eLife assessment

The authors re-analyzed a previously published dataset and identify patterns suggestive of increased bacterial biodiversity in the gut may creating new niches that lead to gene loss in a focal species and promote generation of more diversity. Two limitations are (i) that sequencing depth may not be sufficient to analyze strain-level diversity and (ii) that the evidence is exclusively based on correlations, and the observed patterns could also be explained by other eco-evolutionary processes. The claims should be supported by a more detailed analysis, and alternative hypotheses that the results do not fully exclude should be discussed. Understanding drivers of diversity in natural microbial communities is an important question that is of central interest to biomedically oriented microbiome scientists, microbial ecologists and evolutionary biologists.

eLife assessment

This paper is of broad interest to infer the causal effect of exposures on outcomes. It proposed an interesting idea for the identification of risk factors amongst highly correlated traits in a Mendelian randomization paradigm. The intuition for this method is clearly presented. However, critical details about implementation are missing and its application is not sufficiently demonstrated in the current form.

eLife assessment

This manuscript is relevant to experimental and theoretical neuroscientists interested in the trade-off between chaos and reliability in the brain, and may also pique the interest of the machine learning community, particularly those seeking to understand the computational capacity of recurrent neural networks. The findings are valuable, with practical and theoretical implications for this subfield. Using a spiking neural network model firmly anchored in experimental data from the turtle brain, the authors examine the reliability and flexibility of spike train sequences and determine the differential roles of strong and weak connections. The results show clearly that strong but sparse connections in a sub-network can produce a highly reliable response to single spikes, with reliability and multiplexing across sub-networks controlled by weak connectivity. The strength of evidence for the claims is convincing, using appropriate and validated methodology in line with current state-of-the-art.

eLife assessment

This report illustrates the marked alteration of red blood cell (RBC) morphology that occurs with COVID-19 infection. Of particular importance is the observation that RBC morphology is dramatically affected whether cells are suspended in plasma from healthy vs COVID-infected blood. The claims of the manuscript are well supported by the data, and the approaches used are thoughtful and rigorous. The results are important for consideration of the broader pathophysiology of COVID-19, particularly with regard to the impact on vascular biology.

eLife assessment

This paper directly estimates the fitness cost of loss-of-function mutations in almost every gene in the human genome, providing an interpretable measure of the severity of mutations. The authors then compare datasets of presumably healthy individuals and individuals affected by severe complex disorders or genetic disorders, finding enrichment of de novo loss-of-function mutations in highly constrained genes among probands alongside other illuminating results. This important study will be useful to researchers interested in interpreting and prioritizing disease-causing mutations and in the process of human evolution. Overall, the approach is elegant and the results are of high quality and compelling.

eLife assessment

In this manuscript, the authors address the variable results and data regarding the role of the FAAH variant (C385A at the nucleotide level and P129T at the protein level) in the control of feeding. The authors hypothesize that the variable results might be due to the environmental context, specifically stress related conditions. They designed studies to address the role of glucocorticoids in regulating feeding and metabolism.

eLife assessment

In this study the authors show that neural tuning for object orientation in IT is unaffected by whole-body tilt, suggesting that neurons are encoding objects relative to the gravitational vertical. However, these observations could also be because IT neurons may encode object orientation relative to cues and not due to gravity, or due to dynamic, compensatory torsional eye movements made by the animals. With these concerns adequately addressed, this would be an important study showing that IT neurons may play a role not only in object recognition but more broadly in physical scene understanding.

eLife assessment

This fundamental work reveals a novel direct projection from the lateral entorhinal cortex to the medial entorhinal cortex. Using multiple techniques, the authors provide compelling evidence that fan cells from the lateral entorhinal cortex project to superficial neurons in the medial entorhinal cortex. This newly identified connection may support the combination of spatial inputs with sensory or high-order signals, providing novel insight into potentially how the 'what' (lateral entorhinal cortex) and 'where' (medial entorhinal cortex) features of memory are incorporated.

eLife assessment

This paper will be of interest to those studying DNA replication in the context of chromatin and development. This important study uncovers a new interaction partner for the chromatin protein SuUR and tries to understand how this complex (SUMM4) functions to control under-replication in polytene chromosomes. While the experiments are of high quality and carefully controlled, the data currently do not fully support all the conclusions, particularly as they relate to conclusions about DNA replication timing.

eLife Assessment

In this manuscript, Sell et al., investigate the role of the long non-coding RNA H19 in regulating cellular senescence. Using several cell models they identify upstream and downstream effectors of H19 including let-7 and EZH2. The advances in this work include the identification of a specific cascade of factors connecting H19, senescence and the actions of rapamycin.

eLife assessment

This study presents a valuable finding that adds to a growing body of evidence reporting heritable cell states that can guide fate choices in single cells, in this case the fate of early IFN-I response. The evidence supporting the claims of the authors is solid, although testing the generalizability of the result to other cell types or contexts and strengthening the link to epigenetic regulation would have strengthened the study. Overall, this work will be of interest to a wide set of scientists, including cell biologists, immunologists, and systems biologists.

eLife assessment

This important study reports cryo-EM structures of human ferroportin (FPN), a protein essential for iron transport in humans. This manuscript will be of interest to researchers studying membrane transport mechanisms as well as to those interested in drug design. The structures detail interactions between FPN and the small-molecule inhibitor vamifeport, which is currently in clinical trials for sickle cell disease, and ta new (occluded) protein conformation that is stabilized by a sybody (a nanobody selected from a synthetic library) is identified. Evidence for the mechanism of inhibition by vamifeport is convincing, but evidence for the physiological relevance of the occluded conformation is still incomplete.

