment receptor Draper.

    1. eLife Assessment

      With the goal of investigating the assembly and fragmentation of cellular aggregates, this work investigates cyanobacterial aggregates in a laboratory setting. Investigating the conditions and mechanisms behind aggregation is an important contribution as it yields basic understanding of natural processes and offers potential strategies for control. The combination of computational and experimental investigations in this manuscript provides solid support for the proposed processes for aggregation and fragmentation, with some concerns about the strength of evidence for a subset of claims.

    1. eLife Assessment

      This report details convincing evidence that experience with multilingualism in general, and with larger phonological inventories specifically, is related to differences in the structure of the transverse temporal gyri. The project is notable for using a relatively large sample, and confirming the primary finding in a second sample. The important findings strongly point to experience-dependent plasticity related to language experience as a driver of neuroanatomy of the auditory cortex.

    1. eLife Assessment

      This is an important study providing compelling evidence that the Mediator kinase module mediates an elevated inflammatory response, manifested by heightened cytokine levels, associated with Downs syndrome (DS) via transcriptional changes impacting cell signaling and metabolism that involve mobilization of nuclear receptors by altered lipid metabolites, which has significance for the treatment of DS and other chronic inflammatory conditions. Particular strengths of the study include the combined experimental approaches of transcriptomics, untargeted metabolomics and cytokine screens and the use of sibling matched cell lines (trisomy 21 vs disomy 21) from various donors. Evidence is also provided implicating the Mediator kinase module in controlling mRNA splicing and mitochondrial function that should stimulate new research to elucidate the mechanistic bases for these novel functions.

    1. eLife Assessment

      This study presents a new quantitative method, CROWN-seq, to map the cap-adjacent RNA modification N6,2'-O-dimethyladenosine (m6Am) with single nucleotide resolution. Using thoughtful controls and well-validated reagents, the authors provide compelling evidence that the method is reliable and reproducible. Additionally, the study provides important evidence that m6Am may increase transcription in modified mRNAs. However, the data only demonstrates a correlation between m6Am and transcriptional regulation rather than causality. Overall, this study is poised to advance m6Am research, being of broad interest to the RNA biology and gene regulation fields.

    1. eLife Assessment

      In this article, Cheng et al present an important finding that advances the understanding of mitochondrial stress response(s). The authors employed mass spectrometry-based methods in conjunction with standard molecular and cellular biology techniques to provide compelling evidence that phosphatidylethanolamine-binding protein 1 (PEBP1) acts as a pivotal regulator of the mitochondrial component of integrated stress response. Notwithstanding that this discovery is likely to be of significant interest to researchers across a broad spectrum of disciplines ranging from cell biology to neuroscience, it was thought that further mechanistic dissection of the role of PEBP1 in modulating integrated stress response may further strengthen this study.

    1. eLife Assessment

      This manuscript provides fundamental studies to gain insight into the mutations in the presenilin-1 (PSEN1) gene on proteolytic processing of the amyloid precursor protein (APP). The authors provide compelling evidence using mutations in PSEN to understand what drives alternative substrate turnover with convincing data and rigorous analysis. This deep mechanistic study provides a framework towards the development of small molecule inhibitors to treat AD.

    1. eLife assessment

      The identification of NCS1 as a distal appendage protein that captures preciliary vesicles has important implications for understanding the early steps of ciliary assembly. Furthermore, the work has important implications for the broader understanding of NCS1, which prior to this work was focused on roles in neurotransmission, but now must be considered in a broader context. The investigators used a variety of state-of-the-art methodologies, and the conclusions are convincingly supported by the experimental data. This work will be of interest to cell biologists studying ciliary assembly, human geneticists exploring the pathology of cilia as well as neurobiologists studying NCS1.

    1. eLife Assessment

      This fundamental work substantially advances our understanding of how the glycocalyx of cells provide a non-specific barrier for the interaction of viruses with cell-surface receptors. Using both in vitro experiments and in vivo manipulations they provide solid evidence for the properties of the glycocalyx to serve as an energy barrier as a main attribute of its mode of action. The work will be of broad interest to virologists and the cell biology community that studies host-pathogen interactions.

    1. eLife Assessment

      This manuscript reports valuable findings on the role of the Srs2 protein in turning off the DNA damage signaling response initiated by Mec1 (human ATR) kinase. The data provide solid evidence that Srs2 interaction with PCNA and ensuing SUMO modification is required for checkpoint downregulation. However, while the model that Srs2 acts at gaps after camptothecin-induced DNA damage is reasonable, direct experimental evidence for this is currently lacking. The work will be of interest to cell biologists studying genome integrity.

    1. eLife Assessment

      This study provides useful in vitro evidence to support a mechanism whereby dyslipidemia could accelerate renal functional decline through the activation of the AT1R/LOX1 complex by oxLDL and AngII. As such, it improves the knowledge regarding the complex interplay between dyslipidemia and renal disease and provides a solid basis for the discovery of novel therapeutic strategies for patients with lipid disorders. The methods, data, and analyses partly support the presented findings, although the observed variability and need for further in vivo validation require additional research in this key area.

    1. eLife assessment

      This fundamental work describes for the first time the combined gene expression and chromatin structure at the genome level in isolated chondrocytes and classical (cranial) and non-classical (notochordal) osteoblasts. In a compelling analysis of RNA-Seq and ATAC data, the authors characterize the two osteoblast populations relative to their associated chondrocyte cells and further proceed with a convincing analysis of the crucial entpd5a gene regulatory elements by investigating their respective transcriptional activity and specificity in developing zebrafish.

    1. eLife Assessment

      Graca et al. reports a fundamental missing link in the ethanol metabolism of mycobacteria and illuminates the role of a flavoprotein dehydrogenase that acts as an electron shuttle between an uncommon redox cofactor and the electron transport chain. Overall, the data presented are compelling, supported by a range of well designed and meticulous experiments. The findings will be of broad interest to researchers investigating bacterial metabolism.

    1. eLife Assessment

      In this valuable study, Roiuk et al employed a combination of ribosome profiling and reporter assays to provide convincing evidence that eIF2A is not involved in translational regulation in cultured human cells. In conjunction with several recent publications (spanning yeast to mammalian systems), these findings disaffirm the previously proposed role of eIF2A in directing protein synthesis, including its implication in translational reprogramming under stress. Whilst clearly delinating something eIF2A does not do, identifying cellular role(s) for eIF2A could further strengthen this article.

    1. eLife Assessment

      Notch1 is expressed uniformly throughout the mouse endocardium during the initial stages of heart valve formation, yet it remains unclear how Notch signaling is activated specifically in the AVC region to induce valve formation. To answer this question, the authors used a combination of in vivo and ex vivo experiments in mice to demonstrate ligand-independent activation of Notch1 by circulation induced-mechanical stress and provide evidence for stimulation of a novel mechanotransduction pathway involving post-translational modification of mTORC2 and Protein Kinase C (PKC) upstream of Notch1. These findings represent an important advance in our understanding of valve formation and the conclusions are supported by convincing data.

    1. eLife Assessment

      This manuscript reports useful data suggesting a critical role of two cyclin-dependent kinases, CDK8 and CDK19, in spermatogenesis. However, the data supporting the conclusion remains incomplete. This work may be of interest to reproductive biologists and physicians working on male fertility.

    1. eLife Assessment

      Data presented in this useful report suggest a potentially new model for chemotaxis regulation in the gram-negative bacterium P. putida. Data supporting interactions between CheA and the copper-binding protein CsoR, reveal potential mechanisms for coordinating chemotaxis and copper resistance. There was, however, concern about the large number of CheA interactors identified in the initial screen and it was felt that the study was incomplete without a substantial number of additional experiments to test the model and bolster the authors' conclusions.

    1. eLife Assessment

      This important study identifies a new class of small molecules that activate the integrated stress response (ISR) via the kinase HRI. Convincing evidence, including the image analysis pipeline, indicates that two of these compounds promote mitochondrial elongation and protect against mitochondrial fragmentation caused by chemical stress conditions or by genetic alterations. These findings open an avenue for new strategies for mitochondrial dysfunction targeting linked to ISR alterations.

