eLife Assessment

This study presents TopOMetry, an important novel dimensionality reduction method that addresses a signficant challenge in the analysis of single-cell RNA sequencing data. The authors provide convincing evidence of the method's utility across various tasks, including estimating intrinsic dimensionalities and identifying cell types. The work would benefit from more rigorous validation and a reorganization of the text.

eLife Assessment

This important study provides convincing evidence that emotional information in biological motion can induce different patterns of pupil responses, which could serve as a behavioral marker of an autistic trait. These results broaden our understanding of how emotional biological motion can automatically trigger physiological changes and reveal the potential of using emotional-modulated pupil response to facilitate the diagnosis of social cognitive disorders. The work will be of broad interest to cognitive neuroscience, psychology, affective neuroscience, and vision science.

eLife Assessment

This important study identifies a short amino acid sequence that, when fused in multimeric form to the amino termini of luminal ER proteins, initiates proteasomal degradation via the Hrd1 ER quality control ubiquitin ligase complex. The authors provide solid evidence that this sequence functions as a "degron" for ER proteins. Future work is required to obtain a more detailed view of the properties of this degron, the mechanisms underlying its recognition by ER-resident and cytoplasmic factors, and the in vivo relevance of the findings.

eLife Assessment

Brain inflammation is a hallmark of multiple sclerosis. Using novel spatial transcriptomics methods, the authors provide solid evidence for a gradient of immune genes and inflammatory markers from the meninges toward the adjacent brain parenchyma in a mouse model. This important study advances our understanding of the mechanisms of brain damage in this autoimmune disease.

eLife Assessment

Genetic analysis of complex traits in Drosophila provides a resource for exploring the relationship between genetic and phenotypic variation. The web tool DGRPool presented in this paper makes data and results from the Drosophila Genetic Reference Panel accessible that will enable downstream analyses of genetic association. The findings of this paper are considered to be important, with practical implications beyond a single subfield, supported by convincing evidence using appropriate and validated methodology in line with current state of the art.

Editors Assessment:

This Data Release paper presents the genome of the whippet breed of dog. Demonstrating a streamlined laboratory and bioinformatics workflows with PacBio HiFi long-read whole-genome sequencing that enables the generation of a high-quality reference genome within one week. The genome study being a collaboration between an academic biodiversity institute and a medical diagnostic company. The presented method of working and workflow providing examples that can be used for a wide range of future human and non-human genome projects. The final is 2.47 Gbp assembly being of high quality - with a contig N50 of 55 Mbp and a scaffold N50 of 65.7 Mbp. This reference being scaffolded into 39 chromosome-length scaffolds and the annotation resulting in 28,383 transcripts. The results also looked at the Myostatin gene which can be used for breeding purposes, as these heterozygous animals can have an advantage in dog races. The reviewers making the authors clarify this part a little better with additional results. Overall this study demonstrating how rapidly animal genome research can be carried out through close and streamlined time management and collaboration.

This evaluation refers to version 1 of the preprint

eLife Assessment

This important study shows that a splice variant of the kainate receptor Glu1-1a that inserts 15 amino acids in the extracellular N-terminal region substantially changes the channel's desensitization properties, the sensitivity to glutamate and kainate, and the effects of modulatory Neto proteins. In the revised paper the authors have clarified several points raised by reviewers but the structural portion of the study has not been improved and consequently, more data are needed to determine the molecular mechanism by which the insert changes the functional profile of the channel. Even so, these solid findings advance our understanding of splice variants among glutamate receptors and will be of interest to neuro- and cell-biologists and biophysicists in the field.

eLife Assessment

This study presents an important investigation of water coordination in a specific kinase family with a focus on the regulation of osmosensing protein kinases. X-ray crystallographic approaches combined with functional assays are used to address the hypothesis that bound water participates in the osmosensing mechanism as an allosteric kinase inhibitor. The evidence for changes in kinase conformation and space group of the crystal as a function of added low molecular weight polyethylene glycol is solid. The work will be of considerable interest to the kinase field as well as colleagues studying allosteric regulation of protein function.

eLife Assessment

This fundamental study uses a creative experimental system to directly test Ohno's hypothesis, which describes how and why new genes might evolve by duplication of existing ones. In agreement with existing criticism of Ohno's original idea, the authors present compelling evidence that having two gene copies does not speed up the evolution of a new function as posited by Ohno, but instead leads to the rapid inactivation of one of the copies through the accumulation of mostly deleterious mutations. These findings will be of broad interest to evolutionary biologists and geneticists.

eLife Assessment

In this valuable study, the authors investigate how inflammatory priming and exposure to irradiated Mycobacterium tuberculosis or the bacterial endotoxin LPS impact the metabolism of primary human airway macrophages and monocyte-derived macrophages. The work shows that metabolic plasticity is greater in monocyte-derived macrophages than alveolar macrophages, with solid experimental methods and overall evidence. The findings are relevant to the field of immunometabolism.

eLife Assessment

This study investigates the role of Caspar (Casp), an orthologue of human Fas-associated factor-1, in regulating the number of primordial germ cells that form during Drosophila embryogenesis. The findings are important in that they reveal an additional pathway that contributes to germ cell specification and maintenance. The evidence supporting the conclusions is solid, as the authors identify Casp and its binding partner Transitional endoplasmic reticulum 94 (TER94) as factors that influence germ cell numbers.

eLife Assessment

This important paper addresses the role of fluid flows in nutrient uptake by microorganisms propelled by the action of cilia or flagella. Using a range of mathematical models for the flows created by such appendages, the authors provide convincing evidence that the two strategies of swimming and sessile motion can be competitive. These results will have significant implications for our understanding of the evolution of multicellularity in its various forms.

