Evaluation Summary:

This work presents a new model that leverages imaging and non-imaging data for the prediction of the survival of patients with early-stage NSCLC. The new model sought to demonstrate the roles of imaging and non-imaging features in determining high-risk nodes within the graph neural network, and the results have the potential of broad interest to clinicians within the field of cancer and have a high value towards clinical application.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewer remained anonymous to the authors.)

Evaluation Summary:

This manuscript presents the first molecular dynamics (MD) simulations of full-length membrane-bound Thyroid Stimulating Hormone Receptor (TSHR). The authors find that its linker region (LR) is disordered, contrasting previous models. While this is largely a solid study that would interest researchers working in computational modeling, thyroid hormone metabolism, and signaling, the rationale for the arbitrarily chosen starting model and unclear mechanistic relevance need to be clarified further.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Evaluation Summary:

This paper is of broad interest to clinicians focused on improving sepsis outcomes. The method developed by the authors can identify 10 common pathogens with species-specificity in 4 hours, thus significantly reducing the turnaround time compared to conventional diagnostic methods. Using their method to identify sepsis-causing pathogens early to guide antibiotic treatment, the authors demonstrate high clinical sensitivity and specificity, and some clinical benefit in a real-world scenario.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Evaluation Summary:

Chen et al. demonstrate a pro-survival role of the NRF2/DKK1 axis in mesenchymal stem cells. Furthermore, the authors provide evidence that targeting this pathway can enhance survival in response to liver failure in vivo. These data highlight a novel signaling pathway to enhance efficacy of MSCs in promoting regeneration.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Evaluation Summary:

Carboxysomes enable the efficient fixation of carbon dioxide in specific bacteria. Phase separation has been invoked as a mechanism that drives the formation of carboxysomes. The current work focuses on the biophysical principles of how one of two essential specific protein components enable spatial regulation over carboxysomes. This important work highlights the connection between oligomerization via specific molecular interactions and phase separation. The work is of interest to the areas of biochemistry and carbon dioxide fixation as well as phase separation.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #3 agreed to share their name with the authors.)

Evaluation Summary:

Drosophila ovarian follicle cells have been utilized as a model system to study organogenesis and epithelial tumorigenesis. The analysis of single-cell transcriptomes of follicle cells now shows that transcriptionally distinct cell populations emerge shortly after induction of loss of polarity. Strengths of the work include the use of advanced single cell omics and imaging analyses to identify cell types and factors playing a role the disruption of polarity and the implications of this work for epithelial cancers. The authors' claims are generally well supported by the data and analyses. Weaknesses include the lack of high magnification images and need to clarify motivation for the study and highlight the biology rather than technical advances in the results section. Overall, this work is viewed as an important contribution to cell biologists who work on the epithelial morphogenesis or tumorigenesis.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1, Reviewer #2 and Reviewer #3 agreed to share their name with the authors.)

Evaluation Summary:

This manuscript addresses G protein-coupled receptor signaling and proposes an additional site on Beta-arrestin2 (arrestin 3) as being responsible, in significant part, for the downregulation and likely onward signalling from endosomes of a range of GPCRs. The cell biology appears to be thoroughly carried out and data presented in a statistically appropriate manner. With some textual changes and minor experimental clarification of the route taken and molecules involved, this work will be of broad interest.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #3 agreed to share their name with the authors.)

Evaluation Summary:

The authors use high spatial resolution MEG in humans to link two important components (time - transient bursts, space - waves) of neural sensorimotor dynamics by investigating how transient beta bursts propagate in the brain. The authors find two directions of propagating waves during beta bursts. The work links two fundamental aspects of neural dynamics which may yield new insights into the origins of sensorimotor behavior, with wide appeal to neuroscientists and clinicians. The reviewers considered the methodological work largely sound, although concerns were raised by the reviewers to what extent the travelling waves correspond to underlying neural activity or reflect the generative nature of field potentials.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #3 agreed to share their name with the authors.)

Evaluation Summary:

This paper will be of interest to researchers studying meniscus homeostasis and knee osteoarthritis. It uncovers distinct subtypes of cell populations in inner and outer part of human meniscus using single-cell RNA sequencing. In particular, this work further identifies how alterations in meniscal cell populations may contribute to inflammation and osteoarthritis and thus serves as a resource paper for the field.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #2 agreed to share their name with the authors.)

Evaluation Summary:

This manuscript reports the development of a proteo-genomic screening methodology to identify protein-protein interactions between secreted proteins and their cell surface receptors. The authors use a CRISPRa-based approach to overexpress membrane proteins in cells and then use magnetic cell sorting to identify receptors that bind candidate ligands. This approach leads to the identification of several novel interaction pairs that are validated biochemically, including receptor tyrosine phosphatase ligands and other interactions with implications for immune system function. The work is of interest to a wide variety of fields including biochemistry and signaling.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Evaluation Summary:

The authors provide a summary of single and double mutants in five self-cleaving ribozymes using next-generation sequencing. They dissect their data in terms of epistasis effects, which provides a new angle to understanding ribozyme function. In principle, this allows conclusions to be drawn on bases involved in pairs and in catalysis that have the potential to be of use to the field, although there is also a series of technical weaknesses that should be addressed.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 and Reviewer #2 agreed to share their name with the authors.)

Evaluation Summary:

Identification of transcriptional phenotypes driven by TBI across meningeal immune cell subsets and the effect of aging on these responses is an important and not well-defined area in the field. Multiple complementary and high-end approaches are taken to demonstrate the long-lasting effects that TBI drives in the brain and support the main findings of the manuscript. This manuscript will be of interest to readers in the field(s) of neuroimmunology, aging, and traumatic brain injury.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #2 agreed to share their name with the authors.)

Evaluation Summary:

Menjivar et al. identify a previously unrecognized role of myeloid cell Arginase1 (Arg1) activity in shaping the anti-tumor immune response in pancreatic ductal adenocarcinoma (PDAC). The proposed therapeutic combination is a new approach for pancreatic cancer, with an enhanced response to immune therapy upon arginase inhibition.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 agreed to share their name with the authors.)

Evaluation Summary:

The authors investigate what type and degree of information (either absolute, relative, or a weighted combination of both) is used by bumblebees when retrieving the value of an item. There is recent evidence in humans and birds that suggests that these organisms use a combination of absolute memories and remembering of subjective ranking in these tasks. The authors conclude that bumblebees indeed use remembered ranking, but that they seem not to be able to retain (or at least utilise) absolute property information for very long. The absence of relevant work in invertebrates would make this study a potentially valuable addition to the scientific literature.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #3 agreed to share their name with the authors.)

