Evaluation Summary:

This paper will be of great interest to scientists within the fields of developmental biology and evolution, as well as to researchers that generally use the sea urchin as a model system or those employing single-cell mRNA-sequencing technology. The work provides a comprehensive analysis of the cell state specification of a whole deuterostome organism and proof of principle of the use of single-cell sequencing to identity deep homologies of cell type.

(This preprint has been 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, #2, and #3 agreed to share their names with the authors.)

Evaluation Summary:

This work clearly demonstrates an important role for two specific sodium-permeable ion channels for maintaining the pacemaker-like firing of midbrain dopamine neurons. These neurons have a key role in motivation, reinforcement and locomotion, and have been implicated in Parkinson's disease and multiple neuropsychiatric disorders. The authors also find that the regular firing of these cells is robustly maintained even when one of the two channels is knocked out, through upregulation of the level of the other channel.

(This preprint has been 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 identification of p130 as a substrate of cyclin F adds a new level of understanding about the role of this ubiquitin ligase in cell cycle control. While much of the data are string and of interest, several concerns need to be addressed with the inclusion of new experimental data. This work will be of interest to researchers in the fields of cell cycle 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 #3 agreed to share their name with the authors.)

Evaluation Summary:

It has long been known that nerves regulate the early formation of the blastema during limb regeneration through the promotion of cell proliferation. The manuscript by Wells-Enright et al. provides an interesting new role for nerves during salamander limb regeneration by showing that nerves also determine how much tissue to regenerate. They demonstrate that increased nerve abundance makes bigger limbs while a decrease in nerve abundance generates smaller limbs. Size regulation of organs is a broadly interesting and clinically important problem, which is why this manuscript should be of interest to a large general 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 #2 agreed to share their name with the authors.)

Evaluation Summary:

This paper provides further evidence for hemispheric asymmetry in the cortical control of manual actions based on intracranial (ECoG) recordings in human participants. Specifically, based a linear encoding model, the authors argue that movement encoding is more bilateral in the left hemisphere than the right hemisphere. The paper is well-written and the analyses are largely appropriate for addressing the primary hypothesis, though it would be helpful to detail the variability of electrode placement across individuals (which arises for the clinical intervention being undertaken) and incorporate this variability into the statistical analysis. Given the novelty of this type of human data and the well established question being addressed, this paper will be of interest to both basic and clinical researchers in motor neuroscience.

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

Evaluation Summary:

This manuscript uses viral tracing to identify interneurons, throughout the spinal cord, which synapse onto motoneurons innervating pairs of flexor and extensor hindlimb muscles. Importantly, the data identifies single premotor interneurons which travel to, and presumably regulate the activity of, multiple motor pools. It is possible that these premotor neurons are involved in regulating muscle stiffness across a joint.

(This preprint has been 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:

MicroRNAs (miRNAs) control gene expression during development and play crucial roles in disease. Loss-of-function mutations in key pathway components are embryonically lethal. Here, La Rocca et al. establish an elegant mouse model that enables acute and reversible inhibition of miRNA-guided silencing. Analysis of this model has convincingly demonstrated that miRNA activity is dispensable for homeostasis in most adult tissues, with the notable exception of heart and skeletal muscle. This work provides an extremely useful tool for the study of miRNAs in vivo and provides new insights into the roles of miRNAs in adult mammalian tissues. The findings presented will impact many fields given the well-established roles of miRNAs in normal development and 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. Reviewer #1 and Reviewer #2 agreed to share their names with the authors.)

Evaluation Summary:

This study aims to measure interpersonal and interethnic variation in human microbiomes and metabolomes in the San Franciso, CA, area. The strength of the study is in the level of robust analysis of the microbiota. It is interesting that diet is not one of the apparent associations in this study, yet the relationship of microbiota diversity to body habitus is strong in Caucasian subjects. Overall, the key results of this work nicely confirm that there are dissimilarities in gut microbiomes related to differences in ethnicity of subjects.

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

Evaluation Summary:

This is a strong manuscript due to its sophisticated behavioral analysis and modeling of behavioral output. The system and results provide a framework for future genetic analysis examining the biological basis of sensory behaviors.

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

Evaluation Summary:

This paper is of interest to cell biologists studying the signal transduction regulation of RNP granule assembly and its effects on cell growth. The work provides insight into the novel role of Pak1 kinase in the control of mRNA binding protein Sts5 and determines that Pak1 colocalizes with Processing (P) bodies during starvation and has function in P body dissolution after refeeding. Overall, the data are well presented, and support previous known findings.

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

Evaluation Summary:

This manuscript studies the alignment of malaria parasites (merozoites) at the surface of red blood cells (RBCs), a key element of their reproduction cycle during the blood stage of the disease. Building on a computational model the authors developed previously, which incorporates the stochastic nature of RBC deformations and adhesive bonds between the merozoite and RBC, it is demonstrated that parasite shape plays a key role in its alignment dynamics. In particular, the authors shed new light on the egg-like shape typically observed in Plasmodium merozoites, which has important implications for how effectively the parasite can survive and multiply.

(This preprint has been 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 develops new software tools to analyze and classify single cells with high throughput based on single cell phenotyping using an existing imaging system. The authors show that tissues can be reproducibly decomposed into clusters of cells based on their feature space and that cell composition dynamics can be reliably detected. The main impact is to make single cell phenotyping more tractable, including for samples and organisms for which sequencing-based or fluorescent-labeling-based approaches are not readily available. Applicability was demonstrated in two research model organisms, zebrafish and freshwater snail.

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

Evaluation Summary:

This work is of interest to the field of reproduction. Prior to fertilization, spermatozoa undergo a series of morphological and biochemical changes to become fertilization competent, driven by a rapid and poorly understood signaling cascade, culminating in the acrosome reaction. This latter reaction releases to the outside components from a vesicle, the acrosome, in the spermatozoan head and transforms the head plasma membrane so that sperm can fuse with the egg. The work shows that a G protein modulator GIV/Girdin, influences sperm motility and the acrosome reaction. In so doing it is important for fertilization and is one more strategy to control untimely acrosome reaction. The proposed mechanism is well supported by a variety of different experimental approaches.

(This preprint has been 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 across systems neuroscience or to those interested in how one component of a neural circuit contributes to downstream functions longitudinally. This study investigates how increasing feed forward inhibition in the dentate gyrus-CA3 hippocampal circuit impacts the formation and maintenance of context-specific ensembles in CA1 and the anterior cingulate cortex. However not all the claims of this manuscript are fully 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. Reviewer #1 agreed to share their name with the authors.)

