Evaluation Summary:

This work should be of interest to a broad readership in infectious diseases, especially those people interested in modeling of infections. It combines statistical and mechanistic modeling to find assayable correlates of immunity for vaccines. This method could be relevant to many diseases or vaccines, although the particular markers identified here likely will be limited in their generalizability.

(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 by Jauch-Speer and colleagues uses a CRISPR/Cas9 screening approach in a myeloid cell line to identify C/EBP-delta as a regulator of the alarmins S100A8 and S100A9, which amplify inflammation. This paper is of great interest to macrophage biologists studying macrophage function in inflammatory diseases. In an elegant series of gene targeting and sequencing studies, the authors also characterized epigenetic mechanisms regulating the expression of these pro-inflammatory mediators. Furthermore, human monocytes from cardiovascular patient cohorts showed correlative changes, indicating possible clinical relevance.

(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 presents a novel EEG-based, real-time feedback approach that enables healthy participants to independently self-regulate excitability of the left versus the right hemisphere. Using this unique approach, the authors demonstrate that their paradigm could have the potential to modulate the neural interplay between both hemispheres which is relevant for the field of neurorehabilitation.

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Evaluation Summary:

This study uses dual intracellular and extracellular recordings in different subfields of the hippocampus in awake mice during immobility to investigate the initiation of sharp wave-ripples, synchronous bursts of hippocampal activity thought to be important for memory formation. It provides unique data obtained in vivo across a diversity of hippocampal cell types. Specifically, these findings lead to a model where inhibition of CA3 pyramidal cells is permissive to ripple generation.

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Evaluation Summary:

This paper is of interest for cell biologists studying metabolism and its regulation during the cell cycle, as it demonstrates cross-talk between the CLUH protein, involved in mitochondrial function regulation and metabolism, and astrin, a protein functionally involved in cell division through regulation of centrosome integrity. This physical and functional interaction serves as a hub to integrate the metabolism with cell cycle progression.

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Evaluation Summary:

This article will be of interest to paleobiologists studying the evolution of avian diets and/or prehistoric ecosystem dynamics. The study uses an exceptional new specimen of an early diverging stem bird with a near-complete skull, to reassess diet in the taxon and explore possible early mechanisms for bird-mediated seed dispersal. The claim for frugivory is currently insufficiently supported.

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Evaluation Summary:

This is an interesting paper that uses de novo protein design to probe the effects of oligomerization state on the activity of chimeric antigen receptors (CARS). The successful design of transmembrane domains with specific oligomeric states is an impressive result on its own. The proteins were designed using rotamer-based sequence optimization in Rosetta with an energy function specific for the membrane environment. After experimentally evaluating a couple rounds of designs, the investigators settled on a design protocol that also included screening of the design candidates with docking simulations in alternative oligomerization states to check that the sequences preferred the desired oligomerization state. The designs were experimentally evaluated with gel electrophoresis and X-ray crystallography. In the end, designs that adopted well-defined dimers, trimers, or tetramers were created and carried forward in experiments as CARs.

(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:

In this manuscript the authors conditionally knock out the DNA methyltransferase Dnmt3a in developing excitatory cortical neurons to determine the consequences for chromatin regulation, gene expression, and neuron function. As expected they find widespread loss of DNA methylation at CpA dinucleotides but also an increase in histone methylation (H3K27me3) at many similar regions of the genome, which they speculate may be a mechanism of functional compensation. Overall this study offers new insights into the gene regulatory and neuronal cellular functions of an important chromatin regulatory 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. Reviewer #3 agreed to share their name with the authors.)

Evaluation Summary:

In this manuscript the authors carefully describe the activity of individual neurons within the mouse olfactory tubercle, comprised of the two principal cell types, in the context of odor and tone associative learning. The use of 2-photon microscopy to monitor activity of the neurons is a major step forward and unveiled new insights into the dynamics of these neurons. This manuscript will be of interest to a wide range of readers, including those interested in affective circuits, learning, and sensory processing.

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Evaluation Summary:

This paper will be of broad interest to researchers interested in learning, memory, and/or the hippocampus. It offers a neuroanatomically inspired model of the hippocampus that reconciles its well-known role in episodic memory with its more recently appreciated role in category learning and generalization. The computational simulations are well conducted and support the key conclusions regarding complementary roles of distinct hippocampal pathways for different forms of learning. There are concerns with differentiating the current work from prior reports and the apparent discrepancy between the proposed model and well-established findings of place and concept cell recordings in hippocampus, but thought that these issues could be potentially resolved with additional clarification.

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Evaluation Summary:

The authors examine the impacts of the COVID-19 pandemic on excess mortality in the US up to April 30, 2021. The authors separate direct impacts (caused by COVID-19, coded as such or not) of the pandemic from indirect impacts (disruptions), finding that most excess deaths (90%) are due to direct impacts. Importantly, the authors find that the official COVID-19 death tally is an undercount of these deaths. Moreover, the authors also find that excess deaths due to other causes are the main driver of excess mortality among younger populations. The paper is interesting and well written, although we have some concerns, particularly around the estimation of direct vs. indirect impacts.

(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 shows that spontaneous mutations in cancer cells affecting metabolic pathways do not necessarily result in functional defects, as affected cells may be able to be rescued by gap junction-mediated exchange of metabolites. This is verified in three specific examples, although some of the "quantitative" methods of measuring gap junctional coupling are actually only qualitative in nature. In addition, more experiments are needed to address the effect of Cx31 and Cx43 KD. This paper is of potential interest to a broad readership in cancer biology as well as colleagues studying metabolic pathways.

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Evaluation Summary:

Wahle and colleagues investigate the pervasiveness of the non-canonical arrangement of axons emerging from dendrites rather than the soma of neocortical pyramidal cells of different mammalian species. Using a variety of anatomical techniques, the authors demonstrate that axons can originate directly from pyramidal cell dendrites in species as diverse as rodents, ferret, cats, pigs and primates. Cross-species comparisons indicate that non-primate brains have a higher proportion of axon-carrying-dendrites (AcD) than did brains of macaques or humans. This paper is of potential interest to a broad range of neuroscientists in reporting the distribution of this non-canonical structure and indicating that primate brains may potentially feature axons emanating from dendrites less commonly.

(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 names with the authors.)