Evaluation Summary:

Li et al. use biochemical binding analysis to explore the role of Rabphilin 3A in dense-core vesicle exocytosis in neuroendocrine PC12 cells and in an in vitro SNARE assembly assay. They propose that the Rph3A binding to SNAP25 pre-structures the protein to efficiently assemble with Syntaxin and VAMP2, and thus, promoting the vesicle docking and priming process. This work will be of interest to scientists studying the molecular basis of synaptic vesicle release.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Evaluation Summary:

Iron acquisition is an essential problem for microbial growth and survival. Host defense mechanisms generally reduce iron availability and microbes often find themselves in iron poor environments. This study provides new insights into how the fungal pathogen Candida albicans obtains iron during infection.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 agreed to share their name with the authors.)

Evaluation Summary:

This manuscript will be of interest to readers in the field of microbiology, particularly those interested in bacterial interactions, secretion systems, and stress responses. It identifies the molecules and mechanisms that explain a competitive interaction between two soil-dwelling bacterial species. The data support most of the conclusions of the manuscript, but some controls are lacking and some of the interpretations are not fully justified by the experiments shown.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Evaluation Summary:

This manuscript reports the CryoEM structure of OmcZ cytochrome nanowires of Geobacter sulfurreducens, the third cytochrome nanowire of Geobacter to be structurally resolved. OmcZ differs structurally from these previously determined nanowire structures, showing a different heme chain configuration. Based on these and other differences the authors speculate about the evolutionary origin of these nanowires and the mechanism of long-range electron transport. This manuscript is an important contribution to the field of electron transfer and will be of interest to everyone working in electron transfer and filament formation and interested in their evolution.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 agreed to share their name with the authors.)

Evaluation Summary:

This article seeks to address a key question in protein biophysics: are the amino acid positions (and mutations) that influence allostery conserved across homologs of a protein family? Or is allostery implemented by a distinct set of residues that varies amongst homologs? To address this question, the authors follow an innovative approach that combines deep mutational scanning with machine learning. Significant revisions are required to clarify whether the conclusions of the study are well-supported by the data. The work is potentially highly relevant to protein engineers and biophysicists.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Evaluation Summary:

This paper is of interest to organismal biologists and evolutionary scientists who study cognitive and behavioral sex differences including those with interests in the evolution of complex spatial behaviors. Using intensive field monitoring and experimentally induced navigational challenges, the authors examine two different hypotheses for sex differences in spatial ability in three species of poison frog. A rich and complex story emerges, including from the provision of evidence that is consistent with (but not necessarily yet definitively or exclusively in support of) the hypothesis that androgens may inadvertently affect spatial ability.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #2 agreed to share their name with the authors.)

Evaluation Summary:

This manuscript examines the importance of PKA-dependent mTORC1 activation for the weight-loss effects of liraglutide. The work has the potential to provide important insights, but at present is deemed preliminary as it lacks details on the mouse model and control data and needs a more in-depth analysis of the metabolic phenotype.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #2 and Reviewer #3 agreed to share their name with the authors.)

Evaluation Summary:

This paper is of broad interest to biologists and climate modelers that study the impact of environmental stress (especially multiple stressors) on marine life. The authors show that exposure to low pH (ocean acidification) decreases the ability of two mussel species to survive freezing stress. The authors measure multiple biochemical parameters to try and identify the mechanisms underlying the change in freeze tolerance, but future work will be needed to resolve the underlying mechanism in detail.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Evaluation Summary:

This paper describes the use of three well-established mathematical models of cervical cancer to estimate the impact of COVID-19 related-delays in screening access on cervical cancer incidence and delays in diagnosis. Consistent with previous work and the known biology of cervical cancers, the findings that short delays have relatively small effects on population-level cervical cancer risk are reassuring overall, but the impact of screening interval and screening test performance suggest that existing disparities related to screening access may be exacerbated. These results should be useful for policy makers in planning responses to future pandemics or other sources of sudden restriction of screening availability.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 agreed to share their name with the authors.)

Evaluation Summary:

This paper proposes a computational model that combines biologically detailed elements with more simplified components to provide a comprehensive model of synaptic plasticity. It includes the stochastic character of many of the biophysical processes and introduces a new way to readout the plasticity cascade. It is evaluated against impressively many published experimental studies of hippocampal plasticity. The paper should be of interest not only to computational neuroscience but also to the synaptic neuroscience community but will benefit from a clearer description of assumptions and weaknesses, and a clearer separation of the essential elements in this model from the less critical elements.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 agreed to share their name with the authors.)

Evaluation Summary:

This manuscript, of interest to those studying the evolution of immunity, investigates the evolutionary history of a recently described herbivore-associated molecular pattern (HAMP) receptor, INR, which perceives the caterpillar-derived peptide HAMP, In11. The authors compare INR homologs to identify evolutionarily conserved residues and use chimeric fusion proteins to investigate specificity. The findings presented are valuable and supported by convincing experiments and analysis.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 agreed to share their name with the authors.)

Evaluation Summary:

This paper will be very interesting to the large class of neuroscientists who study functional roles of glycoprotein hormone receptors in the central nervous system. It provides detailed tissue-selective gene and receptor distributions of the three anterior pituitary hormones, and thus likely facilitates further relevant studies by other scientists.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1, Reviewer #2 and Reviewer #3 agreed to share their name with the authors.)

Evaluation Summary:

This manuscript compares COVID-19 mortality during the pre-Omicron and Omicron emergence periods in several countries and finds evidence suggesting the Omicron variant was associated with lower mortality than previous dominant variants. This paper will be of interest to infectious disease scientists both for its content and its methods, as it validates that population-level variant frequency can be a good proxy for individual-level variant data to derive insights on variant biology with population data.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #3 agreed to share their name with the authors.)

Evaluation Summary:

The findings of the paper are of interest to scientists studying the learning of abstract representations. It provides insights into how feedforward networks evolve during a process of learning to map stimuli onto abstract classes via gradient descent. The results are appealing and the analyses thorough. As well, the paper makes some experimental predictions. It could benefit from a deeper discussion on how the findings may generalize to biologically more realistic networks and tasks.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 agreed to share their name with the authors.)

Evaluation Summary:

The early differentiation of germ cells, those that will form egg and sperm, is a critical and nearly universal step in animal development. This paper reveals new layers of molecular and cellular regulation that control this process in the fly, and as such be of broad interest to cell and developmental biologists, especially those interested in critical cell fate decisions. The paper contains a wealth of experimental data demonstrating that processes generally thought to be restricted to somatic cells alter the differentiation of germ cells, but provides only limited functional interpretation of the observed phenotypes.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Evaluation Summary:

This manuscript is of broad interest to neuroscientists studying mechanisms regulating synapse formation and maintenance. Following up on the previous work by the authors on trans-synaptic signaling complexes involving neurexins and cerebellins, this study shows that the basic framework of the complexes operates broadly across different synapses in the brain albeit with subtle differences. The experiments are carefully executed, while some key conclusions could be better supported by additional data.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Evaluation Summary:

The manuscript will be of broad interest to readers in the fields of biochemistry, structural, molecular, and evolutionary biology. It outlines a systematic approach in characterizing nuclear receptor ligands based on the conformational ensemble of the receptor, further exploring the idea that perturbation of the ensemble orchestrates function. The results from the combined use of experiments and simulation are promising, suggesting that the change in the ensemble is responsible for function.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #3 agreed to share their name with the authors.)