Aral Balkan's personal (single-user) Mastodon instance costs him ~50 EUR per month to run.

eLife assessment

This manuscript is extremely useful for describing an R package that provides a valuable pattern and overlay framework for producing colorblind-friendly scatter plots for the field. The utility of this tool for making plots more accessible was demonstrated compellingly. This work will be of broad interest to many biomedical scientists, especially to viewers with color-vision deficiency.

eLife assessment

The authors investigate the cost and benefits of maintaining seemingly redundant multiple copies of the translation machinery components. The authors demonstrate that while redundant multiple copies are beneficial in a nutrient-rich environment, maintaining these extra copies is costly and deleterious in a nutrient-poor environment. This explains why copy numbers of translation machinery genes are under selection according to the environmental niche an organism occupies. The work is very important and the findings exciting and supported by compelling evidence. In particular, the fitness gain upon deletion of translation genes in poor conditions is an insightful observation.

eLife assessment

Giesberg and colleagues provide evidence both in yeast and human cells that fast elongation speeds of RNA polymerases result in a "downstream-shifted" poly(A) profile while the opposite is true for slower speeds of elongating polymerases. GC content of sequences downstream of poly(A) clusters influences the cluster profiles by affecting elongation and thus allowing more time for the 3'-cleavage complex to find the poly(A) site and form the transcript terminus. Although the findings presented in this manuscript are not surprising, they are new and contribute a missing piece to our knowledge of how the transcription machinery determines which poly(A) site to utilize at the end of genes.

eLife assessment

As shown by the authors, the focal adhesion protein, kindlin-2, plays an essential role in liver development in that its genetic inactivation leads to severe fibrosis and death in young mice. This lethality is attributed to increased liver inflammation and cell death. This work will be of interest to readers studying mechanisms of liver development and pathological fibrosis.

eLife assessment

The authors use a clever experimental design and approach to tackle an important set of questions in the field of decision-making. From this work, the authors have a number of intriguing results. However, questions remain regarding the extent to which a number of alternative models and interpretations, not considered in the paper, could account for the observed effects.

eLife assessment

The authors report that, in the murine liver, intermittent fasting alters the homeostatic regenerative programme. This has fundamental implications for the use of murine models to study liver regeneration and cancer and highlights through a series of solid mechanistic studies the role of FGF/Wnt signalling interactions in modulating fasted associated regeneration. It opens up further questions as to why this occurs, how this is beneficial to adapting to a fasting state, and the potential for translation.

eLife assessment

This study, supported by reasonably solid evidence, will be of interest to breast cancer researchers. The finding that EHD2 promotes tumor growth and impacts store-operated calcium entry (SOCE) adds to our understanding of breast cancer cell physiology. If supported by further research, the study provides a rationale for using SOCE inhibitors in a subset of breast cancers, with high expression of EHD2 serving as a potential predictive biomarker for using SOCE inhibitors.

eLife assessment

The paper will be of interest to cognitive neuroscientists in the field of spatial navigation as well as to systems neuroscientists interested in neural representations. Using simultaneous electrophysiological recordings in the anterior thalamus and the retrosplenial cortex, the study investigates the coordination of neurons coding for the head direction in this thalamocortical network. Environmental manipulations led to a near-synchronous update of the head direction signal encoded by the two populations. Further data analysis is needed to support the main claim of the study.

eLife assessment

This paper, which provides useful information on the assembly of volume-regulated anions channels formed by LRRC8 proteins, will be of interest scientists in the field of ion channels. The authors report the structure of a LRRC8C-LRRC8A chimera with native functional properties as a heptameric complex with a lipid-filled pore. This is very interesting and well-presented work, but the evidence supporting the physiological relevance of the heptameric assembly and the hypothesized role of lipids is still incomplete.

eLife assessment

This is an important study that resolves a controversy about a proposed molecular linkage between the fields of mechanobiology and RNA signaling. While prior research had claimed that a specific mechanosensitive ion channel in the gut responds to a specific fecal RNA, this study provides compelling evidence that the mechanosensitive ion channel does not respond to the RNA.

eLife assessment

This paper will interest neuroscientists working in the field(s) of basal ganglia, amygdala, and fear learning. Overall this is an important study that examines the contribution of an understudied brain region to fear conditioning in male subjects. Some conclusions will benefit from additional verification and evaluation of the specificity of the findings to the amygdala-striatal transition zone relative to adjacent regions.

eLife assessment

The fluorescently tagged SYT-1 mouse line will be useful for the field. Importantly, the authors used a comprehensive set of immunohistochemical and physiological experiments to demonstrate that the fluorescence tagging did not alter the function of SYT-1. These are important control experiments that will make the strain useful for physiological experiments in the future. However, the advance of this manuscript is less clear.

eLife assessment

This paper provides important evidence for the impact of the COVID-19 pandemic on cancer screening for breast, cervix, and colorectal cancer in Italy. The authors compared Invitation and examination coverage, as well as conducted telephone interviews, investigated the population screening test coverage, before and during the pandemic, according to educational attainment, perceived economic difficulties and citizenship. Their findings convincingly show that the lockdown and pandemic restrictions caused delays in screening activities but particularly increased the pre-existing individual and geographical inequalities in access.

eLife assessment

The paper describes an online tool, CausalCell, intended for the analysis of causal links in single-cell datasets. Regarding its significance, this work is timely and important, with potentially broad applications as a generally useful tool. However, there are major concerns about the suitability of the tool for its intended purpose, and the extent of validation in the current manuscript is incomplete.

eLife assessment

This paper provides valuable evidence for a weakening of the association between cognitive ability and height from 1957 to 2018 in the UK. The authors find the strength of the association declined over this time frame. These associations were further attenuated after accounting for proxy measures of social class. This paper is a solid contribution to debates about how genetic, environmental, and social factors have affected the joint distribution of height and cognitive ability over the last 60 years.

eLife assessment:

This study by Li et al describes an interesting attempt to predict the functional status of the p53 tumor suppressor in tumors where no DNA mutations in p53 could be identified. To this end, the authors employed SVM models to train the algorithm for the detection of 'p53 inactivation' features contrasting normal and tumor tissues. The approach could be a valuable tool for attributing tumors with unknown p53 status. The authors provide solid evidence supporting their findings and the concept of the study is solid, but in its current formulation, some of the bioinformatic analyses are incomplete, particularly related to the selection of associated genes and the potential mechanism(s).