Evaluation Summary:

This manuscript will appeal to all with an interest in comparative physiology and the molecular biology of age-associated changes in muscle function. The authors draw parallels between aging skeletal muscle in humans and C. elegans, with evidence in support of age-dependent oxidation of the C. elegans ryanodine receptor ortholog, UNC-68, causing loss of the calstabin ortholog, FKB-2. This in turn results in UNC-68 "leakiness", reduced body wall Ca2+ transients and muscle weakness-changes in ryanodine receptor complex structure and function, changes that are similar to those that occur in aging human skeletal muscle despite the dramatic differences in the lifespan of the two organisms. The experimental approaches are generally sound, although the intriguing dataset that is open to multiple 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. The reviewers remained anonymous to the authors.)

Evaluation Summary:

This paper will be of interest to infectious disease epidemiologists and modellers working on situational assessment, and public health researchers focused on COVID19 response. Through an informative case study on the Singaporean COVID19 epidemic, the paper provides estimates of case ascertainment under different levels of border restrictions and public health measures, as well as estimates of the effectiveness of contact tracing in reducing transmission. The combination of data from multiple sources with mathematical modeling provides a powerful tool to assess effectiveness of interventions. Some of the key claims of the manuscript - while plausible - are not directly supported by the analyses, and the methods and modelling assumptions require more detailed exposition.

(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 is an interesting manuscript presenting an ex vivo explant model that allows combining live cell imaging with single-cell transcriptomic analyses. Using mouse models with specific fluorescent reporters that can be used to characterize cellular behaviour in the transplanted tissue and mark individual cells, the authors show that this approach can be used to identify transcriptional differences between cells that differ in cellular movement features during epithelial repair after injury. This is a first step to further expanding the description of cellular heterogeneity, including cellular behavioural as well as transcriptomic features. This manuscript is of broad interest to cell biologists as it describes a new method that links cellular behaviour in intact tissues to single cell sequencing. The method, which relies on the use of a transgenic strain, was demonstrated for cell migration in mouse airway regeneration. It begins to bridge the gap between cellular and molecular phenotyping of single cells but the authors should be clearer the limitations of the technique.

(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 manuscript will be of interest to scientists working on genome organisation and transcriptional control of myelination during mammalian brain development. The authors combine diverse and complimentary experimental approaches to generate insights into how DNA looping contributes to transcriptional regulation in functionally specialised cell types. The experiments have been rigorously performed and the main conclusions are justified.

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Evaluation Summary:

This study reports the results of a transposon inactivation screen to identify essential genes in Mycobacterium abscessus. The authors investigate one hit, the gene encoding the class B penicillin-binding protein, PBP-lipo. They confirm that the PBP-lipo gene is essential despite the presence of a homologous gene and that PBP-lipo is present in other mycobacteria, but not essential in these. They further characterize the consequences of PBP-lipo gene depletion in M. abscessus and demonstrate that the gene product is required for maintaining cell morphology, whilst also participating in a network with other cell wall enzymes. The manuscript will be of interest for researchers working on fundamental aspects of cell wall synthesis in mycobacteria. It may also be relevant for researchers who aim to specifically target M. abscessus using new drugs or drug combinations.

(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 how putative C. elegans H3K9me methyltransferases affect aging by investigating their effects on long-lived daf-2 mutants. They surprisingly find that modifiers of H3K9me1/2, but not H3K9me3, can synergistically extend the lifespan of daf-2 (in some cases, to three times as long as wild-type). They demonstrate that this synergistic effect on lifespan requires the DAF-16 transcription factor and some of its downstream regulatory targets, and compellingly, they show that the effects on lifespan are phenocopied by a small molecular inhibitor known to target a conserved H3K9me1/2 HMT.

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Evaluation Summary:

In this paper, the authors demonstrate that the macrophage efferocytic response in SARS-CoV-2 infection is compromised for two reasons. Internalization of apoptotic SARS-CoV-2 infected cells leads to: 1) A proinflammatory as opposed to an anti-inflammatory response; and 2) reduction in macrophage capacity to perform further efferocytosis

(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 article introduces a geometrical interpretation for the dynamics and function of certain spiking networks, based on earlier work of Machens and Deneve. Given that spiking networks are notoriously hard to understand, the approach could prove useful for many computational neuroscientists. Here, that visualization tool serves to assess how fragile the network is to perturbation of its parameters, such as neuronal death, or spurious noise in excitation and inhibition.

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Evaluation Summary: 

The manuscript reports on a new technical advance in fluorescence microscopy with which changes in the oligomerization of an integral membrane protein can be measured in live cells. The method is used to define the initial steps during activation of the IRE1 signaling arm of the unfolded protein response, leading to the discovery that IRE1 exists as a stable dimer in the absence of stress - which is in contrast to inferences from prior work. In response to stress, the protein assembles into a higher-order oligomer (likely a tetramer), an event that is mediated by the IRE lumenal domain and serves as a prelude to autophosphorylation. While the work will be widely noticed and excitedly discussed in the community, a reconciliation between the different results obtained in this study and in prior work, some of which was reported previously by the same lab, is currently lacking. 

(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:

Yanai et al. used flow cytometry and methlyation profiling to characterize populations of immune cells in the peripheral blood of male rats, finding age-dependent differences in cell composition and DNA methylation profiles, with marked changes occurring at specific time points (e.g., at 15 months and 24 months of age). This raises the possibility that interventions to modify blood aging may be most effective if done prior to these inflection points. This manuscript will be of broad interest to scientists in the geroscience realm and in particular to those using the aging rat as a model for the aging human hematopoietic system.

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Evaluation Summary:

This study employs cutting-edge, multiview light-sheet microscopy and advanced image analysis to investigate how the mechanical interplay of two adjacent tissue layers shapes a developing organ. The finding that genetically-patterned calcium pulses induce local muscle contractions that constrict and fold the adjacent endoderm offers a novel mechanism by which genetically encoded patterning information shapes organs across tissue layers.

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Evaluation Summary:

This paper provides well documented and solid biochemical data to show how phosphorylation of AGO2 modulate its binding to target mRNAs, releasing the complex to allow its recycling in the cell via electrostatic repulsion. This result could explain how a small amount of Ago proteins could target a very large number of mRNA molecules . The data support the key claims of the manuscript, and the approaches used are rigorous. This very well-written and elegant study will be of great interest to those working in the miRNA field as it addresses important open questions concerning the dynamic regulation of mIRNA-mediated gene repression.

