eLife assessment

The manuscript makes a fundamental contribution to our understanding of sugar release by symbiotic dinoflagellates, and is of broad interest for the fields of ecology, marine biology, and cell biology. The experiments, which combine algal culture with targeted metabolomics, transcriptomics and the application of inhibitors, provide substantial, though not entirely complete evidence for an acidic environment mimicking conditions reported for the intracellular organelle that hosts the symbiotic algae, leading to upregulation of algal cellulases, which in turn degrade the algal cell wall and thereby releasing glucose and galactose that can be used as a source of food by the coral host. This is a new idea and could significantly contribute to our understanding of photosymbiosis.

eLife assessment

Using a genetically controlled experimental setting, the authors find that the lack of Polycomb-dependent epigenetic programming in the oocyte and early embryo influences the developmental trajectory through gestation in the mouse. By showing a two-phase outcome of early growth restriction followed by enhancement, the authors address previous inconsistencies in the field. However, the link with placenta function and gene misregulation is not yet fully supported.

eLife assessment

This work addresses the mechanisms of action of the transmembrane proteins TMEM87A and TMEM87B, which are thought to play a role in protein transport, but have been implicated in other processes as well, such as signaling and acting as mechanosensitive ion channels. The study represents an important advance of the understanding of this poorly characterized family of proteins. While the structure is of low resolution, it is well interpreted, and authors take good advantage of AlphaFold2 to gain insights into potential function. The work is of interest to colleagues studying transporters and ion channels.

eLife assessment

This paper is of particular interest to researchers who plan to use focused-ion beam scanning electron microscopes (FIB-SEMs) and require fluorescent data to guide the milling process. The authors describe a valuable after-market upgrade that allows fluorescent data acquisition during FIB-milling without stage repositioning. Technical details of the fluorescent module upgrade together with the sample stage redesign are compellingly documented and will enhance the implementation of this important technology.

eLife assessment

This important paper uses advanced imaging approaches to explore how Piezo1 distributes on surface red blood cells. The study provides compelling evidence that this molecule 'reads' the membrane curvature and clear support for the force-through-membrane model of mechanosensation.

eLife assessment

SARS-CoV-2 nonstructural protein (Nsp1) has emerged as an attractive target as it plays an important role in modulating the host and viral gene expression. This study describes multiple druggable sites in Nsp1. A 1.1Å co-crystal structure of Nsp1 with a fragment, together with computational studies, provides a framework for the rational design of potential antiviral candidates. This important study is methodologically convincing and will be of interest to researchers in the fields of structural virology and rational drug design.

eLife assessment

Conditional deletion and reactivation of a gene in situ remain challenging, and this study therefore addresses a gap in the genetic tool box. The authors introduce a reversible conditional gene inactivation and reactivation method using sequential expression of recombinases, with doxycycline treatment terminating gene transcription, while doxycycline and tamoxifen addition restore gene expression.

eLife assessment

This manuscript will be of broad interest to those working in the genetics of complex diseases, with the results strongly supporting the author's primary claims. Overall, this is an important study that demonstrates the power of proteomics-based systems genetics studies in the mouse.

eLife assessment

The authors report results from experiments and modeling that study the motions of molecules in the dense and dilute phases of biomolecular condensates, with the key finding that molecules in the dense phase of condensates formed by folded domains appear to switch between a confined state with low apparent diffusivity and a mobile state with a high apparent diffusivity that is comparable to that of molecules in the dilute phase. The study provides experimental evidence that is suggestive of phase separation coupled with percolation as the operative mechanism that gives rise to biomolecular condensates.

eLife assessment

This manuscript presents valuable and significant data on how lipids may accumulate in the tubulointerstitial compartment of the diseased kidney, but the work is largely descriptive, using methods that are inadequate for quantification (colorimetric assays versus mass spec), thus rendering data interpretation not very convincing. Therefore, while a major strength is the presentation of innovative ideas, additional experiments would be needed to support the main conclusions.

eLife assessment

This important work will be of interest to neuroscientists working on synaptic transmission and modulation of ion channel activity. This work provides solid evidence of how modulation of Nav1.2 channels by SUMOYLation alters the function of layer 5 pyramidal neurons, using convincing methodology that includes the use of a mouse engineered to eliminate the SUMOYLation site on Nav1.2. Some aspects need to be revised to strengthen data analysis and interpretation.

