eLife assessment

This study provides a methodological report on a modified adaptive sampling approach, multiple walker supervised molecular dynamics (mwSuMD), and its application to G protein-coupled receptors (GPCR), which are the most abundant membrane proteins and key targets for drugs. The mwSuMD approach assists in sampling complex binding processes, leading to some useful findings for GPCR activity, although results may be considered incomplete because the approach may have limited convergence to high-resolution structural data and is lacking other validation. The manuscript explores perhaps too many case studies at the expense of depth of description of methods, reference to existing computational literature, and deeper insight into GPCR activity.

eLife assessment

This important study, which presents novel data on variation in sperm whale communication, contributes to a richer understanding of the social transmission of vocal styles across neighbouring clans. The evidence is solid but could be further improved with some clarification of the specialized measurements and terms used, particularly for comparisons to other taxa. This research will be of interest for bioacoustics and animal communication specialists, particularly those working on social learning and culture.

eLife assessment

This important study highlights the role of SLAM-SAP signaling in shaping innate-like γδ T cell subsets, providing compelling evidence for the importance of SLAM-SAP in immune system regulation, and the potential implications of the findings for tumor surveillance and infectious disease management. The work will be of broad interest to immunologists.

eLife assessment

The study presents important findings on the role of MSI2-HOXA9 translocation in chronic myeloid leukemia. The authors provide convincing evidence supporting the role of this translocation in leukemogenesis by using elegant mouse modeling and in vitro mechanistic studies. Consistent with the reviews, the studies can be strengthened with further murine and cell line experiments.

eLife assessment

This study provides useful data substantiating a role of long noncoding RNAs in liver metabolism and organismal physiology. With murine knockout and knockin models, the authors invoke a previously unidentified role for the lncRNA Snhg3 in fatty liver. While certain findings are backed by solid evidence, other conclusions require more support and should be consolidated with existing paradigms in the field.

eLife assessment

This valuable study analyzes the role of the ciliary transition zone protein rpgrip1l in the development of the scoliotic phenotype in zebrafish. Through convincing proteomic and experimental validation in vivo, the authors demonstrated increased Annexin A2 expression in the brain and increased LCP1+ immune cell infiltration in scoliosis fish. These findings provide additional evidence for the previously proposed role of neuroinflammation in the development of idiopathic scoliosis in zebrafish.

eLife assessment

How misfolded proteins are segregated and cleared is a significant question in mechanistic cell biology, since clearance of these aggregates can protect against pathologies that may otherwise arise. The authors discover a cell cycle stage-dependent clearing mechanism that involves the ER chaperone BiP, the proteosome, and CDK inactivation, but is curiously independent of the APC. These are valuable and interesting new observations, but the evidence supporting these claims is incomplete, and needs to be strengthened and further validated.

eLife assessment

In this important study, Boudjema et al. use cell culture models and advanced microscopic imaging to provide detailed analyses of the cellular events underlying centriole amplification, apical migration, and assembly of hundreds of motile cilia in multi-ciliated cells. This largely descriptive work provides a better understanding of this process that is of interest to cell biologists studying centrioles and cilia. Most of the claims are supported by the data, but the study would benefit from additional analyses regarding the roles of microtubules, which are currently incomplete, and from text editing to improve accessibility and readability, especially for a wider audience.

eLife assessment

This work focuses on the role of Reactive Oxygen Species (ROS) signaling in cyst stem cells of the Drosophila testis. In particular, the authors suggest that ROS can act as signaling molecules between somatic and germ stem cells of the testis. The work is potentially useful, although the evidence that supports the authors' claims is incomplete.

eLife assessment

In their valuable study, Chen et al. investigate the neuronal role of HMMR, a microtubule-associated protein typically associated with cell division. Their findings indicate that HMMR is necessary for proper neuronal morphology and the generation of polymerizing microtubules within neurites, potentially by promoting the function of TPX2. This solid body of work is the first step in deciphering the influence of a mitotic microtubule-associated protein in organizing microtubules in neurons and will be of interest to the neurobiology and cytoskeleton fields.

eLife assessment

This work presents an important technological advance, in the form of a high throughput platform for Single Particle Tracking allowing us to measure millions of cells and thousands of compounds per day. Analysis of the diffusional behaviour of fluorescently-tagged targets permits the identification of, and differentiation between, small molecules that bind directly or affect the target indirectly. The methodology and metrics employed are compelling, leading to the identification of multiple compounds that effectively change the diffusive state of the estrogen receptor, the POC target of the study.

eLife assessment

This study presents a useful description of RNA in extracellular vesicles (EV-RNAs) and highlights the potential to develop biomarkers for the early detection of colorectal cancer (CRC) and precancerous adenoma (AA). The data were analysed using overall solid methodology and would benefit from further validation of predicted lncRNAs and biomarker validation at each stage of CRC/AA to evaluate the potential application to early detection of CRC and AA.

eLife assessment

The study presents a potentially useful approach to genetically modify cells to produce extracellular matrices with altered compositions. The evidence supporting the authors' conclusions regarding the chondrogenicity of lyophilized constructs is considered incomplete, as the study does not adequately demonstrate the formation of a histologically identifiable cartilaginous matrix. The study also lacks several significant details and does not have sufficient power to support the conclusions.

eLife assessment

This is a valuable study in which the authors provide an expression profile of the human blood fluke, Schistosoma mansoni. A strength of this solid study is in its inclusion of in situ hybridisation to validate the predictions of the transcript analysis.

eLife assessment

The manuscript presents valuable findings, using solid techniques and approaches, that shed additional light into how the canine distemper virus (CDV) hemagglutinin might engage cellular receptors and how that engagement impacts host tropism. The structural data and their analysis were thorough and well-presented. The HS-AFM data, which indicate that homodimers may dissociate into monomers - and thus have significant implications for the model of fusion triggering - are very exciting, but require further validation, perhaps by alternate approaches, to bolster the current molecular model of the CDV fusion triggering.