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Evaluation Summary:

Smith et al. examine jaw development across three different species of birds, chick, quail and duck, all of which have jaws of different shapes and sizes. This study provides interesting new data and insights into jaw development 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. The reviewers remained anonymous to the authors.)

Evaluation Summary:

The manuscript by Li et al. identifies the polyether ionophore nanchangmycin as a novel anti-fibrotic compound through a comprehensive chemical library screen. Given the lack of clinically available treatments for liver fibrosis, the anti-activation properties of nanchangmycin could represent a novel therapeutic avenue for the treatment of this disease.

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Evaluation Summary:

The manuscript by Kanda GN, Natsume T et al. describes a robotic artificial intelligence system with a batch Bayesian optimization algorithm that allows to optimise and reliably repeat cell culture protocols. The authors utilise induced pluripotent stem cell-derived retinal pigment epithelial cells as a model culture system of broad interest in regenerative medicine. They demonstrate that the robotic system with Bayesian algorithm accelerates the optimisation of cell culture protocols and increases the quality and quantity of cell products, compared with manual operations - these results will likely inform and strongly impact modern cell culture strategies in regenerative medicine.

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Evaluation Summary: 

This rigorous, carefully designed and executed functional magnetic-resonance imaging study provides compelling evidence against a rigid, fixed model for how working-memory representations are maintained in the human brain. By analyzing patterns and strength of brain activity, the authors show that networks for maintaining contents in mind vary depending on the task demands and foreknowledge of anticipated responses. This manuscript will be of interest to scientists studying working memory, both in humans and in non-human primates. 

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Evaluation Summary: 

This manuscript will be of interest to cognitive and developmental neuroscientists who are interested in brain oscillations and their changes with development. This study decomposes the EEG alpha power, demonstrating the confound of aperiodic activity in true oscillatory power and elucidating opposing relation of periodic and aperiodic components with age. The main approach of this paper is well motivated, and the main conclusions are supported by the analysis, which is applied to multiple large datasets, though there are some minor issues with some of the follow up analyses. Overall, this manuscript makes a timely and important case for the consideration of aperiodic signals in future research. 

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Evaluation Summary:

This study reports on the inference of the evolutionary trajectory of two specialist species that evolved from one generalist species. The process of speciation is explained as an adaptive process and the changing genetic architecture of the process is analyzed in great detail. The genomic dataset is big and the inference from it solid. The authors reach the conclusion that introgression and de novo mutations, but not standing genetic variation, are the main players in this adaptive process. 

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Evaluation Summary:

This paper will be of interest to researchers studying how spoken language is processed in the brain. The results add to our understanding of how brain oscillations track language information at the syllable, word, and sentence level. The analyses are thoughtful and the key claims of the manuscript are largely supported by the data, although some conclusions may require additional 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 #2 agreed to share their name with the authors.)

Evaluation Summary:

This is a very significant new model for papillomavirus infection but all the reviewers have major reservations about the data as they stand, and the quality of some of the data. The manuscript is not publishable without better/more data and a re-write. The work has potential but there is quite a bit of essential experimental work required to make this manuscript sound.

(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:

Persistence of the viral reservoir is hampering HIV cure and thus understanding how these cells persist is important. This study describes a possible way that HIV-infected cells in the reservoir may escape antibody killing. The reservoir cells tend to have less availability of a receptor that binds HIV antibodies that would ordinarily help in killing. These cells are not only less susceptible to antibody killing but also seem to be susceptible to proliferation, which helps maintain the reservoir.

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Evaluation Summary:

This paper provides a new approach, Mixed Neural Likelihood Estimator (MNLE) to build likelihood emulators for simulation-based models where the likelihood is unavailable. The authors show that the MNLE approach is equally accurate but orders of magnitude more efficient than a recent proposal, likelihood approximation networks (LAN), on two variants of the drift-diffusion model (a widely used model in cognitive neuroscience). The comparison between LAN and MNLE approaches could be improved to strengthen the merits of the proposed approach over existing alternatives.

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Evaluation Summary:

Previous studies found that a component of the microbiota, Lactobacillus plantarum, can provide support to its host Drosophila melanogaster during development. They further explore this interaction using defined diets where they find that under conditions that have low levels of some essential amino acids, the bacteria can still promote survival even though the bacteria is not synthesizing the amino acid. Through a screen of bacterial transposon insertion mutants, these authors identify bacterial transfer and ribosomal RNAs as necessary for this effect. And studies in the fly demonstrate that the host kinase GCN2, a protein known to associate with host tRNAs, in enterocytes is the mediator of this response. This manuscript links the intestinal microbiota to host protective responses.

(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, these authors show that BDNF at the axon terminal can be retrogradely transported to promote new protein synthesis in the neuronal cell body and regulate dendritic morphology, which requires activated TrkB, Akt and mTOR in the soma and nuclear phospho-CREB. Although target-derived neurotrophin effects are well-established in the peripheral nervous system, this mechanism of signaling is less well-understood in the CNS. The manuscript presents a comprehensive analysis of the retrograde transport of BDNF/TrkB from the axon terminal to regulate dendritic morphology.

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Evaluation Summary:

This work is relevant to all who are interested in genome editing. The versatile Cas9 nuclease has enabled creative genome editing applications, yet the targetable sequence space is limited by the PAM specificity of the Cas9 RNP. This manuscript expands the Cas9 toolbox by defining the PAM specificity and genome editing activity of a large group of smaller-sized type II-C Cas9s. The results also contribute to our understanding of the diversity of Cas enzymes and show that there is a significant potential in mining for non-trivial genome editing tools amongst highly similar Cas orthologs.

(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 important paper describing the work to develop defined surface coatings for cardiac cell differentiation. The described experiments are convincingly supporting the critical role of fibronectin (FN) in the formation of precardiac mesoderm. The exploration of FN as necessary for pre-cardiac mesoderm formation was explored using various other ECM conditions, endogenous FN knock-out, blocking antibodies against integrin subunits, and inhibition of ILK via small molecule cdp22. In the case of the FN knock-out, experiments included rescue conditions that established a causal link between FN and the formation of precardiac mesoderm. Particularly insightful was the tracking of FN deposition over time with or without exogenously provided FN (i.e., the LN-111 case). This work is of interest to developmental biologists, stem cell biologists, and engineers as they work to optimize defined matrices for differentiation and manufacturing protocols of all cell types including cardiomyocytes.

