Evaluated articles

eLife Assessment

The study presents a valuable conceptual framework by classifying pattern-forming gene subnetworks into three established categories. However, the supporting evidence remains incomplete, as the mathematical generalizations rely on simplified 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 evidence is solid, providing insights into metabolic remodelling under iron-limited conditions.

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.

eLife Assessment

This study presents valuable findings and employs modern analytical approaches on how transient absence of visual input (darkness) affects tactile encoding in the rat somatosensory cortex (S1). The evidence supporting the authors' claims is solid, as population-level neural activity recorded in S1 and decoded by a CNN carries more discriminable texture information in darkness. The underlying basis of this effect remains only partly resolved, however, because it is still unclear which neural features from the CNN drive the decoding and if visual interference is appropriately accounted for, which might confound true neural representational change.

eLife Assessment

This important study provides evidence for dynamic coupling between translation initiation and elongation that can help maintain low ribosome density and translational homeostasis. The authors combine single-molecule imaging with a new approach to analyze mRNA translation kinetics using Bayesian modeling. This work is overall solid and will be of interest to those studying translational regulation.

eLife Assessment

This valuable study provides convincing evidence that MgdE, a conserved mycobacterial nucleomodulin, downregulates inflammatory gene transcription by interacting with the histone methyltransferase COMPASS complex and altering histone H3 lysine methylation. This work will interest microbiologists as well as cell and cancer biologists.

eLife Assessment

This study describes a genetic screen to identify deubiquitinases (DUBs) that counteract the activity of small molecule degraders (PROTACs). The presented data is valuable, identifying OTUD6A and UCHL5 as DUBs that impact the efficacy and potency of PROTAC-mediated degradation in distinct subcellular compartments. While the conclusions are broadly supported and the methods employed are solid, the validation of OTUD6A and UCHL5 mechanisms requires additional study. Overall, these findings merit further evaluation by the targeted protein degradation community when developing and optimizing PROTACs and efforts to achieve compartment-specific degradation.

eLife Assessment

This important study identifies a plant-derived metabolite, betulin, as an effective natural insecticide against aphids and uncovers its specific molecular target. The evidence is compelling, combining greenhouse and field efficacy trials with rigorous molecular, genetic, and electrophysiological approaches that converge on a conserved binding site in the aphid GABA receptor. While additional work is needed to fully assess potential off-target effects and ecological safety, the study provides a strong mechanistic foundation. These findings will be of interest to researchers in plant biology, chemical ecology, and sustainable pest management.

eLife Assessment

This manuscript reports a high-quality genome assembly of the European cuttlefish, Sepia officinalis, a representative species of the Cephalopod lineage. This solid work relies on current best practices in genome sequencing and assembly, combining PacBio HiFi long reads and Hi-C chromatin conformation capture, and on state-of-the-art comparative genomic analyses, including chromosome number evolution and analyses of expanded gene families. The resulting genome will be a valuable resource for researchers interested in cuttlefish biology and comparative genomics in general.

eLife Assessment

This important study advances our understanding of how cellular quality control machinery influences cystic fibrosis (CF) drug responsiveness by systematically analyzing the effects of the chaperone calnexin on more than two hundreds of CFTR (cystic fibrosis transmembrane regulator) variants. The evidence supporting the conclusions is convincing, with a comprehensive deep mutational scanning methodology and rigorous quantitative analysis. The findings reveal that calnexin is critical for both CFTR protein expression and corrector drug efficacy in a variant-specific manner, providing invaluable insights that could guide the development of personalized CF therapies. This work will be of significant interest to researchers in protein folding, CF drug development, and genetic disease therapeutics.

eLife Assessment

In this important contribution, Yan and colleagues describe a powerful and compelling strategy to generate concatamers of the BK channel and their fusion constructs with the auxiliary gamma subunits, which allows exploring contributions of individual subunits of the tetrameric channel to its gating and the study of heteromeric channel complexes of defined composition. Distinct examples are presented, which illustrate great diversity in the stoichiometric control of BK channel gating, depending on the site and nature of molecular perturbations. The molecular approaches could be extended to other membrane proteins whose N and C termini face opposite sides of the membrane.

eLife Assessment

This is a valuable study that explores the role of the conserved transcription factor POU4-2 in the maintenance, regeneration, and function of planarian mechanosensory neurons. The authors present convincing evidence provided by gene expression and functional studies to demonstrate that POU4-2 is required for the maintenance and regeneration of mechanosensory neurons and mechanosensory function in planarians. Furthermore, the authors identify conserved genes associated with human auditory and rheosensory neurons as potential targets of this transcription factor.

eLife Assessment

This study demonstrates the cartilage-protective effects of osteoactivin in inflammatory experimental models. The work offers valuable insights advancing current knowledge regarding regulation of joint inflammation and tissue degeneration. The evidence provided is compelling and suggests that osteoactivin may serve as a promising therapeutic target for inflammatory joint diseases.