Evaluation Summary:

This paper details coordinated work to both measure and model long-range correlations in the primate brain, during either rest or a reach-to-grasp task. The careful analysis shows that these long-range correlations are modulated by behavioral state, and can exist in the absence of common input or long-range anatomical connections. An analytical model is developed that shows how a disordered system with heterogeneous connections can give rise to this kind of long-range correlations, with only short-range direct connections between 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. The reviewers remained anonymous to the authors.)

Evaluation Summary:

This study reports a pivotal role of the conserved edge-strand of the periplasmic metalloprotease BepA in the folding and quality control of an outer membrane protein (OMP), the lipopolysaccharide transporter LptD, in gram-negative bacteria. The authors have discovered that, in addition to proteolytic activity, BepA has a chaperone-like activity and that BepA-mediated quality control of LptD and likely other OMPs occurs during their membrane insertion at the barrel assembly machinery. This result provides new insights into the biogenesis mechanisms of bacterial OMPs and the maintenance of OM integrity.

(This preprint has been 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:

In this study, Kim and co-workers track the dynamics of a large set of different ATP-dependent chromatin remodelers in living cells by utilizing state-of-the-art single-molecule imaging. They report that the remodelers exhibit very high turnover rates at target loci/nucleosomes, find evidence for cooperativity among the remodelers, and reveal the role of ATP hydrolysis in those interactions. These observations allow the authors to put forward a model for tug-of-war activities that modulate the accessibility of promoter regions for transcriptional activity. This manuscript brings important new information to the remodeler and chromatin dynamics 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:

This paper describes a newly developed, publicly available algorithm (iROAR) that was tested on pre-exisiting datasets and is of interest to T and B cell immunologists who perform repertoire analysis via multiplex PCR based techniques. iROAR utilises naturally occurring non-functional sequences to improve and partially correct the amplification bias inherent in multiplex PCR based sequencing technologies.

(This preprint has been 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 is of interest to psychologists and neuroscientist investigating systems memory consolidation. It describes an experimental protocol that allows precise, quantitative behavioural measurements to assess the development and interactions of item and gist memory traces over extended time periods. The study design and hypotheses are elegant and bring together ideas from several other fields of cognitive psychology (working memory, category learning). However, additional analyses, and in particular, comparison of some simple computational models, are needed before the conclusions are justified.

(This preprint has been 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 names with the authors.)

Evaluation Summary: 

This manuscript is of interest to researchers interested in specification and differentiation of the neural crest. This work presents a small single-cell RNAseq dataset from zebrafish trunk neural crest cells during the early stages of migration that identifies the subpopulations of trunk neural crest cells, new genetic markers and a subset of Rohon-Beard neurons. The paper confirms and extends previous work and reports expression of differentiated pigment cell types in the pre-migratory neural crest populations. 

(This preprint has been 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 readers in the field of plant evolutionary biology and paleontology, paleobotany in particular. Using novel 3D reconstruction techniques, the authors provide the first evidence-based reconstruction of Asteroxylon mackiei, the Early Devonian Rhynie chert plant known for a century, and demonstrate that it possessed an extinct pattern of root development transitional to the evolution of true roots in modern club-mosses. The use of multiple lines of evidence and 3D reconstructions based on serial sections of petrified materials provides compelling support for the key conclusions of the paper.

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

Evaluation Summary: 

This study investigates the effect of copy number variants across all genes in Saccharomyces cerevisiae, and the variation across different genetic backgrounds. Interestingly, apart from universal effects common to most of the genetic backgrounds, the authors also report strain-specific effects related to gene copy number variants. 

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

Evaluation Summary: 

This manuscript describes an interesting regulation of the hexosamine biosynthetic pathway (HBP) that is relative specific to the mouse embryonic stem cells (mESC). HBP produces UDP-N-acetylglucosamine, which is used in various protein glycosylation events, thus regulating many biological pathways. Understanding this pathway and its regulation is thus of fundamental 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. Reviewer #1 agreed to share their name with the authors.)

Evaluation Summary:

This paper examines the roles and mechanisms of how subunits of the mitochondrial calcium uniporter complex (MCUcx) regulate calcium uptake by mitochondria, a process that serves to match the rate of ATP generation to cellular metabolic needs. Based on direct electrophysiological recordings of MCUcx, the authors find that the MICU1 subunit potentiates channel activity in a calcium-dependent manner but does not block the channel at low calcium levels, challenging current models of MCU regulation. This work will be of significant interest to biophysicists and cell biologists interested in mitochondrial biology, bioenergetics, and ion channel and calcium signaling mechanisms.

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

Evaluation Summary:

Tonkin-Hill and colleagues present a large set of deep sequencing data from acute SARS-CoV-2 infections with each sample sequenced in duplicate. They use these data to characterize the within-host mutational patterns and diversity and relate them to SARS-CoV-2 diversity in consensus sequences sampled around the globe. It further allows understanding how this variation can or cannot be used to understand transmission dynamics and other applications in genomic epidemiology. 

(This preprint has been 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: 

The experiments reported here directly assess the impact of theta burst transcranial magnetic stimulation on neuronal activity. It will be of high potential interest to researchers using non-invasive brain stimulation. Although the results are highly intriguing, several methodological issues limit the inferences that can be drawn from the data as currently presented. 

(This preprint has been 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 provides important data on the contribution of the vmPFC to temporal discounting, by showing differential modulation of two well-known effects in inter-temporal choice (magnitude effect, episodic future thinking). VMPFC damage abolished the magnitude effect, but not a modulation of discounting via future thinking, a finding of interest to cognitive neuroscientists working on prospection, decision-making and executive control. 

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

Evaluation Summary:

This manuscript is of broad interest to readers in the field of human vision and its cortical topography as well as behavioral and genetic links. The investigation of the neurobiological basis of visual task performance asymmetries represents an important contribution to our understanding of how visual system architecture shapes perception. The key claims of the manuscript are well supported by the data, and the approaches used are thoughtful and rigorous.

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

Evaluation Summary: 

This paper will be of interest to a wide range of systems neuroscientists seeking to understanding the relationship between neuronal activity and behavior. Building on previous technical advances in brain-wide imaging of neuronal activity (Ca signals) in freely moving animals (Caenorhabditis elegans), it demonstrates that a linear regression model is sufficient reconstruct key parameters of locomotion - velocity and body curvature - from the imaging data and documents differences in activity between freely moving and immobilized worms. 

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

Evaluation Summary: 

This study is of potential interest to biologists interested in developmental patterning and the link between cellular identity and behavior. The authors perform experiments in the progenitor zone of avian embryos to propose that heterogeneity of cellular behaviors may drive morphogenesis and underlie cell fate choices. The work is nicely done but might need some additional experimental validation of the proposed hypothesis. 

