Evaluation Summary:

This paper will be of interest to neuroscientists interested in predictive coding. By using complementary neuroimaging and electrophysiological methods to measure brain-wide activation patterns in marmosets in response to sound pattern violations, the authors provide evidence for the hierarchical organization of predictive coding across subcortical and cortical levels of the auditory pathway.

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Evaluation Summary:

This is very much needed work, especially in light of the recent debate regarding whether or not microsaccades are the cause of peripheral attentional effects. A few influential papers have been published recently strongly suggesting that attentional effects are primarily the result of the execution of tiny microsaccades that humans/primates perform during fixation while attending to peripheral stimuli. These past findings have, naturally, a number of implications for the way we interpret visual attention, and raised the question of whether shifts of attention are dependent on microsaccades. By explicitly comparing and quantifying the effects of attention on neuronal responses in the presence and in the absence of microsaccades, this work provides important insights into this debate.

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Evaluation Summary:

This paper is of interest to researchers studying muscle function in the nematode C. elegans and to researchers interested in muscle aging in humans. The work documents the importance of C. elegans alh-6, which encodes a proline catabolic gene, in limiting muscle stress and maintaining locomotory function in aging nematodes. Further work implicates GWAS SNPs in the human homolog ALDH4A1 as potential determinants of specific muscle decline indicators. The suggestion of a conserved role for ALH-6 in aging humans could underlie establishment of a useful biomarker for older age muscle-associated health. However, while the work expands on and reinforces findings in C. elegans, it does not yet rigorously demonstrate a role for ALDH4A1 in muscle function in aging humans.

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Evaluation Summary:

This exciting study reports on the characterization of a novel compound that preferentially targets Nav1.6 voltage-gated sodium channels and shows substantial activity against epilepsy associated SCN8A mutations and seizure activity in a variety of animal models. This compound and approach has significant promise to be translated into a therapeutic for individuals with treatment resistant epilepsy.

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Evaluation Summary:

This study using single cell RNA Seq to profile developing retinal ganglion cells from embryonic and postnatal mouse retina explores the diversification of this class of neurons into specific subtypes. The computational approaches developed identify groups of RGC precursors with largely non-overlapping fates, distinguished by selectively expressed transcription factors that could act as fate determinants. The aim is to show that over time, clusters of cells become "decoupled" as they split into subclusters, and this process is associated with changes in the expression of specific transcription factors. This leads to the proposal that subtype diversification arises as a gradual, asynchronous fate restriction of postmitotic multipotential precursors. These findings enable the prediction of lineage relationships among RGC subtypes and the developmental time when these specification events occur, and should be of great interest to the developmental neurobiology community.

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Evaluation Summary: 

This paper will be of interest to a broad audience of epidemiologists and early childhood researchers as it provides data on the relationship between infection burden in infancy and metabolomic/lipidomic profiles at 12 months of age from a unique cohort of 555 mother-infant dyads. The paper also examines potential biologic pathways that may inform prevention of cardiovascular disease. The series of analyses presented support the preliminary associations outlined and require validation and interventional studies to support the causal relationship between infection, cumulative inflammation burden, and atherosclerosis.

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Evaluation Summary:

In a set of in vitro and in vivo experiments the investigators demonstrated that coating of urinary tract catheters with fibrinogen-degrading substances reduced adhesion and colonization with a broad range of bacteria relevant in the pathogenesis of CAUTI. This approach might, therefore, be interesting for prevention of CAUTI as an alternative to catheters coated with antibiotics.

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Evaluation Summary:

This manuscript which links early markers of inflammation with residual abnormalities on chest CT following SARS-CoV-2 infection. Surprisingly, early surveyed symptoms do not predict long term radiologic outcomes (6 months after infection) while inflammatory markers have stronger predictive value. Residual symptoms are common at the 6 month time point.

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Evaluation Summary:

In this manuscript, a light-gated receptor system (LOV2) linked to T cell receptor signaling machinery is enhanced by addition of an adhesion system enabling robust operation over a larger range of kinetic parameters. This system enables an exploration of how kinetic proofreading processes executed in seconds relate to T cell activation program involving reactions taking minutes to hours.

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Evaluation Summary: 

One hypothesis to explain recent worse-than-expected outcomes of universal test-and-treat HIV prevention trials is population mobility. The authors show phylogenetically that mobility could play a role in transmission events in a large trial in Botswana. This study is of public health interest, has a large sample size for a phylogenetic study in this setting, and overall precise analysis. A few methodological clarifications are still needed to ensure that the data supports the study's claims.

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Evaluation Summary:

This paper will be of interest to neuroscientists studying visual processing and is also more broadly relevant to understanding how sensory systems process information. The paper reveals several new insights into how first-order interneurons in the fly visual system encode visual features that help guide behavior.

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Evaluation Summary:

This paper will be of broad interest to neuroscientists, providing a rich resource for future research. Using available RNAseq data the authors build an easy-to-work-with web platform which will enable researchers to survey the expression patterns of palmitoylating and de-palmitoylating enzymes and their potential co-expressed substrates within the mouse nervous system. Using this map, the authors test hypotheses about the relationship between these enzymes and neurological diseases and generate hypotheses about enzyme/substrate relationships based on expression correlations.

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Evaluation Summary:

This paper will be of interest to neuroscientists studying ingestive behavior and control of body weight. It reveals two distinct subsets of neurons within a little-studied brain area that are both activated by feeding, but only of them contributes to hormone-mediated suppression of feeding. The combination of molecular profiling and functional modulation of the neurons compellingly support the claims of the paper.

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Evaluation Summary:

Matityahu et al investigate the influence of nicotinic acetylcholine receptor signaling on striatal microcircuit function through a combination of slice electrophysiology, optogenetics, and pharmacology. They find that nicotinic signaling delays spiking of striatal projection neurons in response to excitatory input, likely through the tonic release of acetylcholine by cholinergic interneurons onto local GABAergic interneurons and their influence on striatal projection neurons. Understanding how acetylcholine shapes striatal circuits is important, as this neurotransmitter is implicated in multiple movement disorders as well as other basal ganglia-related diseases.

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Evaluation Summary:

Bitzenhofer and colleagues provide unprecedented details of odor response properties of layer 2 cells in LEC. The authors show that firing rates of LEC ensembles conveyed information about odor identify whereas timing of spikes odor intensity and that, on average, fan cells responded earlier than pyramidal neurons, and pyramidal neurons, but not fan cells, changed their peak timing in response to changes in concentrations, providing a basis for temporal coding of odor concentrations. The results provide important information about odor coding in LEC, an understudied area of the brain.

