Evaluated articles

eLife Assessment

In this valuable study, the authors attempt to reconstruct the evolutionary history of a large and widespread group of freshwater fishes (Nemacheilidae) across Eurasia since the early Eocene, based on molecular phylogenetic analysis with very comprehensive samplings including 471 specimens belonging to 250 living species. The authors infer that range expansions of the family were facilitated by tectonic connections, favourable climatic conditions, and orogenic processes, adding to our understanding of the effects of climatic change on biodiversity during the Cenozoic. The molecular evidence is overall solid, but the calibration points from the fossil records used in the analysis have not been clearly demonstrated or cited; the different dates for the calibration points might impact the discussion on the evolutionary history relating to past climatic changes.

eLife Assessment

This important study highlights the key role of the gut-liver axis mediated by LPS in causing hepatic steatosis. The authors provide solid evidence, in vivo, in vitro, and in silico, for the role of acyloxyacyl hydrolase in mediating this effect using KO mice subjected to MASD-inducing diets. The findings are significant for the liver research community and others interested in the gut-liver axis.

eLife Assessment

This study provides convincing evidence that the Kinesin protein family member KIF7 regulates the development of the cerebral cortex and its connectivity and the specificity of Sonic Hedgehog signaling by controlling the details of Gli repressor vs activator functions. This study provides important new insights into general aspects of cortical development.

eLife Assessment

In this useful study, the authors use published scRNA-seq data to highlight the importance of mast cells (MCs) in TB granulomas, reporting a comparative assessment of chymase- and tryptase-expressing MCs in the lungs of tuberculosis-infected individuals and non-human primates, with MC-deficient mice showing reduced lung bacterial burden and pathology during infection. Whilst the findings are helpful, the evidence to support conclusions is inconsistent across models and thus incomplete. Specifically, the data supporting a role for MCs in coordinating cytokine responses to modulate pathology, susceptibility to tuberculosis, and dissemination during infection are weak.

eLife Assessment

This important study provides solid in-vivo evidence that CCR4 regulates the early inflammatory response during atherosclerotic plaque formation. The authors propose that altered T-cell response plays a role in this process, shedding light on mechanisms that may be of interest to medical biologists, biochemists, cell biologists, and immunologists. Further in vivo validation, mechanistic studies, and discussion of results in vitro suggested would be helpful to cement the significance and implications of these findings.

eLife Assessment

This study describes a useful technique to improve imaging depth using confocal microscopy for imaging large, cleared samples. It is as yet unclear if their proposed technique presents a significant advance to the field since their comparisons to existing techniques remain incomplete. However, the work will be of broad interest to many researchers in different fields.

eLife Assessment

This timely and important study used functional near-infrared spectroscopy hyperscanning to examine the neural correlates of how group identification influences collective behavior. The work provides incomplete evidence to indicate that the synchronization of brain activity between different people underlies collective performance and that changes in brain activity patterns within individuals may, in turn, underlie this between-person synchrony. This study will be of interest to researchers investigating the neuroscience of social behaviour.

eLife Assessment

By combining psychophysics and computational modelling based on the Theory of Visual Attention, this study examines the mechanisms underlying self-prioritization by revealing the influence of self-associations on early attentional selection. While the findings are important, the experimental evidence is incomplete. The relationship between consciousness (awareness) and attention, the potential contamination by arousal, the inconsistent and unexpected results, and the distinguishing between social and perceptual tasks need to be addressed or improved. The work will be of interest to researchers in psychology, cognitive science, and neuroscience.

eLife Assessment

This important study advances our understanding of the role of dopamine in modulating pair bonding in mandarin voles by examining dopamine signaling within the nucleus accumbens across various social stimuli using state-of-the-art causal perturbations. The evidence supporting the findings is compelling, particularly cutting-edge approaches for measuring dopamine release as well as the activity of dopamine receptor populations during social bonding. However, statistical analyses were found to lack rigor and clarity, and the lack of complementary experiments in females was noted as a weakness. Additionally, the manuscript would be strengthened by placing findings within a broader framework, such as by highlighting similarities and/or differences between mandarin and prairie voles.

