Evaluated articles

eLife Assessment

This important study presents compelling evidence for dopamine-based representation learning in the mouse olfactory tubercle. While this work suggests that gradient descent in deep networks serves as a helpful framework for understanding neural representations, the empirical evidence provided remains incomplete. Nonetheless, this work will be of significant interest to systems and computational neuroscientists, cognitive scientists, and machine learning theorists.

eLife Assessment

This is an important study that provides evidence that GATA6-dependent programming of peritoneal macrophages helps to regulate lipid metabolism and influences eosinophil survival. The evidence linking GATA6 deficiency to altered lipid profiles and eosinophil accumulation is solid, although the proposed mechanistic pathway connecting sphingolipid remodelling, LTE4 production and eosinophil survival currently remains incomplete. Strengthening these links and/or appropriately calming the conclusions would help to increase the impact of the study.

eLife Assessment

This manuscript presents important work on macrostructure formation in a freshwater filamentous cyanobacterium, focusing on its ability to aggregate and buckle. The authors employ a wide range of experiments and approaches, including time-lapse imaging and 3D theoretical modelling, to establish the physical dynamics of filaments, such as gliding motility and buckling. They demonstrate that, in addition to gliding motility, filament length and flexibility are essential for the ability of cyanobacteria to capture particles and form aggregates. Overall, the study provides convincing evidence and advances our understanding of the role of microbial motility in the environment. It will be of broad interest to biophysicists and environmental microbiologists.

eLife Assessment

This valuable study provides insights into the role of steroid signaling during tumorigenesis in the adult male drosophila accessory gland (functional equivalent of the prostate gland in mammals), hinting at a possible counterintuitive anti-tumoral role of sex hormones during prostate cancer in certain patients. While the Drosophila model provides an elegant way to study the hypothesis derived from the Cancer Atlas analysis, the analyses of public prostate cancer expression data are incomplete and critical knowledge on patients' treatment modalities and normalization across different datasets is missing. This work would be of interest to prostate cancer researchers as it suggests that the absence of androgen receptor signaling in humans could constitute a mechanism promoting tumor escape.

eLife Assessment

This work provides important findings that reveal a mechanistic model of how VDAC2 influences BAX activation in mitochondria during BAX-mediated apoptosis. The experimentally supported model is convincing, with several experiments strengthening its validity. Major strengths include the complementary biochemical, biophysical, structural, and computational approaches, as well as the study's broad relevance.

eLife Assessment

This paper provides a useful assessment of the role of macrophages in the development of functional paw withdrawal, which is a feature in the mouse model of vincristine-induced peripheral neuropathy (VIND). The authors suggest a role for E-selectin as a critical molecule promoting VIPN, acting via immune cell recruitment and inflammasome-mediated signalling; however, their data on NLRP3 inflammasome activation in vivo remains somewhat incomplete. This study will be of interest for immunologists.

eLife Assessment

This important study examines the dynamics of late endosomes and lysosomes (LEL) in cultured astrocytes, leading to a model of how synaptic activity might regulate astrocytic specializations surrounding synapses via the lysosomal calcium channel TRPML1, LEL motility, and proteins involved in regulating actin-membrane association. The experimental work is convincing, including appropriate controls and combining different tools (multiple markers, pharmacology, genetic knock-downs) to test each conclusion, although issues with the specificity of some of the drugs or confounding factors arising from genetic knock-downs limit the strength of some conclusions. Dysfunction in glia-neuron crosstalk as well as lysosomal dysfunction are increasingly recognized as highly relevant for neurodegenerative disease development, so this manuscript will be of interest to the wider neuroscience community, as well as scientists interested in the cell biology of astrocytes and lysosomes.

eLife Assessment

This valuable study reveals a role for lactylation in influenza polymerase function and virus replication. The evidence supporting the claims is solid, although the direct involvement of ATAT1 and SIRT1 in this modification and the functional relevance of the identified sites can be further substantiated. These findings will appeal broadly to influenza virologists studying polymerase regulation, as well as researchers investigating the functional roles of lactylation.

eLife Assessment

The main contribution of this potentially useful manuscript is a standardized comparative MRI resource covering multiple avian clades, complemented by histological cross-validation and diffusion-based connectivity analyses. Such a resource could significantly enhance accessibility to internal avian brain anatomy for evolutionary neurobiology. Its central claim that avian brain compartments exhibit modular diversification aligns with the existing literature. However, uncertainties regarding data availability, concerns with the tractography pipeline, and insufficient recognition of prior work lead to the conclusion that the methods, data, and analyses are incomplete.

eLife Assessment

This work has much novelty, supportive data, and the potential for changing thinking about melanoma biology with the discovery of MRGPRX4 as a relatively melanoma-specific G protein-coupled receptor. MRGPRX4 is normally restricted to peripheral sensory neurons, but it is aberrantly expressed in human melanomas; melanomas with neural-crest-like/invasive features were most likely affected. When ectopically expressed in murine melanocytes, MRGPRX4 drives melanoma development with metastasis; the mechanism appears to involve ligand-independent receptor signaling. Overall, the text presents this as a novel model of oncogenesis driven by re-expression of a sensory GPCR - this is an important study with compelling data.

