eLife Assessment

This report explores the role of matrix metalloprotease MMP21 in left-right patterning in Xenopus. Based on a series of compelling experiments, the authors demonstrate that MMP21 can be secreted and acts upstream of dand5 without affecting cilia flow. The experiments are interesting and valuable; however, the claims by the authors lack consideration of other models that could also explain their findings.

eLife Assessment

This fundamental work presents two clinically relevant BMP4 mutations that contribute to vertebrate development. The compelling evidence, both from wet lab and AI generated predictions, supports that the site-specific cleavage at the BMP4 pro-domain precisely regulates its function and provides mechanistic insight how homodimers and heterodimers behave differently. The work will be of board interest to researchers working on growth factor signaling mechanisms and vertebrate development.

eLife Assessment

This fundamental article significantly advances our understanding of FGF signalling, and in particular highlights the complex modifications affecting this pathway. The evidence for the authors' claims is convincing, combining state of the art conditional gene deletion in the mouse lens with histological and molecular approaches. This work should be of great interest to molecular and developmental biologists beyond the lens community.

eLife Assessment

This is an important study that aims to investigate the behavioral relevance of multisensory responses recorded in the auditory cortex. The experiments are elegant and well-designed and are supported by appropriate analyses of the data. Although solid evidence is presented that is consistent with learning-dependent encoding of visual information in auditory cortex, further work is needed to establish the origin and nature of these non-auditory signals and to definitively rule out any effects of movement-related activity.

eLife Assessment

This work provides a simple, rapid and useful protocol for the isolation of small extracellular vesicles from small volumes of plasma, using two well-known methodologies, in tandem: size exclusion chromatography (SEC) and density gradient ultracentrifugation (DGUC). The authors exhaustively test these methodologies separately and in combination, showing superior results for the SEC-DGUC in terms of purity and yield. The results obtained in this work are convincing, using multiple state-of-art methodologies for the characterization of the isolates that support their conclusions.

eLife Assessment

This valuable study provides a comprehensive description of the Nematostella vectensis matrisome - the genes encoding the proteins of the extracellular matrix. The authors combine new mass spectrometry data with bioinformatic analyses of previously published genomic and single-cell RNAseq data. Although this work will be of interest to biologists working on the evolution of the matrisome, as well as more broadly those working with non-bilaterian animals, in its current state it is incomplete due to the lack of rigorous criteria for manual curation and comprehensive annotation of the predicted matrisome.

eLife Assessment

This important study utilizes single-cell RNA sequencing to reveal the heterogeneity of trans-sialidase-like superfamily gene expression in Trypanosoma cruzi populations. The approach is highly convincing, as it successfully assigns cells to specific developmental forms and highlights the variability in surface protein expression among trypomastigotes. However, while the findings are solid and contribute to the understanding of immune evasion mechanisms, the study would benefit from a more detailed exploration of the regulatory factors governing trans-sialidase expression. Strengthening this aspect would further enhance its impact on researchers studying T. cruzi pathogenesis and host-parasite interactions.

eLife Assessment

The study is useful for advancing spatial transcriptomics through its novel regression-based linear model (glmSMA) that integrates single-cell RNA-seq with spatial reference atlases, though its methodological framework remains incomplete regarding spatial communication applications and feature dependence. The approach demonstrates notable utility by enabling higher-resolution cell mapping across multiple biological systems and spatial platforms compared to existing tools.

eLife Assessment

Kwon et al. present an important paper using a novel approach to estimating rotavirus vaccine efficacy using data from a passive surveillance network in the US. They provide convincing evidence to support their conclusion that using the whole genome, rather than previous use of two surface proteins, enhances our understanding of strain-specific vaccine efficacy. These findings have implications for this vaccine specifically as well as type-specific vaccine evaluation more generally.

eLife Assessment

In this manuscript, Lim and collaborators present a useful system for developing self-amplifying RNA that should not provoke a strong host inflammatory response. However, some of the claims are incomplete; additional experiments to investigate the effects on translation of the gene of interest and replication efficiency of the self-amplifying RNA could strengthen the manuscript.

eLife Assessment

This study reanalyzed previously published scRNA-seq and TCR-seq data to examine the proportion and characteristics of dual-TCR-expressing Treg cells in mice, presenting some useful insights into TCR diversity and immune regulation. However, the evidence is incomplete, particularly with respect to data interpretation, statistical rigor, and the functionality of dual -TCR Treg cells. The study is potentially of interest to immunologists studying T-cell biology.

eLife Assessment

This important study shows, for the first time, the structure and snapshots of the dynamics of the full-length soluble Angiotensin-I converting enzyme dimer. The combination of structural and computational approaches elucidates with convincing evidence the conformational dynamics of the complex and key regions mediating the conformational change. This work provides an example of how conformational heterogeneity can be used to gain insights into protein function.

eLife Assessment

This study presents a useful contribution to understanding zinc regulation of sperm physiology, specifically its inhibitory effects on the sperm-specific potassium channel Slo3. However, the evidence supporting the claims is incomplete, as critical experimental controls are lacking, key mechanistic aspects remain insufficiently explored, and experimental descriptions are often inadequate, making it difficult to fully assess the findings. Strengthening the study with additional electrophysiological recordings in sperm cells, improved imaging controls, and clearer methodological descriptions would enhance its impact and rigor.

eLife Assessment

This important study addresses a topic that is frequently discussed in the literature but is under-assessed, namely correlations among genome size, repeat content, and pathogenicity in fungi. Contrary to previous assertions, the authors found that repeat content is not associated with pathogenicity. Rather, pathogenic lifestyle was found to be better explained by the number of protein-coding genes, with other genomic features associated with insect association status. While the results are considered solid, confidence in the results would be deepened if the authors were to comprehensively account for potential biases stemming from the underlying data quality of the analyzed genomes.