    1. eLife Assessment

      This fundamental work describes for the first time the combined gene expression and chromatin structure at the genome level in isolated chondrocytes and classical (cranial) and non-classical (notochordal) osteoblasts. In a compelling analysis of RNA-Seq and ATAC data, the authors characterize the two osteoblast populations relative to their associated chondrocyte cells and further proceed with a convincing analysis of the crucial entpd5a gene regulatory elements by investigating their respective transcriptional activity and specificity in developing zebrafish.

    1. eLife Assessment

      In this potentially important study, the authors report results of QM/MM simulations and kinetic measurements for the phosphoryl-transfer step in adenylate kinase. The results point to the mechanistic proposal that the transition state ensemble is broader in the most efficient form of the enzyme (i.e., in the presence of Mg2+ in the active site) and thus a different activation entropy. With a broad set of computations and experimental analyses, the level of evidence is considered solid by some reviewers. On the other hand, there remain limitations in the computational analyses, especially regarding free energy profiles using different methodologies (shape of free energy profiles with DFTB vs. PBE QM/MM, and barriers with steered MD and umbrella sampling) and the activation entropy, leading some reviewers to the evaluation that the level of evidence is incomplete.

    1. eLife Assessment

      This valuable work suggests a new physical model of centrosome maturation: a catalytic growth model with a shared enzyme pool. The authors provide compelling evidence to show that the model is able to reproduce various experimental results such as centrosome size scaling with cell size and centrosome growth curves in C. elegans, and that the final centrosome size is more robust to differences in initial centrosome size. While direct experimental support for this theory is currently lacking, the authors propose concrete experiments that could distinguish their shared-enzyme model from previously proposed alternatives.

    1. 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 solid but a higher purity of these fibril types might be required for future studies. This manuscript will be of interest to all scientists in the amyloid formation field.

    1. eLife Assessment

      Cardiolipin is known to play an important role in modulating the assembly and function of membrane proteins in bacterial and mitochondrial membranes. In this study, authors convincingly define the molecular determinants of cardiolipin binding on de novo-designed and native membrane proteins combining the coarse-grained molecular dynamics simulation with the state-of-the-art experimental approaches such as native mass spectrometry and cryogenic electron microscopy. The major findings in this study, which are the identification of degenerate cardiolipin binding motifs and their role in membrane protein stability and activity, will provide much needed insight into the still poorly understood nature of protein-cardiolipin interactions.

    1. eLife Assessment

      The bacterial cell wall is crucial to maintain viability. It has previously been suggested that Gram-positive bacteria have a periplasmic region between the cell membrane and peptidoglycan cell wall that this is maintained by the presence of teichoic acids. In this valuable study, Nguyen et al. make clever use of electron microscopy and metabolic labelling to interrogate the role of teichoic acids in supporting the maintenance of the periplasmic region in Streptococcus pneumoniae. The findings are potentially significant but incomplete to fully support the conclusions drawn.

    1. eLife Assessment

      This study estimates the fraction of apoptotic motor neurons during the development of the zebrafish spinal cord. The results are useful, but incomplete. Importantly, the data are inadequate to support the title or the conclusions presented in the abstract. A correct title could be: "A surprisingly small percentage of early developing zebrafish motor neurons die through apoptosis in non-limb innervating regions of the spinal cord."

    1. eLife Assessment

      This study presents a valuable finding on the role of secretory leukocyte protease inhibitors (SLPI) in developing Lyme disease in mice infected with Borrelia burgdorferi. The evidence supporting the claims of the authors is solid, although there are a few concerns that need to be addressed, including patient sample sizes, and the potential contribution of the greater bacterial burden to the enhanced inflammation. This paper would be of interest to scientists in the infectious inflammatory disease field.

    1. eLife Assessment

      This valuable study investigates how the proteins of the Cdv division system in Metallosphaera sedula archaea sequentially interact with curved membranes in vitro, extending our understanding of this reduced ESCRT-like machinery. While the data support key aspects of protein recruitment and membrane remodeling, missing controls and statistical analysis information, unaddressed discrepancies, and limitations in recapitulating native geometry leave the data incomplete to fully support the proposed conclusions. The work will be of interest to evolutionary and synthetic biologists as membrane biophysicists but would benefit from additional experiments and a more cautious interpretation of results.

    1. eLife Assessment

      This important study reveals a role for IκBα in the regulation of embryonic stem cell pluripotency. The solid data in mouse embryonic stem cells include separation of function mutations in IκBα to dissect its non-canonical role as a chromatin regulator and its canonical function as NF-κB inhibitor. The conclusions could be strengthened by including better markers of differentiation status and additional controls or orthogonal approaches.

    1. eLife Assessment

      This paper reports the analysis of coevolutionary patterns and dynamical information for identifying functionally relevant sites. These findings are considered important due to the broad utility of the unified framework and network analysis capable of revealing communities of key residues that go beyond the residue-pair concept. The data is solid, and the results are clearly presented.

    1. eLife Assessment

      Based on the perceived low efficacy of current therapies targeted to FGFR2 in gastric cancer (GC), the authors investigate an approach which combines SHP2 inhibition with existing FGFR2 inhibitors. The data were largely collected and analysed using solid and validated methodology. There is some useful data regarding combination therapy in a new clinical cohort, which supports previous studies that have reported the potential of targeting RTKs together with phosphatases.

    1. eLife Assessment

      In this manuscript, the authors present useful findings demonstrating that the RNA modification enzyme Mettl5 regulates sleep in Drosophila. Through transcriptome- and proteome-wide analyses, the authors identified downstream targets affected in heterozygous mutants and proposed that Mettl5 regulates the translation and degradation of clock genes to maintain normal sleep function. However, the mechanisms by which Mettl5 achieves these functions, and whether they are direct or indirect, remain incomplete and would benefit from further analysis.

    1. eLife Assessment

      This manuscript describes a method using EM polyclonal epitope mapping to help elucidate endogenous antibodies. Overall the work described is interesting and the contribution will be of use to the field that is expected to only increase in impact and value over time. The significance of the work is considered valuable and the strength of evidence to support its findings is considered solid.

    1. eLife Assessment

      This fundamental work presents two clinically relevant BMP4 mutations that contribute to vertebrate development. The convincing evidence supports that the site-specific cleavage at the BMP4 pro-domain precisely regulates its function and provides mechanistic insight into how homodimers and heterodimers behave differently. The work will be of broad interest to researchers working on growth factor signaling mechanisms and vertebrate development.

    1. eLife Assessment

      This useful study introduces the peptidisc-TPP approach as a promising solution to challenges in membrane proteomics, enabling thermal proteome profiling in a detergent-free system. While the concept is innovative and holds significant potential, the demonstration of its utility and validation remains incomplete. The method presents a strong foundation for broader applications in identifying physiologically and pharmacologically relevant membrane protein-ligand interactions.

    1. eLife Assessment

      This valuable study addresses a gap in our understanding of how the size of the attentional field is represented within the visual cortex. The evidence supporting the role of visual cortical activity is solid, based on a novel modeling analysis of fMRI data. The results will be of interest to psychologists and cognitive neuroscientists.

    1. eLife Assessment

      Understanding bacterial growth mechanisms can potentially help uncover novel drug targets that are crucial for maintaining cellular viability, particularly for bacterial pathogens. In this important study, the authors investigate the role of mycobacterial Wag31 in lipid and peptidoglycan biosynthesis. A detailed analysis of Wag31 domain architecture revealed a role in membrane tethering, more specifically, the N-terminal and C-terminal domains appear to display distinct functional roles therein. Whilst the data presented are of use, the experimental evidence is currently incomplete and does not yet fully support the conclusions made.

