Evaluation Summary:

This manuscript reports the cryo-EM structure of HOPS, a heterohexameric tether that participates in the fusion of late endosomes, autophagosomes, and AP-3 vesicles with lysosomes. The structure will be of interest to a wide range of cell biologists and structural biologists who study membrane traffic. However, while the structural data are elegant, the functional interpretations need further 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 #1 agreed to share their name with the authors.)

Evaluation Summary:

Xing and colleagues present a cryoEM structure of the protein phosphatase 2A (PP2A)-B56 holoenzyme in complex with protein phosphatase methyltransferase-1 (PME-1). The structure reveals that PME-1 blocks the substrate binding site of PP2A by inserting an unstructured loop. This unexpected inhibitory mechanism is also coupled to a large conformation change in the PP2A-B56 holoenzyme and PME-1. Combined with biochemical and cellular assays, the authors suggest how PME-1 can regulate p53-mediated DNA damage responses via inhibiting PP2A. This manuscript will be of importance for structural biologists as well as colleagues in the p53 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 will be of interest to researchers in the phage-microbial host interaction field. Notably, the interplay between bacteria and their viral predators has regained broad interest in recent years given the discovery of numerous innate immunity-like phage defense systems. The identification of phage-mediated counter-defense strategies is therefore not only of prime importance for our basic understanding of predator-prey arms races but also for medical applications such as phage therapy.

(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 is of interest for a wide range of readers who study the biology of lipid modifying enzymes, especially as it relates to interfacial reaction kinetics in biological membranes. This study aimed to obtain detailed biochemical insights into the mutual relationship between PI(4,5)P2 lipids and their kinase PIP5K, which engage in an exciting pattern-forming reaction on membranes. The authors find cooperative recruitment of PIP5K to the membrane, oligomerization-enhanced catalytic efficiency and indications of allosteric regulation. Although of very high interest and featuring mostly convincing data, there are concerns about the interpretation of whether the observed phenomenon is dimer specific or related to higher-order oligomerization. In addition, there are inconsistencies in the data presentation.

(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 reported crystal structure of nearly-full-length cGMP-dependent protein kinase β (PGK1β) provides new insights into how the activity of the PKG catalytic domain is held in check by intramolecular interactions between both the upstream regulatory cGMP-binding domains and the autoinhibitory segment and the catalytic domain, and how cGMP binding to the cGMP-binding domains can relieve these inhibitory constraints leading to an increase in catalytic activity. The structure of the activating PKGIα R177Q CNB-A domain mutant, which resembles a cGMP-bound wild type CNB-A domain, provides a nice explanation for how this point mutation activates PKG Iα and leads to the development of the TAAD (Thoracic Aortic Aneurysms and Dissections) syndrome. The work will be of specific interest to the cyclic nucleotide community, and to the broader signaling community 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. Reviewer #1 and Reviewer #2 agreed to share their names with the authors.)

Evaluation Summary:

This article applies a systems biology approach to understand the mechanism of action of 3-chloropiperidines (a class of anticancer drugs) in cancer cells and evaluate their sensitivity to drugs. It integrates transcriptomic and open-chromatin data and utilizes sound statistical frameworks for building a sensitivity model. The author's methodology can be applied to early-stage drug discovery. This paper will be of interest to the large class of people who tried to understand how omics data will help drug discovery. It sets a new framework to integrate transcriptome and chromatin accessibility data to identify the key mechanisms of action and provide potential disease targets, which will help speed up the early phases of drug discovery.

(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. All three reviewers agreed to share their names with the authors.)

Evaluation Summary:

This study is of interest to the readership interested in the different cell types present in the mouse adult ovary and shows how cellular states change during the four phases of the estrous cycle. This is a valuable resource for 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:

The authors first develop a new flexible and robust method to detect deviations from Mendelian inheritance in genomic data from gametes. The authors then apply this method to study deviations from Mendelian inheritance in human sperm data, but find no evidence for it. Even though this is a negative result, and overall the results are expected based on previous studies. the reviewers agreed that the research is rigorous and valuable.

(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:

Bae et al. examine the regulatory role of the PH domain of the AKT Ser/ Thr kinase, finding a key set of interactions that mediate autoinhibitory interactions between PH and kinase domains. The work provides additional mechanistic understanding of the E17K mutation, a common variant in human cancers. This manuscript will be of great interest to scientists focused on protein kinase regulation and molecular mechanisms that control signal transduction.

(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:

Using data from a tetraplegic individual, the authors show that the neural representations for attempted single finger movements after multiple years after the injury is still organized in a way that is typical for healthy participants. They also show that the representational structure does not change during task training on a simple finger classification task, and that the representational structure - even without active motor outflow or sensory inflow - switches from a motor representation to a sensory representation during the trial. The results have important implications for the use and training of BCI devices in humans.

(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 manuscript shows that bisphosphonate-related osteonecrosis of the jaw, a rare complication of osteoporosis treatment, was prevented in mice using a novel treatment which works by reversing the associated oral inflammation. The work in this manuscript has the potential to be impactful if limitations are addressed. It will be of interest to investigators in the bone and dental fields who conduct pre-clinical 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. The reviewers remained anonymous to the authors.)

Evaluation Summary:

Chaudhary and colleagues follow up their preliminary study on mitochondrial genome copy number in AML with this current study by looking if the expression of specific genes encoding mitochondrial components could provide further insight into AML prognosis. Multivariate analysis was used to identify those genes whose expression was prognostic of patient outcome, which led to the identification of three mitochondrial genes whose expression was used to build a multivariate risk model for childhood AML patients. Altogether, the work by Chaudhary and colleagues interestingly builds on their previous work and suggests that mitochondria may influence AML outcomes, and measuring mitochondrial parameters may help assess patient risk. However, the authors will need to identify the novelty of their findings over the previous reports from their own group.

(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 models the evolution of simple multicellular life cycles using evolutionary game theory. The authors discuss natural selection between different life cycles by modeling growth, fragmentation, and interactions between propagules, discovering conditions for selection of a single life cycle or coexistence of multiple ones. Overall, the model is biologically intuitive, the results are rigorous, and the implications for the evolution of multicellularity are interesting.