eLife Assessment

The IBEX Knowledge-Base is an important tool that will enhance scientific collaboration by providing a centralized, community-driven resource for immunofluorescence imaging and reagent validation. Its detailed use cases, open-source design, and transparent reporting offer compelling evidence of its broad utility and impact in the life sciences. Overall, the resource sets a high standard as a blueprint for future community initiatives in reproducibility and standardization.

eLife Assessment

This manuscript demonstrates that Oct4 overexpression synergizes with Notch inhibition (Rbpj knockout) to promote the conversion of adult murine Müller glia (MG) into bipolar cells. These findings are important as the authors used rigorous genetic lineage tracing (GLAST-CreER; Sun-GFP) to confirm that neurogenesis indeed originates from MGs, addressing a key issue in the field. The single-cell multiomic analyses are convincing, and while functional studies of MG-derived bipolar cells would strengthen the conclusions, they are beyond the scope of this study.

eLife Assessment

This manuscript presents important information as to how adolescent alcohol exposure (AIE) alters pain behavior and relevant neurocircuits, with convincing data. The manuscript focuses on how AIE alters the basolateral amygdala, to the PFC (PV-interneurons), to the periaquaductal gray circuit, resulting in feed-forward inhibition. The manuscript is a detailed study of the role of alcohol exposure in regulating the circuit and reflexive pain, however, the role of the PV interneurons in mechanistically modulating this feed-forward circuit could be more strongly supported.

eLife Assessment

This manuscript presents important information as to how adolescent alcohol exposure (AIE) alters pain behavior and relevant neurocircuits, with convincing data. The manuscript focuses on how AIE alters the basolateral amygdala, to the PFC (PV-interneurons), to the periaquaductal gray circuit, resulting in feed-forward inhibition. The manuscript is a detailed study of the role of alcohol exposure in regulating the circuit and reflexive pain, however, the role of the PV interneurons in mechanistically modulating this feed-forward circuit could be more strongly supported.

eLife Assessment

This study provides a novel and critically important insight into the long-term use of DREADDs to modulate neuronal activity in nonhuman primates. The methods are compelling, demonstrating the peak dynamics and the subsequent stability of chemogenetic effects for 1.5 years, informing experimental designs and interpretation of highly impactful chemogenetic studies in macaques. The protocols, data, and outcomes can serve as guidelines for future experiments. Therefore, the findings will be of significant interest to the field of chemogenetics and may also be of broader interest to researchers and clinicians who seek to utilize viral vectors and/or related genetic technologies.

eLife Assessment

This important study provides compelling insights into the differential impact of intrinsic and synaptic conductances on circuit robustness using computational models of the pyloric network from the crustacean stomatogastric ganglion. The results demonstrate that model networks are more sensitive to perturbations in intrinsic conductances than in synaptic conductances, highlighting the critical role of intrinsic plasticity in stabilizing neuronal networks. These findings underscore the importance of intrinsic plasticity, a crucial yet often overlooked factor in neuronal dynamics. The generality of these conclusions should be tested across diverse networks and functions.

eLife Assessment

This observational study from the UK Biobank provides an important investigation into the associations between menopausal hormone therapy and brain health in a large, population-based cohort of females in the UK. A convincing model of brain aging using an open source algorithm is used. While some modest adverse brain health characteristics were associated with current mHT use and older age at last use, the findings do not support a general neuroprotective effect of mHT nor severe adverse effects on the female brain. This work addresses a topic that is of grave importance since menopausal hormone therapy and its effect on the brain should be better understood in order to provide individualized effective medical support to women going through menopause.

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.

eLife Assessment

This important study includes convincing evidence to show that behavioral measures and hippocampal representations when animals use task-relevant information and ignore irrelevant information do not depend on the medial prefrontal cortex. The results are expected to be of interest to those studying neural mechanisms of cognitive control and functions of associational brain regions.

eLife Assessment

The authors provide a useful summary of ten years of Brain Initiative funding including the historical development, the specific funding mechanisms, and examples of grants funded and work produced. The authors also conduct analyses of the impact on overall funding in Systems and Computational Neuroscience, the raw and field normalized bibliographic impact of the work, the social media impact of the funded work, and the popularity of some tools developed. The evidence for impact is incomplete due to the omission of a comparison group of funded grants.

eLife Assessment

The manuscript presents some useful accounts of experiences funding team projects within the BRAIN Initiative. These would be more appropriate to add to the companion manuscript since the present manuscript contains some overlapping analyses and does not stand well on its own. Therefore the evidence supporting the conclusions is incomplete.

eLife Assessment

This important computational study investigates homeostatic plasticity mechanisms that neurons may employ to achieve and maintain stable target activity patterns. The work extends previous analyses of calcium-dependent homeostatic mechanisms based on ion channel density by considering activity-dependent shifts in channel activation and inactivation properties that operate on faster and potentially variable timescales. The model simulations demonstrate the potential functional importance of these mechanisms, but the evidence is incomplete and would be strengthened by more in-depth analyses and explicit exposition.

eLife Assessment

This fundamental study concerns a model for transgenerational epigenetic inheritance, the learned avoidance by C. elegans of the PA14 pathogenic strain of Pseudomonas aeruginosa. The authors test the impact of procedural alterations made in another study, by Gainey et al., which claimed that transgenerational inheritance in this paradigm lacks robustness, despite this observation having been reported in multiple papers from the Murphy lab. The authors of the present study show that by following a non-standard avoidance protocol, Gainey et al. likely biased their measurements in a way that made it hard to observe learned avoidance. The authors also highlight the importance of bacterial growth conditions, showing that expression of the trigger molecule, the bacterial P11 RNA, which is necessary and sufficient to drive the transgenerational inheritance of the avoidance phenotype, is influenced by temperature. As expression of P11 was not verified by Gainey et al., this provides another explanation for the inability to observe transgenerational epigenetic inheritance. Together, the authors provide compelling and powerful arguments that the original phenomenon is robust and that it can be reproduced in the Murphy lab by following their original protocol precisely, including the use of azide to immobilize the worms at the food source. Overall, this study not only provides guidance for investigators in this experimental paradigm, but it also provides additional understanding of the differences between naïve preference, learned preference, and transgenerational epigenetic inheritance. The present study is therefore of broad interest to anyone studying genetics, epigenetics, or learned behavior.