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.

eLife Assessment

Treatment of pseudomonas aeruginosa (PA) is challenging because of intrinsic and acquired antibiotic resistance to most antibiotic drug classes. Therefore, by using donor B cells in subjects with cystic fibrosis who undergo intermittent or chronic airway PA infections, the authors tried to isolate BCRs against PA virulence factors and examine their biological activities. The data are solid and isolated protective antibodies could be useful for protection against PA.

eLife Assessment

This valuable study addresses one way in which animals identify predator-associated cues and respond in a manner that reflects the imminence of the potential threat. The report shows that, in mice, fresh saliva from a natural predator (cat) elicits a greater defensive response compared to old cat saliva and implicates the vomeronasal organ and ventromedial hypothalamus as part of a circuit that underlies this process. The evidence supporting the main conclusions is solid. This study will be of interest to those interested in aversive behavior, its processes, and mechanisms.

eLife Assessment

This important work shows how a simple geophysical setting of gas flow over a narrow channel of water can create a physical environment that leads to the isothermal replication of nucleic acids. The work presents convincing evidence for an isothermal polymerase chain reaction in careful experiments involving evaporation and convective flows, complimented with fluid dynamics simulations. This work will be of interest to scientists working on the origin of life and more broadly, on nucleic acids and diagnostic applications.

eLife assessment

This important study demonstrates a mechanism underlying the sex-dependent regulation of the susceptibility to gut colonization by Methicillin-resistant Staphylococcus aureus (MRSA). The evidence supporting the conclusion is solid, but additional experiments would strengthen the findings. The work will interest biologists who are working on intestinal infection and immunity.

eLife assessment

This valuable manuscript investigated the role of glutamate signaling in the dorsomedial striatum of rats in a treadmill-based task and reported that it differs in goal-trackers compared to sign-trackers in a way that corresponds to differences in behaviour. The evidence supporting these claims is solid but could be further strengthened by adding more analyses and more detailed descriptions of current analyses. These findings will primarily be of interest to behavioural neuroscientists.

eLife assessment

This important study reports the formation of a new organelle, called giant unilocular vacuole (GUVac), in mammary epithelial cells through a macropinocytosis-like process. The evidence supporting conclusions is convincing, using state-of-the-art cell biology techniques. This work will be of interest to cell biologists and contribute to the understanding of cell survival mechanisms against anoikis.

eLife assessment

This work demonstrates an important regulatory role of the N-terminal disordered tail of small ubiquitin-like modifier (SUMO) proteins, which modulate the function of various proteins in eukaryotic cells. The authors present convincing evidence that the N-terminal tail of SUMO inhibits SUMO's interaction with downstream effector proteins and SUMOylation targets, and that this regulatory mechanism depends on the SUMO paralogue or the phosphorylation of the N-terminal tail. This discovery significantly advances the field by providing a possible explanation of how SUMO paralogues select their effectors and SUMOylation targets.

eLife assessment

This work aimed at deconstructing how sebaceous gland differentiation is controlled in adult skin. Using monoclonal antibodies designed to inhibit specific Notch ligands or receptors, the authors present convincing evidence that the Jag2/Notch1 signaling axis is a crucial regulator of sebocyte progenitor proliferation and sebocyte differentiation. The valuable findings presented here contribute to the growing evidence that Notch signaling is not only key during the development of the skin and its appendages but also regulates cell fate in adult homeostatic tissues. From a translational perspective, it is intriguing that the effect of Jag2 or Notch1 inhibition, which leads to the accumulation of proliferative stem/progenitor cells in the sebaceous gland and prevents sebocyte differentiation, is reversible.

eLife assessment

In this small study involving patients with a history of myocardial infarction, Fawaz et al. found no significant contribution of clonal hematopoiesis and mosaic loss of the Y chromosome to the incidence of myocardial infarction and atherosclerosis. Although the evidence provided by the study is incomplete due to its small sample size, the findings are valuable for guiding future larger studies that will further investigate this significant and controversial subject.

eLife assessment

This important study describes the discovery of a mechanism by which multiple species of bacteria synthesize and localize polar flagella via a novel protein, FipA, which interacts with FlhF. The authors use appropriate methodological approaches (biochemistry, molecular microbiology, quantitative microscopy, and bacterial genetics) to obtain and present convincing results and interpretations. This work will particularly interest those studying bacterial motility and bacterial cell biologists.

eLife assessment

This study presents an assessment of the effect of lactate dehydrogenase (LDH) inhibition on the activity of glycolysis and tricarboxylic acid cycle. The data were collected and analyzed using solid and validated methodology. This paper makes a useful contribution to the field as it considers a control analysis of LDH flux.

eLife assessment

In this valuable work, Lodhiya et al. provide evidence that excessive ATP underlies the killing of the model organism Mycobacterium smegmatis by two mechanistically-distinct antibiotics. Clarification of the role(s) of reactive oxygen species and ADP, as well as discrepancies with existing literature, would strengthen the model proposed. 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.

eLife assessment

This valuable study discusses a hot topic in post-endoscopic retrograde cholangiopancreatography pancreatitis. The new score for predicting post-ERCP pancreatitis offers an idea about the risk of pancreatitis before the procedure. Although most scores depend on intraprocedural manoeuvres, such as the number of attempts to cannulate the papilla, this is a solid retrospective single-center study in one country. To be validated, this score should be done in many countries and on large numbers of patients, nevertheless, this paper should interest gastrointestinal endoscopists.

eLife assessment

This important study combines multiple techniques to investigate how caspase activity regulates non-lethal caspase-dependent processes. Through a combination of various approaches, and the development of new techniques, the authors provide compelling evidence supporting the claim that Fas3G-overexpression promotes non-lethal caspase activation in olfactory receptor neurons.

eLife assessment

This valuable study combines electrophysiology experiments and modeling to investigate the encoding of dynamic patterns of polarized light by identified neurons of the bumblebee central complex. The scientific question and methodology are compelling. However, the evidence supporting the authors' conclusions is incomplete without more comprehensive statistical analyses.