eLife Assessment

This valuable study investigates both online responses to, and offline replay of, visual motion sequences. Sophisticated EEG analyses provide solid evidence for both feature-specific and non-specific sequence representations, though the explanation of the statistical methods used is currently incomplete.

eLife Assessment

This interesting study focuses on a previously reported positive correlation between translational efficiency and protein noise. This is unexpected as typically noise is inversely related to expression and increasing translation efficiency would increase the protein expression and thus be expected to reduce noise in gene expression. Using mathematical modeling and analysis of experimental data the authors argue that this phenomenon arises due to ribosomal demand. However, the work appears incomplete, with the reviewers having raised questions regarding the validity of the assumptions used in the mathematical model as well as the clarity of the presentation.

eLife Assessment

This work presents a valuable finding on how the interplay between transcription factors SOX2 and OCT4 establishes the pluripotency network in early mouse embryos. Despite the high quality of the data, the evidence supporting the claims of the authors is currently incomplete and would benefit from more omics analysis such as H3K4me1 and H3K27ac CUT&Tag. The work will be of interest to biologists working on embryonic development.

eLife Assessment

This valuable study provides a detailed picture of the synapse distributions for a set of visual projection neurons and their downstream partners, in combination with multi-compartmental modelling fitted to electrophysiological data. The model reveals interesting consequences of synapse topography for neuronal computation. The analysis, however, seems incomplete as the authors only analyze passive models of these spiking neurons, and do not attempt to connect their analysis to the bigger picture at the behavioral level.

eLife Assessment

This important study shows that Toxoplasma gondii uses paracrine mechanisms, in addition to cell-intrinsic methods, to evade the host immune system, with MYR1 playing a key role in transporting effector molecules into host cells. The authors present convincing evidence that in vivo, MYR1-deficient parasites can be rescued by wild-type parasites, revealing a limitation in pooled CRISPR screens, where such paracrine effects may obscure the identification of key parasite pathways involved in immune evasion

eLife Assessment

This study reports an important finding on the mechanism underlying the enhancement of anti-viral immune responses by febrile temperatures, especially the role of the conserved heat-shock factor, HSF-1. The data provide compelling support for the authors' model wherein increased temperature in the shrimp Litopenaeus vannamei activates HSF1, which in turn enhances anti-viral response via up-regulation of the nSWD protein and antibacterial peptides. The work, which will be of interest to virologists, immunologists, and cell biologists, would benefit from more discussion of the function and roles of HSF-1 at 25°C vs. 32°C.

eLife Assessment

This important study uses a large dataset from both recent isolates and genomes in databases to provide an analysis of the population structure of the pathogen Salmonella gallinarum. The results regarding regional adaptation and the evolutionary trajectory of the resistome and mobilome remain incomplete, requiring additional details to fully support their claims and assess the value of these insights for future policy interventions regarding this and other pathogens. This work will interest microbiologists and researchers working on genomics, evolution, and antimicrobial resistance.

eLife Assessment

This valuable study on strategies used by Pseudomonas to subvert hots immunity identifies a new immune evasion strategy. The study presents solid evidence on the cleavage of VgrG2B by Caspase 11 and the generation of fragments that inhibit activity of the NLRP3 inflammasome. This work should be of interest to immunologists and microbiologists.

eLife Assessment

This important study reports a detailed quantification of the population dynamics of Salmonella enterica serovar Typhimurium in mice. Bacterial burden and founding population sizes across various organs were quantified, revealing pathways of dissemination and reseeding of the gastrointestinal tract from systemic organs. Using various techniques, including genetic distance measurements, the authors present compelling evidence to support their conclusions, thus presenting new knowledge that will be of broad interest to scientists focusing on infectious diseases.

eLife Assessment

Wang et al's study addresses an important critical gap in our understanding of de novo epithelial polarization using MDCK cell doublets surrounded by ECM, providing convincing evidence through imaging and depletion studies on the role of conserved polarity proteins and the centrosome during this process. While the authors propose a clear hierarchical model, there is a need for further exploration of how microtubule organization contributes to this process. Specifically, live cell imaging of microtubules under mutants and their included ECM conditions, along with a more precise temporal mapping of microtubule dynamics in relation to proteins like Gp135, would strengthen the study's conclusions.