eLife assessment

This study presents valuable new insights into HIV-associated nephropathy (HIVAN) kidney phenotype in the Tg26 transgenic mouse model, and delineates the kidney cell types that express HIV genes and are injured in these HIV-transgenic mice. A series of compelling experiments demonstrated that PKR inhibition can ameliorate HIVAN with reversal of mitochondrial dysfunction (mainly confined to endothelial cells), a prominent feature shared in other kidney diseases. Although there are concerns regarding the specificity of C16 to PKR inhibition, as well as with the in situ hybridization studies, the data suggests that inhibition of PKR and mitochondrial dysfunction has potential clinical significance for HIVAN.

eLife assessment

This valuable study examines the effects of NFKB2 mutations on pituitary gland development through hypothalamic-pituitary organoids. The evidence supporting the main conclusions is solid, although analysis of additional clones to exclude inter-clone variability would strengthen the conclusions. Insight into the mechanism of action of NFKB2 during pituitary development is incomplete. This work will be of interest to endocrinologists and biologists working on pituitary gland development and disease.

eLife assessment

This useful article reports the possible roles of the natural product TRPV1 activator Eugenol on muscle performance and remodeling. It provides as yet incomplete evidence for eugenol, through TRPV1, but nevertheless merits future investigation.

eLife assessment

This study presents a valuable report on the first warm autopsy case of a metastatic prostate cancer patient and the follow-up genomic and epigenomic analysis. The evidence supporting the claims of the authors is solid, although inclusion of more discussion of the study limitation and elaboration of mechanistic link for TP53, CDK12, and CDKN1B mutations would have strengthened the study. The work will be of interest to medical biologists working on prostate cancer.

eLife assessment

This compelling and novel mathematical method assesses drug pro-arrhythmic cardiotoxicity by examining the electrophysiology of untreated cardiac cells. It will be valuable for future drug safety design.

eLife assessment

This study presents valuable findings on diabetogenic risk from colorectal cancer (CRC) treatment. The authors claim that postoperative screening for type 2 diabetes should be prioritized in CRC survivors with overweight/obesity, irrespective of the oncological treatment received. The evidence supporting the claims is solid but requires confirmation in different populations. These results have theoretical or practical implications and will be of interest to endocrinologists, oncologists, general practitioners, gastrointestinal surgeons, and policymakers working on CRC and diabetes.

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. They therefore suggest that antigen switching might have a signal-dependent component. The evidence is mostly compelling, but with some caveats because tagged proteins were used.

eLife assessment

This important study demonstrates widespread introgression between species of cyanobacteria in hot springs in Yellowstone National Park. Using single cell sequencing of hundreds of genomes, the authors provide one of the most convincing demonstrations to date of the importance of selection and hybridization in shaping polymorphism within a natural community. The strong enthusiasm for the paper is only dampened slightly by the methods not being described in the clearest possible manner.

eLife assessment

This work provides valuable insights into mucosal antibody responses against SARS-CoV-2 following intranasal immunization by characterizing a large number of monoclonal antibodies at both mucosal and non-mucosal sites. The evidence supporting the claims is overall solid, although the flow cytometric assessment of antibody-expressing cells would benefit from more rigorous controls. The demonstrated in vitro antiviral activity of antibodies characterized provides a rationale for developing mucosal vaccines, especially if confirmed in vivo and benchmarked against antibodies generated following intramuscular vaccination.

eLife assessment

While decades of research findings have supported the idea that action attenuates predicted touch, recent work has countered this, proposing that action actually enhances predicted touch and the previously observed attenuation is due to tactile contact. This present study resolves these contradictory claims regarding the role of prediction in perception of self-action. This important work provides compelling evidence that self-generated touch is attenuated compared to the same touch externally-generated, and a clear explanation for recent high-profile results that appeared to support the opposite view.

eLife assessment

This work presents useful and potentially valuable findings on how food signals may influence reproduction in the nematode C. elegans. In the current manuscript, the evidence in support of the authors' model is incomplete, and additional experimental data is needed to buttress the authors' conclusions.

eLife assessment

The authors studied the mechanisms by which dead cells are removed from the wounded skin in a process called efferocytosis. By analyzing different cell populations in the skin, the authors find that proteins involved in mediating the cell death and marking the cells as undergoing this process are elevated during distinct times in the wound healing program. Interestingly, these same proteins are elevated even higher in diabetic wounds. Finally the authors demonstrate that blocking the process of efferocytosis alters the wound healing program, thus illustrating its importance in effective wound repair.

eLife assessment

This work is fundamental in providing compelling evidence of mitochondria-encoded RNAs playing a role in controlling nuclear gene expression. How mitochondria and the nucleus communicates is an important but yet not well-appreciated area of biology. Using the iMARI (in situ mapping of RNA-Genome Interactions) technology developed by this team, the authors found that mitochondria-encoded RNAs play an unexpected role in regulating nuclear gene expressions in endothelial cells and intriguingly, depletion or overexpression of a specific mt-caRNA altered stress-induced transcription of nuclear genes encoding for innate inflammation and endothelial activation. Overall, these findings are interesting and supported by experimental confirmation, bulk-RNA-seq, and snRNA and scRNA-seq data and will be of interest to the field studying RNA regulation, gene expression and cell biology.

eLife assessment

Brodsky and colleagues report here an unexpected cis-activation mechanism of caspase-11. The authors use cellular imaging methods and cleavage site mutants to show that the LPS-induced speck formation by caspase-11 depends on the autoprocessing between two subdomains. This new finding opens multiple doors for further investigating how this non-canonical inflammasome is regulated and activated at the molecular level.