eLife assessment

This study investigates the associations of four ICD-related genes in bladder cancer with increased immune cell infiltration and more prolonged survival. The study is valuable because it identifies a risk-scoring model, showing a correlation between high-risk scores based on four ICD-related genes and weak anti-tumour immune function. However, the evidence supporting the association of these genes and immunotherapy response is incomplete.

eLife assessment

This is a mechanistic study showing the effect of combining inhibition of autophagy (through ULK1/2) and KRAS (using sotorasib) on KRAS mutant NSCLC making the study valuable to cancer biologists and more broadly in a clinical setting. The evidence generated by GEM mouse models and cell lines is solid but could be further strengthened by increasing the mouse cohort size. This study holds translational relevance beyond NSCLC to other indications that carry KRAS mutations.

eLife assessment

This is an important work and provides a significant advance in our understanding of mechanosensation in the epidermis. The evidence presented is solid, however, additional work such as testing whether the activation time can be shorter, addressing the mechanism underlying endoplasmic reticulum calcium release, and improving the clarity of writing and rigor of analysis would strengthen the study. This work will be of broad interest to neurobiologists, epithelial cell biologists, and mechanobiologists.

eLife assessment

This fundamental paper reports a new biosensor to study G protein-coupled receptor activation by the pituitary adenylyl cyclase-activating polypeptide (PACAP) in cell culture, ex vivo (mouse brain slices), and in vivo (zebrafish). Convincing data are presented that show the new sensor works, albeit at very high (non-physiological) concentrations of exogenous PACAP. The sensor has not yet been used to detect endogenously released PACAP, raising questions about whether the sensor can be used for its intended purpose. While further work must be pursued to achieve broad in vivo applications under physiological conditions, the new tool will be of interest to cell biologists, especially those studying the large GPCR family.

Evaluation statement (17 January 2024)

The study by Bassetto Jr. et al. presents an elegant and pioneering technique to rapidly manipulate membrane temperature by up to 10 ºC in less than 1.5 ms, thereby enabling high temporal resolution of the temperature dependence of ion channel currents. The approach combines the cut-open oocyte voltage clamp technique with laser illumination to heat the sub-membrane melanosome layer. Temperature is quantified from observed changes in membrane capacitance. Recordings of Kir1.1, TRPM8, and TRPV1 channels are used to validate the effectiveness of the technique. A limitation is that, in its current form, the technique can be used only on melanosome-containing Xenopus oocyte membranes.

Biophysics Colab recommends this study to scientists working on the temperature dependence of ion channels and other membrane proteins.

Biophysics Colab has evaluated this study as one that meets the following criteria: - Rigorous methodology - Transparent reporting - Appropriate interpretation

(This evaluation refers to the version of record for this work, which is linked to and has been revised from the original preprint following peer review.)

eLife assessment

This useful study investigates two secreted Mycobacterium tuberculosis proteins, ESAT-6 and CFP10, using biochemical assays, including a Biolayer Interferometry assay. Solid experimental evidence demonstrates that ESAT-6 forms a tight interaction with CFP10 as a heterodimer at neutral pH and that ESAT-6 also forms a homodimer at acidic pH. Additional, more definitive evidence is required to describe how these proteins disrupt the phagosomal membrane. While improved compared to a previous version, the revised manuscript did not address these concerns adequately.

eLife assessment

This study represents a fundamental contribution to our understanding of how gene expression levels are controlled in bacteria. Through a series of compelling and careful experiments, relying on a mutant that blocks DNA replication but permits growth, and using various methods, the authors reveal how genome concentration rapidly becomes limiting for growth when replication is inhibited. This work contributes to our understanding of the contributions and limiting roles of DNA, mRNA, and ribosomes for growth in bacteria, and will be of considerable interest within both systems biology and microbial physiology.

eLife assessment

This important study could potential provide insight into mechanisms for vaccine-mediated protection, although the evidence for live Leptospira contributing to protection against a pathogenic serovar is still incomplete. The work will be of interest to the scientists interested in host-pathogen interactions and leptospirosis.

eLife assessment

This valuable study reports single-nucleus multiomics-based profiling of transcriptome and chromatin accessibility of mouse XX and XY primordial germ cells (PGCs). Solid data generally support the main conclusions. However, data presentation and interpretation need improvement for clarity and accuracy. The study will be of interest to developmental and reproductive biologists, as well as andrologists.

eLife assessment

This important manuscript provides new insights into the biophysics of the SARS-CoV-2 nucleocapsid. The evidence, which relies on a convincing combination of genetic and biophysical data, nicely supports the conclusions.

eLife assessment

In this fundamental study, the authors use innovative fine-scale motion capture technologies to study visual vigilance with high-acuity vision, to estimate the visual fixation of free-feeding pigeons. The authors present convincing evidence for use of the fovea to inspect predator cues, the behavioral state influencing the latency for fovea use, and the use of the fovea decreasing the latency to escape of both the focal individual and other flock members. The work will be of broad interest to behavioral ecologists.

eLife assessment

This useful study aims to add fresh insights into the sharing of lymphoid and CDP (common DC precursor) lineage origin of plasmacytoid dendritic cells (pDCs). The evidence for a small subset of pDCs sharing its origin with B cell progenitors and depending on BCL11a expression is solid, although further functional characterization of the reported pDC subset would significantly enhance the significance of the study. The study will be of relevance to cellular immunologists interested in the ontogeny of plasmacytoid dendritic cells.

eLife assessment

This useful study identifies amino acid residues in the C. elegans RNA-binding protein NHL-2 that are required for RNA binding in vitro and NHL-2 function in vivo. The evidence in support of the authors' mechanistic model is currently incomplete, as data implicating specific NHL-2 amino acids in RNA binding per se in vivo are not presented. This manuscript will be of interest to scientists working in the area of gene regulation.

eLife assessment

This study presents a light-entrainable synthetic oscillator in bacteria, the optorepressilator. The authors develop a toolbox using optogenetics that makes the cellular oscillator easily controllable. This toolbox is valuable, contributing both to bioengineering and to the understanding of biological dynamical systems. The comparison with a mathematical model, population, and single-cell measurements demonstrate convincingly that the planned system was achieved and is suitable to control and study biological oscillators.

