Evaluated articles

eLife Assessment

This is a valuable study that combines biophysical and evolutionary approaches to understand why particular mutations in the SARS-CoV-2 protein N arose during the COVID-19 pandemic. The evidence is solid and supports the conclusions.

eLife Assessment

The study reports a potential pathway for isoleucine biosynthesis mediated by the underground activity of AHASII, which converts glyoxylate and pyruvate to 2-ketobutyrate. While the findings are valuable in revealing a possible alternative route for isoleucine production, the evidence presented remains incomplete. More comprehensive biochemical experiments are required to substantiate the physiological feasibility of this pathway.

eLife Assessment

This fundamental study provides the first genome-wide characterization of H3K115 acetylation and identifies a striking and previously unappreciated association of this globular-domain histone modification with fragile nucleosomes at CpG island promoters, active enhancers, and CTCF binding sites. While the work is largely descriptive and correlative in nature the evidence is compelling. The authors present multiple, orthogonal genomic and biochemical analyses that consistently support their central conclusions.

eLife Assessment

This important manuscript evaluates how sample size and demographic balance of reference cohorts affect the reliability of normative models. The evidence supporting the conclusions is convincing. This work will be of interest to clinicians and scientists working with normative models.

eLife Assessment

This valuable study compares auditory cortex responses to sounds and cochlear implant stimulation measured with surface electrode grids in rats. Beyond the reduced frequency resolution of cochlear implants observed previously, this study suggests key discrepancies between neuronal representations of cochlear stimulations and natural sounds. The evidence for this result is solid but could be strengthened with a clarification of the methodology and an adaptation of the claim to the actual precision of the measurements. This study is of interest to researchers in the auditory neuroscience field and clinicians implementing treatments with cochlear implants.

eLife Assessment

This important study shows that visual search for upright and rotated objects is affected by rotating participants in a VR and gravitational reference frame. However, the evidence supporting this conclusion is incomplete, given the authors' use of normalized response time and the assumption that object recognition across rotations requires mental rotation.

eLife Assessment

This important study uses simultaneous EEG and fMRI recordings to shed light on the relationship between alpha and gamma oscillations and specific cortical layers. The sophisticated methodology provides solid evidence for correlations between oscillatory power and the strength and contents of fMRI signals in different cortical layers, though some caveats remain. This paper will be of interest to neuroscientists studying the role and mechanisms of alpha and gamma oscillations.

eLife Assessment

This paper presents an important theory and analysis of the role of neurogenesis and inhibitory plasticity in the drift of neural representations in the olfactory system. For one of the findings, regarding the impact of neurogenesis on the drift, the evidence remains incomplete. The reason lies in the differences in variability/drift of the mitral/tufted cell responses observed in the model compared to experimental observations, where these responses remain stable over extended time scales.

eLife Assessment

This study provides important results with regard to the ongoing debate of the relationship between internalizing psychopathology and learning under uncertainty. The methods and analyses are solid, and the results are backed by a large sample size, yet the study could still benefit from a more detailed discussion about the difference in experimental design and analysis compared to previous studies. If these concerns are addressed, this study would be of interest to researchers in clinical and computational psychiatry for the behavioral markers of psychopathological symptoms.

eLife Assessment

This important study uses innovative microfluidics-based single-cell imaging to monitor replicative lifespan, protein localization, and intracellular iron levels in aging yeast cells. The evidence for the proposed role of Ssd1 and reduced nutrients for lifespan through limiting iron uptake is convincing, even though some mechanistic details remain unclear. This work will be of interest to cell biologists working on aging and iron metabolism.

eLife Assessment

The authors describe an interesting approach to studying the dynamics and function of membrane proteins in different lipid environments. The fundamental findings have theoretical and practical implications beyond the study of EGFR to all membrane signalling proteins. The evidence supporting the conclusions is compelling, based on the use of a nanodisk system to study membrane proteins in vitro, combined with state-of-the-art single-molecule FRET. The work will be of broad interest to cell biologists and biochemists.

