Evaluated articles

eLife Assessment

This important study convincingly shows that Vibrio bacteria act as predators of ecologically significant algae that contribute to harmful blooms in the lab, as well as in their natural habitat. While the data strongly suggest that starvation may induce predation, further work is needed to fully establish this link. Similarly, the evidence for a social component in the predation process remains incomplete. This study will be very impactful to those interested in the diversity of microbial predator-prey interactions and controlling toxic algal bloom, but the paper could be strengthened by more clearly showing the degree of replication, by better defining the terms used to describe the observed behaviour, and by providing better support for starvation and collective behaviour.

eLife Assessment

This valuable work presents a novel computational framework for modeling macroscopic traveling waves in the mouse cortex by integrating open-source connectomic and transcriptomic data into a spiking network model. This approach allows the computational model to assign excitatory/inhibitory connections based on neurotransmitter profiles and extends simulations to the 3D domain. The authors present results that demonstrate how spatiotemporal dynamics such as slow oscillations (0.5-4 Hz) emerge and self-organize at the whole-brain scale. This study provides convincing initial insights into the structural basis of traveling waves at the whole-brain scale in the mouse.

eLife Assessment

This fundamental work significantly advances our understanding of gravity sensing and orientation behavior in the ctenophore, an animal of major importance in understanding the evolution of nervous systems. Through comprehensive reconstruction with volumetric electron microscopy, and time-lapse imaging of cilia motion, the authors provide compelling evidence that the aboral nerve net coordinates the activity of balancer cilia. The resemblance to the ciliomotor circuit in marine annelids provides a fascinating example of how neural circuits may convergently evolve to solve common sensorimotor challenges.

eLife Assessment

In this manuscript, the authors investigate the migration of human cortical interneurons under hypoxic conditions using forebrain assembloids and developing human brain tissue, and probe the underlying mechanisms. The study provides the first direct evidence that hypoxia delays interneuron migration and identifies adrenomedullin (ADM) as a potential therapeutic intervention. The findings are important, and the conclusions are convincingly supported by experimental evidence.

eLife Assessment

This fundamental work advances our understanding of how SP5 and SP8 promote neuromesodermal competent progenitors in murine embryos. Generally the evidence is compelling, with strong developmental genetics, transcriptomic, and genomic transcription binding surveys contributing to the strength of the data. Some of the language could be softened to avoid overinterpretation of the data, and figures and diagrams could be improved.

eLife Assessment

This study presents a valuable and rigorous molecular resource, offering subtype-specific insight into the composition of ribosome-associated protein complexes in the developing cerebral cortex. The evidence is compelling in terms of data quality and is strongly supported by the results, given the rigorous technical execution. However, the findings remain primarily descriptive, as the study lacks functional validation to support mechanistic conclusions.

eLife Assessment

In this fundamental manuscript, Richter et al. present a thorough anatomical characterization of the Drosophila melanogaster larval pharyngeal sensory system, which is involved in taste-guided behaviors. This study fills a major gap in the larval sensory map, providing a compelling neuroanatomical foundation for future investigations into sensory circuits and behavior. The data presented here are of exceptional quality and will be of interest to the Drosophila neurobiology community.

eLife Assessment

This important work provides convincing evidence of the cognitive and neural mechanisms that give rise to feelings of shame and guilt, as well as their transformation into compensatory behavior. The authors combine well-designed manipulations of responsibility and harm with computational cognitive modeling and neuroimaging to provide a comprehensive account of how emotions are experienced and acted upon.

eLife Assessment

This manuscript uses modeling approaches to provide mechanistic insight into the structural and dynamic properties of enhancer-promoter interactions in Drosophila. Given the interest in this field, this is a timely approach, and the results give useful insights by providing predictions about the processivity of cohesin loop extrusion in Drosophila and concluding that the compartmental interaction strength is poised near criticality in the coil-globule phase space. The evidence provided to support some of the conclusions is, however, incomplete and would be strengthened by better considering some of the caveats in the data used to constrain the models, such as the use of "homie" genetic elements in the dynamic data. There is insufficient evidence provided for the dynamics being criticality-driven, and in addition, consideration of alternative models would further strengthen the conclusions of the manuscript.

eLife Assessment

This important work describes the adaptation and evaluation of two red-shifted anion channelrhodopsins (RubyACRs) for optogenetic inhibition in Drosophila. The study provides convincing evidence for the effectiveness of RubyACRs in fly neurons, including electrophysiology, calcium imaging, and behavioral analysis. With minor revisions to address potential toxicity and compatibility with 2-photon imaging, this paper and the publicly available fly lines it describes will be resources that are of value to the neuroscience community.

