eLife assessment

In this potentially important study, the authors attempt to explain why hormone replacement therapy with estrogen is not effective in preventing atherosclerosis in post-menopausal women by showing that iron accumulation prevents the hormone replacement therapy benefit through negative regulation of estrogen receptor expression via Mdm2-mediated proteolysis. The strength of evidence is currently incomplete as control groups are missing and there is a lack of clear-cut evidence that this effect is related to the estradiol therapy in addition to the accumulation of iron in the post-menopausal state. The general public as well as specialists might find this work to be of interest.

eLife assessment

This important study reports that a high-fat diet induces biliary epithelial cell proliferation and suggests this may account for the so-called ductular reaction in advanced fatty liver disease. Convincing data support the finding that the transcription factor E2F1 is required for biliary epithelial cell proliferation in mice fed with a high-fat diet, and organoid models indicate that lipid abundance promotes glycolysis in an E2F-dependent manner. These findings are potentially of broad interest to the field of liver biology and disease.

eLife assessment

This paper addresses an important question within adaptive immunity, namely whether the T cell receptor (TCR) repertoire of negatively selected thymocytes shares common features. The authors analyze T cell receptor sequences from mice as they progress through positive selection, CD4/CD8 lineage commitment, and negative selection, to find small but consistent differences between the repertoires at these selection stages. They argue that their findings do not indicate any sequence-specific selection; however, some of the conclusions drawn are currently incompletely supported by the performed analyses.

eLife assessment

This is a very elegant study which clearly demonstrates the existence of CMV specific memory T cells in CMV+ pre-pandemic individuals that are capable of recognising epitopes from SARS-CoV-2. It provides new insights into the development of cross-reactive immune cells that was not anticipated. The study has been elegantly performed and presents important findings. In particular, the discovery of a public TCR which mediates the crossreactivity described is an important finding.

eLife assessment

This paper is of potential interest for skeletal biologist studying osteocytes and skeletal aging. Using a mouse model of partial osteocyte deletion, the authors provide new understanding on the role of osteocytes in regulating other lineage cells in bone, bone marrow, and skeletal muscle. This is an important and logically presented study that offers new insight into the biology of osteocytes. The set of data from the genetic mouse model, bone phenotypic analyses, and scRNA-seq analysis largely support the conclusion.

eLife assessment

Most birds today can lift the upper beak independently of the brain case, enabled by a series of mobile joints and bending zones in the skull. The computed tomography of the skull of a 120-million-year-old toothed bird produced by the authors shows for the first time that the joints were still absent, but also hints at how they may have evolved later. This compelling, important paper is of high interest to evolutionary biologists, vertebrate paleontologists (especially, but by no means only, those working on bird origins) and specialists in biomechanics.

eLife assessment

A commonly held hypothesis about how genetic variants predispose to common diseases and other human traits is that variants have phenotypic effects by altering transcript accumulation. The authors question this view by showing some evidence for shared genetic control of transcript abundance for genes believed to be involved in the traits, and for the traits themselves.

eLife assessment

Functional magnetic resonance imaging (fMRI) yields a notoriously noisy and autocorrelated signal, and the GLMsingle method presented here by Prince and colleagues demonstrably improves the estimation of responses evoked by single trials. This open source toolbox is implemented in a user-friendly manner and will be of interest to researchers using human neuroimaging to study neural responses in condition-rich designs, as is increasingly common in cognitive neuroscience experiments.

eLife assessment

Several mammal species, including dolphins, have evolved to be relatively "hairless". Kowalczyk and colleagues scan the genomes of multiple species to identify genomic regions that appear to have evolved at a faster or slower evolutionary rate along hairless lineages. They identify a number of protein-coding genes as well as noncoding regions that might explain how hairlessness evolved in mammals. This study is of interest to those investigating the development of the skin and its appendages as well as evolutionary biologists, especially those investigating instances of convergent evolution and those developing phylogenomic methods for genome comparisons.

eLife assessment

CRISPR-Cas systems are essential components of an adaptive immune system that protects bacteria and archaea from infection by foreign genetic elements like phages and plasmids. The work presented here demonstrates that some CRISPR systems (i.e., type III-A) rely on host nucleases (i.e., RNase R and PNPase) for faithful processing of CRISPR RNAs. Collectively, this work expands the fundamental understanding of how nucleases involved in RNA metabolism contribute to the adaptive immune response in bacteria.

eLife assessment

This is a valuable study performing elegant experiments making identification of a specific regulator in skeletal muscle regeneration. It will form a foundation for further mechanistic investigation. The work is of importance in the clinical field of muscle injury and regeneration.

eLife assessment

The authors provide a new method to target mouse CSF-cNs via intracerebroventricular injection of adeno-associated virus (AAV) with a neuron-specific promoter, which enabled them to introduce any genes into CSF-cNs. By doing so, they established the structure, connectivity, and function of mouse CSF-cNs in locomotion, recapitulating the findings obtained in zebrafish and lamprey, and extending the recent observations in mice. This study is very conclusive and important for the sensorimotor field.

eLife assessment

This paper on the regulation of microtubule dynamics during C. elegans meiosis will be of interest to scientists in the broad field of microtubule function in both mitosis and meiosis. The experiments are beautifully conducted and presented and generally support the conclusions of the paper. The results are interesting and add to our understanding of the control of microtubule dynamics at the kinetochore and its functional consequences for meiosis.

eLife assessment

Canetta et al. explored the time-dependent effects of inhibition of parvalbumin-positive interneurons in the mouse prefrontal cortex on task learning and cognition. Overall, the study shows that prefrontal cortex PV cell activity during a sensitive period strongly modulates cognitive flexibility and network activity in the adult mouse. This study could progress our understanding of cell behavior in mouse prefrontal cortex.

eLife assessment

This is an important paper that is methodologically solid and highlights structural covariance as the neuroanatomical basis underlying individuality in genetically identical mice. The approach to individuality is very well designed, and the use of brain imaging and anatomical covariance as the underlying mechanism is well thought out. The statistical methods, while overall sound, require further justification and exploration. This paper will be of broad interest to neuroscientists, especially those working in brain plasticity or understanding unique and shared environmental influences on individuality.

eLife assessment

This is an important manuscript that will be of interest to a broad range of researchers studying immunology, obesity and metabolism, as well as the links between maternal health and pathophysiological responses in the offspring. The comprehensive studies using RNA-seq, scRNA-seq, ATAC-seq and scATAC-seq in human umbilical cord monocytes represent an important resource for understanding the transcriptomic and epigenetic shifts in the monocytes of newborns. The experiments involving stimulation of monocytes with pathogens offer convincing evidence for the dysfunction of monocytes in the newborn.