    1. eLife Assessment

      This valuable study combines massively parallel reporter assays and regression analysis to identify sequence features in untranslated regions contributing to the stability of in vitro transcribed mRNA delivered to cells. The strength of evidence presented is solid, although some points about half-life measurements and the relevance of identified sequence features to native transcript stability will inform future discussion surrounding the present study. Taken together, the work will be of interest to a broad swath of colleagues studying post-transcriptional gene regulation and especially to those using massively parallel reporter assays.

    1. eLife Assessment

      This important study enhances our understanding of the foraging behaviour of aerial insectivorous birds. Using solid methodology, the authors have collected extensive data on bird movements and prey availability, which in turn provide support for the main claim of the study. The work will be of broad interest to behavioural ecologists.

    1. eLife Assessment

      In this valuable study, Li et al., set out to understand the mechanisms of audiovisual temporal recalibration - the brain's ability to adjust to the latency differences that emerge due to different (distance-dependent) transduction latencies of auditory and visual signals - through psychophysical measurements and modeling. The analysis and specification of a formal model for this process provide convincing evidence to supports a role for causal inference in recalibration.

    1. eLife Assessment

      This valuable study presents the design of a new device for using high-density electrophysiological probes ('Neuropixels') in freely moving rodents. The evidence demonstrating the system's versatility and ability to record high-quality extracellular data in both mice and rats is compelling. This study will be of significant interest to neuroscientists performing chronic electrophysiological recordings.

    1. eLife Assessment

      The manuscript provides important new insights into the mechanisms of statistical learning in early human development, showing that statistical learning in neonates occurs robustly and is not limited to linguistic features but occurs across different domains. The evidence is convincing and the findings are highly relevant for researchers working in several domains, including developmental cognitive neuroscience, developmental psychology, linguistics, and speech pathology.

    1. eLife Assessment

      This study presents a valuable finding on how the interplay between transcription factors SOX2 and OCT4 establishes the pluripotency network in early mouse embryos. The evidence supporting the claims of the authors is solid, although inclusion of additional omics data would further strengthen the study. The work will be of interest to biologists working on embryonic development and gene regulation.

    1. eLife Assessment

      This analysis of the formation of the oral-aboral body axis in cnidarians, the sister group of bilaterians, is a significant and fundamental contribution to the field of Wnt signalling and planar cell polarity. The evidence supporting the conclusions is compelling and has the potential to contribute to a deeper understanding of the origin and evolution of Wnt signalling in metazoans. These findings will be of broad interest to developmental and evolutionary biologists.

    1. eLife assessment

      This important and detailed study presents the most comprehensive view of the functional organization and requirements for a mother centriole's distal appendage in primary cilia assembly published to date. Crispr-knockouts and super-resolution microscopy analysis of the distal appendage proteins provides convincing evidence to support the claims of the authors. This work will be of high value to cell biologists and biophysicists working on the structure and function of the centrosome as well as human geneticists exploring ciliary pathology.

    1. eLife Assessment

      This important paper explores the impact of early life stress (ELS) on adult brain and behavior. The significance of the convincing findings are that they implicate regulation of non-neuronal cells in the development of brain and behavioral dysfunction associated with ELS. With an elegant combination of behavioral models, morphological and functional assessments using immunostaining, electrophysiology, and viral-mediated loss-of-function approaches, the authors report that astrocyte dysfunction plays a role in ELS responses. The work is of interest to a broad behavioral and cellular neuroscience audience.

    1. eLife Assessment

      This important study combines the use of Fisher Kernels with Hidden Markov models aiming to improve brain-behaviour prediction. The evidence supporting the authors' conclusions is compelling, comparing brain-behaviour prediction accuracies across a range of different traits, including out of sample assessment. This work is timely and will be of interest to neuroscientists working on functional connectivity for brain-behaviour association.

    1. eLife Assessment

      This important modeling study alters a previous model of the intact cat spinal locomotor network to simulate a lateral hemi-section of the spinal cord. The modeling and experimental work described provide convincing evidence that this model is capable of qualitatively predicting alterations to the swing and stance phase durations during locomotion at different speeds on intact or split-belt treadmills. This paper will interest neuroscientists studying vertebrate motor systems, including researchers working on motor dysfunction after spinal cord injury.

    1. eLife Assessment

      This valuable study revealed numerous distinct lineages that evolved within a local human population in Alberta, Canada, leading to persistent cases of E. coli O157:H7 infections for over a decade and highlighting the ongoing involvement of local cattle in disease transmission, as well as the possibility of intermediate hosts and environmental reservoirs. This study also showed a shift towards more virulent stx2a-only strains becoming predominant in the local lineages. The evidence supporting the role played by cattle in the transmission system of human cases of E. coli O157:H7 in Alberta is solid.

    1. eLife Assessment

      This work models reinforcement-learning experiments using a recurrent neural network. It examines if the detailed credit assignment necessary for back-propagation through time can be replaced with random feedback. In this useful study the authors show that it yields a satisfactory approximation but the evidence to support that it holds in general is incomplete. As only short temporal delays are used and the examples simulated are overly simple, the approximation would need to be tested on more complex task and with larger networks.

    1. eLife Assessment

      The current human tissue-based study provides convincing evidence correlating hippocampal expressions of RNA guanine-rich G-quadruplexes with aging and with Alzheimer's Disease presence and severity. The results are important and hold promise for deeper understanding of AD's pathogenesis and potential new therapeutic strategies.

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

    1. eLife Assessment

      In this valuable study the authors use electrophysiology in brain slices and computer modeling and suggest that layer 2/3 pyramidal neurons of the mouse cortex have functional HCN channels on the proximal apical dendrite which allows distinct processing of input at that location from the input to distal apical dendrites. The revisions improved the solid paper but some of the concerns were not addressed sufficiently and many of these concerns could be addressed by further revision.

    1. eLife Assessment

      The revised report provides valuable findings for the field, suggesting a relationship between CRF1 receptors, sociability deficits in morphine-treated male mice yet not females, and a potential mechanism involving oxytocin neurons in the paraventricular nucleus of the hypothalamus. Generally, the strength of evidence is solid in terms of the methods, data, and analyses. This work will be of interest to those interested in social behavior and addiction.

    1. eLife Assessment

      This fundamental study illuminates the dynamics of BRAF in its monomeric and dimeric forms, both in the absence and presence of inhibitors, through a convincing combination of traditional experiments and sophisticated computational analyses. By revealing novel insights into the selectivity and cooperative processes of BRAF inhibitors, it holds significant promise for the development of future therapeutics, particularly against mutant isoforms in cancer. Overall, these findings will be of great interest to structural biologists, medicinal chemists, and pharmacologists.

    1. eLife Assessment

      This study presents valuable evidence of sex differences in oxycodone relapse-related behavior in rats and provides insight into associated synaptic plasticity in the paraventricular thalamus to the nucleus accumbens shell (PVT-NAcSh) circuit. The report reveals that females show heightened cue-induced oxycodone seeking compared to males after 14 days – but not 1 day – of abstinence; however, an increase in synaptic strength from the PVT inputs to the NAcSh was observed in both males and females at 14 days of abstinence. Therefore, whereas the behavioral data and much of the electrophysiology data are solid, the link between them is incomplete. Further investigation of the functional role of the PVT-NAcSh pathway in the observed sex differences in oxycodone relapse and examination of input and cell-type specificity of synaptic alterations would greatly strengthen this study.

    1. eLife Assessment

      Although others have proposed that OHC electromotility subserves cochlear amplification by acting as a "fluid pump", and evidence for this has been found using electrical stimulation of excised cochleae, this important study substantially advances our understanding of cochlear homeostasis. This is the first report to test the pumping effect in vivo and consider its implications for cochlear homeostasis and drug delivery. The manuscript provides convincing evidence for OHC-based fluid flow within the cochlea.

