eLife assessment

This useful study describes expression profiling by scRNA-seq of thousands of cells of recombinant yeast genotypes from a system that models natural genetic variation. The rigorous new method presented here shows promise for improving the efficiency of genotype-to-phenotype mapping in yeast, providing convincing evidence for its efficacy. This revised manuscript focuses on overcoming technical challenges with this approach and identifies several new biological insights that build upon the field of genotype-to-phenotype mapping, a central question of interest to geneticists and evolutionary biologists.

eLife assessment:

This theoretical study makes a useful contribution to our understanding of a subtype of type 2 diabetes – ketosis-prone diabetes mellitus (KPD) – with a potential impact on our broader understanding of diabetes and glucose regulation. The article presents an ordinary differential equation-based model for KPD that incorporates a number of distinct timescales – fast, slow, as well as intermediate, incorporating a key hypothesis of reversible beta cell deactivation. The presented evidence is solid and shows that observed clinical disease trajectories may be explained by a simple mathematical model in a particular parameter regime.

eLife assessment

This valuable study advances our understanding of the histopathological features of type 1 diabetes, in particular in regard to the composition and spatial organization of pancreas infiltrating immune cells. The evidence supporting the conclusions is convincingly grounded in an application of both state-of-the-art high-dimensional in situ immunostaining technology as well as a tailored image analysis strategy. The work will be of broad interest to type 1 diabetes researchers as it contributes to a better understanding of the disease's etiopathology.

eLife assessment

In the revised version of this important study, the authors present a convincing pipeline for insect genome regulatory annotation across 33 insect genomes spanning 5 orders. Despite technical limitations in the field owing to the lack of comprehensive knowledge of enhancer content in any system, the authors employ several independent downstream analyses to support the validity of their enhancer predictions for a subset of these genomes. Taken together, the revised results suggest that this prediction pipeline may have uses in identifying functional enhancers across large phylogenetic distances. Reviewers note caveats that an experimental validation is not yet available in the field to validate a large class of newly identified enhancers across such evolutionary distances, and other pipelines might be of use to compare. This work will be of interest to the computational genomics, evolutionary biology, and gene regulation fields.

eLife assessment

This manuscript compiles existing algorithms into an open-source software package that enables real-time (and offline) motor unit decomposition from muscle activity collected via grids of surface electrodes and indwelling electrode arrays. The package is valuable given that many motor neuroscience labs are using such algorithms and that there exists a host of potential applications for such data. Validation of the software package is compelling, suggesting that it can be successfully applied across a range of muscles and tasks.

eLife assessment

This study describes a useful antibody-free method to map both G-quadruplexes and R-loops in vertebrate cells independently of the BG4 and S9.6 antibodies. It also reveals that the helicase Dhx9 can affect the self-renewal and differentiation capacities of mESCs, perhaps by regulating co-localized G4s and R-loops. The datasets provided might constitute a good starting point for future functional studies, and although the strength of the evidence that DHX9 interferes with the ability of mESCs to differentiate by regulating directly the stability of either G4s or R-loops has been improved compared to a previous version, it is still incomplete.

eLife assessment

In this useful study, a solid machine learning approach based on a broad set of systems to predict the R2 relaxation rates of residues in intrinsically disordered proteins (IDPs) is described. The ability to predict the patterns of R2 will be helpful to guide experimental studies of IDPs. A potential weakness is that the predicted R2 values may include both fast and slow motions, thus the predictions provide only limited new physical insights into the nature of the underlying protein dynamics, such as the most relevant timescale.

eLife assessment

The manuscript proposes an alternative method by SDS-PAGE calibration of Halo-Myo10 signals to quantify myosin molecules in filopodia and discusses different scenarios regarding myosin 10 working models to explain intracellular diffusion and targeting to filopodia. Overall, the paper is elegantly written and the methodology is valuable in its descriptive potential as these are key numbers to know to ultimately decipher the cellular mechanism of Myo10 action as well as understand the molecular composition of a Myo10-generated filopodium. The evidence for the conclusions is compelling, but there are limitations to this study which should be kept in mind when applying this method to other systems.

eLife assessment

This manuscript reveals an important mechanism of KCNQ1/IKs channel gating and PUFA modulation of this mechanism. This mechanism is supported by convincing single channel recordings, macroscopic current recordings and mutational analyses. These findings are of importance to the ion channel field and possibly future therapeutic applications.

eLife assessment

This study presents a valuable finding on the role of cholesterol-binding site on GLP-1 receptors and functionally characterizes the impact of this mutation on receptor behavior in the membrane and downstream signaling. The computational and experimental approaches used in the study to arrive at the conclusions are solid. The clinical ramifications are unclear at this point, but the study is a helpful addition to the scientific community working on receptor biology and drug development.

eLife assessment

Kewenig et al. present a timely and valuable study that extends prior research investigating the neural basis of abstract and concrete concepts by examining how these concepts are processed in a naturalistic stimulus: during movie watching. The authors provide convincing evidence that the varying strength of the relationship between a word and a particular visual scene is associated with a change in the similarity between the brain regions active for concrete and abstract words. This work makes a contribution that will be of general interest within any field that faces the inherent challenge of quantifying context in a multimodal stimulus.

eLife assessment

This important work, leveraging state-of-the-art whole-night sleep EEG-fMRI methods, advances our understanding of the brain states underlying sleep and wakefulness. Despite a small sample size, the authors present convincing evidence for substates within N2 and REM sleep stages, with reliable transition structure, supporting the perspective that there are more than the five canonical sleep/wake states.

eLife assessment

The methods and findings of the current work are important and well-grounded. The strength of the evidence presented is convincing and backed up by rigorous methodology. The work, when elaborated on how to access the app, will have far-reaching implications for current clinical practice.

eLife assessment

This is an important paper that reports in vivo physiological abnormalities in the hippocampus of a rat model of traumatic brain injury (TBI). In this study, authors focused on changes in theta-gamma phase coupling and action potential entrainment to theta, phenomena hypothesized to be critical for cognition. While the authors provide solid evidence of deficits in both features post-TBI, the study would have been stronger with a more hypothesis-driven approach and consideration of alterations of the animal's behavioral state or sensorimotor deficits beyond memory processes.

