eLife assessment

This study presents a valuable finding for the treatment of PCCs by sequencing 16 tumor specimens from five patients with pheochromocytomas by single-cell transcriptomics and proposing a new molecular classification criterion based on the sequencing results and characterization of tumor microenvironmental features. The evidence supporting the claims of the authors is solid, although the inclusion of more patient samples would strengthen the study's conclusions. The work will be of interest to clinicians or medical biologists working on rare pheochromocytomas (PCCs).

eLife assessment

The authors present a potentially useful model involving Ca2+ signaling in inflammasome activation. As it stands, it was felt that the data were not sufficient to support the model and the claims of the study are inadequately presented.

eLife assessment

This important study describes the discovery and further engineering of a red light-activated, chloride-conducting Channelrhodopsin (ACR) that could be used to inhibit neuronal activity. The authors were able to demonstrate some inhibition of neuronal activities in vitro and in vivo with 635 nm light, however the study was incomplete. Adequate controls and direct comparisons to the performance of already-established variants were missing, making it difficult to confirm the future utility of MsACR1 and raACR1.

eLife assessment

This paper describes a new complexity estimator for time series based on state-space modeling, which can directly decompose signal entropy in both time and frequency. The authors compare their estimator to Lempel-Ziv (LZ) complexity using a variety of time series neurophysiological data from humans and non-human primates. This represents a potentially valuable methodological contribution for existing studies using LZ complexity in their analyses, although the paper currently ignores much of the existing literature which has already developed related solutions to the same issues. The strength of the evidence supporting the superiority of the new complexity metric is currently incomplete, and should be backed by additional analyses.

eLife assessment

This paper presents an important contribution to the field of hippocampal registration by introducing a novel surface-based approach that utilizes the topological and morphological features of the hippocampus for anatomical registration across individuals, rather than volumetric-based methods commonly used in the literature. The study provides compelling evidence for the efficacy of this approach using histological samples from three different datasets and offers validation of the method through comparison with traditional volumetric registration. This is important work given the large number of studies that examine hippocampal shape, thickness, and function in large cohorts, providing strong support for the use of hippocampal unfolding methods in future studies.

eLife assessment

This important and compelling study investigates the problem of intracellular acidification induced by commonly-used optogenetic stimulating opsins. The low proton permeability of two high-performance opsins is shown to reduce photostimulated acidification. The findings may be of broad interest in the fields of neuroscience research and optogenetic therapies.

eLife assessment

This study presents important findings indicating that gradients of functional connectivity are present in the human foetal brain, and that these gradients develop further during gestation, particularly in multisensory brain regions. The study uses state-of-the-art connectomic mapping techniques. However, recent findings suggest that such gradients may reflect confounds within the analysis technique more than underlying brain functions. The evidence for the authors' claims therefore currently appears inadequate as it does not account for these potential confounds.

eLife assessment

This important study uses a combination of computational modeling and glutamate imaging to show how a particular synaptic organization referred to as space-time wiring has a limited contribution to a dendritic computation that occurs in the retina. The evidence supporting the claims of the authors is convincing, although the findings are largely confirmatory of previous modeling and experimental results. The work will be of interest to retinal neurobiologists and neurophysiologists interested in dendritic computations.

eLife assessment

The finding that Fusicoccin promotes locomotor recovery after spinal cord injury is useful, and the idea of harnessing small molecules that may affect protein-protein interactions to promote axon regeneration is interesting and worthy of study. However, the main methods, data, and analyses are inadequate to support the primary claim of the manuscript that a 14-3-3-Spastin complex is necessary for the observed Fusicoccin effects.

eLife assessment

Franke et al. explore and characterize the color response properties in the mouse primary visual cortex, revealing specific color opponent encoding strategies across the visual field. The data is solid; however, the evidence supporting some conclusions and details about some procedures are incomplete. In its current form, the paper makes a useful contribution to how color is coded in mouse V1. Significance would be enhanced with some additional analyses and resolution of some technical issues.

eLife assessment

This study presents valuable findings on the roles of the axon growth regulator Sema7a in the formation of peripheral sensory circuits in the lateral line system of zebrafish. The evidence supporting the claims of the authors is solid, although further work directly testing the roles of different sema7a isoforms would strengthen the analysis. The work will be of interest to developmental neuroscientists studying circuit formation.

eLife assessment

This valuable study has the potential to shed mechanistic light on how attention mechanisms that influence competition between multiple visual stimuli are modulated by the relative neural similarity of these stimuli. The study implements an interesting experimental design that provides relevant data, especially for future modeling efforts. However, the presented evidence is considered incomplete due to some features of the design and model, as well as certain analysis choices.

eLife assessment

This study provides a valuable starting point for unraveling the molecular basis of the pathological phenotypes of the repeat expansion in the gene associated with open reading frame 72 in human chromosome 9. The coarse-grained simulation method used by the authors goes beyond the state of the art, investigating a compelling number of binding partners. The evidence supporting the claims of the authors is solid, although validation of the results is needed to further strengthen the major conclusions of the work. The work will be of broad interest to biophysicists and biochemists.

eLife assessment

This paper presents data suggesting the novel finding that stimulating the senses can open the normal barrier to the brain and lead to changes in the brain. However, the paper was unclear in methods and data, which made the strength of evidence for the conclusions seem incomplete. However, the reviewers considered the potential significance of the study to be important.

eLife assessment

This study suggests that PAK3 may play a critical role in cognitive function after cranial irradiation, highlighting a potential therapeutic target to mitigate the adverse effects of radiotherapy. The main finding is of significance, and the evidence is compelling to support their major conclusion. This is an important discovery providing novel insight into the molecular mechanism of how PAK3/LIMK/Cofilin signaling modulates synaptic spine morphology in response to irradiation.

eLife assessment

This paper presents a valuable pipeline based on state-of-the-art analytical software that was used to study genetic pleiotropy between neuropsychiatric disorders. The presented evidence supporting the claims is solid, although the paper is lacking an appropriate comparison to previously published methods as well as a more detailed exploration of some of the findings. The created pipeline is made publicly available and can thus be used by researchers from diverse fields to study different combinations of diseases and traits.