    1. eLife Assessment

      This valuable manuscript presents a thorough analysis of the evolution of Major Histocompatibility Complex gene families across Primates. A key strength of this analysis is the use of state-of-the-art phylogenetic methods to estimate rates of gene gain and loss, but estimates of gene loss may suffer from the issue of genes entirely or partially missing from genome assemblies represented in the public databases used, given the notorious difficulty to properly assemble MHC gene genomic regions. Overall the evidence provided is still convincing, but the manuscript may benefit from discussing approaches that can address the issue of entirely or partially missing genes, in particular how the use of long reads to completely re-assemble complex loci might improve the assessment of the complex evolutionary processes at play in MHC gene families.

    1. eLife Assessment

      The authors present new expression analysis software (TEKRABber) to help analyze expression correlations between transposable elements (TEs) and KRAB zinc finger (KRAB-ZNF) genes in experimentaly validated datasets. The authors use this method to decipher the 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, identified biases and shortcomings in the current analysis pipeline could lead to an unacceptable number of false positive and negative signals and thus impact the conclusions, leaving this work in its current form incomplete.

    1. eLife Assessment

      This study provides useful insights into the ways in which germinal center B cell metabolism, particularly lipid metabolism, affects cellular responses. The authors use sophisticated mouse models to demonstrate that ether lipids are relevant for B cell homeostasis and efficient humoral responses. Although the data were collected from in vitro and in vivo experiments and analyzed using solid and validated methodology, more careful experiments and extensive revision of the manuscript will be required to strengthen the authors' conclusions.

    1. eLife Assessment

      This study is important, advancing our understanding of how humans adapt to uncertainty in dynamic environments by investigating the interplay between two types of uncertainty-volatility (systematic changes in outcomes) and noise (random variability in outcomes). Using an innovative experimental task, reinforcement learning (RL) models, and Bayesian Observer Models (BOM), the authors demonstrate that humans exhibit approximate rationality, often misattributing noise as volatility and adopting suboptimal learning rates in noisy conditions. The evidence is compelling, supported by a well-designed experimental task that independently manipulates noise and volatility, robust behavioral data, and computational modeling; the inclusion of BOM lesioning and physiological validation through pupillometry provides a nuanced understanding of suboptimal human learning. While the study could benefit from expanding the model space (e.g., by including latent state models) and offering greater clarity in task instructions and raw behavioral data, these limitations do not undermine the strength of the findings.

    1. eLife Assessment

      This important study provides insights into the neurodevelopmental trajectories of structural and functional connectivity gradients in the human brain and their potential associations with behaviour and psychopathology. While certain aspects of the methodology are rigorous, the evidence supporting the findings is currently incomplete and would benefit from additional sensitivity analyses to evaluate methodological choices supporting the findings. This study will be of interest to neuroscientists interested in understanding functional connectivity across development.

    1. eLife Assessment

      This is a useful study that adds new data to how different DAG pools influence cellular signaling, and dissects how the enzyme Dip2 modulates the minor lipid signaling DAG pool, which is distinct from the DAG pool utilized in membrane biosynthesis. The paper presents solid evidence on how different DAG pools influence cellular signaling.

    1. eLife Assessment

      This manuscript describes valuable findings regarding the expression pattern of orexin receptors in the midbrain and how manipulating this system influences several behaviors, such as context-induced locomotor activity and exploration. The overall strength of evidence - which includes anatomical, viral manipulation studies, and brain imaging - is solid and broadly substantiates claims in the paper. However, there are several areas in which the conclusions are only partially supported by the combination of methods used. These results have implications for understanding the neural underpinnings of reward and will be of interest to neuroscientists and cognitive scientists with an interest in the neurobiology of reward.

    1. eLife Assessment

      This valuable study suggests that the dosage compensation complex and m6A act in a feedback loop in Drosophila melanogaster. The study provides integrated analyses of RNA sequencing and mapping data of the m6A RNA modification in the context of unbalanced genomes, which suggests that m6A modification status may influence H3K16Ac deposition through regulation of the acetyltransferase MOF. However, it is not clear whether this regulation is directly or indirectly related to m6A regulation. The evidence is considered incomplete due to technical concerns, as quantitative assessments were made using non-quantitative methods.

    1. for - meaning crisis - 50 episodes - John Vervaeke - meaning crisis - summary table of 50 episodes

      meaning crisis - summary table of the title of 50 episodes - 1: Introduction - 2: Flow, Metaphor, and the Axial Revolution - 3: Continuous Cosmos and Modern World Grammar - 4: Socrates and the Quest for Wisdom - 5: Plato and the Cave - 6:Aristotle, Kant, and Evolution - 7: Aristotle's World View and Erich Fromm - 8: The Buddha and "Mindfulness" - 9: Insight - 10: Consciousness - 11: Higher States of Consciousness, Part 1 - 12: Higher States of Consciousness, Part 2 - 13: Buddhism and Parasitic Processing - 14: Epicurians, Cynics, and Stoics - 15: Marcel Aurelius and Jesus - 16:Christianity and Agape - 17:Gnosis and Existential Inertia - 18: Plotinus and Neoplatonism - 19: Augustine and Aquinas - 20: Death of the Universe - 21: Martin Luther and Descartes - 22: Descartes vs. Hobbes - 23: Romanticism - 24: Hegel - 25: The Clash - 26: Cognitive Science - 27:Problem Formulation - 28: Convergence to Relevance Realization - 29: Getting to the Depths of Relevance Realization - 30: Relevance Realization Meets Dynamical Systems Theory - 31: Embodied-Embedded RR as Dynamical-Developmental GI - 32: in the Brain, Insight, and Consciousness - 33: The Spirituality of RR: Wonder/Awe/Mystery/Sacredness - 34: Sacredness: Horror, Music, and the Symbol - 35: The Symbol, Sacredness, and the Sacred - 36: Religio/Perennial Problems/Reverse Eng. Enlightenment - 37: Reverse Engineering Enlightenment: Part 2 - 38: Agape and 4E Cognitive Science - 39: The Religion of No Religion - 40: Wisdom and Rationality? - 41: What is Rationality? - 42: Intelligence, Rationality, and Wisdom - 43: Wisdom and Virtue - 44: Theories of Wisdom - 45: The Nature of Wisdom - 46: Conclusion and the Prophets of the Meaning Crisis - 47: Heidegger - 48: Corbin and the Divine Double - 49: Corbin and Jung - 50: Tillich and Barfield

    1. eLife Assessment

      This work presents important findings of a modulatory effect of yohimbine, an alpha2-adrenergic antagonist that raises noradrenaline levels, on the reconsolidation of emotionally neutral word-picture pairs, depending on the hippocampal and cortical reactivation during retrieval. The evidence supporting the main conclusions is convincing, with an elegant design combining fMRI and psychopharmacology. The work will be of broad interest to researchers working on memory.

    1. eLife Assessment

      This study provides compelling evidence for functional subpopulations of β-cells responsible for Ca2+ signal initiation and maintenance using novel three-dimensional light sheet microscopy imaging and analysis of pancreatic islets. The findings are important as they help decode mechanistic underpinnings of islet calcium oscillations and the resulting pulsatile insulin secretion. The work will be of general interest to cell biologists and particular interest to islet biologists.

    1. eLife Assessment

      This important work presents the development of a novel inhibitor for SARS-CoV-2 Mac1 that has potential utility both as an antiviral therapeutic and as a tool for probing the molecular mechanisms by which infection-induced ADP-ribosylation triggers robust host antiviral responses. The evidence supporting the claims is generally convincing but could be improved if the authors expanded the phenotypic characterization of the compound and its potential effects on both viral and host targets.

    1. eLife Assessment

      This important work substantially advances our understanding of episodic memory by proposing a biologically plausible mechanism through which hippocampal barcode activity enables efficient memory binding and flexible recall. The evidence supporting the conclusions is convincing, with rigorously validated computational models and alignment with experimental findings. The work will be of broad interest to neuroscientists and computational modelers studying memory and hippocampal function.

    1. eLife Assessment

      This valuable study uses dynamic metabolic models to compare perturbation responses in a bacterial system, analyzing whether they return to their steady state or amplify beyond the initial perturbation. The evidence supporting the emergent properties of perturbed metabolic systems to network topology and sensitivity to specific metabolites is solid, although the authors do not explain the origin of some significant inconsistencies between models.