eLife Assessment

This valuable study combines real-time keypoint tracking with transdermal activation of sensory neurons to investigate sensory neuron recruitment in freely moving mice, and builds on the authors' prior work in stationary mice. The evidence supporting the utility of the system is solid, although a more thorough classification of the behavioral responses to nociceptor stimulation would strengthen the work. Importantly, future analyses could include other cutaneous sensory neuron subtypes, and could also be adapted for studying more complex behaviors. The work will be of interest to sensory biologists and pain researchers.

eLife Assessment

This important study conducted experiments to quantify how neural activity independent changes in fluorescence might affect two-photon recordings when using diverse sensors. The researchers found a widespread presence of neural-activity-independent artifacts in two-photon imaging and provide convincing evidence that these artifacts are most likely caused by hemodynamic occlusion. Their findings underscore the importance of accounting for these artifacts when interpreting functional two-photon recordings.

eLife Assessment

This important study combines convincing evolution experiments with molecular and genetic techniques to study how a genetic lesion in MreB that causes rod-shaped cells to become spherical, with concomitant deleterious fitness effects, can be rescued by natural selection. The detailed mechanistic investigation increases our understanding of how mreB contributes to cell wall synthesis and shows how compensatory mutations may reestablish its homogeneity.

eLife Assessment

The authors provide important insights into a system of insect camouflage where a coating of self-made nano-particles (brochosomes) reduces the reflection of UV-light leading to lower predation by spiders. Compelling evidence is provided by micro-UV-Vis spectroscopy, electron microscopy, transcriptome and proteome analysis, histology, in-vivo predation assays and gene knock-downs. The phylogenetic analyses provide evidence that the genes coding for the brochosome proteins are clade-specific and have diversified by gene duplication.

eLife Assessment

In this useful study, the authors perform voltage imaging of CA1 pyramidal cells in head-fixed mice running on a track while local field potentials (LFPs) are recorded. The authors conclude that synchronous ensembles of neurons are differentially associated with different types of LFP patterns, namely theta and ripples. However, evidence for the claims in the paper remains incomplete, due to caveats of the experimental approach and claims that are based on a relatively sparse data set collected with a cutting-edge but still largely untested method.

eLife Assessment

This timely and important study used functional near-infrared spectroscopy hyperscanning to examine the neural correlates of how group identification influences collective behavior. The work provides incomplete evidence to indicate that the synchronization of brain activity between different people underlies collective performance and that changes in brain activity patterns within individuals may, in turn, underlie this between-person synchrony. This study will be of interest to researchers investigating the neuroscience of social behaviour.

eLife Assessment

This study unveils important data describing cell states of olfactory ensheathing cells, and how these cell states may relate to repair after spinal cord injury. The framework used for characterizing these cells is solid. This work will be of interest to stem cell biologists and spinal cord injury researchers.

eLife Assessment

This study reports important findings about pre-saccadic foveal prediction and the extent to which it is influenced by the visibility of the saccade target relative to its background. The research methodology and results make a convincing case that foveal congruency effects develop when salient local contrast variations at the saccade target location can be used to direct the eye movement. This work should be of broad interest to visual neuroscientists, as well as those interested in understanding perception in the context of eye movements and in modeling visually guided actions.

eLife Assessment

This important study reveals that the nucleolar protein Treacle undergoes liquid-liquid phase separation in vitro and in vivo. It provides convincing evidence that the ability of Treacle to form phase-separated condensates is necessary for the proper formation of the fibrillar center of the nucleolus, rRNA transcription, and rDNA repair. These findings will be of interest to the communities studying biomolecular condensates, nucleolar organization, and ribosome biogenesis.

eLife Assessment

This is important work and provides a significant advance in our understanding of mechanosensation in the epidermis. The evidence presented is convincing and, barring a few minor weaknesses, strongly implicates activation of epidermal cells and store-operated calcium entry in the activation of nociceptive neurons innervating that tissue. This work will be of broad interest to neurobiologists, epithelial cell biologists, and mechanobiologists.

eLife Assessment

This valuable study proposes using a rigorous computational model to assess memory deficits in Alzheimer's Disease with the goal of developing an early diagnosis tool for the disease. Using an established mouse model of the disease, the authors studied multiple behavioral tasks and ages with the goal of showing similarities in behavioral deficits across tasks. Using the model, the authors indicate specific deficits in memory (overgeneralization and overdifferentiation) in mice with the transgene for the disease. However, the evidence presented is incomplete as certain concerns remain regarding the interpretation of the behavioral results and the validation of the model fit.

eLife Assessment

This useful study reports datasets on gene expression and chromatin accessibility profiles of spermatogonia at different postnatal ages in mice. Overall, the technical aspects of the sequencing analyses and computational/bioinformatics are solid. This study may be of interest to biomedical researchers working on male germline stem cells and male fertility.

eLife Assessment

Huang and colleagues examined neural responses in mouse anterior cingulate cortex (ACC) during a discrimination-avoidance task. The authors present useful findings that ACC neurons encode primarily post-action variables over extended periods rather than the outcomes or values of those actions. Though the methodological approach was sound, the evidence ruling out alternative explanations is incomplete and requires substantial control analyses.

eLife Assessment

This manuscript by Kaur et al. identifies differential gene expression observed in distinct mouse lung cell populations, namely myeloid and lymphoid cells, upon short-term exposure to e-cig aerosols with various flavors. Their findings are potentially useful because the single-cell sequencing data provides a reference for future studies of genes and cellular pathways that are most affected by e-cig aerosols and their components. However, the evidence is incomplete due to limited statistical analyses and few biological replicates, as well as a lack of experimental validation.