eLife assessment

This paper will be of interest to immunologists and infectious disease experts, as it reports the investigation of a novel treatment of invasive pneumococcal diseases using complement-activating monoclonal antibodies. Using a combination of in vitro and in vivo methods, the authors demonstrate convincingly that the introduction of specific mutations in human monoclonal antibodies that target the surface of pneumococcus bacteria can result in enhanced complement activation after these antibodies bind to the bacterial surface.

eLife assessment

This study shows that cis H3 tail acetylation promotes nucleosome accessibility to H3K4 methyl readers and writers such as MLL1. The findings provide a molecular basis for the long-standing connection between H3 acetylation and H3K4 methylation. Additional evidence is required to fully support the conclusions.

eLife assessment

Authors investigated the role of dopamine (DA) release via GRABDA in the dorsal bed nucleus of the stria terminalis (dBNST) in sign and goal tracking behavior, in response to systemic fentanyl, and to fentanyl self-administration. The behavioral experiments were well-conducted and provide novel information about BNST DA in theories of learning and reinforcement. Identified limitations had to do with acknowledgment and discussion of divergent sources of DA innervation, the low sample size in fentanyl experiments with the exclusion of a large number of animals, and a need for additional analyses of the photometry data and/or control recordings to rule out spontaneous transients in this region.

eLife assessment

The manuscript by Yanis Zekri et al identifies the direct T3 target genes that are important in thyroid hormone signaling in brown adipose tissue (BAT). The findings reported in this manuscript are significant and fundamental to our understanding of thyroid hormone action in response to environmental changes. The strength of the evidence presented with the novel methodological approaches used makes the manuscript exceptional in the area of BAT biology and T3 regulation of adaptive thermogenesis.

eLife assessment

This manuscript examines the inhibition of transmitter release induced by the activation of opioid receptors, both MOR and DOR, using a novel imaging method. The authors specifically examine how the inhibition of transmitter release is changed following prolonged exposure to saturating concentrations of agonists. They showed convincingly that there is a depletion of plasma membrane-associated receptors and suggest that the decline in receptors at the plasma membrane underlies presynaptic tolerance. This work addresses a long-standing question about how tolerance develops at the presynaptic level and indicates that the location of receptors is critically important in the development of tolerance. This work is fundamental and a game changer in the understanding of tolerance at the cellular level.

eLife assessment

This paper will be of interest to neuroscientists who study visual processing or are interested in dendritic integration. The authors used calcium imaging, pharmacology, and electrophysiology to investigate how a large, loom-sensitive neuron in grasshoppers integrates visual input to respond to both light and dark looming objects. These experiments support the finding that the integration is done by two distinct arbors of the neuronal dendritic tree, one of which loses retinotopic information. The authors suggest potential advantages of this dendritic arrangement.

eLife assessment

The complex mechanisms through which diet impact Parkinson's Disease are unclear, limiting the ability to guide patients to an optimal diet. Here, researchers use a mouse model to test the impact of dietary fiber, revealing changes in gut microbes and immune cells in the brain. This study raises intriguing hypotheses about how diet-induced changes in the microbiome could lead to changes in brain function.

eLife assessment

Sanderson developed novel interactive software for visualizing phylogenetic trees representing millions of sequences. This is a fundamental advance over previous software that is typically limited to trees with a few thousand tips. Taxonium has been used intensively by the virus evolution community over the past months and has thus already proven its utility and performance.

eLife assessment

This manuscript examines the functional relationship between neural activities in several cortical areas (such as the primary and secondary motor cortex and the medial prefrontal cortex) and the different sleep states or under anesthesia. The quality of the recordings in infant rats is excellent. Results are important in the field of research into the role of active sleep in the neuronal and circuit mechanisms of early cortical development. Some of the findings presented and hypothesis developed are novel, but the overall demonstration remains incomplete and further in-depth analysis and additional experiments are required to fully support the authors' claims.

eLife assessment

This manuscript will be of interest to researchers within the fields of haematological and bone oncology. It reveals a novel effect of FABP5 inhibition to reduce myeloma growth both in vitro and in vivo, with convincing supporting associations between FABP5 expression and survival in patients with myeloma.