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Evaluation Summary:

This study describes work measuring transcriptional changes through development and later aging. The authors broadly conclude that the transcriptomes of several tissues diverge during development, but re-converge during aging, a pattern that they term "divergence convergence", or DiCo. The trajectories the authors have identified could provide a powerful lens through which to improve our understanding of the basic biology of aging. This paper will be of interest to the aging community, especially to researchers interested in age-dependent gene expression changes and their consequences.

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Evaluation Summary:

The oncogenic virus Human Papillomavirus encodes the E7 protein which is an important contributor to carcinogenesis. Here, the authors show that E7-mediated degradation of the cellular tumor suppressor PTPN14 leads to activation of YAP1 in basal cells of the stratified squamous epithelium. They show that the ability of E7 to extend the lifespan of keratinocytes and facilitate basal cell retention are both activities mediated by the basal-cell specific activation of YAP1 and conclude that this newly discovered function of HPV E7 contributes to its carcinogenic properties. This report will be of great interest for researchers in the HPV and epithelial differentiation fields.

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Evaluation Summary:

This paper describes analysis and modeling of leading edge fluctuations in migrating cells driven by a branched Arp2/3 lamellipodial network. A stochastic model shows how branching contributes to shape stability, and reproduces the measured spectrum and dynamics of leading edge fluctuations. Analysis of the model as a function of branching angle suggests that the Arp2/3 branching angle might be selected to smooth lamellipodial shape. The authors provide new ideas to a big field of research, including Fourier analysis of leading edge fluctuations, which is a novel approach. The modeling methods and model design seem valid and the paper is well written.

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Evaluation Summary:

TRPV4 is an ion channel protein and mutations in TRPV4 gene resulted in different types of skeletal defects. In this study, the authors created two types of TRPV4 mutations (mild V620I and lethal T89I mutations) in human iPS cells through CRISPR-Cas9 gene editing. They identified key molecules potentially involved in TRPV4 mutation-induced changes in chondrocyte activities and concluded that the inhibition of chondrocyte hypertrophy induced by the mutations may cause the bone diseases.

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Evaluation Summary:

This work is of clinical relevance to those interested in the etiology and pathology of hereditary gingival fibromatosis (HGF). The paper discusses two novel findings: identification of a causative role of a missense mutation in the gene encoding the zinc finger protein 862 (ZNF862) that leads to hereditary gingival fibromatosis (HGF), a rare disease characterized by overgrowth of gingivae, in an examined family, and a suggestion of the molecular consequences of that mutation that leads to the disease.

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Evaluation Summary:

This paper will be of great interest to researchers interested in the brain mechanisms of pain. It shows how the connectivity of brain networks associated with sustained pain change over time. These findings are conclusively supported by state-of-the-art fMRI analyses of a tonic pain paradigm in two cohorts of healthy human participants. These insights are important for the understanding of the brain mechanisms of sustained pain which is the hallmark of chronic pain as a major health care problem.

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Evaluation Summary:

This manuscript is of broad interest to readers in the fields of drug addiction and relapse, reinforcement learning and punishment, and those interested in cortical function, particularly the insular cortex. The authors extend a context and punishment-based relapse model to the widely-used drug nicotine and use a number of complementary approaches to support the conclusion that the insular cortex plays a role in nicotine relapse. The experiments were carefully designed and implemented.

(This preprint has been 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:

Padoa-Schioppa and colleagues describe possible neuronal correlates of behavioral biases observed in monkeys making value-based choices when options are presented simultaneously versus sequentially. Building on the lab's previous work detailing functional roles of different neurons in the orbitofrontal cortex, the authors relate different choice biases to different groups of OFC neurons. They propose that these relationships indicate that different biases are likely to arise from specific stages of decision computation. The study results are convincing and represent a significant advance in understanding circuit-level computations underlying decision-making.

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Evaluation Summary:

FGF2 moves directly from the cytoplasm through the plasma membrane in a reaction driven by its subsequent high affinity binding to cell surface heparan sulfate proteoglycans. This study concludes that Glypican-1 is the principal proteoglycan involved, possibly involving a unique tri-sulfated disaccharide binding site in close proximity to the cell surface. While the role of Glypican-1 appears unique to FGF2 rather than part of a generalized direct secretion mechanism, the observations highlight the complexity and significance of proteoglycan variation. The work is well done and generally convincing, but additional support for the authors' conclusion that a specific glycan structure in GPC1 is a specific ligand for FGF2 is required.

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Evaluation Summary: 

This paper is of interest for cell biologists and biophysicists that work on eukaryotic cell motility and the dynamics of the actin cytoskeleton. The authors combine a series of clever biological approaches to fuse small Dictyostelium cells together into 'giant cells' that make it much easier to spatially resolve actin wave dynamics with and without electrical stimulation when cultured on smooth or nano-textured surfaces. Sophisticated and methodical computational approaches are used to analyze these images and relate the data to actin polymerization and wave dynamics parameters using optic flow and associated techniques. This study is mostly descriptive, a full mechanistic explanation of the results remains open, but this compelling experimental system opens up possibilities for the field to analyze the molecular subtleties involved in these cytoskeletal reorganizations.

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Evaluation Summary:

This study adds to the considerable, but often conflicting, work on how neurotransmitter systems contribute to auditory processing dysfunction. The paper details a thorough and careful analysis of an important hypothesis from the point of view of schizophrenia research: do muscarinic and dopaminergic receptors contribute to mismatch negativity effects? The answers could be useful for future treatment allocation in psychosis. The analysis was pre-registered and departures from the planned analysis were well-motivated and clearly described.

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Evaluation Summary:

This paper presents a single-molecule, multi-color microscopy study of the real-time assembly of perfringolysin O, a member of the membrane attack complex perforin cholesterol-dependent cytolysin superfamily. With the ability to resolve different states of the species in the reaction, simultaneously with membrane leakage, this work informs on key aspects of the mechanism including identifying potential assemblies involved in membrane lysis, and how membrane binding, oligomerization, and pore transitioning depends on concentration and pH. While some additional controls are needed to clarify the interpretation of the results, this study will be of interest to many, including those studying cytolysin mechanisms, but also the broader field of single-molecule studies of membrane binding proteins.