eLife assessment

This study presents a useful mathematical analysis of different signaling networks in an attempt to provide general rules that give rise to biphasic responses, a widely observed behavior in biology in which the outputs of the network depend non-monotonically on the inputs. Determining general conditions that underlie this behavior would be useful in engineering synthetic biological systems and for mechanistically understanding biphasic responses in biological systems. However, whereas the mathematical approach and methods are solid, as they stand, the analyses are inadequate to assess how these findings are applicable in nature and which are general.

eLife assessment

This paper presents valuable findings from whole-brain modeling of persistent activity states (underlying working memory) in the mouse brain. The most novel finding is that a spatial gradient of the density of inhibitory neurons supports a corresponding spatial gradient of propensity to support persistent activity. However, the evidence for this finding appears to be incomplete.

eLife assessment

This important work reveals that increased flux towards one carbon metabolism improves neuronal regeneration after injury in C. elegans. The presented data are solid and provide compelling support for this conclusion. The manuscript can still be improved in order to strengthen some of the specific conclusions made and to increase the clarity of the presentation.

eLife assessment

The paper introduces a new, important framework for neural modelling that promises to offer efficient simulation and analysis tools for a wide range of biologically-realistic neural networks. The paper's examples provide solid support for the ease of use and flexibility of the framework, but the comparison to existing solutions (in particular in terms of accuracy and performance) is incomplete. With a more careful evaluation of the tool's strengths and limitations, the work would be of interest to a wide range of computational neuroscientists and researchers working on biologically inspired machine learning applications.

eLife assessment

This valuable study presents a tool for hyperaligning functional brain topography between individuals, which is based on fMRI connectivity data gathered when participants watched different movies. The tool is validated through strong correlations between functional topographic maps generated from a participant's own localizer data and those derived from other participants' data based on this hyperalignment, even when the training and target participants were drawn from different datasets. The study will potentially be of interest to researchers working with a wide range of fMRI datasets.

eLife assessment

The authors establish a Drosophila model to assess the severity of disease-linked alleles of Uba5. Using both in vivo and in vitro experiments, this valuable study demonstrates the alleles fall into mild, intermediate, and severe classes, with convincing evidence to support their conclusion. This well-executed study establishes a model for further characterization of Uba5-related phenotypes in a powerful model system.

eLife assessment

This fundamental study reports differential expression of key genes in full-term placenta between Tibetans and Han Chinese at high elevations, which are more pronounced in the placentae of male than in female fetuses. If validated as functionally relevant, these results will help us understand how human populations adapt to high elevation by mitigating the negative effects of low oxygen on fetal growth. At this time, while the differential gene expression analyses are solid, the downstream analyses offer incomplete support for the connection to hypoxia-specific responses and adaptive genetic variation.

eLife assessment

This important study presents a new apparatus and experimental paradigm to examine deficits in finger control in stroke patients, with the goal of understanding their potential (biomechanical and neural) underpinnings. The paper presents solid experimental design and quantitative analyses to characterise these deficits and infer their origin, but a few technical aspects related to data analysis and statistics could be improved, and alternative interpretations of the results considered. In addition to the scientific results, this novel methodology can be used as a starting point for further research on hand function impairments in stroke, which is of significance for theoretical studies in neuroscience and applied research in rehabilitation.

eLife assessment

In this important paper, the authors report a link between brumation (or "hibernation") and tissue size in frogs, summarizing convincing evidence that extended brumation is associated with smaller brain size and increased investment in reproduction-related tissues. The research is of broad interest to ecologists, evolutionary biologists, and those interested in global change biology, as the dataset involves significant field work and advanced statistical analyses for insights into how expensive tissues in these ectothermic animals respond to environmental seasonality.

eLife assessment

This manuscript describes valuable information on how the extraocular muscles (EOM) are preserved in a mouse model of familial Amyotrophic lateral sclerosis (ALS) that carries a G93A mutation in the Sod1 gene. The authors provide convincing evidence of how the integrity of neuromuscular junction is preserved in EOM but not in limb and diaphragm muscles of G93A mice. Overall, this interesting work provides new evidence regarding the etiopathogenesis of ALS and insights for the development of therapeutic targets to slow the loss of neuromuscular function in ALS.

eLife assessment

This useful study reports on how Notch activity regulates the termination of neurogenesis in central brain during larval-pupal stages in Drosophila. The evidence supporting the claims is solid. The work will be of interest to developmental neurobiologists.

eLife assessment

This study presents the valuable finding that sustained calcium signaling in induced-Treg (iTreg) cells can lead to the loss of Foxp3 expression and iTreg identity by altering the chromatin landscape. The evidence supporting the claims of the authors is convincing. The work will be of interest to immunologists working on Treg cell therapy.

eLife assessment

This valuable study is focused on the requirement of the photoreceptor-specific tetraspanins, ROM1 and PRPH2, for the formation of light-sensitive membrane discs. The evidence supporting the claim that deficiency in one of the proteins can be compensated by the other is convincing, with both established and advanced techniques yielding results that will be of interest to those studying photoreceptor development and membrane curvature.

eLife assessment

This useful study aims to advance our understanding of the structure of the native form of a viral toxin secreted from infected cells. Some of the findings confirm previous reports, but the new claims in this study are only inadequately supported by the methods and analyses used. More rigorous approaches are needed to justify the main conclusion that the structure of the viral toxin derived from infected cells in this study is distinct from previously reported structures of recombinantly expressed versions of the toxin.

eLife assessment

This important study shows, based on analyses of single cell RNA-seq data sets of thymus cells, that transposable elements (TEs) are broadly expressed in thymic stromal cells, especially in medullary thymic epithelial cells and plasamacytoid dendritic cells. The authors also show that at least some TE-derived peptides are presented by MHC-I molecules in the thymus. The results suggest a possible role of TEs in thymic T-cell selection and immune self-tolerance, but the current analyses are incomplete and not yet fully support the claims.

