Evaluated articles

eLife Assessment

This important study reports insights into how the caspase Dcp-1, best known for cell death, can also promote tissue growth in Drosophila, extending the authors' earlier work by identifying regulatory factors that shape this non-lethal activity. The compelling findings identify a physical and functional interaction between Dcp-1 and Bruce, as well as new Dcp-1-interacting proteins that function in autophagy: Sirt1, Fkbp59, Debcl, Buffy, Atg2, and Atg8a. This work helps broaden the understanding of the non-lethal roles of Dcp-1.

eLife Assessment

This study presents a valuable advance by enabling functional mapping of Ca²⁺ responses in live human pancreatic tissue slices, providing new opportunities to study islet heterogeneity and diabetes-related dysfunction in an intact tissue context. The evidence supporting the main conclusions is solid, based on reproducible methodology and functional validation across multiple human donor samples. Key revisions needed include clearer quantification of transduction efficiency and tissue viability, and improved clarification of how CaMPARI2 signals should be interpreted.

eLife Assessment

This paper addresses valuable questions about the evolution of recombination landscape under domestication by examining recombination maps in domesticated chickens and their wild ancestor. However, despite employing a state-of-the-art deep learning method for recombination map inference, the lack of systematic benchmarking and presence of some unexpected patterns raise concerns about the reliability of the inferred maps, thus providing incomplete support for rapid evolution of recombination landscapes. Additionally, due to methodological limitations in testing for intra-genome correlations between evolutionary processes, the current evidence is inadequate to support the associations of recombination with selection and/or introgression in domesticated chickens.

eLife Assessment

Koch et al. describe a valuable novel methodology, SynSAC, to synchronise cells to analyse meiosis I or meiosis II or mitotic metaphase in budding yeast. The authors present convincing data to validate abscisic acid-induced dimerisation to induce a synthetic spindle assembly checkpoint (SAC) arrest that will be of particular importance to analyse meiosis II. The authors use their approach to determine the composition and phosphorylation of kinetochores from meiotic metaphase I and metaphase II that will be of interest to the broader meiosis research community.

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

eLife Assessment

This important study builds on previous work from the same authors to present a conceptually distinct workflow for cryo-EM reconstruction that uses 2D template matching to enable high-resolution structure determination of small (sub-50 kDa) protein targets. The paper provides convincing evidence that the density for small-molecule ligands bound to such targets can be reconstructed without these ligands being present in the template, and it provides an insightful quantification of the level of model bias that remains in the resulting reconstructions. The convenient visualisation of small molecules bound to protein targets of a known structure will be relevant for the pharmaceutical industry.

eLife Assessment

This landmark study is part of an impressive large-scale effort to assess the consistency of published findings in the field of Drosophila immunity. In this article, the authors report an analysis of claims made in approximately 400 research papers from the Drosophila immunity literature. The authors perform validation experiments to test a subset of the claims that are most inconsistent with current understanding in the field. These experiments do not necessarily aim to reproduce the original experiments, but instead to test the repeatability of the result using updated tools and methods. In some cases, the original claim is validated and in others it is not. The conclusions on the consistency of the claims, as presented in this paper, are based on mostly convincing evidence.

eLife Assessment

This paper represents a valuable contribution to our understanding of how local field potential (LFP) oscillations and beta band coordination between the hippocampus and prefrontal cortex of rats may relate to learning. Through a set of appropriate analyses, including oscillation-oscillation coupling, oscillation-spike modulation, and behavioral dependant measurements, the study presents convincing evidence for uncoupled beta activity between the two regions. This work will be of interest to researchers working on interaction of brain regions during spatial learning in rodents.

eLife Assessment

The authors combine a modeling approach, using a digital twin, with electrophysiological evidence in two species to assess the role of inhibition in shaping selectivity in the visual cortex. The results provide a fundamental advance beyond the classic view of sensory coding by proving compelling evidence that many neurons in visual areas exhibit dual-feature selectivity. Overall, the work compellingly showcases how in silico experiments can generate concrete hypotheses about neuronal coding that are difficult to discover experimentally.

eLife Assessment

This important study tackles the challenge of analyzing genome integrity and instability in unicellular pathogens by introducing a novel single-cell genomics approach. It presents compelling evidence that this new tool outperforms standard whole-genome amplification techniques and describes a method that shows promise for probing questions regarding the biology of Leishmania and other microbial eukaryotes.

eLife Assessment

This important study employs a closed-loop, theta-phase-specific optogenetic manipulation of medial septal parvalbumin-expressing neurons in rats and reports that disrupting theta-timescale coordination impairs performance of challenging aspects of spatial behaviors, while sparing hippocampal replay and spatial coding in hippocampal place cells. Technically rigorous experiments were performed, and solid evidence is provided to support the claims. The findings are expected to advance theoretical understanding of learning and memory operations and to provide practical implications for the application of similar optogenetic approaches.