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

Evaluation Summary:

This work describes an important feature of within-host acquisition of antibiotic resistance. This is a follow-up to their recent publication (Bakkeren et al. 2019), and complements their finding of persister cells in the tissues, to show that also chronic, tissue residing bacteria can provide plasmid tissue reservoirs. The experiments the authors performed are elegant and timely. This manuscript will be of interest to readers in the fields of infection biology, plasmid ecology, gut microbiomes, and antimicrobial resistance.

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

Evaluation Summary:

This paper is of interest to a broad audience interested in the coevolutionary arms race between plants and their herbivores. In a thoroughly investigated case study, the detoxification strategy of cockchafer larvae towards the major defensive compound of one of their preferred host plants, dandelion, is revealed and effects on the behavior of the larvae are described.

(This preprint has been 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 study analyzes publicly available genomic and proteomic data to identify host proteins that may be involved in regulation of COVID-19 susceptibility and severity. Several known and new targets are identified, further revealing the complexity of host genetic variation in COVID-19 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:

This paper will be of interest to scientists interested in the biology of the G-protein-coupled receptor Gpr161 and its ciliary regulation of Hedgehog (Hh) signaling. The phenotypes observed in a new GPR161 mutant mouse carrying a hypomorphic allele provide additional information showing which developing tissues are more sensitive to Gpr161 function. However, the data at this stage are insufficient to support the main novel conclusion: the ciliary function of Gpr161 is to regulate Gli3 repressor while the extra-ciliary function is to regulate Gli activator.

(This preprint has been 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 builds upon the recent observation that Schwann cell (SC)-specific loss of the mitochondrial protein Prohibitin-1 results in a rapid, progressive demyelinating peripheral neuropathy in mice associated with mitochondrial dysfunction. They establish pathways as downstream effectors of mitochondrial dysfunction in Schwann cells. The authors provide a comprehensive evaluation of these pathways following the loss of Prophibitin-1 and identify JUN and mTORC1 as potential mediators of myelin disruption.

(This preprint has been 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:

Sitaraman and colleagues address the fundamental question of whether gap junctions facilitate the formation of chemical synapses. To do so they test the function of the gap junction protein, Gjd2b, in early stages of synaptogenesis in larval Zebrafish cerebellar Purkinje neurons. They provide convincing evidence that Gjd2b is necessary for the development of glutamatergic synapses and dendritic arbor growth Purkinje neurons in vivo and that CaMKII plays a role in regulating arbor development. This study will be an important contribution to our understanding of molecular and cellular mechanisms underlying brain development.

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

Evaluation Summary:

Light and light perception are important factors that modulate several aspects of behavior and physiology in all animals, including humans. More specifically, the paper examines circadian cycling of phototransduction regulators in diurnal zebrafish and nocturnal mice, and links them to function at the level of ERGs. Interestingly, the transcriptional cycling is shifted between zebrafish and mice. This work is of relevance to vision researchers, but also of interest to a broader audience of behavioral (neuro)scientists and chronobiologists.

(This preprint has been 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: 

This manuscript provides evidence that loss of N1-methylation of G37 of tRNAs in bacteria on depletion of TrmD results in defects in aminoacylation and peptidyl-transfer, leading to ribosome stalling and phenotypes indicating activation of the stringent response. 

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

Evaluation Summary: 

This paper is of interest to a broad audience in the blood coagulation and fibrinolysis field. Previously undescribed roles in a range of blood clot properties are attributed to a region of the clotting protein fibrinogen, using state-of-the-art methodology. The data support the main conclusions of the paper, open new avenues of investigation for understanding clot properties, and have clinical implications. 

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

Evaluation Summary:

In this work, the authors provide a useful compendium of proteins labeled within SNpc dopaminergic cells using a novel approach. AAV virus was used to conditional express the APEX2 enzyme in dopaminergic neurons (based on DAT-1 Cre genetic technology) to rapidly biotinylate nearby proteins in oriented sections of brain whereby the striatonigral circuit can be spatially parsed for proteomic dissection. In addition to providing a useful new database of proteins for investigators interested in this circuit, the results also provide a more general approach to examining a compartment proteome in neurons and what might be expected in that analysis.

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

Evaluation Summary:

The authors developed an aorta-on-a-chip system to investigate the potential mechanism of Bicuspid Aortic Valve-Thoracic Aortic Aneurysm, BAV-TAA, and to test candidate pharmacologic agents. This study is of broad interest to readers in the field of lab-on-a-chip, biomedicine, biomaterials, etc. However, some important details regarding the development of the model are missing, as are some control data. The authors need to discuss the limitations of this model, such as the inability of their on-a-chip model to recapitulate aortic changes associated with complex pathologic processes such as ECM degradation, inflammation, etc, and discuss the importance of follow-up studies in in vivo 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. The reviewers remained anonymous to the authors.)

Evaluation Summary: 

This study seeks to develop a mathematical framework for estimating rates of chromosome missegregation based on known chromosomal properties and observed aneuploidy rates. A derived model is validated using live-cell imaging before being applied to several previously-described datasets from tumors and organoids. The subject matter is of high interest to aneuploidy and genome evolution researchers. 

(This preprint has been 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 is significant because it addresses a debated question in the field about whether different opioid receptor subtypes expressed in the same cells must function as a unit or function independently. Here the authors show that while mu and delta opioid receptors each signals in a similar manner in response to specific treatments, their interactions are largely independent of one another in modulating the firing and regulation by desensitization and internalization mechanisms in striatal cholinergic interneurons.

(This preprint has been 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: 

Strain variability in bacterial infections is a confounding factor in the treatment and prevention of the associated diseases. Pneumococcal disease is widespread, and the current vaccine targets only a subset of circulating strains, with disease and vaccine efficacy likely varying with the age of the host. Using two large databases of pneumococcal genomes, this study explores the associations between genomic factors and the age of the human host. Ultimately, these data and related studies will establish whether and how vaccines should be differentially designed for children and the elderly. This work will be of interest to those working in bacterial infections and host-pathogen genomics. 

(This preprint has been 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 suggest that that intrinsically generated persistent firing activity of medial septal glutamatergic (VGluT2+) neurons underlies initiation of locomotor activity. In this work, the authors provide evidence for a non-canonical role for persistent firing in initiating locomotion by performing a series of technically difficult experiments to dissect the circuit mechanisms of the persistent firing. This manuscript will be of interest to readers in the field of spatial navigation, motor control, and neural network dynamics. 

(This preprint has been 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: 

Non-nuclear genomes, such as those of mitochondria, contribute to many aspects of cellular function, organismal function, and fitness. Understanding their biology and evolutionary dynamics is thus an essential component eukaryotic evolution. The manuscript addresses an important and complex problem regarding the relationship between mitochondrial mutations, their impacts on gamete function, and the attendant evolutionary processes. The authors present a computational approach to distinguish between three hypotheses about the level of selection most likely to explain the distribution of mitochondrial mutations in human populations. They propose that selection among mitochondria is the most likely process to match empirical, clinical data, for mitochondrial mutation loads. There is, however, currently a mismatch between the fact that the data are derived from numerous different species whose biology is not always comparable, the model, and the title of the paper. 