eLife assessment

This work presents fundamental new insights into the conductivity of freshwater cable bacteria. The evidence supporting the conclusions, which was collected using appropriate techniques, is compelling. The work will be of interest to environmental microbiologists and the microbial electrochemistry community.

eLife assessment

This valuable study reports on several variants of the COVID-2 spike protein that are studied using well-established computational approaches, followed by attempts to validate the findings using experimental approaches. The evidence supporting the claims of the authors is solid, although there are known limitations of the computational approaches. The manuscript would benefit from a deeper discussion of the limitations and better contextualization of the work. The study will be of interest to biophysicists working in the general areas of allostery and protein evolution.

eLife assessment

This useful manuscript explores conditions for epigenetic inheritance by studying the stability of simple network models to permanent and transient perturbations. A novel aspect of the study is that it unifies non-genetic inheritance phenomena across cell divisions of unicellular organisms and in the germline of multicellular organisms. However, the models studied are more a collection of vignettes of numerical studies than a systematic study, therefore the evidence presented remains incomplete. This work will be of interest in the field of epigenetic inheritance as a first step towards building a more systematic theoretical framework.

eLife assessment

This valuable study reports that auxin exposure perturbs feeding behavior, survival rates, lipid metabolism, and gene expression patterns in adult flies. The solid results are based on proper methods and data analyses, which broadly support the conclusions with only minor weaknesses. This work should be interesting to fly geneticists who are interested in using the auxin-inducible gene expression system for inducing target protein degradation acutely.

eLife assessment

This manuscript presents valuable findings that inform our understanding of the genetic underpinnings of the model plant Arabidopsis' resistance to turnip mosaic virus (TuMV). The strength of the evidence in the manuscript is convincing, with very large sample sizes, careful controls, multiple follow-up experiments, and broadening to the evolutionary context. There is very good support for each of the manuscript's conclusions and the work could pave the way for functional studies.

eLife assessment

This study presents important findings that homo- and heterosynaptic plasticity outside of the window at which a weak associative fear memory is formed can transform this memory into a stronger one, and can produce fear memory even when stimuli were not paired. This work therefore expands our views on the role of time- and input-specificity of plasticity in learning processes. The evidence, based on state-of-the-art in vivo manipulations and activity recordings in behaving mice, supporting the conclusions is solid, although further validation of the methods used is required in order to reaffirm the authors' conclusion. Once resolved, the work will be of broad interest to neuroscientists interested in activity-dependent synaptic plasticity and associative memory.

eLife assessment

This study enhances our understanding of the relationship between cortico-hippocampal interactions and behavioral performance. Using an inter-areal coherence metric to gate trial initiation in real time, the authors provide solid evidence that links high hippocampal-prefrontal theta coherence to correct performance on spatial working memory and cue-guided decision-making tasks. Although reviewers agreed that the results do not demonstrate causality between hippocampal-prefrontal synchrony and behavioral performance, the findings are viewed as important given their potential implications for brain-machine interface applications in humans.

eLife assessment

Host cell death is an effective strategy to protect against infection, and is believed to function primarily by the elimination of the intracellular niche for pathogen replication. Abele and colleagues address an important question: does the mode of cell death affect its effectiveness in pathogen clearance? Consistent with prior observations, the authors provide compelling new evidence that the answer can depend on the cell type and/or tissue involved.

eLife assessment

This study describes CLEVER, an improved method for fast and efficient rescue and mutagenesis of SARS-CoV2. While the principle of this method is not new, this work significantly improves upon existing protocols, providing an important advancement in the field of viral infectious clones. Convincing proof-of-concept experiments were performed that demonstrate the utility and efficiency of the method.

eLife assessment

This manuscript provides fundamental findings on the association between sleep regularity and mortality in the UK Biobank, which is a popular topic in recent sleep and circadian research in population-based studies. The study is based on a large accelerometer study with validated follow-up of incident diseases and deaths, and the data quality and large sample size are convincing and strengthen the credibility of the conclusion. This will be of wide interest to researchers in the sleep study field, epidemiologists, practicing clinicians and the general public.

eLife assessment

This small-sized clinical trial comparing nebulized dornase-alfa to the best available care in patients hospitalized with COVID-19 pneumonia is valuable, but in its present form the paper is incomplete.

eLife assessment

This important study unravels the interaction between effort cost, pupil-indexed brain state, and movement (saccadic) vigor during foraging decisions in marmoset monkeys. Based on a normative computational model, the authors derive the prediction that anticipated effort should affect both decisions and movement vigor during foraging; and then provide solid behavioural and pupillometric evidence for this prediction in a foraging task. This paper will be of interest to decision and motor neuroscience as well as to all researchers studying animal behavior.

eLife assessment

This study presents valuable observations indicating that the electrophysiological excitability of cultured sympathetic motor neurons progressively increase during aging, and are inversely correlated with the magnitude of KCNQ currents. The alterations in membrane excitability are broadly relevant for those interested in understanding how the nervous system changes during aging. While the data as a whole are solid in showing that the excitability of sympathetic neurons increases in neurons cultured from older mice, the mechanism of the underlying changes and in vivo relevance is incomplete.

eLife assessment

In Drosophila melanogaster, the Store-operated Ca2+ entry (SOCE) channel, Orai, is required for the development of flight-promoting dopaminergic neurons. Here, Mitra et al. determine that expression of a loss-of-function Orai1 mutant during the 72-96 hour window of pupal development impairs gene expression in dopaminergic flight neurons in part through the expression of Set2, a histone methyltransferase. The authors identify a large number of genes that are controlled by Set2, and show that Set2 is controlled by the Trl/GAF transcription factor. Although the findings reported here are important, the evidence supporting some of the claims is incomplete.

