Evaluated articles

eLife Assessment

This study presents a useful array of analyses of the effects of training and/or instruction to use the method of loci during episodic encoding and retrieval. A major strength of the experiment is the impressive recruitment of memory athletes and the training of novice athletes to use the method of loci, long known to improve the precision of memory recall. That said, the sheer number of results and their organization should be addressed; streamlining the results and placing them, whenever possible, in a theoretical framework. As it stands, the presented work is incomplete with respect to the major conclusions that training itself leads to neural differentiation of prefrontal cortical neural patterns, and the authors need to temper these claims.

eLife Assessment

This important paper provides novel information on the function of the Drosophila ryanodine receptor (RyR) during muscle development. The authors analyze the effects of a rare human mutation that causes myopathy that affects a conserved region of the gene. They present compelling evidence that this variant affects muscle function in flies. These results suggest that Drosophila can be used as a tool for screening additional variants.

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

eLife Assessment

This work provides a map of enhancer-promoter interactions associated with genes controlling the development of a specific neuronal cell population. The study offers a valuable resource and integrates multiple complementary datasets to provide insights into regulatory mechanisms, although the conceptual advances are moderate and the central message could be clearer. The evidence supporting the conclusions is generally solid, but the lack of direct functional testing of key regulatory elements limits the strength of some claims.

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

eLife Assessment

The authors provide valuable findings showing that GM-CSF prevents the loss of ILC3 populations during gut inflammation and inhibits pro-inflammatory cytokine production. They combine a preclinical model of gut inflammation in zebrafish with spatial transcriptomic analysis of samples from Crohn's disease patients. Although the data provided are clear and point to an anti-inflammatory role of GM-CSF, the strength of evidence remains incomplete as no mechanistic insights into GM-CSF regulation of ILCs are provided, and the most significant mechanistic question remains unanswered: what are the signals downstream of GM-CSF that maintain the ILC3 population? This work will be of interest to immunologists.

eLife Assessment

This is a useful study that seeks to elucidate the molecular mechanisms underlying spinal motor circuit assembly. The authors demonstrate that loss of Onecut transcription factors in spinal motor neurons affects the size and spatial distribution of pre-motor interneurons. However, the study in its current form is incomplete: the data and analyses do not fully support the main conclusion that Onecut acts through Neurotrophin-3 to regulate interneuron development in a non-cell autonomous manner. The work will be of broad interest to cell and developmental biologists.

eLife Assessment

This important study examines how chronic pain and opioid exposure interact at the cellular and molecular levels in a reward-related brain region. Using single-nucleus RNA sequencing, the authors map transcriptional changes in the rat ventral tegmental area following chronic inflammatory pain and acute morphine exposure. Notably, their convincing data support that acute morphine, not chronic pain, elicits a stress-related transcriptional response primarily in glial cells rather than neurons, challenging prevailing views of opioid action and supporting growing evidence for glucocorticoid signaling in glial responses. A limitation is the use of a single opioid dose and time point, and further discussion of these constraints would help clarify the broader implications of the findings.

eLife Assessment

The authors developed and validated a gut-on-chip system to mimic the gut environment for studies of Clostridioides difficile infection in vitro. Although the data generated is useful to the field, the evidence provided to support the conclusions is incomplete. Methodology that is not complete, as well as discrepancies regarding the proposed mode of action of lipoxin A4, are significant weaknesses.

eLife Assessment

This valuable study reports a substantial single-cell RNAseq and bulk RNAseq dataset from multiple high-grade serous ovarian cancers, including a single-cell atlas of human fallopian tube epithelium. The bioinformatic analysis investigating the lineage and location of epithelial progenitor cells is convincing, although this will require experimental validation. The work also provides a resource to examine additional features of normal fallopian tubes and ovarian cancers, and for developing methods for early detection and tumour stratification.

eLife Assessment

This study presents important findings that bovine mammary epithelial cells can be infected with both avian and human influenza A viruses, providing a potential site for viral reassortment. The evidence to support these claims is generally solid; however, the evidence suggesting lower permissiveness of cells from other organs is incomplete. The work will be of interest to virologists and evolutionary biologists working on cross-species transmission of viruses and pandemic preparedness.

eLife Assessment

This study characterizes several novel activities of SARS-CoV-2 helicase nsp13, providing valuable insights into potentially new functions of this essential RNA-processing enzyme in the virus life cycle. However, the experimental evidence to support the authors' claims is incomplete. In addition, the placement of the polyhistidine affinity tag on nsp13 may cause artifacts, raising concerns about the interpretation of the results.

eLife Assessment

This useful study presents an improved protocol for long-term in vitro culture of Schistosoma mansoni that enables progression toward sexually dimorphic stages, representing a meaningful advance for studying parasite development and reducing reliance on animal models. The findings show that host-specific culture conditions support essential developmental and metabolic functions required for parasite maturation, although development remains delayed compared to in vivo conditions. The evidence is solid overall, but limited pairing efficiency and the absence of egg production indicate that the system does not yet fully recapitulate complete reproductive development.

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.