Evaluated articles

eLife Assessment

This valuable study is a companion to a paper introducing a theoretical framework and methodology for identifying Cancer Driving Nucleotides (CDNs). The evidence that recurrent SNVs or CDNs are common in true cancer driver genes is convincing, with more limited evidence that many more undiscovered cancer driver mutations will have CDNs, and that this approach could identify these undiscovered driver genes with about 100,000 samples.

eLife Assessment

This important study examined neuronal activity in the dentate nucleus of the cerebellum when monkeys performed a difficult perceptual decision-making task. The authors provide convincing evidence that the cerebellum represents sensory, motor, and behavioral outcome signals that are sent to the attentional system. This paper is of great general interest in that it shows the involvement of the cerebellum in cognitive processes at the neuronal level.

eLife Assessment

In this important study, Baniulyte and Wade provide convincing evidence that translation of a short ORF denoted toiL positioned upstream of the topAI-yjhQP operon is responsive to different ribosome-targeting antibiotics, consequently controlling translation of the TopAI toxin as well as Rho-dependent transcription termination. Strengths of the study include combining a genetic screen to identify 23S rRNA mutations that affect topA1 expression and a creative approach to map the different locations of ribosome stalling within toiL induced by different antibiotics, with ribosome profiling and RNA structure probing by SHAPE to examine consequences of different antibiotics on toiL-mediated regulation. The work leaves unanswered how bacteria benefit by activating expression of the genes using the proposed strategy and the mechanism underlying ToiL's sensing of structurally distinct antibiotics.

eLife Assessment

How secretion is regulated during cell division and how membrane trafficking factors cooperate with the cytoskeleton during cell division remain poorly understood. In this work the authors find protein-protein interactions and localization dependencies between the polymeric septin cytoskeleton and the exocyst complex, using fission yeast as a model organism and using alphafold 3 based structural predictions. The work provides a valuable body of new information that will be of great interest to the cell biology community. The evidence is solid and provides the authors and the community a framework to test if the identified interfaces reflect bona fide interaction sites in vivo and in vitro in future.

eLife Assessment

The study reports an important finding on the role of the global metabolic regulator Crp/cAMP in the formation of antibiotic persister Escherichia coli. The evidence supporting the claims is solid including metabolomic analysis and characterization of many mutant strains.

eLife Assessment

This useful study examined the associations of a healthy lifestyle with comprehensive and organ-specific biological ages defined using common blood biomarkers and body measures. Its large sample size, longitudinal design, and robust statistical analysis provide solid support for the findings, which will be of interest to epidemiologists and clinicians.

eLife Assessment

This study provides compelling data regarding the molecular characterization of a rare tumor type with few treatment options. This fundamental work significantly advances our mechanistic understanding of solitary fibrous tumours, a critical first step towards targeted precision medicine approaches. The results of this study will be of broad interest to cancer biologists and experimental oncologists.

eLife Assessment

This manuscript presents an important machine-learning-based approach to the automated detection of urine and fecal deposits by rodents, key ethological behaviors that have traditionally been very poorly studied. The strength of evidence for the claim is solid, showing accuracy near 90% across several contexts. Training and testing for the specific contexts used by other experimenters, however, is probably warranted to make the model most relevant to the data that may be analyzed.

eLife Assessment

This important paper introduces a theoretical framework and methodology for identifying Cancer Driving Nucleotides (CDNs), primarily based on single nucleotide variant (SNV) frequencies. A variety of solid approaches indicate that a mutation recurring three or more times is more likely to reflect selection rather than being the consequence of a mutation hotspot. The method is rigorously quantitative, though the requirement for larger datasets to fully identify all CDNs remains a noted limitation. The work will be of broad interest to cancer geneticists and evolutionary biologists.

eLife Assessment

Glioblastoma is among the most aggressive cancers without a cure, and its cells are characterized by high mitochondrial membrane potential. This manuscript provides convincing evidence that glioblastoma tumorigenesis is closely linked to mitochondrial stress. The study makes a valuable contribution to the field by advancing our understanding of the metabolic mechanisms driving glioblastoma and highlighting potential therapeutic targets.

