Evaluated articles

eLife assessment

In this study, camera trapping and species distribution models are used to show that human disturbance in mountain forests in the eastern Himalayas pushes medium-sized and large mammal species into narrower habitat space, thus increasing their co-occurrence. While the collected data provide a useful basis for further work, the study presents incomplete evidence to support the claim that increased co-occurrence may indicate positive interactions between species.

eLife assessment

This important study contributes insights into the regulatory mechanisms of a protein governing cell migration at the membrane. The integration of approaches revealing protein structure and dynamics provides convincing data for a model of regulation and suggests a new allosteric role for a solubilized phospholipid headgroup. The work will be interesting to researchers focusing on signaling mechanisms, cell motility, and cancer metathesis.

eLife assessment

This study presents a valuable characterization of the biochemical consequences of a disease-associated point mutation in a nonmuscle actin. The study uses well-characterized in vitro assays to explore function. The data are convincing and should be helpful to others.

eLife assessment

This work uses an interdisciplinary approach combining microfluidics, structural biology, and genetic analyses to provide important findings that show that pathogenic enteric bacteria exhibit taxis toward human serum. The data are compelling and show that the behavior utilizes the bacterial chemotaxis system and the chemoreceptor Tsr, which senses the amino acid L-serine. The work provides an ecological context for the role of serine as a bacterial chemoattractant and could have clinical implications for bacterial bloodstream invasion during episodes of gastrointestinal bleeding.

eLife assessment

This study presents a useful tool for predicting TCR specificity with compelling evidence for improvements over prior art. This work/tool will be broadly relevant to computational biologists and immunologists.

eLife Assessment

This important study addresses two questions: (i) how danger signaling is altered for people with childhood adversities, and (ii) how this differs across different operationalizations of adversity. The latter is of particularly broad interest to multiple fields, given that childhood adversity is operationalized very differently across the literature. The study provides compelling evidence using a large sample size and rigorous statistical methods. These data will be of interest to scientists and clinicians interested in early life adversity, statistical approaches for quantifying stress exposure, or aversive learning.

eLife assessment

BMP signaling plays a vital role in skeletal tissues, and the importance of its role in microtia prevention is novel and promising. This important study sheds light on the role of BMP signaling in preventing microtia in the ear, with solid data broadly supporting the claims of the authors.

eLife assessment

In this important paper, Blin and colleagues develop a high-throughput behavioral assay to test spontaneous swimming and olfactory preference in individual Mexican cavefish larvae. The authors present compelling evidence that the surface and cave morphs of the fish show different olfactory preferences and odor sensitivities and that individual fish show substantial variability in their spontaneous activity that is relevant for olfactory behaviour. The paper will be of interest to neurobiologists working on the evolution of behaviour, olfaction, and the individuality of behaviour.

eLife assessment

This important study reveals the role of skin-resident mast cells in amphibians in mediating antimicrobial responses. The data are compelling and highlight species-specific biology that can cross-inform human mast cell biology in a species that does not rely on IgE as a primary mechanism for antimicrobial skin responses.

eLife assessment

This useful work describes a novel microscopy-based method to correlate the degree of pigmentation with the gene expression profile of human-induced pluripotent stem cell-derived Retinal Pigmented Epithelial (iPSC-RPE) cells at the single cell level. The presented evidence is solid in showing that there is heterogeneous gene expression in iPSC-derived RPE cells, and there is no significant correlation with the pigmentation. By analyzing the expression of some genes related to function, lysosomal- and complement-related pathways were partially enriched in darker cells. This methodology can be used by other researchers interested in analyzing gene expression related to microscopic images.

eLife assessment

This useful study introduces a simple mechanical model of C. elegans locomotion that captures aspects of the worm's behavioral repertoire beyond forward crawling. While the kinetic model (ElegansBot) provides a compromise and starting point to help understand the mechanical components of C. elegans behavior, the claim that this work improves on extant mechanical models is incomplete, including modeling a 3-dimensional turning behavior with a 2-dimensional model without sufficient justification. In addition, the results of the application of the model to previously unstudied behaviors are primarily qualitative and do not produce new predictions.

