Evaluated articles

eLife Assessment

This study presents a useful database resource containing protein conformations generated through molecular dynamics simulations, with extensive quality evaluation and benchmarking. While the database is well-constructed and professionally organized, the evidence supporting its claimed representation of protein conformational landscapes is incomplete, as the short simulation times and starting structure bias prevent true Boltzmann sampling of the conformational space.

eLife Assessment

This study provides valuable insights into mitochondrial cristae organization in Plasmodium falciparum, particularly in the context of its divergent MICOS composition. The authors present convincing evidence, supported by phenotypic and morphological analyses, that cristae junction maintenance can be uncoupled from de novo cristae formation, reinforcing an emerging model of mitochondrial inner membrane organization. Notably, the absence of Mic10 alongside an enlarged and divergent MICOS complex highlights an intriguing evolutionary adaptation, although further characterization of the complex would strengthen the study's overall significance.

[Editors' note: this paper was reviewed by Review Commons.]

eLife Assessment

This study provides valuable insights into how cells maintain sphingolipid homeostasis through transcriptional control and regulated protein degradation in response to changes in sphingolipid levels. The evidence supporting the conclusions is convincing overall, with solid genetic and biochemical approaches, while some mechanistic aspects remain to be clarified. This work will be of interest to researchers studying lipid metabolism and membrane biology.

eLife Assessment

This study presents important findings on the molecular mechanisms governing how the natural killer cell receptor KIR2DL4 interacts with HLA-G and undergoes internalization. The authors provide solid evidence for an allosteric disulfide-bond switch that regulates receptor activity, using a multifaceted approach that includes mutagenesis, mass spectrometry, and imaging. The work would be further strengthened by validating these mechanisms in primary immune cells and providing direct structural evidence for the proposed ligand-binding interface.

eLife Assessment

This study provides a useful demonstration that, at least for the systems examined, aspects of the entropic contribution to protein-ligand binding can be inferred directly from crystallographic data. In doing so, it strengthens a view of crystal structures as heterogeneous ensembles that are amenable to statistical-mechanical analysis rather than purely static models. The analytical approaches are carefully developed and transparently discussed, with thoughtful consideration of both successful and less effective methods, lending solid support to the central conclusions. However, because the analysis is based on a relatively small and narrowly sampled set of protein-ligand complexes, the generality of these findings remains speculative and will require broader validation.

eLife Assessment

This study provides important insights regarding the temporal dynamics of dopamine across sleep/wake transitions in several brain areas. Using multi-site fiber photometry combined with EEG/EMG recordings, the study revealed heterogenous dynamics across both cortical and several subcortical areas. Although the evidence for these observations is solid, evidence for the proposed mechanisms driving DA dynamics is incomplete. Overall, the study may have a substantial impact on several fields working on the neurobiology of DA signaling.

eLife Assessment

This study provides direct and compelling evidence that lamellipodial protrusions dynamically adjust Arp2/3 complex incorporation in response to mechanical counterforces, while also modulating cellular responsiveness to upstream signals like Rac GTPase. By combining endogenous labeling, live-cell imaging, and optogenetic signaling activation, the work demonstrates how adhesion state and physicochemical perturbations reproducibly alter branched actin organization, offering a fundamental advance over previous works. The findings deliver significant insights that will resonate broadly with cell biologists and biochemists studying actin dynamics and mechanotransduction.

eLife Assessment

In this study, Yuan and colleagues perform transcriptomic and epigenomic experiments to study open chromatin regions and transcripts that change upon larval settlement in the sponge Amphimedon. The authors present compelling evidence to show that sponge larvae prepare for receiving an environmental cue (sunset) by extensively modifying their chromatin accessibility in the vicinity of genes that are going to be regulated during metamorphosis. The study represents a fundamental advance in understanding the fine genetic control of larval settlement and has significance beyond the immediate field of sponge larval biology.

eLife Assessment

The study presents important findings revealing previously unresolved conformational dynamics of the heterodimeric type IV ABC transporter TmrAB using single-molecule FRET. The evidence presented is solid, integrating careful experimental design with computational approaches to uncover states that are typically masked and difficult to detect. The work will be of interest to scientists studying the molecular mechanisms of primary active transport processes.

eLife Assessment

This large-scale comparative study of odorant receptor (OR) genes across more than 100 insect species, combining sequence- and structure-based approaches, aims to explore the evolution of this large gene family involved in the detection of odorant signals by olfactory neurons. This useful work uncovers a structural feature unique to the odorant receptor co-receptor Orco that reduces ligand binding affinity. However, the strength of evidence is incomplete: the pipeline for in silico identification of odorant receptor genes lacks validation through comparison with known odorant receptor repertoires from previously studied species, and claims regarding odor response spectra, evolutionary, and ecological interpretations are not fully supported by the analyses.