(This preprint has been 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 explores the under-investigated role of mitochondrial activity and subcellular distribution for alveolar formation by using a variety of transgenic mouse models to delete two specific mitochondrial proteins. The data suggest a new concept for mitochondrial dysfunction driving lung injury and potentially human disease. With some further evidence to support the potential cell-specific role for the observed outcomes and additional mitochondrial assessment, this paper will be of interest to a large group of scientists interested in mitochondrial metabolism in general as well as lung development and disease in particular. 

(This preprint has been 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 presents a theoretical analysis of the abundance of components of the translation machinery (ribosomes, initiation, elongation and release factors, tRNA synthetases) in bacteria. These proteins make up a large fraction of the total proteome and their abundance is closely linked to cell growth. That the stoichiometry of the different components is adjusted such as to maximize the growth rate has been postulated a long time ago, but was so far only studied in detail for ribosomes and EF-Tu, the most abundant elongation factor. Here, the authors extend these earlier works to an unprecedented level of detail and provide a complete analysis based on this idea and derive the optimal stoichiometry for all these factor, which they find to be in good agreement with the observed abundance in different bacteria. This provides new evidence supporting the idea of proteome optimization for maximal growth. 

(This preprint has been 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: 

This study will be of interest to virologists and those working on RNA-protein particles. Strauss and colleagues studied the mechanism of RNA recruitment to ribonucleoprotein condensates using rotavirus. Using multiplexed DNA-barcorded smFISH and DNA-PAINT for direct visualization of the RNP condensates in cells, they observe the early onset of viral transcript oligomerization before the formation of viroplasms and the process of enrichment in RNP condensates. They were able to image all eleven transcripts in an RNP condensate and to quantify the amounts of these transcripts. Based on these findings, the authors suggest a selective RNA enrichment mechanism of rotavirus. The experiments are nicely executed, with good controls. 

(This preprint has been 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: 

Human Herpesvirus 6A (HHV6A) and 6B are common herpesviruses that establish lifelong infection in latent form and can cause severe disease upon reactivation. They are spread by acquired infection of free virus and by germ-line transmission of inherited chromosomally-integrated HHV-6A/6B in telomeres. The authors develop an approach to analyse a hypervariable region of the HHV-6B genome and exploit it to investigate the relationship between acquired and inherited virus, presenting evidence that HHV-6B can readily transition between telomere-integrated and free virus forms. 

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

Evaluation Summary: 

The study by Mika and colleagues uses a comparative transcriptomics approach to identify changes in the expression of genes that specifically occurred during the evolution of the human endometrium. The authors find that hundreds of genes gained or lost endometrial expression in the human lineage and that several of these genes are potentially implicated in the pathophysiology of human pregnancy. The study contributes to ongoing interest in the effect of human evolution on the pathophysiology of human pregnancy, and has the potential to serve as a model of how to study the evolution of pregnancy-associated genomic changes in particular species and tissues. 

(This preprint has been 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:

Bice et al. present new work using an optogenetics-based stimulation to test how this affects stroke recovery in mice. Namely, can they determine if contralateral stimulation of S1 would enhance or hinder recovery after a stroke? They found that stimulation of the cortex contralateral to the site of stroke impairs recovery from this stroke, and impairs the brain mapping and the connectivity that normally emerges in recovery from stroke. This unexpected finding in a mouse model relates to clinical literature on the role of the contralateral cortex in recovery.

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

Evaluation Summary:

This paper is of interest and relevance to clinicians and researchers in the field of muscular dystrophy, a condition that causes loss of muscle function and mobility primarily in older patients. The presented experiments suggest that at least part of the pathology of DM2, a certain form of muscular dystrophy, is caused by defects in a gene that is required for the production of small molecules, called polyamines which are known to support muscle health and function. Interestingly, in a Drosophila model of DM2, feeding with polyamines can restore muscle function. The paper gains broad interest by the demonstration that consistent with the findings in Drosophila, muscle biopsies from human DM2 patients show decreased ODC and polyamine levels, raising the possibility of using polyamines for therapy or prevention.

(This preprint has been 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: 

Previous studies have indicated that neurons in different cortical areas have different intrinsic timescales. In this study, Pinto and colleagues aimed at establishing the functional significance of intrinsic timescales across cortical regions by performing optogenetic silencing of cortical areas in an evidence accumulation task in mice. The results are of broad interest, but the reviewers identified a few important issues that need to be addressed to validate the authors' 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 #3 agreed to share their name with the authors.)

Evaluation Summary:

The manuscript introduces a new tool - BigBrainWarp - which consolidates several of the tools used to analyse BigBrain into a single, easy to use and well documented tool. The BigBrain project produced the first open, high-resolution cell-scale histological atlas of a whole human brain. The tool presented here should make it easy for any researcher to use the wealth of information available in the BigBrain for the annotation of their own neuroimaging data. This is an important resource, with diverse tutorials demonstrating broad application.

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

Evaluation Summary:

The manuscript by Harper et al. examines the cancer risk perceptions, provider communication behaviors and demographic factors influencing the uptake of both, cervical and colorectal cancer screening among 50- to 65-years-old women. Towards those goals, the authors adapted and administered behavioral questions from the Health Information National Trends Survey to a multiethnic population sample in Southeast Michigan. Self-reported cancer screenings for the tumors (as defined by the USPSTF updated guidelines) served as the variable outcome. The study has public health merit in its identification of distinct predictors for cervical cancer and colorectal cancer screenings. The insights from this work on screening behavior differences among women, the perception of cancer risks and impact of positive provider communication, point to the need for exploring new ways for more holistic and integrated cancer prevention with a targeted focus. The strengths of the study include (i) the identification of an unmet need in public health in a neglected patient population, (ii) the track-record of the seasoned investigators, and (iii) the recognition of two potentially actionable insights obtained from the study. Weaknesses of the work include (i) the descriptive and specialized nature of the manuscript, (ii) the regional setting of the study and the question of how generalizable their conclusions would be in other contexts, and (iii) the relatively incremental advance of the reported 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:

Bacterial ParB partition proteins have the novel property that they employ an unusual nucleotide cofactor for complex assembly at their specific DNA binding site, parS. The impact of this study is on our general understanding of this novel class of nucleotide-dependent processes, and the role that nucleotide-protein interactions play in DNA binding and bacterial 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 agreed to share their name with the authors.)