eLife assessment

Chang et al. provide glutamate co-expression profiles in the central noradrenergic system and test the requirement of Vglut2-based glutamatergic release in respiratory and metabolic activity under physiologically relevant gas challenges. Their experiments provide compelling evidence that conditional deletion of Vglut2 in noradrenergic neurons does not impact steady-state breathing or metabolic activity in room air, hypercapnia, or hypoxia. This study provides an important contribution to our understanding of how noradrenergic neurons regulate respiratory homeostasis in conscious adult mice.

eLife assessment

Multimodal experiences that for example contain both visual and tactile components are encoded as associative memories. This manuscript is a valuable contribution supporting structural and functional brain plasticity following associative training protocols that pair together different types of sensory stimuli. The results provide solid support for this plasticity being a basis for cross-modal associative memories.

eLife assessment

This fundamental study provides a unique tool for assessing the range of phosphorylation in insulin reactions due to genetic variation and dietary influence through the utilization of genetically distinct mouse strains. The discoveries of this study hold substantial importance, as they shed light on the interplay between genetic attributes and environmental conditions in shaping the insulin-signaling network within skeletal muscle, a crucial regulator of metabolism. The supporting evidence presented is compelling, and the work is anticipated to captivate a wide audience within the metabolism discipline due to its extensive appeal and by providing inspiration for further hypothesis-driven research.

eLife assessment

This important study presents convincing evidence for the utility of orangutan teeth as terrestrial proxies to reconstruct rainfall regimes, while exploring the potentially conflicting impact of breastfeeding signals. The findings have ramifications for the methods and tools used by the field in the reconstruction of environmental conditions in the historical and archeological past.

eLife assessment

This fundamental work uses computational network models to suggest a possible origin of the wide range of time scales observed in cortical activity. This claim is supported by convincing evidence based on comparisons between mathematical theory, simulations of spiking network models, and analysis of recordings from the orbitofrontal cortex. This manuscript will be of interest to the broad community of systems and computational neuroscience.

eLife assessment

This valuable work explores how transcription factors regulate transcription through cooperative binding to enhancers. Through experiments and modeling, the authors show convincingly that the cooperativity of transcription factor binding regulates transcriptional bursting and the extent of the amount of time that the target promoter remains in an active state.

eLife assessment

This manuscript reports important new results, but it provides incomplete support for its claims. Recent data has shown that schizophrenia-related synaptic alterations induce changes in neural network synchrony, and this manuscript provides the first theoretical understanding of the underlying network mechanisms. Proper support for this result, however, requires a tighter link between the computational model and the experimental data and a more in-depth understanding of the model mechanisms.

eLife assessment

In this important study, Esmaily and colleagues investigate the "confidence matching" between two agents and present a useful exploration of its computational and physiological correlates. Further analyses would be helpful to provide a tighter link between fluctuations of confidence, pupil size, EEG response, and computational variables, to delineate the causal relations between these quantities, which are nevertheless incompletely documented at present.

eLife assessment

This study reveals a novel mechanism of Acetylcholine- Acetylylcholine receptor signaling in regulating gut barrier function in Drosophila, which provides important implications on the pathway played in human diseases, such as Chronic Obstructive Pulmonary DiseaseCOPD. The evidence supporting the claims of the authors is solid.

eLife assessment

The present study provides a valuable new perspective on the optomotor response based on an inversion of the behavior under specific (non-natural) conditions that may help elucidate the principles of this specific behavior. The evidence provided is convincing.

eLife assessment

Using a novel micropipette-based, minimally invasive approach in combination with theoretical and computational analysis, this important work probes tissue mechanics in the Drosophila embryo. The authors provide compelling evidence for the applicability of their method, which reveals important differences between the mechanical properties on the apical and basal tissue sides. This work should be of broad interest to scientists studying tissue mechanics, membranes, and developmental processes.

eLife assessment

This elegantly performed and rigorous study generates new and conceptually important insights into the interaction between an essential malaria parasite invasion ligand (and vaccine candidate) called PfRH5, and its erythrocyte surface integral membrane receptor basigin. The authors provide compelling evidence based on rigorous biochemical assays that erythrocyte basigin is predominantly expressed in a complex with one of two distinct erythrocyte membrane proteins called PMCA and MCT1 and that PfRH5 binds to these complexes better than to isolated basigin. Certain invasion-inhibitory antibodies, that do not prevent binding of PfRH5 to isolated basigin, do in contrast prevent binding to the basigin complexes, explaining the mode of action of these previously enigmatic antibodies and providing valuable data towards the improved design of vaccines based on PfRH5.

eLife assessment

This study provides a potentially useful assessment of the effect of testing contacts of cases in school classes when identified, rather than at the end of quarantine, on both the number of secondary infections and other outcomes including tracing delay and identification of the possible source of infection. The authors find that the intervention likely led to a decrease in tracing delay and an increase in the number of possible sources of infection, though were unable to determine whether secondary transmission decreased, due in part to unmeasured confounding. While the surveillance system described provides a solid dataset appropriate for this analysis, the description of methods, study outcomes, and consideration of potential confounding factors is incomplete.

eLife assessment

The manuscript describes a set of detailed modeling and experimental studies to disentangle the respective roles of gap junctional electrical vs. metabolic coupling mechanisms in the synchronization of islet activity. This is of interest due to the importance of islet synchronization and generally islet network properties in the regulation of insulin secretion from the pancreas. The significance of the findings was judged to be mostly important and the strength of evidence provided was judged to be mostly solid overall.

eLife assessment

In this study, Sparta et al., generated and employed a battery of fluorescent reporters that allowed them to perform time-resolved monitoring of mechanistic target of rapamycin complex 1 (mTORC1) responses to stimuli including glucose, amino acids, and insulin at the single cell resolution. The results of this elegant approach support a model of graded mTORC1 activation in response to the aforementioned stimuli when applied individually or in combination. This model is consistent with continuous adjustment of mTORC1 signaling to changes in cellular environment and opposed to the "on/off" model of mTORC1 function. Considering the pivotal role of mTORC1 in integrating signals such as nutrients, hormones, growth factors, oxygen, and energy status with a plethora of outputs that affect cell fate and organismal physiology, it was thought that this study will be of interests across a variety of biomedical disciplines. Overall, the elegance and robustness of the approach was highly appreciated, though the paper would be strengthened by addressing some technical issues and concerns regarding the positioning of the proposed model of mTORC1 regulation in the field.