eLife assessment

In this valuable study, the authors use deep learning models to provide solid evidence that epithelial wounding triggers bursts of cell division at a characteristic distance away from the wound. The documentation provided by the authors should allow other scientists to readily apply these methods, which are particularly appropriate where unsupervised machine-learning algorithms have difficulties.

eLife assessment

This valuable contribution follows past descriptions of ciliation defects, potentially linked to cholinergic neuronal dysfunction, associated with mutated G2019S Lrrk2 expression. The strength of evidence is considered solid and broadly supportive of the claims concerning well-characterized cilia changes in cholinergic neurons over time in the model; however, additional work may be required to define the specificity of the pRab12 antibody in the IHC technique, dependence on LRRK2, and clarification of the cilia phenotype in sporadic PD brains that exists (for the moment) only in a non-peer-reviewed pre-print, despite the prominence of these (preliminary) results highlighted in the abstract and text of the current manuscript. It is hoped that the authors will begin to address the feedback provided by the expert reviewers to help provide a more mechanistic basis for the audience interested in cholinergic defects associated with Parkinson's disease.

eLife assessment

In this manuscript, Griesius et al analyze the dendritic integration properties of NDNF and OLM interneurons, and the current dataset suggests that even though both cell types display supralinear NMDA receptor-dependent synaptic integration, this may be associated with dendritic calcium transients only in NDNF interneurons. These findings are important because they could shed light on the functional diversity of different classes of interneurons in the mouse neocortex and hippocampus, which in turn can have major implications for understanding information flow in complex neural circuits. They are considered as being currently incomplete, however, due to: (i) the large variability and small sample size of multiple datasets, which prevents a finer evaluation of cellular and molecular mechanisms accounting for the difference in the integrative properties of different interneuron types; (ii) lack of control experiments to rule out that the effect of the NMDA antagonist AP5 on synaptic integration is not confounded by potential phototoxicity damage; (iii) lack of a precise control of the uncaging location.

eLife assessment

This study used electrophysiology and imaging to show that the majority of excitatory cells in the dentate gyrus of adult mice have very slow oscillations during non-rapid eye movement (NREM) sleep. The oscillations were influenced by serotonin when it was released during NREM sleep. Moreover, the serotonin receptor type 1a mediated the effect, and reducing these receptors impaired a type of memory. The significance of the study is important and the strength of the evidence is solid, but revisions to the figures and making conclusions more consistent with the data could improve the significance and strength of evidence.

eLife assessment

This important study by Wong et al. addresses a longstanding question in the field of associative learning regarding how a motivationally relevant event can be inferred from prior learning based on neutral stimulus-stimulus associations. The research provides convincing behavioral and neurophysiological evidence to address this important question. The manuscript will be interesting for researchers in behavioral and cognitive neuroscience.

eLife assessment

This important work combines theory and experiment to assess how humans make decisions about sequences of pairs of correlated observations. The normative theory for evidence integration in correlated environments will be informative for future investigations. However, the developed theory and data analysis seem currently incomplete: it remains to be seen if the derived decision strategy is indeed normative, or only an approximation thereof, and behavioral modelling would benefit from the assessment of alternative models.

Chapter 1 Summary

eLife assessment

This important work identifies a non-autophagic role for ATG5 in lysosomal repair and the trafficking of the glucose transporter GLUT1 to the cell surface, mediated through the retromer complex. The evidence supporting the conclusions is solid.

eLife assessment

Supported by convincing data, this valuable study demonstrates that the Chitinase 3-like protein 1 (Chi3l1) interacts with gut microbiota and protects animals from intestinal injury in laboratory colitis model. The revised manuscript sufficiently addressed the reviewers' comments. The work will be of interest to scientists studying crosstalk between gut microbiota and inflammatory diseases.

eLife assessment

This study provides useful evidence substantiating a role for long noncoding RNAs in liver metabolism and organismal physiology. Using murine knockout and knock-in models, the authors invoke a previously unidentified role for the lncRNA Snhg3 in fatty liver. The revised manuscript has improved and most studies are backed by solid evidence but the study was found to be incomplete and will require future studies to substantiate some of the claims.

eLife assessment

The manuscript by Carbo et al. reports a novel role for the MltG homolog AgmT in gliding motility in M. xanthus. The authors provide convincing data to demonstrate that AgmT is a cell wall lytic enzyme (likely a lytic transglycosylase), its lytic activity is required for gliding motility, and that its activity is required for proper binding of a component of the motility apparatus to the cell wall. The findings are valuable as they contribute to our understanding of the molecular mechanisms underlying the interaction between gliding motility and the bacterial cell wall.

eLife assessment

This useful study describes a single set of label-chase mass spectrometry experiments to confirm the molecular function of YafK as a peptidoglycan hydrolase, and to describe the timing of its attachment to the peptidoglycan. Confirmation of the molecular function of YafK is helpful for further studies to examine the function and regulation of the outer membrane-peptidoglycan link in bacteria. The evidence supporting the molecular function of YafK and that lpp molecules are shuffled on and off the peptidoglycan is solid, however, some of the other data still remain incomplete in the revised version. The work will be of interest to researchers studying lipoproteins in gram negative bacteria.

eLife assessment

This study presents an important finding on the spontaneous emergence of structured activity in artificial neural networks endowed with specific connectivity profiles. The evidence supporting the claims of the authors is convincing, providing direct comparison between the properties of the model and neural data although investigating more naturalistic inputs to the network would have strengthened the main claims. The work will be of interest to systems and computational neuroscientists studying the hippocampus and memory processes.

eLife assessment

This study presents a fundamental finding on how levels of m6A levels are controlled, invoking a consolidated model where degradation of modified RNAs in the cytoplasm plays a primary role in shaping m6A patterns and dynamics, rather than needing active regulation by m6A erasers and other related processes. The evidence is compelling and uses transcriptome-wide data and mechanistic modeling. However, it is possible that m6A-erasers will have roles in specific developmental contexts or conditions, so this model may not apply universally.

eLife assessment

Utilizing transgenic lineage tracing techniques and tissue clearing-based advanced imaging and three-dimensional slices reconstruction, the authors comprehensively mapped the distribution atlas of NFATc1+ and PDGFR-α+ cells in dental and periodontal mesenchyme and tracked their in vivo fate trajectories. This important work extends our understanding of NFATc1+ and PDGFR-α+ cells in dental and periodontal mesenchyme homeostasis, and should provide impact on clinical application and investigation. The strength of this work is compelling in employing CRISPR/Cas9-mediated gene editing to generate two dual recombination systems, and mapped gNFATc1+ and PDGFR-α+cells residing in dental and periodontal mesenchyme, their capacity for progeny cell generation, and their inclusive, exclusive and hierarchical relations in homeostasis, generating a spatiotemporal atlas of these skeletal stem cell population.