(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 is of broad interest to readers in the fields of vitamin D and obesity. It utilises a Mendelian randomization framework to separate the genetically predicted effects of adiposity at two timepoints in the lifecourse, childhood and adulthood. The key claims of the manuscript are well supported by the data. Higher childhood body size had a direct effect on lower vitamin D levels in early life, while in midlife, childhood body size impacted on adult obesity to result in lower vitamin D levels.

(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 focuses on identifying how metabolism can influence the response of cartilage cells to inflammation. This has relevance to the painful disease known as osteoarthritis. Modulation of cell metabolism in the right direction can serve to protect joint cartilage from the negative effects of inflammation which causes onset and disease progression.

(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:

Bouvette et al. describe a new software for fully automated cryo-EM sample screening and data acquisition, making use of deep-learning-based algorithms for the detection of regions and objects of interest. This is the first example of software for fully automated grid screening, which is of great interest to the cryo-EM community, to free skilled researchers and engineers from a serious of tedious tasks, so that they can devote more time to method development or finding answers to interesting biological and medical questions.

(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:

We all have had days where there were multiple distinct memorable experiences that we successfully remember as distinct. This paper for the first time focuses on the important question of whether the resting/sleeping hippocampus maintains a clear distinction between replays of different environments and finds that in fact, replays of different tracks are distinct in the sense that both the right sets of neurons are coactive AND their firing rates in replay reflect their firing rates during experiences.

(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 manuscript by Yue et al describes studies investigating the role of sensory neuron versus arteriole expression of Trpv1 in body temperature control. This is a detail about the contribution of different cells which has significance because of the reported on-target side-effect of hyperthermia by Trpv1-antagonists. The study shows that the effects on body temperature are predominantly produced through sensory neurons. From these studies it is speculated that the actions of Trpv1 might be pharmacologically modified to permit dissociation of the effects on neurogenic inflammation and the undesirable effects on body temperature.

(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. All reviewers agreed to share their names with the authors.)

Evaluation Summary:

This experiment investigated the link between the role of B lymphocytes to neutrophils for the achievement of LPS tolerance. The authors found that B cells can modulate the tissue-damaging properties of neutrophil leukocytes by influencing neutrophil Cxcr4 signaling in a mouse model of bacterial sepsis.

(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 shows a direct link between inflammation and cholesterol metabolism in endothelial cells. Specifically, the authors show a pathway by which the major inflammatory factor, NF kappa B, activates a gene called STARD10, which, in turn, leads to the activation of the cholesterol biosynthetic pathway. The study, therefore, provides important insights into the inter-relationship between cholesterol metabolism and inflammation at the molecular level.

(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 identifies pH as a common factor that underlies eco-evolutionary dynamics related to priority effects, which play an important role in community assembly. Using multiple lines of evidence, the data support the overall conclusions of the manuscript that pH-mediated priority effects in the nectar microbiome are the drivers of alternative community states. This manuscript will be of broad interest to readers in ecology and evolutionary 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 present an analysis of SARS-CoV-2 variant of concern movements into and within the Netherlands. The primary finding is that flight bans (in conjunction with other NPIs) were grossly insufficient at stopping the invasion of new variants into The Netherlands over a one-year period. Although consistent with similar analyses of other regions early in the pandemic, this manuscript provides additional evidence of the inadequacy of flight bans at stopping the spread of variants that are already widespread globally, especially (but not only) when importations continue via ground travel. The reviewers have questioned the rigor of the statistical models and the presentation of the main result, including analyses that were included but do not appear to contribute to the main argument.

(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 interest to scientists working to understand Chlamydia trachomatis persistence, and host pathogen interaction in general. The authors report the surprising observation that the mechanism of restriction of bacterial growth is through the inhibition of c-Myc signaling by IFNg as opposed to IDO-dependent depletion of tryptophan levels, as had been previously suggested.

(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:

Although immunotherapy has revolutionized the cancer field, most tumors do not respond, and in those that do respond, acquired resistance is often inevitable. Several mechanisms have been proposed to be involved in acquired resistance to immunotherapy. In the present study, the authors show that tumor cells from multi-cellular structures protect the inner core of tumor cells via the prevention of penetration by lytic molecules. The formation of these structures is mediated by anti-tumor T cells even with tumors that have retained their immunogenic neoantigens. This work identifies a novel possible resistance mechanism to immune-mediated tumor killing.

(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 sets out to develop a better machine learning-based predictor of survival/prognosis for patients diagnosed with pancreatic cancer, by developing a large combinatorial family of machine learning methods based on a high-dimensional set of -omics and other patient data features; using ten publicly available data sets. A reduced set of features (giving rise to a signature called AIDPS that involves 9 genes) was identified. Unfortunately, the authors used all ten data sets both in the discover stage and in the validation stage of their study. There was also a large mismatch between the initial number of covariates (15,288 genes) and the number of samples (n=1280). The combinatorial ensemble of ML models makes for an unwieldy methodology that is difficult to interpret or duplicate.

(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 Zander et al provides a valuable transcriptomic resource of murine CD4 T cell subsets in chronic viral infection. This study will be of broad interest to a wide range of researchers focused on studying CD4 T cell 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. The reviewers remained anonymous to the authors.)

Evaluation Summary:

Women are a mosaic of two population of cells, one with the paternal X-chromosome and the other with the maternal one in the active state due to random X-chromosome inactivation (XCI) that occurs during embryogenesis. During aging, one of the two populations dominates the other in a significant proportion of women. This skewing of XCI is of unknown etiology and its impact on health remains enigmatic. In this study, Amy L. Robert et al, demonstrate that skewing may not be benign and it is associated with a modest but significant increased risk of cardiovascular disease and 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 #1 agreed to share their name with the authors.)

Evaluation Summary

This study aims to characterise the brain dynamics of different disorders of consciousness by studying patients in a minimally conscious state and those with unresponsive wakefulness syndrome, along with healthy controls. The authors apply elegant analyses to the dynamics of brain functional connectivity to successfully discriminate between healthy controls and patients, revealing reduced metastability and a contracted network repertoire in disorders of consciousness. Overall, the study provides important new information on the mechanisms of disorders of consciousness and the functional brain networks involved.