eLife assessment

This important study describes a high performance computational approach to interrogate how microscopic epistasis and clonal interference affect evolutionary dynamics in a spin glass model of microbial evolution. The study offers several insights that can aid in our understanding of the forces that operate in adaptive evolution. The evidence provided is compelling, with its rigorous use of models and analytical descriptions of how these forces manifest in evolution.

eLife assessment

This important study reports how swallowtail butterflies pattern structures composed of chitin at the nanometer scale to produce structural colors. The work uses state-of-the-art microscopy techniques to convincingly show that F-actin is utilized in these butterflies in a novel way to produce structure, paving the way for further studies on growth regulation leading to precise ultrastructures and structural colors.

eLife assessment

This important manuscript reveals signatures of co-evolution of two nucleosome remodeling factors, Lsh/HELLS and CDCA7, which are involved in the regulation of eukaryotic DNA methylation. The results suggest that the roles for the two factors in DNA methylation maintenance pathways can be traced back to the last eukaryotic common ancestor and that the CDC7A-HELLS-DNMT axis shaped the evolutionary retention of DNA methylation in eukaryotes. The solid evolutionary analyses form an interesting basis for experimental follow-up studies. The work should be of interest to colleagues in the fields of evolutionary biology, chromatin biology and genome biology.

eLife assessment

Large scale cell movements occur during gastrulation in vertebrate embryos but their role in this major morphogenetic transition in formation of the body plan is poorly understood. Using the chick embryo model system, this study makes important advances using elegant methods to show that extension of the primitive streak during gastrulation, occurring through cell proliferation, polarisation and intercalation, and large-scale polonaise cell movements, can be uncoupled. Although the driving mechanism and precise role of these movements remains a mystery, the study provides convincing evidence for the uncoupling through independent approaches, the most creative of which are the effects shown after induction of a supernumerary primitive streak.

eLife assessment

This valuable study uses phylogenetic linear mixed models in a Bayesian framework to explore the relationships between taste qualities and the therapeutic use of botanicals from the ancient Graeco-Roman vademecum. The evidence supporting the authors' conclusions is, however, incomplete, and the paper would benefit from a more exhaustive methodological description. The work is nevertheless of broad relevance to ethnobotanists, pharmacologists, and scientists working on drug discovery, particularly those interested in natural products.

eLife assessment

This important study uncovers a surprising link between two self-cleaving RNAs that belong to the same structural family. The evidence supporting the main conclusions is convincing and based on extensive biochemical and bioinformatic analysis. This research will be of broad interest to RNA molecular biologists and biochemists.

eLife assessment

This valuable study presents a solid transcriptomic analysis of enterochromaffin cells, but there are weaknesses in the functional and physiological data describing the role of enterochromaffin cell mechanosensory receptors (Piezo2 channels) in regulating colonic motility.

eLife assessment

This important study reconstructs the evolutionary history of Heliconius butterflies, a well-established model system for understanding speciation in the presence of gene flow between species. Using a convincing statistical phylogenetic approach that relies on the multispecies coalescent, the authors reconstruct the evolution of the lineage, including the timing of speciation events and the history of gene flow. The new phylogeny will be of interest to all researchers working on Heliconius butterflies, and the phylogenetic approach to investigators aiming to understand the history of lineages that have experienced extensive gene flow.

eLife assessment

This important study reports a new mutant mouse with compromised function of one of the BRCT repeats of TOPBP1, a DNA damage response protein. Mutant mice are viable but males are sterile, owing to the lack of spermatocytes beyond the late pachynema stage of the first meiotic prophase. Using immunofluorescence, phospho-proteomics and single-cell sequencing of cells in the testis, the authors provide solid evidence that the animals are defective in the maintenance (but not the initiation) of sex chromosome inactivation in pachynema. The report is of interest to researchers in the fields of meiosis as well as gene silencing/sex chromosome inactivation.

eLife assessment

The manuscript by Kahraman et al. describes the use of a fluorescent dye for purifying and analyzing human islet alpha cells. The study provides solid evidence that the alpha cells can be purified using this method and the cells remained viable and functional after culturing for several days. The significance of the study is access to a new tool that will be useful for islet biologists and researchers studying diabetes mechanisms.

eLife assessment

This study presents valuable findings that could be utilized for the identification of women at risk for preeclampsia prior to the onset of the disease. The novel aspect of this study lies in the utilization of exosomes with two different sizes. However, the data is incomplete: the patient population has not been well-defined, and the study only measured the proteins at a single time point.

eLife assessment

This important study describes how the composition and stabilization of nanodomains in the plasma membrane are an integral part of plant defence against viruses, with a focus on the calcium-dependent kinase CPK3 and its apparent interaction with a plasma-membrane nano domain scaffold protein from the remorin family. While the evidence for a specific role of CPK3 in limiting viral spread is convincing, the claims regarding the CPK3-remorin interaction would be strengthened by additional experimental support. The work, which will be of interest to plant cell biologists and plant virology, opens new avenues for understanding the role of plasma membrane nanodomains in limiting viral spread.

eLife assessment

This study has uncovered some important initial findings about cellular responses to aneuploidy through analysis of gene expression in a set of donated human embryos. While the study's findings are in general solid, some experiments lack statistical power due to small sample sizes. The authors should try to get much more insight with their data highlighting the novel findings.

eLife assessment

This study has uncovered some interesting findings about the fungal composition and its interaction with bacteria in Caesarean section scar diverticulum (CSD). While the study's findings are valuable and with translation possibilities, the strength of the conclusions obtained is incomplete due to the small sample size and methodological issues indicated by the reviewers such as the lack of controls and the location of samples analyzed.