    1. eLife Assessment

      This study presents an important application of high-content image-based morphological profiling to quantitatively and systematically characterize induced pluripotent stem cell-derived mixed neural cultures cell type compositions. Exceptional evidence through rigorous experimental and computational validations support new potential applications of this cheap and simple assay.

    1. eLife Assessment

      This important study reveals a new mechanism for gene regulation in neurons by an RNA binding protein called RBM20 previously studied in the heart. The methods used are compelling, including the generation of new mouse knockout strains and leading edge sequencing methods for identification of gene regulatory mechanisms. The study shows that neuronal RBM20 governs long pre-mRNAs encoding synaptic proteins in specific neuronal cell types, but the functional consequences of this regulation remain questions for the future.

    1. eLife Assessment

      This valuable study shows a surprising scale-invariance of the covariance spectrum of large-scale recordings in the zebrafish brain in vivo. A solid analysis demonstrates that a Euclidean random matrix model of the covariance matrix recapitulates these properties. The results provide several new and insightful approaches for probing large-scale neural recordings.

    1. eLife Assessment

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

    1. This evaluation refers to version 1 of the preprint

      This work presents the genome of Cardamine chenopodiifolia, an amphicarpic plant (developing two fruit types, one above and another below ground) in the mustard (Brassicaceae) family. Cardamines also known as bittercresses and toothworts. As an octoploid species it has been challenging to create a genome reference for this species, and in this case the authors finally managed to achieve this using PacBio HiFi long-reads and Omni-C technology to assemble a fully phased, chromosome-level genome. Obtaining a 597Mb genome assembled into 32 phased chromosomes (plus mitochondrial and plastid genomes), and only having one gap in the centromeric region of chromosome 9. Peer review asked for additional QC and benchmarking, helping demonstrate the genome quality was very high, with only one gap and a N50 of 18.80Mb. The data presented here potentially helping to develop this species as an emerging model organism in the Brassicaceae for studying the development and evolution of amphicarpy by allopolyploidy.

      This evaluation refers to version 1 of the preprint

    1. Editors Assessment:

      Among hot topics in coral reef research, the difference between anemonefish and other damselfish is currently a popular area of research. In this study the authors provide a new high-quality non-anemonefish genome, which will be of high relevance to further the depth of such analyses. In this case of the sapphire damselfish Chrysiptera cyanea, a widely distributed damselfish in the Indo-Pacific area, often studied to elucidate the roles of various environmental controls on their reproduction, and investigate related hormonal processes To further the potential of biomolecular analyses based on this species, this study generated the first genome of a Chrysiptera fish from a male individual collected in Okinawa, Japan. Using PacBio and HiFI long-read sequencing with 94.5x coverage, a chromosome-scale genome was assembled and 28,173 genes identified and annotated. Peer review gathered more parameters and details on the quality, and the final assembly comprised of 896 Mb pairs across 91 contigs, and a BUSCO completeness of 97.6%. This reference genome should therefore be of high value for future genetic-based approaches, from population structure to gene expression analyses.
      

      This evaluation refers to version 1 of the preprint

    1. eLife assessment

      This paper makes a valuable contribution to the area of balancing selection at the Major histocompatibility complex (MHC), including trans-species polymorphism between humans and other primates, by incorporating a large evolutionary range of species and genes and by using newer methodological approaches to characterize the depth and extent of the trans-species polymorphism across an expanded range of primate taxa. While the presented results solidly support the authors' conclusions, additional analyses would be needed to firmly exclude modes of evolution that could mimic trans-specific polymorphism.

    1. eLife Assessment

      The useful manuscript presents interesting findings in the field of neurodegenerative diseases by highlighting the dual role of phosphorylated ubiquitin (pUb) in cellular proteostasis and neurotoxicity. However, some claims for discovery are supported by unconvincing and incomplete evidence that requires further validation. The poor quality of key immunofluorescent images and questionable quantification analysis raise technical concerns.

    1. eLife Assessment

      This valuable study reports multi-scale molecular dynamics simulations to investigate a class of highly potent antibodies that simultaneously engage with the HIV-1 Envelope trimer and the viral membrane. The work provides insights into how broadly neutralizing antibodies associate with lipids proximal to membrane-associated epitopes to drive neutralization. After extensive revision, the level of evidence is considered solid, although a quantitative assessment of the underlying energetics remain difficult to obtain.

    1. eLife Assessment

      This valuable study presents findings on the mode of action of MOTS-c (mitochondrial open reading frame from the twelve S rRNA type-c), and its impact on monocyte-derived macrophages. The authors present solid evidence for its increased expression in stimulated monocytes/macrophages, its direct bactericidal functions, as well as its role in the modulation of monocyte differentiation into macrophages. Since most of the data were generated from a cell line (THP1), future work is required to validate observations in primary cells and to further support the claims of this work.

    1. eLife Assessment

      This useful study examines patterns of diversity and divergence in two closely related sub-species of Zea mays, patterns that have bearings on local adaptation in maize and teosinte at intermediate geographic scales. The authors suggest that convergent evolution has been facilitated by both standing variation and gene flow, with independent selective sweeps in the two species. While the data themselves are solid, there are limitations concerning population sampling, false positive rates in sweep detection and integration of phenotypic data, which make it difficult to draw definitive conclusions. The work should in principle be of broad interest to colleagues studying the relationship between domesticated species and their progenitors, as well as those studying instances of parallel evolution.

    1. eLife Assessment

      This work presents important findings that the human frontal cortex is involved in a flexible, dual role in both maintaining information in short-term memory, and controlling this memory content to guide adaptive behavior and decisions. The evidence supporting the conclusions is compelling, with a well-designed task, best-practice decoding methods, and careful control analyses. The work will be of broad interest to cognitive neuroscience researchers working on working memory and cognitive control.

    1. eLife Assessment

      The authors provide solid evidence that the likelihood of looking behaviour is predicted by the expected information gain, hence constituting a valuable formal model and explanation of habituation. Such modelling can represent crucial advances in explanation, over-and-above less specified models that can be fitted post hoc to any empirical pattern, although contrast testing with other accounts are desired. The findings would be of interest to researchers studying cognitive development.

    1. eLife Assessment

      This manuscript describes the generation of a fused dorsal-ventral organoid system to model interactions between the cortex and striatum to study the onset and progression of Huntington's disease (HD) and other neurodegenerative disorders. While this approach is valuable, further methodological and analytical work is needed to fully support the interpretations and claims of the authors. Incomplete evidence suggests choroid plexus (ChP) abnormalities form a significant component of HD pathogenesis.

    1. eLife Assessment

      This valuable work explores how synaptic activity encodes information during memory tasks. All reviewers agree that the quality of the work is high. Although experimental data do support the possibility that phospholipase diacylglycerol signaling and synaptotagmin 7 (Syt7) dynamically regulate the vesicle pool required for presynaptic release, concerns remain that the central finding of paired pulse depression at very short intervals was more likely caused by Ca2+ channel inactivation than pool depletion. Overall, this is a solid study although the results warrant consideration of alternative interpretations.

    1. eLife Assessment

      This fundamental study reveals that aging in yeast leads to chromosome mis-segregation due to asymmetric partitioning of chromosomes, driven by disruption of the nuclear pore complex and pre-mRNA leakage. The findings are convincingly supported by carefully-designed experimental data with a combination of genetic, molecular biology and cell biology approaches.

    1. eLife Assessment

      Using highly sophisticated switching linear dynamical systems (SLDS) analyses applied to functional MRI data, this study provides important insights into network dynamics underlying threat processing. After identifying distinct neural network states associated with varying levels of threat proximity, the paper provides compelling evidence of intrinsically and extrinsically driven contributions to these within-state dynamics and between-state transitions. Although the findings could be made more biologically meaningful, this work will be of interest to a wider functional neuroimaging and systems neuroscience community.