eLife assessment

This paper is a fundamental work in developmental biology that supports its findings with compelling evidence drawn from both theoretical and experiment insights. This work will be of interest to researchers in the fields of developmental and stem cell biology as it provides a potentially general mechanism for the control of a proliferative cell population.

eLife assessment

This important work convincingly shows that taste memory formation requires the same circuit substrates and mechanisms as olfactory memory formation. While the exact mechanisms remain to be elucidated, the compelling data and approach represent a valuable foundation for the study of molecular and circuit mechanisms underpinning taste memory formation and the role of brain energy therein. This study will be of particular interest to the large community of scientists studying the mechanisms and circuits of memory formation in the fly and possibly beyond.

eLife assessment

This paper reports on important observations regarding human CD8 T cells that express shared T cell receptors amongst individuals and exhibit poly-specificity directed mainly to several unrelated viral antigens. Although the majority of the claims are convincingly supported by results from both in silico and experimental approaches, mechanistic molecular details underlying poly-specificity remain incomplete. The results from these studies will enhance the ongoing debate on T cell specificity and potentially, will impact fields related to immunology, for example, immunoparasitology, cell biology, and vaccine development.

eLife assessment

The authors of this manuscript set out to improve on a peptide, ProTxII, which had been previously put forward as a promising blocker of Nav1.7 channels and thus offers a possible non-opiate way to block pain. They develop a useful computational workflow that is based on in silico manipulations of the interaction of ProTxII with a Na channel structure determined previously and evaluation of the predicted mutations with electrophysiology. The authors succeed in producing two peptides with improved selectivity for Nav1.7 over other subtypes and capable of producing ion channel block at low concentrations and the experimental evidence presented is solid, and the general applicability of the method is compelling.

eLife assessment

This paper provides evidence that an unhealthy lifestyle during adolescence accelerates epigenetic age in adulthood, and that these associations are largely explained by the effect of shared genetic influences. The main strengths of this valuable paper are the relatively large sample size, longitudinal assessment of lifestyle factors, and sophisticated statistical analyses. The paper is methodologically compelling and will be of interest for a broad audience, including individuals working on methylation, epidemiology, and/or ageing.

eLife assessment

This is a potentially important paper that takes advantage of an unusually comprehensive evolutionary genetic dataset to tease apart the relationship between genetic variation and phenotypic divergence over the ~medium term (50 generations). The questions addressed have broad relevance across evolution, conservation, and agricultural fields, and this paper will particularly appeal to evolutionary biologists. Nonetheless, the strength of evidence is incomplete for the major results and conclusions reported.

eLife assessment

This paper addresses an important question: the relationship between the cell wall and other, primarily lipid, based components of the cell envelope. Building on previous work, the authors provide data suggesting that the activity of a PonA2, non-essential peptidoglycan synthase, promotes membrane partitioning through its role in cell wall synthesis. While the data are consistent with this model, the reviewers felt additional experiments are necessary to fully support the authors' conclusions.

eLife assessment

This paper is of potential interest to any neuroscientist, given it asks how the brain compensates for its own neural transmission delays. This is a problem that runs across neuroscientific disciplines. The authors use a clever and simple design where they study this question in the context of decoding from EEG signals during visual motion processing. They robustly show evidence that the brain can indeed compensate for these delays, although all compensation appears to be afforded by early processing. The manuscript is well-written but can be strengthened by outlining its significance for the broader community as well as some further analyses.

eLife assessment

This manuscript reports an association between TCR convergence and involvement in an antigen-specific response. TCR convergence is assessed as a potential biomarker of response to immune checkpoint blockade (ICB). From jointly analyzing TCR-seq data, single-cell RNA-seq data, and antigen-specific TCR information, the authors provided evidence that convergence is a potential indicator for ongoing T cell antigen-specific response. Overall, the analyses are sound the manuscript is well-written, and the study provides the first evidence that TCRseq alone could be used to predict clinical outcomes.

eLife assessment

The authors present a rich investigation of the evolution of social-movement rules in animal societies under pathogen pressure. The study should be of interest to a broad readership.

eLife assessment

This research focuses on the role of a long noncoding RNA VPS9D1-AS1(VPS) in colorectal cancer (CRC) immune evasion and provides evidence on how it is responsible for escape from cytotoxic T cells killing via amplifying intra-tumoral TGF-β signaling. The findings are of considerable translational significance since VPS9D1-AS1 was validated targetable in this work, and it is of broad interest to readers in cancer biology and immunotherapy.

eLife assessment

Harkin and colleagues explore functional properties of dorsal raphe serotonin neurons using the approach called a generalized integrate-and-fire [aGIF] model, which incorporates a relatively small number of salient biophysical properties of a specific neuron type, and whose parameters are optimized based on voltage dynamics obtained experimentally. The authors make an interesting finding that after-hyperpolarization and A-type potassium currents, in combination with heterogeneous feedforward inhibition from local GABA neurons, give rise to a derivative-like input-output relationship in serotonin neurons.

eLife assessment

This manuscript is of interest to readers in the field of bone biology. It identifies a novel role for the vacuolar ATPase accessory protein ATP6AP2 within the osteoblast lineage and shows that loss of ATP6AP2 in the mature osteoblast results in disorganized bone formation. A similar, but milder, bone disorganization phenotype is also observed when this gene is knocked out in osteocytes. The authors show that this bone phenotype is partially rescued via restoration of MMP14 action.

eLife assessment

This paper reports on the development of an impressive microfluidic platform for the study of motility, and motility transitions, exhibited by single algal cells in circular confinement. Building on previous work that showed a three-state motility repertoire for certain green algae, the present work uses extremely long time series and a variety of physical perturbations to show how those dynamics can be altered by environmental conditions. The work will be of interest to a wide range of scientists studying motility and nonequilibrium dynamics, but its impact would be improved by a more insightful analysis of the voluminous data, with connections to physical principles.

eLife assessment

This paper asks whether a risk score integrating the impact of common genetic variants across the genome (polygenic risk score) on Type II Diabetes is also to any degree predictive of diabetes in pregnancy (Gestational diabetes or GDM).The study population comprises women of South Asian ancestry, who are particularly susceptible to GDM. Strong evidence is presented in favour of the hypothesis of the hypothesis in two sizeable cohorts, one from Canada and the other from the UK. The paper will be useful to those studying women's health in pregnancy, and in particular GDM, which is associated with a number of adverse pregnancy outcomes.