eLife Assessment

The study presents useful findings on the behavioral effects of nicotine exposure, suggesting the Drosophila larva as a potential model organism for studying underlying neural circuits. However, the evidence supporting the claims of the authors is incomplete and would benefit from more rigorous analysis and explanations. The study falls short of identifying the neural mechanisms and is therefore of interest to those with an interest in pharmacology and behavior.

eLife Assessment

This manuscript examines the evolution of molluscan shells using single-cell analyses of the adult mantle of Crassostrea gigas and compares these data with previous datasets from embryonic and larval stages of this species and other spiralians. The authors provide important support for a scenario in which secretory cells are broadly conserved across spiralians, and the incorporation of lineage-restricted genes contributes to the evolution of molluscan shells. While some of the conclusions of the authors are convincing, many aspects of the manuscript remain incomplete and could be improved, especially aspects of cell-type classification and validation.

eLife Assessment

This study presents a valuable perspective on platelet-mediated fibrin compaction, proposing that fibrin fibers undergo "winding" or coiling, an intriguing framework with potential implications for thrombosis and clot mechanics. However, the evidence supporting an active platelet-driven winding mechanism remains incomplete, relying largely on correlative observations without direct or quantitative validation of the proposed dynamics. Overall, the work is thought-provoking and of clear interest to the field, but stronger mechanistic evidence will be required to substantiate the central claims.

eLife Assessment

This study introduces the "Training Village," a valuable system for which solid evidence shows that it enables group-housed rodents to autonomously learn complex tasks while preserving natural social interactions. The platform is flexible, allowing animals to learn multiple tasks sequentially and supporting applications in continual learning. This approach is likely to be of broad interest to behavioral researchers using rodent models in systems and cognitive neuroscience.

eLife Assessment

This fundamental work significantly advances our understanding of the circuit-level implementation of predictive processing by elucidating the functional influence between putative prediction error neurons in layer 2/3 and putative internal representation neurons in layer 5. The evidence demonstrating that neither the hierarchical nor the non-hierarchical variant of predictive processing fully accounts for the presented data is convincing. Moving forward, this line of work would benefit from explicitly comparing different theories, thereby clearly articulating the points raised in this paper.

eLife Assessment

This study provides a valuable contribution to our understanding of the neural basis of perceptual decision-making by jointly modeling behavioral outcomes and EEG signals in a contrast comparison task. The methods and analyses are solid, systematically comparing standard models assuming continuous evidence accumulation with models that track evidence without temporal integration (extrema detection). The authors show that behavior and neural signals are equally consistent with both alternatives, highlighting limitations in current modeling approaches and questioning the generality of evidence accumulation mechanisms.

eLife Assessment

This valuable study explores changes in the Drosophila microbiome in response to environmental temperature over more than ten years. The evidence showing that temperature leads to diversification of bacterial clades is solid, but additional information would help clarify how subspecies competition impacts microbiome composition and the host. The work will interest researchers working with microbiomes, microbial ecology, and evolutionary biology.

eLife Assessment

This manuscript addresses an important question in clinical neuroscience: the use of the theta/beta ratio as a biomarker of attention deficit hyperactivity disorder (ADHD). The study takes an exceptional "multiverse" analysis approach to show that aperiodic activity differences between healthy controls and people with ADHD are driving the apparent theta/beta ratio differences. From a neuroscientific perspective, this is a critical finding because it has a major impact on guiding research on the diagnosis and treatment of ADHD.

eLife Assessment

This valuable study presents a comprehensive comparison of human and macaque monkey behavior across a range of visual perceptual phenomena. The use of a unified oddball visual search paradigm enables direct cross-species comparison while minimizing task-related confounds. It provides solid evidence that visual perception is largely similar between these two species, with some interesting exceptions. These insights into qualitative and quantitative differences between species are relevant for evaluating macaques as a model organism for understanding human vision.

eLife Assessment

This valuable study examined the geometry of visual object representations across hierarchically organized stages of the mouse visual cortex. The use of large-scale training and recording techniques provides solid evidence for changes along the hierarchy that may contribute to invariant object recognition. These findings, particularly if they could be supported by further analyses and clarifications to rule out alternative explanations, including influences of low-level features on behavior and neural activity, help establish the potential usefulness of the mouse to understand the neural basis of object recognition.