eLife assessment

In their paper, Rao, Li et al. explore the mechanisms by which the microtubule-associated protein, doublecortin (DCX), functions in regulating retrograde transport in neurons. They find that DCX affects the dynein-microtubule interaction to perturb its motion. Impressively, they reconstitute a dynein-dynactin-JIP3 complex, validating JIP3 as a bona fide adaptor, and show that DCX disrupts the transport of this processive complex. This mechanism will be useful in understanding how mutations in DCX cause lissencephaly and this paper will be of interest to those in the cytoskeletal and neurobiology fields.

eLife assessment

The ability of organisms to cope with environmental stressors can be modified by their physiological conditions as well as life experience. Here, taking advantage of the tractability of the nematode C. elegans, the authors find that exposure to elevated temperatures enhances defenses against peroxides, agents whose toxicity is enhanced by temperature. The finding that a key thermosensory neuron is required for this phenomenon is an important advance in understanding the underlying mechanism; further, the authors' proposal that this is an "enhancer sensing" phenomenon is interesting and thought-provoking. The multidisciplinary approach and mechanistic detail revealed by this work will make it of interest to readers in the fields of sensory biology, signal transduction, and physiology.

eLife assessment

This manuscript investigates how the fly visual system can encode specific features in the presence of self-generated motion. Using volumetric imaging, it explores the encoding of visual features in population activity in the Drosophila visual glomeruli - a set of visual "feature detectors". Through an elegant combination of neural imaging, visual stimulus manipulations, and behavioral analysis, it demonstrates that two different mechanisms, one based on motor signals and one based on visual input, serve to suppress local features during movements that would corrupt these features. The results of this study open up future directions to determine how motor and visual signals are integrated into visual processing at the level of neural circuits.

eLife assessment

This work offers fundamental insights into how asymmetric behavioral features in optokinetic eye movements can be predicted from visual responses of direction-selective neurons in the retina. The electrophysiological experiments and model-based analyses are carefully performed and offer convincing conclusions. The presentation could improve in clarity for a stronger focus on the most important results.

eLife assessment

The work by Kim et al., used synthetic constructs in Drosophila to examine the relationship between regulators (activator/repressor) and transcription initiation. By measuring regulator concentrations and the corresponding RNA polymerase initiation rates in different synthetic constructs and using a thermodynamic model, the authors concluded that that higher-order cooperativities between the repressor on adjacent binding sites, and that between the repressor and RNA polymerase are needed to explain the observed response curves in RNA polymerase loading rate. This work targets a challenging question in eukaryotic transcription regulation, where higher-order cooperativity between different molecular components, in addition to simple transcription factor binding and unbinding, is often necessary to account for observed promoter behaviors when multiple elements (repressors, mediators, activators) exist.

eLife assessment

This paper will be of interest to cell biologists, structural biologists, and biophysicists studying programmed cell death, membrane transport, and protein-lipid interactions. The simulation data presented offers atomistic detail of how gasdermin-D N-terminal domains assemble on the plasma membrane and trigger the formation of membrane pores which lead to pyroptosis. The study is well designed and the resulting data are rigorously analyzed; however, some clarifications and additional data are required to fully justify the conclusions.

eLife assessment

This manuscript reports a novel role of Mcm2 licensing factor and helicase subunit of the Mcm2-Mcm7 complex in the differentiation of embryonic stem cells into neuronal lineages. A series of compelling experimental manipulations dissect the abnormalities in the formation of heterochromatin at pluripotent genes and the resolution of bivalent chromatin domains at lineage-specific genes in differentiation in response to mutation of the histone binding domain of Mcm2. These findings provide new insights into the replication-independent roles of Mcm2. This paper will be of interest to scientists working on development and embryonal cell differentiation.

eLife assessment

Understanding the integration and contribution of different combinations of environmental cues to the synchronization of the daily oscillator is important, because it provides insight into how organisms might be able to distinguish (and weight) between irregular (or in the tidal zone highly complex) versus regular individual daily changes of light and temperature. The study, which is thoroughly conducted and provides an impressive amount of experimental and analytical work, dissects the effects of sensory conflict on behavior and gene expression rhythms.