eLife assessment

We admired the study by Krehenwinkel and colleagues for its novelty, depth, and ecological breadth, but have questions regarding the laboratory, bioinformatic and statistical methodologies that require clarification. It is likely to make a substantial impact in the field of plant-based arthropod metabarcoding, revealing ecological insights that can be derived from existing bio-banked material. The work, which creatively exploits herbarium material to track arthropod communities, will be interesting to a general audience in addition to ecologists, foresters, phytopathologists, and industry.

eLife assessment

This manuscript will be of interest to cardiovascular clinicians, medical geneticists, pharmaceutical companies, and the general cardiovascular disease research community. The study adds evidence for the causal role of triglyceride to several atherosclerotic cardiovascular diseases. Their use of Mendelian Randomization method is appropriate and provides convincing support to their findings, which may provide insights on the mechanism of TG biology and drug repurposing of TG-lowering agents.

eLife assessment

This fundamental study demonstrates that the two isoforms of the ARPC5 subunit (ARPC5 and ARPC5L) of the Arp2/3 complex have specific functions in regulating cytoplasmic and nuclear actin filament assembly in response to DNA replication stress and T cell receptor signaling in T lymphocytes. The data presented in the manuscript are convincing and of good technical quality, and the study provides interesting new insights into specific cellular roles of different Arp2/3 isoforms in T lymphocytes.

eLife assessment

This work examines the evolutionary origins of acid-sensing ion channels (ASICs), a class of pH-sensing receptors expressed throughout the brain and body. By combining analysis of sequences, functional measurements, and measures of tissue distribution, the authors provide solid evidence that ASICs existed far earlier than previously believed. The present data indicate that ASICs emerged after the split between bilaterians (organisms with two-fold symmetry) and Cnidaria (jellyfish, anemones, corals, etc.), approximately 680 million years ago. This evolutionary and functional analysis of ASIC channels across bilaterian lineages provides relevant information about the evolution of nervous and sensory systems.

eLife assessment

This work, which will be of interest to all who study plant-microbe interactions as well as plant cell biology, addresses a fundamental question in symbiosis, placing a classic nodulation defective mutant (rpg) into a plausible protein complex and establishing a hierarchy of "infectosome" assembly. Evidence includes convincing genetics and subcellular localization of components during establishment and maintenance of infection. The study also includes compelling new FLIM-based imaging techniques to distinguish signals from closely associated domains in plant cells.

eLife assessment

This is an important paper that is of interest to researchers interested in the psychological and neurochemical mechanisms of pain and pain relief. It shows that the perception of pain relief is modulated by controllability, surprise and novelty seeking. Moreover, these modulations are influenced by dopaminergic but not by opioidergic manipulations. These findings are supported by solid evidence.

eLife assessment

The parabrachial nuclei are groups of neurons in the brainstem (one on each side) that integrate information about the state of the body to guide appropriate homeostatic responses. The manuscript by Pauli and Chen et al. is a compelling and much-needed study that characterizes the cell types that make up these nuclei and genetic tools to study them. The result is a highly valuable resource to the academic community.

eLife assessment

This paper, of relevance to a broad range of plant biologists and colleagues in the circandian field, reports important results that demonstrate circadian coordination of characteristic floral development in sunflower. The current manuscript includes convincing observations and possible hypotheses, but the ecological relevance of the temporally-controlled flower development is incompletely shown.

eLife Assessment:

This paper by Möller and colleagues investigates and compares spontaneous turn-taking behavior by pairs of macaque monkeys and human participants in a social coordination game. The study uses a novel format for interaction - the "transparent game" in which subjects play together on a clear glass screen, so that decisions take on properties of continuousness. The results suggest differences between species in their tendencies toward cooperative, mutually beneficial behaviors, with humans exhibiting more prosocial tendencies. Interestingly, training with humans could encourage the monkeys to become less selfish and adopt a turn-taking strategy. The behavior analyses are rigorous and convincingly support the conclusions, and the study is likely to be of interest to researchers in the field of social neuroscience and decision-making, as well as to a more general audience who studies cognition, psychology, economics, especially game theory, and animal behavior.

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

Evaluation Summary:<br /> <br /> This manuscript employs in vitro studies and elegant mouse models to detail how specific pyruvate kinase isoforms impact pancreatic beta-cell ATP/ADP levels, ATP-sensitive K+ channel (KATP channel) activity, calcium handling, and insulin secretion. This is an important study that challenges the current paradigms of KATP-channel regulation, the major signaling mechanism through which pancreatic beta cells couple blood glucose levels to insulin release. Future studies will be necessary to determine whether similar mechanisms are used in human pancreatic beta cells.

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

Evaluation Summary:

The authors leverage genotyping data from the islands of Cabo Verde to study its admixture history and to gain insights into the onset of the Trans-Atlantic Slave Trade. They find that patterns of ancestry between the islands are not the same, suggesting diversity in the founding populations of these islands. These results provide a nice example of how ancestry patterns vary across admixed populations due in part to their unique local history and social practices of that 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 #1 and Reviewer #2 agreed to share their names with the authors.)

eLife Assessment:

The authors aim to predict bacterial enzymes responsible for drug biotransformation, and the work showcases the potential of this approach as a hypothesis generator for characterizing and validating novel bacterial enzymes in vitro. The authors describe the relevance of an accurate input (in terms of reaction completeness, including cofactors and reaction products) as paramount for the quality of the prediction. The conclusions, however, require additional experimental and non-experimental validations.

(This preprint has been 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.)

eLife Assessment:

This manuscript uses a genetically-encoded calcium indicator to assess neural activity across a population of axons connecting the fly's brain to its ventral nerve cord while the tethered fly behaves on a floating ball. Changes in fluorescence signal correlate better with states such as walking, resting, and grooming than with particular limb movements or joint angles, suggesting that specific descending neurons represent the larger behavioral subdivisions. The preparation and large-scale analysis represent a significant step forward in determining how the brain compresses sensory and state information to convey commands to the ventral nervous system for behavior execution by motor circuits.

(This preprint has been 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.)

eLife Assessment:

This paper should be of high interest to scientists within the field of developmental neuroscience. The authors characterize the earliest spontaneous waves of the retina - a topic that is poorly understood. The ability to monitor waves over the entire retina at high resolution is a strength of the work. Weaknesses include reliance on pharmacology and some missing details in the analysis.

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

eLife Assessment:

A comprehensive single-cell transcriptomic study was performed in this study to gain insight into the development of endothelial cells and other co-developing mural cells derived from human induced pluripotent stem cells (hiPSCs) in 3D environment. This study gave us important information about signature genes, trajectories, and cell-cell interactions at various stages of vessel formation. Accordingly, the results of this study could potentially be of valuable interest to scientists working in the fields of stem cells, regenerative medicine, and tissue engineering.