eLife Assessment

This important study suggests that adolescent mice exhibit less accuracy than adult mice in a sound discrimination task when the sound frequencies are very similar. While the evidence supporting this observation is solid, demonstrating that this effect arises from cognitive differences between adolescent and adult mice requires more thorough documentation of task performance, as well as control of impulsivity and baseline licking. The authors should also clarify how difficult and easy trials are interleaved in the task and provide a more comprehensive discussion of the cortical inactivation results in relation to the overall task difficulty.

eLife Assessment

This study presents important information about the role of mu opioid receptors in synaptic communication between the medial habenula and the interpeduncular nucleus. The authors provide solid evidence that mu opioid receptor activation has differential effects on glutamate release from substance P neurons and cholinergic neurons, with a canonical reduction in release from the former but a novel increase in release from the latter. They also show that blocking potassium channels can unmask a nicotinic cholinergic synaptic response that is also facilitated by mu opioid receptor activation. This work will be of interest to those studying the interpeduncular nucleus, as well as the larger neuroscience community studying opioids and motivated behavior.

eLife Assessment

This useful study describes a novel method for imaging NAD(P)H fluorescence lifetime and thus metabolic states in the Drosophila brain. These solid findings support recent work demonstrating the importance of energy homeostasis to sustain memory formation and maintenance. Further efforts to demonstrate the adequacy of the statistical methods and the significance of the observed differences in FLIM signals in the α/β KCs would greatly enhance the manuscript. The approach will be helpful for researchers working with systems where genetic manipulation is challenging.

eLife Assessment

This study provides proof-of-principle data for the use of trained immunity to modulate macrophage interactions with tumours. The study makes a valuable contribution to the field of trained immunity. However, the study is incomplete without vivo data, which would have made the claims in the paper stronger by providing meaningful context for the in vitro experiments that were conducted.

eLife Assessment

Using fMRI-based pRF mapping, this important study presents a novel method to estimate visual field (VF) and VF loss/or potential restoration, through analysis of contrast sensitivity patterns in the early visual cortex. While the approach is very interesting and the evidence supporting the claims of the authors is solid, some methodological concerns need to be addressed. The work will be of interest to researchers in vision/clinical vision, neuroscience, and brain imaging.

eLife Assessment

The medicinal leech preparation is an amenable system in which to understand the neural basis of locomotion. Here a previously identified non-spiking neuron was studied in leech and found to alter the mean firing frequency of a crawl-related motoneuron, which fires during the contraction phase of crawling. The findings are valuable and the experiments were diligently done and generally solid; however, the presentation could improve. The work could be taken to the next level by further experiments, and by providing more overall context for the study.

eLife assessment

The work is interesting in its characterization of a large number of antibiotic persisters from a wild-type strain. Previous work was typically limited to directly observe either high persister strains or a smaller number of wt persisters. Therefore, it sheds new light on the elusive non-dormant persisters present in exponentially growing cultures and should help resolve previous conflicting observations.

eLife Assessment

This important study compares the cortical projections to primary motor and sensory areas originating from the ipsilateral and contralateral hemispheres. Results show that, while there is substantial symmetry between the two hemispheres regarding the areas sending projections to these primary cortical areas, contra-hemispheric projections had more inputs from layer 6 neurons than ipsi-projecting ones. The evidence is compelling and the conclusions are supported by rigorous analyses.

eLife Assessment

This study aims to identify the proteins that compose the electrical synapse, which are much less understood than those of the chemical synapse. The study is useful in terms of both method development and biological advances, as the authors identified more than 50 new proteins and used immunoprecipitation and immunostaining to validate their interaction. However, the current experimental data are considered incomplete, as many key experimental details are missing.

eLife Assessment

This study presents a valuable finding on the importance of the plasma metabolome in glaucoma risk prediction. The evidence supporting the claims of the authors is solid and the work offers insights for the design of protective therapeutic strategies for glaucoma. The authors have addressed the concerns of the reviewers and reported on the limitations of the study.

eLife Assessment

The authors examine the role of Numb, a Notch inhibitor, in intestinal stem cell self-renewal in Drosophila during homeostasis and regeneration. The significance is important as the authors demonstrate the ISC maintenance is reduced when both BMP signaling and Numb expression is reduced. The strength of evidence is convincing as large sample sizes and statistical analyses are provided.

eLife Assessment

This valuable study shows that an odorant that is typically thought of as a repellant actually activates both attractant and repellant olfactory neurons in C. elegans. Solid evidence is provided that nematode worms can integrate signals using different pathways to drive different behavioral responses to the same cue. These findings will be of interest to scientists interested in combinatorial coding in sensory systems.

eLife Assessment

This valuable study sets new standards in analyzing the ultrastructure of insect eyes, which have long served as models for understanding how vision works. The way it describes an entire eye with the resolution of electron microscopy is convincing. On top of this, a miniaturized visual system provides additional, remarkable insights towards understanding optimized solutions.

eLife Assessment

This valuable study sets new standards in analyzing the ultrastructure of insect eyes, which have long served as models for understanding how vision works. The way it describes an entire eye with the resolution of electron microscopy is convincing. On top of this, a miniaturized visual system provides additional, remarkable insights towards understanding optimized solutions.

eLife Assessment

This study presents useful data on sex differences in gene expression across organs of four mice taxa. While the methods and analysis are largely sound, the strength of evidence is solid only in parts and the conclusions drawn from the results are not always appropriate.

eLife Assessment

This valuable study unravels the mechanisms underlying mammalian sperm-oocyte recognition and penetration, shedding light on cross-species interactions. It provides solid evidence that exposure of sperm to oviductal fluid or OVGP1 proteins from bovine, murine, or human sources imparts species-specific zona pellucida (ZP) recognition, ensuring that only sperm from the corresponding species can penetrate the ZP, regardless of its origin. These findings hold significant potential for reproductive biology, offering insights to enhance porcine in vitro fertilization (IVF), which frequently suffers from polyspermy, as well as advancing human IVF through improved intrinsic sperm selection.

eLife Assessment

This is a convincing study of the morphological properties of Purkinje cell dendrites and dendritic spines in adult humans and mice, and the anatomical determinants of multi-innervation by climbing fibers. The data will provide an important resource for the field of cerebellar computation.