eLife assessment

NOX2 is the most well-studied member of the NADPH oxidase family, membrane enzymes that produce reactive oxygen species (ROS), and the proper function of NOX2 is critical for innate immunity against pathogens in mammals. This study reports a high-resolution structure of the NOX2-p22 complex, providing valuable information for a mechanistic understanding of NOX2 activation at the molecular level.

eLife assessment

In this study, Hung et al. address the biology and therapy of chondrosarcoma. The authors provided high-quality data that uncovered a new signaling axis, EZH2/hSULF1/c-Met, that promotes chondrosarcoma growth and progress. The authors also reported evidence showing that c-Met inhibition may be a plausible treatment option for chondrosarcoma. The findings are novel and translational and are of interest to cancer biologists and oncologists.

eLife assessment

Sodium selenate reduced seizures when administered after initiation of epilepsy, complementing earlier work showing efficacy if administered before initiation. The novelty of the results is not much more than the earlier study. Sodium selenate reduced phospho-tau and increased PP2A protein expression, and reversed TLE-associated telomere-shortening. However, whether these effects were critical to the reduced seizures is not clear. Finally, proteome and metabolome data from the animal model of epilepsy is discussed and provide initial insights into the effects of sodium selenate treatment on molecular pathology, however, the data are not well developed so revisions along these lines will be important so conclusions can be made.

eLife Assessment:

Predicting the effect of mutations on protein stability is important both for protein engineering and for helping to decipher the effects of genetic and clinical mutations. The machine learning methodology introduce here is timely in view of the millions of AlphaFold model structures that are now becoming available, which could hypothetically be examined through approaches such as this one. The methodology presented is valuable, but the manuscript would benefit from a substantial amount of comparative data to provide more compelling evidence for the validity of the methods.

eLife assessment

This manuscript addresses the mechanism of ligand specificity of odorant receptors (OR) through mutational analyses and structure prediction. The authors identify a single amino acid substitution that switches ligand specificity between two olfactory receptors. Obtaining structures of OR complexes has been challenging, so such an approach is valuable and will be of interest to scientists within the fields of chemical ecology and sensory neuroscience.

eLife assessment

The manuscript makes an important contribution to understanding the roles of the bee host and microbiome in degrading amygdalin, a dietary secondary metabolite. Several bacterial strains and their enzymes responsible for the deglycosylation of amygdalin are identified. Conclusions are reached convincingly through a comprehensive combination of in vitro and in vivo experiments including gene-expression analysis, proteomics, HPLC-MS, and the use of recombinant E. coli to test enzyme function. As the consequences of microbial-derived amygdalin metabolisation on host health remain uncertain from the experiments conducted, the manuscript could be improved through a clearer discussion of future work needed and in parts more careful wording to not prematurely suggest benefits to the host.

eLife assessment

This paper is of potential interest to neuroscientists expert in cortical circuitry and behavioral role of neuron types. The imaging technique used permitted to detect a specific group of cortical neurons known as vasoactive intestinal peptide (VIP)-expressing interneurons from several cortical regions with high temporal resolution. The main message conveyed by this manuscript is that many VIP-expressing interneurons respond to reward and punishment but also show regional differences. The conclusions drawn are generally supported by the data, but some claims and interpretations require further attention and clarification.

eLife assessment

This large-scale collaborative study is a timely contribution that will be of interest to researchers working in the fields of infectious disease forecasting and epidemic control. This paper provides a comprehensive evaluation of the predictive skills of real-time COVID-19 forecasting models in Europe. The conclusions of the paper are well supported by the data and are consistent with findings from studies in other countries.

eLife assessment

In this valuable contribution, the authors apply an artificial intelligence method to predict the three-dimensional structure of complexes of outer membrane proteins of the Gram-negative bacterium E. coli. Some of the cases presented are compelling, as they explain previously published biochemical data and/or reproduce existing structural data.

eLife assessment

The authors provided strong evidence that the Fusarium oxysporum effector protein FolSpv1 enhances virulence by targeting tomato SlPR1 and preventing the generation of the SlPR1-derived phytocytokine CAPE1, which otherwise positively regulates disease resistance in tomato plants. Strikingly, they show that FolSpv1 translocates SlPR1 from the apoplast back into the nucleus of tomato cell, suggesting a previously unknown mechanism employed by pathogenic microbes.

eLife assessment

The work, which examines how Advanced Glycation End-products (AGEs), commonly found in processed and other cooked foods, affect eating behavior and signaling in the nematode C. elegans, is in a fundamentally important area of research with clear translational potential for humans. Some aspects of the manuscript are compelling, including the well-characterized assays on food intake, while other aspects are still incomplete, such as the mechanistic work on the neural network responsible for the response to AGEs.

eLife assessment

This is an important and timely characterization of a diversity of behaviors male and female rats exhibit during the acquisition of Pavlovian fear conditioning in a conditioned suppression procedure. The data are compelling and provide an exhaustive analysis of behavior in a complex associative learning paradigm that blends aversive Pavlovian and appetitive instrumental elements. The generalizability of these findings to other paradigms could be enhanced, however, with the inclusion of tests of cue responses in a neutral environment. These findings are likely to be of interest to those who study fear conditioning and associative learning more broadly in rodents.

eLife assessment

Primates perceive and detect stimuli differently depending on the stimulus context in which they are embedded, and have a remarkable ability to understand the way in which objects and parts of objects are embedded in natural scenes (scene segmentation). An example of this is figure-ground segmentation, a well documented phenomenon resulting in a "pop-out" of a figure region and corresponding enhanced neural firing rates in visual areas. It is unknown whether mice show similar behavioral and neural signatures as primates. The present study suggests that mice show different segmentation behavior than primates, lacking texture-invariant segmentation of figures and corresponding neural correlates. This reveals a fundamental difference between primates and mice important for researchers working on these species and researchers studying scene segmentation. The findings are further interpreted in terms of neural network architectures (feedforward networks) and are relevant for this field too.

eLife assessment

This study modeled monkeys' behavior in a stimulus-response rule-learning task to show that animals can adopt mixed strategies involving inference for learning latent states and incremental updating for learning action-outcome associations. The task is cleverly designed, the modeling is rigorous, and importantly there are clear distinctions in the behavior generated by different models, which makes the authors' conclusions convincing. The study makes a strong contribution overall, however, there were aspects of the design that were unclear and some alternative accounts that were not considered.