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Evaluation Summary:

In Drosophila neural progenitors (neuroblasts), sequentially-expressed transcription factors (known as temporal transcription factors) ensure the generation of various types of neurons and glia as they divide. However, the mechanisms regulating and finetuning the speed of temporal factor transitions has remained unclear and under-investigated. Here the authors concentrate on a specific temporal transition occurring in medulla neuroblasts and demonstrate that lineage-intrinsic Notch signaling facilitates this transition via at least two identified enhancers. This work provides important insights on the signals and mechanisms that promote temporal transitions in neural progenitors, and therefore regulate cellular diversity in the brain.

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Evaluation Summary:

This manuscript is of broad interest for evolutionary biologists who seek to understand the dynamics of strongly advantageous mutations across time and space. It presents an elegant framework for inferring the strength of natural selection and spread of adaptive variants that accounts for spatially and temporal patterns of genetic variation. The authors extend a previously developed statistical inference method, performs some tests of the performance of their method on simulated data and apply the method to two well-known targets of selection. The development of the method is timely given the growing availability of ancient DNA collections, which have the power to largely increase the accuracy of selection inferences and parameter estimates.

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Evaluation Summary:

Conway and colleagues use a combination of experiments and theory to test models for how kinetochore-fibers are born in mammalian spindles. Their work is consistent with a model where kinetochore-fibers primarily nucleate de novo at kinetochores, rather than arise from search-and-capture of microtubules. This work should be of interest to experimentalists and theorists broadly interested in self-organization, and in cell division.

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Evaluation Summary:

Kiewisz and colleagues performed sophisticated reconstructions of kinetochore-fibers within human spindles using electron tomography, and then analyzed the ultrastructure and organization of their microtubules. This work will not only serve as an incredible resource for the field, but has clear implications for models of kinetochore-fiber and spindle self-organization.

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Evaluation Summary: 

In this manuscript by Kissiov et al. the authors show that enhancers can play an instructive role in controlling stable random monoallelic expression (RME). In order to do so, they initially focus on a limited set of natural killer (NK) receptor genes that are subject to RME, which they investigate using several in vivo genetic models. Furthermore, they also show that RME can be considerably more prevalent than previously thought and that enhancer strength and/or number might influence the extent of RME for different genes. One remaining question may be whether this model may apply to other gene types than hematopoietic-related genes. Overall, this is a highly relevant manuscript with major implications in gene regulation and enhancer biology and, thus, of broad scientific interest. 

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Evaluation Summary:

This theoretical study describes the interaction of a planar brush or film of the resident unstructured components of the nuclear pore complex (NPC) called nucleoporins (FG-nups) and different nuclear transport receptors (NTRs). The authors describe impacts of competitive binding that give rise to enrichment of the NTRs, NTF2 and importin-beta, at different depths of the FG-nup film, which could relate to experimental observations in other studies, as well as evidence that crowding could promote the rate of nuclear transport by modulating FG-NTR binding/unbinding. The conclusions were found to be generally supported by the data, relevant to the field of nuclear transport, and able to make specific predictions that can be experimentally tested in the future, although previous studies in the field and the novelty could be better described.

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Evaluation Summary:

This paper is of interest for neuroscientists studying neocortical neural activity related to social behavior, with a connection to mouse models of neuropsychiatric disorders. The work provides new data on how loss-of-function of postsynaptic scaffolding and adaptor protein IRSp53 (encoded by the BAIAP2 gene) impacts prefrontal cortex activity and social interaction in mice. Overall, the experiments are properly controlled, although further analysis and interpretations are needed.

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Evaluation Summary:

This work reports on a mathematical modeling system and associated software implementation for compound eye vision. A critical advance reported here is the ability to model each ommatidium with independent properties and on a software implementation that runs in real time, with tantalizing applications in both modeling biological systems such as insect compound eyes, and the exploration of the possible applications of compound eye vision in robotics.

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Evaluation Summary:

This manuscript is of potential interest to a large audience in the fields of stem cells, developmental biology and neural regeneration. The authors assess the roles of extrinsic versus intrinsic signalling on differentiation of human neural cells by comparing their differentiation rates across different environments (in vitro, in the human embryo and grafted into a chicken embryo). While the experimental design tests the role of environment on differentiation, some aspects of data analysis need to be clarified and extended to support the conclusions.

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Evaluation Summary:

This manuscript provides insight into the zone-specific regulation of inflammatory gene expression in the fetal membranes prior to labor at term. Specifically, the authors demonstrate distinct epigenetic and mi-RNA control of TLR4 signaling in the amnion and chorion, highlighting the role of this pattern recognition receptor in physiological labor. Overall, the experimental design and data analysis are suitable, though the study would benefit from the inclusion of the analysis of fetal membrane tissues from pregnancy complications and/or in vivo studies.

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Evaluation Summary:

In this study, Tang and colleagues report that the deletion of the fructose-2,6-phosphatase TIGAR leads resistance to cold-induce hypothermia. Using different complementary approaches, they found that this phenotype originates from alteration in cholinergic neurons. In particular, they found that deleting TIGAR in ChAT-expressing neurons recapitulates the phenotype of the global knock-out. Overall, this is a well-performed study that provides evidence for a role of TIGAR in regulating the neuromuscular junction.

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Evaluation Summary: 

In this manuscript, the authors present at interesting strategy for directing simultaneous induction of both mesoderm-derived cardiac and endoderm-derived lung epithelial lineages from human induced pluripotent stem cells (hiPSC). All reviewers found the work to be of interest, but concerns were raised regarding the efficiency of the differentiation process (including % of differentiated cells in the final cultures) . In addition, it is noted that experiments presented are based on analysis of a single hiPSC cell line, and only part of the differentiation was repeated in another cell line, and thus the broader applicability of the presented protocol remains to be established. However, the interesting data support the conclusions presented. It is likely that the presented methods will be very useful for researchers focusing on heart and lung development, and may inspire others to take similar approaches for studying development of other organs. 

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Evaluation Summary:

The authors used phage display deep mutational scanning of SARS-CoV-2 Spike protein to profile antibody epitopes outside of the RBD that were recognized in two cohorts of subjects, which together included mRNA vaccinated, SARS-CoV-2 infected with mild or severe COVID-19 and vaccinated with prior infection. Key findings of the study are that severe COVID-19 and vaccinated individuals had higher binding to Spike protein regions NTD, CTD, and SH-H compared to individuals with mild COVID-19, while mild COVID-19 infections had higher binding to FP than vaccinated or severe COVID-19 individuals. They also reported that vaccinated individuals with or without prior infection were not different and that covariates did not appear to impact the antibody recognition profiles. The authors identified potential escape pathways in these epitope regions, some of which differed between vaccination and infection or drifted over time. The authors acknowledge that this approach is limited to linear epitopes and does not include RBD epitopes. However, the study provides novel insight into the major epitope regions targeted by polyclonal antibodies elicited by vaccination vs. infection, as well as potential pathways for the virus to escape recognition.