    1. eLife Assessment

      In this innovative study, Carpenet C et al explore the use of nanobody-based PET imaging to track proliferative cells after in vivo transplantation in mice, in a fully immunocompetent setting. The development of a unique set of PET tracers and mouse strains to track genetically-unmodified transplanted cells in vivo is an important novel asset that could potentially facilitate cell tracking. The evidence provided is compelling as the new method proposed might facilitate overcoming certain limitations of alternative approaches, such as full sized immunoglobulins and small molecules, while the specific claims would gain further support by additional experimentation and methodological details.

    1. eLife Assessment

      This systematic review presents valuable insights into CCR5 antagonist drugs for neuroprotection and stroke management. The strength of the evidence is convincing, and the review methods and reporting adhere to the expected standards. A sensitivity analysis based on the risk of bias assessment of the included studies would be beneficial, and a more focused/detailed acknowledgment of key limitations of the review would add value to the quality of the reporting and interpretations of the findings.

    1. eLife Assessment

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

    1. eLife Assessment

      This important study presents a finding on the role of the Inferior Colliculus in sensory prediction, cognitive decision-making, and reward prediction. The evidence supporting the claims of the authors is convincing. The work will be of broad interest to sensory neuroscientists.

    1. eLife Assessment

      This valuable study describes how trains of mossy fiber stimulation control cerebellar unipolar brush cell discharges. The dissection of the contributions of relevant glutamate receptors to these transformations is convincing. Overall, the study broadens our understanding of temporal processing in the cerebellar cortex.

    1. eLife Assessment

      This important work advances our understanding of the contribution of tissue-resident immune cells to trained immunity phenotypes. The evidence supporting the claims is convincing, with results that will be of interest to immunologists and scientists studying the host-pathogen interface.

    1. eLife Assessment

      This work provides a valuable contribution to our understanding of the neurobiological mechanisms underlying spatial memory and learning, suggesting that dopamine plays a pivotal role in linking reward context and novelty to memory consolidation processes. The evidence presented to support the main conclusions is solid, although reviewers felt that the strength of evidence could have been further strengthened by more rigorous histological verification of the experimental conditions and the complexity of the experimental manipulations, increased sample sizes, and a more consistent approach to experimental dosing and timing, which will be crucial for confirming the reproducibility and reliability of the observed effects.

    1. eLife Assessment

      This important work uses an innovative approach to understand similarities between haemodynamic and electrophysiological activity of the human brain. The study provides incomplete evidence to indicate that while similar functional brain networks are used in both modalities, there is a tendency for these multi-modal networks to spatially converge at synchronous rather than asynchronous time points. This work will be of interest to neurophysiological and brain imaging researchers.

    1. eLife Assessment

      This important study offers insights into the function and connectivity patterns of a relatively unknown afferent input from the endopiriform to the CA1 subfield of the ventral hippocampus, suggesting a neural mechanism that suppresses the processing of familiar stimuli in favor of detecting memory guided novelty. The strength of evidence is convincing, with careful anatomical and electrophysiological circuit characterization. The work will be of broad interest to researchers studying the neural circuitry of behavior.

    1. eLife Assessment

      This study provides important insights into the brain activity and connectivity underlying speech comprehension, revealing three brain states. The authors present compelling evidence by leveraging hidden Markov modeling of fMRI data to link brain state dynamics to comprehension scores, though the functional role of these states remains under-explored. These findings advance our understanding of how brain state transitions in narrative comprehension relate to stimulus-specific features.

    1. eLife Assessment

      This valuable study reports on electrophysiological recording of the spiking activity of single neurons in the entopeduncular nucleus (EPN) in freely-moving mice performing an auditory discrimination task. The data show that the activity of single EPN neurons is modulated by reward and movement kinematics, with the latter further affected by task contexts (e.g. movement toward or away from a reward location). The results provide solid evidence for the conclusions. There is some ambiguity as to whether the data contain the population of EPN neurons characterized in previous studies that obtained different results. Investigations separating confounding factors would be of benefit. Nonetheless, the work is overall of interest to those who study how the basal ganglia, particularly the EPN, contribute to behavior.

    1. eLife Assessment

      Kreeger et al. convincingly demonstrate that octopus cells in the mouse cochlear nucleus, previously thought to rely primarily on excitatory inputs for coincidence detection, also receive glycinergic inhibitory synaptic inputs that influence their synaptic integration. Using advanced techniques, including genetic mouse models, optogenetics, microscopy, slice physiology, and computational modeling, this important study reveals that inhibition can shunt synaptic currents and alter the timing of dendritic EPSPs, both of which are significant for auditory processing. This research broadens the understanding of octopus cells' roles in sensory processing, highlighting the importance of inhibitory inputs in shaping fast, high-frequency neural response capabilities.

    1. eLife Assessment

      In this manuscript, Abd El Hay and colleagues use an innovative behavioral assay and analysis method, together with standard calcium imaging experiments on cultured dorsal root ganglion (DRG) neurons, to evaluate the consequences of global knockout of TRPV1 and TRPM2, and overexpression of TRPV1, on warmth detection. Compelling evidence is provided for a role of TRPM2 channels in warmth avoidance behavior, but it remains unclear whether this involves channel activity in the periphery or in the brain. In contrast, TRPV1 is clearly implicated at the cellular level in warmth detection. These findings are important because there is substantial ongoing discussion regarding the contribution of TRP channels to different aspects of thermo-sensation.

    1. eLife Assessment

      This study presents valuable evidence concerning the potential for naturalistic movie-viewing fMRI experiments to reveal some features that are correlated with the functional and topographical organization of the developing visual system in awake infants and toddlers. The data are compelling given the difficulty of studying this population, the methodology is original and validated, and the evidence supporting the conclusions is convincing and in line with prior research using resting-state and awake task-based fMRI. This study will be of interest to cognitive neuroscientists and developmental psychologists, and in particular those interested in using fMRI to investigate brain organisation in pediatric and clinical populations with limited tolerance to fMRI.

    1. eLife Assessment

      Using genomic data from ancient and modern samples, this important study investigates the genomic history of cattle in Iberia, focusing on the admixture between domestic cattle and their wild ancestors, aurochs. The authors present convincing evidence for interbreeding between domestic cattle and wild aurochs since the Neolithic period, although the evidence of sex-biased introgression is weak. The authors also show that the aurochs ancestry in cattle stabilized at ~20% since ~4000 years ago and continues into modern breeds; however, the aurochs ancestry is not heightened in a modern breed of Spanish fighting bulls that are bred for aggressiveness. The work will be of interest to evolutionary biologists and quantitative geneticists who seek to understand the genomic history and genetic basis of trait variation of domesticated animals.

    1. eLife Assessment

      This study reveals the important role of upstream open reading frames (uORFs) in limiting the translational variability of downstream coding sequences. Through a combination of computational simulations, comparative analyses of translation efficiency across different developmental stages in two closely related Drosophila species, and manipulative, experimental validation of translation buffering by an uORF for a gene, the authors provide convincing evidence supporting their conclusions. This work will be of broad interest to molecular biologists and geneticists.

    1. eLife Assessment

      This important study of regulatory elements and gene expression in the craniofacial region of the fat-tailed dunnart shows that, compared to placental mammals, marsupial craniofacial tissue develops in a precocious manner, with enhancer regulatory elements as primary driver of this difference. While the results are overall solid, addressing concerns regarding the liftover methods in the context of low conservation of alignable enhancers between dunnart and mouse would benefit the work, enhancing its value for uncovering mechanisms that drive heterochronic processes and as a reference for future mammalian evolution studies.

    1. eLife Assessment

      This study provides important insights into how a specific brain region controls innate responses to odors, showing that different parts of this region govern behaviors related to attraction and aversion. The findings are convincing and supported by a combination of well-executed experimental approaches, including genetic manipulations and neural activity mapping, though the evidence could be strengthened by addressing certain methodological concerns, such as clarifying the rationale for specific experimental choices and exploring alternative techniques.

