Evaluation Summary:

Here, the authors performed a CRISPR/Cas9 loss of function screen in polarized human epithelial cells to identify novel regulators of epithelial polarization and polarized membrane trafficking. This study provides a powerful resource for future investigations to unravel the complexity and diversity of mechanisms underlying epithelial polarization and polarized cargo transport. Furthermore, this dataset may represent an essential contribution to investigating novel congenital diseases associated with these processes, e.g., microvillus inclusion disease and necrotizing enterocolitis. A few experiments are suggested to bolster the authors' conclusions regarding the roles of key hits.

(This preprint has been 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 bridges neurophysiology and biomechanics and is of broad interest in improving our understanding of insect flight control. Here, Putney et al. record the activity of the flight muscles of tethered hawkmoths and demonstrate that the direction of the visual stimulus to which the insect responds can be classified using precisely timed information on muscle activity from a subset of the flight muscles. This is an important step in identifying the mapping from visual input to motor output, albeit that the mapping identified here is qualitative (i.e. classification of visual stimulus direction) rather than quantitative (i.e. prediction of output torque or apparent angular velocity of self-motion).

(This preprint has been 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 very extensive evaluation of the impact of rapid availability of whole-gemome sequencing results from SARS-CoV2 to inform infection control policies in hospital settings. It, most likely, is the largest analysis of its kind, clearly demonstrating the possibilities and challenges with this innovative technique.

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

Evaluation Summary:

This study, which will be of interest to behavioral ecologists, uses highly quantitative video tracking approaches to understand the predictors of predators' success in attacking schooling fish and will be of interest to behavioral, evolutionary, and movement ecologists. While some of the results seem unsurprising (e.g., that predators tend to successfully capture prey that are closer to them), the manuscript as a whole highlights the importance of tracking the perspective of the predator as well as of the prey, and shows that animals that are central to a group may sometimes be the most vulnerable. Although the experiments and data analyses are commendable, the manuscript would benefit from more careful discussion of its overall implications for the evolution of collective behavior, including potential limits of the experimental design.

(This preprint has been 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:

He and collaborators analyse eight samples from six patients with acral melanoma through single-cell RNA sequencing. They describe the tumour microenvironment in these tumours, including descriptions of interactions among distinct cell types and potential biomarkers. The study is thoroughly done. In its final form, this study will help to inform our knowledge of the immune infiltration on the poorly studied acral melanoma subtype, the most common type of the disease in several countries in Africa, Asia and Latin America.

(This preprint has been 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 presents a modeling framework that can be used to track the complex behavioral and immunological landscape of the COVID-19 pandemic over multiple surges and variants in South Africa, which has been validated previously for other regions and time periods. This work may be useful for infectious disease modelers, epidemiologists, and public health officials as they navigate the next phase of the pandemic or seek to understand the history of the epidemic in South Africa.

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

Evaluation Summary:

Patients with Gaucher disease can have significant and crippling neurological manifestations. The study uses novel mouse models of neurodegeneration associated with glucocerebrosidase 1 (GBA1) deficiency. It provides a detailed analysis of the alterations caused by targeted deletion of GBA1, including cellular, genetic and metabolic alterations in neurons, microglia, and infiltrating immune cells. The work defines novel mechanisms driving neuroinflammation in neuronopathic Gaucher 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 manuscript by O'Herron et al. describes an all-optical method combining optogenetic stimulation and 2-photon microscopy imaging to simultaneously manipulate and monitor brain microvasculature contractility in three dimensions. The method employs a spatial light modulator to create three-dimensional activation patterns in the brains of cranial window-model transgenic mice expressing the excitatory opsin, ReaChR, in mural cells (smooth muscle cells and pericytes). This provides a powerful new in vivo technique to control blood flow into the brain and to understand its actions on brain 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, Reviewer #2 and Reviewer #3 agreed to share their name with the authors.)

Evaluation Summary:

This study explores the kinetics of heavy metal staining of tissue using time-lapse imaging with X-ray micro computed tomography (CT). It will be of interest to the wide community of scientists preparing biological samples for electron microscopy (EM), in particular large-volume EM. While at present the relation between CT imaging and EM contrast remains to be quantified, this study has the potential to become a reference for the field in establishing a quantitative tool for assessing and developing staining protocols.

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

Evaluation Summary:

In this study, Ogran and colleagues provide evidence suggesting that T-Cell Leukemia/Lymphoma 1 (TCL1) protein may promote alternative transcription site selection and promoter usage in chronic lymphoid leukemia. It is further proposed that these TCL1-dependent alterations lead to the production of N-terminally truncated versions of proteins including chromatin regulators while bolstering expression of transcription factors including MYC. Collectively, it was found that these results are of broad interest inasmuch as they suggest previously unappreciated rewiring of epigenetic, transcriptional, and translational programs in leukemic cells. To this end, this article should be of significant interest across a variety of fields of biomedical research ranging from regulation of gene expression to cancer research. The paper would be strengthened by mechanistic data linking TCL1 to alterations in transcription site selection and/or alternative promoter usage and by stronger validation of the expression of N-truncated proteins and their functional consequences.

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

Evaluation Summary:

This paper will be of interest to marine biologists, and has particular relevance to those studying symbiotic corals. The use of compelling experimental optical measurements performed in situ allows testing of previous predictions on protein-based pigments that are found in many coral species. Specifically, the study analyzes the role of two classes of pigments, the Red Fluorescent Proteins (RFPs) and the Chromo proteins. It provides direct measurement data that suggest that RFPs can indeed provide additional light to the symbionts by converting the prevalent blue-green light at depth in orange-red light that penetrates more in the tissues of the polyps, thus increasing the number of photons available for photosynthesis. The authors also provide evidence based on light measurement for a possible photoprotective role of Chromoproteins, although the study does not yet provide any direct evidence for an ecological benefit of such light conversion/light protective functions.

(This preprint has been 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:

Osterman and Modragon report the first crystal structure of topoisomerase V in complex with DNA. Topoisomerase V is an unusual protein in that homologs have only been found in the archaeal Methanopyrus genus. The paper is likely of interest to those studying topoisomerase biology and biochemistry, and the wider audience interested in DNA replication and repair transactions.