eLife Assessment

This important study shows that the Nora virus, a natural Drosophila pathogen that also persistently infects many laboratory fly stocks, infects intestinal stem cells (ISCs), leading to a shorter life span and increased sensitivity to intestinal infection with the Pseudomonas bacterium. The authors provide convincing data to support their conclusions. The paper provides new insights into virus-host interactions in the Drosophila gut and serves as a warning for scientists who use the fruit fly as a model to study gut physiology.

eLife Assessment

This important research addresses the effects of subjective control and task difficulty on experienced stress using a novel behavioral task in two, large online samples. Convincing evidence is provided, establishing internal and external task validity and a relationship with individual differences in relevant mental health constructs. Evidence for the core claims could be strengthened by disentangling the effects of controllability from those of reward rate and adjusting data parcellation for computing internal consistency. This work will be of interest to psychologists and clinicians studying controllability, stress, and psychopathology.

eLife Assessment

The authors study the context of the skeletal remains of three individuals and associated sediment samples to conclude that the hominin species Homo naledi intentionally buried their dead. Demonstration of the earliest known instance of intentional funerary practice - with a relatively small-brained hominin engaging in a highly complex behavior that has otherwise been observed from Homo sapiens and Homo neanderthalensis - would represent a landmark finding. The authors have revised their manuscript extensively in light of the reviews of their initial submission, with improved illustration, context, discussion, and theoretical frameworks, leading to an improved case supporting their conclusion that Homo naledi intentionally buried their dead. One of the reviewers concludes that the findings convincingly demonstrate intentional burial practices, while another considers evidence for such an unambiguous conclusion to be incomplete given a lack of definitive knowledge around how the hominins got into the chamber. We look forward to seeing the continued development and assessment of this hypothesis. It is worth noting that the detailed reviews (both rounds) and comprehensive author response are commendable and consequential parts of the scientific record of this study. The editors note that the authors' response repeatedly invokes precedent from previous publications to help justify the conclusions in this paper. While doing so is helpful, the editors also note that scientific norms and knowledge are constantly evolving, and that any study has to rest on its own scientific merit.

eLife Assessment

This study offers valuable insights into the conformational dynamics of the nucleic acid recognition lobe of GeoCas9, a thermophilic Cas9 from Geobacillus stearothermophilus. The authors investigate the influence of local dynamics and allosteric regulation on guide RNA binding affinity and DNA cleavage specificity through advanced NMR techniques and mutagenesis. The revised manuscript incorporates new experimental data, including molecular dynamics simulations and additional RNA binding studies, which provide convincing support for the findings. While the mutations studied do not lead to significant changes in GeoCas9 cleavage activity, the study contributes to a better understanding of the allosteric mechanisms and interdomain communication in Cas9 enzymes, and will be of great interest to biochemists and biophysicists exploring these complex systems.

eLife Assessment

This important study aims to understand the role of endothelial cell differentiation into pericytes in the restoration of blood-brain barrier function after ischemic stroke. Identification of pericytes derived from endothelial cells and the involvement of myeloid cell-derived TGFβ1 signaling are compelling new findings, but the evidence supporting the origin and nature of these pericytes is incomplete and would benefit from more rigorous approaches demonstrating reproducibility. The work will be of interest to researchers whose work focuses on the blood-brain barrier and basic and translational stroke.

eLife Assessment

This work is of fundamental significance and has an exceptional level of evidence for the role of a mutant p53 in regulation of tumorigenesis using an in vivo mouse model. The study is well-conducted and will be of interest to a broad audience including those interested in p53, transcription factors and cancer biology.

eLife Assessment

The manuscript provides valuable findings in the field for understanding the RNAi regulation in plants at the molecular level with a model of how DRB7.2 and DRB4 form a heterodimer and protect dsRNA from DICER activity. The presented data provide a solid basis for the model, but certain measurements could benefit from replicates for robust statistics.

eLife Assessment

In this manuscript, Franco and colleagues describe valuable findings about the chemotactic response of Salmonella to serine and indole, conflicting chemotactic signals. Although the evidence presented is solid, concerns were raised about the novelty of the chemotactic phenomena observed with these two compounds. Also, although the induction of invasion by feces is a novel and interesting finding, the lack of follow-up to this observation was also noted.

eLife Assessment

This solid work, a Research Advance linked to Buchwalter et al., 2019, demonstrates that epitope tagging influences protein fate, serving as a cautionary example of how different tagging and imaging strategies may alter the pattern of endogenous protein trafficking. The information presented will be useful for researchers in the field of membrane trafficking, particularly in guiding their experimental designs. That being said, the study offers limited new insights into the biogenesis or disposal of endogenous Emerin.

eLife Assessment

This study shows that a peptide called galanin can decrease or increase seizure activity in experimental models of seizures depending on the model. The authors use zebrafish and several methods to address the effects of galanin. The study will be useful to researchers who use zebrafish as experimental animals and who are interested in how peptides like galanin regulate seizures. However, the strength of evidence was considered incomplete at the present time due to several limitations of the results.

eLife Assessment

This potentially important model-based study seeks to mimic bat echolocation behavior and flight under high-density conditions. The simulations convincingly suggest that the problem of acoustic jamming in these situations may be less severe than previously thought, a finding that would be of broad interest to scientists working in the fields of bat biology and collective behaviour. However, some aspects of the manuscript were found to lack clarity and concerns were raised about some of the assumptions underlying the parameters used for the simulations, which impact both the modeling results and the conclusions that can be made from the data.

eLife Assessment

In this article, García-Vázquez et al. report valuable findings demonstrating that G2 and S phases expressed protein 1 (GTSE1), is a previously unappreciated non-pocket substrate of the cyclin D/cyclin-dependent kinase (CDK) 4/6 axis. The authors provide convincing evidence showing that this mechanism is triggered in pathological states in which cyclin D levels are elevated (e.g., cancer). Overall, this study holds a promise to improve understanding of the mechanisms underpinning cell cycle progression including its dysregulation in neoplasia and may thus be of broad interest to researchers belonging to diverse biomedical disciplines ranging from cancer research to cell biology.