eLife assessment

This study provides valuable information about the microbiome and metabolome, and their correlation with acute myocardial infarction. However, the relationship established between these variables is limited to a correlation, and therefore the strength of the evidence is incomplete.

eLife Assessment

This valuable study addresses the growing threat of multi-drug-resistant (MDR) pathogens by focusing on the enhanced efficacy of colistin when combined with artesunate and EDTA against colistin-resistant Salmonella strains. The evidence is solid, supported by comprehensive microbiological assays, molecular analyses, and in vivo experiments demonstrating the effectiveness of this synergic combination.

eLife Assessment

This important study by Lee et al. explores the heterogeneous response of non-growing bacteria to the antimicrobial peptide (AMP) tachyplesin. The authors identify a subpopulation of cells that evade lethal damage by limiting the intracellular accumulation of a fluorescently labeled tachyplesin analog. The study provides compelling evidence that reduced drug accumulation underlies the decreased susceptibility of this subpopulation to the AMP. The molecular basis of this phenotype is well supported by the data.

eLife assessment

This manuscript describes an unexpected role of cellular caspases in cleaving Drp1, a protein involved in mitochondrial fission, in virus-infected cells. Drp1 cleavage augments mitochondrial fission, reinforcing MAVS-dependent type-1 IFN response against multiple viruses. The findings presented in this manuscript are important and the strength of evidence is solid. Additional studies may allow for more robust mechanistic substantiation of the proposed model.

eLife Assessment

In this valuable report, the authors investigated the effect of mitochondrial transplantation on post-cardiac arrest myocardial dysfunction (PAMD), which is associated with mitochondrial dysfunction. They convincingly demonstrated that mitochondrial transplantation enhanced cardiac function and increased survival rates after the return of spontaneous circulation (ROSC). They have also shown that myocardial tissues with transplanted mitochondria exhibited increased mitochondrial complex activity, higher ATP levels, reduced cardiomyocyte apoptosis, and lower myocardial oxidative stress post-ROSC.

eLife assessment

Feeding, the circadian rhythm, and the gut microbiota are all intimately linked, motivating new approaches to identify causal relationships while minimizing confounding factors. The authors employ an innovative combination of the stool softener lactulose and a defined 3-member gut microbiota to acutely induce gut bacterial metabolism in mice during the daytime, resulting in changes in the ileal expression of clock genes and altered feeding behavior. Together, this study utilizes solid methods to provide important new insights into the role of gut microbiota in the circadian rhythm, setting the stage for follow-on studies aimed at better understanding the mechanisms responsible.

eLife assessment

This study provides novel insights into COVID-19 immune responses by using the delta of the normalised accessible surface area (DASA) to map IgM responses to the SARS-CoV-2 Membrane protein M1-subtype across multiple European cohorts. The evidence supporting the findings is solid, with thorough validation and comprehensive analysis, although additional clarity on T-independent B cell reactions and the impact of comorbidities would further strengthen the conclusions. The methods and data presented are valuable for advancing diagnostic and prognostic tools for COVID-19, particularly in the context of long COVID.

eLife Assessment

Masroor Ahmad Paddar and colleagues reveal noncanonical roles of ATG5 and membrane ATG8ylation in regulating retromer assembly and function. They identify ATG5's unique non-autophagic role and show that CASM partially contributes to these phenotypes. Although the mechanism by which ATG8ylation regulates the retromer remains unclear, the findings provide important insights with solid supporting evidence.

eLife Assessment

This important work substantially advances our understanding of the molecular mechanisms underlying the timing of the initiation of metamorphosis of the Ciona ascidian tadpole larva. Through the combination of gene knockdown experiments and fluorescent molecular reporters the authors provide compelling evidence about a crosstalk between different G protein mediated signalling pathways and are able to place different signalling molecules within a signalling network. The work will be of interest to molecular, developmental and marine biologists and to scientists working on animal metamorphosis.