Evaluated articles

eLife Assessment

Using a transposon sequencing (TN-seq) approach, the authors identified key genetic determinants of drug tolerance in Mycobacterium abscessus. Given that M. abscessus is inherently resistant to multiple antibiotics, this valuable study makes a significant contribution by uncovering how antibiotic tolerance is linked to reactive oxygen species (ROS) in this non-tuberculous mycobacterial (NTM) species. The solid findings further strengthen the growing evidence that ROS play a central role in the mechanism of antibiotic action and tolerance in mycobacteria. However, the manuscript would benefit from improved clarity of presentation and corrections in the reference section.

eLife Assessment

This paper provides important insight into how early life experience shapes adult behavior in fruit bats. The authors raised juvenile bats either in an impoverished or enriched environment and studied their foraging behaviors. The evidence is convincing that bats raised in enriched environments are more active, bold, and exploratory. The work will be of interest to ethologists and developmental psychologists.

eLife Assessment

This important study provides new insights into the lesser-known effects of the sodium-potassium pump on how nerve cells process signals, particularly in highly active cells like those of weakly electric fish. The computational methods used to establish the claims in this work are compelling and can be used as a starting point for further studies.

eLife Assessment

This manuscript describes the generation of a fused dorsal-ventral organoid system to model interactions between the cortex and striatum to study the onset and progression of Huntington's disease (HD) and other neurodegenerative disorders. While this approach is valuable, further methodological and analytical work is needed to fully support the interpretations and claims of the authors. Incomplete evidence suggests choroid plexus (ChP) abnormalities form a significant component of HD pathogenesis.

eLife Assessment

This valuable work explores how synaptic activity encodes information during memory tasks. All reviewers agree that the work is of very high quality and that the methodological approach is praiseworthy. Although the experimental data support the possibility that phospholipase diacylglycerol signaling and synaptotagmin 7 (Syt7) dynamically regulate the vesicle pool required for presynaptic release, a concern remains that the central finding of paired-pulse depression at very short intervals could be due to a mechanism that does not depend on exocytosis, such as Ca²⁺ channel inactivation, rather than vesicle pool depletion. Overall, this is a solid study although the results still warrant consideration of alternative interpretations.

eLife Assessment

In this important study, the authors provide compelling evidence that the likelihood of looking behaviour is predicted by the expected information gain, hence constituting an invaluable formal model and explanation of habituation. Such modelling represents a crucial advance in explanation, over-and-above less specified models that can be fitted post hoc to any empirical pattern. The findings would be of interest to researchers studying cognitive development, and perception and learning more broadly.

eLife Assessment

This important study presents the development of a novel inhibitor for SARS-CoV-2 Mac1 that has potential utility both as an antiviral therapeutic and as a tool for probing the molecular mechanisms by which infection-induced ADP-ribosylation triggers robust host antiviral responses. Though minor gaps in understanding the compound's precise molecular mechanism of action and its ability to target Mac1 from other coronaviruses remain, the evidence for its effects on SARS-CoV-2 in relevant biological models is compelling.

eLife Assessment

This important theoretical study examines the possibility of encoding genomic information in a collective of short overlapping strands (e.g., the Virtual Circular Genome (VCG) model). The study presents convincing theoretical arguments, simulations and comparisons to experimental data to point at potential features and limitations of such distributed collective encoding of information. The work should be of relevance to colleagues interested in molecular information processing and to those interested in pre-Central Dogma or prebiotic models of self-replication.

eLife Assessment

This fundamental study examines infection of the liver and hepatocytes during tuberculosis infection. The authors convincingly demonstrate that aerosol infection of mice and guinea pigs leads to appreciable infection of the liver as well as the lung. A further strength of the study lies in clinical evaluation of the presence of tuberculosis bacteria in human autopsied liver samples from individuals with miliary tuberculosis and the presence of a clear granuloma-like structure, which will prompt further study.

eLife Assessment

This valuable study presents findings linking prophage carriage to lifestyle regulation in the marine bacterium Shewanella fidelis, with potential implications for niche occupation within a host (Ciona robusta) and mediation of host immune responses. The study leverages a unique animal model system that offers distinct advantages in identifying select phenotypes to present overall solid evidence that supports findings relating to the impact of a prophage on host-microbe interaction. Understanding the role of integrated lysogenic phages in bacterial fitness, both within a host and in the environment, is a significant concept in bacterial eco-physiology, potentially contributing to the success of certain strains.