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Evaluation Summary:

This manuscript studies a topic of interest to developmental biologists using a combination of optogenetics, biophysical concepts, and mathematical modeling. How in plane contractile forces cause out of plane shape changes is a relevant open question, and the optogenetic tools developed in this work provide a new strategy to address the question.

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Evaluation Summary:

This manuscript examines the role of Nephronectin-Integrin a8 signaling in early stages in the avian corneal development. This is an understudied system with numerous gaps in our comprehension how neural crest derived cells migrate into the "open" space between the corneal epithelium and lens and form the corneal endothelium and stroma. Novel insights are generated on the cellular and molecular mechanisms of this critical process of anterior segment morphogenesis.

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Evaluation Summary:

This study employs a novel bioluminescence-based technique to analyze the import of precursor proteins into the mitochondrial matrix in real time. This is an innovative technical advance that can provide mechanistic detail on the kinetic steps of mitochondrial protein import. It has potential applications in other membrane protein transport systems and it could be applicable to studies in applied science such as screening for drugs targeting the mitochondrial import apparatus.

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Evaluation Summary:

The study investigates obesity and adipose distribution on hematopoiesis. It shows that genetically determined adiposity plays a previously underappreciated role in determining blood cell formation and function. The authors performed all the relevant and available MR analyses in the "toolbox". The results support the conclusions. The study will help understand the pathogenesis for clonal hematopoiesis.

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Evaluation Summary:

Karasawa and colleagues examine two gain-of-function mutations in NLRP3, which are known to cause cryopyrin-associated periodic syndromes (auto-inflammatory diseases with different manifestations), and demonstrate that both mutations appear to result in cryo-sensitive aggregated foci when expressed in cells. This is a very impactful and extensive body of work that is of broad interest to the fields of inflammasomes and autoinflammatory diseases. Data presented support the conclusions, and the findings are translational for patients and applicable to our general understanding of inflammasome function. However, specific issues raised by the Reviewers should be addressed.

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Evaluation Summary:

This study provides a sound and novel algorithm to analyze the massive cancer data and its findings greatly help inform novel cancer immunotherapy across various cancer types. Moreover, a 3-gene signature was established based upon Tc1, Tc17, and immune cold tumors to estimate the abundance of monocytic infiltrates that could potentially impact on the overall survival of cancer patients. It might be of great interest to the general audience of cancer biologists, immunologists 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. The reviewer remained anonymous to the authors.)

Evaluation Summary:

This manuscript is of broad interest to readers in the astrocyte and Alzheimer's Disease (AD) fields, and it utilizes state-of-the-art techniques to simultaneously record astrocyte calcium and animal behaviour. The work provides new insight into astrocyte calcium responses in AD, which has important implications for astrocyte pathophysiology. Overall, the data are of high quality and well analyzed.

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Evaluation Summary:

This preclinical study reports on a novel strategy for sepsis. Sepsis induced by Group A Streptococcus (GAS) in mice leads to depletion of bone marrow HSPCs and mortality and infusion of naive donor HSPCs lower mortality but has no effect on bacterial burden. This supports that HSPCs infusion might attenuate the detrimental immune response in sepsis warranting further investigation of this novel concept.

Evaluation Summary:

Using a genome wide screen, the authors identify novel pathways that protect Pseudomonas aeruginosa against Type-6 secretion-mediated by other bacterial species. Importantly these pathways each protect against specific effectors. As an example, the authors further show that one factor Arc3B protects against phospholipase activity by antagonizing the production of lysophospholipids induced by phospholipase-type effectors. These findings uncover potentially conserved and unsuspected bacterial-defense pathways.

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

Evaluation Summary:

This manuscript is of particular interest to readers in the field of pain research. The identification of separate brain systems associated with learning from unexpected pain and learning from unexpected pain relief contributes to understanding of pain avoidance learning. The combination of behavioral data, neuroimaging and computational modeling provide support for many of the central claims of the paper, however weaknesses in the experimental design limit the support for the claims based on the results of the pharmacological manipulation.

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Evaluation Summary:

This work describes how mitochondrial calcium in different regions of pyramidal neurons is controlled by action potentials and synaptic input. The authors show that calcium is controlled in a highly non-linear manner by calcium entry into cells (through voltage-dependent calcium channels) during sequences of action potentials. A particularly interesting finding is the high degree of localization of calcium rises in individual mitochondria in dendrites, and the requirement for both synaptic input and back-propagating action potentials to produce prominent rises of calcium in dendritic mitochondria. The work provides fundamental new information about how calcium entry during action potentials and synaptic input controls mitochondrial function.

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Evaluation Summary:

This new work from Chen et al. reports on a critical question that is whether astrocytes can be converted in situ into dopaminergic neurons in response to the targeting of specific factors using, for example, gene therapy. This is a very strong, elegant and straightforward study. It is of broad interest and of high translational relevance.

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Evaluation Summary:

RIF1 is a protein of the DNA damage response with key roles on genome integrity: it prevents DSB resection and hence accurate HR repair, whilst protecting stalled forks from degradation under replication stress conditions. The authors' main finding is the identification of 3 residues in RIF1 protein, that can be phosphorylated in ATM/ATR-dependent manner. However, this phosphorylation is dispensable for the ability of RIF1 to limit double-strand break resection, but is required to counteract the degradation of stalled replication intermediates mediated by the DNA2 nuclease. Therefore, the manuscript suggests that the three sites can provide a potential switch between the two functions of RIF1. These findings will spark the interest of readers working in the DNA replication and repair fields. However, the actual mechanism by which blocking RIF1 phosphorylation prevents RIF1 function at replication forks still needs to be determined.

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Evaluation Summary:

This manuscript reports the first high-resolution structure of the P4 flippase ATP8B1, which is associated with intrahepatic cholestatic disorder in humans. Using biochemical studies guided by the structure, the authors demonstrate ATP8B1's autoinhibition mechanism, its regulation by lipids and phosphorylation, and a plausible mechanism of disease-associated mutation. These results are an important contribution to the expanding literature in membrane protein dynamics and function.