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 within the fields of DNA replication, developmental biology and oncology. Focusing on the YAP protein, a major regulator of tissue growth and repair, it identifies an interesting new role in DNA replication dynamics, beyond its known role in gene transcription regulation. A series of experimental manipulations support the key claims of the paper. Additional control experiments, as well as mechanistic insight into how RIF1 and YAP interact, and insight into how that interaction influences replication timing would make the paper stronger.

(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 present a manuscript addressing an important unmet need, specifically focused on understanding the effects of high protein on hematopoiesis. This information can be of interest to basic biologists and clinicians who specialize in the areas of various diseases associated with elevated protein concentration (e.g. infections, inflammation, multiple myeloma, renal failure, etc). This is in part what makes for the complexity in studying this entity as the consequences of such disparate diseases are difficult to parcel out as causes of which specific disease manifestations. Furthermore, the presented work is done in an invertebrate model without additional confirmation in other model systems. Taken together, the work, which is plentiful in experiments, provides an incomplete understanding of cause and effect, leading to overinterpretation of results and overstating of derived conclusions.

(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 make an important contribution to our understanding of the universal mechanism of unloading of sugars from the phloem (the vascular tissue dedicated to long-distance sugar transport in plants) into root tip cells. Specifically, the authors investigate the pores (called plasmodesmata) present in the cell wall separating phloem cells from those cells into which sugars get unloaded in roots, which they found to have the same characteristic structure in all plant species investigated. The physical properties of these particular plasmodesmata suggest that they are especially suited for efficient and selective phloem unloading. The paper is relevant for audiences studying plant physiology and development. There are a few criticisms of the modelling 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:

Zaforas et al. conducted a high-quality study on a very complex topic, using advanced layer-specific neuronal recording techniques. Their findings might be especially interesting for pre-clinical and clinical researchers as well as clinicians in the field of SCI-related sensory pathologies such as neuropathic pain. However, methodological limitations prevent clear mechanistic insight into the underlying causes of their effects.

(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 study claims to demonstrate an interplay between awareness and bottom-up attention and explains their joint effects within an established normalization framework. How awareness fits into current computational theory is an important and timely undertaking that has a far-reaching impact on our understanding of visual and cognitive function. Although the study uses control experiments and analyses to reinforce their claims, shortcomings in their experimental approach require further clarification and data to adequately support the study's conclusions.

(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 investigates how prestimulus alpha neural oscillations differentially modulate sensory signal and noise during visual detection and demonstrates that alpha power correlates with the subject's perceptual discriminability but not with decision criterion, supporting that alpha power modulates sensory signals more strongly than noise. The key conceptual claim is directly related to existing claims in the literature, although this is an unusually elegant experimental demonstration of the phenomenon.

(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 study, the authors investigated how predictions modulate performance using a combination of pharmacological experiments, high-density EEG, Bayesian modeling, and machine learning. This is an interesting study with a complex set of analyses. The detailed assessment and interpretation of all the findings could be strengthened by providing a more unified and hypotheses-driven approach.

(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 identifies a novel Shank3 mutation from individuals with ADHD-like syndrome and tests the impacts of this mutation together with other known Shank3 mutations on inter- and intramolecular protein-protein interactions of Shank3 involving the N-terminal SPN and Ank repeats. The results indicate that Shank3 mutations have diverse impacts on the intramolecular SPN-Ank domains and the interaction of Shank3 with other proteins including delta-catenin, fodrin, and CaMKIIa. Overall, the results of the study are novel and of high quality. Considering the lack of detailed biochemical understanding on various Shank3 mutations associated with PMS, ASD, and schizophrenia, this study is a meaningful step forward in the basic understanding of Shank3 functions and related pathophysiology.

(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:

Park and colleagues examined the activity and function of different projection neuron types, pyramidal tract (PT) and intratelencephalic (IT) neurons, in the primary motor cortex using a joystick manipulation task in mice. During forelimb movements, the activity of IT neurons was more correlated with movement kinematics than that of PT neurons was, and inactivation of IT neurons caused larger effects on movement kinematics (amplitude and velocity). The results highlight different activity patterns and functions between PT and IT neurons. Discussion among reviewers focused on two main issues. One centered on the interpretation of the PT neural activity; the second on the evidence underlying the claim of a dissociation between the PT and IT neurons.

“(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 will be of interest to evolutionary biologists and behavioural ecologists. It aims to quantify the fitness benefits of helping with the breeding attempts of others vs. seeking own breeding attempts via dispersal. It is generally considered that helping is less profitable than breeding, but occurs when superior reproductive options are constrained. Using a long-term dataset of birds, the authors call into question this assumption, and propose that both reproductive tactics can in fact have similar fitness returns, resulting in mixed-kin societies.

(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 names with the authors.)

Evaluation Summary:

All reviewers think the study will be really valuable for the field, especially after re-writing to include a detailed comparison with results that were previously published. We all appreciate the clear identification of a gamete sub-population, and also thought that the discovery of low activation of all VSG expression sites was intriguing and will be of considerable interest to those in 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 all agreed to share their names with the authors.)

Evaluation Summary:

This work builds on previous work by the same team, demonstrating that the bacterial protein CspA, which inactivates host complement by binding to the host complement inhibitor FH, is a determinant of host range for the Lyme disease bacterium. Additionally, the authors present phylogenetic analysis of CspA and related protein sequences, which supports the hypothesis that inactivation of host complement has evolved independently in three bacterial genospecies.

(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 describes the development and validation of an automatic approach that leverages machine vision and learning techniques to quantify dynamic facial expressions of emotion. The potential clinical and translational significance of this automated approach is then examined in a "proof-of-concept" follow-on study, which leveraged video recordings of depressed individuals watching humorous and sad video clips.

(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 study provides a compelling and significant advance on the understanding of how gene regulation by the histone methyltransferase MES-4 underlies germ cell survival in C. elegans, with the major claims being nicely substantiated. The critical and surprising finding is that the degeneration of mes-4 mutant primordial germ cells is due to inappropriate upregulation of genes on the silenced X chromosome, and not failure to activate germline-expressed genes, though reduced levels of germline gene expression were observed. An X-linked target of mes-4, lin-15b, is necessary for the degeneration phenotype. The work could be improved by clarification of the relationship between X and autosomal gene expression, especially in consideration with the action of the other histone methyltransferase MET-1, but otherwise it is excellent.