eLife assessment

This valuable study describes engineered dengue virus variants that can be used to dissect epitope specificities in polyclonal sera, and to design candidate vaccine antigens that dampen antibody responses against undesirable epitopes. While the major claims are supported by solid evidence, experiments to distinguish the impact on antibody binding from neutralizing activities would have strengthened the study. This work will be of interest to virologists and structural biologists working on antibody responses to flaviviruses.

eLife assessment

This important study explores numerous lines of evidence for the surprisingly diverse diets of a group of toothed birds that lived over 100 million years ago. The large amount of data the authors collected forms a solid dataset for their statistical analyses. The methods are, to various extents, extensible to other limbed vertebrates. The conclusions in the article itself will be of interest to anyone who studies ecological evolution in birds or dinosaurs more generally, as well as to anyone who studies the impact of the mass extinction event 66 million years ago on ecology and evolution.

eLife assessment

This study describes an important bioinformatics tool for normalizing gene copy number from metagenomic assemblies. The tool is used in a meta-analysis of data from inflammatory bowel disease (IBD) patients and healthy controls. While some of the evidence for the power of the method is compelling, other evidence seems incomplete. The inclusion of additional computational and/or experimental validation would markedly strengthen the study. This paper will likely be of broad interest to researchers studying the role of complex microbial communities in host health and disease.

eLife assessment

This important work provides a comprehensive study of how different cell types of the lateral and dorsomedial hypothalamus are affected by an Influenza H1N1 infection. The evidence presented here is solid; the methodological approach is state-of-the-art, however, the theoretical analysis can be strengthened by further reanalysis of the datasets. This work is of interest to virologists and neurobiologists as the results are promising and open a new door to understanding the effect of respiratory viruses on the physiology of the central nervous system.

eLife assessment

In this valuable paper, the authors analyze the functions of the five C-terminal repeat sequences in the Dux embryonic transcription factor and their role in recruiting cofactors for gene regulation. The evidence is solid and the work is carefully done, although additional experiments could strengthen the overall conclusions of the manuscript.

eLife assessment

This study provides important imaging evidence for the connectopic mapping of the locus coeruleus (LC) and links a rostro-caudal gradient to heterogeneous functional organisation of this structure. Using a well-established gradient approach applied to large 3T and 7T fMRI datasets, the study demonstrates a change in LC functional gradients with increasing age. Overall, the study provides solid evidence and highlights the importance of using more specific spatial definitions of the LC based on distinct connectivity patterns in future studies.

eLife assessment

The role of CRB3A/B in ciliogenesis was discovered several years ago in epithelial cells and in vivo, but the mechanism by which CRB3A/B regulates ciliogenesis has been unknown. Here, the authors confirm the requirement of CRB3A/B expression for primary ciliogenesis in both mouse and human cells and propose a mechanism by which CRB3A/B promotes ciliogenesis. The results are useful but currently incomplete: further experimentation and data analysis are needed to support some of the authors' central claims.

eLife assessment

This study presents valuable insights into the circuit mechanisms of how the fly nervous system modulates ingestive behaviors in response to metabolic conditions. The authors present convincing findings on how downstream neurons connected to Interoceptive Subesophageal zone Neurons modulate nutrient and/or water ingestion in Drosophila melanogaster.

eLife assessment

There is a tremendous need to increase agricultural productivity with means that are both practical and efficient. Drawing on data from variable field environments, this important study provides a theoretical framework for the identification of new factors with presumed relevance for crop growth. This framework can be applied in the context of both agricultural and ecological studies. There is solid evidence for several of the authors' claims, but the impact of the study is limited due to missing functional validation of candidate species in the field. Plant biologists and ecologists working in agricultural and natural environments will find the work interesting.

eLife assessment

There is a tremendous need to find practical and efficient means in order to increase agricultural productivity. Drawing on data from variable field environments, this study provides a valuable theoretical framework to identify new factors that could increase agricultural production. There is solid evidence to support the authors' claims, though following the fate of candidate species after introduction into rice fields would have strengthened the study. Plant biologists and ecologists working in nature and fields will find the work interesting.

eLife assessment

This fundamental study provides a framework for leveraging systems genetics data to dissect mechanisms of gut physiology. The authors provide compelling analyses to highlight diverse modes of interrogating intestinal inflammation, dietary response, and consequent impacts on IBD. As a resource, it will have great utility for linking genetic variation and diet to gut-related pathophysiologies.

eLife assessment

This valuable study contributes to understanding how retinal activity shapes the response properties of excitatory and inhibitory neurons in a major visual target, the superior colliculus. The evidence supporting the claim is convincing: the work is technically excellent yet the interpretation of these results assumes an unbiased sampling and integration of the RGC axon in the SC, a caveat pointed out by the authors. Overall, this study provides insights into the integration of visual information from the eye to the brain, and this work will be of interest to visual neuroscientists.

eLife assessment

This fundamental study leverages natural genetic diversity in mice to discover candidate genes for insulin sensitivity, followed by experimental identification of compounds that can modulate insulin sensitivity, and finally initial mechanistic investigation of the mode of action. The generalized approach presented here – the integration of systems genetics data with drug discovery – supported by compelling evidence, will be a guide for others who seek to translate insights from mammalian genetics to drug discovery.

eLife assessment

This important study leverages natural genetic diversity in mice to discover candidate genes for insulin sensitivity, followed by experimental identification of compounds that can modulate insulin sensitivity, and finally initial mechanistic investigation of the mode of action. The generalized approach presented here – the integration of systems genetics data with drug discovery – supported by convincing evidence, will be a guide for others who seek to translate insights from mammalian genetics to drug discovery.

eLife assessment

This valuable manuscript attempts to identify the brain regions and cell types involved in habituation to dark flash stimuli in larval zebrafish. Habituation being a form of learning widespread in the animal kingdom, the investigation of neural mechanisms underlying it is a worthwhile endeavor. The authors use a combination of behavioral analysis, neural activity imaging, and pharmacological manipulation to investigate brain-wide mechanisms of habituation. However, the data presented are incomplete and do not show a robust causative link between pharmacological manipulations, neural activity patterns, and behavioral outcomes.