eLife assessment

This is a valuable contribution to the electric fish community, and to studies of active sensing, in that it provides evidence that a well-studied behavior (chirping) may serve in active sensing rather than communication. This is likely to stimulate follow-up behavioral and physiological studies to determine whether the active sensing component of the behavior is pre-eminent, or whether their major function is communication. For the most part, the evidence for increased chirping in more cluttered environments and the relationship between chirping and movement are convincing. However, the evidence used to argue that chirping does not vary with behavioral context is less so, and the arguments against a communicative function of chirps are not strong. The main conclusions are only supported by correlations and remain for now at the level of an interesting hypothesis to explore.

eLife assessment

The authors present an algorithm and workflow for the inference of developmental trajectories from single-cell data, including a mathematical approach to increase computational efficiency. While such efforts are in principle useful, the absence of benchmarking against synthetic data and a wide range of different single-cell data sets make this study incomplete. Based on what is presented, one can neither ultimately judge if this will be an advance over previous work nor whether the approach will be of general applicability.

eLife assessment

This important study introduces a biologically constrained model of telencephalic area of adult zebrafish to highlight the significance of precisely balanced memory networks in olfactory processing. The authors convincingly show that their model performs better in multiple situations (for e.g. in terms of network stability and shaping the geometry of representations), compared to traditional attractor networks and persistent activity. However the study lacks a mechanistic understanding of the results in terms of parameter sensitivity analysis. The work supports recent studies reporting functional E/I subnetworks in several sensory cortexes, and will be of interest to both theoretical and experimental neuroscientists studying network dynamics based on structured excitatory and inhibitory interactions.

eLife assessment

This important work presents a creative and thoughtful analysis of mouse foraging behavior and its dependence on body reference frame-based vs world reference frame-based cues. It convincingly demonstrates that a robust map capable of supporting taking novel shortcuts is learned based primarily on self-motion cues from a known starting location and this can be done in contexts where there is little reliance on distal visual landmarks; this may be a unique finding outside of the human literature. The discussion is rich with ideas about the role of the hippocampus in supporting the behavior that should be interesting to test in future analyses of brain recordings as mice perform the tasks considered by the study.

eLife assessment

This important study by Yogesh and Keller provides a set of results describing the response properties of cholinergic input and its functional impacts in the mouse visual cortex. They found that cholinergic inputs are elevated by locomotion in a binary manner regardless of locomotor speeds, and activation of cholinergic input differently modulated the activity of Later 2/3 and Layer 5 visual cortex neurons induced by bottom-up (visual stimuli) and top-down (visuomotor mismatch) inputs. The experiments are cutting-edge and well-executed, and the results are convincing.

eLife assessment

This important study has practical and theoretical implications for understanding rhythm perception and production in human cognition. The evidence for individual frequency preferences and a deterioration in frequency adaptation with age is convincing. These findings will inform existing models of rhythm perception and production, and the reported effects of age may have clinical implications.

eLife assessment

This magnetoencephalography study reports important new findings regarding the nature of memory reactivation during cued recall. It replicates previous work showing that such reactivation can be sequential or clustered, with sequential reactivation being more prevalent in low performers. It adds convincing evidence, even though based on limited amounts of data, that high memory performers tend to show simultaneous (i.e., clustered) reactivation, varying in strength with item distance in the learned graph structure. The study will be of interest to scientists studying memory replay.

eLife assessment

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

eLife assessment

In this manuscript, the authors have identified Rapamycin, a common pharmacological tool, thought to only bind to the mTOR kinase, as an off-target modulator of the ion channel TRPM8, the main cold sensor in mammals. This is a valuable study, that presents solid evidence for its claims. The NMR methods employed need to be better validated in order to become a tool for the community.

eLife assessment

This study presents valuable observations indicating that the excitability of cultured sympathetic motor neurons increases in neurons cultured from aged mice, and is inversely correlated with the amplitude of KCNQ currents. The alterations in membrane excitability are relevant for aging-related changes in neuronal membrane properties. While the study documents interesting changes in membrane excitability in cultured neurons with aging, the mechanisms underlying these changes are not clear and physiological relevance of the results to the intact circuits is incomplete.

eLife assessment

In this important paper, Blin and colleagues develop a high-throughput behavioral assay to test spontaneous swimming and olfactory preference in individual Mexican cavefish larvae. The authors present compelling evidence that the surface and cave morphs of the fish show different olfactory preferences and odor sensitivities and that individual fish show substantial variability in their spontaneous activity that is relevant for olfactory behaviour. The paper will be of interest to neurobiologists working on the evolution of behaviour, olfaction, and the individuality of behaviour.

eLife assessment

This study provides valuable insights and allows for hypothesis generation around diet-microbe-host interactions in alcohol use disorder. The strength of the evidence is convincing: the work is done in a rigorous manner and includes well-characterized and described human samples. Limitations include the cross-sectional study design, and the authors should clarify their experimental groups and definitions.

eLife assessment

Leveraging state-of-the-art experimental and analytical approaches, this valuable study characterizes the recruitment and activation of large populations of human motor units during slow isometric contractions in two lower limb muscles. Evidence for many claims is solid, however, the main claim that this study reveals rate coding of entire motoneuron pools requires additional data in more dynamic conditions.

eLife assessment

In this useful study, the authors tested a novel approach to eradicate the HIV reservoir by constructing a herpes simplex virus (HSV)-based therapeutic vaccine. The approach was tested in experimental infections of chronically SIV-infected, antiretroviral therapy (ART)-treated macaques with extent of rebound after ART interruption as a measure of the size of the HIV reservoir. While mean viremia at rebound was lower in the HSV vaccine-treated group, the evidence presented appear to be be incomplete because the group size was small and the viral load at rebound was highly variable.

eLife assessment

This important work by Veneditto and colleagues developed a new modeling approach, called a mixture-of-agent hidden Markov model (MoA-HMM), in which choice behaviors are modeled as transitions between discrete states defined by different weighting of several reinforcement learning and decision strategies. The authors apply this approach to their previous data collected from rats performing the two-step task, and show that this method provides better fits to the data than previous methods, and predicts fluctuations in neural and other behavioral data. The reviewers found this study to be overall convincing, and the method is of general interest to the field.