(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:

Dongre et al. build on previous social learning research on wild vervet monkeys to investigate the role of a particular social behaviour, muzzle-muzzle contact, in aiding the acceptance of a novel food and provide interesting observations on the potential for male monkeys immigrating from one social group to another in spreading this novel behaviour. With a more robust and transparent analysis, this manuscript has the potential to provide significant insights into innovation and social learning in animals.

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 will be of interest to scientists studying neuroinflammation and searching for potential therapeutic targets. The findings here have revealed the effects of an anti-inflammatory cytokine, human IL-37 (hIL-37), in the central nervous system of mice. The data support the conclusions within the current mouse models. Since hIL-37 is not naturally expressed in mice, more evidence related to human cells or tissues would strengthen the physiological significance.

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:

Rabies-mediated monosynaptic retrograde tracing is a powerful method to characterize the connectivity of neural circuits. The CVS-N2c strain of rabies virus shows significantly higher efficiency of transsynaptic spread and less toxicity than the more commonly used SAD B19 strain but has been limited in use by an arduous and lengthy packaging process and low resultant titers. Here, Sumser et al. present a method that significantly speeds up the production process while reducing off-target expression. They also introduce a suite of novel reagents (34 novel plasmids) for monosynaptic tracing with the CVS-N2c strain that they commendably, have already deposited with Addgene. The work is an important advance that will reinvigorate rabies-mediated circuit tracing.

(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:

Cohesin is an evolutionarily conserved protein complex that plays essential roles in mitotic chromosome structure and function. Previous studies suggest that multiple activities of cohesin are required only prior to the onset of chromosome segregation. Using a Mcd1-AID and a Mcd1-TEV to either degrade or cleave cohesin's kleisin subunit Mcd1 of the yeast Saccharomyces cerevisiae, this study shows that cohesion plays also a role in anaphase organizing the centromeric regions, providing new evidence that cohesin function is critical for chromosome structure and segregation during and after the onset of chromosome segregation. The work is of relevance for students of chromosome biology and cell division.

(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:

Results from observational studies examining an association between the antihypertensive drugs and the risk of breast cancer reported inconsistent findings. This study uses a two-sample Mendelian randomization approach (MR), which overcomes the limitation of observational studies by using genetic variants as a proxy for modifiable exposures, to investigate the relationship between the use of antihypertensive medication and breast cancer risk. Using publicly available data and including a comprehensive assessment of antihypertensive drugs, the authors identified two SNPs that were associated with breast cancer risk. While the findings suggest that antihypertensive medication use may be associated with breast cancer risk, there are some methodological issues that need to 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:

FLT3 (Fms Related Receptor Tyrosine Kinase 3) activation occurs in a subset of acute myeloid leukemia (AML) cases and is associated with poor prognosis. This work is focused on the mechanisms of resistance to FLT3 inhibitors in AML. The authors show that the combination of the FLT3 inhibitor and an mTORC1 inhibitor reduces tumor burden and prevents relapse in FLT3 mutant AML. This paper is of interest in scientists and physicians investigating AML as well as scientists studying signaling pathways.

(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:

Overall, this study will make significant contributions to developmental neuroscience and vision science as they attempt to study how prenatal and postnatal maturation influence structural-functional measurements in the early and high-level visual cortex. These results will be of broad interest as it is a novel attempt to study processes that might be innate or genetically wired and those that emerge due to worldly experiences within the sensory systems. The authors are addressing an important and timely question based on a large and impressive infant database.

(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 demonstrates that artificial neural networks can be used to accurately predict the responses of biologically-detailed neuron models to synaptic inputs, and hence to approximate the behaviour of networks of such neurons. This study potentially opens the door to massively reduced simulation times for biologically-detailed neuronal network simulations without recourse to supercomputers and hence will be of broad interest to computational neuroscientists.

(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 novel insights into the potential function of innexin proteins, which are electrical synapse-forming proteins with often quite enigmatic in vivo functions. The authors describe here potential functions in synapse tiling. The paper should be of interest to researchers with interests in molecular mechanisms governing nervous system 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 #3 agreed to share their name with the authors.)

Evaluation Summary:

In this paper the authors report an updated theoretical model describing in mathematical terms how the Hsf1 transcription factor is activated in yeast in response to heat shock, and demonstrate that rather than denatured mature proteins, Hsf1 activation involves newly synthesized proteins that sequester the Hsp70 chaperone away from the inactive Hsp70/Hsf1 complex, releasing active Hsf1. They also describe a general role for the Sis1 co-chaperone in maintaining the fitness of yeast cells under stress conditions, such as heat shock, that is independent of regulation of Hsf1.

(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 bioinformatically analyze previous scRNA-seq datasets of the developing mouse soft palate to identify differential signaling pathway activities in the heterogeneous palatal mesenchyme. Identifying TGF-beta signaling pathway activity with the perimysial cells, they hypothesize and test whether TGF-beta signaling in the perimysial cells might regulate palatal muscle formation. This paper will be of high interest to developmental biologists interested in the molecular regulation of tissue interactions that occur during mammalian palate morphogenesis.

(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 of interest to readers curious about collective behavior, biological rhythms, and models of synchronized oscillations. The authors study a remarkable species of fireflies in which individual males flash non-rhythmically and erratically, but sufficiently large groups flash rhythmically and synchronously. Unlike nearly all previous models of biological oscillations, the authors' model accounts for their data quantitatively and with no adjustable parameters, at least in the experimental set-up considered.

(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 provides insight into the identity of the sodium channel controlling excitability in proprioceptors. Using pharmacology, gene KO, behavior, and histology, the authors show quite convincingly that NaV1.1 in sensory neurons is essential for normal motor behavior and contributes to proprioceptor excitability. The work has interesting implications for human subjects with inherited variants of Nav1.1.

(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:

Some children conceived by assisted reproductive technologies (ART) exhibit metabolic differences compared to those conceived naturally, and the causes are unknown. This work reveals possible explanations for the metabolic differences and provides opportunities to improve ART and prevent the differences. This is a valuable contribution and will be of special interest to practitioners of ART, as well as to developmental and reproductive 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 #2 agreed to share their name with the authors.)