eLife Assessment

This manuscript is useful as it demonstrates that Rv2577, a Fe³⁺/Zn²⁺-dependent metallophosphatase, is secreted by Mycobacterium bovis BCG and localizes to the nucleus of mammalian cells, altering transcriptional and inflammatory responses. However, the study is incomplete as it lacks activity validation in macrophage cells and with virulent Mycobacterium tuberculosis strains. It is necessary to confirm Rv2577 secretion from a virulent strain and to clarify the direct or indirect role of MmpE in modulating host pathways, together with mechanistic insight into how MmpE influences lysosomal biogenesis and trafficking.

eLife Assessment

This important study applies a novel signal decomposition method to disentangle distinct signals contributing to the decision-making process, and provides convincing evidence for the operation of separate sensory encoding, attentional orienting, and ramping evidence accumulation signals. These findings are consistent with previous work, except for the absence of a motor component, which may relate to limitations of the analysis approach.

eLife Assessment

This manuscript reports the development and characterization of iGABASnFR2, a genetically encoded GABA sensor that demonstrates substantially improved performance compared to its predecessor, iGABASnFR1. The work is comprehensive and methodologically rigorous, combining high-throughput mutagenesis, functional screening, structural analysis, biophysical characterization, and in vivo validation. The significance of the findings is fundamental, and the supporting evidence is compelling. iGABASnFR2 represents a notable advance in GABA sensor engineering, enabling enhanced imaging of GABA transmission both in brain slices and in vivo, and constitutes a timely, technically robust addition to the molecular toolkit for neuroscience research.

eLife Assessment

This manuscript introduces a potentially valuable large-scale fMRI dataset pairing vision and language, and employs rigorous decoding analyses to investigate how the brain represents visual, linguistic, and imagined content. The current manuscript blurs the line between a resource paper and a theoretical contribution, and the evidence for truly modality-agnostic representations remains incomplete at this stage. Clarifying the conceptual aims and strengthening both the dataset technicality and the quantitative analyses would improve the manuscript's significance for the fields of cognitive neuroscience and multimodal AI.

eLife Assessment

This useful study uses fiber photometry, implantable lenses, and optogenetics to show that a subset of subthalamic nucleus neurons is active during movement, and that active but not passive avoidance depends in part on STN projections to substantia nigra. The strength of the evidence for these claims is solid, whereas evidence supporting the claims that STN is involved in cautious responding or the speed of avoidance is incomplete. This paper will be of interest to basic and applied behavioural neuroscientists working on avoidance if suitably streamlined to support the strongest claims.

eLife Assessment

This is an important study that takes a key step towards understanding developmental disorders linked to mutations in the O-GlcNAc transferase enzyme by generating a mouse model harboring the C921Y mutation. The study thoroughly examines behavioral and anatomical differences in these mice and finds behavioral hyperactivity and learning/memory deficits, as well as phenotypic differences in skull and brain formation. However, the experimental evidence is incomplete owing to discrepancy in OGT protein/RNA levels in the C921Y mutant mice in this paper and the previous paper ("Neurodevelopmental defects in a mouse model of O-GlcNAc transferase intellectual disability "). This line of research will benefit from investigation of the differences in associated glycoproteins and mechanistic insights. This study will be of interest to those studying neurodevelopment, learning and behavior, or associated brain mechanisms.

eLife Assessment

This study provides new important insights concerning pathogen variant-specific reproduction parameters from molecular sequencing and case finding. The methods for inferring which variants will likely emerge in subsequent epidemic cycles are solid. This article is of broad interest to infectious disease epidemiology researchers and mathematical modellers of the COVID-19 pandemic.

eLife Assessment

This valuable study combined careful computational modeling, a large patient sample, and replication in an independent general population sample to provide a computational account of a difference in risk-taking between people who have attempted suicide and those who have not. It is proposed that this difference reflects a general change in the approach to risky (high-reward) options and a lower emotional response to certain rewards. Evidence for the specificity of the effect to suicide, however, is incomplete, which would require additional analyses.

eLife Assessment

This valuable study concerns a highly interesting and biologically relevant topic, the regulation of the PIN auxin transporter, which is of broad interest to the plant biology community. The authors propose NPY1 to act downstream of PID in auxin-mediated development by modulating PIN phosphorylation, which, if experimentally solidified, would expand our understanding of PIN regulation. While the genetic evidence is solid, the mechanistic role of NPY1 and the functional relevance of phosphorylated PIN residues are still uncertain. There are also concerns regarding experimental rigor and methodological transparency.

eLife Assessment:

This study addresses valuable questions about the neural mechanisms underlying statistical learning of room acoustics, combining robust behavioral measures with non-invasive brain stimulation. The behavioral findings are strong and extend previous work in psychoacoustics, but the TMS results are modest, with methodological limitations and over-interpretation that weaken the mechanistic conclusions. The strength of evidence is therefore incomplete, and a more cautious interpretation of the stimulation findings, alongside strengthened analyses, would improve the manuscript.