eLife assessment

This study provides useful insights into the mechanisms of electron transport in STEAP proteins, consistent with current models. The work strengthens and supports previously published biochemical and structural data, and the experimental results are of solid technical quality. The manuscript will be of interest to colleagues who work on STEAP proteins and related electron transfer systems.

eLife assessment

This study presents useful insights into core genome mutations that could have contributed to the emergence of the Staphylococcus aureus lineage USA300, a frequent cause of community-acquired infections. The solid approach used is innovative in combining genome-wide association studies and RNA-expression analyses, both applied to extensive publicly available datasets. This strategy reduces the rate of false positives attributed to high genome-wide linkage disequilibrium. It is noted that this method cannot be used for most phenotype-genotype studies, especially those requiring essential population structure correction, and it can therefore not be readily replicated in different datasets.

eLife assessment

Understanding how genomic regulatory elements interact to control spatiotemporal gene expression is essential to explaining cell type diversification, function, and delineating genetic variation and disease. In this important study, the authors provide solid evidence showing that, in general, enhancers influence gene expression in an additive way. The findings contribute to ongoing discussions about the selectivity and combination of regulatory elements. Improved clarity regarding the statistical analysis, computational methods, and definitions used would strengthen the conclusions.

eLife assessment

This manuscript describes an important NMR investigation of allosteric interactions within Abl kinase. The authors identify helix I as a major element that couples the Abl active site with the myristate-binding pocket. The convincing findings have implications for understanding Abl kinase activation and how to target Abl kinase in diseases.

eLife assessment

This study provides a valuable resource that documents the protein-protein interactions (PPI) network for alpha-arrestins in both human and Drosophila based on affinity purification/mass spectrometry and the SAINTexpress method followed by a series of bioinformatic and functional assessments. Through these, the authors confirmed the roles of known and novel interactions, including proteins involved in RNA splicing and helicase, GTPase-activating proteins, and ATP synthase. This study represents a convincing example of how to adopt comparative molecular interactions and how to interpret the functional implications.

eLife assessment

In this study, the authors (1) build a detailed model of the process whereby visual information is stored in neuronal activity from the moment that a stimulus is presented until some time later when such information needs to be recalled, and (2) test numerous mechanistic assumptions by fitting the model to rich psychophysical experiments performed by human participants. The evidence supporting the claims is convincing, utilizing detailed model comparison to evaluate potential mechanisms. Overall, the results represent a valuable advance in our understanding of how sensory representations are encoded in and then recalled from, working memory.

eLife assessment

This is a fundamental work that significantly advances our understanding of the role of mossy cells in the dentate gyrus in Fragile X Syndrome. Carefully designed experiments provide evidence that changes in their excitability occur due to up-regulation of Kv7 currents. While the evidence supporting the authors' conclusions is solid, some of their claims did not consider other potential factors and explanations. The work will be of interest to neuroscientists working on unveiling the mechanisms of Fragile X pathology.

eLife assessment

This study presents useful findings from a large sample of participants from the UK Biobank on the relationship between menopause (including status, type, and age of onset), cognition, neuroanatomical measures derived from magnetic resonance imaging, and Alzheimer's disease. The strength of evidence is incomplete, and the study would benefit from clearer methodological descriptions, more careful consideration of potential confounds, and better theoretical integration with prior work in the field. This paper will be of interest to people working in the fields of cognitive neuroscience, endocrinology, and dementia.

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 data provided. 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

In this important study, the authors integrated genetic and genomic datasets from humans and mice to unveil shared networks and pathways associated with coronary artery disease. Their compelling analysis led to the identification of new regulatory genes and pathways in vascular tissues and in the liver, allowing for a more in-depth understanding of the pathogenesis of coronary artery disease.

eLife assessment

This study and associated data is compelling, novel, important, and well-carried out. The study demonstrates a novel finding that different chemotherapeutic agents can induce nucleolar stress, which manifests with varying cellular and molecular characteristics. The study also proposes a mechanism for how a novel type of nucleolar stress driven by CDK inhibitors may be regulated. The study sheds light on the importance of nucleolar stress in defining the on-target and off-target effects of chemotherapy in normal and cancer cells.

eLife assessment

This study reports that neural activity in the auditory cortex (field L) of singing male songbirds can be modulated by social context. These potentially important findings indicate that the presence of a female conspecific alters the response of auditory cortical neurons to the male bird's own song and to perturbations of auditory feedback that the bird has been trained to expect. While they extend recent work showing that the activity of dopaminergic neurons in songbirds is also affected by an audience, the evidence presented is incomplete since it is unclear how much of the apparent modulation of cortical neurons may be due to other factors, such as changes in the recorded neurons or their properties over time, which will require additional analyses to work out.

eLife assessment

This important study discovered DBT as a novel gene implicated in the resistance to MG132-mediated cytotoxicity and potentially also in the pathogenesis of ALS and FTD, two fatal neurodegenerative diseases. The authors provided solid evidence to support a mechanism by which loss of DBT suppresses MG132-mediated toxicity. While activation of autophagy is shown to be associated with DBT knockdown, it remains unclear if this is the underlying mechanism driving improved survival.

eLife assessment

This fundamental study provides an unprecedented understanding of the roles of different combinations of NaV channel isoforms in nociceptors' excitability, with relevance for the design of better strategies targeting NaV channels to treat pain. Although the experimental combination of electrophysiological, modeling, imaging, molecular biology, and behavioral data is convincing and supports the major claims of the work, some conclusions need to be strengthened by further evidence or discussion. The work may be of broad interest to scientists working on pain, drug development, neuronal excitability, and ion channels.