Evaluation Summary:

Boddé et al propose a new approach for species identification in the genus Anopheles. The approach uses an amplicon panel, a kmer-based similarity metric, and a variant auto-encoder to minimize issues of sequence alignment between divergent lineages. The authors provide strong evidence that their approach works well for most samples. The work will be of potential interest to practitioners in the field of parasite carrying mosquitoes.

(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:

Nutrition profoundly affects neural development. The Uemura lab previously reported that C4da neurons elaborate complex dendrites when larvae grow on low-yeast diets, a phenomenon called neural sparing. In this current study, they define the molecular mechanism underlying the nutrition-mediated phenomenon and identify that the inter-organ Wingless/Ror/Akt pathway between the neuron and its adjacent muscles is necessary and sufficient to mediate dendrite overbranching in the low-yeast 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 #1 and Reviewer #2 agreed to share their name with the authors.)

Evaluation Summary:

In this paper, the authors generate and analyze new genome and gene expression data to understand better the evolution of the white-throated sparrow supergene region, which contains 1000 genes and determines whether a bird has a tan or a white stripe. The study nicely illustrates how the cessation of recombination that results from a chromosomal inversion can become a source of evolutionary novelty. The lack of recombination can result in the accumulation of deleterious variation leading to degeneration, but it can also (as here) facilitate genomic diversification and adaptation. The results will be of interest to a broad array of researchers studying genome architecture and phenotypic diversity and 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 #2 agreed to share their name with the authors.)

Evaluation Summary:

This study will be of interest to the large class of researchers who perform brain-behavior correlation analysis in the neuroimaging field, especially those related to neurodevelopment. The authors found that controlling for socioeconomic and maternal behavioral confounders, in addition to the usual demographic variables, generally attenuated such associations in ADHD using two independent large cohorts. The findings highlighted the importance of careful confounder selection and control for robust brain-behavior associations.

(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 extensive study dissects the different gene expression patterns in a large set of different human lower limb muscles. It is an extensive transcriptome study. Its potential importance is that it points out insights into their differing changes in particular muscle diseases associated with specific gene defects.

(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 helical shape of the bacterial pathogen Helicobacter pylori is important for its ability to colonize the human gut. Building on previous work identifying a complex of proteins required for generating helicity, this study focuses on the molecular mechanisms by which this complex modulates cell shape. Based on results from genetic, cytological, and pull-down experiments, the authors propose that one member of the complex, the bactofilin CcmA, interacts with two other complex members to generate helicity through a combination of cell wall synthesis and degradation. While data is supportive of this idea, the conclusions of the study require additional experimental support to rule out competing models.

(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 manuscript, the authors focus on the fungus B. bassiana, which is resistant to the toxin cyclosporine A. Through a mutant screen, the authors identify the key gene that mediates the sequestration of the toxin in vacuoles. They further show that this gene can be transferred to a distinct fungus and also to plants to protect against a toxin-producing fungal pathogen. Therefore, this work may lead to novel disease control strategies against fungal pathogens.

(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 interesting, timely and important because it presents a way to understand the transmission potential of a virus even when there are very few local cases. This has a high public health communication and preparedness value. The paper is clearly written, and the results fit with the known epidemiology of the various outbreaks that occurred in Australia in 2020. The paper is likely to be of broad interest within and outside the field of epidemiological modelling.

(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:

The manuscript by Routledge et al. describes the role of Reggie-1/Flottilin2 in the formation of filopodia-like membrane protrusions called cytonemes and which were shown to be conserved between gastric cancer cells and Zebrafish. Authors demonstrate that Flot2 is present on the cytoneme along with Wnt3 in gastric cancer and with Wnt8a in Zebrafish. Furthermore, Flot2 is also present with Ror2 on the cytoneme and together they are believed to modulate cytoneme formation. This study extended the previous studies and provides new details about regulatory events controlling a cell biological process that will be of interest to those in the Wnt and cytoneme 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. The reviewers remained anonymous to the authors.)

Evaluation Summary:

The neural correlates of voluntary action is one of the most intriguing questions in neuroscience, but studying it at laboratory settings is incredibly difficult. Here, the authors have used an impressive range of methods and analyses approaches in mice to investigate the neural activity preceding voluntary action in mice. Using widefield calcium imaging in mice to study volition is novel and welcome but the great strength of this paper is its wide range of analyses approaches. There remains a question to what extent the findings reveal specific properties of 'voluntary action,'.

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 investigated the mechanism of the cadherin-catenin F-actin catch bond interaction, a fundamental cell-cell adhesive structure that can be both dynamic and force-activated. Force measurements with purified protein components demonstrate that the catch bond results from a force-dependent switch of the actin-binding domain of αE-catenin between a five-helix bundle and a four-helix bundle bound on F-actin. The findings are interesting and well supported by experimental data, and will be interesting to the broader field of cytoskeleton function and functional structural 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 #1 agreed to share their name with the authors.)

Evaluation Summary:

This work by Cheng et al evaluates the contribution of regulation of gene expression at the RNA and protein level by leveraging copy number variations in a large cohort of cancer samples. Importantly they find that there is rarely compensatory regulation at the RNA and protein level together, but depending on the gene, expression is either compensated at one or the other. The paper is very intriguing and the findings are of interest to a broad readership.

(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 describes a biochemical analysis of the roles of Ub chain length on Ub-dependent segregase activity of yeast and human p97 and the role of UBX proteins on the disassembly of the CMG replicative helicase complex. The human p97 complex does not segregate substrates with shorter ubiquitin chains as efficiently as does the yeast complex but the human complex can be enhanced in vitro by 3 UBX proteins - FAF1, FAF2, and UBXN7. Cellular studies indicate a partial role for FAF1 and UBXN7 in cells. The paper would be strengthened by additional mechanistic understanding of how the UBX domain functions in activation of segregase activity and the contribution of this pathway in 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. The reviewers remained anonymous to the authors.)