eLife Assessment

This is an important study demonstrating the importance of S100A4+ alveolar macrophages in the earlier stages of tumour development and suggesting a role in angiogenesis. As such this convincing study is of interest to cancer biologists focused on early tumour development and those interested in the development of therapeutics that may specifically target early cancers.

eLife Assessment

How misfolded proteins are segregated and cleared is a significant question in cell biology, since clearance of these aggregates can protect against pathologies that may otherwise arise. The authors discover a cell cycle stage-dependent clearing mechanism that involves the ER chaperone BiP, the proteosome, and CDK inactivation, but is curiously independent of the anaphase promoting complex (APC). These are valuable and interesting new observations, but the evidence supporting these claims is partially incomplete. New experiments and/or toning down the conclusions and highlighting what has not been learned may be appropriate and can then spur more work in the field.

eLife Assessment

Cardiolipin is known to play an important role in modulating the assembly and function of membrane proteins in bacterial and mitochondrial membranes. Here, 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, the characterization of their dynamic features, and the role in membrane protein stability and activity, will provide much needed insight into the still poorly understood nature of protein-cardiolipin interactions.

eLife Assessment

This important study provides insights into the role of maternal behavior in the learning and ontogeny of vocalization. It finds evidence that the maternal behavior of sac-winged bats (Saccopteryx bilineata) can influence the learned territorial songs of their pups. The behavioral analyses are convincing, using longitudinal acoustic recordings and behavioral monitoring of individual mother-pup pairs across development and multiple wild bat colonies. The work will be relevant to a broad audience interested in the evolution and development of social behavior as well as sensory-motor learning.

eLife Assessment

This valuable contribution to the field evaluated the function of the cytoskeletal protein ABBA in mediating key aspects of mitosis of neuronal precursor cells. The authors provide compelling evidence that ABBA interactions with its signaling partners is related to the development of at least some cases of microcephaly — a developmental anomaly associated with intellectual disability and other neurological findings.

eLife Assessment

This important Research Advance presents compelling 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.

eLife Assessment

In this valuable study, the authors integrate several datasets to describe how the genome interacts with nuclear bodies across distinct cell types and in Lamin A and LBR knockout cells. They provide convincing evidence to support their claims and particularly find that specific genomic regions segregate relative to the equatorial plane of the cell when considering their interaction with various nuclear bodies.

eLife Assessment

Using multiple techniques previously validated by the authors, this study identified INTS12, a component of the Integrator complex involved in 3' processing of small nuclear RNAs U1 and U2, as a factor promoting HIV-1 latency. The work is valuable, based on a sound strategy for screening targets to activate HIV latency and the solid mechanistic insights it provides on INTS12 repression of transcriptional elongation. Future studies are needed to explore INTS12 as a drug target against HIV/AIDS.

eLife Assessment

This valuable study investigates both online responses to, and offline replay of, visual motion sequences. Sophisticated EEG analyses provide convincing evidence for both feature-specific and non-specific sequence representations. These intriguing findings will be of interest to perception and learning researchers alike.

eLife Assessment

This important study uses reinforcement learning to study how turbulent odor stimuli should be processed to yield successful navigation. The authors find that there is an optimal memory length over which an agent should ignore blanks in the odor to discriminate whether the agent is still inside the plume or outside of it, complementing recent studies using recurrent neural networks and finite state controllers to identify optimal strategies for navigating a turbulent plume. The strength of evidence is compelling, presenting a novel approach to understanding optimal representations for navigation in stochastic sensory environments.

eLife Assessment

In this important and compelling study, Sánchez-León et al. investigate the effects of tDCS on the firing of single cerebellar neurons in awake and anesthetized mice. They find heterogeneous responses depending on the orientation of the recorded Purkinje cell. The paper may well explain part of the controversial and ambiguous outcomes of various clinical trials.

eLife Assessment

This important study provides significant insights into the dynamics of attentional re-orienting within visual working memory, demonstrating how expected and unexpected memory tests influence attention focus and re-focus. The evidence supporting these conclusions is convincing, with the use of state-of-the-art methodologies. This work will be of interest to cognitive neuroscientists studying attention and memory.

eLife Assessment

This study by Li et al. presents important findings on the metabolism-independent role of nuclear IDH1 in chromatin regulation during erythropoiesis. The authors provide convincing evidence that IDH1 deficiency disrupts H3K79 methylation and nuclear architecture, contributing to dyserythropoiesis. Their findings offer invaluable mechanistic insights with potential therapeutic implications for erythroid disorders and hematologic malignancies.

eLife Assessment

This study provides a potentially useful investigation into the positive role of BDNF/TrkB signaling in implanted dental pulp stem cells to enhance dentin regeneration in the context of dental caries. Some of the key methods used need to be much better documented, and the data should be strengthened and added to in support of several of the claims of functional benefit, which are inadequately supported at present. Additional details for the validation of the reagents and techniques are needed to support the interpretation of the results.

eLife Assessment

The authors propose that the kinase MARK2 regulates the Golgi's reorientation towards the cell's leading edge through the regulation of microtubule binding protein CAMSAP2 and its binding to USO1. While the model is interesting and the study is useful, the quantification of an insufficient number of cells and insufficient description of the methods and biological replicates mean the results are inadequate to support the model.