(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 analyzes data from 150 previously published phylogenies of plants and animals from the Neotropics. A range of diversification models is fit in order to characterize patterns of diversification through time and across space. The authors reveal five biogeographic provinces within which long-term diversification has occurred, but they find that contrasting patterns of diversification for lineages are better explained by their phylogenetic relationship than by biogeographic province, such that the observed modern diversity of seed plants and tetrapods is a consequence of the groups' contrasting diversification dynamics. This paper is of potential interest to a broad audience of biologists who are working on the evolution of large-scale biodiversity, diversity hotspots, lineage diversification, and biogeography.

(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:

Kim et al. investigate interactions between Seipin transmembrane domains and triacylglycerol using molecular dynamics simulations. They identify the leading steps in droplet formation and provide a physical basis for understanding the initial phases of this process, highlighting the importance of transmembrane helices in the function of seipin protein. This paper will be of interest to cell biologists and biophysicists aiming to unveil and understand how lipid droplets are formed inside cells. The topic is important given that lipid droplets are key organelles used for energy storage, and that the failure in their formation can result in various metabolic diseases.

(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 provides a novel insight into regulation of osteogenesis by ERK-mTOR pathway. The authors proposed that the effect of Erk pathway would be mediated mTOR2-SGK1. The mitochondrial metabolisms appears to be involved in this regulation. This study is well performed, and the manuscript is clearly written.

(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 is an elegant imaging experiment in humans that shows that visual area hMT+, but not other candidate brain areas, signal the perceived motion path in a visual drift illusion. Using a powerful computational decoding approach, the results show a perceptual representation of the illusory position in space for moving stimuli even when the actual retinal position of the stimulus is kept stable. Such a representation and the underlying neural mechanisms are of broad importance for our understanding of the neural basis of sensory perception.

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Evaluation Summary:

In this manuscript, the authors map the cellular landscape in the tongue, which is an underrated immunological organ, with a main focus on tissue-resident myeloid cells under homeostatic and inflammatory conditions. They identify two major subsets of macrophages, which occupy distinct anatomical niches and develop from local precursors, while under immune compromised conditions they can also be replenished from circulating hematopoietic precursors. These findings provide an important basis for future investigations of the tongue immune function in the context of infection, inflammation, and neoplastic diseases.

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Evaluation Summary: 

The authors study the important problem of how to achieve accurate oscillation robustly in biological networks where noise level may be high. The authors adopted a comprehensive approach and study how different network configurations affect oscillation. This work makes an important contribution to the field, as it offers the first comprehensive survey of networks motifs capable of oscillation, with further characterization of their robustness. 

(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 employs a diverse array of approaches including single cell RNA sequencing, bioinformatic analyses, and whole genome bisulfite sequencing to propose a mechanism underlying their findings that will interest scientists broadly in fields of metabolism, development, and epigenetics.

(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: 

Nagle and colleagues studied the determinants of key physical properties of multicellular assemblies, using magnetic flattening of spheroids. Their key and insightful result is that intermediate filaments could also be implicated in the setting the elastic properties of these assemblies, shedding light on this central cellular component and how their modifications could be important to the understanding of some pathologies. The paper would be strengthened by additional experiments to better support the claims. 

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Evaluation Summary: 

Genetic forms of deafness are a major health challenge. This study deciphers the cochlear roles of Repressor element 1-silencing transcription factor (REST), a gene involved in the DFNA27 dominant form of deafness, using the mouse as a model system. This study provides evidence for a pathophysiological mechanism of deafness and shows how genes involved in different forms of deafness may interact together. The manuscript will be interesting to readers who work in the field of hearing research, REST regulation, or Kv7.4 regulation. 

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Evaluation Summary:

This work develops a new method to probe protein-protein interactions using proximity-assisted photoactivation, in which a receiver fluorophore (longer wavelength) can be photoactivated by the excitation of a nearby sender fluorophore (shorter wavelength). This new method is validated through in-depth characterization, comparison with FRET, and application to known systems of protein-protein interactions. While the new method bears the potential to expand the tool kit for probing protein-protein interactions, further characterizations of its photoactivation properties and comparisons with existing methods would be needed to inform researchers interested to apply this method to their own 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 #2 and Reviewer #3 agreed to share their name with the authors.)

Evaluation Summary:

Kinetochores are large protein complexes that mediate faithful chromosome segregation in eukaryotes. The authors develop an in vitro system to study interactions between kinetochores and microtubules in yeast cell extracts and detect a role for a kinesin motor protein in the generation of kinetochore movements. This paper should be interesting to researchers working in the field of mitosis, molecular motors, the cell cycle, the cytoskeleton, and, more broadly, for those studying macromolecular complexes with reconstitution and in vitro imaging approaches.

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Evaluation Summary:

This manuscript is of interest to neuroscientists willing to deepen their knowledge related to the role of the insula and to any scientist interested in oscillatory activities. The substantial dataset and the novel methodological approach provide interesting insights on the functional organization of this brain region.

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Evaluation Summary:

This study should be of broad interest to all virologists and many students of molecular genetics. It examines the constraints in a part of the HIV 1 genome that encodes important functional regions of two proteins, Rev and Env, in overlapping reading frames. It is convincingly shown that functional segregation occurs in a part of the overlap region that is critical for both proteins, which has important implications for HIV biology and may aid in the design of future HIV therapies.

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Evaluation Summary: 

DNA replication forks can become arrested either in a cellular program or by accident. In fission yeast, DNA replication fork arrests at the locus called the RTS1 are mediated by a DNA binding protein, Rtf1. In this paper, by combining genetics, proteomics, and genomics approaches, the authors nicely showed the role of Rtf2 as a fork barrier to mediate the splicing of rtf1 mRNA. The splicing-mediated control of protein abundance provides a new regulatory mechanism for the programmed DNA replication barrier. 

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Evaluation Summary:

This paper addresses how cells can robustly maintain direction during movement by ignoring noise in concentration gradients while also being able to adapt to new signals in those gradients. The authors study this tension in EGFR signaling by postulating a form of cellular memory in a theoretical framework based on dynamical systems and bifurcation theory. The authors also carry out experiments that raise interesting unresolved questions. This paper will be of interest to scientists of all stripes working on cell motility and for theorists who take a dynamical systems view of biological phenomena. 