eLife assessment

This study presents fundamental new insight into the regulatory apparatus of PI3Kgamma, a crucial kinase in signaling pathways that control the immune response and cancer. A suite of biophysical and biochemical approaches provide convincing evidence for new sites of allosteric control over enzyme activity. The rigorous findings provide structure and dynamic information that may be exploited in efforts to control PI3Kgamma activity in a therapeutic setting.

eLife assessment

This paper demonstrates valuable evidence for genetic redundancy of the COUPTF transcription factors in hippocampal development by creating conditional compound knockouts in combination. Authors aim to demonstrate specific and complementary roles of the two COUPTF homologues. The paper uses convincing methods that includes both anatomic and behavioral studies for the roles of these factors. However, the strength of evidence was incomplete, due to the use of a Cre line that was not adequately described, and lack of concordance with expression domains of the COUPTF factors with the published literature dampened enthusiasm. This concern is expressed by reviewers in the interpretation of some of the finding that may require additional experiments in the future.

eLife assessment:

This valuable study, of interest for students of the biology of genomes, uses simulations in combination with published data to examine how many TADs remain after cohesin depletion. The authors suggest that a significant subset of chromosome conformations do not require cohesin, and that knowledge of specific epigenetic states can be used to identify regions of the genome that still interact in the absence of cohesin. The theoretical approaches and quantitative analysis are state-of-the-art, and the data quality and strength of the conclusions are solid. However, because "physical boundaries (of domains?)" in the model appear to be a consequence of preserved TADs, rather than the other way around, the functional insights are limited.

eLife assessment

This valuable study presents a novel analysis of a large human intracranial electrophysiological recording dataset. The study challenges the traditional view that neural responses to word lists exhibit smoothly drifting contexts over time, showing that items just after a boundary have a characteristic response that occurs repeatedly. The evidence is incomplete, however, leaving open the possibility for alternative explanations.

eLife assessment

This convincing study, which is based on a survey of researchers, finds that women are less likely than men to submit articles to elite journals. It also finds that there is no relation between gender and reported desk rejection. The study is an important contribution to work on gender bias in the scientific literature.

eLife assessment

This study, of interest to cell biologists, presents valuable findings on the positioning mechanics of microtubule asters in Drosophila embryo explants. While the experimental setting is artificial (centrosomes are detached from nuclei and the cell cycle is arrested in interphase in these explants), it extends the framework of aster positioning from recently published work. The authors reach the conclusion that asters interact via pushing forces, an interesting conclusion supported by solid evidence. The identification of motors and MAPs functioning in the aster positioning mechanism would further strengthen the study.

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 get 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

This study presents a useful inventory of the joint effects of genetic and environmental factors on psychotic-like experiences, and identifies cognitive ability as a potential underlying mediating pathway. The data were analyzed using solid and validated methodology based on a large, multi-center dataset. The claim that these findings are of relevance to psychosis risk and have implications for policy changes are partially supported by the results.

eLife assessment

This valuable study examines the ancestral function of Hippo pathway kinases in contractility and cell density in the ameboid organism Capsaspora owczarzaki, a unicellular animal that is a close relative of multicellular animals. There is solid evidence for Hippo kinases regulating contractility and cell density but not proliferation in C. owczarzaki. The work complements previous work on the Hippo effector Yorkie homolog in this species, although the unavailability of extensive genetic tools in this species precludes informative epistasis experiments. The work would be of interest to evolutionary and developmental biologists.

eLife assessment

This important study combines extensive phenotyping of genome-wide deletion mutants and machine learning-based prediction to generate a large scale resource for understanding the functions of thousands of fission yeast protein-coding genes. This resource is supported by convincing phenotyping data and state-of-the-art bioinformatic analyses and will be of interest to many geneticists.

eLife assessment

This important study advances our understanding of the functions and regulation of the Drosophila transcriptional regulator Bonus, an ortholog of mammalian TIF1 family members. Solid evidence, leveraging both in vivo and in vitro studies, reveals the molecular requirements for Bonus' function as a transcriptional repressor, including a key role for sumoylation.

eLife assessment

This important study expands on current knowledge of allosteric diversity in the human kinome by C-terminal splicing variants using as a paradigm DCLK1. The authors provide convincing evolutionary and some mechanistic evidence how C-terminal isoform specific variants generated by alternative splicing can regulate catalytic activity by means of coupling specific phosphorylation sites to dynamical and conformational changes controlling active site and substrate pocket occupancy, as well as protein-protein interactions. The data will be of interest to researchers in the kinase and signal transduction field.

eLife assessment

This important study in the protozoan parasite Toxoplasma gondii significantly advances our understanding of calcium signaling mediated by the kinase CDPK1 in this species. The authors' conclusions are supported by convincing evidence, with rigorous biochemical experiments and microscopy analysis. The work will be of broad interest to researchers in the fields of signal transduction and protozoan biology.

eLife assessment

This work presents important insights regarding the mechanism underlying the assembly, maintenance, and disassembly of a very stable microtubule-based structure, termed quiescent-cell nuclear microtubule (Q-nMT) bundle, formed in quiescent yeast cells to ensure cell survival and viability. Some of the evidence is solid, but some of the major claims are only incompletely supported and require additional analyses using state-of-the-art methodology and more precise descriptions.

eLife assessment

This study provides a clearly presented and thoughtfully analyzed single cell-resolution dataset of gene expression in wildtype and mutant zebrafish skin. These data are used by the authors to develop and test hypotheses about cell lineage relationships and signaling interactions between cell types in the skin, allowing them to identify roles for several signaling pathways and the hypodermis in scale and pigment cell development. These findings constitute a fundamental contribution to the field, and the rigor of the analyses make this manuscript compelling.

eLife assessment

This study presents valuable findings on genetic risk factors for type 1 diabetes and celiac disease using a large cohort from the Environmental Determinants of Diabetes in the Young (TEDDY) study. The evidence supporting the claims of the authors is solid, although the inclusion of the genetic effect of this locus on individuals with different genetic backgrounds would have strengthened the study. The work will be of interest to population geneticists working on diabetes and celiac disease.