eLife assessment

In this fundamental study, the authors describe a new data processing pipeline that can be used to discover causal interactions from time-lapse imaging data. The utility of this pipeline was convincingly illustrated using tumor-on-chip ecosystem data. The newly developed pipeline could be used to better understand cell-cell interactions and could also be applied to perform temporal causal discovery in other areas of science, meaning this work could potentially have a wide range of applications.

eLife assessment

This valuable study characterizes the variability in spacing and direction of entorhinal grid cells and shows how this variability can be used to disambiguate locations within an environment. These claims are supported by solid evidence, yet some aspects of the methodology should be clarified. This study will be of interest to neuroscientists working on spatial navigation and, more generally, on neural coding.

eLife assessment

In this useful study, the authors show that N-acetylation of synuclein increases clustering of synaptic vesicles in vitro and that this effect is mediated by enhanced interaction with lysophosphatidylcholine. While the evidence for enhanced clustering is largely solid, the biological significance remains unclear.

eLife assessment

The manuscript introduces an important and innovative non-AI computational method for segmenting noisy grayscale images, with a particular focus on identifying immunostained potassium ion channel clusters. This method significantly enhances accuracy over basic threshold-based techniques while remaining user-friendly and accessible, even for researchers with limited computational backgrounds. The evidence supporting the method's efficacy is convincing. Its practical application and ease of use make it a tool that will benefit a wide range of laboratories.

eLife assessment

This useful experiment seeks to better understand how memory interacts with incoming visual information to effectively guide human behavior. Using several methods, the authors identify two distinct pathways relating visual processing to the default mode network: one that emphasizes semantic cognition, and the other, spatial cognition. The evidence presented is solid and will be of interest to cognitive and systems neuroscientists.

eLife assessment

This important study shows a significant role for Mushashi-2 (Msi2) in lung adenocarcinoma. The authors provided solid data that support the requirement for Msi2 in tumor growth and progression, although the study would have been strengthened by including more patient samples and additional evidence regarding Msi2+ cells being more responsive to transformation. These findings are of interest to both the lung cancer and the RNA binding protein fields.

eLife assessment

This fundamental study provides compelling evidence for dysgranular insular involvement in top-down and bottom-up interoceptive processing by building on previous evidence using state-of-the-art methods. Its translational application in ADE patients corroborates the assumption that the mid-insula may indeed be a locus of 'interoceptive disruption' in psychiatric disorders, which underscores the study's high relevance for both body-brain as well as clinical research.

eLife assessment

This is a potentially valuable contribution, reporting a deletion analysis of the MSL1 gene to assess how different parts of the protein product interact with the MSL2 protein and roX RNA to affect the association of the MSL complex with the male X chromosome of Drosophila. However, the framework that the MSL complex mediates dosage compensation is outdated and has flaws, and the evidence is currently considered inadequate to support the claims. Because there are many ways to alter viability, sex-specific viability is insufficient to make claims regarding dosage compensation.

eLife assessment

This important study combines genetic analysis, biochemistry, and structural modeling to reveal new insights into how changes in protein-protein structure activate signal transduction as part of the bacterial general stress response. The data, collected using validated and standard methods, and the interpretations are solid, although additional experimental structural evidence would strengthen the proposed model and its potential application to other systems. This manuscript, which provides multiple avenues for follow-up studies, will be of broad interest to microbiologists, structural biologists, and cell biologists.

eLife assessment

This study provides potentially highly valuable new insight into the role of Fgf signalling in SUFU mutation-linked cerebellar tumors and indicates novel therapeutic interventions via inhibition of Fgf signalling. The evidence supporting the major claims, however, is at this point currently incomplete. A more robust analysis of gene expression patterns and deeper mechanistic insight would significantly enhance this study, which could have wide-ranging implications for the treatment of specific cerebellar tumors.

eLife assessment

This manuscript presents a valuable new quantitative crosslinking mass spectrometry approach using novel isobaric crosslinkers. The data are solid and the method has potential for a broad application in structural biology if more isobaric crosslinking channels are available and the quantitative information of the approach is exploited in more depth.

eLife assessment

The authors present a valuable study exploring the interaction between JNK signaling and high sucrose feeding. The strength of evidence supporting these observations is solid, including multi-tissue transcriptomic and metabolic analyses, followed by network modeling approaches to define the organs and pathways involved. Reviewers provided several suggestions to improve the manuscript including clarifications of model and analyses, as well as explanations for within-group variations and confirming RNA-seq results at the level of metabolite processes highlighted.

eLife assessment

Recent studies have demonstrated that depletion of nuclear TDP-43 leads to loss of its nuclear function resulting in changes in gene expression and splicing of target mRNAs. This study developed a sensitive and robust sensor for TDP-43 activity that should impact the field's ability to monitor whether TDP-43 is functional or not. Though limited to cell culture, the evidence presented is convincing and is the first demonstration that a GFP on/off system can be used to assess TDP-43 mutants as well as loss of soluble TDP-43. The findings are valuable and may represent a novel tool to investigate TDP-43-associated disease mechanisms.

eLife assessment

This work describes how the toxin-antitoxin (TA) system, which uses the cyclic di-GMP as an antitoxin, controls both the persistence of antibiotics linked to biofilms and the integrity of the bacterial genome. The authors present solid evidence linking cyclic di-GMP and the toxin HipH. The work is valuable because it establishes the relationship between bacterial persistence and biofilm resilience, which lays a strong basis for future research on the formation of bacterial biofilms and antibiotic resistance.

eLife assessment

This important study evaluates the outcomes of a single-institution pilot program designed to provide graduate students and postdoctoral fellows with internship opportunities in areas representing diverse career paths in the life sciences. The data convincingly show the benefit of internships to students and postdocs, their research advisors, and potential employers, without adverse impacts on scientific productivity. This work will be of interest to multiple stakeholders in graduate and postgraduate life sciences education and should stimulate further research into how such programs can best be broadly implemented.

