Evaluated articles

eLife Assessment

This valuable study shows the impact of the metabolic state of bacteria on phage infection. The experimental results, based on various phages infecting E. coli, are solid and consistent with a two-step adsorption mathematical model, although the detailed evidence supporting this model is currently incomplete. This study should be of interest to the communities working on cell metabolism and on host-pathogen interactions.

eLife Assessment

Zandvoort and colleagues describe respiration-brain coupling in the context of apnoea in human newborns. The authors have addressed an important question and supported their claims with solid data. The rigor of the findings could perhaps be further strengthened with some relatively minor changes to the analysis methodology.

eLife Assessment

This study presents valuable and compelling evidence that β-glucan-induced trained immunity can protect against intestinal inflammation by reprogramming innate immune cells toward a reparative phenotype. The authors employ a convincing combination of functional assays, adoptive transfers, and single-cell transcriptomics to uncover mechanistic insights and demonstrate the therapeutic potential of innate immune memory in IBD. While the work is robust, addressing the underlying epigenetic mechanisms and including additional controls would further reinforce the trained immunity-specific interpretation.

eLife Assessment

The authors addressed an important biological question, namely the role of glutamine metabolism in humoral responses, and they obtained solid conclusions. The strength of this study is that the authors used state-of-the-art transgenic mouse models together with in vitro analysis, thereby providing significant insights into the question posed. The following would strengthen the manuscript: i) adding more in-depth functionality/physiological relevance in the discussion part, and ii) regarding the experiments, the inclusion of more appropriate controls and a clearer and more accurate description of the methods.

eLife Assessment

This compelling work describes how the cell cycle-regulating phosphatase subunit, RepoMan, is regulated by the oxygen-dependent, metabolite-sensing hydroxylase PHD1. The characterisation of how proline hydroxylation alters signalling at the molecular and cellular level provides important evidence to enhance our understanding of how 2-oxoglutarate-dependent dioxygenases influence the cell cycle and mitosis.

eLife Assessment

This work characterizes the function and localization of SLC4A1 variants associated with distal renal tubular acidosis in human patients. Cell culture and limited animal studies provide partial but incomplete support to the authors' claim that the variants disrupt normal protein degradative flux by alkalinizing the intracellular pH. The study is valuable in providing preliminary evidence for future exploration of the link between intracellular pH regulation by SLC4A1 and kidney cell function in vivo.

eLife Assessment

This study presents a valuable comparison of the efficiency and precision of two prime editing methods to introduce single-nucleotide variants and longer exogenous DNA sequences into the zebrafish genome. Solid data support the conclusion that the PE2 prime editor Nickase is more effective at introducing single-nucleotide variants, while the PEn prime editor nuclease is more effective at integrating short sequences from 3 up to 30 base pairs, for both somatic and germline editing. The results will be of interest to the zebrafish community, in particular to model human disease variants in this model organism.

eLife Assessment

This valuable study demonstrates that it is possible to decode information about characters and locations from single-unit responses in the human brain to a narrative movie, using a convincing technical approach to capture information in population-level dynamics. The study introduces an exciting dataset of single-unit responses in humans during a naturalistic and dynamic movie stimulus, with recordings from multiple regions within the medial temporal lobe. Using both a traditional firing-rate analysis as well as a population decoding analysis to connect these neural responses to the visual content of the movie, they show that in this dataset, the decoding of semantic scene features (e.g., the person currently on screen), but not scene transitions, is surprisingly driven by classically non-responsive neurons. Based on these findings, the authors argue that dynamic naturalistic semantic information may be processed within the medial temporal lobe at the population level.

eLife Assessment

This study presents valuable findings by demonstrating that specific GPCR subtypes induce distinct extracellular vesicle miRNA signatures, highlighting a potential novel mechanism for intercellular communication with implications for receptor pharmacology within the field. The data is compelling, however, more evidence is needed to determine whether the distinct extracellular vesicle miRNA signatures result from GPCR-dependent miRNA expression or GPCR-dependent incorporation of miRNAs into extracellular vesicles.