(This preprint has been 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 examined the nature of projections from the prefrontal cortex (PFC) to the nucleus accumbens (NAc) and to the ventral tegmental area (VTA). The authors show that PFC projections to NAc and VTA are largely non-overlapping, originate in different layers of PFC, and express different molecular markers. This study provides high-quality data to the long-standing question.

(This preprint has been 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 potential interest to readers in the fields of working memory and neural coding. It presents a model of a neural circuit that learns to optimally represent its inputs subject to an information capacity limit and claims that this model can account for a range of empirical phenomena in the visual working memory literature. However, the fit to empirical data is qualitative and in some cases unconvincing, certain aspects of the neural model seem difficult to square with established neurophysiology, and there is insufficient conceptual or quantitative comparison with other models in the WM literature that seek to explain the same 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:

The methods presented in this work are of potential broad interest across different domains of human neuroscience. Reliable methods for pushing the limits of spatial resolution for mesoscopic scale imaging of the living human cortex are of wide interest and utility. The image quality and high-spatial resolution of the data are exceptionally high. The paper in its current form demonstrates the application of the developed methods to a few exemplary cortical regions and sequences.

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

Evaluation Summary:

This paper will be of interest to basic and clinical neurophysiologists who are focused on understanding neural mechanisms that influence recovery following spinal cord injury (SCI). The work compares the afferent regulation of motor output to soleus muscle in controls and individuals with SCI. The results indicate differences between groups such that there is less facilitation in the SCI group during muscle contraction.

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

Evaluation Summary:

Schubert and coworkers report the development of a novel CRISPR-based screening method that allows probing interactions between (a large set of) specific mutations and the abundance of specific proteins, and, more generally, investigate the spectrum of effects that (point) mutations can have on protein abundance. This complements existing strategies for measuring effects of genetic perturbations on transcript levels, which is important as for some proteins mRNA and protein levels do not correlate well. The ability to measure proteins directly therefore promises to close an important gap in our understanding of the links between genotype and phenotype, and the strategy is broadly applicable beyond the current study.

(This preprint has been 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 study shows that individuals with unsuppressed HIV infection had poorer T cell polyfunctionality and lower cross-reactive responses to SARS-CoV-2 variants compared to those who were HIV negative or aviremic. The conclusions of this paper are well supported by the data and will be of interest to clinicians, immunologists, and public health practitioners, particularly in Southern Africa.

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

Evaluation Summary:

This study tests the potential of using a combination of mosquito-based approaches, transgenesis and paratransgenesis, for malaria control relative to the use of the individual technologies. The results show that a combination of approaches can be more powerful at preventing the transmission of malaria parasites, opening the possibility of using similar combination approaches to reduce the malaria burden. The findings will be interesting for a broad audience of mosquito biologists and malaria researchers, but as they are limited to a specific transgenic-paratransgenic combination, more work will be needed to determine the true potential of this strategy for disease control.

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

Evaluation Summary:

This manuscript describes the unexpected observation of selenium exchange into an iron-sulfur cluster cofactor of a component of nitrogenase. The work sets the stage for future mechanistic study of this phenomenon. It also provides a roadmap for the study of sulfide exchange in other classes of iron-sulfur cluster enzymes.

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

Evaluation Summary:

The manuscript by Luo et al. showed that the cytokine receptor DR3 is selectively expressed on thymic NKT17 cells and DR3 ligation leads to the activation of NKT17 cells in the thymus. Overall, The presented experiment are properly executed, controlled and presented. The finding that DR3 acts as a costimulatory molecule for thymic NKT17 cells is interesting. The mechanism and the functional relevance of this finding remain wanting.

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

Evaluation Summary:

By using single-cell RNA sequencing, elegant computational approaches, protein validation, and in vitro functional assays, this study characterizes the cellular composition and gene expression profiles of the human placenta in mid-gestation. The findings and dataset provided by the authors represent an important resource for readers interested in human development and placenta biology. However, conclusions require additional experimental support.

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

Evaluation Summary:

This study uses social media data (namely twitter) to analyse factors of covid-vaccine acceptance. It first trains a classifier to detect whether a tweets pro-vaccine, neutral, or against. Using then a large corpus of accounts, it investigates multiple factors explaining this position in a light counterfactual analysis. The central finding is that the most socioeconomically disadvantaged groups are more likely to hold polarized opinions on COVID-19 vaccines; other findings inclduing that personal pandemic experience has an important impact on acceptance, or that interest in politics modulates acceptance. This study a good example of what machine learning can do with social media data; however it is also a good example of the high data-demands and limitations of a machine learning approach. The correlations found are plausible but the causal implications are not evidenced strongly enough to guide public policy.

(This preprint has been 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 work will be of interest to cell biologists studying the mechanism of asymmetric cell division and its diversity across species. Building on their earlier work, the authors show that that there is considerable variability in the mechanics of the spindle among six nematode species studied here. While the authors' main conclusion is plausible - that spindle oscillations require high force and low viscosity - stronger support by the data would be needed.

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

Evaluation Summary:

This study is an extension of previous work by the same authors, which established a two step high-throughput screening approach to monitor germination and growth of fungal spores of the human pathogen Cryptococcus neoformans and identified an FDA-approved drug with antifungal activity (DOI: 10.1128/AAC.00994-19). The current work extends this approach to three libraries of drug-like molecules comprising 75,000 candidate compounds and employs automated image analysis methods to identify classes of inhibition phenotypes. The key result of this work is the identification of 191 inhibitors, of which 76 could be grouped in to 8 classes based on chemical structure - inhibitors that share structural similarities tend to share phenotypic impact.

(This preprint has been 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 demonstrates an inactive protease in Pseudomonas aeruginosa, CtpA, is regulated by am outer membrane lipoprotein LbcA. Using crystallization and EM strategies, they also provide a complex structure; however, the precise mechanism of regulation is speculative due to the flexible arrangement of protein domains.

(This preprint has been 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 demonstrates that a cysteine residue (C152) in the vWA domain of the type-iV pili tip-associated protein, PilY1 impacts surface sensing, biofilm formation and cyclic-di-GMP signaling in Pseduomonas aeruginosa. Well-executed experiments provide insight into the events that initiate cell adhesion and colonisation, the understanding of which has important implications for human health. The work will be of interest to microbiologists in general.