eLife assessment

This useful study summarises the effect of optical stimulation of the A13 region on locomotion in healthy mice and experimental Parkinsonism and could potentially be of interest to basic and clinical neuroscientists. Behavioural analyses and evidence for pro-locomotor effects of stimulation are solid. However, anatomical analyses are incomplete and do not yield mechanistic insights due to various issues with specificity, sample size, statistical analysis, and data presentation in the present form of the study.

eLife assessment

This study provides valuable insights into how researchers can use perceptual metamers to formally explore the limits of visual representations at different processing stages. While the study is overall convincing in terms of approach and results, issues were identified with respect to novelty, sample size, incomplete psychophysical methodology, and better motivation of the models tested.

eLife assessment

This is a valuable study of Eph-Ephrin signaling mechanisms generating pathological changes in amyotropic lateral sclerosis. There are exciting findings bearing on the role of glial cells in this pathology. The study emerges with solid evidence for a novel astrocyte-mediated mechanism for disease propagation. It may help identify potential therapeutic targets.

eLife assessment

This paper provides a fundamental expansion of vestibular compensation into transient and partial dysfunction, as well as insights into the adaptation of visual reflexes in this process. The conclusions are convincingly supported with paired histological and behavioral measurements, which are additionally modeled for further interpretation. This work would be of interest to neuroscientists working in multisensory integration and recovery mechanisms.

eLife assessment

This study provides valuable findings about pre-saccadic foveal prediction and the extent to which it is influenced by the visibility of the saccade target relative to its background. The results and research methodology are technically solid, but there are questions about the interpretation of data which if addressed, would benefit our understanding of this phenomenon. This work should be of broad interest to visual neuroscientists, as well as those interested in understanding perception in the context of eye movements and in modeling visually guided actions.

eLife assessment

In this study, the authors develop a useful strategy for fluorophore-tagging endogenous proteins in human induced pluripotent stem cells (iPSCs) using a split mNeonGreen approach. Experimentally, the methods are solid, and the data presented support the author's conclusions. Overall, these methodologies should be useful to a wide audience of cell biologists who want to study protein localization and dynamics at endogenous levels in iPSCs.

eLife assessment

This study describes a method to track MHC class II binding peptides on dendritic cell (DC) surfaces using a tetracystein tag and a thiol-reactive dye, which can then be investigated in vitro and in vivo. This is a valuable study for the impact on immunology and potentially other areas where the detection of cell-associated peptides is required. The methods are convincing based on the use of MHC class I/II deficient mice that have significantly reduced signal, but the non-zero background is detected, and it is not clear that this is lower than if the peptides were directly labelled with fluorophores.

eLife assessment

This study presents a valuable finding on the mechanism of glucocorticoid-induced osteonecrosis of the femoral head. The data were collected and analyzed using solid and validated methodology and can be used as a starting point for functional studies of the development of glucocorticoid-induced osteonecrosis. This paper would be of interest to cell biologists and biophysicists working on the potential pharmacological treatments for glucocorticoid-induced osteonecrosis.

eLife assessment

The authors have shown a valuable tumor suppressive function of the non-core regions of RAG1/2 recombinases, by using a set of animal models. The work is solid and the conclusions are supported by their data. Some areas of mechanistic work can be improved.

eLife assessment

The authors studied key characteristics of MYC-driven cancers: dysregulated pre-mRNA splicing and altered metabolism. The reviewers agree that this is an interesting study and that the findings are important. Overall the data was considered solid although the paper would benefit from revisions. The manuscript has the potential to be of broad interest to cancer biologists due to its therapeutic implications.

eLife assessment

The study provides important insights into the mechanisms underlying ulcerative colitis, a chronic and debilitating gastrointestinal condition. The article provides solid evidence of the role of the vesicular trafficking protein Rab7 in regulating the colonic mucus system and its implications in ulcerative colitis.

eLife assessment

The findings of this valuable manuscript advance our understanding of the significance of Bestrophin isoform 4 (BEST4) in suppressing colorectal cancer (CRC) progression. The authors used appropriate and validated methodology, such as the knockout of BEST4 using CRISPR/Cas9 in CRC cells, to provide a solid foundation for elucidating the potential link between BEST4 and CRC progression.

eLife assessment

This paper proposes a valuable new method for the assessment of the mean kurtosis for diffusional kurtosis imaging by utilizing a recently introduced sub-diffusion model. The evidence supporting the claims that this technique is robust and accurate in brain imaging is incomplete. The work could be of interest in the research and clinical arena.

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 proportion 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 presents an important open-source resource for high-throughput behavioral screening. The protocols employ inexpensive, off the shelf hardware, and allow real-time analysis of hundreds of behaving flies. Although these protocols were developed using Drosophila melanogaster, they could easily be applied to other models. The evidence in support of the conclusions is solid and the revisions carried out by the authors go a long way towards providing the user with an integrated system that is also more user-friendly.

