Evaluated articles

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 not 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 solid 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 solid. Its ecological design and sophisticated computational modeling are major strengths. The article would benefit from adding details on hypotheses, VR implementation, sample size determination, modeling, analysis, and pain specificity.

eLife Assessment

The study presents valuable theoretical insights by attempting to classify pattern-forming gene subnetworks and exploring their potential mechanisms. However, the results are incomplete, as they rely on oversimplified models, limited classifications, and assumptions that may not hold in more complex or realistic scenarios.

eLife Assessment

This work provides high-precision single-cell data on the relationship between DnaA activity and cell size, offering important insights for the field of cell cycle control. These findings motivate a novel and intriguing hypothesis for DNA replication initiation -the "extrusion model"- in which DNA-binding proteins modulate free DnaA availability in response to biomass-DNA imbalance. While the current indirect evidence does not fully establish the model, an experimental perturbation involving H-NS offers convincing support for its plausibility, laying the groundwork for future investigation.

eLife Assessment

This well-designed, valuable study uses isotope tracing to analyse how iron limitation alters TCA cycle metabolism in Mycobacterium tuberculosis, revealing potential antibiotic targets for non-replicating bacteria in the host. The findings provide insights into metabolic remodelling under iron-limited conditions. Whilst some of the evidence is solid, the data around the GABA shunt is incomplete, requiring genetic validation, as was done for the glyoxylate shunt. Questions remain about the underlying mechanisms and their specific role in M. tuberculosis pathogenesis.

eLife Assessment

This important paper reports the development of proteins and small molecules that induce degradation of a clinically-relevant oncogenic transcription factor, LMO2. The findings provide a proof of concept that PROTAC-type chemicals can be developed against intrinsically disordered proteins. The methods provide a blueprint for rational design of PROTACs starting from intracellular antibody paratopes. Overall, the paper is supported by solid evidence and will be of interest to chemical biologists and cancer pharmacologists.

eLife Assessment

This valuable work substantially advances our understanding of prognostic value of total gfDNA in gastric cancer. The evidence supporting the conclusions is solid, supported by a large, well-classified patient cohort and controlled clinical variables. The work will be of broad interest to scientists and clinical pathologist working in the field of gastric cancer.

eLife Assessment

This is a valuable computational study of odor responses in the early olfactory system of insects and vertebrates. The study addresses the question of how information about odor concentration is encoded by second-order neurons in the invertebrate and vertebrate olfactory system; it offers insights into the transformation of neural signals from receptors to second-order neurons. While reanalysis of published data presents solid evidence supporting compression of concentration information, incomplete analysis is provided to resolve how this observation could be reconciled with the need to preserve information about changes in stimulus intensity. This work will be of interest to neuroscientists studying sensory processing broadly and olfaction specifically.

eLife Assessment

This useful paper examined the mechanism of planar cell polarity (PCP) using Drosophila pupal wing, investigating how 'cellular level', 'molecular level' and 'tissue level' mechanisms intersect to establish PCP. This represents progress for the field and the conclusions are mostly backed up by solid data. Whereas the manuscript is sound overall, remaining concerns could be addressed by textual clarification of the concepts used in the manuscript.

[Editors' note: this paper was reviewed by Review Commons and revised by the authors.]

eLife Assessment

This manuscript reports a large series of experiments to investigate specific aspects of plant adaptation, leveraging genetic and genomic resources of Arabidopsis thaliana. The study provides convincing evidence for local adaptation in this highly selfing plant. This is an important dataset contributing to the developing understanding of non-linear selection in plants and beyond.

eLife Assessment

This manuscript presents an in-depth analysis of gene expression across multiple brown algal species with differing life histories, providing convincing evidence for the conservation of life cycle-specific gene expression. While largely descriptive, the study is an important step forward in understanding the core cellular processes that differ between life cycle phases, and its findings will be of broad interest to developmental and evolutionary biologists.

eLife Assessment

This valuable study provides a 3D standardised anatomical atlas of the brain of an orb-weaving spider. The authors describe the brain's shape and its inner compartments-the neuropils-and add information on the distribution of a number of neuroactive substances such as neurotransmitters and neuropeptides. Through the use of histological and microscopy methods the authors provide a more complete view of an arachnid brain than previous studies and also presents convincing evidence about the organisation and homology of brain regions. The work will serve as a reference for future studies on spider brains and will enables comparisons of brain regions with insects so that the evolution of these structures can be inferred across arthropods.