Evaluation Summary:

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

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Evaluation Summary:

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

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Evaluation Summary:

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

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Evaluation Summary:

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

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Evaluation Summary:

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

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Evaluation Summary:

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

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Evaluation Summary:

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

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Evaluation Summary:

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

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Evaluation Summary:

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

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Evaluation Summary:

This paper describes novel insights into the potential function of innexin proteins, which are electrical synapse-forming proteins with often quite enigmatic in vivo functions. The authors describe here potential functions in synapse tiling. The paper should be of interest to researchers with interests in molecular mechanisms governing nervous system development.

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Evaluation Summary:

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

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Evaluation Summary:

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

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Evaluation Summary:

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

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Evaluation Summary:

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

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Evaluation Summary:

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

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Evaluation Summary:

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

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Evaluation Summary:

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

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Evaluation Summary:

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

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Evaluation Summary:

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

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Evaluation Summary:

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

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Evaluation Summary:

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

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Evaluation Summary:

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

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Evaluation Summary:

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

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Evaluation Summary:

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

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Evaluation Summary:

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

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Evaluation Summary:

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

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Evaluation Summary:

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

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Evaluation Summary:

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

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Evaluation Summary:

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

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Evaluation Summary:

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

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Evaluation Summary:

This work is potentially very important to dissect the immune repertoire of T/B cells, which is one of the most critical/difficult parts for the adaptive immune system to achieve antigen specificity. These conclusions and proposed methods will require additional experimental support and further validation in different disease conditions.

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Evaluation Summary:

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

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Evaluation Summary:

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

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Evaluation Summary:

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

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Evaluation Summary:

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

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Evaluation Summary:

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

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Evaluation Summary:

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

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Evaluation Summary:

This very clear paper, which will be of interest to scientists in the field of evolutionary biology, investigates the effect of population structure on the efficacy of selection on a single locus. The results are based on analytical computations and numerical simulations, conducted in a scientifically rigorous manner. Although the conclusions are currently limited, the paper could serve as a solid basis for a more ambitious investigation.

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Evaluation Summary:

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

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Evaluation Summary:

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

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Evaluation Summary:

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

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Evaluation Summary:

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

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Evaluation Summary:

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

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Evaluation Summary:

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

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Evaluation Summary:

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

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Evaluation Summary:

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

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Evaluation Summary:

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

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Evaluation Summary:

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

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Evaluation Summary:

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

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Evaluation Summary:

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

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Evaluation Summary:

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

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Evaluation Summary:

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

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Evaluation Summary:

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

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

Evaluation Summary:

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

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Evaluation Summary:

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

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

Evaluation Summary:

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

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Evaluation Summary:

This paper proposes a novel mechanism used by the visual system to recruit interneurons into the visual thalamus. The primary claims that retinal ganglion cell axons secrete Shh in the visual thalamus that induces FGF15 expression by astrocytes, that then attract interneurons are sound. Because Shh signaling, interneuron migration, and astrocyte functions are studied by a large number of neuroscientists this study will have a high impact on the field.

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Evaluation Summary:

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

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Evaluation Summary:

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

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

Evaluation Summary:

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

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

Evaluation Summary:

Prostate cancer cellular heterogeneity is a major problem for disease progression and treatment resistance. This body of work addresses the cellular identity and populations that make up prostate cancer using single-cell sequencing technology and state-of-the-art mouse models. The cellular identities, associated signaling networks, and immune complexes accompanying the heterogeneity of the prostate are identified in this work and a resource is provided for scientists in the field.

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Evaluation Summary:

This study reports on the diagnostic utility of TRIO-based whole-exome sequencing (WES) in a cohort of 123 unrelated patients with suspected monogenic inborn errors of immunity. The authors further explored the diagnostic rate in this cohort by focusing their analyses on the identification of de novo variants (DNVs). This manuscript will be of interest to medical geneticists, immunologists, and physicians working with patients with primary immunodeficiencies.

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

Evaluation Summary:

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

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Evaluation Summary:

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

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Evaluation Summary:

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

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Evaluation Summary:

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

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

Evaluation Summary:

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

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

Evaluation Summary:

This paper presents an artificial neuronal network which, from action and visual inputs, develops representations of space comparable to those found in the navigational system of the brain. They show that the representations developed by this network can be used in novel environments and in a reinforcement learning task. This demonstration of representations in absolute coordinates from agent-centered information is a significant contribution to neuroscientists as well as machine learning.

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

Evaluation Summary:

This report identified NK-extracellular-vesicle (NK-EV)-associated microRNAs and characterized them by small RNA next-generation sequencing. They found that NK-EVs promote Th1 polarization and activation of monocyte and monocyte-derived dendritic cells. The findings are potentially important for understanding NK cell function.

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Evaluation Summary:

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

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

Evaluation Summary:

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

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Evaluation Summary:

This study provides important new information regarding the functions and behavior of lung tissue-resident alveolar macrophages in the context of acute lung injury. New data regarding the impact of hypoxia via HIF-1 on biology of these critical cells are provided and importantly suggesting an impact on the outcome of lung injury.

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

Evaluation Summary:

This study asks how diverse signals are integrated at the cellular level to generate adaptive behaviors. The authors show that prolonged food deprivation (i.e. fasting) of C. elegans broadly alters gene expression in food sensing neurons, thereby altering foraging behavior and chemosensory neuron responses to food. The fasting-induced genes include many chemoreceptors, one of which mediates responses to specific volatile components of food. Finally, they show that food controls the expression of a fasting-induced chemoreceptor via multiple external (i.e. sensory) and internal (potentially metabolic) cues. The paper is of importance to scientists with an interest in adaptive behaviour as well as the cellular and molecular mechanisms underlying integration of stimuli.