In "AI Image Generators Often Give Racist and Sexist Results: Can They Be Fixed?" by Ananya, the article dives deeper into sources of racial and gender bias in AI images and how to confront the issues.

eLife assessment

This study makes an important effort to observe and quantify synaptic integration in a large and active network of cultured neurons, using simultaneous patch-clamp and large-scale extracellular recordings. They developed a method to distinguish excitatory and inhibitory contributions, show compelling evidence that the subthreshold activity of these neurons is dominated by few presynaptic neurons. They provide convincing statistics about connectivity and network dynamics.

eLife assessment

Using microscopy experiments and theoretical modelling, the authors present convincing evidence of cellular coordination in the gliding filamentous cyanobacterium Fluctiforma draycotensis. The results are important for the understanding of cyanobacterial motility and the underlying molecular and mechanical pathways of cellular coordination.

eLife assessment

The authors present a solid statistical framework for using sibling phenotype data to assess whether there is evidence for de-novo or rare variants causing extreme trait values. Their valuable method is promising and will be of interest to researchers studying complex trait genetics.

eLife assessment

This manuscript describes the mapping of natural DNA sequence variants that affect gene expression and its noise, as well as cell cycle timing, using as input single-cell RNA-sequencing of progeny from crosses between wild yeast strains. The method represents an important advance in the study of natural genetic variation. The findings, especially given the follow-up validation of the phenotypic impact of a mapped locus of major effect, provide convincing support for the rigor and utility of the method.

eLife assessment

This important study investigates neurobiological mechanisms underlying the maintenance of stable, functionally appropriate rhythmic motor patterns during changing environmental conditions - temperature in this study in the crab Cancer borealis stomatogastric central neural pattern generating circuits producing the rhythmic pyloric motor pattern, which is naturally subjected to temperature perturbations over a substantial range. The authors present compelling evidence that the neuronal hyperpolarization-activated inward current (Ih), known to contribute to rhythm control, plays a vital role in the ability of these circuits to appropriately adjust the frequency of rhythmic neural activity in a smooth monotonic fashion while maintaining the relative timing of different phases of the activity pattern that determines proper functional motor coordination transiently and persistently to temperature perturbations. This study will be of interest to neurobiologists studying rhythmic motor circuits and systems and their physiological adaptations.

eLife assessment

This important study highlights cell types preserving long-lived proteins and lays a foundation for identifying exceptionally long-lived proteins in the ovary. Convincing evidence describes helpful data about protein turnover and identifies long-lived macromolecules in oocytes and somatic cells during mouse ovarian aging. This work will be of interest to researchers working on aging and reproductive health.

eLife assessment

This potentially valuable study examines the role of IL17-producing Ly6G PMNs as a reservoir for Mycobacterium tuberculosis to evade host killing activated by BCG immunisation. The authors report that IL17-producing polymorphonuclear neutrophils harbour a significant bacterial load in both wild-type and IFNg-/- mice and that targeting IL17 and Cox2 improved disease outcomes whilst enhancing BCG efficacy. Although the authors suggest that targeting these pathways may improve disease outcomes in humans, the evidence as it stands is incomplete and requires additional experimentation for the study to realise its full impact.

eLife assessment

This useful study investigates the role of Complement 3a Receptor 1 (C3aR) in the pathogenesis of Metabolic Dysfunction-Associated Steatotic Liver Disease (MASLD) using mouse models with specific target deletions in various cell types. While the relevance of C3aR in inflammatory contexts has been established, the authors provide helpful but incomplete evidence that C3aR does not contribute significantly to MASLD pathogenesis in their models, a claim that would require additional experiments for support.

eLife assessment

This important study demonstrates that interferon beta stimulation induces WTAP transition from aggregates to liquid droplets, coordinating m6A modification of a subset of mRNAs that encode interferon-stimulated genes and restricting their expression. The evidence presented is solid, supported by microscopy, immunoprecipitations, m6A sequencing, and ChIP, to show that WTAP phosphorylation controls phase transition and its interaction with STAT1 and the methyltransferase complex.

eLife assessment

This valuable study confirms the association between the human leukocyte antigen (HLA)-II region and tuberculosis (TB) susceptibility in genetically admixed South African populations, specifically identifying a near-genome-wide significant association in the HLA-DPB1 gene, which originates from KhoeSan ancestry. Whilst some of the evidence supporting the association between the HLA-II region and TB susceptibility is solid, the analysis is incomplete and requires further work for the study to achieve its full value. The work will be of interest to those studying the genetic basis of tuberculosis susceptibility/infection resistance.

eLife assessment

This valuable study presents compelling evidence that a single member of the Ly49 gene family (Ly49a) provides sufficient inhibitory signaling to license NK cell activity when its H-2Dd ligand is present. There is also convincing evidence of the effect of Ly49a expression on in vitro killing and IFNgamma production. The use of the authors' system to investigate additional Ly49 receptors, such as Ly49c/i on the H2b background, could provide information on their relative contribution to NK cell licensing. Improvements to the presentation with respect to figure clarity and terminology would allow a better understanding of this complex system by non-experts.

eLife assessment

This paper reports the synthesis of covalent inhibitors bearing a unique fragment as a protected covalent warhead for irreversible binding to histidine in carbonic anhydrase (CA) enzymes. These findings are important due to the broad utility of the approach for covalent drug discovery applications and could have long-term impacts on related covalent targeting approaches. The data convincingly support the main conclusions of the paper.

eLife assessment

This study presents an important platform for mapping mutation effects onto higher-level protein structural information, addressing a significant gap in current research. While the work is ambitious and incorporates often-overlooked aspects of higher-order structure, the strength of the evidence supporting some results seems incomplete. The quaternary structure modeling appears to underestimate oligomeric proteins compared to previous studies, and the mutation analysis lacks crucial baseline information. Despite these limitations, the method has potential for broader applications and generalization to additional organisms, warranting further development and refinement.

eLife assessment

This study focuses on the role of a T-cell-specific receptor, ctla-4, in a new zebrafish model of IBD-like phenotype. Although implicated in IBD diseases, the function of ctla-4 has been hard to study in mice as the KO is lethal. Ctla-4 mutant zebrafish exhibited significant intestinal inflammation and dysbiosis, mirroring the pathology of inflammatory bowel disease (IBD) in mammals, providing a new valuable model to the field of IBD research. However, although many of the results are solid, the methods as provided are incomplete, without information on methods for many data panels.