Evaluation Summary: 

This paper addresses researchers interested in architecture and function of the insect central complex as it represents the first comprehensive projectome dataset of any central complex outside Drosophila. The authors use the bumblebee as representative for hymenopterans with their navigation skills. Further, they mine their data for conserved and diverged aspects compared to fly (Drosophila) knowledge and hypothesize how the differences may relate to diverged neural circuit function. Hence, they provide an excellent and comprehensive descriptive resource providing a point of reference for others and a starting point for comparative studies of neural circuits. In particular, this study is the first comprehensive description of columnar neurons in the bumblebee central complex, described through the lens of the recently published fruit fly connectome of the same, homologous neuropil. The comparative approach used here holds promise for describing neural circuits in bees and flies in shared frame of reference. The authors use an approach that reflects a compromise between quick collection of electron microscopy (EM) data and being able to fully reconstruct all neurons in the bumble bee's central complex. The authors are transparent about the method's limitations and draw appropriate 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 and Reviewer #2 agreed to share their names with the authors.)

Evaluation Summary:

This interesting, timely and well-done study focuses on the mechanism underlying nevus growth arrest, which has received renewed attention as a result of recent studies that question the dogma that such arrest is mediated by oncogene-induced senescence. Through experiments involving both cultured primary human melanocytes and cells derived from clinical samples, the authors show that Braf-oncogene-induced nevus cell growth arrest results from microRNA-dependent suppression of the mitotic kinase Aurkb, which influences whether Braf activity is proliferative versus antiproliferative. While the conclusions made within the manuscript are justified, and there is sound acknowledgment of certain pitfalls that could be addressed in future research, more expansive sample sizes and further in vivo work would aid in providing more clinical relevance. This manuscript would appeal to researchers in the melanoma field, especially those studying the underlying mechanisms behind phenotypic plasticity and tumor heterogeneity.

(This preprint has been 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 rigorously conducted meta-analytic study, the authors investigated the functional and structural abnormalities associated with developmental dyslexia across languages. Convergent and divergent functional and structural changes as well as language-universal and language-specific brain alternations related to dyslexia are found. In general, the study has generated important results and the findings are of interest to readers in educational psychology/neuroscience fields, especially those focusing on reading development and dyslexia. The analytic approach used in this study is cutting-edge, the data support the main claims, and a detailed discussion is presented. 

(This preprint has been 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: 

How the bacterium E.coli decides when to divide is an interesting, important, unsolved and highly controversial topic of interest to readers across disciplines, including microbiology, cell biology and statistical physics. Popular "single process" models invoke regulation at the step of replication initiation or at the step of cell division per se, whereas these authors have previously proposed a "concurrent cycles" model in which both processes are relevant, with different prominences in different situations. Consistent with the authors' motivating hypothesis, in the particular perturbed condition investigated in this work, a process different from DNA replication becomes increasingly important for division control as the degree of perturbation increases, which provides a new challenge to models for cell division control. 

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

Evaluation Summary:

This study describes reduced antibody cross-reactivity between the SARS-CoV-2 B.1.1.7 variant and the parental strain or the B.1.351 variant. Asymmetric antibody responses and reduced neutralizing antibodies against heterogeneous variants have been demonstrated in multiple studies. The current study reports reduction of B.1.1.7 COVID-19 sera against the SARS-CoV-2 parental strain and B.1.351. This observation is interesting and could be useful for future vaccine development. The work is of interest to virologists and infectious disease specialists.

(This preprint has been 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 provides an experimental and computational method for the identification and reconstruction of full-length circRNAs using nanopore sequencing,. With a better comparison to other existing methods in the field and a clearer demonstration of the advantages of the described methodology, the work would be of great interest to researchers in the circular RNA 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. Reviewer #3 agreed to share their name with the authors.)

Evaluation Summary:

This paper is of great interest for researchers working in the filed of cell adhesion and cell migration. The authors show for the first time that alpha5beta1 ligand spacing profoundly influences the collective migration behaviour of keratinocytes. They demonstrate that this parameter can outcompete the well-known and studied influence of substrate stiffness.

(This preprint has been 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 perform a tour-de-force study of classical conditioning in fly larvae. Experiments are original, findings are exciting, and we expect this paper to have a substantial impact. There is potentially an issue in the assay of larvae preference taking an hour of unrewarded presentation of CO2, while the training and extinction happen on much shorter scales, muddying the ability to interpret the results. A mathematical model of the conditioning process is also missing, which also makes interpretation harder.

(This preprint has been 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 interesting study aiming to link the evolutionary effects of dietary mismatch in humans to increased inflammatory responses and risk of chronic diseases. To uncover more insights into the causal links, the study used a non-human primate (macaque) model to show that the dietary switch from a Mediterranean to a modern Western diet leads to the polarisation of monocyte cell populations toward a more pro-inflammatory state, which in addition to increasing the chronic health risk can also impose behavioural changes such as anxiety and social isolation. The results of this study are convincing, interesting, and have fundamental importance in evolutionary biology, immunology and psychology. The extent to which these findings can be extrapolated to human populations remains to be 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 #1 and Reviewer #2 agreed to share their names with the authors.)

Evaluation Summary:

Although the role of membrane potential in Cell Permeable Peptides (CPP) translocation has been consistently described in artificial systems, this multi scale study, combining cell biology, genetics and in silico approaches, further extends this topic to a live cell context where it shows that internalization stops when the membrane polarization is decreased by the removal of potassium channels. It proposes an original mechanism of CPP translocation based on water pore formation, which should be of interest for biophysicists, cell biologists and for applications such as drug delivery.

(This preprint has been 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:

Glioblastomas, like many tumors, consist of a cohort of actively dividing cells and a substantially larger fraction of non-proliferating cells. The standard of care involves the administration of a chemotherapy drug (temozolomide (TMZ)) whose antitumor activity is thought to be dependent on a toxic intermediate produced during DNA replication. In this report, the authors show how this compound is also processed by the interaction of two DNA repair pathways which produce the same intermediate without the requirement for DNA replication. The paper will be of interest to those scientists concerned with the implications of DNA damage and repair for cancer chemotherapy, particularly for tumors as deadly as glioblastoma.

(This preprint has been 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 study reports that calsyntenin-3, a synaptic adhesion molecule, is expressed in cerebellar Purkinje cells and that acute knockout of calsyntenin-3 increases excitatory synapse density and decreases inhibitory synapse density. The manuscript provides compelling evidence that elimination of calsyntenin-3 from cells in the cerebellar cortex alters the E/I balance for Purkinje cells by increasing the strength of excitatory parallel fiber inputs and decreasing the strength of inhibitory inputs. However, it would have been far better to selectively target Purkinje cells, but that was not done. This is the first study showing that a particular synaptic adhesion molecule regulates excitatory and inhibitory synapse in opposite directions.