eLife assessment

This fundamental work demonstrates the importance of considering overlapping modes of functional organization (i.e. gradients) in the hippocampus, showing associations between with aging, dopaminergic receptor distribution and episodic memory. The evidence supporting the conclusions is solid, although some clarifications about testing procedures and a discussion of the limitations of the dopaminergic receptor mapping techniques employed should be provided along with analysis code. The work will be of broad interest to basic and clinical neuroscientists.

eLife assessment

This study offers valuable insight into the remarkable resistance of tardigrades to ionizing radiation by showing that radiation treatment induces a suite of DNA repair proteins and by identifying a strongly induced tardigrade-specific DNA-binding protein that can reduce the number of double-strand breaks in human U2OS cells. The evidence of upregulation of repair proteins is convincing, and the case for a role of the newly identified protein in repair can be strengthened as genetic tools for tardigrades become better developed. The results will interest the fields of DNA repair and radiobiology as well as tardigrade biologists.

eLife assessment

The manuscript presents a machine-learning method to predict protein hotspot residues. The validation is incomplete, along with the misinterpretation of the results with other current methods like FTMap.

eLife assessment

This is an important study characterizing the unique expression of mouse Schlemm's canal endothelial cells (SECs), which function in the aqueous humor outflow pathway of the eye. The work convincingly identifies novel biomarkers for SECs and molecular markers for inner wall and outer wall SECs, followed by targeted RNA and protein expression validation in mouse eyes. Gene networks and pathways were analyzed for their potential contribution to glaucoma pathogenesis.

eLife assessment

This study reports single-cell RNA sequencing results of lung adenocarcinoma, comparing 4 treatment-naive and 5 post-neoadjuvant chemotherpy tumor samples. Of interest is the delineation of two macrophage subtypes : Anti-mac cells (CD45+CD11b+CD86+) and Pro-mac cells (CD45+CD11b+ARG+), with the proportion of Pro-mac/pro-tumorigenic cells significantly increasing in LUAD tissues after neoadjuvant chemotherapy. In terms of significance, the findings might be useful but only if robust statistical comparisons (currently missing) can be provided. As it stands, the level of supportive evidence is inadequate.

eLife assessment

The paper uses published data and a proposed cell-based model to understand how growth and death mechanisms lead to the observed data. This work provides an important insight into the early stages of tumour development. From the work provided here, the results are solid, showing a thorough analysis. However, the work has not fully specified the model, which can lead to some questions around the model's suitability.

eLife assessment

This useful study reports on the impact of antibiotic pressure on the genomic stability of the mc2155 strain of Mycobacterium smegmatis, a model for Mycobacterium tuberculosis. The study concludes that exposure to antibiotics did not lead to the emergence of new adaptive mutations in laboratory settings, contradicting the prevailing theory of antibiotic resistance development through drug-induced microevolution. While the genomic analysis provided detailed insights into the stability of M. smegmatis following exposure to standard TB treatment antibiotics, the evidence presented for antibiotic pressure not contributing to the occurrence of new adaptive mutations is still incomplete.

eLife assessment

This paper presents a valuable optimization algorithm for determining the spatio-temporal organization of chromatin. The algorithm identifies the polymer model that best fits population averaged Hi-C data and makes predictions about the spatio-temoral organization of specific genomic loci such as the oncogenic Myc locus. While the algorithm will be of value to biologists and physicists working in the field of genome organization, the provided methodological details and evidence are incomplete to fully substantiate the conclusions. In particular, the following would be beneficial: analysis of single-cell data, the inclusion of loci beyond Myc, testing the dependence of results on the chosen parameters, providing more details on CTCF occupancy at loop anchors, and better substantiating the claim about predictions of single-cell heterogeneity.

eLife assessment

This valuable study presents a series of results aimed at uncovering the involvement of the endosomal sorting protein SNX4 in neurotransmitter release. While the evidence supporting the conclusions is solid, the molecular mechanisms remain unclear, and the study would significantly benefit from additional experiments to strengthen its findings. This paper will be of interest to cell biologists and neurobiologists.

eLife assessment

This valuable study assesses through simulations how several known features of local cortical circuits - interneuron subtypes, their specific targeting of dendritic compartments, and certain brain rhythms - together affect the integration of synaptic inputs by a pyramidal cell into a spiking output signal. Employing several carefully considered simulation setups they convincingly demonstrate that beta rhythms are best suited to modulate and control dendritic Ca-spikes while gamma rhythms affect their coupling to somatic spiking, or how basal inputs are directly integrated into somatic spikes. However, the baseline setup may be idealized for the generation of the events in question and it would be beneficial if the similarity to the in-vivo activity regime was demonstrated further. The results will be relevant for neuroscientists studying local circuits or developing more abstract theories at the systems level.

eLife assessment

This valuable paper presents convincing evidence that changing the constraint of how long to stop at an intermediate target significantly influences the degree of coarticulation of two sequential reaching movements, as well as their response to mechanical perturbations. Using an optimal-control framework, the authors offer a normative explanation of how both co-articulated and separated sequential movement can be understood as an optimal solution to the task requirements.

eLife assessment

This study provides important evidence that links acetylcholine responses in the sensory cortex to motor actions during perceptual tasks, rather than to rewards. The evidence for the association between acetylcholine responses and motor actions is solid, but does not demonstrate the causal link implied by the title and abstract. The manuscript would benefit from a more detailed description of results and methodologies. This study is of broad interest to the neuroscience field.

eLife assessment

This valuable study examines the role of a host in conditions that shift pathogenicity of opportunistic microbes. The use of single-cell microbial transcriptomics and metabolomics to demonstrate the host's effects on pathogen dynamics is interesting and convincing. However, the connection to host antimicrobial peptides driving these effects is incomplete and would benefit from additional evidence and improved explanation in the text. This paper has the potential to be of broad interest to those working in host-microbe (microbiome and pathogen) interactions.