eLife assessment

Leafhoppers coat their body surface with nanoparticles, called brochosomes, which are an evolutionary innovation in this insect clade. The important paper adds significant evidence for the biological role of these structures consisting of a reflection effect of UV light as a defense against predatory spiders. Convincing support is provided for a new functional aspect of brochosomes, elucidating the emergence of the underlying genes and the principles of self-assembly of these biological nanoparticles.

eLife assessment

This paper reports a novel mechanism of regulation of the heat shock response in plants that acts as a brake to prevent hyperactivation of the stress response. The findings are valuable to understand and potentially manipulate the plant's response to heat stress and the presented evidence is overall solid. However, in some cases, the data are either poorly presented or insufficient to support the primary claims.

eLife assessment

This important study reveals a novel mechanism by which hypoxia-ischemia damages the neonatal brain and how hypothermia protects from brain injury. The paper presents an interesting combination of state-of-the-art optical measurements, mitochondrial assays, and the use of various control experiments providing solid evidence for the derived conclusions. Reviewers caution that possible adverse effects of prolonged anesthesia, as well as pain and stress after a major surgical procedure might influence the outcomes and should be carefully considered. This work will be of interest to the fields of hypoxia and brain metabolism research.

eLife assessment

This important study provides a comprehensive assessment of mitochondrial function across age and sex in mice. The strength of evidence supporting this resource is compelling, given the exhaustive number of tissues profiled and in-depth analyses performed.

eLife assessment

This study offers a valuable description of the layer-and sublayer specific outputs of the somatosensory cortex based on compelling evidence obtained with modern tools for the analysis of brain connectivity, together with functional validation of the connectivity using optogenetic approaches in vivo. Beyond bridging together, in one dataset, the results of disparate studies, this effort brings new insights on layer specific outputs, and on differences between primary and secondary somatosensory areas. This study will be of interest to neuroanatomists and neurophysiologists.

eLife assessment

The authors presented a valuable bioinformatics pipeline for screening and identifying inhibitory receptors for potential drug targets. They provided solid evidence showing a sequential reduction in the search space through various screening tools and algorithms and demonstrated that this pipeline can be used to "rediscover" known targets. Further experimental validation on putative and unknown inhibitory receptors will strengthen the evidence reported in this work. This study will be of interest to bioinformaticians and computational biologists working on immune regulation, sequence screening, and target identification of immune checkpoint inhibitors.

eLife assessment

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

eLife assessment

This paper presents a valuable automated method to track individual mammalian cells as they progress through the cell cycle using the FUCCI system. The authors have developed a technique for analyzing cells that grow in suspension and used their method to look at different tumor cell lines that grow in suspension and determine the effect of drugs that directly affect the cell cycle. They show solid evidence that the method can be applied to both adherent and non-adherent cell lines. This paper will be of interest to cell biologists investigating cell cycle effects.

eLife assessment

This study presents a valuable finding and developed ME3BP-7 as a novel microencapsulated formulation of 3BP, which specifically targets MCT1-overexpressing PDAC cells. It demonstrates its specificity and efficacy in vitro and in PDAC mouse models, with significant anti-tumor effects and improved serum stability. Overall, the evidence supporting the authors' claims is solid.

eLife assessment

This important study identifies a new class of small molecules that activate the integrated stress response via the kinase HRI. Solid evidence indicates that two of these compounds promote mitochondrial elongation. The findings would be strengthened if the mutant cells with reduced fusion activity of Mfn2 were analyzed for the rescue of mitochondrial functions.

eLife assessment

This important manuscript shows that axonal transport of Wnd is required for its normal degradation by the Hiw ubiquitin ligase pathway. In Hiw mutants, the Wnd protein accumulates in nerve terminals. In the absence of axonal transport, Wnd levels also rise and lead to excessive JNK signaling, disrupting neuronal function. These are interesting findings supported by convincing data. However, how Rab11 is involved in Golgi processing or axonal transport of Wnd is not resolved as it is clear that Rab11 is not travelling with Wnd to the axon.

eLife assessment

This study presents valuable findings from an observational dataset in a riverine ecosystem about the effects of genetic and species diversity, across multiple trophic levels, on ecosystem functions. However, the support for these findings is currently incomplete because raw data are not provided and there is insufficient information in the manuscript for readers to understand and assess the statistical analyses and conclusions. The work will be of broad interest to ecologists.

eLife assessment

This study provides direct evidence showing that Kv1.8 channels provide the basis for several potassium currents in the two types of sensory hair cells found in the mouse vestibular system. This is an important finding because the nature of the channels underpinning the unusual potassium conductance gK,L in type I hair cells has been under scrutiny for many years. The experimental evidence is compelling and the analysis is rigorous. The study will be of interest to cell and molecular biologists as well as vestibular and auditory neuroscientists.

eLife assessment

This fundamental study enhances our understanding of how somatic variants in microglia might influence the onset and progression of neurodegenerative diseases such as Alzheimer's. The evidence supporting the conclusions is compelling, with the authors employing a multi-faceted approach to identify an enrichment of potentially pathogenic somatic mutations in Alzheimer's disease microglia. This research will be of significant interest to those investigating somatic mutations, Alzheimer's disease, microglial biology and cell signalling pathways.

eLife assessment

This fundamental study has the potential to substantially advance our understanding of human locomotion in complex real-world settings and opens up new approaches to studying (visually guided) behavior in natural settings outside the lab. The evidence supporting the conclusions is overall compelling. Whereas detailed analyses represent multiple ways to visualize and quantify the rich and complex natural behavior, some of the specific conclusions remain more suggestive at this point. The work will be of interest to neuroscientists, kinesiologists, computer scientists, and engineers working on human locomotion.