eLife Assessment

This important study shows that self-supervised pretraining on related fungal genomes can substantially improve sequence-to-expression prediction in budding yeast. The evidence for the main conclusion is convincing, with careful comparisons to models trained from random initialization and clear gains on held-out expression data. The broader claims about the optimal evolutionary scope and transfer of regulatory grammar are less fully supported.

eLife Assessment

This important study investigates how experimentally introducing two facultative bacterial endosymbionts into the Russian wheat aphid, Diuraphis noxia, affects aphid performance, dispersal, and damage to cereal host plants and the authors provide solid evidence for contrasting symbiont-associated phenotypes under controlled conditions: Rickettsiella increases plant damage while reducing wing production and dispersal, whereas Regiella reduces feeding damage and, at some time points, aphid population growth. The stable establishment of these novel symbiont-host associations and complementary experiments spanning individual aphids, whole plants, populations, and mesocosms are notable strengths and the revised manuscript better clarifies the experimental approaches and the context dependence of symbiont effects; however, the underlying mechanisms remain unresolved, horizontal transmission is inferred rather than directly demonstrated, and limited replication and temporal variability constrain some population-level conclusions. Potential applications to pest management therefore require further validation under field conditions. The study will interest researchers working on insect symbiosis, plant-insect interactions, and biologically based pest management.

eLife Assessment

Using a range of complementary approaches, this study examines how type I and type II interferon (IFN) programs exert opposing effects on macrophage responses relevant to tuberculosis. The work addresses a key biological question and provides valuable mechanistic insights. However, the data to support several key conclusions is incomplete and requires further strengthening; in particular, the role of ferritin needs to be established more definitively, the TNF stimulation findings should be validated in the context of M. tuberculosis infection, and in vivo evidence is needed to support the proposed therapeutic strategy. Additionally, aspects of iron metabolism, lipid peroxidation, and the translatability of the findings between mouse and human macrophages would benefit from greater clarity and deeper mechanistic investigation.

eLife Assessment

This study presents important findings that genome-wide DNA double-strand breaks trigger large-scale genomic amplification (DIGA), which does not require origin re-licensing, but is dependent on some proteins that are involved in break-induced replication (BIR). While the findings and model are compelling, the evidence supporting the claims is largely incomplete, as it depends primarily on a single assay to examine amplification. This work will be of interest to scientists in the DNA repair, replication, and cell cycle fields, as well as cancer biologists.

eLife Assessment

This study presents a valuable finding on a potential new regulatory mechanism for cellular proliferation in the mammalian cochlea, taking advantage of the organoid-forming potential of cells from the greater epithelial ridge (GER), or Kolliker's organ, a transient structure in the developing cochlea. The authors highlight three potential regulators - galectin 1, galectin 3, and Myc - providing solid evidence for potential roles in modulating the proliferation of cochlear GER cells using gene expression studies, single-cell profiling, pharmacological inhibition, and genetic overexpression both in vitro and in vivo. However, some of the analyses and interpretations are incomplete, and a better understanding of how the compounds and the gene overexpression studies affect the cells and modulate cell survival/death would aid a fuller interpretation of the data.

eLife Assessment

This valuable study provides a proof of concept for the utility of transcriptomic methods to develop novel diagnostic tests for bovine tuberculosis. A comprehensive analysis using a suite of machine learning models provides convincing evidence for the use of mRNA biomarkers to distinguish between infected and disease-free animals. The analysis also provides major insights into both the levels of individual variation in expression between animals as well as systematic changes with respect to the time from infection.

eLife Assessment

This valuable study advances our understanding of habituation and related potentiation behavior in a single-celled organism, Stentor. The authors provide convincing evidence for their claims in the form of extensive data on habituation behavior. The work will be of interest to cell biologists, neuroscientists, and also scientists broadly interested in behavior in non-neural organisms.

eLife Assessment

In this study, electroencephalography was recorded during a binocular-rivalry paradigm in which participants viewed a target and a distractor stimulus. The stimuli were independently frequency-tagged, allowing the researchers to track target and distractor processing over time. The findings suggest that parietal alpha oscillations initially segregate competing inputs, followed by frontal theta activity associated with suppression of distractor representations. The significance of these findings is valuable, although the strength of the evidence remains incomplete, because of specific experiment design choices and methodological limitations.

eLife Assessment

This important study integrates mouse genetics with sequencing, electrophysiological and behavioral tools to uncover the behavioral role and molecular profile of a developmentally defined subpopulation in the lateral septum. The data collected and analyzed are convincing, highlighting the role of this subpopulation in threat avoidance and stress, providing a framework by which developmental origin is linked to mature neuronal function. The work will be of interest to biologists and neuroscientists working on development and behavior.

eLife Assessment

This important paper provides evidence that visual representations, as observed through drawing, preferentially preserve topological features over metric features. Across three experiments with different age groups and creative converging methods, they demonstrate that holes and T-junctions are relatively preserved as compared to topologically irrelevant L-junctions, and Euclidian features like length or precise angle. Together, these data provide convincing evidence for topology as an organizing principle for spatial representation, but the work would be strengthened by considering a broader range of topological features, or by ruling out alternative accounts, like preserved memory for complex features, motor production limitations, or noisy compression, that may produce a similar pattern without a topological prior.