eLife assessment

It's been widely known that the amino acid Glycine can work as a cytoprotectant and inhibit pyroptosis-associated plasma membrane rupture. However, a long-standing question has been: how does Glycine cytoprotection work? The authors observed that Glycine treatment phenocopied deficiency of NINJ1 (a recently reported cell surface molecule critical for plasma membrane rupture), and can inhibit aggregation of NINJ1. Understanding the intrinsic mechanism by which Glycine affects NINJ1 could provide a significant advance in the cell death field.

eLife assessment

The study by Kim et al. combines extracellular recordings from olfactory sensory neurons (OSNs) in locusts with computational modelling approaches to investigate the dynamics of odour responses. The authors demonstrate that OSN responses can be grouped into four distinct response motifs, with OSNs showing different motifs in an odour-dependent manner. Using computational modelling the authors provide some evidence that these diverse response motifs expand the coding space and could facilitate odour discrimination and navigation. This study can be of high relevance to both experimental and theoretical neuroscientists investigating odour coding and odour-driven behaviours such as navigation. In its present form, while the experimental data and analysis are of the highest quality, the modelling part needs to be expanded to fully support the experimental measurements.

eLife assessment

The interesting manuscript shows that breast cancer cells that are poorly migratory in culture can be more metastatic in mice. This is due, at least in part, to the secretion of extracellular vesicles containing the the crosslinking enzyme Transglutaminase-2, which can activate fibroblasts in the tumours. These fibroblasts can then promote metastatic phenotypes. This study demonstrates how cancer cells can manipulate the cells around them in order to disseminate.

eLife assessment

Hearing is mediated by hair cells in the cochlea, which synapse onto the primary dendrites of the auditory nerve. This study shows how deletion of a postsynaptic glutamate receptor subtype strongly influences inner hair cell-spiral ganglion cell synapse formation. Thus pre- and post-synaptic changes are dynamically intertwined, providing insights into how pathological outcomes arise from synaptic perturbations.

eLife assessment

This paper should be of broad interest to developmental biologists who seek to understand spatiotemporal control of myosin-based force generation during tissue morphogenesis during early development. The central conclusions are well-grounded in rigorous quantitative data analysis and modeling. The results challenge current views of how gene expression patterns control myosin II anisotropies and provide new testable hypotheses on the role and importance of tissue geometry.

eLife assessment

The authors identify co-deletion of the mitochondrial AAA+ ATPase ATAD1 with the tumor suppressor PTEN as a factor modifying cancer prognosis, based on a new mechanism of increasing sensitivity to proteotoxic stress induced by proteasome inhibition. The authors also identify the mitochondrial E3 ubiquitin ligase MARCH5 as a gene whose deletion is synthetically lethal with ATAD1. These findings suggest that the use of proteasome-targeting agents may be useful in patients with tumors dually deleted for ATAD1 and PTEN. The study is based on convincing evidence, and makes an innovative contribution to the understanding of the biology of tumors with 10q23 deletions.

eLife Assessment

This report describes evidence that the main driving force for stimulation of glycolysis in dentate granule cell neurons in acute hippocampal slices from mouse by electrical activity comes from influx of Na+ including Na+ exchanging into the cell for Ca2+. The findings are presented very clearly and the authors' interpretations seem reasonable. This is important and impactful because it identifies the major energy demand in excited neurons that stimulates glycolysis to supply more ATP.

eLife assessment

This well-presented and sophisticated study provides significant proof-of-concept for the application of the ForensOMICS approach as a new pathway for forensic taphonomy with great promise to advance future research. The solid foundation of the research combining metabolomics, proteomics, and lipidomics is considered very exciting, strong, and expands the boundaries of forensics research.

eLife assessment

The transcription factor DUX4 is emerging as a key molecule in early mammalian development and in diverse pathologies including muscular dystrophy and solid tumors. While DUX4 has been linked to immune evasion, the mechanisms have not been delineated. In this study, the authors demonstrate that DUX4 functions as a negative regulator of interferon signaling by inhibiting STAT1, thereby suppressing interferon-stimulated gene induction. These studies provide a critical mechanistic link between DUX4 expression and the modulation of immune signaling pathways.

eLife assessment

This manuscript contains fundamental work on hormonal and neurobiological processing of social experience in humans. It sheds compelling new light on potential mechanisms underlying how humans place social experiences in context, demonstrating how oxytocin and cortisol might interact to modulate higher-level processing and contextualizing of familiar vs. stranger encounters.

eLife assessment

In this important manuscript the authors use a powerful cross-specifies approach and cutting-edge experimental methods to examine possible shifts in the excitatory and inhibitory balance in both an animal model of Parkinsonism and in human patients with Parkinson's disease. Their solid findings support such a shift, wherein untreated Parkinson's disease is characterized by excessive activity in the subthalamic nucleus. While a strong paper, there are concerns with some of the methodological choices and their implications.

eLife assessment

In this important study, the authors examine transport and synaptic activity in the corticostriatal circuit in both microfluidic devices and in mice. They convincingly show that the Huntingtin protein regulates the anterograde transport of synaptic vesicle precursors in coordination with the molecular motor KIF1A. Activated Huntingtin recruits KIF1A, accelerates synaptic vesicle precursor's transport, modifies synaptic transmission and motor skill learning in mice. This work sheds new light on the role of axonal transport in synaptic function under physiological and pathological conditions related to Huntington's disease.

eLife assessment

This study presents an atlas of glial cell morphology in Drosophila, from distinct locations at different periods of life. The authors integrate morphological information with the transcriptomic signatures of those cells and find that morphological diversity among glial cells of a given class is not a strong predictor of transcriptional identity. The study is of great value as connecting morphology with scRNA sequencing analysis is rarely done and is a necessary step for understanding the underlying biology of these cells. While the weak morphotype-transcriptomic link in many cases may be due to low sequencing resolution, nonetheless, the data are of very high quality and the study will be a very useful resource for the glial biology field.