eLife assessment

This study examines how self-citations in selected neurology, neuroscience, and psychiatry journals differ according to geography, gender, seniority, and subfield. The evidence supporting the claims is mostly convincing, but certain aspects of the analysis would benefit from further work. Overall, the article is a valuable addition to the literature on self-citations

eLife assessment

This manuscript is an important contribution toward understanding the mechanisms of transcriptional bursting. The evidence is considered solid. Questions regarding the broader advance, details of the analysis, and the models used in the analysis were addressed by the authors.

eLife assessment

This work presents a valuable mouse model for a liver-specific depletion of the Survival Motor Neuron (SMN) protein, where the liver retains 30% of functional full-length SMN protein. The authors provide a profile of phenotypic changes in liver-specific SMN depleted mice: while evidence supporting their claims are generally solid, the phenotype is mild and mechanistic understanding remains to be determined.

eLife assessment

This important work has substantially advanced our understanding of the molecular basis of symmetry breaking and lineage specification in preimplantation mammalian embryos. The results generated using live imaging are compelling. Quantification of the functional assays is convincing and would be improved by increasing the number of embryos in the evaluations and clearly stating how many embryos are evaluated per experiment.

eLife assessment

This important study explores the impact of pH changes and cancer mutations on nucleosome interactions and higher-order chromatin structures. The evidence supporting the main conclusions is solid, based on rigorous computational methods, including pKa prediction, electrostatic force calculation, and molecular dynamics simulations. The findings provide insights into how protonation states and cancer-associated mutations affect nucleosome electrostatics and chromatin organization, making this work of broad interest to chromatin biologists, cancer researchers, and computational biophysicists.

eLife assessment

This valuable study investigates how inter-organ communication between the tracheal stem cells and the fat body plays a key role in the directed migration of tracheal stem cells in Drosophila pupae. While the experimental data are extensive and complementary, the evidence presented to substantiate some of the conclusions appears incomplete and requires further clarification and additional experiments. The work would be of interest to researchers in the fields of developmental biology and cancer biology.

eLife assessment

This study presents valuable findings on the relative cerebral blood volume of non-human primates that move us closer to uncovering the functional and architectonic principles that govern the interplay between neuronal and vascular networks. The evidence of areal variations is solid, but that of vessel counting and laminar analysis is incomplete. The lack of a direct comparison of their approach against better-established MRI-based methods for measuring hemodynamics and vascular structure weakens the evidence provided in the current paper version. The work will be of interest to NHP imaging scientists.

eLife assessment

In this elegant and thorough 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 is important in that it may well explain part of the controversial and ambiguous outcomes of various clinical trials. It is a well-written paper on a deeply analyzed dataset and the methods in the paper are generally convincing, with the current version having some weaknesses in statistical reporting and power.

eLife assessment

This work presents valuable 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 conclusion is incomplete so far, particularly considering concerns about the median-splitting approach for reaction times and hippocampal activity. The work will be of broad interest to researchers working on memory.

eLife assessment

This study provides valuable evidence on the relationship between morphine-induced social deficits, corticotropin-releasing factor receptors, and alterations in neuronal activity in the paraventricular nucleus of the hypothalamus of mice (PVN). Convincing approaches and methods were used to show that the CRF1 receptor plays a role in sociability deficits occurring after acute morphine administration. Conclusions regarding mechanistic connections between the effect of modulation of CRF 1 receptor on sociability and PVN neuronal firing are, however, incompletely supported.

eLife assessment

This study combines experimental and theoretical approaches to examine metabolites at the single-cell level in tea plants. The authors skilfully integrated various tools available for this type of research, and meticulously presented and illustrated every step of the survey. The overall quality of the work is convincing, and it represents an important contribution to our understanding of the compartmentalization of biosynthesis pathways.

eLife assessment

This useful study provides data suggesting that subcellular localization of the spatial regulator of cell division, MinD, is an intrinsic feature of the protein's ability to associate with the membrane as both a dimer and a monomer. These findings distinguish the behavior of MinD in B. subtilis from its counterpart in E. coli and suggest that there is not a need to invoke additional localization factors. However, all three reviewers agreed that the study is incomplete: experimentally, quantitation and assessment of MinD behavior in the presence of proteins previously implicated in its localization are missing, among other assays, and the molecular modeling necessary to support the authors' conclusion that their data support a reaction-diffusion model is completely absent. Finally, the manuscript itself is difficult to read with an overly long discussion and disorganized introduction and results sections, and it will require significant revision.

eLife assessment

This important work by Zheng and colleagues uses a large cohort database from Shanghai to identify that post-infection vaccination among previously vaccinated individuals provides significant low to moderate protection against re-infection. The evidence supporting the conclusion is convincing with some limitations, e.g., lack of symptom severity as an outcome, and no inclusion of time since infection as an independent variable). This study will be of interest to vaccinologists, public health officials and clinicians.

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.

eLife assessment

In this important study, Bu et al investigate how cell overcrowding triggers a mechano-transduction pathway involving TRPV4 channels, focusing on high-grade ductal carcinoma in situ (DCIS) cells. The authors show that cell crowding in these malignant cells leads to a reduction in cell volume and promotes a pro-invasive phenotype through calcium homeostasis and TRPV4 channel trafficking to the plasma membrane; this phenomenon is specific to invasive cell lines like MCF10CA and DCIS and is corroborated by patient tissue samples. The work suggests the role of TRPV4 in cell motility and mechanical sensing, offering potential therapeutic insights for targeting cancer metastasis. While the study presents robust and convincing data, the absence of TRPV4 genetic ablation is a critical limitation, which would further confirm its role in these processes.

eLife assessment

This study provides novel insights into COVID-19 immune responses by using the delta of the normalised accessible surface area (DASA) to map IgM responses to the SARS-CoV-2 Membrane protein M1-subtype across multiple European cohorts. The evidence supporting the findings is solid, with thorough validation and comprehensive analysis, although additional clarity on T-independent B cell reactions and the impact of comorbidities would further strengthen the conclusions. The methods and data presented are valuable for advancing diagnostic and prognostic tools for COVID-19, particularly in the context of long COVID.