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

eLife Assessment

This manuscript offers an exploration of the immune cells in the oyster Crassostrea gigas, by correlating distinct hemocyte morphotypes with specific single-cell transcriptional profiles. The evidence supporting the conclusion is convincing, deriving from the comprehensive dataset that not only captures unicellular diversity but also associates these cells with distinct immune roles, making it an important resource for the broader research community. There are some concerns on the data presentation that leave some questions.

eLife Assessment

Kin selection and inclusive fitness have generated significant controversy. While not entirely new, this paper reconsiders the general form of Hamilton's rule in which benefits and costs are defined as regression coefficients, with higher-order coefficients being added to accommodate non-linear interactions. The paper is a valuable contribution to the field with convincing, systematic analysis, giving clarity to long-standing debates.

eLife Assessment

This valuable study advances our understanding of genome annotations for chiton genomes. It provides a solid estimation of syntentic relationships for the chromosomes of the four new genomes plus an analysis linking these to other available chiton genomes, and an update for how these relate to molluscan genomes.

eLife Assessment

This useful study employs AlphaFold2 to predict interactions among 20 nuage proteins, identifying five novel interaction candidates, three of which are validated experimentally through co-immunoprecipitation. Expanding the analysis to 430 oogenesis-related proteins and screening ~12,000 Drosophila proteins for interactions with Piwi, the study identifies 164 potential binding partners, demonstrating how computational predictions can streamline experimental validation. This study provides a solid basis for further investigations into eukaryotic protein interaction networks.

eLife Assessment

This study explores how complement protein C3 and its signalling may modulate immune training in alveolar macrophages. The findings are an important contribution to the field of trained immunity. The data presented is mainly solid, but incomplete in parts.

eLife Assessment

This study provides compelling evidence that kinesin's stepping mechanism is governed by strain-induced conformational changes in its nucleotide-binding pockets. Using pre-steady state kinetics and single-molecule assays, the authors demonstrate that the neck linker's conformation differentially modulates nucleotide affinity and detachment rates, establishing an asynchronous chemo-mechanical cycle that prevents simultaneous detachment. Supported by cryo-EM structural data, the work presents an important advance in our understanding of kinesin's hand-over-hand movement.

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

eLife Assessment

This valuable study tackles the well-established overflow metabolism issue by applying a coarse-grained metabolic flux model to predict how individual cells execute various energy strategies, such as respiration versus fermentation. The model's population average is convincing enough to align with experimental observations on overflow metabolism. The potential source of metabolic or proteomic heterogeneity of individual cells remains an open question to be studied. How individual cells adjust their metabolic strategies also requires future study of the underlying mechanisms. Overall, this work provides a key aspect on cell-to-cell variability on general metabolic response.

eLife Assessment

This valuable study uses state-of-the-art neural encoding and video reconstruction methods to achieve a substantial improvement in video reconstruction quality from mouse neural data, providing a convincing demonstration of how reconstruction performance can be improved by combining these methods. The findings showed that model ensembling and the number of neurons used for reconstruction were key determinants of reconstruction accuracy, but the theoretical contribution to understanding neural encoding was less clear. The treatment of how image masking improved reconstruction performance was also incomplete.

eLife Assessment

This manuscript provides valuable novel insights into the role of interpersonal guilt in social decision-making by showing that responsibility for a partner's bad lottery outcomes influences happiness. Through the integration of neuroimaging and computational modelling methods, and by combining findings from two studies, the authors provide solid support for their claims.

eLife Assessment

This is an important study showing that people who are hungry (vs. sated) put more weight on taste (vs. health) in their food choices. The experiment is well-designed and includes choice behavior, eye-tracking, and state-of-the-art computational modeling, resulting in compelling evidence supporting the conclusions. The manuscript could be further improved through appropriate revisions to data analysis and interpretation.

eLife Assessment

The manuscript by Mancl et al. provides valuable mechanistic insights into the conformational dynamics of Insulin Degrading Enzyme (IDE), a zinc metalloprotease involved in the clearance of various bioactive peptides. Supported by a convincing combination of cryo-EM, SEC-SAXS, enzymatic assays, and molecular dynamics simulations, the study characterizes the dynamic transitions between IDE's open and closed states in the presence of a sub-saturating concentration of insulin. This work contributes to a refined model of IDE's functional cycle, enhancing our understanding of its role in proteolysis.

eLife Assessment

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

eLife Assessment

This important contribution to the field demonstrates the role of a single transcription factor with cell-autonomous functions in the differentiation of two distinct neuronal populations in regulating the interactions between those cells in a non-autonomous manner to generate their final organized projection pattern. There are additional quantifications and controls that would enhance the convincing nature of the study and would raise the strength of the evidence from incomplete if they were performed.

eLife Assessment

This paper provides an important proposal for why learning can be much faster and more accurate if synapses have a fast component that immediately corrects errors, as well as a slower component that corrects behavior averaged over a longer timescale. It is convincingly shown that integrating these two learning timescales improves performance compared to classical strategies, particularly in terms of robustness and generalization when learning new target signals. However, the biological plausibility and justification for the proposed rapid learning mechanism require further elaboration and supporting mechanistic examples.

eLife Assessment

This work presents an important genetic toolkit for Drosophila neurobiologists to access and manipulate neuronal lineages during development and adulthood. The evidence supporting the fidelity of this toolkit is convincing. This work will interest Drosophila neurobiologists in general, and some of the genetic tools may be used outside the nervous system. The conceptual approaches used in this paper are likely transferable to other fields as comparable data and genomic methods are obtained.

eLife Assessment

This study introduces a useful toolkit for zebrafish transgenesis, significantly enhancing the flexibility and efficiency of transgene generation for immunological applications. The authors provide supporting evidence through well-designed experiments, demonstrating the toolkit's utility in generating diverse and functional transgenic lines. While the findings are solid, additional functional validation and broader comparisons to existing systems would strengthen the overall evidence base and ensure broader relevance to the zebrafish field, thereby increasing the significance of the study.

eLife Assessment

This manuscript introduces Opto-PKCε, an optogenetic tool that enabled important findings derived from interactome and phosphoproteome studies. Light-dependent recruitment of Opto-PKCε to the plasma membrane revealed the specific phosphorylation of the insulin receptor at Thr 1160. In turn, recruitment to mitochondria led to phosphorylation of the complex I subunit NDUFS4, correlating with reduced spare respiratory capacity. The evidence supporting these conclusions is solid, although additional clarification on data analysis would further enhance readability.

eLife Assessment

The study reports valuable findings on the nature of genotype-by-climate interaction, parameterised in a framework that allows integrating genetics and ecophysiological variation in switchgrass. The evidence provided is solid overall but the analysis could be improved to better support some of the claims.

eLife Assessment

This paper reports the fundamental finding of how Raman spectral patterns correlate with proteome profiles. The authors then go further to show that this can be used to infer global stochiometric regulation of the proteomes. These findings are likely general and the authors provide compelling evidence by analyzing bacterial and human cells but there are some suggestions provided below to make the work clearer and more accessible for it to reach a broader audience.