(This preprint has been 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 in the field of collective behavior addresses how naïve and experienced individuals (i.e., homing pigeons) pool information in order to navigate while flying back home. The authors show that the passage of information is largely democratic, meaning information passes both ways, and that, unexpectedly, exploration of the route is initiated both by naïve and experienced birds. The work provides a new perspective on information sharing during collective 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 study uses the approach of labeling neurons with distinct birthdates so they can be differentiated in experiments performed later in development. The authors then test morphological, functional and circuit inputs/outputs patterns of these neurons by using immunohistochemistry, slice electrophysiology, retrograde labelling, morphological reconstructions and behavioral assays. The manuscript is likely to make a strong impact in the field of developmental neuroscience and a good impact related to more general cellular and molecular neuroscience.

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

Evaluation Summary:

This manuscript will be of interest to epidemiologists and population biologists interested in outbreak dynamics in populations with complex social structures, such as emergent viral infections of humans. The study offers a functional, differential-equation (DE)-based framework for capturing the transition from emergence to endemicity without the huge over-compensation cycles typically predicted by DE models but rarely seen in natural populations. The model framework currently offers insights into the drivers of epidemic dynamics and, after further testing and calibration, may be useful for assessing control strategies for emerging infectious 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. Reviewer #2 agreed to share their name with the authors.)

Evaluation Summary:

The work will be of interest to anyone interested in signal transduction, and especially those studying GPCRs and membrane receptors. Dimerization and oligomerization of G protein-coupled membrane receptors (GPCRs) are expected to be critical for receptor function. This intriguing study helps understand the usually underestimated role of GPCR soluble domains. The authors discovered that oligomerization of a GPCR can be mediated by multiple weak interactions between soluble domains that are "tunable" by environmental factors, thus possibly modulating the function of this important class of membrane receptor proteins. What remains to be shown is how oligomerization alters receptor 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 #1 and Reviewer #2 agreed to share their name with the authors.)

Evaluation Summary:

The authors ask why the APOE4 allele has persisted, often at high frequencies, in human populations despite its associations to heart disease and Alzheimer's disease. They consider the hypothesis that APOE4 may be advantageous in a high pathogen and high physical environment settings (as opposed to a low pathogen industrial lifestyle) through an in-depth characterization of the Tsimane in Bolivia. The study is of broad interest with an insightful dataset; the conclusions are somewhat limited by the nature and current description and treatment of 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:

This submission reports an approach to identify bacterial specific carboxyesterases that can be exploited to activate prodrugs of antibiotics in Staphylococcus aureus. The main premise is that charged functional groups found in some antibiotics prevent entry of these into bacteria, an effect that can be circumvented through esterification of the antibiotic to allow entry. Thereafter, activation of the antibiotic will occur in the bacterial cytoplasm through hydrolysis by bacterial esterases. This could lead to new antibiotic delivery strategies.

(This preprint has been 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:

Drosophila species have long served as an important model system for genetics and genomics. The authors have developed an important community resource of high standard genomes for many species across the Drosophila clade. This resource will serve to empower the next generation of Drosophila research and provides an important road map for similar efforts in other groups of organisms.

(This preprint has been 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 the first digital adult zebrafish brain anatomy atlas that includes ten highly informative markers for different brain regions and cell types. The authors utilize new clearing techniques to enable staining of the whole fixed zebrafish adult brains, and light sheet microscopy fluorescent imaging to obtain high resolution three-dimensional data. Several individual dataset for each marker are registered and aligned to an anatomical model using fluorescent cell nuclei and autofluorescence patterns by state of the art volume registration algorithms. The results appear to be of high quality. The authors also provide a detailed and state-of-the-art anatomical annotation of brain regions. Using ten different antibodies to fluorescently label different neuron types, stem cells and glia, proliferation zones, and some specific anatomical regions, the authors demonstrate the utility of their database. This will be a valuable resource for neurobiology research in zebrafish.

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

Evaluation Summary:

This manuscript will be of interest to developmental geneticists interested in neuroscience, as it demonstrates how spinal motor neurons maintain their unique identities in adulthood after fate decisions are made in the embryo. The work here suggests that a Hox transcription factor acts as a terminal selector to control motor neuron identity, thus mirroring recent studies in C. elegans, and pointing towards this type of gene regulation as important in building diverse nervous 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 agreed to share their name with the authors.)

Evaluation Summary:

This is a well conducted study that examines the potential role of senescent cells in fracture healing. Furthermore, the authors have used senolytic agents to examine if targeting cellular senescence will have a significant impact on fracture healing phenotype. The manuscript is succinctly written, and the methods and results are well described. These data provide the first demonstration for a potential role for cellular senescence in regulating fracture healing. The authors’ conclusions are largely supported by the experimental 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. Reviewers #1, #2, and #3 agreed to share their names with the authors.)

Evaluation Summary:

In this study, Knight and colleagues investigate the role of the ribosome and translational control in colorectal tumours. A mutation of a protein of the large ribosomal subunit, RPL24, is used to suppress tumours driven by two mutations found commonly in cancer, in APC and KRAS. The authors identify a mechanistic output of the RPL24 BST mutation, eEF2 phosphorylation, which they demonstrate is a major effector in inhibiting tumour cell translation and proliferation. By targeting the eEF2 kinase eEF2K, they restore protein synthesis in RPL24 mutant cells. The conclusion is well supported by the experimental data presented, which implies that translation elongation can be a potential therapeutic target of KRAS mutated CRC. Importantly, Rpl24Bst in wildtype intestine does not affect epithelial cell proliferation and differentiation, suggesting that translation elongation can be used as tumour-specific target.

(This preprint has been 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:

Tian et al. used a battery of biophysical techniques to compare wild-type SARS-CoV-2 with two variants (B.1.1.7 and B.1.351). The authors obtained evidence consistent with the receptor-binding domain (RBD) of the variants exhibiting higher affinity ACE2, providing a possible explanation for their higher transmission. However, the effects are modest, and further work will be needed to confirm that this difference explains the increased transmission of the variants. Despite the need for follow-up studies, the paper is among the first to show definitively that the N501Y mutation confers enhanced binding to ACE2.

(This preprint has been 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 addresses an interesting and important question in evolutionary biology: how does the variance in fitness (components) vary between the sexes? In particular, it aims to evaluate whether there is a larger sex difference in systems with strong sexual selection. This study will be of considerable interest to researchers working on sexual coevolution and the role of sexual selection in promoting adaptation. However, there are some concerns regarding the limitations of the data and methods in support of the 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 #3 agreed to share their name with the authors.)

Evaluation Summary:

This study will be of interest to scientists involved in high-level vision. The data provide a compelling demonstration of the causal role of three key visual areas in context-based object recognition. The key claims of the manuscript are supported by the data, and are strengthened by the pre-registration of each of the three experiments.