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

Evaluation Summary:

This study is timely and important for all scientists and policymakers with an interest in producing, using or interpreting estimates of the effective reproductive number, R, as an indicator of epidemic growth when case counts are low (e.g. at the very beginning or end of an epidemic). However, the utility and accuracy of these methods is not evaluated in the context of less-than-ideal surveillance, including time-varying case observation and long delays, which is currently the case in most countries and they fail to evaluate the performance of the metrics in real 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 manuscript is of broad interest to readers interested in heterogeneity in immune cell populations with single-cell RNA sequencing, and for students of human T cell biology. It uses and reanalyses published single-cell RNA sequencing data dataset for this purpose. However, it does not adequately address major technical concerns, and therefore the interpretations are not robustly supported.

(This preprint has been 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 shows that it is possible to detect high-abundance peptide antigens in nerve cells at the electron microscope (EM) level in sections of formaldehyde-fixed monkey brain after the sections have been stored for several years in an antifreeze solution in the freezer. The topic of utilizing formalin fixed tissue for research, especially with the numerous "brain banks" worldwide, is an important topic especially if one wishes to conduct studies in post mortem human tissue. The authors used antibodies to detect the presence of vasopressin gene-related products (i.e., neurophysin II and copeptin) in the hypothalamus and pituitary of the monkey brain. This paper is of interest to anatomists who work on AVP neurons in non-human primate. Due to issues with tissue quality, methodology and interpretation, the experimental approach described in this paper may not be as useful for studying fixed and archived brain sections as the authors conclude.

(This preprint has been 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 paper addresses a subject of potential great interest regarding the evolution of gene regulation and of enhancer landscapes. Available chromatin looping and gene expression data in mouse and human are analyzed to compare diverse properties of genome-wide promoter-centered maps, including associations with gene expression. It is shown that there is conservation of regulatory landscape across the two species, and that the extent of conservation in the TSS-distal landscape is associated with gene expression similarities. These overall results are in agreement with a large body of work in the field.

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

Evaluation Summary:

This manuscript extends the evidence that ribosomal DNA has substantial interindividual variation, and presents evidence that variants are associated with differences in DNA methylation. The authors show that some rDNA types respond to environmental signals during in utero development, whereas others are changed during the aging process - thus broadening the known communication between development/nutrition/aging and the cellular protein synthesis machinery. These findings have relevance for the influence of such epialleles on gene expression and disease risk.

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

Evaluation Summary:

This manuscript reports a new approach to the important and challenging problem of predicting T cell receptor:peptide-MHC interactions, one that relies on molecular model building (with previously published tools) followed by feature extraction and machine learning. The strengths of the study are more conceptual than practical: the overall framework and analytical approach; a balanced, critical assessment of the method's performance (which does not shy away from negative results); some observations on TCR:pMHC docking geometry. On the practical side, the classifier does not appear to generalize well to unseen epitopes (neither do the published tools it's compared to), so at the end of the day it's not clear that it will be preferable to simpler sequence-based 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:

In this study, the authors used a chick and a mouse model and human tissues to analyze the role of the conserved protein TALPID3/KIAA0586, previously linked to ciliogenesis, in gut development. Using a multi-species approach, the authors conclude that TALPID3 has an evolutionary conserved role in regulating gut patterning along the radial axis, apparently orchestrated by neural crest cells in a non-cell-autonomous manner and mediated by perturbation of Sonic Hedgehog signaling and the composition of extracellular matrix.

(This preprint has been 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 will be interesting for people performing all optical electrophysiology. It describes a new combination of previously available genetic tools to allow simultaneous optogenetic manipulation and optical electrophysiology. The manuscript does not provide a major conceptual advance but provides good evidence that this assay can be employed for large-scale screening in hIPSC-derived 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:

In their manuscript, Eira et al. investigate the role of transthyretin in promoting axon elongation by modulating microtubule dynamics. The data point to a possible role of transthyretin in regulating microtubule dynamics by modulating tubulin acetylation levels during axon outgrowth. With additional support to strengthen this conclusion, the paper will be of interest to those in the neurodevelopment, neurodegeneration, and microtubule cytoskeleton fields.

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

Evaluation Summary:

This behavioural study in healthy participants examines how people trade-off a brief phasic pain stimulus with a monetary reward, reporting a quadratic effect of pain on decision making. It supports and adds to previous findings of a context-dependency deriving from the distribution of rewards, which is a deviation from conventional rational choice theory (which proposes that a particular level of pain should carry the same price, regardless of small context changes). Broadly, the reviewers found the work well executed and the data compelling, but there were some suggestions for alternative explanations that are not ruled out given the current 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.)

Public Evaluation Summary:

Determining when cells acquire their individual identity is critical for understanding the patterning and growth of embryos. The authors use state-of-the-art methods to map the lineages of cells that emerge during the earliest stages of development in chick embryos and that contribute to the central and peripheral nervous system. The authors have characterised the gene signature of ectoderm sub-clusters and used algorithms to infer lineage trajectories using the dataset. However, the analysis of placode and neural crest emergence is not clear-cut or well supported by in vivo experiments in the embryo. The work overall will be of broad interest to developmental and stem cell biologists, as well as neurobiologists interested in the understanding of the neural and neural crest gene regulatory networks.

(This preprint has been 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 paper, the authors use a mathematical model of plant and water dynamics in drylands to show that drylands adaptive capacity to respond to changes, via spatial self-organization in space, has also beneficial effects in preserving its biodiversity and ecosystem functions. The current study extends previous work by considering a trait diversity gradient that ranges from stress-tolerant to fast-growing plant species.

(This preprint has been 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:

In this manuscript, the authors explore mechanisms involved in predation of other bacteria by Myxococcus xanthus. They identify two gene clusters, which encode proteins with homology to proteins of the Tad pilus system and some of which are important for predation. The work represents a good starting point for understanding how Myxococcus cells may engage in contact-dependent killing of other bacteria.

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

Evaluation Summary:

This manuscript will be of interest to geneticists seeking to establish rules that govern gene regulation. To explain why a sequence enhances, rather than silences, gene transcription the authors draw our attention away from the binding of a single transcription factor, to focus instead on the number and diversity of transcription factor molecules that bind to it. Using a relatively simple metric called sequence information content they appear to be able to improve the prediction of enhancer over silencer sequences. A concern is whether the silencers are true silencers, or whether they only act as such in this specific experimental paradigm.