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Evaluation Summary:

This manuscript addresses a significant and timely topic in translational control and will be of interest to researchers studying molecular biology or diseases impacted by the Integrated Stress Response (ISR). The combination of biochemical, structural, and in-cell experiments constitutes a comprehensive study that supports the proposed model for allosteric regulation of the active/inactive states of the eIF2B complex. The findings are relevant to neuropathologies, infectious and inflammatory diseases, diabetes, and metabolic disorders.

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Evaluation Summary:

This study assess the role of SMCHD1 provided by the oocyte at fertilization in the regulation of Xist expression in the embryo. They also provide preliminary analysis of the downstream effects of faulty Xist expression, on X chromosome silencing. This work has implications in epigenetics and embryonic development and aims at an audience interested in gene dosage regulation in mammals. Although of potential interest, some further analytical and experimental work is needed to understand how SMHCD1 works on the early stages of X inactivation.

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Evaluation Summary:

When the subjects are instructed to produce saccades away from suddenly appearing visual targets under time pressure, early saccades tend to be directed incorrectly to the peripheral target, suggesting that exogenous and endogenous signals that are related to the target position and instruction, respectively, compete to control the motor responses. In this study, the authors provide further evidence for the independence of these two processes by showing that they can account for temporal evolution of correct saccades regardless of the instruction, stimulus luminance or motor bias.

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Evaluation Summary:

This paper tests the hypothesis that subjective cognitive impairment (SCI) is linked to hyperreactivity to uncertainty. Using an information-gathering task, the authors demonstrate that individuals with subjective cognitive impairment sample more than controls under uncertainty. Despite the clear strengths of the experimental design and the novel insights into SCI, some of the findings rely on problematic between-subject correlation analyses that should be corrected. Furthermore, alternative accounts of the main findings are consistent with the data.

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Evaluation Summary:

This paper employs innovative approaches to elegantly tackle the question of how we are able to learn an object category with just a single example, and what features we use to distinguish that category. Through a collection of rigorous experiments and analytical methods, the paper demonstrates people's impressive abilities at rapid category learning and highlights the important role of distinctive features for determining category membership. This paper and its approach will be of interest to those who study learning, memory, and perception, while also contributing to a growing field which uses naturalistic drawing as a window into high-level cognition.

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Evaluation Summary:

This paper describes a new structure for a complex between a bifurcating electron transfer flavoprotein (ETF) and its client dehydrogenase. Because electrons are being supplied by the dehydrogenase, the ETF executes confurcation in contrast to all of those elucidated so far, which function in the opposite direction to effect bifurcation. As electron-confurcation and electron-bifurcation have emerged as important paradigms of cellular bioenergetics, the data reported herein pave the way for future exploration of similar electron transfer systems and lay the ground for understanding their structural basis. The work will be of relevance to all who are interested in the mechanisms of enzymes.

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Evaluation Summary:

The authors measure dry mass and its density in growing and proliferating cells at high temporal resolution and with high precision. Using this method to study mitotic cells, the authors show that some cell types lose dry mass early in mitosis by a mechanism involving exocytosis. This work improves upon the authors' method to measure the mass of single cells and its thought-provoking conclusion is that dividing cells 'clean out' their contents to give the daughter cells a clean start.

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Evaluation Summary: 

Overall, this study explores the differentiation of human pacemaker cells from human iPSCs, demonstrating different subtypes of pacemaker cells, and highlighting the role of Wnt and TGFbeta signaling in the formation of sinoatrial note cardiomyocyte subtypes. 

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Evaluation Summary:

This manuscript is of interest to cardiovascular and developmental biologists as it describes Dnajb6 as a novel gene linked with Sick Sinus Syndrome. The claims are mostly supported by observations using zebrafish dnajb6b trap line and Dnajb6 heterozygous mouse models. However, the paper would be strengthened be clarification of some experimental aspects and a discussion of the potential connection of DNAJB6 to the Sick Sinus Syndrome in humans.

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Evaluation Summary: 

This paper will be of interest to public health specialists and cancer scientists working in cancer prevention. The work presents valuable data on how the COVID-19 pandemic has impacted breast cancer screening indicators compared with previous years. Overall, the results support the assertion that while many key indicators have not been substantially impacted, the screening participation rate declined and fewer cancers were screen-detected in 2020-21. 

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Evaluation Summary:

This paper uses an innovative cell-free system to identify antiviral factors that interact with HSV-1 in cells. In addition to cataloging many capsid-interacting factors, the paper probes the antiviral mechanism of one of these, MxB. The data provide strong support for an intriguing model in which MxB "punches" holes in HSV-1 capsids, releasing viral DNA and potentially triggering host DNA sensors. However, the binding of a variety of factors to the capsid appears able to bind to and shield the capsids from MxB attack, suggesting a new perspective on how viruses might evade some host defenses.

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Evaluation Summary:

This manuscript will be of interest to readers in the field of infection and cell biology. The authors follow up their previous study to further deepen our understanding of host-pathogen interactions that contribute to transkingdom contact sites. The authors show that the Chlamydia effector protein IncV tethers ER to the bacterial vacuole in a manner dependent on the phosphorylation of its C-terminus by the host kinase CK2. In addition, the authors show that IncV recruits the host kinase CK2 to the bacterial vacuole in manner required for its phosphorylation and ER tethering. Overall, the data justify most of the key claims put forward by the authors. Nonetheless, clarification is required concerning the chain of events and the phosphorylation events required for VAP binding.

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Evaluation Summary:

The paper uses hybrid mouse lines to estimate the heritability of the microbiome and map variants in the mouse genome that are associated with the composition of the microbiome. The findings are of broad interest to microbiome researchers and improve on knowledge in the field, as they focus on mucosa-associated (rather than fecal) microbiome profiles and report a novel correlation between heritability and cospeciation rates. The results are intriguing, but technical and biological confounders are incompletely addressed in the manuscript's present form, potentially leading to surprisingly high estimates of microbiome trait heritability relative to previous work.

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Evaluation Summary:

The authors report a preregistered study which tests the effects of targeted memory reactivation (TMR), which is typically studied in the context of declarative memory, on motor memory consolidation during sleep. In a nap study, the authors use a standard TMR paradigm. Their results suggest a key role of oscillatory activity for motor memory consolidation, where distinct features of the slow oscillation spindle interaction mediate memory formation. Overall, this is a timely interesting. It is scientifically rigorous and transparently reported. The claims are well supported by the data.

