Evaluated articles

eLife Assessment

In this valuable study, the authors develop new approaches to investigate mRNA imprinting, a phenomenon in which RNA-protein complexes form in the nucleus to influence the fate of transcripts in the cytoplasm. They propose that the Pol II subunit Rpb4 serves as a key node in this pathway, recruiting proteins involved in cytoplasmic processes. Notably, some of the candidates identified in this study were previously thought to function exclusively in the cytoplasm. However, the evidence remains incomplete, as key controls are lacking and alternative explanations have not been fully addressed; additional validation would help strengthen the authors' conclusions.

eLife Assessment

This valuable study by Zhu et al. offers a high-resolution evolutionary framework for spider silk proteins (spidroins) through long-read transcriptomics across a broad phylogenetic range, with theoretical implications for protein family evolution, biomaterials, and silk biology. By identifying putative ancestral spidroin templates in early-diverging spiders, the authors make a significant contribution to understanding genetic innovations underlying silk diversification. The long-read sequencing approach is well-suited to these highly repetitive genes. However, the support is incomplete: key claims regarding direct ancestry between silk protein families, the independent origin of certain silk types, and the co-option of flagelliform spidroins in non-web-building spiders rely on absence-based inferences and indirect phylogenetic reasoning that the data cannot yet fully substantiate, and some gene family assignments overreach the available molecular evidence.

eLife Assessment

This potentially important paper questions the evolutionary origin of the tunicate endoderm, using single-cell sequencing on a developmental series of the ascidian Styela clava that covers metamorphosis and gut development. The authors base their conclusions on a comparison with the development of mouse gut endoderm, where they point out similarities in the origin of tissues, perhaps representing a case of "deep homology". This work has the potential to make a significant contribution to the field of chordate evolution, but in its current form, the evidence it presents is incomplete and is limited by a problematic discussion of evolutionary implications and by major issues regarding the clarity and cogency of data presentation.

eLife Assessment

This study presents a valuable methodological contribution exploiting the DEER background decay to quantify supramolecular packing in amyloid fibrils. The evidence is incomplete: the observation of D < 1 is inconsistent with the theoretical lower bound of the model, and it remains unclear whether this reflects a genuine systematic limitation or falls within experimental uncertainty.

eLife Assessment

In this work, the authors demonstrated that blue light mediated mitochondrial contacts attenuated blue light induced mitochondrial dysfunction, and validated this in human cells and C. elegans. This valuable work has the potential to provide novel perspectives into the field of mitochondrial biology but the supporting data are incomplete.

eLife Assessment

This manuscript presents a valuable analysis of how locomotion modulates the activity of different subtypes of cortical neurons in the mouse primary visual cortex, showing that locomotion more strongly increases responses in sensitizing than in depressing excitatory cells. This data is then used to constrain a model of the responses. While the data are very interesting, the analyses remain incomplete, in particular due to concerns surrounding the modelling.

eLife Assessment

This manuscript reports an important study in which the authors apply smFRET imaging to probe HIV-1 Env conformational dynamics in the presence of antibodies. Previous implementations of smFRET imaging of HIV-1 Env, which focus on gp120 conformation, have yielded limited information on antibodies that target gp41. Through the cutting-edge application of smFRET imaging, the study provides convincing insights into the mechanisms of action of relevant antibodies.

eLife Assessment

This study provides valuable insights into the cellular dynamics underlying accelerated tooth regeneration in a vertebrate model. Using single-nucleus RNA sequencing across multiple time points, the authors present a well-structured analysis of cell populations, trajectories, and intercellular signaling events associated with this process. The strength of evidence is solid but incomplete, as the conclusions are primarily supported by computational inference, without experimental validation of key findings.

eLife Assessment

This paper provides a valuable observation that imiquimod, a compound often used to induce a psoriasis-like skin inflammation in mice, has a TLR7-independent effect acting through the unfolded protein response and binding to Gelsolin. However, the mechanism connecting Gelsolin to skin inflammation presented in this paper is incomplete and requires further investigation. These findings are of interest to the field of skin immunology.

eLife assessment

This study provides an important and biologically plausible account of how human perceptual judgments of heading direction are influenced by a specific pattern of motion in optic flow fields known as retinal curl. By combining psychophysical experiments and neural modeling, the authors demonstrate that what was previously considered an incidental "nuisance" signal actually serves as a functional control signal for estimating heading and steering toward a fixated target. While the evidence for the role of curl signals is convincing and advances our understanding of vision-based navigation, the work's impact would be strengthened by situating these findings among other cues that contribute to heading estimation, and by clarifying both the time course of these computations and their generalizability across different navigational contexts.