(This preprint has been 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 potentially an interesting paper in which extensive MD simulations are used to probe the effect of phosphorylation of a tyrosine residue on the conformational ensemble of Ras GTPase. The insights form the basis for a screen of small molecule(s) that disrupt interaction with its target Raf kinase, and predictions are tested experimentally. Overall, the integrated approach is of interest to a wide range of biochemist and protein scientists and could potentially be used to modulate the activities of other proteins.

(This preprint has been 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 the function of N6-methyladenosine (m6A) modification in developing retina. Enriched scRNA-seq and MeRIP-seq data will be an excellent resource for neurodevelopmental community.

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

Evaluation Summary:

This manuscript provides a comprehensive analysis of expression patterns and genomic features of long non-coding RNAs (lncRNAs) in the human developing gonad, using available single-cell RNA-seq datasets from both somatic and germ cells. Using multiple genetic strategies in an in vitro system of female germ cell differentiation, the study further shows a positive regulatory function of the LNC1845 lncRNA on its protein-coding neighbor LHX8, known to have a role in ovarian follicle development. This study has potential interest for reproductive biologists and for the non-coding 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 #2 agreed to share their name with the authors.)

Evaluation Summary:

This manuscript will interest a large community of molecular biologists studying translation and mRNA decay. The study provides a large-scale comparison of the roles of protein factors in No-Go Decay (NGD) and Codon-Optimality-Mediated Decay (COMD) in the yeast S. cerevisiae. A major strength of the manuscript is the direct comparison between one mRNA with a single strong translational stall and another similar mRNA with many slow translation sites (caused by changes in the genetic code). The analysis of both the factors that cause decay of these mRNAs as well as the ribosome states on the different mRNAs has the potential to reveal the molecular basis for the different mechanisms of mRNA quality control.

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

Evaluation Summary:

The authors advance our understanding of the molecular underpinnings of allostery in GPCRs by showing the effects of allosteric modulators of mGluR2 on receptor conformation at distinct sites in the presence and absence of orthosteric modulators. This is important as drugs and drug candidates acting outside the site where the orthosteric or endogenous ligands bind are harder to identify. This work provides insights into allosteric changes at the level of individual receptors and provides a new path for drug discovery and is this of interest to colleagues studying GPCRs in health and disease.

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

Evaluation Summary:

The work describes the energetic constraints and preferred operating conditions of these "strategies" in particular on how nature has solved the problem of low energy "headroom'" required to prevent deleterious back reactions while maintaining efficient energy storage. The differences between the species are quite interesting and show that nature has evolved multiple solutions to fundamental limitations. Given the importance of understanding and improving the efficiency of photosynthesis, and the new insights revealed, the work will be of interest to a broad audience.

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

Evaluation Summary:

Menicucci et al. investigate the implication of sleep in the maintenance of ocular dominance plasticity in adult humans. This is an interesting study as it shows that sleep can maintain the changes in ocular dominance obtained after applying an eye-path on the dominant eye for two hours. This contrasts with the rapid decline of these changes during quiet wake in darkness. The authors further report correlations between sleep oscillations and the magnitude of the plasticity effect. These results highlight a possible implication of sleep in a new form of plasticity

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

Evaluation Summary:

In this study, the role of different cortical areas on three distinct tasks all relying on the same virtual maze set-up was examined using optogenetic interventions and calcium imaging. The paper is potentially of interest to people interested in understanding the neural substrates of learning and how these can be impacted by previous knowledge and experience of stimuli. It could also be of use to behavioral neuroscientists when considering possible order effects of 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 agreed to share their name with the authors.)

Evaluation Summary:

This paper addresses a very notable gap that exists between evolutionary computing and experimental evolution. While artificial and computational approaches have long been used as an analogy for biological systems (with studies that have produced findings relevant for evolutionary theory), few studies have directly used methods and results from evolutionary computing to directly inform the shape and structure of experimental evolution studies. This study's approach is creative, and its approaches and results may be of use to both computational and experimental audiences. Lastly, this study can spawn future ones that draw even more connections between evolutionary computation/artificial life and evolutionary theory.

(This preprint has been 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 probes the mechanism of postsynaptic retinoic acid (RA) signaling on presynaptic function. BDNF has important roles in synaptic plasticity, but how retrograde BDNF signaling is controlled following synaptic inactivity is unclear. The authors use genetic tools to localize the action of different components of the pathway to pre- or post-synaptic compartments and use biochemical approaches to define a molecular link between retinoic acid and local translation of distinct BDNF transcripts. The findings presented here fill a gap in our knowledge regarding how presynaptic function is adaptively modulated by BDNF by highlighting the role of RA in this process. The experiments have been well-executed and the data provide compelling support for the model proposed by the authors.

(This preprint has been 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 report on the coordination mechanisms between oscillations recorded in the CA1 subfield of the hippocampus, prefrontal cortex, and olfactory bulb and cell ensemble activity in CA1 and prefrontal cortex that are associated with odor-cued decision making. The findings support the hypothesis that the beta rhythm plays a role in coordinating CA1-prefrontal cortex ensembles associated with an animal's accurate decisions. Sensory-guided decision-making is of broad significance to many readers who are studying executive functions and cognitive behaviors, and the observations reported in this manuscript provide insights into mechanisms that may support these functions and 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 #1 agreed to share their name with the authors.)

Evaluation Summary:

Houy and co-workers investigated the function of Munc13-1 and ubMunc13-2 in chromaffin cells and the interaction with phorbol esters (PMA). They combined calcium uncaging, capacitance measurements, amperometry, and activity-dependent movements of the EGFP-labeled Munc13 proteins. This study reveals that phorbolesters have a stimulatory effect via ubMunc13-2 but an inhibitory effect via Munc13-1. These opposing effects of the two Munc13 paralogs are surprising considering the closely related domain architectures.