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

Evaluation Summary:

This manuscript is of interest to readers interested in how brain gene expression patterns differ between humans and other animals. The authors develop an innovative approach to map correspondences between the gene expression profiles of human and mouse brains, finding that the profiles of sensorimotor areas are more similar than those of transmodal association cortex. This thus contributes to our understanding of the genetic mechanisms that may drive differences in brain organization across species. The study is methodologically sound and the key claims are supported by the data.

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Evaluation Summary:

Berryer et al. report on an automated and quantitative platform to study the number of synaptic inputs formed in networks of human excitatory neurons and astrocytes in vitro. The authors tested the utility of the platform by screening a large collection of small molecules and identified several modulators of synapse density, which were validated in follow-up experiments. The automated platform substantially extends what is currently available, particularly with respect to the automation of the initial analysis steps. The positive hits identified here, the inhibitors of bromodomain and extraterminal (BET) family of gene expression regulators, are important, and will likely contribute to the understanding of the mechanisms of human synapse assembly.

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

Evaluation Summary:

This paper will be of interest to neurobiologists and developmental biologists. Identifying novel mechanisms that prevent excessive neuronal migration is an important contribution to the field of neural development. The key conclusions of the paper are well 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 #3 agreed to share their name with the authors.)

Evaluation Summary:

The authors found elevated Hsp 27 levels in brains from Alzheimer disease patients. Hsp27 co-localized with p-Tau, efficiently prevented pTau fibrillation in vitro, and mitigated neuropathology of pTau aggregation in a Drosophila tauopathy model. A series of biochemical assays is presented to supporrt the claim that Hsp27 prevents abnormal Tau aggregation and p-Tau pathology. Overall, the study is well designed and presented, and the data convincingly support this major conclusion, which is relevant to colleagues studying neurodegeneration.

(This preprint has been reviewed 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:

Pond et al. established a 2D patient-derived organoid screening platform to study tissue patterning and kinase pathway dynamics. They aim to understand how the spacing of different colonic cell types and their communication are regulated. They found that apoptosis induces Erk signaling waves that prime cell movement and are essential to maintain tissue patterning in the organoid monolayers. The work presented here is of importance to the field and provides insights into how Erk waves driven by apoptosis can help maintain gut homeostasis.

(This preprint has been 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 article introduces "DetecDiv", a high throughput, deep learning method to perform automated cell-division tracking in yeast. The performance of the method, estimated to be 100 times faster than manual annotation, overcomes current time processing limitations that are inherent to large single cell datasets. In particular, DetecDiv allows to automatically get quantitative measurements of replicative life span in yeast. The method is of broad interest for quantitative biology as it can be used to study yeast cells dynamics across their lifespan.

(This preprint has been reviewed 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, which will be of interest to basic scientists and clinicians in the fields of dental and craniofacial malformations, explores the validity and usefulness of mouse teeth as a model for studying the role of enhancers in human dental development and disease, based on a multi-layered integrated analysis of genetic data with different available data from mice and humans. The results from the study can provide a useful tool for the manipulation of expression of reporter or other genes in a tooth- or enamel-specific 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 #1 agreed to share their name with the authors.)

Evaluation Summary:

The web-based software developed in this study will be of interest to researchers who develop CRISPR-based diagnostic methods. The use of CRISPR-Cas to rapidly identify specific mutations in both cancer and infection is an evolving field with good potential to play a role in future research and diagnostics. This software will facilitate the implementation of such technologies and is therefore useful.

(This preprint has been reviewed 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 builds on previous work to design yeast display libraries representing full viral proteomes with overlapping 15-mer peptides binding to specific HLA-DR alleles, and therefore potentially immunogenic for CD4 T cell responses. The authors use SARS-CoV-2 and dengue viruses as proof of concept and identify a number of potentially immunogenic peptides not predicted by current algorithms. The methods are interesting and promising and will be of interest to a wide range of researchers in immunological and infectious disease studies.

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Evaluation Summary:

This paper will be of interest to scientists interested in intergenerational transmission of phenotypes through genetic pathways. The authors propose an innovative and sound method to leverage the adoption of a design for disentangling prenatal and postnatal genetic effects. Additional analyses are needed to address the limitations of the model applied to the specific dataset that was used to illustrate the method.

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Evaluation Summary:

The authors analyze the mechanisms of entropically driven cooperativity in the human thymidylate synthase (hTS), an enzyme essential for DNA replication and a promising target for anticancer drugs. The authors conclude that the cooperative binding of dUMP ligands to its two identical sites arises from a disproportionate reduction in the enzyme's conformational entropy upon binding the first ligand. The results provide rare insights into the mechanisms of ligand binding for an essential human protein and should be of great interest to readers interested in enzyme structure/dynamics/function relationships, cooperativity and allostery, and possible drug targeting of thymidylate synthase.

(This preprint has been reviewed 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 uses a species-hybrid model in which functional human white and thermogenic adipose tissues develop in mice. Interestingly, human adipose tissue is fully able to recruit mouse vascular networks and sympathetic innervation during human adipocyte development. These findings provide novel and valuable information about the development of human thermogenic adipose tissue.

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

Evaluation Summary:

Here, 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).

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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.

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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.

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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.)