eLife assessment

This manuscript proposes that metformin protects against elevated intraocular pressure and oxidative injury by regulating cytoskeleton remodeling through the integrin/ROCK pathway, thus providing a new direction for further exploration toward the treatment of primary open-angle glaucoma as well as investigation of oxidative injury in multiple settings.

eLife assessment

This work is of high relevance to developmental and quantitative biologists with an interest in morphogen-mediated position decoding. A general mathematical model formulation is presented that is nevertheless accessible to a broad audience. Model tests via perturbation experiments in the Drosophila wing disc look promising and inspire a new round of data generation.

eLife assessment

Using a heterologous model system of budding yeast, authors find that nuclear translocation of beta-catenin is mediated by Kap104, the ortholog of Transportin (TNPO)1/2. A TNPO1 binding motif was identified in the C-terminal region of beta-catenin, which serves as a nuclear localization signal, and mutation of the motif inhibits beta-catenin mediated transcription. The manuscript serves as a staring point to study how much this motif contributes to nuclear localization of full-length beta-catenin in mammalian cells and to assess whether inhibiting TNPO1 interaction can reduce hyperactivation of beta-catenin signaling.

eLife assessment

This manuscript puts forward a new idea that topography in neural networks helps to remove noise from inputs. The authors show that there is a critical level of topography that is needed for network to denoise inputs. At present, the analysis is limited to inputs that are constant in time.

eLife assessment

This is an important paper reporting that an adenosine methyltransferase in the model plant Arabidopsis functions to target a key RNA component of the spliceosome, as in fission yeast, and thereby contributes to intron recognition. By contrast, the authors report no major role for the methyltransferase in targeting mRNAs, as reported in previous studies in Arabidopsis. While some of the evidence is convincing, other evidence is incomplete. The conclusions that mRNAs are not a significant target and that specific intronic sequences define sensitivity to the methyltransferase require additional support.

eLife assessment

This study delineates the transcriptomics of lung neuroendocrine cells and provides important new information on the nature of these cells in normal mouse lungs and in a sample of a human lung carcinoid. It will inform future studies investing the roles of PNECs in health and disease.

eLife assessment

Dhurhandar and colleagues developed a computational method that predicts discriminability of odor mixtures based on chemical structures of component molecules. The model first transforms chemical structures into natural language descriptions of odor, and then perform Lasso regressions to obtain a compact transformation into discriminability. The results suggest that the model performs better compared to that without transformation to language descriptions, yet, there are some issues that need to be addressed to make strong conclusions.

eLife assessment

This study applies AlphaFold to the CHESS selection of transcripts with the goal of generating predicted 3D protein structures and a quality measure of folding, the pLDDT score. From these data, the authors build a database for result exploration, documented by several examples, including proteins, where the authors propose the pLDDT score as a measure of presumed superior biological functionality over other isoforms. These results will be highly relevant for anyone working with proteins that occur in different isoforms.

eLife assessment

This important study reveals the role of polygenic scores for four commonly diagnosed cancers with high genetic predisposition (breast, prostate, colorectal, and lung) in East Asian populations, which is developed in participants of European descent. The data is convincing that is derived from a prospective cohort including 21,694 Singaporean participants of East Asian descent. The work will be of interest and provide great help to disease specialists in the field.

eLife assessment

In learning to walk, infants must balance the need to explore their movement repertoire with the need to establish regular movement patterns. Using a longitudinal approach, this paper suggests that while young infants generate high variability from a small number of regular patterns ('primitives'), older infants use a greater number of primitives with less variability. These interesting conclusions are not currently fully supported by the small and somewhat selective sample of data, and some alternative explanations need to be considered more thoroughly.

eLife assessment

This paper will be of interest to those studying retinal angiogenesis and endothelial cell biology. The authors performed rigorous data analysis and presented a logical, well-written report. The key conclusions of the manuscript are supported by the data and uncover a novel factor for retinal endothelial cell growth.

eLife assessment

This study takes a fresh view of the hypothesis that right inferior frontal gyrus is critical in inhibitory control in humans, as assessed by the widely-used stop signal task. It applies recent development in modeling and EEG measures in patients with focal brain damage, yielding causal insights. It will be of interest to neuroscientists and clinical researchers who study the brain basis of response control. Reviewers found this to be a strong, hypothesis-driven study that makes new progress on an important topic.

eLife assessment

This manuscript reports data consistent with a new and unanticipated phenomenon: that Cre or its mRNA may be transmitted between tissues in the mouse and that the male reproductive tract (epididymis) appears to be the most common target of such transported molecules. The data serve as a timely warning to mouse researchers about an unexpected complication of Cre-mediated gene manipulation.

eLife assessment

Type II topoisomerases are essential players in virtually every aspect of genome organization and function of all organisms. The in vitro data presented here clearly demonstrate that eukaryotic type II topoisomerases phase separate under physiological conditions, forming liquid-liquid condensates, and that the outcomes of type topoisomerase II activity on DNA are altered in these condensates. The experiments and methods are sound, clearly described, and fully support the insightful and carefully formulated interpretation of the data. This work has broad implications for dissecting and delineating the myriad fundamental roles of this centrally important molecule.

eLife assessment

This study reports an interesting analysis of evolutionary variation in forelimb/hand bone shapes in relation to functional and developmental variation along the proximo-distal axis. The authors found expected and compelling patterns of evolutionary shape variation along the proximo-distal axis but less expected, yet equally compelling, patterns of shape integration. This paper will be of interest to researchers working on macroevolutionary patterns and sources of morphological diversity.

eLife assessment

This study builds upon previous results of the authors to study the neural computations within the basal ganglia that support behavioral proactive inhibition. Here, the authors identify features of neural activity in the SNr that correlate with proactive inhibition, including changes in firing rate and neural variability, and how both of these variables are influenced by an animal's outcome history. The analyses are rigorous and provide important insights into the neural dynamics in the basal ganglia that support proactive inhibition.