eLife assessment

This useful study characterises motor and somatosensory cortex neural activity during naturalistic eating and drinking tongue movement in nonhuman primates. The data, which include both electrophysiology and nerve block manipulations, will be of value to neuroscientists and neural engineers interested in tongue use. However, data analysis needs to be improved to strengthen the inadequate support for some of the main claims in the paper.

eLife assessment

The authors combined molecular dynamics simulations and experiments to study the role of ATP as a hydrotrope of protein aggregates. The topic is of major current interest and thus the study potentially makes an important contribution to the community. With the revised version, the level of evidence is considered generally solid, although there remains concern regarding the unusually high ATP concentration used in the simulation.

eLife assessment

The authors developed a method to allow a hypothermic agent, neurotensin, to cross the blood-brain barrier so it could potentially protect the brain from seizures and the adverse effects of seizures. The work is important because it is known that cooling the brain can protect it but developing a therapeutic approach based on that knowledge has not been done. The paper is well presented and the data are convincing. Revisions to clarify some of the methods and results improved the paper and more data about tolerability would improve the paper further.

eLife assessment

In this manuscript, the authors present valuable findings on the apparent role of a salience-network anterior insula node in directing fronto-parietal and default-mode network activity within a tripartite network during control of memory, drawn from an impressive invasive human neurophysiological dataset. We commend the use of a large intracranial EEG dataset to approach this question. While many aspects of the evidence are solid, there are some remaining points which are methodologically incomplete and could be further improved with some specific control analyses and word changes.

eLife assessment

This study provides compelling data that defines the structure of the S. cerevisiae APC/C. The structure reveals overall conservation of its mechanism of action compared to the human APC/C but some important differences that indicate that activation by co-activator binding and phosphorylation are not identical to the human APC/C. Thus this study will be of considerable value to the field.

eLife assessment

In this useful study, the authors investigate the regulatory mechanisms related to toxin production and pathogenicity in Aspergillus flavus. Their observations indicate that the SntB protein regulates morphogenesis, aflatoxin biosynthesis, and the oxidative stress response. The data supporting the conclusions are compelling and contribute significantly the advancing the understanding of SntB function.

eLife assessment

The regulation of mitosis and the dynamics of the mitotic spindle in it are central to cell division with high fidelity and crucial for normal division and development and defects therein can lead to disease. A key component of ensuring the fidelity is the "spindle assembly checkpoint". This valuable study using convincing experimental approaches in fission yeast has revealed novel links between the MAP-kinase signalling pathway modulating the spindle assembly checkpoint.

eLife assessment

This valuable study characterises receptors for calcitonin-related peptides from a deuterostomian animal, the echinoderm Apostichopus japonicus, by a combination of heterologous expression, pharmacological experiments, and the quantification of gene-expression levels. The authors provide solid evidence for a functional calcitonin-related peptide system in the sea cucumber, but some of the phylogenetic and statistical analyses and the evidence of a physiological function are incomplete. This work should be of interest to scientists studying the signaling pathways, functions, and evolution of neuropeptides, and could be of relevance to improving the culture conditions of this economically key species.

eLife assessment

This valuable paper uses the ChEC-seq2 technique to investigate RNA polymerase II (RNAPII) binding patterns in yeast and demonstrates that this technique is a complementary method for investigating transcription mechanisms, especially slow steps at the initiation and termination regions. The authors use ChEC-seq2 data to investigate RNAPII kinetics and obtain solid data providing new insights into transcription regulation. This study highlights the importance of careful methodological comparisons in understanding RNAPII dynamics.

eLife assessment

The manuscript by Li and coworkers analyzed astrocytic differentiation of midbrain floor plate-patterned neural cells originating from human iPS cells, with a LMX1A reporter. This valuable work identifies transcriptomic differences at the single-cell level, between astrocytes generated from LMX1A reporter positive or negative cells, as well as non-patterned astrocytes and neurons. The evidence is solid, but the paper can be strengthened by further analyses of the transcriptomic data, and astrocytic morphology; also, searching for some of the differentially expressed genes by immunohistochemistry in different regions of the mammalian brain, or in human specimens, would be very informative.

eLife assessment

In this valuable study, García-Vázquez et al. provide solid evidence suggesting that G2 and S phases expressed protein 1 (GTSE1), is a previously unappreciated non-pocket substrate of cyclin D1-CDK4/6 kinases. To this end, this study holds a promise to significantly contribute to an improved understanding of the mechanisms underpinning cell cycle progression. Notwithstanding these clear strengths of the article, it was thought that the study may benefit from establishing the precise role of cyclin D1-CDK4/6 kinase-dependent GTSE1 phosphorylation in the context of cell cycle progression, obtaining more direct evidence that cyclin D1-CDK4/6 kinase phosphorylate indicated sites on GTSE1 (e.g., S454) and mapping a degron in GTSE1 whose function may be blocked by cyclin D1-CDK4/6 kinase-dependent phosphorylation.

eLife assessment

This study presents a valuable optimization algorithm to identify polymer models that best fit population-averaged chromosome contact data that will be of interest to physicists and biologists working on chromatin organization. The conclusions are supported by solid evidence.