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Evaluation Summary:

This study will be of interest to readers in the field of virus discovery. This study attempts to identify predictors of human-infective RNA virus discovery and predict high risk areas in a recent period in the United States, China and Africa using an ecological modelling framework. The study has potential to inform future discovery efforts for human-infective viruses . However it is not clear that key claims of the manuscript are currently fully supported.

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Evaluation Summary:

This paper is of interest to researchers studying cardiac regeneration and regeneration in general. Given the multiple papers characterizing interstitial cell types during mammalian cardiac injury response, this type of characterization in one of the leading regeneration model systems is overdue. The authors utilize single cell sequencing approaches to identify dynamics and key features of interstitial cell populations during zebrafish cardiac regeneration, which largely supports the claims of the paper. The data presented here have the potential to serve as a valuable reference resource for future studies, although some of the conclusions, in particular those on the function of tal1 and mmp14, are not yet sufficiently supported by data.

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Evaluation Summary:

This work analyzes how meaningful connections develop in the nervous system. Studying the dissociated neuronal cultures, the authors find that the information processing connections develop after 5-10 days. The direction of the information flow is influenced by neuronal bursting properties: the early bursting neurons emerge as sources and late bursting neurons become sinks in the information flow.

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Evaluation Summary: 

This manuscript reports that ppGpp accumulation is necessary for acclimation to nitrogen starvation in a model plant Arabidopsis. The authors also showed a ppGpp-mediated downregulation of chloroplast gene transcription and a coordinated plastid-nuclear gene expression under nitrogen deficiency. This represents a solid new step in our understanding of plant responses to nitrogen-limiting conditions as well as on the role of ppGpp in plants and possibly throughout the green lineage.

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Evaluation Summary:

The study presents novel results on spontaneous fluctuations in pupil dilation in relation to the spectral dynamics in a large sample of human participants. The study is based on MEG recordings allowing for quantifying these relations in time and space. The data provide important new insight into the temporal and spatial characteristics of pupil-linked changes in cortical states which form the basis for incorporating this insight in future clinical and cognitive neuroscience studies.

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Evaluation Summary:

The possibility that local or systemic hypoxia regulates aspects of the immune system has attracted widespread interest over the last decade or more. Previous work has implicated regulatory T cells in at least some of these responses, and has demonstrated that over-activation of a specific hypoxia inducible factor (HIF) isoform, HIF-2alpha has the potential to driven pro-inflammatory lymphoproliferative responses characterized by defective regulatory T cells. The current work demonstrates that genetic activation of these hypoxia-signalling pathways that is restricted to the regulatory T cell lineage is sufficient to drive this type of immune activation. The work is important since it provides a focus for study of the mechanism, for which the authors make a proposal based on mis-localization of regulatory T cells. It is also important in focussing a key questions (requiring further study) as to whether physiological or pathological hypoxia, specifically affecting these cells, will drive such a response and/or whether the lymphoproliferative phenotype could be affected adversely or beneficially by agents that are being used to upregulate or downregulate hypoxia-signalling pathways in other settings.

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Evaluation Summary:

The study by Kano et al. provides experimental evidence that specific features of the human eye, namely shape and sclera depigmentation, enhance the ability to detect gaze direction of individuals. The study is notable for being the first to adopt a comparative experimental approach, testing both humans and chimpanzees, to demonstrate that white sclera can enhance gaze discrimination in both species, particularly when visibility is poor.

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Evaluation Summary: 

This study addresses the the potential effects of saturated vs. unsaturated fatty acids on kidney proximal tubule injury in diabetic kidney disease. They find that compared to saturated fatty acids, unsaturated fatty acids prevent ER stress by stimulating triacylglycerol formation. 

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Evaluation Summary:

This manuscript from Bishop et al aims to quantify the hypoxic and hyperoxic ventilatory response in the marmoset, an increasingly more common primate research model. The strongest contribution of the paper is the presentation of an analysis toolkit to perform unsupervised analyses of respiratory data, which are not widely available.

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Evaluation Summary:

This is an intriguing study using cleverly designed stimuli to investigate the representation of physical stability in the human brain. This paper will be of interest to readers wondering when human cognition uses generalizable pattern matching similar to that used by machine learning algorithms, and when it relies on more specialized processes evolved for specific tasks. The well-crafted experiments generally support the authors' major claim.

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Evaluation Summary:

This manuscript describes the presence of two discernable populations of pancreatic delta cells in a zebrafish model. One of these subsets of delta cells is suggested to facilitate the regeneration of functional beta cell mass following beta cell ablation. This observation is of interest to investigators studying islet regeneration.

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Evaluation Summary:

This is a fascinating article on the discovery of an unusual form of bacterial multicellularity: an organism that can exist in dense, filamentous multicellular structures and clusters of coccobacillus daughter cells. Experiments that mimic the periodic immersion that the bacteria experience in their natural cave environment suggest that water immersion plays a role in this life-cycle dynamics. This work, while rather qualitative, will nevertheless likely attract great interest from a diverse range of scientists working on multicellularity, the biophysics of cell packing, and geobiological problems.

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Evaluation Summary: 

In a previous study the authors showed that the quorum sensing signal molecule 2-aminoacetophenone (2-AA) produced by Pseudomonas aeruginosa enables persistence in host tissue of this pathogen. They propose that this effect depends on a Warburg-like metabolic reprogramming effect in macrophages. 

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Evaluation Summary:

The work supports the hypothesis that novel specific enymes evolved to modify metabolic pathways, allowing phototrophs to shift from growth under photoautotrophic and photomixotrophic growth conditions.

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Evaluation Summary:

Rutz et al. outline LOTUS, a new open-source database that links natural product structures with the organisms they are present in. It contains over 700,000 referenced structure-organism pairs and search tools that make mining the database intuitive and efficient. The LOTUS Initiative comprises an important data harmonization/integration effort over previous databases. The results are distributed to the public through Wikidata, which additionally supports future curation. This new resource is likely to be of great interest to natural product researchers as well as across fields of biology including ecology, evolution, and biochemistry.

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Evaluation Summary:

This is a challenging study exploring the effects of a commonly used analgesic, remifentanil, on brain and spinal cord related pain processing in humans. It is of considerable interest to the pain research, neuroimaging and opioid neuroscience communities and are also relevant to clinicians who commonly use opioid infusions. The authors have used sophisticated methods for combined brain and spinal cord functional magnetic resonance imaging to examine the influence of an intravenous opioid on pain processing in the ascending and descending pain pathways in healthy subjects. The authors have conducted a comprehensive assessment in large numbers of subjects and have explored both changes in amplitude of activity as well as connectivity. Their detailed analysis strengthens findings from previous human and animal studies and extend to demonstrate novel changes in connectivity in the descending pathway to the spinal cord although these data are potentially compatible with alternative interpretations and may need to be reinforced by further analysis.