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Evaluation Summary:

Bao and colleagues present a chemical genetics study to identify novel compounds extending lifespan in C. elegans, and they proceed to investigate the mechanisms of action of their most potent compound. Based on the known target TRPV4 of the screening hit, the authors provide evidence for the involvement of a C. elegans homolog (osm-9) in the observed phenomenon, although this evidence is not completely conclusive. This study will be of interest to researchers working on drug discovery, repurposing and lead optimization in the context of ageing.

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Evaluation Summary:

This paper is of interest for cancer biologists studying the role microRNAs in tumor growth. The work provides links between over-expression of microRNAs, downregulation of a ubiquitin ligase, inhibition of JNK and reduced tumor growth. Some of the data are properly controlled and analyzed. However, the key claims of the manuscript are not entirely supported by the data, and additional controls are needed.

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Evaluation Summary:

The manuscript shows that retinal ganglion cell light responses in awake mice differ substantially from those under two forms for anesthesia and previously attained ex vivo recordings. This difference is central to our understanding of how ganglion cell responses relate to behavior. There are a few technical issues and issues about how the work is presented that could be strengthened.

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Evaluation Summary:

This paper demonstrates that deletion of MKK6 reduces life span in mice, and leads to cardiac hypertrophy that progresses to cardiac dilatation and fibrosis with age. The authors also demonstrate that the mechanism for this phenomenon is through reduced p38a activation while causing MKK3-p38g/d hyperphosphorylation and increased mTOR signaling. The authors extend previous studies (that demonstrate a role for P38 proteins as downstream effector of MKK6) and identify the isoform of P38 that plays a role in this process. Overall, the studies in this paper are conducted carefully and most of the conclusions are based on the reported data.

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Evaluation Summary:

This manuscript uses a micropatterned cell culture system to explore the mechanism of human primordial germ cell-like cell specification from human pluripotent stem cells, and proposes a previously unrecognized role of NODAL signaling operating downstream of BMP signaling. The strength of the manuscript is the development of a simple and efficient in vitro system that is potentially suitable for exploring the mechanism of human primordial germ cell-like cell specification. With a more rigorous validation of the identity of the studied cells and more discussion relating the findings to developmental mechanisms in vivo, this study will be of interest to stem cell and developmental biologists.

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Evaluation Summary: 

This is a very elegant study that through cross-species analysis describes the evolution of ubiquitin ligase adaptor protein LZTR1-mediated degradation of RAS-related GTPase RIT1 as a principal regulatory mechanism for RIT1 function and its role in Noonan syndrome, a prominent subgroup of RASopathy disorders. Extensive genetic experiments in Drosophila and mouse suggest that important pathological phenotypes observed in LZTR1-linked RASopathy models are mediated by its ubiquitination target RIT1 and less by the canonical RAS isoforms. While the work further supports the connection between LZTR1 mediated RIT1 level modulation, it does not fully rule out the significance of canonical RAS isoforms in LZTR1-associated RASopathies in humans. 

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Evaluation Summary:

This work will be of interest to theorists in microbial systems biology. It shows that taking protein degradation into account improves theoretical predictions of bacterial growth laws at low growth rates. The theoretical aspects of this work are solid. Some underlying assumptions of the model and key predictions remain to be validated experimentally.

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Evaluation Summary:

In this manuscript, the authors discovered a new function of Rai14, an F-actin binding protein, in dendritic spine dynamics. They showed that Rai14 is localized at the spine neck and regulate spine density and function. Heterozygous Rai14 knockout mice showed impaired learning and memory and depressive-like behavior. Overall, this study provides novel insights into the molecular mechanisms underlying spine dynamics and depressive-like behavior. The main conclusions are supported by the data.

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Evaluation Summary:

The paper is of interest to scientists who study neuroanatomy or the many behavioural phenotypes that have been proposed to be associated with left-right asymmetry of the human brain. The authors' new tool appears to provide clues to identify individuals based on shape asymmetry.

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Evaluation Summary:

Krasniewski and colleagues leveraged single-cell transcriptomics to identify subpopulations of macrophages in the skeletal muscle of aging male mice. They identify several new resident subpopulations of skeletal muscle macrophages, spanning a range of polarization states using novel markers, and they identify a shift in relative abundances of these subpopulations with age, leading to a functional shift in inflammatory marker expression and phagocytic capacity. The study overall is an interesting and timely investigation of skeletal muscle macrophage populations and transcriptomics in both healthy young and old mice, and should be a valuable resource for the inflammaging and muscle biology field.

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Evaluation Summary:

This manuscript by Nakane et al investigates phototaxis of the rod shaped bacteria Thermosynechococcus vulcanus. This is important because most our knowledge on phototaxis is only emerging on round-shaped cyanobacteria. In the study, the authors demonstrate that T. vulcanus can chemotax positively or negatively to light depending on the light source. They identify a photoreceptor complex that drives negative phototaxis and propose that it impacts motility by increasing cdiGMP levels, which in turn would regulate the motility complex, formed by bi-polar Type-IV pili. Provided that the link between light induced cdi-GMP and spatial TFP activity is established, the work would provide a new mechanistic framework to explain TFP-driven phototaxis. This is an important topic because TFPs are emerging as spatially-regulated motility machineries in a large number of bacterial systems and linking their activity to receptors and secondary messengers is a current unresolved question.

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Evaluation Summary:

Medley et al. study A. mexicanus, an extreme-adapted organism with important connections to human health. The authors test metabolic responses in this natural model of elevated blood glucose and extensive body fat deposits, conditions generally expected to predispose to higher risk for metabolic syndrome and higher frailty. The work is rigorous and will provide a reference for future studies aimed at dissecting the mechanistic basis underlying metabolic shifts in this uniquely attractive model. The authors also provide an open and accessible window into their data and analyses by sharing a Shiny app.

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Evaluation Summary:

Analyzing the long-distance migration of centrioles to the dendrite tip of multicilated olfactory neurons in mice, Ching et al. use expansion microscopy to show that centrioles migrate as clusters, which mature as they reach the apical surface. The super-resolution data are impressive and the claims are generally supported by the data. Although the manuscript is largely descriptive, it is an important addition to the field, and will be of broad interest to cell biologists.

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Evaluation Summary:

This paper will be of interest to the structural biology community and people working on cryogenic fluorescence microscopy. This paper is a clear step forward in the use of single-molecule localization microscopy at angstrom resolution, thanks to low-temperature polarized super-resolution imaging and advanced data processing algorithms.