Evaluation Summary:

This paper investigates scenarios in which the environment changes during the course of a decision, and shows that optimal behavior can be highly complex. It will be of broad interest to researchers in psychology, behavioural economics, and neuroscience interested in decision-making in real-world tasks. It also awaits detailed empirical testing.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #3 agreed to share their name with the authors.)

Evaluation Summary:

A murine genetic platform reducing fibroblast expression shows normal background indicators of cardiac structure and contractile function. Yet it shows a reduced functional compromise, on ischemic or hypertrophic challenge. This suggests its value for studies of the effect of fibrosis following normal or pathological change.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 agreed to share their name with the authors.)

Evaluation Summary:

This paper develops evolutionary simulations to identify the type of molecular networks that can give rise to size control. We now know a lot about the functional consequences and underlying molecular biology of different cell size control strategies, but comparatively less about which factors select for particular mechanisms. The authors address this point in an evolutionary framework. They show that the evolution of a specific cell size control mechanism is dependent on the cell cycle structure. The paper will interest researchers in development, evolution, and physics of biological systems.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 and Reviewer #2 agreed to share their name with the authors.)

COVID-19 vaccine tracker and landscape. (2022, April 22). https://www.who.int/publications/m/item/draft-landscape-of-covid-19-candidate-vaccines

Evaluation Summary:

This paper addresses the mechanism of entrapment of DNA in the cohesin SMC complex. Through a series of biochemical studies, the paper convincingly demonstrates that DNA enters cohesin rings through the hinge and SMC3/SCC1 interfaces. How such entrapment is regulated is important for different biological activities including sister chromatid cohesion and the formation of DNA loops. The paper will be of interest to researchers in SMC biology, DNA recombination and 3D genome organization.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #2 agreed to share their name with the authors.)

Evaluation Summary:

Adult zebra finch song is highly stereotyped, and it is driven by correspondingly stereotyped neural sequences in premotor cortical nucleus HVC. By imaging HVC activity in juvenile birds isolated from social contact with tutors, the authors discover that stereotyped HVC sequences can exist even without exposure to tutor song. Interestingly, after tutoring, existing sequences in the HVC of isolate birds transitioned from being uncoupled to vocal output to highly coupled to newly copied tutor syllables. Together, these data provide a fascinating glimpse into mechanistic foundations of how nature and nurture work together to a learned motor sequence.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #2 agreed to share their name with the authors.)

Evaluation Summary:

The complete metamorphosis of the higher insects is one of the most fascinating and complex processes in nature: The discrepancy in form and function between larvae, pupa, and adult insects is breathtaking, begging the question of how these forms and functions can so seamlessly follow each other. For the highest-order brain centre of the insects, the mushroom body, the authors provide a masterpiece analysis of this process at the cellular level. Given the breadth and depth of the data that the authors present, the current study will serve as a reference for the field of developmental neuroscience for many years to come; this study is eagerly awaited in the field. Perhaps ever more importantly, the insights into the relationship between evolutionary development and individual development at the cellular level might have a profound and lasting conceptual impact on life and natural sciences.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #3 agreed to share their name with the authors.)

Evaluation Summary:

This study builds on previous observations of arginine depletion in the pancreatic tumor microenvironment, with the goal of developing and using a cell culture medium (TIFM) that better recapitulates nutrient levels in the TME. With this system, the authors identify arginine biosynthesis as an adaptation of pancreatic cancer cells to arginine starvation. This work reinforces a timely message that builds upon the push for optimizing and reformulating cell culture media, so as to improve fidelity, and better recapitulation of physiological/pathophysiological cellular behavior. The latter is in turn critical for translational and therapeutic applications. The work will be of interest to tumor biologists.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 and Reviewer #2 agreed to share their names with the authors.)

Evaluation Summary:

The research presented in this manuscript is focused on testing the role of peroxiredoxin (Prdx5) and heterogeneous nuclear ribonucleoprotein K (hnRNPK) in bone biology and osteoporosis. Using cell-base and animal models, as well as various experimental methodologies the authors demonstrated that Prdx5 is upregulated during osteogenesis but suppressed during osteoclastogenesis. This novel function Prdx5 was found to be associated with binding and regulation of hnRNPK which controls the expression of genes involved in osteoclastogenesis, such as osteocalcin (Ocn).

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #2 agreed to share their name with the authors.)

Evaluation Summary:

This paper provides insight into a potentially new genetically defined subset of prostate tumors driven by concurrent loss of two tumor suppressor genes. This study both validates previous findings and provides new data that is compelling overall. With some additional statistical and biochemical evidence to support the conclusions, the work would be of interest to cancer biologists studying molecular mechanisms of prostate cancer.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #3 agreed to share their name with the authors.)

Evaluation Summary:

The authors identify a novel developmental role for the beta-adrenergic system in the regulation of mammalian cardiac regenerative capacity. Using genetic and pharmacological loss-of-function approaches, the authors identify a link between Yap and β-adrenergic receptor blockade. The conditional genetic loss-of-function studies are a particular strength of the manuscript and provide strong support for the Gas/Yap-dependent nature of the cardiomyocyte proliferative response to beta adrenergic blockade. Given the widespread use of beta blockers in the clinical management of heart failure, the findings are potentially very important. However, further evidence is required to substantiate the induction of bona fide cardiomyocyte proliferation and cardiac regeneration and clarify the associated mechanisms.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 agreed to share their name with the authors.)

Evaluation Summary:

This work is a bioinformatic analysis of HML-2-like proviruses found in the genomes of Rhesus Macaques, which convincingly argues that an HML-2 provirus underwent an ancient recombination event with a HERV-K (HML-8) related virus. The authors also provide data to suggest that the recombinant retrovirus may have acquired a distinct mechanism for the regulation of expression of spliced and unspliced transcripts. This paper should be of broad interest to virologists as it uses molecular 'fossil-like' evidence contained in the genomes of modern pirates to document the generation of what could be considered a previously undescribed retrovirus species, through recombination.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 and Reviewer #2 agreed to share their name with the authors.)