(This preprint has been 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.)

eLife Assessment:

This is a rigorous evaluation of whether the compression of time cells in the hippocampus follows the Weber-Fechner Law, using a hierarchical Bayesian model that simultaneously accounts for the firing pattern at the trial, cell, and population levels. The two key results are that the time field width increases linearly with delay, even after taking into account the across trial response variability, and that the time cell population is distributed evenly on a logarithmic time scale. Overall, the paper is well written, the experiment and data analysis are technically sound, and the conclusions are mostly well supported.

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

eLife Assessment:

This manuscript sheds light on the biology of embryonal rhabdomyosarcoma, a common pediatric muscle tumor, by exploiting an established zebrafish model. Specifically, new knowledge is revealed of how the p53 tumor suppressor contributes to progression and extent of disease. This paper will be of interest not only to pediatric oncologists but also the broader cancer research community given the frequency of TP53 mutations as secondary lesions in human cancer.

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

eLife Assessment:

The authors perform a Transposon-Sequencing screen to determine bacterial factors (including receptors) important for infection by two phages in the model bacterium Corynebacterium glutamicum. Using their established high-density transposon library, they identify genes required for infection with the phages Cog and CL31. They also identified a spontaneous phage-resistant mutant that led to the discovery of a gene involved in mycolic acid synthesis. Overall, the work is of broad interest to scientists in the field of cell wall biogenesis, phage infection, and bacterial cell biology.

(This preprint has been 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.)

eLife Assessment:

In this manuscript, the authors perform an extensive systematic analysis of membrane contacts sites to uncover novel proteins required for tethering organelles and modulation of membrane contacts. The authors identify over 100 new potential contact site proteins and effectors including proteins associated with the recently discovered plasma membrane-LD (pClip) and Golgi-peroxisome (GoPo) contact sites. Further, the authors identify and characterize novel lipid transport proteins associated with the pClip as well as Lec1, an ER-Lipid droplet contact site associated protein which contains a novel putative lipid binding domain and may facilitate ergosterol transport between the plasma membrane and lipid droplets.

(This preprint has been 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.)

eLife Assessment:

This manuscript presents a biophysical study of the nature of the mechanosensitivity of voltage-gated sodium channels. The identification of a voltage-independent mechanosensitive step is well founded, the proposal that this step is the intracellular gate is plausible speculation. It is expected to be of interest to scientists studying the physical basis of mechanosensitivity in electrophysiology.

(This preprint has been 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.)

eLife Assessment:

This manuscript presents the cryo-EM structure of the Yta7 chromatin remodeler, which provides new mechanistic insight into how this AAA+ protein unfolds histone H3 in yeast for DNA replication. The study details the putative role of the C-terminal bromodomains, as well as an N-terminal bromo-interaction motif, in engaging nucleosomes for subsequent capture of the H3 tail for ATP-driven translocation by the upper AAA1 ring. The accompanying functional work helps establish the proposed nucleosome recognition mechanism, providing a structural framework that may be generally used by AAA+ nucleosome remodelers. The work will be of interest to colleagues in chromatin biology as well as all who study the very large family of AAA-ATPases.

(This preprint has been 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.)

eLife Assessment:

This paper demonstrates an integrated labeling and block face fluorescence imaging method that enables the rapid evaluation of biological specimens as large as an E18 mouse embryo with single cell resolution. Such capabilities will likely be of great interest to developmental biologists and pathologists. While the approach can be considered a major step forward, additional experimental support is necessary to gauge how quantitative the method is.

(This preprint has been 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:

By the use of liver specific gene knock-out approaches Tang et al have clearly documented an important role for an endoplasmic reticulum sorting receptor, SURF4, in the efficient secretion of PCSK9, a protein in circulation that binds to and enhances the intracellular uptake and degradation of the low density lipoprotein receptor. As a consequence of liver specific knock-outs, adult mice survive well with an exceptionally lower level of circulating cholesterol, triglycerides and various lipoproteins. These compelling results reinforce the prospect for the development of therapeutic approaches in cholesterol and LDL reduction by targeting the intracellular association of PCSK9 and the SURF4 receptor. The work is elegant and complete with the only concern that some of the work and results overlap work published previously by some of these authors.

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

Evaluation Summary:

In this manuscript entitled "Dietary palmitic acid induces innate immune memory via ceramide production that enhances severity of acute septic shock and clearance of infection" Seufert and colleagues have investigated how saturated fatty acids increase susceptibility of the host in a murine model of LPS-mediated septic shock. Pretreatment of macrophages with palmitic acid (PA) was found to reprogram macrophages towards hyper-inflammatory phenotype, which was dependent on ceremide. Importantly, depletion of macrophages intracellular ceremide with oleic acid reversed their hyper-inflammatory phenotype. Interestingly, while PA was harmful in the LPS-acute septic shock model, it was beneficial in clearance of C. albicans in Rag-deficient mice lacking both B and T cells. While this is an exciting study, the presented data don't fully support the central hypothesis and the link with trained immunity is currently weak.

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

eLife Assessment:

In this manuscript the authors describe targeted, imaging-based RNAi screens to identify novel modulators of nuclear size and shape — two traits that are diagnostic and prognostic for many human diseases including cancers. The work provides novel insights into how and what dictates nuclear morphology, further decoupling key different components of lamins, chromatin, and the nuclear envelope, but there are some notable concerns regarding the scoring approach applied in the screen and hit validation. The authors also provide new evidence that lamin A may directly bind to (modified) histone H3 and how histone H3 disease mutations impact nuclear shape; this aspect of the manuscript would benefit from a more thorough analysis.

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

eLife Assessment:

Replogle et al. present their design of a compact and functionally validated dual sgRNA libary and dCas9-effector protein that will enable new forms of CRISPRi-based screening in mammalian cells. Quantitative comparisons to previously published standards demonstrate strengths and weaknesses, which, along with the protocols and design strategies outlined, should enable end users to rapidly adopt their approach.

(This preprint has been 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.)

eLife Assessment:

This paper presents a new mathematical model describing biologically plausible feedback that glial cells might use to properly modify the conduction velocity in axons and promote optimal timing of neural impulses through changes in myelination. This problem is of great importance in the field of neuronal plasticity. The mathematical model is solid and predicts that individual oligodendrocytes are able to modify their myelination pattern in response to correlated action potentials. This work provides an important step forward by providing the theory for myelin-mediated neuronal plasticity. The study will benefit from adapting physiological parameters for oligodendrocytes that are guided by experimental data.