    1. eLife Assessment

      This important manuscript presents a thorough analysis of trans-specific polymorphism (TSP) in Major Histocompatibility Complex gene families across primates. The analysis makes the most of currently available genomic data and methods to substantially increase the amount and evolutionary time that TSPs can be observed, but both false negative TSPs due to missing genes at the assembly and/or annotation level, as well as false positives due to read mismapping with missing paralogs, could be assessed and discussed more. Overall the evidence provided is convincing, and the manuscript may benefit from discussing the future use of more complete assemblies made from long reads to reduce the occurrence of both missing and false TSPs.

    1. eLife Assessment

      This valuable study presents a resource for researchers using Drosophila to study neural circuits, in the form of a collection of split-Gal4 lines with an online search engine, which will facilitate the mapping of neuronal circuits. The evidence is convincing to demonstrate the utility of these new tools, and of the search engine, for understanding expression patterns in adults and larvae, and differences between the sexes. These resources will be of broad interest to Drosophila researchers in the field of neurobiology.

    1. eLife Assessment

      This important study reports on PI3KR mutations and a paradoxical mechanism of PI3KR signaling. The strength of evidence for the study is mostly convincing, as conclusions are supported by a variety of mutational strategies and cellular systems to look at interactions among signaling pathways.

    1. eLife Assessment

      This important study provides insights into the physiological role of RIPK1 in liver physiology, particularly during short-term fasting. The discovery that RIPK1 deficiency sensitizes the liver to acute injury and hepatocyte apoptosis is based on convincing evidence, highlighting the importance of RIPK1 in maintaining liver homeostasis under metabolic stress. The work will be of relevance to anyone studying liver pathologies.

    1. eLife Assessment

      This important collection of over 800 new cell type-specific driver lines will be an invaluable resource for researchers studying associative learning in Drosophila. Thoroughly characterized and well documented, this collection will permit researchers to selectively target neurons that deliver information to, or receive it from, the memory center of the fly brain called the Mushroom Body. Given the wealth of new drivers and the genetic access they provide to over 300 cell types, this compelling work will be of interest not only to researchers studying the mechanisms of associative learning but more generally to those dissecting sensorimotor circuits in the fly nervous system.

    1. eLife Assessment

      This paper presents useful results that extend our understanding of how the visual cortex encodes temporal structure, providing new information about sequence representations in the upper layers of the visual cortex. The evidence for prediction errors is solid, however, support for other claims regarding sparsification and simplification of activity following training is incomplete. The main concerns pertain to the confounds associated with restricted ordering within blocks that does not allow for separate plasticity mechanisms operating on different time scales.

    1. eLife Assessment

      This paper addresses an important topic (normative trajectory modelling), seeking to provide a method aiming to accurately reflect the individual deviation of longitudinal/temporal change compared to the normal temporal change characterized based on a pre-trained population normative model. The evidence provided for the new methods is solid.

    1. eLife Assessment

      Yonk and colleagues provide a valuable, timely, and in-depth study showcasing the role of thalamostriatal inputs in learning and action selection. After characterizing the synaptic properties of these inputs onto different striatal cell types in vitro, they provide solid evidence that posterior medial thalamic nucleus (POm) terminals in striatum are activated during reward expectation and arousal. The overall function of this pathway and the degree to which results are confounded by viral contamination of surrounding nuclei and movements remain open questions.

    1. eLife Assessment

      Somatostatin-expressing neurons of the entopeduncular nucleus (EPNSst+) provide a limbic output of the basal ganglia and co-release GABA and Glutamate in their projection to the lateral habenula, a structure that is key for reward-based learning. Combining fiber photometry and computational modeling, the authors provide compelling evidence that EPNSst+ neural activity represents movement, choice direction and reward outcomes in a probabilistic switching task but, surprisingly, neither chronic genetic silencing of these neurons nor selectively elimination glutamate release affected behavioral performance in well-trained animals. This valuable study shows that despite its representation of key task variables, EPNSst+ neurons are dispensable for ongoing performance in a task requiring outcome monitoring to optimize reward. This work will be of interest to those interested in neural circuits, learning, and/or decision making.

    1. eLife Assessment

      Cav2 voltage-gated calcium channels play key roles in regulating synaptic strength and plasticity. In contrast to mammals, invertebrates like Drosophila encode a single Cav2 channel, raising questions on how diversity in Cav2 is achieved from a single gene. Here, the authors present solid evidence that two alternatively spliced Cac isoforms enable important changes in Cav2 expression, localization, and function in synaptic transmission and plasticity at the Drosophila neuromuscular junction. How the isoforms affect synaptic calcium channel levels remains less clear. This study provides insights into the roles of voltage-gated calcium channel splice isoforms in synaptic transmission.

    1. eLife Assessment

      This important study presents an evaluation of several tools used for detecting Identity-By-Descent (IBD) segments in highly recombining genomes, using simulated data to replicate the high recombination and low marker density of Plasmodium falciparum, the parasite responsible for malaria. Most of the evidence presented by the authors is solid demonstrating that users should be cautious calling IBD when SNP density is low and recombination rate is high. This study will be of interest to scientists working in the field of genome evolution and infectious diseases.

    1. eLife Assessment

      This useful observational study was conducted in Dar es Salaam, Tanzania, to investigate potential associations between genetic variation in Mycobacterium tuberculosis and human host vs. disease severity. The authors conclude that human genetic ancestry did not contribute to tuberculosis severity, but the evidence for this conclusion is currently incomplete, as the analysis did not fully leverage the genome-wide data available in a human-strain association study, and there was no comparison group from the general population (or household controls), to which the ancestry findings could be compared. The findings have significance for the understanding of the influence of host / bacillary genetics on tuberculosis disease.

    1. eLife Assessment

      This important study introduces a fully differentiable variant of the Gillespie algorithm as an approximate stochastic simulation scheme for complex chemical reaction networks, allowing kinetic parameters to be inferred from empirical measurements of network outputs using gradient descent. The concept and algorithm design are convincing and innovative. While the proofs of concept are promising, the determination of the range of applicability and of the errors is incomplete, leaving open some questions about implications for more complex systems that cannot be addressed by existing methods. This work has the potential to be of significant interest to a broad audience of quantitative and synthetic biologists.

    1. eLife Assessment

      This study presents a platform to implement closed-loop experiments in mice based on auditory feedback. The authors provide solid evidence that their platform enables a variety of closed-loop experiments using neural or movement signals, indicating that it will be a valuable resource to the neuroscience community. However, the demonstration experiments could be strengthened by increasing the sample size for several groups in the neurofeedback experiments, as well as a more thorough description of the results in the text.

    1. eLife Assessment

      This important study conducted experiments to quantify how changes in blood flow results in apparent fluorescence changes when imaging neural activity sensors using two-photon microscopy. While the study highlights the prevalence neural-activity independent artifacts in two-photon imaging, the evidence linking the observed signals to hemodynamic occlusion remains incomplete.

    1. eLife Assessment

      This study examined how multidimensional social relationships influence social attention in rhesus macaques, linking individual and group-level behaviors to attentional processes. The findings that oxytocin altered social attention and its relationship to both social tendencies and dyadic relationships are important, as recent technological advances allow for the exploration of neuronal activities and mechanisms in free-moving macaques. This work is convincing and will be of interest to those studying the interplay between social dynamics and information processing in primates.

    1. eLife Assessment

      This valuable study uses a novel method to record spine calcium responses without the confounds of backpropagating action potentials to study how the dendritic integration of large numbers of inputs generates the tuned output of cortical neurons. While the results are generally solid, the study would benefit from more details, characterizations, and quantifications, including better validation of the method to suppress backpropagating action potentials.

    1. eLife Assessment

      This study presents a valuable finding on a new role of glia in activity-dependent synaptic remodeling using the Drosophila NMJ as a model system. The evidence supporting the claims of the authors is solid. However, the unaddressed cell-type specific mechanisms of Shv secretion and regulation on the extracellular glutamate levels and lack of details on the methods for statistical analysis have hindered further evaluation of the claims. The work will be of interest to neuroscientists working on glia-neuron interaction and synaptic remodeling.