Evaluation Summary:

This paper can provide novel basic science insights into how brain responses at different frequencies signal sensory information. An analysis of intracranial recordings in 121 human participants shows that low-frequency local field potentials and high-frequency (>30 Hz) broadband activity in response to face stimuli have largely similar spatial, functional, and timing properties. However, it is essential to show that the two response types can be reliably disambiguated and to critically discuss the generalizability of the 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. Reviewer #1 agreed to share their name with the authors.)

Evaluation Summary:

This paper studies how pheromone-sensing neurons of the vomeronasal organ establish and maintain cell identity. A role for a particular transcription factor, AP-2e, is investigated using targeted gene knockout and rescue, and observations reveal an unexpected plasticity in the cell identity of mature sensory neurons. This paper should be of broad interest to neuroscientists and cell biologists studying mechanisms of cell development and differentiation.

(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 potentially very important to dissect the immune repertoire of T/B cells, which is one of the most critical/difficult parts for the adaptive immune system to achieve antigen specificity. These conclusions and proposed methods will require additional experimental support and further validation in different disease 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 #2 agreed to share their name with the authors.)

Evaluation Summary:

In this manuscript Nunes Santos et al. use a combination of computation and experimental methods to identify and characterize a cis-regulatory element that mediates expression of the quail Slow Myosin Heavy Chain III (SMyHC III) gene in the heart. The study contributes to our understanding of how genes can be expressed differentially in the atrial and ventricular chambers of the heart. The evidence for the newly-identified gene regulatory sequence, and its origin, in exclusively directing these gene expression differences could be stronger. This study is of potential interest to readers in the fields of developmental biology, evolution, gene regulation, and biology of repeats.

(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:

Wei- Jai et al., demonstrate the protein Human liver DnaJ-like protein (HLJ1) converts misfolded IL-12p35 homodimers to monomers in sepsis. This contributes to increased IL-12 activity, in macrophages which in turn leads to an increased production of IFN-gamma production and lethality in mice. This study suggests that HLJ1 plays an role in regulating IFN dependent mortality and future studies may determine a therapeutic role in blocking this protein.

(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 would be of interest to all researchers who work in understanding the mechanisms involved in podocyte slit diaphragm homeostasis and maintenance of the glomerular filtration barrier. The work provides substantial new insights into nephrin dynamics and the mechanisms of slit diaphragm maintenance. A series of compelling experiments depicted that dynamin-mediated endocytosis was involved in ectopic nephrin turnover and that flotillin-mediated turnover of nephrin occurred within the slit diaphragm was needed to maintain filter permeability in-vivo.

(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:

This paper presents a novel and potentially highly useful approach to monitor circadian rhythms in specific tissues. The elegant reporter that the authors have built has the potential to become an important tool for understanding how different body clocks respond to various inputs and genetic manipulations. The authors already apply it to show that different clocks appear to be responding differently to loss of signaling from a key circadian neuropeptide in Drosophila melanogaster. However, it is difficult to determine whether these results, as currently presented and analyzed, provide new insight into the relationship between brain and peripheral clocks. The work is of interest to the community of biologists studying biological rhythms.

(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 addresses a potential role for the box C/D Small Nucleolar Ribonucleoprotein complex at the intersection of mitochondrial homeostasis and cellular responses to infection and environmental stress in the context of the C. elegans system. The presented data can be explained in multiple ways and can serve as starting point for further research in this interesting and important area.

“(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 study, the authors present a numerical model of ant raft shape dynamics. It is an interesting topic, the experimental movies are exciting, and the idea that ant rafts make protrusions is new. The goal seems to be to explain how local interactions can lead to the perpetual protrusions of the raft. Since the biological significance of the results has not been clarified, the paper is likely to be primarily interesting to engineers and experts on robotics.

(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 very clear paper, which will be of interest to scientists in the field of evolutionary biology, investigates the effect of population structure on the efficacy of selection on a single locus. The results are based on analytical computations and numerical simulations, conducted in a scientifically rigorous manner. Although the conclusions are currently limited, the paper could serve as a solid basis for a more ambitious 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. Reviewer #1 and Reviewer #2 agreed to share their names with the authors.)

Evaluation Summary:

This paper is of interest to biochemists studying DNA replication and genome maintenance in eukaryotic cells. The work details a structure-function analysis of an interaction between two proteins that are critical for genome stability. A mutation that disrupts this interaction may have no adverse effects under unperturbed conditions but causes telomeric DNA damage when cells experience replication stress. However, the structural nature of the damage and cellular consequences are not sufficiently explored.

(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 reports a novel function of non-coding RNA miR-22 in the regulation of tumor-associated angiogenesis. The presented data suggest a possible link between microRNA and endothelial cell function. If the underlying mechanisms were further explored, this work would be interesting for people working on microRNA function in endothelial cells. Furthermore, considering the increasing interest of combination of anti-angiogenesis agents with anti-PD1 immunotherapy, this work may attract readers interested in immunology.

(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:

High-throughput approaches that accurately assess drug target vulberbility in Mycobacterium tuberculosis, the causative agent of tuberculosis, are urgently needed to develop new treatment options for this dreaded disease. This paper applies a CRISPRi based approach to investigate gene essentiality and vulnerability on a diverse set of 96 genes. While the key observations of the study support previous findings, the approach reported here is useful for identification and characterization of novel drug targets. The study will be of interest to microbiologists and those interested in diverse aspects of bacterial metabolism.

(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 provides an attempt to understand the crosstalk between to islet cell types during beta cell regeneration following partial pancreatectomy. It combines lineage tracing, single cell sequencing and light microscopy to describe islet cell heterogeneity and interactions in the regenerating mouse pancreas. The concept of protective signaling resulting from the direct interactions between beta and delta cells is compelling and would be of interest to scientists in the field of endocrine pancreas development and regeneration. However, the conclusions derived from the sequencing data 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. The reviewers remained anonymous to the authors.)

Evaluation Summary:

This study investigates how deficiency in the RNA splicing factor SON impairs centriole assembly, which may underlie ciliopathy-like phenotypes in humans with SON mutations and is thus of interest to both cell biologists and clinicians. Using RNA-sequencing analysis and advanced imaging techniques the authors discover a large number of known and new SON splicing targets and attempt to identify those crucial for SON knockdown defects. However, knockdown of a subset of targets did not fully recapitulate SON depletion phenotypes and only led to the relatively vague conclusion that the observed centriole assembly defects were caused by impaired protein trafficking around the centrosome.