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

eLife Assessment:

This study presents a large sample of participants ranging from 6-18 years investigating the association between white matter measures and reading using a sophisticated analysis. The results show a clear association between intra-axonal volume and single-word reading abilities. In sum, this valuable study complements other large-scale studies by applying sophisticated fixel-based analyses.

(This preprint has been 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.)

eLife Assessment:

This is a very valuable study that describes the bone phenotype and mechanism of the action of the obesity gene Ksr2. That there is a site-selective bone phenotype is interesting as is the identification of KSR2 as an actionable target.

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

eLife Assessment:

The authors use their expertise in live-cell imaging and mathematical modeling to explore the relationship between chromatin structure, gene positioning and transcriptional co-regulation, using two publicly available datasets encompassing chromatin tracing and transcriptional activity. The resulting analysis reveals a weak association between transcription and proximity, but needs more statistical validation to strengthen the validity of the conclusions. With some clarifications and revisions, several findings, such as coupling of spatiotemporal positioning with activity, in-depth analysis of existing imaging/ChIP-seq datasets, could make this work impactful to both specialists and non-specialists.

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

eLife Assessment:

Juette and coworkers employed single-molecule fluorescence, cryogenic-electron microscopy structures, and in vivo measurements to investigate the mechanism whereby two natural products with potential as cancer therapeutics, didemnin B and ternatin-4, act. The compounds are shown to inhibit tRNA accommodation within the ribosomal A site during translation elongation by interfering with movement of eukaryotic elongation factor 1 alpha after its activation by the GTPase activation site of the ribosome, with the degree and nature of this restriction differing subtly between the two compounds, leading to more marked differences in their effects on global translation and cell growth. The compelling results of this interdisciplinary work solidify prior conclusions, particularly on didemnin B, and illuminate the similarities and differences on how these two drugs interfere with the normal functioning of the elongating ribosome in vitro and inhibit protein synthesis and cell growth in vivo. Some revisions of figures and text are required to clarify the results and the authors' interpretations.

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

eLife Assessment:

This manuscript describes a highly novel barcoding strategy for forward genetic lineage tracing of tumor cells in vitro and in the in vivo environment. The technique, coined WILDseq, can be used to track cells present in vitro which are enriched or depleted in the in vivo environment. Treatment further contributes to clonal expansion and retraction and emergence of populations with sensitivity to alternate agents. The studies are rigorously conducted and are highly impactful.

(This preprint has been 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.)

eLife Assessment:

The authors sought to enhance antibody binding to target antigens via reversible catenation, as an alternative to affinity maturation, beginning by computationally establishing parameters under which this type of binding enhancement via avidity effects would occur, and then following up with proof-of-principle experiments. While computational predictions and experiments are in excellent agreement, some controls that would further strengthen data interpretation are lacking. If generally applicable, the approach would accelerate efforts to develop antibodies with enhanced binding potency relative to their progenitors, applicable to any area of research employing antibodies.

(This preprint has been 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.)

eLife Assessment:

This study is a useful extension of previous work on the relationship between body size and cancer risk and the mechanisms by which large-bodied mammals reduce their cancer risk. Through solid analyses of the genomes and several aspects of the cell biology of sloths, armadillos and their relatives, the study explores whether the evolution of large body size in their relatives (some extinct) was correlated with genomic changes such as the duplication of tumor suppressor genes, experimentally demonstrating that cells of Xenarthrans (sloths, armadillos, anteaters) are exceptionally sensitive to DNA damage. The study concerns a topic of great interest and contributes to our understanding of how cancer risk has evolved in mammals.

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eLife Assessment:

This manuscript will be of interest to microbial ecologists and biogeochemists working on soil carbon cycling and responses to climate warming. This study uses an elegant experiment to show that standing variation, both phylogenetic and phenotypic, enables microbial community adaptation to higher temperatures. The authors' conclusions are supported by the data, and this work lays a foundation for future experimental and modeling studies.

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Evaluation Summary:

This is an interesting discovery of a role for NINL in antiviral defense through modulation of interferon signaling. They found that there is diversifying selection of this factor as well as viral antagonism. This discovery paves the way to a better understanding of how viruses and hosts co-evolve.

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Evaluation Summary:

The manuscript by Kane et al. described transcriptional profiles of various subsets of activated iNKT cells using longitudinal scRNA-Seq analysis. The finding that IL-10 producing iNKT cells have a cMAF-associated gene signature similar to Tr1 cells is novel. Overall, the data is well presented, however, functional consequences of some findings require further investigation.

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Evaluation Summary:

This is one of the most thorough assessments to date of suppression gene drives against mosquitoes. The models specifically consider the spatial dynamics of gene drives and whether a form of group selection may prevent the drive from eradicating the population, with mosquito ecology parameters. This manuscript will be of interest to those working in the technical development of gene drives, those predicting how such genetically modified insects would spread in the wild, and those evaluating the technology from regulatory and funding standpoints.

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Evaluation Summary:

In this study, the authors identified that NFATc1 acts as a key regulator of articular chondrocyte differentiation during early mouse development. Using multiple pulse-chase experiments the authors found that NFATc1 expressing cells generated most of the articular chondrocytes, but not growth plate chondrocytes. Interestingly, NFATc1 expression in chondrocytes diminished as mice aged, suggesting that NFATc1 expressing progenitors are no longer expressing NFATc1 after articular cartilage development. This is an important study since it provides valuable evidence to reveal the regulatory mechanism of articular chondrocyte differentiation. The data presented in this manuscript, in general, support their conclusion.

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Evaluation Summary:

The authors suggest that PINK1-dependent endothelial mitophagy is pro-inflammatory by increasing the release of mitochondrial formyl peptides, one of the mitochondrial DAMPs. This study is important to identify the origin of serum formyl peptides during inflammation and to propose a new role of mitophagy in inflammation, which may be context and/or tissue specific.

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Evaluation Summary:

This study will be of interest to a broad audience of microbiologists by providing one of the few examples of a clear phenotype for a toxin-antitoxin system. The conclusion that an oxygen-regulated toxin-antitoxin system is required for an important step in biofilm development in the model organism Caulobacter crescentus is well supported by the data and experiments are well designed and controlled. Some possible limitations in interpretations from incompletely controlled phenotype reporters should be resolved by simple experiments.