    1. eLife Assessment

      In this important manuscript, Ryan et al perform a genome-wide CRISPR based screen to identify genes that modulate TDP-43 levels in neurons. They identify a number of genes and pathways and highlight the BORC complex, which is required for anterograde lysosome transport as one such regulator of TDP-43 protein levels. Overall, this is a convincing study, which opens the door for additional future investigations on the regulation of TDP-43.

    1. eLife Assessment

      This valuable study by Cui et al. investigates mechanisms generating sighs, which are crucial for respiratory function and linked to emotional states. Utilizing advanced methods in mice, they provide solid evidence that increased excitability in specific preBötzinger complex neuronal subpopulations expressing Neuromedin B receptors, gastrin-releasing peptide receptors, or somatostatin can induce sigh-like large amplitude inspirations. With additional technical clarifications and further elaboration of the limitations in terms of how the results are interpreted in the revised manuscript, the study will interest neuroscientists studying respiratory neurobiology and rhythmic motor systems.

    1. eLife Assessment

      In this revised manuscript, Dong et al. investigate the role of the small Ras-like GTPase Rab10 in the exocytosis of DCVs in mouse hippocampal neurons, showing that Rab10 depletion hinders DCV exocytosis independently of its effects on neurite outgrowth. Upon revising their work, these findings provide compelling evidence that Rab10 depletion leads to altered ER morphology, impaired ER-based calcium buffering, and decreased ribosomal protein expression, which collectively contributes to defective DCV secretion. The study comes to the fundamental conclusion that Rab10 is critical for DCV release by ensuring ER calcium homeostasis.

    1. eLife Assessment

      This important study develops and exploits novel ideas in dendritic integration and implements these ideas in a neural network. Historically, dendritic plateau potentials were thought to exist primarily for maintaining neurons in a depolarized state for 100s of milliseconds, but this study presents a new perspective that dendritic plateau potentials are equally effective in much shorter integration windows. The computational evidence supporting the article's claims is compelling.

    1. eLife Assessment

      This study aggregates across five fMRI datasets and reports that a network of brain areas previously associated with response inhibition processes, including several in the basal ganglia, are more active on failed stop than successful stop trials. This study is valuable as a well-powered investigation of fMRI measures of stopping, and following revisions provides solid evidence for its conclusions.

    1. eLife Assessment

      In this fundamental study, the authors describe ELF3 as a candidate driver of luminal progenitor transformation, such that its up-regulation during replicative stress conditions and in BRCA1 deficient cells may permit cell proliferation by suppressing genome instability. While the work is certainly of interest, the supporting data remain incomplete as luminal progenitor cells could not be isolated, which would be needed in order to definitively determine whether ELF3 is a driver of transformation in these cells. Overall this paper may offer insight into mechanisms by which BRCA1 deficiency fuels breast tumorigenesis.

    1. eLife Assessment

      This important work advances our understanding of factors influencing efficacy assessments and biomarker viability for complement-directed gene therapy against age-related macular degeneration. The data presented is convincing and offers insights and teachings for the design of gene therapy and complement-targeted therapeutics in the eye and more broadly for future ocular biomarker studies.

    1. eLife Assessment

      In this valuable study, the authors propose a model wherein the bacterial redox state plays a crucial role in the differentiation of Chlamydia trachomatis into elementary and reticulate bodies. They provide solid evidence to argue that a highly oxidising environment favours the formation of elementary bodies while a reducing condition slows down development. Overall, the study convincingly demonstrates that Chlamydial redox states play a role in differentiation, an observation that may have implications for the study of other bacterial systems.

    1. eLife Assessment

      This is a valuable study on the efficacy of a live attenuated vaccine that was tested in different animal models and the evidence is convincing. The study has been strengthened after revisions.

    1. eLife Assessment

      In this important study, the authors investigate the biogenesis of extracellular vesicles in mycobacteria and provide several observations to link VirR with vesiculogenesis, peptidoglycan metabolism, lipid metabolism, and cell wall permeability. The authors have done a commendable job of comprehensively examining the phenotypes associated with the VirR mutant using various techniques. The evidence presented in the revised manuscript is convincing and creates several avenues for further research.

    1. eLife Assessment

      The authors performed extensive coarse-grained molecular dynamics simulations of 140 different prion-like domain variants to interrogate how specific amino acid substitutions determine the driving forces for phase separation. The analyses are solid, and the derived predictive scaling laws can aid in identifying potential phase-separating regions in uncharacterized proteins. Overall, this is a valuable contribution to the field of biomolecular condensates. It exemplifies how data-driven methodologies can uncover new insights into complex biological phenomena.

    1. eLife Assessment

      The authors propose that positive biodiversity-ecosystem functioning relationships found in experiments have been exaggerated because commonly used statistical analyses are flawed. To remedy this, a new type of analysis based on a concept of "partial density monoculture yield" is proposed. However, the presented concept and analysis methods are not reproducibly described (how can partial density monoculture yield experimentally be assessed?), do not appear to be complete, and are inadequate for hypothesis testing. The reviewers found that the authors misinterpret current research in the field and made limited efforts to understand or address the reviewer comments about this study.

    1. eLife Assessment

      This neuroimaging and electrophysiology study in a small cohort of congenital cataract patients with sight recovery aims to characterize the effects of early visual deprivation on excitatory and inhibitory balance in visual cortex. While contrasting sight-recovery with visually intact controls suggested the existence of persistent alterations in Glx/GABA ratio and aperiodic EEG signals, it provided only incomplete evidence supporting claims about the effects of early deprivation itself. The reported data were considered valuable, given the rare study population. However, the small sample sizes, lack of a specific control cohort and multiple methodological limitations will likely restrict usefulness to scientists working in this particular subfield.

    1. eLife Assessment

      This valuable study provides insights into the structure and function of bacterial contractile injection systems that are present in the cytoplasm of many Streptomyces strains. A convincing high-resolution model of the structure of extended forms of the cytoplasmic contractile injection system assembly from Streptomyces coelicolor is presented, with some investigation of the membrane protein CisA in attachment of the extended assembly to the inner face of the cytoplasmic membrane and the firing of the system. The work expands the current understanding of these diverse bacterial nanomachines.

    1. eLife Assessment

      This is a valuable study and a promising development for the field of open-source microscopy for educational purposes. The strengths include the low cost of constructing the microscope, impressive performance and detailed resources including a dedicated website and YouTube channel. The claims are generally supported by solid evidence, however, the manuscript would be strengthened by inclusion of further details on standard performance metrics (e.g. signal to noise ratio etc.) compared to existing systems and further details and clarification on the microscope, construction and operation.

    1. eLife Assessment

      The work presented in this paper provides an important insight into how early life experience shapes adult behavior in fruit bats. The authors raised juvenile bats either in an impoverished or enriched environment and studied their foraging behaviors. The evidence is convincing that bats raised in enriched environments are more active, bold, and exploratory, although further exploration of the data and clarification of the analysis would strengthened the evidence. The work will be of interest to ethologists and developmental psychologists.

    1. eLife Assessment

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

    1. eLife Assessment

      This fundamental study examines infection of the liver and hepatocytes during Mycobacterium tuberculosis infection using different systems including aerosol infection of mice and guinea pigs to demonstrate appreciable infection of the liver as well as the lung. The authors present convincing evidence that hepatocyte infection leads to metabolic dysfunction that promotes M. tuberculosis growth, in part potentially mediated by a nuclear receptor called PPARg. Overall, this is an interesting paper on an area of tuberculosis research which has been understudied, representing a significant advancement in the field.

    1. eLife Assessment

      This important theoretical study examines the possibility of encoding genomic information in a collective of short overlapping strands (e.g., the Virtual Circular Genome (VCG) model). The study presents solid theoretical arguments, simulations and comparisons to experimental data to point at potential features and limitations of such distributed collective encoding of information. The work should be of relevance to colleagues interested in molecular information processing and to those interested in pre-Central Dogma or prebiotic models of self-replication.