(This preprint has been 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 manuscript, the authors specifically look at the interaction between epidural stimulation of the spinal cord and the descending input evoked voluntarily in 2 intact monkeys. The results show that spinal stimulation could facilitate or suppress voluntarily evoked EMG and wrist torque, depending on voluntarily evoked activity as well as the stimulation parameters. This shows that spinal stimulation could enhance the descending inputs in cases of partial lesions. The conclusions of this paper are well supported by data, although they could be made stronger with additional analysis and clarification.

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

Evaluation Summary:

This manuscript will be of general interest to Drosophila researchers, whose work has long relied on the tools generated by the Gene Disruption Project (GDP). This manuscript provides a notable update on the work of the GDP. In it, the authors demonstrate the efficacy of new, streamlined transformation vectors, which they use to generate several hundred novel gene-specific Gal4 driver lines using CRISPR technology. The new vectors promise to allow the GDP to complete its goal of creating null mutations for every gene in the fly genome. The elegant functionality of the new vectors will also likely be of interest to workers outside of Drosophila.

(This preprint has been 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, which is of interest to membrane biologists and colleagues in signal transduction, examines the interesting question of whether LRRK2 recruitment to membranes may regulate its activity. Membrane association involves binding to membrane-tethered Rab GTPases via LRRK2's armadillo domain, and the authors propose an elegant feedforward mechanism to describe how recruitment could lead to Rab phosphorylation, but not all features of the feed-forward model are directly supported by 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 manuscript by Fox, Birman, and Gardner combines human behavioral experiments with spatial attention manipulation and computational modeling (image-computable convolutional neural network models) to investigate the computational mechanisms that may underlie improvements in behavioral performance when deploying spatial attention. Through carefully controlled manipulations of computational architecture and parameters, the authors dissociate the effects of different tuning properties (e.g. tuning gain vs. tuning shifts) and conclude that increases in gain are the primary means by which attention improves behavioral performance. The analyses and results are technically sound and clearly presented, but the generality of the conclusions is limited by certain modeling/task choices made in 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: 

This paper will be of interest to microbiologists, clinicians, and public health workers with an interest in the possible impact of antibiotic use and regulations. The scope of the study is unusually high, integrating economic and geographical factors as well as genomic data among others. However, reasonable alternative explanations can be identified such that the data do not strongly favor the preferred hypothesis put forward by the authors. 

(This preprint has been 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 finds that the levels of many immune markers are higher in vaginal samples in women taken after initiation of vaginal sex than before initiation of vaginal sex. This result may indicate that initiation of vaginal sex potentially influences vaginal immune responses, but it is possible that unmeasured confounding and selection bias might contribute to some of the difference across samples. This study will be of highest interest to those interested in how immune markers can change within individuals over 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. The reviewers remained anonymous to the authors.)

Evaluation Summary: 

The manuscript presents a high-quality quantitative analysis of plant embryo cell division in 3D. Authors combine computer modeling with detailed microscopy imaging to reveal underlying patterns and biases in cell divisions. The manuscript will likely be of interest to cell and developmental biologists. The conclusion can be straightened following additional analysis and data interpretation. 

(This preprint has been 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 explores the establishment and spread of antimalarial drug-resistant P. falciparum parasites using a combination of transmission modeling and model emulation. The authors add an important component to the broader understanding by jointly considering multiple factors driving drug 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 analyses the synaptic connections of two subsets of clock neurons in the Drosophila brain, the small ventral lateral neurons and the dorsal lateral neurons that control the sleep-wake behavior. The study reveals interesting features of the clock network, including the high heterogeneity of the LNd subset and the existence of non-clock cells that are predicted to act as "inter-clock neurons". The manuscript will be of interest to chronobiologists and neuroscientists working on neuronal networks, and it provides new insights into circadian clock network organization that may be of general value. The data analysis is rigorous, and the conclusions are justified 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 study provides a comprehensive analysis of the effects of polymorphism in an immune gene (the immunoglobulin E receptor Fcer1a) on immune responses, resistance to infection, and reproductive fitness in a wild rodent population. The authors claim to have found evidence for sex-specific effects of Fcer1a polymorphism, a result that would have broad implications for our understanding of the maintenance of genetic variation. The support for this claim is currently rather weak.

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

Evaluation Summary:

This manuscript is of interest to several fields, in particular to microbiologists and structural biologists interested in pore-forming proteins and peptides. The data presented reveal insights into the mode of action of a newly identified peptide toxin secreted by Candida albicans (candidalysin). Using different techniques the authors propose and test a model for membrane perforation by candidalysin and identify an intriguing inactive mutant. While the presented data supports the main conclusions of the paper some of the initial assumptions need further assessment while the described mutants could benefit from more extensive characterization.

(This preprint has been 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 collected human samples from a rare cancer type in which evolutionary features have not been well-defined. They describe the clonal evolution through sampling at precancerous, primary tumour, and metastatic stages. Whole exome sequencing was performed and one of the mutation types was confirmed with other techniques.

(This preprint has been 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 will be of interest for researchers studying the functions of microbial communities, microbial ecology and interactions. Using the Kombucha tea (KT) microbiome as a case study, Huang et al. provide a framework for simplifying complex communities into core communities that capture aspects of complex communities. Authors demonstrated that core communities can facilitate a mechanistic understanding of how microbes interact, especially when member species are individually culturable. The work presents a fresh, novel approach for the coarse-grained analysis of complex microbiomes.

(This preprint has been 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 analyses the inhibitory role of IL-10 producing regulatory T-cells in a mouse cytomegalovirus infection model. The authors report that IL-10 producing CD4+T-cells express genes of chronically activated Th1-cells, are clonally expanded and inhibit anti-viral T-cell responses via arginase, an enzyme that breaks down an essential amino acid for T-cell activation. The manuscript presents some novel and potentially important data; however, it requires the provision of additional experimental data and clarifications.

(This preprint has been 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 will be of interest to a broad audience of cancer biologists, especially those interested in esophageal cancer or treatment strategies involving ATR inhibition. It provides novel information about how FDA-approved antiretroviral compound Arbidol is a potential ATR inhibitor, which is of interest in the treatment of multiple tumor types. The key claims of the manuscript are supported by in silico, in vitro, and in vivo 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 #2 agreed to share their name with the authors.)