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Evaluation Summary:

This manuscript provides strong evidence that adaptation in cone photoreceptors of the primate retina can subtly change the balance of excitatory and inhibitory inputs to On parasol ganglion cells and thereby fundamentally affect how these cells integrate visual information. This study provides important mechanistic insight into the previous observation that On parasol cells display nonlinear spatial stimulus integration under standard reversing gratings but linearly integrate signals in the context of natural scenes. The findings will be of great interest to visual neuroscientists.

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Evaluation Summary:

Using computational modeling and dynamic clamp recordings, this work supports the concept that hyperexcitability of cortical circuits in a familial mouse model of Alzheimer's disease is caused by impairments of biophysical properties of Kv3 channels in parvalbumin-positive cortical interneurons. Overall, the work is clear and interesting but some further analysis is required to provide compelling support to the central claims.

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Evaluation Summary:

This paper addresses an important problem in control of episodic memory. This paper develops a computationally-based proposal about how semantic, working memory, and episodic memory systems might learn to interact so that stored episodic memories can optimally contribute to reconstruction of semantic memory for event sequences. This is an understudied area and this present work can make a major theoretical contribution to this domain with new predictions. The reviewers were positive about the contribution.

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Evaluation Summary:

Giove and colleagues demonstrate an intriguing dissociation of neurovascular (as measured with BOLD-fMRI) and neurometabolic (measured with fMRS) responses during perception. This is a thought-provoking study that makes one wonder about the signals we measure with human neuroimaging, especially fMRI. It will therefore be of great interest to the broad community of neuroimagers, as well as perception researchers.

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Evaluation Summary:

This paper uses an anatomically-constrained neural network model to investigate how looming visual stimuli - i.e. stimuli likely to collide with an organism - could be detected. The authors find one dominant solution to this problem reproduces both the computational properties and neural responses of known collision detecting neurons in the fruit fly, Drosophila melanogaster, without ever being trained on neural data. Their findings shed light on why biological collision detection circuits may have converged on particular solutions. A similar approach could reveal important computational features in other circuits.

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Evaluation Summary:

Kidney organoid cultures derived from human induced pluripotent stem cells represent a new tool with which to study renal morphogenesis in both normal and pathological states. In the current study, the authors have combined morphological evaluation with proteomics to elucidate aspects of the temporal sequence of basement membrane composition during normal renal development and in the setting of a pathogenic collagen type IV alpha 5 chain variant associated with Alport syndrome, an inherited kidney disease. This model system may help us to better understand the pathogenesis of inherited diseases that affect renal basement membrane composition.

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Evaluation Summary: 

The work evaluates the production of P. falciparum sexual stage parasites in blood samples from asymptomatic parasite carriers through the dry season and symptomatic malaria patients in the wet season. Sexual stage parasites are required for malaria transmission via mosquito, but historically their low levels in peripheral blood have limited analysis. The work here monitored asexual and sexual stage parasitemia and found that the relative expression of early gametocyte genes, including ap2-g, is similar in samples from asymptomatic and asymptotic individuals. The data was used to model gametocyte availability from the initial symptomatic infection through the chronic phase and advances the understanding of factors that contribute to malaria transmission. 

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Evaluation Summary:

The potential mechanism of METTL3 N6-methyltransferase in the chemotherapeutic response is poorly defined. Herein, Li and colleagues describe a pathway where METTL3 promoted EGF expression through m6A modification, which further upregulated RAD51 expression, resulting in enhanced HR activity. METTL3 knockdown results in DNA damage accumulation, which renders breast cancer cells sensitive to adriamycin treatment.

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Evaluation Summary:

This manuscript investigates the role of role of the VEGFA signaling cascade, which is widely known to regulate formation of blood vessels, in muscle satellite cells and muscular diseases. on studying the relationship between muscle stem cells (MuSCs) and blood vessels. The authors identified the FLT1-AKT1 axis as an important effector of VEGFA on MuSC survival. They conducted a series of in silico, in vitro and in vivo experiments and showed that VEGFA-FLT1-AKT signaling promotes satellite cell survival both the physiologic and myopathy conditions. The paper will be interesting not only for muscle biologists, but also cell biologists and the general life science field.

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Evaluation Summary:

This manuscript reports a surprising discovery in C. elegans: upon losing its normal sensory properties, the ADL nociceptive/pheromone sensing neuron relays and thereby enhances oxygen behavioral responses via neuropeptide signaling. This effect could be interpreted as cross-modal sensory plasticity or more general a cross-modulation between sensory circuits, a still open question that should be addressed in a revision. The study is relevant to scientists working on sensory neurobiology and neuronal plasticity.

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Evaluation Summary:

In this paper, Sahinyan and colleagues developed a method for analyzing chromatin accessibility in single murine myofibers. This goal was achieved by adapting the previously published OMNI-ATAC protocol to the specific properties of the myofiber environment. To demonstrate the validity of this method, they isolated myofibers from uninjured and regenerating murine EDL muscles dissected from wild type animals. In a second experiment, this method was applied to isolate myofibers from mdx mice, a model of Duchenne Muscular Dystrophy. The resulting datasets were further compared to the one generated from purified muscle stem cells.

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Evaluation Summary:

The study by Cantero-Recasens et al. aims to investigate if mucus secreted by colorectal cancers would impact the effect of the frequently used chemotherapy treatment, FOLFIRI as it has been reported that mucinous carcinomas are more treatment resistant. They further investigate the role of some mucus secretion regulatory genes in this context. The conclusions made on the effect of the mucus secretion regulatory genes are well supported, though the link to the function of mucus in reducing treatment availability needs some further clarifications.

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Evaluation Summary:

In their manuscript, Lu et al. use a combination of experimental approaches to determine how cellular components are transported from nurse cells into the growing oocyte during Drosophila egg development. The authors demonstrate that the minus-end directed microtubule motor, dynein, generates cortical flow by gliding microtubules along the cell cortex. This flow is capable of propelling cargoes through the ring canals into the growing oocyte via a bulk cytoplasmic transport mechanism. This action is distinct from dynein's cargo transport functions, as the authors are able to replace dynein with a minus-end directed kinesin linked to the cortex and observe the same phenomenon. Overall, this work had broad significance to cell biologists and developmental biologists interested in intracellular transport functions and oocyte development.