eLife assessment

This proof-of-concept study focuses on an A->G DNA base editing strategy that converts CAG repeats to CAA repeats in the human HTT gene, which causes Huntington's disease (HD). These studies are conducted in human HEK293 cells engineered with a 51 CAG canonical repeat and in HD knock-in mice harboring 105+ CAG repeats. The findings of this study are valuable for the HD field, applying state-of-the-art techniques. However, the key experiments have yet to be performed in neuronal systems or brains of these mice: actual disease-rectifying effects relevant to patients have yet to observed, leaving the work incomplete.

eLife assessment

This important study reports on the genome evolution of a poorly studied fungal group. By combining long-read sequencing and different bioinformatic analyses, the authors show that the giant genome of Entomophthora muscae expanded due to extensive transposable element activity. The strength of evidence is compelling and the authors are to be commended for their multiple comparative analyses of gene content along with transparently written and visualized techniques, data curation, and methods. This paper will be of relevance to fungal biologists as well as to evolutionary biologists interested in the study of genome size dynamics.

eLife assessment

The study presents valuable findings where two-domain thermodynamic model for TetR accurately predicts in vivo phenotype changes brought about as a result of various mutations. The evidence provided is compelling and features the first innovative observations with a computational model that captures the structural behavior, much more than the current single-domain models.

eLife Assessment

This study presents valuable findings on what networks of genes were impacted by introgression from Denisovans, to identify the biological functions involved in high-altitude adaptation in Tibet. This study applies solid and previously validated methodology to identify genes with signatures of both introgression and positive selection. This paper would be of interest to population geneticists, anthropologists, and scientists studying the genetic basis underlying high-altitude adaptation.

eLife assessment

This manuscript investigates how chloroplasts are broken down during light-limiting conditions as plants reorganize their energy-producing organelles during carbon limitation. The authors provide compelling live-cell imaging data of plastids and solid quantification of events, documenting that buds form on the surface of chloroplasts and pinch away, then associate with the vacuole via a mechanism that depends on autophagy machinery, but not plastid division machinery. This manuscript provides valuable groundwork for other scientists studying the regulation and breakdown of energy-producing organelles, including chloroplasts and mitochondria.

eLife assessment

This study provides useful information by identifying the cell type (macrophages) in synovial tissues involved in the pathogenesis of post-traumatic osteoarthritis (OA) and clarifying distinct transcriptomic signatures that may be a good therapeutic target for OA. However, the analysis performed so far is incomplete, with a main weakness being the lack of data to confirm the authors' speculation about the underlying mechanisms.

eLife Assessment

The manuscript reports fundamental findings supported by convincing data that supports the biological mechanism for optimal nodulation in soybean. The results are of relevance to understanding the signaling pathways (specifically those dependent on RIN4/RPM1-interacting protein 4) underpinning beneficial rhizobia symbiosis, while repressing the immune response.

eLife Assessment

This study presents valuable evidence concerning the potential for naturalistic movie-viewing fMRI experiments to reveal some features that are correlated with the functional and topographical organization of the developing visual system in awake infants and toddlers. The data are compelling given the difficulty of studying this population, the methodology is original and validated, and the evidence supporting the conclusions is convincing and in line with prior research using resting-state and awake task-based fMRI. This study will be of interest to cognitive neuroscientists and developmental psychologists, and in particular those interested in using fMRI to investigate brain organisation in pediatric and clinical populations with limited tolerance to fMRI.

eLife assessment

This important study reports the generation of genetic tools for manipulating several tissues at the same time in Drosophila. The authors provide convincing evidence that this allows for the generation of LexA and QF2 driver lines, which will be of great utility for understanding inter-organ communication. Making the tools available through the Drosophila stock center and plasmid depository will ensure that they are easily accessed by many researchers.