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, assays to detect this are still incomplete and require further refinement. The work will be of interest to microbiologists studying metabolism and post-translational modifications.

eLife assessment

This valuable study has characterized the unique expression of Schlemm's canal endothelial cells (SECs) using FACS-sorted specific cell bulk RNA-Seq and scRNA-/snRNA-Seq of mouse SECs. The compelling study identified novel biomarkers for SECs and molecular markers for two inner wall SEC states and outwall SECs in mouse eyes. Significant gene networks and pathways were elucidated for their potential contribution to glaucoma pathogenesis, providing targets for further research in relation to glaucoma.

eLife assessment

This important study introduces and evaluates the efficacy of a novel form of non-invasive brain stimulation in humans: kilohertz transcranial magnetic perturbation (kTMP). The evidence provided for the ability of kTMP to increase cortical excitability with minimal sensation is compelling, with two separate replication experiments. Although exploratory in nature, this work represents new avenues for non-invasive brain stimulation research that has potential long-term appeal for both clinical and research applications. This paper will be of significant interest to neuroscientists interested in brain stimulation.

eLife assessment

This study provides valuable insights and allows for hypothesis generation around diet-microbe-host interactions in alcohol use disorder. The strength of the evidence is convincing: the work is done in a rigorous manner in a well-described cohort of patients with AUD before and after withdrawal. There are several weaknesses, including validating the metabolites identified by metabolomics, the cross-sectional study design, the lack of a healthy control group, and the descriptive nature of such clinical cohort studies. Nevertheless, the study provides a wealth of new data that may be the basis for future studies that test causality and elucidate the role of single metabolites in the psychiatric sequela of AUD.

eLife assessment

This important study describes changes in excitability in motor neurons of the peripheral autonomous nervous system during aging. The manuscript provides convincing evidence indicating that sympathetic neurons from aged mice show higher excitability compared to neurons from young mice which was linked to decreased activity of KCNQ2/3 potassium channels. This research has implications for understanding the age-related changes that occur in the peripheral nervous system.

eLife assessment

This study presents useful findings for how sevoflurane anesthesia modulates the activity of corticotropin-releasing hormone neurons in the paraventricular nucleus of the hypothalamus and how manipulation of such PVHCRH neurons influences anesthesia and post-anesthesia responses. The technical approaches are solid and the data presented is largely clear. Whether PVHCRH neurons are critical for the mechanisms of sevoflurane anesthesia is a direction for the future.

eLife assessment

This valuable study explores a new strategy of lysin-derived antimicrobial peptide-primed screening to find peptidoglycan hydrolases from bacterial proteomes. Using this strategy, the authors identified five peptidoglycan hydrolases from Acinetobacter baumannii, which they tested on various Gram-positive and Gram-negative pathogens for antimicrobial activity. The revised manuscript addressed most of the prior concerns, and the data presented are solid and will be of interest to microbiologists.

eLife assessment

This study presents useful findings on the efficacy and mechanism of linalool protection against Saprolegnia parasitica oomycetes in the grass carp model. The evidence is incomplete since the claims are partially justified, thus there is a need for more experimental data and more rigorous statistical data analysis . Revisions according to the recommendations will improve the work, making it of interest to scientists within the fields of aquaculture, ichthyology, microbiology, and drug discovery.

eLife assessment

This study presents a useful finding on the interplay of CCL5 and miR-324-5p during ischemic stroke injury. Despite its importance, the evidence supporting the claims of the authors is incomplete. In particular, the lack of methodological information, inappropriate statistical testing, a flawed culture system, and the temporal mismatch in the expression of CCL5 and miR-324-5p following stroke have hindered further evaluation of the claims. The work will be of interest to neuroscientists working on brain injury such as stroke.

eLife assessment

This important study investigates the sensitivity to endogenous cosolvents of three families of intrinsically disordered proteins involved with desiccation. The findings, drawn from well-designed experiments and calculations, suggest a functional synergy between sensitivity to small molecule solutes and convergent desiccation protection strategy. The evidence is found to be convincing, and the authors provide appropriate caveats since the study's conclusions are based on a small number of proteins. This work will be of interest to biochemists and biophysicists interested in the conformation-function relationship of intrinsically disordered proteins.

eLife assessment

This study provides an important insight into the mechanisms of cooperation between Hsp70 and its cochaperones during reactivation of aggregated proteins. Based on convincing evidence, the authors demonstrate that the co-chaperone Hsp110 boosts disaggregation activity by enhancing Hsp70 recruitment to protein aggregates. This work is of broad interest to biochemists and cell biologists working in the protein homeostasis field.

eLife assessment

This fundamental study demonstrates a novel method for imaging glutamate receptors in situ via cryo-ET. The use of cutting-edge methods is well-described and is compelling. This paper is broadly relevant to biophysicists and neuroscientists.

eLife assessment

This revised study presents valuable evidence that a combination of endothelial cells, astrocytes, and neuroblastoma cells of human origin can integrate to form an in vitro brain blood barrier, that recapitulates key aspects of its natural counterpart, especially at short times. Convincingly, the mechanism by which neuroblastoma-secreted GDNF increases Claudin-5 and VE-cadherin is described. To substantiate the role of GDNF in vivo, authors demonstrated that knock-down of this neurotrophic factor, increased the permeability of the brain blood barrier in mice. This in vitro system can be used to study the permeability of the human brain blood barrier to different drugs.

eLife assessment

The present study provides valuable evidence on the neurochemical mechanisms underlying working memory in obesity. The authors' approach considering specific working memory operations (maintenance, updating) and putative dopaminergic genes is solid, though the inclusion of a more direct measure of dopamine signaling would have strengthened the work.

eLife assessment

This valuable manuscript reports alterations in autophagy present in dopaminergic neurons differentiated from iPSCs of patients with WDR45 mutations. The authors identified compounds that improved the defects present in mutant cells by generating isogenic iPSC without the mutation and performing an automated drug screening. The methodological approaches are solid, but the claims still need to be completed; showing the effects of the identified compounds on iron-related alterations is crucial. The effects of these drugs in vivo would be a great addition to the study.

eLife assessment

The aim of this valuable study is to identify novel genes involved in sleep regulation and memory consolidation. It combines transcriptomic approaches following memory induction with measurements of sleep and memory to discover molecular pathways underlying these interlinked behaviors. The authors explore transcriptional changes in specific mushroom body neurons and suggest roles for two genes involved in RNA processing, Polr1F and Regnase-1, in the regulation of sleep and memory. Although this work exploits convincing and validated methodology, the strength of the evidence is incomplete to support the main claim that these two genes establish a definitive link between sleep and memory consolidation.