eLife assessment

This manuscript provides an improved version of the little skate genome, which will be of great interest to the field of comparative genomics and evolutionary biology. The authors use the genome to compare gene expression and chromatin accessibility profiles in motor neurons of the little skate and other species (mouse, chicken), aiming to predict conserved and divergent gene regulatory mechanisms underlying motor neuron development. While the manuscript contributes a valuable resource to the field, more rigorous analyses and experimental validation are needed to support the major claims of this study.

eLife assessment

This study provides a valuable analysis of the splicing landscape in colon cancer cells that have properties intermediate between those typically found in primary cancers ("epithelial") and those that are spreading by metastasis ("mesenchymal"). The strength of evidence provided is wide ranging and convincing, and supports current ideas that changes in the way that RNA from particular genes is processed plays a key role in cancer spread.

eLife assessment

Organoids mimic the architecture and function of their cognate organs and have potential as replacements for animal models. Here the authors generated canine organoids from multiple adult tissues, including endometrium, lung, and pancreas, in addition to previously generated organoids from the kidney, bladder, and liver. However more methodological detail and functional characterization are required before this toolbox can be optimally utilized by wider scientific community.

eLife assessment

This manuscript constitutes an important foray into the conformational rearrangements throughout various domains of the notoriously difficult-to-study P2X7 receptor, with a focus on the enigmatic intracellular 'ballast' domain. This is of broad interest to those studying the role of enzymatically active intracellular domains of membrane proteins. The authors provide convincing evidence that the ballast domain is unlikely to undergo major conformational changes upon ATP-induced gating, but additional experimental support is required on the facilitation process and to elucidate the consequences exerted by intracellular factors.

eLife assessment

This study investigates factors that control egg size plasticity in a social insect, the honey bee Apis mellifera. It finds that honey bee queens vary egg size in response to size of their colony, and that the gene Rho1 is involved in egg-size determination. These findings inform our understanding of maternal control over egg size, a key form of maternal investment. The work is relevant to colleagues studying reproduction and social insects.

eLife assessment

This manuscript reports the results of an observational study in 312 cancer patients to assess post-acute sequelae of SARS-CoV-2 infection (PASC). Their descriptive results provide details on the type of persistent symptoms as well as their frequency among cancer patients. This is valuable information to inform clinical policies regarding disease management in cancer patients.

eLife assessment

The premise behind this manuscript is important and timely for muscle biologists and for stem cell biologists. The identification of heterogenous distribution of factors across the myofiber is an important contribution for dissecting how muscle stem cell diversity in a tissue is achieved. However, the mechanism of action proposed by the authors will require additional experimental support.

eLife assessment

This study provides empirical support for how brain function at the system level, particularly network segregation, influences cognitive abilities even in the oldest-old range of human aging. The findings are potentially interesting to understand successful aging.

eLife assessment

This manuscript provides insights into the architecture of the yeast histone acetyltransferase complex NuA4 and is of broad interest to those studying transcription and chromatin modification. The cryo-EM data are of very high quality, and enable the authors to devise a structural model that is in much better agreement with biochemical data than previously reported models. This structure represents an important puzzle piece towards a molecular understanding of chromatin modification.

eLife assessment

This study connects changes in single-cell twitching motility due to substrate stiffness to multicellular phenotypes. It is likely to have a broad impact on those studying microbiology and multicellular communities as it assesses the influence of single-cell behavior on multicellular processes. However, some of the presented data conflict with previously published literature, raising questions about the nature of these differences.

eLife assessment

This paper will be of broad interest to anyone aiming to understand the neural basis of human touch perception. This is an important paper that provides compelling evidence for peripheral tactile encoding of orientation that reflects perceptual capabilities, by using a wide range of stimulus conditions. The results will be valuable to inform both future experiments and computational investigations into the neural representation and processing of small tactile spatial features at the edge of perceptual resolvability and on the emergence of invariant representations in touch more generally.

eLife assessment

This manuscript will be of interest to those working on non-neuronal bioelectricity, particular synthetic biologists and bioengineers. The primary contribution is the ability to leverage engineered gene circuits to control cellular membrane potential. We find issue, however, with the presentation of the data in this work as electrical communication since the synchronous behavior largely arises from external chemical stimuli.