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 significant 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 manuscript aims to identify the pacemaker cells in the lymphatic collecting vessels - the cells that initiate the autonomous action potentials and contractions needed to drive lymphatic pumping. Through the exemplary use of existing approaches (genetic deletions and cytosolic calcium detection in multiple cell types), the authors convincingly determine that lymphatic muscle cells are the origin of the action potential that triggers lymphatic contraction. This fundamental discovery establishes a new standard for the field of lymphatic physiology.

eLife assessment

This study presents valuable findings on the presence of 6mA in the Drosophila genome and challenges previous findings regarding the role of TET in 6mA modification. The evidence supporting the claims is solid, and the paper has the potential to stimulate re-evaluations of the significance and regulatory mechanisms of 6mA DNA modifications in Drosophila.

eLife assessment

This fundamental study advances our understanding of how Notch signaling activates transcription by analyzing the dynamics of the Mastermind transcriptional co-activator and its role in the activation complex. The evidence is compelling with precise quantitative measurements. The evidence presented by the authors features methods, data, and analyses that are currently state-of-the-art but have not previously been applied to how transcription is regulated in the Notch pathway.

eLife assessment

This valuable work on the paleovegetation history of Iceland has implications for the field of paleoecology, and the deglaciation history of Iceland and additional localities in Northern America and Europe via woody shrub colonization. The study uses a sedimentary ancient DNA metabarcoding approach to study this historic process. The strength of evidence is solid, with the methods (analysis of sedimentary DNA) and data analyses broadly supporting the claims.

eLife assessment

This study presents initial findings in the generation of 3D cell constructs from endometrial cell mixtures seeded in Matrigel scaffold and treated with hormones as a proof of concept. While the study findings are valuable, functional validation to demonstrate its robustness is lacking, and therefore the strength of evidence is incomplete. The term organoids might not be appropriate to describe this in vitro model.

eLife assessment

The current manuscript presents a cryo-EM structure of a tripartite ATP-independent periplasmic (TRAP) transporter that contributes to Haemophilus influenzae virulence. Convincing biophysical and cryo-EM experiments yield a valuable molecular model, but evidence to support some of the mechanistic conclusions is currently incomplete.

eLife assessment

This valuable paper examines gene expression differences between male and female individuals over the course of flower development in the dioecious angiosperm Trichosantes pilosa. The authors show that male-biased genes evolve faster than female-biased and unbiased genes. This is frequently observed in animals, but this is the first report of such a pattern in plants. In spite of the limited sample size, the evidence is mostly solid and the methods appropriate for a non-model organism. The resources produced will be used by researchers working in the Cucurbitaceae, and the results obtained advance our understanding of the mechanisms of plant sexual reproduction and its evolutionary implications: as such they will broadly appeal to evolutionary biologists and plant biologists.

eLife assessment

This important study combines in vitro experiments with simulations to identify the mechanisms governing modulation of microtubule dynamics by GTP hydrolysis. The authors introduce a convincing new approach by using a mixed GDP/GMPCPP lattice and varying GDP concentration to reveal that the nucleotide at the interface of two tubulin dimers determines the strength of the interaction between two dimers. Overall, the findings will be of interest to biophysicists and cell biologists, especially in the field of microtubule biology.

eLife assessment

This important study uses CRISPRi to silence multiple effectors in the pathogen, Legionella pneumophila. It provides a technique that will allow researchers to address functional redundancy amongst effectors, a problem that has persisted even after decades of study. The methodology used is convincing, and further improvement (such as using multiple guides per gene) can lead to the identification of novel virulence factors.

eLife assessment

One of the most promising strategies in development of drugs targeting kinases is provided by using allosteric control that allows specific regulation and study of kinase function without directly targeting the active site. This important paper reviews convincingly the current repertoire of tools for regulating the activity of protein kinases with the ultimate goal of developing novel approaches in treating diseases associated with signal dysregulation.

eLife assessment

One of the most promising strategies in development of drugs targeting kinases is provided by using allosteric control that allows specific regulation and study of kinase function without directly targeting the active site. This important manuscript provides a convincing review of the current repertoire of tools for regulating the activity of protein kinases with the ultimate goal of developing novel approaches in treating diseases associated with signal dysregulation.

eLife assessment

This valuable study provides convincing evidence that acute experimental pain induces changes of cortical excitability. Although the modality specificity of the findings is not fully clear, the findings will be of interest to researchers interested in the brain mechanisms of pain.

eLife assessment

This study provides the fundamental insight that TGN46, a single-pass membrane protein, acts as a cargo receptor for proteins at the Trans-Golgi Network that are destined for secretion. Compelling evidence shows that the luminal domain of TGN46 is crucial for the incorporation of the soluble secretory protein PAUF into CARTS. The clear effect but partial block of secretion after depletion of TGN46 points to the need for further exploration of the process.

eLife assessment

This valuable study of Iceland's paleovegetation history has implications for the field of paleoecology, as well as shrubification in the Arctic. It presents solid evidence that postglacial colonisation by birch was later than willow in Iceland and nearby areas, based on a new analysis with multiple lines of existing evidence, including one new site with sedimentary ancient DNA. The study would benefit from a clearer description of key methods and results, and more critical reflection on the assessment of colonisation lags and the predictive use of paleo datasets.

eLife assessment

The OpenApePose database presented in this manuscript will be important for many applications within primatology and the behavioural sciences, and a beneficial resource for developing additional tools using computer-vision based methods. The authors have rigorously tested the utility of this database to clearly demonstrate its convincing potential, especially in relation to current alternatives. The transparent and open nature of this work will surely be beneficial to advancing automated methods for pose estimation both in captive and wild settings, and for image and video processing.

eLife assessment

This manuscript used the sci-Plex system for screening compounds to improve the Ascl1-induced reprogramming from Müller glia to bipolar neurons in vitro, followed by in vivo characterization of two promising compounds in mice. The findings are valuable for future studies to develop cell replacement strategies for treatment of retinal degeneration. The strength of evidence is solid, featuring a scalable drug screening design, albeit with limited mechanistic insights.