eLife assessment

This study presents a valuable set of experiments to test whether Bombus terrestris bumblebees can detect lethal-level doses of a series of pesticides in nectar-mimicking sugary solutions. Behavioural essays were coupled with electrophysiological measurements to show that B. terrestris mouthparts cannot detect high levels of the tested pesticides. If confirmed using pesticide formulas, and other bumblebee species, the study will be of general interest in environmental science research. Most experimental data are compelling, and the conclusions are solid, but the write-up would benefit from being more to the point and less overgeneralizing.

eLife assessment

The findings of this work on the protective role of Leucine in LPS-induced cytokine release syndrome by modulating macrophage polarization are potentially valuable in establishing the link between metabolic regulation of macrophage function and inflammatory responses. The evidence supporting the conclusions that the mTORC1/LXRa axis but not the STAT6 pathway mediates Leucine-promoted M2 polarization are is solid. The manuscript is well written, but the mechanistic studies are incomplete, hence should be improved.

eLife assessment

This convincing study demonstrates a potentially important role for the factor Numb in skeletal muscle excitation-contraction coupling. Numb knockout reduced contractile force. The authors thus demonstrate a novel role for Numb in calcium release in skeletal muscle.

eLife assessment

This study presents a valuable finding on the association between DUX4 expression with features of immune evasion in human tissue and clinical outcomes in patients with advanced urothelial cancer. The evidence supporting the claims of the authors is convincing, using a range of corroborative statistical techniques. While of significant interest to those working on the immune biology of urothelial cancer and drug discovery, this work does not provide any mechanistic insights into the role of DUX4 and immune suppression and the assessment on clinical samples forms the discovery part of a biomarker program, requiring further cohorts for validation.

eLife assessment

The authors have made important contributions to our understanding of the pathogenesis of erectile dysfunction (ED) in diabetic patients. They have identified the gene Lbh, expressed in pericytes of the penis and decreased in diabetic animals. Overexpression of Lbh appears to counteract ED in these animals. The authors also confirm Lbh as a potential marker in cavernous tissues in both humans and mice. While solid evidence supports Lbh's functional role as a marker gene, further research is needed to elucidate the specific mechanisms by which it exerts its effects. This work is of interest to those working in the fields of ED and angiogenesis.

eLife assessment

This manuscript presents a useful method for a comprehensive numerical simulation to systematically characterise the effect of heterogeneity in either the initial conditions or the biophysical parameters on the dynamic behaviour of protein signalling networks. Nevertheless, the presentation and detail of their model appear incomplete to fully support the main claims of the manuscript.

eLife assessment

The authors set out to study the development of high altitude polycythemia, which affects mice in a hypoxia chamber and humans staying at a hypoxic atmosphere at high altitude. The findings are useful both for initiating the discussion of the hypothesis that splenic red pulp macrophages, central to red cell survival, are impacted by hypoxia, and for providing some data that partially supports this hypothesis. However, the current data are inadequate to fully support the authors' conclusions that RPM are inefficient during hypoxia, reducing erythrophagocytosis, and new data provides evidence of the opposite conclusion, given that RBC lifespan is decreased (rather than increased) in response to hypoxia, suggesting that RPM are more efficient at erythrophagocytosis.

eLife assessment

The authors generate a new formulation built upon a previous nanoparticle platform to generate a new system termed bicontinuous nanospheres (BCN), allowing for the dual incorporation of lipid and protein antigens. The authors generate mycolic acid (MA)-loaded BCN and perform a series of characterization studies to demonstrate the superior performance of this new formulation relative to the original one in terms of antigen persistence, a quality needed to sustain responses after vaccination. This work provides important new insights relevant to the TB vaccine field and it suggests that alternative antigens to proteins could be used in TB vaccine formulations. The data are convincing and will be of interest to individuals working on tuberculosis, vaccines and basic immunology.

eLife assessment

This work is useful as it highlights the importance of data analysis strategies in influencing outcomes during differential gene expression testing. While the manuscript has the potential to enhance awareness regarding data analysis choices in the community, its value could be further enhanced by providing a more comprehensive comparison of alternative methods and discussing the potential differences in preprocessing, such as scFLOW. The current analysis, although insightful, appears incomplete in addressing these aspects.

eLife assessment

This valuable study illuminates molecular movements of acid-sensing ion channels by combining compelling advanced chemical biology and biophysical techniques. The evidence for the main claim, lack of interaction of molecular termini, is solid and challenges prior models. Some other claims warrant further evidence. This work will pique interest in the ion channel signaling field, providing a fresh perspective.

eLife assessment

This work provides useful data related to vomeronasal sensory neuron tuning to urine from different sexes, inbred strains, and wild mice, as well as a catalog of nonvolatile molecules and proteins that are present in these urine sources, as assessed by mass spectrometry. Evidence linking specific nonvolatile molecules or proteins to vomeronasal neural activity is incomplete; specific candidate ligands derived from urine, or fractions thereof, are not directly tested on the vomeronasal sensory neurons. A large category of vomeronasal ligands that are known to be present in urine (small nonvolatiles) were not evaluated. This work provides a foundation for future research that will determine which molecules drive sex- and strain-specific vomeronasal responses.

eLife assessment

This intracranial EEG study presents important neural evidence supporting the high spatial specificity (receptive field) of visually-driven alpha-band oscillation in human brains and its potential role in exogenous cuing attention. The evidence supporting the claims is solid, although more control analyses to exclude other explanations could further strengthen the conclusion. The work challenges the predominant view about the role of alpha-band oscillation in visual attention and advocates that stimulus-driven alpha suppression is precisely tuned and might contribute to exogenous spatial attention.

eLife assessment

In this useful study, the authors use a computational model to investigate how recurrent connections influence the firing patterns of grid cells, which are thought to play a role in encoding an animal's position in space. The work suggests that a one-dimensional network architecture may be sufficient to generate the hexagonal firing patterns of grid cells, a possible alternative to attractor models based on recurrent connectivity between grid cells. However, the support for this proposal was incomplete, as the model was inconsistent with certain key features of grid cell organization.