eLife assessment

This paper by Einarsson and colleagues presents a comprehensive analysis on how human genetic variability impacts both gene expression and promoter. Using a new resource of CAGE data in lymphoblastoid cell lines from 108 individuals, they uncover a series of features that distinguish promoters with highly variable expression across individuals from those exhibiting low variability. The authors propose various explanations for the observed results. A few additional analyses and a more pragmatic interpretation of their data may help consolidate or refine the models proposed.

eLife assessment

Seipin is a multifunctional Endoplasmic Reticulum localised protein associated with seemingly unrelated human diseases. Here the authors establish a correlation between the expression of a particular mutant form of Seipin associated in humans with motor neuron disease and altered intracellular calcium dynamics and allied proteotoxic stress. The paper is noted for the clues it provides into how these cellular defects arise and for offering a plausible, but yet unproven hypothesis for the cellular pathology that may account for the human disease phenotype.

eLife assessment

Dingus et al. have developed an innovative approach for improving the intracellular stability of nanobodies. Working with a set of 75 nanobodies, the authors have identified key amino acid changes that can improve the stability of nanobodies expressed within the cell that might be generalized to other nanobodies.

eLife assessment

The replication protein A (RPA) plays a critical role in DNA replication, DNA repair, and recombination by interacting with various proteins. This paper describes the structure of an N-terminus OB-fold of the 70kD subunit of human replication protein A (RPA70N or DNA-binding domain-F) bound to peptides from five different proteins, HELB, ATRIP, BLM, RMI1, and WRN. This paper provides useful knowledge regarding the structural flexibility of RPA70N in the binding to the different interacting peptides. The structural and biochemical analyses of the interaction of RPA70N with the different peptides provide solid evidence for the presented conclusion. The work will be of interest to those studying DNA replication, recombination and repair.

eLife assessment

This study provides new experimental data and detailed modeling of the partitioning of low copy plasmids under the control of the ParABS system in bacteria. The dynamics of the partition complex is tracked over many generations, providing useful data to constrain the models. The authors propose a model which can manifest either regular positioning or oscillations depending on the model parameters. The research will be of interest to biologists and biophysicists interested in cellular dynamics and internal organization in bacteria.

eLife assessment

This high-quality study characterizes a key enzyme in asexual red blood stages of the malaria parasites that is used to salvage lipid precursors needed for membrane biogenesis and parasite growth in red blood cells. A previously identified glycerophosphodiesterase (PfGDPD), is shown to mediate the hydrolysis of host lyso-phosphatidycholine to generate choline, which in turn is required for parasite de novo phosphatidylcholine synthesis. Extensive analysis of the localization, growth phenotype and lipidomic profiles of PfGDPD deficient parasites indicate that this salvage pathway is essential for lipid homeostasis and asexual parasite development.

eLife assessment

Jneid et al find that an entomopathogenic strain of B. thuringiensis and its Cry1A toxins, which are widely used to combat lepidopteran pests, disrupt intestinal epithelial homeostasis in Drosophila-an insect that is generally considered non-suceptible. They demonstrate that the Cry1A toxins act by altering E-cadherin-based adhesion between intestinal stem cells and their new progeny. The findings carry potential implications for unintended, broad effects of B. thuringiensis in agricultural settings.

eLife assessment

This work, which will be of interest to scientists in the field of hematology and ubiquitin biology, identifies previously unrecognized functions and regulatory mechanisms of an E3 ubiquitin ligase during erythrocyte progenitor maintenance and differentiation. This work has the potential to reveal that the exchange of scaffold proteins of a modular E3 ligase can have an effect on cell fate and reveal a novel mechanism of E2 enzyme regulation during differentiation. However, additional work is needed to support the major claims.

eLife assessment

This paper describes the anatomy of important fossil remains of the dwarf dinosaur Europasaurus, providing compelling evidence for precociality. Only a handful of papers provide detailed information on sauropod neuroanatomy - as such this paper will be of interest to a relatively wide range of researchers, in particular vertebrate palaeontologists, and comparative anatomists.

eLife assessment

The manuscript is of broad interest in the field of muscle physiology and structure. The authors developed nanobodies against different domains of the giant Drosophila proteins Sallimus and Projectin, which are titin homologs, and used them to define their organization along sarcomeres of distinct fly muscles. This is an important contribution to understand the functional architecture of the muscle; it suggests that in invertebrates two proteins fulfil the role of the vertebrate titin in bridging the A-band and the I-band.

This manuscript was co-submitted with: https://www.biorxiv.org/content/10.1101/2022.04.13.488177v1

eLife assessment

This work provides valuable knowledge to the ongoing research to establish an algorithm to shorten the duration of hepatitis C therapy with direct-acting antivirals. This is an important study that is a nice addition to previous reports evaluating the utility of response-guided therapy for shortening the duration of HCV treatment. Given the disease burden and the high costs of treatment, especially in low-income countries, this is a major goal that was also advocated by the WHO. Although the main objective (shortening therapy to 4 weeks) was not adequately achieved (<90% success rate), the study's results may suggest that re-treatment in case of failure is safe and efficient, although further studies with a larger number of patients are needed for confirmation.

eLife assessment

Igf2 and H19 are the two best-studied imprinted genes in mice. Taking advantage of the varying levels of H19 and Igf2 expression in three existing mouse models, the authors dissect the role of H19 and Igf2 in cardiac and placental development. Their findings suggest that an accurate dosage of both H19 and Igf2 is critical for normal embryonic development, especially the development of the heart and placenta. The work is of interest to colleagues studying imprinting as well as mammalian development.

eLife assessment

The authors find a significant and unexpected consequence of hypoxia in lung fibroblasts and smooth muscle cells - decreased lactate production - a finding that is important in the field of pulmonary hypertension. Additional orthogonal assessments of lactate production will strengthen the conclusions put forward.

eLife assessment

The authors present very exciting findings on the cranial bone defect repair using cutting-edge multiphoton imaging to study the role of different vessel subtypes and related oxygen and metabolic microenvironments. The study used microscopy to visualize the oxygen distribution and energy metabolism within the defects at different time points during the process of bone healing. This allows one to understand the pathophysiological progressions of bone diseases and regeneration. It will also provide critical information to optimize the therapeutic bone healing and regeneration approach for different clinical situations.