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Evaluation Summary:

This manuscript describes the mesenchymal cells expressed Axin1 as a key regulator for Wnt and BMP signaling pathway which is essential for lower limb development. Fibular hemimelia (FH) is a rare genetic disorder with unknown mechanisms. Their data clearly demonstrated that inhibition of β-catenin and BMP signaling genetically and pharmacologically could largely reverse fibular hemimelia phenotype in mice. In general, the manuscript is clear, well written, and concise, the study is well-structured and various techniques have been used to validate the data. It presents as a thorough study highlighting the importance of Axin1/ β-catenin/BMP signaling in FH development, and, furthermore, the interpretation of the results and the following conclusions are convincing.

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Evaluation Summary:

This paper reports the structure of the M protein of SARS-CoV-2, as determined by cryoEM. The structure is well-determined and reveals a homodimer with overall similar structure as ORF3a, another virally encoded protein. The surface charge distribution is skewed towards positive at the C-terminal domain, which suggests roles in interactions with viral N and S proteins, and possibly viral RNA. The work is of relevance to virologists, especially those studying SARS-CoV-2.

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Evaluation Summary:

This is a valuable manuscript that addresses an important question and provides interesting mechanistic insights into the roles of specific regions of the IR and IGF1R in their activation. While many of the data convincingly support the conclusions, in some areas the data are incomplete so we are left with an unfinished picture of the mechanisms of activation of the IR and IGF1R, and why they differ.

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Evaluation Summary:

This manuscript reports useful data on how human papillomavirus 8E6 protein regulates DSB repair pathways in human cells. The data support the claim that 8E6 promotes alternative end-joining through binding and destabilizing the p300 acetyltransferase, but the study remains relatively descriptive and incomplete as it is not yet clear which alternative end-joining pathway is involved lacking a test of a direct involvement of DNA polymerases theta (POLθ).

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Evaluation Summary:

This is an interesting and timely paper that presents thermodynamic and structural (NMR) analyses of six KOW domains from the NusG superfamily of transcription factors. The authors identify a second fold-switching member of the NusG superfamily, VcRfaH, and investigate the physical basis of this fold-switching transition. The authors also compare the thermodynamic and structural properties of six fold-switching and single-folding KOW domains from different organisms, and show that fold-switching domains are less thermodynamically stable than their single-folding counterparts. This work will be of great interest for scientists in the fields of protein folding (theory and experiment), structural biophysics, and advanced protein NMR spectroscopy.

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Evaluation Summary:

This is a useful quantification of the links of vascular disease on the development of subsequent mental health issues. It uses a robust dataset to quantify this association. Further work to focus the analyses, ensure claims are supported by the data, and consider alternative explanations is needed.

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Evaluation Summary:

This manuscript has the potential to be of interest to a broad range of behavioral scientists. It provides insights into how biases can affect value-based behavior in invertebrates, similar to what has been reported in humans. However, there are a number of potential confounders that need to be addressed before drawing robust conclusions from the data reported.

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Evaluation Summary:

This is a valuable paper that uses solid computational modeling approaches to link plasticity in the hippocampal circuit with behavioral learning. The work focuses on reinforcement learning, a theoretical framework for how animals can optimize learning by extracting the statistical structure of the sensory environments. While a vast range of experimental data regarding the physiological properties of neurons in the hippocampus exists, reinforcement learning often lacks such physiological details. The manuscript begins to fill this gap, by developing a spiking computational model of the hippocampus that can implement reinforcement learning and capture some features of hippocampal physiology.

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Evaluation Summary:

In this elegant study, Leyhr et al. identify the first potent nkx3.2 jaw joint enhancer, which they show to be deeply conserved across gnathostomes and likely to be absent from jawless fishes. The data support the hypothesis that this enhancer arose with the origin of hinged jaws during vertebrate evolution and is required for some aspects of early joint development in zebrafish. The work has important implications both for our basic understanding of enhancer function and evolution as well as potential genetic causes of craniofacial defects in humans.

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Evaluation Summary:

This paper will be of interest to readers who perform extracellular recordings with high-density electrodes. It provides a proof of principle that high-density recordings allow assessing the interactions of pairs of neurons within local cortical networks in nonhuman primates.

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Evaluation Summary:

The authors identify a new FOXP2-CPED1 gene fusion in prostate cancer that leads to the increased expression of FOXP2 and subsequent transformation of non-cancer cells. Increased FOXP2 was shown to promote prostate cancer in part through the increased expression and activation of the receptor tyrosine kinase MET, a known driver of prostate cancer. Notably, the authors created new genetically engineered mouse models of FOXP2 and FOXP2-CPED1 overexpression in prostate luminal epithelial cells which was sufficient to cause prostatic intraepithelial neoplasia in these mice with lesions that confirmed increased MET signaling. Oncogenes are typically interesting drug targets or interact with possible drug targets, and the manuscript could thus have a significant societal impact on better understanding drivers of the disease.

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Evaluation Summary:

The authors combined atomistic simulations and continuum mechanics models to probe how structural features of the M2 channel impact the local membrane properties and stability of the channel in membranes of different curvatures. The insights gained in this work can potentially lead to novel strategies that screen for drug molecules that stabilize fission-incompetent conformations of the M2 channel. The multi-scale computational approach will find utility to many problems in membrane reshaping.

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Evaluation Summary:

This manuscript is a timely contribution to the CRISPR/Cas field: the mode of function of the type III-E Cas7-11 CRISPR-Cas system. This is an RNA-guided RNA targeting system only characterized last year. In contrast to Cas13 systems, Cas7-11 does not possess collateral damaging activity, hence does not show cytotoxicity when introduced into human cells. These are highly desirable traits in practical applications. High resolution mechanistic studies would be essential for driving the further development of Cas7-11 based biotechnology applications.

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Evaluation Summary:

This important study shows that methods currently used to predict which animals species might be at risk of infection by SARS-CoV-2, by looking at features of the host cell receptor the virus binds to, are fundamentally flawed, with exceptionally strong support for this conclusion. Much work on the potential host range of SARS-CoV-2 has focused on measuring the susceptibility of different species' ACE2 receptors to sarbecovirus entry and extending predictions to other unmeasured species based on ACE2 sequence features. Mollentze and colleagues show that ACE2 sequences are not more than a proxy for generic species relationships. In other words, species phylogeny alone can provide equivalent predictive power, allowing for predictions of mammalian susceptibility to sarbecovirus infection for the many species for which ACE2 sequences are not known yet.