Evaluation Summary:

This paper is an extensive analysis of the underlying basis of desiccation resistance in 50 Drosophila species from diverse habitats. The work suggests that the longer methyl-branched alkanes (mbCHC) of the cuticular hydrocarbons are critical for this resistance. The study, which informs on the evolution of desiccation resistance in flies, is well done, although the main hypothesis is currently only partially supported by coating experiments, which presently lack controls and would be greatly strengthened by "replacement" experiments to add mbCHCs to flies without CHCs. The work is of relevance to evolutionary biologists in general.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Evaluation Summary:

This is an important paper that addresses a key mechanism that underlies the canonical computation of direction selectivity in the retina. By using fluorescence imaging of glutamate release from excitatory interneurons combined with a computational model of dendritic integration, the authors make a convincing case that the kinetics of glutamate release contributes to the direction-selectivity of individual neural processes in retinal neurons. This work will appeal to visual neuroscientists as well as cellular physiologists interested in dendritic computations.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #3 agreed to share their name with the authors.)

Evaluation Summary:

In this manuscript, of interest to the fields of animal immunity and epigenetics, the authors investigate the crosstalk between PML Nuclear Bodies and HIRA, a member of the H3.3 histone chaperone complex, during inflammatory stress. This study raises interesting perspectives on how availability of HIRA could be regulated by PML Nuclear Bodies for histone deposition onto interferon-stimulated genes, which in turn, could be relevant for immune-response mediated gene regulation.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Evaluation Summary:

Synaptic plasticity can take place on the presynaptic and/or postsynaptic sites, and these two sites of plasticity are known to involve distinct mechanisms. Using a combined approach of physiology, Drosophila genetics, and behaviour, this study provides evidence that postsynaptic mechanisms underlie plasticity for olfactory learning. This complements the field knowledge that olfactory associative learning largely relies on the presynaptic mechanism in mushroom body neurons. The paper also emphasizes the similarities in learning and memory mechanisms between vertebrates and invertebrates.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 agreed to share their name with the authors.)

Evaluation Summary:

The paper provides fundamental information through the identification of an E3 ligase and kinase/phosphatase regulatory machinery that regulates the inner nuclear membrane protein SUN2 using a GFP-based assay. The data reveal a model involving extraction of ubiquitylation of SUN2 from the membrane by p97, which is an important contribution to the field. Although the biochemical evidence is solid on the GFP-tagged SUN2 protein, one question is the extent to which this pathway works on endogenous SUN2 and the extent to which this is a quality control mechanism for turnover of unassembled SUN2 or whether it acts on the fully assembled complex.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #3 agreed to share their name with the authors.)

Evaluation Summary:

This is a very fundamental study that challenges the paradigm that histones H3 and H4 are imported to the nucleus primarily as heterodimers. Instead this study provides compelling evidence that H3 and H4 are imported by importin 5 as monomers and dimerize on chaperones in the nucleus. The work is of relevance to colleagues studying nuclear import and epigenetic regulation.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1, Reviewer #2 and Reviewer #3 agreed to share their name with the authors.)

Evaluation Summary:

The authors show that MiR-27a affects osteoclast-mediated bone resorption but not osteoblast-mediated bone formation during skeletal remodeling. Through gene profiling and bioinformatics study authors also identify the specific target of miR-27a in the osteoclast gene. MiR-27a exerts its effects on osteoclast differentiation through modulation of P62. This paper is of interest to scientists within the field of bone biology. The manuscript data analysis and conclusion are clear and directly supporting the previous known findings.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Evaluation Summary:

This study used 2017-2018 Afrobarometer surveys of more than 45,000 individuals to examine the association between the ownership of mobile phones and proximity to a health clinic in 33 African countries. Findings show that about 40% of people own smartphones and those who live closer to health clinics are more likely to own a mobile phone. This manuscript will be of interest to all people who are involved in the design and implementation of mHealth interventions in Africa.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 and Reviewer #2 agreed to share their names with the authors.)

Evaluation Summary:

Regulation of NAD and its intermediary metabolites is of critical importance in axon degeneration and in neurodegenerative disease. In mammals, the SARM1 NADase has been shown to be a metabolic sensor activated by an increase in the NMN/NAD+ ratio and SARM1 activation then leads to catastrophic energetic collapse and axon degeneration in disease and injury. This manuscript clarifies the role of NMN in activating the axon degeneration trigger dSARM in Drosophila. The authors analyze the signaling role of NMN, a NAD precursor metabolite involved in injury-induced axon degeneration, by overexpressing NMN-D, a prokaryotic enzyme that consumes NMN, using a stabilized version allowing for prolonged NMN depletion, and find that it is strongly protective in several in vivo injury paradigms in flies. This paper will be of interest to those in the neurodegeneration/axon injury field in general as an extensive set of optimized reagents is presented, confirming the crucial role of for exploring NAD-related axon degenerative pathways, and providing tools for neuroscientists to use Drosophila as a model for neurodegenerative research.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #2 agreed to share their name with the authors.)

Evaluation Summary:

This work will be of interest to behavioral neuroscientists with a focus on social behavior. The interrogation of the transcriptional signature of pair-bonding, in both short and long-term, is unique and made possible with the use of the monogamous vole. That there is a "degrading" of the transcriptome of pair bonding following separation is evident but there is a gap in understanding how the gene expression changes relate to behavior.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 agreed to share their name with the authors.)

Evaluation Summary:

This study presents an in-depth analyses of carbon oxidation state and hydration state of proteomes in different taxa and environmental settings, which contributes to our understanding of how microbial communities are shaped by their surroundings. The study has merit, but there also some technical weaknesses.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 agreed to share their name with the authors.)

Evaluation Summary:

Deposition of hyperphosphorylated misfolded tau is a hallmark of many neurodegenerative diseases, but the exact mechanisms by which misfolded tau spreads to adjacent areas of the brain are not known. In this manuscript, which will be of broad interest to cell biologists and neuroscientists, the authors suggest that tau fibrils that translocate directly through the cell membrane induce aggregation of cytosolic tau. While the results appear stunning, there are alternative explanations to the authors' hypothesis that require further investigation.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Evaluation Summary:

Vignogna et al. used yeast genetics, experimental evolution and biochemistry to investigate human congenital disorders of glycosylation, often caused by mutations in PMM2. They took advantage of the observation that the budding yeast gene SEC53 is almost identical to human PMM2, and used experimental evolution to find interactors of SEC53/PMM2. Mutations in genes corresponding to other human CDG genes, including PGM1, were overrepresented. The mechanisms of how reduced pgm1 activity could compensate for defects of sec53 are not yet clear.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #2 and Reviewer #3 agreed to share their name with the authors.)

Evaluation Summary:

The authors of this study characterize human Fip1, an important component of the 3' end processing machinery. They use X-ray crystallography to determine the molecular basis of the interactions between Fip1 and CPSF30 (at a 2:1 stoichiometry) and between Fip1 and CstF77 (at a 2:2 stoichiometry). Together with biochemical assays, they suggest that Fip1 may be central to regulating transitions with CPSF. The work will of relevance to colleagues interested in transcription and RNA processing.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #3 agreed to share their name with the authors.)