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Evaluation Summary:

This paper is of interest to scientists within the field of apicomplexans cytoskeleton and malaria parasite proliferation. A series of compelling experimental manipulations identify potential new pellicle proteins and dissect the role of a protein acyl-transferase for the development of the intraerythrocytic stages of Plasmodiun yoelii and the palmitoylation status of two potential substrates.

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Evaluation Summary:

In this paper, the authors identify topological metrics in gene-regulatory networks that potentially predict the kinds of phenotypic steady-states that the network allows. In particular, they apply their results to the epithelial-mesenchymal plasticity, showing that the relevant gene regulatory networks are structured as ‘teams' that may be 'strong', yielding stable phenotypes, or 'weak', yielding unstable phenotypes prone to plasticity. The work would be of interest to researchers interested in systems biology and the nonlinear dynamics of biological systems, as well as biologists interested in gene regulatory networks and their (mis)functioning in cancer cells.

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Evaluation Summary:

This study focus follows this group's previous work on EROS and NOX2. In this current study the authors examine neutrophil EROS in the generation of superoxide by the NADPH oxidase. They demonstrate how EROS is involved in the maturation of gp91phox and expand our knowledge on the role of EROS in regulating expression of the P2x7 ion channel.

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Evaluation Summary:

The authors have systematically examined relationships between muscle length and force potentiation in young adults using very carefully conducted and controlled measurements by dynamometry and estimated using patellar tendon shear wave speed. The paper should be of interest to those who study human performance.

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Evaluation Summary:

The paper addresses the highly timely questions of how to quantify aperiodic and periodic neural activity. This was done by extending previous work by embracing time-resolved parametrization of both simulated, noninvasive EEG and intracranial data. The new approach is termed Spectral Parametrization Resolved in Time (SPRiNT) and the paper shows that the slope of aperiodic activity is linked with both behaviour and age. The method thus demonstrates the importance of evaluating the state-dependence of aperiodic activity and dynamic properties of oscillatory components in a time-resolved manner.

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Evaluation Summary:

Synaptotagmins are Ca2+ sensors for synchronous neurotransmitter release. However, despite intense study it remains unclear exactly how the binding of 5 Ca2+ ions to Synaptotagmin's two C2 domains leads to the observed Ca2+ dependence of vesicle fusion. This study puts forward a novel mechanistic model of neurotransmitter vesicle fusion (vesicle exocytosis) which is relatively simple but significantly more detailed than the widely used phenomenological models of calcium-dependent fast exocytosis.

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Evaluation Summary:

The observations from high quality in vivo and in vitro recordings of tagged CHR neurons are supported by a computational model that suggests feedback inhibition may regulate the activity patterns of CRH neurons in distinct states, and represent an important contribution. The authors also present an unexpected observation that uncovers interesting neural dynamics that will provide the impetus for new studies exploring firing characteristics in discrete physiological and emotional states. Previous work reaching an opposite conclusion and likely effects of urethane on in vivo recordings are not discussed.

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Evaluation Summary:

This manuscript provides a comprehensive unbiased analysis of the fucosylation secretome and correlates with drug response in cancer. It uses a combination of bioinformatic based analyses of multiple datasets and cell based data to identify changes in the secretome and correlates this to drug responses to several targeted therapies.

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Evaluation Summary:

This manuscript is of interest to protein biochemists, protein engineers, and those interested in molecular evolution. The computation and experiments presented in this paper are very logical and rigorously performed. The results provide an example of how protein interaction specificity can be rewired using a small number of mutations, in the context of ancestral sequence reconstruction.

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Evaluation Summary:

The work reports collection of DNA from 400-plus individuals from the Kalinago territory of Dominica, and shows their relationships with other ancestries, along with a more specific genetic analysis of skin pigmentation. The material is clearly rare and hard to obtain and the analyses are extremely interesting. The work will be of interest to all studying human populations.

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Evaluation Summary:

In this work, the authors describe a protocol for coating supports for transmission electron microscopy with graphene. The approach uses a commercially available PMMA/graphene pad and the authors provide a new process for PMMA removal after graphene transfer. This work has the potential to be an important methodological step forward - if a way were found to remove amorphous residue from the surface of graphene. The work has the potential to be of broad interest to the many structural biologists using cryo-EM techniques.

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Evaluation Summary:

This work investigates natural variation in plant growth plasticity in Arabidopsis thaliana. Notably, the paper shows that plants from cold regions show less growth response to temperature than plants from warmer regions and this variation in response is consistent with local adaptation. These results have clear relevance for those specialized in working on A. thaliana life history.

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Evaluation Summary:

This work is of interest for readers in the field of bone regeneration, and more broadly to readers in the field of tissue repair and regenerative medicine. The authors took advantage of a well-established in vivo model, live imaging, pharmacological inhibition and genetic strategies to dissect the interrelations of key cellular events in zebrafish fin regeneration. The finding of how distinct generic injury responses are differentially regulated, and are functioning independently from each other, is a valuable piece of information for the community.

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Evaluation Summary:

This is an interesting simulation-based study focusing on the genomic epidemiology of Mycobacterium tuberculosis. The work nicely relates key biological and epidemiological parameters to how M. tuberculosis isolates cluster together, and to the terminal branch lengths in M. tuberculosis phylogenies. These concepts have both been applied to comparative studies of M. tuberculosis success and have often been interpreted as reflecting differences in transmission. The author finds that clustering and terminal branch lengths can also be modified by differences in the latent period, the mutation rate or the sampling fraction. This work will be of broad interest to readers studying tuberculosis epidemiology and transmission modelling.

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Evaluation Summary:

The authors describe a new tool to completely block both evoked and spontaneous release in a selective manner using the GAL4 system in Drosophila. Surprisingly, they see no effects on either pre or postsynaptic development when both evoked and spontaneous release are blocked, in contrast to prior studies in the field. Overall, the results are provocative and will be of interest to the field. The study contradicts a number of published works, so it is important for the field to see the data and be able to evaluate it themselves.

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Evaluation Summary:

Information about the environment obtained through sensory organs is processed and utilized at multiple levels in the brain. In this study, the authors use a variety of modern genetic and optophysiological tools to uncover the function and connectivity of glutamatergic neurons in a higher brain center of Drosophila - the lateral horn. They find that these neurons do not only encode chemical odor identity, but also the hedonic value (attractive or repulsive) of odors. This advances our understanding of how odors are represented in the brain will be of value to those who are interested in odour coding and behavioural valence of various odours.