eLife assessment

This manuscript is of interest to researchers investigating genetic mechanisms of aging and transcriptional regulation of developmental processes in mesenchyme-derived tissues. In this study, fibroblast cell lines from patients with and without Hutchinson-Gilford Progeria were compared to pinpoint the molecular mechanisms leading to the phenotypes of persons with this condition. The identification of five major dysregulated functional hubs in fibroblast cell lines derived from Hutchinson-Gilford Progeria Syndrome (HGPS) patients provides a unique opportunity for others working on this disorder to utilize animal models to validate the authors' hypotheses.

eLife assessment

The authors show that the amino terminus of dystroglycan is required for the production of full-length matriglycan, and in its absence, a shorter matriglycan is produced that is still capable of binding laminin. alpha-DGN deficient mice have abnormal neuromuscular synapses and reduced lengthening contraction-induced force. Overall, the well-controlled and convincing data mostly support the main conclusions, which will be of interest to scientists in membrane biology, muscle biology, and glycobiology.

eLife assessment

This work makes an important contribution to the study of the cell cycle and inferring mechanisms by studying correlations in division timing between single cells. By treating the problem in a general way and computing over lineage trees, the authors can infer timescales in the underlying mechanism. This approach is able to detect a general role of circadian rhythms in cell cycle control. The method is validated on data sets from bacterial and mammalian cells and can suggest when additional measurements are needed to distinguish competing models. This paper is of broad interest to scientists in the fields of cell growth, cell division, and cell-cycle control.

eLife assessment

When sensory inputs, such as vision or sound, are chronically disabled, the loss of input activity is counterbalanced by the upregulation of synaptic activity. In this study, the authors provide evidence that instead of synapses that directly represent the sensory information, synapses that show correlated intrinsic network activity are the ones that undergo the change upon sensory deprivation. This fundamental and important paper will be useful to readers in the fields of experience-dependent plasticity, sensory cortical coding, and homeostatic plasticity. While the key claims of the manuscript are well supported by the data, minor changes are suggested for clarification, including the fact that the present study has addressed homeostatic responses in adult animals rather than in juvenile animals with which homeostatic plasticity has been actively studied to date.

eLife assessment

The manuscript by Wardwell-Ozgo and co-authors describes a thorough and interesting study that explores the mechanisms through which a hormone receptor can both repress and activate gene transcription. They have conducted an impressive number of experiments all aimed at showing that by using their new transgenic tool, and Ecdysone Receptor (EcR) ligand binding domain sponge, they can demonstrate that EcR activity is important for eliciting both types of ecdysone responses, repression, and activation, in the Drosophila wing disc and that the EcR binding partner Smarter is essential for the repressive function. The differences in expression levels have however not been quantified, which would lend greater support to their claims.

eLife assessment

This paper will be of interest to scientists studying species-specific immune responses and those studying how transposable elements rewire transcriptional regulatory networks. The work describes a new class of TEs that may act as enhancers of immune genes in mice. A combination of computational and experimental data supports most but not all conclusions in the paper.

eLife assessment

This article is a valuable contribution to the field of neuroimaging. The paper proposes a deep neural network for brain extraction that generalises across domains, including species, scanners, and MRI sequences. Although in some sense brain extraction is not a challenging problem for deep learning, domain generalisation can be. The authors provide solid evidence that their approach works though it may need to be precisely matched to the training data.

eLife assessment

This paper is of interest to cell biologists studying the mechanisms and control of microtubule nucleation. In this work, the authors use a novel protocol for the purification of gamma-TuRCs and for the production of gamma-TuNA that enables them to demonstrate a clear activating effect of gamma-TuNA on microtubule nucleation that depends on the dimerization of gamma-TuNA protein chains.

eLife assessment

This paper will be of interest to the audience in the fields of genome stability and B lymphocyte biology for highlighting the role of R loop metabolism in maintaining genome integrity during antigen gene diversification. Although RNA:DNA hybrids and R loops have been described at the immunoglobulin (Ig) loci long ago, their contribution to Ig heavy chain (Igh) class switch recombination and Igh locus integrity have not been fully elucidated yet. Overall, the experiments and results generally support this conclusion; however, several aspects of the model put forward are highly speculative in the current form.

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.

(This preprint has been 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.)