Evaluation Summary:

This is an in-depth and rigorous analysis of transcriptomic changes in myogenic cells lacking dystrophin. Studies are made in both a mouse model and human subjects. the paper bears on possible roles of such alterations in pathogenesis of Duchenne muscular dystrophy. They draw attention to new therapeutic interventions for this condition.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Evaluation Summary:

Individual cells may act in response to stimuli or in a self-organized fashion. The relative weight of these two modes determines in the end to which degree cells or rather organs/organisms carry function. This study reports an example of very complex self-organization of actin waves as the coexistence of slowly moving broad waves of high F-actin concentration and rapidly propagating planar F-actin pulses. The paper is interesting for everybody interested in conceptual questions like signalling versus self-organization, in cellular morpho-dynamics and theory of dynamic patterns.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Evaluation Summary:

This work is of interest to neuroscientists and medical professionals involved in the study of Alzheimer's disease and related neurodegenerative conditions. The findings provide important information about how potential network-based structural and metabolic imaging biomarkers are associated with memory performance during distinct disease stages, in line with previous hypothetical biomarker models. The study is conceptually and methodologically sound, although some aspects of the analysis and reporting of the results could be further clarified.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #2 agreed to share their name with the authors.)

Evaluation Summary:

Barber et al present a manuscript discussing predictive factors for chemotherapy efficacy in head and neck squamous cancer (HNSCC). The paper is well written, and its style/formatting are optimal. The baseline signature moderately predicted outcome, and the data after one cycle further improved the algorithm, though this decreases its utility as a pure predictive tool. It is interesting that a subpopulation of monocytes, a subset of white peripheral cells long suspected to correlate with outcomes in HNSCC was one of the key drivers of the algorithm. However the overall impact in the field of this work seems limited by a number of factors, including that the authors focused on immune cell subpopulations and exosomes, which narrows the scope (no cytokines or other biomarkers were included); the signatures were not prospectively validated on an independent cohort; the algorithm was developed around a first-line therapy that is no longer considered to be the standard of care for HNSCC; and, while most of the conclusions are supported by the data, some of the caveats (such as the lack of a validation cohort, key in predictive biomarker development), are not addressed.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Evaluation Summary:

The study is overall well-planned and the amount of data presented by the authors is impressive. The work nicely incorporates animal-level physiology (echocardiography data), tests for known canonical markers of hypertrophy, and then delves into an unbiased analysis of the transcriptome and proteome of LV tissue in bulk. The techniques and analyses in the study are adequately executed and within the realm of expertise of the Lakatta laboratory. This study is a necessary and crucial first step to extensively phenotype this mouse line and generate hypotheses for further work.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 agreed to share their name with the authors.)

Evaluation Summary:

Park et al.'s work provides insight into the infection processes of the human pathogen Coxiella burnetii with unprecedented detail. Their time course of cellular infection reveals the timing of key events and detects a previously unrecognized membrane structure. This work will shed new insight into the infection process of this pathogen allowing new targets for the treatment of infection with Coxiella.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #2 agreed to share their name with the authors.)

Evaluation Summary:

In this paper, the authors show that autobiographical memory recall is related to a specific biophysical property of the parahippocampal cingulum bundle, the so-called MR g-ratio. This paper will be of interest to neuroscientists studying associations between brain structure and cognitive processes. The data support the main conclusions of the paper. However, it is unclear how reliable the results are and whether the findings would generalize to situations beyond the specific one studied.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Evaluation Summary:

This study seeks to develop the use of a FRET-based sensor for the formation of the folded 'interacting heads motif' structure for cardiac myosin, which is thought by some to represent a super-relaxed state with lower basal ATPase activity. This study offers some evidence that there is a relationship between the super-relaxed state and the 'interacting heads motif' structure, and that a specific dilated cardiomyopathy mutant in this myosin stabilizes the 'interacting heads motif' conformation. This paper will be of interest to muscle and cardiovascular biologists as it provides important insights into the correlation of structural and functional states of motor proteins in the context of cardiac muscle. The data qualitatively support this correlation and suggest a new mode of action of disease-causing mutations that lead to impaired contractile function.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #2 agreed to share their name with the authors.)

Evaluation Summary:

This study by Krug et al. uses the turquoise killifish, an emerging model for biomedical research, to generate a valuable live-imaging platform. Initially, the authors generate a transparent killifish they named Klara. Specifically, using optimized CRISPR approaches, they simultaneously inactivate three genes that are required for the formation of primary pigment cells in fish (melanophores, iridophores, xanthophores) and next, to monitor cell-cycle arrest and cellular senescence, they generate a cdkn1a-GFP reporter line using HDR-mediated integration. The paper would benefit from a further description of the HDR approach, the genetic models, and improved figures. Together, this platform will be an extremely valuable resource with broad application, including for aging research, physiology, toxicology, and regeneration.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1, Reviewer #2 and Reviewer #3 agreed to share their name with the authors.)

Evaluation Summary:

This pre-registration study by Kerrén et al. used a proactive interference task in combination with MEG recordings on humans to test predictions of a previous computational model postulating that neural representations of competing memories are associated with varied phases of the hippocampus theta-band rhythm. Their results largely confirmed the hypothesis and suggest that reactivations of target and competitor memories indeed occur at different phases of theta oscillations, which is further related to the intrusion effect in behavior.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #2 agreed to share their name with the authors.)

Evaluation Summary:

Using an elegant combination of cutting-edge techniques, the authors show that in the neuromuscular junction of the nematode C. elegans two different classes of voltage-activated calcium channels differentially trigger exocytosis of distinct pools of synaptic vesicles, one docked to the active zone and a second one localized more distant from the active zone. These findings will be of broad interest to neuroscientists interested in the mechanisms of calcium-mediated release of neurotransmitters at chemical synapses.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1, Reviewer #2 and Reviewer #3 agreed to share their name with the authors.)

Evaluation Summary:

The authors describe a newly developed software, ProteInfer, that analyses protein sequences to predict their functions. It is based on a single convolutional neural network scan for all known domains in parallel. This software provides a convincing approach for all computational scientists as well as experimentalists working near the interface of machine learning and molecular biology.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #2 agreed to share their name with the authors.)