eLife assessment

Understanding how genomic regulatory elements control spatiotemporal gene expression is essential for explaining cell type diversification, function, and the impact of genetic variation on disease. This important study provides solid evidence that enhancers generally combine additively to influence gene expression. Moreover, promoters, particularly weaker ones, can exhibit supra-additivity when integrating enhancer effects. These findings highlight the context-dependent nature of enhancer-promoter interactions in gene regulation, and contribute to ongoing discussions about the selectivity and combination of regulatory elements.

eLife assessment

This is a valuable contribution to our understanding of how different cell stressors (ethanol or heat-shock) elicit unique responses at the genomic and topographical level under the regulation of yeast transcription factor Hsf1, providing solid evidence documenting the temporal coupling (or lack thereof) between Hsf1 aggregation and long-range communication among co-regulated heat-shock loci versus chromatin remodeling and transcriptional activation. A particular strength is the combination of genomic and imaging-based experimental approaches applied to genetically engineered in vivo systems.

eLife assessment

This manuscript investigates how chloroplasts are broken down during light-limiting conditions as plants reorganize their energy-producing organelles during carbon limitation. The authors provide compelling live-cell imaging data of plastids and solid quantification of events, documenting that buds form on the surface of chloroplasts and pinch away, then associate with the vacuole via a mechanism that depends on autophagy machinery, but not plastid division machinery. This manuscript provides valuable groundwork for other scientists studying the regulation and breakdown of energy-producing organelles, including chloroplasts and mitochondria.

eLife assessment

This study provides valuable insights into the role of actin dynamics in regulating the transition of fusion models during homotypic fusion between late endosomes. The evidence supporting the authors' claims is convincing. However, while the observations are significant, the study could benefit from further exploration of the mechanistic details and physiological relevance.

eLife assessment

This is an important behavioral, pharmacological intervention study of the effects of the catecholamine reuptake inhibitor methylphenidate (MPH) on value-based decision-making using a combination of aversive and appetitive Pavlovian to Instrumental Transfer (PIT) in a human cohort (n=100). The design used drug dosing after learning, allowing the convincing interpretation of catecholamines being involved in the decision process, an effect dependent on baseline working memory capacity. The results also challenge the view that catecholamines operate by modulating behavioural invigoration alone.

eLife assessment

This important study offers a powerful empirical test of a highly influential hypothesis in population genetics. It incorporates a large number of animal genomes spanning a broad phylogenetic spectrum and treats them in a rigorous unified pipeline, providing the convincing negative result that effective population size scales neither with the content of transposable elements nor with overall genome size. These observations demonstrate that there is still no simple, global hypothesis that can explain the observed variation in transposable element content and genome size in animals.

eLife assessment

This valuable study investigates the immune system's role in pre-eclampsia. The authors map the immune cell landscape of the human placenta and find an increase in macrophages and Th17 cells in patients with pre-eclampsia. Following mouse studies, the authors suggest that the IGF1-IGF1R pathway might play a role in how macrophages influence T cells, potentially driving the pathology of pre-eclampsia. There is solid evidence in this study that will be of interest to immunologists and developmental biologists, however, some of the conclusions require additional detail and/or more appropriate statistical tests.

eLife assessment

This important work advances our understanding of how mechanical forces transmitted by blood flow contribute to cardiac development by identifying id2b as a flow-responsive factor that is required for valve development and calcium-mediated cardiac contractility and its downstream mechanism of action. However, the evidence supporting the conclusions is incomplete and would benefit from more rigorous approaches. With additional support of the main conclusions, the work will be of interest to those working on developmental biology, heart development, and congenital heart disease.

eLife assessment

This valuable work analyzes how specialized cells in the auditory cells, known as the octopus cells, can detect coincidences in their inputs at the submillisecond time scale. While previous work indicated that these cells receive no inhibitory inputs, the present study unambiguously demonstrates that these cells receive inhibitory glycinergic inputs. The physiologic impact of these inputs needs to be studied further. It remains incomplete at present but could be improved by addressing caveats related to similar sizes of excitatory postsynaptic potentials and spikes in the octopus neurons.

eLife assessment

This study presents a valuable finding on the role of dopamine receptor D2R in dopaminergic neurons DAN-c1 and mushroom body neurons (Y201-GAL4 pattern) on aversive and appetitive conditioning. The evidence supporting the claims of the authors is solid and promotes the investigation using fly larvae, which have interesting advantages in the time required for obtaining experimental animals and the use of optogenetics. The work will be of interest to researchers studying neuronal control of behaviour and learning and memory in general.

eLife assessment

This important study investigates the relationship between transcription factor condensate formation, transcription, and 3D gene clustering of the MET regulon in the model organism S. cerevisiae. The authors provide solid experimental evidence that transcription factor condensates enhance transcription of MET-regulated genes, but evidence for the role of Met4 IDRs and Met4-containing condensates in mediating target gene clustering in the MET regulon is not as strong. This paper will be of interest to molecular biologists working on chromatin and transcription, although its impact would be strengthened by further investigation.

eLife assessment

In this important study, the findings have theoretical and practical implications beyond a single subfield; the work supports the role of breast carcinoma amplified sequence 2 (Bcas2) in positively regulating primitive wave hematopoiesis through amplification of beta-catenin-dependent (canonical) Wnt signaling. The study is convincing, using appropriate and validated methodology in line with the current state-of-the-art; there is a first-rate analysis of a strong phenotype with highly supportive mechanistic data. The findings shed light on the controversial question of whether, when, and how canonical Wnt signaling may be involved in hematopoietic development. The work will be of interest to hematologists but also to developmental biologists.

eLife assessment

The authors present 16 new well-preserved specimens from the early Cambrian Chengjiang biota. These specimens potentially represent a new taxon which could be useful in sorting out the problematic topology of artiopodan arthropods - a topic of interest to specialists in Cambrian arthropods. The authors provide solid anatomical and phylogenetic evidence in support of a new interpretation of the homology of dorsal sutures in trilobites and their relatives.

eLife assessment

This important computational study provides new insights into how neural dynamics may lead to time-evolving behavioral errors as observed in certain working-memory tasks. By combining ideas from efficient coding and attractor neural networks, the authors construct a two-module network model to capture the sensory-memory interactions and the distributed nature of working memory representations. They provide convincing evidence supporting that their two-module network, although none of the alternative circuit structures they considered can account for error patterns reported in orientation-estimation tasks with delays.