eLife assessment

This valuable study explores the sequence characteristics and conservation of high-occupancy target loci, which are genomic regions bound by a multitude of transcription factors, at promoters and enhancers throughout the human genome. The computational analyses presented in this study are solid, although the evidence for some claims is inadequate. This study would be a helpful resource for researchers performing ChIP-seq based analyses of transcription factor binding.

eLife assessment

This important study addresses the challenge of antimicrobial resistance by targeting plasmid proteins that interfere with plasmid transfer as a novel strategy to limit the spread of antibiotic resistance genes. While the evidence presented is solid, the work would benefit from a clear integration of the approaches used and more thorough analyses to fully assess the effectiveness of this strategy. This study will interest those working on plasmid transfer and antimicrobial resistance.

eLife assessment

This important study presents new knowledge of the spermatogonial stem cell (SSC) niche in trans women after gender-affirming hormone therapy (GAHT). While the evidence supporting the claims is convincing, weaknesses identified by both reviewers should be addressed. The work will be of interest to researchers and clinicians working in the field of sexual medicine and andrology.

eLife assessment

This important work reports that genome-wide patterns of relaxed purifying selection on genes involved in male fertility may represent a response to the reduced sperm competition in the gorillas' mating system. However, the evidence supporting the conclusion is incomplete and needs to be strengthened. This work will be of interest to researchers working on evolution and reproductive biology.

eLife assessment

Using a set of animal models, this valuable paper shows tumor suppressive function of the non-core regions of RAG1/2 recombinases. The conclusions are supported by solid evidence.

eLife assessment

This valuable study reports on a series of artificial selection experiments for microbiomes that confer drought tolerance to rice plants. A major strength is the solid experimental design with multiple soils, which will likely guide others in designing their experiments, but the study has also shortcomings in that the rescuing effect is not benchmarked against healthy well-watered plants, the sterilized controls do not add much information, and the dispersal between inocula confounds the interpretation of the results. In addition, while the type of work presented here is a first step towards the eventual goal of plant microbiome engineering, that goal is still mainly an ambition. The abstract would benefit from this being made clear, and the presentation would overall benefit from more extensive consideration of recent developments in the field.

eLife assessment

This article is a valuable addition to the growing literature on the developmental patterning of insect wings. Using CRISPR mutagenesis and localization of mRNA, the authors present solid evidence that the transcription factor Mirror is necessary for specifying the morphological identity of the most posterior regions of butterfly wings. The manuscript would benefit from more careful use of terminology and appropriate citation of related Drosophila literature, and there are also some concerns about whether the phenotype represents transformation or loss which might be clarified through a closer look at ultrastructure. With a clearer presentation of terminology, this paper would be of general interest to developmental and evolutionary biologists.

eLife assessment

This valuable paper describes the stiffness of meiotic chromosomes in both oocytes and spermatocytes. The authors identify differences in stiffness between meiosis I and II chromosomes, as well as an age-dependent increase in stiffness in meiosis I (and meiosis II) chromosomes, results that are highly significant for the field of chromosome biology. The mechanisms underlying age-dependent changes in chromosome stiffness remain unclear, and the evidence to suggest that changes in stiffness are independent of cohesin, which is known to deteriorate with age, is incomplete.

eLife assessment

This useful paper explores a mathematical model of subsecond time perception, testing potential neural mechanisms behind the linear psychophysical law, Weber's law, and dopaminergic modulation of subjective durations. The model employed readout units to decode an interval. Nevertheless, the work is incomplete and presented as data-driven, but there is no analysis of empirical data.

eLife assessment

This study presents a useful strategy in which the authors devised a simple method to attenuate Candida albicans and deliver a live whole-cell vaccine in a mouse model of systemic candidiasis. The reviewers are not convinced about the completeness of the study: the strength of the evidence is incomplete and could be augmented with additional experiments to more fully characterize vaccine efficacy and host immune responses.

eLife assessment

This valuable study addresses the interpretation of patterns of synonymous and nonsynonymous diversity in microbial genomes. The authors present solid theoretical and computational evidence that adaptive mutations that revert the amino acids to an earlier state can significantly impact the observed ratios of synonymous and nonsynonymous mutations in human commensal bacteria. This paper will be of interest to microbiologists with a background in evolution.

eLife assessment

This important work identifies a p. aeruginosa strain and enzyme that can degrade 1-naphthylamine, a harmful industrial pollutant. Data resulting from in vivo and structural approaches are compelling, but additional mutagenesis would further test and establish the broad substrate specificity of NpaA1. With this additional data, this paper would be of high interest to biologists and enzymologists studying biodegradation of industrial pollutants.

eLife assessment

This valuable study offers new insight into the role of centrosome protein ninein in skeletal development through an analysis of the skeletal phenotype of ninein-deficient mice. While there is solid evidence supporting the conclusion that the absence of ninein leads to transient skeletal abnormalities and a lasting reduction in osteoclastogenesis, the evidence to substantiate the claim that enhanced ossification is attributed to reduced osteoclast formation/activity is insufficient. This work will be of interest to scientists in bone biology and skeletal development field.

eLife assessment

Using anchored phylogenomic analyses, this valuable study sheds new light on the evolutionary history of the plant diet of Belidae weevil beetles and their geographic distribution. Using convincing methodological approaches, the authors suggest a continuous association of certain belid lineages with Araucaria hosts, since the Mesozoic era. While the biogeographical analysis has weaknesses due to uncertainties in vicariance explanations, the study overall offers contributions to understanding the evolutionary dynamics of Belidae and provides novel insights into ancient community ecology.

eLife assessment

This paper provides useful information about how the ionome of Arabidopsis thaliana adapts to very high CO2-levels, backed up by solid evidence and carefully designed studies. The work will be of interest to anyone studying natural genetic variation as well as the response of plants to altered CO2 levels in the atmosphere.

eLife assessment

This important work identifies a previously uncharacterized capacity for songbird to recover vocal targets even without sensory experience. The evidence supporting this claim is convincing, with technically difficult and innovative experiments exploring goal-directed vocal plasticity in deafened birds. This work has broad relevance to the fields of vocal and motor learning.

