Evaluated articles

eLife Assessment

This study reports important negative results, showing that genetically removing the RNA-binding protein PTBP1 in astrocytes is insufficient to convert them into neurons, thereby challenging previous claims in the field. It also offers a compelling analysis of PTBP1's role in regulating astrocyte-specific splicing. The evidence is strong, as the experiments are technically sound, carefully controlled, and supported by both imaging and transcriptomic analyses.

eLife Assessment

This manuscript presents a valuable methodological approach to investigating context-dependent activity of cis-regulatory activity within defined genomic loci. The authors combine a locus-specific massively parallel reporter assay, enabling unbiased and high-coverage profiling of enhancer activity across large genomic regions, with a degenerate reporter assay to identify nucleotides critical for enhancer function. The data supporting the conclusions are solid, highlighted by successful identification and characterization of both previously known and new regulatory elements across multiple developmental stages, cell types, and species. While the approach has inherent limitations in sensitivity, and indirect assignment of regulatory elements to target genes, it provides a flexible platform for nominating candidate cis-regulatory elements across defined loci.

eLife Assessment

This useful study characterizes the evolution of medial prefrontal cortex activity during the learning of an odor-based choice task. The evidence provided is solid, providing quantification of functional classes of cells over the course of learning using the longitudinal calcium recordings in prefrontal cortex, and quantification of prefrontal sequences. However, the experimental design appears to provide limited evidence to support strong conclusions regarding the functional relevance of neural sequences. The study will be of interest to neuroscientists investigating learning and decision-making processes.

eLife Assessment

This important study presents JABS, an open-source platform that integrates hardware and user-friendly software for standardized mouse behavioral phenotyping. The work has practical implications for improving reproducibility and accessibility in behavioral neuroscience, especially for linking behavior to genetics across diverse mouse strains. The strength of evidence is convincing, with comprehensive validation of the platform's components and enthusiastic reviewer support.

eLife Assessment

This valuable study introduces a modern and accessible PyTorch reimplementation of the widely used SpliceAI model for splice site prediction. The authors provide convincing evidence that their OpenSpliceAI implementation matches the performance of the original while improving usability and enabling flexible retraining across species. These advances are likely to be of broad interest to the computational genomics community.

eLife Assessment

This important study is the first characterization of the phenotype caused by a lack of Eml3 expression in mice. Mutant animals present a disrupted pial basement membrane, leading to focal extrusions from the cerebral cortex, called ectopias. The methodology is convincing and the conclusions are solid, although further investigations on the molecular and cellular mechanisms are required to improve the manuscript. This work would be of interest to neural development biologists and human geneticists working on brain disorders.

eLife Assessment

This valuable study reports the physiological function of a putative transmembrane UDP-N-acetylglucosamine transporter called SLC35G3 in spermatogenesis. The conclusion that SLC35G3 is a new and essential factor for male fertility in mice and probably in humans is supported by convincing data. This study will be of interest to reproductive biologists and physicians working on male infertility.

eLife Assessment

In this manuscript, Wafer and Tandon et al. present a thoughtful and well-designed genetic screen for regulators of adipose remodeling using zebrafish as a model system. This work is valuable because it uncovers several genes associated with adipose tissue hyperplastic hypertrophic morphology and diet-induced remodelingthe hat have considerable potential health impact. The rigorous phenotypic analyses and compelling evidence make this work a key resource for the field.

eLife Assessment

Qiu et al. present multiple dimeric structures of GPR3, which reveal the binding mode of the inverse agonist AF64394. The findings provide important insights into the regulation of GPCR3 and potentially other related orphan GPCRs. The authors present convincing evidence of their claims through thoughtful analysis of their cryo-EM structures, mutagenesis, and cell-based assays. This work will be of interest to GPCR investigators, especially those studying the signaling of orphan receptors.

eLife Assessment

This study provides important insights into the crosstalk between ATG2A with components of the early secretory pathway. While the mechanisms governing autophagic membrane expansion remain yet to be fully understood, in this study the authors employ an elegant proximity labelling approach and identify two ER-Golgi intermediate compartment (ERGIC)-localized proteins. Through a series of complementary experiments combining microscopy and biochemistry, the authors identify ARFGAP1 and Rab1A as components of early autophagic membranes, which accumulate at the periphery of pre-autophagosomal structures induced by loss of ATG2. The overall study is well executed and the evidence supporting the claims is convincing.