Evaluation Summary:

This manuscript will be of interest to stem cell and developmental biologists who aim to use newly emerging brain organoid models to understand the structure and function of the developing human brain. It presents a technological advance in imaging and describes an innovative method for labeling and tracking of cells within organoids to enable the assessment of dynamic processes within the intact organoid. The method is validated in a disease model and addresses a challenge in the field of human stem cell modeling of assessing cells within the 3D structure.

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

Evaluation Summary:

This study provides computational predictions on optimal combinations of broadly neutralizing antibodies for treating HIV-1, based on the finding that population diversity alone permits the prediction of the timing of viral escape from broadly neutralizing antibodies. The idea behind the approach used is good, although the analyses and computational data/results highlight important limitations of the modeling approach. Nonetheless, the study should be of broad interest to those studying viral responses to therapeutic interventions as well as to both evolutionary and computational biologists.

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

Evaluation Summary:

This paper is of potential interest to a broad audience in the fields of germ cell biology and cytoskeleton, as it implies a microtubule-based motor function in intra-manchette cargo transport in developing sperm tail. However, some conclusions of this paper require stronger experimental support.

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

Evaluation Summary:

This study combines behavioral data from guinea pigs and data from a classifier model to ask what auditory features are important for classifying vocalisations. This study is likely to be of interest to both computational and experimental neuroscientists, in particular auditory neurophysiologists and cognitive and comparative neuroscientists. A strength of this work is that a model trained on natural calls was able to predict some aspects of responses to temporally and spectrally altered cues. However, additional data, analysis, or modelling would be required to support some of the stronger claims.

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

Evaluation Summary:

In this manuscript, effective force-distance curves between cells are inferred for various tissues. This study is potentially interesting for researchers interested in tissue dynamics, because computer models of growing cellular tissues are becoming an increasingly important tool to understand experimental data and eventually predict medical interventions.

(This preprint has been 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 described a role of Vitamin C in promoting plasma cell differentiation by remodeling the epigenome via TET (Ten Eleven Translation) family proteins. Overall, most of experiments are properly executed, controlled and presented. This paper will be of interest to scientists in molecular immunologists, particularly those involved in of epigenetic mechanisms of B cell differentiation to plasma cells.

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

Evaluation Summary:

The manuscript shows that OTOP proton channels are proton-gated with distinct pH sensitivities, and identifies regions on the proteins that alter pH-dependent gating. The main claims are well supported by the data. These findings are likely to be of interest to researchers studying acid/base physiology, sensory physiology, or ion channel biophysics.

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

Evaluation Summary:

This manuscript puts forward a new toolkit of viruses for manipulation and visualization of zebrafish neural circuits. The authors overcome several challenges in the field and present a set of resources likely to be of high value to the zebrafish 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:

Hososhima et al. characterize a marine virus Heliorhodopsin as the first of its class to show ion transport activity. These bacteriorhodopsin homologs have been recently described and the present careful characterization of V2HeR3 represents an important step in the understanding of these interesting membrane proteins. Though the experiments are carried out carefully and the results, in general, support the conclusions, some experiments are needed and the interpretation of results needs to be clarified.

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

Evaluation Summary:

This paper is of interest to neuroscientists studying the interaction between working memory, decision making, cell types, and neural oscillations. It introduces a detailed model of different brain areas which interact giving rise to the complex pattern of oscillations that are observed during a visual attention task. Additionally, the model reproduces the phase-dependent behavioral performance observed experimentally during such a task. This provides a new level of precision in our understanding of how rhythmic attention works in the brain.

(This preprint has been 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 presents a creative, unique, and well-explained theoretical analysis of the shapes adopted by chromosome-attached microtubule bundles during manipulation with glass microneedles inside dividing cells. The overall conclusion is that the bundles are laterally anchored to other structures in the mitotic apparatus within several micrometers of their chromosome-attached ends, but relatively freer at their pole-proximal ends. This interesting work should appeal broadly to cell biologists and biophysicists. 

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

Evaluation Summary:

This paper is mainly for an audience of genetic epidemiologists interested in the evaluation and portability of polygenic scores. The authors show that a polygenic risk score to predict prostate cancer risk is very informative for individuals that are classified on three different ancestry categories. The authors show that the polygenic risk score can be used to predict the risk to develop prostate cancer as a function of age. This paper provides evidence that genetic information could be used to provide guidance to clinicians on when to perform screenings to detect prostate cancer in patients.

(This preprint has been 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 contributes to a circuit-based understanding of how sweet and bitter tastes are integrated with hunger state to drive feeding initiation in Drosophila. Anatomical, behavioral, and neuronal activity data support a multi-step pathway from sensory input to motor output. This manuscript, thus, contributes to our understanding of how multiple sensory cues are integrated with an internal state to reach a behavioral decision.

(This preprint has been 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:

Through the use of multiplexed in situ hybridization with careful embryo staging, this manuscript represents exemplary documentation of dynamic gene expression patterns in early fly development. By comparison of these patterns in various mutant combinations, a simple logical model for specification of expression is proposed. This manuscript will be of broad significance to developmental biologists interested in embryo segmentation and gene regulatory networks underpinning patterning.

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

Evaluation Summary:

This paper is of interest to scientists interested in the functions of the hippocampus, as well as those in the field of sensorimotor timing. The reported data and findings point towards the possibility that the hippocampus supports specific and generalized learning of short time intervals relevant to behavior. While the conclusions are mostly supported by the evidence, further clarification of methodology as well as additional analyses and discussion would strengthen 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. The reviewers remained anonymous to the authors.)

Evaluation Summary:

The authors use a combination of proteome-specific protein complex structures and publicly available ribosome profiling data to show that cotranslational assembly is favored by large N-terminal intermolecular interfaces. The manuscript represents an important contribution to the field of protein biosynthesis pathways by suggesting an intuitive evolutionary mechanism that can promote co-translational assembly pathways in mammalians, yeast, and bacteria.

(This preprint has been 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:

Second order conditioning is a higher form of learning where a previously conditioned stimulus (e.g. odor A by food) is used to condition the perception of another stimulus (e.g. odor B by odor A). Yamada et al. have used the fly to identify a neural circuit in the insect mushroom body underpinning second order conditioning. This work elegantly combines neural circuit mapping, electrophysiology and modeling to put forward a mechanistic model for this highly conserved form of 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:

The authors measured the heartbeat and touch perception while people touched a variety of surfaces. The results indicate that people's heart rates and heartbeats vary systematically according to the type of touch performed and how difficult it was to perceive the grooved surfaces. The paradigm and the results appear very interesting though the specific analyses of choice and their presentation require some improvement to make a more convincing case.