Evaluation Summary:

The authors aim to tackle a fundamental question with their study: whether there is a direct age-associated increase of transcriptional noise. To investigate this question, they develop tools to analyze single-cell sequencing data from mouse and human aging datasets. Ultimately, application of their novel tool (Scallop) suggests that transcriptional noise does not change with age, changes in transcriptional noise can be attributed to other sources such as subtle shifts in cell identity. This study is in principle of broad interest, but it currently lacks a definitive demonstration of the robustness of Scallop. Systematic testing of this new package would ultimately strengthen the key conclusion of the work and give additional users more confidence when using the tool to estimate expression noise.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Evaluation Summary:

In addition to providing extensive proteomics profiling datasets. this manuscript is fundamental that sheds light on the importance of appropriate experimental design for mouse disease model which have been overlooked so far. The results look quite solid based on the proper methodology. This type of work is extremely valuable to many biomedical scientists in the field for conducting reproducible research especially in the preclinical studies and properly interpreting the results.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #3 agreed to share their name with the authors.)

Evaluation Summary:

This paper will be of interest to scientists within the field of neuromuscular disorders and has potential clinical relevance. It reveals a novel targeted strategy to improve the pathophysiology of children with neonatal brachial plexus injury. The key claims of the manuscript are well supported by the data, and the approaches used are thoughtful and rigorous.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 agreed to share their name with the authors.)

Evaluation Summary:

This is a paper that will be of particular interest to neuroscientists with a focus on food intake and neural responses to food ingestion. This paper provides new insights into how the body responds to weight loss and helps identify those that may not be successful.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Evaluation Summary:

The authors use theoretical models to examine the joint evolution of different cheating strategies: selfish cheating (not contributing to a common good), and manipulative cheating (inducing a competitor to preferentially provide benefits to the cheat). The models seem well formulated and the results robust. That said, improvements could be made to the presentation to clarify the assumptions and wider applicability of the model. An improved article would provide a better understanding of the mechanisms behind cheating, which would be of interest to readers working on the evolution of cooperation, potentially opening up new directions for theoretical and empirical work.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Evaluation Summary:

This work has potential value for researchers in several areas of cognitive and systems neuroscience. Range adaptation is a widespread property in neuronal circuits, and a network mechanism that relates neuronal adaptation to behavioral outputs is a valuable addition to the literature. However, limitations in the current framing and analyses leave some uncertainty about the interpretation of the results and their broader applicability.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Evaluation Summary:

This manuscript tackles the timely and interesting research question of whether meningeal lymphatic drainage is required for the control of brain infection with Toxoplasma gondii. It contains a sophisticated experimental approach using cutting-edge methods, it has an easy-to-follow narrative, and comes up with an interesting albeit negative finding which the authors even tried to explain by an additional set of experiments. Although there are some limitations and weaknesses of the paper in its present form it will certainly contribute to the growing body of literature on how the once "immune-privileged" CNS is protected against environmental challenges.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #2 agreed to share their name with the authors.)

Evaluation Summary:

This manuscript shows that mutations in the gene encoding an enhancer chromatin-modifying enzyme MLL3 cooperate with Myc overexpression to drive hepatocellular carcinoma in mouse models. The authors identify Cyclin Dependent Kinase Inhibitor 2A (Cdkn2a) as a critical direct target gene of MLL3. Overall, the manuscript makes a compelling case that MLL3 is a hepatocellular carcinoma tumor suppressor that directly binds and activates the Cdkn2a locus. This study provides important insights for cancer biologists and those interested in specific epigenetic mechanisms that regulate liver cancer development. Editorial and some experimental suggestions were made to strengthen the work.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 and Reviewer #2 agreed to share their name with the authors.)

Evaluation Summary:

By performing homeostatic longitudinal IgH repertoire analysis of human memory B cells and plasma cells, authors draw two major unique conclusions; first, a high degree of clonal persistence in individual memory B cell subsets with inter individual convergence in memory B and plasma cells; second, reactivation of persisting memory B cells with new rounds of affinity maturation during proliferation and differentiation into plasma cells. These conclusions provide a significant insight into how human memory B and plasma cells are generated in a homeostatic condition.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #2 agreed to share their name with the authors.)

Evaluation Summary:

Keine et al study the role of the RhoGTPase Rac1 in neurotransmitter release by ablating this protein at an age when synapses are in an almost mature stage. They describe an increase in synaptic strength, which they interpret as an increase in release probability or fusogenicity of synaptic vesicles. They also describe subtle effects in the timing of release, which point towards a mild defect in positional priming. The study delivers important information on the role of Rac1.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #2 agreed to share their name with the authors.)

Evaluation Summary:

This study develops a resource allocation model for E. coli growing under steady-state conditions. The model describes both growth rate and yield and has been subjected to validation by comparison with a compiled data set. The manuscript addresses an important problem of interest to a wide range of investigators. At the same time, the authors would need to explore different assumptions for the housekeeping proteome fraction (phi_q) to ensure the model is robust.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Evaluation Summary:

The current study examined in detail the role of oxytocin neurons in the hypothalamus in regulating food intake. The current study extends our understanding of the role of this peptide in regulating complex behaviors.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Evaluation Summary:

Hu and colleagues describe the discovery and characterization of a new class of reversible palmitoylation (PLM) binding site TEAD inhibitors. X-ray co-crystallographic analysis reveals that the ligand class, identified from a screen of 30,000 small molecules, binds to a new site within the auto-PLM site. The TM2 lead compound inhibits the growth of NF2-deficient cell lines. The discovery has the potential to significantly impact the design and development of new effective TEAD inhibitors. Some clarification or additional data are required to support and justify some of the authors' claims regarding the molecular significance of this new class of inhibitors.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Evaluation Summary:

Recent studies of the brainstem locus coeruleus (LC) noradrenaline system have demonstrated a partially modular organization in which specific classes of neurons can serve distinct functions or exhibit module-specific co-activity. However, how noradrenaline cell classes function in a modular way is not clear. The authors have accomplished a technical feat by recording up to eight LC neurons at once using ex-vivo, multi-patch recordings. In doing so, two empirically-derived classes of LC neurons were identified and the analysis of electrical coupling between these neurons established some principles of local circuit communication occurring preferentially within the defined cell classes.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 agreed to share their name with the authors.)

Evaluation Summary:

This manuscript is of interest to individuals working on genome stability and B lymphocyte development. Using knockouts for the genes encoding the structure-selective endonucleases GEN1 and MUS81 in mice, the authors show that the absence of both proteins is incompatible with embryonic development, with selective loss in mature B-cells inhibiting germinal center formation. This is the first study of these enzymes in an organismic context and in primary cells, revealing insight into the in vivo consequences of loss of MUS81 and GEN1 functions not previously accessible through studies in cultured cells.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 agreed to share their name with the authors.)

Evaluation Summary:

This paper explores the use of 2D high-resolution template-matching (2DTM) to locate and discriminate highly similar macromolecules within cryo-EM images of focused ion beam-milled cells. It demonstrates that differences in the 2DTM signal-to-noise ratios for located targets against multiple search templates can effectively segregate a mixed population of similar structures, as well as present a formal analysis strategy for probabilistic assignment of species within the mixed population. Because the identification of distinct structural states of macromolecular complexes inside the cell is a fundamental problem in 3D visual proteomics, this paper will be of broad interest to both structural and cell biologists.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 and Reviewer #3 agreed to share their name with the authors.)