eLife assessment

Through anchored phylogenomic analyses, this important study offers fresh insights into the evolutionary history of the plant diet and geographic distribution of Belidae weevil beetles. Employing robust methodological approaches, the authors propose that certain belid lineages have maintained a continuous association with Araucaria hosts since the Mesozoic era. Although the biogeographical analysis is somewhat limited by uncertainties in vicariance explanations, this convincing study enhances our understanding of Belidae's evolutionary dynamics and provides new perspectives on ancient community ecology.

eLife assessment

This study investigated the involvement of programmed cell death (PCD) in Arabidopsis thaliana root cap cells and its effect on microbial colonization. The authors have reported the importance of timely corpse clearance in the root cap and a root cap-specific transcription factor in controlling microbial colonization by beneficial fungi. By demonstrating the connection between transcriptional control of PCD and microbial colonization, this study provides fundamental insights into how relationships are established and regulated at the root-microbiome interface. The strength of the evidence presented is convincing, providing a foundation for further research concerning the spatial and temporal dynamics of microbiome recruitment along the root axis.

eLife assessment

This important manuscript presents several structures of the Kv1.2 voltage-gated potassium channel, based on state-of-the-art cryoEM techniques and algorithms. The authors present solid evidence for structures of an inactivating mutant of Kv1.2, DTX-bound Kv1.2 and of Kv1.2 in potassium-free solution (with presumably sodium ions bound within the selectivity filter). These structures advance our knowledge of the molecular basis of the slow inactivation process of potassium channels.

eLife assessment

This manuscript describes valuable findings on 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 supports claims in the paper, however, there are several areas in which the conclusions are only partially supported by the statistical evidence. 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.

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 volumetric ratio, and mitochondrial morphology. The data were collected using a solid methodology, however, the analysis of the functional vesicle pools is incomplete, 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.

eLife assessment

This study describes the formation of a penetration ring in the rice blast fungus Magnaporthe oryzae during host cell invasion. The work provides useful insights into how the penetration ring facilitates the transition of penetration pegs into invasive hyphae, which leads to a better understanding of plant-pathogen interactions. However, the evidence supporting the function of this novel infection structure remains incomplete and further work is needed to help clarify the exact role of the penetration ring in the infection process.

eLife assessment

This valuable work discusses the phylogenetic conservation of the hippocampal region and primary sensory cortical regions in mammalian species. The authors propose that species-specific differences in behavior and mnemonic functions may be due to differences in cortico-hippocampal connectivity patterns. However, the manuscript, in its present form, is speculative, and the strength of evidence for this proposition is incomplete.

eLife assessment

This research investigates the precision of numerosity perception in two different tasks and concludes that human performance aligns with an efficient coding model optimized for current environmental statistics and task goals. The findings may have important implications for our understanding of numerosity perception as well as the ongoing debate on different efficient coding models. However, the evidence presented in the paper to support the conclusion is still incomplete and could be strengthened by further modeling analysis or experimental data that can address potential confounds.

eLife assessment

This important study reports that slow fluctuations of serotonin release during wakefulness and non-REM sleep correspond to periods of either increased arousal or enhanced offline information processing. The evidence supporting the claim is convincing, and the methodology used in the study will benefit many in the field. The work will be of interest to neuroscientists working on sleep, memory, and neuromodulation.

eLife assessment

This valuable study aims to understand the function of ProSAP-interacting protein 1 (Prosapip1) in the brain. Using a conditional Prosapip1 KO mouse (floxed prosapip1 crossed with Syn1-Cre line), the authors performed analysis including protein biochemistry, synaptic physiology, and behavioral learning. Solid evidence from this study supports a role of Prosapip 1 in synaptic protein composition, synaptic NMDA responses, LTP, and spatial memory. Addressing some of the technical and methodological weaknesses may further improve the significance of the study.

eLife assessment

This study presents a fundamental finding to the field interested in recurrent processing and its neuromodulatory underpinnings, finding unexpectedly that memantine (blocking NMDA-receptors) enhances the decoding of features thought to rely on NMDA-receptors. The evidence is solid and would be improved by further persuading the readership of the likely functional underpinnings of this direction of result and why there was no behavioural effect. These findings will be of interest to a wide community of researchers studying consciousness, sensory processing, attention, and neurotransmitters.

eLife assessment

This study explores the role of protein synthesis in spinal cord neurons in the regulation of chronic pain. Using innovative techniques, this valuable study outlines cell-type specific gene changes that occur in the spinal cord in the early and late phases of nerve injury. The presented evidence and methods used are, however, incomplete: there are several major technical and analysis issues that need to be addressed, and in addition, deeper gene expression analysis and additional controls would have strengthened the conclusions. This work will be of broad interest to biologists studying pathological plasticity in circuits.

Security depends on cryptographically verifiable primitives. Cryptography is native to binary, which makes text-based human readable Protocols (like JSON) awkward.

eLife assessment

This important study reports the discovery of a novel nucleotide ubiquitylation activity by the DTX3L E3 ligase. Solid evidence is presented for ubiquitin attachment to single-stranded oligonucleotides. This very interesting biochemical finding can be used as a starting point for studies to establish relevance in a physiological setting.

eLife assessment

This important study investigates the molecular mechanisms underpinning how the tumor necrosis factor alpha-induced protein, TIPE, regulates aerobic glycolysis to promote tumor growth in melanoma. Solid data using multiple independent approaches provide new insights into the molecular mechanisms underpinning aerobic glycolysis, also known as the Warburg Effect, in melanoma cells. However, further investigation of a potential oncogenic effect of TIPE in melanoma patients is warranted and more advanced metabolomic and bioenergetic assays could be employed. The work will be of interest to biomedical researchers working in cancer and metabolism.

eLife assessment

In this study, Ferling and colleagues provide convincing evidence demonstrating that myeloid cells exert distinct, cargo-dependent responses during and after phagocytosis. These important findings establish previously unrecognized insights into the function(s) of myeloid cells in immunosurveillance and are thus likely to be broadly impactful across the spectrum of biomedical disciplines including immunology and cell biology. Notwithstanding these clear strengths of the article, some minor issues were noted pertinent to the relative opaqueness of the mechanisms underpinning context-specific RhoA activation.