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Evaluation Summary:

By integrating a range of computational techniques, the authors generated a structural model for the AT3 domain, which is predicted to adopt a new fold. The key features of the structural model are consistent with the activity of the enzyme as an acyltransferase, with a transmembrane channel that can accommodate an acyl-CoA donor, and an outer cavity formed with a second domain that can accommodate a nascent LPS molecule as substrate. Overall, the study will help stimulate specific experimental analyses that can further evaluate and improve the model for better mechanistic understanding of this class of enzymes. The work will be of interest to structural biologists, and all studying acyltransferase enzymes.

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Evaluation Summary:

The authors dissect the phenotypes of bone-marrow derived myeloid cells in a murine model of pulmonary vasculitis with relevance to human disease, revealing the association of novel phenotypic subsets associated with lung injury, yet the role of these subsets in regulating or contributing to tissue injury is less clearly determined.

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Evaluation Summary:

The work presented by Masson et al. highlights experimental approaches using spatial indentation and contrast-enhanced 3-D x-ray imaging to topographically map cartilage thickness in mouse knee joints. This methods described have the potential to impact the field of musculoskeletal biomechanics, especially for researchers using mouse models to study cartilage wear and disease, given the high resolution and sensitivity of the described approaches.

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Evaluation Summary:

This work describes mouse ovary morphogenesis from E14.5 to birth using recently developed methods combining CUBIC and iDISCO and optimized 3D imaging using light sheet microscopy. The manuscript is of interest to all developmental biologists as it will serve as a reference to whole embryo morphogenesis, in particular vertebrate ovary morphogenetic processes.

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Evaluation Summary:

Grande and colleagues provide new insights into how different regions of the entorhinal cortex functionally interact with specific cortical brain areas and how, in turn, subregions of the entorhinal cortex interact with the hippocampus during 'scene' and 'object' processing. This paper is relevant to cognitive neuroscientists with an interest in the entorhinal cortex - hippocampal pathways and 'scene' and 'object' representation in the medial temporal lobe. The study is well-motivated, well-designed and appropriately analysed to address the research questions. Most conclusions of the paper are well supported by the data.

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Evaluation Summary:

The authors use an elegant experimental design to study genetic variation in the ubiquitin-proteasome degradation system in yeast. They identify a large number of QTLs for naturally occurring variation, and they elucidate the causal variants and likely functional mechanisms of several of these. The paper illustrates an innovative new approach to high-throughput QTL mapping for specific molecular processes and it will be of interest to colleagues aiming to harness natural variation for understanding a range of biological processes.

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Evaluation Summary:

This manuscript described the effects of two different CoronaVac vaccination schedules in a Chilean adult population. They find that a 0 and 28-day two-dose schedule produced superior levels of neutralizing antibodies and antibodies with a great breadth of interaction across variants compared to a 0 and 14-day two-dose schedule. They find no differences in T cell responses or total antibody levels between the two groups. These findings demonstrate that a short two-week two-dose interval should provide sufficient immunity to reduce the likelihood of serious outcomes during a COVID infection.

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Evaluation Summary:

This study bridges the gap between connectomic data from the fly hemibrain and driver lines needed for functional experiments through a new freely available computational tool, NeuronBridge. It demonstrates that this software provides users with the ability to identify the same neurons within different driver lines, and the opportunity to match expression of neurons in a driver line with those in a connectomic database. Overall, this manuscript does a commendable job of describing an important resource for the community, which will hopefully be built upon via collaborative science of many groups as the field develops.

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Evaluation Summary:

This manuscript addresses a long-standing question regarding the highly variable cellular composition and functions as well as immune environments along the epididymis. Using multiple mouse models (bacterial infection and parabiosis between WT and Ccr2 KO) in conjunction with powerful scRNA-seq analyses, the authors provided solid evidence supporting the notion that resident immune cells are strategically positioned along the epididymal duct, potentially providing different immunological environments required for sperm maturations and elimination of pathogens ascending the urogenital tract.

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Evaluation Summary:

The manuscript by Noel et al reports parallel neurophysiological responses from the three brain areas MST, 7a and dlPFC of monkeys during a novel behavioural paradigm developed by the same group previously. The continual nature of this paradigm with a closed action-perception loop makes the animal behaviour more naturalistic compared to classical paradigms with artificial breaks between sensory stimulation and action. Findings of neurophysiology under such a paradigm are novel and of broad interest to cognitive and systems neuroscientists. The data presented in the paper support the claim of distributed neural coding in which task-specific sub-networks may form.

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Evaluation Summary:

This is an important and delicately designed study that uses integrated tools to reveal underlying mechanisms of repair of the endometrium at menstruation. It combines single cell sequencing analysis and lineage tracing technologies to strongly prove that repair-specific cells originate from the fibroblast cell clusters and PDGFRα+ endometrial fibroblasts undergo MET and can become incorporated into the luminal epithelium of the post repair tissue.

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Evaluation Summary:

The manuscript is well organized and clearly written. The discussion provides the required information to easily understand the relevance of each finding. the authors demonstrated using an osteocyte cell model that connexin43 is localized to mitochondria and that this is enhanced in response to oxidative stress. Several lines of evidence were presented showing that mitochondrial connexin43 forms functional hemichannels and that connexin43 is required for optimal mitochondrial respiration and ATP generation. These aspects were major strengths of the study.

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Evaluation Summary:

This work provides substantial new insights into how semantic association strength influences the function and relationships across brain regions along a topographical structure of cerebral cortex. A principal gradient with the separation of default mode network from sensory-motor systems represents a hallmark of the retrieval of strong conceptual links. This study will be of interest to cognitive neuroscientists, especially those who are interested in semantic cognition.

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Evaluation Summary:

This paper uses a new statistical approach called within family Mendelian randomization and asserts that claims of childhood BMI affecting a range of psychiatric traits are unfounded and were mainly caused by confounders that this new approach is able to better identify and control for. They do find a role for maternal BMI on a child's risk for developing depression. The main issue raised is that they do not convincingly show if they do not replicate the old association of childhood BMI with a range of psychiatric traits due to their technique simply having lower power to detect the signal or due to a true lack of this effect.

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Evaluation Summary:

The authors investigate how HIV-1 infection affects the immune response in the context of SARS-CoV-2 infection by characterising the circulating B cell response. They conclude that people with HIV-1 infection, who become infected by SARS-CoV-2, produce B cell responses via an extra-follicular pathway to a greater degree than people who do not have HIV-1 infection. These findings imply that in HIV-1 infected individuals, long-term B cell and antibody responses against SARS-CoV-2 might not be as robust and durable compared to those in people without HIV-1 infection. The manuscript will be of interest to infectious disease specialists, virologists, and immunologists.