(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 interest to the chromosome biology field and SMC researchers in particular. The study provides cell biological, biochemical, and structural modeling evidence that a new Nse5-like protein named SIMC1 is a paralog of SLF1, and that the two compete for SLF2-Smc5/6 binding. The authors also show that SIMC1 targets SMC5/6 to polyomavirus replication centers through its SUMO binding motifs (SIMs), supporting a role for SIMC1 in Smc5/6 recruitment for viral restriction.

(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:

Burl and Rondini et al. elucidate the transcriptional profile of the stromal vascular fraction of murine brown adipose tissue in the context of thermogenic stimulation. The authors combined systems and reductionist approaches to show the reliance of mature brown adipocytes on adrenergic activation to indirectly stimulate progenitor proliferation and differentiation and the involvement of dendritic cells in this process. Overall, this is a timely and well-rounded work that will provide beneficial data for public use and further resolve the complexities underlying brown adipose physiology.

(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:

This paper is one of the first demonstrations that expression quantitative trait loci (eQTL) affecting human microRNAs are linked to brain development affecting brain structure and function. These findings will have a broad impact on the genomics, neural development, and microRNA fields. The datasets produced here (developmental changes in miRNAs, new human miRNAs) will likely be used for further discoveries. However, some claims need to be tempered.

(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:

DNA methylation inheritance through the UHRF1-DNMT1 signaling axis is becoming increasingly appreciated as a ubiquitin-regulated process. This study builds on the observation that UHRF1 multi mono-ubiquitinates the PCNA-associated protein PAF15, and that, similarly to H3 substrates, these mono-ubiquitin sites are bound by DNMT1 and may contribute to its S-phase chromatin association. The authors focus on players involved in ubiquitin removal and PAF15 release from chromatin and they identify the deubiquitinase USP7 and the DNA replication regulator ATAD5 as important to this termination process. While manipulation of these factors using Xenopus egg extracts shows quite striking effects on DNMT1 chromatin association, effects on DNA methylation are minimal and this brings to question the importance and potential impact of the pathway involving PAF15. In addition, how the findings from Xenopus egg extracts translate to regulation of DNA methylation maintenance in mammalian cells is currently unclear.

(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 evaluates the effects of two distinct dietary methods that cause obesity in mice (high fat vs high starch) on insulin sensitivity and glucose homeostasis. Through a series of nicely performed physiology experiments, the authors demonstrated that high starch feeding causes obesity without deleterious effects on insulin sensitivity. This work will have an impact in the field and help define the important lipid mediators of metabolic 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 #3 agreed to share their name with the authors.)

Evaluation Summary:

Predicting if a tumour has aggressive or metastatic characteristics would be of great utility in the clinic as it would help patient stratification and management. In this manuscript, Carrier and collaborators derive a signature for melanoma aggressiveness relying on methylated regions of tumour and cell line genomes. The identification of a 4-gene methylation biomarker for melanoma aggressiveness and survival is an important contribution. This manuscript is of relevance to clinicians and melanoma researchers interested in biomarker 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 #1 and Reviewer #2 agreed to share their name with the authors.)

Evaluation Summary:

This is an important paper querying odor responses in the olfactory bulb at low concentrations. Classical studies have revealed a 'combinatorial code' for odorant recognition, with individual odorants represented by combinations of broadly tuned and low-affinity olfactory receptors. Here, the authors perform a large-scale analysis of odor responses across glomeruli and surprisingly observe that odorant receptors instead generally display remarkably narrow tuning profiles.

(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 shows that Drosophila can perform olfactory unimodal sensory preconditioning, an example of higher-order conditioning that may guide behaviour through inferred value. This is of conceptual significance for the brain, behavioural, and to some extent, the social sciences, because it shows that a conditioned response to a stimulus can occur even when the stimulus itself was never paired with punishment, for example.

(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 submission represents a holistic approach to how pentraxin 3 (PTX3) modulates susceptibility to experimental infection by Streptococcus pneumoniae. The authors have built robust findings on the importance of PTX3 for the survival of mice and they have extensively investigated all different aspects of the mechanism of PTX3 protection. One main strength of the manuscript is its usage of bone marrow chimeras in addition to total as well as tissue-specific mouse strains that support their claims.

(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:

In this paper, the authors demonstrate that a reversible amination network that allows nitrogen transfer via transaminases for synthesis of several amino acids can be constructed in laboratory strains through clever and carefully designed experiments. As a result, this work should be of interest to microbiologists, biochemists, synthetic biologists, and biotechnologists.

(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:

Nicastro et al. uncover a new input for the central metabolic regulator TOR complex 1 (TORC1) , namely manganese (Mn) levels, in budding yeast and they show that this dependence on Mn is conserved in humans. TORC1 is a central coordinator of multiple inputs to guide cellular decisions of catabolism vs anabolism, and information on an additional way to modulate its activity will be highly influential in both basic cell biology as well as therapeutic 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 #1

Evaluation Summary:

Mitochondria have their own DNA, which is much more likely to gain mutation (due to error-prone DNA polymerase). It is widely appreciated that there are quality control mechanisms such that functional mitochondria are passed from one generation to the next. The proposed mechanisms include a passive mechanism (generation of the bottleneck) as well as an active mechanism (selective removal of non-functional mitochondria), but the processes are not fully understood. This manuscript presents fascinating observations as to how C. elegans germline may remove mitochondria by creating bottlenecks as well as selectively removing non-functional mitochondria. Building upon the authors' previous finding that the C. elegans primordial germ cells (PGCs) shed much of cytoplasm during embryogenesis through 'cannibalism', they now describe that a bulk of mitochondria are removed from PGCs through this process.

(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 describes a new antibody to identify human neutrophil extracellular traps (NETs) also in tissue samples. The paper might not only introduce an important novel tool for many areas of biomedical research, but it also touches cell biological questions of importance. The usefulness of the NET-specific antibody is impressively developed in the paper, while the mechanistic concepts are not yet fully established.