eLife assessment

This study provides evidence that the quality of research in female-dominated fields of research is systematically undervalued by the research community. The authors' findings are based on analyses of data from a research assessment exercise in New Zealand and data on funding success rates in Australia, Canada, the European Union and the United Kingdom. This work is an important contribution to the discourse on gender biases in academia, underlining the pervasive influence of gender on whole fields of research, as well as on individual researchers. The evidence supporting the conclusions is solid, but the work would benefit from further explorations into the nuances of specific fields of fields of research.

eLife assessment

In this study, the authors developed a cell-based screening assay for the identification of small molecule inhibitors of nonsense-mediated decay (NMD). They used it to validate a novel small molecule SMG1 kinase inhibitor that inhibits NMD in cultured cells leading to the expression of neoantigens from NMD-targeted genes, and in vivo slows tumor growth of cells with a significant number of out-of-frame indel mutations. The conclusions are supported by convincing evidence, and the significance of this work consists in the development of a novel and very promising NMD inhibitor drug that acts as an inhibitor of the SMG1 NMD kinase and is suitable for use in animals. This is an important advance for the field, as previous NMD inhibitors were not specific, lacked efficacy, or were very toxic and hence not suitable for animal application.

eLife assessment

In this study, the authors present convincing evidence to demonstrate theta cycle skipping by individual neurons of the lateral septum, which they then relate to population coding of future trajectories encapsulated by theta cycles. This valuable finding furthers our understanding of how the septum conveys navigational information downstream.

eLife assessment

This study presents valuable findings on the potential role of a peptide typically associated with feeding in the control of a pituitary hormone, FSH, which is a critical regulator of reproductive physiology. The evidence supporting the main claims of the authors is thought-provoking but incomplete. In particular, the authors demonstrate that the peptide is sufficient to regulate FSH, but they have not established its necessity. The work will be of interest to reproductive biologists, especially those with an interest in the endocrine control of fertility.

eLife assessment

This important study provides a comprehensive analysis of ITP and its role as an anti-diuretic and metabolic hormone in Drosophila. The evidence supporting the conclusion is solid in general with combined genetic, comparative genomic approaches, classical physiological techniques, and biochemical assays. However, the evidence of direct binding between ITPa and Gyc76C and their physiological functions is incomplete. This work represents a contribution to the field of neuropeptides and neurohormones in insects and other animals.

eLife assessment

This important study investigates the structural organization of a series of diblock elastin-like polypeptide condensates. The methodology is highly compelling, as it combines multiscale simulations and fluorescence lifetime imaging microscopy experiments. The results increase our understanding of model biomolecular condensates.

eLife assessment:

This work describes an easily implemented method for measuring solid food intake in Drosophila, which is necessary for studying the consumption of experimentally challenging diets, such as high-fat foods, as well as their nutritional impacts on the organism. It is a valuable technical contribution with solid evidence supporting the conclusions, filling a significant gap in the field.

eLife assessment

This study reports some useful information on the mechanisms by which a high-fat diet induces arrhythmias in the model organism Drosophila. Specifically, the authors propose that adipokinetic hormone (Akh) secretion is increased with this diet, and through binding of Akh to its receptor on cardiac neurons, arrhythmia is induced. The presented data, however, incompletely support the conclusions, with a number of concerns identified, such as the need for editorial clarifications, issues with experimental design (including additional control experiments), and over or misinterpretation of some of the experimental data. Nonetheless, some of the data will be helpful to those who wish to extend the research to a more complex model system, such as the mouse.

eLife assessment

This fundamental study for the first time defines genetically the role of the Clock gene in basal metazoa, using the cnidarian Nematostella vectensis. With convincing evidence, the study provides insight into the early evolution of circadian clocks. Clock in this species is necessary for daily rhythms under constant conditions, but not under a rhythmic light/dark cycle, suggesting that the major role of the circadian oscillator in this species could be a stabilizing function under non-rhythmic environmental conditions.

eLife assessment

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

eLife assessment

This study addresses the effects of estrogen on the kisspeptin1 subset of neurons in the arcuate nucleus of the hypothalamus of female mice after ovaries were surgically removed. The authors repeat some of their prior work and provide new and interesting findings about the effects of estrogen on currents mediated by calcium and potassium channels, suggest a neurotransmitter "switch", and suggest Trpc5 regulates Kisspeptin 1 neuron excitability. While useful in its significance, there are concerns that the evidence for some conclusions is incomplete. This study will be of interest to endocrinologists and reproductive biologists.

eLife assessment

Unlocking the potential of molecular genetic tools (optogenetics, chemogenetics, sensors, etc.) for the study of systems neuroscience in nonhuman primates requires the development of effective regulatory elements for cell-type specific expression to facilitate circuit dissection. This study provides a valuable building block, by carefully characterizing the laminar expression profile of two viral vectors, one designed for general GABA+ergic neurons and the second for parvalbumin+ cell-type selective expression in the marmoset primary visual cortex. The authors provide solid evidence for the first enhancer S5E2 and incomplete evidence for the second one, h56D. This study contributes to our understanding of these tools but is limited by the understandably small number of animals used.

eLife assessment

This study presents an important contribution to cardiac arrhythmia research by demonstrating long noncoding RNA Dachshund homolog 1 (lncDACH1) tunes sodium channel functional expression and affects cardiac action potential conduction and rhythms. The evidence supporting the major claims are solid. The work will be of broad interest to cell biologists and cardiac electrophysiologists.

eLife assessment

This study provides an important cell atlas of the gill of the mussel Gigantidas platifrons using a single nucleus RNA-seq dataset, a resource for the community of scientists studying deep sea physiology and metabolism and intracellular host-symbiont relationships. The evidence supporting the conclusions is convincing with high-quality single-nucleus RNA-sequencing and transplant experiments. This work will be of broad relevance for scientists interested in host-symbiont relationships across ecosystems.