eLife assessment

The study presents a potentially valuable approach by combining two measurements (pHLA binding and pHLA-TCR binding) to improve predictions of which mutations in colorectal cancer are likely to be presented to and recognised by the immune system. While this approach is promising, the evidence supporting the primary claim remains somewhat incomplete. The experimental validation of the computational predictions with actual immune responses is still limited, despite the increase in sample size from 4 to 8 in this revision.

eLife assessment

This important manuscript demonstrates that UGGT1 is involved in preventing the premature degradation of endoplasmic reticulum (ER) glycoproteins through the re-glucosylation of their N-linked glycans following release from the calnexin/calreticulin lectins. The authors include a wealth of convincing data in support of their findings, although extending these findings to other types of substrates, such as secreted proteins, could further demonstrate the global importance of this mechanism for protein trafficking through the secretory pathway. This will work will be of interest to scientists interested in ER protein quality control, proteostasis, and protein trafficking.

eLife assessment

This fundamental study reports the most comprehensive neurotransmitter atlas of any organism to date, using fluorescent knock-in reporter lines. The work is comprehensive, rigorous, and compelling. The tool will be used by broad audience of scientists interested in neuronal cell type differentiation and function, and could be a seminal reference in the field.

eLife assessment

The study presents compelling evidence that the melanocortin system originating in the arcuate nucleus of the hypothalamus plays a crucial role in puberty onset, representing a significant advance in our understanding of reproductive biology. The work, which represents a fundamental advance, employs innovative approaches and benefits from the combined expertise of two respected laboratories, enhancing the robustness of the findings. Given the potential impact on human health and the strength of the evidence presented, this work will likely influence the field substantially and may inform future clinical applications.

eLife assessment

This work introduces a Python package, Avian Vocalization Analysis (AVN) that provides several key analysis pipelines for segmentation, annotation, and visualization of zebra finch song. AVN can be used to predict the stage of song development, quantify acoustic similarity, and detect abnormalities associated with deprived auditory feedback or social isolation. The methods are solid and are likely to provide a useful tool for scientists aiming to automate the analysis of large datasets of zebra finch vocalizations.

eLife assessment

Zhou et al. introduce cascading neural activations, known as 'replay', into a context-maintenance and retrieval model (CMR) that has been previously used to capture a range of memory phenomena. The proposed 'CMR-replay' model outperforms its CMR predecessor in a compelling way, and thus, the work makes important strides towards understanding the empirical memory literature as well as some of the cognitive functions of replay. Notable limitations include the scope of the model with respect to established aspects of memory consolidation, such as the stages and physiology of sleep, and the lack of integration with highly relevant associative and deep learning theories.

eLife assessment

This study presents valuable findings with practical and theoretical implications for drug discovery, particularly in the context of repurposing CIP for the treatment of Babesia spp. The evidence is convincing overall, as the data and analyses support the main claims. However, a few assertions are only partially substantiated. If the authors can strengthen these areas with additional evidence, the paper could attract greater interest from scientists in drug discovery, computational biology, and microbiology.

eLife assessment

This important study provides solid mechanistic and modeling data suggesting that the polar localization of MinCD in Bacillus subtilis is largely due to differences in diffusion rates between monomeric and dimeric MinD. This finding is exciting as it negates the necessity for a third, localization determinant, in this system as has been previously proposed. The work is generally strong but is incomplete without some additional quantitative analysis, as well as clarification of the underlying assumptions and details used for the modeling experiments.

eLife assessment

This work provides solid evidence that Transforming Growth Factor β Activated Kinase 1 (TAK1) regulates esophageal squamous cell carcinoma (ESCC) tumor proliferation and metastasis. The findings are valuable to the field of molecular tumor biology in general and to the understanding of ESCC tumor invasiveness and metastatic potential.

eLife assessment

This valuable study characterized a new set of small molecules targeting the interaction between ELF3-MED23, with one of the reported compounds representing a promising novel therapeutic strategy, The evidence supporting the conclusions is convincing. This article will be of interest to medical and cell biologists working on cancer and, particularly, on HER2-overexpression cancers.

eLife assessment

The manuscript establishes a sophisticated mouse model for acute retinal artery occlusion (RAO) by combining unilateral pterygopalatine ophthalmic artery occlusion (UPOAO) with a silicone wire embolus and carotid artery ligation, generating ischemia-reperfusion injury upon removal of the embolus. This clinically relevant model is useful for studying the cellular and molecular mechanisms of RAO. The data overall are solid, presenting a novel tool for screening pathogenic genes and promoting further therapeutic research in RAO.

eLife assessment

This study presents an important computational tool for the quantification of the cellular composition of human tissues profiled with ATAC-seq. The methodology and its application results on breast cancer tumor tissues are convincing. It advances existing methods by utilizing a comprehensive reference profile for major cancer-relevant cell types, compatible with a widely-used cell type deconvolution tool.

eLife assessment

This important study provides convincing evidence that both psychiatric dimensions (e.g. anhedonia, apathy, or depression) and chronotype (i.e., being a morning or evening person) influence effort-based decision-making. This is of importance to researchers and clinicians alike, who may make inferences about behaviour and cognition without taking into account whether the individual may be tested or observed out-of-sync with their phenotype. The current study can serve as a starting point for more targeted investigation of the relationship between chronotype, altered decision making and psychiatric illness.

eLife assessment

This important work provides insights into the neural mechanisms regulating specific parental behaviors. By identifying a key role for oxytocin synthesizing cells in the paraventricular nucleus of the hypothalamus and their projections to the medial prefrontal cortex in promoting pup care and inhibiting infanticide, this study advances our understanding of the neurobiological basis of these contrasting behaviors in male and female mandarin voles. The evidence supporting the authors' conclusions is solid, and this work should be of interest to researchers studying neuropeptide control of social behaviors in the brain.

eLife assessment

This fundamental work demonstrates that ABHD6 regulates AMPAR gating kinetics in a TARP γ-2-dependent manner. The evidence in this study is compelling. This study will be of interest to readers in the field of synaptic transmission.