eLife assessment

This study shows that unlike prior reports, cortical spreading depression does not lead to spontaneous activity in the majority of meningeal afferent sensory neurons but that it increases sensitivity to mechanical deformation of the meninges. This has important implications for headache disorders like migraine where cortical spreading depression is thought to contribute to the pathology, but how this occurs is unclear. The current work uses convincing methods in awake and freely moving animals compared to prior studies of this nature that used recordings in anesthetized animals.

eLife assessment

The findings of this study are valuable as they provide new insights into the role of acetylcholine in modulating sensory processing in the auditory cortex. This paper reports a systematic measurement of cell activity in the auditory cortex before and after applying ACh during an oddball and cascade sequence of auditory stimuli in anesthetized rats. The results presented are solid given the rigorous experimental design and statistical analysis. The conclusions are provocative and will interest researchers in auditory neuroscience and neuromodulation, as well as clinicians and individuals with auditory processing disorders. However, the findings support multiple interpretations, beyond that offered by the authors.

eLife assessment

This manuscript reports a useful computational study of the effects of axon de-myelination and re-myelination on models of working memory, with potential applications implications in disorders such as multiple sclerosis. In its present form, the provided evidence is partly incomplete due to certain modeling choices and lack of clarity on model details, but these shortcomings could be addressed.

eLife assessment

Building on their own prior work, the authors present valuable findings that add to our understanding of cortical astrocytes, which respond to synaptic activity with calcium release in subcellular domains that can proceed to larger calcium waves. The proposed concept of a spatial "threshold" is based on solid evidence from in vivo and ex vivo imaging data and the use of mutant mice. However, details of the specific threshold should be taken with caution and appear incomplete unless supported by additional experiments with higher resolution in space and time.

eLife assessment

Schnell et al report important differences between the strategies used by rodents and humans when discriminating different visual objects. The evidence supporting these findings is convincing, showing that rat performance was influenced far more by low-level cues compared to humans. It is, however, unclear to what extent these differences can be explained by the lower visual acuity of rats. This work will be of general interest to vision and cognition researchers, particularly those studying object vision.

eLife assessment

This study provides a valuable contribution to the study of eye-movements in reading, revealing that attention-weights from a deep neural network show a statistically reliable fit to the word-level reading patterns of humans. Its evidence is convincing and strengthens a line of research arguing that attention in reading reflects task optimization. The work would be of interest to psychologists, neuroscientists, and machine learning researchers.

eLife assessment

The authors provide an important series of metabolic measurements characterizing group dynamics in fish, rationalizing that schooling behavior presents several benefits. The strength of evidence supporting this conclusion is solid, but the methodological and analytical approaches taken could be strengthened. Similarly, numerous test-based clarifications and improved statistical analyses could significantly strengthen the study and underlying interpretations.

eLife assessment

This valuable study reports comprehensive multi-omic data on the changes induced in young and aged male mouse tail fibroblasts after treatment with chemical reprogramming factors. The authors claim that chemical reprogramming factors induce changes consistent with a reduction of cellular 'biological' age (e.g., correlations with established aging markers in whole tissues). However, the study relies on previously identified aging markers (instead of aging in the tail fibroblast system itself), and thus, at this stage, the evidence in support of the observed molecular changes truly reflecting changes in biological age in the study system is still incomplete.

eLife assessment

This valuable study investigates evolutionary aspects around a single amino acid polymorphism in an immune peptide of Drosophila melanogaster,. This polymorphism is known to be under long-term balancing selection. Using alleles with different substitutions, the investigators found that one allele provides better survival after systemic infections by a bacterial pathogen, but that the alternative allele endows its carriers with a longer lifespan under certain conditions. The authors suggest that these contrasting fitness effects of the two alleles contribute to balancing their long-term evolutionary fate. The strength of the provided evidence is still incomplete and would benefit from more rigorous approaches.

eLife assessment

This study presents valuable finding regarding the role of life history differences in determining population size and demography. The evidence for the claims is still partially incomplete, with concerns about generation times and population structure. Nonetheless, the work will be of considerable interest to biologists thinking about the evolutionary consequences of life history changes.

eLife assessment

This is a fundamental study addressing a long-standing mystery in splicing regulation. The authors provide compelling evidence that splicing can occur post-transcriptionally. The work will be of broad interest to anyone studying gene regulation.

eLife assessment

This important study reports the cryo-electron microscopy structure of a multi-protein complex that recognizes the 5'-end cap of mRNAs and plays a critical role in mRNA export. The structural analyses and biochemical assays in this study provide convincing evidence to support the major claims of the authors, although the inclusion of more functional characterizations in cell-based systems would have strengthened the study. This paper would be of interest to structural biologists and RNA biologists working on mRNA metabolism.

eLife assessment

This work presents the application of protein language models in combination with current methods for the detection of distant evolutionary relationships. While the results are important, they are supported by incomplete, preliminary evidence. A more comprehensive benchmark and clarification of technical details may turn this exploratory study into an algorithm ready for wide use.

eLife assessment

This study presents important findings on a transcription-independent component of the early recovery of proteasome activity from a short pulse of proteasome inhibitor treatment. While the evidence supporting this conclusion is solid, experimental support forthe proposal of an alternative regulatory process operative at the level of proteasome assembly, is incomplete. Lacking is experimental quantification of the effect of proteasome inhibition on the rate at which newly synthesized subunits are assembled into proteasomes.

eLife assessment

This is a valuable study that convincingly demonstrates that quantification of EpCAM+/CD24+/Vimentin+ cells in the stroma of human oral cancers followed by machine learning algorithms can be used as a prognostic indicator of metastasis.