eLife assessment

In this important study, the authors describe a novel function for RAPSYN in bcr-abl fusion associated leukemia, presenting convincing evidence that RAPSYN stabilizes the oncogenic BCR-ABL fusion protein. Compared to an earlier version of the manuscript, the authors have added data using primary samples that strengthen the conclusions.

eLife assessment

The authors provide important insights into the pathogenesis of erectile dysfunction (ED) in patients with diabetes. The authors present compelling evidence, using single-cell transcriptomic analysis in both mouse and human cavernous tissues, to support their claims regarding the key roles of pericytes in diabetic ED. The identification of LBH as a potential pericyte-specific marker in both mouse and human tissues further strengthens their findings. This well-written manuscript offers novel and significant contributions to the field, identifying potential therapeutic targets for further investigation.

eLife assessment

The studies described here are useful; they are broadly applicable to all antibody discovery subfields but do not add significant improvement to techniques already published. The findings are incomplete with respect to the methodology since details that are crucial in order to repeat the experiment are lacking (such as a timestamp) and they do not take into account multiple recent papers that have tested similar strategies. These studies will be of interest to a specialized audience working on making antibodies to infectious agents.

eLife assessment

The authors present valuable findings on trends in hind limb morphology through the evolution of titanosaurian sauropod dinosaurs, the land animals that reached the most remarkable gigantic sizes. The solid results include the use of 3D geometric morphometrics to examine the femur, tibia, and fibula to provide new information on the evolution of this clade and on evolutionary trends between morphology and allometry. Further justification of the ontogenetic stages of the sampled individuals would help strengthen the manuscript's conclusions, and the inclusion of additional large-body mass taxa could provide expanded insights into the proposed trends.

eLife assessment

This fundamental work significantly advances our understanding of how FOG1 nuclear localization is regulated during erythropoiesis and megakaryopoiesis, including the role of EPO and MPL/TPO signaling in this process. The authors provide compelling evidence using both K562 and CD34+ cells that heat shock cognate B (HSCB) can promote the proteasomal degradation of TACC3 to regulate the nuclear localization of FOG1, and that this function is independent of its role in iron-sulfur cluster (ISC) biogenesis. Together these data will be of interest to the fields of hematopoiesis and cell biology.

eLife assessment

This useful work shows that the experimental application of serotonin to locust antennal lobes induces an increased feeding-related response to some odorants (even in food-satiated animals). To explain how the odorant-specific effects are seen despite similar consequences of 5-HT modulation on all projection neuronal types, the authors propose a simple quantitative model built around projection with different downstream connections. While they are consistent with the authors' conclusions, the current panel of experiments is incomplete and additional future work will be required to fully support the conclusions the authors currently draw from their observations.

eLife assessment

This important study builds on a previous publication (with partially overlapping authors), demonstrating that T. brucei has a continuous endomembrane system, which probably facilitates high rates of endocytosis. Using a range of cutting-edge approaches, the authors present compelling evidence that an actomyosin system, with the myosin TbMyo1 as the molecular motor, is localized close to the endosomal system in the bloodstream form (BSF) of Trypanosoma brucei. It shows convincingly that actin plays a role in the organization and integrity of the endosomal system, and that the trypanosome Myo1is an active motor that interacts with actin and transiently associates with endosomes, but a role of Myo1 in endomembrane function in vivo was not directly demonstrated. This work should be of interest to cell biologists and microbiologists working on the cytoskeleton, and unicellular eukaryotes.

eLife assessment

Following small molecule screens, this study provides convincing evidence that 7,8 dihydroxyflavone (DHF) is a competitive inhibitor of pyridoxal phosphatase. These results are important since they offer an alternative mechanism for the effects of 7,8 dihdroxyflavone in cognitive improvement in several mouse models. This paper is also significant due to the interest in the phosphatases and neurodegeneration fields.

eLife assessment

This study focuses on nuclear pore complex dysfunction in a mouse model of Alzheimer's disease related Aβ pathology. If future revisions can adequately respond to the reviewer comments, the findings may eventually be useful in supporting the idea that nuclear cytoplasmic transport defects occur prior to plaque deposition in this disease model and may be caused by Alzheimer's disease pathology. However, even after revision, the work suffers from overinterpretation of some of the data and remains incomplete in several respects.

eLife assessment

This valuable study reports a chemogenetic screen for resistance and sensitivity towards three compounds that inhibit cell cycle progression: camptothecin, colchicine, and palbociclib. Following up on the palbociclib results, the authors provide solid evidence that knockdown of the PRC2.1 complex, likely through increasing D-type cyclin expression, confers resistance to palbociclib. The generality of the results would be improved by demonstrating the effect of PRC2.1 on cyclin expression and cell cycle progression in more than one cell line.

eLife assessment

The authors explore ER stress signalling mediated by ATF6 using a genome-wide gene depletion screen. They find that the ER chaperone Calreticulin binds and directly represses ATF6; this proposed function for Calreticulin is intriguing and constitutes an important finding. The evidence presented is based on CHO genetic evidence and biochemical results and is convincing.

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 the evidence that nuclear condensates per se drive MET gene clustering is incomplete and would benefit from further experimental analyses. This paper will be of interest to molecular biologists working on chromatin and transcription, although its impact would be strengthened by revising the literature citations and including additional experimental work.

eLife assessment

Wounds are commonly infected, which can lead to delayed or poor wound healing, thereby significantly impacting morbidity and overall quality of life for patients. This manuscript uses single cell RNA sequencing to try to understand the impact of infection on various cell types during wound healing in a mouse model. The methodology is solid and the results provide a valuable 'atlas' of the cellular changes associated with infected and uninfected wounds which will be of interest to the field.

eLife assessment

The current manuscript re-examines an established claim in the literature that human PANX-1 is regulated by Src kinase phosphorylation at two tyrosine residues, Y199 and Y309. This issue is important for our understanding of Pannexin channel regulation. The authors present an extensive series of experiments that fail to detect PANX-1 phosphorylation at these sites. Although the authors' approach is more rigorous than the previous studies, this work relies primarily on negative results that are not unambiguously definitive; the work nonetheless provides a compelling reason for the field to reexamine conclusions drawn in earlier studies.