(This preprint has been 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:

This manuscript is of interest to scientists within the fields of actin cytoskeleton, cellular neurobiology and neurodevelopment. It explores how actin regulators are coordinated to trigger the formation of branches in neuronal dendritic arbor. Experiments are very well performed. Conclusions of the manuscript are convincingly supported by the results, although strict dependence of Cobl and Cobl-like in dendritic branch formation should perhaps be confirmed with additional experiments or tuned down. Results concerning the spatiotemporal relationship between the molecular players involved are more preliminary and few findings already published by the same group in previous articles should be expunged from this 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. Reviewer #1 agreed to share their name with the authors.)

Evaluation Summary:

This paper compares the properties of UV cone output synapses in different regions of the zebrafish retina using a combination of electron microscopy, quantitative imaging and computational modeling. They relate these differences to ultrastructural differences in synaptic ribbons and evaluate them using a previously-developed biophysical model for the operation of the synapse. The finding of regional differences in ribbon behavior is novel and suggests an under-appreciated degree of control of release by ribbon structure and behavior. The presentation of some of the results, particularly the model, could be strengthened.

(This preprint has been 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:

Capturing the rate and degree of protein turnover in tissues rich in collagen, proteoglycans and glycoproteins over the life span provides valuable information about how these tissues age and can increase our understanding of age-related disease. Using a Stable Isotope Labeling (SILAC) method to examine protein retention, new protein incorporation and protein turnover in three high collage content tissues, the authors show that turnover is low in older mice in these tissues, but the depth of the data generated provide a detailed examination of what low turnover means at a level we have not previously had. This paper would be of interest to a broad range of scientists studying connective tissues in the context of development and ageing.

(This preprint has been 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, which will be of interest to neuroscientists in the fields of learning and memory, somatosensation, and motor behavior, uses systems neuroscience tools to expand our view how the postero-medial (POm) nucleus of the thalamus contributes to goal-directed behavior. The reviewers suggested additional ontogenetic experiments to clarify the nature and specificity of those roles. They also indicated that certain alternative explanations to the experimental observations could be addressed for a more balanced presentation and interpretation of the results.

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

Evaluation Summary:

Understanding genes that control susceptibility to infection is critically important. In this manuscript Ji et al. identify the gene SP140 as the driving mutation resulting in susceptibility to a range of bacterial pathogens located within the severe susceptibility to tuberculosis (SST1) in mice. While our understanding of how SP140 functions remains unknown, the identification of a single gene within this locus that regulates Type I IFN is impactful and will be of broad interest for immunologists and microbiologists alike.

(This preprint has been 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 unravels a detailed bipartite signaling mechanism, activation of which results in epithelial inflammation and cell motility. The paper is potentially of broad interest to cancer biologists and epithelial cell biologists. The data generated using the combination of genetic analyses, chemical inhibitors, and state-of-the-art confocal microscopy is of exceptionally high quality and supports the majority of the claims made in this paper.

(This preprint has been 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 utilizes holographic microscopy to study the swimming behaviour of flagellated forms of Leishmania mexicana in the presence or absence of host cell stimuli. Infective metacyclic promastigotes were found to swim faster than actively dividing procyclic promastigotes and to display different average trajectories. The swimming trajectories of these parasite stages were also altered in the presence of macrophages, promoting chemotaxis towards target host cells. The findings provide new insights into promastigote flagellar function and role of swimming behaviour in promoting pathogenesis.

(This preprint has been 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 assessed multivariate relations between a dimensionality-reduced symptom space and brain imaging features, using a large database of individuals with psychosis-spectrum disorders (PSD). Demonstrating both high stability and reproducibility of their approaches, this work showed a promise that diagnosis or treatment of PSD can benefit from a proposed data-driven brain-symptom mapping framework. It is therefore of broad potential interest across cognitive and translational neuroscience.

(This preprint has been 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:

Cohen and Baldassano present analyses of a large publicly available set of neuroimaging data from children and adolescents watching an animated movie, and is likely be of interest to neuroscientists interested in methods for analyzing naturalistic neuroimaging data, or those interested in the development of narrative processing in the brain. The results are not embedded in a strong theoretical framework and it is not yet clear which hypotheses are supported and which are refuted. However, the methodological approach developed here is a valuable addition to the repertoire of developmental neuroscience.

(This preprint has been 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:

The ability to fully resolve the whole genome of viral pathogens is often hampered by a multitude of different obstacles, one of which is optimally amplifying different regions of the genome. Part of this challenge lies in designing the best primers pairs that can consistently amplify PCR products despite the presence of changes (mutations) in the genome. The work described by Jaworski and colleagues can potentially provide an alternative approach that does not depend on primer pairs to fully sequence one such viral pathogen, SARS-CoV-2, and can also be applied towards other viral families.

(This preprint has been 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 combines 2D and 3D cryo-electron microscopy to show that cellular keratin intermediate filaments have heterogenous diameter, protofilament number and protofilament arrangement. This demonstrates the challenge for future high resolution structure determination of these essential filaments as well as providing the basis for understanding how this heterogeneity facilitates their 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 #1 and Reviewer #2 agreed to share their names with the authors.)

Evaluation Summary:

Vinbert et al. provide a conceptual replication on individual differences in conditioned skin conductance response during fear acquisition training and BOLD fMRI in a large sample (N=285) of healthy individuals (mono- and dizygotic twins). The authors report results that are in line with previous work and new results from a whole-brain analysis and suggest unique and shared contributions of individual brain regions. This is a timely and well-conducted replication study, the sample size is large for this area, and there are robustness (multiverse) analyses in place to ensure that findings are not driven by particular analysis choices.

(This preprint has been 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 will be of interest both to marine biologists and to biophysicists studying voltage-gated proton channels. It describes cloning and full biophysical characterization of the first ion channel ever identified in reef-building coral species, and develops a mechanistic model for understanding regulation of voltage-gated proton channels.

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

Evaluation Summary:

This is a well-performed study that defines the role of purported host cell receptors in the entry of hantaviruses into human endothelial cells. This is an important study as it applies CRISPR-mediated deletion studies for candidate receptors in the same endothelial cell line (TIME).

(This preprint has been 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 will be of interest to neuroscientists studying the effects of cholinergic modulation throughout the brain. It provides strong support for the view that activity in the basal forebrain cholinergic system is not monolithic, but varies across the rostrocaudal axis, consistent with previous reports of differential connectivity of these areas. Strong evidence for regional differences in cholinergic responses collected simultaneously under multiple behavioral conditions provides valuable context for interpreting variability in existing and future studies.