eLife assessment

This study provided a valuable finding demonstrating the spatial relationship between dendritic spines and mitochondria. The authors combined the analysis of ultra-structure data and functional data, which gives an excellent spatial and functional resolution to understand how mitochondria positioning is correlated to synaptic function and response in an in vivo model. Specifically, the authors provided convincing evidence and showed that dendritic mitochondria are positioned in spines with a diversity of orientation tuning, spines that display heterogeneous responses, and in areas of low local calcium activity.

eLife assessment

The manuscript offers useful descriptive insights into the potential influence of whole-brain lactate and pH levels on the manifestation of behavioral phenotypes seen in diverse animal models of neuropsychiatric disorders. However, reviewers have raised concerns about the potential loss of specificity in capturing regional and cell-type-specific effects when relying solely on whole-brain analysis methods. While the evidence supporting the conclusions is largely solid, the robustness of these conclusions could be enhanced by the inclusion of additional data and further analysis.

eLife assessment

This important study uses a range of technical approaches to investigate the responses of zona incerta neurons to movement and sensory stimuli. The majority of neurons exhibited movement-related activity but only a small propotion were modulated by whisker deflections. The major conclusion of the study is that the zona incerta distributes a general motor signal. The evidence supporting this claim is solid, although the study would be improved by greater transparency and discussion of experimental methods and histological verification of recording sites, viral spread, and which territories of the zona incerta were investigated. The work will be of interest to behavioral and physiological neuroscientists.

eLife assessment

This study provides potentially important, new insights about the combination of information from the two eyes in humans. The data includes frequency tagging of each eye's inputs and measures reflecting both cortical (EEG) and sub-cortical processes (pupillometry). The strength of supporting evidence is solid, suggesting that temporal modulations are combined differently than spatial modulations, with additional differences between subcortical and cortical pathways. However, questions remain as to exactly how information is combined, how the findings relate to the extant literature and more broadly, to the interests of vision scientists at large.

eLife assessment:

This work advances on two Aso et al 2014 eLife papers to describe further resources valuable for the field. This paper adds more MBON split-Gal4s convincingly describing their anatomy, connectivity and function.

eLife assessment

This important study reports the physiological role of ZMYND21 in the regulation of sperm flagellar development and male fertility. The data supporting the conclusion are solid, although the inclusion of more patients and ultrastructural studies would have further strengthened the study. This work will be of interest to clinicians and researchers who work on either sperm biology or ciliopathy due to cilial defects.

eLife assessment

This work is a valuable advance in our understanding of a very interesting biological phenomenon: the role of trophic eggs in ant caste determination. The evidence supporting the unexpected finding that feeding larvae trophic eggs promotes the development of the non-reproductive caste is compelling. However, even though there is a description of how trophic and fertile eggs differ in composition, the evidence of its significance for caste determination is incomplete.

eLife assessment

The manuscript describes valuable theoretical calculations focusing on the structural changes in the photosynthetic reaction center postulated by others based on time-resolved crystallography using X-ray free-electron laser (XFEL) (Dods et al., Nature, 2021). The authors provide solid arguments that calculated changes in redox potential Em and deformations using the XEFL structures may reflect experimental errors rather than real structural changes.

eLife assessment

This important study identifies the gene Bm-mamo as a new regulator of pigmentation in the silkworm Bombyx mori, a function that was previously unsuspected because the extensively studied Drosophila mamo gene is involved in gamete production. The evidence supporting the role of Bm-nano in pigmentation is convincing, including high-resolution linkage mapping of two mutant strains, expression profiling, and reproduction of the mutant phenotypes with state-of-the-art RNAi and CRISPR knock-out assays. The part of the work that concerns potential effector genes that Bm-mamo may regulate relies on in vitro and in silico analysis and can be used as a starting point for future in vivo studies. The work will be of interest to evolutionary biologists and geneticists interested in color patterns and in evolution of gene networks in general.

eLife assessment

This work presents convincing evidence for the presence of wooly mammoth/rhinoceros ancient environmental DNA (aeDNA) far from the time likely to host living individuals: what is effectively a genetic version of a geological inclusion. These are important findings that will have ramifications for the interpretation and conclusions extracted from aeDNA more generally.

eLife assessment

This manuscript describes a useful tool for quantitative assessment of sarcomere structures in healthy and perturbed cardiomyocytes grown in vitro. The work is solid, and the methods, data and analyses broadly support the claims with only minor weaknesses. The tool will be relevant to biologists working on and interested in obtaining quantitative information on sarcomere structure, function and development.

eLife assessment

This study addresses an important question in sensory neuroscience: how the olfactory system distinguishes decreases in stimulus intensity from decreases in neural responses due to adaptation. Based on a combination of electrophysiological and behavioral analyses, solid evidence establishes that neural coding changes differently between intensity reductions and adaptation. Intriguingly, behavioral responses tend to increase as the neural responses decrease, suggesting that core features of the odor response persist through adaptation. While the experimental results are convincing overall, the conclusions would be strengthened by more refined statistical analysis and data quantification.

Evaluation statement (24 May 2023)

Yang et al. present valuable information about ligand interactions with the serotonin transporter SERT, innovatively purified from pig brain using Fab fragments. The approach of using natively expressed SERT is notable for its potential insight into binding of endogenous membrane components such as lipids. Data distinguishing binding of the psychostimulants methamphetamine and cocaine add to our knowledge of substrate and inhibitor interactions with SERT and allow direct comparison with the closely related dopamine transporter DAT. The authors carefully state the limitations of their findings, including the possibility that the monomeric transporter stable in detergent micelles might exist in a multimeric state in native membranes.

Biophysics Colab considers this to be a convincing study and recommends it to scientists interested in the structure, mechanism and ligand interactions of neurotransmitter transporters.

(This evaluation by Biophysics Colab refers to version 2 of this preprint, which has been revised in response to peer review of version 1.)