eLife assessment

The authors present an important study of a multi-cellular platform involving co-culturing of various hiPSC-derived hepatocyte like cells, cholangiocytes, stellate cells and macrophages to mimic the liver microenvironment. The aggregates are then treated with fatty acids and examined through transcriptomic and functional assays. The techniques and methodologically are sound, and the evidence supporting the conclusion is convincing, although more clinically relevant data demonstrating the effect of some potential pharmacological agents on the platform would serve to strengthen the study.

eLife assessment

The work by Lewis and co-workers presents important findings on the role of myosin structure/energetics on the molecular mechanisms of hibernation by comparing muscle samples from small and large hibernating mammals. The solid methodological approaches have revealed insights into the mechanisms of non-shivering thermogenesis and energy expenditure.

eLife assessment

This valuable study reports a potential connection between the seminal microbiome and sperm quality/male fertility. The data are generally convincing, but the statistical methods employed need further justification. This study will be of interest to clinicians and biomedical researchers who work on microbiome and male fertility.

eLife assessment

This study provides fundamental new knowledge into the role of reversible cysteine oxidation and reduction in protein kinase regulation. The data provide convincing evidence that intra-molecular disulfide bonds serve a repressive regulatory role in the Brain Selective Kinases (BRSK) 1 & 2; part of the as yet understudied 'dark kinome'. The findings will be of broad interest to biochemists, structural biologists, and those interested in the rational design and development of next-generation kinase inhibitors.

eLife assessment

In this interesting study, Drożdżyk and colleagues analyze the ability of placental CALHM orthologs to form stable complexes, identifying that CALHM2 and CALHM4 form heterooligomeric channels. The authors then determine cryo-EM structures of heterooligomeric CALHM2 and CALHM4 that reveal a distinct arrangement in which the two orthologs can interact, but preferentially segregate in the channel. This is an important study; the data provide compelling support for the interpretations and overall, the work is clearly described.

eLife assessment

In this valuable manuscript, Yeo et al. describe new methods for assessing the intracellular itinerary of Botulinum neurotoxin A (BoNT/A), a potent toxin used in clinical and cosmetic applications. The current manuscript challenges previously held views on how the catalytic portion of the toxin makes its way from the endocytic compartment to the cytosol, to meet its substrates. The approach taken is deemed innovative and the experiments are carefully performed, presenting solid evidence for some of the drawn conclusion; however, the conclusions one may draw from the experimental results are somewhat limited, as it is possible that the scope of their findings could be restricted to the specific neuron model and molecular tools that were used. This paper could be of interest to both cell biologists and physicians.

eLife assessment

This valuable paper describes innovative force measurements of the bending modulus of gliding cyanobacteria, along with measurements of the critical buckling length of the cells, which in combination lead to insight into how these cells produce the force necessary to move. Quantitative analysis convincingly shows that the propulsive force and resistive friction coefficient are strongly coupled, which supports propulsion based on adhesion forces rather than slime extrusion.

eLife assessment

This study investigates associations between retrotransposon element expression and methylation with age and inflammation, using multiple public datasets. The study is valuable because a systematic analysis of retrotransposon element expression during human aging ishas beenlacking. However, the data provided are incomplete due to the sole reliance on microarray expression data for the core analysis of the paper.

eLife assessment

This valuable paper characterizes a murine model for congenital cystic airway abnormalities (CPAM). In contrast to previous assumptions that only epithelial cells are involved in the formation of pulmonary cysts, the authors provide compelling new evidence that defective BMP signaling in lung mesenchymal cells can disrupt airway development. Knowing that proper BMP signaling in mesenchymal cells is required for normal cyst-free lungs could potentially pave the way to understanding and preventing CPAM in infants at risk for this common disorder, which can be fatal if untreated. The relevance of the murine model could be enhanced by further molecular and histological comparison with human cysts.

eLife assessment

This important study presents a novel pipeline for the large-scale genomic prediction of members of the non-ribosomal peptide group of pyoverdines based on a dataset from nearly 2000 Pseudomonas genomes. The advance presented in this study is largely based on solid evidence, although some main claims are only incompletely supported. This study on bacterial siderophores has broad theoretical and practical implications beyond a singular subfield.

eLife assessment

In this manuscript the authors present high-speed atomic force microscopy (HSAFM) to analyze real-time structural changes in actin filaments induced by cofilin binding. This important study enhances our understanding of actin dynamics which plays a crucial role in a broad spectrum of cellular activities. However, some technical questions remain, making the data interpretation incomplete.

eLife assessment

This manuscript reports important in vitro biochemical and in planta experiments to study the receptor activation mechanism of plant membrane receptor kinase complexes with non-catalytic intracellular kinase domains. Several lines of evidence convincingly show that one such putative pseudokinase, the immune receptor EFR achieves an active conformation following phosphorylation by a co-receptor kinase, and then in turn activates the co-receptor kinase allosterically to enable it to phosphorylate down-stream signaling components. This manuscript will be of interest to scientists focusing on cell signalling and allosteric regulation.

eLife assessment

This study provides an important finding that the local abundance of metabolites impacts the biology of the tumor microenvironment by utilizing kidney tumors from patients and adjacent normal tissues. The evidence supporting the claims of the authors is convincing. The work will of interest to the research community working on metabolism and kidney cancer especially.

eLife assessment

This study provides valuable evidence indicating that SynGap1 regulates the synaptic drive and membrane excitability of parvalbumin- and somatostatin-positive interneurons in the auditory cortex. Since haplo-insufficiency of SynGap1 has been linked to intellectual disabilities without a well-defined underlying cause, the central question of this study is timely. However, the support for the authors' conclusions is incomplete in general and some parts of the experimental evidence are inadequate. Specifically, the manuscript requires further work to properly evaluate the impact on synaptic currents, intrinsic excitability parameters, and morphological features.

eLife assessment

This study presents an important new technology for transdifferentiation of fibroblasts into muscle cells. The data and methods used for analysis were compelling. This study will have broad interest to cellular reprogramming biologists in particular as well as the general public.