Evaluated articles

eLife Assessment

Avoidance of UV and blue light by the nematode C. elegans is mediated by the unusual transmembrane protein LITE-1, a non-canonical photoreceptor. In this valuable work, the authors provide convincing evidence that LITE-1 function is also required for avoidance of very high concentrations of the food-associated cue diacetyl, suggesting that it may also function as a diacetyl chemoreceptor. While the evidence for this idea is incomplete, these intriguing findings suggest an unexpected complexity in the function of this unusual photoreceptor.

eLife Assessment

This study examines how the neuronal cytoskeleton contributes to the formation of the axonal membrane-associated periodic skeleton (MPS) in embryonic dorsal root ganglia (DRG) neurons, using STED imaging. Conclusions are supported by convincing methods, data, and analyses. This useful work confirms previous data and improves our understanding of the roles of microtubules and actin dynamics in the chronological recruitment of MPS components.

eLife Assessment

This is a methodologically rich manuscript that is important for revealing the center-surround inhibition profile of expectation in orientation space. The analyses are compelling in validating the critical role of predictive coding feedback. The findings provide novel insights into how expectation optimizes perception via enhancement and suppression.

eLife Assessment

This study introduces a valuable simulation-based inference (SBI) framework to identify degenerate compensatory mechanisms that stabilize network activity despite neuronal hyperexcitability, a feature common to many brain disorders. By estimating posterior distributions of network parameters, the authors highlight factors such as threshold potential and interneuron-to-principal cell connectivity as key compensators for increased intrinsic excitability and interneuron loss. While the approach is promising and could become a key tool for probing network degeneracy, the study is currently incomplete. To fully realize its potential, the framework requires improved scalability and more rigorous cross-validation.

eLife Assessment

This study provides valuable insights into humans' ability to generalize knowledge of learned graph structures to new experiences that share the same structure but are built from different stimuli. However, the evidence for the authors' claims is incomplete, with the main claims of structural generalization and compositionality only partially supported by MEG and behavioral data. This study will be of interest to cognitive neuroscientists studying structure learning and generalization.

eLife Assessment

This valuable study used genetic and pharmacological manipulations of insulin/IGF signaling in renal glomerular podocytes to address the role of insulin/IGF axis in podocytes. Solid data are presented to demonstrate that co-inhibition of insulin/IGF signaling in podocytes led to aberrant splicing of mRNAs, which could contribute to the loss of podocytes in vitro and in vivo in mice. As it stands, the study lacks the assessment of developmental phenotype of podocytes in the mouse model.

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

eLife Assessment

This paper performs a valuable critical reassessment of anatomical and functional data, proposing a reclassification of the mouse visual cortex in which almost all the higher visual areas are consolidated into a single area V2. However, the evidence supporting this unification is incomplete, as the key experimental observations that the model attempts to reproduce do not accurately reflect the literature. This study will likely be of interest to neuroscientists focused on the mouse visual cortex and the evolution of cortical organization.

eLife Assessment

In their important manuscript, Gangadharan, Kober and Rice focus on how Stu2/XMAP215-family microtubule polymerases use their TOG domains to catalytically promote microtubule growth, testing whether their mechanism follows an enzyme-like kinetic model similar to that of actin polymerases. The authors integrate measurements including microtubule polymerization rates and TOG-tubulin binding kinetics to convincingly show that Stu2 follows an enzyme-like model where tight tubulin binding enables efficient polymerization, revealing a shared mechanism with actin polymerases despite their evolutionary divergence. This work will be of general interest to the cell biology and biophysics communities.

eLife Assessment

This manuscript revisits the well-studied KdpFABC potassium transport system from bacteria with a convincing set of new higher resolution structures, a protein expression strategy that permits purification of the active wildtype protein, and insight obtained from mutagenesis and activity assays. The thorough and thoughtful mechanistic analyses make this a valuable contribution to the membrane transport field.

eLife Assessment

This important study reports that two distinct waves of ovarian follicles contribute to oocyte production in mice. The paper provides large amounts of data that will benefit future studies, although the methods and analysis are considered incomplete at present. Justification for the criteria of wave 1 follicles would benefit from further explanation and discussion. This work will be of interest to ovarian biologists and physicians working on female infertility.

eLife Assessment

This important study tackles an interesting aspect of fungal physiology: how a mitochondria-associated gene influences production of the secondary metabolite DON and fungicide sensitivity. The authors have improved the manuscript and the supporting evidence is convincing, although some uncertainties remain around descriptions of the methods.

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 mechanisms and inclusion of the experiments performed, but not presented, will 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.