Evaluation Summary:

The notion of transcription factors as composed of interchangeable parts where DNA binding activity can be separated from activation activity has been a dominant paradigm in molecular biology for decades. However, recent evidence suggests that activation domains may contribute to binding specificity as well. This paper describes the use of single-molecule imaging of endogenously tagged transcription factors to dissect how transcription factors move in the nucleus and how these dynamics are related to functional protein domains. These results will be of interest to the transcription and gene regulation fields, but the conclusions require additional experimental support.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #3 agreed to share their name with the authors.)

Evaluation Summary:

The authors describe their work on an atlas of associations between polygenic scores for 129 different traits representing a variety of quantitative phenotypes and diseases, and a large set of metabolites measured in up to 83,000 participants in the UK Biobank. These associations are all available via a public browser, and may be used to identify candidate intermediate phenotypes, as well as potential biomarkers of disease.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #2 and Reviewer #3 agreed to share their name with the authors.)

Evaluation Summary:

This study investigates the potential role of kin selection in driving social behaviours among siblings in wild mountain gorillas. Using an impressive dataset of 14 years for 157 individuals the authors find some evidence for kin recognition in guiding biases for affiliative and aggressive behaviours. However, the results of the current study will be more convincing if a number of major concerns with the analysis can be addressed.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Evaluation Summary:

This paper will be of broad interest to clinicians and scientists in the area, providing clinical trial data on how the efficacy of monoclonal antibodies targeting SARS-CoV-2 varies according to the variant of concern. The clinical outcome data were consistent with previously reported in vitro data, which are being used to inform the clinical use of monoclonal antibodies. However, as the trial was stopped early, conclusions regarding the efficacy and safety of the individual monoclonal antibodies are limited.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #3 agreed to share their name with the authors.)

Evaluation Summary:

The origin of virulence in pathogenic microbes is not understood for many microbial species. The concept of 'accidental virulence' was proposed as a mechanism by which a microbe could acquire the capacity for virulence through interaction with other microbial species, such as amoeba. This paper adds an important new dimension to that concept by showing that the capacity for virulence can emerge from abiotic interactions, such as adherence to plastic.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 agreed to share their name with the authors.)

Evaluation Summary:

The work by Volante et al. studied a new plasmid partition system, in which the authors discovered that four or more contiguous ParS sequence repeats are required to assemble a stable partitioning ParAB complex and to activate the ParA ATPase. The work reveals a new plasmid partitioning mechanism in which the mechanic property of DNA and its interaction with the partition complex may drive the directional movement of the plasmid.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Evaluation Summary:

In this interesting study the authors combined innovative object-based conflict assays with optogenetic silencing to probe the role of the perirhinal cortex in motivational conflict. The manuscript is well-written and the approach was adequate. The findings provide new insight into how conflicting motivation is processed and would benefit from additional analysis and experimental investigation to more conclusively support the interpretations.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #2 and Reviewer #3 agreed to share their name with the authors.)

Evaluation Summary:

In this manuscript, the authors identify enhancer-associated (e)RNAs that are specifically associated with esophageal adenocarcinoma. Based on combining the data with analyses of patient gene expression data and epigenetic data from cell lines, they conclude that eRNAs are markers of enhancers relevant to the transition from Barrett's esophagus to cancer. This work provides new insights into the epigenetic alterations that occur in cancer progression, and it will be of interest to the cancer and epigenetics fields.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #3 agreed to share their name with the authors.)

Evaluation Summary:

This paper describes results obtained from multi-cellular imaging of CA1 cells using large-field-of-view miniscopes in rats performing a shock avoidance task. By exploiting behavioral (barriers) and pharmacological (scopolamine) manipulations the authors explore cell remapping dynamics during aversive learning. This work will be of interest to the neuroscience community by setting new methodological standards and providing data for across-species comparisons.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 and Reviewer 3 agreed to share their name with the authors.)

Evaluation Summary:

The current paper is of interest to cell biologists studying ciliogenesis and specifically vertebrate photoreceptors, which are specialized cilia. The study shows that mutations in the small GTP binding protein ARL3 known to cause dominant inherited retinal dystrophies in humans result in ARL3 hyperactivity, disrupting the normal ciliary gradient of ARL3 activity and leading to altered retinal development. The authors demonstrate restored normal nuclear distribution by overexpression of ARL3 effectors, suggesting that the active mutants disrupt nuclear migration, at least in part, by sequestering ARL3 effectors. Overall, the experiments are properly controlled, executed, and analyzed and involve a series of extensive biochemical analyses complemented with in vivo phenotypic assessment. The development of a method to analyze snapshots of the interaction between ARL3 and its interactors is also a strength of the paper, however, significant concerns remain regarding links between nuclear migration failure and ciliogenesis in the outer segment, and alternative possibilities that could explain the phenotype of the ARL3 Y90C mutant with respect to its sequestration of the GEF ARL13B. Addressing these major concerns would improve the manuscript and could have considerable impact on the field.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 agreed to share their name with the authors.)

Evaluation Summary:

The authors show the utility of an AAV-based approach in non-human primates to develop an improved model of Huntington's disease. They have presented a very thorough, carefully executed, body of work that will be of benefit to a range of researchers studying HD or developing therapies for HD. While this extends the work from an earlier paper (that presented the tools used to induce phenotypes) the results presented are new, relevant, and important to the community.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Evaluation Summary:

In this work, the authors test a multivalent vaccine design they term Mos-tri-RBD, consisting of three linked spike receptor binding domains, one based on Omicron sub-lineage BA.1 and the others with different SARS-CoV-2 variant mutations. Immunization with this construct either as a prime or booster vaccine resulted in better neutralization of the Omicron and Beta variants relative to the same design, but with the ancestral receptor binding domain, and supports the notion that vaccination with variant sequences may broaden the neutralization capacity of vaccines against divergent variants.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #2 agreed to share their name with the authors.)

Evaluation Summary

This study investigates the question of whether distinct brain areas differentially encode time during the learning of a simple motor timing task. The key novel result is that early in training the dynamics of the medial prefrontal cortex (mPFC) provides the best code for time, but later in training, the basal ganglia and in particular, the striatum provides a better code. In addition, the study shows that inactivation of mPFC produces a delayed learning effect, while inactivation of the striatum after learning led to impaired performance. The observation that temporal coding and the necessity of brain area for task performance transfers from medial prefrontal cortex to the striatum during learning is an intriguing observation for our understanding of the neural mechanisms underlying temporal processing in sensorimotor control.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 agreed to share their name with the authors.)