eLife assessment

This study presents important findings on the early development of cardiac and respiratory interoceptive sensitivity based on an investigation of infants aged 3, 9 and 18 months and on extensive statistical analyses. The evidence supporting the conclusions are convincing although the research faced technical and recruitment challenges that limit the findings interpretation and generalizability. This study will be of significant interest to developmental psychologists and neuroscientists working on interoception and its influence on socio-cognitive development.

eLife assessment

This valuable study advances the understanding of granuloma formation by identifying a key chemokine receptors in containing infection by a specific species of bacteria. The evidence supporting this is solid, providing a spatial transcriptomic dataset spanning granuloma formation and resolution by a specific species of bacteria. The work should be of interest to microbiologists and immunologists.

eLife assessment

By developing a framework to integrate metagenomic and metabolomic data with genome-scale metabolic models, this study establishes a toolkit to investigate trophic interactions between microbiota members in situ. The authors apply this method to the native rhizosphere bacterial communities of apple rootstocks, producing solid evidence and numerous detailed hypotheses on specific trophic exchanges and resource dependencies. The framework represents a valuable method to disentangle features of microbial interaction networks and will be of interest to microbiome scientists as well as plant and computational biologists.

eLife assessment

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

eLife assessment

This fundamental state-of-the-art modeling study explores neural mechanisms underlying walking control in cats, demonstrating the probability of three different states of operation of the spinal circuitry generating locomotion at different speeds. The authors' biophysical modeling sufficiently reproduces and provides explanations for experimental data on how the locomotor cycle and phase durations depend on treadmill walking speed and points to new principles of circuit functional architecture and operating regimes underlying how spinal circuits interact with supraspinal signals and limb sensory feedback signals to produce different locomotor behaviors at different speeds, which are major unresolved problems in the field. The modeling evidence is compelling, especially in advancing our understanding of locomotion control mechanisms and will interest neuroscientists studying the neural control of movement.

eLife assessment

This manuscript describes the impact of modulating signaling by a key regulatory enzyme, Dual Leucine Zipper Kinase (DLK), on hippocampal neurons. The results are interesting and will be important for scientists interested in synapse formation, axon specification, and cell death. The methods and interpretation of the data are solid, but the study can be further strengthened with some additional studies and controls.

eLife assessment

Data presented in this useful report suggest a potentially new model for chemotaxis regulation in the gram-negative bacterium P. putida. Data supporting interactions between CheA and the copper-binding protein CsoR, reveal potential mechanisms for coordinating chemotaxis and copper resistance. There was, however concern about the large number of CheA interactors identified in the initial screen and it was felt that the study was incomplete without a substantial number of additional experiments to test the model and bolster the authors' conclusions.

eLife assessment

In this manuscript, Chen et al. used cryo-ET and in vitro reconstituted system to demonstrate that the autoinhibited form of LRRK2 can also assemble into filaments on the microtubule surface, with a new interface involving the N-terminal repeats that were disordered in the previous active-LRRK2 filament structure. The structure obtained in this study is the highest resolution of LRRK2 filaments done by subtomogram averaging, representing a major technical advance compared to the previous paper from the same group. This is an important study, especially considering the pharmacological implications of the effect of inhibitors of the protein. The strengths of the data are convincing, but the study would be considerably strengthened if the authors addressed several discrepancies relating to their earlier work, and explored the physiological significance of the new interfaces and the incomplete decoration of microtubules described here.

eLife assessment

The authors provide convincing data that identify a novel, non-opioid biologic from human birth tissue products with anti-nociceptive properties in a preclinical mouse model of surgical pain. This important study highlights the potential use of naturally derived biologics from human birth tissues as safe and sustainable pain treatment options that do not possess the adverse side effects associated with opioids and synthetic pharmaceuticals. Whether these results will translate to the clinic remains to be seen, nevertheless, these preclinical findings are promising.

eLife assessment

Saijilafu et al. describe that MLCK and MLCP bidirectionally regulate NMII phosphorylation ultimately impinging on axonal growth during regeneration in the central and peripheral nervous systems. However, the evidence is in most cases incomplete, since some key controls are missing, some major claims are too broad to be supported by data and some claims and evidence present internal contradictions. In sum, this knowledge is potentially useful for the field due to the relevance of identifying mechanisms that regulate axonal regeneration, providing some claims inconsistencies are better supported and properly discussed.

eLife assessment

This study presents a useful demonstration that a specific protein fragment may induce the loss of synapses in Alzheimer's disease. The evidence supporting the data is solid but incomplete and would benefit from additional experiments. The application of the findings is limited because blocking the formation of the protein fragment has not benefited patients in several clinical trials.

eLife assessment

Examination of (a)periodic brain activity has gained particular interest in the last few years in the neuroscience fields relating to cognition, disorders, and brain states. Using large EEG/MEG datasets from younger and older adults, the current study provides compelling evidence that age-related differences in aperiodic EEG/MEG signals can be driven by cardiac rather than brain activity. Their findings have important implications for all future research that aims to assess aperiodic neural activity, suggesting control for the influence of cardiac signals is essential.

eLife assessment

This study demonstrates the potential role of 17α-estradiol in modulating neuronal gene expression in the aged hypothalamus of male rats, identifying key pathways and neuron subtypes affected by the drug. While the findings are useful and provide a foundation for future research, the strength of supporting evidence is incomplete due to the lack of female comparison, a young male control group, unclear link to 17α-estradiol lifespan extension in rats, demonstration of physiological effects of the treatment, and insufficient analysis of glial cells and cellular senescence in CRH neurons.

eLife assessment

This study presents a valuable combination of X-ray and cryo-EM structures of the bacterial adhesin PrgB, an atypical microbial cell surface-anchored polypeptide that binds DNA. There is convincing support for the claims regarding the overall function and importance of individual domains. The model for PrgB's binding of eDNA is thought-provoking, but the evidence for it based on low-resolution volumes of cryoEM data is incomplete. If additional experimental evidence for the model is produced, this work will be impactful in the field of bacterial adhesins, conjugation, and biofilm formation, as it focuses on a clinically relevant Gram-positive pathogen, whereas most work in the field has been focused on Gram-negative model systems.

eLife assessment

This valuable work describes a novel role of Vangl2, a core planar cell polarity protein, in mechanistically linking the inflammatory NF-kB pathway to selective autophagic protein degradation. Using solid methods, the authors also establish the functional significance of the proposed mechanism in sepsis. The work may advance our understanding of NF-kB control, particularly in the context of aberrant inflammation. However, some gaps remain, and additional studies are needed to unequivocally establish the role of Vangl2 in regulating NF-kB signaling.