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Evaluation Summary:

This manuscript describes a useful dataset for those interested in regulatory variation. The large scale of variants surveyed offers the potential to look for dependencies between nearby TF binding events at the same accessible site, and will likely be useful to those interested in dissecting sequence determinants of transcription-factor binding genome-wide.

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Evaluation Summary:

The strength of this paper is identifying a novel factor Bach2 that might be involved in the generation and/or maintenance of NK cells. To date, the full molecular network guiding the development, maturation and maintenance of NK cells has not been fully defined and Bach2 has not yet been investigated.

(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:

Stolyarova et al. investigate a highly polymorphic species, the fungus Schizophyllum commune, finding that compared to synonymous mutations, levels of linkage disequilibrium between nonsynonymous mutations are higher within genes than between genes. The authors propose this observation may be explained by compensatory interactions between nonsynonymous alleles, pointing to the presence of positive epistasis. This paper should be of interest to population geneticists and evolutionary biologists studying the role of natural selection.

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Evaluation Summary:

The manuscript by Liu et al., aims to develop a novel MRI-based approach to monitor virus specific CD8+ T cells and their relationship to cerebrovascular pathology in living brains. Using a mouse model of VSV brain infection, they show that MRI approaches can be used to identify microbleeds in the brain, and these microbleeds occur independent of immune cell influx. Furthermore, the transfer of low numbers of virus specific CD8+ T cells can reduce cerebrovascular bleeding. The capacity to track virus specific T cells and cerebrovascular pathology in real time in living brains would be a major technological advance.

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Evaluation Summary: 

Peyregne et al. studied the genes encoding proteins of the spindle apparatus. These genes have an elevated number of nonsynonymous substitutions in modern humans, and by comparison of modern and archaic alleles the authors identify that some Neanderthals had already the modern human haplotype at the KNL1 gene, raising the possibility that Neanderthals acquired it from modern humans. This study will be of interest to evolutionary biologists and anthropologists, because it supports the hypothesis that modern humans and Neanderthals interacted more than once in the past. 

(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:

Pseudomonas aeruginosa regulates the production of many cooperative traits through quorum sensing cell-cell signaling. The authors carried out transcriptomic studies of experimental evolved populations of P. aeruginosa and observed that the size of the quorum sensing regulon decreases when only a few but not all the cooperative processes regulated quorum sensing are required for growth. Their findings are consistent with the hypothesis that quorum sensing regulated genes can be counter selected rapidly when not beneficial. This study is of interest for microbiologists studying quorum-sensing, and evolutionary biologists studying the evolution of cooperative 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. The reviewers remained anonymous to the authors.)

Evaluation Summary:

The primary audience that will be keenly interested in these findings will be those with an interest in T cell development and thymic function, however given the broad applicability of transendothelial migration, there will also likely be broader interest in these findings. The manuscript provides key new insight into the importation of hematopoietic progenitors into the thymus to initiate T cell development. Overall, the main claims of the paper are well supported by the studies presented, although some clarification is needed regarding some experimental details, in particular the thymus reconstitution model used to test the effects of CD47-SIRPa inhibition in immunotherapy.

(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:

By addressing shortcomings in rabies viral-mediated labeling of monosynaptic inputs to ventral tegmental area dopamine neurons, this study provides a previously unattained precision local inputs to VTA dopamine neurons. Main findings include the preservation of a medial to lateral topography in the projection patterns within VTA microcircuitry, prominence of inhibition of DA neurons from the substantial nigra pars reticulata (SNr), DA-DA transmission, and inputs from raphe serotonin neurons. The precise local VTA connectivity described here is important for identifying how dopamine neurons compute reward, prediction, and movement-related signals during behavior, and thus is likely to be of interest to neuroscientists interest in those processes and the midbrain dopamine system.

(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 reports the phenotype of a zebrafish banp mutant that was identified in a screen for eye defects. Banp is known to regulate the transcription of a number of genes including those important in oncogenesis. In vivo function of Banp, especially in the context of normal development, remains to be better understood. The current study fills this knowledge gap and identifies the roles of banp during replication stress responses and mitosis. With somewhat more careful interpretation of the data and a clearer presentation of the results and their potential impact, this study will be of interest to scientists studying development, DNA damage responses and apoptosis.

(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 revisits a classical magnetic resonance imaging technique to image the brain's vasculature, showing that small blood vessels, deemed too difficult to image, could be targeted effectively with extremely high resolution imaging. This proof-of-concept, both theoretical and experimental, may be of use to build detailed models of brain physiology and detect fine alterations of the vessels in 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. The reviewers remained anonymous to the authors.)

Evaluation Summary:

Zhao et al. present an interesting proposal for the evolution of complex multimodal signals based on the analysis of the mating display of small torrent frogs. Combining observational and experimental evidence, they suggest that male limb movements, which are used to swat away blood-sucking midges, have become attractive to female frogs, enhancing the acoustic mating call of these males.

(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 connection between double-strand break (DSB) formation and chromosome pairing/synapsis during meiosis is not fully understood. In this paper, the authors show that the formation of DSBs is regulated by the DNA damage response (DDR) machinery. The paper will be of interest to the broad meiosis and DDR communities. While the main conclusions of the manuscript appear to be well-supported by the data, some gaps are present and the manuscript would therefore benefit from additional (mostly minor) changes.

(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 Family with sequence similarity 49 member B (Fam49b) protein is a newly discovered negative regulator of TCR signaling that has been shown to suppress Rac-1 activity in cultured T cell lines. In this study, the authors investigate the role of Fam49a and Fam49b in T cell development. The phenotype of mice lacking Fam49b mice suggests that it may be due to increased negative selection. The experiments are well performed and the results are convincing. Including data from TCR transgenic mice will solidify the view of the authors and greatly improve the impact of the manuscript.

(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:

Here, using a novel bioluminescence-based assay, authors dissect the sequence features of client proteins that influence SecA/SecYEG-mediated protein translocation across the bacterial inner membranes. Combined with rigorous kinetic modeling, this study pushes the description of this important cellular pathway towards a highly detailed level, which will potentially advance our understanding of ATP-driven protein secretion mechanisms in bacteria. The main conclusions are well supported, and the paper will be interesting to both those in the field of protein transport and to a broader audience.

(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.)