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

Evaluation Summary:

This paper is an impressive and deep look at a very important problem: understanding the genetic underpinnings of evolution acting on a quantitative trait. The authors analytically study the response to an abrupt shift in phenotypic optimum, in terms of both phenotype and genetic basis (how various alleles/loci contribute to this response). The basic assumptions are classic, but the methods and findings are new (especially finite population effects) and well supported by clear analytical approximations and extensive simulation checks. The main finding is that the relative contribution of large vs moderate effect alleles changes substantially and predictably over a long-term period after the shift, even though the phenotypic changes are already undetectable over this period.

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

Evaluation Summary:

This study investigates on how weight loss by bariatric surgery or weight-matched dietary intervention impairs breast cancer growth as well as immunotherapy. This study can potentially provide some therapeutic intervention strategies on combining vertical sleeve gastrectomy and immunotherapy in treating breast cancer.

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

Evaluation Summary:

This is an exemplary manuscript describing the creation of a novel mouse model to study bone marrow adipocytes. The authors demonstrate that these cells play a critical role in the pathophysiology of myeloid cell lineage regeneration as well as the maintenance of bone mass and hematopoietic progenitors during times of limited energy (e.g. caloric restriction).

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

Evaluation Summary:

In this paper, Ekman and colleagues present novel evidence, using a visual sequence task in fMRI, that the early visual cortex (V1) and the hippocampus both represent perceptual sequences in the form of a predictive "successor" representation, where the current state is represented in terms of its future (successor) states in a temporally discounted fashion. In both brain structures, there was evidence for upcoming, but not preceding steps in the sequence, and these results were found only in the temporal but not spatial domain. This study suggests that the hippocampus and V1 represent temporally structured information in a predictive, future-oriented manner.

(This preprint has been 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 provides evidence that murine acid ceramidase (Ac) is required for normal erythropoiesis and development of rodent malaria. The findings are of interest in understanding molecular processes involved in regulating erythropoiesis, as well as the potential to develop host-directed therapies for malarial parasites that target human reticulocytes.

(This preprint has been 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:

Haggerty et al. reported findings examining how changes in brain function are involved in alcohol binge drinking, with a selective focus on the synaptic and circuit alterations that occur in the anterior insular cortex inputs within the dorsolateral striatum. They show that chronic alcohol drinking produces glutamatergic synaptic adaptations and by stimulating this circuit, binge drinking could be reduced without altering either water consumption or general performance for select reinforcing, anxiogenic or locomotor behaviors. The results of this study may specifically improve our understanding of the neurocircuitry mediating a common alcohol use disorder associated behavior referred to as "front-loading" or excessive drinking during the very beginning of the session.

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

Evaluation Summary:

This manuscript reports the complex interactions that take place in the uterus between the endometrium and the blastocyst during and after embryonic diapause, a period of suspended animation that occurs in some mammals including the mouse, the model used here. The authors showed that one gene, Foxa2, interacts with two other genes, Msx1 and LIF, to control the success and duration of diapause. This will be of broad interest to researchers in the field of developmental biology and reproduction. It is a carefully done study, providing new information on the complex process that is diapause in which an embryo goes into suspended animation until it receives appropriate signaling from the uterine endometrial secretions to reactivate.

(This preprint has been 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 study intergenerational adaptation patterns in four relatively closely related nematode species, using previously established experimental procedures. Phenotypic and transcriptomic data are used to compare responses to stress triggers in the offspring generation between the species. The authors conclude that at least some of the responses are evolutionary conserved.

(This preprint has been 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 for scientists studying human genetic adaptation and disease. The work improves on previous studies addressing the question of recent positive selection on genes underlying Mendelian diseases, by examining larger datasets of disease genes as well as carefully controlling for confounding factors that could result in disease genes and non-disease genes showing different patterns of genetic variation. The authors suggest that interference between strongly deleterious recessive mutations can reduce adaptation at disease genes, although this conclusion is weakened by the fact that the signal is only observed in Africa.

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

Evaluation Summary:

This paper is of interest to a broad range of neuroscientists, particularly those interested in ApoE biology and Alzheimer's disease (AD), as it reveals a novel mechanism that counteracts AD-linked amyloid plaque burden and synapse dysfunction in mice. Overall, the methodology is sound, sophisticated, and employs animal models that more closely mimic human diseases, and the results are interesting and compelling. Whilst the mechanistic hypothesis proposed by the authors is consistent with the data, plausible alternative explanations remain.

(This preprint has been 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 presents a method to characterize diverse neural activity patterns arising from a small invertebrate circuit. This is of practical interest to invertebrate neuroscientists. The application of unsupervised methods to characterize qualitatively distinct regimes of spiking neural circuits is very interesting. The challenges and lessons learned in this study are therefore of broader interest to those seeking to quantitatively characterize large sets of neural data across many subjects. The survey could be improved by further validation of the derived clusters.

(This preprint has been 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:

There has been a great deal of recent interest in the neural basis for offset responses given their hypothesised importance to perception. This tests the relevance of offset responses to duration perception in a mouse model in addition to examining the brain basis. The work is thorough and well executed. The work demonstrates offset responses that occurs for the first time in auditory cortex distinct from A1 where prevention of offsets by activating cells causes worsening of behavioural performance.

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

Evaluation Summary:

The manuscript addresses an important question with broad relevance to the fields of virology, reproductive biology and immunology, and cell death. The primary conclusion of viral-induced cell death is well supported. Some mechanistic details of the pathway remain unclear.

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

Evaluation Summary:

This paper documents in wild bonobos significant physiological changes in response to becoming a sibling for the first time. The authors find that new siblings' cortisol increases dramatically, while their neopterin (a marker of immune function) decreases. This paper will be of interest to those who study development, life history transitions, and colleagues at the intersection of physiology and behavior, in particular in primates and other mammals with slow life histories.