eLife assessment

Tilk and colleagues present a computational analysis of tumor transcriptomes to investigate the hypothesis that the large number of somatic mutations in some tumors is detrimental such that these detrimental effects are mitigated by an up-regulation by pathways and mechanisms that prevent protein misfolding. The authors address this question by fitting a model that explains the log expression of a gene as a linear function of the log number of mutations in the tumor and show that specific categories of genes (proteasome, chaperones, ...) tend to be upregulated in tumors with a large number of somatic mutations. Some of the associations presented could arise through confounding, but overall the authors present solid evidence that mutational load is associated with higher expression of genes involved in mitigation of protein misfolding – an important finding with general implications for our understanding of cancer evolution.

eLife assessment

This important manuscript reveals signatures of co-evolution of two nucleosome remodeling factors, Lsh/HELLS and CDCA7, which are involved in the regulation of eukaryotic DNA methylation. The results suggest that the roles for the two factors in DNA methylation maintenance pathways can be traced back to the last eukaryotic common ancestor and that the CDC7A-HELLS-DNMT axis shaped the evolutionary retention of DNA methylation in eukaryotes. The evolutionary analyses are solid, although more refined phylogenetic approaches could have strengthened some of the claims. Overall, this study could be used by researchers studying DNA methylation pathways in different organisms, and it should be of general interest to colleagues in the fields of evolutionary biology, chromatin biology and genome biology.

eLife assessment

The specific questions taken up for study by the authors – in mice of HDAC and Polycomb function in the context of vascular endothelial cell (EC) gene expression relevant to the blood-brain barrier, (BBB) – are potentially useful in the context of vascular diversification in understanding and remedying situations where BBB function is compromised. The strength of the evidence presented is incomplete, and to elaborate, it is known that the culturing of endothelial cells can have a strong effect on gene expression. This is a significant issue as we are not given how long the cells were cultured and how the above point was addressed.

eLife assessment

This study presents fundamental new insight into the regulatory apparatus of PI3Kγ, a kinase in signaling pathways that control the immune response and cancer. A suite of biophysical and biochemical approaches provide convincing evidence for new sites of allosteric control over enzyme activity. The rigorous findings provide structure and dynamic information that may be exploited in efforts to control PI3Kγ activity in a therapeutic setting.

eLife assessment

This fundamental study has successfully identified four key transcription factors (MECOM, PAX8, SOX17, and WT1) that exhibit synergistic effects and are potentially responsible for the transformation of fallopian tube secretory epithelial cells into high-grade serous 'ovarian' cancer cells. Convincing data strongly support the drawn conclusion and significantly contribute to our understanding of the etiology of this devastating cancer. The implications of this finding are substantial, as it provides molecular insights that can potentially pave the way for innovative diagnostics and therapeutics in the field of gynecological oncology. Enhancing the clarity and impact of this study would be achieved through improvements in data presentation.

eLife assessment

The bacterial neurotransmitter:sodium symporter homoglogue LeuT is an well-established model system for understanding the basis for how human monoamine transporters, such as the dopamine and serotonin, couple ions with neurotransmitter uptake. Here the authors provide convincing data to show that the K+ catalyses the return step of the transport cycle in LeuT by binding to one of the two sodium sites. The paper is an important contribution, but it's still unclear exactly where K+ binds in LeuT, and how to incorporate K+ binding into a transport cycle mechanism.

eLife assessment

There was a range of opinion among three highly expert reviewers from different perspectives in the field. This is a significant topic and it was felt that the contribution at present is valuable to those in the field. However, it was agreed after consultation that the description of the simulation methodology was inadequate.

eLife assessment

This valuable study is of relevance for those interested in mechanism required for infections of humans by Klebsiella pneumoniae. The authors apply TraDIS (high-density TnSeq) to K. pneumoniae with the goal of identifying genes required for survival under various infection-relevant conditions. In general, the evidence supporting the identity of the identified genes is convincing, but testing additional individual genes to validate the list inferred from TraDIS data, in addition to complementing the mutants, would help to provide full support for the claims made. Additional work would also help to unravel novel mechanisms beyond the ones reported.

eLife assessment

This valuable study reports on the structure and function of capsid size-determining external scaffolding protein encoded by a Vibrio phage satellite. The structural work is of high quality and the presented reconstructions are compelling, but some of the experiments could benefit from a more rigorous statistical analysis of capsid sizes and shapes. The paper offers an advance in the field of phage and virus structure and assembly with implications for understanding the evolution of phage satellites.

eLife assessment

This important study illustrates the value of museum samples for understanding past genetic variability in the genomes of populations and species, including those that no longer exist. The authors present genomic sequencing data for the extinct Xerces Blue butterfly and report convincing evidence of declining population sizes and increases in inbreeding beginning 75,000 years ago, which strongly contrasts to the patterns observed in similar data from its closest relative, the extant Silvery Blue butterfly. Such long-term population health indicators may be used to highlight still extant but especially vulnerable-to-extinction insect species – irrespective of their current census population size abundance.

eLife assessment

This paper is a valuable step in multi-subject behavioral modeling using an extension of the Variational Autoencoder (VAE) framework. Using a novel partition of the latent space and in tandem with a recently proposed regularization scheme, the paper provides a rich set of computational analyses analyzing social behavior data of mice with results that represent the state-of-the-art in this subfield. The strength of evidence is convincing, with the methodology being well documented and the results being reproducible, although some additional quantifications would have been helpful to fully gauge the circumstances where the approach would be most effectively applied.

eLife assessment

This article presents important results describing how the gathering, integration, and broadcasting of information in the brain changes when consciousness is lost either through anesthesia or injury. They provide convincing evidence to support their conclusions, although the paper relies on a single analysis tool (partial information decomposition) and could benefit from a clearer explication of its conceptual basis, methodology, and results. The work will be of interest to both neuroscientists and clinicians interested in basic and clinical aspects of consciousness.

eLife assessment

This valuable study focuses on the impact of growth feedback on the performance of artificial gene circuits capable of achieving adaptive responses, a significant problem in synthetic biology. Through solid computational analysis, the authors identify specific failure mechanisms, as well as core topologies associated with robust performance based on systematic analysis of over four hundred circuit topologies. The results will be of interest to those working on engineering gene circuits for diverse applications.