Evaluation statement (22 August 2023)

Bansal et al. present an atomistic view of the transition cascade of the class F GPCR Smoothened (Smo). The extensive long-range molecular dynamics simulations together with stochastic modelling provide theoretical insight into Smo activation and how this is modulated by different ligands. The work identifies testable hypotheses for functional studies of Smo and other class F GPCRs. Future simulations of regions beyond the seven-transmembrane bundle, particularly the cysteine-rich domain, will afford a more complete understanding of receptor activation.

Biophysics Colab considers this to be a convincing computational study and recommends it to scientists interested in the conformational dynamics of class F GPCRs.

(This evaluation by Biophysics Colab refers to version 2 of this preprint, which has been revised in response to peer review of version 1.)

eLife assessment

This important study uses the brain endocast of a ~1.9-million-year-old hominin fossil from Kenya, attributed to genus Homo, to show that the organization of the Broca's area in members of early Homo was primitive. Specifically, the prefrontal sulcal pattern in this early Homo specimen more closely resembles that of chimpanzees than of modern humans. Because Broca's area is associated with speech function, the compelling evidence from this study is relevant for understanding the timing and trajectory of evolution of speech related traits in our genus. Coupled with its potential implications for taxonomic classification, this study will be of interest to paleoanthropologists, paleontologists, archaeologists, and neuroscientists.

eLife assessment

This fundamental study advances the analytic toolset and understanding of long-term series of biological (freshwater) communities, and the impact of humans on these. The authors highlight the value of including not only spatiotemporal scales in biodiversity assessments but also some of the possible drivers of biodiversity loss. Analyzing their joint contribution as environmental stressors, the authors provide compelling evidence that ecosystem assessment methods currently used by environmental regulators throughout Europe are not fit-for-purpose, and they identify several alternatives, more robust indicators of freshwater ecosystem health. The work is timely and will be of interest to ecologists, modelers and global warming scientists in general.

eLife assessment

This valuable study presents an exhaustive structural analysis of a complete tripartite HipBST toxin-antitoxin system of the Enteropathogenic E. coli O127:H6, which represents a fascinating variation on the well-studied HipAB toxin-antitoxin system. The convincing data show that major features of the canonical HipAB system have been rerouted to form the tripartite HipBST, revealing a new mode of inhibition of a toxin kinase.

eLife assessment:

This study reports a meta-analysis of published data to address an issue that is topical and potentially useful for understanding how the sites of initiation of DNA replication are specified in human chromosomes. The work focuses on the role of the Origin Recognition Complex (ORC) and the Mini-Chromosome Maintenance (MCM2-7) complex in localizing origins of DNA replication in human cells. While some aspects of the paper are of interest, the analysis of published data is in parts inadequate to allow for the broad conclusion that, in contrast to multiple observations with other species, sites in the human genome for binding sites for ORC and MCM2-7 do not have extensive overlap with the location of origins of DNA replication.

eLife assessment

This important study combines experiments and mathematical modelling to enhance our understanding of the interplay between the two flight muscles in birds during slow flight. The evidence for the findings is compelling, deriving from a combination of novel methods for measuring wing shape and force production, and validated methods in muscle physiology. This work will be of broad interest to comparative biomechanists.

eLife assessment

This fundamental work substantially advances our understanding of animals' foraging behaviour, by monitoring the movement and body posture of barn owls in high resolution, in addition to assessing their foraging success. With a large dataset, the evidence supporting the main conclusions is convincing. This work provides new evidence for motion-induced sound camouflage and has broad implications for understanding predator-prey interactions.

eLife assessment

This study shows important evidence of the correlation between social tolerance and communicative complexity in a comparison of three macaque species. Notably, the authors use an innovative, detailed methodology for quantifying facial expressions during social interactions. The results are convincing regarding a positive association between social complexity and facial behaviour, which should stimulate further comparative research in this field.

eLife assessment

This important study makes use of AlphaFold2 to predict the models of tens of cohesin subcomplexes from different species. The models, which are in most cases consistent with published cohesin mutants with defects in cohesin function in vitro and in vivo, provide convincing evidence that leads to testable hypotheses of cohesin dynamics and regulation. More broadly, this study serves as an example of how to use AlphaFold2 to build models of protein complexes that involve the docking of flexible regions to globular domains.

eLife assessment

This important study reveals for the first time that ferroptotic stress may play critical roles in regulating tooth germ development. While the evidence presented is solid, it insufficiently supports several of the claims, due to a lack of in-depth analysis.

eLife assessment

Trypanosoma brucei evades mammalian humoral immunity through the expression of different variant surface glycoprotein genes. In this fundamental paper, the authors extend previous observations that TbRAP1 both interacts with PIP5Pase and binds PI(3,4,5)P3, indicating a role for PI(3,4,5)P3 binding and suggesting that antigen switching is signal dependent. While much of the evidence is compelling, the work would benefit from further controls to rule out that any of the observed effects come from the protein tags used.

eLife assessment

This valuable study provides an experimental paradigm and state-of-the-art analysis method to study the existence of call types and transition differences among Mongolian gerbil families in a naturalistic environment. While the evidence supporting the authors' claims is solid, the conclusions would be significantly strengthened by additional analyses and a larger number of families and pup generations. The work will likely be of interest to the auditory neuroscience and vocal neuroethology communities.

eLife assessment

This valuable paper examines the role of the WRNIP1 AAA+ ATPase in regulating R-loop formation, which induces a conflict with active replication forks and transcription. The authors provide convincing evidence to support a role of the ubiquitin-binding UBZ domain of WRNIP1 in R-loop suppression generated by this conflict. The work is of interest to researchers who work on genome stability/instability.

eLife assessment

This important study reports jAspSnFR3, a biosensor that enables high spatiotemporal resolution of aspartate levels in living cells. To develop this sensor, the authors used a structurally guided amino acid substitution in a glutamate/aspartate periplasmic binding protein to switch its specificity towards aspartate. The in vitro and in cellulo functional characterization of the biosensor is convincing, but evidence of the sensor's effectiveness in detecting small perturbations of aspartate levels and information on its behavior in response to acute aspartate elevations in the cytosol are still lacking.