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

Evaluation Summary: 

This is an interesting study, conducted in mice, that demonstrates for the first time the presence of a large population of cytotoxic CD4+ T lymphocytes in infection with Trypanosoma cruzi, a relevant human pathogen. At present, the relevance of these cells in protective immunity engendered by the host remains unclear. Additional experiments are needed to characterize the functionality of these cytotoxic CD4 T cells vis-a-vis the canonical Th1 T cells. This paper can be of interest to scientists interested in immune responses to parasitic infections. 

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

Evaluation Summary:

The manuscript will be of interest to a broad audience in structural biology, biochemistry, and enzymology. The work demonstrates the use of a cutting-edge approach in protein crystallography to investigate and visualize the complex mechanism of an enzyme, the paradigm being Mn-dependent ribonucleotide reductase R2b in complex with flavin-bound NrdI at different redox states. The work is timely and has implications for future investigation of complex biochemical processes.

(This preprint has been 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:

Using an impressive experimental design, Tang et al. analyzed the effects of intraspecific (genetic) and interspecific (species) diversity in ecosystem processes carried out by forest communities. The results show that both species and genotype diversity influence productivity via changes in overall functional diversity, herbivory, and soil fungal diversity. This study will be important to ecologists and environmentalists interested in ecosystem processes and restoration efforts.

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

Evaluation Summary:

The manuscript shows an important role for Cav2.3 channels in SNI-mediated allodynia and firing properties of PV-expressing APT neurons. Mechanisms that underlie adaptations in chronic pain models are extremely important for the development of novel therapeutics for chronic pain and this could be a significant contribution in that regard. However, the discussion asserts that these studies are the "first direct evidence that supra-spinal Cav3.2 channels play a fundamental role in pain pathophysiology." This is an overstatement as Chen and colleagues examined the role of these channels in the anterior cingulate cortex in CCI-mediated neuropathic pain (Shen, et al., 2015, Molecular Pain).

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

Evaluation Summary:

Ribeiro M et al investigate the ability of a novel bispecific CD19-CD47 antibody to enhance the cell mediated killing mediated by existing drug combinations - anti-CD20 plus PIK3d/CK1E inhibitor. The novelty of this study is the restriction to CD19 positive lymphoma cells, thus potentially avoiding toxicity to non-lymphoma lineages, and the gene expression profiling to identify up regulation of GPR183 after combined treatment of CD19/47 plus CD20/PI3K/CK1E vs CD19/47 alone. Genetic and drug studies suggest that GPR183 is essential for the full activity of the triplet drug combination.

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

Evaluation summary:

This study investigates the neural basis of the hidden causal structure between visual and proprioceptive signals in the primate premotor and parietal circuit during reaching tasks executed in a virtual reality environment, where information between the two modalities can be dissociated. Modelling is used to characterize the proprioceptive drift of the monkeys when integrating bimodal information. The key novel result is that premotor neurons represent the integration of bimodal information for small disparities and the segregation for large disparities between the proprioceptive and visual information, while parietal cells show reaching tuning changes that support the updating sensory uncertainty between tasks. Overall, the experiments are technically sound, and the conclusions are mostly well supported. However, a simpler framing of the paper could make the main message easier to grasp, the analysis of Bayesian models seems to lack major details, the statistical reporting is below standard, and a large part of the extensive literature on the role of premotor and parietal cortex in visuomotor behavior is lacking.

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

Evaluation Summary:

This paper suggests that assembly of CaV2.3 with b2a/b2e splice variants confers biophysical properties that enable these channels to contribute to calcium-dependent pacemaking in dopaminergic neurons. The findings could have implications for why these neurons are vulnerable to degeneration in Parkinson's disease. The work will be of interest to ion channel biophysicists and neuroscientists.

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

Evaluation Summary:

The authors use a comparative genomics approach to predict gene function, in particular genes that have a role in eye development. After identifying the convergent loss of SERPINE3 with vision loss across mammals, the authors confirmed its involvement in eye development by characterizing zebrafish knockouts. This work highlights the power of comparative genomics to generate hypotheses that can be experimentally validated. This work is relevant to a broad audience interested in evolution and adaptation as well as for those studying eye development and eye pathologies.

(This preprint has been 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 provide evidence suggesting the gene expression profile of a specific subset of dendritic cells define features of specific forms of non-infectious uveitis. This work suggests specific pathways in these cells that may have mechanistic import in inflammatory eye disease. This manuscript is of interested to immunologists studying autoimmunity and ocular immunity. While the paper is largely descriptive, the data it presents should serve as a valuable resource for generating hypotheses about the pathogenesis of ocular autoimmune disease.

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

Evaluation Summary:

This article proposes methodology and accompanying software for robustly fitting dose-response curves where response is a number between 0 and 1. When response is transformed using the common logistic transformation, values close to 0 or 1 become large in magnitude, unduly influencing the fitted curve after back-transformation and introducing bias in the estimate of certain parameters. The proposed approach, called Robust and Efficient Assessment of Potency, is less perturbed by these extreme measurements.

(This preprint has been 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 combines new and previously generated data on hand preference to show that hand preference strength, but not direction, is predicted by ecology and phylogeny across primates. By drawing on the most expansive data set to date on experimentally determined hand preference, it calls existing hypotheses on the evolution of hand preference into question and shows that the strength of lateralization in humans is uniquely extreme. Its results are of interest to evolutionary anthropologists, primatologists, and evolutionary morphologists. However, concerns about intraspecific variation and the accuracy of handedness estimates for poorly sampled species are incompletely addressed by the manuscript in its current form.

(This preprint has been 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 of this manuscript, which is of interest to the cancer community, identify the chromatin regulator WDR5 as a possible new drug target in triple negative breast cancer. Targeted therapeutics for this patient population are of high scientific and clinical interest, and the authors provide a compelling case that co-targeting WDR5 along with mTOR provides a promising new therapeutic strategy.

(This preprint has been 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 provides a detailed structural and biophysical characterization of several complexes of the p52 homodimer of NF kB and different DNA binding sites. The main topic is the investigation of why the central base pair(s) have a strong influence on the transcriptional activity of the homodimer. The authors correlate structural changes with measurements of kinetic on and off rates to develop a model that explains the differences in activity. The paper is of interest to all working on understanding how transcriptional activity is regulated.

(This preprint has been 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.)