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Evaluation Summary:

This paper is of interest to skeletal biologists studying skeletal development and tissue regeneration. The study applies a well-established and elegant axolotl limb regeneration model and transgenic reporter strains to reveal the potential role of osteoclast-mediated resorption in limb regeneration.

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Evaluation Summary:

This important paper uses molecular simulations to explain how actomyosin networks transition from small clusters to the cortex or ring-shaped actin networks. The authors provide compelling evidence that variation in filament turnover rate and myosin concentration triggers a phase transition of these networks. The predictions of this model are consistent with observations made in T cells, where actin ring formation can be induced following their activation by antibodies.

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Evaluation Summary:

Knowledge of the protein composition of defined sub-cellular compartments is of key importance for the characterization of protein machines that mediate defined cellular functionalities. The current paper presents a novel mouse line that will serve as a helpful tool in this context - a Cre-inducible APEX2 reporter mouse line for acute ex-vivo proximity biotinylation. The paper documents the successful use of the novel reporter line to assess circuit-specific proteomes and phosphoproteomes in the corticostriatal system during development. The corresponding data largely align with the published record, but potentially new biological insights deduced from bioinformatic analyses of proteomic data were not followed up by experimental validation. In sum, the new APEX2 reporter mouse line will be of substantial interest to researchers in many fields of mammalian biology. The extent of 'new biology' provided is rather limited, but will be of interest to readers in neurodevelopment.

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Evaluation Summary:

This paper will be of interest to researchers studying control of respiration and also those developing functional magnetic resonance imaging methodology. The work provides insight into the relationship between brain activity (measured directly) and non-invasive functional magnetic resonance imaging measures. The authors find that the respiration signal is associated with the gamma band in the cingulate cortex, and both the gamma signal and respiration signal correlate with distributed neuronal networks across the brain. This contributes to our knowledge of the contribution of respiration on neuro and neuro-vascular signals during resting conditions.

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Evaluation Summary:

The authors developed a set of synthetic proteins, Designed Ankyrin Repeat Proteins (DARPins), that bind gephyrin, the main scaffold protein at inhibitory postsynaptic sites, and characterize them extensively to study gephyrin cluster morphology and biochemistry. In several aspects, DARPins outperform traditional antibodies. This study is clear, well organized and well written, demonstrating that DARPins can be important tools synaptic, cellular and circuit neuroscience fields.

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Evaluation Summary:

These studies establish a role for the D2 pseudophosphatase domain of the PTPRK receptor-like phosphotyrosine phosphatase in recruiting Afadin, a cell-cell junction protein that is reported to be a PTPRK substrate, for dephosphorylation by the active D1 phosphatase domain. These findings suggest that the D2 pseudophosphatase domains of RPTPKs might have a general function as platforms to recruit specific phosphotyrosine substrates.

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Evaluation Summary:

The present manuscript examines cortical representations of basic visual attributes following a manipulation shown to enhance plasticity in the adult brain: binocular dark exposure for several days, followed by light re-introduction. The work has fundamental therapeutic and conceptual implications, and will be of potential interest to a broad readership of vision scientists, neuroscientists, clinicians and modelers. The paper is well-written and based on sophisticated experiments. The evidence provided convincingly supports the authors' contention that dark exposure does not have a negative impact on visual representations in V1. The study uses a generally appropriate study design. However, it would benefit from the addition of some key experimental details, and additional analyses and statistical tests to explore alternative interpretations of results.

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Evaluation Summary:

Protein-RNA interactions are involved in many diseases and targeting them with drugs can be valuable. Because protein-RNA complexes are considered difficult to target both computationally and experimentally, an integrated computational-experimental approach to solve this limitation is introduced. The approach is demonstrated by targeting the mRNA-binding protein YB-1, which works remarkably well. Inhibitors in the micromolar range are detected, including a previously approved drug. The main strength here is the proof of concept that protein-RNA interactions are targetable. However, additional data are required to support the central claims of the paper.

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Evaluation Summary:

Bacteria living in stressful and fluctuating environments need to respond to changing conditions. Many species, including Mycobacterium tuberculosis, the causative agent of tuberculosis, use cAMP as a secondary messenger to sense and respond to specific stimuli. What distinguishes M. tuberculosis, is that its genome encodes for at least 15 adenylate cyclases, enzymes that synthesize cAMP from ATP. The authors characterized one specific adenylate cyclase, Rv3645, and demonstrate that it is the most significant contributor to cAMP levels and mediates fatty acid metabolism and antibiotic resistance. This manuscript will be of broad interest to readers in the field of tuberculosis drug discovery and bacterial metabolism.

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Evaluation Summary:

This work presents a series of enhancements to the PhIP-seq method of autoantibody discovery, with the goal of improving scaling to larger cohorts and increasing disease specificity. The strength of the paper is the validation of the high throughput format, although results from screening patient samples confirm or only modestly extend previous data.

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Evaluation Summary:

KdpFABC is a bacterial potassium uptake transporter made up of a channel-like subunit (KdpA) and a P-type ATPase (KdpB). When potassium levels are low (< 2 mM), the transporter actively and selectively uptakes potassium, but must be switched off again to prevent excessive K+ accumulation. Although structures of KdpFABC have been determined before, the structural basis for inhibition by phosphorylation is unknown. Here, the authors have determined the structure of KdpABC in an arrested (off-state) that is in a distinct conformation from previously determined P-type ATPase structures. More detailed structural comparisons are needed to more convincingly show this, however, and the protein required to inhibit KdpABC by phosphorylation remains unknown. This paper will be of interest to researchers in the microbiology and transporter communities.

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Evaluation Summary:

The manuscript reports a new tissue clearing procedure that is faster (clearing within 48 hours), uses less hazardous chemicals, and importantly appears to result in less tissue volume change compared to other methods. The simple protocol adds further to the toolbox of tissue clearing methods and is one that is likely to be even more popular than many current methods, although the scope of tissue on which it can be used and rigorous comparisons to existing protocols have not been fully investigated.

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Evaluation Summary:

In their study, Gicking et al. study the physical properties of artificial complexes composed of the dynein-dynactin-BicD2 (DDB) complex linked to one of three classes of kinesins (1, 2, or 3) via a DNA scaffold. They find that all three kinesins can move to the plus-end of microtubules when coupled to the DDB complex. This is surprising because motors in the kinesin-2 and kinesin-3 families have been shown to have a higher load sensitivity. However, the authors show that the faster reattachment kinetics of these motors compensate for their faster detachment rates under load. This work is relevant to both the biophysics field for advancing knowledge in fundamental science, and in the neuroscience field since disruption of neuronal transport leads to a variety of neurodegenerative diseases.

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