eLife Assessment

This important study introduces an advance in multi-animal tracking by reframing identity assignment as a self-supervised contrastive representation learning problem. It eliminates the need for segments of video where all animals are simultaneously visible and individually identifiable, and significantly improves tracking speed, accuracy, and robustness with respect to occlusion. This innovation has implications beyond animal tracking, potentially connecting with advances in behavioral analysis and computer vision. The strength of support for these advances is compelling overall, although there were some remaining minor methodological concerns.

eLife Assessment

This useful study presents interesting observations on the potential importance of extracellular transport of human papillomaviruses along actin protrusions by retrograde flow. The focus on the events of HPV infection between ECM binding and keratinocyte-specific receptor binding is unique and interesting. However, the evidence supporting the conclusions is incomplete, and additional experimental support is needed. Because conclusions drawn regarding HS interactions are largely based on experiments using a single HS mAb, the specificity of this mAb needs to be described in more detail, either based on the literature or further experimentation.

eLife Assessment

The authors collected time-course RNA-seq data from four tree species in natural environments and analyzed seasonal patterns of gene expression. This fundamental study substantially advances our understanding of how seasonal environments shape gene expression. The evolutionary effects of seasonal environments on gene expression are rarely studied at this scale and the dataset is extensive. The evidence supporting the conclusions is compelling, with caveats and limitations clearly described. The work will be of broad interest to colleagues studying evolution and gene expression.

eLife Assessment

The study provides valuable technical advances to generate and isolate neural rosettes. The technique is robust, as indicated by both reviewers. The evidence is solid, as shown in orthogonal characterization by flow cytometry, morphology, and scRNA-seq. Comparison with the manual-rosette-picking protocol will enhance the validity of the claims.

eLife Assessment

This valuable study provides outlines the mechanism by which repeated vaccination broadens the breadth of antibody responses against epitope unmatched virus strains. The authors' mathematical model is solid and incorporates various parameters that regulate B cell activation and antibody response.

eLife Assessment

Cryptovaranoides, a Late Triassic animal (some 230 Ma old), was originally described as a possibly anguimorph squamate, i.e., more closely related to snakes and some extant lizards than to other extant lizards, making Squamata much older than previously thought and providing a new calibration date inside it. Following a rebuttal and a defense, this fourth important contribution to the debate makes a convincing argument that Cryptovaranoides is not a squamate. Further comparisons to potentially closely related animals such as early lepidosauromorphs would greatly benefit this study, and parts of the text require clarification.

eLife Assessment

This important study presents a sequence-based method for predicting drug-interacting residues in intrinsically disordered proteins (IDPs), addressing a significant challenge in understanding small-molecule:IDP interactions. The findings have solid support through examples underscoring the role of aromatic interactions. While predicted binding sites remain coarse, validation was done on a total of 10 IDPs at varying depths. The method builds on the authors' previous work and, with ad hoc modifications, is poised to benefit this emerging field.

eLife Assessment

This fundamental work provides solid evidence that advances our understanding of the physical mechanisms underlying bacterial cell division by examining the role of membrane tension and FtsZ condensation in sequential stages of division. The effect of accDA overexpression on membrane tension was carefully characterized. To further enhance rigor, the authors could consider examining orthogonal perturbations to membrane tension, addressing membrane tension vs. fluidity, and addressing the ability of FtsZ to bend membranes in cells.

eLife Assessment

This important study presents the rational redesign and engineering of interleukin-7. The data from the integrated approach of using computational, biophysical, and cellular experiments are convincing. This paper is broadly relevant to those studying immunomodulation using biologics.

eLife Assessment

This study examines an important question regarding the developmental trajectory of neural mechanisms supporting facial expression processing. Leveraging a rare intracranial EEG (iEEG) dataset including both children and adults, the authors reported that facial expression recognition mainly engaged the posterior superior temporal cortex (pSTC) among children, while both pSTC and the prefrontal cortex were engaged among adults. In terms of strength of evidence, the solid methods, data and analyses broadly support the claims with minor weaknesses.

eLife Assessment

This work presents a useful investigation of functional and structural brain changes following navigation and verbal memory training. The analyses of whole-brain volumetric changes are convincing and support the study's main conclusion regarding the lack of a volumetric whole-brain plasticity effects. Some analyses are compelling in demonstrating the presence of longitudinal behavioural effects, the presence of functional activation changes, and the lack of hippocampal volume changes.