Evaluation Summary:

In this manuscript, the authors explore the circuit mechanism underlying mating-induced change of odor preference in Drosophila. Olfactory cues during mating induce a long-lasting increase in attraction to polyamines in female flies. The authors use a combination of neurogenetics, imaging, and behaviour to identify elements of the mushroom body and lateral horn circuitry involved in this behaviour. The importance of mushroom body plasticity in female postmating changes highlights a novel pathway for these changes and reveals the variety of mechanisms by which the brain can encode experience and adapt behavior. This paper will be of interest to scientists within the field of reproductive behaviors and neuroscience of internal states.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 agreed to share their name with the authors.)

Evaluation Summary:

This study uses media-based conversion of stem cell cultures towards to investigate how cell cycle regulation affects the transition of cell populations between pluripotent and differentiated states. Through a detailed analysis of cell cycle properties in different primed subpopulations, under a range of growth conditions, the authors propose that both the maintenance of pluripotency as well as the conversion towards a more differentiated state is influenced by selective shortening of the cell cycle in different primed subpopulations. By using new reporter systems and long-term imaging, this study thus sheds new light on the old question of whether extracellular signals control differentiation in cell populations through selection or induction.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Evaluation Summary:

Prior work has linked posterior urethral valves (PUV), a common cause of end stage renal disease in children, with chromosomal abnormalities and rare copy number variants, but the genetic causes of PUV remain incompletely defined. In this study, the authors have used diverse ancestry whole-genome sequencing association studies to identify two novel genes and an enrichment of rare duplications and inversions affecting candidate cis-regulatory elements as possible causes of this rare condition, illustrating the potential for this approach to other rare conditions.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #3 agreed to share their name with the authors.)

Evaluation Summary:

This manuscript reports a new method for high-throughput analysis of C. elegans feeding behaviour that overcomes shortcomings of existing methods. It is a useful technique that will be interesting for scientists studying feeding dynamics in worms.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #2 agreed to share their name with the authors.)

Evaluation Summary:

This manuscript describes cellular and developmental defects at late embryonic stages during Wolbachia-induced cytoplasmic incompatibility (CI), which occurs when male insects harboring the endosymbiont bacteria Wolbachia fertilize eggs of uninfected females, triggering embryonic lethality, usually at the first nuclear division. This work presents evidence that the mechanism of late embryonic defects is independent from the ones responsible for early embryonic defects. The experiments are technically superb, and the strength of evidence provided is compelling, including beautiful single-embryo PCR analyses and convincing light microscopy. While the overall significance might be limited, the knowledge will be useful to those in the fields of cytoplasmic incompatibilities and insect embryo development.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 and Reviewer #2 agreed to share their names with the authors.)”

Evaluation Summary:

This manuscript, contains fundamental findings that substantially advance understanding of an important research question, mostly uses appropriate and validated methodology in line with the current state-of-the-art, with good support for the claims, and the message of the manuscript will have a profound and lasting influence on neuroscience. In essence, the manuscript reports that dopamine converts spike-timing-dependent synaptic depression into potentiation that requires cAMP/PKA second messenger cascade and protein synthesis. The mechanism enables a separate synaptic input to induce heterosynaptic potentiation in previously primed synapses, which is shown in a network model to have desirable computational properties. The significance of the findings is threefold: First, it is the longest-lasting synaptic eligibility trace identified so far; second, the mechanism enables memory linking between temporally separate events; and third, it indicates a novel function of postsynaptic reactivation events. In addition, the finding may inspire new reinforcement learning algorithms in machine learning.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Evaluation Summary:

This work will be of interest to the field of researchers that generate human stem cell-derived kidney organoids to model genetic kidney diseases. It describes a novel and crucial role of the protein CEP83 in mesoderm patterning, which further determines whether kidney tissues can form correctly. Using cutting-edge technologies the authors provide strong data, which support the key claims of this manuscript. This work is of high impact due to the relevance of CEP83 mutations in human kidney disease.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 agreed to share their name with the authors.)

Evaluation Summary:

This manuscript describes de novo dominant toxic mutations in CRMP1 in 3 probands with a shared neurodevelopmental phenotype. The authors show that the mutations lead to reduced protein production from recombinant expression and that the mutations correlate with shorter neurites in cultured cells. This is the first report of mutations in CRMP1 in humans, encoding a cytoskeletal regulator protein. The results could have implications for physicians, geneticists, neurodevelopmental scientists, and cell biologists.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 agreed to share their name with the authors.)

Evaluation Summary:

The study is of interest to researchers in the field of cell biology, especially mechanosensing. The work identifies a new context to evaluate the activity of MSL proteins in mechanosensing by identifying two novel suppressors of MSL10 as components of the ER-PM contact sites (EPCS). The work has significance for both the plant and the animal science community providing the basics for various avenues of further research in the area of mechanobiology.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 and Reviewer #2 agreed to share their name with the authors.)

Evaluation Summary:

This manuscript tackles the important question of what proteins regulate asymmetrical cell division in Mycobacteria. This will be of interest to all individuals interested in bacterial physiology. The data are sound, but some of the conclusions need to be tempered or bolstered, in relation to the models proposed.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Evaluation Summary:

This manuscript is an important body of work that addresses the role of the integrated stress response (ISR) and the role of the GCN2 protein kinase in prostate cancer. The studies comprehensively elucidate how GCN2 and amino acid transporters and uptake promote prostate cancer proliferation, as well as the therapeutic potential of inhibiting this pathway. This work, therefore, provides insights for both identification of new mechanisms and experimental therapeutics in prostate cancer.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #2 agreed to share their name with the authors.)

Evaluation Summary:

Fluid flows in networks are ubiquitous, and in many living systems the networks are not static but instead can rearrange over time. Using vascular networks formed by the slime mold Physarum polycephalum, Marcbach et al. demonstrate that there is a time delay between the change in the flow and the change in the network geometry. They present a mechanical model of vein-radius adaptation leveraging the negative normal stress response of the actin cytoskeletal network lining the vein walls. More generally, the authors make use of the unique advantage of this simple model vascular system to connect the local shear rate to the network reorganisation and how it depends on its architecture. There are features to their work that are new to the literature and that can be impactful in advancing the field.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Evaluation Summary:

This manuscript examines the role of transposable element (TE) expression and the transcription factor FOXO on aging of Drosophila melanogaster. Increased TE expression in aged organisms compared to their younger counterparts has been observed in several animals, including Drosophila. Here, the authors show that artificially inducing transcription of a specific TE can reduce fly lifespan and exacerbate some aging phenotypes-paraquat resistance and rhythmicity. The authors also argue that the detrimental effects of increased TE expression can be rescued by FOXO expression, although this is less convincing.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)