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Evaluation Summary:

This manuscript will be of interest to readers in the field of immunology and especially in the induction of immune tolerance in the thymus. The work uses several mouse models to substantially broaden the current understanding of MHCII/TCR -mediated cell-cell crosstalk in the thymus and suggests a novel mechanism that contributes to the generation of functional and self-tolerant T-cells.

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Evaluation Summary:

This paper presents a mathematical model for prioritizing drugs for prostate cancer patients based on signal network database. The manuscript is of broad interest to the field of oncology and precision medicine. The methodology developed is sophisticated and relevant to real patient prostate cancer data. The predictions from the model are validated in an experimental setting and provide suggestions for the personalisation of prostate cancer treatment. The study can serve as a roadmap for future development of predictive, personalized models.

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Evaluation Summary: 

This study demonstrates that differences in areas outside the regions that encode the TCR genes can affect the properties of TCRs that get made. This paper will be of interest to a broad swathe of immunologists who study such variable lymphocyte receptors. It combines several large datasets in an extremely statistically rigorous analysis, producing results consistent with but substantially expanding upon the prior knowledge of the field. 

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Evaluation Summary:<br> This work elegantly fuses cryo-EM, x-ray crystallography, and in vitro transport experiments to describe the structural basis for functional diversity in the SLC11/NRAMP family of membrane transporters. This work identifies factors responsible for selectivity of classical NRAMPS for transition metal ions (Fe, Mn) and the NRMT clade for alkali metal ion (Mg). Although selectivity is much discussed in transport of divalent metal ions, this is an outstanding example of a study that gets to the bottom of the structural determinants governing this behavior. 

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Evaluation Summary: 

The regulation of cell growth is crucial for our understanding of how cells control their size as well as how they balance cell mass and volume. While recent studies carefully measured single cell mass trajectories during the cell cycle, revealing complex growth patterns, the volume growth patterns of animal cells are poorly understood. In this interesting study, Cadart et al. now present high-precision measurements of 1700 HeLa cell growth trajectories and offering evidence for the mechanisms that regulate volume growth-rate fluctuations. This is an important demonstration of cell autonomous volume regulation.

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Evaluation Summary:

The manuscript by Carrasquilla and colleagues applied Mendelian Randomization (MR) techniques to study causal relationship of physical activity and obesity. Their results support the causal effects of physical activity on obesity, and bi-directional causal effects of sedentary time and obesity. One strength of this work is the use of CAUSE, a recently developed MR method that is robust to common violations of MR assumptions. The conclusion reached could potentially have a large impact on an important public health problem.

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Evaluation Summary:

This addresses an important area of excitation contraction coupling failure of potential clinical translational importance. They report that progressive depolarization of the resting potential upon excitation contraction coupling results in a persistence of action potential generation in the face of a failure of Ca2+ release.

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Evaluation Summary:

Nowicka et al., evaluated radiation dose and time dependent changes in the levels of selected serum miRNAs in human patients who received partial or complete myeloablative total body irradiation (TBI) and propose a panel of circulating miRNAs as potential radiation biodoismeters. The team employed next generation sequencing approach for discovery (or rediscovery) and quantification of selected responders by qRT-PCR using non-responsive miRNAs purified from exosomes in serum for evaluation of relative changes. Excellent bioinformatics and bio statistical methods are employed. However, critical biomarkers they propose as radiation biodosimeters have already been identified and published earlier. There is little novelty here and the translational significance of the study is moderate.

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Evaluation Summary:

This article will be of interest to behavioral ecologists studying activity patterns in wild animals. Using accelerometry, rather than polysomnography, opens up exciting opportunities for studying animal sleep under natural conditions for relatively long periods.

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Evaluation Summary:

Oligogenic inheritance is likely to be an important mode of disease risk for many male infertility traits, but few validated examples exist. This clear documentation of oligogenic effects on mouse sperm is significant for both the sperm abnormality field and for the broader male infertility community.

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Evaluation Summary:

Circadian disruption is widespread in our modern 24/7 society, leading to an increased prevalence of common diseases including type 2 diabetes. The authors conducted an unbiased screen for small-molecule compounds that can restore the attenuated insulin secretion from pancreatic beta cells caused by a disrupted circadian clock. They identified ivermectin and its clock-controlled target, the P2Y1 receptor, which regulate glucose-stimulated Ca2+ influx and insulin secretion in beta cells.

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Evaluation Summary:

The manuscript details the function of the N-Myc downstream regulated gene 1 (NDRG1) during induced hypoxia using the anoxic developing zebrafish as a model system. With some additional support for the central claim of a switch for metabolic suppression, this paper will be of interest to scientists with a focus on kidney development, factors that regulate hypoxic survival, and metabolism in response to stress conditions.

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Evaluation Summary:

This paper is of potential interest to investigators in the bone field. The study provides evidence of CypD regulation of osteoblast differentiation and offers new insights into it's transcriptional regulation. Overall, although the findings are compelling and have the potential to advance the field, several conclusions require additional data or clarification and there are some missed opportunities to strengthen the manuscript.

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Evaluation Summary:

This paper will be of interest to the large class of neuroscientists who investigate brain plasticity. It identifies short-term plasticity in a subcortical region, the ventral division of the pulvinar, following monocular deprivation in adult humans. The work is believed to extend our research focus on the topic of ocular dominance plasticity from mainly the cortex to a larger brain network including the subcortical stages of visual processing. This is an intriguing possibility, but further evidence is required to fully support the claims.

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Evaluation Summary:

This is a multifaceted study of the epithelial to mesenchymal transition (EMT) in live cells. EMT is relevant for cancer, development, and wound healing. The authors were able to discern two possible cell transition path categories without multi-color labeling or other advanced experimental approaches, which could be impactful. The study draws on a wide range of experimental, data science, and modelling tools and techniques.

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Evaluation Summary:

The overarching goal of this study was to identify eco-evolutionary feedbacks between plant community diversity and global change drivers. The authors aimed to test the hypothesis that a decline in species richness due to various global change drivers selects for traits that will make species more vulnerable to the further effects of these drivers, amplifying thus the initial diversity decline. This research is of prime importance to botanists, plant ecologists and ecosystem ecologists wanting to understand the effects of global change on plant diversity and productivity.