eLife Assessment

This valuable study introduces an innovative experimental design to address a crucial and timely issue in microbial ecology: the potential bias in soil microbial community analyses caused by extracellular DNA degradation. While the evidence showing variable degradation rates of extracellular DNA is convincing, additional conceptual, methodological, and statistical clarifications could reinforce the claims and the study's contribution to the field. This research will appeal to microbial ecologists and researchers interested in using molecular techniques to evaluate microbial community structure.

eLife Assessment

In this study, the authors use microCT to image an intact hatchling octopus and segment major organ systems, including the vascular, respiratory, digestive, and nervous systems. The resulting dataset is of good quality, and its release through a public web interface is a valuable resource for the community to explore cephalopod mesoscale anatomy. However, the authors claim to have elucidated previously uncharacterized chemotactile pathways from the suckers to the brain, for which there is incomplete evidence, as microCT does not reveal structural connectivity. In addition, the language is often overly complex, obscuring the main points and making it difficult to assess the strength of individual claims. This article would benefit from more cautious framing of the anatomical findings and complementary neuronal tracing experiments to support the proposed pathways.

eLife Assessment

This important study advances a new computational approach to measure and visualize gene expression specificity across different tissues and cell types. The framework is potentially helpful for improving the way gene expression specificity is defined across biological datasets, especially among single-cell datasets. The evidence supporting the method is generally solid, although further evaluation of the method's robustness and comparison to other approaches would strengthen the conclusions.

eLife Assessment

This important study provides a comprehensive multi-omics characterization of Leishmania donovani stage differentiation, offering insights into the molecular basis of parasite adaptation across host environments. The authors present convincing evidence that stage transitions are not driven by genomic variation but instead rely on coordinated post-transcriptional regulation, including mRNA turnover, translation, and protein degradation. Although experimental validation of these findings and conclusions remains to be completed, the integration of diverse, high-quality datasets establishes a robust resource that will be of broad utility to researchers investigating Leishmania biology and life-cycle progression.

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

eLife Assessment

This study provides valuable insights into how HIV-1 Env modulates the nanoscale organization and dynamics of the CXCR4 co-receptor on T cells, using quantitative imaging and functional approaches, the authors present convincing evidence that gp120 engagement promotes CD4-dependent clustering and altered mobility of CXCR4, distinct from the effects of the natural ligand CXCL12. Some concerns were raised regarding the interpretation of the single-particle tracking analyses, and additional clarification or analysis may help strengthen the conclusions. The physiological relevance of the findings could be further enhanced by validation with infectious virus and by more clearly integrating the CXCR4R334X mutant observations into the central mechanistic narrative. The work will be of interest to researchers studying HIV entry and membrane receptor organization.

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

eLife Assessment

In light of the diverse functions associated with the Dorsal Raphe Nucleus across vertebrate species, this important study presents findings on the role of serotonin in promoting behavioral quiescence through the regulation of neuromotor populations. Combining optogenetics with brain-wide activity analyses, the study provides convincing evidence of interest to researchers in neuromodulation and translational medicine fields.

eLife Assessment

This study presents important findings for the understanding of central brain circuits that underlie nociception-induced escape. Using a laser-based nociception assay, chronic neuronal silencing, trans-Tango anatomical tracing, and reference to connectomic data, the authors propose that nociceptive signals (from painless- and trpA1-expressing neurons) converge on a subset of dopaminergic neurons (subsets of PPL1 and PAM), which in turn engage mushroom body output neurons (MBONs) to shape escape latency. However, methods and controls fall short of fully supporting the findings, rendering the evidence incomplete. This study will be of interest to scientists studying nociception and learning and memory circuits.

eLife Assessment

This valuable work identifies a subpopulation of neurons in the larval zebrafish pallium that responds differentially to varying threat levels, potentially mediating the categorization of negative valence. The evidence supporting these claims is solid; however, the study would be strengthened by more sophisticated analyses of functional imaging results, behavioral confirmation of stimulus valence, and further evidence linking the functionally distinct clusters to their molecular identity. This work will be of interest to systems neuroscientists investigating the circuit-level encoding of emotion and defensive behavior.

eLife Assessment

This manuscript presents important findings that challenge traditional models of speech processing by demonstrating that theta-gamma phase-amplitude coupling in the auditory cortex is primarily a stimulus-driven alignment to external acoustic structures rather than an intrinsic neural oscillatory mechanism. The evidence supporting these claims is convincing, grounded in a robust cross-linguistic acoustic analysis and high-fidelity, time-resolved intracranial recordings.

eLife Assessment

This is a potentially important study comparing infants (8 months) and adults with respect to rhythmic EEG response properties during periodic and aperiodic visual stimulation. The results provide solid evidence for a ~4 Hz EEG response in infants that emerges independently of stimulation frequency. At this stage, additional work will be required to conclusively establish that this theta-band effect reflects genuine neural resonance rather than oculomotor processes.