eLife assessment

This paper reports a valuable new set of new results. The main claim is that the projection from adult-born granule cells in the dentate gyrus to the hippocampal subfield CA2 is necessary for the retrieval of social memories formed during development. However, the reviewers agreed that evidence for this major claim is currently incomplete.

eLife assessment

This important study illustrates the value of museum samples for understanding past genetic variability in the genomes of populations and species, including those that no longer exist. The authors present genomic sequencing data for the extinct Xerces Blue butterfly and report convincing evidence of declining population sizes and increases in inbreeding beginning 75,000 years ago, which strongly contrasts to the patterns observed in similar data from its closest relative, the extant Silvery Blue butterfly. Such long-term population health indicators may be used to highlight still extant but especially vulnerable-to-extinction insect species – irrespective of their current census population size abundance.

eLife assessment

This study presents valuable new insights from the protist Tetrahymena regarding radial spokes, conserved protein complexes that are relevant for cilia motility. The work employs interdisciplinary approaches to provide convincing support for radial spoke composition with some experiments, but there are weaker areas with partially incomplete support, such as relying on knockouts alone rather than including localization studies of tagged proteins.

eLife assessment

The study presents a tool for searching molecular dynamics simulation data, making such data sets accessible for open science. The authors provide convincing evidence that it is possible to identify useful molecular dynamics simulation data sets and their analysis can produce valuable information.

eLife assessment

The demonstration that the PARG dePARylation enzyme is required in S phase to remove polyADP-ribose (PAR) protein adducts that are generated in response to the presence of unligated Okazaki fragments is potentially valuable, but the evidence is incomplete, and identification of relevant PARylated PARG substrates in S-phase is needed to understand the role of PARylation and dePARylation in S-phase progression. Their observation that human ovarian cancer cells with low levels of PARG are more sensitive to a PARG inhibitor, presumably due to the accumulation of high levels of protein PARylation, suggests that low PARG protein levels could serve as a criterion to select ovarian cancer patients for treatment with a PARG inhibitor drug.

eLife assessment:

This valuable study provides molecular-level insights into the functional mechanism of bacterial ice-nucleating proteins, detailing electrostatic interactions in the domain architecture of multimeric assemblies. The evidence supporting the claims of the authors is solid, with results from protein engineering experiments, functional assays, and cryo-electron tomography, while the proposed structural model of protein self-assembly remains hypothetical. The work is of broad interest to researchers in the fields of protein structural biology, biochemistry, and biophysics, with implications in microbial ecology and atmospheric glaciation.

eLife assessment

This is an important study because it provides evidence that specific neuronal firing patterns in deep cerebellar nuclei map onto specific behavioral movement disorder phenotypes. The optogenetic manipulations and resulting neuronal and behavioral outcomes are highly compelling, but the development of the classifier tool was incomplete. This study contributes to the fields of cerebellar physiology and movement disorders because it puts forth a map of relationships between neuronal firing patterns and multiple distinct movement phenomena, providing a comprehensive view that goes beyond most studies which typically examine one phenomenon in isolation.

eLife assessment

This study provides valuable insight into the role of miR-199a/b-5p in cartilage formation. The evidence supporting the significance of the identified miRNA and its target mRNA transcripts is convincing, however further experiments and a broader contextual analysis are warranted to draw a more robust conclusion. This paper will likely primarily benefit scientists focused on diseases related to this biological process, such as osteoarthritis. Furthermore, researchers interested in miRNAs as a broader subject may find the computational model development methodology particularly helpful.

eLife assessment

This fundamental work quantifies the stochastic dynamics of neural population activity in the lateral intraparietal area (LIP) of the macaque monkey brain during single perceptual decisions. These single-trial dynamics have been subject to intense debate in neuroscience, and they have implications for modelling decision-making in various fields including neuroscience and psychology. Through a combination of state-of-the-art recordings from many LIP neurons and theory-driven data analyses, the authors provide solid evidence for the notion that single-trial neural population dynamics in LIP encode the decision variable postulated by the drift-diffusion model of decision-making.

eLife assessment

This study offers a compelling molecular model for the organization of rootlets, a critical organelle that links cilia to the basal body, ensuring proper anchoring. While previous research has explored rootlet structure and organization, this study delivers an unprecedented level of resolution, important to the centrosome and cilia field. The model proposed by the authors will serve as a reference for future studies.

eLife assessment

The authors developed a tool to improve our understanding of tissue-specific activation of Free Fatty Acid receptor 2 (FFA2). Convincing in vitro and in vivo validation of the tool is presented via the development of new antibody reagents that constitute an important advance in the field. Some of the technical details could be presented more clearly.

eLife assessment

This manuscript describes an important web resource for kinases connected to cytokines. The compelling information will be highly used by researchers across a number of fields including analysts, modelers, and wet lab experimentalists – and clinician-researchers – who are looking to improve our understanding of pathologies and means to correct them through modulating the immune response.

eLife assessment

This valuable work by Rivera et al. probes to understand how the regulation of oligodendrocyte progenitor cell (OPC) remyelination and function contributes to the treatment of multiple sclerosis. The authors provide incomplete evidence for the platelets to mediate OPC differentiation and remyelination. Both reviewers have raised significant questions. This work will be of broad interest to biologists in general.

eLife assessment

The authors used ribosome profiling in conjunction with standard biochemical approaches to investigate the role of eIF2A in translation initiation in yeast under optimal growth conditions or stress. The convincing data demonstrate that eIF2A does not play a substantial role in translation initiation in yeast. These important findings challenge the current view that eIF2A substitutes for eIF2 under stress and are thus anticipated to spur future investigation on the role(s) of eIF2A. Considering the broad scope of cellular functions attributed to eIF2A, this study should be of interest to a wide spectrum of biomedical researchers ranging from those studying mechanisms of translation regulation to virologists and cancer biologists.

eLife assessment

This important study proposes a new method for tracking neurons recorded with Neuropixel electrodes across days. The methods and the strength of the evidence are convincing, but the authors do not adequately address whether their approach can be generalized to other brain areas, species, behaviors, or tools. Overall, this method will be potentially of interest to many neuroscientists who want to study long-term activity changes of individual neurons in the brain.