eLife assessment

This fundamental work substantially advances our understanding of how cells can tightly modulate small GTPase activity to build and maintain neighboring cytoskeletal structures, in this case microvilli. The evidence supporting these claims is compelling and is supported by both protein-protein interaction assays as well as cell biological studies. The work will be of interest to cell biologist studying the cytoskeleton as well as those interested in G-protein mediated regulation.

eLife assessment

The study is an important advancement to the consideration of antimalarial drug resistance: the authors make use of both modelling results and supporting empirical evidence to demonstrate the role of malaria strain diversity in explaining biogeographic patterns of drug resistance. The theoretical methods and the corresponding results are convincing, with the novel model presented moving beyond existing models to incorporate malaria strain diversity and antigen-specific immunity. This work is likely to be interesting to malaria researchers and others working with antigenically diverse infectious diseases.

eLife assessment

This study presents potentially valuable results on glutamine-rich motifs in relation to protein expression and alternative genetic codes. The author's interpretation of the results is so far only supported by incomplete evidence, due to a lack of acknowledgment of alternative explanations, missing controls and statistical analysis and writing unclear to non experts in the field. These shortcomings could be at least partially overcome by additional experiments, thorough rewriting, or both.

eLife assessment

BTK, a TEC-family tyrosine kinase activated by the B-cell antigen receptor, contains a variety of regulatory domains and it is subject to complex regulation by membrane phospholipids, protein ligands, phosphorylation, and dimerization. This study presents convincing evidence, utilizing various biophysical techniques, to support a model for BTK activation that will be valuable for the field. Overall, the study enhances the understanding of BTK's activation mechanism, autoinhibition, and allosteric control, challenging previous assumptions about BTK.

eLife assessment

This study is valuable as it sheds light on the pivotal role played by alterations in glycan metabolism within chondrocytes in the onset of cartilage degeneration and early onset of osteoarthritis (OA) through the process of hypertrophic differentiation of chondrocytes, giving insights into the identification of nascent markers for early-stage OA. Although the methods, data, and analyses broadly support the claims, the data shown by the authors are incomplete because the mechanism by which cartilage degeneration induced by changes in glycometabolism occurs has not been fully elucidated. The authors' deductions stand to gain further credence through undertaking additional experiments aimed at analyzing the mechanisms underlying the changes in glycometabolism in cartilage, such as the meticulous identification of the target glycan molecules bearing core fucose and analysis of endochondral ossification in cartilage-specific Fut8 KO mice.

eLife assessment

This useful work provides insight into the formation of associations between the nucleolus and Promyelocytic leukemia nuclear bodies (PML-NBs). The work showed that these associations depend on both the formation of DNA double-strand breaks and the impaired RNA Polymerase I transcription, and also is modulated by the homologous recombination. The evidence supporting the claims is incomplete and the paper needs more experimental support on the dynamics of the association and mechanistic insight into the signaling for its formation.

eLife assessment

This useful study could potentially represent a step forward towards personalized medicine by combining cell-based data and a prior-knowledge network to derive Boolean-based predictive logic models to uncover altered protein/signaling networks within cancer cells. However, the level of evidence supporting the conclusions is inadequate, and further validation of the reported approach is required. If properly validated, these findings could be of interest to medical biologists working in the field of cancer and would inform drug development and treatment choices in the field of oncology.

eLife assessment

This is an important study that characterizes a surprising interaction between two different cytokine/hormone receptors using nanoscale resolution (dSTORM) microscopy. The study provides solid evidence that the interaction is ligand-dependent, and is mediated by the receptor-associated intracellular signalling molecule JAK2. While at present limited to growth hormone and prolactin receptors in a limited number of cell lines, there are potentially broad implications for cytokine signalling, as such JAK2-mediated interactions could occur between a range of different cytokines. Moreover, the specific hormone interactions shown in the manuscript may have important implications for understanding how these hormones can have differential effects in breast cancer, under different conditions.

eLife assessment

This is a useful study that uses a microfluidic method to evaluate the ability of single human white blood cells to produce combinations of cytokines. The evidence that this takes place is solid. The paper highlights polyfunctionality using similar data to a prior work from the same group.

eLife assessment

This study presents a valuable finding on the putative molecular patterns underlying characteristic morphological regions observed in colorectal cancer (CRC). The authors provide a morphological framework through which clinicians might improve the performance of molecular signatures and consequently predict the clinical response of patients with better accuracy. The evidence supporting the claims of the authors is solid. The work will be of interest to clinicians and cancer biologists working in the field of CRC.

eLife assessment

This paper presents valuable findings that shed light on the mental organisation of knowledge about real-world objects. It provides diverse if incomplete evidence from behaviour, brain, and large language models that this knowledge is divided categorically between relatively small objects that are at the relevant scale for direct manipulation and larger objects that are outside the typical scope of human affordances for action.

eLife assessment

This important study offers new and convincing support for the idea that about a third of mouse liver DNAse hypersensitivity sites (DHS) showing male-biased chromatin opening are sex-biased because of the male-specific cyclic action of growth hormone pulses to alter chromatin accessibility, as compared to the relative ineffectiveness of the more static pattern of growth hormone secretion in females. Supporting evidence is found in the impact of hypophysectomy and growth hormone treatment on chromatin accessibility, and the binding of specific transcription factors and epigenetic marks at STAT5-sensitive sites. This work uncovers mechanisms that impact sex differences in liver function and will be of broad interest to endocrinologists and hepatologists.

eLife assessment

This useful study addresses epilepsy caused by the loss of a molecule called Pten, resulting in hyperactivity of the mTOR pathway. The findings suggest that inhibiting two molecules called mTORC1 and mTORC2 can reduce epilepsy symptoms but there is much less effect when inhibited separately. The evidence supporting the conclusions is currently incomplete, but could be strengthened after additional experiments.