eLife Assessment

This interesting study adapts machine learning tools to analyze movements of a chromatin locus in living cells in response to serum starvation. The machine learning approach developed is useful, the experiments are well controlled, and the data are solid. The study would be greatly strengthened by testing key predictions made using perturbation experiments. This work will be of interest to those studying chromosome biology and gene expression patterns.

eLife Assessment

The present study employed transcriptomics to investigate the impact of methionine restriction (MR) and cold exposure (CE) on liver and adipose tissues in mice. The authors demonstrate that responses to MR and CE are tissue-specific, while both MR and CE have a similar effect on beige adipose tissue. While these findings are somewhat descriptive, this work is considered important, as it provides a comprehensive resource for enhancing our understanding of these lifestyle interventions. The study is of high scientific quality, and the analyses are convincing.

eLife Assessment

This useful study investigates how intrinsically disordered domains can interact to dictate the sub-cellular localization of a major innate immune sensor termed cGAS. The data from various cellular and biochemical assays are mostly solid, but the main conclusions from these experiments need to be validated further. This paper is relevant to immunologists, especially those interested in cytosolic DNA-sensing pathways.

eLife Assessment

In this valuable study, through carefully executed and rigorously controlled experiments, the authors challenged a previously reported role of the Death Receptor 6 (DR6/Tnfrsf21) in Wallerian degeneration (WD). Using two DR6 knockout mouse lines and multiple WD assays, both in vitro and in vivo, the authors provided convincing evidence that loss of DR6 in mice does not protect peripheral axons from WD after injury, at least in the specific contexts of the mice and analyses performed in this study. Due to the lack of certain specific parameters from previous studies (sex, age, mouse strains etc.), the exact reasons underlying the observed inconsistencies between current and previous reports on the protective effects of DR6 remains to be determined. Overall, this is a carefully executed study providing invaluable information toward understanding DR6's role (or lack thereof) in axon degeneration.

eLife Assessment

In their study, Brown et. al. provide an important advance in understanding the architecture of the mycobacterial outer membrane. Using all-atom simulations of model mycomembranes, the work reports compelling structural insights into how α-mycolic acids and outer leaflet lipids (PDIM and PAT) shape membrane organisation. The work revealed membrane heterogeneity with ordered inner leaflets and disordered outer leaflets that provide a molecular explanation for the resilience of the mycobacterial envelope.

eLife Assessment

This useful study introduces a computational pipeline for designing RNA in situ fluorescence hybridization probes that could improve the sensitivity and specificity of RNA detection in cells. While the approach is novel and the preliminary data suggestive, the evidence supporting a clear advantage over existing probe design strategies is incomplete. The work will be of interest to researchers developing or using molecular tools for imaging RNA in cells.

eLife Assessment

This important study addresses the timely and interesting question of how itaconate generation emerged in evolution, using taxonomic analysis of the gene and enzyme cis-aconitate decarboxylase (CAD). The authors provide solid evidence identifying three CAD branches in metazoans and showing that the early metazoan paleo-form indeed generates aconitate and is already linked to innate immunity. They further provide limited evidence suggesting that taxonomic differences in subcellular localisation of this enzyme may allow for innate immune signalling without compromising cellular energetics. The implications of the study will be of high interest to the field of innate host defence and immunometabolism.

eLife Assessment

This set of experiments provides important knowledge for how the infralimbic cortex is recruited to inhibit behavior after extinction training. The evidence supporting the conclusions is convincing with multiple sophisticated behavioral designs providing converging lines of evidence, though reviewers note possible alternative interpretations and limitations of small group sizes in some cases. This work will be of interest to those interested in cortical function, learning and memory, aversive behavior, and/or related psychiatric factors.

eLife Assessment

The paper presents a valuable finding that the human brain and models that incorporate sentence structures can capture sentence-level semantics beyond word meaning, while large language models behave differently. The evidence supporting the authors' claims is solid, though the stimuli are highly controlled and some analyses could be more thorough. This work will be of interest to researchers in language neuroscience and those developing language models.