eLife assessment

Wang, Carlson, and colleagues investigate sensory adaptations in the fruit pest Drosophila suzukii, which prefers ripe over overripe fruit. This study focuses on changes in sensory pathways for sugars and food texture, which may contribute to ecological shifts. Several interesting physiological and molecular adaptations are observed in D. suzukii, but it remains unclear whether these observed changes account for behavioral changes.

eLife assessment

This study addresses a fundamental question about the origin and evolution of selfish genetic elements, focusing on the paradoxical abundance of toxin-antidote elements in selfing Caenorhabditis species. The authors propose for the C. elegans peel-1 zeel-1 locus fitness advantages; if these the findings can be supported with additional data, they will be of considerable interest to the field due to their wider implications for the evolution of such systems.

eLife assessment

The purpose of the study was to evaluate the transcription factor NF-kB, a common transcription factor that is thought to mediate muscle atrophy, in the setting of a rotator cuff injury. The authors used gain of function and loss of function NF-kB inhibitors to show that, surprisingly, NF-kB does not seem to be a major mediator of muscle atrophy in this model (as compared to other atrophy models), but there are sex-related differences. They found that male mice were more likely to have atrophy regulated by autophagy, both of which are interesting, novel findings.

eLife assessment

This manuscript presents a valuable framework and blueprint for the study, in artificial systems, of the principles and mechanisms that underlie proprioception in biological systems. Using artificial neural networks trained on synthetic hand movement data, the authors present solid, albeit incomplete, evidence that action recognition can explain important features of the mechanisms that underlie proprioception in biological systems. Experiments with architectures trained using losses that, in addition to action, take into account velocity and/or other states, could strengthen the authors' findings.

eLife assessment’

This paper is of interest to a broad audience of cell biologists, and researchers who work with cultured endothelial cells. The work uncovers the impact of culture conditions on transcriptional changes of endothelial cells and demonstrates that some of these changes can be recovered by sheer forces or coculture. The authors provide valuable datasets which will be a good resource for the community.

eLife assessment

This manuscript provides a valuable and policy-relevant contribution to our understanding of SARS-CoV-2 viral kinetics in the Omicron era. The authors exploit a rich and unique dataset from the National Basketball Association to describe post-infection viral kinetics and explore evidence for differential kinetics by immune history and demographics. The authors show (as others have) that most people remain with high viral loads 5 days post positive test (though less so in groups who are tested in a more realistic manner), and that older individuals and those who were boosted (but had a poor initial response to the primary vaccine series) were more likely to remain with high viral loads longer after an Omicron infection, while also describing rebound frequencies after Omicron infections.

eLife assessment

In peripheral nerve injury, an immune response occurs to ensure debris clean-up and potential repair, however, there has not yet been a census of cell types and gene expression as these lesions undergo clearance and eventual repair. Zhao et al generate a transcriptional resource by performing scRNAseq on both the naive, injured, and repairing sciatic nerve. They identify the composition of different cell types, gene signatures, and cell-cell communication and contrast these with signatures from the blood, and compare the injured site with distal nerve segments after injury. To dissociate the immune response from injury versus Wallerian degeneration, they use SARM1 KO mice (which exhibits delayed neurodegeneration) and observe that there is still injury-induced immune influx. Overall, this is a convincing study and useful resource for the field of neuronal repair and neural-immune interactions with a clear presentation of the animals and time points, with some follow-up experiments and validation.

eLife assessment

This manuscript uses large-scale neural imaging and network models to show how spontaneous dynamics emerge in such ensembles and how such activity influences behavior. It is a strong addition to the field for explaining many of the observed neural activity patterns and their heterogeneities.

eLife assessment

This paper will be of interest to scientists working on cilia, intraflagellar transport, and structural modeling. Using an integrative modeling approach, the paper provides a fundamental structural model for a part of the molecular machinery that is responsible for cilium assembly. However, additional approaches would improve confidence in the as yet incomplete structure model.

eLife assessment

This paper is an important contribution to the microglia field and will be of interest to a broad readership in the fields of neurobiology, cell biology and immunology. This work describes fundamental mechanisms of efferocytosis by microglia and uses impressive imaging in zebrafish, in combination with molecular manipulations, to provide compelling data of how centrosome movements synchronize with phagocytic cup formation during microglial efferocytosis of neuronal corpses in vivo.

eLife assessment

This paper is of interest for somatosensory neurobiologists studying how polymodality is achieved in peripheral sensory neurons. The work identifies roles in cold nociception and not mechanosensation in chloride transport for a number of ion channels.

eLife assessment

The manuscript makes a fundamental contribution to our understanding of sugar release by symbiotic dinoflagellates, and is of broad interest for the fields of ecology, marine biology, and cell biology. The experiments, which combine algal culture with targeted metabolomics, transcriptomics and the application of inhibitors, provide substantial, though not entirely complete evidence for an acidic environment mimicking conditions reported for the intracellular organelle that hosts the symbiotic algae, leading to upregulation of algal cellulases, which in turn degrade the algal cell wall and thereby releasing glucose and galactose that can be used as a source of food by the coral host. This is a new idea and could significantly contribute to our understanding of photosymbiosis.

eLife assessment

Using a genetically controlled experimental setting, the authors find that the lack of Polycomb-dependent epigenetic programming in the oocyte and early embryo influences the developmental trajectory through gestation in the mouse. By showing a two-phase outcome of early growth restriction followed by enhancement, the authors address previous inconsistencies in the field. However, the link with placenta function and gene misregulation is not yet fully supported.

eLife assessment

This work addresses the mechanisms of action of the transmembrane proteins TMEM87A and TMEM87B, which are thought to play a role in protein transport, but have been implicated in other processes as well, such as signaling and acting as mechanosensitive ion channels. The study represents an important advance of the understanding of this poorly characterized family of proteins. While the structure is of low resolution, it is well interpreted, and authors take good advantage of AlphaFold2 to gain insights into potential function. The work is of interest to colleagues studying transporters and ion channels.