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Evaluation Summary: 

Nichols et al. developed and characterized the first fluorescent sensors for several nicotinic receptor partial agonists relevant to smoking cessation. It is potentially a major advance for the field. They leveraged crystallography to understand the mechanism by which the ligands enhance fluorescence, then characterized top sensors for sensitivity, selectivity, and kinetics, and their utility in plasma membrane and ER sensing in neurons and cell lines. The tools developed by this team will enable investigators to track nicotinic receptor partial agonists in different subcellular compartments with relatively fast time resolution. 

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Evaluation Summary: 

This carefully executed study suggests new mechanisms by which Serum Response Factor (Srf) regulates transcription. The manuscript reports the effects that loss of Srf function has on different neural crest lineages in the mouse. The authors conclude that within neural crest, the main function of Srf is in the cardiac neural crest lineage where it regulates cytoskeletal genes. 

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Evaluation Summary:

This study investigated the role of transient receptor potential vanilloid 4 (TRPV4) in pressure overload-induced cardiac hypertrophy. The expression of TPRV4 is increased in both heart failure and pressure overload-induced cardiac hypertrophy models. The TRPV4 deletion or inhibition ameliorated the hypertrophy cardiac pathology. The authors propose that TRPV4 is a potential therapeutic target for cardiac hypertrophy.

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Evaluation Summary:

This paper will be of broad interest to readers who study anatomical connections of the brain. It demonstrates the efficacy of a cutting-edge viral tracing technique in mapping excitatory projections in macaque monkeys. The work describes the generation of a projectome from the macaque vlPFC cortex across the rest of the brain using AAV2/9-CaMKIIa-Tau-GFP labeling and imaging with high-throughput serial two-photon tomography. The comparison with imaging techniques available in humans (diffusion tractography) will also be of interest to research in human brain anatomy.

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Evaluation Summary:

This manuscript will be of interest to researchers interested in the influence of prenatal exposures on infant health. The authors investigate the impact of the season of conception on child DNA methylation levels in two independent cohorts from the Gambia and identify a set of CpGs that are tightly regulated during development. The data support the main conclusions of the manuscript, but some of the analyses could be improved (i.e. possible presence of residual confounding). There is also limited evidence for the functional importance of the observed associations. 

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

Evaluation Summary:

This paper is of interest to cell biologists, biochemists and biophysicists interested in how adhesion and signaling proteins at the cell surface help cells (and especially neurons) interact and perform self/non-self-recognition and self-avoidance. The authors provide the first extensive biophysical dataset examining a large subset of potential trans (across two cells) and cis (on the surface of the same cell) interactions between different isoforms of the ~60 clustered protocadherins (cPcdhs). There data show that all tested trans interactions are strictly homophilic and that not all possible cis interactions are equivalent. These results provide additional layers of complexity and constraints on how this protein family can provide neurons with the ability to perform self-recognition and self-avoidance.

(This preprint has been reviewed 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 presents evidence that autophagosomes fuse with phagosomes and that this promotes the degradation of phagocytosed cell corpses. The study also resolves controversy in the field about the question why genes involved in autophagy affect cell corpse engulfment and degradation. With some additional data to solidify the main conclusions, the work will be of interest to a broad cell biology 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 name with the authors.)

Evaluation Summary:

This paper will be of interest to the lipid metabolism and transporter communities. Fatty acids that are too long to be transported into mitochondria are instead transported into peroxisomes for their break down i.e., beta-oxidation. The authors have determined the cryo-EM structure of human ABC transporter ABCD1 (ALDP), which translocates very-long-chain fatty acids (VLCFA) conjugated to coenzyme A across peroxisomal membranes, in complex with its substrate. While the work is well done, it is unclear what new mechanistic insights are gained from the ALDP structure. Also, the proposed conformational differences based on AlphaFold models should be taken with caution.

(This preprint has been reviewed 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:

The authors have discovered that the transcription factor Zfp335 is an important regulator of early T cell development in the thymus. This paper will be of interest to scientists within the field of T cell development. The approaches used are thoughtful and rigorous and the key claims are supported by the data. Whether or not Zfp335 specifically controls beta-selection via the gene targets described requires additional experimentation.

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

Evaluation Summary:

This manuscript by Yu et al. captures the transcriptional heterogeneity of mouse POMC neurons across hypothalamic development. This study unifies multiple other observations about the role for other neuron al cell types that express POMC transiently during development. The paper is an important resource understanding of the diversity of POMC neuron classes and their relationship to other cell types in the arcuate nucleus.

(This preprint has been 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 broad interest to the DNA-repair and structural biology field. The paper describes new insights into the interaction between ATM and Nsb1, proteins central to repairing DNA double-strand breaks in humans. Overall, the structural cryo-electron microscopy data is solid and the data well analyzed and presented with key claims directly related to and supporting previous known findings.

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

Evaluation Summary:

This manuscript will be of interest for researchers interested in DNA repair and transcriptional regulation. The authors provide a series of well-executed and designed high-resolution sequencing data demonstrating that transcription factor (TF) binding perturbs alkylation base damage formation as well as inhibits its repair via base excision repair (BER) at TF binding sites. Moreover, they demonstrate differences between nucleotide excision repair and BER at TF binding sites that are consistent with the different repair mechanism of these two pathways. These results should have an important and timely impact on the field.

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

Evaluation Summary:

The study reports the development of high-throughput droplet digital PCR to detect Plasmodium falciparum parasites carrying pfhrp2 and pfhrp3 gene deletions. These mutations usually cause false-negative RDT results on malaria tests. Although there are several PCR-based detection methods already available, the assay is useful as an alternative, particularly in countries and settings where droplet digital PCR is routinely used. The strength lies in its capability to detect hrp2 and hrp3 deletions in samples with multiclonal (more than one clone) infections. This has the potential to assist in surveillance for pfhrp2/3 deletions programs where RDTs designed to detect HRP2 are the primary test leading to false negative results, particularly in medium to high transmission settings. The study will be of interest to those studying infectious diseases.

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

Evaluation Summary:

This paper will be of interest to neuroscientists, particularly those studying defensive behaviors. The authors provide novel insights into the mechanisms by which the brain computes contextual information associated with innate threats in mice. The experimental approach and data analysis are mostly adequate and the study provides the first causal evidence of a hippocampus-anterior hypothalamic pathway mediating spatial fear memory of ethological threats. The implementation of more robust statistical tests, as well as more detailed Methods and Discussion sections should serve to strengthen an already elegant 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.)