eLife Assessment

This is a valuable study that investigates the role of the long non-coding RNA Dreg1 for the development, differentiation, or maintenance of group 2 ILC (ILC2). The authors generate Dreg1-/- mice and show solid evidence for a reduction of group 2 innate lymphoid cells (ILC2). However, the strength of evidence supporting and analysing the impact of Dreg1 on Gata3 expression, a transcription factor required for ILC2 cell fate decisions, remains incomplete. This study will be of interest to immunologists.

eLife Assessment

This important study combines anatomical tracing, tissue clearing, and functional manipulations to demonstrate lateralized brainstem control of hepatic glucose metabolism and identify a site of sympathetic nerve crossover supplying the liver. The evidence supporting the anatomical organization of hepatic sympathetic innervation is compelling, and the functional studies provide solid support for a role of asymmetric sympathetic outflow in regulating glucose homeostasis. While some uncertainty remains regarding the contribution of sensory innervation and the extent to which these findings generalize beyond mice, the work provides an invaluable advance in understanding neural regulation of liver metabolism.

eLife Assessment

In this valuable study, the authors conducted an impressive amount of atomistic simulations with a glycosylated HIV-1 envelope glycoprotein (Env) trimer in a realistic asymmetric lipid bilayer. The aim was to probe how Env transmembrane domain, cytoplasmic tail, and membrane environment influence ectodomain orientation and antibody epitope exposure. The simulations convincingly show that ectodomain motion is dominated by tilting relative to the membrane and explicitly demonstrate the role of membrane asymmetry in modulating the protein conformation and orientation, and the results are contextualized well in the revised version. Additional analyses of the authors' deposited MD trajectories could serve as invaluable extensions of this work to probe, for example, for exposure of cryptic epitopes and potential allosteric coupling.

eLife Assessment

This study provides a useful application of computational modelling to examine how people with chronic pain learn under uncertainty, contributing to efforts to link pain with motivational processes. However, the evidence supporting the main claims is incomplete, as the modelling differences are not reflected in observable behaviour or pain measures, and the interpretation extends beyond what the data can substantiate. The conclusions would benefit from a clearer explanation of the behavioural differences that underlie the computational findings.

eLife Assessment

This important study establishes an environmental sampling workflow for the discovery of bacteriophages capable of infecting antibiotic-resistant pathogens. The authors convincingly demonstrate the effectiveness of the approach, even with the limited sampling scheme and the current challenges in viral taxonomy. This study will interest researchers working on bacterial infections, environmental microbiology, and phage-based alternatives for addressing antimicrobial resistance.

eLife Assessment

This important study uses an optimized IOR-Stroop fMRI paradigm to dissociate integration and segregation processes and to show that attentional orienting modulates conflict processing at both the semantic and response levels. The evidence is compelling, supporting the integration-segregation theory of exogenous attention in inhibition of return while also deepening our understanding of how attentional orienting shapes downstream cognitive processing. The work will therefore be of broad interest to researchers in attention and cognitive control.

eLife Assessment

This important work contributes a transcriptional dataset that identifies potential genes involved in axon initial growth and axon regrowth, followed by a characterization of axon phenotypes after knockdown of a subset of these genes. Focused experiments on a single gene, Pmvk, highlight the potential role of the mevalonate pathway in axon regrowth. The methods are convincing, though partially incomplete. The data establish a basis for further studies on axonal development and will be of interest to both developmental neurobiologists and those seeking to develop molecular tools to target, monitor, and manipulate axon morphology and function.

eLife Assessment

This fundamental work shows that a history of cocaine self-administration disrupts the orbitofrontal cortex's ability to encode similarities between distinct sensory stimuli that possess identical task information - hidden states. The evidence supporting these conclusions is compelling, with methods and analyses spanning self-administration, a novel 'figure 8' sequential odor task, recordings from 3,881 single units, and sophisticated firing analyses revealing complex orbitofrontal representations of task structure. These results will be of broad interest to psychologists, neuroscientists, and clinicians.

eLife Assessment

This is a potentially important paper attempting to identify neutral correlates of memory engram expression in humans, and how they change during forgetting. The questions posed are clear and novel. The methods employed, namely behavioral analysis, high-resolution functional magnetic resonance imaging, and representational similarity analysis, are advanced, integrative, and appropriate. The experiments are well designed and combine analysis of recollection and familiarity of object/face associations. However, substantial questions remain as to the validity of the incomplete statistical analyses applied to the imaging data, as well as the parsing of and interpretation of the behavioral data.

eLife Assessment

This valuable study links psychological theories of chunking with a physiological implementation based on short-term synaptic plasticity and synaptic augmentation. The theoretical derivation for increased memory capacity via hierarchical chunking is solid. However, the model robustness and biological grounding of the mechanism - including many aspects that were hard-wired, chunking cues, and parameter ranges - as well as its evaluation in the task settings that motivated the study, are incomplete. Additional simulations to test robustness in more cognitively and biologically realistic settings, a systematic parameter analysis, and stronger links to prior work would substantially strengthen the manuscript and increase its impact across disciplines.