eLife Assessment

This work describes a valuable method, SICKO, for real-time longitudinal quantification of bacterial colonization in the gut of individual C. elegans. The authors present convincing evidence to support the validity of the approach. SICKO provides an experimental framework that will enable progress in our understanding of host-microbe interactions.

eLife Assessment

This work is a valuable study that presents a detailed analysis of translation, driven by the untranslated regions of the Japanese encephalitis virus. It reports a role for the RNA helicase DDX3 in promoting a cap-independent translation mechanism. The conclusions are based on generally solid evidence, although there are some weaknesses in the overall model based on suboptimal experimental approaches and over-interpretation of some of the data. Addressing deficiencies noted in peer review could elevate the impact of the study.

eLife Assessment

This fundamental study uncovers the unique molecular features of Arabidopsis phloem companion cells that highly express FLOWERING LOCUS T (FT). These FT-expressing cells constitute a distinct subpopulation marked by elevated ATP biosynthesis and co-expression of small mobile proteins such as FLP1 and BFT, highlighting a fine balance between florigen and anti-florigen signals. Motif analyses and transgenic studies further identify NIGT1 transcription factors as direct, nitrogen-inducible repressors of FT, providing a mechanism for delayed flowering under nitrogen-rich conditions. Together, the compelling findings show that florigen-producing companion cells integrate energy metabolism, systemic protein signals, and nutrient-responsive repression to fine-tune the seasonal and nutritional regulation of flowering.

eLife Assessment

The manuscript provides an important assessment of the number and distribution of different retrovirus env genes present in primate genomes in the form of ancient endogenous retroviruses (ERV loci) and the potential role that viral recombination played in the diversification of retrovirus env genes and their propagation in the primate germline over millions of years. The paper convincingly describes how intermixing/recombination occurs with this viruses, representing a conceptual advance with potentially broad implications.

eLife Assessment

This important work substantially advances our understanding of reactive oxygen species (ROS) as a regenerative signal during postnatal cerebellum repair by activating adaptive progenitor reprogramming. The evidence supporting the conclusions is compelling, with rigorous genomic assays and in vivo analyses. This work will be of broad interest to biologists working on stem cells, neurodevelopment and regenerative medicine.

eLife Assessment

This study presents a valuable finding regarding the role of Arp2/3 and the actin nucleators N-WASP and WAVE complexes in myoblast fusion. The data presented is convincing, and the work will be of interest to biologists studying skeletal muscle stem cell biology in the context of skeletal muscle regeneration.

eLife Assessment

This valuable study sets new standards in analyzing the ultrastructure of insect eyes, which have long served as models for understanding how vision works. The way it describes an entire eye with the resolution of electron microscopy is convincing. On top of this, a miniaturized visual system provides additional, remarkable insights towards understanding optimized solutions.

eLife Assessment

The study evaluates the feasibility, safety, and tolerability of neoadjuvant radiotherapy followed by a CDK4/6 inhibitor (dalpiciclib) and hormonal therapy in treatment-naive patients with unilateral early-stage HR+/HER2- breast cancer. The findings are convincing, with a strong scientific rationale supported by integrated correlative studies. The trial is considered to be important as the outcomes could inform the design of larger, future studies. The limitations of the study have been acknowledged and outlined in this manuscript, which include only a small cohort of patients (n=12), which was not adequately powered to definitively assess the efficacy or safety of this combinatorial treatment approach.

eLife Assessment

This study provides important insights into how cryptic pockets play a role in shaping binding preferences of protein-nucleic acid interactions. By combining biochemical assays and state-of-the-art molecular dynamics simulations, mechanism underlying viral protein 35 (VP35) homologs to bind the backbone of double stranded RNA is presented. The evidence is compelling for molecular determinants that suggest two different dsRNA binding modes for VP35 and also underscores the evolutionary importance of these pockets.

eLife Assessment

This study provides an important and timely analysis of invasive and non-invasive Streptococcus pyogenes emm89 isolates, which have become a dominant serotype in the past decade. Using genome sequencing of 311 strains from Japan and comparing them with 666 global strains, the authors present compelling evidence in support of the identification of genetic factors linked to the invasive phenotype of emm89. The findings are both theoretically and practically significant in medical microbiology.