eLife Assessment

This paper develops a fundamental theory that explains how the brain can hold in working memory not only the identity but also the order of presented stimuli. Previous theories did not explain the ability of people to immediately recall the correct order of the stimulus presentation. The authors present compelling evidence that this can be achieved through synaptic augmentation, an experimentally observed phenomenon with a time scale of tens of seconds.

eLife Assessment

This important study uses data from OpenAlex on more than 50 million journal articles in over 50,000 research journals to examine the dynamics of interdisciplinarity and international collaboration in research journals. The data analytics used to quantify disciplinary and national diversity are convincing, and support the claims that journals have become more diverse in both aspects. The revisions made by the authors have addressed the small number of concerns the reviewers had about the original version.

eLife Assessment

This useful study examines excitation/inhibition (E/I) balance in the CA3-CA1 circuit of the hippocampus. Experimental and computational modeling results are presented. The computational modeling results were viewed as a novel advance supported by solid evidence, but incomplete evidence was provided to support the paper's main experimental claims due to deficiencies in the experimental methodology and concerns about the neurobiological relevance of the experimental observations.

eLife Assessment

This valuable study provides evidence that the integration of the nuclear envelope into the endoplasmic reticulum provides a mechanism for mechanical integration across this continuous membrane system. This work opens up new avenues for studying organelle membrane tension homeostasis. The evidence was found to be convincing and carefully quantified, with minor limitations that we expect to be further explored in future work.

eLife Assessment

This important work shows that corticotrophin-releasing factor is delivered monosynaptically to dorsal striatal cholinergic interneurons from the central amygdala and bed nucleus of the stria terminalis. CRF increases cholinergic interneuron firing and release of acetylcholine, and this action is attenuated by pre-exposure to ethanol, suggesting a potential role in stress- and alcohol use disorders. This revision addressed prior concerns, presented convincing evidence supporting the conclusions, and set the stage for additional studies.

eLife Assessment

This fundamental study presents a compelling and comprehensive analysis of the newly defined Lipocone superfamily, offering unprecedented insights into the evolutionary origins of Wnt proteins. The authors provide evidence that this superfamily evolved from membrane proteins. The work is exemplary in its use of sequence analysis and structural modeling and will be of broad interest to researchers studying protein evolution and enzymology.

[Editors' note: this paper was reviewed by Review Commons.]

eLife Assessment

The authors study how apolipoprotein L1 variants impact inflammation and lipid accumulation in macrophages. The findings will be useful for researchers investigating macrophage metabolism and inflammation. The discovery that the polyamine spermidine in part mediates such effects is interesting, but the supporting evidence for a physiologically relevant role is currently incomplete due to the lack of relevant in vivo studies.

eLife Assessment

This fundamental study shows how past experiences shape perception across short, medium, and long time scales, using a single behavioural paradigm and reanalysed EEG data. It provides convincing evidence for two processes across all scales: an attention-dependent mechanism that speeds responses to expected events, and an attention-independent mechanism where expected events are encoded less precisely, consistent with feedforward dampening. The work offers a unifying account of temporal context effects, though stronger brain-behaviour links, integration with serial dependence attraction and repulsion models, and extension to other timescale definitions would further strengthen the contribution.

eLife Assessment

This important study explores the regulation of collective cell migration and tissue patterning in the zebrafish posterior lateral line primordium by SoxB1 transcription factors. The authors provide evidence that SoxB1 genes interact with Wnt and Fgf signaling pathways to control neuromast deposition and spacing, a process central to sensory organ development. The work offers mechanistic insight into the self-organization of migrating tissues and adds to the understanding of how transcriptional networks integrate with signaling pathways during morphogenesis. However, the strength of the evidence supporting several key conclusions is incomplete due to insufficient validation of mutant and knockdown tools, lack of quantitative analysis, and unclear experimental design details; additional quantification and more rigorous verification of gene knockdown or loss-of-function tools are needed to support the proposed model.

eLife Assessment

This study provides valuable findings regarding potential correlates of protection against the African swine fever virus. The evidence supporting the claims is solid, and the results are highly relevant to the field. Further analysis using larger number of animals and other virus strains will help validate the importance of these findings and assess the relevance of the immune parameters associated with protection. The work will be of broad interest to veterinary immunologists, and particularly those working on African swine fever.