(This preprint has been 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.)

summary text new

Evaluation Summary:

This article is of general interest to scientists who perform two-photon calcium imaging in vivo and explore the link between function and structure in real neural networks. The development of efficient approaches to estimate true correlations between large sets of noisy individual neurons based on realistic and thus limited observation time is a key to better understand functional local circuits. The effectiveness of the proposed method is illustrated by simulations and applied on real data, but several steps in its procedure remain to be clarified in the current form of the manuscript to be usable by a wide range of users.

(This preprint has been 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 examined the neural mechanism underlying stimulus-outcome associations. Using a series of sophisticated experiments with otpogenetics and pharmacogenetics, the authors show that interactions between the basolateral amygdala (BLA) and the lateral part of the orbitofrontal cortex (lOFC) play critical role in learning to predict the identity of outcome predicted by a cue, but not in learning to predict reward generally. These results extend our understanding of how BLA and lOFC regulate the formation of associative learning and subsequent decision-making.

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

Evaluation Summary:

In this work, Holz and colleagues develop a computational stochastic model of lamellipodial actin network growth and turnover to address an unresolved important question: how do these networks remain wide enough, maintain angular order, and actually increase the filament length behind the leading edge? They compare the filament organization and rate of incorporation/detachment of actin subunits with experimental data published in the literature. A main result from this study is that frequent filament fragmentation and annealing are key events in the reorganization of branched actin networks. The paper is well written, contains very thorough and fair literature review, is accurate, well documented. The result is novel and significant.

(This preprint has been 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:

Cell movement is essential for development and tissue homeostasis. While the cellular machineries involved in movement have been well studied, how cells maintain a persistent direction of motion is less well understood. Here, Coppey's team shows that movement persistence emerges from the coupling of two cellular systems: protrusions at the leading edge and polarity of secretion. This coupling is controlled by the small GTPase Cdc42. The authors propose a physical model that recapitulates the coupling, defines two key parameters and explains persistent cell migration.

(This preprint has been 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 will be of interest to cell biologists interested in understanding processes that regulate the biogenesis of the primary cilium, and to others interested in ciliopathies (ie disorders of the primary cilium). The authors have identified a novel pathway that controls the generation and length of primary cilia and show that its effects are mediated at least in part through its effects on regulating the cytoskeleton. They suggest that this pathway may also have clinical relevance for autosomal dominant polycystic disease, but the data and rationale underlying this part of the study wold need to be strengthened. 

(This preprint has been 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 researchers working on a broad range of questions in evolutionary biology, from the evolution of multicellularity to senescence and cancer. With their model, the authors study an often-neglected aspect of cellular differentiation and division of labour. While the model is relatively simple, the premise and the findings are thought-provoking and this study can potentially provide the groundwork for further investigation.

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

Evaluation Summary:

Kasper et al. have analyzed intra-ocular cells in four subjects with HLA-B27-associated acute anterior uveitis, 2 subjects with HLA-B27-negative anterior uveitis, and one subject with bacterial endophthalmitis using several assay techniques including single cell RNA-Seq, fluorescence activated cell sorting, and quantification of multiple cytokines. They discovered a unique pattern in HLA-B27 positive uveitis that exclusively featured plasmacytoid and classical dendritic cells (cDC) infiltrate and plasma cells. These might provide hints for the pathogenesis of this disease. 

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

Evaluation Summary: 

This manuscript is of potential interest to experimental haematologists studying initiation and maintenance factors in leukaemia. Overall, the study is well designed and the data is clearly presented. However, in some places the analysis lacks depth and technological sophistication, and the novel insights are limited without additional experimentation. 

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

Evaluation Summary: 

The study by Vanacker et al examines the effect of activating GFAP expressing cells within the POA and ARC on the activity of GnRH and TAC2 neurons as well as LH levels. The authors found that activation of GFAP POA cells activated GnRH neurons and increased circulating LH levels, limited to intact males. Activation of ARC GFAP cells failed to alter TAC2 activity or LH levels. Inhibition of POA GFAP cells or activation of POA GFAP cells in females failed to alter the firing rate of GnRH neurons. The study is largely well done and clearly presented. 

(This preprint has been 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 will be of interest to structural biologists, enzymologists, and cell biologists. The kinase complex mTORC1, a master regulator of cell growth, can be inhibited by another protein, DEPTOR. This protein is of general interest for several reasons, including the hope that understanding how DEPTOR works will lead to new strategies for therapeutically tuning mTORC1 activity. This study provides insights into the binding and inhibitory effects of DEPTOR on mTORC1. Solving a few technical questions will improve the work.

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

Evaluation Summary: 

Zappia et al investigate the function of E2F transcriptional activity in the development of Drosophila, with the aim of understanding which targets the E2F/Dp transcription factors control to facilitate development. They characterize changes in gene expression by proteomic profiling, and characterize Dp loss phenotypes in muscle, fat body, and the whole body. They document low levels of glycolytic intermediates and circulating trehalose, which is traced to loss of Dp in the fat body. Strikingly, this phenotype and the resulting lethality during the pupal stage (metamorphosis) can be rescued by increasing dietary sugar. Hence the authors provides new insights in the function of E2F/Dp. 

(This preprint has been 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 reports the atomic structure of XKR9, a membrane protein that is implicated in initiating the process to get rid of cells that are undergoing programmed cell death (apoptosis). The protein of interest was originally proposed to be a lipid channel, but the work presented here suggests that it is unlikely to function in this capacity alone. As a first step in this nascent field, the paper should be of interest to membrane structural biologists, and those working on lipid transport 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 #3 agreed to share their name with the authors.)

Evaluation Summary:

Yamagata et al., present a new transgenic mouse where the cells expressing the gene Scn1a also express green fluorescent protein. This new model is an important contribution to the study of Dravet Syndrome- an epileptic disorder, that is often drug-resistant, where ~80% of patients have loss-of-function mutations in SCN1A. This study confirms the well-known presence of Scn1a in interneurons and identifies Scn1a-expressing subpopulations of cortical neurons that could also potentially contribute to the symptoms of Dravet Syndrome.

(This preprint has been 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 is of interest to the broad malaria research community and especially those who work on drug resistance. The authors provide a summary of their surveys of African and Southeast Asian Plasmodium falciparum parasites for the Kelch 13 gene, a marker of artemisinin resistance. The contribution of several K13 mutations to artemisinin resistance is investigated in different genetic backgrounds and confirms the lack of a barrier for the potential emergence of artemisinin resistance in African parasites. These findings are of prime importance in the context of public health perspective on managing the risk of resistance appearing in Africa.

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

Evaluation Summary:

Stress granules are a critical component in the defense against certain viruses. The mechanisms regulating stress granules induced but the NF90 pathway are not well defined. Here, the authors use biochemical, cell-based, and in vivo approaches to make the novel discovery that Tim3 functions as a negative regulator of NF90-mediated antiviral 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.)