Evaluated articles

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 reports the characterization of newly identified genetic variants of SLC4A1 in patients with distal renal tubular acidosis. Cell culture studies supplemented with histological analysis of a previously established disease mouse model provide convincing evidence that some of the variants increase intracellular pH, reduce ATP synthesis, and attenuate autophagic degradative flux. The study is valuable in establishing a mechanistic framework for future exploration of the link between intracellular pH and mutations in SLC4A1 in vivo.

eLife Assessment

This study presents a 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. Convincing 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 sequences from 3 up to 46 base pairs, for both somatic and germline editing. The results will be valuable for 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 evidence is solid, however, more experiments are 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, which is supported through compelling evidence, has implications beyond animal tracking, potentially connecting with advances in behavioral analysis and computer vision.

eLife Assessment

This study provides valuable insight into the role of actin protrusions in mediating early pre-endoyctic steps of human papillomavirus entry at the cell surface. Using state-of-the-art microscopy in an immortalized keratinocyte model, the authors present convincing evidence that filopodia actively promote the transfer of heparin sulfate-coated virions from the extracullar matrix to the viral entry factor CD151. These findings provide a strong framework for future studies aimed at further resolving the dynamics of virion transfer and receptor engagement.

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.

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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.

eLife Assessment

The authors developed a fundamental computational method, which is intended to automatically process bioluminescence imaging-derived tumour images across anatomical regions and over time. This allows quantitative analysis of such data, and the authors applied it to describe the spatiotemporal distribution of tumour cells in response to CD19-targeted CAR-T cells that contained either CD28 or 4-1BB costimulatory domains. Some operational limitations were identified, which relate to the pipeline's reliance on predefined regions of interest instead of aligning signal sites with anatomical information, scaling, and limitations in taking animal pose into account. Overall, the authors provide compelling evidence for the functionality of their computational approach towards automated analysis of bioluminescence imaging data, while applying it to a current topic of wide interest in cell therapy research.

eLife Assessment

This important study investigates changes in oscillatory activity across cortical and subcortical areas during stroke recovery in a nonhuman primate model. The authors distinguish between global and local oscillatory bursts, providing solid evidence that these two types of bursts correlate with distinct aspects of movement; additionally, they show that the likelihood of these bursts occurring follows opposing trends during recovery. The study could be further improved by accounting for inter-individual differences and by some technical improvements, such as employing more robust burst detection methods and more stringent analyses.

eLife Assessment

This manuscript describes convincing and very interesting findings that substantially advance our understanding of a major research question on the role of Cx32 hemichannels in the Schwann cell paranode. It provides an interdisciplinary integration of imaging, in silico approaches, and functional data. This important study proposes a new mechanism with profound physiological relevance and provides new insights into glial modulation of electrical conduction in sensory/motor myelinated nerves.

eLife Assessment

The article presents important findings of a dissociation between phasic and tonic pain functions in adaptive behavior, combining immersive VR, computational modeling, skin conductance, and EEG data. The methodology used is convincing. Its ecological design and sophisticated computational modeling are major strengths.