(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 proposes a novel mechanism used by the visual system to recruit interneurons into the visual thalamus. The primary claims that retinal ganglion cell axons secrete Shh in the visual thalamus that induces FGF15 expression by astrocytes, that then attract interneurons are sound. Because Shh signaling, interneuron migration, and astrocyte functions are studied by a large number of neuroscientists this study will have a high 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 and Reviewer #2 agreed to share their names with the authors.)

Evaluation Summary:

The authors use single-cell RNA-sequencing, single-cell ATAC-sequencing, a CRISPR-based lineage tracing system, and a novel computational pipeline to characterize heritable expression changes. Aspects of this work were found to be both impactful and technically sound, but there is a concern with the scalability/generalizability of the approach, the use of the single cell ATAC-sequencing data, and some technical aspects of the computational pipeline. This work will appeal to groups working on lineage tracing and 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. Reviewer #2 agreed to share their name with the authors.)

Evaluation Summary:

The authors show that a widely used knock-out mouse for Mertk carries multiple additional changes in its genome, affecting the expression of a number of genes besides Mertk. They show that, although the line was back-crossed to the C57 background, these changes are due to the original 129P2 genome of the embryonic stem cells in which the knock-out was originally created. Through the generation of two new knock-out mouse strains, in C57 embryonic stem cells, the authors here show only part of the phenotype of the original Mertk knock-out mouse can be reproduced. Overall, this study raises awareness as to the limitations of the Mertk-/- v1 model and limits direct inference of Mertk-/-v1 observed phenotypes to Mertk deficiency alone.

(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:

The authors here present how specific fatty acids modulate the bactericidal effect of the antibiotic vancomycin. The authors find that palmitoleic acid significantly increases the bactericidal activity of vancomycin and investigate the mechanism responsible. The key finding will be of interest to a broad audience of researchers focused on microbiology, host-pathogen interactions, and antimicrobial development, as well as to clinicians that treat antibiotic-recalcitrant infections.

(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:

Prostate cancer cellular heterogeneity is a major problem for disease progression and treatment resistance. This body of work addresses the cellular identity and populations that make up prostate cancer using single-cell sequencing technology and state-of-the-art mouse models. The cellular identities, associated signaling networks, and immune complexes accompanying the heterogeneity of the prostate are identified in this work and a resource is provided for scientists in 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 study reports on the diagnostic utility of TRIO-based whole-exome sequencing (WES) in a cohort of 123 unrelated patients with suspected monogenic inborn errors of immunity. The authors further explored the diagnostic rate in this cohort by focusing their analyses on the identification of de novo variants (DNVs). This manuscript will be of interest to medical geneticists, immunologists, and physicians working with patients with primary immunodeficiencies.

(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:

Monteiro de Assis et al. demonstrate a role for T3 in modulating circadian metabolic rhythms both systemically and within the liver. The findings extend the molecular framework in which organismal metabolism is coordinated in a circadian fashion.

(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 investigates the consequences of Disrupted-in-schizophrenia-1 (Disc1) gene knock out in the medial prefrontal cortex (mPFC) of mice. This work marks a potentially significant contribution to elucidate cortical circuits alterations in this genetic model of schizophrenia. The main message is that communication between cortical pyramidal neurons and fast spiking interneurons is altered with consequence on cortical network activities. The data generally support the conclusions made but analyses of electrophysiological data should improve.

(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 is of relevance to the field of DNA repair. It uses a cleverly designed new recombination assay in yeast to address the impact of DNA break position on global genome mobility. A centromere-proximal DNA double-strand break (DSB) induces an H2A(X) phosphorylation-dependent global mobility that accelerates but is not essential for DSB repair, while a centromere-distal DSB triggers global mobility that is essential for repair and which depends on H2A(X) phosphorylation, Rad9 and Rad51. Together, these data support a model where global genome mobility promotes homologous recombination repair, particularly for centromere-distal DSBs, and help settle some recent controversy in 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 #3 agreed to share their name with the authors.)

Evaluation Summary:

This paper is potentially of broad interest to researchers in the chromosome biology field. With specific loading sequences identified, the condensin DC complex studied here provides an elegant system to investigate the in vivo activities of SMC complexes. Combining Hi-C, ChIP-seq and RNA-seq, the authors have a comprehensive suite of assays to probe their questions. However, not all of their major conclusions are currently supported by the 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:

Mechanisms for controlling gene dosage and uniparental gene expression vary widely across the eukaryotic tree, with many such mechanisms still unknown. Montgomery et al. describe an epigenetic mechanism used to modulate paternal chromosome gene dosage during the transient diploid state of the primarily haploid plant, Marchantia polymorpha. This fascinating case of genome-wide genomic imprinting will be of broad interest to evolutionary biologists, epigeneticists, and those focused on understanding the context and mechanisms of gene dosage 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. The reviewers remained anonymous to the authors.)

Evaluation Summary:

This paper presents an artificial neuronal network which, from action and visual inputs, develops representations of space comparable to those found in the navigational system of the brain. They show that the representations developed by this network can be used in novel environments and in a reinforcement learning task. This demonstration of representations in absolute coordinates from agent-centered information is a significant contribution to neuroscientists as well as 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 report identified NK-extracellular-vesicle (NK-EV)-associated microRNAs and characterized them by small RNA next-generation sequencing. They found that NK-EVs promote Th1 polarization and activation of monocyte and monocyte-derived dendritic cells. The findings are potentially important for understanding NK cell 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:

The authors set out to investigate the roles of SMAD4 and TGFbeta in regulating memory CD8 T cell differentiation during viral infection. To achieve their goal, the authors utilized a variety of available tools including, gene expression, mice that lack certain regulatory genes, and different tissue tissue culture approaches. Although the in vitro experiments yielded interesting results that will interest students of T cell immunology/biology, there is an absence of results from in vivo studies that would validate the in vitro observations.

(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 outstanding manuscript evaluating a mutation commonly seen in AML and MDS in a spliceosome protein called SF3B1. The authors link this spliceosome mutation to altered transcripts and ultimately to cell cycle proteins and differentiation. This paper will be of high interest for oncologists in that it demonstrates that AML and MDS cells with this mutation can be targeted in a precision medicine approach.

(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.)