Editors Assessment:

As volumes of viral and bacterial sequence data grow exponentially, the field of computational phylogenetics now demands resources to manage the burgeoning scale of this input data. This study introduces CompactTree, a C++ library designed for ultra-large phylogenetic trees with millions of tips. To address these scalability issues while maintaining ease of incorporation into external code bases, CompactTree is a header-only library with enhanced performance utilizing minimal dependencies, optimized node representation, and memory-efficient tree structure schemes. Resulting in significantly reduced memory footprints and improved processing times. Peer review requested some more detail on the functionality and some real-world examples, demonstrating the current utility of the tool. Although primarily supporting the (text-based) Newick format, the increased and extensibility scalability holds promise for multiple biological and epidemiological applications supporting more complex formats such as Nexus and NeXML. The tool is open source (GPLv3 licensed) and available in GitHub: https://niema.net/CompactTree

This evaluation refers to version 1 of the preprint

eLife Assessment

This valuable study identifies a protein called adenosine deaminase-related growth factor (ADGF) as a key regulator of tip formation in the slime mold Dictyostelium discoideum. The authors convincingly show that ADGF catalyses the formation of ammonia from adenosine, allowing ammonia to initiate tip formation, and then elucidate pathways upstream and downstream from ADGF. The authors discuss the intriguing possibility that mammalian ADGF may also similarly regulate development.

eLife Assessment

This important study by Liu et al. presents a comprehensive structure-function analysis of the presynaptic protein UNC-13, leading to new insights into how its distinct domains control neurotransmitter release. The methods, data, and analyses are convincing, and the genetic and electrophysiological approaches support many of their conclusions. The work will be of interest to neuroscientists studying synaptic transmission, as it provides a foundation for future mechanistic studies of Munc13/UNC-13 family proteins.

eLife Assessment

This valuable work investigates the social interactions of mice living together in a system of multiple connected cages. It provides solid evidence for a statistical approach capturing changes in social interactions after manipulating prefrontal cortical plasticity. This research will be of broad interest to researchers studying animal social behaviour.

eLife Assessment

The study presents valuable insights into the role of periosteal stem cells in bone marrow regeneration. The evidence is convincing. The data broadly support their claims and in line with state-of-art methodology. Future study on their model will help to strengthen their discovery further.

eLife Assessment

This useful study introduces a deep learning-based algorithm that tracks animal postures with reduced drift by incorporating transformers for more robust keypoint detection. The efficacy of this new algorithm for single-animal pose estimation was demonstrated through comparisons with two popular algorithms. The strength of evidence is solid but would benefit from consideration of issues in multi-animal tracking. This work will be of interest to those interested in animal behavior tracking.

eLife Assessment

This useful manuscript reports on the crystal structures of two glycosaminoglycan (GAG) lyases from the PL35 family, along with in vitro enzyme activity assays and comprehensive structure-guided mutagenesis. The authors have addressed key concerns by incorporating additional docking analyses, validating the role of His188 in alginate degradation, and providing ICP-MS data to examine Mn²⁺ binding. While these improvements enhance the study, the study is incomplete due to the lack of enzyme-substrate complex structures and reliance on modeling which still limit mechanistic insight. Nonetheless, the revised manuscript presents a more complete analysis that will be of interest to specialists in carbohydrate-active enzymes.

eLife Assessment

This important work advances our understanding of how the SARS-CoV-2 Nsp16 protein is regulated by host E3 ligases to promote viral mRNA capping. Support for the overall claims in the revised manuscript is convincing . This work will be of interest to those working in host-viral interactions and the role of the ubiquitin-proteasome system in viral replication.

eLife Assessment

This study provides a valuable contribution to our understanding of causal inference in visual perception. The evidence provided through multiple well-designed psychophysical experiments is convincing. The current study targets very specific visual features of launch events, future work will be able to build on this to study the implementation of causal inference in general.

eLife Assessment

Cichlid fishes have attracted attention from a wide range of biologists because of their<br /> extensive species diversification at the ecological and phenotypic levels. In this important study, the authors have partially revealed the mechanism behind lip thickening in cichlid fishes, which has evolved independently across three lakes in Africa. To explore this phenomenon, the authors used histological comparison, proteomics, and transcriptomics, all of which are well suited for their objectives. With compelling evidence, this contribution provides insights into parallel evolution in polygenic traits and holds significant value for the field.

eLife Assessment

This important manuscript investigates the role of olfactory cues in Pieris brassicae larvae, focusing on their interactions with the host plant Brassica oleracea and the parasitoid wasp Cotesia glomerata. The authors' demonstration that impaired olfactory perception reduces caterpillar performance and increases susceptibility to parasitism is solid. These findings highlight the ecological significance of olfaction in mediating feeding behavior and predator avoidance in herbivorous insects.

eLife Assessment

This study presents a valuable open-source and cost-effective method for automating the quantification of male aggression and courtship in Drosophila melanogaster. The work as presented provides solid evidence that the use of the behavioral setup that the authors designed - using readily available laboratory equipment and standardised high-performing classifiers they developed using existing software packages - accurately and reliably characterises social behavior in Drosophila. The work will be of interest to Drosophila neurobiologists and particularly to those working on male social behaviors.

eLife Assessment

This study presents a valuable finding on predator threat detection in C. elegans and the role of neuropeptide systems in defensive behavioral strategies. The evidence supporting the conclusions is solid, although additional analyses and control experiments would strengthen the claims of the study. Overall, the work is of interest to the C. elegans community as well as neuroethologists and ecologists studying predator-prey interactions.