eLife assessment

This paper is of particular interest to researchers who plan to use focused-ion beam scanning electron microscopes (FIB-SEMs) and require fluorescent data to guide the milling process. The authors describe a valuable after-market upgrade that allows fluorescent data acquisition during FIB-milling without stage repositioning. Technical details of the fluorescent module upgrade together with the sample stage redesign are compellingly documented and will enhance the implementation of this important technology.

eLife assessment

This important paper uses advanced imaging approaches to explore how Piezo1 distributes on surface red blood cells. The study provides compelling evidence that this molecule 'reads' the membrane curvature and clear support for the force-through-membrane model of mechanosensation.

eLife assessment

SARS-CoV-2 nonstructural protein (Nsp1) has emerged as an attractive target as it plays an important role in modulating the host and viral gene expression. This study describes multiple druggable sites in Nsp1. A 1.1Å co-crystal structure of Nsp1 with a fragment, together with computational studies, provides a framework for the rational design of potential antiviral candidates. This important study is methodologically convincing and will be of interest to researchers in the fields of structural virology and rational drug design.

eLife assessment

Conditional deletion and reactivation of a gene in situ remain challenging, and this study therefore addresses a gap in the genetic tool box. The authors introduce a reversible conditional gene inactivation and reactivation method using sequential expression of recombinases, with doxycycline treatment terminating gene transcription, while doxycycline and tamoxifen addition restore gene expression.

eLife assessment

This manuscript will be of broad interest to those working in the genetics of complex diseases, with the results strongly supporting the author's primary claims. Overall, this is an important study that demonstrates the power of proteomics-based systems genetics studies in the mouse.

eLife assessment

The authors report results from experiments and modeling that study the motions of molecules in the dense and dilute phases of biomolecular condensates, with the key finding that molecules in the dense phase of condensates formed by folded domains appear to switch between a confined state with low apparent diffusivity and a mobile state with a high apparent diffusivity that is comparable to that of molecules in the dilute phase. The study provides experimental evidence that is suggestive of phase separation coupled with percolation as the operative mechanism that gives rise to biomolecular condensates.

eLife assessment

This manuscript presents valuable and significant data on how lipids may accumulate in the tubulointerstitial compartment of the diseased kidney, but the work is largely descriptive, using methods that are inadequate for quantification (colorimetric assays versus mass spec), thus rendering data interpretation not very convincing. Therefore, while a major strength is the presentation of innovative ideas, additional experiments would be needed to support the main conclusions.

eLife assessment

This important work will be of interest to neuroscientists working on synaptic transmission and modulation of ion channel activity. This work provides solid evidence of how modulation of Nav1.2 channels by SUMOYLation alters the function of layer 5 pyramidal neurons, using convincing methodology that includes the use of a mouse engineered to eliminate the SUMOYLation site on Nav1.2. Some aspects need to be revised to strengthen data analysis and interpretation.

eLife assessment

This paper will be of interest to immunologists and infectious disease experts, as it reports the investigation of a novel treatment of invasive pneumococcal diseases using complement-activating monoclonal antibodies. Using a combination of in vitro and in vivo methods, the authors demonstrate convincingly that the introduction of specific mutations in human monoclonal antibodies that target the surface of pneumococcus bacteria can result in enhanced complement activation after these antibodies bind to the bacterial surface.

eLife assessment

This study shows that cis H3 tail acetylation promotes nucleosome accessibility to H3K4 methyl readers and writers such as MLL1. The findings provide a molecular basis for the long-standing connection between H3 acetylation and H3K4 methylation. Additional evidence is required to fully support the conclusions.

eLife assessment

Authors investigated the role of dopamine (DA) release via GRABDA in the dorsal bed nucleus of the stria terminalis (dBNST) in sign and goal tracking behavior, in response to systemic fentanyl, and to fentanyl self-administration. The behavioral experiments were well-conducted and provide novel information about BNST DA in theories of learning and reinforcement. Identified limitations had to do with acknowledgment and discussion of divergent sources of DA innervation, the low sample size in fentanyl experiments with the exclusion of a large number of animals, and a need for additional analyses of the photometry data and/or control recordings to rule out spontaneous transients in this region.

eLife assessment

The manuscript by Yanis Zekri et al identifies the direct T3 target genes that are important in thyroid hormone signaling in brown adipose tissue (BAT). The findings reported in this manuscript are significant and fundamental to our understanding of thyroid hormone action in response to environmental changes. The strength of the evidence presented with the novel methodological approaches used makes the manuscript exceptional in the area of BAT biology and T3 regulation of adaptive thermogenesis.

eLife assessment

This manuscript examines the inhibition of transmitter release induced by the activation of opioid receptors, both MOR and DOR, using a novel imaging method. The authors specifically examine how the inhibition of transmitter release is changed following prolonged exposure to saturating concentrations of agonists. They showed convincingly that there is a depletion of plasma membrane-associated receptors and suggest that the decline in receptors at the plasma membrane underlies presynaptic tolerance. This work addresses a long-standing question about how tolerance develops at the presynaptic level and indicates that the location of receptors is critically important in the development of tolerance. This work is fundamental and a game changer in the understanding of tolerance at the cellular level.

eLife assessment

This paper will be of interest to neuroscientists who study visual processing or are interested in dendritic integration. The authors used calcium imaging, pharmacology, and electrophysiology to investigate how a large, loom-sensitive neuron in grasshoppers integrates visual input to respond to both light and dark looming objects. These experiments support the finding that the integration is done by two distinct arbors of the neuronal dendritic tree, one of which loses retinotopic information. The authors suggest potential advantages of this dendritic arrangement.

eLife assessment

The complex mechanisms through which diet impact Parkinson's Disease are unclear, limiting the ability to guide patients to an optimal diet. Here, researchers use a mouse model to test the impact of dietary fiber, revealing changes in gut microbes and immune cells in the brain. This study raises intriguing hypotheses about how diet-induced changes in the microbiome could lead to changes in brain function.

eLife assessment

Sanderson developed novel interactive software for visualizing phylogenetic trees representing millions of sequences. This is a fundamental advance over previous software that is typically limited to trees with a few thousand tips. Taxonium has been used intensively by the virus evolution community over the past months and has thus already proven its utility and performance.